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Sample records for marker individualized dedicare

  1. Individual Identifiability Predicts Population Identifiability in Forensic Microsatellite Markers.

    PubMed

    Algee-Hewitt, Bridget F B; Edge, Michael D; Kim, Jaehee; Li, Jun Z; Rosenberg, Noah A

    2016-04-01

    Highly polymorphic genetic markers with significant potential for distinguishing individual identity are used as a standard tool in forensic testing [1, 2]. At the same time, population-genetic studies have suggested that genetically diverse markers with high individual identifiability also confer information about genetic ancestry [3-6]. The dual influence of polymorphism levels on ancestry inference and forensic desirability suggests that forensically useful marker sets with high levels of individual identifiability might also possess substantial ancestry information. We study a standard forensic marker set-the 13 CODIS loci used in the United States and elsewhere [2, 7-9]-together with 779 additional microsatellites [10], using direct population structure inference to test whether markers with substantial individual identifiability also produce considerable information about ancestry. Despite having been selected for individual identification and not for ancestry inference [11], the CODIS markers generate nontrivial model-based clustering patterns similar to those of other sets of 13 tetranucleotide microsatellites. Although the CODIS markers have relatively low values of the F(ST) divergence statistic, their high heterozygosities produce greater ancestry inference potential than is possessed by less heterozygous marker sets. More generally, we observe that marker sets with greater individual identifiability also tend toward greater population identifiability. We conclude that population identifiability regularly follows as a byproduct of the use of highly polymorphic forensic markers. Our findings have implications for the design of new forensic marker sets and for evaluations of the extent to which individual characteristics beyond identification might be predicted from current and future forensic data.

  2. A Combined Marker of Inflammation in Individuals with Mania

    PubMed Central

    Dickerson, Faith; Stallings, Cassie; Origoni, Andrea; Vaughan, Crystal; Katsafanas, Emily; Khushalani, Sunil; Yolken, Robert

    2013-01-01

    Background Markers of immune activation have been associated with mania but have not been examined in combination. We studied the association between mania and an inflammation score based on four immune markers. Methods A total of 57 individuals with mania were assessed at up to three time points: the day of hospital admission, evaluation several days later, and six-month follow-up. Also assessed were 207 non-psychiatric controls and 330 individuals with recent onset psychosis, multi-episode schizophrenia, or bipolar disorder depression. A combined inflammation score was calculated by factor analysis of the levels of class-specific antibodies to the NR peptide of the NMDA receptor; gliadin; Mason-Pfizer monkey virus protein 24; and Toxoplasma gondii. Inflammation scores among groups were compared by multivariate analyses. The inflammation score of the mania group at evaluation was studied as a predictor of re-hospitalization in the follow-up period. Results The combined inflammation score of the mania group at hospital admission and at evaluation differed significantly from that of the non-psychiatric controls (t = 3.95, 4.10, p<.001). The inflammation score was significantly decreased at six month follow-up (F = 5.85, p = 0.004). There were not any significant differences in the inflammation scores of any of the other psychiatric groups and that of the controls. Within the mania group, an elevated inflammation score at evaluation predicted re-hospitalization (Hazard ratio = 7.12, p = .005). Conclusions Hospitalization for mania is associated with immune activation. The level of this activation is predictive of subsequent re-hospitalization. Interventions for the modulation of inflammation should be evaluated for the therapy of individuals with mania. PMID:24019926

  3. Individual Markers of Resilience in Train Traffic Control

    PubMed Central

    Lo, Julia C.; Pluyter, Kari R.; Meijer, Sebastiaan A.

    2015-01-01

    Objective: The aim of this study was to examine individual markers of resilience and obtain quantitative insights into the understanding and the implications of variation and expertise levels in train traffic operators’ goals and strategic mental models and their impact on performance. Background: The Dutch railways are one of the world’s most heavy utilized railway networks and have been identified to be weak in system and organizational resilience. Method: Twenty-two train traffic controllers enacted two scenarios in a human-in-the-loop simulator. Their experience, goals, strategic mental models, and performance were assessed through questionnaires and simulator logs. Goals were operationalized through performance indicators and strategic mental models through train completion strategies. Results: A variation was found between operators for both self-reported primary performance indicators and completion strategies. Further, the primary goal of only 14% of the operators reflected the primary organizational goal (i.e., arrival punctuality). An incongruence was also found between train traffic controllers’ self-reported performance indicators and objective performance in a more disrupted condition. The level of experience tends to affect performance differently. Conclusion: There is a gap between primary organizational goals and preferred individual goals. Further, the relative strong diversity in primary operator goals and strategic mental models indicates weak resilience at the individual level. Application: With recent and upcoming large-scale changes throughout the sociotechnical space of the railway infrastructure organization, the findings are useful to facilitate future railway traffic control and the development of a resilient system. PMID:26721290

  4. Language Individuation and Marker Words: Shakespeare and His Maxwell's Demon

    PubMed Central

    Marsden, John; Budden, David; Craig, Hugh; Moscato, Pablo

    2013-01-01

    Background Within the structural and grammatical bounds of a common language, all authors develop their own distinctive writing styles. Whether the relative occurrence of common words can be measured to produce accurate models of authorship is of particular interest. This work introduces a new score that helps to highlight such variations in word occurrence, and is applied to produce models of authorship of a large group of plays from the Shakespearean era. Methodology A text corpus containing 55,055 unique words was generated from 168 plays from the Shakespearean era (16th and 17th centuries) of undisputed authorship. A new score, CM1, is introduced to measure variation patterns based on the frequency of occurrence of each word for the authors John Fletcher, Ben Jonson, Thomas Middleton and William Shakespeare, compared to the rest of the authors in the study (which provides a reference of relative word usage at that time). A total of 50 WEKA methods were applied for Fletcher, Jonson and Middleton, to identify those which were able to produce models yielding over 90% classification accuracy. This ensemble of WEKA methods was then applied to model Shakespearean authorship across all 168 plays, yielding a Matthews' correlation coefficient (MCC) performance of over 90%. Furthermore, the best model yielded an MCC of 99%. Conclusions Our results suggest that different authors, while adhering to the structural and grammatical bounds of a common language, develop measurably distinct styles by the tendency to over-utilise or avoid particular common words and phrasings. Considering language and the potential of words as an abstract chaotic system with a high entropy, similarities can be drawn to the Maxwell's Demon thought experiment; authors subconsciously favour or filter certain words, modifying the probability profile in ways that could reflect their individuality and style. PMID:23826143

