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Sample records for scale gene-associated marker

  1. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

    Energy Technology Data Exchange (ETDEWEB)

    Catfish Genome Consortium; Wang, Shaolin; Peatman, Eric; Abernathy, Jason; Waldbieser, Geoff; Lindquist, Erika; Richardson, Paul; Lucas, Susan; Wang, Mei; Li, Ping; Thimmapuram, Jyothi; Liu, Lei; Vullaganti, Deepika; Kucuktas, Huseyin; Murdock, Christopher; Small, Brian C; Wilson, Melanie; Liu, Hong; Jiang, Yanliang; Lee, Yoona; Chen, Fei; Lu, Jianguo; Wang, Wenqi; Xu, Peng; Somridhivej, Benjaporn; Baoprasertkul, Puttharat; Quilang, Jonas; Sha, Zhenxia; Bao, Baolong; Wang, Yaping; Wang, Qun; Takano, Tomokazu; Nandi, Samiran; Liu, Shikai; Wong, Lilian; Kaltenboeck, Ludmilla; Quiniou, Sylvie; Bengten, Eva; Miller, Norman; Trant, John; Rokhsar, Daniel; Liu, Zhanjiang

    2010-03-23

    Background-Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. Results-A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35percent of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. Conclusions-This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.

  2. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies.

    Science.gov (United States)

    Wang, Shaolin; Peatman, Eric; Abernathy, Jason; Waldbieser, Geoff; Lindquist, Erika; Richardson, Paul; Lucas, Susan; Wang, Mei; Li, Ping; Thimmapuram, Jyothi; Liu, Lei; Vullaganti, Deepika; Kucuktas, Huseyin; Murdock, Christopher; Small, Brian C; Wilson, Melanie; Liu, Hong; Jiang, Yanliang; Lee, Yoona; Chen, Fei; Lu, Jianguo; Wang, Wenqi; Xu, Peng; Somridhivej, Benjaporn; Baoprasertkul, Puttharat; Quilang, Jonas; Sha, Zhenxia; Bao, Baolong; Wang, Yaping; Wang, Qun; Takano, Tomokazu; Nandi, Samiran; Liu, Shikai; Wong, Lilian; Kaltenboeck, Ludmilla; Quiniou, Sylvie; Bengten, Eva; Miller, Norman; Trant, John; Rokhsar, Daniel; Liu, Zhanjiang

    2010-01-22

    Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35% of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.

  3. Gene-associated markers provide tools for tackling illegal fishing and false eco-certification

    DEFF Research Database (Denmark)

    Eg Nielsen, Einar; Cariani, Alessia; Aoidh, Eoin Mac

    2012-01-01

    Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch...... certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays...

  4. Microgeographical population structure and adaptation in Atlantic cod Gadus morhua: spatio-temporal insights from gene-associated DNA markers

    DEFF Research Database (Denmark)

    Poulsen, Nina Aagaard; Hemmer-Hansen, Jakob; Loeschcke, V.

    2011-01-01

    populations, indicating long-term temporal adaptive stability driven by strong local selection. In an environmentally dynamic area, on the other hand, patterns of genetic structuring were more variable. Overall, our results not only suggest separation of populations under both evolutionary and ecological...... paradigms, but also illustrate the usefulness of the spatio-temporal approach for making inferences about the dynamics and geographical distribution of adaptive genetic variation in natural populations.......Recent technical advances have stimulated studies on spatial scales of adaptive genetic variation in marine fishes. However, very few studies have combined spatial and temporal sampling to investigate adaptive genetic structuring at local and microgeographical scales, i.e. scales at which neutral...

  5. Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array

    Directory of Open Access Journals (Sweden)

    Kaltenboeck Ludmilla

    2011-01-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs have become the marker of choice for genome-wide association studies. In order to provide the best genome coverage for the analysis of performance and production traits, a large number of relatively evenly distributed SNPs are needed. Gene-associated SNPs may fulfill these requirements of large numbers and genome wide distribution. In addition, gene-associated SNPs could themselves be causative SNPs for traits. The objective of this project was to identify large numbers of gene-associated SNPs using high-throughput next generation sequencing. Results Transcriptome sequencing was conducted for channel catfish and blue catfish using Illumina next generation sequencing technology. Approximately 220 million reads (15.6 Gb for channel catfish and 280 million reads (19.6 Gb for blue catfish were obtained by sequencing gene transcripts derived from various tissues of multiple individuals from a diverse genetic background. A total of over 35 billion base pairs of expressed short read sequences were generated. Over two million putative SNPs were identified from channel catfish and almost 2.5 million putative SNPs were identified from blue catfish. Of these putative SNPs, a set of filtered SNPs were identified including 342,104 intra-specific SNPs for channel catfish, 366,269 intra-specific SNPs for blue catfish, and 420,727 inter-specific SNPs between channel catfish and blue catfish. These filtered SNPs are distributed within 16,562 unique genes in channel catfish and 17,423 unique genes in blue catfish. Conclusions For aquaculture species, transcriptome analysis of pooled RNA samples from multiple individuals using Illumina sequencing technology is both technically efficient and cost-effective for generating expressed sequences. Such an approach is most effective when coupled to existing EST resources generated using traditional sequencing approaches because the reference ESTs facilitate

  6. A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia.

    Directory of Open Access Journals (Sweden)

    Mikołaj Słabicki

    Full Text Available DNA repair is essential to maintain genome integrity, and genes with roles in DNA repair are frequently mutated in a variety of human diseases. Repair via homologous recombination typically restores the original DNA sequence without introducing mutations, and a number of genes that are required for homologous recombination DNA double-strand break repair (HR-DSBR have been identified. However, a systematic analysis of this important DNA repair pathway in mammalian cells has not been reported. Here, we describe a genome-scale endoribonuclease-prepared short interfering RNA (esiRNA screen for genes involved in DNA double strand break repair. We report 61 genes that influenced the frequency of HR-DSBR and characterize in detail one of the genes that decreased the frequency of HR-DSBR. We show that the gene KIAA0415 encodes a putative helicase that interacts with SPG11 and SPG15, two proteins mutated in hereditary spastic paraplegia (HSP. We identify mutations in HSP patients, discovering KIAA0415/SPG48 as a novel HSP-associated gene, and show that a KIAA0415/SPG48 mutant cell line is more sensitive to DNA damaging drugs. We present the first genome-scale survey of HR-DSBR in mammalian cells providing a dataset that should accelerate the discovery of novel genes with roles in DNA repair and associated medical conditions. The discovery that proteins forming a novel protein complex are required for efficient HR-DSBR and are mutated in patients suffering from HSP suggests a link between HSP and DNA repair.

  7. Human CLOCK gene-associated attention deficit hyperactivity disorder-related features in healthy adults: quantitative association study using Wender Utah Rating Scale.

    Science.gov (United States)

    Jeong, Seong Hoon; Yu, Je-Chun; Lee, Chang Hwa; Choi, Kyeong-Sook; Choi, Jung-Eun; Kim, Se Hyun; Joo, Eun-Jeong

    2014-02-01

    Circadian rhythm disturbance is highly prevalent in attention deficit hyperactivity disorder (ADHD). Recently, the association between the CLOCK gene and ADHD has been demonstrated in clinical samples, and the CLOCK gene's role was thought to be mediated by rhythm dysregulation. Meanwhile, ADHD has been suggested as the extreme end of a continuously distributed trait that can be found in the general population. Therefore, we examined two possibilities: (1) an ADHD-related continuous trait may be associated with the CLOCK gene, and (2) this association may be mediated by the degree of individuals' evening preference. To explore these possibilities, we performed a quantitative trait locus association study with a sample of 1,289 healthy adults. The Wender Utah Rating Scale (WURS) and the Composite Scale of Morningness (CSM) were utilized to measure the quantitative traits. Quantitative association analysis was performed using PLINK software. We found that rs1801260 (=T3111C) was associated with WURS scores in both allele-wise (p = 0.018) and haplotype-wise analyses (range of p values: 0.0155-0.0171) in male participants only. After controlling for the CSM total score as a covariate, the strength of the association did not change at all, suggesting that the association was not mediated by evening preference. Despite the very weak association signal, our results provide evidence that the CLOCK gene's association with ADHD in clinical samples may be generalizable to traits measured in the normal population. However, as our results failed to show a mediating role of evening preference, ongoing efforts are needed to identify the mechanisms by which the CLOCK gene determines ADHD-related traits.

  8. Distribution of genes associated with yield potential and water ...

    Indian Academy of Sciences (India)

    Supplementary data: Distribution of genes associated with yield potential and water-saving in. Chinese Zone II wheat detected by developed functional markers. Zhenxian Gao, Zhanliang Shi, Aimin Zhang and Jinkao Guo. J. Genet. 94, 35–42. Table 1. Functional markers for high-yield or water-saving genes in wheat and ...

  9. Contact and Alignment Marker Technology for Atomic Scale Device Fabrication

    NARCIS (Netherlands)

    Zuiddam, M.R.; Rogge, S.; Drift, E. van der; Ilge, B.; Palasantzas, G.

    1998-01-01

    This article reports on the technology to link atomic scale structures to macroscopic contact pads. Dedicated processes for electrode pattern formation in several materials have been developed and characterised. For pattern formation in CoSi2 a thermal compromise between proper silicide formation

  10. Distribution of genes associated with yield potential and water ...

    Indian Academy of Sciences (India)

    Distribution of genes associated with yield potential and water-saving in Chinese Zone II wheat detected by developed functional markers. ZHENXIAN GAO1,∗, ZHANLIANG SHI1, AIMIN ZHANG2 and JINKAO GUO1. 1Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, Hebei 050041, People's ...

  11. Sugarcane genes associated with sucrose content

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    Vincentz Michel GA

    2009-03-01

    Full Text Available Abstract Background - Sucrose content is a highly desirable trait in sugarcane as the worldwide demand for cost-effective biofuels surges. Sugarcane cultivars differ in their capacity to accumulate sucrose and breeding programs routinely perform crosses to identify genotypes able to produce more sucrose. Sucrose content in the mature internodes reach around 20% of the culms dry weight. Genotypes in the populations reflect their genetic program and may display contrasting growth, development, and physiology, all of which affect carbohydrate metabolism. Few studies have profiled gene expression related to sugarcane's sugar content. The identification of signal transduction components and transcription factors that might regulate sugar accumulation is highly desirable if we are to improve this characteristic of sugarcane plants. Results - We have evaluated thirty genotypes that have different Brix (sugar levels and identified genes differentially expressed in internodes using cDNA microarrays. These genes were compared to existing gene expression data for sugarcane plants subjected to diverse stress and hormone treatments. The comparisons revealed a strong overlap between the drought and sucrose-content datasets and a limited overlap with ABA signaling. Genes associated with sucrose content were extensively validated by qRT-PCR, which highlighted several protein kinases and transcription factors that are likely to be regulators of sucrose accumulation. The data also indicate that aquaporins, as well as lignin biosynthesis and cell wall metabolism genes, are strongly related to sucrose accumulation. Moreover, sucrose-associated genes were shown to be directly responsive to short term sucrose stimuli, confirming their role in sugar-related pathways. Conclusion - Gene expression analysis of sugarcane populations contrasting for sucrose content indicated a possible overlap with drought and cell wall metabolism processes and suggested signaling and

  12. Identification of a Simple Sequence Repeat molecular-marker set for large-scale analyses of pear germplasm

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    Gabriel Dequigiovanni

    2012-01-01

    Full Text Available Simple Sequence Repeats (SSR are molecular markers suitable to assess the genetic variation of germplasm resources; however, large-scale SSR use requires protocol optimization. The present work aimed to identify SSR markers, developed for pear and other fruit species that are effective in characterizing pear germplasm collections and in demonstrating their use in providing support for genetic breeding programs. From a total of 62 SSR markers investigated, 23 yielding reproducible and polymorphic patterns were used to genotype a sample of 42 pear accessions of the Brazilian Pear Germplasm Bank (PGB. When compared to these 23 SSR markers, a subset of eleven markers, selected based on He, PIC and PId, was used to distinguish individual accessions and perform cluster analysis with similar efficacy. Genetic diversity analysis clustered the European, Japanese and Chinese accessions in distinct groups. This markers subset constitutes a valuable tool for several applications related to pear genetic resources management and breeding.

  13. The full-scale anaerobic digestion microbiome is represented by specific marker populations.

    Science.gov (United States)

    De Vrieze, Jo; Raport, Linde; Roume, Hugo; Vilchez-Vargas, Ramiro; Jáuregui, Ruy; Pieper, Dietmar H; Boon, Nico

    2016-11-01

    Anaerobic digestion is a well-established microbial-based technology for the treatment of organic waste streams and subsequent biogas recovery. A robust and versatile microbial community to ensure overall stability of the process is essential. Four full-scale anaerobic digestion plants were followed for one year to link operational characteristics with microbial community composition and structure. Similarities between digesters, community dynamics and co-occurrence between bacteria and archaea within each digester were analysed. Free ammonia concentration (>200 mg N L-1) and conductivity (>30 mS cm-1) hindered acetoclastic methanogenesis by Methanosaetaceae. Thus, methanogenesis was pushed to the hydrogenotrophic pathway carried out by Methanobacteriales and Methanomicrobiales. Firmicutes dominated the overall bacterial community in each of the digesters (>50%), however, principal coordinate analysis of Bray-Curtis indices showed that each of the four digesters hosted a unique microbial community. The uniqueness of this community was related to two phylotypes belonging to the Syntrophomonas genus (Phy32 and Phy34) and to one unclassified bacterium (Phy2), which could both be considered marker populations in the community. A clear differentiation in co-occurrence of methanogens with several bacteria was observed between the different digesters. Our results demonstrated that full-scale anaerobic digestion plants show constant dynamics and co-occurrence patterns in function of time, but are unique in terms of composition, related to the presence of marker populations. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. An optimized microsatellite marker set for detection of Metarhizium anisopliae genotype diversity on field and regional scales.

    Science.gov (United States)

    Oulevey, Catherine; Widmer, Franco; Kölliker, Roland; Enkerli, Jürg

    2009-09-01

    Thirty-three Metarhizium anisopliae isolates sampled across Switzerland as well as 35 and 36 M. anisopliae isolates sampled from two field sites were assembled in three isolate collections. All isolates were analyzed using 27 newly developed and 14 previously published microsatellite markers. The 41 markers allowed for detection of 25 genotypes in the Swiss collection while 30 and 11 genotypes were detected in the two field collections. This indicated high genetic diversity on a regional as well as on a field scale. In order to improve genotyping efficiency, an optimized marker set, which allows discrimination of a large number of genotypes with as few markers as possible was developed. The optimized marker set consisted of 16 common markers, which provided resolution close to maximal resolution in all three collections (91-93 %). The results demonstrated that optimized marker sets have to be validated before large scale application to previously unassessed collections in order to avoid suboptimal resolution. This genetic tool will be valuable for analyses of genetic population structure of M. anisopliae in different habitats on a regional as well as on a field scale.

  15. Application of large-scale sequencing to marker discovery in plants

    Indian Academy of Sciences (India)

    2012-10-15

    Oct 15, 2012 ... 1Queensland Alliance for Agriculture and Food Innovation, The University of Queensland,. Brisbane QLD 4072, Australia ... tions for DNA marker discovery employed a range of tech- niques to deal with the lack of ...... Henry RJ 2010 Plant resources for food fuel and conservation. (London: Earthscan). Hill H ...

  16. Comparison of clinical and biochemical markers of dehydration with the clinical dehydration scale in children: a case comparison trial.

    Science.gov (United States)

    Tam, Ron K; Wong, Hubert; Plint, Amy; Lepage, Nathalie; Filler, Guido

    2014-06-16

    The clinical dehydration scale (CDS) is a quick, easy-to-use tool with 4 clinical items and a score of 1-8 that serves to classify dehydration in children with gastroenteritis as no, some or moderate/severe dehydration. Studies validating the CDS (Friedman JN) with a comparison group remain elusive. We hypothesized that the CDS correlates with a wide spectrum of established markers of dehydration, making it an appropriate and easy-to-use clinical tool. This study was designed as a prospective double-cohort trial in a single tertiary care center. Children with diarrhea and vomiting, who clinically required intravenous fluids for rehydration, were compared with minor trauma patients who required intravenous needling for conscious sedation. We compared the CDS with clinical and urinary markers (urinary electrolytes, proteins, ratios and fractional excretions) for dehydration in both groups using receiver operating characteristic (ROC) curves to determine the area under the curve (AUC). We enrolled 73 children (male = 36) in the dehydration group and 143 (male = 105) in the comparison group. Median age was 32 months (range 3-214) in the dehydration and 96 months (range 2.6-214 months, p dehydration group and 0 in the comparison group (p dehydrated group: difference in heart rate, diastolic blood pressure, urine sodium/potassium ratio, urine sodium, fractional sodium excretion, serum bicarbonate, and creatinine measurements. The best markers for dehydration were urine Na and serum bicarbonate (ROC AUC = 0.798 and 0.821, respectively). CDS was most closely correlated with serum bicarbonate (Pearson r = -0.3696, p = 0.002). Although serum bicarbonate is not the gold standard for dehydration, this study provides further evidence for the usefulness of the CDS as a dehydration marker in children. Registered at ClinicalTrials.gov (NCT00462527) on April 18, 2007.

  17. Large-scale transcriptome analyses reveal new genetic marker candidates of head, neck, and thyroid cancer

    DEFF Research Database (Denmark)

    Reis, Eduardo M; Ojopi, Elida P B; Alberto, Fernando L

    2005-01-01

    with detailed clinical data about tumor origin, the information reported here is now publicly available on a dedicated Web site as a resource for further biological investigation. This first in silico reconstruction of the head, neck, and thyroid transcriptomes points to a wealth of new candidate markers......A detailed genome mapping analysis of 213,636 expressed sequence tags (EST) derived from nontumor and tumor tissues of the oral cavity, larynx, pharynx, and thyroid was done. Transcripts matching known human genes were identified; potential new splice variants were flagged and subjected to manual...... curation, pointing to 788 putatively new alternative splicing isoforms, the majority (75%) being insertion events. A subset of 34 new splicing isoforms (5% of 788 events) was selected and 23 (68%) were confirmed by reverse transcription-PCR and DNA sequencing. Putative new genes were revealed, including...

  18. Development and small-scale validation of a novel pigeon-associated mitochondrial DNA source tracking marker for the detection of fecal contamination in harvested rainwater.

    Science.gov (United States)

    Waso, M; Khan, S; Khan, W

    2018-02-15

    The current study was aimed at designing and validating (on a small-scale) a novel pigeon mitochondrial DNA (mtDNA) microbial source tracking (MST) marker for the detection of pigeon fecal matter in harvested rainwater. The pigeon mtDNA MST marker was designed to target the mtDNA Cytochrome b gene by employing mismatch amplification mutation assay kinetics. The pigeon marker was validated by screening 69 non-pigeon and 9 pigeon fecal samples. The host-sensitivity of the assay was determined as 1.00 while the host-specificity of the assay was 0.96. Harvested rainwater samples (n=60) were screened for the prevalence of the marker with the mtDNA Cytochrome b marker detected in 78% of the samples. Bayes' theorem was applied to calculate the conditional probability of the marker detecting true pigeon contamination and the marker subsequently displayed a 99% probability of detecting true pigeon contamination in the harvested rainwater samples. In addition, the mtDNA Cytochrome b marker displayed high concurrence frequencies versus heterotrophic bacteria (78.3%), E. coli (73.3%), total coliforms (71.1%) and fecal coliforms (66.7%). This study thus validates that targeting mtDNA for the design of source tracking markers may be a valuable tool to detect avian fecal contamination in environmental waters. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Weighing Scale-Based Pulse Transit Time is a Superior Marker of Blood Pressure than Conventional Pulse Arrival Time

    Science.gov (United States)

    Martin, Stephanie L.-O.; Carek, Andrew M.; Kim, Chang-Sei; Ashouri, Hazar; Inan, Omer T.; Hahn, Jin-Oh; Mukkamala, Ramakrishna

    2016-12-01

    Pulse transit time (PTT) is being widely pursued for cuff-less blood pressure (BP) monitoring. Most efforts have employed the time delay between ECG and finger photoplethysmography (PPG) waveforms as a convenient surrogate of PTT. However, these conventional pulse arrival time (PAT) measurements include the pre-ejection period (PEP) and the time delay through small, muscular arteries and may thus be an unreliable marker of BP. We assessed a bathroom weighing scale-like system for convenient measurement of ballistocardiography and foot PPG waveforms - and thus PTT through larger, more elastic arteries - in terms of its ability to improve tracking of BP in individual subjects. We measured “scale PTT”, conventional PAT, and cuff BP in humans during interventions that increased BP but changed PEP and smooth muscle contraction differently. Scale PTT tracked the diastolic BP changes well, with correlation coefficient of -0.80 ± 0.02 (mean ± SE) and root-mean-squared-error of 7.6 ± 0.5 mmHg after a best-case calibration. Conventional PAT was significantly inferior in tracking these changes, with correlation coefficient of -0.60 ± 0.04 and root-mean-squared-error of 14.6 ± 1.5 mmHg (p < 0.05). Scale PTT also tracked the systolic BP changes better than conventional PAT but not to an acceptable level. With further development, scale PTT may permit reliable, convenient measurement of BP.

  20. Identification of genes associated with multiple cancers via integrative analysis

    Directory of Open Access Journals (Sweden)

    Huang Jian

    2009-11-01

    Full Text Available Abstract Background Advancement in gene profiling techniques makes it possible to measure expressions of thousands of genes and identify genes associated with development and progression of cancer. The identified cancer-associated genes can be used for diagnosis, prognosis prediction, and treatment selection. Most existing cancer microarray studies have been focusing on the identification of genes associated with a specific type of cancer. Recent biomedical studies suggest that different cancers may share common susceptibility genes. A comprehensive description of the associations between genes and cancers requires identification of not only multiple genes associated with a specific type of cancer but also genes associated with multiple cancers. Results In this article, we propose the Mc.TGD (Multi-cancer Threshold Gradient Descent, an integrative analysis approach capable of analyzing multiple microarray studies on different cancers. The Mc.TGD is the first regularized approach to conduct "two-dimensional" selection of genes with joint effects on cancer development. Simulation studies show that the Mc.TGD can more accurately identify genes associated with multiple cancers than meta analysis based on "one-dimensional" methods. As a byproduct, identification accuracy of genes associated with only one type of cancer may also be improved. We use the Mc.TGD to analyze seven microarray studies investigating development of seven different types of cancers. We identify one gene associated with six types of cancers and four genes associated with five types of cancers. In addition, we also identify 11, 9, 18, and 17 genes associated with 4 to 1 types of cancers, respectively. We evaluate prediction performance using a Leave-One-Out cross validation approach and find that only 4 (out of 570 subjects cannot be properly predicted. Conclusion The Mc.TGD can identify a short list of genes associated with one or multiple types of cancers. The identified genes

  1. Molecular markers discriminate closely related species Encarsia diaspidicola and Encarsia berlesei (Hymenoptera: Aphelinidae): biocontrol candidate agents for white peach scale in Hawaii.

    Science.gov (United States)

    De León, Jesse H; Neumann, Gabor; Follett, Peter A; Hollingsworth, Robert G

    2010-06-01

    We genetically characterized Encarsia diapsidicola Silvestri and Encarsia berlesei Howard (Hymenoptera: Aphelinidae) by two molecular methods: phylogenetic analysis of the cytochrome oxidase subunit I gene (COI) and intersimple sequence repeat-polymerase chain reaction (ISSR-PCR) DNA fingerprinting. These two closely related endoparasitoids are candidate biological control agents for the white peach scale, Pseudaulacaspis pentagona Targioni-Tozetti (Hemiptera: Diaspididae), in Hawaii. We developed species-specific COI molecular markers that discriminated the two species, and we tested the utility of the E. diaspidicola-specific COI marker to detect parasitism of white peach scale. The COI sequence data uncovered 46-bp differences between the two Encarsia spp. The level of COI genetic divergence between the two species was 9.7%, and the two clustered into their own clade on a parismonious phylogram. ISSR-PCR readily discriminated the two Encarsia spp. because each was observed with fixed species-specific banding patterns. The COI molecular markers were specific for each species because cross-reactivity was not observed with nontarget species. The E. diaspidicola-specific COI markers were successful at detecting parasitism of white peach scale by E. diaspidicola by 24 h. Both molecular marker types successfully discriminated the two Encarsia spp., whereas the COI markers will be useful as tools to assess levels of parasitism in the field and to study competitive interactions between parasitoids.

  2. Predictive functional profiling using marker gene sequences and community diversity analyses of microbes in full-scale anaerobic sludge digesters.

    Science.gov (United States)

    Gao, Jing; Liu, Guoji; Li, Hongping; Xu, Li; Du, Lili; Yang, Bo

    2016-07-01

    Anaerobic digestion (AD) is widely used in treating the sewage sludge, as it can reduce the amount of sludge, eliminate pathogens and produce biofuel. To enhance the operational performance and stability of anaerobic bioreactors, operational and conventional chemical data from full-scale sludge anaerobic digesters were collected over a 2-year period and summarized, and the microbial community diversity of the sludge sample was investigated at various stages of the AD process. For the purpose of distinguishing between the functional and community diversity of the microbes, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) software was used to impute the prevalence of 16S rDNA marker gene sequences in the difference in various sludge samples. Meanwhile, a taxa analysis was also carried out to investigate the different sludge samples. The microbial community diversity analysis of one AD sludge sample showed that the most dominant bacterial genera were Saccharicrinis, Syntrophus, Anaerotruncus and Thermanaerothrix. Among archaea, acetoclastic Methanosaeta represented 56.0 %, and hydrogenotrophic Methanospirillum, Methanoculleus, Methanothermus and Methanolinea accounted for 41.3 % of all methanogens. The taxa, genetic and functional prediction analyses of the feedstock and AD sludge samples suggested great community diversity differences between them. The taxa of bacteria in two AD sludge samples were considerably different, but the abundances of the functional KEGG pathways took on similar levels. The numbers of identified pathogens were significantly lower in the digested sludge than in the feedstock, but the PICRUSt results showed the difference in "human diseases" abundances in the level-1 pathway between the two sludge samples was small.

  3. Multiplex-endonuclease genotyping approach (MEGA): a tool for the fine-scale detection of unlinked polymorphic DNA markers.

    NARCIS (Netherlands)

    Agbo, E.C.; Duim, B.; Majiwa, P.A.O.; Buscher, P.; Claassen, E.; Pas, te M.F.W.

    2003-01-01

    Restriction enzyme-detectable polymorphisms have been used for assessing genetic differences and generating informative genetic markers. The most detailed fingerprinting analyses have been obtained using the AFLP (amplified fragment length polymorphism) technique, which accesses subsets of

  4. Multiplex-endonuclease genotyping approach (MEGA): a tool for the fine-scale detection of unlinked polymorphic DNA markers

    NARCIS (Netherlands)

    Agbo, Eddy Chukwura; Duim, Birgitta; Majiwa, Phelix A. O.; Büscher, Philippe; Claassen, Eric; te Pas, Marinus F. W.

    2003-01-01

    Restriction enzyme-detectable polymorphisms have been used for assessing genetic differences and generating informative genetic markers. The most detailed fingerprinting analyses have been obtained using the AFLP (amplified fragment length polymorphism) technique, which accesses subsets of

  5. Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing

    Science.gov (United States)

    2013-01-01

    Background The genetics and molecular biology of sesame has only recently begun to be studied even though sesame is an important oil seed crop. A high-density genetic map for sesame has not been published yet due to a lack of sufficient molecular markers. Specific length amplified fragment sequencing (SLAF-seq) is a recently developed high-resolution strategy for large-scale de novo SNP discovery and genotyping. SLAF-seq was employed in this study to obtain sufficient markers to construct a high-density genetic map for sesame. Results In total, 28.21 Gb of data containing 201,488,285 pair-end reads was obtained after sequencing. The average coverage for each SLAF marker was 23.48-fold in the male parent, 23.38-fold in the female parent, and 14.46-fold average in each F2 individual. In total, 71,793 high-quality SLAFs were detected of which 3,673 SLAFs were polymorphic and 1,272 of the polymorphic markers met the requirements for use in the construction of a genetic map. The final map included 1,233 markers on the 15 linkage groups (LGs) and was 1,474.87 cM in length with an average distance of 1.20 cM between adjacent markers. To our knowledge, this map is the densest genetic linkage map to date for sesame. 'SNP_only’ markers accounted for 87.51% of the markers on the map. A total of 205 markers on the map showed significant (P sesame. The map was constructed using an F2 population and the SLAF-seq approach, which allowed the efficient development of a large number of polymorphic markers in a short time. Results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for sesame, but will also serve as a reference for positioning sequence scaffolds on a physical map, to assist in the process of assembling the sesame genome sequence. PMID:24060091

  6. Polymorphisms of two neuroendocrine–correlated genes associated ...

    African Journals Online (AJOL)

    In this study, insulin-like growth factor binding protein 2 (IGFBP-2) and signal transducers activators of transcription 5b (STAT5b) gene were studied as candidate gene associated with body weight and reproductive traits of the Jinghai Yellow chicken. Single nucleotide polymorphisms (SNPs) of the IGFBP-2 and STAT5b ...

  7. Evaluation of gene association methods for coexpression network construction and biological knowledge discovery.

    Science.gov (United States)

    Kumari, Sapna; Nie, Jeff; Chen, Huann-Sheng; Ma, Hao; Stewart, Ron; Li, Xiang; Lu, Meng-Zhu; Taylor, William M; Wei, Hairong

    2012-01-01

    Constructing coexpression networks and performing network analysis using large-scale gene expression data sets is an effective way to uncover new biological knowledge; however, the methods used for gene association in constructing these coexpression networks have not been thoroughly evaluated. Since different methods lead to structurally different coexpression networks and provide different information, selecting the optimal gene association method is critical. In this study, we compared eight gene association methods - Spearman rank correlation, Weighted Rank Correlation, Kendall, Hoeffding's D measure, Theil-Sen, Rank Theil-Sen, Distance Covariance, and Pearson - and focused on their true knowledge discovery rates in associating pathway genes and construction coordination networks of regulatory genes. We also examined the behaviors of different methods to microarray data with different properties, and whether the biological processes affect the efficiency of different methods. We found that the Spearman, Hoeffding and Kendall methods are effective in identifying coexpressed pathway genes, whereas the Theil-sen, Rank Theil-Sen, Spearman, and Weighted Rank methods perform well in identifying coordinated transcription factors that control the same biological processes and traits. Surprisingly, the widely used Pearson method is generally less efficient, and so is the Distance Covariance method that can find gene pairs of multiple relationships. Some analyses we did clearly show Pearson and Distance Covariance methods have distinct behaviors as compared to all other six methods. The efficiencies of different methods vary with the data properties to some degree and are largely contingent upon the biological processes, which necessitates the pre-analysis to identify the best performing method for gene association and coexpression network construction.

  8. Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae transcriptome permits large-scale unigene assembly and SSR marker discovery.

    Directory of Open Access Journals (Sweden)

    Haibin Wang

    Full Text Available BACKGROUND: Simple sequence repeats (SSRs are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST sequences have been acquired to date, so the number of available EST-SSR markers is very low. METHODOLOGY/PRINCIPAL FINDINGS: Illumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59% unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all of the assays were transferable across species and that they exposed a significant amount of allelic diversity. CONCLUSIONS/SIGNIFICANCE: SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera.

  9. Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring

    DEFF Research Database (Denmark)

    Bekkevold, Dorte; Helyar, Sarah J.; Limborg, Morten T.

    2015-01-01

    Regulations on the exploitation of populations of commercially important fish species and the ensuing consumer interest in sustainable products have increased the need to accurately identify the population of origin of fish and fish products. Although genomics-based tools have proven highly useful...... the method's suitability to address specific biological questions, as well as management applications. We analyse temporally replicated collections from two areas, the Skagerrak (n = 81, 84, 66) and the western Baltic (n = 52, 52). Both areas harbour heavily fished mixed-origin stocks, complicating...

  10. A robust linkage map of the porcine autosome based on gene-associated SNPs

    DEFF Research Database (Denmark)

    Vingborg, Rikke K K; Gregersen, Vivi R; Zhan, Bujie

    2009-01-01

    conserved synteny. A total of 330 previously unmapped genes and ESTs were mapped to the porcine autosome while ten genes were mapped to unexpected locations. Conclusions The linkage map presented here shows high accuracy in gene order. The pedigree family network as well as the large amount of meiotic......Background Genetic linkage maps are necessary for mapping of mendelian traits and quantitative trait loci (QTLs). To identify the actual genes, which control these traits, a map based on gene-associated single nucleotide polymorphism (SNP) markers is highly valuable. In this study, the SNPs were...... genotyped in a large family material comprising more than 5,000 piglets derived from 12 Duroc boars crossed with 236 Danish Landrace/Danish Large White sows. The SNPs were identified in sequence alignments of 4,600 different amplicons obtained from the 12 boars and containing coding regions of genes derived...

  11. Multiple SNP markers reveal fine-scale population and deep phylogeographic structure in European anchovy (Engraulis encrasicolus L.).

    KAUST Repository

    Zarraonaindia, Iratxe

    2012-07-30

    Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian

  12. Genetic structure of earthworm populations at a regional scale: inferences from mitochondrial and microsatellite molecular markers in Aporrectodea icterica (Savigny 1826).

    Science.gov (United States)

    Torres-Leguizamon, Magally; Mathieu, Jérôme; Decaëns, Thibaud; Dupont, Lise

    2014-01-01

    Despite the fundamental role that soil invertebrates (e.g. earthworms) play in soil ecosystems, the magnitude of their spatial genetic variation is still largely unknown and only a few studies have investigated the population genetic structure of these organisms. Here, we investigated the genetic structure of seven populations of a common endogeic earthworm (Aporrectodea icterica) sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale. Because combining markers with distinct modes of inheritance can provide extra, complementary information on gene flow, we compared the patterns of genetic structure revealed using nuclear (7 microsatellite loci) and mitochondrial markers (COI). Both types of markers indicated low genetic polymorphism compared to other earthworm species, a result that can be attributed to ancient bottlenecks, for instance due to species isolation in southern refugia during the ice ages with subsequent expansion toward northern Europe. Historical events can also be responsible for the existence of two divergent, but randomly interbreeding mitochondrial lineages within all study populations. In addition, the comparison of observed heterozygosity among microsatellite loci and heterozygosity expected under mutation-drift equilibrium suggested a recent decrease in effective size in some populations that could be due to contemporary events such as habitat fragmentation. The absence of relationship between geographic and genetic distances estimated from microsatellite allele frequency data also suggested that dispersal is haphazard and that human activities favour passive dispersal among geographically distant populations.

  13. Genetic structure of earthworm populations at a regional scale: inferences from mitochondrial and microsatellite molecular markers in Aporrectodea icterica (Savigny 1826.

    Directory of Open Access Journals (Sweden)

    Magally Torres-Leguizamon

    Full Text Available Despite the fundamental role that soil invertebrates (e.g. earthworms play in soil ecosystems, the magnitude of their spatial genetic variation is still largely unknown and only a few studies have investigated the population genetic structure of these organisms. Here, we investigated the genetic structure of seven populations of a common endogeic earthworm (Aporrectodea icterica sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale. Because combining markers with distinct modes of inheritance can provide extra, complementary information on gene flow, we compared the patterns of genetic structure revealed using nuclear (7 microsatellite loci and mitochondrial markers (COI. Both types of markers indicated low genetic polymorphism compared to other earthworm species, a result that can be attributed to ancient bottlenecks, for instance due to species isolation in southern refugia during the ice ages with subsequent expansion toward northern Europe. Historical events can also be responsible for the existence of two divergent, but randomly interbreeding mitochondrial lineages within all study populations. In addition, the comparison of observed heterozygosity among microsatellite loci and heterozygosity expected under mutation-drift equilibrium suggested a recent decrease in effective size in some populations that could be due to contemporary events such as habitat fragmentation. The absence of relationship between geographic and genetic distances estimated from microsatellite allele frequency data also suggested that dispersal is haphazard and that human activities favour passive dispersal among geographically distant populations.

  14. PCAN: phenotype consensus analysis to support disease-gene association.

    Science.gov (United States)

    Godard, Patrice; Page, Matthew

    2016-12-07

    Bridging genotype and phenotype is a fundamental biomedical challenge that underlies more effective target discovery and patient-tailored therapy. Approaches that can flexibly and intuitively, integrate known gene-phenotype associations in the context of molecular signaling networks are vital to effectively prioritize and biologically interpret genes underlying disease traits of interest. We describe Phenotype Consensus Analysis (PCAN); a method to assess the consensus semantic similarity of phenotypes in a candidate gene's signaling neighborhood. We demonstrate that significant phenotype consensus (p disease-gene associations, using a combination of high quality String interactions + Metabase pathways and use Joubert Syndrome to demonstrate the ease with which a significant result can be interrogated to highlight discriminatory traits linked to mechanistically related genes. We advocate phenotype consensus as an intuitive and versatile method to aid disease-gene association, which naturally lends itself to the mechanistic deconvolution of diverse phenotypes. We provide PCAN to the community as an R package ( http://bioconductor.org/packages/PCAN/ ) to allow flexible configuration, extension and standalone use or integration to supplement existing gene prioritization workflows.

  15. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery.

    Science.gov (United States)

    Kaur, Sukhjiwan; Cogan, Noel O I; Pembleton, Luke W; Shinozuka, Maiko; Savin, Keith W; Materne, Michael; Forster, John W

    2011-05-25

    Lentil (Lens culinaris Medik.) is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality. Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 106 expressed sequence tags (ESTs). De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR)-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism. A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.

  16. Transcriptome sequencing of lentil based on second-generation technology permits large-scale unigene assembly and SSR marker discovery

    Directory of Open Access Journals (Sweden)

    Materne Michael

    2011-05-01

    Full Text Available Abstract Background Lentil (Lens culinaris Medik. is a cool-season grain legume which provides a rich source of protein for human consumption. In terms of genomic resources, lentil is relatively underdeveloped, in comparison to other Fabaceae species, with limited available data. There is hence a significant need to enhance such resources in order to identify novel genes and alleles for molecular breeding to increase crop productivity and quality. Results Tissue-specific cDNA samples from six distinct lentil genotypes were sequenced using Roche 454 GS-FLX Titanium technology, generating c. 1.38 × 106 expressed sequence tags (ESTs. De novo assembly generated a total of 15,354 contigs and 68,715 singletons. The complete unigene set was sequence-analysed against genome drafts of the model legume species Medicago truncatula and Arabidopsis thaliana to identify 12,639, and 7,476 unique matches, respectively. When compared to the genome of Glycine max, a total of 20,419 unique hits were observed corresponding to c. 31% of the known gene space. A total of 25,592 lentil unigenes were subsequently annoated from GenBank. Simple sequence repeat (SSR-containing ESTs were identified from consensus sequences and a total of 2,393 primer pairs were designed. A subset of 192 EST-SSR markers was screened for validation across a panel 12 cultivated lentil genotypes and one wild relative species. A total of 166 primer pairs obtained successful amplification, of which 47.5% detected genetic polymorphism. Conclusions A substantial collection of ESTs has been developed from sequence analysis of lentil genotypes using second-generation technology, permitting unigene definition across a broad range of functional categories. As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.

  17. Mapping the MMPI-2/MMPI-2-RF Restructured Clinical Scales Onto Mood Markers in an Israeli Sample.

    Science.gov (United States)

    Shkalim, Eleanor; Ben-Porath, Yossef S; Almagor, Moshe

    2016-01-01

    This study cross-culturally evaluated the Minnesota Multiphasic Personality Inventory-2/MMPI-2 Restructured Form (MMPI-2/MMPI-2-RF) emotion-focused Restructured Clinical (RC) Scales to examine whether their patterns of associations with positive affect (PA) and negative affect (NA) are as expected based on Tellegen, Watson, and Clark's ( 1999a , 1999b ) mood model. The sample was composed of 100 men and 133 women from psychiatric settings in Israel who completed the MMPI-2 and the Mood Check List (MCL; Zevon & Tellegen, 1982 ). Results indicated that RCd was substantially correlated with both PA and NA in opposite directions, and that RC2 and RC7 were more highly correlated with PA and NA, respectively. Further, when compared with their Clinical Scale counterparts, RC2 and RC7 exhibited comparable convergent validities and improved discriminant properties. Findings provide support for Tellegen et al.'s ( 2003 ) goal to link the RC scales to contemporary conceptualizations of mood.

  18. Influence of Adalimumab on the Expression Profile of Genes Associated with the Histaminergic System in the Skin Fibroblasts In Vitro

    Directory of Open Access Journals (Sweden)

    Dominika Wcisło-Dziadecka

    2018-01-01

    Full Text Available Objective. The aim of this study was to evaluate the influence of adalimumab on expression profile of genes associated with the histaminergic system in Normal Human Dermal Fibroblast (NHDF cells stimulated with 8.00 μg/ml of adalimumab and the identification of miRNAs regulating these genes’ expression. Methods. NHDFs were cultured with or without the presence of adalimumab for 2, 8, and 24 hours. The expression profile of genes and miRNA were determined with the use of microarray technology. Results. Among 22283 ID mRNA, 65 are associated with the histaminergic system. It can be observed that 15 mRNAs differentiate NHDFs cultures with adalimumab form control. The analysis of miRNAs showed that, among 1105 ID miRNA, 20 miRNAs are differentiating in cells treated with adalimumab for 2 hours, 9 miRNA after 8 hours, and only 3 miRNAs after 24 hours. Conclusion. It was also determined that miRNAs play certain role in the regulation of the expression of genes associated with the histaminergic system. The results of this study confirmed the possibility of using both genes associated with this system as well as miRNAs regulating their expression, as complementary molecular markers of sensitivity to the adalimumab treatment.

  19. Trehalose as a stress marker of the physiological impact of mixing on yeast production: scale-down reactors and mini-bioreactors investigations

    Directory of Open Access Journals (Sweden)

    Thonart, P.

    2010-01-01

    Full Text Available Trehalose is a reserve carbohydrate produced by Saccharomyces cerevisiae under stress conditions and used as a cryoprotectant during freeze drying. So the cellular content of trehalose is an important parameter to control in industrial context. Scale-down reactors have been used to produce Saccharomyces cerevisiae. These reactors permit to mimic the hydrodynamic conditions experienced by cells during large scale production. Three types of scale-down reactors have been tested, differing by the geometry of the non-mixed part and the recirculation flow rate. The results show that cells cultivated in scale-down reactors produced less trehalose compared to the reference reactor. These results are completed by the study of the expression of the TPS2 promoter coupled with a green fluorescent protein (GFP. TPS2 is a gene coding for a subunit of the enzymatic complex responsible of trehalose synthesis. This strain was produced in mini-bioreactors which are shake flasks equipped with a dissolved oxygen probe. This approach allows using trehalose, or related enzymes, as a cellular marker of the stress encountered by yeast in industrial process.

  20. Major histocompatibility complex and other allergy-related candidate genes associated with insect bite hypersensitivity in Icelandic horses.

    Science.gov (United States)

    Klumplerova, Marie; Vychodilova, Leona; Bobrova, Olga; Cvanova, Michaela; Futas, Jan; Janova, Eva; Vyskocil, Mirko; Vrtkova, Irena; Putnova, Lenka; Dusek, Ladislav; Marti, Eliane; Horin, Petr

    2013-04-01

    Insect bite hypersensitivity (IBH) is an allergic dermatitis of horses caused by bites of insects. IBH is a multifactorial disease with contribution of genetic and environmental factors. Candidate gene association analysis of IBH was performed in a group of 89 Icelandic horses all born in Iceland and imported to Europe. Horses were classified in IBH-affected and non-affected based on clinical signs and history of recurrent dermatitis, and on the results of an in vitro sulfidoleukotriene (sLT)-release assay with Culicoides nubeculosus and Simulium vittatum extract. Different genetic markers were tested for association with IBH by the Fisher's exact test. The effect of the major histocompatibility complex (MHC) gene region was studied by genotyping five microsatellites spanning the MHC region (COR112, COR113, COR114, UM011 and UMN-JH34-2), and exon 2 polymorphisms of the class II Eqca-DRA gene. Associations with Eqca-DRA and COR113 were identified (p initial screen, no marker from the panel was significantly (p studies.

  1. DDPC: Dragon database of genes associated with prostate cancer

    KAUST Repository

    Maqungo, Monique

    2010-09-29

    Prostate cancer (PC) is one of the most commonly diagnosed cancers in men. PC is relatively difficult to diagnose due to a lack of clear early symptoms. Extensive research of PC has led to the availability of a large amount of data on PC. Several hundred genes are implicated in different stages of PC, which may help in developing diagnostic methods or even cures. In spite of this accumulated information, effective diagnostics and treatments remain evasive. We have developed Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC. We believe this resource will serve as a source of useful information for research on PC. DDPC is freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/ddpc/ and http://cbrc .kaust.edu.sa/ddpc/. The Author(s) 2010.

  2. DDPC: Dragon Database of Genes associated with Prostate Cancer.

    Science.gov (United States)

    Maqungo, Monique; Kaur, Mandeep; Kwofie, Samuel K; Radovanovic, Aleksandar; Schaefer, Ulf; Schmeier, Sebastian; Oppon, Ekow; Christoffels, Alan; Bajic, Vladimir B

    2011-01-01

    Prostate cancer (PC) is one of the most commonly diagnosed cancers in men. PC is relatively difficult to diagnose due to a lack of clear early symptoms. Extensive research of PC has led to the availability of a large amount of data on PC. Several hundred genes are implicated in different stages of PC, which may help in developing diagnostic methods or even cures. In spite of this accumulated information, effective diagnostics and treatments remain evasive. We have developed Dragon Database of Genes associated with Prostate Cancer (DDPC) as an integrated knowledgebase of genes experimentally verified as implicated in PC. DDPC is distinctive from other databases in that (i) it provides pre-compiled biomedical text-mining information on PC, which otherwise require tedious computational analyses, (ii) it integrates data on molecular interactions, pathways, gene ontologies, gene regulation at molecular level, predicted transcription factor binding sites on promoters of PC implicated genes and transcription factors that correspond to these binding sites and (iii) it contains DrugBank data on drugs associated with PC. We believe this resource will serve as a source of useful information for research on PC. DDPC is freely accessible for academic and non-profit users via http://apps.sanbi.ac.za/ddpc/ and http://cbrc.kaust.edu.sa/ddpc/.

  3. DNA mutation motifs in the genes associated with inherited diseases.

    Science.gov (United States)

    Růžička, Michal; Kulhánek, Petr; Radová, Lenka; Čechová, Andrea; Špačková, Naďa; Fajkusová, Lenka; Réblová, Kamila

    2017-01-01

    Mutations in human genes can be responsible for inherited genetic disorders and cancer. Mutations can arise due to environmental factors or spontaneously. It has been shown that certain DNA sequences are more prone to mutate. These sites are termed hotspots and exhibit a higher mutation frequency than expected by chance. In contrast, DNA sequences with lower mutation frequencies than expected by chance are termed coldspots. Mutation hotspots are usually derived from a mutation spectrum, which reflects particular population where an effect of a common ancestor plays a role. To detect coldspots/hotspots unaffected by population bias, we analysed the presence of germline mutations obtained from HGMD database in the 5-nucleotide segments repeatedly occurring in genes associated with common inherited disorders, in particular, the PAH, LDLR, CFTR, F8, and F9 genes. Statistically significant sequences (mutational motifs) rarely associated with mutations (coldspots) and frequently associated with mutations (hotspots) exhibited characteristic sequence patterns, e.g. coldspots contained purine tract while hotspots showed alternating purine-pyrimidine bases, often with the presence of CpG dinucleotide. Using molecular dynamics simulations and free energy calculations, we analysed the global bending properties of two selected coldspots and two hotspots with a G/T mismatch. We observed that the coldspots were inherently more flexible than the hotspots. We assume that this property might be critical for effective mismatch repair as DNA with a mutation recognized by MutSα protein is noticeably bent.

  4. Candidate gene association studies in syndromic and non-syndromic cleft lip and palate

    Energy Technology Data Exchange (ETDEWEB)

    Daack-Hirsch, S.; Basart, A.; Frischmeyer, P. [Univ. of Iowa, IA (United States)] [and others

    1994-09-01

    Using ongoing case ascertainment through a birth defects registry, we have collected 219 nuclear families with non-syndromic cleft lip and/or palate and 111 families with a collection of syndromic forms. Syndromic cases include 24 with recognized forms and 72 with unrecognized syndromes. Candidate gene studies as well as genome-wide searches for evidence of microdeletions and isodisomy are currently being carried out. Candidate gene association studies, to date, have made use of PCR-based polymorphisms for TGFA, MSX1, CLPG13 (a CA repeat associated with a human homologue of a locus that results in craniofacial dysmorphogenesis in the mouse) and an STRP found in a Van der Woude syndrome microdeletion. Control tetranucleotide repeats, which insure that population-based differences are not responsible for any observed associations, are also tested. Studies of the syndromic cases have included the same list of candidate genes searching for evidence of microdeletions and a genome-wide search using tri- and tetranucleotide polymorphic markers to search for isodisomy or structural rearrangements. Significant associations have previously been identified for TGFA, and, in this report, identified for MSX1 and nonsyndromic cleft palate only (p = 0.04, uncorrected). Preliminary results of the genome-wide scan for isodisomy has returned no true positives and there has been no evidence for microdeletion cases.

  5. Assessment of molecular markers for anti-malarial drug resistance after the introduction and scale-up of malaria control interventions in western Kenya.

    Science.gov (United States)

    Shah, Monica; Omosun, Yusuf; Lal, Ashima; Odero, Christopher; Gatei, Wangeci; Otieno, Kephas; Gimnig, John E; ter Kuile, Feiko; Hawley, William A; Nahlen, Bernard; Kariuki, Simon; Walker, Edward; Slutsker, Laurence; Hamel, Mary; Shi, Ya Ping

    2015-02-14

    Although it is well known that drug pressure selects for drug-resistant parasites, the role of transmission reduction by insecticide-treated bed nets (ITNs) on drug resistance remains unclear. In this study, the drug resistance profile of current and previous first-line anti-malarials in Kenya was assessed within the context of drug policy change and scale-up of ITNs. National first-line treatment changed from chloroquine (CQ) to sulphadoxine-pyrimethamine (SP) in 1998 and to artemether-lumefantrine (AL) in 2004. ITN use was scaled-up in the Asembo, Gem and Karemo areas of western Kenya in 1997, 1999 and 2006, respectively. Smear-positive samples (N = 253) collected from a 2007 cross-sectional survey among children in Asembo, Gem and Karemo were genotyped for mutations in pfcrt and pfmdr1 (CQ), dhfr and dhps (SP), and at pfmdr-N86 and the gene copy number in pfmdr1 (lumefantrine). Results were compared among the three geographic areas in 2007 and to retrospective molecular data from children in Asembo in 2001. In 2007, 69 and 85% of samples harboured the pfmdr1-86Y mutation and dhfr/dhps quintuple mutant, respectively, with no significant differences by study area. However, the prevalence of the pfcrt-76T mutation differed significantly among areas (p dhps-436A, or dhps-613T. From 2001 to 2007, there were significant increases in the pfcrt-76T mutation from 82 to 94% (p dhps quintuple mutant from 62 to 82% (p drug pressure from the continued use of CQ, SP, and mechanistically similar drugs, such as amodiaquine and cotrimoxazole. There was no clear evidence that differences in transmission intensity, as a result of ITN scale-up, influenced the prevalence of drug resistance molecular markers.

  6. Identification of methylated genes associated with aggressive bladder cancer.

    Directory of Open Access Journals (Sweden)

    Carmen J Marsit

    Full Text Available Approximately 500,000 individuals diagnosed with bladder cancer in the U.S. require routine cystoscopic follow-up to monitor for disease recurrences or progression, resulting in over $2 billion in annual expenditures. Identification of new diagnostic and monitoring strategies are clearly needed, and markers related to DNA methylation alterations hold great promise due to their stability, objective measurement, and known associations with the disease and with its clinical features. To identify novel epigenetic markers of aggressive bladder cancer, we utilized a high-throughput DNA methylation bead-array in two distinct population-based series of incident bladder cancer (n = 73 and n = 264, respectively. We then validated the association between methylation of these candidate loci with tumor grade in a third population (n = 245 through bisulfite pyrosequencing of candidate loci. Array based analyses identified 5 loci for further confirmation with bisulfite pyrosequencing. We identified and confirmed that increased promoter methylation of HOXB2 is significantly and independently associated with invasive bladder cancer and methylation of HOXB2, KRT13 and FRZB together significantly predict high-grade non-invasive disease. Methylation of these genes may be useful as clinical markers of the disease and may point to genes and pathways worthy of additional examination as novel targets for therapeutic treatment.

  7. DCAF4, a novel gene associated with leucocyte telomere length

    Science.gov (United States)

    Mangino, Massimo; Christiansen, Lene; Stone, Rivka; Hunt, Steven C; Horvath, Kent; Eisenberg, Dan T A; Kimura, Masayuki; Petersen, Inge; Kark, Jeremy D; Herbig, Utz; Reiner, Alex P; Benetos, Athanase; Codd, Veryan; Nyholt, Dale R; Sinnreich, Ronit; Christensen, Kaare; Nassar, Hisham; Hwang, Shih-Jen; Levy, Daniel; Bataille, Veronique; Fitzpatrick, Annette L; Chen, Wei; Berenson, Gerald S; Samani, Nilesh J; Martin, Nicholas G; Tishkoff, Sarah; Schork, Nicholas J; Kyvik, Kirsten Ohm; Dalgård, Christine; Spector, Timothy D; Aviv, Abraham

    2015-01-01

    Background Leucocyte telomere length (LTL), which is fashioned by multiple genes, has been linked to a host of human diseases, including sporadic melanoma. A number of genes associated with LTL have already been identified through genome-wide association studies. The main aim of this study was to establish whether DCAF4 (DDB1 and CUL4-associated factor 4) is associated with LTL. In addition, using ingenuity pathway analysis (IPA), we examined whether LTL-associated genes in the general population might partially explain the inherently longer LTL in patients with sporadic melanoma, the risk for which is increased with ultraviolet radiation (UVR). Results Genome-wide association (GWA) meta-analysis and de novo genotyping of 20 022 individuals revealed a novel association (p=6.4×10−10) between LTL and rs2535913, which lies within DCAF4. Notably, eQTL analysis showed that rs2535913 is associated with decline in DCAF4 expressions in both lymphoblastoid cells and sun-exposed skin (p=4.1×10−3 and 2×10−3, respectively). Moreover, IPA revealed that LTL-associated genes, derived from GWA meta-analysis (N=9190), are over-represented among genes engaged in melanoma pathways. Meeting increasingly stringent p value thresholds (p<0.05, <0.01, <0.005, <0.001) in the LTL-GWA meta-analysis, these genes were jointly over-represented for melanoma at p values ranging from 1.97×10−169 to 3.42×10−24. Conclusions We uncovered a new locus associated with LTL in the general population. We also provided preliminary findings that suggest a link of LTL through genetic mechanisms with UVR and melanoma in the general population. PMID:25624462

  8. Marker chromosomes.

    Science.gov (United States)

    Rao, Kiran Prabhaker; Belogolovkin, Victoria

    2013-04-01

    Marker chromosomes are a morphologically heterogeneous group of structurally abnormal chromosomes that pose a significant challenge in prenatal diagnosis. Phenotypes associated with marker chromosomes are highly variable and range from normal to severely abnormal. Clinical outcomes are very difficult to predict when marker chromosomes are detected prenatally. In this review, we outline the classification, etiology, cytogenetic characterization, and clinical consequences of marker chromosomes, as well as practical approaches to prenatal diagnosis and genetic counseling.

  9. Large scale fusion of gray matter and resting-state functional MRI reveals common and shared biological markers across the psychosis spectrum in the B-SNIP cohort

    Directory of Open Access Journals (Sweden)

    Zheng eWang

    2015-12-01

    Full Text Available To investigate whether aberrant interactions between brain structure and function present similarly or differently across probands with psychotic illnesses (schizophrenia (SZ, schizoaffective disorder (SAD, and bipolar I disorder with psychosis (BP and whether these deficits are shared with their first-degree non-psychotic relatives. A total of 1199 subjects were assessed, including 220 SZ, 147 SAD, 180 psychotic BP, 150 first-degree relatives of SZ, 126 SAD relatives, 134 BP relatives and 242 healthy controls. All subjects underwent structural MRI (sMRI and resting-state functional MRI (rs-fMRI scanning. Joint independent analysis (jICA was used to fuse sMRI gray matter (GM and rs-fMRI amplitude of low frequency fluctuations (ALFF data to identify the relationship between the two modalities. Joint ICA revealed two significantly fused components. The association between functional brain alteration in a prefrontal-striatal-thalamic-cerebellar network and structural abnormalities in the default mode network (DMN was found to be common across psychotic diagnoses and correlated with cognitive function, social function and Schizo-Bipolar Scale (SBS scores. The fused alteration in the temporal lobe was unique to SZ and SAD. The above effects were not seen in any relative group (including those with cluster-A personality. Using a multivariate fused approach involving two widely used imaging markers we demonstrate both shared and distinct biological traits across the psychosis spectrum. Further, our results suggest that the above traits are psychosis biomarkers rather than endophenotypes.

  10. SNP-SNP interaction network in angiogenesis genes associated with prostate cancer aggressiveness.

    Science.gov (United States)

    Lin, Hui-Yi; Amankwah, Ernest K; Tseng, Tung-Sung; Qu, Xiaotao; Chen, Dung-Tsa; Park, Jong Y

    2013-01-01

    Angiogenesis has been shown to be associated with prostate cancer development. The majority of prostate cancer studies focused on individual single nucleotide polymorphisms (SNPs) while SNP-SNP interactions are suggested having a great impact on unveiling the underlying mechanism of complex disease. Using 1,151 prostate cancer patients in the Cancer Genetic Markers of Susceptibility (CGEMS) dataset, 2,651 SNPs in the angiogenesis genes associated with prostate cancer aggressiveness were evaluated. SNP-SNP interactions were primarily assessed using the two-stage Random Forests plus Multivariate Adaptive Regression Splines (TRM) approach in the CGEMS group, and were then re-evaluated in the Moffitt group with 1,040 patients. For the identified gene pairs, cross-evaluation was applied to evaluate SNP interactions in both study groups. Five SNP-SNP interactions in three gene pairs (MMP16+ ROBO1, MMP16+ CSF1, and MMP16+ EGFR) were identified to be associated with aggressive prostate cancer in both groups. Three pairs of SNPs (rs1477908+ rs1387665, rs1467251+ rs7625555, and rs1824717+ rs7625555) were in MMP16 and ROBO1, one pair (rs2176771+ rs333970) in MMP16 and CSF1, and one pair (rs1401862+ rs6964705) in MMP16 and EGFR. The results suggest that MMP16 may play an important role in prostate cancer aggressiveness. By integrating our novel findings and available biomedical literature, a hypothetical gene interaction network was proposed. This network demonstrates that our identified SNP-SNP interactions are biologically relevant and shows that EGFR may be the hub for the interactions. The findings provide valuable information to identify genotype combinations at risk of developing aggressive prostate cancer and improve understanding on the genetic etiology of angiogenesis associated with prostate cancer aggressiveness.

  11. SNP-SNP interaction network in angiogenesis genes associated with prostate cancer aggressiveness.

    Directory of Open Access Journals (Sweden)

    Hui-Yi Lin

    Full Text Available Angiogenesis has been shown to be associated with prostate cancer development. The majority of prostate cancer studies focused on individual single nucleotide polymorphisms (SNPs while SNP-SNP interactions are suggested having a great impact on unveiling the underlying mechanism of complex disease. Using 1,151 prostate cancer patients in the Cancer Genetic Markers of Susceptibility (CGEMS dataset, 2,651 SNPs in the angiogenesis genes associated with prostate cancer aggressiveness were evaluated. SNP-SNP interactions were primarily assessed using the two-stage Random Forests plus Multivariate Adaptive Regression Splines (TRM approach in the CGEMS group, and were then re-evaluated in the Moffitt group with 1,040 patients. For the identified gene pairs, cross-evaluation was applied to evaluate SNP interactions in both study groups. Five SNP-SNP interactions in three gene pairs (MMP16+ ROBO1, MMP16+ CSF1, and MMP16+ EGFR were identified to be associated with aggressive prostate cancer in both groups. Three pairs of SNPs (rs1477908+ rs1387665, rs1467251+ rs7625555, and rs1824717+ rs7625555 were in MMP16 and ROBO1, one pair (rs2176771+ rs333970 in MMP16 and CSF1, and one pair (rs1401862+ rs6964705 in MMP16 and EGFR. The results suggest that MMP16 may play an important role in prostate cancer aggressiveness. By integrating our novel findings and available biomedical literature, a hypothetical gene interaction network was proposed. This network demonstrates that our identified SNP-SNP interactions are biologically relevant and shows that EGFR may be the hub for the interactions. The findings provide valuable information to identify genotype combinations at risk of developing aggressive prostate cancer and improve understanding on the genetic etiology of angiogenesis associated with prostate cancer aggressiveness.

  12. Systematic identification of latent disease-gene associations from PubMed articles.

    Science.gov (United States)

    Zhang, Yuji; Shen, Feichen; Mojarad, Majid Rastegar; Li, Dingcheng; Liu, Sijia; Tao, Cui; Yu, Yue; Liu, Hongfang

    2018-01-01

    Recent scientific advances have accumulated a tremendous amount of biomedical knowledge providing novel insights into the relationship between molecular and cellular processes and diseases. Literature mining is one of the commonly used methods to retrieve and extract information from scientific publications for understanding these associations. However, due to large data volume and complicated associations with noises, the interpretability of such association data for semantic knowledge discovery is challenging. In this study, we describe an integrative computational framework aiming to expedite the discovery of latent disease mechanisms by dissecting 146,245 disease-gene associations from over 25 million of PubMed indexed articles. We take advantage of both Latent Dirichlet Allocation (LDA) modeling and network-based analysis for their capabilities of detecting latent associations and reducing noises for large volume data respectively. Our results demonstrate that (1) the LDA-based modeling is able to group similar diseases into disease topics; (2) the disease-specific association networks follow the scale-free network property; (3) certain subnetwork patterns were enriched in the disease-specific association networks; and (4) genes were enriched in topic-specific biological processes. Our approach offers promising opportunities for latent disease-gene knowledge discovery in biomedical research.

  13. Molecular markers in maize breeding

    Directory of Open Access Journals (Sweden)

    Treskić Sanja

    2011-01-01

    Full Text Available Today the marker assisted selection (MAS is being routinely applied in breeding programs of large private companies. However, the implementation of molecular markers for commercial use in small companies and public sec- tor is on a considerably smaller scale. Numerous researches on QTL mapping, theoretical analysis and simulation models for MAS give impetus to new research on the validation of quantitative trait loci and the application of molecular markers in maize breeding. This paper presents basic concepts related to MAS, the principles of QTL mapping, marker-trait association analysis and examples of successful application of markers in breeding for qualitative and quantitative traits.

  14. Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology.

    Science.gov (United States)

    Hallingbäck, Henrik R; Fogelqvist, Johan; Powers, Stephen J; Turrion-Gomez, Juan; Rossiter, Rachel; Amey, Joanna; Martin, Tom; Weih, Martin; Gyllenstrand, Niclas; Karp, Angela; Lagercrantz, Ulf; Hanley, Steven J; Berlin, Sofia; Rönnberg-Wästljung, Ann-Christin

    2016-05-01

    Willow species (Salix) are important as short-rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker-assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnäs, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype-by-environment interactions (G × E) on trait-marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation (Radj2) explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR < 0.2) with bud burst. The rare homozygous genotype exhibited 0.4-1.0 lower bud burst scores than the other genotype classes on a five-grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small Radj2 estimates and to considerable G × E interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32-0.61).

  15. Common alleles in candidate susceptibility genes associated with risk and development of epithelial ovarian cancer

    DEFF Research Database (Denmark)

    Notaridou, Maria; Quaye, Lydia; Dafou, Dimitra

    2011-01-01

    Common germline genetic variation in the population is associated with susceptibility to epithelial ovarian cancer. Microcell-mediated chromosome transfer and expression microarray analysis identified nine genes associated with functional suppression of tumorogenicity in ovarian cancer cell lines...

  16. Polymorphisms in FGFBP1 and FGFBP2 genes associated with carcass and meat quality traits in chickens.

    Science.gov (United States)

    Felício, A M; Boschiero, C; Balieiro, J C C; Ledur, M C; Ferraz, J B S; Moura, A S A M T; Coutinho, L L

    2013-01-24

    In the past, the focus of broiler breeding programs on yield and carcass traits improvement led to problems related to meat quality. Awareness of public concern for quality resulted in inclusion of meat quality traits in the evaluation process. Nevertheless, few genes associated with meat quality attributes are known. Previous studies mapped quantitative trait loci for weight at 35 and 42 days in a region of GGA4 flanked by the microsatellite markers, MCW0240 and LEI0063. In this region, there are 2 fibroblast growth factor binding protein (FGFBP) genes that play an important role in embryogenesis, cellular differentiation, and proliferation in chickens. The objective of this study was to identify and associate single nucleotide polymorphisms (SNPs) in FGFBP1 and FGFBP2 with performance, carcass, and meat quality in experimental and commercial chicken populations. In the commercial population, SNP g.2014G>A in FGFBP1 was associated with decreased carcass weight (P A in FGFBP2 was associated with thawing loss and meat redness content (P meat redness content. The diplotypes were associated with thawing loss, lightness, and redness content. The SNPs evaluated in the present study may be used as markers in poultry breeding programs to aid in improving growth and meat quality traits.

  17. (SSR) markers

    African Journals Online (AJOL)

    uwerhiavwe

    Variability was observed for six ... rapid increase in climate change, so there is need to develop high yielding ... the past decade including assessment of genetic diversity in maize ... The SSR gel images and marker data were processed using.

  18. A seven-marker signature and clinical outcome in malignant melanoma: a large-scale tissue-microarray study with two independent patient cohorts.

    Directory of Open Access Journals (Sweden)

    Stefanie Meyer

    Full Text Available BACKGROUND: Current staging methods such as tumor thickness, ulceration and invasion of the sentinel node are known to be prognostic parameters in patients with malignant melanoma (MM. However, predictive molecular marker profiles for risk stratification and therapy optimization are not yet available for routine clinical assessment. METHODS AND FINDINGS: Using tissue microarrays, we retrospectively analyzed samples from 364 patients with primary MM. We investigated a panel of 70 immunohistochemical (IHC antibodies for cell cycle, apoptosis, DNA mismatch repair, differentiation, proliferation, cell adhesion, signaling and metabolism. A marker selection procedure based on univariate Cox regression and multiple testing correction was employed to correlate the IHC expression data with the clinical follow-up (overall and recurrence-free survival. The model was thoroughly evaluated with two different cross validation experiments, a permutation test and a multivariate Cox regression analysis. In addition, the predictive power of the identified marker signature was validated on a second independent external test cohort (n=225. A signature of seven biomarkers (Bax, Bcl-X, PTEN, COX-2, loss of β-Catenin, loss of MTAP, and presence of CD20 positive B-lymphocytes was found to be an independent negative predictor for overall and recurrence-free survival in patients with MM. The seven-marker signature could also predict a high risk of disease recurrence in patients with localized primary MM stage pT1-2 (tumor thickness ≤2.00 mm. In particular, three of these markers (MTAP, COX-2, Bcl-X were shown to offer direct therapeutic implications. CONCLUSIONS: The seven-marker signature might serve as a prognostic tool enabling physicians to selectively triage, at the time of diagnosis, the subset of high recurrence risk stage I-II patients for adjuvant therapy. Selective treatment of those patients that are more likely to develop distant metastatic disease could

  19. Identification of maize genes associated with host plant resistance or susceptibility to Aspergillus flavus infection and aflatoxin accumulation.

    Directory of Open Access Journals (Sweden)

    Rowena Y Kelley

    Full Text Available BACKGROUND: Aspergillus flavus infection and aflatoxin contamination of maize pose negative impacts in agriculture and health. Commercial maize hybrids are generally susceptible to this fungus. Significant levels of host plant resistance have been observed in certain maize inbred lines. This study was conducted to identify maize genes associated with host plant resistance or susceptibility to A. flavus infection and aflatoxin accumulation. RESULTS: Genome wide gene expression levels with or without A. flavus inoculation were compared in two resistant maize inbred lines (Mp313E and Mp04:86 in contrast to two susceptible maize inbred lines (Va35 and B73 by microarray analysis. Principal component analysis (PCA was used to find genes contributing to the larger variances associated with the resistant or susceptible maize inbred lines. The significance levels of gene expression were determined by using SAS and LIMMA programs. Fifty candidate genes were selected and further investigated by quantitative RT-PCR (qRT-PCR in a time-course study on Mp313E and Va35. Sixteen of the candidate genes were found to be highly expressed in Mp313E and fifteen in Va35. Out of the 31 highly expressed genes, eight were mapped to seven previously identified quantitative trait locus (QTL regions. A gene encoding glycine-rich RNA binding protein 2 was found to be associated with the host hypersensitivity and susceptibility in Va35. A nuclear pore complex protein YUP85-like gene was found to be involved in the host resistance in Mp313E. CONCLUSION: Maize genes associated with host plant resistance or susceptibility were identified by a combination of microarray analysis, qRT-PCR analysis, and QTL mapping methods. Our findings suggest that multiple mechanisms are involved in maize host plant defense systems in response to Aspergillus flavus infection and aflatoxin accumulation. These findings will be important in identification of DNA markers for breeding maize lines

  20. Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain

    Science.gov (United States)

    Krienen, Fenna M.; Yeo, B. T. Thomas; Ge, Tian; Buckner, Randy L.; Sherwood, Chet C.

    2016-01-01

    The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute’s human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections. PMID:26739559

  1. Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain.

    Science.gov (United States)

    Krienen, Fenna M; Yeo, B T Thomas; Ge, Tian; Buckner, Randy L; Sherwood, Chet C

    2016-01-26

    The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute's human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections.

  2. MMPI-A scores and high points of male juvenile delinquents: scales 4, 5, and 6 as markers of juvenile delinquency.

    Science.gov (United States)

    Morton, Todd L; Farris, Kelly L; Brenowitz, Lisa H

    2002-09-01

    The Minnesota Multiphasic Personality Inventory-Adolescent (MMPI-A) clinical, supplementary, and content scale score patterns for 655 male delinquents were examined. Low scores on Scale 5 (Masculinity/Femininity) were found to be the most frequent deviation, followed by elevations on Scales 6 (Paranoia) and 4 (Psychopathic Deviate). This is consistent with previous research, although the importance of Scale 5 deviations has been little noted because of the traditional focus on scale elevations only. Classification analysis indicated that a combination of MMPI-A scales discriminated between this delinquent sample and the normative sample, with a sensitivity of 90%-95% and a specificity of 80%-85%. This level of sensitivity was maintained in a replication sample (N = 473).