  5. Diversity, population structure, and individual behaviour of parasitoids as seen using molecular markers.

    PubMed

    van Nouhuys, Saskya

    2016-04-01

    Parasitoids have long been models for host-parasite interactions, and are important in biological control. Neutral molecular markers have become increasingly accessible tools, revealing previously unknown parasitoid diversity. Thus, insect communities are now seen as more speciose. They have also been found to be more complex, based on trophic links detected using bits of parasitoid DNA in hosts, and host DNA in adult parasitoids. At the population level molecular markers are used to determine the influence of factors such as host dynamics on parasitoid population structure. Finally, at the individual level, they are used to identify movement of individuals. Overall molecular markers greatly increase the value of parasitoid samples collected, for both basic and applied research, at all levels of study. PMID:27436653

  6. Markers

    ERIC Educational Resources Information Center

    Healthy Schools Network, Inc., 2011

    2011-01-01

    Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

  7. The effectiveness of indigestible markers for identifying individual animal feces and their prevalence of use in North American zoos.

    PubMed

    Fuller, Grace; Margulis, Susan W; Santymire, Rachel

    2011-01-01

    Techniques for analyzing hormone metabolites in animal excreta have created many opportunities for noninvasive monitoring of health, reproduction, and welfare in zoo animals, but can be difficult to implement when individual samples are not readily identifiable in animal groups. A common approach to this problem is to feed animals an indigestible marker that subsequently appears in feces, but there has been little systematic research on the use of such "fecal markers." First, we used an online survey to assess the prevalence of fecal marker use in North American zoological institutions. Second, we conducted a series of experimental tests utilizing commonly employed fecal markers in a variety of typical zoo taxa to determine the: (1) effectiveness of several markers to accurately distinguish samples in a variety of species, (2) minimum quantity of marker needed for detection, and (3) length of time between ingestion and detection in the feces. The majority of the 45 institutions that completed the survey reported using fecal markers with their collections. The survey also revealed that the most frequently used markers are seeds/grains and food colorants, with the former generally used in Carnivora and the latter in Primates. Our experimental data confirmed the success of these taxa/marker combinations and also revealed that food colorants function as markers in a variety of avian, reptilian, and mammalian species. Our data describe successful fecal markers for a wide variety of zoo taxa and should, therefore, be useful for zoological managers and researchers needing to employ fecal markers in future investigations.

  8. Individual identification from genetic marker data: developments and accuracy comparisons of methods.

    PubMed

    Wang, Jinliang

    2016-01-01

    Genetic marker-based identification of distinct individuals and recognition of duplicated individuals has important applications in many research areas in ecology, evolutionary biology, conservation biology and forensics. The widely applied genotype mismatch (MM) method, however, is inaccurate because it relies on a fixed and suboptimal threshold number (TM ) of mismatches, and often yields self-inconsistent pairwise inferences. In this study, I improved MM method by calculating an optimal TM to accommodate the number, mistyping rates, missing data and allele frequencies of the markers. I also developed a pairwise likelihood relationship (LR) method and a likelihood clustering (LC) method for individual identification, using poor-quality data that may have high and variable rates of allelic dropouts and false alleles at genotyped loci. The 3 methods together with the relatedness (RL) method were then compared in accuracy by analysing an empirical frog data set and many simulated data sets generated under different parameter combinations. The analysis results showed that LC is generally one or two orders more accurate for individual identification than the other methods. Its accuracy is especially superior when the sampled multilocus genotypes have poor quality (i.e. teemed with genotyping errors and missing data) and highly replicated, a situation typical of noninvasive sampling used in estimating population size. Importantly, LC is the only method that guarantees to produce self-consistent results by partitioning the entire set of multilocus genotypes into distinct clusters, each cluster containing one or more genotypes that all represent the same individual. The LC and LR methods were implemented in a computer program COLONY for free download from the Internet.

  9. Empirical Selection of Informative Microsatellite Markers within Co-ancestry Pig Populations Is Required for Improving the Individual Assignment Efficiency.

    PubMed

    Li, Y H; Chu, H P; Jiang, Y N; Lin, C Y; Li, S H; Li, K T; Weng, G J; Cheng, C C; Lu, D J; Ju, Y T

    2014-05-01

    The Lanyu is a miniature pig breed indigenous to Lanyu Island, Taiwan. It is distantly related to Asian and European pig breeds. It has been inbred to generate two breeds and crossed with Landrace and Duroc to produce two hybrids for laboratory use. Selecting sets of informative genetic markers to track the genetic qualities of laboratory animals and stud stock is an important function of genetic databases. For more than two decades, Lanyu derived breeds of common ancestry and crossbreeds have been used to examine the effectiveness of genetic marker selection and optimal approaches for individual assignment. In this paper, these pigs and the following breeds: Berkshire, Duroc, Landrace and Yorkshire, Meishan and Taoyuan, TLRI Black Pig No. 1, and Kaohsiung Animal Propagation Station Black pig are studied to build a genetic reference database. Nineteen microsatellite markers (loci) provide information on genetic variation and differentiation among studied breeds. High differentiation index (FST) and Cavalli-Sforza chord distances give genetic differentiation among breeds, including Lanyu's inbred populations. Inbreeding values (FIS) show that Lanyu and its derived inbred breeds have significant loss of heterozygosity. Individual assignment testing of 352 animals was done with different numbers of microsatellite markers in this study. The testing assigned 99% of the animals successfully into their correct reference populations based on 9 to 14 markers ranking D-scores, allelic number, expected heterozygosity (HE) or FST, respectively. All miss-assigned individuals came from close lineage Lanyu breeds. To improve individual assignment among close lineage breeds, microsatellite markers selected from Lanyu populations with high polymorphic, heterozygosity, FST and D-scores were used. Only 6 to 8 markers ranking HE, FST or allelic number were required to obtain 99% assignment accuracy. This result suggests empirical examination of assignment-error rates is required if

  10. Cerebrospinal fluid markers including trefoil factor 3 are associated with neurodegeneration in amyloid-positive individuals.

    PubMed

    Paterson, R W; Bartlett, J W; Blennow, K; Fox, N C; Shaw, L M; Trojanowski, J Q; Zetterberg, H; Schott, J M

    2014-07-29

    We aimed to identify cerebrospinal fluid (CSF) biomarkers associated with neurodegeneration in individuals with and without CSF evidence of Alzheimer pathology. We investigated 287 Alzheimer's Disease Neuroimaging Initiative (ADNI) subjects (age=74.9±6.9; 22/48/30% with Alzheimer's disease/mild cognitive impairment/controls) with CSF multiplex analyte data and serial volumetric MRI. We calculated brain and hippocampal atrophy rates, ventricular expansion and Mini Mental State Examination decline. We used false discovery rate corrected regression analyses to assess associations between CSF variables and atrophy rates in individuals with and without amyloid pathology, adjusting in stages for tau, baseline volume, p-tau, age, sex, ApoE4 status and diagnosis. Analytes showing statistically significant independent relationships were entered into reverse stepwise analyses. Adjusting for tau, baseline volume, p-tau, age, sex and ApoE4, 4/83 analytes were significantly independently associated with brain atrophy rate, 1/83 with ventricular expansion and 2/83 with hippocampal atrophy. The strongest CSF predictor for the three atrophy measures was low trefoil factor 3 (TFF3). High cystatin C (CysC) was associated with higher whole brain atrophy and hippocampal atrophy rates. Lower levels of vascular endothelial growth factor and chromogranin A (CrA) were associated with higher whole brain atrophy. In exploratory reverse stepwise analyses, lower TFF3 was associated with higher rates of whole brain, hippocampal atrophy and ventricular expansion. Lower levels of CrA were associated with higher whole brain atrophy rate. The relationship between low TFF3 and increased hippocampal atrophy rate remained after adjustment for diagnosis. We identified a series of CSF markers that are independently associated with rate of neurodegeneration in amyloid-positive individuals. TFF3, a substrate for NOTCH processing may be an important biomarker of neurodegeneration across the Alzheimer

  11. Serum Vitamin A and Inflammatory Markers in Individuals with and without Chronic Obstructive Pulmonary Disease

    PubMed Central

    Caram, L. M. O.; Amaral, R. A. F.; Ferrari, R.; Tanni, S. E.; Correa, C. R.; Paiva, S. A. R.; Godoy, I.

    2015-01-01

    Background. Vitamin A is essential for the preservation and integrity of the lung epithelium and exerts anti-inflammatory effects. Objective. Evaluating vitamin A in the serum and sputum and testing its correlation with inflammatory markers in individuals with or without COPD. Methods. We evaluated dietary intake, serum and sputum vitamin A, tumor necrosis factor alpha, interleukin- (IL-) 6, IL-8, and C-reactive protein in 50 COPD patients (age = 64.0 ± 8.8 y; FEV1 (forced expiratory volume in the first second) (%) = 49.8 ± 16.8) and 50 controls (age = 48.5 ± 7.4 y; FEV1 (%) = 110.0 ± 15.7). Results. COPD exhibited lower serum vitamin A (1.8 (1.2–2.1) versus 2.1 (1.8–2.4) μmol/L, P < 0.001) and lower vitamin A intake (636.9 (339.6–1349.6) versus 918.0 (592.1–1654.6) RAE, P = 0.05) when compared with controls. Sputum concentration of vitamin A was not different between groups. Sputum vitamin A and neutrophils were negatively correlated (R2 = −0.26; P = 0.03). Smoking (0.197, P = 0.042) exhibited positive association with serum vitamin A. COPD was associated with lower serum concentrations of vitamin A without relationship with the systemic inflammation. Conclusions. Serum concentration of vitamin A is negatively associated with the presence of COPD and positively associated with smoking status. Sputum retinol is quantifiable and is negatively influenced by neutrophils. Although COPD patients exhibited increased inflammation it was not associated with serum retinol. PMID:26339144

  12. Individuation in Slovene emerging adults: its associations with demographics, transitional markers, achieved criteria for adulthood, and life satisfaction.

    PubMed

    Zupančič, Maja; Komidar, Luka; Levpušček, Melita Puklek

    2014-12-01

    The study investigated associations of Slovene emerging adults' age, gender, living situation, romantic relationship, and employment status with aspects of individuation in relation to mother and father. Controlling for demographic variables and transitional markers of adulthood, we further explored the contribution of individuation measures to individuals' perceptions of achieved criteria for adulthood and life satisfaction. The participants provided self-reports on the Individuation Test for Emerging Adults, the Satisfaction With Life Scale, and the list of Achieved Criteria for Adulthood. Age and living out of parental home were positively associated with self-reliance in relation to both parents, whereas female gender was related to higher levels of connectedness and seeking parental support. Along with age and involvement in a romantic relationship, connectedness and self-reliance predicted adulthood criteria attainment and life satisfaction. The results support the models of individuation that emphasize growing autonomy and retaining connectedness to parents as pathways towards personal adjustments.

  13. Cancer chronomics I. Origins of timed cancer treatment: early marker rhythm-guided individualized chronochemotherapy.

    PubMed

    Halberg, Franz; Prem, Konald; Halberg, Francine; Norman, Catherine; Cornélissen, Germaine

    2006-01-01

    A 21-year old patient who presented in 1973 with a rare and highly malignant ovarian endodermal sinus tumor with spillage into the peritoneal cavity is alive and well today after receiving chronochemotherapy. During the first four courses of treatment, medications were given at different circadian stages. Complete blood counts and marker variables such as mood, vigor, nausea, and temperature were monitored around the clock and analyzed by cosinor to seek times of highest tolerance. Remaining treatment courses were administered at a time corresponding to the patient's best drug tolerance, rather than extrapolating the timing of optimal cyclophosphamide administration from also-implemented parallel laboratory studies on mice. Notwithstanding remaining hurdles in bringing chronochemotherapy to the clinic for routine care, merits of marker rhythm-guided chronotherapy documented in this and other case reports have led to the doubling of the two-year disease-free survival of patients with large perioral tumors in a clinical trial.