  3. (SSR) markers

    African Journals Online (AJOL)

    HP-PROBOOK

    2016-10-05

    Oct 5, 2016 ... Cluster analysis was constructed using DARwin program version 6.0. Forty eight (48) coconut individuals were clustered into three groups. Key words: Coconut palm (Cocos nucifera ... markers, cluster analysis, diversity. INTRODUCTION ... industry in Kenya (Muhammed et al., 2013). Furthermore, the slow ...

  4. (SRAP) markers

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-03

    Jun 3, 2009 ... are a very powerful tool for characterization and genetic diversity estimation. Many molecular marker techniques have been successfully used in identification and genetic diversity analysis in mulberry, such as RAPD (Xiang et al., 1995; Feng et al., 1996; Zhao and Pan, 2004),. AFLP (Sharma and Sharma, ...

  5. (SSR) markers

    African Journals Online (AJOL)

    SAM

    2014-07-30

    Jul 30, 2014 ... and attempt crosses for genetic improvement of the crop. Key words: Capsicum, genetic diversity, molecular characterization, simple sequence repeats (SSR) markers. INTRODUCTION. Chilli pepper (Capsicum annuum L.) (Solanaceae) has a chromosome number 2n=2x=24. It is indigenous to South.

  6. (SSR) markers

    African Journals Online (AJOL)

    Yomi

    2012-04-03

    Apr 3, 2012 ... Oilseed rape (Brassica napus L.) is an important oilseed crop worldwide. The objective of this research was to study the genetic diversity and relationships of B. napus accessions using simple sequence repeat (SSR). A set of 217 genotypes was characterized using 37 SSR markers of mapping on the B.

  7. (RAPD) markers

    African Journals Online (AJOL)

    Administrator

    2011-09-21

    Sep 21, 2011 ... Biotechnol. Biotechnol. Equip.14: 16-18. Belaj A, Satovic Z, Cipriani G, Baldoni L, Testolin R, Rallo L, Trujillo I. (2003). Comparative study of the discriminating capacity of RAPD,. AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive. Theor. Appl. Genet. 107: 736-744 ...

  8. Genetic structure of earthworm populations at a regional scale: inferences from mitochondrial and microsatellite molecular markers in Aporrectodea icterica (Savigny 1826)

    National Research Council Canada - National Science Library

    Torres-Leguizamon, Magally; Mathieu, Jérôme; Decaëns, Thibaud; Dupont, Lise

    2014-01-01

    ... (Aporrectodea icterica) sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale...

  9. Genetic Structure of Earthworm Populations at a Regional Scale: Inferences from Mitochondrial and Microsatellite Molecular Markers in Aporrectodea icterica (Savigny 1826): e101597

    National Research Council Canada - National Science Library

    Magally Torres-Leguizamon; Jérôme Mathieu; Thibaud Decaëns; Lise Dupont

    2014-01-01

    ... (Aporrectodea icterica) sampled in northern France to explore how historical species range changes, microevolutionary processes and human activities interact in shaping genetic variation at a regional scale...

  10. FABP4 is a leading candidate gene associated with residual feed intake in growing Holstein calves.

    Science.gov (United States)

    Cohen-Zinder, Miri; Asher, Aviv; Lipkin, Ehud; Feingersch, Roi; Agmon, Rotem; Karasik, David; Brosh, Arieh; Shabtay, Ariel

    2016-05-01

    Ecological and economic concerns drive the need to improve feed utilization by domestic animals. Residual feed intake (RFI) is one of the most acceptable measures for feed efficiency (FE). However, phenotyping RFI-related traits is complex and expensive and requires special equipment. Advances in marker technology allow the development of various DNA-based selection tools. To assimilate these technologies for the benefit of RFI-based selection, reliable phenotypic measures are prerequisite. In the current study, we identified single nucleotide polymorphisms (SNPs) associated with RFI phenotypic consistency across different ages and diets (named RFI 1-3), using DNA samples of high or low RFI ranked Holstein calves. Using targeted sequencing of chromosomal regions associated with FE- and RFI-related traits, we identified 48 top SNPs significantly associated with at least one of three defined RFIs. Eleven of these SNPs were harbored by the fatty acid binding protein 4 (FABP4). While 10 significant SNPs found in FABP4 were common for RFI 1 and RFI 3, one SNP (FABP4_5; Amarkers for RFI-based selection for FE in the Holstein breed, following a larger-scale validation. Copyright © 2016 the American Physiological Society.

  11. DCAF4, a novel gene associated with leucocyte telomere length

    DEFF Research Database (Denmark)

    Mangino, Massimo; Christiansen, Lene; Stone, Rivka

    2015-01-01

    BACKGROUND: Leucocyte telomere length (LTL), which is fashioned by multiple genes, has been linked to a host of human diseases, including sporadic melanoma. A number of genes associated with LTL have already been identified through genome-wide association studies. The main aim of this study was t...

  12. Ranking of disease gene associations from large corpora of scientific publications

    OpenAIRE

    ter Horst, Hendrik

    2015-01-01

    The extraction of disease-gene associations from biomedical publications is a widely inves- tigated field of research. In previous work, a frequent method was to implement natural language processing tools that use semantic information to find such associations. How- ever, most of these approaches are restricted to single documents. Retrieval systems that predict novel associations across various documents often lack the ability to deal with the huge amount of resulting candida...

  13. Brain Atrophy Estimated from Structural Magnetic Resonance Imaging as a Marker of Large-Scale Network-Based Neurodegeneration in Aging and Stroke

    OpenAIRE

    Michele Veldsman

    2017-01-01

    Brain atrophy is a normal part of healthy aging, and stroke appears to have neurodegenerative effects, accelerating this atrophy to pathological levels. The distributed pattern of atrophy in healthy aging suggests that large-scale brain networks may be involved. At the same time, the network wide effects of stroke are beginning to be appreciated. There is now widespread use of network methods to understand the brain in terms of coordinated brain activity or white matter connectivity. Examinin...

  14. Marker Detection in Aerial Images

    KAUST Repository

    Alharbi, Yazeed

    2017-04-09

    The problem that the thesis is trying to solve is the detection of small markers in high-resolution aerial images. Given a high-resolution image, the goal is to return the pixel coordinates corresponding to the center of the marker in the image. The marker has the shape of two triangles sharing a vertex in the middle, and it occupies no more than 0.01% of the image size. An improvement on the Histogram of Oriented Gradients (HOG) is proposed, eliminating the majority of baseline HOG false positives for marker detection. The improvement is guided by the observation that standard HOG description struggles to separate markers from negatives patches containing an X shape. The proposed method alters intensities with the aim of altering gradients. The intensity-dependent gradient alteration leads to more separation between filled and unfilled shapes. The improvement is used in a two-stage algorithm to achieve high recall and high precision in detection of markers in aerial images. In the first stage, two classifiers are used: one to quickly eliminate most of the uninteresting parts of the image, and one to carefully select the marker among the remaining interesting regions. Interesting regions are selected by scanning the image with a fast classifier trained on the HOG features of markers in all rotations and scales. The next classifier is more precise and uses our method to eliminate the majority of the false positives of standard HOG. In the second stage, detected markers are tracked forward and backward in time. Tracking is needed to detect extremely blurred or distorted markers that are missed by the previous stage. The algorithm achieves 94% recall with minimal user guidance. An average of 30 guesses are given per image; the user verifies for each whether it is a marker or not. The brute force approach would return 100,000 guesses per image.

  15. Genetic epidemiology of bladder cancer: scaling up in the identification of low-penetrance genetic markers of bladder cancer risk and progression.

    Science.gov (United States)

    Malats, Núria

    2008-09-01

    Bladder cancer is an increasingly important international public health problem. As a multifactorial disease, both environmental and genetic factors are involved in its development and progression. This neoplasm is a paradigm for the participation of low-penetrance genetic variants (GSTM1-null and NAT2-slow) and provides the best established gene-environment interaction in cancer (NAT2-slow * tobacco). Genetic variants in nucleotide excision and double strand break DNA repair pathways have provided promising results, ERCC2-XPD rs238406 being the most consistent variant associated with an increased of bladder cancer risk, by itself and by interacting with tobacco. Variants in other pathways such as cell-cycle control, 1-C metabolism and inflammation have been studied, although the results are inconsistent. Three very large whole genome association studies are being undertaken using the same genotyping platform. Their results will be available soon. Genetic variants have seldom been considered as markers of prognosis or response to therapy in this tumour. The results of these studies are inconclusive. Other issues that need to be addressed are the role of genetic variants in different population subgroups--defined by ethnicity, gender and age, among others--and the association with bladder cancer subphenotypes according to clinical, pathological and molecular characteristics of the tumour. This endeavour can only be achieved by integrating multidisciplinary tools and information. Can this information be applied better to identify high-risk populations? Can the information be used to better assess prognosis or predict response to therapy? These questions require large, well-designed, multicentre studies to be conducted. Funding agencies should be aware of these needs.

  16. Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease.

    Directory of Open Access Journals (Sweden)

    Lela Lackey

    Full Text Available Genome-wide association studies aim to correlate genotype with phenotype. Many common diseases including Type II diabetes, Alzheimer's, Parkinson's and Chronic Obstructive Pulmonary Disease (COPD are complex genetic traits with hundreds of different loci that are associated with varied disease risk. Identifying common features in the genes associated with each disease remains a challenge. Furthermore, the role of post-transcriptional regulation, and in particular alternative splicing, is still poorly understood in most multigenic diseases. We therefore compiled comprehensive lists of genes associated with Type II diabetes, Alzheimer's, Parkinson's and COPD in an attempt to identify common features of their corresponding mRNA transcripts within each gene set. The SERPINA1 gene is a well-recognized genetic risk factor of COPD and it produces 11 transcript variants, which is exceptional for a human gene. This led us to hypothesize that other genes associated with COPD, and complex disorders in general, are highly transcriptionally diverse. We found that COPD-associated genes have a statistically significant enrichment in transcript complexity stemming from a disproportionately high level of alternative splicing, however, Type II Diabetes, Alzheimer's and Parkinson's disease genes were not significantly enriched. We also identified a subset of transcriptionally complex COPD-associated genes (~40% that are differentially expressed between mild, moderate and severe COPD. Although the genes associated with other lung diseases are not extensively documented, we found preliminary data that idiopathic pulmonary disease genes, but not cystic fibrosis modulators, are also more transcriptionally complex. Interestingly, complex COPD transcripts are more often the product of alternative acceptor site usage. To verify the biological importance of these alternative transcripts, we used RNA-sequencing analyses to determine that COPD-associated genes are

  17. Increased Transcript Complexity in Genes Associated with Chronic Obstructive Pulmonary Disease

    Science.gov (United States)

    Lackey, Lela; McArthur, Evonne; Laederach, Alain

    2015-01-01

    Genome-wide association studies aim to correlate genotype with phenotype. Many common diseases including Type II diabetes, Alzheimer’s, Parkinson’s and Chronic Obstructive Pulmonary Disease (COPD) are complex genetic traits with hundreds of different loci that are associated with varied disease risk. Identifying common features in the genes associated with each disease remains a challenge. Furthermore, the role of post-transcriptional regulation, and in particular alternative splicing, is still poorly understood in most multigenic diseases. We therefore compiled comprehensive lists of genes associated with Type II diabetes, Alzheimer’s, Parkinson’s and COPD in an attempt to identify common features of their corresponding mRNA transcripts within each gene set. The SERPINA1 gene is a well-recognized genetic risk factor of COPD and it produces 11 transcript variants, which is exceptional for a human gene. This led us to hypothesize that other genes associated with COPD, and complex disorders in general, are highly transcriptionally diverse. We found that COPD-associated genes have a statistically significant enrichment in transcript complexity stemming from a disproportionately high level of alternative splicing, however, Type II Diabetes, Alzheimer’s and Parkinson’s disease genes were not significantly enriched. We also identified a subset of transcriptionally complex COPD-associated genes (~40%) that are differentially expressed between mild, moderate and severe COPD. Although the genes associated with other lung diseases are not extensively documented, we found preliminary data that idiopathic pulmonary disease genes, but not cystic fibrosis modulators, are also more transcriptionally complex. Interestingly, complex COPD transcripts are more often the product of alternative acceptor site usage. To verify the biological importance of these alternative transcripts, we used RNA-sequencing analyses to determine that COPD-associated genes are frequently

  18. DISEASES: text mining and data integration of disease-gene associations.

    Science.gov (United States)

    Pletscher-Frankild, Sune; Pallejà, Albert; Tsafou, Kalliopi; Binder, Janos X; Jensen, Lars Juhl

    2015-03-01

    Text mining is a flexible technology that can be applied to numerous different tasks in biology and medicine. We present a system for extracting disease-gene associations from biomedical abstracts. The system consists of a highly efficient dictionary-based tagger for named entity recognition of human genes and diseases, which we combine with a scoring scheme that takes into account co-occurrences both within and between sentences. We show that this approach is able to extract half of all manually curated associations with a false positive rate of only 0.16%. Nonetheless, text mining should not stand alone, but be combined with other types of evidence. For this reason, we have developed the DISEASES resource, which integrates the results from text mining with manually curated disease-gene associations, cancer mutation data, and genome-wide association studies from existing databases. The DISEASES resource is accessible through a web interface at http://diseases.jensenlab.org/, where the text-mining software and all associations are also freely available for download. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

  19. Candidate genes associated with testicular development, sperm quality, and hormone levels of inhibin, luteinizing hormone, and insulin-like growth factor 1 in Brahman bulls.

    Science.gov (United States)

    Fortes, Marina R S; Reverter, Antonio; Hawken, Rachel J; Bolormaa, Sunduimijid; Lehnert, Sigrid A

    2012-09-01

    Bull fertility is an important target for genetic improvement, and early prediction using genetic markers is therefore a goal for livestock breeding. We performed genome-wide association studies to identify genes associated with fertility traits measured in young bulls. Data from 1118 Brahman bulls were collected for six traits: blood hormone levels of inhibin (IN) at 4 mo, luteinizing hormone (LH) following a gonadotropin-releasing hormone challenge at 4 mo, and insulin-like growth factor 1 (IGF1) at 6 mo, scrotal circumference (SC) at 12 mo, ability to produce sperm (Sperm) at 18 mo, and percentage of normal sperm (PNS) at 24 mo. All the bulls were genotyped with the BovineSNP50 chip. Sires and dams of the bull population (n = 304) were genotyped with the high-density chip (∼800 000 polymorphisms) to allow for imputation, thereby contributing detail on genome regions of interest. Polymorphism associations were discovered for all traits, except for Sperm. Chromosome 2 harbored polymorphisms associated with IN. For LH, associated polymorphisms were located in five different chromosomes. A region of chromosome 14 contained polymorphisms associated with IGF1 and SC. Regions of the X chromosome showed associations with SC and PNS. Associated polymorphisms yielded candidate genes in chromosomes 2, 14, and X. These findings will contribute to the development of genetic markers to help select cattle with improved fertility and will lead to better annotation of gene function in the context of reproductive biology.

  20. Revealing genes associated with vitellogenesis in the liver of the zebrafish (Danio rerio by transcriptome profiling

    Directory of Open Access Journals (Sweden)

    Hyslop Terry

    2009-03-01

    Full Text Available Abstract Background In oviparous vertebrates, including fish, vitellogenesis consists of highly regulated pathways involving 17β-estradiol (E2. Previous studies focused on a relatively small number of hepatic expressed genes during vitellogenesis. This study aims to identify hepatic genes involved in vitellogenesis and regulated by E2, by using zebrafish microarray gene expression profiling, and to provide information on functional distinctive genes expressed in the liver of a vitellogenic female, using zebrafish as a model fish. Results Genes associated with vitellogenesis were revealed by the following paired t-tests (SAM comparisons: a two-month old vitellogenic (Vit2 females were compared with non-vitellogenic (NV females, showing 825 differentially expressed transcripts during early stages of vitellogenesis, b four-month old vitellogenic (Vit4 females were compared with NV females, showing 1,046 differentially expressed transcripts during vitellogenesis and c E2-treated males were compared with control males, showing 1,828 differentially expressed transcripts regulated by E2. A Venn diagram revealed 822 common transcripts in the three groups, indicating that these transcripts were involved in vitellogenesis and putatively regulated by E2. In addition, 431 transcripts were differentially expressed in Vit2 and Vit4 females but not in E2-treated males, indicating that they were putatively not up-regulated by E2. Correspondence analysis showed high similarity in expression profiles of Vit2 with Vit4 and of NV females with control males. The E2-treated males differed from the other groups. The repertoire of genes putatively regulated by E2 in vitellogenic females included genes associated with protein synthesis and reproduction. Genes associated with the immune system processes and biological adhesion, were among the genes that were putatively not regulated by E2. E2-treated males expressed a large array of transcripts that were not associated

  1. SNP detection using RNA-sequences of candidate genes associated with puberty in cattle.

    Science.gov (United States)

    Dias, M M; Cánovas, A; Mantilla-Rojas, C; Riley, D G; Luna-Nevarez, P; Coleman, S J; Speidel, S E; Enns, R M; Islas-Trejo, A; Medrano, J F; Moore, S S; Fortes, M R S; Nguyen, L T; Venus, B; Diaz, I S D P; Souza, F R P; Fonseca, L F S; Baldi, F; Albuquerque, L G; Thomas, M G; Oliveira, H N

    2017-03-22

    Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3.1.1) and analyzed in five cattle breeds; Brangus, Brahman, Nellore, Angus, and Holstein. Two approaches used the Brangus data for SNP discovery 1) pooling all samples, and 2) within each individual sample. These approaches revealed 1157 SNPs. These were compared with those identified in the pooled samples of the other breeds. Overall, 172 SNPs within 13 genes (CPNE5, FAM19A4, FOXN4, KLF1, LOC777593, MGC157266, NEBL, NRXN3, PEPT-1, PPP3CA, SCG5, TSG101, and TSHR) were concordant in the five breeds. Using Ensembl's Variant Effector Predictor, we determined that 12% of SNPs were in exons (71% synonymous, 29% nonsynonymous), 1% were in untranslated regions (UTRs), 86% were in introns, and 1% were in intergenic regions. Since these SNPs were discovered in RNA, the variants were predicted to be within exons or UTRs. Overall, 160 novel transcripts in 42 candidate genes and five novel genes overlapping five candidate genes were observed. In conclusion, 1157 SNPs were identified in 62 candidate genes associated with puberty in Brangus cattle, of which, 172 were concordant in the five cattle breeds. Novel transcripts and genes were also identified.

  2. Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees.

    Directory of Open Access Journals (Sweden)

    Hui Liu

    2016-06-01

    Full Text Available The emerging field of sociogenomics explores the relations between social behavior and genome structure and function. An important question is the extent to which associations between social behavior and gene expression are conserved among the Metazoa. Prior experimental work in an invertebrate model of social behavior, the honey bee, revealed distinct brain gene expression patterns in African and European honey bees, and within European honey bees with different behavioral phenotypes. The present work is a computational study of these previous findings in which we analyze, by orthology determination, the extent to which genes that are socially regulated in honey bees are conserved across the Metazoa. We found that the differentially expressed gene sets associated with alarm pheromone response, the difference between old and young bees, and the colony influence on soldier bees, are enriched in widely conserved genes, indicating that these differences have genomic bases shared with many other metazoans. By contrast, the sets of differentially expressed genes associated with the differences between African and European forager and guard bees are depleted in widely conserved genes, indicating that the genomic basis for this social behavior is relatively specific to honey bees. For the alarm pheromone response gene set, we found a particularly high degree of conservation with mammals, even though the alarm pheromone itself is bee-specific. Gene Ontology identification of human orthologs to the strongly conserved honey bee genes associated with the alarm pheromone response shows overrepresentation of protein metabolism, regulation of protein complex formation, and protein folding, perhaps associated with remodeling of critical neural circuits in response to alarm pheromone. We hypothesize that such remodeling may be an adaptation of social animals to process and respond appropriately to the complex patterns of conspecific communication essential for

  3. DNA-microarrays identification of Streptococcus mutans genes associated with biofilm thickness

    Directory of Open Access Journals (Sweden)

    Feldman Mark

    2008-12-01

    Full Text Available Abstract Background A biofilm is a complex community of microorganisms that develop on surfaces in diverse environments. The thickness of the biofilm plays a crucial role in the physiology of the immobilized bacteria. The most cariogenic bacteria, mutans streptococci, are common inhabitants of a dental biofilm community. In this study, DNA-microarray analysis was used to identify differentially expressed genes associated with the thickness of S. mutans biofilms. Results Comparative transcriptome analyses indicated that expression of 29 genes was differentially altered in 400- vs. 100-microns depth and 39 genes in 200- vs. 100-microns biofilms. Only 10 S. mutans genes showed differential expression in both 400- vs. 100-microns and 200- vs. 100-microns biofilms. All of these genes were upregulated. As sucrose is a predominant factor in oral biofilm development, its influence was evaluated on selected genes expression in the various depths of biofilms. The presence of sucrose did not noticeably change the regulation of these genes in 400- vs. 100-microns and/or 200- vs. 100-microns biofilms tested by real-time RT-PCR. Furthermore, we analyzed the expression profile of selected biofilm thickness associated genes in the luxS- mutant strain. The expression of those genes was not radically changed in the mutant strain compared to wild-type bacteria in planktonic condition. Only slight downregulation was recorded in SMU.2146c, SMU.574, SMU.609, and SMU.987 genes expression in luxS- bacteria in biofilm vs. planktonic environments. Conclusion These findings reveal genes associated with the thickness of biofilms of S. mutans. Expression of these genes is apparently not regulated directly by luxS and is not necessarily influenced by the presence of sucrose in the growth media.

  4. Expression of genes associated with carbohydrate metabolism in cotton stems and roots

    Directory of Open Access Journals (Sweden)

    Scheffler Jodi

    2009-01-01

    Full Text Available Abstract Background Cotton (Gossypium hirsutum L is an important crop worldwide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. Domesticated cotton makes these reserves available to developing seeds which impacts seed yield. The goals of these analyses were to identify genes and physiological pathways that establish cotton stems and roots as physiological sinks and investigate the role these pathways play in cotton development during seed set. Results Analysis of field-grown cotton plants indicated that starch levels peaked about the time of first anthesis and then declined similar to reports in greenhouse-grown cotton plants. Starch accumulated along the length of the stem and the shape and size of the starch grains from stems were easily distinguished from transient starch. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with starch synthesis, starch degradation, hexose metabolism, raffinose synthesis and trehalose synthesis. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in selected tissues. Conclusion In domesticated cotton starch stored prior to flowering was available to support seed production. Starch accumulation observed in young field-grown plants was not observed in greenhouse grown plants. A suite of genes associated with starch biosynthesis was identified. The pathway for starch utilization after flowering was associated with an increase in expression of a glucan water dikinase gene as has been implicated in utilization of transient starch. Changes in raffinose levels and levels of expression of genes controlling trehalose and raffinose biosynthesis were also observed in vegetative

  5. Association Analysis Suggests SOD2 as a Newly Identified Candidate Gene Associated With Leprosy Susceptibility.

    Science.gov (United States)

    Ramos, Geovana Brotto; Salomão, Heloisa; Francio, Angela Schneider; Fava, Vinícius Medeiros; Werneck, Renata Iani; Mira, Marcelo Távora

    2016-08-01

    Genetic studies have identified several genes and genomic regions contributing to the control of host susceptibility to leprosy. Here, we test variants of the positional and functional candidate gene SOD2 for association with leprosy in 2 independent population samples. Family-based analysis revealed an association between leprosy and allele G of marker rs295340 (P = .042) and borderline evidence of an association between leprosy and alleles C and A of markers rs4880 (P = .077) and rs5746136 (P = .071), respectively. Findings were validated in an independent case-control sample for markers rs295340 (P = .049) and rs4880 (P = .038). These results suggest SOD2 as a newly identified gene conferring susceptibility to leprosy. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  6. Genes associated with early development, apoptosis and cell cycle regulation define a gene expression profile of adenoid cystic carcinoma.

    Science.gov (United States)

    Patel, Ketan J; Pambuccian, Stefan E; Ondrey, Frank G; Adams, George L; Gaffney, Patrick M

    2006-11-01

    Adenoid cystic carcinoma (ACC) is an uncommon salivary gland malignancy characterized by indolent yet relentless growth that exhibits inherent resistance to systemic chemotherapy, surgical salvage and conventional radiotherapy. We used microarray analysis to characterize gene expression changes associated with ACC. Eight ACC patient specimens were compared with normal parotid gland tissue and the ACC3 cell line. Differentially expressed genes were identified (512 total) using supervised analysis methods and functional categories assigned using OntoExpress. Genes associated with morphogenesis, neurogenesis, proliferation and apoptosis characterized ACC tumors. Genes associated with saliva production and immune response characterized normal parotid tissues while the ACC3 cell line expressed genes primarily associated with proliferation, chromosome maintenance and the cell cycle. These results demonstrate that ACC tumors express genes associated with early developmental processes including morphogenesis and neurogenesis implicating oncogenic events that result in dedifferentiation of normal salivary glands.

  7. Identification of Differentially Expressed Genes Associated with Apple Fruit Ripening and Softening by Suppression Subtractive Hybridization.

    Directory of Open Access Journals (Sweden)

    Zongying Zhang

    Full Text Available Apple is one of the most economically important horticultural fruit crops worldwide. It is critical to gain insights into fruit ripening and softening to improve apple fruit quality and extend shelf life. In this study, forward and reverse suppression subtractive hybridization libraries were generated from 'Taishanzaoxia' apple fruits sampled around the ethylene climacteric to isolate ripening- and softening-related genes. A set of 648 unigenes were derived from sequence alignment and cluster assembly of 918 expressed sequence tags. According to gene ontology functional classification, 390 out of 443 unigenes (88% were assigned to the biological process category, 356 unigenes (80% were classified in the molecular function category, and 381 unigenes (86% were allocated to the cellular component category. A total of 26 unigenes differentially expressed during fruit development period were analyzed by quantitative RT-PCR. These genes were involved in cell wall modification, anthocyanin biosynthesis, aroma production, stress response, metabolism, transcription, or were non-annotated. Some genes associated with cell wall modification, anthocyanin biosynthesis and aroma production were up-regulated and significantly correlated with ethylene production, suggesting that fruit texture, coloration and aroma may be regulated by ethylene in 'Taishanzaoxia'. Some of the identified unigenes associated with fruit ripening and softening have not been characterized in public databases. The results contribute to an improved characterization of changes in gene expression during apple fruit ripening and softening.

  8. Expression of candidate genes associated with obesity in peripheral white blood cells of Mexican children.

    Science.gov (United States)

    Ulloa-Martínez, Marcela; Burguete-García, Ana I; Murugesan, Selvasankar; Hoyo-Vadillo, Carlos; Cruz-Lopez, Miguel; García-Mena, Jaime

    2016-10-01

    Obesity is a chronic, complex, and multifactorial disease, characterized by excess body fat. Diverse studies of the human genome have led to the identification of susceptibility genes that contribute to obesity. However, relatively few studies have addressed specifically the association between the level of expression of these genes and obesity. We studied 160 healthy and obese unrelated Mexican children aged 6 to 14 years. We measured the transcriptional expression of 20 genes associated with obesity, in addition to the biochemical parameters, in peripheral white blood cells. The detection of mRNA levels was performed using the OpenArray Real-Time PCR System (Applied Biosystems). Obese children exhibited higher values of fasting glucose (p = 0.034), fasting insulin (p = 0.004), low-density lipoprotein (p = 0.006), triglycerides (p Analysis of transcriptional expression data showed a difference for ADRB1 (p = 0.0297), ADIPOR1 (p = 0.0317), GHRL (p = 0.0060) and FTO (p = 0.0348) genes. Our results suggest that changes in the expression level of the studied genes are involved in biological processes implicated in the development of childhood obesity. Our study contributes new perspectives for a better understanding of biological processes involved in obesity. The protocol was approved by the National Committee and Ethical Committee Board from the Mexican Social Security Institute (IMSS) (IMSS FIS/IMSS/PRIO/10/011).

  9. Identification of Differentially Expressed Genes Associated with Apple Fruit Ripening and Softening by Suppression Subtractive Hybridization.

    Science.gov (United States)

    Zhang, Zongying; Jiang, Shenghui; Wang, Nan; Li, Min; Ji, Xiaohao; Sun, Shasha; Liu, Jingxuan; Wang, Deyun; Xu, Haifeng; Qi, Sumin; Wu, Shujing; Fei, Zhangjun; Feng, Shouqian; Chen, Xuesen

    2015-01-01

    Apple is one of the most economically important horticultural fruit crops worldwide. It is critical to gain insights into fruit ripening and softening to improve apple fruit quality and extend shelf life. In this study, forward and reverse suppression subtractive hybridization libraries were generated from 'Taishanzaoxia' apple fruits sampled around the ethylene climacteric to isolate ripening- and softening-related genes. A set of 648 unigenes were derived from sequence alignment and cluster assembly of 918 expressed sequence tags. According to gene ontology functional classification, 390 out of 443 unigenes (88%) were assigned to the biological process category, 356 unigenes (80%) were classified in the molecular function category, and 381 unigenes (86%) were allocated to the cellular component category. A total of 26 unigenes differentially expressed during fruit development period were analyzed by quantitative RT-PCR. These genes were involved in cell wall modification, anthocyanin biosynthesis, aroma production, stress response, metabolism, transcription, or were non-annotated. Some genes associated with cell wall modification, anthocyanin biosynthesis and aroma production were up-regulated and significantly correlated with ethylene production, suggesting that fruit texture, coloration and aroma may be regulated by ethylene in 'Taishanzaoxia'. Some of the identified unigenes associated with fruit ripening and softening have not been characterized in public databases. The results contribute to an improved characterization of changes in gene expression during apple fruit ripening and softening.

  10. Tdd-3, a tRNA gene-associated poly(A) retrotransposon from Dictyostelium discoideum.

    Science.gov (United States)

    Winckler, T; Tschepke, C; de Hostos, E L; Jendretzke, A; Dingermann, T

    1998-04-01

    The full-length 5218-bp sequence of the mobile genetic element Tdd-3 from Dictyostelium discoideum is described. Tdd-3 encodes two overlapping open reading frames (ORFs) flanked by non-redundant, untranslated regions. The deduced amino acid sequence of ORF2 is homologous to reverse transcriptases (RTs) encoded by the class of poly(A) retrotransposons. ORF2 also encodes a putative protein domain related to the family of apurinic/apyrimidinic (AP) endonucleases, whose retroelement-encoded homologs have recently been proposed to represent the integrase function of poly(A) retrotransposons. Comparison of several genomic Tdd-3 copies revealed that element insertion is orientation specific and occurs about 100 bp downstream of tRNA genes in the D. discoideum genome. These properties of Tdd-3 suggest that the element is a tRNA gene-associated poly(A) retroelement present in the D. discoideum genome. Analysis of several cloned cDNAs derived from Tdd-3-specific plus strand RNAs indicate that the element is transcribed and polyadenylated during the growth of D. discoideum cells.

  11. Identification of Differentially Expressed Genes Associated with Prognosis of B Acute Lymphoblastic Leukemia

    Science.gov (United States)

    Jaime-Perez, Jose Carlos; Carrillo-Sanchez, Karol; Ramos-Del Hoyo, Maria Guadalupe; Lugo-Trampe, Angel; Gutierrez-Aguirre, Cesar Homero; Gonzalez-Llano, Oscar; Salazar-Riojas, Rosario; Hidalgo-Miranda, Alfredo; Gomez-Almaguer, David

    2015-01-01

    Background. Acute lymphoblastic leukemia type B (B-ALL) is a neoplastic disorder with high mortality rates. The aim of this study was to validate the expression profile of 45 genes associated with signaling pathways involved in leukemia and to evaluate their association with the prognosis of B-ALL. Methods. 219 samples of peripheral blood mononuclear cells obtained from 73 B-ALL patients were studied at diagnosis, four, and eight weeks after starting treatment. Gene expression was analyzed by quantitative real-time polymerase chain reaction. Results. Normalized delta Cq values of 23 genes showed differences between B-ALL and controls at diagnosis time (P values < 0.05). There were significant associations between B-ALL patients relapse/death and the expression levels of IL2RA, SORT1, DEFA1, and FLT3 genes at least in one of the times evaluated (P values < 0.05 and odds ratio ranges: 3.73–27). The association between FLT3 deregulation and relapse/death was a constant in the times studied and their overexpression significantly increased the odds of relapse/death in a range of 3.73 and 6.05 among study population (P values < 0.05). Conclusions. Overexpression of FLT3 and DEFA1 genes retained independent prognostic significance for B-ALL outcome, reflected as increased risks of relapse/death among the study population. PMID:25802479

  12. Factors affecting interactome-based prediction of human genes associated with clinical signs.

    Science.gov (United States)

    González-Pérez, Sara; Pazos, Florencio; Chagoyen, Mónica

    2017-07-17

    Clinical signs are a fundamental aspect of human pathologies. While disease diagnosis is problematic or impossible in many cases, signs are easier to perceive and categorize. Clinical signs are increasingly used, together with molecular networks, to prioritize detected variants in clinical genomics pipelines, even if the patient is still undiagnosed. Here we analyze the ability of these network-based methods to predict genes that underlie clinical signs from the human interactome. Our analysis reveals that these approaches can locate genes associated with clinical signs with variable performance that depends on the sign and associated disease. We analyzed several clinical and biological factors that explain these variable results, including number of genes involved (mono- vs. oligogenic diseases), mode of inheritance, type of clinical sign and gene product function. Our results indicate that the characteristics of the clinical signs and their related diseases should be considered for interpreting the results of network-prediction methods, such as those aimed at discovering disease-related genes and variants. These results are important due the increasing use of clinical signs as an alternative to diseases for studying the molecular basis of human pathologies.

  13. [Identification of variants in LMF1 gene associated with primary hypertriglyceridemia].

    Science.gov (United States)

    Lamiquiz-Moneo, Itziar; Bea, Ana M; Mateo-Gallego, Rocío; Baila-Rueda, Lucía; Cenarro, Ana; Pocoví, Miguel; Civeira, Fernando; de Castro-Orós, Isabel

    2015-01-01

    The majority of severe primary hypertriglyceridemia (HTG) are diagnosed in adults, and their molecular bases have not yet been fully defined. The promoter, coding regions and intron-exon boundaries of LMF1 were sequenced in 112 patients with severe primary hipertrigliceridemia (defined as TG above 500mg/dl). Five patients (4.46%) were carriers of four rare variants in the LMF1 gene associated with HTG, which participate in lipoprotein lipase (LpL) function. Also, we have identified two common variants, c.194-28 T>G and c.729+18C>G that were associated with HTG, with a different allelic frequency to that observed in the general population. A bioinformatic analysis of all found variants was conducted, defining the following as potentially harmful: p.Arg364Gln, p.Arg451Trp, p.Pro562Arg and p.Leu85Leu. Our results suggest that LMF1 mutations are involved in a substantial proportion of cases with severe HTG, putting together the moderate-aggressive effect of rare mutations with polymorphisms classically associated with this disease. Copyright © 2014 Sociedad Española de Arteriosclerosis. Published by Elsevier España. All rights reserved.

  14. A candidate gene association study of bone mineral density in an Iranian population.

    Directory of Open Access Journals (Sweden)

    Seyed Alireza Dastgheib

    2016-10-01

    Full Text Available The genetic epidemiology of variation in bone mineral density (BMD and osteoporosis is not well studied in Iranian populations and needs more research. We report a candidate gene association study of BMD variation in a healthy cross sectional study of 501 males and females sampled from the IMOS study Shiraz, Iran. We selected to study the association with 21 SNPs located in the 7 candidate genes LRP5, RANK, RANKL, OPG, P2RX7, VDR and ESR1. BMD was measured at the three sites L2-L4, neck of femur and total hip. Association between BMD and each SNP was assessed using multiple linear regression assuming an allele dose (additive effect on BMD (adjusted for age and sex. Statistically significant (at the unadjusted 5% level associations were seen with 7 SNPs in 5 of the candidate genes. Two SNPs showed statistically significant association with more than one BMD site. Significant association was seen between BMD at all three sites with the VDR SNP rs731246 (L2-L4 p=0.038; neck of femur p=0.001 and total hip p<0.001. The T allele was consistently associated with lower BMD than the C allele. Significant association was also seen for the P2RX7 SNP rs3751143 where the G allele was consistently associated with lower BMD than the T allele, (L2-L4 p=0.069; neck of femur p=0.024, total hip p=0.045.

  15. Identification of Differentially Expressed Genes Associated with Prognosis of B Acute Lymphoblastic Leukemia

    Directory of Open Access Journals (Sweden)

    Idalia Garza-Veloz

    2015-01-01

    Full Text Available Background. Acute lymphoblastic leukemia type B (B-ALL is a neoplastic disorder with high mortality rates. The aim of this study was to validate the expression profile of 45 genes associated with signaling pathways involved in leukemia and to evaluate their association with the prognosis of B-ALL. Methods. 219 samples of peripheral blood mononuclear cells obtained from 73 B-ALL patients were studied at diagnosis, four, and eight weeks after starting treatment. Gene expression was analyzed by quantitative real-time polymerase chain reaction. Results. Normalized delta Cq values of 23 genes showed differences between B-ALL and controls at diagnosis time (P values < 0.05. There were significant associations between B-ALL patients relapse/death and the expression levels of IL2RA, SORT1, DEFA1, and FLT3 genes at least in one of the times evaluated (P values < 0.05 and odds ratio ranges: 3.73–27. The association between FLT3 deregulation and relapse/death was a constant in the times studied and their overexpression significantly increased the odds of relapse/death in a range of 3.73 and 6.05 among study population (P values < 0.05. Conclusions. Overexpression of FLT3 and DEFA1 genes retained independent prognostic significance for B-ALL outcome, reflected as increased risks of relapse/death among the study population.

  16. Geodetic Control Points, NGS_Control Points - Published National Geodetic Survey Markers located in Glynn County that were either set or recovered by County staff., Published in 2009, 1:24000 (1in=2000ft) scale, Glynn County Government.

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — Geodetic Control Points dataset current as of 2009. NGS_Control Points - Published National Geodetic Survey Markers located in Glynn County that were either set or...

  17. A database of annotated promoters of genes associated with common respiratory and related diseases

    KAUST Repository

    Chowdhary, Rajesh

    2012-07-01

    Many genes have been implicated in the pathogenesis of common respiratory and related diseases (RRDs), yet the underlying mechanisms are largely unknown. Differential gene expression patterns in diseased and healthy individuals suggest that RRDs affect or are affected by modified transcription regulation programs. It is thus crucial to characterize implicated genes in terms of transcriptional regulation. For this purpose, we conducted a promoter analysis of genes associated with 11 common RRDs including allergic rhinitis, asthma, bronchiectasis, bronchiolitis, bronchitis, chronic obstructive pulmonary disease, cystic fibrosis, emphysema, eczema, psoriasis, and urticaria, many of which are thought to be genetically related. The objective of the present study was to obtain deeper insight into the transcriptional regulation of these disease-associated genes by annotating their promoter regions with transcription factors (TFs) and TF binding sites (TFBSs). We discovered many TFs that are significantly enriched in the target disease groups including associations that have been documented in the literature. We also identified a number of putative TFs/TFBSs that appear to be novel. The results of our analysis are provided in an online database that is freely accessible to researchers at http://www.respiratorygenomics.com. Promoter-associated TFBS information and related genomic features, such as histone modification sites, microsatellites, CpG islands, and SNPs, are graphically summarized in the database. Users can compare and contrast underlying mechanisms of specific RRDs relative to candidate genes, TFs, gene ontology terms, micro-RNAs, and biological pathways for the conduct of metaanalyses. This database represents a novel, useful resource for RRD researchers. Copyright © 2012 by the American Thoracic Society.

  18. A Multiomics Approach to Identify Genes Associated with Childhood Asthma Risk and Morbidity.

    Science.gov (United States)

    Forno, Erick; Wang, Ting; Yan, Qi; Brehm, John; Acosta-Perez, Edna; Colon-Semidey, Angel; Alvarez, Maria; Boutaoui, Nadia; Cloutier, Michelle M; Alcorn, John F; Canino, Glorisa; Chen, Wei; Celedón, Juan C

    2017-10-01

    Childhood asthma is a complex disease. In this study, we aim to identify genes associated with childhood asthma through a multiomics "vertical" approach that integrates multiple analytical steps using linear and logistic regression models. In a case-control study of childhood asthma in Puerto Ricans (n = 1,127), we used adjusted linear or logistic regression models to evaluate associations between several analytical steps of omics data, including genome-wide (GW) genotype data, GW methylation, GW expression profiling, cytokine levels, asthma-intermediate phenotypes, and asthma status. At each point, only the top genes/single-nucleotide polymorphisms/probes/cytokines were carried forward for subsequent analysis. In step 1, asthma modified the gene expression-protein level association for 1,645 genes; pathway analysis showed an enrichment of these genes in the cytokine signaling system (n = 269 genes). In steps 2-3, expression levels of 40 genes were associated with intermediate phenotypes (asthma onset age, forced expiratory volume in 1 second, exacerbations, eosinophil counts, and skin test reactivity); of those, methylation of seven genes was also associated with asthma. Of these seven candidate genes, IL5RA was also significant in analytical steps 4-8. We then measured plasma IL-5 receptor α levels, which were associated with asthma age of onset and moderate-severe exacerbations. In addition, in silico database analysis showed that several of our identified IL5RA single-nucleotide polymorphisms are associated with transcription factors related to asthma and atopy. This approach integrates several analytical steps and is able to identify biologically relevant asthma-related genes, such as IL5RA. It differs from other methods that rely on complex statistical models with various assumptions.

  19. Candidate gene associated with a mutation causing recessive polycystic kidney disease in mice

    Energy Technology Data Exchange (ETDEWEB)

    Moyer, J.H.; Lee-Tischler, M.J.; Kwon, H.Y.; Schrick, J.J. (Univ. of Tennessee Graduate School of Biomedical Sciences, Oak Ridge, TN (United States)); Avner, E.D.; Sweeney, W.E. (Univ. of Washington, Seattle, WA (United States)); Godfrey, V.L.; Cacheiro, N.L.A.; Woychik, R.P. (Oak Ridge National Lab., TN (United States)); Wilkinson, J.E. (Univ. of Tennessee, Knoxville, TN (United States))

    1994-05-27

    A line of transgenic mice was generated that contains an insertional mutation causing a phenotype similar to human autosomal recessive polycystic kidney disease. Homozygotes displayed a complex phenotype that included bilateral polycystic kidneys and an unusual liver lesion. The mutant locus was cloned and characterized through use of the transgene as a molecular marker. Additionally, a candidate polycystic kidney disease (PKD) gene was identified whose structure and expression are directly associated with the mutant locus. A complementary DNA derived from this gene predicted a peptide containing a motif that was originally identified in several genes involved in cell cycle control.

  20. Novel genes associated with amyotrophic lateral sclerosis: diagnostic and clinical implications.

    Science.gov (United States)

    Chia, Ruth; Chiò, Adriano; Traynor, Bryan J

    2018-01-01

    The disease course of amyotrophic lateral sclerosis (ALS) is rapid and, because its pathophysiology is unclear, few effective treatments are available. Genetic research aims to understand the underlying mechanisms of ALS and identify potential therapeutic targets. The first gene associated with ALS was SOD1, identified in 1993 and, by early 2014, more than 20 genes had been identified as causative of, or highly associated with, ALS. These genetic discoveries have identified key disease pathways that are therapeutically testable and could potentially lead to the development of better treatments for people with ALS. Since 2014, seven additional genes have been associated with ALS (MATR3, CHCHD10, TBK1, TUBA4A, NEK1, C21orf2, and CCNF), all of which were identified by genome-wide association studies, whole genome studies, or exome sequencing technologies. Each of the seven novel genes code for proteins associated with one or more molecular pathways known to be involved in ALS. These pathways include dysfunction in global protein homoeostasis resulting from abnormal protein aggregation or a defect in the protein clearance pathway, mitochondrial dysfunction, altered RNA metabolism, impaired cytoskeletal integrity, altered axonal transport dynamics, and DNA damage accumulation due to defective DNA repair. Because these novel genes share common disease pathways with other genes implicated in ALS, therapeutics targeting these pathways could be useful for a broad group of patients stratified by genotype. However, the effects of these novel genes have not yet been investigated in animal models, which will be a key step to translating these findings into clinical practice. WHERE NEXT?: The identification of these seven novel genes has been important in unravelling the molecular mechanisms underlying ALS. However, our understanding of what causes ALS is not complete, and further genetic research will provide additional detail about its causes. Increased genetic knowledge will

  1. Changes in mitochondrial DNA alter expression of nuclear encoded genes associated with tumorigenesis

    Energy Technology Data Exchange (ETDEWEB)

    Jandova, Jana; Janda, Jaroslav [Southern Arizona VA Healthcare System, Department of Medicine, Dermatology Division and Arizona Cancer Center, University of Arizona, 1515 N Campbell Avenue, Tucson, AZ 857 24 (United States); Sligh, James E, E-mail: jsligh@azcc.arizona.edu [Southern Arizona VA Healthcare System, Department of Medicine, Dermatology Division and Arizona Cancer Center, University of Arizona, 1515 N Campbell Avenue, Tucson, AZ 857 24 (United States)

    2012-10-15

    genes associated with tumorigenesis. Black-Right-Pointing-Pointer MMP-9 is up-regulated and Col1a1 is down-regulated in mutant cybrids. Black-Right-Pointing-Pointer GM6001 reduced the enhanced motility of mutant cybrids caused by up-regulated MMP-9. Black-Right-Pointing-Pointer The MMP-9 expression and invasiveness of mutant cybrids were reduced by Bay 11-7802.

  2. Differential regulation of the foraging gene associated with task behaviors in harvester ants

    Directory of Open Access Journals (Sweden)

    Kleeman Lindsay

    2011-08-01

    Full Text Available Abstract Background The division of labor in social insect colonies involves transitions by workers from one task to another and is critical to the organization and ecological success of colonies. The differential regulation of genetic pathways is likely to be a key mechanism involved in plasticity of social insect task behavior. One of the few pathways implicated in social organization involves the cGMP-activated protein kinase gene, foraging, a gene associated with foraging behavior in social insect species. The association of the foraging gene with behavior is conserved across diverse species, but the observed expression patterns and proposed functions of this gene vary across taxa. We compared the protein sequence of foraging across social insects and explored whether the differential regulation of this gene is associated with task behaviors in the harvester ant, Pogonomyrmex occidentalis. Results Phylogenetic analysis of the coding region of the foraging gene reveals considerable conservation in protein sequence across insects, particularly among hymenopteran species. The absence of amino acid variation in key active and binding sites suggests that differences in behaviors associated with this gene among species may be the result of changes in gene expression rather than gene divergence. Using real time qPCR analyses with a harvester ant ortholog to foraging (Pofor, we found that the brains of harvester ant foragers have a daily fluctuation in expression of foraging with mRNA levels peaking at midday. In contrast, young workers inside the nest have low levels of Pofor mRNA with no evidence of daily fluctuations in expression. As a result, the association of foraging expression with task behavior within a species changes depending on the time of day the individuals are sampled. Conclusions The amino acid protein sequence of foraging is highly conserved across social insects. Differences in foraging behaviors associated with this gene among

  3. Novel genes associated with enhanced motility of Escherichia coli ST131.

    Science.gov (United States)

    Kakkanat, Asha; Phan, Minh-Duy; Lo, Alvin W; Beatson, Scott A; Schembri, Mark A

    2017-01-01

    Uropathogenic Escherichia coli (UPEC) is the cause of ~75% of all urinary tract infections (UTIs) and is increasingly associated with multidrug resistance. This includes UPEC strains from the recently emerged and globally disseminated sequence type 131 (ST131), which is now the dominant fluoroquinolone-resistant UPEC clone worldwide. Most ST131 strains are motile and produce H4-type flagella. Here, we applied a combination of saturated Tn5 mutagenesis and transposon directed insertion site sequencing (TraDIS) as a high throughput genetic screen and identified 30 genes associated with enhanced motility of the reference ST131 strain EC958. This included 12 genes that repress motility of E. coli K-12, four of which (lrhA, ihfA, ydiV, lrp) were confirmed in EC958. Other genes represented novel factors that impact motility, and we focused our investigation on characterisation of the mprA, hemK and yjeA genes. Mutation of each of these genes in EC958 led to increased transcription of flagellar genes (flhD and fliC), increased expression of the FliC flagellin, enhanced flagella synthesis and a hyper-motile phenotype. Complementation restored all of these properties to wild-type level. We also identified Tn5 insertions in several intergenic regions (IGRs) on the EC958 chromosome that were associated with enhanced motility; this included flhDC and EC958_1546. In both of these cases, the Tn5 insertions were associated with increased transcription of the downstream gene(s), which resulted in enhanced motility. The EC958_1546 gene encodes a phage protein with similarity to esterase/deacetylase enzymes involved in the hydrolysis of sialic acid derivatives found in human mucus. We showed that over-expression of EC958_1546 led to enhanced motility of EC958 as well as the UPEC strains CFT073 and UTI89, demonstrating its activity affects the motility of different UPEC strains. Overall, this study has identified and characterised a number of novel factors associated with enhanced

  4. Discovering genes associated with dormancy in the monogonont rotifer Brachionus plicatilis

    Directory of Open Access Journals (Sweden)

    Kube Michael

    2009-03-01

    Full Text Available Abstract Background Microscopic monogonont rotifers, including the euryhaline species Brachionus plicatilis, are typically found in water bodies where environmental factors restrict population growth to short periods lasting days or months. The survival of the population is ensured via the production of resting eggs that show a remarkable tolerance to unfavorable conditions and remain viable for decades. The aim of this study was to generate Expressed Sequence Tags (ESTs for molecular characterisation of processes associated with the formation of resting eggs, their survival during dormancy and hatching. Results Four normalized and four subtractive libraries were constructed to provide a resource for rotifer transcriptomics associated with resting-egg formation, storage and hatching. A total of 47,926 sequences were assembled into 18,000 putative transcripts and analyzed using both Blast and GO annotation. About 28–55% (depending on the library of the clones produced significant matches against the Swissprot and Trembl databases. Genes known to be associated with desiccation tolerance during dormancy in other organisms were identified in the EST libraries. These included genes associated with antioxidant activity, low molecular weight heat shock proteins and Late Embryonic Abundant (LEA proteins. Real-time PCR confirmed that LEA transcripts, small heat-shock proteins and some antioxidant genes were upregulated in resting eggs, therefore suggesting that desiccation tolerance is a characteristic feature of resting eggs even though they do not necessarily fully desiccate during dormancy. The role of trehalose in resting-egg formation and survival remains unclear since there was no significant difference between resting-egg producing females and amictic females in the expression of the tps-1 gene. In view of the absence of vitellogenin transcripts, matches to lipoprotein lipase proteins suggest that, similar to the situation in dipterans, these

  5. Genetic diversity detection of the domestic horse (Equus caballus by genes associated with coat color

    Directory of Open Access Journals (Sweden)

    Luz Correa A

    2015-09-01

    Full Text Available Objective. To assess the population structure and genetic diversity in populations of domestic horse (Equus caballus in the municipality Cienaga de Oro-Córdoba (Colombia. Materials and methods. Random sampling were conducted between August and October 2013, in adult animals on farms seven districts, which was carried out phenotypic characterization of each animal, based on autosomal markers encoding morphological Extension (E , Agouti (A, Cream (C, White (W, Gray (G, Tobiano (TO, Overo (O and Roan (RN. Population genetic parameters: allele frequency, genetic diversity, gene flow, Hardy-Weinberg equilibrium and genetic distance were calculated through the program POPGENE 1.31; the genetic structure was assessed using the program FSTAT v. 2.9.3.2. Results. 341 individuals were analyzed in the seven populations studied, where the Extension gene Was the MOST faq frequently as the Overo and Tobiano genes showed the lowest values. Insignificant values of genetic variability and population recorded a global level, likewise, low genetic differentiation among populations, accompanied by a high gene flow was obtained; an excess of heterozygotes at population and global level was observed; to this is added the presence of Hardy-Weinberg equilibrium in all populations relative to the markers studied and low genetic distance values were reported. Conclusions. The populations are highly genetically related, a situation that may result from the existing geographical proximity between them, favoring genetic exchange and the establishment of a metapopulation.

  6. Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm.

    Directory of Open Access Journals (Sweden)

    Diego Micheletti

    Full Text Available Peach was domesticated in China more than four millennia ago and from there it spread world-wide. Since the middle of the last century, peach breeding programs have been very dynamic generating hundreds of new commercial varieties, however, in most cases such varieties derive from a limited collection of parental lines (founders. This is one reason for the observed low levels of variability of the commercial gene pool, implying that knowledge of the extent and distribution of genetic variability in peach is critical to allow the choice of adequate parents to confer enhanced productivity, adaptation and quality to improved varieties. With this aim we genotyped 1,580 peach accessions (including a few closely related Prunus species maintained and phenotyped in five germplasm collections (four European and one Chinese with the International Peach SNP Consortium 9K SNP peach array. The study of population structure revealed the subdivision of the panel in three main populations, one mainly made up of Occidental varieties from breeding programs (POP1OCB, one of Occidental landraces (POP2OCT and the third of Oriental accessions (POP3OR. Analysis of linkage disequilibrium (LD identified differential patterns of genome-wide LD blocks in each of the populations. Phenotypic data for seven monogenic traits were integrated in a genome-wide association study (GWAS. The significantly associated SNPs were always in the regions predicted by linkage analysis, forming haplotypes of markers. These diagnostic haplotypes could be used for marker-assisted selection (MAS in modern breeding programs.

  7. Construction of a high-density genetic map and the X/Y sex-determining gene mapping in spinach based on large-scale markers developed by specific-locus amplified fragment sequencing (SLAF-seq).

    Science.gov (United States)

    Qian, Wei; Fan, Guiyan; Liu, Dandan; Zhang, Helong; Wang, Xiaowu; Wu, Jian; Xu, Zhaosheng

    2017-04-04

    Cultivated spinach (Spinacia oleracea L.) is one of the most widely cultivated types of leafy vegetable in the world, and it has a high nutritional value. Spinach is also an ideal plant for investigating the mechanism of sex determination because it is a dioecious species with separate male and female plants. Some reports on the sex labeling and localization of spinach in the study of molecular markers have surfaced. However, there have only been two reports completed on the genetic map of spinach. The lack of rich and reliable molecular markers and the shortage of high-density linkage maps are important constraints in spinach research work. In this study, a high-density genetic map of spinach based on the Specific-locus Amplified Fragment Sequencing (SLAF-seq) technique was constructed; the sex-determining gene was also finely mapped. Through bio-information analysis, 50.75 Gb of data in total was obtained, including 207.58 million paired-end reads. Finally, 145,456 high-quality SLAF markers were obtained, with 27,800 polymorphic markers and 4080 SLAF markers were finally mapped onto the genetic map after linkage analysis. The map spanned 1,125.97 cM with an average distance of 0.31 cM between the adjacent marker loci. It was divided into 6 linkage groups corresponding to the number of spinach chromosomes. Besides, the combination of Bulked Segregation Analysis (BSA) with SLAF-seq technology(super-BSA) was employed to generate the linkage markers with the sex-determining gene. Combined with the high-density genetic map of spinach, the sex-determining gene X/Y was located at the position of the linkage group (LG) 4 (66.98 cM-69.72 cM and 75.48 cM-92.96 cM), which may be the ideal region for the sex-determining gene. A high-density genetic map of spinach based on the SLAF-seq technique was constructed with a backcross (BC1) population (which is the highest density genetic map of spinach reported at present). At the same time, the sex-determining gene X/Y was mapped

  8. Fine Mapping and Transcriptome Analysis Reveal Candidate Genes Associated with Hybrid Lethality in Cabbage (Brassica Oleracea).

    Science.gov (United States)

    Xiao, Zhiliang; Hu, Yang; Zhang, Xiaoli; Xue, Yuqian; Fang, Zhiyuan; Yang, Limei; Zhang, Yangyong; Liu, Yumei; Li, Zhansheng; Liu, Xing; Liu, Zezhou; Lv, Honghao; Zhuang, Mu

    2017-06-05

    Hybrid lethality is a deleterious phenotype that is vital to species evolution. We previously reported hybrid lethality in cabbage (Brassica oleracea) and performed preliminary mapping of related genes. In the present study, the fine mapping of hybrid lethal genes revealed that BoHL1 was located on chromosome C1 between BoHLTO124 and BoHLTO130, with an interval of 101 kb. BoHL2 was confirmed to be between insertion-deletion (InDels) markers HL234 and HL235 on C4, with a marker interval of 70 kb. Twenty-eight and nine annotated genes were found within the two intervals of BoHL1 and BoHL2, respectively. We also applied RNA-Seq to analyze hybrid lethality in cabbage. In the region of BoHL1, seven differentially expressed genes (DEGs) and five resistance (R)-related genes (two in common, i.e., Bo1g153320 and Bo1g153380) were found, whereas in the region of BoHL2, two DEGs and four R-related genes (two in common, i.e., Bo4g173780 and Bo4g173810) were found. Along with studies in which R genes were frequently involved in hybrid lethality in other plants, these interesting R-DEGs may be good candidates associated with hybrid lethality. We also used SNP/InDel analyses and quantitative real-time PCR to confirm the results. This work provides new insight into the mechanisms of hybrid lethality in cabbage.

  9. Porcine Is a Positional Candidate Gene Associated with Growth and Fat Deposition

    Directory of Open Access Journals (Sweden)

    Bong Hwan Choi

    2012-12-01

    Full Text Available Crosses between Korean and Landrace pigs have revealed a large quantitative trait loci (QTL region for fat deposition in a region (89 cM of porcine chromosome 4 (SSC4. To more finely map this QTL region and identify candidate genes for this trait, comparative mapping of pig and human chromosomes was performed in the present study. A region in the human genome that corresponds to the porcine QTL region was identified in HSA1q21. Furthermore, the LMNA gene, which is tightly associated with fat augmentation in humans, was localized to this region. Radiation hybrid (RH mapping using a Sus scrofa RH panel localized LMNA to a region of 90.3 cM in the porcine genome, distinct from microsatellite marker S0214 (87.3 cM. Two-point analysis showed that LMNA was linked to S0214, SW1996, and S0073 on SSC4 with logarithm (base 10 of odds scores of 20.98, 17.78, and 16.73, respectively. To clone the porcine LMNA gene and to delineate the genomic structure and sequences, including the 3′untranslated region (UTR, rapid amplification of cDNA ends was performed. The coding sequence of porcine LMNA consisted of 1,719 bp, flanked by a 5’UTR and a 3’UTR. Two synonymous single nucleotide polymorphisms (SNPs were identified in exons 3 and 7. Association tests showed that the SNP located in exon 3 (A193A was significantly associated with weight at 30 wks (p<0.01 and crude fat content (p<0.05. This association suggests that SNPs located in LMNA could be used for marker-assisted selection in pigs.

  10. Detecting marker-disease association by testing for Hardy-Weinberg disequilibrium at a marker locus.

    Science.gov (United States)

    Nielsen, D M; Ehm, M G; Weir, B S

    1998-01-01

    We review and extend a recent suggestion that fine-scale localization of a disease-susceptibility locus for a complex disease be done on the basis of deviations from Hardy-Weinberg equilibrium among affected individuals. This deviation is driven by linkage disequilibrium between disease and marker loci in the whole population and requires a heterogeneous genetic basis for the disease. A finding of marker-locus Hardy-Weinberg disequilibrium therefore implies disease heterogeneity and marker-disease linkage disequilibrium. Although a lack of departure of Hardy-Weinberg disequilibrium at marker loci implies that disease susceptibilityweighted linkage disequilibria are zero, given disease heterogeneity, it does not follow that the usual measures of linkage disequilibrium are zero. For disease-susceptibility loci with more than two alleles, therefore, care is needed in the drawing of inferences from marker Hardy-Weinberg disequilibria. PMID:9867708

  11. Embryonic Stem Cell Markers

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    Lan Ma

    2012-05-01

    Full Text Available Embryonic stem cell (ESC markers are molecules specifically expressed in ES cells. Understanding of the functions of these markers is critical for characterization and elucidation for the mechanism of ESC pluripotent maintenance and self-renewal, therefore helping to accelerate the clinical application of ES cells. Unfortunately, different cell types can share single or sometimes multiple markers; thus the main obstacle in the clinical application of ESC is to purify ES cells from other types of cells, especially tumor cells. Currently, the marker-based flow cytometry (FCM technique and magnetic cell sorting (MACS are the most effective cell isolating methods, and a detailed maker list will help to initially identify, as well as isolate ESCs using these methods. In the current review, we discuss a wide range of cell surface and generic molecular markers that are indicative of the undifferentiated ESCs. Other types of molecules, such as lectins and peptides, which bind to ESC via affinity and specificity, are also summarized. In addition, we review several markers that overlap with tumor stem cells (TSCs, which suggest that uncertainty still exists regarding the benefits of using these markers alone or in various combinations when identifying and isolating cells.

  12. Gene expression changes in HLA mismatched mixed lymphocyte cultures reveal genes associated with allorecognition.

    Science.gov (United States)

    Nicolaidou, V; Stylianou, C; Koumas, L; Vassiliou, G S; Bodman-Smith, K B; Costeas, P

    2015-04-01

    Human leucocyte antigen (HLA) compatibility is the main factor determining the occurrence of graft-vs-host disease (GVHD) in patients. It has also been shown that minor histocompatibility antigen differences as well as genetic polymorphisms that are not sequenced by standard methodology for HLA typing can play a role. We used mixed lymphocyte cultures (MLCs) as a functional cellular test and investigated gene expression changes driven by HLA incompatibility in an effort to better understand the mechanisms involved in the disease. Gene expression profile of HLA matched and HLA mismatched MLC identified differentially regulated genes and pathways. We found that a great number of genes related to immune function were differentially regulated; these genes were also found to be associated with GVHD and graft rejection. The majority of differentially regulated genes were interferon-gamma (IFNγ)-inducible genes and IFNγ neutralisation in MLCs abrogated their induction. The microRNA-155, a recently identified target for acute GVHD (aGVHD), was also found to be significantly induced in HLA mismatched MLC but not in the matched setting and its induction was not diminished by blocking IFNγ. In this proof-of-principle study we show gene expression changes in mismatched MLC that represent alloreactive responses, correlate with markers involved in GVHD and can potentially be useful in the study of the biological processes involved in this disease. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  13. Mapping and expression of genes associated with raspberry fruit ripening and softening.

    Science.gov (United States)

    Simpson, Craig G; Cullen, Danny W; Hackett, Christine A; Smith, Kay; Hallett, Paul D; McNicol, Jim; Woodhead, Mary; Graham, Julie

    2017-03-01

    QTL mapping identifies a range of underlying and unrelated genes with apparent roles in raspberry fruit ripening and softening that show characteristic developing fruit expression profiles. Fruit softening is an important agronomical trait that involves a complex interaction of plant cell processes. We have used both qualitative and quantitative scoring of fruit firmness, length, mass, and resistance to applied force to identify QTL in a raspberry mapping population. QTLs were located primarily on linkage group (LG) 3 with other significant loci on LG 1 and LG 5 and showed mostly additive effects between the two parents. The expression of key genes that underlie these QTLs with roles in cell-wall solubility, water uptake, polyamine synthesis, transcription, and cell respiration was tested across five stages of fruit development, from immature green to red ripe fruit, using real-time RT-qPCR. Gene expression patterns showed variable expression patterns across fruit development with a highly significant positive and negative correlation between genes, supporting precise regulation of expression of different cell processes throughout raspberry fruit development. Variable timing in expression was also found in some genes at different fruit development stages between soft and firm cultivars. Multiple processes have a role to play in fruit softening and this will require development of multiple marker combinations to genes that characterise raspberry fruit softening.

  14. The urine marker test

    DEFF Research Database (Denmark)

    Elbe, Anne-Marie; Jensen, Stine Nylandsted; Elsborg, Peter

    2016-01-01

    of this new method via two questionnaires (n = 253). Furthermore, a third study (n = 91) investigated whether ingestion of the marker can identify the urine as coming from a specific person and whether the marker interferes with the detection of prohibited substances. RESULTS AND CONCLUSIONS: The results...... indicate that this new method finds wide acceptance both from athletes who have only heard about the procedure and those who have actually tested the new method. Furthermore, the marker, which can identify urine as coming from a specific person, does not interfere with the detection of prohibited...... that athletes are actually delivering their own urine. A method that can be used to alleviate the negative impact of a supervised urination procedure and which can also identify urine as coming from a specific athlete is the urine marker test. Monodisperse low molecular weight polyethylene glycols (PEGs...

  15. VT Roadside Historic Markers

    Data.gov (United States)

    Vermont Center for Geographic Information — Roadside Historic Site Marker program has proven an effective way to commemorate Vermont’s many people, events, and places of regional, statewide, or national...

  16. Polymorphisms in inflammatory and immune response genes associated with cerebral cavernous malformation type 1 severity

    Science.gov (United States)

    Choquet, Hélène; Pawlikowska, Ludmila; Nelson, Jeffrey; McCulloch, Charles E.; Akers, Amy; Baca, Beth; Khan, Yasir; Hart, Blaine; Morrison, Leslie; Kim, Helen

    2014-01-01

    , respectively. TGFBR2 rs9823731 was significantly associated with ICH as well as with total and large lesion counts (P≤0.017). Further, IL-4 rs9327638, CD14 rs778588, IL-6R rs114660934 and MSR1 rs62489577 were associated with two markers of disease severity. Finally, the whole pathway was associated with total lesion count (P=0.005) with TLR-4 rs10759930, CD14 rs778588, IL-6R rs114660934 and IGH rs57767447 mainly bearing this association. Eicosanoid signaling, extracellular pattern recognition and immune response sub-pathways were also associated with total lesion count. Conclusions These results suggest that polymorphisms in inflammatory and immune response pathways contribute to variability in CCM1 disease severity and might be used as predictors of disease severity. In particular, TGFBR2 rs9823731 was associated with all three markers of CCM1 disease severity tested, suggesting that TGFBR2 might be a key participant in the mechanism underlying CCM1 disease severity and phenotype variability. However, further longitudinal studies in larger sample sizes are needed to confirm these findings. PMID:25472749

  17. Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.).

    Science.gov (United States)

    Hedley, Peter E; Russell, Joanne R; Jorgensen, Linzi; Gordon, Sandra; Morris, Jenny A; Hackett, Christine A; Cardle, Linda; Brennan, Rex

    2010-09-14

    The detrimental effects of mild winter temperatures on the consistency of cropping of blackcurrant (Ribes nigrum L.) in parts of Europe have led to increasing interest in the genetic control of dormancy release in this species. This study examined patterns of gene expression in leaf buds of blackcurrant to identify key differential changes in these profiles around the time of budbreak. Using leaf bud tissue of blackcurrant, a cDNA library was generated as a source of blackcurrant ESTs for construction of a custom microarray, which was used to identify differential gene expression during dormancy release. Gene activity was lowest in early stages of dormancy, increasing to reach a maximum around the time of budbreak. Genes with significantly changing expression profiles were clustered and evidence is provided for the transient activity of genes previously associated with dormancy processes in other species. Expression profiling identified candidate genes which were mapped onto a blackcurrant genetic linkage map containing budbreak-related QTL. Three genes, which putatively encode calmodulin-binding protein, beta tubulin and acetyl CoA carboxylase respectively, were found to co-localise with budbreak QTL. This study provides insight into the genetic control of dormancy transition in blackcurrant, identifying key changes in gene expression around budbreak. Genetic mapping of ESTs enabled the identification of genes which co-localise with previously-characterised blackcurrant QTL, and it is concluded that these genes have probable roles in release of dormancy and can therefore provide a basis for the development of genetic markers for future breeding deployment.

  18. Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.

    Directory of Open Access Journals (Sweden)

    Hedley Peter E

    2010-09-01

    Full Text Available Abstract Background The detrimental effects of mild winter temperatures on the consistency of cropping of blackcurrant (Ribes nigrum L. in parts of Europe have led to increasing interest in the genetic control of dormancy release in this species. This study examined patterns of gene expression in leaf buds of blackcurrant to identify key differential changes in these profiles around the time of budbreak. Results Using leaf bud tissue of blackcurrant, a cDNA library was generated as a source of blackcurrant ESTs for construction of a custom microarray, which was used to identify differential gene expression during dormancy release. Gene activity was lowest in early stages of dormancy, increasing to reach a maximum around the time of budbreak. Genes with significantly changing expression profiles were clustered and evidence is provided for the transient activity of genes previously associated with dormancy processes in other species. Expression profiling identified candidate genes which were mapped onto a blackcurrant genetic linkage map containing budbreak-related QTL. Three genes, which putatively encode calmodulin-binding protein, beta tubulin and acetyl CoA carboxylase respectively, were found to co-localise with budbreak QTL. Conclusions This study provides insight into the genetic control of dormancy transition in blackcurrant, identifying key changes in gene expression around budbreak. Genetic mapping of ESTs enabled the identification of genes which co-localise with previously-characterised blackcurrant QTL, and it is concluded that these genes have probable roles in release of dormancy and can therefore provide a basis for the development of genetic markers for future breeding deployment.

  19. Candidate gene association study of BMI-related loci, weight, and adiposity in old age.

    Science.gov (United States)

    Murphy, Rachel A; Nalls, Michael A; Keller, Margaux; Garcia, Melissa; Kritchevsky, Stephen B; Tylavsky, Frances A; Newman, Anne B; Tranah, Gregory J; Eiriksdottir, Gudny; Gudnason, Vilmundur; Harris, Tamara B

    2013-06-01

    Most genome-wide association studies are confined to middle-aged populations. It is unclear whether associations between single nucleotide polymorphisms (SNPs) and obesity persist in old age. We aimed to relate 10 body mass index (BMI)-associated SNPs to weight, BMI, % fat, visceral and subcutaneous adipose tissue in Health ABC and AGES-Reykjavik comprising 4,846 individuals of European Ancestry, and 1,139 African Americans over age 65. SNPs were scaled using effect estimates from candidate SNPs. In Health ABC, a SNP near GNPDA2 was modestly associated with weight and SAT area (p = .008, p = .001). Risk score (sum of scaled SNPs) was associated with weight, BMI, and SAT area (p BMI, visceral adippose tissue, subcutaneous adipose tissue, or % fat in AGES-Reykjavik. In African Americans, a SNP near SEC16B was weakly associated with weight (p = .04). In this sample of older adults, no BMI-associated SNPs were associated with weight or adiposity.

  20. Oil palm (Elaeis guineensis Jacq. tissue culture ESTs: Identifying genes associated with callogenesis and embryogenesis

    Directory of Open Access Journals (Sweden)

    Ooi Leslie CL

    2008-05-01

    , in order to confirm whether these genes are suitable as early markers for embryogenesis, the genes need to be tested on earlier stages of tissue culture and a wider range of genotypes. This collection of ESTs is an important resource for genetic and genome analyses of the oil palm, particularly during tissue culture development.

  1. Oil palm (Elaeis guineensis Jacq.) tissue culture ESTs: identifying genes associated with callogenesis and embryogenesis.

    Science.gov (United States)

    Low, Eng-Ti L; Alias, Halimah; Boon, Soo-Heong; Shariff, Elyana M; Tan, Chi-Yee A; Ooi, Leslie Cl; Cheah, Suan-Choo; Raha, Abdul-Rahim; Wan, Kiew-Lian; Singh, Rajinder

    2008-05-29

    early markers for embryogenesis, the genes need to be tested on earlier stages of tissue culture and a wider range of genotypes. This collection of ESTs is an important resource for genetic and genome analyses of the oil palm, particularly during tissue culture development.

  2. Cloning and expression profiling of the VLDLR gene associated with egg performance in duck (Anas platyrhynchos

    Directory of Open Access Journals (Sweden)

    Peng Xiu-li

    2011-08-01

    and be used as a genetic marker to improve egg performance in ducks.

  3. Genes associated to lactose metabolism illustrate the high diversity of Carnobacterium maltaromaticum

    DEFF Research Database (Denmark)

    Iskandar, Christelle F.; Cailliez-Grimal, Catherine; Rahman, Abdur

    2016-01-01

    , III and IV. These data suggest that these genes evolved thanks to horizontal transfer, genetic duplication and translocation. We hypothesize that the lac and gal genes evolved in C. maltaromaticum according to a complex scenario that mirrors the high population diversity....... genomic analysis revealed that the species C. maltaromaticum exhibits genes related to the Leloir and the tagatose-6-phosphate (Tagatose-6P) pathways. More precisely, strains can bear genes related to one or both pathways and several strains apparently do not contain homologs related to these pathways....... Analysis at the population scale revealed that the Tagatose-6P and the Leloir encoding genes are disseminated in multiple phylogenetic lineages of C. maltaromaticum: genes of the Tagatose-6P pathway are present in the lineages I, II and III, and genes of the Leloir pathway are present in the lineages I...

  4. Season of Birth and Dopamine Receptor Gene Associations with Impulsivity, Sensation Seeking and Reproductive Behaviors

    Science.gov (United States)

    Eisenberg, Dan T. A.; Campbell, Benjamin; MacKillop, James; Lum, J. Koji; Wilson, David S.

    2007-01-01

    Background Season of birth (SOB) has been associated with many physiological and psychological traits including novelty seeking and sensation seeking. Similar traits have been associated with genetic polymorphisms in the dopamine system. SOB and dopamine receptor genetic polymorphisms may independently and interactively influence similar behaviors through their common effects on the dopaminergic system. Methodology/Principal Findings Based on a sample of 195 subjects, we examined whether SOB was associated with impulsivity, sensation seeking and reproductive behaviors. Additionally we examined potential interactions of dopamine receptor genes with SOB for the same set of traits. Phenotypes were evaluated using the Sociosexual Orientation Inventory, the Barratt Impulsivity Scale, the Eysenck Impulsivity Questionnaire, the Sensation Seeking Scale, and the Delay Discounting Task. Subjects were also asked about their age at first sex as well as their desired age at the birth of their first child. The dopamine gene polymorphisms examined were Dopamine Receptor D2 (DRD2) TaqI A and D4 (DRD4) 48 bp VNTR. Primary analyses included factorial gender×SOB ANOVAs or binary logistic regression models for each dependent trait. Secondary analysis extended the factorial models by also including DRD2 and DRD4 genotypes as independent variables. Winter-born males were more sensation seeking than non-winter born males. In factorial models including both genotype and season of birth as variables, two previously unobserved effects were discovered: (1) a SOB×DRD4 interaction effect on venturesomeness and (2) a DRD2×DRD4 interaction effect on sensation seeking. Conclusion These results are consistent with past findings that SOB is related to sensation seeking. Additionally, these results provide tentative support for the hypothesis that SOB modifies the behavioral expression of dopaminergic genetic polymorphism. These findings suggest that SOB should be included in future studies of

  5. Season of birth and dopamine receptor gene associations with impulsivity, sensation seeking and reproductive behaviors.

    Directory of Open Access Journals (Sweden)

    Dan T A Eisenberg

    2007-11-01

    Full Text Available Season of birth (SOB has been associated with many physiological and psychological traits including novelty seeking and sensation seeking. Similar traits have been associated with genetic polymorphisms in the dopamine system. SOB and dopamine receptor genetic polymorphisms may independently and interactively influence similar behaviors through their common effects on the dopaminergic system.Based on a sample of 195 subjects, we examined whether SOB was associated with impulsivity, sensation seeking and reproductive behaviors. Additionally we examined potential interactions of dopamine receptor genes with SOB for the same set of traits. Phenotypes were evaluated using the Sociosexual Orientation Inventory, the Barratt Impulsivity Scale, the Eysenck Impulsivity Questionnaire, the Sensation Seeking Scale, and the Delay Discounting Task. Subjects were also asked about their age at first sex as well as their desired age at the birth of their first child. The dopamine gene polymorphisms examined were Dopamine Receptor D2 (DRD2 TaqI A and D4 (DRD4 48 bp VNTR. Primary analyses included factorial genderxSOB ANOVAs or binary logistic regression models for each dependent trait. Secondary analysis extended the factorial models by also including DRD2 and DRD4 genotypes as independent variables. Winter-born males were more sensation seeking than non-winter born males. In factorial models including both genotype and season of birth as variables, two previously unobserved effects were discovered: (1 a SOBxDRD4 interaction effect on venturesomeness and (2 a DRD2xDRD4 interaction effect on sensation seeking.These results are consistent with past findings that SOB is related to sensation seeking. Additionally, these results provide tentative support for the hypothesis that SOB modifies the behavioral expression of dopaminergic genetic polymorphism. These findings suggest that SOB should be included in future studies of risky behaviors and behavioral genetic

  6. A Diagnostic Marker to Discriminate Childhood Apraxia of Speech from Speech Delay: IV. the Pause Marker Index

    Science.gov (United States)

    Shriberg, Lawrence D.; Strand, Edythe A.; Fourakis, Marios; Jakielski, Kathy J.; Hall, Sheryl D.; Karlsson, Heather B.; Mabie, Heather L.; McSweeny, Jane L.; Tilkens, Christie M.; Wilson, David L.

    2017-01-01

    Purpose: Three previous articles provided rationale, methods, and several forms of validity support for a diagnostic marker of childhood apraxia of speech (CAS), termed the pause marker (PM). Goals of the present article were to assess the validity and stability of the PM Index (PMI) to scale CAS severity. Method: PM scores and speech, prosody,…

  7. A Complex Network of MicroRNAs Expressed in Brain and Genes Associated with Amyotrophic Lateral Sclerosis

    Directory of Open Access Journals (Sweden)

    Santosh Shinde

    2013-01-01

    Full Text Available Amyotrophic Lateral Sclerosis (ALS is a rare neurological disease affecting mainly motor neurons and often leads to paralysis and death in extreme cases. For exploring the role of microRNAs in genes regulation in ALS disease, miRanda was employed for prediction of target sites of miRNAs expressed in various parts of brain and CNS on 35 genes associated with ALS. Similar search was conducted using TargetScan and PicTar for prediction of target sites in 3′ UTR only. 1456 target sites were predicted using miRanda and more target sites were found in 5′ UTR and CDS region as compared to 3′ UTR. 11 target sites were predicted to be common by all the algorithms and, thus, these represent the most significant sites. Target site hotspots were identified and were recognized as hotspots for multiple miRNAs action, thus, acting as favoured sites of action for the repression of gene expression. The complex interplay of genes and miRNAs brought about by multiplicity and cooperativity was explored. This investigation will aid in elucidating the mechanism of action of miRNAs for the considered genes. The intrinsic network of miRNAs expressed in nervous system and genes associated with ALS may provide rapid and effective outcome for therapeutic applications and diagnosis.

  8. Genetic characterization of inbred lines of Chinese cabbage by DNA markers; towards the application of DNA markers to breeding of F1 hybrid cultivars

    Directory of Open Access Journals (Sweden)

    Kazutaka Kawamura

    2016-03-01

    Full Text Available Chinese cabbage (Brassica rapa L. var. pekinensis is an important vegetable in Asia, and most Japanese commercial cultivars of Chinese cabbage use an F1 hybrid seed production system. Self-incompatibility is successfully used for the production of F1 hybrid seeds in B. rapa vegetables to avoid contamination by non-hybrid seeds, and the strength of self-incompatibility is important for harvesting a highly pure F1 seeds. Prediction of agronomically important traits such as disease resistance based on DNA markers is useful. In this dataset, we identified the S haplotypes by DNA markers and evaluated the strength of self-incompatibility in Chinese cabbage inbred lines. The data described the predicted disease resistance to Fusarium yellows or clubroot in 22 Chinese cabbage inbred lines using gene associated or gene linked DNA markers.

  9. [Markers of brain tumors].

    Science.gov (United States)

    Fumagalli, R; Pezzotta, S; Bernini, F; Racagni, G

    1984-05-19

    Biological markers of tumors are compounds or enzymatic activities measurable in body fluids. Their presence or concentration must be linked to tumoral growth. The markers of the central nervous system tumors are detected in CSF. Alpha-feto-protein, carcinoembryonic antigen, human chorionic gonadotropin, adenohypophyseal peptide hormones, enzymes, etc., have found some application in the early diagnosis of leptomeningeal metastasis. Other applications involve the early detection and recurrency of primary brain tumors, as well as the evaluation of efficacy of their therapy. The tests based on the CSF content of desmosterol and polyamines have been studied extensively. Their rationale is discussed and specificity, sensitivity, efficiency and predictive value are considered. Experimental results concerning a new possible biochemical marker, based on CSF concentration of cyclic adenosine monophosphate, are reported.

  10. Tumor Markers: An Overview

    Directory of Open Access Journals (Sweden)

    Ajay G Nayak

    2010-01-01

    Full Text Available Oral cancer is a potentially fatal disease that has been the bane of clinicians throughout the world. Though various modalities of management exist, early detection still provides the best hope for any cancer patient Advances in molecular diagnosis have led to a plethora of choices being available in the fight against cancer. Abnormal cellular products elucidated from malignant cells can be detected and measured in various body tissues and fluids and constitute tumor markers. The various clinical applications and their limitations are covered in the brief overview to help the oral medicine specialist understand the relevant advances made in the field of tumor markers.

  11. Influence of Productivity on the Acquisition of Inflectional Markers

    DEFF Research Database (Denmark)

    Kjærbæk, Laila; Basbøll, Hans; Christensen, René dePont

    marker for a grammatical category (e.g. the PL suffix -s) and a minor number of exceptions to this default rule. We find this distinction rather inexpedient since this is not the case for all languages (e.g. Danish, German). In order to address this issue we have developed a scale with three degrees......-schwa (/ɐ/) suffix without phonemic stem change. Semi-Productive: e–schwa (/ə/) and zero suffix without phonemic stem change. Unproductive: markers with phonemic stem change and markers with the foreign suffixes s, a and i. Hypothesis We predict the error direction to go from Unproductive to Semi......-Productive or Unproductive PL marker. Children overgeneralize the Fully Productive and Semi-Productive PL markers but never the Unproductive. The error direction goes from Unproductive to Semi-Productive to Fully Productive PL markers....

  12. Magik Markers Trehvis

    Index Scriptorium Estoniae

    2008-01-01

    Müra-rock'i viljelevast USA duost Magik Markers (ansambel osaleb režissöör Veiko Õunapuu uue mängufilmi "Püha Tõnu kiusamine" võtetel, kontsert 15. nov. Tartus klubis Trehv, vt. www.magikmarkers.audiosport.org.)

  13. (DArT) markers

    Indian Academy of Sciences (India)

    2EH Graham Centre for Agricultural Innovation (NSW Department of Industry and Investment and Charles Sturt. University), P. O. Box 588 Wagga Wagga, .... between-cluster variance in relative hybridization intensity as a percentage of the total .... markers tend to cluster on one or two linkage groups. The data of both sets of ...

  14. The Swift Turbidity Marker

    Science.gov (United States)

    Omar, Ahmad Fairuz; MatJafri, Mohd Zubir

    2011-01-01

    The Swift Turbidity Marker is an optical instrument developed to measure the level of water turbidity. The components and configuration selected for the system are based on common turbidity meter design concepts but use a simplified methodology to produce rapid turbidity measurements. This work is aimed at high school physics students and is the…

  15. Identification and characterization of genes associated with tapping panel dryness from Hevea brasiliensis latex using suppression subtractive hybridization

    Directory of Open Access Journals (Sweden)

    Chen Chunliu

    2010-07-01

    Full Text Available Abstract Background Tapping panel dryness (TPD is one of the most serious threats to natural rubber production. Although a great deal of effort has been made to study TPD in rubber tree, the molecular mechanisms underlying TPD remain poorly understood. Identification and systematical analyses of the genes associated with TPD are the prerequisites for elucidating the molecular mechanisms involved in TPD. The present study is undertaken to generate information about the genes related to TPD in rubber tree. Results To identify the genes related to TPD in rubber tree, forward and reverse cDNA libraries from the latex of healthy and TPD trees were constructed using suppression subtractive hybridization (SSH method. Among the 1106 clones obtained from the two cDNA libraries, 822 clones showed differential expression in two libraries by reverse Northern blot analyses. Sequence analyses indicated that the 822 clones represented 237 unique genes; and most of them have not been reported to be associated with TPD in rubber tree. The expression patterns of 20 differentially expressed genes were further investigated to validate the SSH data by reverse transcription PCR (RT-PCR and real-time PCR analysis. According to the Gene Ontology convention, 237 unique genes were classified into 10 functional groups, such as stress/defense response, protein metabolism, transcription and post-transcription, rubber biosynthesis, etc. Among the genes with known function, the genes preferentially expressed were associated with stress/defense response in the reverse library, whereas metabolism and energy in the forward one. Conclusions The genes associated with TPD were identified by SSH method in this research. Systematic analyses of the genes related to TPD suggest that the production and scavenging of reactive oxygen species (ROS, ubiquitin proteasome pathway, programmed cell death and rubber biosynthesis might play important roles in TPD. Therefore, our results not only

  16. Identification and characterization of genes associated with tapping panel dryness from Hevea brasiliensis latex using suppression subtractive hybridization

    Science.gov (United States)

    2010-01-01

    Background Tapping panel dryness (TPD) is one of the most serious threats to natural rubber production. Although a great deal of effort has been made to study TPD in rubber tree, the molecular mechanisms underlying TPD remain poorly understood. Identification and systematical analyses of the genes associated with TPD are the prerequisites for elucidating the molecular mechanisms involved in TPD. The present study is undertaken to generate information about the genes related to TPD in rubber tree. Results To identify the genes related to TPD in rubber tree, forward and reverse cDNA libraries from the latex of healthy and TPD trees were constructed using suppression subtractive hybridization (SSH) method. Among the 1106 clones obtained from the two cDNA libraries, 822 clones showed differential expression in two libraries by reverse Northern blot analyses. Sequence analyses indicated that the 822 clones represented 237 unique genes; and most of them have not been reported to be associated with TPD in rubber tree. The expression patterns of 20 differentially expressed genes were further investigated to validate the SSH data by reverse transcription PCR (RT-PCR) and real-time PCR analysis. According to the Gene Ontology convention, 237 unique genes were classified into 10 functional groups, such as stress/defense response, protein metabolism, transcription and post-transcription, rubber biosynthesis, etc. Among the genes with known function, the genes preferentially expressed were associated with stress/defense response in the reverse library, whereas metabolism and energy in the forward one. Conclusions The genes associated with TPD were identified by SSH method in this research. Systematic analyses of the genes related to TPD suggest that the production and scavenging of reactive oxygen species (ROS), ubiquitin proteasome pathway, programmed cell death and rubber biosynthesis might play important roles in TPD. Therefore, our results not only enrich information about

  17. Association of genetic loci with sleep apnea in European Americans and African-Americans: the Candidate Gene Association Resource (CARe.

    Directory of Open Access Journals (Sweden)

    Sanjay R Patel

    Full Text Available Although obstructive sleep apnea (OSA is known to have a strong familial basis, no genetic polymorphisms influencing apnea risk have been identified in cross-cohort analyses. We utilized the National Heart, Lung, and Blood Institute (NHLBI Candidate Gene Association Resource (CARe to identify sleep apnea susceptibility loci. Using a panel of 46,449 polymorphisms from roughly 2,100 candidate genes on a customized Illumina iSelect chip, we tested for association with the apnea hypopnea index (AHI as well as moderate to severe OSA (AHI≥15 in 3,551 participants of the Cleveland Family Study and two cohorts participating in the Sleep Heart Health Study.Among 647 African-Americans, rs11126184 in the pleckstrin (PLEK gene was associated with OSA while rs7030789 in the lysophosphatidic acid receptor 1 (LPAR1 gene was associated with AHI using a chip-wide significance threshold of p-value<2×10(-6. Among 2,904 individuals of European ancestry, rs1409986 in the prostaglandin E2 receptor (PTGER3 gene was significantly associated with OSA. Consistency of effects between rs7030789 and rs1409986 in LPAR1 and PTGER3 and apnea phenotypes were observed in independent clinic-based cohorts.Novel genetic loci for apnea phenotypes were identified through the use of customized gene chips and meta-analyses of cohort data with replication in clinic-based samples. The identified SNPs all lie in genes associated with inflammation suggesting inflammation may play a role in OSA pathogenesis.

  18. Association of genetic variation with systolic and diastolic blood pressure among African Americans: the Candidate Gene Association Resource study

    Science.gov (United States)

    Fox, Ervin R.; Young, J. Hunter; Li, Yali; Dreisbach, Albert W.; Keating, Brendan J.; Musani, Solomon K.; Liu, Kiang; Morrison, Alanna C.; Ganesh, Santhi; Kutlar, Abdullah; Ramachandran, Vasan S.; Polak, Josef F.; Fabsitz, Richard R.; Dries, Daniel L.; Farlow, Deborah N.; Redline, Susan; Adeyemo, Adebowale; Hirschorn, Joel N.; Sun, Yan V.; Wyatt, Sharon B.; Penman, Alan D.; Palmas, Walter; Rotter, Jerome I.; Townsend, Raymond R.; Doumatey, Ayo P.; Tayo, Bamidele O.; Mosley, Thomas H.; Lyon, Helen N.; Kang, Sun J.; Rotimi, Charles N.; Cooper, Richard S.; Franceschini, Nora; Curb, J. David; Martin, Lisa W.; Eaton, Charles B.; Kardia, Sharon L.R.; Taylor, Herman A.; Caulfield, Mark J.; Ehret, Georg B.; Johnson, Toby; Chakravarti, Aravinda; Zhu, Xiaofeng; Levy, Daniel; Munroe, Patricia B.; Rice, Kenneth M.; Bochud, Murielle; Johnson, Andrew D.; Chasman, Daniel I.; Smith, Albert V.; Tobin, Martin D.; Verwoert, Germaine C.; Hwang, Shih-Jen; Pihur, Vasyl; Vollenweider, Peter; O'Reilly, Paul F.; Amin, Najaf; Bragg-Gresham, Jennifer L.; Teumer, Alexander; Glazer, Nicole L.; Launer, Lenore; Zhao, Jing Hua; Aulchenko, Yurii; Heath, Simon; Sõber, Siim; Parsa, Afshin; Luan, Jian'an; Arora, Pankaj; Dehghan, Abbas; Zhang, Feng; Lucas, Gavin; Hicks, Andrew A.; Jackson, Anne U.; Peden, John F.; Tanaka, Toshiko; Wild, Sarah H.; Rudan, Igor; Igl, Wilmar; Milaneschi, Yuri; Parker, Alex N.; Fava, Cristiano; Chambers, John C.; Kumari, Meena; JinGo, Min; van der Harst, Pim; Kao, Wen Hong Linda; Sjögren, Marketa; Vinay, D.G.; Alexander, Myriam; Tabara, Yasuharu; Shaw-Hawkins, Sue; Whincup, Peter H.; Liu, Yongmei; Shi, Gang; Kuusisto, Johanna; Seielstad, Mark; Sim, Xueling; Nguyen, Khanh-Dung Hoang; Lehtimäki, Terho; Matullo, Giuseppe; Wu, Ying; Gaunt, Tom R.; Charlotte Onland-Moret, N.; Cooper, Matthew N.; Platou, Carl G.P.; Org, Elin; Hardy, Rebecca; Dahgam, Santosh; Palmen, Jutta; Vitart, Veronique; Braund, Peter S.; Kuznetsova, Tatiana; Uiterwaal, Cuno S.P.M.; Campbell, Harry; Ludwig, Barbara; Tomaszewski, Maciej; Tzoulaki, Ioanna; Palmer, Nicholette D.; Aspelund, Thor; Garcia, Melissa; Chang, Yen-Pei C.; O'Connell, Jeffrey R.; Steinle, Nanette I.; Grobbee, Diederick E.; Arking, Dan E.; Hernandez, Dena; Najjar, Samer; McArdle, Wendy L.; Hadley, David; Brown, Morris J.; Connell, John M.; Hingorani, Aroon D.; Day, Ian N.M.; Lawlor, Debbie A.; Beilby, John P.; Lawrence, Robert W.; Clarke, Robert; Collins, Rory; Hopewell, Jemma C.; Ongen, Halit; Bis, Joshua C.; Kähönen, Mika; Viikari, Jorma; Adair, Linda S.; Lee, Nanette R.; Chen, Ming-Huei; Olden, Matthias; Pattaro, Cristian; Hoffman Bolton, Judith A.; Köttgen, Anna; Bergmann, Sven; Mooser, Vincent; Chaturvedi, Nish; Frayling, Timothy M.; Islam, Muhammad; Jafar, Tazeen H.; Erdmann, Jeanette; Kulkarni, Smita R.; Bornstein, Stefan R.; Grässler, Jürgen; Groop, Leif; Voight, Benjamin F.; Kettunen, Johannes; Howard, Philip; Taylor, Andrew; Guarrera, Simonetta; Ricceri, Fulvio; Emilsson, Valur; Plump, Andrew; Barroso, Inês; Khaw, Kay-Tee; Weder, Alan B.; Hunt, Steven C.; Bergman, Richard N.; Collins, Francis S.; Bonnycastle, Lori L.; Scott, Laura J.; Stringham, Heather M.; Peltonen, Leena; Perola, Markus; Vartiainen, Erkki; Brand, Stefan-Martin; Staessen, Jan A.; Wang, Thomas J.; Burton, Paul R.; SolerArtigas, Maria; Dong, Yanbin; Snieder, Harold; Wang, Xiaoling; Zhu, Haidong; Lohman, Kurt K.; Rudock, Megan E.; Heckbert, Susan R.; Smith, Nicholas L.; Wiggins, Kerri L.; Shriner, Daniel; Veldre, Gudrun; Viigimaa, Margus; Kinra, Sanjay; Prabhakaran, Dorairajan; Tripathy, Vikal; Langefeld, Carl D.; Rosengren, Annika; Thelle, Dag S.; MariaCorsi, Anna; Singleton, Andrew; Forrester, Terrence; Hilton, Gina; McKenzie, Colin A.; Salako, Tunde; Iwai, Naoharu; Kita, Yoshikuni; Ogihara, Toshio; Ohkubo, Takayoshi; Okamura, Tomonori; Ueshima, Hirotsugu; Umemura, Satoshi; Eyheramendy, Susana; Meitinger, Thomas; Wichmann, H.-Erich; Cho, Yoon Shin; Kim, Hyung-Lae; Lee, Jong-Young; Scott, James; Sehmi, Joban S.; Zhang, Weihua; Hedblad, Bo; Nilsson, Peter; Smith, George Davey; Wong, Andrew; Narisu, Narisu; Stančáková, Alena; Raffel, Leslie J.; Yao, Jie; Kathiresan, Sekar; O'Donnell, Chris; Schwartz, Steven M.; Arfan Ikram, M.; Longstreth, Will T.; Seshadri, Sudha; Shrine, Nick R.G.; Wain, Louise V.; Morken, Mario A.; Swift, Amy J.; Laitinen, Jaana; Prokopenko, Inga; Zitting, Paavo; Cooper, Jackie A.; Humphries, Steve E.; Danesh, John; Rasheed, Asif; Goel, Anuj; Hamsten, Anders; Watkins, Hugh; Bakker, Stephan J.L.; van Gilst, Wiek H.; Janipalli, Charles S.; Radha Mani, K.; Yajnik, Chittaranjan S.; Hofman, Albert; Mattace-Raso, Francesco U.S.; Oostra, Ben A.; Demirkan, Ayse; Isaacs, Aaron; Rivadeneira, Fernando; Lakatta, Edward G.; Orru, Marco; Scuteri, Angelo; Ala-Korpela, Mika; Kangas, Antti J.; Lyytikäinen, Leo-Pekka; Soininen, Pasi; Tukiainen, Taru; Würz, Peter; Twee-Hee Ong, Rick; Dörr, Marcus; Kroemer, Heyo K.; Völker, Uwe; Völzke, Henry; Galan, Pilar; Hercberg, Serge; Lathrop, Mark; Zelenika, Diana; Deloukas, Panos; Mangino, Massimo; Spector, Tim D.; Zhai, Guangju; Meschia, James F.; Nalls, Michael A.; Sharma, Pankaj; Terzic, Janos; Kranthi Kumar, M.J.; Denniff, Matthew; Zukowska-Szczechowska, Ewa; Wagenknecht, Lynne E.; Fowkes, Gerald R.; Charchar, Fadi J.; Schwarz, Peter E.H.; Hayward, Caroline; Guo, Xiuqing; Bots, Michiel L.; Brand, Eva; Samani, Nilesh J.; Polasek, Ozren; Talmud, Philippa J.; Nyberg, Fredrik; Kuh, Diana; Laan, Maris; Hveem, Kristian; Palmer, Lyle J.; van der Schouw, Yvonne T.; Casas, Juan P.; Mohlke, Karen L.; Vineis, Paolo; Raitakari, Olli; Wong, Tien Y.; Shyong Tai, E.; Laakso, Markku; Rao, Dabeeru C.; Harris, Tamara B.; Morris, Richard W.; Dominiczak, Anna F.; Kivimaki, Mika; Marmot, Michael G.; Miki, Tetsuro; Saleheen, Danish; Chandak, Giriraj R.; Coresh, Josef; Navis, Gerjan; Salomaa, Veikko; Han, Bok-Ghee; Kooner, Jaspal S.; Melander, Olle; Ridker, Paul M.; Bandinelli, Stefania; Gyllensten, Ulf B.; Wright, Alan F.; Wilson, James F.; Ferrucci, Luigi; Farrall, Martin; Tuomilehto, Jaakko; Pramstaller, Peter P.; Elosua, Roberto; Soranzo, Nicole; Sijbrands, Eric J.G.; Altshuler, David; Loos, Ruth J.F.; Shuldiner, Alan R.; Gieger, Christian; Meneton, Pierre; Uitterlinden, Andre G.; Wareham, Nicholas J.; Gudnason, Vilmundur; Rettig, Rainer; Uda, Manuela; Strachan, David P.; Witteman, Jacqueline C.M.; Hartikainen, Anna-Liisa; Beckmann, Jacques S.; Boerwinkle, Eric; Boehnke, Michael; Larson, Martin G.; Järvelin, Marjo-Riitta; Psaty, Bruce M.; Abecasis, Gonçalo R.; Elliott, Paul; van Duijn , Cornelia M.; Newton-Cheh, Christopher

    2011-01-01

    The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10−8) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10−8). The top IBC association for SBP was rs2012318 (P= 6.4 × 10−6) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10−6) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexity. PMID:21378095

  19. Pathways-driven sparse regression identifies pathways and genes associated with high-density lipoprotein cholesterol in two Asian cohorts.

    Directory of Open Access Journals (Sweden)

    Matt Silver

    2013-11-01

    Full Text Available Standard approaches to data analysis in genome-wide association studies (GWAS ignore any potential functional relationships between gene variants. In contrast gene pathways analysis uses prior information on functional structure within the genome to identify pathways associated with a trait of interest. In a second step, important single nucleotide polymorphisms (SNPs or genes may be identified within associated pathways. The pathways approach is motivated by the fact that genes do not act alone, but instead have effects that are likely to be mediated through their interaction in gene pathways. Where this is the case, pathways approaches may reveal aspects of a trait's genetic architecture that would otherwise be missed when considering SNPs in isolation. Most pathways methods begin by testing SNPs one at a time, and so fail to capitalise on the potential advantages inherent in a multi-SNP, joint modelling approach. Here, we describe a dual-level, sparse regression model for the simultaneous identification of pathways and genes associated with a quantitative trait. Our method takes account of various factors specific to the joint modelling of pathways with genome-wide data, including widespread correlation between genetic predictors, and the fact that variants may overlap multiple pathways. We use a resampling strategy that exploits finite sample variability to provide robust rankings for pathways and genes. We test our method through simulation, and use it to perform pathways-driven gene selection in a search for pathways and genes associated with variation in serum high-density lipoprotein cholesterol levels in two separate GWAS cohorts of Asian adults. By comparing results from both cohorts we identify a number of candidate pathways including those associated with cardiomyopathy, and T cell receptor and PPAR signalling. Highlighted genes include those associated with the L-type calcium channel, adenylate cyclase, integrin, laminin, MAPK

  20. Characterization of the 'Xiangshui' lemon transcriptome by de novo assembly to discover genes associated with self-incompatibility.

    Science.gov (United States)

    Zhang, Shuwei; Ding, Feng; He, Xinhua; Luo, Cong; Huang, Guixiang; Hu, Ying

    2015-02-01

    Seedlessness is a desirable character in lemons and other citrus species. Seedless fruit can be induced in many ways, including through self-incompatibility (SI). SI is widely used as an intraspecific reproductive barrier that prevents self-fertilization in flowering plants. Although there have been many studies on SI, its mechanism remains unclear. The 'Xiangshui' lemon is an important seedless cultivar whose seedlessness has been caused by SI. It is essential to identify genes involved in SI in 'Xiangshui' lemon to clarify its molecular mechanism. In this study, candidate genes associated with SI were identified using high-throughput Illumina RNA sequencing (RNA-seq). A total of 61,224 unigenes were obtained (average, 948 bp; N50 of 1,457 bp), among which 47,260 unigenes were annotated by comparison to six public databases (Nr, Nt, Swiss-Prot, KEGG, COG, and GO). Differentially expressed genes were identified by comparing the transcriptomes of no-, self-, and cross-pollinated stigmas with styles of the 'Xiangshui' lemon. Several differentially expressed genes that might be associated with SI were identified, such as those involved in pollen tube growth, programmed cell death, signal transduction, and transcription. NADPH oxidase genes associated with apoptosis were highly upregulated in the self-pollinated transcriptome. The expression pattern of 12 genes was analyzed by quantitative real-time polymerase chain reaction. A putative S-RNase gene was identified that had not been previously associated with self-pollen rejection in lemon or citrus. This study provided a transcriptome dataset for further studies of SI and seedless lemon breeding.

  1. Identification and characterization of potential NBS-encoding resistance genes and induction kinetics of a putative candidate gene associated with downy mildew resistance in Cucumis

    Directory of Open Access Journals (Sweden)

    Wan Hongjian

    2010-08-01

    Full Text Available Abstract Background Due to the variation and mutation of the races of Pseudoperonospora cubensis, downy mildew has in recent years become the most devastating leaf disease of cucumber worldwide. Novel resistance to downy mildew has been identified in the wild Cucumis species, C. hystrix Chakr. After the successful hybridization between C. hystrix and cultivated cucumber (C. sativus L., an introgression line (IL5211S was identified as highly resistant to downy mildew. Nucleotide-binding site and leucine-rich repeat (NBS-LRR genes are the largest class of disease resistance genes cloned from plant with highly conserved domains, which can be used to facilitate the isolation of candidate genes associated with downy mildew resistance in IL5211S. Results Degenerate primers that were designed based on the conserved motifs in the NBS domain of resistance (R proteins were used to isolate NBS-type sequences from IL5211S. A total of 28 sequences were identified and named as cucumber (C. sativus = CS resistance gene analogs as CSRGAs. Polygenetic analyses separated these sequences into four different classes. Quantitative real-time polymerase chain reaction (qRT-PCR analysis showed that these CSRGAs expressed at different levels in leaves, roots, and stems. In addition, introgression from C. hystrix induced expression of the partial CSRGAs in cultivated cucumber, especially CSRGA23, increased four-fold when compared to the backcross parent CC3. Furthermore, the expression of CSRGA23 under P. cubensis infection and abiotic stresses was also analyzed at different time points. Results showed that the P. cubensis treatment and four tested abiotic stimuli, MeJA, SA, ABA, and H2O2, triggered a significant induction of CSRGA23 within 72 h of inoculation. The results indicate that CSRGA23 may play a critical role in protecting cucumber against P. cubensis through a signaling the pathway triggered by these molecules. Conclusions Four classes of NBS-type RGAs were

  2. Candidate gene association study in type 2 diabetes indicates a role for genes involved in beta-cell function as well as insulin action.

    Directory of Open Access Journals (Sweden)

    Inês Barroso

    2003-10-01

    Full Text Available Type 2 diabetes is an increasingly common, serious metabolic disorder with a substantial inherited component. It is characterised by defects in both insulin secretion and action. Progress in identification of specific genetic variants predisposing to the disease has been limited. To complement ongoing positional cloning efforts, we have undertaken a large-scale candidate gene association study. We examined 152 SNPs in 71 candidate genes for association with diabetes status and related phenotypes in 2,134 Caucasians in a case-control study and an independent quantitative trait (QT cohort in the United Kingdom. Polymorphisms in five of 15 genes (33% encoding molecules known to primarily influence pancreatic beta-cell function-ABCC8 (sulphonylurea receptor, KCNJ11 (KIR6.2, SLC2A2 (GLUT2, HNF4A (HNF4alpha, and INS (insulin-significantly altered disease risk, and in three genes, the risk allele, haplotype, or both had a biologically consistent effect on a relevant physiological trait in the QT study. We examined 35 genes predicted to have their major influence on insulin action, and three (9%-INSR, PIK3R1, and SOS1-showed significant associations with diabetes. These results confirm the genetic complexity of Type 2 diabetes and provide evidence that common variants in genes influencing pancreatic beta-cell function may make a significant contribution to the inherited component of this disease. This study additionally demonstrates that the systematic examination of panels of biological candidate genes in large, well-characterised populations can be an effective complement to positional cloning approaches. The absence of large single-gene effects and the detection of multiple small effects accentuate the need for the study of larger populations in order to reliably identify the size of effect we now expect for complex diseases.

  3. Large-scale analysis of differential gene expression in coffee genotypes resistant and susceptible to leaf miner–toward the identification of candidate genes for marker assisted-selection

    Science.gov (United States)

    2014-01-01

    Background A successful development of herbivorous insects into plant tissues depends on coordination of metabolic processes. Plants have evolved complex mechanisms to recognize such attacks, and to trigger a defense response. To understand the transcriptional basis of this response, we compare gene expression profiles of two coffee genotypes, susceptible and resistant to leaf miner (Leucoptera coffella). A total of 22000 EST sequences from the Coffee Genome Database were selected for a microarray analysis. Fluorescence probes were synthesized using mRNA from the infested and non-infested coffee plants. Array hybridization, scanning and data normalization were performed using Nimble Scan® e ArrayStar® platforms. Genes with foldchange values +/-2 were considered differentially expressed. A validation of 18 differentially expressed genes was performed in infected plants using qRT-PCR approach. Results The microarray analysis indicated that resistant plants differ in gene expression profile. We identified relevant transcriptional changes in defense strategies before insect attack. Expression changes (>2.00-fold) were found in resistant plants for 2137 genes (1266 up-regulated and 873 down-regulated). Up-regulated genes include those responsible for defense mechanisms, hypersensitive response and genes involved with cellular function and maintenance. Also, our analyses indicated that differential expression profiles between resistant and susceptible genotypes are observed in the absence of leaf-miner, indicating that defense is already build up in resistant plants, as a priming mechanism. Validation of selected genes pointed to four selected genes as suitable candidates for markers in assisted-selection of novel cultivars. Conclusions Our results show evidences that coffee defense responses against leaf-miner attack are balanced with other cellular functions. Also analyses suggest a major metabolic reconfiguration that highlights the complexity of this response. PMID

  4. Alcoholism: Current Marker Research

    Science.gov (United States)

    1984-03-01

    mongolism are high-risk candidates for certain types of leukemia. Similarly, hemophiliacs have a correspondingly high incidence of color blindness . (4...genetically determined characteristics such as color blindness and blood type. GENETIC MARKER STUDIES In 1966 Dr. Cruz-Coke and Dr. Varela reported that...their study had linked color blindness , cirrhosis of the liver and alcoholism. They further hypothesized the existence of a sex-linked carrier gene

  5. Hepatocellualar carcinoma serum markers.

    Science.gov (United States)

    Bertino, Gaetano; Ardiri, Annalisa; Malaguarnera, Michele; Malaguarnera, Giulia; Bertino, Nicoletta; Calvagno, Giuseppe Stefano

    2012-08-01

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in some areas of the world. In most cases, HCC is diagnosed at a late stage. Therefore, the prognosis of patients with HCC is generally poor. The recommended screening strategy for patients with cirrhosis includes the determination of serum α-fetoprotein (AFP) levels and an abdominal ultrasound every 6 months to detect HCC at an earlier stage. AFP, however, is a marker characterized by poor sensitivity and specificity, and abdominal ultrasound is highly dependent on the operator's experience. In addition to AFP, Lens culinaris agglutinin-reactive AFP (AFP-L3), des-γ-carboxy prothrombin (DCP), glypican-3 (GPC-3), osteopontin (OPN), and several other biomarkers (such as squamous cell carcinoma antigen-immunoglobulin M complexes [SCCA-IgM], alpha-1-fucosidase [AFU], chromogranin A [CgA], human hepatocyte growth factor, insulin-like growth factor) have been proposed as markers for the early detection of HCC. For these markers, we describe the mechanisms of production, and their diagnostic and prognosis roles. None of them is optimal; however, when used together, their sensitivity in detecting HCC is increased. Recent research has shown that some biomarkers have mitogenic and migratory activities in the angiogenesis of HCC and are a factor of tumor growth. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. Platelet-to-lymphocyte ratio as a novel marker of in-hospital and long-term adverse outcomes among patients with acute pulmonary embolism: A single center large-scale study.

    Science.gov (United States)

    Ozcan Cetin, Elif Hande; Cetin, Mehmet Serkan; Canpolat, Ugur; Akdi, Ahmet; Aras, Dursun; Temizhan, Ahmet; Aydogdu, Sinan

    2017-02-01

    The interaction of platelets with leukocytes is a well-known process both in progression and prognosis of acute pulmonary embolism (PE). Recently, platelet to lymphocyte ratio (PLR) is emerged as an indirect inflammatory indicator which was shown to be associated with adverse cardiovascular events in various clinical conditions, including acute PE. However, the long-term prognostic value of PLR in acute PE has not been investigated thoroughly. Therefore, we aimed to assess the impact of PLR on both in-hospital and long-term adverse outcomes in acute PE. A total of 459 patients with definite diagnosis of acute PE between January 2009 and January 2016 were enrolled. On admission, blood sampling to calculate PLR and detailed clinical data were obtained. Patients were divided into tertiles according to the admission PLR levels. Simplified PE severity index (sPESI) score and computerized tomography (CT) based pulmonary artery obstruction index were calculated for each patient. Mean sPESI score of the study population was 1.6. A total of 34 patients (7.4%) died during index hospitalization. At median 28.8months follow-up, all-cause mortality was observed in 81 patients (1.9%). Patients in the highest tertile of PLR revealed a higher rate of in-hospital adverse events including cardiogenic shock, the necessity for thrombolytic therapy and in-hospital mortality as well as long-term all-cause mortality. In multivariate analysis, the PLR was found to be a significant predictor of both in-hospital adverse events (OR: 1.588, 95% CI:1.116-2.154, p=0.004) and long-term all-cause mortality (OR:1.746, 95% CI:1.211-2.865, p=0.001). The PLR, as a simple, inexpensive and available marker of inflammatory and prothrombotic status, seemed to be a novel predictor of in-hospital and long-term adverse outcomes in patients with acute PE. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. Premenstrual asthma and atopy markers.

    Science.gov (United States)

    Pereira-Vega, Antonio; Sánchez, José L; Maldonado, José A; Borrero, Fátima; Rico, Ignacio Vázquez; Vázquez, Rosa; Alvarez, Francisco; Ignacio, José M; Romero, Pedro; Gil, Francisco L

    2010-09-01

    The frequency of atopy in women with premenstrual asthma (PMA) and its possible effect on the premenstrual exacerbation of asthma are unknown. To analyze the relation between atopy markers (total IgE, Phadiatop, and specific IgE) and PMA. Asthmatic women of reproductive age completed a questionnaire about respiratory symptoms and recorded peak flow during an entire menstrual cycle to be classified as asthmatic patients with or without PMA. Their asthma severity was graded according to the 2005 Global Initiative for Asthma scale. PMA was defined as a clinical or functional exacerbation (>or=20%) in the premenstrual phase compared with the preovulatory phase. Blood tests for several atopy markers were conducted for: total IgE and screening for aeroallergens (Phadiatop) and specific IgE. Blood determinations were performed in 59 asthmatic women, of whom 31 (53%) had PMA. Twenty-six patients with PMA (84%) and 12 without PMA (43%) had total IgE values greater than 100 kU/L (P=.001). Twenty-one patients with PMA (68%) and 14 without PMA (50%) tested positive for Phadiatop (P=.17). Those who were positive for Phadiatop were also tested for specific IgE. No relation was found between specific IgE and PMA; values for ryegrass (63%), olive (60%), and Dermatophagoides pteronyssinus (54%) exceeded 0.35 kU/L. PMA seems to be closely linked to total IgE levels but not to specific allergens. The atopy affects the clinical manifestations of PMA in women of reproductive age. Copyright © 2010 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  8. A whole genome SNP genotyping by DNA microarray and candidate gene association study for kidney stone disease

    Science.gov (United States)

    2014-01-01

    Background Kidney stone disease (KSD) is a complex disorder with unknown etiology in majority of the patients. Genetic and environmental factors may cause the disease. In the present study, we used DNA microarray to genotype single nucleotide polymorphisms (SNP) and performed candidate gene association analysis to determine genetic variations associated with the disease. Methods A whole genome SNP genotyping by DNA microarray was initially conducted in 101 patients and 105 control subjects. A set of 104 candidate genes reported to be involved in KSD, gathered from public databases and candidate gene association study databases, were evaluated for their variations associated with KSD. Results Altogether 82 SNPs distributed within 22 candidate gene regions showed significant differences in SNP allele frequencies between the patient and control groups (P AHSG, CD44, and HAO1, encoding osteocalcin, fetuin-A, CD44-molecule and glycolate oxidase 1, respectively, were further assessed for their associations with the disease because they carried high proportion of SNPs with statistical differences of allele frequencies between the patient and control groups within the gene. The total of 26 SNPs showed significant differences of allele frequencies between the patient and control groups and haplotypes associated with disease risk were identified. The SNP rs759330 located 144 bp downstream of BGLAP where it is a predicted microRNA binding site at 3′UTR of PAQR6 – a gene encoding progestin and adipoQ receptor family member VI, was genotyped in 216 patients and 216 control subjects and found to have significant differences in its genotype and allele frequencies (P = 0.0007, OR 2.02 and P = 0.0001, OR 2.02, respectively). Conclusions Our results suggest that these candidate genes are associated with KSD and PAQR6 comes into our view as the most potent candidate since associated SNP rs759330 is located in the miRNA binding site and may affect mRNA expression level

  9. A large insertion in intron 2 of the TYRP1 gene associated with American Palomino phenotype in American mink

    DEFF Research Database (Denmark)

    Cirera Salicio, Susanna; Markakis, Marios Nektarios; Kristiansen, Thea

    2016-01-01

    A number of American mink phenotypes display a range of brownish colours. One of these phenotypes, namely American Palomino (b (P) b (P) ) (AP) has been found to be associated with the tyrosinase-related protein 1 (TYRP1) gene by genotyping microsatellite markers in one sire family. Trials...

  10. Selection of genes associated with variations in the Circle of Willis in gerbils using suppression subtractive hybridization.

    Directory of Open Access Journals (Sweden)

    Zhenkun Li

    Full Text Available Deformities in the Circle of Willis (CoW can significantly increase the risk of cerebrovascular disease in humans. However, the molecular mechanisms underlying these deformities have not been understood. Based on our previous studies, variations in the CoW of gerbils are hereditary. A normal CoW is observed in approximately 60% of gerbils, a percentage that also applies to humans. Thus, gerbil is an ideal experimental model for studying variations in the CoW. To study the mechanisms underlying these variations, we selected genes associated with different types of the CoW using suppression subtractive hybridization (SSH. After evaluating the efficiency of SSH using quantitative real-time polymerase chain reaction (qPCR on subtracted and unsubtracted cDNA and Southern blotting on SSH PCR products, 12 SSH libraries were established. We identified 4 genes (CST3, GNAS, GPx4 and PFN2 associated with variations in the CoW. These genes were identified with qPCR and Western blotting using 70 expressed sequence tags from the SSH libraries. Cloning and sequencing allowed us to demonstrate that the 4 genes were closely related to mouse genes. We may assume that these 4 genes play an important role in the development of variations in the CoW. This study provides a foundation for further research of genes related to development of variations in the CoW and the mechanisms of dysmorphosis of cerebral vessels.

  11. Selection of Genes Associated with Variations in the Circle of Willis in Gerbils Using Suppression Subtractive Hybridization

    Science.gov (United States)

    Li, Zhenkun; Huo, Xueyun; Zhang, Shuangyue; Lu, Jing; Li, Changlong; Guo, Meng; Fu, Rui; He, Zhengming; Du, Xiaoyan; Chen, Zhenwen

    2015-01-01

    Deformities in the Circle of Willis (CoW) can significantly increase the risk of cerebrovascular disease in humans. However, the molecular mechanisms underlying these deformities have not been understood. Based on our previous studies, variations in the CoW of gerbils are hereditary. A normal CoW is observed in approximately 60% of gerbils, a percentage that also applies to humans. Thus, gerbil is an ideal experimental model for studying variations in the CoW. To study the mechanisms underlying these variations, we selected genes associated with different types of the CoW using suppression subtractive hybridization (SSH). After evaluating the efficiency of SSH using quantitative real-time polymerase chain reaction (qPCR) on subtracted and unsubtracted cDNA and Southern blotting on SSH PCR products, 12 SSH libraries were established. We identified 4 genes (CST3, GNAS, GPx4 and PFN2) associated with variations in the CoW. These genes were identified with qPCR and Western blotting using 70 expressed sequence tags from the SSH libraries. Cloning and sequencing allowed us to demonstrate that the 4 genes were closely related to mouse genes. We may assume that these 4 genes play an important role in the development of variations in the CoW. This study provides a foundation for further research of genes related to development of variations in the CoW and the mechanisms of dysmorphosis of cerebral vessels. PMID:25973917

  12. A Novel Homozygous Frameshift Mutation in Exon 2 of Gene Associated with Severe Obesity: A Case Report

    Directory of Open Access Journals (Sweden)

    Ashwaq Shukri Altawil

    2016-01-01

    Full Text Available Background Monogenic obesity is a rare type of obesity caused by a mutation in a single gene. Patients with monogenic obesity may develop early onset of obesity and severe metabolic abnormalities. Case Presentation A two-and-half-year-old girl was presented to our clinic because of excessive weight gain and hyperphagia. She was born at full term, by normal vaginal delivery with birth weight of 2.82 kg and no complications during pregnancy. The patient was the second child of two healthy, non-obese Saudis with known consanguinity. She gained weight rapidly leading to obesity at the age of three months. Methods The demographic data and clinical features were recorded. Blood samples were collected and tested for endocrine and metabolic characteristics and genetic studies. Mutations of the LEP gene were screened. The coding exons 2 and 3 and the corresponding exon–intron boundaries were amplified by polymerase chain reaction using specific primers, analyzed by direct sequencing using an ABI sequencer 3500 xL GA (Applied Biosystems, and evaluated using the JSI SeqPilot software. The resulting sequence data were compared with the reference MM_0002302. Conclusion We report a novel homozygous frameshift mutation c.144delin TAC (G1n49Thrfs * 23 in exon 2 of the LEP gene associated with extreme obesity.

  13. A novel mutation in the NOD2 gene associated with Blau syndrome: a Norwegian family with four affected members.

    Science.gov (United States)

    Milman, N; Ursin, K; Rødevand, E; Nielsen, F C; Hansen, T V O

    2009-01-01

    Blau syndrome is a chronic granulomatous disease with an autosomal dominant trait characterized by the triad granulomatous dermatitis, arthritis, and uveitis. It is caused by mutations in the NOD2 gene, also termed the CARD15 gene. To report a novel mutation in the NOD2 gene associated with Blau syndrome. The proband was a 68-year-old ethnic Norwegian male who had uveitis and arthritis since 10 years of age followed by lifelong recurrent arthritis and chronic eye involvement. Genetic analysis showed a heterozygous c.1814 C>A, T605N mutation in NOD2 that has not previously been described. All of his three children had Blau syndrome and had inherited the NOD2 mutation. The proband's first son had exanthema, arthritis, and uveitis from 10 years of age and later presented with granulomatous lymphadenopathy, granulomatous parotitis, and granulomatous intestinal inflammation. The proband's daughter had arthritis, uveitis, and exanthema from 3 years of age. The proband's second son had uveitis, exanthema, and arthritis from 1.5 years of age. None of the cases had any involvement of the heart or lungs. We report a novel Blau syndrome-associated mutation with an autosomal dominant heritage. Most likely the mutation has arisen de novo in the proband. Genetic counselling and antenatal diagnostics should be available to the involved families.

  14. Genome-wide analysis of Epstein-Barr virus identifies variants and genes associated with gastric carcinoma and population structure.

    Science.gov (United States)

    Yao, Youyuan; Xu, Miao; Liang, Liming; Zhang, Haojiong; Xu, Ruihua; Feng, Qisheng; Feng, Lin; Luo, Bing; Zeng, Yi-Xin

    2017-10-01

    Epstein-Barr virus is a ubiquitous virus and is associated with several human malignances, including the significant subset of gastric carcinoma, Epstein-Barr virus-associated gastric carcinoma. Some Epstein-Barr virus-associated diseases are uniquely prevalent in populations with different geographic origins. However, the features of the disease and geographically associated Epstein-Barr virus genetic variation as well as the roles that the variation plays in carcinogenesis and evolution remain unclear. Therefore, in this study, we sequenced 95 geographically distinct Epstein-Barr virus isolates from Epstein-Barr virus-associated gastric carcinoma biopsies and saliva of healthy donors to detect variants and genes associated with gastric carcinoma and population structure from a genome-wide spectrum. We demonstrated that Epstein-Barr virus revealed the population structure between North China and South China. In addition, we observed population stratification between Epstein-Barr virus strains from gastric carcinoma and healthy controls, indicating that certain Epstein-Barr virus subtypes are associated with different gastric carcinoma risks. We identified that the BRLF1, BBRF3, and BBLF2/BBLF3 genes had significant associations with gastric carcinoma. LMP1 and BNLF2a genes were strongly geographically associated genes in Epstein-Barr virus. Our study provides insights into the genetic basis of oncogenic Epstein-Barr virus for gastric carcinoma, and the genetic variants associated with gastric carcinoma can serve as biomarkers for oncogenic Epstein-Barr virus.

  15. A Novel Homozygous Frameshift Mutation in Exon 2 of LEP Gene Associated with Severe Obesity: A Case Report.

    Science.gov (United States)

    Altawil, Ashwaq Shukri; Mawlawi, Horia Ahmad; Alghamdi, Khalid Ateeq; Almijmaj, Faten Fohaid

    2016-01-01

    Monogenic obesity is a rare type of obesity caused by a mutation in a single gene. Patients with monogenic obesity may develop early onset of obesity and severe metabolic abnormalities. A two-and-half-year-old girl was presented to our clinic because of excessive weight gain and hyperphagia. She was born at full term, by normal vaginal delivery with birth weight of 2.82 kg and no complications during pregnancy. The patient was the second child of two healthy, non-obese Saudis with known consanguinity. She gained weight rapidly leading to obesity at the age of three months. The demographic data and clinical features were recorded. Blood samples were collected and tested for endocrine and metabolic characteristics and genetic studies. Mutations of the LEP gene were screened. The coding exons 2 and 3 and the corresponding exon-intron boundaries were amplified by polymerase chain reaction using specific primers, analyzed by direct sequencing using an ABI sequencer 3500 xL GA (Applied Biosystems), and evaluated using the JSI SeqPilot software. The resulting sequence data were compared with the reference MM_0002302. We report a novel homozygous frameshift mutation c.144delin TAC (G1n49Thrfs*23) in exon 2 of the LEP gene associated with extreme obesity.

  16. Frequency of mutations in the genes associated with hereditary sensory and autonomic neuropathy in a UK cohort.

    LENUS (Irish Health Repository)

    Davidson, G L

    2012-08-01

    The hereditary sensory and autonomic neuropathies (HSAN, also known as the hereditary sensory neuropathies) are a clinically and genetically heterogeneous group of disorders, characterised by a progressive sensory neuropathy often complicated by ulcers and amputations, with variable motor and autonomic involvement. To date, mutations in twelve genes have been identified as causing HSAN. To study the frequency of mutations in these genes and the associated phenotypes, we screened 140 index patients in our inherited neuropathy cohort with a clinical diagnosis of HSAN for mutations in the coding regions of SPTLC1, RAB7, WNK1\\/HSN2, FAM134B, NTRK1 (TRKA) and NGFB. We identified 25 index patients with mutations in six genes associated with HSAN (SPTLC1, RAB7, WNK1\\/HSN2, FAM134B, NTRK1 and NGFB); 20 of which appear to be pathogenic giving an overall mutation frequency of 14.3%. Mutations in the known genes for HSAN are rare suggesting that further HSAN genes are yet to be identified. The p.Cys133Trp mutation in SPTLC1 is the most common cause of HSAN in the UK population and should be screened first in all patients with sporadic or autosomal dominant HSAN.

  17. An analysis of exome sequencing for diagnostic testing of the genes associated with muscle disease and spastic paraplegia

    Science.gov (United States)

    Dias, Cristina; Sincan, Murat; Cherukuri, Praveen F.; Rupps, Rosemarie; Huang, Yan; Briemberg, Hannah; Selby, Kathryn; Mullikin, James C.; Markello, Thomas C.; Adams, David R.; Gahl, William A.; Boerkoel, Cornelius F.

    2012-01-01

    In this study we assess exome sequencing (ES) as a diagnostic alternative for genetically heterogeneous disorders. Since ES readily identified a previously reported homozygous mutation in the CAPN3 gene for an individual with an undiagnosed limb girdle muscular dystrophy, we evaluated ES as a generalizable clinical diagnostic tool by assessing the targeting efficiency and sequencing-coverage of 88 genes associated with muscle disease (MD) and spastic paraplegia (SPG). We used three exome-capture kits on 125 individuals. Exons constituting each gene were defined using the UCSC and CCDS databases. The three exome-capture kits targeted 47–92% of bases within the UCSC-defined exons, and 97%–99% of bases within the CCDS-defined exons. An average of 61.2–99.5% and 19.1–99.5% of targeted bases per gene were sequenced to 20X coverage within the CCDS-defined MD and SPG coding exons, respectively. Greater than 95–99% of targeted known mutation positions were sequenced to ≥1X coverage and 55–87% to ≥20X coverage in every exome. We conclude therefore that ES is a rapid and efficient first tier method to screen for mutations, particularly within the CCDS annotated exons, although its application requires disclosure of the extent of coverage for each targeted gene and supplementation with second tier Sanger sequencing for full coverage. PMID:22311686

  18. Molecular markers in melanoma.

    Science.gov (United States)

    Kashani-Sabet, M

    2014-01-01

    The last few years have witnessed the dawn of the molecular era in melanoma treatment. With the advent of successful therapy targeting mutant BRAF, melanoma is leading the field of cancer research in the molecular approach to therapy of advanced disease. Attempting to keep pace with advances in therapy are advances in the molecular assessment of melanoma progression, facilitated by the availability of genome-wide approaches to interrogate the malignant phenotype. At the DNA level, this has included approaches such as comparative genomic hybridization. At the RNA level, this has consisted of gene expression profiling using various assay methodologies. In certain instances, markers identified using these platforms have been further examined and developed using fluorescence in situ hybridization and immunohistochemical analysis. In this article, we will review recent progress in the development of novel molecular markers for melanoma that are nearing clinical application. We will review developments in the molecular classification of melanoma, in the molecular diagnosis of melanoma, and in the molecular assessment of melanoma prognosis. © 2013 British Association of Dermatologists.

  19. Inflammatory markers and extent and progression of early atherosclerosis

    DEFF Research Database (Denmark)

    Willeit, Peter; Thompson, Simon G; Agewall, Stefan

    2016-01-01

    BACKGROUND: Large-scale epidemiological evidence on the role of inflammation in early atherosclerosis, assessed by carotid ultrasound, is lacking. We aimed to quantify cross-sectional and longitudinal associations of inflammatory markers with common-carotid-artery intima-media thickness (CCA...... in its assessment within a limited time period. Our findings for 'inflammatory load' suggest important combined effects of the three inflammatory markers on early atherosclerosis....

  20. Serologic Markers of Autism Spectrum Disorder.

    Science.gov (United States)

    Khramova, T V; Kaysheva, Anna L; Ivanov, Y D; Pleshakova, T O; Iourov, I Y; Vorsanova, S G; Yurov, Y B; Schetkin, A A; Archakov, A I

    2017-08-01

    According to WHO data, about 67 million people worldwide are affected by autism, and this number grows by 14% annually. Among the possible causes of autism are genetic modifications, organic lesions of the central nervous system, metabolic disorders, influence of viral and bacterial infections, chemical influence to the mother's body during pregnancy, etc. The conducted research shows that research papers published until today do not name any potential protein markers that meet the requirements of the basic parameters for evaluating the efficiency of disease diagnostics, in particular high sensitivity, specificity, and accuracy. Conducting proteomic research on a big scale in order to detect serologic markers of protein nature associated with development of autism spectrum disorders seems to be highly relevant.

  1. Colorful seashells: Identification of haem pathway genes associated with the synthesis of porphyrin shell color in marine snails

    KAUST Repository

    Williams, Suzanne T.

    2017-10-30

    Very little is known about the evolution of molluskan shell pigments, although Mollusca is a highly diverse, species rich, and ecologically important group of animals comprised of many brightly colored taxa. The marine snail genus Clanculus was chosen as an exceptional model for studying the evolution of shell color, first, because in Clanculus margaritarius and Clanculus pharaonius both shell and foot share similar colors and patterns; and second, because recent studies have identified the pigments, trochopuniceus (pink-red), and trochoxouthos (yellow-brown), both comprised of uroporphyrin I and uroporphyrin III, in both shell and colored foot tissue of these species. These unusual characteristics provide a rare opportunity to identify the genes involved in color production because, as the same pigments occur in the shell and colored foot tissue, the same color-related genes may be simultaneously expressed in both mantle (which produces the shell) and foot tissue. In this study, the transcriptomes of these two Clanculus species along with a third species, Calliostoma zizyphinum, were sequenced to identify genes associated with the synthesis of porphyrins. Calliostoma zizyphinum was selected as a negative control as trochopuniceus and trochoxouthos were not found to occur in this species. As expected, genes necessary for the production of uroporphyrin I and III were found in all three species, but gene expression levels were consistent with synthesis of uroporphyrins in mantle and colored foot tissue only in Clanculus. These results are relevant not only to understanding the evolution of shell pigmentation in Clanculus but also to understanding the evolution of color in other species with uroporphyrin pigmentation, including (mainly marine) mollusks soft tissues and shells, annelid and platyhelminth worms, and some bird feathers.

  2. Identification of potential crucial genes associated with steroid-induced necrosis of femoral head based on gene expression profile.

    Science.gov (United States)

    Lin, Zhe; Lin, Yongsheng

    2017-09-05

    The aim of this study was to explore potential crucial genes associated with the steroid-induced necrosis of femoral head (SINFH) and to provide valid biological information for further investigation of SINFH. Gene expression profile of GSE26316, generated from 3 SINFH rat samples and 3 normal rat samples were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified using LIMMA package. After functional enrichment analyses of DEGs, protein-protein interaction (PPI) network and sub-PPI network analyses were conducted based on the STRING database and cytoscape. In total, 59 up-regulated DEGs and 156 downregulated DEGs were identified. The up-regulated DEGs were mainly involved in functions about immunity (e.g. Fcer1A and Il7R), and the downregulated DEGs were mainly enriched in muscle system process (e.g. Tnni2, Mylpf and Myl1). The PPI network of DEGs consisted of 123 nodes and 300 interactions. Tnni2, Mylpf, and Myl1 were the top 3 outstanding genes based on both subgraph centrality and degree centrality evaluation. These three genes interacted with each other in the network. Furthermore, the significant network module was composed of 22 downregulated genes (e.g. Tnni2, Mylpf and Myl1). These genes were mainly enriched in functions like muscle system process. The DEGs related to the regulation of immune system process (e.g. Fcer1A and Il7R), and DEGs correlated with muscle system process (e.g. Tnni2, Mylpf and Myl1) may be closely associated with the progress of SINFH, which is still needed to be confirmed by experiments. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Elongation factor 1 alpha1 and genes associated with Usher syndromes are downstream targets of GBX2.

    Science.gov (United States)

    Roeseler, David A; Sachdev, Shrikesh; Buckley, Desire M; Joshi, Trupti; Wu, Doris K; Xu, Dong; Hannink, Mark; Waters, Samuel T

    2012-01-01

    Gbx2 encodes a DNA-binding transcription factor that plays pivotal roles during embryogenesis. Gain-and loss-of-function studies in several vertebrate species have demonstrated a requirement for Gbx2 in development of the anterior hindbrain, spinal cord, inner ear, heart, and neural crest cells. However, the target genes through which GBX2 exerts its effects remain obscure. Using chromatin immunoprecipitation coupled with direct sequencing (ChIP-Seq) analysis in a human prostate cancer cell line, we identified cis-regulatory elements bound by GBX2 to provide insight into its direct downstream targets. The analysis revealed more than 286 highly significant candidate target genes, falling into various functional groups, of which 51% are expressed in the nervous system. Several of the top candidate genes include EEF1A1, ROBO1, PLXNA4, SLIT3, NRP1, and NOTCH2, as well as genes associated with the Usher syndrome, PCDH15 and USH2A, and are plausible candidates contributing to the developmental defects in Gbx2(-/-) mice. We show through gel shift analyses that sequences within the promoter or introns of EEF1A1, ROBO1, PCDH15, USH2A and NOTCH2, are directly bound by GBX2. Consistent with these in vitro results, analyses of Gbx2(-/-) embryos indicate that Gbx2 function is required for migration of Robo1-expressing neural crest cells out of the hindbrain. Furthermore, we show that GBX2 activates transcriptional activity through the promoter of EEF1A1, suggesting that GBX2 could also regulate gene expression indirectly via EEF1A. Taken together, our studies show that GBX2 plays a dynamic role in development and diseases.

  4. Elongation factor 1 alpha1 and genes associated with Usher syndromes are downstream targets of GBX2.

    Directory of Open Access Journals (Sweden)

    David A Roeseler

    Full Text Available Gbx2 encodes a DNA-binding transcription factor that plays pivotal roles during embryogenesis. Gain-and loss-of-function studies in several vertebrate species have demonstrated a requirement for Gbx2 in development of the anterior hindbrain, spinal cord, inner ear, heart, and neural crest cells. However, the target genes through which GBX2 exerts its effects remain obscure. Using chromatin immunoprecipitation coupled with direct sequencing (ChIP-Seq analysis in a human prostate cancer cell line, we identified cis-regulatory elements bound by GBX2 to provide insight into its direct downstream targets. The analysis revealed more than 286 highly significant candidate target genes, falling into various functional groups, of which 51% are expressed in the nervous system. Several of the top candidate genes include EEF1A1, ROBO1, PLXNA4, SLIT3, NRP1, and NOTCH2, as well as genes associated with the Usher syndrome, PCDH15 and USH2A, and are plausible candidates contributing to the developmental defects in Gbx2(-/- mice. We show through gel shift analyses that sequences within the promoter or introns of EEF1A1, ROBO1, PCDH15, USH2A and NOTCH2, are directly bound by GBX2. Consistent with these in vitro results, analyses of Gbx2(-/- embryos indicate that Gbx2 function is required for migration of Robo1-expressing neural crest cells out of the hindbrain. Furthermore, we show that GBX2 activates transcriptional activity through the promoter of EEF1A1, suggesting that GBX2 could also regulate gene expression indirectly via EEF1A. Taken together, our studies show that GBX2 plays a dynamic role in development and diseases.

  5. Quantitative trait loci and candidate genes associated with starch pasting viscosity characteristics in cassava (Manihot esculenta Crantz).

    Science.gov (United States)

    Thanyasiriwat, T; Sraphet, S; Whankaew, S; Boonseng, O; Bao, J; Lightfoot, D A; Tangphatsornruang, S; Triwitayakorn, K

    2014-01-01

    Starch pasting viscosity is an important quality trait in cassava (Manihot esculenta Crantz) cultivars. The aim here was to identify loci and candidate genes associated with the starch pasting viscosity. Quantitative trait loci (QTL) mapping for seven pasting viscosity parameters was carried out using 100 lines of an F1 mapping population from a cross between two cassava cultivars Huay Bong 60 and Hanatee. Starch samples were obtained from roots of cassava grown in 2008 and 2009 at Rayong, and in 2009 at Lop Buri province, Thailand. The traits showed continuous distribution among the F1 progeny with transgressive variation. Fifteen QTL were identified from mean trait data, with Logarithm of Odds (LOD) values from 2.77-13.01 and phenotype variations explained (PVE) from10.0-48.4%. In addition, 48 QTL were identified in separate environments. The LOD values ranged from 2.55-8.68 and explained 6.6-43.7% of phenotype variation. The loci were located on 19 linkage groups. The most important QTL for pasting temperature (PT) (qPT.1LG1) from mean trait values showed largest effect with highest LOD value (13.01) and PVE (48.4%). The QTL co-localised with PT and pasting time (PTi) loci that were identified in separate environments. Candidate genes were identified within the QTL peak regions. However, the major genes of interest, encoding the family of glycosyl or glucosyl transferases and hydrolases, were located at the periphery of QTL peaks. The loci identified could be effectively applied in breeding programmes to improve cassava starch quality. Alleles of candidate genes should be further studied in order to better understand their effects on starch quality traits. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.

  6. Microarray-based detection and expression analysis of new genes associated with drug resistance in ovarian cancer cell lines

    Science.gov (United States)

    Januchowski, Radosław; Sterzyńska, Karolina; Zawierucha, Piotr; Ruciński, Marcin; Świerczewska, Monika; Partyka, Małgorzata; Bednarek-Rajewska, Katarzyna; Brązert, Maciej; Nowicki, Michał; Zabel, Maciej; Klejewski, Andrzej

    2017-01-01

    Purpose The present study is to discover a new genes associated with drug resistance development in ovarian cancer. Methods We used microarray analysis to determine alterations in the level of expression of genes in cisplatin- (CisPt), doxorubicin- (Dox), topotecan- (Top), and paclitaxel- (Pac) resistant variants of W1 and A2780 ovarian cancer cell lines. Immunohistochemistry assay was used to determine protein expression in ovarian cancer patients. Results We observed alterations in the expression of 22 genes that were common to all three cell lines that were resistant to the same cytostatic drug. The level of expression of 13 genes was upregulated and that of nine genes was downregulated. In the CisPt-resistant cell line, we observed downregulated expression of ABCC6, BST2, ERAP2 and MCTP1; in the Pac-resistant cell line, we observe upregulated expression of ABCB1, EPHA7 and RUNDC3B and downregulated expression of LIPG, MCTP1, NSBP1, PCDH9, PTPRK and SEMA3A. The expression levels of three genes, ABCB1, ABCB4 and IFI16, were upregulated in the Dox-resistant cell lines. In the Top-resistant cell lines, we observed increased expression levels of ABCG2, HERC5, IFIH1, MYOT, S100A3, SAMD4A, SPP1 and TGFBI and decreased expression levels of MCTP1 and PTPRK. The expression of EPHA7, IFI16, SPP1 and TGFBI was confirmed at protein level in analyzed ovarian cancer patients.. Conclusions The expression profiles of the investigated cell lines indicated that new candidate genes are related to the development of resistance to the cytostatic drugs that are used in first- and second-line chemotherapy of ovarian cancer. PMID:28611294

  7. Genomics and relative expression analysis identifies key genes associated with high female to male flower ratio in Jatropha curcas L.

    Science.gov (United States)

    Gangwar, Manali; Sood, Hemant; Chauhan, Rajinder Singh

    2016-04-01

    Jatropha curcas, has been projected as a major source of biodiesel due to high seed oil content (42 %). A major roadblock for commercialization of Jatropha-based biodiesel is low seed yield per inflorescence, which is affected by low female to male flower ratio (1:25-30). Molecular dissection of female flower development by analyzing genes involved in phase transitions and floral organ development is, therefore, crucial for increasing seed yield. Expression analysis of 42 genes implicated in floral organ development and sex determination was done at six floral developmental stages of a J. curcas genotype (IC561235) with inherently higher female to male flower ratio (1:8-10). Relative expression analysis of these genes was done on low ratio genotype. Genes TFL1, SUP, AP1, CRY2, CUC2, CKX1, TAA1 and PIN1 were associated with reproductive phase transition. Further, genes CUC2, TAA1, CKX1 and PIN1 were associated with female flowering while SUP and CRY2 in female flower transition. Relative expression of these genes with respect to low female flower ratio genotype showed up to ~7 folds increase in transcript abundance of SUP, TAA1, CRY2 and CKX1 genes in intermediate buds but not a significant increase (~1.25 folds) in female flowers, thereby suggesting that these genes possibly play a significant role in increased transition towards female flowering by promoting abortion of male flower primordia. The outcome of study has implications in feedstock improvement of J. curcas through functional validation and eventual utilization of key genes associated with female flowering.

  8. Markers of hepatic fibrosis.

    Science.gov (United States)

    Caballería, Llorenç; Torán, Pere; Caballería, Joan

    2017-10-18

    Chronic liver diseases constitute a major health problem. Chronic liver inflammation, defined by the degree of hepatic fibrosis, is asymptomatic in a significant percentage of patients; hence, the disease often remains undiagnosed until it has reached very advanced phases and, frequently, when the damage is irreversible. Ideally, patients should be screened during the initial phases of chronic inflammation, thus allowing for the effective management of the natural evolution of the disease by stopping or delaying its course. Standard diagnostic methods (transaminase determination or abdominal ultrasonography) do not allow for the early diagnosis of the degree of fibrosis. A liver biopsy is the invasive method of choice to screen for fibrosis, however, due to its limitations, non-invasive diagnostic methods such as elastography or serological markers are increasingly used as a good alternative for the early diagnosis of the degree of fibrosis. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

  9. Molecular marker applications in plants.

    Science.gov (United States)

    Hayward, Alice C; Tollenaere, Reece; Dalton-Morgan, Jessica; Batley, Jacqueline

    2015-01-01

    Individuals within a population of a sexually reproducing species will have some degree of heritable genomic variation caused by mutations, insertion/deletions (INDELS), inversions, duplications, and translocations. Such variation can be detected and screened using molecular, or genetic, markers. By definition, molecular markers are genetic loci that can be easily tracked and quantified in a population and may be associated with a particular gene or trait of interest. This chapter will review the current major applications of molecular markers in plants.