  14. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae)

    PubMed Central

    Jan, Catherine

    2016-01-01

    The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species. PMID:27688959

  15. Individual Differences in the Alignment of Structural and Functional Markers of the V5/MT Complex in Primates

    PubMed Central

    Large, I.; Bridge, H.; Ahmed, B.; Clare, S.; Kolasinski, J.; Lam, W. W.; Miller, K. L.; Dyrby, T. B.; Parker, A. J.; Smith, J. E. T.; Daubney, G.; Sallet, J.; Bell, A. H.; Krug, K.

    2016-01-01

    Extrastriate visual area V5/MT in primates is defined both structurally by myeloarchitecture and functionally by distinct responses to visual motion. Myelination is directly identifiable from postmortem histology but also indirectly by image contrast with structural magnetic resonance imaging (sMRI). First, we compared the identification of V5/MT using both sMRI and histology in Rhesus macaques. A section-by-section comparison of histological slices with in vivo and postmortem sMRI for the same block of cortical tissue showed precise correspondence in localizing heavy myelination for V5/MT and neighboring MST. Thus, sMRI in macaques accurately locates histologically defined myelin within areas known to be motion selective. Second, we investigated the functionally homologous human motion complex (hMT+) using high-resolution in vivo imaging. Humans showed considerable intersubject variability in hMT+ location, when defined with myelin-weighted sMRI signals to reveal structure. When comparing sMRI markers to functional MRI in response to moving stimuli, a region of high myelin signal was generally located within the hMT+ complex. However, there were considerable differences in the alignment of structural and functional markers between individuals. Our results suggest that variation in area identification for hMT+ based on structural and functional markers reflects individual differences in human regional brain architecture. PMID:27371764

  16. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae).

    PubMed

    Jan, Catherine; Fumagalli, Luca

    2016-01-01

    The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species. PMID:27688959

  17. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae)

    PubMed Central

    Jan, Catherine

    2016-01-01

    The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

  18. Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae).

    PubMed

    Jan, Catherine; Fumagalli, Luca

    2016-01-01

    The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis, A. oratrix, A. pretrei, A. rhodocorytha, Anodorhynchus leari, Ara rubrogenys and Primolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

  19. Workflow for high-content, individual cell quantification of fluorescent markers from universal microscope data, supported by open source software.

    PubMed

    Stockwell, Simon R; Mittnacht, Sibylle

    2014-01-01

    Advances in understanding the control mechanisms governing the behavior of cells in adherent mammalian tissue culture models are becoming increasingly dependent on modes of single-cell analysis. Methods which deliver composite data reflecting the mean values of biomarkers from cell populations risk losing subpopulation dynamics that reflect the heterogeneity of the studied biological system. In keeping with this, traditional approaches are being replaced by, or supported with, more sophisticated forms of cellular assay developed to allow assessment by high-content microscopy. These assays potentially generate large numbers of images of fluorescent biomarkers, which enabled by accompanying proprietary software packages, allows for multi-parametric measurements per cell. However, the relatively high capital costs and overspecialization of many of these devices have prevented their accessibility to many investigators. Described here is a universally applicable workflow for the quantification of multiple fluorescent marker intensities from specific subcellular regions of individual cells suitable for use with images from most fluorescent microscopes. Key to this workflow is the implementation of the freely available Cell Profiler software(1) to distinguish individual cells in these images, segment them into defined subcellular regions and deliver fluorescence marker intensity values specific to these regions. The extraction of individual cell intensity values from image data is the central purpose of this workflow and will be illustrated with the analysis of control data from a siRNA screen for G1 checkpoint regulators in adherent human cells. However, the workflow presented here can be applied to analysis of data from other means of cell perturbation (e.g., compound screens) and other forms of fluorescence based cellular markers and thus should be useful for a wide range of laboratories.

  20. Preoperative serum markers for individual patient prognosis in stage I-III colon cancer.

    PubMed

    Giessen-Jung, Clemens; Nagel, Dorothea; Glas, Maria; Spelsberg, Fritz; Lau-Werner, Ulla; Modest, Dominik Paul; Schulz, Christoph; Heinemann, Volker; Di Gioia, Dorit; Stieber, Petra

    2015-09-01

    Carcinoembryonic antigen (CEA) remains the only recommended biomarker for follow-up care of colorectal cancer (CRC), but besides CEA, several other serological parameters have been proposed as prognostic markers for CRC. The present retrospective analysis investigates a comprehensive set of serum markers with regard to cancer-specific survival (CSS) and disease-free survival (DFS). A total of 472 patients with colon cancer underwent surgery for curative intent between January 1988 and June 2007. Preoperative serum was analyzed for the following parameters: albumin, alkaline phosphatase (aP), beta-human chorionic gonadotropin (βhCG), bilirubin, cancer antigen 125 (CA 125), cancer antigen 19-9 (CA 19-9), CA 72-4, CEA, C-reactive protein (CRP), cytokeratin-19 soluble fragment (CYFRA 21-1), ferritin, gamma-glutamyltransferase (γGT), glutamate oxaloacetate transaminase (GOT), glutamate pyruvate transaminase (GPT), hemoglobin, haptoglobin, interleukin-6, interleukin-8, creatinine, lactate dehydrogenase (LDH), serum amyloid A (SAA), and 25-hydroxyvitamin D. After a median follow-up period of 5.9 years, the overall 3- and 5-year CSS was 91.7 and 84.9 % and DFS rates were 82.7 % (3 years) and 77.6 % (5 years). Multivariate analyses confirmed preoperative CEA as an independent prognostic factor with regard to CSS and DFS. CA 19-9 and γGT also provided prognostic value for CSS and DFS, respectively. Younger age was negatively associated with DFS. According to UICC stage, CEA provided significant prognostic value with regard to CSS and DFS, while CA 19-9 was only prognostic for CSS. Combined analysis is able to identify patients with favorable prognosis. In addition to tumor baseline parameters, preoperative CEA could be confirmed as prognostic marker in colon cancer. CA 19-9 and γGT also provide additional prognostic value with regard to survival and recurrence in stage III and stage I disease, respectively. The combined use of CEA together with CA 19-9 and γGT improve

  1. Platelet leukocyte aggregates and markers of platelet aggregation, immune activation and disease progression in HIV infected treatment naive asymptomatic individuals.