  10. Oral cancer risk and molecular markers.

    Science.gov (United States)

    Chimenos-Küstner, Eduardo; Font-Costa, Imma; López-López, José

    2004-01-01

    The clinical appearance and, especially, the degree of dysplasia that may be shown by pre-cancerous lesions in the oral cavity suggest a potential for malignisation. An increasing number of studies are seeking new, more specific markers that would help to determine the degree of cell alteration and enable a better understanding of the degree of malignant degeneration of these cells. The present review considers the most recent findings for these markers, grouping them into families: tumour growth markers; markers of tumour suppression and anti-tumour response; angiogenesis markers; markers of tumour invasion and metastatic potential; cell surface markers; intracellular markers; markers derived from arachidonic acid; and enzymatic markers.

  11. A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs.

    Science.gov (United States)

    Gondret, Florence; Vincent, Annie; Houée-Bigot, Magalie; Siegel, Anne; Lagarrigue, Sandrine; Causeur, David; Gilbert, Hélène; Louveau, Isabelle

    2017-03-21

    Animal's efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI). Pigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age. Transcriptomics data were generated from longissimus muscle, liver and two adipose tissues using a porcine microarray and analyzed for the line effect (n = 24 pigs per line). The most apparent effect of the line was seen in muscle, whereas subcutaneous adipose tissue was the less affected tissue. Molecular data were analyzed by bioinformatics and subjected to multidimensional statistics to identify common biological processes across tissues and key genes participating to differences in the genetics of feed efficiency. Immune response, response to oxidative stress and protein metabolism were the main biological pathways shared by the four tissues that distinguished pigs from the low or high RFI lines. Many immune genes were under-expressed in the four tissues of the most efficient pigs. The main genes contributing to difference between pigs from the low vs high RFI lines were CD40, CTSC and NTN1. Different genes associated with energy use were modulated in a tissue-specific manner between the two lines. The gene expression program related to glycogen utilization was specifically up-regulated in muscle of pigs from the low RFI line (more efficient). Genes involved in fatty acid oxidation were down-regulated in muscle but were promoted in adipose tissues of the same pigs when compared with pigs from the high RFI line (less efficient). This underlined opposite line-associated strategies for energy use in skeletal muscle and adipose tissue. Genes related to cholesterol synthesis

  12. Genome Wide Association Study Identifies 20 Novel Promising Genes Associated with Milk Fatty Acid Traits in Chinese Holstein

    Science.gov (United States)

    Li, Cong; Sun, Dongxiao; Zhang, Shengli; Wang, Sheng; Wu, Xiaoping; Zhang, Qin; Liu, Lin; Li, Yanhua; Qiao, Lv

    2014-01-01

    Detecting genes associated with milk fat composition could provide valuable insights into the complex genetic networks of genes underling variation in fatty acids synthesis and point towards opportunities for changing milk fat composition via selective breeding. In this study, we conducted a genome-wide association study (GWAS) for 22 milk fatty acids in 784 Chinese Holstein cows with the PLINK software. Genotypes were obtained with the Illumina BovineSNP50 Bead chip and a total of 40,604 informative, high-quality single nucleotide polymorphisms (SNPs) were used. Totally, 83 genome-wide significant SNPs and 314 suggestive significant SNPs associated with 18 milk fatty acid traits were detected. Chromosome regions that affect milk fatty acid traits were mainly observed on BTA1, 2, 5, 6, 7, 9, 13, 14, 18, 19, 20, 21, 23, 26 and 27. Of these, 146 SNPs were associated with more than one milk fatty acid trait; most of studied fatty acid traits were significant associated with multiple SNPs, especially C18:0 (105 SNPs), C18 index (93 SNPs), and C14 index (84 SNPs); Several SNPs are close to or within the DGAT1, SCD1 and FASN genes which are well-known to affect milk composition traits of dairy cattle. Combined with the previously reported QTL regions and the biological functions of the genes, 20 novel promising candidates for C10:0, C12:0, C14:0, C14:1, C14 index, C18:0, C18:1n9c, C18 index, SFA, UFA and SFA/UFA were found, which composed of HTR1B, CPM, PRKG1, MINPP1, LIPJ, LIPK, EHHADH, MOGAT1, ECHS1, STAT1, SORBS1, NFKB2, AGPAT3, CHUK, OSBPL8, PRLR, IGF1R, ACSL3, GHR and OXCT1. Our findings provide a groundwork for unraveling the key genes and causal mutations affecting milk fatty acid traits in dairy cattle. PMID:24858810

  13. The Infinitive Marker across Scandinavian

    DEFF Research Database (Denmark)

    Christensen, Ken Ramshøj

    2007-01-01

    In this paper I argue that the base-position of the infinitive marker in the Scandinavian languages and English share a common origin site. It is inserted as the top-most head in the VP-domain. The cross-linguistic variation in the syntactic distribution of the infinitive marker can be accounted...

  14. (SSR) marker development for tomato

    African Journals Online (AJOL)

    -

    2012-09-18

    Sep 18, 2012 ... semi automated and fully automated robotics for liquid handling and genotyping steps. As several of our developed SSR markers were mapped to informative sequences, they are called EST-. SSR putatives. The set of EST-SSR markers would be informative for phylogenetics analysis and genetic mapping.

  15. Beta-2 Microglobulin Tumor Marker

    Science.gov (United States)

    ... https://www.cancer.gov/about-cancer/diagnosis-staging/diagnosis/tumor-markers-fact-sheet. Accessed on 4/10/17. (January ... http://www.cancer.gov/cancertopics/factsheet/Detection/tumor-markers. Accessed June ... Mosby's Diagnostic and Laboratory Test Reference 10th Edition: Mosby, Inc., ...

  16. Genome-Wide Association Study Reveals Novel Genes Associated with Culm Cellulose Content in Bread Wheat (Triticum aestivum, L.

    Directory of Open Access Journals (Sweden)

    Simerjeet Kaur

    2017-11-01

    Full Text Available Plant cell wall formation is a complex, coordinated and developmentally regulated process. Cellulose is the most dominant constituent of plant cell walls. Because of its paracrystalline structure, cellulose is the main determinant of mechanical strength of plant tissues. As the most abundant polysaccharide on earth, it is also the focus of cellulosic biofuel industry. To reduce culm lodging in wheat and for improved ethanol production, delineation of the variation for stem cellulose content could prove useful. We present results on the analysis of the stem cellulose content of 288 diverse wheat accessions and its genome-wide association study (GWAS. Cellulose concentration ranged from 35 to 52% (w/w. Cellulose content was normally distributed in the accessions around a mean and median of 45% (w/w. Genome-wide marker-trait association study using 21,073 SNPs helped identify nine SNPs that were associated (p < 1E-05 with cellulose content. Four strongly associated (p < 8.17E-05 SNP markers were linked to wheat unigenes, which included β-tubulin, Auxin-induced protein 5NG4, and a putative transmembrane protein of unknown function. These genes may be directly or indirectly involved in the formation of cellulose in wheat culms. GWAS results from this study have the potential for genetic manipulation of cellulose content in bread wheat and other small grain cereals to enhance culm strength and improve biofuel production.

  17. Genes associated with MUC5AC expression in small airway epithelium of human smokers and non-smokers

    Directory of Open Access Journals (Sweden)

    Wang Guoqing

    2012-06-01

    -related regulator and mucus hypersecretory-related ion channel. As a validation cohort, we assessed the MUC5AC-associated core gene list in the small airway epithelium of an independent set of healthy smokers (n = 72. There was up-regulation of MUC5AC in the small airway epithelium of smokers (2.3-fold, p -8 associated with a coordinated up-regulation of MUC5AC-associated core gene expression pattern in the small airway epithelium of smokers (p  Conclusion The identification of the genes associated with increased airway mucin production in humans should be useful in understanding the pathogenesis of airway mucus hypersecretion and identifying therapeutic targets. Author summary Mucus hypersecretion contributes to the morbidity and mortality of smoking-related lung diseases, especially chronic obstructive pulmonary disease (COPD, which starts in the small airways. Little is known about the gene networks associated with the synthesis and secretion of mucins in the human small airway epithelium. Taking advantage of the knowledge that MUC5AC is a major mucin secreted by the small airway epithelium, the expression of MUC5AC in small airway epithelium is highly regulated at the transcriptional level and our observation that healthy nonsmokers have variable numbers of MUC5AC+ secretory cells in the human small airway epithelium, we compared genome-wide gene expression of the small airway epithelium of high vs low MUC5AC expressors from 60 nonsmokers to identify the genes associated with MUC5AC expression. This novel strategy enabled identification of a 73 “MUC5AC-associated core gene” list with 9 categories, which control a series of processes from mucin biosynthesis to mucus secretion. The coordinated gene expression pattern of MUC5AC-associated core genes were corroborated in an independent cohort of 72 healthy smokers. Deep sequencing of small airway epithelium RNA confirmed these observations. This finding will be useful in identifying therapeutic targets to treat small

  18. A new insertion/deletion fragment polymorphism of inhibin-α gene associated with follicular cysts in Large White sows.

    Science.gov (United States)

    Li, Wanhong; Chen, Shuxiong; Li, Hongjiao; Liu, Zhuo; Zhao, Yun; Chen, Lu; Zhou, Xu; Li, Chunjing

    2016-05-18

    Ovarian follicular cysts are anovulatory follicular structures that lead to infertility. Hormones play key roles in the formation and persistence of cysts. Inhibins are heterodimeric gonadal glycoprotein hormones that belong to the transforming growth factor-β superfamily. These hormones suppress the secretion of follicle-stimulating hormone. In this report, partial fragment of inhibin-α (INHA) subunit gene of Large White pig was detected from the genomic DNA by polymerase chain reaction. The sequence showed a 283 bp fragment insertion/deletion (I/D) polymorphism in INHA subunit gene. A total of 49 Large White sows with cystic follicles and 152 normal sows were screened for this polymorphism. The relationship of INHA I/D polymorphisms with follicular cysts was investigated. The distribution of I/D was significantly different between cystic and normal sows, thereby suggesting that the INHA subunit gene might be a potential biological marker for breeding programs in pig.

  19. Odontogenic Tumor Markers - An Overview

    Science.gov (United States)

    Premalatha, B R; Patil, Shankargouda; Rao, Roopa S; Reddy, Narendranatha P; Indu, M

    2013-01-01

    The practice of pathology is currently undergoing significant change, due to advances in the field of molecular pathology. Tumor markers are molecules that help the pathologists for confirmatory diagnosis of histopathologically confounding lesions. Odontogenic tumors are relatively rare with estimated incidence of less than 0.5 cases/ 100,000 population per year. Odontogenic tumors can pose diagnostic challenges because of overlapping histology. But, appropriate diagnosis is crucial as their treatment modality and prognosis differ; in these situations tumor markers can be helpful. But lack of comprehensive literature on specific markers for odontogenic tumors imposes pathologists to think aimlessly about various markers to arrive at an appropriate diagnosis. With this background, it is our attempt at compiling diagnostically important odontogenic tumor markers. Also, a note is added on tumor behaviour studies in common clinically important odontogenic tumors: Ameloblastoma and Keratocystic odontogenic tumor. How to cite this article: Premalatha B R, Patil S, Rao R S, Reddy N P, Indu M. Odontogenic Tumor Markers - An Overview. J Int Oral Health 2013; 5(2):65-75. How to cite this article: Premalatha B R, Patil S, Rao R S, Reddy N P, Indu M. Odontogenic Tumor Markers - An Overview. J Int Oral Health 2013; 5(2):65-75 PMID:24155593

  20. Ideal, nonideal, and no-marker variables: The confirmatory factor analysis (CFA) marker technique works when it matters.

    Science.gov (United States)

    Williams, Larry J; O'Boyle, Ernest H

    2015-09-01

    A persistent concern in the management and applied psychology literature is the effect of common method variance on observed relations among variables. Recent work (i.e., Richardson, Simmering, & Sturman, 2009) evaluated 3 analytical approaches to controlling for common method variance, including the confirmatory factor analysis (CFA) marker technique. Their findings indicated significant problems with this technique, especially with nonideal marker variables (those with theoretical relations with substantive variables). Based on their simulation results, Richardson et al. concluded that not correcting for method variance provides more accurate estimates than using the CFA marker technique. We reexamined the effects of using marker variables in a simulation study and found the degree of error in estimates of a substantive factor correlation was relatively small in most cases, and much smaller than error associated with making no correction. Further, in instances in which the error was large, the correlations between the marker and substantive scales were higher than that found in organizational research with marker variables. We conclude that in most practical settings, the CFA marker technique yields parameter estimates close to their true values, and the criticisms made by Richardson et al. are overstated. (c) 2015 APA, all rights reserved).

  1. Single nucleotide polymorphism of SREBF-1 gene associated with an increased risk of endometrial cancer in Chinese women.

    Directory of Open Access Journals (Sweden)

    Chun-Ping Qiu

    Full Text Available Elevated levels of sterol regulatory element-binding protein-1 (SREBP-1 have been found in endometrial cancer (EC, suggesting that it is essential to the development of EC. Obesity and diabetes have been established as known risk factors of EC, while SREBF-1 gene polymorphisms have also been found to be associated with obesity and type II diabetes. Therefore, we hypothesize that single nucleotide polymorphism (SNP in SREBF-1 gene may be associated with increased risk of EC.We analyzed the sequence of SREBF-1 in tissue samples from 30 EC cases and 6 benign controls using high throughput method. Based on the primary results, we selected one SNP (rs2297508 as a genetic marker to conduct a hospital-based case-control study with 139 EC cases and 129 benign controls. The samples were examined under the microscope to determine their histopathology prior to the SNP analysis using RT-PCR.Through sequence analysis, we found 10 SNPs of SREBF-1 associated with EC, including 3 new SNPs. Fourteen percent of EC showed the rs2297508 SNP with C allele, while only 7% had the C allele was present in benign controls (p = 0.027, OR = 1.983. Additionally, the C allele was associated with cancer differentiation (p<0.05 and the depth of myometrial invasion (p<0.05.Our study indicates that SNP (rs2297508 of SREBF-1 may serve as a genetic predisposition factor for the development of EC and screening of such genetic marker may be helpful in its early detection.

  2. Application of molecular markers in apple breeding

    Directory of Open Access Journals (Sweden)

    Marić Slađana

    2010-01-01

    Full Text Available Apple is economically the most important species of genus Malus Miller. In respect of production, trade and consumption, it ranks first among deciduous fruit and third on a global scale among all fruit species. Apple breeding is carried out on a large scale in several scientific institutes throughout the world. Due to this activity, apple is a fruit species with the highest number of described monogenic traits; 76 genes, encoding morphological traits, pest and disease resistance, as well as 69 genes encoding enzymes. The development of molecular markers (RFLPs, AFLPs, SCARs and SSRs has allowed the mapping of the apple genome and the development of several saturated genetic maps, to which genes controlling important traits are assigned. Markers flanking these genes not only play an important role in selecting parental combinations and seedlings with positive traits, but they are also particularly important in detecting recessive traits, such as seedless fruit. In addition they enable pre-selection for polygenic quantitative traits. In recent years, particular attention has been paid to biochemical and physiological processes involved in the pathway of important traits e.g., ripening and the storage capability of apple fruit.

  3. Analogy of ISSR and RAPD markers for comparative analysis of ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-12-03

    Dec 3, 2008 ... (PCR) technology has offered new marker systems for diagnosis of genetic diversity in large scale studies (Saiki et al., 1988). Over the last 15 years, polymerase chain reaction technology has led to the development of two simple and quick techniques called random amplified polymorphic DNA (RAPD) and ...

  4. Prenatal Screening Using Maternal Markers.

    Science.gov (United States)

    Cuckle, Howard

    2014-05-09

    Maternal markers are widely used to screen for fetal neural tube defects (NTDs), chromosomal abnormalities and cardiac defects. Some are beginning to broaden prenatal screening to include pregnancy complications such as pre-eclampsia. The methods initially developed for NTDs using a single marker have since been built upon to develop high performance multi-maker tests for chromosomal abnormalities. Although cell-free DNA testing is still too expensive to be considered for routine application in public health settings, it can be cost-effective when used in combination with existing multi-maker marker tests. The established screening methods can be readily applied in the first trimester to identify pregnancies at high risk of pre-eclampsia and offer prevention though aspirin treatment. Prenatal screening for fragile X syndrome might be adopted more widely if the test was to be framed as a form of maternal marker screening.

  5. Prenatal Screening Using Maternal Markers

    Directory of Open Access Journals (Sweden)

    Howard Cuckle

    2014-05-01

    Full Text Available Maternal markers are widely used to screen for fetal neural tube defects (NTDs, chromosomal abnormalities and cardiac defects. Some are beginning to broaden prenatal screening to include pregnancy complications such as pre-eclampsia. The methods initially developed for NTDs using a single marker have since been built upon to develop high performance multi-maker tests for chromosomal abnormalities. Although cell-free DNA testing is still too expensive to be considered for routine application in public health settings, it can be cost-effective when used in combination with existing multi-maker marker tests. The established screening methods can be readily applied in the first trimester to identify pregnancies at high risk of pre-eclampsia and offer prevention though aspirin treatment. Prenatal screening for fragile X syndrome might be adopted more widely if the test was to be framed as a form of maternal marker screening.

  6. Potential blood-based markers of celiac disease.

    Science.gov (United States)

    Bragde, Hanna; Jansson, Ulf; Fredrikson, Mats; Grodzinsky, Ewa; Söderman, Jan

    2014-10-09

    Blood-based diagnostics has the potential to simplify the process of diagnosing celiac disease (CD). Although high levels of autoantibodies against tissue transglutaminase (anti-TG2) are strongly indicative of active CD, several other scenarios involve a need for additional blood-based CD markers. We investigated the levels of messenger RNA (mRNA) in whole blood (n = 49) and protein in plasma (n = 22) from cases with active CD (n = 20), with confirmed CD and normalized histology (n = 15), and without a CD diagnosis (n = 14). Group differences were analyzed using Kruskal-Wallis one-way analysis of variance by ranks. We also investigated correlations between levels of potential markers, histopathology according to the modified Marsh scale, and CD risk gradient based on HLA type, using Spearman rank correlation. The relation between HLA-DQ2 gene dose effect and the expression levels of selected blood-based markers was investigated using the Mann-Whitney U test. Finally, the diagnostic performance of anti-TG2, potential blood-based CD markers, and logistic regression models of combined markers was evaluated using receiver operating characteristic (ROC) curve analysis. CXCL11 protein levels and TNFRSF9 and TNFSF13B mRNA levels were identified as potential CD markers. These are all affected by or involved in the regulation of the NF-κB complex. CXCL11 protein levels and IL21 and IL15 mRNA levels were correlated with histopathology according to the modified Marsh scale, as were the established CD markers. HLA genotype risk and HLA-DQ2 gene dose effect did not show any significant relations with either the potential CD markers or the established CD markers. ROC curve analysis revealed a slight, non-significant increase in the area under the curve for the combined use of anti-TG2 and different constellations of potential blood-based CD markers compared to anti-TG2 alone. The CD markers identified in this study further emphasize the significance of

  7. Prenatal Screening Using Maternal Markers

    OpenAIRE

    Howard Cuckle

    2014-01-01

    Maternal markers are widely used to screen for fetal neural tube defects (NTDs), chromosomal abnormalities and cardiac defects. Some are beginning to broaden prenatal screening to include pregnancy complications such as pre-eclampsia. The methods initially developed for NTDs using a single marker have since been built upon to develop high performance multi-maker tests for chromosomal abnormalities. Although cell-free DNA testing is still too expensive to be considered for routine application ...

  8. Breast cancer statistics and markers

    Directory of Open Access Journals (Sweden)

    Mallika Siva Donepudi

    2014-01-01

    Full Text Available Breast cancer is one of the familiar diseases in women. Incidence and mortality due to cancer, particularly breast cancer has been increasing for last 50 years, even though there is a lacuna in the diagnosis of breast cancer at early stages. According to World Health Organization (WHO 2012 reports, breast cancer is the leading cause of death in women, accounting 23% of all cancer deaths. In Asia, one in every three women faces the risk of breast cancer in their lifetime as per reports of WHO 2012. Here, the review is been focused on different breast cancer markers, that is, tissue markers (hormone receptors, human epidermal growth factor-2, urokinase plasminogen activator, plasminogen activator inhibitor, p53 and cathepsin D, genetic markers (BRAC1 and 2 and gene expression microarray technique, etc., and serum markers (CA 15.3, BR 27.29, MCA, CA 549, carcinoembryonic antigen, oncoproteins, and cytokeratins used in present diagnosis, but none of the mentioned markers can diagnose breast cancer at an early stage. There is a disquieting need for the identification of best diagnosing marker, which can be able to diagnose even in early stage of breast carcinogenesis.

  9. Pharmacogenomic study reveals new variants of drug metabolizing enzyme and transporter genes associated with steady-state plasma concentrations of risperidone and 9-hydroxyrisperidone in Thai autism spectrum disorder patients

    Directory of Open Access Journals (Sweden)

    Sadeep Medhasi

    2016-12-01

    Full Text Available The present study sought to investigate the genetic variants in drug metabolizing enzyme and transporter (DMET genes associated with steady-state plasma concentrations of risperidone among Thai autism spectrum disorder (ASD patients. ASD patients taking risperidone for at least one month were enrolled for this pharmacogenomic study. Genotyping profile was obtained using Affymetrix DMET Plus array interrogating 1931 variants in 231 genes. Steady-state plasma risperidone and 9-hydroxyrisperidone were measured using liquid chromatography/tandem mass spectrometry (LC-MS/MS assay. The final analysis included 483 markers for 167 genes. Six variants, ABCB11 (c.3084A>G, c.*420A>G, c.*368G>A, and c.*236G>A and ADH7 (c.690G>A and c.-5360G>A, were found to be associated with plasma concentrations of risperidone. 9-Hydroxyrisperidone and the total active-moiety levels were associated with six gene variants, SCLO1B1 (c.-11187G>A and c.521T>C, SLCO1B3 (c.334G>T, c.699A>G, and c.1557G>A, and SLC7A5 c.*438C>G. Polymorphisms in UGT2B4 c.*448A>G and CYP2D6 (c.1661G>C, c.4180G>C, and c.-2178G>A showed considerable but not significant associations with metabolic ratio. This pharmacogenomic study identifies new genetic variants of DMET genes in monitoring risperidone therapy.

  10. A large insertion in intron 2 of the TYRP1 gene associated with American Palomino phenotype in American mink.

    Science.gov (United States)

    Cirera, Susanna; Markakis, Marios Nektarios; Kristiansen, Thea; Vissenberg, Kris; Fredholm, Merete; Christensen, Knud; Anistoroaei, Razvan

    2016-04-01

    A number of American mink phenotypes display a range of brownish colours. One of these phenotypes, namely American Palomino (b (P) b (P) ) (AP) has been found to be associated with the tyrosinase-related protein 1 (TYRP1) gene by genotyping microsatellite markers in one sire family. Trials for amplifying the genomic DNA and cDNA at the beginning of intron 2 of AP TYRP1 revealed the presence of a large insertion of approximately eight kb. The insertion most likely disrupts different elements necessary for the splicing of intron 2 of the TYRP1 gene. In AP RNAseq data indicate, however, the presence of the wild-type (wt) transcript at very low levels and Western blot reveals three products when using an antibody raised against middle part of the TYRP1 protein. One individual from another brown mink phenotype-commercially named Dawn-was also investigated at the molecular level by long-range PCR and the same size insertion appears to be present. By this we suggest that certain modifiers of TYRP1 would induce different brown colour degradation, which results in at least two different phases of brown.

  11. Identification of Exonic Nucleotide Variants of the Gene Associated with Carcass Traits and Fatty Acid Composition in Korean Cattle

    Directory of Open Access Journals (Sweden)

    Dong-yep Oh

    2014-10-01

    Full Text Available The thyroid hormone responsive protein (THRSP gene is a functional gene that can be used to indicate the fatty acid compositions. This study investigates the relationships of exonic single nucleotide polymorphisms (SNPs in the THRSP gene and fatty acid composition of muscle fat and marbling score in the 612 Korean cattle. The relationships between fatty acid composition and eight SNPs in the THRSP gene (g.78 G>A, g.173 C>T, g.184 C>T, g.190 C>A, g.194 C>T, g.277 C>G, g.283 T>G and g.290 T>G were investigated, and according to the results, two SNPs (g.78 G>A and g.184 C>T in exon 1 were associated with fatty acid composition. The GG and CC genotypes of g.78 G>A and g.184 C>T had higher unsaturated fatty acid (UFA and monounsaturated fatty acid (MUFA content (pA and g.184 C>T had significantly relationships with UFAs and MUFAs. Two SNPs in the THRSP gene affected fatty acid composition, suggesting that GG and CC genotypes and the ht1*ht1 group (Val/Ala haplotype can be markers to genetically improve the quality and flavor of beef.

  12. Novel Mutation in the TSC2 Gene Associated with Prenatally Diagnosed Cardiac Rhabdomyomas and Cerebral Tuberous Sclerosis

    Directory of Open Access Journals (Sweden)

    Chih-Ping Chen

    2006-01-01

    Full Text Available Cardiac rhabdomyomas are prenatal echocardiographic markers for tuberous sclerosis complex (TSC. TSC is caused by mutations in the genes TSC1 and TSC2. We report a 28-year-old, gravida 5, para 2, woman with an uncomplicated pregnancy until prenatal ultrasound at 34 weeks' gestation revealed fetal cardiac tumors. Ultrafast magnetic resonance imaging (MRI at 36 weeks' gestation showed cardiac rhab-domyomas and small subependymal tubers. At 39 weeks' gestation, a 2262 g female infant was delivered uneventfully. Postnatal echocardiography confirmed cardiac rhabdomyomas and MRI verified small cerebral subependymal tubers. Mutational analysis of TSC1 and TSC2 genes using denaturing high-performance liquid chromatography and direct sequencing of the genes was performed and revealed that the parents had wildtype DNA, while the proband was heterozygous for a novel de novo nonsense mutation, c.4830 G > A, in exon 36 of the TSC2 gene, resulting in a change of codon 1610 TGG (tryptophan to TGA (stop codon. The mutation predicted a W1610X premature termination of the tuberin protein. These findings support an association between a TSC2 de novo nonsense mutation and prenatally detected cardiac rhabdomyomas and cerebral tuberous sclerosis. Familial molecular analysis of TSC1 and TSC2 in cases with prenatally diagnosed cardiac rhabdomyomas and cerebral tuberous sclerosis lesions is helpful in prenatal diagnosis and genetic counseling.

  13. Cytokine gene associations with self-report ratings of morning and evening fatigue in oncology patients and their family caregivers.

    Science.gov (United States)

    Dhruva, Anand; Aouizerat, Bradley E; Cooper, Bruce; Paul, Steven M; Dodd, Marylin; West, Claudia; Wara, William; Lee, Kathryn; Dunn, Laura B; Langford, Dale J; Merriman, John D; Baggott, Christina; Cataldo, Janine; Ritchie, Christine; Kober, Kord M; Leutwyler, Heather; Miaskowski, Christine

    2015-03-01

    The purpose of this study was to evaluate for differences in variations in pro- and anti-inflammatory cytokine genes between participants who were classified as having low and high levels of morning and evening fatigue and to evaluate for differences in phenotypic characteristics between these two groups. In a sample of 167 oncology outpatients with breast, prostate, lung, or brain cancer and 85 of their family caregivers, growth mixture modeling was used to identify latent classes of individuals based on ratings of morning and evening fatigue obtained prior to, during, and for 4 months following completion of radiation therapy. Differences in single nucleotide polymorphisms and haplotypes in 15 cytokine genes were evaluated between the latent classes. Multiple logistic regression was used to assess the effect of phenotypic and genotypic characteristics on morning and evening fatigue class membership. Associations were found between morning fatigue and number of comorbidities as well as variations in tumor necrosis factor alpha (TNFA) rs1800629 and rs3093662. Evening fatigue was associated with caring for children at home and variations in interleukin 4 (IL4) rs2243248 and TNFA rs2229094. Younger age and lower performance status were associated with both morning and evening fatigue. These findings suggest that inflammatory mediators are associated with the development of morning and evening fatigue. However, because different phenotypic characteristics and genomic markers are associated with diurnal variations in fatigue, morning and evening fatigue may be distinct but related symptoms. © The Author(s) 2014.

  14. Cytokine Gene Associations with Self-report Ratings of Morning and Evening Fatigue in Oncology Patients and Their Family Caregivers

    Science.gov (United States)

    Dhruva, Anand; Aouizerat, Bradley E.; Cooper, Bruce; Paul, Steven M.; Dodd, Marylin; West, Claudia; Wara, William; Lee, Kathryn; Dunn, Laura B.; Langford, Dale J.; Merriman, John D.; Baggott, Christina; Cataldo, Janine; Ritchie, Christine; Kober, Kord M.; Leutwyler, Heather; Miaskowski, Christine

    2017-01-01

    The purpose of this study was to evaluate for differences in variations in pro- and anti-inflammatory cytokine genes between participants who were classified as having low and high levels of morning and evening fatigue and to evaluate for differences in phenotypic characteristics between these two groups. In a sample of 167 oncology outpatients with breast, prostate, lung, or brain cancer and 85 of their family caregivers, growth mixture modeling (GMM) was used to identify latent classes of individuals based on ratings of morning and evening fatigue obtained prior to, during, and for 4 months following completion of radiation therapy. Differences in single nucleotide polymorphisms (SNPs) and haplotypes in 15 cytokine genes were evaluated between the latent classes. Multiple logistic regression was used to assess the effect of phenotypic and genotypic characteristics on morning and evening fatigue class membership. Associations were found between morning fatigue and number of comorbidities as well as variations in TNFA rs1800629 and rs3093662. Evening fatigue was associated with caring for children at home and variations in IL4 rs2243248 and TNFA rs2229094. Younger age and lower performance status was associated with both morning and evening fatigue. These findings suggest that inflammatory mediators are associated with the development of morning and evening fatigue. However, because different phenotypic characteristics and genomic markers are associated with diurnal variations in fatigue, morning and evening fatigue may be distinct but related symptoms. PMID:24872120

  15. The Variability of Growth Hormone Gene Associated with Ultrasound Imaging of Longissimus dorsi Muscle and Perirenal Fat in Rabbits

    Directory of Open Access Journals (Sweden)

    T. I. Amalianingsih

    2014-04-01

    Full Text Available Identification of genes in rabbits correlated to economic traits were intended to improve and develop their genetic quality. The objective of this research was to analyze the variability of growth hormone gene (GH in three rabbit breeds, i.e. Rex, Satin, and Reza (Rex and Satin crosses then was associated with ultrasound imaging of Longissimus dorsi muscle and perirenal fat thickness. Identification of the variability of growth hormone gene was analyzed using PCR RFLP technique from blood samples of 33 mature male rabbits in Indonesian Research Institute for Animal Production (IRIAP. Thickness of Longissimus dorsi muscle and perirenal fat were imaged and measured by using ultrasound unit at 2nd to 3rd lumbar vertebrae in the left body side. PCR product of GH gene fragment (231 base pair /bp was digested with restriction enzyme Bsh1236I. PCR-RFLP patterns were allele T resulted in an undigested fragment of 231 bp; allele C resulted in fragment of 169 bp and 62 bp. The result showed that Bsh1236I GH gene had three genotypes, i.e. CC, TT, and CT. There were signifficant association of Longissimus dorsi muscle thickness between rabbit breed (P<0.05. There was no significant association between GH Bsh1236I gene polymorphism and imaging ultrasound of Longissimus dorsi muscle and perirenal fat thickness. The association of characteristic genotype of GH|Bsh1236I gene with measurement phenotype was not significant, however it had potency as marker assisted selection (MAS.

  16. Imaging markers for Alzheimer disease

    Science.gov (United States)

    Bocchetta, Martina; Chételat, Gael; Rabinovici, Gil D.; de Leon, Mony J.; Kaye, Jeffrey; Reiman, Eric M.; Scheltens, Philip; Barkhof, Frederik; Black, Sandra E.; Brooks, David J.; Carrillo, Maria C.; Fox, Nick C.; Herholz, Karl; Nordberg, Agneta; Jack, Clifford R.; Jagust, William J.; Johnson, Keith A.; Rowe, Christopher C.; Sperling, Reisa A.; Thies, William; Wahlund, Lars-Olof; Weiner, Michael W.; Pasqualetti, Patrizio; DeCarli, Charles

    2013-01-01

    Revised diagnostic criteria for Alzheimer disease (AD) acknowledge a key role of imaging biomarkers for early diagnosis. Diagnostic accuracy depends on which marker (i.e., amyloid imaging, 18F-fluorodeoxyglucose [FDG]-PET, SPECT, MRI) as well as how it is measured (“metric”: visual, manual, semiautomated, or automated segmentation/computation). We evaluated diagnostic accuracy of marker vs metric in separating AD from healthy and prognostic accuracy to predict progression in mild cognitive impairment. The outcome measure was positive (negative) likelihood ratio, LR+ (LR−), defined as the ratio between the probability of positive (negative) test outcome in patients and the probability of positive (negative) test outcome in healthy controls. Diagnostic LR+ of markers was between 4.4 and 9.4 and LR− between 0.25 and 0.08, whereas prognostic LR+ and LR− were between 1.7 and 7.5, and 0.50 and 0.11, respectively. Within metrics, LRs varied up to 100-fold: LR+ from approximately 1 to 100; LR− from approximately 1.00 to 0.01. Markers accounted for 11% and 18% of diagnostic and prognostic variance of LR+ and 16% and 24% of LR−. Across all markers, metrics accounted for an equal or larger amount of variance than markers: 13% and 62% of diagnostic and prognostic variance of LR+, and 29% and 18% of LR−. Within markers, the largest proportion of diagnostic LR+ and LR− variability was within 18F-FDG-PET and MRI metrics, respectively. Diagnostic and prognostic accuracy of imaging AD biomarkers is at least as dependent on how the biomarker is measured as on the biomarker itself. Standard operating procedures are key to biomarker use in the clinical routine and drug trials. PMID:23897875

  17. A novel frameshift mutation in BLM gene associated with high sister chromatid exchanges (SCE) in heterozygous family members.

    Science.gov (United States)

    Ben Salah, Ghada; Hadj Salem, Ikhlas; Masmoudi, Abderrahmen; Kallabi, Fakhri; Turki, Hamida; Fakhfakh, Faiza; Ayadi, Hamadi; Kamoun, Hassen

    2014-11-01

    The Bloom syndrome (BS) is an autosomic recessive disorder comprising a wide range of abnormalities, including stunted growth, immunodeficiency, sun sensitivity and increased frequency of various types of cancer. Bloom syndrome cells display a high level of genetic instability, including a 10-fold increase in the sister chromatid exchanges (SCE) level. Bloom syndrome arises through mutations in both alleles of the BLM gene, which was identified as a member of the RecQ helicase family. In this study, we screened a Tunisian family with three BS patients. Cytogenetic analysis showed several chromosomal aberrations, and an approximately 14-fold elevated SCE frequency in BS cells. A significant increase in SCE frequency was observed in some family members but not reaching the BS patients values, leading to suggest that this could be due to the heterozygous profile. Microsatellite genotyping using four fluorescent dye-labeled microsatellite markers revealed evidence of linkage to BLM locus and the healthy members, sharing higher SCE frequency, showed heterozygous haplotypes as expected. Additionally, the direct BLM gene sequencing identified a novel homozygous frameshift mutation c.3617-3619delAA (p.K1207fsX9) in BS patients and a heterozygous BLM mutation in the family members with higher SCE frequency. Our findings suggest that this latter mutation likely leads to a reduced BLM activity explaining the homologous recombination repair defect and, therefore, the increase in SCE. Based on the present data, the screening of this mutation could contribute to the rapid diagnosis of BS. The genetic confirmation of the mutation in BLM gene provides crucial information for genetic counseling and prenatal diagnosis.

  18. Virus-induced gene silencing-based functional characterization of genes associated with powdery mildew resistance in barley.

    Science.gov (United States)

    Hein, Ingo; Barciszewska-Pacak, Maria; Hrubikova, Katarina; Williamson, Sandie; Dinesen, Malene; Soenderby, Ida E; Sundar, Suresh; Jarmolowski, Artur; Shirasu, Ken; Lacomme, Christophe

    2005-08-01

    We successfully implemented virus-induced gene silencing (VIGS) in barley (Hordeum vulgare) for the functional characterization of genes required for Mla13-mediated resistance toward the biotrophic barley pathogen Blumeria graminis f. sp. hordei. Initially, barley cultivars were screened for their ability to host the barley stripe mosaic virus (BSMV)-VIGS vector by allowing its replication and systemic movement without causing excessive symptoms. Phytoene desaturase silencing leading to photobleaching was used as a phenotypic marker alongside reverse transcription-PCR data to characterize the silencing response at the molecular level. Barley cultivar Clansman, harboring the Mla13 resistance gene, was chosen as the most suitable host for BSMV-VIGS-based functional characterization of Rar1, Sgt1, and Hsp90 in the Mla-mediated resistance toward powdery mildew. BSMV-induced gene silencing of these candidate genes, which are associated in many but not all race-specific pathways, proved to be robust and could be detected at both mRNA and protein levels for up to 21 d postinoculation. Systemic silencing was observed not only in the newly developed leaves from the main stem but also in axillary shoots. By examining fungal development from an incompatible mildew strain carrying the cognate Avr13 gene on plants BSMV silenced for Rar1, Sgt1, and Hsp90, a resistance-breaking phenotype was observed, while plants infected with BSMV control constructs remained resistant. We demonstrate that Hsp90 is a required component for Mla13-mediated race-specific resistance and that BSMV-induced VIGS is a powerful tool to characterize genes involved in pathogen resistance in barley.

  19. Virus-Induced Gene Silencing-Based Functional Characterization of Genes Associated with Powdery Mildew Resistance in Barley1

    Science.gov (United States)

    Hein, Ingo; Barciszewska-Pacak, Maria; Hrubikova, Katarina; Williamson, Sandie; Dinesen, Malene; Soenderby, Ida E.; Sundar, Suresh; Jarmolowski, Artur; Shirasu, Ken; Lacomme, Christophe

    2005-01-01

    We successfully implemented virus-induced gene silencing (VIGS) in barley (Hordeum vulgare) for the functional characterization of genes required for Mla13-mediated resistance toward the biotrophic barley pathogen Blumeria graminis f. sp. hordei. Initially, barley cultivars were screened for their ability to host the barley stripe mosaic virus (BSMV)-VIGS vector by allowing its replication and systemic movement without causing excessive symptoms. Phytoene desaturase silencing leading to photobleaching was used as a phenotypic marker alongside reverse transcription-PCR data to characterize the silencing response at the molecular level. Barley cultivar Clansman, harboring the Mla13 resistance gene, was chosen as the most suitable host for BSMV-VIGS-based functional characterization of Rar1, Sgt1, and Hsp90 in the Mla-mediated resistance toward powdery mildew. BSMV-induced gene silencing of these candidate genes, which are associated in many but not all race-specific pathways, proved to be robust and could be detected at both mRNA and protein levels for up to 21 d postinoculation. Systemic silencing was observed not only in the newly developed leaves from the main stem but also in axillary shoots. By examining fungal development from an incompatible mildew strain carrying the cognate Avr13 gene on plants BSMV silenced for Rar1, Sgt1, and Hsp90, a resistance-breaking phenotype was observed, while plants infected with BSMV control constructs remained resistant. We demonstrate that Hsp90 is a required component for Mla13-mediated race-specific resistance and that BSMV-induced VIGS is a powerful tool to characterize genes involved in pathogen resistance in barley. PMID:16040663

  20. Candidate gene association study conditioning on individual ancestry in patients with type 2 diabetes and metabolic syndrome from Mexico City.

    Science.gov (United States)

    Cruz, M; Valladares-Salgado, A; Garcia-Mena, J; Ross, K; Edwards, M; Angeles-Martinez, J; Ortega-Camarillo, C; de la Peña, J Escobedo; Burguete-Garcia, A I; Wacher-Rodarte, N; Ambriz, R; Rivera, R; D'artote, A L; Peralta, J; Parra, Esteban J; Kumate, J

    2010-05-01

    Type 2 diabetes (T2D) is influenced by diverse environmental and genetic risk factors. Metabolic syndrome (MS) increases the risk of cardiovascular disease and diabetes. We analysed 14 cases of polymorphisms located in 10 candidate loci, in a sample of patients with T2D and controls from Mexico City. We analysed the association of 14 polymorphisms located within 10 genes (TCF7L2, ENPP1, ADRB3, KCNJ11, LEPR, PPARgamma, FTO, CDKAL1, SIRT1 and HHEX) with T2D and MS. The analysis included 519 subjects with T2D defined according to the ADA criteria, 389 with MS defined according to the AHA/NHLBI criteria and 547 controls. Association was tested with the program ADMIXMAP including individual ancestry, age, sex, education and in some cases body mass index (BMI), in a logistic regression model. The two markers located within the TCF7L2 gene showed strong associations with T2D (rs7903146, T allele, odd ratio (OR) = 1.76, p = 0.001 and rs12255372, T allele, OR = 1.78, p = 0.002), but did not show significant association with MS. The non-synonymous rs4994 polymorphism of the ADRB3 gene was associated with T2D (Trp allele, OR = 0.62, p = 0.001) and MS (Trp allele, OR = 0.74, p = 0.018). Nominally significant associations were also observed between T2D and the SIRT1 rs3758391 SNP and MS and the HHEX rs5015480 polymorphism. Variants located within the gene TCF7L2 are strongly associated with T2D but not with MS, providing support to previous evidence indicating that polymorphisms at the TCF7L2 gene increase T2D risk. In contrast, the non-synonymous ADRB3 rs4994 polymorphism is associated with T2D and MS.

  1. Biological Markers and Salivary Cortisol

    DEFF Research Database (Denmark)

    Hansen, Åse Marie; Gunnarsson, Lars-Gunnar; Harris, Anette

    2011-01-01

    This chapter focuses on salivary cortisol in relation to biological markers. Specifically, associations with conventional cardiovascular risk factors and metabolic abnormalities (body mass index, waist circumference, waist/hip ratio, lipid status, glucose, blood pressure, heart rate and heart rate...... variability), markers related to inflammation (C-reactive protein, cytokines and tumor necrosis factor-alpha) and other stress hormones (adrenaline and noradrenaline) were studied. The focus was on healthy adult populations; studies on patient populations and pregnant women were excluded. Studies on genome...... variations and pharmacological interventions were also excluded. After meeting all exclusion criteria, 42 papers remained. In total, 273 associations between salivary cortisol and any of the markers mentioned were studied, comprising 241 associations on metabolic abnormalities, 30 on inflammation, and 2...

  2. Serum markers of liver fibrosis

    DEFF Research Database (Denmark)

    Veidal, Sanne Skovgård; Bay-Jensen, Anne-Christine; Tougas, Gervais

    2010-01-01

    BACKGROUND: Fibrosis is a central histological feature of chronic liver diseases and is characterized by the accumulation and reorganization of the extracellular matrix. The gold standard for assessment of fibrosis is histological evaluation of a percutaneous liver biopsy. Albeit a considerable......-epitopes, may be targeted for novel biochemical marker development in fibrosis. We used the recently proposed BIPED system (Burden of disease, Investigative, Prognostic, Efficacy and Diagnostic) to characterise present serological markers. METHODS: Pubmed was search for keywords; Liver fibrosis, neo......, a systematic use of the neo-epitope approach, i.e. the quantification of peptide epitopes generated from enzymatic cleavage of proteins during extracellular remodeling, may prove productive in the quest to find new markers of liver fibrosis....

  3. FBLN4 as candidate gene associated with long-term and short-term survival with primary glioblastoma

    Directory of Open Access Journals (Sweden)

    Li F

    2017-01-01

    showed that the expression patterns of FBLN4 and IGFBP-2 serve as independent prognostic indicators for overall survival (P<0.01 and P<0.05, respectively. Conclusion: To our knowledge, this is the first report describing FBLN4 as a prognostic factor for GBM patient survival, demonstrating that increased GBM survival time correlates with decreased FBLN4 expression. Understanding FBLN4 expression patterns could aid in the creation of powerful tools to predict clinical prognoses of GBM patients. Keywords: glioblastoma, FBLN4, IGFBP-2, tumor marker, prognosis

  4. RNA-Seq identifies SNP markers for growth traits in rainbow trout.

    Directory of Open Access Journals (Sweden)

    Mohamed Salem

    Full Text Available Fast growth is an important and highly desired trait, which affects the profitability of food animal production, with feed costs accounting for the largest proportion of production costs. Traditional phenotype-based selection is typically used to select for growth traits; however, genetic improvement is slow over generations. Single nucleotide polymorphisms (SNPs explain 90% of the genetic differences between individuals; therefore, they are most suitable for genetic evaluation and strategies that employ molecular genetics for selective breeding. SNPs found within or near a coding sequence are of particular interest because they are more likely to alter the biological function of a protein. We aimed to use SNPs to identify markers and genes associated with genetic variation in growth. RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each identified SNP markers associated with growth-rate. The allelic imbalances (the ratio between the allele frequencies of the fast growing sample and that of the slow growing sample were considered at scores >5.0 as an amplification and <0.2 as loss of heterozygosity. A subset of SNPs (n = 54 were validated and evaluated for association with growth traits in 778 individuals of a three-generation parent/offspring panel representing 40 families. Twenty-two SNP markers and one mitochondrial haplotype were significantly associated with growth traits. Polymorphism of 48 of the markers was confirmed in other commercially important aquaculture stocks. Many markers were clustered into genes of metabolic energy production pathways and are suitable candidates for genetic selection. The study demonstrates that RNA-Seq at low sequence coverage of divergent populations is a fast and effective means of identifying SNPs, with allelic imbalances between phenotypes. This technique is

  5. MarkerMiner 1.0: A new application for phylogenetic marker development using angiosperm transcriptomes.

    Science.gov (United States)

    Chamala, Srikar; García, Nicolás; Godden, Grant T; Krishnakumar, Vivek; Jordon-Thaden, Ingrid E; De Smet, Riet; Barbazuk, W Brad; Soltis, Douglas E; Soltis, Pamela S

    2015-04-01

    Targeted sequencing using next-generation sequencing (NGS) platforms offers enormous potential for plant systematics by enabling economical acquisition of multilocus data sets that can resolve difficult phylogenetic problems. However, because discovery of single-copy nuclear (SCN) loci from NGS data requires both bioinformatics skills and access to high-performance computing resources, the application of NGS data has been limited. We developed MarkerMiner 1.0, a fully automated, open-access bioinformatic workflow and application for discovery of SCN loci in angiosperms. Our new tool identified as many as 1993 SCN loci from transcriptomic data sampled as part of four independent test cases representing marker development projects at different phylogenetic scales. MarkerMiner is an easy-to-use and effective tool for discovery of putative SCN loci. It can be run locally or via the Web, and its tabular and alignment outputs facilitate efficient downstream assessments of phylogenetic utility, locus selection, intron-exon boundary prediction, and primer or probe development.

  6. Nutrigenomic studies on hilsa to evaluate flesh quality attributes and genes associated with fatty acid metabolism from the rivers Hooghly and Padma.

    Science.gov (United States)

    Ganguly, Satabdi; Mahanty, Arabinda; Mitra, Tandrima; Mohanty, Sasmita; Das, Basanta Kumar; Mohanty, Bimal Prasanna

    2018-01-01

    The Indian shad hilsa (Tenualosa ilisha), a commercially important food fish rich in oils, enjoys high consumer preference in the South Asian countries owing to its unique flavour and culinary properties. The present study was undertaken with the primary objective of determining the flesh quality attributes of hilsa in terms of nutritive value (gross chemical composition, amino acid, fatty acid and mineral composition), pH, water holding capacity (WHC) and expression of genes associated with fatty acid metabolism and flesh quality. Additionally, comparative studies on the flesh quality attributes in hilsa from two distributaries of river Ganga i.e. Hooghly and Padma were also carried out. A high WHC (>80%) suggested juicy and tender nature of hilsa meat. The protein content was 18-21% in hilsa from both the rivers and essential amino acid lysine, valine and functional amino acids leucine and arginine were significantly higher in Hooghly hilsa (Pattributes of hilsa has enriched the knowledgebase. Further, from comparative nutrient analysis on hilsa from river Hooghly and Padma, it was observed that Hooghly hilsa is superior in terms of oil content, ω-3 PUFAs EPA and DHA and essential amino acids; however, the expression profile of genes associated with flesh quality were found to be similar. Thus, within the scope of the present study, Hooghly hilsa (medium size category, 500-700g size) was found to be nutritionally superior. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Concepts of scale and scaling

    Science.gov (United States)

    Jianguo Wu; Harbin Li

    2006-01-01

    The relationship between pattern and process is of great interest in all natural and social sciences, and scale is an integral part of this relationship. It is now well documented that biophysical and socioeconomic patterns and processes operate on a wide range of spatial and temporal scales. In particular, the scale multiplicity and scale dependence of pattern,...

  8. Protein species as diagnostic markers

    NARCIS (Netherlands)

    Steffen, Pascal; Kwiatkowski, Marcel; Robertson, Wesley D.; Zarrine-Afsar, Mash; Deterra, Diana; Richter, Verena; Schlueter, Hartmut

    2016-01-01

    Many diseases are associated with protein species perturbations. A prominent example of an established diagnostic marker is the glycated protein species of hemoglobin, termed HbA1c. HbA1c concentration is increased in the blood of diabetes mellitus patients due to their poor control of blood glucose

  9. Dopaminergic, Serotonergic, and Oxytonergic Candidate Genes Associated with Infant Attachment Security and Disorganization? In Search of Main and Interaction Effects

    Science.gov (United States)

    Luijk, Maartje P. C. M.; Roisman, Glenn I.; Haltigan, John D.; Tiemeier, Henning; Booth-LaForce, Cathryn; van IJzendoorn, Marinus H.; Belsky, Jay; Uitterlinden, Andre G.; Jaddoe, Vincent W.V.; Hofman, Albert; Verhulst, Frank C.; Tharner, Anne; Bakermans-Kranenburg, Marian J.

    2011-01-01

    Background and methods In two birth cohort studies with genetic, sensitive parenting, and attachment data of more than 1,000 infants in total, we tested main and interaction effects of candidate genes involved in the dopamine, serotonin, and oxytocin systems (DRD4, DRD2, COMT, 5-HTT, OXTR) on attachment security and disorganization. Parenting was assessed using observational rating scales for parental sensitivity (Ainsworth, Bell, & Stayton, 1974), and infant attachment was assessed with the Strange Situation Procedure. Results We found no consistent additive genetic associations for attachment security and attachment disorganization. However, specific tests revealed evidence for a co-dominant risk model for COMT Val158Met, consistent across both samples. Children with the Val/Met genotype showed higher disorganization scores (combined effect size d = 0.22, CI = 0.10; 0.34, p < .001). Gene-by-environment interaction effects were not replicable across the two samples. Conclusions This unexpected finding might be explained by a broader range of plasticity in heterozygotes, which may increase susceptibility to environmental influences or to dysregulation of emotional arousal. This study is unique in combining the two largest attachment cohorts with molecular genetic and observed rearing environment data to date. PMID:21749372

  10. Biochemical Markers in Neurocritical Care

    Directory of Open Access Journals (Sweden)

    Omidvar Rezae

    2016-07-01

    Full Text Available During the past two decades, a variety of serum or cerebrospinal fluid (CSF biochemical markers in daily clinical practice have been recommended to diagnose and monitor diverse diseases or pathologic situations. It will be essential to develop a panel of biomarkers, to be suitable for evaluation of treatment efficacy, representing distinct phases of injury and recovery and consider the temporal profile of those. Among the possible and different biochemical markers, S100b appeared to fulfill many of optimized criteria of an ideal marker. S100b, a cytosolic low molecular weight dimeric calciumbinding protein from chromosome 21, synthesized in glial cells throughout the CNS, an homodimeric diffusible, belongs to a family of closely related protein, predominantly expressed by astrocytes and Schwann cells and a classic immunohistochemical marker for these cells, is implicated in brain development and neurophysiology. Of the 3 isoforms of S-100, the BB subunit (S100B is present in high concentrations in central and peripheral glial and Schwann cells, Langerhans and anterior pituitary cells, fat, muscle, and bone marrow tissues. The biomarker has shown to be a sensitive marker of clinical and subclinical cerebral damage, such as stroke, traumatic brain injury, and spinal cord injury. Increasing evidence suggests that the biomarker plays a double function as an intracellular regulator and an extracellular signal of the CNS. S100b is found in the cytoplasm in a soluble form and also is associated with intracellular membranes, centrosomes, microtubules, and type III intermediate filaments. Their genomic organization now is known, and many of their target proteins have been identified, although the mechanisms of regulating S100b secretion are not completely understood and appear to be related to many factors, such as the proinflammatory cytokines, tumor necrosis factor alpha (TNF-a, interleukin (IL-1b, and metabolic stress. 

  11. Urinary oxidative stress markers in children with autism.

    Science.gov (United States)

    Damodaran, Lakshmi Priya Malarveni; Arumugam, Geetha

    2011-01-01

    Oxidative stress caused by increased production of free radicals and impaired functions of antioxidants remains as the major factor associated with the pathophysiology of many neuropsychiatric diseases. The objective of the present study was to analyze the oxidative stress markers in urine sample since the collection of blood from these children is highly meticulous and also to evaluate whether these urinary markers can be correlated with the severity of autism. The subjects of the study were 45 autistic children with different grades of severity (low functioning autism (LFA), medium functioning autism (MFA), and high functioning autism (HFA) according to Childhood Autism Rating Scale (CARS), n=15 children in each group and 50 healthy children (age and sex matched). The boys and girls ratio involved in this study was 4:1, and they were of age 4-12 years. We determined the urinary levels of oxidative stress markers like thiobarbituric acid-reacting substances, lipid hydroperoxides, 4-hydroxy nonenal, protein carbonyls, sulfhydryl groups, total antioxidant capacity, total peroxide content, oxidative stress index, and also UA/Cr ratio in autistic children. The study observed a significant elevation in the level of oxidative stress markers in autistic children when compared with normal children. The level of antioxidants excreted in urine was found to be significantly low in autistic children. These findings when correlated with the degrees of severity, oxidative stress markers showed positive correlation with increasing order of severity (LFA>MFA>HFA), whereas antioxidants showed negative correlation. The study reveals that the urinary levels of oxidative stress markers can be considered as the measure of oxidative stress index in autistic children. The significant correlation between the severity of autism with urinary lipid peroxidation products also support the use of oxidative stress markers and antioxidants as biomarkers of autism.

  12. Migrainomics - identifying brain and genetic markers of migraine.

    Science.gov (United States)

    Nyholt, Dale R; Borsook, David; Griffiths, Lyn R

    2017-12-01

    Migraine is one of the world's most prevalent and disabling disorders and imposes an enormous socioeconomic burden. The exact causes of migraine are unknown, and no recognizable diagnostic pathological changes have been identified. Specific identifiable markers of migraine would aid diagnosis and could provide insight into the pathogenesis of the condition, with the potential to direct development of new therapeutics. In the past few years, advances in neuroimaging and genetic studies have provided the most substantial progress towards the identification of markers. A growing number of brain imaging studies have provided important insights into the brain mechanisms that underlie migraine symptoms during and between migraine attacks. Similarly, large-scale genome-wide association studies have identified genetic variants associated with the common forms of migraine - migraine with aura and migraine without aura. In total, 44 independent single-nucleotide polymorphism loci have been robustly associated with the risk of migraine and provide new evidence for the involvement of vascular mechanisms. Both imaging and genetics, therefore, have excellent potential as markers of migraine. In this Review, we provide a summary of results regarding current and potential neuroimaging and genetic markers of migraine, consider what conclusions can be drawn from these markers about migraine mechanisms and discuss the potential of combining imaging and genetics.

  13. Voice analysis as an objective state marker in bipolar disorder

    DEFF Research Database (Denmark)

    Faurholt-Jepsen, M.; Busk, Jonas; Frost, M.

    2016-01-01

    Changes in speech have been suggested as sensitive and valid measures of depression and mania in bipolar disorder. The present study aimed at investigating (1) voice features collected during phone calls as objective markers of affective states in bipolar disorder and (2) if combining voice...... features with automatically generated objective smartphone data on behavioral activities (for example, number of text messages and phone calls per day) and electronic self-monitored data (mood) on illness activity would increase the accuracy as a marker of affective states. Using smartphones, voice...... the Hamilton Depression Rating Scale 17-item and the Young Mania Rating Scale, respectively, by a researcher blinded to smartphone data. Data were analyzed using random forest algorithms. Affective states were classified using voice features extracted during everyday life phone calls. Voice features were found...

  14. Transcriptional profiling of human liver identifies sex-biased genes associated with polygenic dyslipidemia and coronary artery disease.

    Directory of Open Access Journals (Sweden)

    Yijing Zhang

    Full Text Available Sex-differences in human liver gene expression were characterized on a genome-wide scale using a large liver sample collection, allowing for detection of small expression differences with high statistical power. 1,249 sex-biased genes were identified, 70% showing higher expression in females. Chromosomal bias was apparent, with female-biased genes enriched on chrX and male-biased genes enriched on chrY and chr19, where 11 male-biased zinc-finger KRAB-repressor domain genes are distributed in six clusters. Top biological functions and diseases significantly enriched in sex-biased genes include transcription, chromatin organization and modification, sexual reproduction, lipid metabolism and cardiovascular disease. Notably, sex-biased genes are enriched at loci associated with polygenic dyslipidemia and coronary artery disease in genome-wide association studies. Moreover, of the 8 sex-biased genes at these loci, 4 have been directly linked to monogenic disorders of lipid metabolism and show an expression profile in females (elevated expression of ABCA1, APOA5 and LDLR; reduced expression of LIPC that is consistent with the lower female risk of coronary artery disease. Female-biased expression was also observed for CYP7A1, which is activated by drugs used to treat hypercholesterolemia. Several sex-biased drug-metabolizing enzyme genes were identified, including members of the CYP, UGT, GPX and ALDH families. Half of 879 mouse orthologs, including many genes of lipid metabolism and homeostasis, show growth hormone-regulated sex-biased expression in mouse liver, suggesting growth hormone might play a similar regulatory role in human liver. Finally, the evolutionary rate of protein coding regions for human-mouse orthologs, revealed by dN/dS ratio, is significantly higher for genes showing the same sex-bias in both species than for non-sex-biased genes. These findings establish that human hepatic sex differences are widespread and affect diverse cell

  15. A Genome-Wide Scan of DNA Methylation Markers for Distinguishing Monozygotic Twins.

    Science.gov (United States)

    Du, Qingqing; Zhu, Guijun; Fu, Guangping; Zhang, Xiaojing; Fu, Lihong; Li, Shujin; Cong, Bin

    2015-12-01

    Identification of individuals within pairs of monozygotic (MZ) twins remains unresolved using common forensic DNA typing technology. For some criminal cases involving MZ twins as suspects, the twins had to be released due to inability to identify which of the pair was the perpetrator. In this study, we performed a genome-wide scan on whole blood-derived DNA from four pairs of healthy phenotypically concordant MZ twins using the methylated DNA immunoprecipitation sequencing technology to identify candidate DNA methylation markers with capacity to distinguish MZ twins within a pair. We identified 38 differential methylation regions showing within-pair methylation differences in all four MZ pairs. These are all located in CpG islands, 17 of which are promoter-associated, 17 are intergenic islands, and four are intragenic islands. Genes associated with these markers are related with cell proliferation, differentiation, and growth and development, including zinc finger proteins, PRRX2, RBBP9, or are involved in G-protein signaling, such as the regulator of G-protein signaling 16. Further validation studies on additional MZ twins are now required to evaluate the broader utility of these 38 markers for forensic use.

  16. Physical mapping of genetic markers on the short arm of chromosome 5

    Energy Technology Data Exchange (ETDEWEB)

    Gersh, M.; Goodart, S.A.; Overhauser, J. [Thomas Jefferson Univ., Philadelphia, PA (United States)

    1994-12-01

    The deletion of the short arm of chromosome 5 is associated with the cri-du-chat syndrome. In addition, loss of this portion of a chromosome is a common cytogenetic marker in a number of malignancies. However, to date, no genes associated with these disorders have been identified. Physical maps are the first step in isolating causative genes, and genes involved in autosomal recessive disorders are now routinely mapped through the identification of linked markers. Extensive genetic maps based upon polymorphic short tandem repeats (STRs) have provided researchers with a large number of markers to which such disorders can be genetically mapped. However, the physical locations of many of these STRs have not been determined. Toward the goal of integrating the human genetic maps with the physical maps, a 5p somatic cell hybrid deletion mapping panel that was derived from patients with 5p deletions or translocations was used to physically map 47 STRs that have been used to construct genetic maps of 5p. These data will be useful in the localization of disease genes that map to 5p and may be involved in the etiology of the cri-du-chat syndrome. 26 refs., 1 fig.

  17. Chronic vortioxetine treatment in rodents modulates gene expression of neurodevelopmental and plasticity markers.

    Science.gov (United States)

    Waller, Jessica A; Tamm, Joseph A; Abdourahman, Aicha; Pehrson, Alan L; Li, Yan; Cajina, Manuel; Sánchez, Connie

    2017-02-01

    The multimodal antidepressant vortioxetine displays an antidepressant profile distinct from those of conventional selective serotonin reuptake inhibitors (SSRIs) and serotonin-norepinephrine reuptake inhibitors (SNRIs) and possesses cognitive-enhancing properties in preclinical and clinical studies. Recent studies have begun to investigate molecular mechanisms that may differentiate vortioxetine from other antidepressants. Acute studies in adult rats and chronic studies in a middle-aged mouse model reveal upregulation of several markers that play a central role in synaptic plasticity. However, the effect of chronic vortioxetine treatment on expression of neuroplasticity and neurodevelopmental biomarkers in naïve rats has not been evaluated. In the present study, we demonstrate that vortioxetine at a range of doses regulates expression of genes associated with plasticity in the frontal cortex, hippocampus, region encompassing the amygdala, as well as in blood, and displays similar effects relative to the SSRI fluoxetine in adult naïve rats. These genes encode immediate early genes (IEGs), translational regulators, and the neurodevelopmental marker Sema4g. Similar findings detected in brain regions and in blood provide a potential translational impact, and vortioxetine appears to consistently regulate signaling in these networks of neuroplasticity and developmental markers. Copyright © 2016 Elsevier B.V. and ECNP. All rights reserved.

  18. Genotyping in the MHC locus: potential for defining predictive markers in sarcoidosis

    Directory of Open Access Journals (Sweden)

    Seitzer Ulrike

    2001-10-01

    Full Text Available Abstract In sarcoidosis, host genetic factors are discussed as contributing to disease susceptibility and course. Since tumor necrosis factor (TNF-α is a central mediator of granuloma formation and since elevated TNF-α levels are found during active phases of sarcoidosis, genetic polymorphisms correlating with influences on TNF-α levels are of special interest. The complete sequencing of the MHC region and the increase in the number of identified gene polymorphisms in this locus associated with TNF-α production offer the opportunity of detecting new genes associated with sarcoidosis and perhaps of defining disease-associated haplotypes that bear the potential of serving as predictive markers for this disease.

  19. Early bichemical markers of effects: Enzyme induction, oncogene activation and markers of oxidative damage

    DEFF Research Database (Denmark)

    Poulsen, Henrik E.; Loft, Steffen

    1995-01-01

    Early bichemical marker, enzyme induction, oncogene activation, oxidative damage, low-density lipoprotein......Early bichemical marker, enzyme induction, oncogene activation, oxidative damage, low-density lipoprotein...

  20. The Unintentional Procrastination Scale.

    Science.gov (United States)

    Fernie, Bruce A; Bharucha, Zinnia; Nikčević, Ana V; Spada, Marcantonio M

    2017-01-01

    Procrastination refers to the delay or postponement of a task or decision and is often conceptualised as a failure of self-regulation. Recent research has suggested that procrastination could be delineated into two domains: intentional and unintentional. In this two-study paper, we aimed to develop a measure of unintentional procrastination (named the Unintentional Procrastination Scale or the 'UPS') and test whether this would be a stronger marker of psychopathology than intentional and general procrastination. In Study 1, a community sample of 139 participants completed a questionnaire that consisted of several items pertaining to unintentional procrastination that had been derived from theory, previous research, and clinical experience. Responses were subjected to a principle components analysis and assessment of internal consistency. In Study 2, a community sample of 155 participants completed the newly developed scale, along with measures of general and intentional procrastination, metacognitions about procrastination, and negative affect. Data from the UPS were subjected to confirmatory factor analysis and revised accordingly. The UPS was then validated using correlation and regression analyses. The six-item UPS possesses construct and divergent validity and good internal consistency. The UPS appears to be a stronger marker of psychopathology than the pre-existing measures of procrastination used in this study. Results from the regression models suggest that both negative affect and metacognitions about procrastination differentiate between general, intentional, and unintentional procrastination. The UPS is brief, has good psychometric properties, and has strong associations with negative affect, suggesting it has value as a research and clinical tool.

  1. RNA-Seq analysis reveals genes associated with resistance to Taura syndrome virus (TSV) in the Pacific white shrimp Litopenaeus vannamei.

    Science.gov (United States)

    Sookruksawong, Suchonma; Sun, Fanyue; Liu, Zhanjiang; Tassanakajon, Anchalee

    2013-12-01

    Outbreak of Taura syndrome virus (TSV) is one of the major pathogens of the Pacific white shrimp Litopenaeus vannamei. Although selective breeding for improvement of TSV resistance in L. vannamei has been successfully developed and has led to a great benefit to the shrimp farming industry worldwide. The molecular mechanisms underlying the viral resistance in shrimp remain largely unknown. In the present study, we conducted the first transcriptomic profiling of host responses in hemolymph and hemocytes in order to identify the differentially expressed genes associated with resistance to TSV in L. vannamei. High-throughput RNA-Seq was employed, obtaining 193.6 and 171.2 million high-quality Illumina reads from TSV-resistant and susceptible L. vannamei lines respectively. A total of 61,937 contigs were generated with an average length of 546.26 bp. BLASTX-based gene annotation (E-value vannamei. Copyright © 2013 Elsevier Ltd. All rights reserved.

  2. Transcriptional analysis of genes associated with stress and adhesion in Lactobacillus acidophilus NCFM during the passage through an in vitro gastrointestial tract model

    DEFF Research Database (Denmark)

    Weiss, Gudrun Margarethe; Jespersen, Lene

    2010-01-01

    The aim of the present study was to investigate the transcription of genes associated with stress and adhesion in Lactobacillus acidophilus NCFM during the passage through an in vitro gastrointestinal tract model. As acidified milk exerted a protective effect on the bacteria leading to increased...... survival, the gene expression studies were carried out with pre-inoculation of L. acidophilus NCFM in acidified milk. The induction of the genes encoding the stress-related proteins GroEL, DnaK and ClpP, and adhesion-related genes encoding mucin-binding proteins, fibronectin-binding protein and S...... juice, but they were significantly upregulated during incubation in duodenal juice and bile (6- to 7-fold). A significant induction of the gene encoding the S-layer protein was not detected. Our results give a better understanding of the functionality of L. acidophilus NCFM and other probiotics during...

  3. Inflammation markers in essential hypertension.

    Science.gov (United States)

    Tsounis, Dimitrios; Bouras, Georgios; Giannopoulos, Georgios; Papadimitriou, Charalampos; Alexopoulos, Dimitrios; Deftereos, Spyridon

    2014-01-01

    Essential hypertension is a common health disorder with uncertain etiology and unclear pathophysiology. There is evidence that various systems interact in uncertain ways and mechanisms to cause hypertension. It is also well known that inflammation is a key feature in the initiation, progression and clinical implication of several cardiovascular diseases. Recently, it has become evident that the immune system and inflammatory response are also essential in the pathogenesis of hypertension. Many inflammation markers such as CRP, cytokines, and adhesion molecules have been found elevated in hypertensive patients supporting the role of inflammation in the pathogenesis of hypertension. Also, in normotensive individuals, these markers have been associated with the risk of developing hypertension, whereas in hypertensive patients they have been associated with target organ damage as well as with the risk for future cardiovascular events. Thus, understanding the role of inflammation in hypertension provides new insights for novel therapeutic approaches, targeting inflammation for the treatment of hypertension and its complications.

  4. The Infinitive Marker across Scandinavian

    Directory of Open Access Journals (Sweden)

    Ken Ramshøj Christensen

    2007-04-01

    Full Text Available In this paper I argue that the base-position of the infinitive marker in the Scandinavian languages and English share a common origin site. It is inserted as the top-most head in the VP-domain. The cross-linguistic variation in the syntactic distribution of the infinitive marker can be accounted for by assuming that it undergoes head movement. This movement is optional in Danish, English, Norwegian, and Early Modern Danish and is not feature-driven. In Faroese, Icelandic, and Swedish, on the other hand, it is triggered by φ-feature checking on Finº. In Icelandic and Swedish these φ-features are strong and induce obligatory vº→Finº movement, whereas they are weak in Faroese and do not induce vº→Finº movement.

  5. Studies on meat color, myoglobin content, enzyme activities, and genes associated with oxidative potential of pigs slaughtered at different growth stages

    Directory of Open Access Journals (Sweden)

    Qin Ping Yu

    2017-12-01

    Full Text Available Objective This experiment investigated meat color, myoglobin content, enzyme activities, and expression of genes associated with oxidative potential of pigs slaughtered at different growth stages. Methods Sixty 4-week-old Duroc×Landrace×Yorkshire pigs were assigned to 6 replicate groups, each containing 10 pigs. One pig from each group was sacrificed at day 35, 63, 98, and 161 to isolate longissimus dorsi and triceps muscles. Results Meat color scores were higher in pigs at 35 d than those at 63 d and 98 d (p<0.05, and those at 98 d were lower than those at 161 d (p<0.05. The total myoglobin was higher on 161 d compared with those at 63 d and 98 d (p<0.05. Increase in the proportions of metmyoglobin and deoxymyoglobin and a decrease in oxymyoglobin were observed between days 35 and 161 (p<0.05. Meat color scores were correlated to the proportion of oxymyoglobin (r = 0.59, p<0.01, and negatively correlated with deoxymyoglobin and metmyoglobin content (r = −0.48 and −0.62, p<0.05. Malate dehydrogenase (MDH activity at 35 d and 98 d was higher than that at 161 d (p<0.05. The highest lactate dehydrogenase/MDH ratio was achieved at 161 d (p<0.05. Calcineurin mRNA expression decreased at 35 d compared to that at 63 d and 98 d (p<0.05. Myocyte enhancer factor 2 mRNA results indicated a higher expression at 161 d than that at 63 d and 98 d (p<0.05. Conclusion Porcine meat color, myoglobin content, enzyme activities, and genes associated with oxidative potential varied at different stages.

  6. Serotonin, neural markers and memory

    Directory of Open Access Journals (Sweden)

    Alfredo eMeneses

    2015-07-01

    Full Text Available Diverse neuropsychiatric disorders present dysfunctional memory and no effective treatment exits for them; likely as result of the absence of neural markers associated to memory. Neurotransmitter systems and signaling pathways have been implicated in memory and dysfunctional memory; however, their role is poorly understood. Hence, neural markers and cerebral functions and dysfunctions are revised. To our knowledge no previous systematic works have been published addressing these issues. The interactions among behavioral tasks, control groups and molecular changes and/or pharmacological effects are mentioned. Neurotransmitter receptors and signaling pathways, during normal and abnormally functioning memory with an emphasis on the behavioral aspects of memory are revised. With focus on serotonin, since as it is a well characterized neurotransmitter, with multiple pharmacological tools, and well characterized downstream signaling in mammals’ species. 5-HT1A, 5-HT4, 5-HT5, 5-HT6 and 5-HT7 receptors as well as SERT (serotonin transporter seem to be useful neural markers and/or therapeutic targets. Certainly, if the mentioned evidence is replicated, then the translatability from preclinical and clinical studies to neural changes might be confirmed. Hypothesis and theories might provide appropriate limits and perspectives of evidence

  7. Prognostic molecular markers in cancer - quo vadis?

    Science.gov (United States)

    Søland, Tine M; Brusevold, Ingvild J

    2013-09-01

    Despite the tremendous number of studies of prognostic molecular markers in cancer, only a few such markers have entered clinical practise. The lack of clinical prognostic markers clearly reflects limitations in or an inappropriate approach to prognostic studies. This situation should be of great concern for the research community, clinicians and patients. In the present review, we evaluate immunohistochemical prognostic marker studies in oral squamous cell carcinomas (OSCC) from 2006 to 2012. We comment upon general issues such as study design, assay methods and statistical methods, applicable to prognostic marker studies irrespective of cancer type. The three most frequently studied markers in OSCC are reviewed. Our analysis revealed that most new molecular markers are reported only once. To draw conclusions of clinical relevance based on the few markers that appeared in more than one study was problematic due to between-study heterogeneity. Currently, much valuable tissue material, time and money are wasted on irrelevant studies. © 2013 John Wiley & Sons Ltd.

  8. Vocatives and discourse markers in textualinteractive grammar

    Directory of Open Access Journals (Sweden)

    Eduardo Penhavel

    2012-12-01

    Full Text Available In this paper, we discuss the class of Vocatives and the class of Discourse Markers as proposed within Textualinteractive Grammar, and we try to demonstrate that Vocatives can work as Discourse Markers.

  9. Ureohydrolases as dominant selectable markers in yeast

    NARCIS (Netherlands)

    Daran, J.G.; Pronk, J.T.; Romagnoli, G.

    2015-01-01

    The invention relates to a nucleic acid molecule encoding a novel selection marker. Said marker is a guanidinobutyrase from Kluyveromyces lactis, which, when expressed in Saccharomyces, allows the growth of the yeast in the presence of guanidinobutyrate as the sole nitrogen source. Said marker can

  10. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.).

    Science.gov (United States)

    Qiu, Lijun; Yang, Chun; Tian, Bo; Yang, Jun-Bo; Liu, Aizhong

    2010-12-16

    The castor bean (Ricinus communis L.), a monotypic species in the spurge family (Euphorbiaceae, 2n = 20), is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85%) in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs) provide valuable resources to develop gene-associated SSR markers. In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A) with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He) with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean. Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly useful for both genetic mapping and population structure

  11. From Subordinate Marker to Discourse Marker: que in Andean Spanish

    Directory of Open Access Journals (Sweden)

    Anna María Escobar

    2005-06-01

    Full Text Available This paper proposes an analysis of a redundant use of que ('that' found in Andean Spanish as an expression which has undergone a grammaticalization process. Evidence suggests that the function of que as subordinate marker is much more generalized in this variety than in other dialects of Spanish. que is found to be used as a marker introducing both nominal and adjectival clauses, suggesting that adjectival subordinates behave as nominal subordinates in this variety of Spanish. An intrusive que appears in restricted syntactic and semantic contexts with clauses that have nominal and adjectival functions, and even appears replacing adverbial expressions in some adverbial subordinates (temporal, spatial, and manner. Furthermore, it is found to be sensitive to the degree of the argument’s thematic/semantic function in the subordinate clause. In particular, it seems to occur more often with low-agency arguments in adjectival and nominal contexts, and, in nominal subordinates, tends to appear with a restricted set of epistemic and evidential main verbs (e.g. creer 'to believe', saber 'to know', decir 'to say'. The analysis suggests that que has developed a new function in this variety of Spanish, namely, one of indicating that the information contained in the subordinate clause does not constitute background information (as would be expected in non-contact varieties of Spanish but instead contains information relevant to the discourse.

  12. Immunological markers of rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    Agnieszka Matuszewska

    2016-03-01

    Full Text Available Rheumatoid arthritis (RA is the most common connective tissue disease of autoimmune origin. The disease is characterized by chronic inflammation leading to bone erosions and organ involvement. RA is a progressive disease. It affects the quality of life, leading to disability and death mainly due to premature cardiovascular disease. Early diagnosis and appropriate treatment are essential for prognosis and quality of life improvement. In 2010 the American College of Rheumatology (ACR and The European League Against Rheumatism (EULAR established new RA classification criteria. Besides clinical symptoms it includes two immunologic criteria: rheumatoid factor (RF and anti-citrullinated protein antibodies (anti-CCP antibodies. RF is the first well-known RA immunologic marker. It is observed in 80-85% of patients with RA. Elevated serum level of RF has been associated with increased disease activity, radiographic progression, and the presence of extraarticular manifestations. The sensitivity of RF is 50-90%, and specificity is 50-95%. Anti-CCP antibodies appear to be a more specific marker than RF. They are often present at the very beginning of the disease, or even years before the first symptoms. The prognostic value of anti-CCP antibodies is well established. High serum level of anti-CCP correlates with poor prognosis and early erosions of the joints. The sensitivity of anti-CCP2 is 48-80%, and specificity is 96-98%. New immunologic markers include anti-carbamylated protein antibodies (anti-CarP and antibodies against heterogeneous nuclear ribonucleoproteins (anti-hnRNP A2/B1, RA33. Scientists aim to identify a highly sensitive and specific biomarker of the disease that not only has diagnostic and prognostic value but also may predict the response to treatment.

  13. Immunological markers of rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    Agnieszka Matuszewska

    2016-03-01

    Full Text Available Rheumatoid arthritis (RA is the most common connective tissue disease of autoimmune origin. The disease is characterized by chronic inflammation leading to bone erosions and organ involvement. RA is a progressive disease. It affects the quality of life, leading to disability and death mainly due to premature cardiovascular disease. Early diagnosis and appropriate treatment are essential for prognosis and quality of life improvement.In 2010 the American College of Rheumatology (ACR and The European League Against Rheumatism (EULAR established new RA classification criteria. Besides clinical symptoms it includes two immunologic criteria: rheumatoid factor (RF and anti-citrullinated protein antibodies (anti-CCP antibodies. RF is the first well-known RA immunologic marker. It is observed in 80-85% of patients with RA. Elevated serum level of RF has been associated with increased disease activity, radiographic progression, and the presence of extraarticular manifestations. The sensitivity of RF is 50-90%, and specificity is 50-95%. Anti-CCP antibodies appear to be a more specific marker than RF. They are often present at the very beginning of the disease, or even years before the first symptoms. The prognostic value of anti-CCP antibodies is well established. High serum level of anti-CCP correlates with poor prognosis and early erosions of the joints. The sensitivity of anti-CCP2 is 48-80%, and specificity is 96-98%.New immunologic markers include anti-carbamylated protein antibodies (anti-CarP and antibodies against heterogeneous nuclear ribonucleoproteins (anti-hnRNP A2/B1, RA33. Scientists aim to identify a highly sensitive and specific biomarker of the disease that not only has diagnostic and prognostic value but also may predict the response to treatment.

  14. Maslowian Scale.

    Science.gov (United States)

    Falk, C.; And Others

    The development of the Maslowian Scale, a method of revealing a picture of one's needs and concerns based on Abraham Maslow's levels of self-actualization, is described. This paper also explains how the scale is supported by the theories of L. Kohlberg, C. Rogers, and T. Rusk. After a literature search, a list of statements was generated…

  15. Helicity scalings

    Energy Technology Data Exchange (ETDEWEB)

    Plunian, F [ISTerre, CNRS, Universite Joseph Fourier, Grenoble (France); Lessinnes, T; Carati, D [Physique Statistique et Plasmas, Universite Libre de Bruxelles (Belgium); Stepanov, R, E-mail: Franck.Plunian@ujf-grenoble.fr [Institute of Continuous Media Mechanics of the Russian Academy of Science, Perm (Russian Federation)

    2011-12-22

    Using a helical shell model of turbulence, Chen et al. (2003) showed that both helicity and energy dissipate at the Kolmogorov scale, independently from any helicity input. This is in contradiction with a previous paper by Ditlevsen and Giuliani (2001) in which, using a GOY shell model of turbulence, they found that helicity dissipates at a scale larger than the Kolmogorov scale, and does depend on the helicity input. In a recent paper by Lessinnes et al. (2011), we showed that this discrepancy is due to the fact that in the GOY shell model only one helical mode (+ or -) is present at each scale instead of both modes in the helical shell model. Then, using the GOY model, the near cancellation of the helicity flux between the + and - modes cannot occur at small scales, as it should be in true turbulence. We review the main results with a focus on the numerical procedure needed to obtain accurate statistics.

  16. Prognostic markers of canine pyometra

    Directory of Open Access Journals (Sweden)

    M.C. Sant'Anna

    2014-12-01

    Full Text Available The pyometra is a disease that affects middle age and elderly female dogs during diestrus. Hormonal, microbiological, biochemical and hematological aspects are well described. However, few studies have evaluated the role of each in the prognosis of canine pyometra. The aim of this study was to identify markers associated with clinical worsening of dogs with pyometra. We prospectively evaluated 80 dogs with pyometra treated surgically. Group 1 consisted of dogs that were discharged within 48 hours after surgery and Group 2 consisted of those who required prolonged hospitalization or died. The findings of hematological, biochemical and blood lactate levels were compared between groups and variables such as bacterial multidrug resistance, systemic inflammatory response syndrome (SIRS, hyperlactatemia and increased creatinine were analyzed through the dispersion of frequencies between groups. Among the variables studied, the presence of SIRS and elevated serum creatinine >2.5mg/mL were effective in predicting the worsening of the disease and can be used as prognostic markers of canine pyometra.

  17. Framing scales and scaling frames

    NARCIS (Netherlands)

    Lieshout, van M.; Dewulf, A.; Aarts, M.N.C.; Termeer, C.J.A.M.

    2009-01-01

    Policy problems are not just out there. Actors highlight different aspects of a situation as problematic and situate the problem on different scales. In this study we will analyse the way actors apply scales in their talk (or texts) to frame the complex decision-making process of the establishment

  18. The potential value of the neutral comet assay and the expression of genes associated with DNA damage in assessing the radiosensitivity of tumor cells.

    Science.gov (United States)

    Jayakumar, Sundarraj; Bhilwade, Hari N; Pandey, Badri N; Sandur, Santosh K; Chaubey, Ramesh C

    2012-10-09

    The assessment of tumor radiosensitivity would be particularly useful in optimizing the radiation dose during radiotherapy. Therefore, the degree of correlation between radiation-induced DNA damage, as measured by the alkaline and the neutral comet assays, and the clonogenic survival of different human tumor cells was studied. Further, tumor radiosensitivity was compared with the expression of genes associated with the cellular response to radiation damage. Five different human tumor cell lines were chosen and the radiosensitivity of these cells was established by clonogenic assay. Alkaline and neutral comet assays were performed in γ-irradiated cells (2-8Gy; either acute or fractionated). Quantitative PCR was performed to evaluate the expression of DNA damage response genes in control and irradiated cells. The relative radiosensitivity of the cell lines assessed by the extent of DNA damage (neutral comet assay) immediately after irradiation (4Gy or 6Gy) was in agreement with radiosensitivity pattern obtained by the clonogenic assay. The survival fraction of irradiated cells showed a better correlation with the magnitude of DNA damage measured by the neutral comet assay (r=-0.9; Pcomet assay (r=-0.73; Pcomet assay was better than alkaline comet assay for assessment of radiosensitivities of tumor cells after acute or fractionated doses of irradiation. © 2012 Elsevier B.V. All rights reserved.

  19. Occurrence of virulence genes associated with diarrheagenic Escherichia coli isolated from raw cow's milk from two commercial dairy farms in the Eastern Cape Province, South Africa.

    Science.gov (United States)

    Caine, Lesley-Anne; Nwodo, Uchechukwu U; Okoh, Anthony I; Ndip, Roland N; Green, Ezekiel

    2014-11-18

    Escherichia coli remains a public health concern worldwide as an organism that causes diarrhea and its reservoir in raw milk may play an important role in the survival and transport of pathogenic strains. Diarrheagenic E. coli strains are diverse food-borne pathogens and causes diarrhea with varying virulence in humans. We investigated the prevalence of pathogenic E. coli in raw milk from two commercial dairy farms. Four hundred raw milk samples, 200 from each dairy farm, were screened for the presence of fliCH7, eagR, ial, eagg, lt, and papC genes. In dairy farm A, 100 E. coli were identified based on culture, oxidase and Gram staining, while 88 isolates from dairy farm B were identified in the same manner. Gene detection showed fliCH7 27 (54%) to be the highest gene detected from farm A and lt 2 (4%) to be the lowest. The highest gene detected in dairy farm B was fliCH7 16 (43.2%) and papC 1 (2.7%) was the least. The amplification of pathogenic genes associated with diarrheagenic E. coli from cows' raw milk demonstrates that potentially virulent E. coli strains are widely distributed in raw milk and may be a cause of concern for human health.

  20. Occurrence of Virulence Genes Associated with Diarrheagenic Escherichia coli Isolated from Raw Cow’s Milk from Two Commercial Dairy Farms in the Eastern Cape Province, South Africa

    Directory of Open Access Journals (Sweden)

    Lesley-Anne Caine

    2014-11-01

    Full Text Available Escherichia coli remains a public health concern worldwide as an organism that causes diarrhea and its reservoir in raw milk may play an important role in the survival and transport of pathogenic strains. Diarrheagenic E. coli strains are diverse food-borne pathogens and causes diarrhea with varying virulence in humans. We investigated the prevalence of pathogenic E. coli in raw milk from two commercial dairy farms. Four hundred raw milk samples, 200 from each dairy farm, were screened for the presence of fliCH7, eagR, ial, eagg, lt, and papC genes. In dairy farm A, 100 E. coli were identified based on culture, oxidase and Gram staining, while 88 isolates from dairy farm B were identified in the same manner. Gene detection showed fliCH7 27 (54% to be the highest gene detected from farm A and lt 2 (4% to be the lowest. The highest gene detected in dairy farm B was fliCH7 16 (43.2% and papC 1 (2.7% was the least. The amplification of pathogenic genes associated with diarrheagenic E. coli from cows’ raw milk demonstrates that potentially virulent E. coli strains are widely distributed in raw milk and may be a cause of concern for human health.

  1. Genome-Wide Analysis Identifies IL-18 and FUCA2 as Novel Genes Associated with Diastolic Function in African Americans with Sickle Cell Disease.

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    Julio D Duarte

    Full Text Available Diastolic dysfunction is common in sickle cell disease (SCD, and is associated with an increased risk of mortality. However, the molecular pathogenesis underlying this development is poorly understood. The aim of this study was to identify a gene expression profile that is associated with diastolic function in SCD, potentially elucidating molecular mechanisms behind diastolic dysfunction development.Diastolic function was measured via echocardiography in 65 patients with SCD from two independent study populations. Gene expression microarray data was compared with diastolic function in both study cohorts. Candidate genes that associated in both analyses were tested for validation in a murine SCD model. Lastly, genotyping array data from the replication cohort was used to derive cis-expression quantitative trait loci (cis-eQTLs and genetic associations within the candidate gene regions.Transcriptome data from both patient cohorts implicated 7 genes associated with diastolic function, and mouse SCD myocardial expression validated 3 of these genes. Genetic associations and eQTLs were detected in 2 of the 3 genes, FUCA2 and IL18.FUCA2 and IL18 are associated with diastolic function in SCD patients, and may be involved in the pathogenesis of the disease. Genetic polymorphisms within the FUCA2 and IL18 gene regions are also associated with diastolic function in SCD, likely by affecting expression levels of the genes.

  2. Molecular pathology in adult gliomas: diagnostic, prognostic, and predictive markers.

    LENUS (Irish Health Repository)

    Jansen, Michael

    2010-07-01

    Over the past 10 years, there has been an increasing use of molecular markers in the assessment and management of adult malignant gliomas. Some molecular signatures are used diagnostically to help pathologists classify tumours, whereas others are used to estimate prognosis for patients. Most crucial, however, are those markers that are used to predict response to certain therapies, thereby directing clinicians to a particular treatment while avoiding other potentially deleterious therapies. Recently, large-scale genome-wide surveys have been used to identify new biomarkers that have been rapidly developed as diagnostic and prognostic tools. Given these developments, the pace of discovery of new molecular assays will quicken to facilitate personalised medicine in the setting of malignant glioma.

  3. The Japanese Keigo Verbal Marker

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    Ely Triasih Rahayu

    2013-07-01

    Full Text Available This research studies Japanese keigo in the office domain, a case study at XXX Corporation Japan. Keigo consists of sonkeigo, kenjougo, and teineigo. Each of those speech levels is going to be analyzed based on linguistic and nonlinguistic factors. In this qualitative research, the data are in form of natural conversations gained by using several techniques such as recording, observation, and interview. Natural conversations were obtained through the recording process done with a tape recorder at XXX Corporation. There were 20 respondents coming from business fields to fill in the questionnaire and five informants for the interview.This research shows that keigo has lexical, morphological, and syntactical verbal markers. There are some nonlinguistic factors influencing the implementation of keigo in the office domain, especially the position gap and age.

  4. Molecular Markers for Food Traceability

    Directory of Open Access Journals (Sweden)

    Paula Martins-Lopes

    2013-01-01

    Full Text Available DNA analysis with molecular markers has opened a way to understand complex organism's genome. It is presently being widely applied across different fields, where food takes a preeminent position. Constant outbreaks of foodborne illnesses are increasing consumer's attention towards more detailed information related to what they are consuming. This overview reports on the areas where food traceability has been considered, and the problems that still remain to be bypassed in order to be widely applied. An outline of the most broadly used PCR-based methods for food traceability is described. Applications in the area of detection of genetically modified organisms, protected denomination of origin, allergenic and intolerance reactions are detailed in order to understand the dimension of the performed studies.

  5. DNA markers in plant improvement: an overview.

    Science.gov (United States)

    Kumar, L S

    1999-09-01

    The progress made in DNA marker technology has been tremendous and exciting. DNA markers have provided valuable tools in various analyses ranging from phylogenetic analysis to the positional cloning of genes. The development of high-density molecular maps which has been facilitated by PCR-based markers, have made the mapping and tagging of almost any trait possible. Marker-assisted selection has the potential to deploy favorable gene combinations for disease control. Comparative studies between incompatible species using these markers has resulted in synteny maps which are useful not only in predicting genome organization and evolution but also have practical application in plant breeding. DNA marker technology has found application in fingerprinting genotypes, in determining seed purity, in systematic sampling of germplasm, and in phylogenetic analysis. This review discusses the use of this technology for the genetic improvement of plants.

  6. Genetic determinants of the ankle-brachial index : A meta-analysis of a cardiovascular candidate gene 50K SNP panel in the candidate gene association resource (CARe) consortium

    NARCIS (Netherlands)

    Wassel, Christina L.; Lamina, Claudia; Nambi, Vijay; Coassin, Stefan; Mukamal, Kenneth J.; Ganesh, Santhi K.; Jacobs, David R.; Franceschini, Nora; Papanicolaou, George J.; Gibson, Quince; Yanek, Lisa R.; van der Harst, Pim; Ferguson, Jane F.; Crawford, Dana C.; Waite, Lindsay L.; Allison, Matthew A.; Criqui, Michael H.; McDermott, Mary M.; Mehra, Reena; Cupples, L. Adrienne; Hwang, Shih-Jen; Redline, Susan; Kaplan, Robert C.; Heiss, Gerardo; Rotter, Jerome I.; Boerwinkle, Eric; Taylor, Herman A.; Eraso, Luis H.; Haun, Margot; Li, Mingyao; Meisinger, Christa; O'Connell, Jeffrey R.; Shuldineri, Alan R.; Tybjaerg-Hansen, Anne; Frikke-Schmidt, Ruth; Kollerits, Barbara; Rantner, Barbara; Dieplinger, Benjamin; Stadler, Marietta; Mueller, Thomas; Haltmayer, Meinhard; Klein-Weigel, Peter; Summerer, Monika; Wichmann, H. -Erich; Asselbergs, Folkert W.; Navis, Gerjan; Mateo Leach, Irene; Brown-Gentry, Kristin; Goodloe, Robert; Assimes, Themistocles L.; Becker, Diane M.; Cooke, John P.; Absher, Devin M.; Olin, Jeffrey W.; Mitchell, Braxton D.; Reilly, Muredach P.; Mohler, Emile R.; North, Kari E.; Reiner, Alexander P.; Kronenberg, Florian; Murabito, Joanne M.

    Background: Candidate gene association studies for peripheral artery disease (PAD), including subclinical disease assessed with the ankle-brachial index (ABI), have been limited by the modest number of genes examined. We conducted a two stage meta-analysis of similar to 50,000 SNPs across similar to

  7. Scaling down

    Directory of Open Access Journals (Sweden)

    Ronald L Breiger

    2015-11-01

    Full Text Available While “scaling up” is a lively topic in network science and Big Data analysis today, my purpose in this essay is to articulate an alternative problem, that of “scaling down,” which I believe will also require increased attention in coming years. “Scaling down” is the problem of how macro-level features of Big Data affect, shape, and evoke lower-level features and processes. I identify four aspects of this problem: the extent to which findings from studies of Facebook and other Big-Data platforms apply to human behavior at the scale of church suppers and department politics where we spend much of our lives; the extent to which the mathematics of scaling might be consistent with behavioral principles, moving beyond a “universal” theory of networks to the study of variation within and between networks; and how a large social field, including its history and culture, shapes the typical representations, interactions, and strategies at local levels in a text or social network.

  8. Elevated tumour marker: an indication for imaging?

    LENUS (Irish Health Repository)

    McMahon, Colm J

    2012-02-01

    INTRODUCTION: The purpose of this study was to evaluate the utility of imaging examinations in patients with elevated tumour markers when (a) the tumour marker is not validated for as a primary diagnostic test; (b) the patient had no personal history of cancer and (c) the patient had no other imaging indication. MATERIALS AND METHODS: Patients without known cancer who had abnormal carcinoembryonic antigen, CA19-9, CA125 and\\/or CA15-3 serology over a one-year period were included. A retrospective medical record review was performed to assess the number of these cases who underwent imaging because of \\'elevated tumour marker\\' in the absence of a clinical indication for imaging. The number and result of these imaging studies were evaluated. RESULTS: Eight hundred and nineteen patients were included. Of those, 25 patients (mean age: 67.8 [range 41-91] y), were imaged to evaluate: \\'elevated tumour marker\\'. They underwent 29 imaging studies (mean [+\\/-standard deviation (SD)] per patient = 1.2 [+\\/-0.4]), and had 42 elevated tumour marker serology tests (mean [+\\/-SD] per patient = 1.7 [+\\/-0.7]). Four patients had >1 imaging test. No patient had an imaging study which diagnosed a malignancy or explained the elevated tumour marker. CONCLUSION: The non-judicious use of tumour markers can prompt further unnecessary investigations including imaging. In this study, there was no positive diagnostic yield for imaging performed for investigation of \\'elevated tumour marker\\'. \\'Elevated tumour marker\\

  9. Candidate gene association mapping of Sclerotinia stalk rot resistance in sunflower (Helianthus annuus L.) uncovers the importance of COI1 homologs.

    Science.gov (United States)

    Talukder, Zahirul I; Hulke, Brent S; Qi, Lili; Scheffler, Brian E; Pegadaraju, Venkatramana; McPhee, Kevin; Gulya, Thomas J

    2014-01-01

    Functional markers for Sclerotinia basal stalk rot resistance in sunflower were obtained using gene-level information from the model species Arabidopsis thaliana. Sclerotinia stalk rot, caused by Sclerotinia sclerotiorum, is one of the most destructive diseases of sunflower (Helianthus annuus L.) worldwide. Markers for genes controlling resistance to S. sclerotiorum will enable efficient marker-assisted selection (MAS). We sequenced eight candidate genes homologous to Arabidopsis thaliana defense genes known to be associated with Sclerotinia disease resistance in a sunflower association mapping population evaluated for Sclerotinia stalk rot resistance. The total candidate gene sequence regions covered a concatenated length of 3,791 bp per individual. A total of 187 polymorphic sites were detected for all candidate gene sequences, 149 of which were single nucleotide polymorphisms (SNPs) and 38 were insertions/deletions. Eight SNPs in the coding regions led to changes in amino acid codons. Linkage disequilibrium decay throughout the candidate gene regions declined on average to an r (2) = 0.2 for genetic intervals of 120 bp, but extended up to 350 bp with r (2) = 0.1. A general linear model with modification to account for population structure was found the best fitting model for this population and was used for association mapping. Both HaCOI1-1 and HaCOI1-2 were found to be strongly associated with Sclerotinia stalk rot resistance and explained 7.4 % of phenotypic variation in this population. These SNP markers associated with Sclerotinia stalk rot resistance can potentially be applied to the selection of favorable genotypes, which will significantly improve the efficiency of MAS during the development of stalk rot resistant cultivars.

  10. Scaling Rules!

    Science.gov (United States)

    Malkinson, Dan; Wittenberg, Lea

    2015-04-01

    Scaling is a fundamental issue in any spatially or temporally hierarchical system. Defining domains and identifying the boundaries of the hierarchical levels may be a challenging task. Hierarchical systems may be broadly classified to two categories: compartmental and continuous ones. Examples of compartmental systems include: governments, companies, computerized networks, biological taxonomy and others. In such systems the compartments, and hence the various levels and their constituents are easily delineated. In contrast, in continuous systems, such as geomorphological, ecological or climatological ones, detecting the boundaries of the various levels may be difficult. We propose that in continuous hierarchical systems a transition from one functional scale to another is associated with increased system variance. Crossing from a domain of one scale to the domain of another is associated with a transition or substitution of the dominant drivers operating in the system. Accordingly we suggest that crossing this boundary is characterized by increased variance, or a "variance leap", which stabilizes, until crossing to the next domain or hierarchy level. To assess this we compiled sediment yield data from studies conducted at various spatial scales and from different environments. The studies were partitioned to ones conducted in undisturbed environments, and those conducted in disturbed environments, specifically by wildfires. The studies were conducted in plots as small as 1 m2, and watersheds larger than 555000 ha. Regressing sediment yield against plot size, and incrementally calculating the variance in the systems, enabled us to detect domains where variance values were exceedingly high. We propose that at these domains scale-crossing occurs, and the systems transition from one hierarchical level to another. Moreover, the degree of the "variance leaps" characterizes the degree of connectivity among the scales.

  11. Combined analysis of murine and human microarrays and ChIP analysis reveals genes associated with the ability of MYC to maintain tumorigenesis.

    Directory of Open Access Journals (Sweden)

    Chi-Hwa Wu

    2008-06-01

    Full Text Available The MYC oncogene has been implicated in the regulation of up to thousands of genes involved in many cellular programs including proliferation, growth, differentiation, self-renewal, and apoptosis. MYC is thought to induce cancer through an exaggerated effect on these physiologic programs. Which of these genes are responsible for the ability of MYC to initiate and/or maintain tumorigenesis is not clear. Previously, we have shown that upon brief MYC inactivation, some tumors undergo sustained regression. Here we demonstrate that upon MYC inactivation there are global permanent changes in gene expression detected by microarray analysis. By applying StepMiner analysis, we identified genes whose expression most strongly correlated with the ability of MYC to induce a neoplastic state. Notably, genes were identified that exhibited permanent changes in mRNA expression upon MYC inactivation. Importantly, permanent changes in gene expression could be shown by chromatin immunoprecipitation (ChIP to be associated with permanent changes in the ability of MYC to bind to the promoter regions. Our list of candidate genes associated with tumor maintenance was further refined by comparing our analysis with other published results to generate a gene signature associated with MYC-induced tumorigenesis in mice. To validate the role of gene signatures associated with MYC in human tumorigenesis, we examined the expression of human homologs in 273 published human lymphoma microarray datasets in Affymetrix U133A format. One large functional group of these genes included the ribosomal structural proteins. In addition, we identified a group of genes involved in a diverse array of cellular functions including: BZW2, H2AFY, SFRS3, NAP1L1, NOLA2, UBE2D2, CCNG1, LIFR, FABP3, and EDG1. Hence, through our analysis of gene expression in murine tumor models and human lymphomas, we have identified a novel gene signature correlated with the ability of MYC to maintain tumorigenesis.

  12. Physiological performance and differential expression profiling of genes associated with drought tolerance in root tissue of four contrasting varieties of two Gossypium species.

    Science.gov (United States)

    Singh, Ruchi; Pandey, Neha; Kumar, Anil; Shirke, Pramod A

    2016-01-01

    Root growth in drying soil is generally limited by a combination of mechanical impedance and water stress. As the major function of root tissue is water and nutrient uptake, so it imparts an important role in plant growth and stress management. Previously, we have studied physiological performance and expression profiling of gene associated with drought tolerance in leaf tissue of four cotton varieties. Here, we have further continued our studies with the root tissue of these varieties. The Gossypium hirsutum species JKC-770 is drought-tolerant and KC-2 is drought-sensitive, while Gossypium herbaceum species JKC-717 is drought-tolerant and RAHS-187 is drought-sensitive. JKC-770 and JKC-717 the drought-tolerant varieties showed a comparatively high glutathione-S-transferase, superoxide dismutase, proline along with their gene expression, and low malondialdehyde content indicating low membrane damage and better antioxidative defense under drought condition. The expression levels of cellulose synthase, xyloglucan:xyloglucosyl transferase, and glycosyl hydrolases suggest modulation in cell wall structure and partitioning of sugars towards osmoprotectants instead of cell wall biosynthesis in tolerant varieties. Heat shock proteins and serine/threonine protein phosphotases show upregulation under drought condition, which are responsible for temperature tolerance and protein phosphorylation, respectively. These effects many metabolic processes and may be playing a key role in drought tolerance and adaptability of JKC-770 towards drought tolerance. The long-term water use efficiency (WUE) estimated in terms of carbon isotope discrimination (∆(13)C) in the root tissues showed maximum depletion in the ∆(13)C values in JKC-770 variety, while minimum in RAHS-187 under drought stress with reference to their respective control, suggesting a high WUE in JKC-770 variety.

  13. Natural Cubic Spline Regression Modeling Followed by Dynamic Network Reconstruction for the Identification of Radiation-Sensitivity Gene Association Networks from Time-Course Transcriptome Data.

    Science.gov (United States)

    Michna, Agata; Braselmann, Herbert; Selmansberger, Martin; Dietz, Anne; Hess, Julia; Gomolka, Maria; Hornhardt, Sabine; Blüthgen, Nils; Zitzelsberger, Horst; Unger, Kristian

    2016-01-01

    Gene expression time-course experiments allow to study the dynamics of transcriptomic changes in cells exposed to different stimuli. However, most approaches for the reconstruction of gene association networks (GANs) do not propose prior-selection approaches tailored to time-course transcriptome data. Here, we present a workflow for the identification of GANs from time-course data using prior selection of genes differentially expressed over time identified by natural cubic spline regression modeling (NCSRM). The workflow comprises three major steps: 1) the identification of differentially expressed genes from time-course expression data by employing NCSRM, 2) the use of regularized dynamic partial correlation as implemented in GeneNet to infer GANs from differentially expressed genes and 3) the identification and functional characterization of the key nodes in the reconstructed networks. The approach was applied on a time-resolved transcriptome data set of radiation-perturbed cell culture models of non-tumor cells with normal and increased radiation sensitivity. NCSRM detected significantly more genes than another commonly used method for time-course transcriptome analysis (BETR). While most genes detected with BETR were also detected with NCSRM the false-detection rate of NCSRM was low (3%). The GANs reconstructed from genes detected with NCSRM showed a better overlap with the interactome network Reactome compared to GANs derived from BETR detected genes. After exposure to 1 Gy the normal sensitive cells showed only sparse response compared to cells with increased sensitivity, which exhibited a strong response mainly of genes related to the senescence pathway. After exposure to 10 Gy the response of the normal sensitive cells was mainly associated with senescence and that of cells with increased sensitivity with apoptosis. We discuss these results in a clinical context and underline the impact of senescence-associated pathways in acute radiation response of normal

  14. FAR1 and FAR2 regulate the expression of genes associated with lipid metabolism in the rice blast fungus Magnaporthe oryzae.

    Directory of Open Access Journals (Sweden)

    Mohammad Termizi bin Yusof

    Full Text Available The rice blast fungus Magnaporthe oryzae causes plant disease via specialised infection structures called appressoria. These dome-shaped cells are able to generate enormous internal pressure, which enables penetration of rice tissue by invasive hyphae. Previous studies have shown that mobilisation of lipid bodies and subsequent lipid metabolism are essential pre-requisites for successful appressorium-mediated plant infection, which requires autophagic recycling of the contents of germinated spores and germ tubes to the developing appressorium. Here, we set out to identify putative regulators of lipid metabolism in the rice blast fungus. We report the identification of FAR1 and FAR2, which encode highly conserved members of the Zn2-Cys6 family of transcriptional regulators. We generated Δfar1, Δfar2 and Δfar1Δfar2 double mutants in M. oryzae and show that these deletion mutants are deficient in growth on long chain fatty acids. In addition, Δfar2 mutants are also unable to grow on acetate and short chain fatty acids. FAR1 and FAR2 are necessary for differential expression of genes involved in fatty acid β-oxidation, acetyl-CoA translocation, peroxisomal biogenesis, and the glyoxylate cycle in response to the presence of lipids. Furthermore, FAR2 is necessary for expression of genes associated with acetyl-CoA synthesis. Interestingly, Δfar1, Δfar2 and Δfar1Δfar2 mutants show no observable delay or reduction in lipid body mobilisation during plant infection, suggesting that these transcriptional regulators control lipid substrate utilization by the fungus but not the mobilisation of intracellular lipid reserves during infection-related morphogenesis.

  15. Using diverse U.S. beef cattle genomes to identify missense mutations in EPAS1, a gene associated with pulmonary hypertension [version 2; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Michael P. Heaton

    2016-10-01

    Full Text Available The availability of whole genome sequence (WGS data has made it possible to discover protein variants in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in global beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene (EPAS1, a gene associated with pulmonary hypertension in Angus cattle. The identity and quality of genomic sequences were verified by comparing WGS genotypes to those derived from other methods. The average read depth, genotype scoring rate, and genotype accuracy exceeded 14, 99%, and 99%, respectively. The 96 genomes were used to discover four amino acid variants encoded by EPAS1 (E270Q, P362L, A671G, and L701F and confirm two variants previously associated with disease (A606T and G610S. The six EPAS1 missense mutations were verified with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assays, and their frequencies were estimated in a separate collection of 1154 U.S. cattle representing 46 breeds. A rooted phylogenetic tree of eight polypeptide sequences provided a framework for evaluating the likely order of mutations and potential impact of EPAS1 alleles on the adaptive response to chronic hypoxia in U.S. cattle. This public, whole genome resource facilitates in silico identification of protein variants in diverse types of U.S. beef cattle, and provides a means of translating WGS data into a practical biological and evolutionary context for generating and testing hypotheses.

  16. Transcriptome Analysis of the Intracellular Facultative Pathogen Piscirickettsia salmonis: Expression of Putative Groups of Genes Associated with Virulence and Iron Metabolism.

    Directory of Open Access Journals (Sweden)

    Alvaro Machuca

    Full Text Available The intracellular facultative bacteria Piscirickettsia salmonis is one of the most important pathogens of the Chilean aquaculture. However, there is a lack of information regarding the whole genomic transcriptional response according to different extracellular environments. We used next generation sequencing (NGS of RNA (RNA-seq to study the whole transcriptome of an isolate of P. salmonis (FAVET-INBIOGEN using a cell line culture and a modified cell-free liquid medium, with or without iron supplementation. This was done in order to obtain information about the factors there are involved in virulence and iron acquisition. First, the isolate was grown in the Sf21 cell line; then, the bacteria were cultured into a cell-free liquid medium supplemented or not with iron. We identified in the transcriptome, genes associated with type IV secretion systems, genes related to flagellar structure assembly, several proteases and sigma factors, and genes related to the development of drug resistance. Additionally, we identified for the first time several iron-metabolism associated genes including at least two iron uptake pathways (ferrous iron and ferric iron uptake that are actually expressed in the different conditions analyzed. We further describe putative genes that are related with the use and storage of iron in the bacteria, which have not been previously described. Several sets of genes related to virulence were expressed in both the cell line and cell-free culture media (for example those related to flagellar structure; such as basal body, MS-ring, C-ring, proximal and distal rod, and filament, which may play roles in other basic processes rather than been restricted to virulence.

  17. Immune signature of metastatic breast cancer: Identifying predictive markers of immunotherapy response.

    Science.gov (United States)

    Kim, Ji-Yeon; Lee, Eunjin; Park, Kyunghee; Park, Woong-Yang; Jung, Hae Hyun; Ahn, Jin Seok; Im, Young-Hyuck; Park, Yeon Hee

    2017-07-18

    In breast cancer (BC), up to 10-20% patients were known to have clinical benefit with immune checkpoint inhibitors, and biomarkers are needed for optimal use of this multi-potential therapeutic strategy. Accordingly, we conducted an experiment to identify expression of genes associated with immune checkpoints that represent potential targets of cancer immunotherapy. We performed whole-transcriptome sequencing and whole-exome sequencing using 37 refractory BC specimens. In the immune pathway gene set expression analysis, we found that HER2 expression and previous taxane treatment were positively correlated with high expression of immune gene set expression (p = 0.070 and 0.008, respectively). The nine genes associated with immune checkpoints - PDCD1(PD-1), CD274(PD-L1), CD276(B7-H3), CTLA-4, IDO1, LAG3, VTCN1, HAVCR2, and TNFRSF4(OX40) - interacted with each other. In addition, HER2 expression also affected the expression levels of these genes (p = 0.044). Lastly, expression of immune checkpoint genes and tissue-infiltrating lymphocytes were positively correlated in metastatic BCs (p immune checkpoint genes and immune pathway gene sets. Further study of the BC immune signature with large-scale, translational data sets is warranted.

  18. Stereotactic core needle breast biopsy marker migration: An analysis of factors contributing to immediate marker migration.

    Science.gov (United States)

    Jain, Ashali; Khalid, Maria; Qureshi, Muhammad M; Georgian-Smith, Dianne; Kaplan, Jonah A; Buch, Karen; Grinstaff, Mark W; Hirsch, Ariel E; Hines, Neely L; Anderson, Stephan W; Gallagher, Katherine M; Bates, David D B; Bloch, B Nicolas

    2017-11-01

    To evaluate breast biopsy marker migration in stereotactic core needle biopsy procedures and identify contributing factors. This retrospective study analyzed 268 stereotactic biopsy markers placed in 263 consecutive patients undergoing stereotactic biopsies using 9G vacuum-assisted devices from August 2010-July 2013. Mammograms were reviewed and factors contributing to marker migration were evaluated. Basic descriptive statistics were calculated and comparisons were performed based on radiographically-confirmed marker migration. Of the 268 placed stereotactic biopsy markers, 35 (13.1%) migrated ≥1 cm from their biopsy cavity. Range: 1-6 cm; mean (± SD): 2.35 ± 1.22 cm. Of the 35 migrated biopsy markers, 9 (25.7%) migrated ≥3.5 cm. Patient age, biopsy pathology, number of cores, and left versus right breast were not associated with migration status (P> 0.10). Global fatty breast density (P= 0.025) and biopsy in the inner region of breast (P = 0.031) were associated with marker migration. Superior biopsy approach (P= 0.025), locally heterogeneous breast density, and t-shaped biopsy markers (P= 0.035) were significant for no marker migration. Multiple factors were found to influence marker migration. An overall migration rate of 13% supports endeavors of research groups actively developing new biopsy marker designs for improved resistance to migration. • Breast biopsy marker migration is documented in 13% of 268 procedures. • Marker migration is affected by physical, biological, and pathological factors. • Breast density, marker shape, needle approach etc. affect migration. • Study demonstrates marker migration prevalence; marker design improvements are needed.

  19. Fiducial marker for correlating images

    Science.gov (United States)

    Miller, Lisa Marie [Rocky Point, NY; Smith, Randy J [Wading River, NY; Warren, John B [Port Jefferson, NY; Elliott, Donald [Hampton Bays, NY

    2011-06-21

    The invention relates to a fiducial marker having a marking grid that is used to correlate and view images produced by different imaging modalities or different imaging and viewing modalities. More specifically, the invention relates to the fiducial marking grid that has a grid pattern for producing either a viewing image and/or a first analytical image that can be overlaid with at least one other second analytical image in order to view a light path or to image different imaging modalities. Depending on the analysis, the grid pattern has a single layer of a certain thickness or at least two layers of certain thicknesses. In either case, the grid pattern is imageable by each imaging or viewing modality used in the analysis. Further, when viewing a light path, the light path of the analytical modality cannot be visualized by viewing modality (e.g., a light microscope objective). By correlating these images, the ability to analyze a thin sample that is, for example, biological in nature but yet contains trace metal ions is enhanced. Specifically, it is desired to analyze both the organic matter of the biological sample and the trace metal ions contained within the biological sample without adding or using extrinsic labels or stains.

  20. Syntactical Marker {-Nya} In Indonesian

    Directory of Open Access Journals (Sweden)

    I Nyoman Sedeng

    2015-10-01

    Full Text Available This study discusses the syntactic marker {-nya} in Indonesian, and aims at finding the answers to the three research questions; (i what hosts can be appended by {-nya},(iiwhat syntactic functions can be filled by {-nya}, and (iii what is the meaning of {-nya}contextually. The data to support the analysis was collected from the source with the help of a data collection tool [antconc3.2.1w window2007]. Two theories are relevant to the discussion of {-nya}, namely; morphosyntactic theory that searched the occurrence of {-nya} in a text and discourse theory to discover the meaning of {-nya} contextually. The result of analysis showed three occurrence of {-nya}; pronoun clitics, determiner, and as adverbial formation. As a core argument {-nya} can be attached to the nasal verbs, passive verbs, zero intransitive verbs, and category of nouns, prepositions, and reflexive pronouns. As adverbial formation {-nya} is attached to the adjective, bound root, and is combined with {se-} to form confix {se-baik-nya}. As pronoun, {-nya} can serve as; Grammatical Subjects and Objects, Possessive determiner, Oblique Agent, Reflexive pronoun. As determiner it is always attached to the noun, forming nouns from verbs, and as an adverbial it can serve as an adjunct, conjunct, and disjunct. The meaning of {-nya} with pronominal category should be traced in the text and always refers to the third person singular.

  1. Efficient marker data utilization in genomic prediction

    DEFF Research Database (Denmark)

    Edriss, Vahid

    of editing marker data, methods to handle missing genotypes and prediction using haplotypes constructed with an advanced method. The results of this study show that the accuracy of genomc prediction increases by: optimal criteria for marker data editing parameters, proper handling of missing genotypes using...

  2. Molecular marker analysis of 'Shatangju' and 'Wuzishatangju ...

    African Journals Online (AJOL)

    ARL4

    Citrus assisted-selection breeding, genetic diversity analysis, population genetics and molecular evolutionary genetics (Wang et al., 2000; Gong et al., 2008). Molecular marker techniques are new types of genetic markers and have greatly promoted Citrus breeding as a whole. Currently, random amplified polymorphic DNA.

  3. (L.) Dunal using RAPD and AFLP markers

    African Journals Online (AJOL)

    A strong correlation was observed between morphology and molecular marker systems. Identification of specific markers to wild as well as cultivated accessions is yet another important finding in the present study. Such genetic diversity is useful in facilitating the development of large number of new varieties through ...

  4. Characterization of novel polymorphic microsatellite markers from ...

    Indian Academy of Sciences (India)

    ysis, marker-assist selective breeding in fisheries animals. ∗For correspondence. E-mail: Xiuliwang417@sina.com. and linkage mapping (Jackson et al. 2003). Traditionally, microsatellite markers were expensive to develop. However, expressed sequence tags (ESTs) were explored as a new source of microsatellite ...

  5. European side markers effect on traffic safety

    NARCIS (Netherlands)

    Roelfsema, A.; Theeuwes, J.; Alferdinck, J.W.A.M

    1999-01-01

    In 1993 new European legislation regarding side-markers for passenger cars became effective. Volvo requested the TNO-Human Factors Research Institute (HFRI) to investigate the possible safety benefit of this European side-markers configuration. A test panel at TNO- HFRI was used to determine the

  6. (L.) Dunal using RAPD and AFLP markers

    African Journals Online (AJOL)

    ajl yemi

    2011-10-26

    Oct 26, 2011 ... PCO generated using UPGMA (3D view). et al., 2003). A high degree of correlation between marker systems has also been reported in wheat and safflower (Bohn et al., 1999). However, Powell et al. (1996) observed little correlation between various marker systems in soybean. The incongruity between ...

  7. High-throughput retrotransposon-based fluorescent markers: improved information content and allele discrimination

    Directory of Open Access Journals (Sweden)

    Baker David

    2009-07-01

    Full Text Available Abstract Background Dense genetic maps, together with the efficiency and accuracy of their construction, are integral to genetic studies and marker assisted selection for plant breeding. High-throughput multiplex markers that are robust and reproducible can contribute to both efficiency and accuracy. Multiplex markers are often dominant and so have low information content, this coupled with the pressure to find alternatives to radio-labelling, has led us to adapt the SSAP (sequence specific amplified polymorphism marker method from a 33P labelling procedure to fluorescently tagged markers analysed from an automated ABI 3730 xl platform. This method is illustrated for multiplexed SSAP markers based on retrotransposon insertions of pea and is applicable for the rapid and efficient generation of markers from genomes where repetitive element sequence information is available for primer design. We cross-reference SSAP markers previously generated using the 33P manual PAGE system to fluorescent peaks, and use these high-throughput fluorescent SSAP markers for further genetic studies in Pisum. Results The optimal conditions for the fluorescent-labelling method used a triplex set of primers in the PCR. These included a fluorescently labelled specific primer together with its unlabelled counterpart, plus an adapter-based primer with two bases of selection on the 3' end. The introduction of the unlabelled specific primer helped to optimise the fluorescent signal across the range of fragment sizes expected, and eliminated the need for extensive dilutions of PCR amplicons. The software (GeneMarker Version 1.6 used for the high-throughput data analysis provided an assessment of amplicon size in nucleotides, peak areas and fluorescence intensity in a table format, so providing additional information content for each marker. The method has been tested in a small-scale study with 12 pea accessions resulting in 467 polymorphic fluorescent SSAP markers of which

  8. Nuclear scales

    Energy Technology Data Exchange (ETDEWEB)

    Friar, J.L.

    1998-12-01

    Nuclear scales are discussed from the nuclear physics viewpoint. The conventional nuclear potential is characterized as a black box that interpolates nucleon-nucleon (NN) data, while being constrained by the best possible theoretical input. The latter consists of the longer-range parts of the NN force (e.g., OPEP, TPEP, the {pi}-{gamma} force), which can be calculated using chiral perturbation theory and gauged using modern phase-shift analyses. The shorter-range parts of the force are effectively parameterized by moments of the interaction that are independent of the details of the force model, in analogy to chiral perturbation theory. Results of GFMC calculations in light nuclei are interpreted in terms of fundamental scales, which are in good agreement with expectations from chiral effective field theories. Problems with spin-orbit-type observables are noted.

  9. Markers of assimilation of problematic experiences in dementia within the LivDem project.

    Science.gov (United States)

    Cheston, Richard; Gatting, Lauren; Marshall, Ann; Spreadbury, John H; Coleman, Peter

    2017-05-01

    This study aimed to determine whether the Markers of Assimilation of Problematic Experiences in Dementia scale (MAPED) can be used to identify whether the way in which participants talk about dementia changed during the group. All eight sessions of a LivDem group, which were attended by participants were recorded and transcribed. An initial analysis identified 160 extracts, which were then rated using the MAPED system. Inter-rater reliability was 61% and following a resolution meeting, 35 extracts were discarded, leaving 125 extracts with an agreed marker code. All of the participants were identified as producing a speech marker relating to dementia, and these varied between 0 (warding off) to 6 (problem solution). Examples of these markers are provided. The proportion of emergence markers (indicating the initial stages of assimilation) compared to later markers changed significantly between the first four sessions and the final sessions. This difference was still significant even when the markers produced by the most verbal participant, Graham, were excluded. The use of process measures within psychotherapy complements more conventional outcome measures and has both theoretical and clinical implications.

  10. Methods comparison for microsatellite marker development: Different isolation methods, different yield efficiency

    Science.gov (United States)

    Zhan, Aibin; Bao, Zhenmin; Hu, Xiaoli; Lu, Wei; Hu, Jingjie

    2009-06-01

    Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology, quantitative genetics and genomics. Therefore, it is extremely necessary to select several versatile, low-cost, efficient and time- and labor-saving methods to develop a large panel of microsatellite markers. In this study, we used Zhikong scallop ( Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency, while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time- and cost-saving, it is difficult to obtain a large number of microsatellite markers, mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study, we recommend two methods, microsatellite-enriched library construction method and FIASCO-colony hybridization method, for large-scale microsatellite marker development. Both methods were derived from the microsatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.

  11. Markers of Early Vascular Ageing.

    Science.gov (United States)

    Kotsis, Vasilios; Antza, Christina; Doundoulakis, Ioannis; Stabouli, Stella

    2017-01-01

    Cardiovascular damage is clinically manifested as coronary artery disease, heart failure, stroke and peripheral artery disease. The prevalence of these adverse conditions is higher with advancing age. Although many patients present cardiovascular damage late in their life, it is common to see patients with early atherosclerosis in cardiovascular intensive care units at ages lower than 50 years in men and 55 for women. In this review of the literature we identified risk factors of early vascular damage. The classic risk factors such as age, gender, diabetes mellitus, dyslipidemia, smoking, alcohol, hypertension, obesity, family history and newer biomarkers such as hs-CRP, folic acid, homocysteine, fibrinogen are neither strong nor predictive of the individual patient's risk to present early cardiovascular disease. All these risk factors have been used to propose risk scores for possible future events but we still lack a single strong marker indicating new onset of disease that will predict the future independently of the classical factors. The role of vascular imaging techniques to identify patients with subclinical atherosclerotic vascular damage before clinical disease, including the effect of known and unknown risk factors on the vascular tree, seems to be very important for intensifying preventive measures in high risk patients. Early arteriosclerosis measured from pulse wave velocity is associated with reduced arterial elasticity and is associated with future cardiovascular events. Vascular measurements may better represent the continuum of cardiovascular disease from a young healthy to an aged diseased vessel that is going to produce adverse clinical events. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  12. Bone metabolism markers in sports medicine.

    Science.gov (United States)

    Banfi, Giuseppe; Lombardi, Giovanni; Colombini, Alessandra; Lippi, Giuseppe

    2010-08-01

    Bone mass can be viewed as the net product of two counteracting metabolic processes, bone formation and bone resorption, which allow the skeleton to carry out its principal functions: mechanical support of the body, calcium dynamic deposition and haemopoiesis. Besides radiological methods, several blood and urinary molecules have been identified as markers of bone metabolic activity for estimating the rates and direction of the biological activities governing bone turnover. The advantages for the use of bone metabolism markers are that they are potentially less dangerous than radiological determinations, are more sensitive to changes in bone metabolism than radiological methods and are easily collected and analysed. The disadvantages are that they have high biological variability. Physical exercise is a known source of bone turnover and is recommended for preventing osteoporosis and bone metabolism problems. There are numerous experiments on bone metabolism markers after acute exercise, but not after long-term training and during or after a whole competition season. Moreover, few studies on bone metabolism markers have evaluated their performance in elite and top-level athletes, who have a higher bone turnover than sedentary individuals. Despite discrepant results among studies, most have shown that short exercise is insufficient for modifying serum concentrations of bone metabolism markers. Marker variations are more evident after several hours or days after exercise, bone formation markers are more sensitive than bone resorption markers, and stimulation of osteoblast and/or osteoclast functions is exercise dependent but the response is not immediate. The response depends on the type of exercise; the markers seem to be less sensitive to resistance exercise and the intensity of exercise is not discriminate. Comparisons between trained subjects and untrained controls have demonstrated the influence of exercise on bone turnover. During training, carboxy

  13. The QT Scale: A Weight Scale Measuring the QTc Interval.

    Science.gov (United States)

    Couderc, Jean-Philippe; Beshaw, Connor; Niu, Xiaodan; Serrano-Finetti, Ernesto; Casas, Oscar; Pallas-Areny, Ramon; Rosero, Spencer; Zareba, Wojciech

    2017-01-01

    Despite the strong evidence of the clinical utility of QTc prolongation as a surrogate marker of cardiac risk, QTc measurement is not part of clinical routine either in hospital or in physician offices. We evaluated a novel device ("the QT scale") to measure heart rate (HR) and QTc interval. The QT scale is a weight scale embedding an ECG acquisition system with four limb sensors (feet and hands: lead I, II, and III). We evaluated the reliability of QT scale in healthy subjects (cohort 1) and cardiac patients (cohorts 2 and 3) considering a learning (cohort 2) and two validation cohorts. The QT scale and the standard 12-lead recorder were compared using intraclass correlation coefficient (ICC) in cohorts 2 and 3. Absolute value of heart rate and QTc intervals between manual and automatic measurements using ECGs from the QT scale and a clinical device were compared in cohort 1. We enrolled 16 subjects in cohort 1 (8 w, 8 m; 32 ± 8 vs 34 ± 10 years, P = 0.7), 51 patients in cohort 2 (13 w, 38 m; 61 ± 16 vs 58 ± 18 years, P = 0.6), and 13 AF patients in cohort 3 (4 w, 9 m; 63 ± 10 vs 64 ± 10 years, P = 0.9). Similar automatic heart rate and QTc were delivered by the scale and the clinical device in cohort 1: paired difference in RR and QTc were -7 ± 34 milliseconds (P = 0.37) and 3.4 ± 28.6 milliseconds (P = 0.64), respectively. The measurement of stability was slightly lower in ECG from the QT scale than from the clinical device (ICC: 91% vs 80%) in cohort 3. The "QT scale device" delivers valid heart rate and QTc interval measurements. © 2016 Wiley Periodicals, Inc.

  14. Gene expression markers in circulating tumor cells may predict bone metastasis and response to hormonal treatment in breast cancer.

    Science.gov (United States)

    Wang, Haiying; Molina, Julian; Jiang, John; Ferber, Matthew; Pruthi, Sandhya; Jatkoe, Timothy; Derecho, Carlo; Rajpurohit, Yashoda; Zheng, Jian; Wang, Yixin

    2013-11-01

    Circulating tumor cells (CTCs) have recently attracted attention due to their potential as prognostic and predictive markers for the clinical management of metastatic breast cancer patients. The isolation of CTCs from patients may enable the molecular characterization of these cells, which may help establish a minimally invasive assay for the prediction of metastasis and further optimization of treatment. Molecular markers of proven clinical value may therefore be useful in predicting disease aggressiveness and response to treatment. In our earlier study, we identified a gene signature in breast cancer that appears to be significantly associated with bone metastasis. Among the genes that constitute this signature, trefoil factor 1 (TFF1) was identified as the most differentially expressed gene associated with bone metastasis. In this study, we investigated 25 candidate gene markers in the CTCs of metastatic breast cancer patients with different metastatic sites. The panel of the 25 markers was investigated in 80 baseline samples (first blood draw of CTCs) and 30 follow-up samples. In addition, 40 healthy blood donors (HBDs) were analyzed as controls. The assay was performed using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) with RNA extracted from CTCs captured by the CellSearch system. Our study indicated that 12 of the genes were uniquely expressed in CTCs and 10 were highly expressed in the CTCs obtained from patients compared to those obtained from HBDs. Among these genes, the expression of keratin 19 was highly correlated with the CTC count. The TFF1 expression in CTCs was a strong predictor of bone metastasis and the patients with a high expression of estrogen receptor β in CTCs exhibited a better response to hormonal treatment. Molecular characterization of these genes in CTCs may provide a better understanding of the mechanism underlying tumor metastasis and identify gene markers in CTCs for predicting disease progression and

  15. Prevalence of Plasmodium falciparum Molecular Markers of Antimalarial Drug Resistance in a Residual Malaria Focus Area in Sabah, Malaysia.

    Directory of Open Access Journals (Sweden)

    Nor Azrina Norahmad

    Full Text Available Chloroquine (CQ and fansidar (sulphadoxine-pyrimethamine, SP were widely used for treatment of Plasmodium falciparum for several decades in Malaysia prior to the introduction of Artemisinin-based Combination Therapy (ACT in 2008. Our previous study in Kalabakan, located in south-east coast of Sabah showed a high prevalence of resistance to CQ and SP, suggesting the use of the treatment may no longer be effective in the area. This study aimed to provide a baseline data of antimalarial drug resistant markers on P. falciparum isolates in Kota Marudu located in the north-east coast of Sabah. Mutations on genes associated with CQ (pfcrt and pfmdr1 and SP (pfdhps and pfdhfr were assessed by PCR amplification and restriction fragment length polymorphism. Mutations on the kelch13 marker (K13 associated with artemisinin resistance were determined by DNA sequencing technique. The assessment of pfmdr1 copy number variation associated with mefloquine resistant was done by real-time PCR technique. A low prevalence (6.9% was indicated for both pfcrt K76T and pfmdr1 N86Y mutations. All P. falciparum isolates harboured the pfdhps A437G mutation. Prevalence of pfdhfr gene mutations, S108N and I164L, were 100% and 10.3%, respectively. Combining the different resistant markers, only two isolates were conferred to have CQ and SP treatment failure markers as they contained mutant alleles of pfcrt and pfmdr1 together with quintuple pfdhps/pfdhfr mutation (combination of pfdhps A437G+A581G and pfdhfr C59R+S108N+I164L. All P. falciparum isolates carried single copy number of pfmdr1 and wild type K13 marker. This study has demonstrated a low prevalence of CQ and SP resistance alleles in the study area. Continuous monitoring of antimalarial drug efficacy is warranted and the findings provide information for policy makers in ensuring a proper malaria control.

  16. Augmented Reality Marker Hiding with Texture Deformation.

    Science.gov (United States)

    Kawai, Norihiko; Sato, Tomokazu; Nakashima, Yuta; Yokoya, Naokazu

    2017-10-01

    Augmented reality (AR) marker hiding is a technique to visually remove AR markers in a real-time video stream. A conventional approach transforms a background image with a homography matrix calculated on the basis of a camera pose and overlays the transformed image on an AR marker region in a real-time frame, assuming that the AR marker is on a planar surface. However, this approach may cause discontinuities in textures around the boundary between the marker and its surrounding area when the planar surface assumption is not satisfied. This paper proposes a method for AR marker hiding without discontinuities around texture boundaries even under nonplanar background geometry without measuring it. For doing this, our method estimates the dense motion in the marker's background by analyzing the motion of sparse feature points around it, together with a smooth motion assumption, and deforms the background image according to it. Our experiments demonstrate the effectiveness of the proposed method in various environments with different background geometries and textures.

  17. Identification of Non-HLA Genes Associated with Celiac Disease and Country-Specific Differences in a Large, International Pediatric Cohort.

    Science.gov (United States)

    Sharma, Ashok; Liu, Xiang; Hadley, David; Hagopian, William; Liu, Edwin; Chen, Wei-Min; Onengut-Gumuscu, Suna; Simell, Ville; Rewers, Marian; Ziegler, Anette-G; Lernmark, Åke; Simell, Olli; Toppari, Jorma; Krischer, Jeffrey P; Akolkar, Beena; Rich, Stephen S; Agardh, Daniel; She, Jin-Xiong

    2016-01-01

    There are significant geographical differences in the prevalence and incidence of celiac disease that cannot be explained by HLA alone. More than 40 loci outside of the HLA region have been associated with celiac disease. We investigated the roles of these non-HLA genes in the development of tissue transglutaminase autoantibodies (tTGA) and celiac disease in a large international prospective cohort study. A total of 424,788 newborns from the US and European general populations and first-degree relatives with type 1 diabetes were screened for specific HLA genotypes. Of these, 21,589 carried 1 of the 9 HLA genotypes associated with increased risk for type 1 diabetes and celiac disease; we followed 8676 of the children in a 15 y prospective follow-up study. Genotype analyses were performed on 6010 children using the Illumina ImmunoChip. Levels of tTGA were measured in serum samples using radio-ligand binding assays; diagnoses of celiac disease were made based on persistent detection of tTGA and biopsy analysis. Data were analyzed using Cox proportional hazards analyses. We found 54 single-nucleotide polymorphisms (SNPs) in 5 genes associated with celiac disease (TAGAP, IL18R1, RGS21, PLEK, and CCR9) in time to celiac disease analyses (10-4>P>5.8x10-6). The hazard ratios (HR) for the SNPs with the smallest P values in each region were 1.59, 1.45, 2.23, 2.64, and 1.40, respectively. Outside of regions previously associated with celiac disease, we identified 10 SNPs in 8 regions that could also be associated with the disease (Pceliac disease (CTLA4, P = 1.3x10-6, HR = 0.76 and LPP, P = 2.8x10-5, HR = .80) and 6 SNPs in 5 regions not previously associated with celiac disease (Pceliac disease development with 5 non-HLA regions previously associated with the disease and 8 regions not previously associated with celiac disease. We identified 5 regions associated with development of tTGA. Two loci associated with celiac disease progression reached a genome-wide association

  18. α-Phellandrene alters expression of genes associated with DNA damage, cell cycle, and apoptosis in murine leukemia WEHI-3 cells.

    Science.gov (United States)

    Lin, Jen-Jyh; Yu, Chien-Chih; Lu, Kung-Wen; Chang, Shu-Jen; Yu, Fu-Shun; Liao, Ching-Lung; Lin, Jaung-Geng; Chung, Jing-Gung

    2014-08-01

    α-phellandrene (α-PA) is a cyclic monoterpene, present in natural plants such as Schinus molle L. α-PA promotes immune responses in mice in vivo. However, there is no available information on whether α-PA affects gene expression in leukemia cells. The present study determined effects of α-PA on expression levels of genes associated with DNA damage, cell cycle and apoptotic cell death in mouse leukemia WEHI-3 cells. WEHI-3 cells were treated with 10 μM α-PA for 24 h, cells were harvested and total RNA was extracted, and gene expression was analyzed by cDNA microarray. Results indicated that α-PA up-regulated 10 genes 4-fold, 13 by over 3-fold and 175 by over 2-fold; 21 genes were down-regulated by over 4-fold, 26 genes by over 3-fold and expression of 204 genes was altered by at leas 2-fold compared with the untreated control cells. DNA damage-associated genes such as DNA damage-inducer transcript 4 and DNA fragmentation factor were up-regulated by 4-fold and over 2-fold, respectively; cell-cycle check point genes such as cyclin G2 and cyclin-dependent kinases inhibitor 2D and IA (p21) were up-regulated by over 3-fold and over 2-fold, respectively; apoptosis-associated genes such as BCL2/adenovirus EIB interacting protein 3, XIAP-associated factor 1, BCL2 modifying factor, caspase-8 and FADD-like apoptosis regulator were over 2-fold up-regulated. Furthermore, DNA damage-associated gene TATA box binding protein was over 4-fold down-regulated, and D19Ertd652c (DNA segment) over 2-fold down-regulated; cell cycle-associated gene cyclin E2 was over 2-fold down-regulated; apoptosis associated gene growth arrest-specific 5 was over 9-fold down-regulated, Gm5426 (ATP synthase) was over 3-fold down-regulated, and death box polypeptide 33 was over 2-fold down-regulated. Based on these observations, α-PA altered gene expression in WEHI-3 cells in vitro. Copyright© 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  19. MOLECULAR MARKERS FOR METASTATIC PROSTATE ADENOCARCINOMA

    Directory of Open Access Journals (Sweden)

    I. S. Kunin

    2012-01-01

    Full Text Available The search of molecular markers of metastasing and prognosis in prostate cancer remains an urgent task. In this study, we investigated the relationship of gene expression heparanase-1 (HPSE1 and D-glucuronil C5-epimerase (GLCE with early disease relapse and metastasis of a 2,5−3 years after diagnosis. It was shown that the ratio of the expression levels of genes HPSE1/GLCE > 1 may serve as a prognostic relapse marker and trends of the tumour to metastasis. The data obtained suggest to use this option as a molecular marker for the diagnostics of metastatic process and the disease prognosis.

  20. New microsatellite markers for bananas (Musa spp).

    Science.gov (United States)

    Amorim, E P; Silva, P H; Ferreira, C F; Amorim, V B O; Santos, V J; Vilarinhos, A D; Santos, C M R; Souza Júnior, M T; Miller, R N G

    2012-04-27

    Thirty-four microsatellite markers (SSRs) were identified in EST and BAC clones from Musa acuminata burmannicoides var. Calcutta 4 and validated in 22 Musa genotypes from the Banana Germplasm Bank of Embrapa-CNPMF, which includes wild and improved diploids. The number of alleles per locus ranged from 2 to 14. The markers were considered highly informative based on their polymorphism information content values; more than 50% were above 0.5. These SSRs will be useful for banana breeding programs, for studies of genetic diversity, germplasm characterization and selection, development of saturated genetic linkage maps, and marker assisted selection.

  1. Tumor markers of breast cancer: New prospectives

    OpenAIRE

    Ahmed M. Kabel

    2017-01-01

    Tumor markers are substances produced by the tumors or by other cells of the body in response to cancer or certain benign conditions. Although most of these markers are made by the normal cells as well as by cancer cells, they are produced at much higher levels in cancerous conditions. These markers are used to evaluate the patient's response to treatment and to detect the presence of metastasis or recurrence. Breast cancer is one of the most common malignancies in females worldwide. The CA 2...

  2. Voice analysis as an objective state marker in bipolar disorder

    Science.gov (United States)

    Faurholt-Jepsen, M; Busk, J; Frost, M; Vinberg, M; Christensen, E M; Winther, O; Bardram, J E; Kessing, L V

    2016-01-01

    Changes in speech have been suggested as sensitive and valid measures of depression and mania in bipolar disorder. The present study aimed at investigating (1) voice features collected during phone calls as objective markers of affective states in bipolar disorder and (2) if combining voice features with automatically generated objective smartphone data on behavioral activities (for example, number of text messages and phone calls per day) and electronic self-monitored data (mood) on illness activity would increase the accuracy as a marker of affective states. Using smartphones, voice features, automatically generated objective smartphone data on behavioral activities and electronic self-monitored data were collected from 28 outpatients with bipolar disorder in naturalistic settings on a daily basis during a period of 12 weeks. Depressive and manic symptoms were assessed using the Hamilton Depression Rating Scale 17-item and the Young Mania Rating Scale, respectively, by a researcher blinded to smartphone data. Data were analyzed using random forest algorithms. Affective states were classified using voice features extracted during everyday life phone calls. Voice features were found to be more accurate, sensitive and specific in the classification of manic or mixed states with an area under the curve (AUC)=0.89 compared with an AUC=0.78 for the classification of depressive states. Combining voice features with automatically generated objective smartphone data on behavioral activities and electronic self-monitored data increased the accuracy, sensitivity and specificity of classification of affective states slightly. Voice features collected in naturalistic settings using smartphones may be used as objective state markers in patients with bipolar disorder. PMID:27434490

  3. ABCG2 is a potential marker of tumor-initiating cells in breast cancer.

    Science.gov (United States)

    Sicchieri, Renata Danielle; da Silveira, Willian Abraham; Mandarano, Larissa Raquel Mouro; de Oliveira, Tatiane Mendes Gonçalves; Carrara, Hélio Humberto Angotti; Muglia, Valdair Francisco; de Andrade, Jurandyr Moreira; Tiezzi, Daniel Guimarães

    2015-12-01

    The existence of tumor-initiating cells (TICs) within solid tumors has been hypothesized to explain tumor heterogeneity and resistance to cancer therapy. In breast cancer, the expression of CD44 and CD24 and the activity of aldehyde dehydrogenase 1 (ALDH1) can be used to selectively isolate a cell population enriched in TICs. However, the ideal marker to identify TICs has not been established. The aim of this study was to evaluate the expression of novel potential markers for TIC in breast carcinoma. We prospectively analyzed the expression of CD44, CD24, ABCG2, and CXCR4, and the activity of ALDH1 by using flow cytometry in 48 invasive ductal carcinomas from locally advanced and metastatic breast cancer patients who were administered primary chemotherapy. A mammosphere assay was employed in 30 samples. The relationship among flow cytometric analyses, ABCG2 gene expression, and clinical and pathological responses to therapy was analyzed. The GSE32646 database was analyzed in silico to identify genes associated with tumors with low and high ABCG2 expression. We observed that the presence of ABCG2(+) cells within the primary tumor was the only marker to predict the formation of mammospheres in vitro (R (2) = 0.15, p = 0.029). Quantitative polymerase chain reaction (qPCR) revealed a positive correlation between ABCG2 expression and the presence of ABCG2(+) cells within the primary tumor. The expression of ABCG2 was predictive of the response to neoadjuvant chemotherapy in our experiments and in the GSE32646 dataset (p = 0.04 and p = 0.002, respectively). The in silico analysis demonstrated that ABCG2(Up) breast cancer samples have a slower cell cycle and a higher expression of membrane proteins but a greater potential for chromosomal instability, metastasis, immune evasion, and resistance to hypoxia. Such genetic characteristics are compatible with highly aggressive and resistant tumors. Our results support the hypothesis that the presence of ABCG2

  4. Fatigue as Prognostic Risk Marker of Mental Sickness Absence in White Collar Employees

    NARCIS (Netherlands)

    Roelen, C.A.M.; Heymans, M.W.; van Rhenen, W.; Groothoff, J.W.; Twisk, J.W.R.; Bultmann, U.