    PubMed

    Nkambule, Bongani B; Davison, Glenda; Ipp, Hayley

    2015-11-01

    Platelet aggregates play a crucial role in the immune defence mechanism against viruses. Increased levels of lipopolysaccharide have been reported in human immunodeficiency virus (HIV) infected individuals. Platelets are capable of interacting with bacterial LPS and subsequently forming platelet leukocyte aggregates (PLAs). This study aimed at determining the levels of circulating PLAs in treatment naïve HIV infected individuals and correlating them, with markers of immune activation, disease progression and platelet aggregation. Thirty-two HIV negative and 35 HIV positive individuals were recruited from a clinic in the Western Cape. Platelet monocyte and platelet neutrophil aggregates were measured using flow cytometry at baseline and were correlated with markers of platelet activation (CD62P); aggregation (CD36); monocyte and neutrophil activation (CD69); monocyte tissue factor expression (CD142); immune activation (CD38 on T+ cells); D-dimers (a marker of active coagulation); CD4 count and viral load. Platelet monocyte aggregates were also measured post stimulation with lipopolysaccharide. PMA levels were higher in HIV 25.26 (16.16-32.28) versus control 14.12 (8.36-18.83), p = 0.0001. PMAs correlated with %CD38/8 expression (r = 0.54624, p = 0.0155); CD4 count (r = -0.6964, p = 0.0039) viral load (r = 0.633, p < 0.009) and monocyte %CD69 expression (r = 0.757, p = 0.030). In addition the %PMAs correlated with platelet %CD36 (r = 0.606, p = 0.017). The HIV group showed increased levels of %CD62P 5.44 (2.72-11.87) versus control 1.15 (0.19-3.59), p < 0.0001; %CD36 22.53 (10.59-55.15) versus 11.01 (3.69-26.98), p = 0.0312 and tissue factor (CD142) MFI 4.84 (4.01-8.17) versus 1.74 (1.07-9.3), p = 0.0240. We describe increased levels of circulating PMAs which directly correlates with markers of immune activation, disease progression and platelet aggregation in HIV treatment naïve individuals.

  2. Evaluation of preoperative serum markers for individual patient prognosis in stage I-III rectal cancer.

    PubMed

    Giessen, Clemens; Nagel, Dorothea; Glas, Maria; Spelsberg, Fritz; Lau-Werner, Ulla; Modest, Dominik Paul; Michl, Marlies; Heinemann, Volker; Stieber, Petra; Schulz, Christoph

    2014-10-01

    Several independent serum biomarkers have been proposed as prognostic and/or predictive markers for colorectal cancer (CRC). To this date, carcinoembryonic antigen (CEA) remains the only recommended serological CRC biomarker. The present retrospective analysis investigates the prognostic value of several serum markers. A total of 256 patients with rectal cancer underwent surgery for curative intent in a university cancer center between January 1988 and June 2007. Preoperative serum was retrospectively analyzed for albumin, alkaline phosphatase (aP), beta-human chorionic gonadotropin, bilirubin, CA 125, cancer antigen 19-9, cancer antigen 72-4 (CA 72-4), CEA, CRP, CYFRA 21-1, ferritin, gamma-glutamyl transpeptidase, glutamate oxaloacetate transanunase, glutamate pyruvate transaminase, hemoglobin, haptoglobin, interleukin-6, interleukin-8, creatinine, lactate-dehydrogenase, serum amyloid A (SAA), and 25-hydroxyvitamin D. Cancer-specific survival (CSS) and disease-free survival (DFS) were estimated. Median follow-up time was 8.4 years. Overall 3- and 5-year CSS was 88.6 and 78.9 %, respectively. DFS rates were 72.8 % (3 years) and 67.5 % (5 years). Univariate analysis of CSS indicated aP, CA 72-4, CEA, and SAA as prognostic factors, while aP, CEA, and SAA were also prognostic with regard to DFS. Multivariate analysis confirmed SAA together with T and N stage as prognostic factors. According to UICC stage, CEA and SAA add prognostic value in stages II and III with regard to DFS and CSS, respectively. The combined use of CEA and SAA is able to identify patients with favorable and poor prognosis. In addition to tumor baseline parameters, routine analysis of SAA together with CEA provided markedly improved prognostic value on CSS and DFS in resected rectal cancer. PMID:25027407

  3. Relationship between physical activity and markers of oxidative stress in independent community-living elderly individuals.

    PubMed

    Fraile-Bermúdez, A B; Kortajarena, M; Zarrazquin, I; Maquibar, A; Yanguas, J J; Sánchez-Fernández, C E; Gil, J; Irazusta, A; Ruiz-Litago, F

    2015-10-01

    The aim of the present study was to examine the relationship between objective data of physical activity and markers of oxidative stress in older men and women. Participants were old adults, aged≥60years (61 women and 34 men) who were all capable of performing basic daily activities by themselves and lived on their own. To describe physical activity we used objective data measured by accelerometers which record active and sedentary periods during everyday life for five days. Determination of oxidative stress was conducted from three perspectives: determination plasma total antioxidant status (TAS), plasma antioxidant enzyme activities, i.e., glutathione peroxidase (GPx), catalase (CAT) and superoxide dismutase (SOD), and membrane lipid peroxidation (TBARS). In the group of women, those who met physical activity recommendations (WR) had lower level of TAS. In addition, the moderate to vigorous physical activity (MVPA) was negatively correlated with TAS. Simultaneously, MVPA was correlated with increase in the GPx antioxidant enzyme activity, and the counts per minute were positively correlated with CAT activity. In the group of men, the cpm and the MVPA were negatively correlated with lipid peroxidation while lifestyle physical activity was positively correlated with CAT activity. These findings suggest that MVPA in the elderly although it is related to a decrease in the TAS in women, induces adaptive increase in antioxidant enzyme activity and decreases lipid peroxidation in both women and men. These results suggest that at this time of life, it is not only the amount of physical activity performed that is important but also its intensity.