    2014-01-01

    Purpose: To investigate fatigue as prognostic risk marker for identifying working employees at risk of long-term sickness absence (SA). Methods: At baseline, fatigue was measured in 633 white collar employees with the checklist individual strength (CIS) including scales for fatigue severity, reduced

  5. Fatigue as prognostic risk marker of mental sickness absence in white collar employees

    NARCIS (Netherlands)

    Roelen, C. A. M.; Heymans, M. W.; van Rhenen, W.; Groothoff, J. W.; Twisk, J. W. R.; Bültmann, U.

    2014-01-01

    To investigate fatigue as prognostic risk marker for identifying working employees at risk of long-term sickness absence (SA). At baseline, fatigue was measured in 633 white collar employees with the checklist individual strength (CIS) including scales for fatigue severity, reduced concentration,

  6. Reproducibility testing of RAPD, AFLP and SSR markers in plants by a network of European laboratories

    NARCIS (Netherlands)

    Jones, C.J.; Edwards, K.J.; Castiglione, S.; Winfield, M.O.; Sala, F.; Wiel, van de C.C.M.; Bredemeijer, G.M.M.; Vosman, B.; Matthes, M.; Daly, A.; Brettschneider, R.; Bettini, P.; Buiatti, M.; Maestri, E.; Malcevschi, A.; Marmiroli, N.; Aert, R.; Volckaert, G.; Ru, J.; eda,; Linacero, R.; Vazquez, A.; Karp, A.

    1997-01-01

    A number of PCR-based techniques can be used to detect polymorphisms in plants. For their wide-scale usage in germplasm characterisation and breeding it is important that these marker technologies can be exchanged between laboratories, which in turn requires that they can be standardised to yield

  7. Discovery of DNA methylation markers in cervical cancer using relaxation ranking

    NARCIS (Netherlands)

    Ongenaert, Mate; Wisman, G. Bea A.; Volders, Haukeline H.; Koning, Alice J.; van der Zee, Ate G. J.; van Criekinge, Wim; Schuuring, Ed

    2008-01-01

    Background: To discover cancer specific DNA methylation markers, large-scale screening methods are widely used. The pharmacological unmasking expression microarray approach is an elegant method to enrich for genes that are silenced and re-expressed during functional reversal of DNA methylation upon

  8. Fatigue as Prognostic Risk Marker of Mental Sickness Absence in White Collar Employees

    NARCIS (Netherlands)

    Roelen, C. A. M.; Heymans, M. W.; van Rhenen, W.; Groothoff, J. W.; Twisk, J. W. R.; Bultmann, U.

    Purpose To investigate fatigue as prognostic risk marker for identifying working employees at risk of long-term sickness absence (SA). Methods At baseline, fatigue was measured in 633 white collar employees with the checklist individual strength (CIS) including scales for fatigue severity, reduced

  9. Nuclear microsatellite markers for population genetic studies in sugar maple (Acer saccharum Marsh.

    Directory of Open Access Journals (Sweden)

    Sudhir Khodwekar

    2015-12-01

    Full Text Available A set of seven new nuclear microsatellite markers (nSSRs was developedfor sugar maple (Acer saccharum Marsh. using paired-end Illumina sequencing. Out of 96 primers screened in a panel of six unrelated individuals, seven markers amplified polymorphic products. The utility of these markers, in addition to six already published microsatellites, for genetic variation and gene flow studies was assessed. Out of the seven newly developed markers, three amplified multiple fragments and were interpreted as dominant (absence/presence markers, while four markers amplified a maximum of two amplification products per sample. The six published microsatellites and three of the four newly developed markers showed regular segregation in an open-pollinated single tree progeny. Observed heterozygosity (Ho and expected heterozygosity (He in 48 individuals from one population ranged from 0.436 to 0.917 and from 0.726 to 0.894, respectively. Dominant markers revealed 64 variable positions and moderate genetic variation within the population (He = 0.102, Shannon’s I = 0.193. Paternity analyses in the program CERVUS at co-dominant markers showed effective dispersal of pollen in the sugar maple population both at 95% and 80% confidence levels. Dependent on the confidence level, the mean pollen dispersal distance within the population ranged from 33.25 m to 38.75 m and gene flow from utside the stand from 78% to 82%. The absence of fine-scale Spatial Genetic Structure (SGS suggested effective dispersal of both seeds and pollen.

  10. Efficiency of RAPD, ISSR, AFLP and ISTR markers for the detection of polymorphisms and genetic relationships in camote de cerro (Dioscorea spp.

    Directory of Open Access Journals (Sweden)

    Ana Paulina Velasco-Ramírez

    2014-03-01

    Conclusion: This indicates an important level of genetic differences despite the fact that the plant is asexually propagated. Based on the diversity statistics, any marker tested in present work can be recommended for use in large-scale genetic studies of populations. However, the low correlations among different molecular marker systems show the importance of the complementarity of the information that is generated by different markers for genetic studies involving estimation of polymorphism and relationships.

  11. Simultaneous Analysis of Bioactive Markers from Orthosiphon ...

    African Journals Online (AJOL)

    RP-HPLC) method for the analysis of the crude extracts of Orthosiphon stamineus. Methods: A simple and facile analytical method was developed using RP- HPLC with UV detection for the identification and quantitation of bioactive markers ...

  12. Simultaneous Analysis of Bioactive Markers from Orthosiphon ...

    African Journals Online (AJOL)

    Erah

    Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Penang,. Malaysia. Abstract ... the identification and quantitation of bioactive markers present in O. stamineus extracts. Four different bioactive ... Orthosiphon stamineus plant was cultivated and propagated under ...

  13. Tumor markers of breast cancer: New prospectives

    Directory of Open Access Journals (Sweden)

    Ahmed M. Kabel

    2017-04-01

    Full Text Available Tumor markers are substances produced by the tumors or by other cells of the body in response to cancer or certain benign conditions. Although most of these markers are made by the normal cells as well as by cancer cells, they are produced at much higher levels in cancerous conditions. These markers are used to evaluate the patient's response to treatment and to detect the presence of metastasis or recurrence. Breast cancer is one of the most common malignancies in females worldwide. The CA 27-29, CA 15-3, CA27.29, carcinoembryonic antigen, tissue polypeptide specific antigen, p53, cathepsin D, cyclin E, nestin and HER-2 are tumor markers that are often expressed in people with breast cancer. They play a crucial role in diagnosis, monitoring response to therapy, early detection of metastasis and determination of recurrence in patients with breast cancer.

  14. Identifying Early Diagnosis Markers of Prostate Cancer

    National Research Council Canada - National Science Library

    Huang, Shuang

    2004-01-01

    .... We reasoned that the success and accuracy in early diagnosis of prostate cancer may be significantly improved if a panel of prostate cancer-specific markers can be identified and used in combination...

  15. Diagnostic markers for germ cell neoplasms

    DEFF Research Database (Denmark)

    Rajpert-De Meyts, Ewa; Nielsen, John E; Skakkebaek, Niels E

    2015-01-01

    This concise review summarises tissue and serum markers useful for differential diagnosis of germ cell tumours (GCTs), with focus on the most common testicular GCTs (TGCTs). GCTs are characterised by phenotypic heterogeneity due to largely retained embryonic pluripotency and aberrant somatic...... to gain-of function mutations in survival-promoting genes (e.g. FGFR3, HRAS), thus this tumour has a different expression profile than GCNIS-derived TGCT. Clinically most informative markers for GCT, except teratoma, are genes expressed in primordial germ cell/gonocyte and embryonic pluripotency......-related, such as placental-like alkaline phosphatase (PLAP), OCT4 (POU5F1), NANOG, AP-2g (TFAP2C) and LIN28. These genes are not expressed in normal adult germ cells, hence are useful immunohistochemical markers for GCNIS and GCT subtypes in tissue specimens. Some of these markers can also be used for immunocytochemistry...

  16. Genetics and biological markers in urachal cancer.

    Science.gov (United States)

    Behrendt, Mark A; van Rhijn, Bas W G

    2016-10-01

    Urachal cancer (UraC) is a rare tumor entity that usually develops at the basis of the remnant embryologic urachus. Consisting of mostly adenocarcinomas, most patients present with secondary symptoms due to an advanced stage with urinary bladder infiltration. One third of patients are already metastasized at presentation rendering them unsuitable for curative surgical treatment. In order to improve staging, treatment and follow-up, adequate knowledge about the genetic origin and potential markers is necessary. This paper reviews the English literature until December 2015. Pathologists argue for and against metaplasia or remnant enteric cells as origin for the adenomatous tissue found in UraC. Mutations in KRAS, BRAF, GNAS and Her2 have been associated with UraC. Immunohistochemical (IHC) markers like CEA, 34βE12, Claudin-18 and RegIV are indicative for mucous producing UraC. So far, IHC markers fail as prognosticators when matched to clinical data. Little is known about serum markers for UraC. CEA, CA19-9, CA125 and CA724 are mentioned as being elevated in UraC by some reports. Regarding the literature for biological markers in UraC, knowledge is mostly derived from case reports or cohort studies mentioning markers or predictors. More genetic research is needed to show whether UraC stems from progenitor cells of the cloaca or is due to metaplasia of transitional cells. Few IHC markers have shown indicative potential for UraC. A useful panel for differential diagnostics and clinicopathologic prognostication needs to be developed. Serum markers show very little potential for neither diagnosis nor follow-up in UraC. Further research on larger cohorts is necessary.

  17. Detection of immunocytological markers in photomicroscopic images

    Science.gov (United States)

    Friedrich, David; zur Jacobsmühlen, Joschka; Braunschweig, Till; Bell, André; Chaisaowong, Kraisorn; Knüchel-Clarke, Ruth; Aach, Til

    2012-03-01

    Early detection of cervical cancer can be achieved through visual analysis of cell anomalies. The established PAP smear achieves a sensitivity of 50-90%, most false negative results are caused by mistakes in the preparation of the specimen or reader variability in the subjective, visual investigation. Since cervical cancer is caused by human papillomavirus (HPV), the detection of HPV-infected cells opens new perspectives for screening of precancerous abnormalities. Immunocytochemical preparation marks HPV-positive cells in brush smears of the cervix with high sensitivity and specificity. The goal of this work is the automated detection of all marker-positive cells in microscopic images of a sample slide stained with an immunocytochemical marker. A color separation technique is used to estimate the concentrations of the immunocytochemical marker stain as well as of the counterstain used to color the nuclei. Segmentation methods based on Otsu's threshold selection method and Mean Shift are adapted to the task of segmenting marker-positive cells and their nuclei. The best detection performance of single marker-positive cells was achieved with the adapted thresholding method with a sensitivity of 95.9%. The contours differed by a modified Hausdorff Distance (MHD) of 2.8 μm. Nuclei of single marker positive cells were detected with a sensitivity of 95.9% and MHD = 1.02 μm.

  18. Tyrosinase-positive oculocutaneous albinism in Southern African blacks: P gene-associated haplotypes suggest a major mutation in the 5{prime} region of the gene

    Energy Technology Data Exchange (ETDEWEB)

    Ramsay, M.; Stevens, G.; Beukering, J. van [Univ. of the Witwatersrand, Johannesburg (South Africa)] [and others

    1994-09-01

    Tyrosinase-positive oculocutaneous albinism (ty-pos OCA) occurs with a prevalence of 1 in 3900 among Southern African (SA) blacks. The major contributors to morbidity and mortality are skin cancer and decreased visual acuity. Two distinct phenotypes occur, namely individuals with ephelides (darkly pigmented patches) and those without. There is complete concordance with regard to ephelus status among siblings. The disorder is linked to markers on chromosome 15q11.2-q12, and no obligatory cross-overs were observed with polymophic markers at the human homolog, P, of the mouse pink eyed dilute gene, p. Contrary to what has been shown for Caucasoid ty-pos OCA, this condition shows locus homogeneity among SA blacks. The P gene is an excellent candidate for ty-pos OCA and mutations in this gene will confirm its role in causing the common form of albinism in SA. Numerous P gene mutations have been described in other populations. In an attempt to detect mutations, the P gene cDNA was used to search for structural rearrangements or polymorphisms. Six polymorphisms (plR10/Scal, 912/Xbal, 912/HincII, 912/TaqI, 1412/TaqI [two systems] and 1412/HindIII) were detected with subclones of the P cDNA and haplotypes were determined in each family. None were clearly associated with an albinism-related rearrangement. However, strong linkage disequilibrium was observed with alleles at loci toward the 5{prime} region of the gene ({triangle}=0.65, 0.57 and 0.80 for the three polymorphisms detected with the 912 subclone), suggesting a major ty-pos OCA mutation in this region. Haplotype analysis provides evidence for a major mutation associated with the same haplotype in individuals with ephelides (8/12 OCA chromosomes) and those without ephelides (24:30). The presence of other ty-pos OCA associated haplotypes indicates several other less common mutations.

  19. Comparison of genetic detection efficiency of different markers ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-06-03

    combined genetic markers for the relations among populations. Key words: Genetic markers, genetic differentiation, genetic detection efficiency. ..... transporter gene moderate depression in maltreated children. Proc. Natl. Acad. Sci.

  20. Identification of Non-HLA Genes Associated with Celiac Disease and Country-Specific Differences in a Large, International Pediatric Cohort.

    Directory of Open Access Journals (Sweden)

    Ashok Sharma

    Full Text Available There are significant geographical differences in the prevalence and incidence of celiac disease that cannot be explained by HLA alone. More than 40 loci outside of the HLA region have been associated with celiac disease. We investigated the roles of these non-HLA genes in the development of tissue transglutaminase autoantibodies (tTGA and celiac disease in a large international prospective cohort study.A total of 424,788 newborns from the US and European general populations and first-degree relatives with type 1 diabetes were screened for specific HLA genotypes. Of these, 21,589 carried 1 of the 9 HLA genotypes associated with increased risk for type 1 diabetes and celiac disease; we followed 8676 of the children in a 15 y prospective follow-up study. Genotype analyses were performed on 6010 children using the Illumina ImmunoChip. Levels of tTGA were measured in serum samples using radio-ligand binding assays; diagnoses of celiac disease were made based on persistent detection of tTGA and biopsy analysis. Data were analyzed using Cox proportional hazards analyses.We found 54 single-nucleotide polymorphisms (SNPs in 5 genes associated with celiac disease (TAGAP, IL18R1, RGS21, PLEK, and CCR9 in time to celiac disease analyses (10-4>P>5.8x10-6. The hazard ratios (HR for the SNPs with the smallest P values in each region were 1.59, 1.45, 2.23, 2.64, and 1.40, respectively. Outside of regions previously associated with celiac disease, we identified 10 SNPs in 8 regions that could also be associated with the disease (P<10-4. A SNP near PKIA (rs117128341, P = 6.5x10-8, HR = 2.8 and a SNP near PFKFB3 (rs117139146, P<2.8x10-7, HR = 4.9 reached the genome-wide association threshold in subjects from Sweden. Analyses of time to detection of tTGA identified 29 SNPs in 2 regions previously associated with celiac disease (CTLA4, P = 1.3x10-6, HR = 0.76 and LPP, P = 2.8x10-5, HR = .80 and 6 SNPs in 5 regions not previously associated with celiac disease (P<10

  1. Biochemical Analysis of Four Missense Mutations in the HSD17B3 Gene Associated With 46,XY Disorders of Sex Development in Egyptian Patients.

    Science.gov (United States)

    Engeli, Roger T; Tsachaki, Maria; Hassan, Heba A; Sager, Christoph P; Essawi, Mona L; Gad, Yehia Z; Kamel, Alaa K; Mazen, Inas; Odermatt, Alex

    2017-09-01

    molecular modeling provides insight into disease mechanism. However, the stability of mutant proteins in vivo cannot be predicted by this approach. The 17β-HSD3 G289S substitution, previously reported in other patients with 46,XY DSD, is a polymorphism that does not cause the disorder; thus, further sequence analysis was required and disclosed a mutation in SRD5A2, explaining the cause of 46,XY DSD in these patients. Engeli RT, Tsachaki M, Hassan HA, et al. Biochemical Analysis of Four Missense Mutations in the HSD17B3 Gene Associated With 46,XY Disorders of Sex Development in Egyptian Patients. J Sex Med 2017;14:1165-1174. Copyright © 2017 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.

  2. A multiplex immunoassay method for simultaneous quantification of iron, vitamin A and inflammation status markers.

    Directory of Open Access Journals (Sweden)

    Eleanor Brindle

    Full Text Available Deficiencies of vitamin A and iron affect a significant portion of the world's population, and efforts to characterize patterns of these deficiencies are hampered by a lack of measurement tools appropriate for large-scale population-based surveys. Vitamin A and iron are not easily measured directly, so reliable proxy markers for deficiency status have been identified and adopted. Measurement of inflammatory markers is necessary to interpret vitamin A and iron status markers, because circulating levels are altered by inflammation. We developed a multiplex immunoassay method for simultaneous measurement of five markers relevant to assessing inflammation, vitamin A and iron status: α-1-acid glycoprotein, C-reactive protein, retinol binding protein 4, ferritin and soluble transferrin receptor. Serum and plasma specimens were used to optimize the assay protocol. To evaluate assay performance, plasma from 72 volunteers was assayed using the multiplex technique and compared to conventional immunoassay methods for each of the five markers. Results of the new and conventional assay methods were highly correlated (Pearson Correlations of 0.606 to 0.991, p<.0001. Inter-assay imprecision for the multiplex panel varied from 1% to 8%, and all samples fell within the limits of quantification for all assays at a single dilution. Absolute values given by the multiplex and conventional assays differed, indicating a need for further work to devise a new standard curve. This multiplexed micronutrient immunoassay technique has excellent potential as a cost effective tool for use in large-scale deficiency assessment efforts.

  3. A multiplex immunoassay method for simultaneous quantification of iron, vitamin A and inflammation status markers.

    Science.gov (United States)

    Brindle, Eleanor; Stevens, Daniel; Crudder, Christopher; Levin, Carol E; Garrett, Dean; Lyman, Chris; Boyle, David S

    2014-01-01

    Deficiencies of vitamin A and iron affect a significant portion of the world's population, and efforts to characterize patterns of these deficiencies are hampered by a lack of measurement tools appropriate for large-scale population-based surveys. Vitamin A and iron are not easily measured directly, so reliable proxy markers for deficiency status have been identified and adopted. Measurement of inflammatory markers is necessary to interpret vitamin A and iron status markers, because circulating levels are altered by inflammation. We developed a multiplex immunoassay method for simultaneous measurement of five markers relevant to assessing inflammation, vitamin A and iron status: α-1-acid glycoprotein, C-reactive protein, retinol binding protein 4, ferritin and soluble transferrin receptor. Serum and plasma specimens were used to optimize the assay protocol. To evaluate assay performance, plasma from 72 volunteers was assayed using the multiplex technique and compared to conventional immunoassay methods for each of the five markers. Results of the new and conventional assay methods were highly correlated (Pearson Correlations of 0.606 to 0.991, pquantification for all assays at a single dilution. Absolute values given by the multiplex and conventional assays differed, indicating a need for further work to devise a new standard curve. This multiplexed micronutrient immunoassay technique has excellent potential as a cost effective tool for use in large-scale deficiency assessment efforts.

  4. Large-Scale Candidate Gene Analysis in Whites and African Americans Identifies IL6R Polymorphism in Relation to Atrial Fibrillation The National Heart, Lung, and Blood Institute's Candidate Gene Association Resource (CARe) Project

    NARCIS (Netherlands)

    Schnabel, Renate B.; Kerr, Kathleen F.; Lubitz, Steven A.; Alkylbekova, Ermeg L.; Marcus, Gregory M.; Sinner, Moritz F.; Magnani, Jared W.; Wolf, Philip A.; Deo, Rajat; Lloyd-Jones, Donald M.; Lunetta, Kathryn L.; Mehra, Reena; Levy, Daniel; Fox, Ervin R.; Arking, Dan E.; Mosley, Thomas H.; Mueller-Nurasyid, Martina; Young, Taylor R.; Wichmann, H. -Erich; Seshadri, Sudha; Farlow, Deborah N.; Rotter, Jerome I.; Soliman, Elsayed Z.; Glazer, Nicole L.; Wilson, James G.; Breteler, Monique M. B.; Sotoodehnia, Nona; Newton-Cheh, Christopher; Kaeaeb, Stefan; Ellinor, Patrick T.; Alonso, Alvaro; Benjamin, Emelia J.; Heckbert, Susan R.

    2011-01-01

    Background-The genetic background of atrial fibrillation (AF) in whites and African Americans is largely unknown. Genes in cardiovascular pathways have not been systematically investigated. Methods and Results-We examined a panel of approximately 50 000 common single-nucleotide polymorphisms (SNPs)

  5. CytoGTA: A cytoscape plugin for identifying discriminative subnetwork markers using a game theoretic approach.

    Directory of Open Access Journals (Sweden)

    S Farahmand

    Full Text Available In recent years, analyzing genome-wide expression profiles to find genetic markers has received much attention as a challenging field of research aiming at unveiling biological mechanisms behind complex disorders. The identification of reliable and reproducible markers has lately been achieved by integrating genome-scale functional relationships and transcriptome datasets, and a number of algorithms have been developed to support this strategy. In this paper, we present a promising and easily applicable tool to accomplish this goal, namely CytoGTA, which is a Cytoscape plug-in that relies on an optimistic game theoretic approach (GTA for identifying subnetwork markers. Given transcriptomic data of two phenotype classes and interactome data, this plug-in offers discriminative markers for the two classes. The high performance of CytoGTA would not have been achieved if the strategy of GTA was not implemented in Cytoscape. This plug-in provides a simple-to-use platform, convenient for biological researchers to interactively work with and visualize the structure of subnetwork markers. CytoGTA is one of the few available Cytoscape plug-ins for marker identification, which shows superior performance to existing methods.

  6. Modified FOLFOX-6 chemotherapy in advanced gastric cancer: Results of phase II study and comprehensive analysis of polymorphisms as a predictive and prognostic marker

    Directory of Open Access Journals (Sweden)

    Lee Se-Hoon

    2008-05-01

    Full Text Available Abstract Background The objective of this study was to evaluate the efficacy and toxicity of infusional 5-fluorouracil (5-FU, folinic acid and oxaliplatin (modified FOLFOX-6 in patients with advanced gastric cancer (AGC, as first-line palliative combination chemotherapy. We also analyzed the predictive or prognostic value of germline polymorphisms of candidate genes associated with 5-FU and oxaliplatin. Methods Seventy-three patients were administered a 2 hour infusion of oxaliplatin (100 mg/m2 and folinic acid (100 mg/m2 followed by a 46 hour continuous infusion of 5-FU (2,400 mg/m2. Genomic DNA from the patients' peripheral blood mononuclear cells was extracted. Ten polymorphisms within five genes were investigated including TS, GSTP, ERCC, XPD and XRCC. Results The overall response rate (RR was 43.8%. Median time to progression (TTP and overall survival (OS were 6.0 months and 12.6 months, respectively. Toxicities were generally tolerable and manageable. The RR was significantly higher in patients with a 6-bp deletion homozygote (-6 bp/-6 bp in TS-3'UTR (55.0% vs. 30.3% in +6 bp/+6 bp or +6 bp/-6 bp, p = 0.034, and C/A or A/A in XPD156 (52.0% vs. 26.1% in C/C, p = 0.038. The -6 bp/-6 bp in TS-3'UTR was significantly associated with a prolonged TTP and OS. In a multivariate analysis, the 6-bp deletion in TS-3'UTR was identified as an independent prognostic marker of TTP (hazard ratio = 0.561, p = 0.032. Conclusion Modified FOLFOX-6 chemotherapy appears to be active and well tolerated as first line chemotherapy in AGC patients. The 6-bp deletion in TS-3'UTR might be a candidate to select patients who are likely to benefit from 5-FU based modified FOLFOX-6 in future large scale trial.

  7. On identification problems requiring linked autosomal markers.

    Science.gov (United States)

    Egeland, Thore; Sheehan, Nuala

    2008-06-01

    This paper considers identification problems based on DNA marker data. The topics we discuss are general, but we will exemplify them in a simple context. There is DNA available from two persons. There is uncertainty about the relationship between the two individuals and a number of hypotheses describing the possible relationship is available. The task is to determine the most likely pedigree. This problem is fairly standard. However, there are some problems that cannot be solved using DNA from independently segregating loci. For example, the likelihoods for (i) grandparent-grandchild, (ii) uncle-niece and (iii) half-sibs coincide for such DNA data and so these relations cannot be distinguished on the basis of markers normally used for forensic identification problems: the likelihood ratio comparing any pair of hypotheses will be unity. Sometimes, but not in the examples we consider, other sources of DNA like mtDNA or sex chromosomes can help to distinguish between such equally likely possibilities. Prior information can likewise be of use. For instance, age information can exclude alternative (i) above and also indicate that alternative (iii) is apriori more likely than alternative (ii). More generally, the above problems can be solved using linked autosomal markers. To study the problem in detail and understand how linkage works in this regard, we derive an explicit formula for a pair of linked markers. The formula extends to independent pairs of linked markers. While this approach adds to the understanding of the problem, more markers are required to obtain satisfactory results and then the Lander-Green algorithm is needed. Simulation experiments are presented based on a range of scenarios and we conclude that useful results can be obtained using available freeware (MERLIN and R). The main message of this paper is that linked autosomal markers deserve greater attention in forensic genetics and that the required laboratory and statistical analyses can be performed

  8. Human Leukocyte Antigen Class I Genes Associated With Stevens-Johnson Syndrome and Severe Ocular Complications Following Use of Cold Medicine in a Brazilian Population.

    Science.gov (United States)

    Wakamatsu, Tais H; Ueta, Mayumi; Tokunaga, Katsushi; Okada, Yukinori; Loureiro, Renata R; Costa, Karita A; Sallum, Juliana Maria F; Milhomens, José Arthur; Inoue, Chikara; Sotozono, Chie; Gomes, José Álvaro P; Kinoshita, Shigeru

    2017-04-01

    individuals of both ethnic groups (Pardo: OR, 12.2; 95% CI, 1.19-125.0; P = .03; and European: OR, 21.2; 95% CI, 0.97-465.0; P = .04). An association was observed only in the European cohort for HLA-B*44:03 (OR, 5.50; 95% CI, 1.47-20.50; P = .01) and HLA-C*12:03 (OR, 8.79; 95% CI, 1.83-42.20; P = .008). This study suggests that HLA-A*66:01 might be a marker for CM-SJS/TEN with SOCs in Brazilian individuals of Pardo and European ancestry and that HLA-B*44:03 and HLA-C*12:03 might be markers only in those of European ancestry. Moreover, HLA-A*11:01 might be a marker of resistance to CM-SJS/TEN with SOCs.

  9. Cytoskeletal proteins and stem cell markers gene expression in human bone marrow mesenchymal stromal cells after different periods of simulated microgravity

    Science.gov (United States)

    Gershovich, P. M.; Gershovich, J. G.; Zhambalova, A. P.; Romanov, Yu. A.; Buravkova, L. B.

    2012-01-01

    Mesenchymal stem (stromal) cells (MSCs) are present in a variety of tissues during prenatal and postnatal human development. In adult organism, they are prevalent in bone marrow and supposed to be involved in space-flight induced osteopenia. We studied expression of various genes in human bone marrow MSCs after different terms of simulated microgravity (SMG) provided by Random Positioning Machine. Simulated microgravity induced transient changes in expression level of genes associated with actin cytoskeleton, especially after 48 h of SMG. However, after 120 h exposure in SMG partial restoration of gene expression levels (relative to the control) was found. Similar results were obtained with bmMSCs subjected to 24 h readaptation in static state after 24 h in SMG. Analysis of 84 genes related to identification, growth and differentiation of stem cells revealed that expression of nine genes was changed slightly after 48 h in SMG. More pronounced changes in gene expression of "stem cells markers" were observed after 120 h of simulated microgravity. Among 84 investigated genes, 30 were up-regulated and 24 were down-regulated. Finally, MSCs osteogenesis induced by long-term (10-20 days) simulation of microgravity was accompanied by down-regulation of gene expression of the main osteogenic differentiation markers ( ALPL, OMD) and master transcription osteogenic factor of MSCs ( Runx2). Thus, our study demonstrated that changes in expression level of some genes associated with actin cytoskeleton and stem cell markers are supposed to be one of the mechanisms, which contribute to precursor's cellular adaptation to the microgravity conditions. These results can clarify genomic mechanisms through which SMG reduces osteogenic differentiation of bmMSCs.

  10. Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean

    Science.gov (United States)

    Burt, Andrew J.; William, H. Manilal; Perry, Gregory; Khanal, Raja; Pauls, K. Peter; Kelly, James D.; Navabi, Alireza

    2015-01-01

    Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co–4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co–4 is localized. Three SCAR markers with known linkage to Co–4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK–4 loci found in previous studies. It is possible that the Co–4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases. PMID:26431031

  11. Development of SSR Markers Based on Transcriptome Sequencing and Association Analysis with Drought Tolerance in Perennial Grass Miscanthus from China

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    Gang Nie

    2017-05-01

    Full Text Available Drought has become a critical environmental stress affecting on plant in temperate area. As one of the promising bio-energy crops to sustainable biomass production, the genus Miscanthus has been widely studied around the world. However, the most widely used hybrid cultivar among this genus, Miscanthus × giganteus is proved poor drought tolerance compared to some parental species. Here we mainly focused on Miscanthus sinensis, which is one of the progenitors of M. × giganteus providing a comparable yield and well abiotic stress tolerance in some places. The main objectives were to characterize the physiological and photosynthetic respond to drought stress and to develop simple sequence repeats (SSRs markers associated with drought tolerance by transcriptome sequencing within an originally collection of 44 Miscanthus genotypes from southwest China. Significant phenotypic differences were observed among genotypes, and the average of leaf relative water content (RWC were severely affected by drought stress decreasing from 88.27 to 43.21%, which could well contribute to separating the drought resistant and drought sensitive genotype of Miscanthus. Furthermore, a total of 16,566 gene-associated SSRs markers were identified based on Illumina RNA sequencing under drought conditions, and 93 of them were randomly selected to validate. In total, 70 (75.3% SSRs were successfully amplified and the generated loci from 30 polymorphic SSRs were used to estimate the genetic differentiation and population structure. Finally, two optimum subgroups of the population were determined by structure analysis and based on association analysis, seven significant associations were identified including two markers with leaf RWC and five markers with photosynthetic traits. With the rich sequencing resources annotation, such associations would serve an efficient tool for Miscanthus drought response mechanism study and facilitate genetic improvement of drought resistant for

  12. Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.

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    Yang Jun-Bo

    2010-12-01

    Full Text Available Abstract Background The castor bean (Ricinus communis L., a monotypic species in the spurge family (Euphorbiaceae, 2n = 20, is an important non-edible oilseed crop widely cultivated in tropical, sub-tropical and temperate countries for its high economic value. Because of the high level of ricinoleic acid (over 85% in its seed oil, the castor bean seed derivatives are often used in aviation oil, lubricants, nylon, dyes, inks, soaps, adhesive and biodiesel. Due to lack of efficient molecular markers, little is known about the population genetic diversity and the genetic relationships among castor bean germplasm. Efficient and robust molecular markers are increasingly needed for breeding and improving varieties in castor bean. The advent of modern genomics has produced large amounts of publicly available DNA sequence data. In particular, expressed sequence tags (ESTs provide valuable resources to develop gene-associated SSR markers. Results In total, 18,928 publicly available non-redundant castor bean EST sequences, representing approximately 17.03 Mb, were evaluated and 7732 SSR sites in 5,122 ESTs were identified by data mining. Castor bean exhibited considerably high frequency of EST-SSRs. We developed and characterized 118 polymorphic EST-SSR markers from 379 primer pairs flanking repeats by screening 24 castor bean samples collected from different countries. A total of 350 alleles were identified from 118 polymorphic SSR loci, ranging from 2-6 per locus (A with an average of 2.97. The EST-SSR markers developed displayed moderate gene diversity (He with an average of 0.41. Genetic relationships among 24 germplasms were investigated using the genotypes of 350 alleles, showing geographic pattern of genotypes across genetic diversity centers of castor bean. Conclusion Castor bean EST sequences exhibited considerably high frequency of SSR sites, and were rich resources for developing EST-SSR markers. These EST-SSR markers would be particularly

  13. HLA class II gene associations in African American Type 1 diabetes reveal a protective HLA-DRB1*03 haplotype

    Science.gov (United States)

    Howson, J M M; Roy, M S; Zeitels, L; Stevens, H; Todd, J A

    2013-01-01

    Aims Owing to strong linkage disequilibrium between markers, pinpointing disease associations within genetic regions is difficult in European ancestral populations, most notably the very strong association of the HLA-DRB1*03-DQA1*05:01-DQB1*02:01 haplotype with Type 1 diabetes risk, which is assumed to be because of a combination of HLA-DRB1 and HLA-DQB1. In contrast, populations of African ancestry have greater haplotype diversity, offering the possibility of narrowing down regions and strengthening support for a particular gene in a region being causal. We aimed to study the human leukocyte antigen (HLA) region in African American Type 1 diabetes. Methods Two hundred and twenty-seven African American patients with Type 1 diabetes and 471 African American control subjects were tested for association at the HLA class II genes, HLA-DRB1, HLA-DQA1, HLA-DQB1 and 5147 single nucleotide polymorphisms across the major histocompatibility complex region using logistic regression models. Population admixture was accounted for with principal components analysis. Results Single nucleotide polymorphism marker associations were explained by the HLA associations, with the major peak over the class II loci. The HLA association overall was extremely strong, as expected for Type 1 diabetes, even in African Americans in whom diabetes diagnosis is heterogeneous. In addition, there were unique features: the HLA-DRB1*03 haplotype was split into HLA-DRB1*03:01, which confers greatest susceptibility in these samples (odds ratio 3.17, 95% CI 1.72–5.83) and HLA-DRB1*03:02, an allele rarely observed in Europeans, which confers the greatest protection in these African American samples (odds ratio 0.22, 95% CI 0.09–0.55). Conclusions The unique diversity of the African HLA region we have uncovered supports a specific and major role for HLA-DRB1 in HLA-DRB1*03 haplotype-associated Type 1 diabetes risk. PMID:23398374

  14. Development of polymorphic microsatellite markers for the human botfly, Dermatobia hominis (Diptera: Oestridae).

    Science.gov (United States)

    Bitarello, Bárbara Domingues; Torres, Tatiana Teixeira; Lyra, Mariana Lúcio; DE Azeredo-Espin, Ana Maria Lima

    2009-01-01

    In this report, we describe the development of 17 polymorphic microsatellite markers for the human botfly, Dermatobia hominis, an obligatory parasite of mammals of great veterinary importance in Latin America. The number of alleles ranged from 5 to 21 per locus, with a mean of 12.2 alleles per locus. The expected heterozygosity ranged from 0.2571 to 0.9206 and from 0.2984 to 0.9291 in two populations from Brazil. These markers should provide a high resolution tool for assessment of the fine-scale genetic structure of natural populations of the human botfly. © 2009 The Authors. Journal compilation © 2009 Blackwell Publishing Ltd.

  15. Molecular markers. Amplified fragment length polymorphism

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    Pržulj Novo

    2005-01-01

    Full Text Available Amplified Fragment Length Polymorphism molecular markers (AFLPs has been developed combining procedures of RFLPs and RAPDs molekular markers, i.e. the first step is restriction digestion of the genomic DNA that is followed by selective amplification of the restricted fragments. The advantage of the AFLP technique is that it allows rapid generation of a large number of reproducible markers. The reproducibility of AFLPs markers is assured by the use of restriction site-specific adapters and adapter-specific primers for PCR reaction. Only fragments containing the restriction site sequence plus the additional nucleotides will be amplified and the more selected nucleotides added on the primer sequence the fewer the number of fragments amplified by PCR. The amplified products are normally separated on a sequencing gel and visualized after exposure to X-ray film or by using fluorescent labeled primers. AFLP shave proven to be extremely proficient in revealing diversity at below the species level. A disadvantage of AFLP technique is that AFLPs are essentially a dominant marker system and not able to identify heterozygotes.

  16. Systemic markers of inflammation in periodontitis.

    Science.gov (United States)

    Loos, Bruno G

    2005-11-01

    This literature review summarizes current knowledge on the systemic levels of selected markers of inflammation in periodontitis. From samples of peripheral blood the following cellular factors are discussed: total number of white blood cells, red blood cells, and thrombocytes. Further, plasma levels of acute-phase proteins, cytokines, and coagulation factors are reviewed. From the available literature it appears that the total numbers of leukocytes and plasma levels of C-reactive protein are consistently higher in periodontitis patients compared to healthy controls. Numbers of red blood cells and levels of hemoglobin are lower in periodontitis and there is a trend towards anemia of chronic disease. Most systemic markers of inflammation discussed in this review are also regarded as predictive markers for cardiovascular diseases. Therefore, changes in these markers in periodontitis may be part of the explanation why periodontitis is associated with cardiovascular diseases and/or cerebrovascular events in epidemiological studies. It is hypothesized that possibly daily episodes of a bacteremia originating from periodontal lesions are the cause for the changes in systemic markers in periodontitis; the cumulative size of all periodontal lesions in the untreated severe patient may amount to 15 to 20 cm2.

  17. Candidate gene association study of type 2 diabetes in a nested case-control study of the EPIC-Potsdam cohort - role of fat assimilation.

    Science.gov (United States)

    Fisher, Eva; Nitz, Inke; Lindner, Inka; Rubin, Diana; Boeing, Heiner; Möhlig, Matthias; Hampe, Jochen; Schreiber, Stefan; Schrezenmeir, Jürgen; Döring, Frank

    2007-02-01

    To search for common variants etiological for type 2 diabetes, we screened 15 genes involved in fat assimilation for sequence variants. Approximately 55 kb in promoter and coding regions, and intron/splice sites were sequenced by cycle sequencing. In the set of 15 genes, 71 single nucleotide polymorphisms (SNPs) were detected. 33 SNPs were presumed to be functionally significant and were genotyped in 192 incident type 2 diabetes subjects and 384 matched controls from the European Prospective Investigation into Cancer and Nutrition-Potsdam cohort. A total of 27 SNPs out of 15 genes showed no statistical association with type 2 diabetes in our study. Six SNPs demonstrated nominal association with type 2 diabetes, with the most significant marker (FABP6 Thr79Met) having an adjusted odds ratio of 0.45 (95% CI 0.22-0.92) in homozygous Met allele carriers. Evidence for an association with disease status was also found for a novel Arg109Cys (g.2129C > T) variant of colipase, 5'UTR (rs2084202) and Met71Val (rs8192506) variants of diazepam-binding inhibitor, Arg298His (rs13283456) of PTGES2, and a novel promoter variant (g.-1324G > A) of SLC27A5. The results presented here provide preliminary evidence for the association of common variants in genes involved in fat assimilation with the genetic susceptibility of type 2 diabetes. However, they definitely need further verification.

  18. Differential Expression of Genes Associated with the Progression of Renal Disease in the Kidneys of Liver-Specific Glucokinase Gene Knockout Mice

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    Gang Niu

    2013-03-01

    Full Text Available Liver glucokinase (GCK deficient mice possess mild renal complications associated with diabetes. To investigate the progression of kidney disease and identify candidate genes involved in the pathogenesis of renal damage, we examined changes in tissue structure and gene expression in the kidneys of liver-specific GCK knockout (gckw/− mice and age-matched normal wild-type control (gckw/w mice as they aged. Suppression subtractive hybridization (SSH was used to identify candidate genes that showed a pattern of differential expression between kidneys of gckw/− and gckw/w mice at 60 weeks of age. Differential expression of the candidate genes was examined by real-time qPCR in liver-specific gckw/− and gckw/w mice at 16, 26, 40, 60, and 85 weeks of age. Among the candidate genes, only glutathione peroxidase-3 (GPX3 was confirmed to show differential expression by qPCR in the 60-week old mice, however two others genes, MALAT1 and KEG, showed significant changes at other ages. This study shows that liver-specific glucokinase deficient mice display changes in kidney morphology by 40 weeks of age, and that renal complication may be correlated with a reduction in GPX3 levels. Since decreased GPX3 mRNA expression was observed at 26 weeks, which is younger than the age when pathological changes can be seen in kidney biopsies, GPX3 may serve as an early marker for kidney damage.

  19. DNA methylation levels in candidate genes associated with chronological age in mammals are not conserved in a long-lived seabird.

    Science.gov (United States)

    De Paoli-Iseppi, Ricardo; Polanowski, Andrea M; McMahon, Clive; Deagle, Bruce E; Dickinson, Joanne L; Hindell, Mark A; Jarman, Simon N

    2017-01-01

    Most seabirds do not have any outward identifiers of their chronological age, so estimation of seabird population age structure generally requires expensive, long-term banding studies. We investigated the potential to use a molecular age biomarker to estimate age in short-tailed shearwaters (Ardenna tenuirostris). We quantified DNA methylation in several A. tenuirostris genes that have shown age-related methylation changes in mammals. In birds ranging from chicks to 21 years of age, bisulphite treated blood and feather DNA was sequenced and methylation levels analysed in 67 CpG sites in 13 target gene regions. From blood samples, five of the top relationships with age were identified in KCNC3 loci (CpG66: R2 = 0.325, p = 0.019). In feather samples ELOVL2 (CpG42: R2 = 0.285, p = 0.00048) and EDARADD (CpG46: R2 = 0.168, p = 0.0067) were also weakly correlated with age. However, the majority of markers had no clear association with age (of 131 comparisons only 12 had a p-value < 0.05) and statistical analysis using a penalised lasso approach did not produce an accurate ageing model. Our data indicate that some age-related signatures identified in orthologous mammalian genes are not conserved in the long-lived short tailed shearwater. Alternative molecular approaches will be required to identify a reliable biomarker of chronological age in these seabirds.

  20. DNA methylation levels in candidate genes associated with chronological age in mammals are not conserved in a long-lived seabird.

    Directory of Open Access Journals (Sweden)

    Ricardo De Paoli-Iseppi

    Full Text Available Most seabirds do not have any outward identifiers of their chronological age, so estimation of seabird population age structure generally requires expensive, long-term banding studies. We investigated the potential to use a molecular age biomarker to estimate age in short-tailed shearwaters (Ardenna tenuirostris. We quantified DNA methylation in several A. tenuirostris genes that have shown age-related methylation changes in mammals. In birds ranging from chicks to 21 years of age, bisulphite treated blood and feather DNA was sequenced and methylation levels analysed in 67 CpG sites in 13 target gene regions. From blood samples, five of the top relationships with age were identified in KCNC3 loci (CpG66: R2 = 0.325, p = 0.019. In feather samples ELOVL2 (CpG42: R2 = 0.285, p = 0.00048 and EDARADD (CpG46: R2 = 0.168, p = 0.0067 were also weakly correlated with age. However, the majority of markers had no clear association with age (of 131 comparisons only 12 had a p-value < 0.05 and statistical analysis using a penalised lasso approach did not produce an accurate ageing model. Our data indicate that some age-related signatures identified in orthologous mammalian genes are not conserved in the long-lived short tailed shearwater. Alternative molecular approaches will be required to identify a reliable biomarker of chronological age in these seabirds.

  1. Genetic markers as therapeutic target in rheumatoid arthritis: A game changer in clinical therapy?

    Science.gov (United States)

    Ali, A M Mohamed Thoufic; Vino, S

    2016-11-01

    Rheumatoid arthritis (RA) is a chronic, inflammatory, multi-systemic autoimmune disease unremitted by genetic and environmental factors. The factors are crucial but inadequate in the development of disease; however, these factors can be representative of potential therapeutic targets and response to clinical therapy. Insights into the contribution of genetic risk factors are currently in progress with studies querying the genetic variation, their role in gene expression of coding and non-coding genes and other mechanisms of disease. In this review, we describe the significance of genetic markers architecture of RA through genome-wide association studies and meta-analysis studies. Further, it also reveals the mechanism of disease pathogenesis investigated through the mutual findings of functional and genetic studies of individual RA-associated genes, which includes HLA-DRB1, HLA-DQB1, HLA-DPB1, PADI4, PTPN22, TRAF1-C5, STAT4 and C5orf30. However, the genetic background of RA remains to be clearly depicted. Prospective efforts of the post-genomic and functional genomic period can travel toward real possible assessment of the genetic effect on RA. The discovery of novel genes associated with the disease can be appropriate in identifying potential biomarkers, which could assist in early diagnosis and aggressive treatment.

  2. Absence of the Genetic Marker IS6110 from a Strain of Mycobacterium tuberculosis Isolated in Ontario

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    Susan T Howard

    1998-01-01

    Full Text Available A 35-year-old female patient from Waterloo, Ontario was diagnosed with pulmonary tuberculosis in June 1995. Records indicated that the patient had emigrated from Laos circa 1990. A culture grown from a bronchoalveolar lavage specimen was identified as Mycobacterium tuberculosis by standard biochemical methods. Drug-susceptibility testing indicated the strain was resistant to pyrazinamide (PZA, and a mutation was detected within pncA, a gene associated with PZA resistance. Sequence data from the 16S rRNA gene and the 16S/23S rRNA gene spacer confirmed that the strain was a member of the M tuberculosis complex, and analysis of the mpcA and pncA genes supported the identification of the strain as M tuberculosis rather than Mycobacterium bovis. However, the insertion element IS6110, which is used for epidemiological tracing of M tuberculosis, was not detected in this strain by either restriction fragment length polymorphism analysis or by polymerase chain reaction. Two other genetic markers associated with the M tuberculosis complex, IS1081 and the direct repeat element, were present. The arrival of immigrants with tuberculosis from southeast Asia, where most strains of M tuberculosis lacking IS6110 have been traced, has important implications for epidemiological studies of tuberculosis in North America.

  3. Inflammatory cardiovascular risk markers in obstructive sleep apnoea syndrome.

    LENUS (Irish Health Repository)

    Ryan, Silke

    2012-02-01

    Obstructive sleep apnoea syndrome (OSAS) represents a highly prevalent disease and is recognized as a major public health burden. Large-scale epidemiological studies have demonstrated an independent relationship between OSAS and various cardiovascular disorders. The pathogenesis of cardiovascular complications in OSAS is not completely understood, but given the complexity of the disorder, a multifactorial etiology is likely. Inflammatory processes have emerged as critical in the pathogenesis of atherosclerosis in general and they mediate many of the stages of atheroma formation. Circulating levels of several markers of inflammation have been associated with future cardiovascular risk. These markers include cell adhesion molecules such as intercellular adhesion molecule-1 (ICAM-1) and selectins, cytokines such as tumour necrosis factor alpha (TNF-alpha) and interleukin 6 (IL-6), chemokines such as IL-8, and C-reactive protein (CRP). There is increasing evidence that inflammatory processes also play a central role in the cardiovascular pathophysiology of OSAS. This is supported by cell culture and animal studies identifying a preferential activation of inflammatory pathways by intermittent hypoxia (IH), the hallmark of OSAS. A number of studies have selectively examined the expression of inflammatory factors in OSAS patients with different conclusions. These different findings may have been contributed to by a number of methodological factors such as small subject numbers, inadequately matched study populations, particularly in terms of body mass index (BMI), and inclusion of patients with pre-existing cardiovascular or metabolic diseases. This review will focus on the potential role of various inflammatory markers in OSAS with a critical analysis of the current literature.

  4. TFF3 Expression as Stratification Marker in Borderline Epithelial Tumors of the Ovary.

    Science.gov (United States)

    El-Balat, Ahmed; Schmeil, Iryna; Karn, Thomas; Becker, Sven; Sänger, Nicole; Holtrich, Uwe; Arsenic, Ruza

    2017-05-03

    Borderline tumors (BOT) of the ovary account for 10% to 20% of ovarian neoplasms. Like ovarian cancer, BOT encompass several different histological subtypes (serous, mucinous, endometrioid, clear cell, transitional cell and mixed) with serous (SBOT) and mucinous (MBOT) the most common. Current hypotheses suggest low-grade serous carcinoma may develop in a stepwise fashion from SBOT whereas the majority of high grade serous carcinomas develop rapidly presumably from inclusion cysts or ovarian surface epithelium. The pathogenesis of mucinous ovarian tumors is still puzzling. Molecular markers could help to better define relationships between such entities. Trefoil factor-3 (TFF3) is an estrogen-regulated gene associated with prognosis in different types of cancer. It has also been included in a recent marker panel predicting subtypes of ovarian carcinoma. We analyzed the expression of TFF3 by immunohistochemistry in a cohort of 137 BOT and its association with histopathological features. Overall expression rate of TFF3 was 21.9%. None of the BOT with serous and endometrioid histology displayed strong TFF3 expression. On the other hand, TFF3 was highly expressed in 61.4% of MBOT cases and 33.3% of BOT with mixed histology (P < 0.001) suggesting a potential function of the protein in that subtypes. Associations of TFF3 expression with FIGO stage and micropapillary pattern were significant in the overall cohort but confounded by their correlation with histological subtypes. The highly specific expression of TFF3 in MBOT may help to further clarify potential relationships of tumors with mucinous histology and warrants further studies.

  5. Delta-like 1 homolog (dlk1: a marker for rhabdomyosarcomas implicated in skeletal muscle regeneration.

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    Louise H Jørgensen

    Full Text Available Dlk1, a member of the Epidermal Growth Factor family, is expressed in multiple tissues during development, and has been detected in carcinomas and neuroendocrine tumors. Dlk1 is paternally expressed and belongs to a group of imprinted genes associated with rhabdomyosarcomas but not with other primitive childhood tumors to date. Here, we investigate the possible roles of Dlk1 in skeletal muscle tumor formation. We analyzed tumors of different mesenchymal origin for expression of Dlk1 and various myogenic markers and found that Dlk1 was present consistently in myogenic tumors. The coincident observation of Dlk1 with a highly proliferative state in myogenic tumors led us to subsequently investigate the involvement of Dlk1 in the control of the adult myogenic programme. We performed an injury study in Dlk1 transgenic mice, ectopically expressing ovine Dlk1 (membrane bound C2 variant under control of the myosin light chain promotor, and detected an early, enhanced formation of myotubes in Dlk1 transgenic mice. We then stably transfected the mouse myoblast cell line, C2C12, with full-length Dlk1 (soluble A variant and detected an inhibition of myotube formation, which could be reversed by adding Dlk1 antibody to the culture supernatant. These results suggest that Dlk1 is involved in controlling the myogenic programme and that the various splice forms may exert different effects. Interestingly, both in the Dlk1 transgenic mice and the DLK1-C2C12 cells, we detected reduced myostatin expression, suggesting that the effect of Dlk1 on the myogenic programme might involve the myostatin signaling pathway. In support of a relationship between Dlk1 and myostatin we detected reciprocal expression of these two transcripts during different cell cycle stages of human myoblasts. Together our results suggest that Dlk1 is a candidate marker for skeletal muscle tumors and might be involved directly in skeletal muscle tumor formation through a modulatory effect on the

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

    DEFF Research Database (Denmark)

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

    2010-01-01

    Plant geneticists consider molecular marker assisted selection a useful additional tool in plant breeding programs to make selection more efficient. Standards for organic agriculture do not exclude the use of molecular markers as such, however for the organic sector the appropriateness of molecular...... markers is not self-evident and is often debated. Organic and low-input farming conditions require breeding for robust and flexible varieties, which may be hampered by too much focus on the molecular level. Pros and contras for application of molecular markers in breeding for organic agriculture...... was the topic of a recent European plant breeding workshop. The participants evaluated strengths, weaknesses, opportunities, and threats of the use of molecular markers and we formalized their inputs into breeder’s perspectives and perspectives seen from the organic sector’s standpoint. Clear strengths were...

  7. Overview of cardiac markers in heart disease.

    Science.gov (United States)

    Jarolim, Petr

    2014-03-01

    Cardiac troponins I and T have been the cornerstone of diagnostics of acute coronary syndrome for almost 20 years. Natriuretic peptides have established themselves in heart failure during the last decade. These and additional promising biomarkers, such as ST-2, galectin-3, GDF-15, copeptin, midregional proadrenomedullin, and the markers of glomerular filtration rate and kidney injury, are reviewed in groups corresponding to the pathophysiological processes they probe--cardiomyocyte injury, myocyte stress, inflammation, oxidative stress, plaque instability, extracellular-matrix remodeling, or those markers grouped in the neurohormone category. Biomarkers linking the renal and cardiac functions and microRNAs and metabolomic markers are addressed as well. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Markers of metastatic carcinoma of breast origin.

    Science.gov (United States)

    Gown, Allen M; Fulton, Regan S; Kandalaft, Patricia L

    2016-01-01

    This review summarizes the three major breast-associated markers that can be of assistance in evaluating metastatic carcinomas for which a breast primary diagnosis is entertained. These markers include gross cystic disease fluid protein-15 (GCDFP-15), mammaglobin, and GATA3. The first two are cytoplasmic markers that show comparable sensitivities for breast cancer, although relatively few of the published studies have employed the same antibodies against the target molecule, making direct comparisons challenging. GATA3 is a nuclear transcription factor that shows superior sensitivity to GCDFP-15 and mammaglobin. However, the specificity of GATA3 can pose challenges, inasmuch as carcinomas of the bladder and other sites can show significant levels of positivity. Determination of the optimal panel of antibodies employed in a given clinical setting will thus depend on the non-breast tumours included in the differential diagnosis. © 2015 John Wiley & Sons Ltd.

  9. Noninvasive Retinal Markers in Diabetic Retinopathy

    DEFF Research Database (Denmark)

    Blindbæk, Søren Leer; Torp, Thomas Lee; Lundberg, Kristian

    2017-01-01

    The retinal vascular system is the only part of the human body available for direct, in vivo inspection. Noninvasive retinal markers are important to identity patients in risk of sight-threatening diabetic retinopathy. Studies have correlated structural features like retinal vascular caliber...... and fractals with micro- and macrovascular dysfunction in diabetes. Likewise, the retinal metabolism can be evaluated by retinal oximetry, and higher retinal venular oxygen saturation has been demonstrated in patients with diabetic retinopathy. So far, most studies have been cross-sectional, but these can only...... disclose associations and are not able to separate cause from effect or to establish the predictive value of retinal vascular dysfunction with respect to long-term complications. Likewise, retinal markers have not been investigated as markers of treatment outcome in patients with proliferative diabetic...

  10. [Molecular classification and markers of malignant melanoma].

    Science.gov (United States)

    Tímár, József; Hársing, Judit; Somlai, Beáta

    2013-06-01

    Pathological classification of malignant melanoma did not change in the past decade, it was just completed with UV-induced skin alterations. A new feature, however, is the establishment of molecular classification of melanoma indicating that beside the most frequent genetic alterations (BRAF, NRAS, CKIT mutations) there is a wide variety of rare molecular subclasses. Unfortunately, none of these genetic alterations can be used to discriminate benign lesions from malignant ones. The frequently used "melanoma" markers are mostly melanosomal markers, therefore they are not helpful for this diagnostic purpose either. More recently, novel FISH kits have been developed analyzing characteristic copy number alterations specific for malignant melanoma. Though melanosomal markers are helpful in differencial diagnostics, the presence of normal melanocytes in various tissues (lymph nodes, intestine or brain) requires application of molecular techniques when melanoma metastasis is in question.

  11. Liver fibrosis markers in alcoholic liver disease.

    Science.gov (United States)

    Chrostek, Lech; Panasiuk, Anatol

    2014-07-07

    Alcohol is one of the main factors of liver damage. The evaluation of the degree of liver fibrosis is of great value for therapeutic decision making in patients with alcoholic liver disease (ALD). Staging of liver fibrosis is essential to define prognosis and management of the disease. Liver biopsy is a gold standard as it has high sensitivity and specificity in fibrosis diagnostics. Taking into account the limitations of liver biopsy, there is an exigency to introduce non-invasive serum markers for fibrosis that would be able to replace liver biopsy. Ideal serum markers should be specific for the liver, easy to perform and independent to inflammation and fibrosis in other organs. Serum markers of hepatic fibrosis are divided into direct and indirect. Indirect markers reflect alterations in hepatic function, direct markers reflect extracellular matrix turnover. These markers should correlate with dynamic changes in fibrogenesis and fibrosis resolution. The assessment of the degree of liver fibrosis in alcoholic liver disease has diagnostic and prognostic implications, therefore noninvasive assessment of fibrosis remains important. There are only a few studies evaluating the diagnostic and prognostic values of noninvasive biomarkers of fibrosis in patients with ALD. Several noninvasive laboratory tests have been used to assess liver fibrosis in patients with alcoholic liver disease, including the hyaluronic acid, FibroTest, FibrometerA, Hepascore, Forns and APRI indexes, FIB4, an algorithm combining Prothrombin index (PI), α-2 macroglobulin and hyaluronic acid. Among these tests, Fibrotest, FibrometerA and Hepascore demonstrated excellent diagnostic accuracy in identifying advanced fibrosis and cirrhosis, and additionally, Fibrotest was independently associated with survival. Therefore, the use of biomarkers may reduce the need for liver biopsy and permit an earlier treatment of alcoholic patients.

  12. Towards Common Balkan Lexical Evidential Markers

    Directory of Open Access Journals (Sweden)

    Maxim M. Makartsev

    2012-08-01

    Full Text Available A simple listing of lexical evidential markers in Bulgarian, Macedonian and Albanian uncovers unusual problems, because a significant part of the markers are common, both due to genetic relations between the languages (e.g. Bulg. and Maced. spored and to areal factors (e.g. Turk. word güya / gûya was loaned into Bulg. dialectal gyoa, Maced. ǵoa and Alb. gjoja; this marker also exists in Serb.. But these common markers with the same etymology do not necessarily have similar meanings, which is both a theoretical problem for the description of the language data and a practical issue for translation between the languages. As Bulgarian, Macedonian and Albanian have grammatical evidential systems as well, there is a question how the lexical evidential markers interact with evidential forms. Here the distinction between analytic and holistic reading can be quite helpful, as it clarifies the role of each of the components in constructions. In the article it is analysed on the basis of translations between the Balkan languages. The definition of evidentiality I employ in this article is the one stated by A. Aikhenvald: “evidentiality is a linguistic category whose primary meaning is [the] source of information. […] [T]his covers the way in which the information was acquired, without necessarily relating to the degree of [the] speaker’s certainty concerning the statement or whether it is true or not” [Aikhenvald 2004: 3]. It is well known that there is a certain variety of domains for expressing evidentiality; first and foremost there is a distinction between lexical and grammatical markers.1 In the following article I will concentrate on the common lexical evidential markers in Albanian, Bulgarian, and Macedonian, with a short introduction to grammatical evidentiality in these languages. _______________________ 1 As for the grammatical evidential markers in the Balkan languages, there is a tradition of their analysis dating back to the second

  13. Towards Common Balkan Lexical Evidential Markers

    Directory of Open Access Journals (Sweden)

    Maxim M. Makartsev

    2012-08-01

    Full Text Available A simple listing of lexical evidential markers in Bulgarian, Macedonian and Albanian uncovers unusual problems, because a significant part of the markers are common, both due to genetic relations between the languages (e.g. Bulg. and Maced. spored and to areal factors (e.g. Turk. word güya / gûya was loaned into Bulg. dialectal gyoa, Maced. ǵoa and Alb. gjoja; this marker also exists in Serb.. But these common markers with the same etymology do not necessarily have similar meanings, which is both a theoretical problem for the description of the language data and a practical issue for translation between the languages. As Bulgarian, Macedonian and Albanian have grammatical evidential systems as well, there is a question how the lexical evidential markers interact with evidential forms. Here the distinction between analytic and holistic reading can be quite helpful, as it clarifies the role of each of the components in constructions. In the article it is analysed on the basis of translations between the Balkan languages. The definition of evidentiality I employ in this article is the one stated by A. Aikhenvald: “evidentiality is a linguistic category whose primary meaning is [the] source of information. […] [T]his covers the way in which the information was acquired, without necessarily relating to the degree of [the] speaker’s certainty concerning the statement or whether it is true or not” [Aikhenvald 2004: 3]. It is well known that there is a certain variety of domains for expressing evidentiality; first and foremost there is a distinction between lexical and grammatical markers.1 In the following article I will concentrate on the common lexical evidential markers in Albanian, Bulgarian, and Macedonian, with a short introduction to grammatical evidentiality in these languages._______________________1 As for the grammatical evidential markers in the Balkan languages, there is a tradition of their analysis dating back to the second

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

    Science.gov (United States)

    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

  15. Prolactin-induced protein as a potential therapy response marker of adjuvant chemotherapy in breast cancer patients

    Science.gov (United States)

    Jablonska, Karolina; Grzegrzolka, Jedrzej; Podhorska-Okolow, Marzenna; Stasiolek, Mariusz; Pula, Bartosz; Olbromski, Mateusz; Gomulkiewicz, Agnieszka; Piotrowska, Aleksandra; Rys, Janusz; Ambicka, Aleksandra; Ong, Siew Hwa; Zabel, Maciej; Dziegiel, Piotr

    2016-01-01

    Many studies are dedicated to exploring the molecular mechanisms of chemotherapy-resistance in breast cancer (BC). Some of them are focused on searching for candidate genes responsible for this process. The aim of this study was typing the candidate genes associated with the response to standard chemotherapy in the case of invasive ductal carcinoma. Frozen material from 28 biopsies obtained from IDC patients with different responses to chemotherapy were examined using gene expression microarray, Real-Time PCR (RT-PCR) and Western blot (WB). Based on the microarray results, further analysis of candidate gene expression was evaluated in 120 IDC cases by RT-PCR and in 224 IDC cases by immunohistochemistry (IHC). The results were correlated with clinical outcome and molecular subtype of the BC. Gene expression microarray revealed Prolactin-Induced Peptide (PIP) as a single gene differentially expressed in BC therapy responder or non-responder patients (p G1, G2 vs. G3 cases (p=0.0027 and p=0.0013, respectively). Microarray analysis characterized PIP gene as a candidate for BC standard chemotherapy response marker. Analysis of clinical data suggests that PIP may be a good prognostic and predictive marker in IDC patients. Higher levels of PIP were related to longer DFS and MFS but not with OS. PMID:27293986

  16. Red-legged partridge (Alectoris rufa de-novo transcriptome assembly and identification of gene-related markers

    Directory of Open Access Journals (Sweden)

    Natalia Sevane

    2017-03-01

    Full Text Available The red-legged partridge (Alectoris rufa has a great socio-economic importance as a game species and is reared by millions in farms in several European countries. The ability to respond to a wide spectrum of pathogens and environmental changes is key for farm-reared animals that, as such, face even higher pathogen exposure and specifically for those submitted to restocking programs. In this study, RNA-sequencing and de-novo assembly of genes expressed in different immune tissues were performed. The raw FASTQ files were submitted to the NCBI SRA database with accession number PRJNA289204. A total of 94.2 million reads were obtained and assembled into 51,403 contigs using OASES software. The final annotated partridge immune transcriptome comprises almost 7000 unigenes, available as FASTA in the supplementary material. A total of 12,828 microsatellites and 33,857 Single Nucleotide Polymorphisms (SNPs were identified. The candidate gene sequences and the large number of potential genetic markers from the red-legged partridge transcriptome reliably identified through the use for the first time of a high coverage 100-bp paired-end RNA-seq protocol, provide new tools for future studies in this and related species, thus contributing to the ongoing development of genomic resources in avian species. Further investigation into candidate genes and gene-associated markers will help to uncover individual variability in the resistance to infections and other external aggressions in partridges.

  17. The Terpene Synthase Gene Family of Carrot (Daucus carota L.: Identification of QTLs and Candidate Genes Associated with Terpenoid Volatile Compounds

    Directory of Open Access Journals (Sweden)

    Jens Keilwagen

    2017-11-01

    Full Text Available Terpenes are an important group of secondary metabolites in carrots influencing taste and flavor, and some of them might also play a role as bioactive substances with an impact on human physiology and health. Understanding the genetic and molecular basis of terpene synthases (TPS involved in the biosynthesis of volatile terpenoids will provide insights for improving breeding strategies aimed at quality traits and for developing specific carrot chemotypes possibly useful for pharmaceutical applications. Hence, a combination of terpene metabolite profiling, genotyping-by-sequencing (GBS, and genome-wide association study (GWAS was used in this work to get insights into the genetic control of terpene biosynthesis in carrots and to identify several TPS candidate genes that might be involved in the production of specific monoterpenes. In a panel of 85 carrot cultivars and accessions, metabolite profiling was used to identify 31 terpenoid volatile organic compounds (VOCs in carrot leaves and roots, and a GBS approach was used to provide dense genome-wide marker coverage (>168,000 SNPs. Based on this data, a total of 30 quantitative trait loci (QTLs was identified for 15 terpenoid volatiles. Most QTLs were detected for the monoterpene compounds ocimene, sabinene, β-pinene, borneol and bornyl acetate. We identified four genomic regions on three different carrot chromosomes by GWAS which are both associated with high significance (LOD ≥ 5.91 to distinct monoterpenes and to TPS candidate genes, which have been identified by homology-based gene prediction utilizing RNA-seq data. In total, 65 TPS candidate gene models in carrot were identified and assigned to known plant TPS subfamilies with the exception of TPS-d and TPS-h. TPS-b was identified as largest subfamily with 32 TPS candidate genes.

  18. 78 FR 35567 - Safety Zone; Lower Mississippi River, Mile Marker 219 to Mile Marker 229, in the Vicinity of Port...

    Science.gov (United States)

    2013-06-13

    ... Captain of the Port, New Orleans has implemented a safety zone from mile marker 219 to mile marker 225... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Lower Mississippi River, Mile Marker 219 to Mile Marker 229, in the Vicinity of Port Allen Lock AGENCY: Coast Guard, DHS. ACTION: Temporary final...

  19. The role of Molecular Markers in Improvement of Fruit Crops

    Directory of Open Access Journals (Sweden)

    Zahoor Ahmad BHAT

    2010-06-01

    Full Text Available Markers have been used over the years for the classification of plants. Markers are any trait of an organism that can be identified with confidence and relative easy, and can be followed in a mapping population on another hand markers be defined as heritable entities associated with the economically important trait under the control of polygenes. Morphological markers can be detected with naked eye (naked eye polymorphism or as difference in physical or chemical properties of the macromolecules. In other words, there are two types of genetic markers viz. morphological markers or naked eye polymorphism and non-morphological markers or molecular markers. Morphological markers include traits such as plant height, disease response, photoperiod, sensitivity, shape or colour of flowers, fruits or seeds etc. Molecular markers include biochemical constituents. Morphological markers have many limitations for being used as markers particularly in fruit crops because of long generation time and large size of fruit trees besides being influenced by environment. Consequently, molecular markers could be appropriate choice to study and preserve the diversity in any germplasm. Molecular markers have diverse applications in fruit crop improvement, particularly in the areas of genetic diversity and varietal identification studies, gene tagging, disease diagnostics, pedigree analysis, hybrid detection, sex differentiation and marker assisted selection.

  20. Isolation and characterization of polymorphic microsatellite markers ...

    African Journals Online (AJOL)

    Development of highly polymorphic co-dominant markers will be important for the molecular and genomic research in flax. Two microsatellite-enriched flax genomic libraries were constructed for trinucleotide TTC and ATC motifs. A total of 206 new microsatellite-containing sequences were identified and classified.

  1. Interpreting Whole-Genome Marker Data

    Science.gov (United States)

    Weir, Bruce S.

    2013-01-01

    The challenges of whole-genome data, when genotypes are available from hundreds of thousands of genetic markers, are explored for four topics in statistical genetics: Hardy-Weinberg testing, estimating linkage disequilibrium from unphased genotypic data, association mapping and characterizing population structure. PMID:24273615

  2. Surrogate markers of atherosclerosis: impact of statins

    NARCIS (Netherlands)

    Kastelein, John J. P.; Wiegman, Albert; de Groot, Eric

    2003-01-01

    Carotid artery intima-media thickness (IMT) measured by ultrasound has been shown to be correlated with existing cardiovascular disease (CVD) and predictive of CVD in individuals without clinically evident disease. Carotid IMT is now widely used as a surrogate marker for atherosclerotic disease. A

  3. Lymphocyte markers: diagnostic help or costly vogue?

    Science.gov (United States)

    Preud'homme, J L

    1984-01-01

    Lymphocyte marker studies are routinely performed in a large number of laboratories. Reading the literature and answering daily requests from clinicians for such studies lead me to wonder whether the methodological problems, interpretation, and indications of these investigations are fully understood by everybody and whether the need for these costly technics is overestimated or not.

  4. RAPD markers demonstrate genetic diversity in Pterocarpus ...

    African Journals Online (AJOL)

    RAPD markers demonstrate genetic diversity in Pterocarpus angolensis from Zimbabwe and Zambia. E Chisha-Kasumu, S Woodward, A Price. Abstract. Understanding the availability, extent and apportionment of genetic variability in natural populations of the southern African savanna tree Pterocarpus angolensis can ...

  5. Molecular markers unravel intraspecific and interspecific genetic ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Genetics; Volume 92; Issue 2. Molecular markers unravel intraspecific and interspecific genetic variability in Plantago ovata and some of its wild allies. Shivanjali Kotwal Manoj K. Dhar Balbir Kour Kuldeep Raj Sanjana Kaul. Research Note Volume 92 Issue 2 August 2013 pp 293-298 ...

  6. Identification of Prostate Cancer Prognostic Markers

    Science.gov (United States)

    2016-10-01

    role in cellular energetics and growth. So far, our results suggest that genomic alterations may serve as prognostic markers that would improve the...shRNA vectors with better knockdown efficiency . Stable ECI1- knockdown cells would be ultimately used to perform rescue experiments for the phenotypes

  7. SNP marker detection and genotyping in tilapia

    NARCIS (Netherlands)

    Bers, van N.E.M.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Dibbits, B.W.; Komen, J.

    2012-01-01

    We have generated a unique resource consisting of nearly 175 000 short contig sequences and 3569 SNP markers from the widely cultured GIFT (Genetically Improved Farmed Tilapia) strain of Nile tilapia (Oreochromis niloticus). In total, 384 SNPs were selected to monitor the wider applicability of the

  8. Microsatellite Instability Markers Status in Colorectal Cancer

    Directory of Open Access Journals (Sweden)

    Giti Esmailnia

    2014-12-01

    Full Text Available Background: Colorectal cancer (CRC is the third most prevalent and the third leading cause of cancer-related deaths in Iran. Our aim was to investigate five mononucleotide statuses among Iranian patients with sporadic colorectal cancer. Materials and Methods: In this experimental study 80 sporadic CRC patients were evaluated for microsatellite instability (MSI. The pentaplex panel including 5 quasi mononucleotide microsatellite markers (NR-21, BAT-26, BAT-25, NR-27 and NR-24 was used. The MSI analysis was performed on paired tumoral DNA from cancerous tissues and genomic DNA from whole blood. MSI carriers were identified by analysis of tumor tissue using polymerase chain reaction. Results: Our findings showed that microsatellite instability was detected in 36 of 80 cases (45% with colorectal cancer. MSI analysis revealed that 17 cases of MSI-H (21%, 19 MSI-L (23% and 44 microsatellite stable tumors (55%. Instability is observed in the tumoral DNA compared to the DNA from the normal DNA sample. The most instable markers were NR-21, NR-24 in which instability was detected in 45% of patients. Conclusion: Using a panel including 3 mentioned MSI markers should be more promising markers for identifying MSI status in patients with sporadic colorectal cancer.