  4. Early Markers of Atherosclerotic Disease in Individuals with Excess Weight and Dyslipidemia

    PubMed Central

    Menti, Eduardo; Zaffari, Denise; Galarraga, Thais; Lessa, João Regis da Conceição e; Pontin, Bruna; Pellanda, Lucia Campos; Portal, Vera Lúcia

    2016-01-01

    Background Excessive weight is a cardiovascular risk factor since it generates a chronic inflammatory process that aggravates the endothelial function. Objective To evaluate the endothelial function in individuals with excess weight and mild dyslipidemia using brachial artery flow-mediated dilation (BAFMD), and the association of endothelial function with anthropometric and biochemical variables. Methods Cross-sectional study that included 74 individuals and evaluated anthropometric variables (body mass index [BMI], waist-hip ratio [WHR], waist circumference [AC], and percentage of body fat [PBF]), biochemical (blood glucose, insulinemia, ultrasensitive C-reactive protein, fibrinogen, total cholesterol, HDL-cholesterol, triglycerides, and LDL-cholesterol) and endothelial function (BAFMD, evaluated by ultrasound). The statistical analysis was performed with SPSS, version 16.0. To study the association between the variables, we used chi-square, Student's t and Mann-Whitney tests, and Pearson's correlation. Logistic regression analyzed the independent influence of the factors. Values of p < 0.05 were considered significant. Results The participants had a mean age of 50.8 years, and 57% were female. BMI, WC, WHR, and PBF showed no significant association with BAFMD. The male gender (p = 0.02) and higher serum levels of fibrinogen (p = 0.02) were significantly and independently associated with a BAFMD below 8%. Conclusions In individuals with excess weight and mild untreated dyslipidemia, male gender and higher levels of fibrinogen were independently associated with worse BAFMD. PMID:27142650

  5. Is there a genetic contribution to cultural differences? Collectivism, individualism and genetic markers of social sensitivity.

    PubMed

    Way, Baldwin M; Lieberman, Matthew D

    2010-06-01

    Genes and culture are often thought of as opposite ends of the nature-nurture spectrum, but here we examine possible interactions. Genetic association studies suggest that variation within the genes of central neurotransmitter systems, particularly the serotonin (5-HTTLPR, MAOA-uVNTR) and opioid (OPRM1 A118G), are associated with individual differences in social sensitivity, which reflects the degree of emotional responsivity to social events and experiences. Here, we review recent work that has demonstrated a robust cross-national correlation between the relative frequency of variants in these genes and the relative degree of individualism-collectivism in each population, suggesting that collectivism may have developed and persisted in populations with a high proportion of putative social sensitivity alleles because it was more compatible with such groups. Consistent with this notion, there was a correlation between the relative proportion of these alleles and lifetime prevalence of major depression across nations. The relationship between allele frequency and depression was partially mediated by individualism-collectivism, suggesting that reduced levels of depression in populations with a high proportion of social sensitivity alleles is due to greater collectivism. These results indicate that genetic variation may interact with ecological and social factors to influence psychocultural differences.

  6. Increased inflammatory markers identified in the dorsolateral prefrontal cortex of individuals with schizophrenia.

    PubMed

    Fillman, S G; Cloonan, N; Catts, V S; Miller, L C; Wong, J; McCrossin, T; Cairns, M; Weickert, C S

    2013-02-01

    Upregulation of the immune response may be involved in the pathogenesis of schizophrenia with changes occurring in both peripheral blood and brain tissue. To date, microarray technology has provided a limited view of specific inflammatory transcripts in brain perhaps due to sensitivity issues. Here we used SOLiD Next Generation Sequencing to quantify neuroimmune mRNA expression levels in the dorsolateral prefrontal cortex of 20 individuals with schizophrenia and their matched controls. We detected 798 differentially regulated transcripts present in people with schizophrenia compared with controls. Ingenuity pathway analysis identified the inflammatory response as a key change. Using quantitative real-time PCR we confirmed the changes in candidate cytokines and immune modulators, including interleukin (IL)-6, IL-8, IL-1β and SERPINA3. The density of major histocompatibility complex-II-positive cells morphologically resembling microglia was significantly increased in schizophrenia and correlated with IL-1β expression. A group of individuals, most of whom had schizophrenia, were found to have increased inflammatory mRNA expression. In summary, we have demonstrated changes in an inflammatory response pathway that are present in ∼40% of people diagnosed with schizophrenia. This suggests that therapies aimed at immune system attenuation in schizophrenia may be of direct benefit in the brain. PMID:22869038

  7. Genetic marker of norepinephrine synthesis predicts individual differences in post-error slowing: a pilot study.

    PubMed

    Colzato, Lorenza S; de Rover, Mischa; van den Wildenberg, Wery P M; Nieuwenhuis, Sander

    2013-11-01

    When our brain detects the commission of an error, we slow down immediately thereafter: a phenomenon called post-error slowing (PES). Some researchers have speculated that slowing after unexpected errors or negative feedback is related to the activity of the neuromodulatory locus coeruleus-norepinephrine system. In the present pilot study, we tested whether individual differences in the size of PES are related to differences in genetic predisposition related to norepinephrine synthesis. In a sample of 100 healthy adults, we studied the dependency of an individual's size of PES on the DBH5'-ins/del polymorphism-a variation in the DBH gene associated with the production of the enzyme dopamine β-hydroxylase, which catalyzes the conversion of dopamine to norepinephrine. DBH5'-ins/del heterozygotes, who have intermediate levels of plasma DβH activity, showed increased PES in a Simon task compared to del/del homozygotes and ins/ins homozygotes, who have low and high levels of plasma DβH activity, respectively. This outcome pattern presents preliminary evidence that the size of PES varies with DβH activity and, presumably, NE release according to an inverted U-shape: intermediate levels of DβH activity and NE release are associated with larger post-error adjustments. PMID:23962674