  9. Mapping markers linked to porcine salmonellosis susceptibility

    NARCIS (Netherlands)

    Galina-Pantoja, L.; Siggens, K.; Schriek, M.G.; Heuven, H.C.M.|info:eu-repo/dai/nl/314417818

    2009-01-01

    Anim Genet. 2009 Jun 3. [Epub ahead of print] Mapping markers linked to porcine salmonellosis susceptibility. Galina-Pantoja L, Siggens K, van Schriek MG, Heuven HC. PIC/Genus, 100 Bluegrass Commons Blvd, Hendersonville, TN 37075, USA. The goal of this study was to identify pig chromosomal regions

  10. Using microsatellite markers to assess genetic diversity ...

    African Journals Online (AJOL)

    bobby

    2013-05-15

    May 15, 2013 ... YAO et al. 2809. Table 1. Populations of tall coconut palm including three parental (G0) and three regenerated (G1) populations investigated in the present study of the genetic diversity by microsatellite markers. Population code, origin and sample size are also shown. Population. Generation. Codea. Origin.

  11. Random amplified polymorphic DNA (RAPD) marker associated ...

    African Journals Online (AJOL)

    Jane

    2011-06-29

    Jun 29, 2011 ... between the studied provenances were less than 39%. Key words: Acacia Senegal, provenance variation, random amplified polymorphic DNA (RAPD) marker, salt tolerance, seed germination, seedling growth. INTRODUCTION. Salinity is the major factor limiting plants growth, widely spread and has more ...

  12. Predicting the relationship between molecular marker ...

    African Journals Online (AJOL)

    hope&shola

    2010-11-08

    Nov 8, 2010 ... Genetic diversity for restriction fragment length polymorphisms and heterosis for two diallel sets of maize inbreds. Theor. Appl. Genet. 80: 488-496. Mezeneer N, Ghesquire A, Marmey P, Combes MC, Guideror E (1997). Assessment of RAPD markers to detect genetic change in protoplast derived rice plants.

  13. Structural assessment of backcrossing using microsatellite markers ...

    African Journals Online (AJOL)

    Backcrossing, coupled with marker or gene assisted selection, can be used to introgress a specific gene or chromosomal region from one population into another. The objective of this study was to assess the genomic structure of cattle produced by backcrossing for loci that are unlinked to a locus that was being introgressed ...

  14. Random amplified polymorphic DNA (RAPD) marker associated ...

    African Journals Online (AJOL)

    Jane

    2011-06-29

    Jun 29, 2011 ... bands detected were polymorphic for the provenances of A. senegal and the dissimilarity indices between the studied provenances were less than 39%. Key words: Acacia Senegal, provenance variation, random amplified polymorphic DNA (RAPD) marker, salt tolerance, seed germination, seedling growth ...

  15. Molecular marker genes for ectomycorrhizal symbiosis

    Science.gov (United States)

    Shiv Hiremath; Carolyn McQuattie; Gopi Podila; Jenise. Bauman

    2013-01-01

    Mycorrhizal symbiosis is a mutually beneficial association very commonly found among most vascular plants. Formation of mycorrhiza happens only between compatible partners and predicting this is often accomplished through a trial and error process. We investigated the possibility of using expression of symbiosis specific genes as markers to predict the formation of...

  16. Bridging the Gap Between Large-scale Data Sets and Analyses: Semi-automated Methods to Facilitate Length Polymorphism Scoring and Data Analyses.

    Science.gov (United States)

    Amplified fragment length polymorphism (AFLP) markers can be developed more quickly and at a lower cost than microsatellite and single nucleotide polymorphism markers, which makes them ideal markers for large-scale studies of understudied taxa — such as species at risk. However,...

  17. Marker formation vs. marker offset - on the resolution potential of tectono-geomorphic records

    Science.gov (United States)

    Zielke, Olaf

    2017-04-01

    Understanding the recurrence and actual size of large and damaging earthquakes is an important step towards mitigating the hazard of future seismic events. Coseismically displaced geomorphic and stratigraphic markers are commonly utilized to constrain the recurrence history of surface-rupturing events. An underlying assumption of this approach is that the formation of new geomorphic markers is (distinctly) more frequent than the occurrence of surface-rupturing earthquakes that will disrupt and offset them (the markers). If this assumption is valid, then the offsets that are caused by individual earthquakes can be distinguished, providing valuable information on the causative earthquake size and its variability. Many of the currently existing earthquake recurrence models, such as the characteristic, the uniform-slip, and the variable-slip earthquake model were formulated following this general approach and the underlying assumption. However, whether this assumption is valid or not is essentially never tested or questioned. How sensitive are those recurrence models with regards to the validity of the afore-mentioned assumption that marker formation is more frequent than marker offset? Could it be that the observed recurrence characteristics represent the properties of climatic forcing rather than tectonic activity? To address this question, I utilize a statistical model in which I create markers and then displace them by sampling from a number of different probability distributions for marker formation and offset. In doing so, I create a library of recurrence patterns in which the corresponding patterns depend on timing and relative strength of marker formation and marker offset events. In my presentation I compare these model results with reported earthquake recurrence data (i.e., slip accumulation patterns). This comparison indicates that the surface displacement of ground-rupturing earthquakes is required to exhibit some form of "characteristic" behavior (with

  18. PDGFRβ Is a Novel Marker of Stromal Activation in Oral Squamous Cell Carcinomas.

    Directory of Open Access Journals (Sweden)

    Vinay K Kartha

    Full Text Available Carcinoma associated fibroblasts (CAFs form the main constituents of tumor stroma and play an important role in tumor growth and invasion. The presence of CAFs is a strong predictor of poor prognosis of head and neck squamous cell carcinoma. Despite significant progress in determining the role of CAFs in tumor progression, the mechanisms contributing to their activation remain poorly characterized, in part due to fibroblast heterogeneity and the scarcity of reliable fibroblast surface markers. To search for such markers in oral squamous cell carcinoma (OSCC, we applied a novel approach that uses RNA-sequencing data derived from the cancer genome atlas (TCGA. Specifically, our strategy allowed for an unbiased identification of genes whose expression was closely associated with a set of bona fide stroma-specific transcripts, namely the interstitial collagens COL1A1, COL1A2, and COL3A1. Among the top hits were genes involved in cellular matrix remodeling and tumor invasion and migration, including platelet-derived growth factor receptor beta (PDGFRβ, which was found to be the highest-ranking receptor protein genome-wide. Similar analyses performed on ten additional TCGA cancer datasets revealed that other tumor types shared CAF markers with OSCC, including PDGFRβ, which was found to significantly correlate with the reference collagen expression in ten of the 11 cancer types tested. Subsequent immunostaining of OSCC specimens demonstrated that PDGFRβ was abundantly expressed in stromal fibroblasts of all tested cases (12/12, while it was absent in tumor cells, with greater specificity than other known markers such as alpha smooth muscle actin or podoplanin (3/11. Overall, this study identified PDGFRβ as a novel marker of stromal activation in OSCC, and further characterized a list of promising candidate CAF markers that may be relevant to other carcinomas. Our novel approach provides for a fast and accurate method to identify CAF markers without

  19. PDGFRβ Is a Novel Marker of Stromal Activation in Oral Squamous Cell Carcinomas.

    Science.gov (United States)

    Kartha, Vinay K; Stawski, Lukasz; Han, Rong; Haines, Paul; Gallagher, George; Noonan, Vikki; Kukuruzinska, Maria; Monti, Stefano; Trojanowska, Maria

    2016-01-01

    Carcinoma associated fibroblasts (CAFs) form the main constituents of tumor stroma and play an important role in tumor growth and invasion. The presence of CAFs is a strong predictor of poor prognosis of head and neck squamous cell carcinoma. Despite significant progress in determining the role of CAFs in tumor progression, the mechanisms contributing to their activation remain poorly characterized, in part due to fibroblast heterogeneity and the scarcity of reliable fibroblast surface markers. To search for such markers in oral squamous cell carcinoma (OSCC), we applied a novel approach that uses RNA-sequencing data derived from the cancer genome atlas (TCGA). Specifically, our strategy allowed for an unbiased identification of genes whose expression was closely associated with a set of bona fide stroma-specific transcripts, namely the interstitial collagens COL1A1, COL1A2, and COL3A1. Among the top hits were genes involved in cellular matrix remodeling and tumor invasion and migration, including platelet-derived growth factor receptor beta (PDGFRβ), which was found to be the highest-ranking receptor protein genome-wide. Similar analyses performed on ten additional TCGA cancer datasets revealed that other tumor types shared CAF markers with OSCC, including PDGFRβ, which was found to significantly correlate with the reference collagen expression in ten of the 11 cancer types tested. Subsequent immunostaining of OSCC specimens demonstrated that PDGFRβ was abundantly expressed in stromal fibroblasts of all tested cases (12/12), while it was absent in tumor cells, with greater specificity than other known markers such as alpha smooth muscle actin or podoplanin (3/11). Overall, this study identified PDGFRβ as a novel marker of stromal activation in OSCC, and further characterized a list of promising candidate CAF markers that may be relevant to other carcinomas. Our novel approach provides for a fast and accurate method to identify CAF markers without the need for

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

    Science.gov (United States)

    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. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  1. Efficacy and safety of ultrasound-guided implantation of fiducial markers in the liver for stereotactic body radiation therapy.

    Science.gov (United States)

    Park, So Hyun; Won, Hyung Jin; Kim, So Yeon; Shin, Yong Moon; Kim, Pyo Nyun; Yoon, Sang Min; Park, Jin-Hong; Kim, Jong Hoon

    2017-01-01

    Stereotactic body radiation therapy (SBRT) for the treatment of a malignancy in the liver requires the perilesional implantation of fiducial markers for lesion detection. The purpose of this study is to evaluate the efficacy and safety of ultrasound (US) -guided marker implantation for SBRT. We retrospectively reviewed 299, US-guided, intrahepatic fiducial markers implanted in 101 patients between November 2013 and September 2014. SBRT-planning CT images were analyzed to determine the technical success of the implantation, the mean distance between the tumor margin and the marker, with the ideal location of fiducials defined as the distance between a marker and a tumor less than 3 cm and the distance between markers greater than 2 cm according to the tumor conspicuity seen on gray-scale US and the artifact obscuring tumor margins. We also evaluated procedure-related major and minor complications. Technical success was achieved in 291 (97.3%) fiducial marker implantations. The mean distance between the tumor and the marker was 3.1 cm (S.D., 2.1 cm; range, 0-9.5 cm). Of 101 patients, 72 lesions (71.3%, 2.2 ± 1.0 cm; range, 0-3.0 cm) had fiducial markers located in an ideal location. The ideal location of fiducials was more common in visible lesions than in poorly conspicuous lesions (90.2% vs. 52.0%, P hardening artifacts obscuring the tumor margins. There were no major complications, although 12 patients (11.9%) developed minor complications. US-guided implantation of fiducial markers in the liver is an effective and safe procedure with only rare complications.

  2. Testing for Hardy-Weinberg equilibrium at biallelic genetic markers on the X chromosome.

    Science.gov (United States)

    Graffelman, J; Weir, B S

    2016-06-01

    Testing genetic markers for Hardy-Weinberg equilibrium (HWE) is an important tool for detecting genotyping errors in large-scale genotyping studies. For markers at the X chromosome, typically the χ(2) or exact test is applied to the females only, and the hemizygous males are considered to be uninformative. In this paper we show that the males are relevant, because a difference in allele frequency between males and females may indicate HWE not to hold. The testing of markers on the X chromosome has received little attention, and in this paper we lay down the foundation for testing biallelic X-chromosomal markers for HWE. We develop four frequentist statistical test procedures for X-linked markers that take both males and females into account: the χ(2) test, likelihood ratio test, exact test and permutation test. Exact tests that include males are shown to have a better Type I error rate. Empirical data from the GENEVA project on venous thromboembolism is used to illustrate the proposed tests. Results obtained with the new tests differ substantially from tests that are based on female genotype counts only. The new tests detect differences in allele frequencies and seem able to uncover additional genotyping error that would have gone unnoticed in HWE tests based on females only.

  3. Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance

    Directory of Open Access Journals (Sweden)

    A.D. Chowdhury

    2016-11-01

    Full Text Available Salt stress is a major problem in most of the rice growing areas in the world. A major QTL Saltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice. This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated with salt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1 to 9 score at EC = 10 dSm-1 under controlled environmental conditions. Seven new breeding lines including three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 and can be good sources of new genes/alleles for salt tolerance. Simple sequence repeat (SSR marker RM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information content value varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54 lines were clearly separated into two major clusters. Fourteen haplotypes were identified based on Saltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminate between the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assisted selection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 on chromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.

  4. Fatigue as prognostic risk marker of mental sickness absence in white collar employees.

    Science.gov (United States)

    Roelen, C A M; Heymans, M W; van Rhenen, W; Groothoff, J W; Twisk, J W R; Bültmann, U

    2014-06-01

    To investigate fatigue as prognostic risk marker for identifying working employees at risk of long-term sickness absence (SA). At baseline, fatigue was measured in 633 white collar employees with the checklist individual strength (CIS) including scales for fatigue severity, reduced concentration, reduced motivation, and reduced physical activity. SA was medically certified by an occupational physician in the 3rd or 4th SA week with diagnostic codes according to the 10th version of the International Classification of Diseases. Medically certified SA was retrieved at the individual level from an occupational health register after 1-year follow-up. CIS scores were investigated as prognostic risk markers predicting medically certified SA and particularly SA certified as mental SA. 614 employees (N = 378 men and N = 236 women) had complete data and were eligible for analysis; 63 (10 %) had medically certified SA of whom 39 (6 %) had mental SA. Fatigue severity and total CIS scores were associated with medically certified SA in men, but poorly discriminated between men with and without medically certified SA. Fatigue severity, reduced concentration, reduced motivation, and total CIS scores were also associated with mental SA in men. CIS and its reduced concentration scale were valid prognostic risk markers of mental SA. CONCLUSION Fatigue was a prognostic risk marker of mental SA in white collar men. The CIS should be further validated as a screening tool for the risk of mental SA in white collar working populations.

  5. Whole-Genome Analysis of Candidate genes Associated with Seed Size and Weight in Sorghum bicolor Reveals Signatures of Artificial Selection and Insights into Parallel Domestication in Cereal Crops.

    Science.gov (United States)

    Tao, Yongfu; Mace, Emma S; Tai, Shuaishuai; Cruickshank, Alan; Campbell, Bradley C; Zhao, Xianrong; Van Oosterom, Erik J; Godwin, Ian D; Botella, Jose R; Jordan, David R

    2017-01-01

    Seed size and seed weight are major quality attributes and important determinants of yield that have been strongly selected for during crop domestication. Limited information is available about the genetic control and genes associated with seed size and weight in sorghum. This study identified sorghum orthologs of genes with proven effects on seed size and weight in other plant species and searched for evidence of selection during domestication by utilizing resequencing data from a diversity panel. In total, 114 seed size candidate genes were identified in sorghum, 63 of which exhibited signals of purifying selection during domestication. A significant number of these genes also had domestication signatures in maize and rice, consistent with the parallel domestication of seed size in cereals. Seed size candidate genes that exhibited differentially high expression levels in seed were also found more likely to be under selection during domestication, supporting the hypothesis that modification to seed size during domestication preferentially targeted genes for intrinsic seed size rather than genes associated with physiological factors involved in the carbohydrate supply and transport. Our results provide improved understanding of the complex genetic control of seed size and weight and the impact of domestication on these genes.

  6. A Comparison Between Denaturing Gradient Gel Electrophoresis and Denaturing High Performance Liquid Chromatography in Detecting Mutations in Genes Associated with Hereditary Non-Polyposis Colorectal Cancer (HNPCC and the Identification of 9 New Mutations Previously Unidentified by DGGE

    Directory of Open Access Journals (Sweden)

    Meldrum Cliff J

    2003-12-01

    Full Text Available Abstract Denaturing high performance liquid chromatography is a relatively new method by which heteroduplex structures formed during the PCR amplification of heterozygote samples can be rapidly identified. The use of this technology for mutation detection in hereditary non-polyposis colorectal cancer (HNPCC has the potential to appreciably shorten the time it takes to analyze genes associated with this disorder. Prior to acceptance of this method for screening genes associated with HNPCC, assessment of the reliability of this method should be performed. In this report we have compared mutation and polymorphism detection by denaturing gradient gel electrophoresis (DGGE with denaturing high performance liquid chromatography (DHPLC in a set of 130 families. All mutations/polymorphisms representing base substitutions, deletions, insertions and a 23 base pair inversion were detected by DHPLC whereas DGGE failed to identify four single base substitutions and a single base pair deletion. In addition, we show that DHPLC has been used for the identification of 5 different mutations in exon 7 of hMSH2 that could not be detected by DGGE. From this study we conclude that DHPLC is a more effective and rapid alternative to the detection of mutations in hMSH2 and hMLH1 with the same or better accuracy than DGGE. Furthermore, this technique offers opportunities for automation, which have not been realised for the majority of other methods of gene analysis.

  7. The role of rheumatoid arthritis genetic susceptibility markers in the prediction of erosive disease in patients with early inflammatory polyarthritis: results from the Norfolk Arthritis Register

    Science.gov (United States)

    Plant, Darren; Thomson, Wendy; Lunt, Mark; Flynn, Edward; Martin, Paul; Eyre, Steven; Farragher, Tracey; Bunn, Diane; Worthington, Jane; Symmons, Deborah

    2011-01-01

    Objectives. Recent whole-genome and candidate gene association studies in RA have identified a number of single nucleotide polymorphisms (SNPs) that predispose to disease with moderate risk. It remains poorly understood how recently identified genetic factors may contribute to RA severity. We therefore sought to investigate the role of recently identified RA susceptibility SNP markers in predicting erosive outcome in patients with recent-onset inflammatory polyarthritis (IP). Methods. DNA and X-ray data were available for 1049 patients who were registered between 1990 and 2003 with the Norfolk Arthritis Register (NOAR); a primary care-based inception cohort of patients with recent-onset IP. Demographic and clinical data were recorded at inclusion, and at yearly assessments thereafter. Patients were genotyped for 18 SNP markers. The presence of serum anti citrullinated peptide antibodies (ACPAs) was assessed in samples collected at inclusion to the NOAR. The association of serological and genetic markers with poor radiological (Larsen) score at Years 1 and 5, and erosions at Years 1 and 5 was investigated. Results. Baseline ACPA positivity was associated with erosive disease and higher radiological damage. SNP markers within the TRAF1/C5 locus were associated with erosive disease at Year 1 [rs2900180: odds ratio (OR) 1.53 (95% CI 1.14, 2.05)] and Year 5 [rs2900180: OR 1.47 (95% CI 1.07, 2.02)]. None of the SNP markers tested was associated with Larsen score. Conclusion. Our results are in keeping with a previous report and suggest that the TRAF1/C5 region is associated with risk of development of radiological erosions in IP/RA patients. The finding requires replication in other large data sets. PMID:20219786

  8. Markers for blood-brain barrier integrity

    DEFF Research Database (Denmark)

    Saunders, Norman R; Dziegielewska, Katarzyna M; Møllgård, Kjeld

    2015-01-01

    known when first introduced, but seem to have been forgotten since. Understanding these limitations is important because Evans blue is still the most commonly used marker of brain barrier integrity and those using it seem oblivious to problems arising from its in vivo application. The introduction......In recent years there has been a resurgence of interest in brain barriers and various roles their intrinsic mechanisms may play in neurological disorders. Such studies require suitable models and markers to demonstrate integrity and functional changes at the interfaces between blood, brain......, and cerebrospinal fluid. Studies of brain barrier mechanisms and measurements of plasma volume using dyes have a long-standing history, dating back to the late nineteenth-century. Their use in blood-brain barrier studies continues in spite of their known serious limitations in in vivo applications. These were well...

  9. Predictive markers of honey bee colony collapse.

    Directory of Open Access Journals (Sweden)

    Benjamin Dainat

    Full Text Available Across the Northern hemisphere, managed honey bee colonies, Apis mellifera, are currently affected by abrupt depopulation during winter and many factors are suspected to be involved, either alone or in combination. Parasites and pathogens are considered as principal actors, in particular the ectoparasitic mite Varroa destructor, associated viruses and the microsporidian Nosema ceranae. Here we used long term monitoring of colonies and screening for eleven disease agents and genes involved in bee immunity and physiology to identify predictive markers of honeybee colony losses during winter. The data show that DWV, Nosema ceranae, Varroa destructor and Vitellogenin can be predictive markers for winter colony losses, but their predictive power strongly depends on the season. In particular, the data support that V. destructor is a key player for losses, arguably in line with its specific impact on the health of individual bees and colonies.

  10. Predictive markers of honey bee colony collapse.

    Science.gov (United States)

    Dainat, Benjamin; Evans, Jay D; Chen, Yan Ping; Gauthier, Laurent; Neumann, Peter

    2012-01-01

    Across the Northern hemisphere, managed honey bee colonies, Apis mellifera, are currently affected by abrupt depopulation during winter and many factors are suspected to be involved, either alone or in combination. Parasites and pathogens are considered as principal actors, in particular the ectoparasitic mite Varroa destructor, associated viruses and the microsporidian Nosema ceranae. Here we used long term monitoring of colonies and screening for eleven disease agents and genes involved in bee immunity and physiology to identify predictive markers of honeybee colony losses during winter. The data show that DWV, Nosema ceranae, Varroa destructor and Vitellogenin can be predictive markers for winter colony losses, but their predictive power strongly depends on the season. In particular, the data support that V. destructor is a key player for losses, arguably in line with its specific impact on the health of individual bees and colonies.

  11. Biomolecular Markers in Cancer of the Tongue

    Directory of Open Access Journals (Sweden)

    Daris Ferrari

    2009-01-01

    Full Text Available The incidence of tongue cancer is increasing worldwide, and its aggressiveness remains high regardless of treatment. Genetic changes and the expression of abnormal proteins have been frequently reported in the case of head and neck cancers, but the little information that has been published concerning tongue tumours is often contradictory. This review will concentrate on the immunohistochemical expression of biomolecular markers and their relationships with clinical behaviour and prognosis. Most of these proteins are associated with nodal stage, tumour progression and metastases, but there is still controversy concerning their impact on disease-free and overall survival, and treatment response. More extensive clinical studies are needed to identify the patterns of molecular alterations and the most reliable predictors in order to develop tailored anti-tumour strategies based on the targeting of hypoxia markers, vascular and lymphangiogenic factors, epidermal growth factor receptors, intracytoplasmatic signalling and apoptosis.

  12. Collagen markers in peritoneal dialysis patients

    DEFF Research Database (Denmark)

    Graff, J; Joffe, P; Fugleberg, S

    1995-01-01

    Possible relationships between the dialysate-to-plasma creatinine equilibration ratio (D/Pcreatinine 4 hour), duration of peritoneal dialysis treatment, number of peritonitis episodes, and mass appearance rates of three connective tissue markers [carboxyterminal propeptide of type I procollagen...... (PICP), aminoterminal propeptide of type III procollagen (PIIINP), and carboxyterminal telopeptide of type I collagen (ICTP)] were studied in 19 nondiabetic peritoneal dialysis patients. The absence of correlation between the mass appearance rates of the markers and the duration of dialysis treatment...... as well as the number of peritonitis episodes supports the concept that peritoneal dialysis does not cause persistent changes in the deposition and degradation rates of collagen. A correlation between the D/Pcreatinine 4 hr and the PICP mass appearance rates was found. Since it is unlikely...

  13. DNA markers for Portuguese olive oil fingerprinting.

    Science.gov (United States)

    Martins-Lopes, Paula; Gomes, Sónia; Santos, Elisabete; Guedes-Pinto, Henrique

    2008-12-24

    The certification of olive oil has led to the definition of Protected Denomination of Origin (PDO) producing regions in European countries. PDO products should be protected, and a solution could be by using DNA fingerprinting. In this work we evaluate the efficiency of RAPD, ISSR, and SSR molecular markers for olive oil varietal identification and their possible use in certification purposes. Twenty-three Portuguese olive oil samples (11 obtained monovarietal and 12 purchased commercial oils) were screened by means of two RAPD, four ISSR, and four SSR markers. The quality of amplified products was used to evaluate the reproducibility and the level of polymorphism. Principal component analysis was performed with DCENTER using unweighted pair group mathematical average (UPGMA) that allowed group formation according to olive oil varietal geographic origin.

  14. Learner Autonomy Scale: A Scale Development Study

    Science.gov (United States)

    Orakci, Senol; Gelisli, Yücel

    2017-01-01

    The goal of the study is to develop a scale named "Learner Autonomy Scale" (LAS) for determining the learner autonomy of the students toward English lesson. The proposal scale, composed of 29 items, was applied to two study groups in Turkey. The group of Exploratory Factor Analysis that aims to determine the psychometric properties…

  15. Drawing organic photovoltaics using paint marker pens

    Science.gov (United States)

    Suzuki, Kaori; Izawa, Seiichiro; Chen, Yujiao; Nakano, Kyohei; Tajima, Keisuke

    2017-11-01

    Active layers for organic photovoltaic devices (OPVs) were prepared by hand drawing with paint marker pens containing solutions of the materials. Although the pen-coated organic films were visually non-uniform with quite high surface roughness, OPV devices using these films exhibited similar or slightly better performances than those using spin-coated films. As such, the pen-coating technique represents an easily accessible, inexpensive, and highly material-efficient method for fabricating OPVs.

  16. ONLINE RESOURCES Development of Novel microsatellite markers ...

    Indian Academy of Sciences (India)

    sony vaio

    Rymer P.D., Harris S. and Boshier D. 2014 Isolation and characterization of microsatellite markers for the neotropical tree Pachir aquinata (Malvaceae). Conserv. Genet ... Sonah H., Deshmukh R.K., Sharma A., Singh V.P., Gupta D.K., Gacche R.N., Rana J.C., Singh. N.K. and Sharma T.R. 2011 Genome wide distribution and ...

  17. MACD - an imaging marker for cardiovascular disease

    DEFF Research Database (Denmark)

    Ganz, Melanie; de Bruijne, Marleen; Nielsen, Mads

    2010-01-01

    Despite general acceptance that a healthy lifestyle and the treatment of risk factors can prevent the development of cardiovascular diseases (CVD), CVD are the most common cause of death in Europe and the United States. It has been shown that abdominal aortic calcifications (AAC) correlate strongly...... imaging markers described. Finally we present that the MACD index predicts cardiovascular death with a hazard ratio of approximately four....

  18. Genetic Markers for Differentiating Aspirin-Hypersensitivity

    OpenAIRE

    Kim, Seung-Hyun; Park, Hae-Sim

    2006-01-01

    Aspirin-induced asthma (AIA) and aspirin-induced urticaria/angioedema (AIU) are two major aspirin-related allergies. We summarize recent findings related to their molecular genetic mechanisms in order to identify genetic susceptibility markers for differentiating AIU and AIA. The overproduction of cysteinyl leukotriene has been suggested as a mechanism in both AIU and AIA. Increased expression of CYSLTR1 with CYLSTR1 and CYSLTR2 polymorphisms are new findings in AIA, while the ALOX5 promoter ...

  19. Automated genotyping of dinucleotide repeat markers

    Energy Technology Data Exchange (ETDEWEB)

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

    1994-09-01

    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  20. DNA marker technology for wildlife conservation

    OpenAIRE

    Arif, Ibrahim A.; Haseeb A. Khan; Bahkali, Ali H.; Al Homaidan, Ali A.; Ahmad H. Al Farhan; Al Sadoon, Mohammad; Shobrak, Mohammad

    2011-01-01

    Use of molecular markers for identification of protected species offers a greater promise in the field of conservation biology. The information on genetic diversity of wildlife is necessary to ascertain the genetically deteriorated populations so that better management plans can be established for their conservation. Accurate classification of these threatened species allows understanding of the species biology and identification of distinct populations that should be managed with utmost care...

  1. Markers of T Cell Senescence in Humans

    Directory of Open Access Journals (Sweden)

    Weili Xu

    2017-08-01

    Full Text Available Many countries are facing the aging of their population, and many more will face a similar obstacle in the near future, which could be a burden to many healthcare systems. Increased susceptibility to infections, cardiovascular and neurodegenerative disease, cancer as well as reduced efficacy of vaccination are important matters for researchers in the field of aging. As older adults show higher prevalence for a variety of diseases, this also implies higher risk of complications, including nosocomial infections, slower recovery and sequels that may reduce the autonomy and overall quality of life of older adults. The age-related effects on the immune system termed as “immunosenescence” can be exemplified by the reported hypo-responsiveness to influenza vaccination of the elderly. T cells, which belong to the adaptive arm of the immune system, have been extensively studied and the knowledge gathered enables a better understanding of how the immune system may be affected after acute/chronic infections and how this matters in the long run. In this review, we will focus on T cells and discuss the surface and molecular markers that are associated with T cell senescence. We will also look at the implications that senescent T cells could have on human health and diseases. Finally, we will discuss the benefits of having these markers for investigators and the future work that is needed to advance the field of T cell senescence markers.

  2. Prognostic DNA Methylation Markers for Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Siri H. Strand

    2014-09-01

    Full Text Available Prostate cancer (PC is the most commonly diagnosed neoplasm and the third most common cause of cancer-related death amongst men in the Western world. PC is a clinically highly heterogeneous disease, and distinction between aggressive and indolent disease is a major challenge for the management of PC. Currently, no biomarkers or prognostic tools are able to accurately predict tumor progression at the time of diagnosis. Thus, improved biomarkers for PC prognosis are urgently needed. This review focuses on the prognostic potential of DNA methylation biomarkers for PC. Epigenetic changes are hallmarks of PC and associated with malignant initiation as well as tumor progression. Moreover, DNA methylation is the most frequently studied epigenetic alteration in PC, and the prognostic potential of DNA methylation markers for PC has been demonstrated in multiple studies. The most promising methylation marker candidates identified so far include PITX2, C1orf114 (CCDC181 and the GABRE~miR-452~miR-224 locus, in addition to the three-gene signature AOX1/C1orf114/HAPLN3. Several other biomarker candidates have also been investigated, but with less stringent clinical validation and/or conflicting evidence regarding their possible prognostic value available at this time. Here, we review the current evidence for the prognostic potential of DNA methylation markers in PC.

  3. Leptin as local inflammatory marker in COPD.

    Science.gov (United States)

    Broekhuizen, R; Vernooy, J H J; Schols, A M W J; Dentener, M A; Wouters, E F M

    2005-01-01

    Chronic inflammation of the lung is a characteristic finding in chronic obstructive pulmonary disease (COPD). Leptin is a pleiotropic cytokine thought to play a role in host response to inflammation. As recent studies have shown that leptin receptors are present in the lung, this study aimed to determine if leptin is detectable in induced sputum of COPD patients and if there is a relationship between leptin and other inflammatory markers in sputum. Sputum was induced in 14 male patients with moderate COPD (FEV1: 56 (15) % pred.). Leptin, total tumour necrosis factor (TNF)-alpha, and C-reactive protein (CRP) were analyzed in induced sputum supernatant by ELISA. Leptin was also determined in EDTA plasma. Leptin was detectable in induced sputum of 10 COPD patients. A significant relationship was found between sputum leptin and CRP (r = 0.943, P leptin and sputum leptin were inversely correlated (r = -0.643, P leptin is detectable in induced sputum of patients with moderate COPD and is related to other inflammatory markers. The observed correlations between leptin and inflammatory markers in sputum may indicate that leptin is involved in the local inflammatory response in COPD.

  4. Early markers of adult obesity: a review

    Science.gov (United States)

    Brisbois, T D; Farmer, A P; McCargar, L J

    2012-01-01

    Summary The purpose of this review was to evaluate factors in early childhood (≤5 years of age) that are the most significant predictors of the development of obesity in adulthood. Factors of interest included exposures/insults in the prenatal period, infancy and early childhood, as well as other socio-demographic variables such as socioeconomic status (SES) or birth place that could impact all three time periods. An extensive electronic and systematic search initially resulted in 8,880 citations, after duplicates were removed. Specific inclusion and exclusion criteria were set, and following two screening processes, 135 studies were retained for detailed abstraction and analysis. A total of 42 variables were associated with obesity in adulthood; however, of these, only seven variables may be considered as potential early markers of obesity based on the reported associations. Possible early markers of obesity included maternal smoking and maternal weight gain during pregnancy. Probable early markers of obesity included maternal body mass index, childhood growth patterns (early rapid growth and early adiposity rebound), childhood obesity and father's employment (a proxy measure for SES in many studies). Health promotion programmes/agencies should consider these factors as reasonable targets to reduce the risk of adult obesity. PMID:22171945

  5. Bone Remodelling Markers in Rheumatoid Arthritis

    Directory of Open Access Journals (Sweden)

    Patrice Fardellone

    2014-01-01

    Full Text Available Bone loss in rheumatoid arthritis (RA patients results from chronic inflammation and can lead to osteoporosis and fractures. A few bone remodeling markers have been studied in RA witnessing bone formation (osteocalcin, serum aminoterminal propeptide of type I collagen (PINP, serum carboxyterminal propeptide of type I collagen (ICTP, bone alkaline phosphatase (BAP, osteocalcin (OC, and bone resorption: C-terminal telopeptide of type 1 collagen (I-CTX, N-terminal telopeptide of type 1 collagen (I-NTX, pyridinolines (DPD and PYD, and tartrate-resistant acid phosphatase (TRAP. Bone resorption can be seen either in periarticular bone (demineralization and erosion or in the total skeleton (osteoporosis. Whatever the location, bone resorption results from activation of osteoclasts when the ratio between osteoprotegerin and receptor activator of nuclear factor kappa-B ligand (OPG/RANKL is decreased under influence of various proinflammatory cytokines. Bone remodeling markers also allow physicians to evaluate the effect of drugs used in RA like biologic agents, which reduce inflammation and exert a protecting effect on bone. We will discuss in this review changes in bone markers remodeling in patients with RA treated with biologics.

  6. Fecal Molecular Markers for Colorectal Cancer Screening

    Directory of Open Access Journals (Sweden)

    Rani Kanthan

    2012-01-01

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

  7. HLA markers in familial Lichen sclerosus.

    Science.gov (United States)

    Aslanian, Flavia M N P; Marques, Maria Teresa Q; Matos, Haroldo J; Pontes, Luciane F S; Porto, Luis Cristóvão S; Azevedo, Lucia M S; Filgueira, Absalom L

    2006-10-01

    Lichen sclerosus (LS) has been identified with increased frequency in families,often associated with HLA markers, mainly DQ7. A genetic co-etiology seems likely in this setting. Moreover, there is an association of LS with autoimmune disorders, such as the presence of anti-thyroid peroxidase autoantibodies (anti-TPO), a hallmark of autoimmune thyroid diseases. In 3 families affected by LS, we verified their HLA markers, and identified previously undiagnosed cases of LS and autoimmune disorders. 30 individuals were examined with history, skin biopsy, HLA class I and II typing by PCR-SSP, and measurement of anti-TPO, free thyroxine and thyroidstimulating hormones (TSH) levels. There were 8 cases of LS, 50 % of them anti-TPO+. Autoimmune disorders were found in 40 % (total) and in 87.5 % of those affected. Most common HLA markers were B*15, B*57, CW*03, CW*07, CW*18, DRB1*04, DRB1*07, DRB4*. The three latter have been previously associated with LS. New cases of LS and autoimmune disorders can be detected in first degree relatives of patients with LS. The presence of anti-TPO antibodies strongly suggests autoimmune thyroiditis. There is intra-familial association between the haplotype HLA-B*15 -DRB1*04 -DRB4* and anti-TPO,emphasizing their link with thyroiditis. New familial approaches might help to make clear the pathogenesis of LS and its association with autoimmune diseases.

  8. Haptocorrin as marker of disease progression in fibrolamellar hepatocellular carcinoma

    DEFF Research Database (Denmark)

    Lildballe, Dorte Launholt; Nguyen, Khoa Tran; Poulsen, Steen Seier

    2011-01-01

    No valid markers are routinely available to follow disease progression in patients with fibrolamellar hepatocellular carcinoma (FLHCC). We report data suggesting that the vitamin B12 binding protein haptocorrin (HC) may prove a suitable marker....

  9. Lipid-related markers and cardiovascular disease prediction

    DEFF Research Database (Denmark)

    Di Angelantonio, Emanuele; Gao, Pei; Pennells, Lisa

    2012-01-01

    The value of assessing various emerging lipid-related markers for prediction of first cardiovascular events is debated.......The value of assessing various emerging lipid-related markers for prediction of first cardiovascular events is debated....

  10. Characterization of fifteen SNP markers by mining EST in sea ...

    Indian Academy of Sciences (India)

    pdf]. Introduction. Fifteen single nucleotide polymorphism (SNP) markers were validated and characterized in the sea cucumber ... ers are powerful tools for conservation and management of natural resources, and for marker-assisted selection in.

  11. Triacylglycerol markers of mature human milk.

    Science.gov (United States)

    Morera, S; Castellote, A I; Jauregui, O; Casals, I; López-Sabater, M C

    2003-12-01

    To determine which triacylglycerol (TAG) species in mature human milk are less affected by external factors and may thus be considered as TAG markers, as well as to determine which species are most influenced by these external conditions. Furthermore, we examine the correlation between the TAG markers and their fatty acids (FAs). Six healthy women from Barcelona (Catalonia, Spain). In order to obtain the maximum variability of sampling conditions, 40 mature human milk samples were collected from different mothers, on different days, at different times of the day, and from different breasts during and after both the baby's and mother's meal. TAG and FA profiles were determined and correlated. The TAG composition was determined by high-performance liquid chromatography with an evaporative light-scattering detector, and also with atmospheric pressure chemical ionisation mass spectrometry. FAs compositions were determined by gas chromatography. The results were analysed using the SPSS statistical package and proved to be more variable than might have been found in a more restrictive sample design. Nevertheless, despite these conditions, some TAG species were found in relatively constant levels in mature human milk, and could thus be considered as markers of the mature milk TAG profile. TAG species that we can classify in this group were: LaMO, CaPO, LaCaO, LaPCa, LaOL, MPLn, LLO, LaOO, MPL, and MOL. The names do not indicate the location of fatty acids in the glycerol molecule. On the other hand, concentrations of other TAG species vary considerably between samples and consequently these may be understood to be especially affected by the external factors. TAGs like PaLS, MPO, PaOO, PPP, MPS, SPP, LOO, PPO, MOS, SSP, POL, and SOS are in this second group. Correlation between the TAG markers and their FAs was examined by Pearson's test and a significant correlation was found for some FAs. The TAG species present in mature human milk are affected in different ways by

  12. Expressed sequence tag analysis of adult human optic nerve for NEIBank: Identification of cell type and tissue markers

    Directory of Open Access Journals (Sweden)

    Peterson Katherine

    2009-09-01

    Full Text Available Abstract Background The optic nerve is a pure white matter central nervous system (CNS tract with an isolated blood supply, and is widely used in physiological studies of white matter response to various insults. We examined the gene expression profile of human optic nerve (ON and, through the NEIBANK online resource, to provide a resource of sequenced verified cDNA clones. An un-normalized cDNA library was constructed from pooled human ON tissues and was used in expressed sequence tag (EST analysis. Location of an abundant oligodendrocyte marker was examined by immunofluorescence. Quantitative real time polymerase chain reaction (qRT-PCR and Western analysis were used to compare levels of expression for key calcium channel protein genes and protein product in primate and rodent ON. Results Our analyses revealed a profile similar in many respects to other white matter related tissues, but significantly different from previously available ON cDNA libraries. The previous libraries were found to include specific markers for other eye tissues, suggesting contamination. Immune/inflammatory markers were abundant in the new ON library. The oligodendrocyte marker QKI was abundant at the EST level. Immunofluorescence revealed that this protein is a useful oligodendrocyte cell-type marker in rodent and primate ONs. L-type calcium channel EST abundance was found to be particularly low. A qRT-PCR-based comparative mammalian species analysis reveals that L-type calcium channel expression levels are significantly lower in primate than in rodent ON, which may help account for the class-specific difference in responsiveness to calcium channel blocking agents. Several known eye disease genes are abundantly expressed in ON. Many genes associated with normal axonal function, mRNAs associated with axonal transport, inflammation and neuroprotection are observed. Conclusion We conclude that the new cDNA library is a faithful representation of human ON and EST data

  13. Numerical Modeling of Deep Mantle Convection: Advection and Diffusion Schemes for Marker Methods

    Science.gov (United States)

    Mulyukova, Elvira; Dabrowski, Marcin; Steinberger, Bernhard

    2013-04-01

    Thermal and chemical evolution of Earth's deep mantle can be studied by modeling vigorous convection in a chemically heterogeneous fluid. Numerical modeling of such a system poses several computational challenges. Dominance of heat advection over the diffusive heat transport, and a negligible amount of chemical diffusion results in sharp gradients of thermal and chemical fields. The exponential dependence of the viscosity of mantle materials on temperature also leads to high gradients of the velocity field. The accuracy of many numerical advection schemes degrades quickly with increasing gradient of the solution, while the computational effort, in terms of the scheme complexity and required resolution, grows. Additional numerical challenges arise due to a large range of length-scales characteristic of a thermochemical convection system with highly variable viscosity. To examplify, the thickness of the stem of a rising thermal plume may be a few percent of the mantle thickness. An even thinner filament of an anomalous material that is entrained by that plume may consitute less than a tenth of a percent of the mantle thickness. We have developed a two-dimensional FEM code to model thermochemical convection in a hollow cylinder domain, with a depth- and temperature-dependent viscosity representative of the mantle (Steinberger and Calderwood, 2006). We use marker-in-cell method for advection of chemical and thermal fields. The main advantage of perfoming advection using markers is absence of numerical diffusion during the advection step, as opposed to the more diffusive field-methods. However, in the common implementation of the marker-methods, the solution of the momentum and energy equations takes place on a computational grid, and nodes do not generally coincide with the positions of the markers. Transferring velocity-, temperature-, and chemistry- information between nodes and markers introduces errors inherent to inter- and extrapolation. In the numerical scheme

  14. Mental health symptoms as prognostic risk markers of all-cause and psychiatric sickness absence in office workers

    NARCIS (Netherlands)

    Roelen, C.A.M.; Rhenen, van W.; Hoedeman, R.; Groothoff, J.W.; Klink, van der J.J.L.; Bültmann, U.

    2013-01-01

    To investigate mental health symptoms as prognostic risk markers of all-cause and psychiatric sickness absence (SA). Methods: Mental health symptoms were measured in 1137 office workers with the Four-Dimensional Symptom Questionnaire (4DSQ), including scales for distress, depression, anxiety and

  15. Mental health symptoms as prognostic risk markers of all-cause and psychiatric sickness absence in office workers

    NARCIS (Netherlands)

    Roelen, Corne A. M.; Hoedeman, Rob; van Rhenen, Willem; Groothoff, Johan W.; van der Klink, Jac J. L.; Bultmann, Ute

    Background: To investigate mental health symptoms as prognostic risk markers of all-cause and psychiatric sickness absence (SA). Methods: Mental health symptoms were measured in 1137 office workers with the Four-Dimensional Symptom Questionnaire (4DSQ), including scales for distress, depression,

  16. 38 CFR 38.632 - Headstone or marker application process.

    Science.gov (United States)

    2010-07-01

    ... appropriate instances, a new emblem of belief for inscription on a Government-furnished headstone or marker... inscription on a new, first Government-furnished headstone or marker for a deceased eligible individual, the... applications. A request to inscribe a new emblem on a Government-furnished headstone or marker shall be granted...

  17. Thirty novel microsatellite markers for the coastal pelagic fish ...

    Indian Academy of Sciences (India)

    is still needed as a supplement of genetic markers for further studies such as the evaluation of population genetic structure and mating pattern. Here, we developed 30 new microsatellite markers for S. japonicus collected from two distant locations in the East. Keywords. microsatellite marker; SSR; genetic variation; Scomber ...

  18. Rice genetic marker database: An identification of single nucleotide ...

    African Journals Online (AJOL)

    ... characterization table of 12,829 potential SNPs in 3,356 genes. The QTL marker database provides 175 QTL markers information with 942 polymorphic markers on each of the 12 chromosomes in rice. Users are assisted in tracing any new structures of the chromosomes and gene positional functions through comparisons ...

  19. Genetic markers and their application in livestock breeding in South ...

    African Journals Online (AJOL)

    The ultimate use of DNA markers would be to identify quantitative trait loci (QTL) in order to practice genotypic selection. This paper reviews DNA markers (RAPD, DFP, RFLP AFLP, minisatellites, microsatellites, SNP) and provides a brief overview of the current application of these markers in animal breeding.

  20. Status of clean gene (selection marker-free) technology

    African Journals Online (AJOL)

    SERVER

    2007-12-28

    Dec 28, 2007 ... marker genes in transgenic plants on health and safety grounds. One of the major apprehensions with the commercialization of transgene products has been the concern that selectable marker genes or their products may be toxic or allergenic when consumed. When anti- biotic selection markers having ...

  1. The Pragmatic Markers Anyway , Okay , and Shame : A South ...

    African Journals Online (AJOL)

    Pragmatic markers are “a class of short, recurrent linguistic items that generally have little lexical import but serve significant pragmatic functions in conversation” (Andersen 2001:39). While pragmatic markers are receiving growing consideration in the literature, pragmatic markers in South African English have been given ...

  2. Application of molecular markers in breeding for bean common ...

    African Journals Online (AJOL)

    Application of molecular markers in breeding for bean common blight resistance in South Africa. ... resistance and presence of all markers found in Vax 4 confirmed transfer of resistance. Marker-assisted selection can successfully be implemented in breeding for common bacterial blight resistance in South African materials.

  3. Possible Biochemical Markers in Protein-Energy Malnutrition and ...

    African Journals Online (AJOL)

    The biochemical markers studied did not show any unusual values at the time of the assays, but serum glucose and albumin levels showed potential as diagnostic markers for the two disease conditions. Keywords: Biochemical markers, spectrophotometry, protein-energy malnutrition, Western Kenya East and Central ...

  4. Molecular marker analysis to differentiate a clonal selection of ...

    African Journals Online (AJOL)

    Three AFLP markers were polymorphic; two markers were present only in Centennial Seedless, whereas one was present only in Manjari Naveen. These markers will be useful for establishing genetic identity, variety registration and protection of breeder's right. Keywords: Vitis vinifera, AFLP, microsatellites, clonal selection

  5. Chromosomal location of genomic SSR markers associated with ...

    Indian Academy of Sciences (India)

    ... we selected 16 SSR markers mapped only in one genome of chromosome group 2 around 1–21 cM distance to these diagnostic markers based on the SSR consensus map of wheat. Out of 16 SSRs, Xwmc658 identified resistant F2 individuals as a diagnostic marker for yellow rust disease and provided the location of ...

  6. Molecular markers for drought tolerance in bread wheat

    African Journals Online (AJOL)

    aghomotsegin

    2013-05-22

    May 22, 2013 ... this study to characterize drought tolerance in six wheat genotypes with developed marker assisted drought tolerance. Four of ..... Abdel-Tawab FM, Eman MF, Bahieledin A, Asmhan AM, Moselihy. (2003). Marker RAPD and ISSR marker related to drought tolerance in Rice. Egypt. J. Genet. Cytol. 36:195- ...

  7. Genetic and biological markers in drug abuse and alcoholism

    Energy Technology Data Exchange (ETDEWEB)

    Braude, M.C.; Chao, H.M.

    1986-01-01

    This book contains 11 selections. Some of the titles are: Polymorphic Gene Marker Studies; Pharmacogenetic Approaches to the Prediction of Drug Response; Genetic Markers of Drug Abuse in Mouse Models; Genetics as a Tool for Identifying Biological Markers of Drug Abuse; and Studies of an Animal Model of Alcoholism.

  8. Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome

    NARCIS (Netherlands)

    Silfverberg-Dilworth, E.; Matasci, C.L.; Weg, van de W.E.; Kaauwen, van M.P.W.; Walser, M.; Kodde, L.P.; Soglio, V.; Gianfranceschi, L.; Durel, C.E.; Costa, F.; Yamamoto, T.; Koller, B.; Gessler, C.; Patocchi, A.

    2006-01-01

    A new set of 148 apple microsatellite markers has been developed and mapped on the apple reference linkage map Fiesta x Discovery. One-hundred and seventeen markers were developed from genomic libraries enriched with the repeats GA, GT, AAG, AAC and ATC; 31 were developed from EST sequences. Markers

  9. Construction of Saccharomyces cerevisiae strains with enhanced ethanol tolerance by mutagenesis of the TATA-binding protein gene and identification of novel genes associated with ethanol tolerance.

    Science.gov (United States)

    Yang, Jungwoo; Bae, Ju Yun; Lee, Young Mi; Kwon, Hyeji; Moon, Hye-Yun; Kang, Hyun Ah; Yee, Su-Bog; Kim, Wankee; Choi, Wonja

    2011-08-01

    Since elevated ethanol is a major stress during ethanol fermentation, yeast strains tolerant to ethanol are highly desirable for the industrial scale ethanol production. A technology called global transcriptional machinery engineering (gTME), which exploits a mutant library of SPT15 encoding the TATA-binding protein of Saccharomyces cerevisiae (Alper et al., 2006; Science 314: 1565-1568), seems to a powerful tool for creating ethanol-tolerant strains. However, the ability of created strains to tolerate high ethanol on rich media remains unproven. In this study, a similar strategy was used to obtain five strains with enhanced ethanol tolerance (ETS1-5) of S. cerevisiae. Comparing global transcriptional profiles of two selected strains ETS2 and ETS3 with that of the control identified 42 genes that were commonly regulated with twofold change. Out of 34 deletion mutants available from a gene knockout library, 18 were ethanol sensitive, suggesting that these genes were closely associated with ethanol tolerance. Eight of them were novel with most being functionally unknown. To establish a basis for future industrial applications, strains iETS2 and iETS3 were created by integrating the SPT15 mutant alleles of ETS2 and ETS3 into the chromosomes, which also exhibited enhanced ethanol tolerance and survival upon ethanol shock on a rich medium. Fermentation with 20% glucose for 24 h in a bioreactor revealed that iETS2 and iETS3 grew better and produced approximately 25% more ethanol than a control strain. The ethanol yield and productivity were also substantially enhanced: 0.31 g/g and 2.6 g/L/h, respectively, for control and 0.39 g/g and 3.2 g/L/h, respectively, for iETS2 and iETS3. Thus, our study demonstrates the utility of gTME in generating strains with enhanced ethanol tolerance that resulted in increase of ethanol production. Strains with enhanced tolerance to other stresses such as heat, fermentation inhibitors, osmotic pressure, and so on, may be further created by

  10. Associations of Physical Activity Intensities with Markers of Insulin Sensitivity.

    Science.gov (United States)

    Jelleyman, Charlotte; Edwardson, Charlotte L; Henson, Joseph; Gray, Laura J; Rowlands, Alex V; Khunti, Kamlesh; Davies, Melanie J; Yates, Thomas

    2017-12-01

    Objectively measured physical activity (PA) intensity has traditionally been categorized as light, moderate, and vigorous using laboratory calibrated cut points. The relative contribution of time spent across a spectrum of accelerometer-determined intensities on health outcomes is less clear. This study aimed to assess the relationship between objectively measured PA intensity on a continuous scale and markers of insulin sensitivity (IS). Participants at high risk of type 2 diabetes mellitus were recruited from primary care (Leicestershire, UK). PA was measured using an ActiGraph accelerometer. Fasting and postchallenge glucose and insulin levels were assessed using an oral glucose tolerance test. IS was calculated using the Matsuda-IS and the HOMA-IS indices. Log-linear regression modeling was used to assess the relationship between PA intensity, in increments of 500 counts per minute, with markers of IS. Models were controlled for known confounders. Complete data were available for 569 participants. PA intensity was favorably associated with fasting and 2 h of insulin and IS, with the association increasing in magnitude with each increment of 500 counts per minute. Differences in HOMA-IS per 10 min of PA ranged from 12.4% (95% confidence interval = 3.7%-21.8%) to 26.8% (11.0%-44.7%) within the moderate-intensity PA category (from 2000-2499 to 3500-3999 counts per minute). For Matsuda-IS, these differences were 22.0% (10.3%-34.9%) and 34.7% (13.9%-59.3%), respectively. Significant associations for fasting insulin were no longer observed after controlling for body mass index, whereas differences associated with 2-h insulin and IS were attenuated but still significant. PA of any intensity may positively influence glucose regulation and insulin sensitivity in individuals at high risk of type 2 diabetes mellitus in a dose-response manner. Further research is required to identify the intensity thresholds at which clinically relevant benefits occur in this population.

  11. Tumor markers in pancreatic cancer: a European Group on Tumor Markers (EGTM) status report.

    LENUS (Irish Health Repository)

    Duffy, M J

    2012-02-01

    Pancreatic ductal adenocarcinoma is one of the most difficult malignancies to diagnose and treat. The aim of this article is to review how tumor markers can aid the diagnosis and management of patients with this malignancy. The most widely used and best validated marker for pancreatic cancer is CA 19-9. Inadequate sensitivity and specificity limit the use of CA 19-9 in the early diagnosis of pancreatic cancer. In non-jaundiced patients, however, CA 19-9 may complement other diagnostic procedures. In patients with resectable pancreatic cancer, presurgical and postresection CA 19-9 levels correlate with overall survival. In advanced disease, elevated pretreatment levels of CA 19-9 are associated with adverse patient outcome and thus may be combined with other factors for risk stratification. Most, but not all, reports indicate that serial levels of CA 19-9 correlate with response to systemic therapy. Use of CA 19-9 kinetics in conjunction with imaging is therefore recommended in monitoring therapy. Although several potential serum and tissue markers for pancreatic cancer are currently undergoing evaluation, none are sufficiently validated for routine clinical use. CA 19-9 thus remains the serum pancreatic cancer marker against which new markers for this malignancy should be judged.

  12. Small and large scale genomic DNA isolation protocol for chickpea ...

    African Journals Online (AJOL)

    Both small and large scale preparations were essentially suitable for PCR and Southern blot hybridization analyses, which are the key steps in crop improvement programme through marker development and genetic engineering techniques. Key words: Cicer arietinum L., phenolics, restriction enzyme digestion, PCR ...

  13. Transposable Element Junctions in Marker Development and Genomic Characterization of Barley

    Directory of Open Access Journals (Sweden)

    Mona Mazaheri

    2014-03-01

    Full Text Available Barley is a model plant in genomic studies of Triticeae species. However, barley’s large genome size and high repetitive sequence content complicate the whole-genome sequencing. The majority of the barley genome is composed of transposable elements (TEs. In this study, TE repeat junctions (RJs were used to develop a large-scale molecular marker platform, as a prerequisite to genome assembly. A total of 10.22 Gb of barley nonassembled 454 sequencing data were screened with RJPrimers pipeline. In total, 9,881,561 TE junctions were identified. From detected RJs, 400,538 polymerase chain reaction (PCR-based RJ markers (RJMs were designed across the genome, with an average of 39 markers/Mb. The utility of designed markers was tested using a random subset of RJMs. Over 94% of the markers successfully amplified amplicons, among which ∼90% were genome specific. In addition to marker design, identified RJs were utilized to detect 1190,885 TEs across the genome. In gene-poor regions of the genome elements comprised the majority of TEs (∼65%, while in gene-rich regions , , and were the main transposons, each representing an average ∼23% of total TEs. The numerous RJ primer pairs developed in this study will be a valuable resource for barley genomic studies including genomic selection, fine mapping, and genome assembly. In addition, the results of this study show that characterizing RJs provides insight into TE composition of species without a sequenced genome but for which short-read sequence data is available.

  14. A systematic review of the effect of yogurt consumption on chronic diseases risk markers in adults.

    Science.gov (United States)

    Dumas, Audrée-Anne; Lapointe, Annie; Dugrenier, Marilyn; Provencher, Véronique; Lamarche, Benoît; Desroches, Sophie

    2017-06-01

    We reviewed randomised controlled trials (RCTs) that have assessed the effects of yogurt containing Lactobacillus bulgaricus and Streptococcus thermophilus (LBST) on metabolic risk markers of chronic diseases in adults. We performed a systematic search in July 2016 in the scientific databases PubMed, EMBASE and The Cochrane Library. Included studies were RCTs that assessed the impact of consuming yogurt containing LBST as a treatment, and that evaluated at least one metabolic risk marker for chronic diseases compared with a control diet or a diet supplemented in another food/ingredient in healthy or chronically ill adults. Seven RCTs involving 278 participants were included in the review. Studies were conducted in the USA, France, Spain, Iran and Canada. Five studies were undertaken in healthy adults, and two were conducted among lactose malabsorbers. All studies investigated changes in blood lipids and glucose homoeostasis, with different doses of yogurt, durations of the supplementation and risks markers assessed. Consumption of LBST yogurt significantly reduced total cholesterol concentrations, ratio of total cholesterol to HDL-C and plasma glucose compared to a control yogurt-free diet or diet supplemented in another food/ingredient in two out of the seven studies. The majority of included RCTs presented high to unclear methodological risks of bias, which raises questions about the validity of their findings. Data from this systematic review indicate that the consumption of LBST yogurt shows either favourable or neutral effects on metabolic risk markers when compared with a control treatment in controlled research settings. RCTs investigating the effect of LBST yogurt consumption on metabolic risk markers of chronic diseases are scarce and presented considerable variation in methodologies making comparison between studies difficult. Further large-scale, well-designed studies assessing the impact of LBST yogurt, in particular in comparison with a control yogurt

  15. On the possibility of magnetic nano-markers use for hydraulic fracturing in shale gas mining

    Science.gov (United States)

    Zawadzki, Jaroslaw; Bogacki, Jan

    2016-04-01

    Recently shale gas production became essential for the global economy, thanks to fast advances in shale fracturing technology. Shale gas extraction can be achieved by drilling techniques coupled with hydraulic fracturing. Further increasing of shale gas production is possible by improving the efficiency of hydraulic fracturing and assessing the spatial distribution of fractures in shale deposits. The latter can be achieved by adding magnetic markers to fracturing fluid or directly to proppant, which keeps the fracture pathways open. After that, the range of hydraulic fracturing can be assessed by measurement of vertical and horizontal component of earth's magnetic field before and after fracturing. The difference in these components caused by the presence of magnetic marker particles may allow to delineate spatial distribution of fractures. Due to the fact, that subterranean geological formations may contain minerals with significant magnetic properties, it is important to provide to the markers excellent magnetic properties which should be also, independent of harsh chemical and geological conditions. On the other hand it is of great significance to produce magnetic markers at an affordable price because of the large quantities of fracturing fluids or proppants used during shale fracturing. Examining the properties of nano-materials, it was found, that they possess clearly superior magnetic properties, as compared to the same structure but having a larger particle size. It should be then possible, to use lower amount of magnetic marker, to obtain the same effect. Although a research on properties of new magnetic nano-materials is very intensive, cheap magnetic nano-materials are not yet produced on a scale appropriate for shale gas mining. In this work we overview, in detail, geological, technological and economic aspects of using magnetic nano-markers in shale gas mining. Acknowledgment This work was supported by the NCBiR under Grant "Electromagnetic method to

  16. 76 FR 60733 - Safety Zone; Mississippi River, Mile Marker 230 to Mile Marker 234, in the Vicinity of Baton...

    Science.gov (United States)

    2011-09-30

    .... Basis and Purpose The Captain of the Port New Orleans has implemented a safety zone from mile marker 230... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; Mississippi River, Mile Marker 230 to Mile Marker 234, in the Vicinity of Baton Rouge, LA AGENCY: Coast Guard, DHS. ACTION: Temporary final rule...

  17. 75 FR 59620 - Natchez Fireworks Safety Zone; Lower Mississippi River, Mile Marker 365.5 to Mile Marker 363...

    Science.gov (United States)

    2010-09-28

    ..., Mile Marker 365.5 to Mile Marker 363, Natchez, MS AGENCY: Coast Guard, DHS. ACTION: Temporary final... Mississippi River from mile marker 365.5 to 363 extending the entire width of the river. This safety zone is... W12-140, 1200 New Jersey Avenue, SE., Washington, DC 20590, between 9 a.m. and 5 p.m., Monday through...

  18. Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms.

    Science.gov (United States)

    N'Diaye, Amidou; Haile, Jemanesh K; Fowler, D Brian; Ammar, Karim; Pozniak, Curtis J

    2017-01-01

    unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly.

  19. Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms

    Directory of Open Access Journals (Sweden)

    Amidou N’Diaye

    2017-08-01

    making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly.

  20. Mammographic density and epithelial histopathologic markers

    Directory of Open Access Journals (Sweden)

    Killeen Jeffrey

    2009-06-01

    Full Text Available Abstract Background We explored the association of mammographic density, a breast cancer risk factor, with hormonal and proliferation markers in benign tissue from tumor blocks of pre-and postmenopausal breast cancer cases. Methods Breast cancer cases were recruited from a case-control study on breast density. Mammographic density was assessed on digitized prediagnostic mammograms using a computer-assisted method. For 279 participants of the original study, we obtained tumor blocks and prepared tissue microarrays (TMA, but benign tissue cores were only available for 159 women. The TMAs were immunostained for estrogen receptor alpha (ERα and beta (ERβ, progesterone receptor (PR, HER2/neu, Ki-67, and Proliferating Cell Nuclear Antigen (PCNA. We applied general linear models to compute breast density according to marker expression. Results A substantial proportion of the samples were in the low or no staining categories. None of the results was statistically significant, but women with PR and ERβ staining had 3.4% and 2.4% higher percent density. The respective values for Caucasians were 5.7% and 11.6% but less in Japanese women (3.5% and -1.1%. Percent density was 3.4% higher in women with any Ki-67 staining and 2.2% in those with positive PCNA staining. Conclusion This study detected little evidence for an association between mammographic density and expression of steroid receptors and proliferation markers in breast tissue, but it illustrated the problems of locating tumor blocks and benign breast tissue samples for epidemiologic research. Given the suggestive findings, future studies examining estrogen effects in tissue, cell proliferation, and density in the breast may be informative.

  1. A SOMATIC-MARKER THEORY OF ADDICTION

    Science.gov (United States)

    Verdejo-García, Antonio; Bechara, Antoine

    2009-01-01

    Similar to patients with ventromedial prefrontal cortex (VMPC) lesions, substance abusers show altered decision-making, characterized by a tendency to choose the immediate reward, at the expense of negative future consequences. The somatic-marker model proposes that decision-making depends on neural substrates that regulate homeostasis, emotion and feeling. According to this model, there should be a link between alterations in processing emotions in substance abusers, and their impairments in decision-making. A growing evidence from neuroscientific studies indicate that core aspects of addiction may be explained in terms of abnormal emotional/homeostatic guidance of decision-making. Behavioural studies have revealed emotional processing and decision-making deficits in substance abusers. Neuroimaging studies have shown that altered decision-making in addiction is associated with abnormal functioning of a distributed neural network critical for the processing of emotional information, and the experience of “craving”, including the VMPC, the amygdala, the striatum, the anterior cingulate cortex, and the insular/somato-sensory cortices, as well as non-specific neurotransmitter systems that modulate activities of neural processes involved in decision-making. The aim of this paper is to review this growing evidence, and to examine the extent of which these studies support a somatic-marker theory of addiction. We conclude that there are at least two underlying types of dysfunctions where emotional signals (somatic-markers) turns in favor of immediate outcomes in addiction: (1) a hyperactivity in the amygdala or impulsive system, which exaggerates the rewarding impact of available incentives, and (2) hypoactivity in the prefrontal cortex or reflective system, which forecasts the long-term consequences of a given action. PMID:18722390

  2. Connective tissue markers of rheumatoid arthritis

    DEFF Research Database (Denmark)

    Møller, H J

    1998-01-01

    Rheumatoid arthritis (RA) is a common systemic autoimmune disorder of unknown aetiology. The most common outcome of RA is a progressive development of joint destruction and deformity. Early introduction of disease-modifying antirheumatic drugs seems important for prevention of the long term...... of rheumatoid factor contributes to the classification of arthritis as RA, and acute phase reactants are useful for quantifying and comparing the level of inflammatory activity in the course of a given patient. There is, however, a lack of sensitive and specific biochemical markers for RA, and frontline...

  3. Bacterial and fungal markers in tobacco smoke

    Energy Technology Data Exchange (ETDEWEB)

    Szponar, B., E-mail: szponar@iitd.pan.wroc.pl [Lund University, Dept. of Laboratory Medicine, Soelvegatan 23, 223 62 Lund (Sweden); Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolfa Weigla 12, 53-114 Wroclaw (Poland); Pehrson, C.; Larsson, L. [Lund University, Dept. of Laboratory Medicine, Soelvegatan 23, 223 62 Lund (Sweden)

    2012-11-01

    Previous research has demonstrated that cigarette smoke contains bacterial and fungal components including lipopolysaccharide (LPS) and ergosterol. In the present study we used gas chromatography-mass spectrometry to analyze tobacco as well as mainstream and second hand smoke for 3-hydroxy fatty acids (3-OH FAs) of 10 to 18 carbon chain lengths, used as LPS markers, and ergosterol, used as a marker of fungal biomass. The air concentrations of LPS were 0.0017 nmol/m{sup 3} (N = 5) and 0.0007/m{sup 3} (N = 6) in the smoking vs. non-smoking rooms (p = 0.0559) of the studied private houses, and 0.0231 nmol/m{sup 3} (N = 5) vs. 0.0006 nmol/m{sup 3} (N = 5) (p = 0.0173), respectively, at the worksite. The air concentrations of ergosterol were also significantly higher in rooms with ongoing smoking than in rooms without smoking. A positive correlation was found between LPS and ergosterol in rooms with smoking but not in rooms without smoking. 3-OH C14:0 was the main 3-OH FA, followed by 3-OH C12:0, both in mainstream and second hand smoke and in phenol:water smoke extracts prepared in order to purify the LPS. The Limulus activity of the phenolic phase of tobacco was 3900 endotoxin units (EU)/cigarette; the corresponding amount of the smoke, collected on filters from 8 puffs, was 4 EU/cigarette. Tobacco smoking has been associated with a range of inflammatory airway conditions including COPD, asthma, bronchitis, alveolar hypersensitivity etc. Significant levels of LPS and ergosterol were identified in tobacco smoke and these observations support the hypothesis that microbial components of tobacco smoke contribute to inflammation and airway disease. -- Highlights: Black-Right-Pointing-Pointer Air concentration of bacterial and fungal markers is significantly higher in rooms with ongoing smoking than without smoking. Black-Right-Pointing-Pointer Bacterial LPS correlates with fungal marker in rooms with ongoing smoking but not without smoking. Black-Right-Pointing-Pointer LPS

  4. [Circadian markers and genes in bipolar disorder].

    Science.gov (United States)

    Yeim, S; Boudebesse, C; Etain, B; Belliviera, F

    2015-09-01

    Bipolar disorder is a severe and complex multifactorial disease, characterized by alternance of acute episodes of depression and mania/hypomania, interspaced by euthymic periods. The etiological determinants of bipolar disorder yet, are still poorly understood. For the last 30 years, chronobiology is an important field of investigation to better understand the pathophysiology of bipolar disorder. We conducted a review using Medline, ISI Database, EMBase, PsyInfo up to January 2015, using the following keywords combinations: "mood disorder", "bipolar disorder", "depression", "unipolar disorder", "major depressive disorder", "affective disorder", for psychiatric conditions; and "circadian rhythms", "circadian markers", "circadian gene", "clock gene", "melatonin" for circadian rhythms. The search critera was presence of word in any field of the article. Quantitative and qualitative circadian abnormalities are associated with bipolar disorders both during acute episodes and euthymic periods, suggesting that these altered circadian rhythms may represent biological trait markers of the disorder. These circadian dysfunctions were assessed by various validated tools including polysomnography, actigraphy, sleep diaries, chronotype assessments and blood melatonin/cortisol measures. Other altered endogenous circadian activities have also been reported in bipolar patients, such as hormones secretion, core body temperature or fibroblasts activity. Moreover, these markers were also altered in healthy relatives of bipolar patients, suggesting a degree of heritability. Several genetic association studies have also showed associations between multiple circadian genes and bipolar disorder, such as CLOCK, ARTNL1, GSK3β, PER3, NPAS2, NR1D1, TIMELESS, RORA, RORB, and CSNK1ε. Thus, these circadian gene variants may contribute to the genetic susceptibility of the disease. Furthermore, the study of the clock system may help to better understand some phenotypic aspects like the

  5. Collagen markers in peritoneal dialysis patients

    DEFF Research Database (Denmark)

    Graff, J; Joffe, P; Fugleberg, S

    1995-01-01

    (PICP), aminoterminal propeptide of type III procollagen (PIIINP), and carboxyterminal telopeptide of type I collagen (ICTP)] were studied in 19 nondiabetic peritoneal dialysis patients. The absence of correlation between the mass appearance rates of the markers and the duration of dialysis treatment...... as well as the number of peritonitis episodes supports the concept that peritoneal dialysis does not cause persistent changes in the deposition and degradation rates of collagen. A correlation between the D/Pcreatinine 4 hr and the PICP mass appearance rates was found. Since it is unlikely...

  6. Medline search engine for finding genetic markers with biological significance.

    Science.gov (United States)

    Xuan, Weijian; Wang, Pinglang; Watson, Stanley J; Meng, Fan

    2007-09-15

    Genome-wide high density SNP association studies are expected to identify various SNP alleles associated with different complex disorders. Understanding the biological significance of these SNP alleles in the context of existing literature is a major challenge since existing search engines are not designed to search literature for SNPs or other genetic markers. The literature mining of gene and protein functions has received significant attention and effort while similar work on genetic markers and their related diseases is still in its infancy. Our goal is to develop a web-based tool that facilitates the mining of Medline literature related to genetic studies and gene/protein function studies. Our solution consists of four main function modules for (1) identification of different types of genetic markers or genetic variations in Medline records (2) distinguishing positive versus negative linkage or association between genetic markers and diseases (3) integrating marker genomic location data from different databases to enable the retrieval of Medline records related to markers in the same linkage disequilibrium region (4) and a web interface called MarkerInfoFinder to search, display, sort and download Medline citation results. Tests using published data suggest MarkerInfoFinder can significantly increase the efficiency of finding genetic disorders and their underlying molecular mechanisms. The functions we developed will also be used to build a knowledge base for genetic markers and diseases. The MarkerInfoFinder is publicly available at: http://brainarray.mbni.med.umich.edu/brainarray/datamining/MarkerInfoFinder.

  7. Assessing Date Palm Genetic Diversity Using Different Molecular Markers.

    Science.gov (United States)

    Atia, Mohamed A M; Sakr, Mahmoud M; Adawy, Sami S

    2017-01-01

    Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.

  8. Exploring Geochemical Markers of the Anthropocene in River Sediments: Southern New England

    Science.gov (United States)

    Tran, J.