  8. Hepatitis B virus markers in anti-HBc only positive individuals.

    PubMed

    Weber, B; Melchior, W; Gehrke, R; Doerr, H W; Berger, A; Rabenau, H

    2001-07-01

    Isolated reactivity to hepatitis B virus (HBV) core antigen (anti-HBc) is observed relatively frequently in immunocompromised individuals, intravenous drug abusers (IVDA), and in the presence of HCV infection. The reason for the lack of HBsAg is not clear. The aim of the present study was to investigate which factors (genetic variability of S gene, low-level HBsAg, and immune complexes may be responsible for the failure of HBsAg detection with commercial HBsAg screening assays. Dilution series of two recombinant HBsAg escape mutants and dilutions of serum samples from chronic HBV carriers with multiple insertions in the a determinant and different HBsAg subtypes were tested with a highly sensitive assay that detects wild-type HBsAg (Elecsys HBsAg, Roche Diagnostics, Penzberg, Germany) and two assays that detect HBV wild-type and escape mutants (Murex HBsAg Version 3, Murex and Enzygnost HBsAg 5.0, Dade Behring, Marburg, Germany). Elecsys HBsAg showed in comparison to Murex HBsAg Version 3 and Enzygnost HBsAg 5.0 a reduced sensitivity for escape mutant detection. On the other hand, the best performance for HBsAg subtype detection was obtained with Elecsys HBsAg. In the second part of the study, a selected panel of isolated anti-HBc reactive (n = 104) serum samples (AxSYM Core) was submitted to testing by Elecsys HBsAg, Murex HBsAg Version 3, Enzygnost HBsAg 5.0, and HBsAg detection after immune complex dissociation (ICD) and anti-HBs determination with two different assays (AxSYM Ausab and Elecsys Anti-HBs). To assess the specificity of anti-HBc test results, all the samples were tested by a second anti-HBc assay (Elecsys Anti-HBc). Quantitative HBV DNA detection was undertaken with a commercially available HBV PCR assay (Amplicor HBV Monitor). HCV infection was present in 65.4% of anti-HBc only reactive individuals. Five AxSYM Core positive samples were negative by Elecsys Anti-HBc. Overall, 15 (14.4%) AxSYM Ausab negative samples gave positive results with Elecsys

  9. Potential novel markers to discriminate between active and latent tuberculosis infection in Chinese individuals.

    PubMed

    Bai, Xue-juan; Liang, Yan; Yang, You-rong; Feng, Jin-dong; Luo, Zhan-peng; Zhang, Jun-Xian; Wu, Xue-qiong

    2016-02-01

    Latent tuberculosis infection (LTBI) constitutes the main reservoir for reactivation tuberculosis. The finding of potential biomarkers for differentiating between TB and LTBI is very necessary. In this study, the immunological characteristics and potential diagnostic utility of Rv2029c, Rv2628 and Rv1813c proteins were assessed. These three proteins stimulated PBMCs from ELISPOT-positive LTBI subjects produced higher levels of IFN-γ in comparison with TB patients and ELISPOT-negative healthy subjects (p<0.05). BCG vaccination and non-TB respiratory disease had little influence on the immunological responses of Rv2029c and Rv2628 proteins (p>0.05). The LTBI diagnostic performance of Rv2029c was higher than Rv2628 and Rv1813c by ROC evaluation. But Rv2628 had much higher specificity than Rv2029c in active TB patients and uninfected healthy subjects. The IgG level against Rv1813c was higher in the TB group than in LTBI and uninfected healthy subjects (p<0.05). These results suggest that T cell response to Rv2628 and antibody against Rv1813c might be applicable as biomarkers to distinguish TB from LTBI and uninfected individuals.

  10. Is there a genetic contribution to cultural differences? Collectivism, individualism and genetic markers of social sensitivity

    PubMed Central

    Lieberman, Matthew D.

    2010-01-01

    Genes and culture are often thought of as opposite ends of the nature–nurture spectrum, but here we examine possible interactions. Genetic association studies suggest that variation within the genes of central neurotransmitter systems, particularly the serotonin (5-HTTLPR, MAOA-uVNTR) and opioid (OPRM1 A118G), are associated with individual differences in social sensitivity, which reflects the degree of emotional responsivity to social events and experiences. Here, we review recent work that has demonstrated a robust cross-national correlation between the relative frequency of variants in these genes and the relative degree of individualism–collectivism in each population, suggesting that collectivism may have developed and persisted in populations with a high proportion of putative social sensitivity alleles because it was more compatible with such groups. Consistent with this notion, there was a correlation between the relative proportion of these alleles and lifetime prevalence of major depression across nations. The relationship between allele frequency and depression was partially mediated by individualism–collectivism, suggesting that reduced levels of depression in populations with a high proportion of social sensitivity alleles is due to greater collectivism. These results indicate that genetic variation may interact with ecological and social factors to influence psychocultural differences. PMID:20592043

  11. Attention and Working Memory-Related EEG Markers of Subtle Cognitive Deterioration in Healthy Elderly Individuals.

    PubMed

    Deiber, Marie-Pierre; Meziane, Hadj Boumediene; Hasler, Roland; Rodriguez, Cristelle; Toma, Simona; Ackermann, Marine; Herrmann, François; Giannakopoulos, Panteleimon

    2015-01-01

    Future treatments of Alzheimer's disease need the identification of cases at high risk at the preclinical stage of the disease before the development of irreversible structural damage. We investigated here whether subtle cognitive deterioration in a population of healthy elderly individuals could be predicted by EEG signals at baseline under cognitive activation. Continuous EEG was recorded in 97 elderly control subjects and 45 age-matched mild cognitive impairment (MCI) cases during a simple attentional and a 2-back working memory task. Upon 18-month neuropsychological follow-up, the final sample included 55 stable (sCON) and 42 deteriorated (dCON) controls. We examined the P1, N1, P3, and PNwm event-related components as well as the oscillatory activities in the theta (4-7 Hz), alpha (8-13 Hz), and beta (14-25 Hz) frequency ranges (ERD/ERS: event-related desynchronization/synchronization, and ITC: inter-trial coherence). Behavioral performance, P1, and N1 components were comparable in all groups. The P3, PNwm, and all oscillatory activity indices were altered in MCI cases compared to controls. Only three EEG indices distinguished the two control groups: alpha and beta ERD (dCON >  sCON) and beta ITC (dCON <  sCON). These findings show that subtle cognitive deterioration has no impact on EEG indices associated with perception, discrimination, and working memory processes but mostly affects attention, resulting in an enhanced recruitment of attentional resources. In addition, cognitive decline alters neural firing synchronization at high frequencies (14-25 Hz) at early stages, and possibly affects lower frequencies (4-13 Hz) only at more severe stages. PMID:26401557

  12. Transcriptomic, biochemical and individual markers in transplanted Daphnia magna to characterize impacts in the field.