    2015-12-01

    The sedimentary record of New England is complex. From glacial till to colonial land use to the industrial revolution, any sediment preserved is intertwined and muddled by humans. Recent studies support the idea that any anthropogenic markers in the sediment record are site specific. Southern New England is marked by a myriad of practices including farming, charcoal kilns, hatting, mill dams, and iron furnaces. While specific markers of the anthropocene have been identified, little work has been done to correlate and quantify these noted markers across multiple basins. Specifically, a combination of x-ray fluorescence (XRF), x-ray diffraction (XRD), and grain size analysis were done on sediment cores taken within Southern New England across various watersheds. We present a combination of geochemical analysis and detrital zircon geochronology in order identify and account for basin differences. This in turn results in a more comprehensive trans-basin understanding of the anthropocene in this region. We observe strong evidence that supports the idea of geochemical markers anthropocene which include an increase in Mercury and Lead content in the sediments. Additionally, in basins where mill dams are present we observe sediment records consistent with flood events and dam degradation. While still fairly novel and understudied, our results provide insight to the much often question topic of the anthropocene in relation to this particular region and the potential pitfalls of doing large scale anthropogenic dating.

  9. Stable maintenance of multiple plasmids in E. coli using a single selective marker.

    Science.gov (United States)

    Schmidt, Calvin M; Shis, David L; Nguyen-Huu, Truong D; Bennett, Matthew R

    2012-10-19

    Plasmid-based genetic systems in Escherichia coli are a staple of synthetic biology. However, the use of plasmids imposes limitations on the size of synthetic gene circuits and the ease with which they can be placed into bacterial hosts. For instance, unique selective markers must be used for each plasmid to ensure their maintenance in the host. These selective markers are most often genes encoding resistance to antibiotics such as ampicillin or kanamycin. However, the simultaneous use of multiple antibiotics to retain different plasmids can place undue stress on the host and increase the cost of growth media. To address this problem, we have developed a method for stably transforming three different plasmids in E. coli using a single antibiotic selective marker. To do this, we first examined two different systems with which two plasmids may be maintained. These systems make use of either T7 RNA polymerase-specific regulation of the resistance gene or split antibiotic resistance enzymes encoded on separate plasmids. Finally, we combined the two methods to create a system with which three plasmids can be transformed and stably maintained using a single selective marker. This work shows that large-scale plasmid-based synthetic gene circuits need not be limited by the use of multiple antibiotic resistance genes.

  10. Discovery of potential DNA methylation markers for forensic tissue identification using bisulphite pyrosequencing.

    Science.gov (United States)

    Vidaki, Athina; Giangasparo, Federica; Syndercombe Court, Denise

    2016-10-01

    The presence of specific body fluids at crime scenes could be linked with particular types of crime, therefore attributing a DNA profile to a specific tissue could increase the evidential significance of a match with a suspect. Current methodologies such as tissue-specific mRNA profiling are useful but drawbacks include low tissue specificity and applicability to degraded samples. In this study, the potential of 11 tissue-specific differentially methylated regions, initially identified following large-scale methylation analysis of whole blood, buccal cells and sperm, was explored in order to identify markers for blood, saliva and semen. Bisulphite pyrosequencing analysis supported previous findings, but tissue-specific differentially methylated regions for blood and buccal cells did not show enough specificity to be proposed as markers for blood and saliva, respectively. For some CpGs, a large inter-individual variation in methylation levels was also observed. Two of the semen markers (cg04382920 and cg11768416) were used for further validation on a large set of stains. These two semen-specific assays showed high sensitivity (as low as 50 pg) and stability. Future experiments will shed light on the usefulness of these markers in forensic casework. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Comparison of SNP and CAPS markers application in genetic research in wheat and barley.

    Science.gov (United States)

    Shavrukov, Yuri

    2016-01-27

    Barley and bread wheat show large differences in frequencies of Single Nucleotide Polymorphism (SNP) as determined from genome-wide studies. These frequencies have been estimated as 2.4-3 times higher in the entire barley genome than within each diploid genomes of wheat (A, B or D). However, barley SNPs within individual genes occur significantly more frequently than quoted. Differences between wheat and barley are based on the origin and evolutionary history of the species. Bread wheat contains rarer SNPs due to the double genetic 'bottle-neck' created by natural hybridisation and spontaneous polyploidisation. Furthermore, wheat has the lowest level of useful SNP-derived markers while barley is estimated to have the highest level of polymorphism. Different strategies are required for the development of suitable molecular markers in these cereal species. For example, SNP markers based on high-throughput technology (Infinium or KASP) are very effective and useful in both barley and bread wheat. In contrast, Cleaved Amplified Polymorphic Sequences (CAPS) are more widely and successfully employed in small-scale experiments with highly polymorphic genetic regions containing multiple SNPs in barley, but not in wheat. However, preliminary 'in silico' search databases for assessing the potential value of SNPs have yet to be developed. This mini-review summarises results supporting the development of different strategies for the application of effective SNP and CAPS markers in wheat and barley.

  12. Scaling of Metabolic Scaling within Physical Limits

    Directory of Open Access Journals (Sweden)

    Douglas S. Glazier

    2014-10-01

    Full Text Available Both the slope and elevation of scaling relationships between log metabolic rate and log body size vary taxonomically and in relation to physiological or developmental state, ecological lifestyle and environmental conditions. Here I discuss how the recently proposed metabolic-level boundaries hypothesis (MLBH provides a useful conceptual framework for explaining and predicting much, but not all of this variation. This hypothesis is based on three major assumptions: (1 various processes related to body volume and surface area exert state-dependent effects on the scaling slope for metabolic rate in relation to body mass; (2 the elevation and slope of metabolic scaling relationships are linked; and (3 both intrinsic (anatomical, biochemical and physiological and extrinsic (ecological factors can affect metabolic scaling. According to the MLBH, the diversity of metabolic scaling relationships occurs within physical boundary limits related to body volume and surface area. Within these limits, specific metabolic scaling slopes can be predicted from the metabolic level (or scaling elevation of a species or group of species. In essence, metabolic scaling itself scales with metabolic level, which is in turn contingent on various intrinsic and extrinsic conditions operating in physiological or evolutionary time. The MLBH represents a “meta-mechanism” or collection of multiple, specific mechanisms that have contingent, state-dependent effects. As such, the MLBH is Darwinian in approach (the theory of natural selection is also meta-mechanistic, in contrast to currently influential metabolic scaling theory that is Newtonian in approach (i.e., based on unitary deterministic laws. Furthermore, the MLBH can be viewed as part of a more general theory that includes other mechanisms that may also affect metabolic scaling.

  13. Navigated marker placement for motion compensation in radiotherapy

    Science.gov (United States)

    Winterstein, A.; März, K.; Franz, A. M.; Hafezi, M.; Fard, N.; Sterzing, F.; Mehrabi, A.; Maier-Hein, L.

    2015-03-01

    Radiotherapy is frequently used to treat unoperated or partially resected tumors. Tumor movement, e.g. caused by respiration, is a major challenge in this context. Markers can be implanted around the tumor prior to radiation therapy for accurate tracking of tumor movement. However, accurate placement of these markers while keeping a secure margin around the target and while taking into account critical structures is a difficult task. Computer-assisted needle insertion has been an active field of research in the past decades. However, the challenge of navigated marker placement for motion compensated radiotherapy has not yet been addressed. This work presents a system to support marker implantation for radiotherapy under consideration of safety margins and optimal marker configuration. It is designed to allow placement of markers both percutaneously and during an open liver surgery. To this end, we adapted the previously proposed EchoTrack system which integrates ultrasound (US) imaging and electromagnetic (EM) tracking in a single mobile modality. The potential of our new marker insertion concept was evaluated in a phantom study by inserting sets of three markers around dedicated targets (n=22) simultaneously spacing the markers evenly around the target as well as placing the markers in a defined distance to the target. In all cases the markers were successfully placed in a configuration fulfilling the predefined criteria. This includes a minimum distance of 18.9 ± 2.4 mm between marker and tumor as well as a divergence of 2.1 ± 1.5 mm from the planned marker positions. We conclude that our system has high potential to facilitate the placement of markers in suitable configurations for surgeons without extensive experience in needle punctions as high quality configurations were obtained even by medical non-experts.

  14. Celiac disease markers in patients with liver diseases: A single center large scale screening study

    Czech Academy of Sciences Publication Activity Database

    Drastich, P.; Honsová, E.; Lodererová, A.; Jarešová, M.; Pekáriková, Aneta; Hoffmanová, I.; Tučková, Ludmila; Tlaskalová-Hogenová, Helena; Špičák, J.; Sánchez, Daniel

    2012-01-01

    Roč. 18, č. 43 (2012), s. 6255-6262 ISSN 1007-9327 R&D Projects: GA AV ČR IAA500200709; GA ČR GA310/07/0414 Institutional support: RVO:61388971 Keywords : Tissue transglutaminase * Anti-tissue transglutaminase antibodies * Autoimmune liver disease s Subject RIV: EC - Immunology Impact factor: 2.547, year: 2012

  15. Application of large-scale sequencing to marker discovery in plants

    Indian Academy of Sciences (India)

    Sequencing genomic DNA enriched for genes by hybridization with probes for all or some of the known genes simplifies sequencing and analysis of differences in gene sequences between large numbers of genotypes and genes especially when working with complex genomes. Examples of application of the ...

  16. Is there an association between the Expanded Disability Status Scale and inflammatory markers in multiple sclerosis?

    Directory of Open Access Journals (Sweden)

    Isil Guzel

    2016-02-01

    Methods: We reviewed the data of 127 patients (91 women and 36 men who were retrospectively diagnosed as MS according to the revised Mc Donald's criteria who were seen at our facility between January 2007 and December 2012. Patients were divided into two groups according to EDSS score: Group 1, EDSS 5. Additionally, NLR and CRP levels may be discriminative factors of adverse clinical outcomes.

  17. Outlier SNP markers reveal fine-scale genetic structuring across European hake populations (Merluccius merluccius)

    DEFF Research Database (Denmark)

    Milano, I.; Babbucci, M.; Cariani, A.

    2014-01-01

    Shallow population structure is generally reported for most marine fish and explained as a consequence of high dispersal, connectivity and large population size. Targeted gene analyses and more recently genome-wide studies have challenged such view, suggesting that adaptive divergence might occur...

  18. Black Pineleaf Scale (FIDL)

    Science.gov (United States)

    Katharine A. Sheehan; Mario A. Melendez; Shana Westfall

    1998-01-01

    The black pineleaf scale (Nuculaspis californica (Coleman)) belongs to a group of sucking insects called armored scales. Concealed under their protective shells, these scales insert their mouthparts into their hosts, removing sap and, possibly, injecting toxic enzymes secreted in the saliva. Armored scales are important pests of agricultural and ornamental plants;...

  19. Postprostatectomy ultrasound-guided transrectal implantation of gold markers for external beam radiotherapy. Technique and complications rate

    Energy Technology Data Exchange (ETDEWEB)

    Langenhuijsen, J.F.; Kiemeney, L.A.L.M.; Witjes, J.A. [Radboud Univ. Nijmegen Medical Center, Nijmegen (Netherlands). Dept. of Urology; Donker, R. [Medical Center Alkmaar (Netherlands). Dept. of Radiation Oncology; McColl, G.M.; Lin, E.N.J.T. van [Radboud Univ. Nijmegen Medical Center, Nijmegen (Netherlands). Dept. of Radiation Oncology

    2013-06-15

    Background and purpose: Postprostatectomy radiotherapy (RT) improves survival in adjuvant and salvage settings. The implantation technique and complications rate of gold markers in the prostate bed for high-precision RT were analyzed. Patients and methods: Patients undergoing postprostatectomy RT for prostate-specific antigen (PSA) relapse or high-risk disease were enrolled in the study. Under transrectal ultrasound guidance, three fine gold markers were implanted in the prostate bed and the technical difficulties of insertion were documented. Patients received our self-designed questionnaires concerning complications and pain. The influence of anticoagulants and coumarins on bleeding was analyzed, as was the effect of potential risk factors on pain. Results: In 77 consecutive patients, failure of marker implantation or marker migration was seen in six cases. Rectal bleeding was reported by 10 patients and 1 had voiding complaints. No macroscopic hematuria persisting for more than 3 days was observed. Other complications included rectal discomfort (n = 2), nausea (n = 1), abdominal discomfort (n = 1), and pain requiring analgesics (n = 4). No major complications were reported. On a 0-10 visual analogue scale (VAS), the mean pain score was 3.7. No clinically significant risk factors for complications were identified. Conclusion: Transrectal implantation of gold markers in the prostate bed is feasible and safe. Alternatives like cone beam computed tomography (CBCT) should be considered, but the advantages of gold marker implantation for high-precision postprostatectomy RT would seem to outweigh the minor risks involved. (orig.)

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

    Directory of Open Access Journals (Sweden)

    Tiejun Zhang

    Full Text Available 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.

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

    Science.gov (United States)

    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.

  2. Fluorescence markers in some New Zealand honeys.

    Science.gov (United States)

    Bong, Jessie; Loomes, Kerry M; Schlothauer, Ralf C; Stephens, Jonathan M

    2016-02-01

    The fluorescence characteristics of various New Zealand honeys were investigated to establish if this technique might detect signatures unique to manuka (Leptospermum scoparium) and kanuka (Kunzea ericoides) honeys. We found unique fluorescence profiles for these honeys which distinguished them from other New Zealand honey floral types. Two excitation-emission (ex-em) marker wavelengths each for manuka and kanuka honeys were identified; manuka honey at 270-365 (MM1) and 330-470 (MM2) nm and kanuka honey at 275-305 (KM1) and 445-525 (KM2) nm. Dilution of manuka and kanuka honeys with other honey types that did not possess these fluorescence profiles resulted in a proportional reduction in fluorescence signal of the honeys at the marker wavelengths. By comparison, rewarewa (Knightia excelsa), kamahi (Weinmannia racemosa), and clover (Trifolium spp.) honeys did not exhibit unique fluorescence patterns. These findings suggests that a fluorescence-based screening approach has potential utility for determining the monoflorality status of manuka and kanuka honeys. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Uniparental genetic markers in South Amerindians

    Directory of Open Access Journals (Sweden)

    Rafael Bisso-Machado

    2012-01-01

    Full Text Available A comprehensive review of uniparental systems in South Amerindians was undertaken. Variability in the Y-chromosome haplogroups were assessed in 68 populations and 1,814 individuals whereas that of Y-STR markers was assessed in 29 populations and 590 subjects. Variability in the mitochondrial DNA (mtDNA haplogroup was examined in 108 populations and 6,697 persons, and sequencing studies used either the complete mtDNA genome or the highly variable segments 1 and 2. The diversity of the markers made it difficult to establish a general picture of Y-chromosome variability in the populations studied. However, haplogroup Q1a3a* was almost always the most prevalent whereas Q1a3* occurred equally in all regions, which suggested its prevalence among the early colonizers. The STR allele frequencies were used to derive a possible ancient Native American Q-clade chromosome haplotype and five of six STR loci showed significant geographic variation. Geographic and linguistic factors moderately influenced the mtDNA distributions (6% and 7%, respectively and mtDNA haplogroups A and D correlated positively and negatively, respectively, with latitude. The data analyzed here provide rich material for understanding the biological history of South Amerindians and can serve as a basis for comparative studies involving other types of data, such as cultural data.

  4. Writing on water with permanent markers

    Science.gov (United States)

    Khodaparast, Sepideh; Boulogne, François; Stone, Howard A.

    2016-11-01

    Permanent markers create a continuous thin stain on a surface, which, after drying, can only be removed by high pressure cleaning or organic solvents. The stains of the markers are hydrophobic and thus effectively resist rinsing by water. We introduce a peeling technique based on surface tension, which benefits from this hydrophobicity, to transfer complex two-dimensional marks onto the air-water interface. As an air-water meniscus reaches the stain edge, the surface tension applies a detachment force to the thin layer. If larger than the adhesion of the stain on the substrate, the surface tension can peel off the entire layer. We examine the efficiency of this peeling method for elastic thin films in an experimental model made of thin polystyrene films of well-controlled geometrical properties adhering on clean glass substrates. We investigate the effect of film thickness and interface velocity. At low interface velocities U cleaning the water proof stains without solvent and fabrication of flexible wearable electronics. This research is supported by Grant from Swiss National Science Foundation (P2ELP2-158896).

  5. Hyperglycaemia, oxidative stress and inflammatory markers.

    Science.gov (United States)

    Butkowski, Eugene G; Jelinek, Herbert F

    2017-11-01

    The increasing prevalence of hyperglycaemia implicates a state of oxidative stress and inflammation. Traditional and emerging biomarkers associated with increasing hyperglycaemia were assessed to clarify their role they play in hyperglycaemia. 309 participants attending a rural diabetic screening program were categorised into control and quintile groups based upon glucose levels: 1st quintile - 6.1 mmol/L. Significant results were obtained for anthropometric data and biochemical markers - glucose, HbA1c and total cholesterol (P < 0.001); oxidative stress: glutathione (P < 0.001), glutathione:glutathione disulfide and 8-hydroxy-2-deoxyguanosine (P < 0.05). Interleukin -1β and inflammatory marker ratios IL-6/IL-10, IL-1β/IL-10, MCP-1/IL-10, IGF-1/IL-10 and IL-6/IL-1β were significant (P < 0.05). This study provided further evidence that inflammatory and oxidative stress biomarkers may contribute to diagnostic information associated with preclinical increases in BGL. Further we have provided a unique study in the analysis of ratios of inflammatory biomarkers and correlations with increasing BGL.

  6. Biological markers of Alzheimer?s disease

    Directory of Open Access Journals (Sweden)

    Leonardo Cruz de Souza

    2014-03-01

    Full Text Available The challenges for establishing an early diagnosis of Alzheimer’s disease (AD have created a need for biomarkers that reflect the core pathology of the disease. The cerebrospinal fluid (CSF levels of total Tau (T-tau, phosphorylated Tau (P-Tau and beta-amyloid peptide (Aβ42 reflect, respectively, neurofibrillary tangle and amyloid pathologies and are considered as surrogate markers of AD pathophysiology. The combination of low Aβ42 and high levels of T-tau and P-Tau can accurately identify patients with AD at early stages, even before the development of dementia. The combined analysis of the CSF biomarkers is also helpful for the differential diagnosis between AD and other degenerative dementias. The development of these CSF biomarkers has evolved to a novel diagnostic definition of the disease. The identification of a specific clinical phenotype combined with the in vivo evidence of pathophysiological markers offers the possibility to make a diagnosis of AD before the dementia stage with high specificity.

  7. Heritability of markers of bone metabolism

    Science.gov (United States)

    Smith, Scott M.; Zwart, S. R.; Hargens, A. R.

    2005-01-01

    Several classic twin studies show genetic effects on markers of bone health, including bone mineral density and parathyroid hormone (PTH). This study was performed to assess the relative contribution of genetics to biochemical markers of bone metabolism. Fifteen sets of identical twins (8 male, 7 female) were housed in a clinical research center where diet was controlled (15% protein, 55% carbohydrate, 30% fat) for 3 consecutive days. Each day, 24-h urine pools were collected and N-telopeptide (NTX), deoxypyridinoline (DPD), calcium, and serum PTH were measured. The broad-sense heritability factor (H2) is an estimation of the portion of the total variance of a given phenotype that is attributable to genetic variance. H2 was estimated from the correlation coefficient of the phenotype data. H2 for NTX was 94% for males and 80% for females, DPD was 88% for males and 97% for females, urinary calcium excretion was 97% for males and 90% for females, and PTH was 92% for males and 79% for females. Since environmental variability was minimized for the 3 days of data collection, these heritability factors are likely overestimated. Nonetheless, the data support the concept that PTH is a predominantly heritable trait, and suggest that NTX, DPD, and calcium excretion are as well. These biochemical data support the previously documented heritability of bone health.

  8. Mucocutaneous Leishmaniasis: clinical markers in presumptive diagnosis.

    Science.gov (United States)

    Diniz, João Luiz Cioglia Pereira; Costa, Manoel Otávio da Rocha; Gonçalves, Denise Utsch

    2011-06-01

    Mucocutaneous Leishmaniasis (ML) can lead to serious sequela; however, early diagnosis can prevent complications. To evaluate clinical markers for the early diagnosis of ML. A series study of 21 cases of ML, which were evaluated through clinical interview, nasal endoscopy, biopsy and the Montenegro test. A skin scar and previous diagnosis of cutaneous leishmaniasis (CL) were reported in 8(38%) patients, and 13(62%) of them denied having had previous CL and had no scar. Nasal/oral symptom onset until the ML diagnosis varied from 5 months to 20 years, mean value of 6 years. In the Montenegro test, the average size of the papule was 14.5 mm, which did not correlate with disease duration (p=0.87). The nose was the most often involved site and the extension of the injured mucosa did not correlate with disease duration. The parasite was found in 2 (9.52%) biopsy specimens. ML diagnosis was late. Finding the parasite in the mucosa, cutaneous scar and/or previous diagnosis of CL were not clinical markers for ML. ML diagnosis must be based on the Montenegro test, chronic nasal and/or oral discharge and histological findings ruling out other granulomatous diseases.

  9. Evaluation of DNA markers for fish identification

    Directory of Open Access Journals (Sweden)

    Maurizio Gilli

    2013-02-01

    Full Text Available Species substitution is a common commercial fraud, mainly applied to fish species. It is thus important to have analytical methods for species identification. DNA analysis can be a suitable technique: some mitochondrial genes are actually recognized as valuable markers for species discrimination. Aim of this work was thus to evaluate the capability of cytb and COI genes to discriminate the species of fish (n=89 which are commonly substituted. In the last four years of activity on field, the laboratory analysed, using the FINS method (Forensically Informative Nucleotide Sequencing, 146 samples, belonging to several fish species, sent by veterinary officers in the frame of their activities of control: in this work, results about number and kind of fraud are reported. Additionally, samples directly purchased by the lab were examined. The obtained results showed that the genetic markers have a high discriminatory power and that the method is highly suitable. The frequent detection of species substitution in the samples collected on field showed the importance of controlling this kind of frauds in the fish market.

  10. Markers of acute stress in pigs.

    Science.gov (United States)

    Breineková, K; Svoboda, M; Smutná, M; Vorlová, L

    2007-01-01

    This study explores the biological validation of markers of acute stress in pigs subjected to transportation for slaughter. The stress markers selected for monitoring were neopterin and cortisol. Their levels in pig serum were measured for two porcine stress syndrome genotypes, NN and Nn, after a 30-min transport to a slaughterhouse. Blood samples were withdrawn before transport (control group) and immediately after the animals' arrival (experimental group). The values of neopterin and cortisol measured before the transport were 5.60+/-1.65 nmol/l and 273.54+/-66.17 nmol/l respectively. After the transfer, the concentration of cortisol rose significantly compared to the control (355.69+/-85.13 nmol/l, p<0.01). Neopterin concentrations in the serum (8.25+/-1.60 nmol/l) were also significantly higher (p<0.01) after transportation. The elevated concentrations of both analytes were found to be independent of the genotype. These results document the stimulation of the endocrine system and the immune system that develops in animals undergoing transportation for slaughter.

  11. Clinical and Biological Markers in Hypereosinophilic Syndromes

    Directory of Open Access Journals (Sweden)

    Paneez Khoury

    2017-12-01

    Full Text Available Hypereosinophilic syndromes (HES are rare, heterogeneous syndromes characterized by markedly elevated eosinophil counts in the blood and/or tissue and evidence of eosinophil-associated pathology. Although parasitic infections, drug hypersensitivity, and other disorders of defined etiology can present as HES (associated HES, treatment is directed at the underlying cause rather than the eosinophilia itself. A number of additional subtypes of HES have been described, based on clinical and laboratory features. These include (1 myeloid HES—a primary disorder of the myeloid lineage, (2 lymphocytic variant HES—eosinophilia driven by aberrant or clonal lymphocytes secreting eosinophil-promoting cytokines, (3 overlap HES—eosinophilia restricted to a single organ or organ system, (4 familial eosinophilia—a rare inherited form of HES, and (5 idiopathic HES. Since clinical manifestations, response to therapy, and prognosis all differ between HES subtypes, this review will focus on clinical and biological markers that serve as markers of disease activity in HES (excluding associated HES, including those that are likely to be useful only in specific clinical subtypes.

  12. Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: a review.

    Science.gov (United States)

    Kaur, Shubhneet; Panesar, Parmjit S; Bera, Manab B; Kaur, Varinder

    2015-01-01

    Sequencing of rice genome has facilitated the understanding of rice evolution and has been utilized extensively for mining of DNA markers to facilitate marker-assisted breeding. Simple sequence repeat (SSR) markers that are tandemly repeated nucleotide sequence motifs flanked by unique sequences are presently the maker of choice in rice improvement due to their abundance, co-dominant inheritance, high levels of allelic diversity, and simple reproducible assay. The current level of genome coverage by SSR markers in rice is sufficient to employ them for genotype identification and marker-assisted selection in breeding for mapping of genes and quantitative trait loci analysis. This review provides comprehensive information on the mapping and applications of SSR markers in investigation of rice cultivars to study their genetic divergence and marker-assisted selection of important agronomic traits.

  13. Tumor markers in breast cancer- European Group on Tumor Markers recommendations

    DEFF Research Database (Denmark)

    Molina, Rafael; Barak, Vivian; van Dalen, Arie

    2005-01-01

    in the selection of patients for treatment with hormone therapy, while HER-2 is essential in selecting patients with advanced breast cancer for treatment with Herceptin (trastuzumab). Urokinase plasminogen activator and plasminogen activator inhibitor 1 are recently validated prognostic markers for lymph node...

  14. Development of diagnostic markers from disease resistance QTLs for marker-assisted breeding in peanut

    Science.gov (United States)

    Breeding for disease resistance in peanut cultivars has been constrained due to both a narrow genetic base and a low degree of polymorphism. Earlier attempts have resulted in the development of a few hundreds of simple sequence repeat (SSR) markers in peanut that could define broad QTL on the physic...

  15. De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas

    Directory of Open Access Journals (Sweden)

    Huang Lifei

    2010-12-01

    Full Text Available Abstract Background The tuberous root of sweetpotato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing is needed to generate enormous transcript sequences from sweetpotato root for gene discovery and molecular marker development. Results In this study, more than 59 million sequencing reads were generated using Illumina paired-end sequencing technology. De novo assembly yielded 56,516 unigenes with an average length of 581 bp. Based on sequence similarity search with known proteins, a total of 35,051 (62.02% genes were identified. Out of these annotated unigenes, 5,046 and 11,983 unigenes were assigned to gene ontology and clusters of orthologous group, respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG indicated that 17,598 (31.14% unigenes were mapped to 124 KEGG pathways, and 11,056 were assigned to metabolic pathways, which were well represented by carbohydrate metabolism and biosynthesis of secondary metabolite. In addition, 4,114 cDNA SSRs (cSSRs were identified as potential molecular markers in our unigenes. One hundred pairs of PCR primers were designed and used for validation of the amplification and assessment of the polymorphism in genomic DNA pools. The result revealed that 92 primer pairs were successfully amplified in initial screening tests. Conclusion This study generated a substantial fraction of sweetpotato transcript sequences, which can be used to discover novel genes associated with tuberous root formation and development and will also make it possible to construct high density microarrays for further characterization of gene expression profiles during these processes. Thousands of cSSR markers identified in the present study can enrich molecular markers

  16. Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5’ accessions

    Science.gov (United States)

    2012-01-01

    Background Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for fire blight resistance has been reported on linkage group 3 of Malus ‘Robusta 5’. In this study we identified markers derived from putative fire blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. Results When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand ‘Malling 9’ X ‘Robusta 5’ population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German ‘Idared’ X ‘Robusta 5’ population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90). In the US ‘Otawa3’ X ‘Robusta5’ population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in fire blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor

  17. Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5’ accessions

    Directory of Open Access Journals (Sweden)

    Gardiner Susan E

    2012-04-01

    Full Text Available Abstract Background Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL for fire blight resistance has been reported on linkage group 3 of Malus ‘Robusta 5’. In this study we identified markers derived from putative fire blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. Results When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand ‘Malling 9’ X ‘Robusta 5’ population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1 and a closely linked class 3 peroxidase gene. While the QTL detected in the German ‘Idared’ X ‘Robusta 5’ population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90. In the US ‘Otawa3’ X ‘Robusta5’ population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in fire blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY

  18. Frailty Markers and Treatment Decisions in Patients Seen in Oncogeriatric Clinics: Results from the ASRO Pilot Study.

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    Anaïs Farcet

    Full Text Available Comprehensive Geriatric Assessment (CGA is the gold standard to help oncologists select the best cancer treatment for their older patients. Some authors have suggested that the concept of frailty could be a more useful approach in this population. We investigated whether frailty markers are associated with treatment recommendations in an oncogeriatric clinic.This prospective study included 70 years and older patients with solid tumors and referred for an oncogeriatric assessment. The CGA included nine domains: autonomy, comorbidities, medication, cognition, nutrition, mood, neurosensory deficits, falls, and social status. Five frailty markers were assessed (nutrition, physical activity, energy, mobility, and strength. Patients were categorized as Frail (three or more frailty markers, pre-frail (one or two frailty markers, or not-frail (no frailty marker. Treatment recommendations were classified into two categories: standard treatment with and without any changes and supportive/palliative care. Multiple logistic regression models were used to analyze factors associated with treatment recommendations.217 patients, mean age 83 years (± Standard deviation (SD 5.3, were included. In the univariate analysis, number of frailty markers, grip strength, physical activity, mobility, nutrition, energy, autonomy, depression, Eastern Cooperative Oncology Group Scale of Performance Status (ECOG-PS, and falls were significantly associated with final treatment recommendations. In the multivariate analysis, the number of frailty markers and basic Activities of Daily Living (ADL were significantly associated with final treatment recommendations (p<0.001 and p = 0.010, respectively.Frailty markers are associated with final treatment recommendations in older cancer patients. Longitudinal studies are warranted to better determine their use in a geriatric oncology setting.

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

    Science.gov (United States)

    2012-01-01

    marker-assisted selection in the Australian national lupin breeding program. Conclusions We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8) of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species. PMID:22805587

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

    Directory of Open Access Journals (Sweden)

    Yang Huaan

    2012-07-01

    fingerprinting method for marker-assisted selection in the Australian national lupin breeding program. Conclusions We demonstrated that more than 30 molecular markers linked to a target gene of agronomic trait of interest can be identified from a small portion (1/8 of one sequencing run on HiSeq2000 by applying NGS based RAD sequencing in marker development. The markers developed by the strategy described in this study are all co-dominant SNP markers, which can readily be converted into high throughput multiplex format or low-cost, simple PCR-based markers desirable for large scale marker implementation in plant breeding programs. The high density and closely linked molecular markers associated with a target trait help to overcome a major bottleneck for implementation of molecular markers on a wide range of germplasm in breeding programs. We conclude that application of NGS based RAD sequencing as DNA fingerprinting is a very rapid and cost-effective strategy for marker development in molecular plant breeding. The strategy does not require any prior genome knowledge or molecular information for the species under investigation, and it is applicable to other plant species.

  1. Anthropopression markers in lake bottom sediments

    Science.gov (United States)

    Nadolna, Anna; Nowicka, Barbara

    2014-05-01

    Lakes are vulnerable to various types of anthropogenic disturbances. Responses of lake ecosystems to environmental stressors are varied and depend not only on the type of a factor but also on the lake natural resistance to degradation. Within the EULAKES project an evaluation of anthropogenic stress extent in a flow-through, postglacial, ribbon lake (Lake Charzykowskie) was carried out. It was assumed, that this impact manifests unevenly, depending on a type and degree of the pressure on the shore zones, water quality of tributaries, lake basin shape and dynamics of a water movement. It was stated, that anthropogenic markers are substances accumulated in bottom sediments as a result of allochthonous substances inflow from the catchment and atmosphere. Along the selected transects 105 samples from the top layer of sediments (about 20 cm) was collected representing the contemporary accumulation (about 15 years). The content of selected chemical elements and compounds was examined, including nutrients (TN and TP), heavy metals (arsenic, cadmium, lead, chromium, nickel, copper, zinc, mercury, iron, and manganese) and pesticides (DDT, DDD, DDE, DMDT , γ-HCH). The research was conducted in the deepest points of each lake basin and along the research transects - while choosing the spots, the increased intensity of anthropogenic impact (ports, roads with heavy traffic, wastewater discharge zones, built-up areas) was taken into consideration. The river outlets to the lake, where there are ecotonal zones between limnic and fluvial environment, were also taken into account. Analysis of the markers distribution was carried out against the diversity of chemical characteristics of limnic sediments. Ribbon shape of the lake basin and the dominant wind direction provide an opportunity of easy water mixing to a considerable depth. Intensive waving processes cause removal of the matter from the littoral zone towards lake hollows (separated by the underwater tresholds), where the

  2. Markers of neurodevelopmental impairments in early-onset psychosis

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    Petruzzelli MG

    2015-07-01

    Full Text Available Maria Giuseppina Petruzzelli,1 Lucia Margari,1 Francesco Craig,1 Maria Gloria Campa,1 Domenico Martinelli,2 Adriana Pastore,3 Marta Simone,1 Francesco Margari3 1Child and Adolescence Neuropsychiatry Unit, Department of Basic Medical Sciences, Neuroscience and Sense Organs, University “Aldo Moro” of Bari, 2Department of Medical and Surgical Sciences; University of Foggia, Foggia, 3Psychiatry Unit, Department of Basic Medical Sciences, Neuroscience and Sense Organ, University “Aldo Moro” of Bari, Bari, Italy Background: The aim of this study was to assess the association between the clinical and neurobiological markers of neurodevelopmental impairments and early-onset schizophrenia spectrum psychosis. Methods: A sample of 36 patients with early-onset schizophrenia spectrum psychosis was compared to a control sample of 36 patients with migraine. We assessed early childhood neurodevelopmental milestones using a modified version of the General Developmental Scale, general intellectual ability using the Wechsler Intelligence Scale for Children–Revised or Leiter International Performance Scale–Revised for patients with speech and language abnormalities, and neurological soft signs with specific regard to subtle motor impairment. Results: Subjects with early-onset psychosis had a higher rate of impaired social development (P=0.001, learning difficulties (P=0.04, enuresis (P=0.0008, a lower intelligence quotient (P<0.001, and subtle motor impairments (P=0.005 than control subjects. Conclusion: We suggest that neurodevelopment in early-onset psychosis is characterized by a global impairment of functional and adaptive skills that manifests from early childhood, rather than a delay or limitation in language and motor development. The current evidence is based on a small sample and should be investigated in larger samples in future research. Keywords: early-onset psychosis, early-onset schizophrenia, neurodevelopment, social cognition

  3. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea.

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    Yash Paul Khajuria

    Full Text Available The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777 of an inter-specific reference mapping population. High amplification efficiency (87%, experimental validation success rate (81% and polymorphic potential (55% of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48% detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%. An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777 having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7-23 cM longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped

  4. Inflammatory markers and extent and progression of early atherosclerosis

    DEFF Research Database (Denmark)

    Willeit, Peter; Thompson, Simon G; Agewall, Stefan

    2016-01-01

    BACKGROUND: Large-scale epidemiological evidence on the role of inflammation in early atherosclerosis, assessed by carotid ultrasound, is lacking. We aimed to quantify cross-sectional and longitudinal associations of inflammatory markers with common-carotid-artery intima-media thickness (CCA-IMT......) in the general population. METHODS: Information on high-sensitivity C-reactive protein, fibrinogen, leucocyte count and CCA-IMT was available in 20 prospective cohort studies of the PROG-IMT collaboration involving 49,097 participants free of pre-existing cardiovascular disease. Estimates of associations were...... calculated within each study and then combined using random-effects meta-analyses. RESULTS: Mean baseline CCA-IMT amounted to 0.74 mm (SD = 0.18) and mean CCA-IMT progression over a mean of 3.9 years to 0.011 mm/year (SD = 0.039). Cross-sectional analyses showed positive linear associations between...

  5. Cognitive, emotional and social markers of serial murdering.

    Science.gov (United States)

    Angrilli, Alessandro; Sartori, Giuseppe; Donzella, Giovanna

    2013-01-01

    Although criminal psychopathy is starting to be relatively well described, our knowledge of the characteristics and scientific markers of serial murdering is still very poor. A serial killer who murdered more than five people, KT, was administered a battery of standardized tests aimed at measuring neuropsychological impairment and social/emotional cognition deficits. KT exhibited a striking dissociation between a high level of emotional detachment and a low score on the antisocial behavior scale on the Psychopathy Checklist-Revised (PCL-R). The Minnesota Multiphasic Personality Inventory-2 showed a normal pattern with the psychotic triad at borderline level. KT had a high intelligence score and showed almost no impairment in cognitive tests sensitive to frontal lobe dysfunction (Wisconsin Card Sorting Test, Theory of Mind, Tower of London, this latter evidenced a mild impairment in planning performance). In the tests on moral, emotional and social cognition, his patterns of response differed from matched controls and from past reports on criminal psychopaths as, unlike these individuals, KT exhibited normal recognition of fear and a relatively intact knowledge of moral rules but he was impaired in the recognition of anger, embarrassment and conventional social rules. The overall picture of KT suggests that serial killing may be closer to normality than psychopathy defined according to either the DSM IV or the PCL-R, and it would be characterized by a relatively spared moral cognition and selective deficits in social and emotional cognition domains.

  6. Development of Microsatellite Markers for a Tropical Seagrass, Syringodium filiforme (Cymodoceaceae

    Directory of Open Access Journals (Sweden)

    Alexandra L. Bijak

    2014-10-01

    Full Text Available Premise of the study: A total of 17 polymorphic microsatellite markers were developed for the tropical Atlantic seagrass Syringodium filiforme (Cymodoceaceae, enabling analysis of population genetic structure in this species for the first time. Methods and Results: The 17 primers amplified di- and trinucleotide repeats revealing two to eight alleles per locus among the South Florida populations tested. In the analysis of two populations from the Florida Keys (Florida, USA, observed heterozygosity ranged from 0.063 to 0.905, although sampling was from relatively closely located populations so heterozygosity is expected to be higher across larger spatial scales. Multiplex PCRs consisting of two 6-plex and one 5-plex reactions were developed to maximize genotyping efficiency. Conclusions: We present here 17 polymorphic markers that will be useful for the study of clonality and population structure of S. filiforme, a marine plant that forms extensive habitat throughout the tropical Atlantic and Caribbean.

  7. Towards Common Balkan Lexical Evidential Markers

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    Maxim M. Makartsev

    2012-08-01

    1 As for the grammatical evidential markers in the Balkan languages, there is a tradition of their analysis dating back to the second half of the 19th century for Albanian and Bulgarian. Comparative analysis of evidential forms in the Balkan languages conducted by Victor Friedman [Friedman 1982, 1986, 1999], Grace Fielder [Fielder 1994, 1996, 1997, 1998, 1999], and several other linguists, has answered some questions about what is common among Balkan languages and what is unique for each of them in the domain of grammaticalised evidentiality. There is a great deal of literature on grammatical evidentiality in general and it is scarcely possible to cite it all within a single article, but a recent study [Aikhenvald 2004] contains the main bibliography on the issue.

  8. Oligothiophenes as Fluorescent Markers for Biological Applications

    Directory of Open Access Journals (Sweden)

    Antonio Manetto

    2012-01-01

    Full Text Available This paper summarizes some of our results on the application of oligothiophenes as fluorescent markers for biological studies. The oligomers of thiophene, widely known for their semiconductor properties in organic electronics, are also fluorescent compounds characterized by chemical and optical stability, high absorbance and quantum yield. Their fluorescent emission can be easily modulated via organic synthesis by changing the number of thiophene rings and the nature of side-chains. This review shows how oligothiophenes can be derivatized with active groups such as phosphoramidite, N-hydroxysuccinimidyl and 4-sulfotetrafluorophenyl esters, isothiocyanate and azide by which the (biomolecules of interest can be covalently bound. This paper also describes how molecules such as oligonucleotides, proteins and even nanoparticles, tagged with oligothiophenes, can be used in experiments ranging from hybridization studies to imaging of fixed and living cells. Finally, a few multilabeling experiments are described.

  9. Genetic markers for flowering in perennial ryegrass

    DEFF Research Database (Denmark)

    Paina, Cristiana; Byrne, Stephen; Andersen, Jeppe Reitan

    2011-01-01

    Perennial ryegrass (Lolium perenne L.) is the principal forage grass utilized in Danish agriculture and underpins the beef and dairy sectors. It is characterized as having high digestibility, high nutritional value, and high productivity during vegetative growth. However, at the reproductive growth...... stage there is a significant reduction in digestibility due to an increase in the stem to leaf ratio. Thus, the controlled inhibition or delay of flowering would result in a significant increase of forage quality. Traditional breeding programs have been successfully breeding new varieties of perennial...... ryegrass for decades. However, it can take more than ten years to develop a new variety and involves intensive phenotyping at all stages of selection. It is envisaged that with the aid of molecular markers, breeding programs can be accelerated and gains increased. Our goal is to develop and validate...

  10. Calprotectin--a novel marker of obesity

    DEFF Research Database (Denmark)

    Mortensen, Ole Hartvig; Nielsen, Anders Rinnov; Erikstrup, Christian

    2009-01-01

    obese subjects or subjects with type 2 diabetes. METHODOLOGY/PRINCIPAL FINDINGS: Plasma calprotectin and skeletal muscle S100A8 mRNA levels were measured in a cohort consisting of 199 subjects divided into four groups depending on presence or absence of type 2 diabetes (T2D), and presence or absence...... of obesity. There was a significant interaction between obesity and T2D (p = 0.012). Plasma calprotectin was increased in obese relative to non-obese controls (pobese and non-obese patients with T2D (p = 0.62). S100A8 mRNA levels in skeletal muscle were...... not influenced by obesity or T2D. Multivariate regression analysis (adjusting for age, sex, smoking and HOMA2-IR) showed plasma calprotectin to be strongly associated with BMI, even when further adjusted for fitness, CRP, TNF-alpha or neutrophil number. CONCLUSIONS/SIGNIFICANCE: Plasma calprotectin is a marker...

  11. Hepatitis and thrombocytopenia: markers of dengue mortality.

    Science.gov (United States)

    Krishnamoorthy, Smitha; Bhatt, Arun N; Mathew, Celine Thalappillil; Ittyachen, Abraham M

    2017-04-01

    Dengue fever is of great concern to public health in India as it contributes significantly to the burden of healthcare. The aim of our study was to measure mortality in dengue and its association with hepatitis and thrombocytopenia. Our study was performed in a tertiary care setting in the state of Kerala in southern India. Adult patients admitted in the year 2013 were included. Among 1308 confirmed dengue patients, the mortality rate was 1.76%. Hepatitis and thrombocytopenia were present in over 80% of all patients, but severe hepatitis was seen in 11.4% and severe thrombocytopenia in 9.3%. These were markers of fatal outcome. Other factors significantly associated with mortality were age >60 years, male sex, diabetes and the presence of any co-morbidity.

  12. Converging intracranial markers of conscious access.

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    Raphaël Gaillard

    2009-03-01

    Full Text Available We compared conscious and nonconscious processing of briefly flashed words using a visual masking procedure while recording intracranial electroencephalogram (iEEG in ten patients. Nonconscious processing of masked words was observed in multiple cortical areas, mostly within an early time window (<300 ms, accompanied by induced gamma-band activity, but without coherent long-distance neural activity, suggesting a quickly dissipating feedforward wave. In contrast, conscious processing of unmasked words was characterized by the convergence of four distinct neurophysiological markers: sustained voltage changes, particularly in prefrontal cortex, large increases in spectral power in the gamma band, increases in long-distance phase synchrony in the beta range, and increases in long-range Granger causality. We argue that all of those measures provide distinct windows into the same distributed state of conscious processing. These results have a direct impact on current theoretical discussions concerning the neural correlates of conscious access.

  13. Paternally inherited markers in bovine hybrid populations.

    Science.gov (United States)

    Verkaar, E L C; Vervaecke, H; Roden, C; Romero Mendoza, L; Barwegen, M W; Susilawati, T; Nijman, I J; Lenstra, J A

    2003-12-01

    The genetic integrity of crossfertile bovine- or cattle-like species may be endangered by species hybridization. Previously, amplified fragment length polymorphism, satellite fragment length polymorphism and microsatellite assays have been used to analyze the species composition of nuclear DNA in taurine cattle, zebu, banteng and bison populations, while mitochondrial DNA reveals the origin of the maternal lineages. Here, we describe species-specific markers of the paternally transmitted Y-chromosome for the direct detection of male-mediated introgression. Convenient PCR-restriction fragment length polymorphism and competitive PCR assays are shown to differentiate the Y-chromosomes of taurine cattle, American bison and European bison, and to detect the banteng origin of Indonesian Madura and Bali cattle bulls.

  14. Chemical markers in Veronica sect. Hebe

    DEFF Research Database (Denmark)

    Johansen, Maria; Larsen, Tania Surrow; Mattebjerg, Maria Ahlm

    2007-01-01

    The content of iridoid glucosides and other water soluble compounds of Veronica sect. Hebe, three species and two hybrids were investigated. V. (Hebe) elliptica and V. (Hebe) brachysiphon, both from sect. Apertae were chemically different since the former contained two esters of 6-O......-rhamnopyranosylcatalpol while the latter had a 6-O-catalpol ester, compounds characteristic for most Veronica species. V. (Hebe) odora, from sect. Buxifoliatae as well as two hybrids presumably between this and two different "whipcord" species were also investigated. The parent species contained two 6-O-catalpol esters, one...... and hebridoside as well as 1-O-benzoyl b-rutinose had not previously been described from nature. The results confirm previous studies in that esters of 6-O-rhamnopyranosylcatalpol could be useful chemical markers in Veronica sect. Hebe....

  15. SNP marker discovery in koala TLR genes.

    Directory of Open Access Journals (Sweden)

    Jian Cui

    Full Text Available Toll-like receptors (TLRs play a crucial role in the early defence against invading pathogens, yet our understanding of TLRs in marsupial immunity is limited. Here, we describe the characterisation of nine TLRs from a koala immune tissue transcriptome and one TLR from a draft sequence of the koala genome and the subsequent development of an assay to study genetic diversity in these genes. We surveyed genetic diversity in 20 koalas from New South Wales, Australia and showed that one gene, TLR10 is monomorphic, while the other nine TLR genes have between two and 12 alleles. 40 SNPs (16 non-synonymous were identified across the ten TLR genes. These markers provide a springboard to future studies on innate immunity in the koala, a species under threat from two major infectious diseases.

  16. SNP marker discovery in koala TLR genes.

    Science.gov (United States)

    Cui, Jian; Frankham, Greta J; Johnson, Rebecca N; Polkinghorne, Adam; Timms, Peter; O'Meally, Denis; Cheng, Yuanyuan; Belov, Katherine

    2015-01-01

    Toll-like receptors (TLRs) play a crucial role in the early defence against invading pathogens, yet our understanding of TLRs in marsupial immunity is limited. Here, we describe the characterisation of nine TLRs from a koala immune tissue transcriptome and one TLR from a draft sequence of the koala genome and the subsequent development of an assay to study genetic diversity in these genes. We surveyed genetic diversity in 20 koalas from New South Wales, Australia and showed that one gene, TLR10 is monomorphic, while the other nine TLR genes have between two and 12 alleles. 40 SNPs (16 non-synonymous) were identified across the ten TLR genes. These markers provide a springboard to future studies on innate immunity in the koala, a species under threat from two major infectious diseases.

  17. Predictive and therapeutic markers in ovarian cancer

    Science.gov (United States)

    Gray, Joe W.; Guan, Yinghui; Kuo, Wen-Lin; Fridlyand, Jane; Mills, Gordon B.

    2013-03-26

    Cancer markers may be developed to detect diseases characterized by increased expression of apoptosis-suppressing genes, such as aggressive cancers. Genes in the human chromosomal regions, 8q24, 11q13, 20q11-q13, were found to be amplified indicating in vivo drug resistance in diseases such as ovarian cancer. Diagnosis and assessment of amplification levels certain genes shown to be amplified, including PVT1, can be useful in prediction of poor outcome of patient's response and drug resistance in ovarian cancer patients with low survival rates. Certain genes were found to be high priority therapeutic targets by the identification of recurrent aberrations involving genome sequence, copy number and/or gene expression are associated with reduced survival duration in certain diseases and cancers, specifically ovarian cancer. Therapeutics to inhibit amplification and inhibitors of one of these genes, PVT1, target drug resistance in ovarian cancer patients with low survival rates is described.

  18. Macrophage serum markers in pneumococcal bacteremia

    DEFF Research Database (Denmark)

    Møller, Holger Jon; Moestrup, Søren K; Weis, Nina

    2006-01-01

    with pneumococcal bacteremia. DESIGN: Observational cohort study. SETTING: Five university hospitals in Denmark. PATIENTS: A total of 133 patients with Streptococcus pneumoniae bacteremia (positive blood culture) and 133 age- and gender-matched controls. INTERVENTIONS: Samples were collected for biochemical...... analyses at the time of first positive blood culture. MEASUREMENTS AND MAIN RESULTS: sCD163 was highly correlated with other macrophage markers and was significantly elevated (median [25-75 percentiles], 4.6 mg/L [2.8-8.9]) compared with healthy controls (2.7 mg/L [2.1-3.3], p ... were observed in patients who needed intensive care (hemodialysis, p = .0011; hypotension, p = .0014; mechanical ventilation, p = .0019). Significantly lower levels of sCD163, ferritin, transcobalamin, and suPAR (but not C-reactive protein) were measured in patients > or =75 yrs. In patients

  19. "Tooth marker" to diagnose diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Dipti Bhatnagar

    2009-01-01

    Full Text Available During clinical examination of patients to diagnose oral diseases, it was observed that many patients had Cuspal destruction with saucer shaped cavity, ill defined pits and fissures with flattening of occlusal surface in the First permanent molars. The tooth is slightly yellowish in color. Many people who are having this tooth were diabetic. The tooth appeared as Attrition Pattern. A research has been carried out to find out whether this tooth has any relevance to diabetes mellitus. Incidence of attrition pattern among non diabetic, diabetic patients and Incidence of diabetes among attrition patients were carried out. Further gingival biopsies were taken to find out microangiopathy and PAS positive in vessels of connective tissue among diabetic, non diabetic and patients with attrition pattern. The observations of Research are correlated with one another and it was found that the attrition pattern have significant relation to diabetes. The use of attrition pattern as a marker to diagnose diabetes has been discussed.

  20. Keratinocyte specific markers isolated using phage display

    DEFF Research Database (Denmark)

    Jensen, K.B.; Jensen, Ole Nørregaard; Ravn, P.

    2003-01-01

    Specific molecular markers for various normal and pathogenic cell states and cell types provide knowledge of basic biological systems and have a direct application in targeted therapy. We describe a proteomic method based on the combination of new and improved phage display antibody technologies...... display method was applied to analysis of human skin keratinocytes resulting in the isolation of a panel of antibodies. Fourteen of these antibodies were further characterized, half of which predominantly recognized keratinocytes in a screen of a range of different cell types. Three cognate keratinocyte...... antigens were subsequently identified by mass spectrometry as laminin-5, plectin, and fibronectin. The combination of phage display technology with mass spectrometry methods for protein identification is a general and promising approach for proteomic analysis of cell surface complexity....

  1. Magnetic Resonance Imaging (MRI) Markers for MRI-Guided High-Dose-Rate Brachytherapy: Novel Marker-Flange for Cervical Cancer and Marker Catheters for Prostate Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Schindel, Joshua; Muruganandham, Manickam [Department of Radiation Oncology, University of Iowa, Iowa City, Iowa (United States); Pigge, F. Christopher [Department of Chemistry, University of Iowa, Iowa City, Iowa (United States); Anderson, James [Department of Radiation Oncology, University of Iowa, Iowa City, Iowa (United States); Kim, Yusung, E-mail: yusung-kim@uiowa.edu [Department of Radiation Oncology, University of Iowa, Iowa City, Iowa (United States)

    2013-06-01

    Purpose: To present a novel marker-flange, addressing source-reconstruction uncertainties due to the artifacts of a titanium intracavitary applicator used for magnetic resonance imaging (MRI)-guided high-dose-rate (HDR) brachytherapy (BT); and to evaluate 7 different MRI marker agents used for interstitial prostate BT and intracavitary gynecologic HDR BT when treatment plans are guided by MRI. Methods and Materials: Seven MRI marker agents were analyzed: saline solution, Conray-60, copper sulfate (CuSO{sub 4}) (1.5 g/L), liquid vitamin E, fish oil, 1% agarose gel (1 g agarose powder per 100 mL distilled water), and a cobalt–chloride complex contrast (C4) (CoCl{sub 2}/glycine = 4:1). A plastic, ring-shaped marker-flange was designed and tested on both titanium and plastic applicators. Three separate phantoms were designed to test the marker-flange, interstitial catheters for prostate BT, and intracavitary catheters for gynecologic HDR BT. T1- and T2-weighted MRI were analyzed for all markers in each phantom and quantified as percentages compared with a 3% agarose gel background. The geometric accuracy of the MR signal for the marker-flange was measured using an MRI-CT fusion. Results: The CuSO{sub 4} and C4 markers on T1-weighted MRI and saline on T2-weighted MRI showed the highest signals. The marker-flange showed hyper-signals of >500% with CuSO{sub 4} and C4 on T1-weighted MRI and of >400% with saline on T2-weighted MRI on titanium applicators. On T1-weighted MRI, the MRI signal inaccuracies of marker-flanges were measured <2 mm, regardless of marker agents, and that of CuSO{sub 4} was 0.42 ± 0.14 mm. Conclusion: The use of interstitial/intracavitary markers for MRI-guided prostate/gynecologic BT was observed to be feasible, providing accurate source pathway reconstruction. The novel marker-flange can produce extremely intense, accurate signals, demonstrating its feasibility for gynecologic HDR BT.

  2. Tumour Markers and Kidney Function: A Systematic Review

    Directory of Open Access Journals (Sweden)

    Giuseppe Coppolino

    2014-01-01

    Full Text Available Tumour markers represent useful tools in diagnosis and clinical management of patients with cancer, because they are easy to use, minimally invasive, and easily measured in either blood or urine. Unfortunately, such an ideal marker, as yet, does not exist. Different pathological states may increase the level of a tumour marker in the absence of any neoplasia. Alternatively, low levels of tumour markers could be also found in the presence of neoplasias. We aimed at reviewing studies currently available in the literature examining the association between tumour markers and different renal impairment conditions. Each tumour marker was found to be differently influenced by these criteria; additionally we revealed in many cases a lack of available published data.

  3. A new fiducial marker for Image-guided radiotherapy of prostate cancer: clinical experience.

    Science.gov (United States)

    Carl, Jesper; Nielsen, Jane; Holmberg, Mats; Højkjaer Larsen, Erik; Fabrin, Knud; Fisker, Rune V

    2008-01-01

    A new fiducial marker for image guided radiotherapy (IGRT) based on a removable prostate stent made of Ni Ti has been developed during two previous clinical feasibility studies. The marker is currently being evaluated for IGRT treatment in a third clinical study. The new marker is used to co-register MR and planning CT scans with high accuracy in the region around the prostate. The co-registered MR-CT volumes are used for delineation of GTV before planning. In each treatment session the IGRT system is used to position the patient before treatment. The IGRT system use a stereo pair of kV images matched to corresponding Digital Reconstructed Radiograms (DRR) from the planning CT scan. The match is done using mutual gray scale information. The pair of DRR's for positioning is created in the IGRT system with a threshold in the Look Up Table (LUT). The resulting match provides the necessary shift in couch coordinates to position the stent with an accuracy of 1-2 mm within the planned position. At the present time 39 patients have received the new marker. Of the 39 one has migrated to the bladder. Deviations of more than 5 mm between CTV outlined on CT and MR are seen in several cases and in anterior-posterior (AP), left-right (LR) and cranial-caudal (CC) directions. Intra-fraction translation movements up to +/- 3 mm are seen as well. As the stent is also clearly visible on images taken with high voltage x-rays using electronic portal images devices (EPID), the positioning has been verified independently of the IGRT system. The preliminary result of an on going clinical study of a Ni Ti prostate stent, potentially a new fiducial marker for image guided radiotherapy, looks promising. The risk of migration appears to be much lower compared to previous designs.

  4. Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum).

    Science.gov (United States)

    Russell, Joanne R; Bayer, Micha; Booth, Clare; Cardle, Linda; Hackett, Christine A; Hedley, Pete E; Jorgensen, Linzi; Morris, Jenny A; Brennan, Rex M

    2011-10-28

    Deep-level second generation sequencing (2GS) technologies are now being applied to non-model species as a viable and favourable alternative to Sanger sequencing. Large-scale SNP discovery was undertaken in blackcurrant (Ribes nigrum L.) using transcriptome-based 2GS 454 sequencing on the parental genotypes of a reference mapping population, to generate large numbers of novel markers for the construction of a high-density linkage map. Over 700,000 reads were produced, from which a total of 7,000 SNPs were found. A subset of polymorphic SNPs was selected to develop a 384-SNP OPA assay using the Illumina BeadXpress platform. Additionally, the data enabled identification of 3,000 novel EST-SSRs. The selected SNPs and SSRs were validated across diverse Ribes germplasm, including mapping populations and other selected Ribes species.SNP-based maps were developed from two blackcurrant mapping populations, incorporating 48% and 27% of assayed SNPs respectively. A relatively high proportion of visually monomorphic SNPs were investigated further by quantitative trait mapping of theta score outputs from BeadStudio analysis, and this enabled additional SNPs to be placed on the two maps. The use of 2GS technology for the development of markers is superior to previously described methods, in both numbers of markers and biological informativeness of those markers. Whilst the numbers of reads and assembled contigs were comparable to similar sized studies of other non-model species, here a high proportion of novel genes were discovered across a wide range of putative function and localisation. The potential utility of markers developed using the 2GS approach in downstream breeding applications is discussed.

  5. Ghost marker detection and elimination in marker-based optical tracking systems for real-time tracking in stereotactic body radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Guanghua, E-mail: yan@ufl.edu; Li, Jonathan; Huang, Yin; Mittauer, Kathryn; Lu, Bo; Liu, Chihray [Department of Radiation Oncology, University of Florida, Gainesville, Florida 32610 (United States)

    2014-10-15

    Purpose: To propose a simple model to explain the origin of ghost markers in marker-based optical tracking systems (OTS) and to develop retrospective strategies to detect and eliminate ghost markers. Methods: In marker-based OTS, ghost markers are virtual markers created due to the cross-talk between the two camera sensors, which can lead to system execution failure or inaccuracy in patient tracking. As a result, the users have to limit the number of markers and avoid certain marker configurations to reduce the chances of ghost markers. In this work, the authors propose retrospective strategies to detect and eliminate ghost markers. The two camera sensors were treated as mathematical points in space. The authors identified the coplanar within limit (CWL) condition as the necessary condition for ghost marker occurrence. A simple ghost marker detection method was proposed based on the model. Ghost marker elimination was achieved through pattern matching: a ghost marker-free reference set was matched with the optical marker set observed by the OTS; unmatched optical markers were eliminated as either ghost markers or misplaced markers. The pattern matching problem was formulated as a constraint satisfaction problem (using pairwise distances as constraints) and solved with an iterative backtracking algorithm. Wildcard markers were introduced to address missing or misplaced markers. An experiment was designed to measure the sensor positions and the limit for the CWL condition. The ghost marker detection and elimination algorithms were verified with samples collected from a five-marker jig and a nine-marker anthropomorphic phantom, rotated with the treatment couch from −60° to +60°. The accuracy of the pattern matching algorithm was further validated with marker patterns from 40 patients who underwent stereotactic body radiotherapy (SBRT). For this purpose, a synthetic optical marker pattern was created for each patient by introducing ghost markers, marker position

  6. Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

    Science.gov (United States)

    Kim, Sung-Ryul; Ramos, Joie; Ashikari, Motoyuki; Virk, Parminder S; Torres, Edgar A; Nissila, Eero; Hechanova, Sherry Lou; Mauleon, Ramil; Jena, Kshirod K

    2016-12-01

    development of other genes associated with useful agronomic traits.

  7. Candidate Gene Associations with Withdrawn Behavior

    Science.gov (United States)

    Rubin, David H.; Althoff, Robert R.; Ehli, Erik A.; Davies, Gareth E.; Rettew, David C.; Crehan, Eileen T.; Walkup, John T.; Hudziak, James J.

    2013-01-01

    Background: Social withdrawal is a core neuropsychiatric phenomenon in developmental psychopathology. Its presence predicts psychopathology across many domains, including depression, psychosis, autism, anxiety, and suicide. Withdrawn behavior is highly heritable, persistent, and characteristically worsens without intervention. To date, few studies…

  8. Novel candidate genes associated with hippocampal oscillations.

    NARCIS (Netherlands)

    Jansen, R.; Timmerman, J.; Loos, M.; Spijker, S.; van Ooyen, A.; Brussaard, A.B.; Mansvelder, H.D.; Smit, A.B.; de Gunst, M.; Linkenkaer-Hansen, K.

    2011-01-01

    The hippocampus is critical for a wide range of emotional and cognitive behaviors. Here, we performed the first genome-wide search for genes influencing hippocampal oscillations. We measured local field potentials (LFPs) using 64-channel multi-electrode arrays in acute hippocampal slices of 29 BXD

  9. Technologies for Assessing Behavioral and Cognitive Markers of Suicide Risk

    Science.gov (United States)

    2017-10-01

    hopelessness, reassurance seeking) and cognitive (e.g., attentional fixation on suicide-related information) markers could provide new method for...AWARD NUMBER: W81XWH-15-1-0632 TITLE: Technologies for Assessing Behavioral and Cognitive Markers of Suicide Risk PRINCIPAL INVESTIGATOR: Brian...CONTRACT NUMBER Technologies for Assessing Behavioral and Cognitive Markers of Suicide Risk 5b. GRANT NUMBER W81XWH-15-1-0632 5c. PROGRAM

  10. NEW MARKERS FOR CARDIOVASCULAR RISK: FROM STUDIES TO CLINICAL GUIDELINES

    Directory of Open Access Journals (Sweden)

    D. A. Anichkov

    2014-11-01

    Full Text Available New markers for cardiovascular disease (CVD risk are the subject of an intensive discussion in the scientific literature. The biomarkers (newlipid parameters, inflammatory markers and signs of subclinical atherosclerosis are candidates to be included in models to assess the cumulative risk of CVD. The paper considers the basic studies dealing with new markers of CVD risk and their place in current clinical recommendations.

  11. Plant breeding with marker-assisted selection in Brazil

    OpenAIRE

    Sakiyama,Ney Sussumu; Ramos, Helaine Christine Cancela; Caixeta, Eveline Teixeira; Pereira,Messias Gonzaga

    2014-01-01

    Over the past three decades, molecular marker studies reached extraordinary advances, especially for sequencing and bioinformatics techniques. Marker-assisted selection became part of the breeding program routines of important seed companies, in order to accelerate and optimize the cultivar developing processes. Private seed companies increasingly use marker-assisted selection, especially for the species of great importance to the seed market, e.g. corn, soybean, cotton, and sunflower. In the...

  12. Established and emerging biological activity markers of inflammatory bowel disease

    DEFF Research Database (Denmark)

    Nielsen, O H; Vainer, B; Madsen, S M

    2000-01-01

    Assessment of disease activity in inflammatory bowel disease (IBD), i.e., ulcerative colitis (UC) and Crohn's disease (CD), is done using clinical parameters and various biological disease markers. Ideally, a disease marker must: be able to identify individuals at risk of a given disorder...... warranted to identify and assess the clinical importance and applicability of new laboratory markers for the diagnosis or the disease activity of IBD....

  13. On Quantitative Rorschach Scales.

    Science.gov (United States)

    Haggard, Ernest A.

    1978-01-01

    Two types of quantitative Rorschach scales are discussed: first, those based on the response categories of content, location, and the determinants, and second, global scales based on the subject's responses to all ten stimulus cards. (Author/JKS)

  14. Atlantic Salmon Scale Measurements

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Scales are collected annually from smolt trapping operations in Maine as wellas other sampling opportunities (e.g. marine surveys, fishery sampling etc.). Scale...

  15. De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers.

    Science.gov (United States)

    Xanthopoulou, Aliki; Ganopoulos, Ioannis; Psomopoulos, Fotis; Manioudaki, Maria; Moysiadis, Theodoros; Kapazoglou, Aliki; Osathanunkul, Maslin; Michailidou, Sofia; Kalivas, Apostolos; Tsaftaris, Athanasios; Nianiou-Obeidat, Irini; Madesis, Panagiotis

    2017-07-30

    The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes. In the current study we used these databases to perform comparative transcriptome analysis in order to identify genes with potential roles in fruit morphology and fruit size. Differential Gene Expression (DGE) analysis between cv. 'Munchkin' (small-fruit) and cv. 'Big Moose' (large-fruit) revealed a variety of candidate genes associated with fruit morphology with significant differences in gene expression between the two cultivars. In addition, we have set the framework for generating EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. The results of the present study will contribute to both further understanding the molecular mechanisms regulating fruit morphology and furthermore identifying the factors that determine fruit size. Moreover, they may lead to the development of molecular marker tools for selecting genotypes with desired morphological traits. Copyright © 2017. Published by Elsevier B.V.

  16. Secretagogin is a new neuroendocrine marker in the human prostate

    DEFF Research Database (Denmark)

    Adolf, Katja; Wagner, Ludwig; Bergh, Anders

    2007-01-01

    marker in carcinoid tumors of the lung and the gastrointestinal tract. The present study analyzes the expression of secretagogin in normal and malign prostate tissue. METHODS: We analyzed immunoreactivity for secretagogin, chromogranin A (CgA), neuron specific enolase (NSE), and synaptophysin (SYN...... and co-localized with the NE markers CgA and NSE. The expression of secretagogin is significantly correlated to CgA (P marker in the prostate with more extended...... immunoreactivity compared to the NE markers CgA, SYN, and NSE. Secretagogin is widely expressed in prostatic adenocarcinoma as opposed to adenocarcinomas in other organs....

  17. The Marker State Space (MSS method for classifying clinical samples.

    Directory of Open Access Journals (Sweden)

    Brian P Fallon

    Full Text Available The development of accurate clinical biomarkers has been challenging in part due to the diversity between patients and diseases. One approach to account for the diversity is to use multiple markers to classify patients, based on the concept that each individual marker contributes information from its respective subclass of patients. Here we present a new strategy for developing biomarker panels that accounts for completely distinct patient subclasses. Marker State Space (MSS defines "marker states" based on all possible patterns of high and low values among a panel of markers. Each marker state is defined as either a case state or a control state, and a sample is classified as case or control based on the state it occupies. MSS was used to define multi-marker panels that were robust in cross validation and training-set/test-set analyses and that yielded similar classification accuracy to several other classification algorithms. A three-marker panel for discriminating pancreatic cancer patients from control subjects revealed subclasses of patients based on distinct marker states. MSS provides a straightforward approach for modeling highly divergent subclasses of patients, which may be adaptable for diverse applications.

  18. Advances of selectable marker genes in plastid genetic engineering.

    Science.gov (United States)

    He, Yong; Luo, An; Mu, Lian-Sheng; Chen, Qiang; Zhang, Yan; Yeh, Kai-Wun; Tian, Zhi-Hong

    2017-09-20

    Plastid genetic engineering is a safer, more precise, and more efficient transgene expression system than the nuclear genetic transformation system. It has been widely used in basic research and biotechnology applications as the next-generation transgenic technology in plants. Similar to nuclear genetic transformation, selection markers are needed in plastid genetic engineering to identify 'true' transformants and acquire homoplasmy. Because of the high copy number of plastids, maternal inheritance of the plastid genome, and the long process of homogenization of transplastomic plants, the selection markers for plastid genetic engineering are different from those used in the nuclear transformation system. At present, antibiotic resistance genes are the most commonly used selectable markers in the transplastomic selections. However for biosafety reasons, they needed to be replaced with either alternative markers or marker-free systems for the plastid genetic engineering. In this review, we have evaluated and summarized the positive and negative features of the selectable markers and marker elimination strategies commonly used in the plastid engineering research in the literature on plastid genetic engineering research. In addition, we have reviewed the features of the reporter genes used in plastid genetic engineering. We hope this review can help improving the current and developing new selectable markers and marker removal systems, and further promote the development of plastid genetic engineering, especially on the monocotyledonous plants.

  19. [ETAP: A smoking scale for Primary Health Care].

    Science.gov (United States)

    González Romero, Pilar María; Cuevas Fernández, Francisco Javier; Marcelino Rodríguez, Itahisa; Rodríguez Pérez, María Del Cristo; Cabrera de León, Antonio; Aguirre-Jaime, Armando

    2016-05-01

    To obtain a scale of tobacco exposure to address smoking cessation. Follow-up of a cohort. Scale validation. Primary Care Research Unit. Tenerife. A total of 6729 participants from the "CDC de Canarias" cohort. A scale was constructed under the assumption that the time of exposure to tobacco is the key factor to express accumulated risk. Discriminant validity was tested on prevalent cases of acute myocardial infarction (AMI; n=171), and its best cut-off for preventive screening was obtained. Its predictive validity was tested with incident cases of AMI (n=46), comparing the predictive power with markers (age, sex) and classic risk factors of AMI (hypertension, diabetes, dyslipidaemia), including the pack-years index (PYI). The scale obtained was the sum of three times the years that they had smoked plus years exposed to smoking at home and at work. The frequency of AMI increased with the values of the scale, with the value 20 years of exposure being the most appropriate cut-off for preventive action, as it provided adequate predictive values for incident AMI. The scale surpassed PYI in predicting AMI, and competed with the known markers and risk factors. The proposed scale allows a valid measurement of exposure to smoking and provides a useful and simple approach that can help promote a willingness to change, as well as prevention. It still needs to demonstrate its validity, taking as reference other problems associated with smoking. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

  20. New development and validation of 50 SSR markers in breadfruit (Artocarpus altilis, Moraceae) by next-generation sequencing.

    Science.gov (United States)

    De Bellis, Fabien; Malapa, Roger; Kagy, Valérie; Lebegin, Stéphane; Billot, Claire; Labouisse, Jean-Pierre

    2016-08-01

    Using next-generation sequencing technology, new microsatellite loci were characterized in Artocarpus altilis (Moraceae) and two congeners to increase the number of available markers for genotyping breadfruit cultivars. A total of 47,607 simple sequence repeat loci were obtained by sequencing a library of breadfruit genomic DNA with an Illumina MiSeq system. Among them, 50 single-locus markers were selected and assessed using 41 samples (39 A. altilis, one A. camansi, and one A. heterophyllus). All loci were polymorphic in A. altilis, 44 in A. camansi, and 21 in A. heterophyllus. The number of alleles per locus ranged from two to 19. The new markers will be useful for assessing the identity and genetic diversity of breadfruit cultivars on a small geographical scale, gaining a better understanding of farmer management practices, and will help to optimize breadfruit genebank management.