    PubMed

    Rivetti, Claudia; Campos, Bruno; Faria, Melissa; De Castro Català, Nuria; Malik, Amrita; Muñoz, Isabel; Tauler, Romà; Soares, Amadeu M V M; Osorio, Victoria; Pérez, Sandra; Gorga, Marina; Petrovic, Mira; Mastroianni, Nicola; de Alda, Miren López; Masiá, Ana; Campo, Julian; Picó, Yolanda; Guasc, Helena; Barceló, Damià; Barata, Carlos

    2015-01-15

    Daphnia magna individuals were transplanted across 12 sites from three Spanish river basins (Llobregat, Ebro, Jucar) showing different sources of pollution. Gene transcription, feeding and biochemical responses in the field were assessed and compared with those obtained in re-constituted water treatments spiked with organic eluates obtained from water samples collected at the same locations and sampling periods. Up to 166 trace contaminants were detected in water and classified by their mode of action into 45 groups that included metals, pharmaceuticals, pesticides, illicit drugs, and other industrial compounds. Physicochemical water parameters differentiated the three river basins with Llobregat having the highest levels of conductivity, metals and pharmaceuticals, followed by Ebro, whereas the Jucar river had the greatest levels of illicit drugs. D. magna grazing rates and cholinesterase activity responded similarly than the diversity of riparian benthic communities. Transcription patterns of 13 different genes encoding for general stress, metabolism and energy processes, molting and xenobiotic transporters corroborate phenotypic responses differentiated sites within and across river basins. Principal Component Analysis and Partial Least Square Projections to Latent Structures regression analyses indicated that measured in situ responses of most genes and biomarkers and that of benthic macroinvertebrate diversity indexes were affected by distinct environmental factors. Conductivity, suspended solids and fungicides were negatively related with the diversity of macroinvertebrates cholinesterase, and feeding responses. Gene transcripts of heat shock protein and metallothionein were positively related with 11 classes of organic contaminants and 6 metals. Gene transcripts related with signaling paths of molting and reproduction, sugar, protein and xenobiotic metabolism responded similarly in field and lab exposures and were related with high residue concentrations of

  13. The chronic effects of whey proteins on blood pressure, vascular function, and inflammatory markers in overweight individuals.

    PubMed

    Pal, Sebely; Ellis, Vanessa

    2010-07-01

    Limited evidence suggests that dairy whey protein may be the major dairy component that is responsible for health benefits currently associated with increased dairy consumption. Whey proteins may reduce blood pressure and improve cardiovascular health. This study evaluated the effects of whey protein supplementation on blood pressure, vascular function and inflammatory markers compared to casein and glucose (control) supplementation in overweight/obese individuals. The subjects were randomized to either whey protein, casein or glucose supplementation for 12 weeks according to a parallel design. In all, 70 men and women with a mean (+/-s.e.m.) BMI (kg/m(2)) of 31.3 +/- 0.8 completed the study. Systolic blood pressure (SBP) decreased significantly at week 6 compared to baseline in the whey and casein groups, (P = 0.028 and P = 0.020, respectively) and at week 12 (P = 0.020, and P = 0.017, respectively). Diastolic blood pressure (DBP) decreased significantly compared to baseline in the whey and casein groups (P = 0.038 and P = 0.042, respectively) at week 12. DBP decreased significantly in the whey and casein groups (P = 0.025, P = 0.038, respectively) at week 12 compared to the control group. Augmentation index (AI) was significantly lower from baseline at 12 weeks (P = 0.021) in the whey group. AI decreased significantly in the whey group at 12 weeks compared to control (P = 0.006) and casein (P = 0.006). There were no significant changes in inflammatory markers within or between groups. This study demonstrated that supplementation with whey protein improves blood pressure and vascular function in overweight and obese individuals.

  14. The complexity of the genotype-phenotype relationship and the limitations of using genetic "markers" at the individual level.

    PubMed

    Templeton, A R

    1998-01-01

    Many associations have recently been discovered between phenotypic variation and genetic loci, causing some to advocate what Robert Sinsheimer has called "a new eugenics" that would treat genetic "defects" in individuals prone to a disease. The first premise of this vision is that genetic association studies reveal the biological cause of the phenotypic variation. Once the responsible genes are known, the second premise is that we should focus upon changing "nature" rather than "nurture" by correcting the "defective" genes. The first premise is flawed because associations between genetic markers and phenotypes can be spurious, as shown by an example. Moreover, it is shown that using non-causative but associated genetic markers one at a time (the normal practice) can lead to incorrect predictions of disease risk for many individuals. Going from association to causation is a non-trivial step scientifically that has rarely been done in much of the human genetic research. Even when a particular locus does contribute to the phenotypic variation of interest, the first premise remains flawed because phenotypes in general arise from complex interactions among genes and between genes and environments as shown for genes associations with coronary artery disease (CAD). The ability of current molecular genetic tools to "fix" defective genotypes is extremely limited, but even if the technological problems could be overcome, the studies on CAD reveal no obvious "defective" gene to fix because the genetic effects are so context dependent (upon both other genes and environmental factors). Contrary to the second premise of the new eugenics, the more we learn about how different genotypes show variable responses to environments, the more important the environment becomes for individual treatment. The paradigm of a "defective gene" may work for classical Mendelian genetic diseases that are due to loss-of-function mutations. However, such mutations affect only a small portion of

  15. Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls

    PubMed Central

    Damgaard, Christian; Jensen, Lars J.; Holmstrup, Palle

    2016-01-01

    Background The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients with periodontitis and dental caries to healthy individuals. Methods Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically with LysC and trypsin. The resulting peptide mixtures were cleaned up by solid-phase extraction and separated online with 2 h gradients by nano-scale C18 reversed-phase chromatography connected to a mass spectrometer through an electrospray source. The eluting peptides were analyzed on a tandem mass spectrometer operated in data-dependent acquisition mode. Results We identified a total of 35,664 unique peptides from 4,161 different proteins, of which 1,946 and 2,090 were of bacterial and human origin, respectively. The human protein profiles displayed significant overexpression of the complement system and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease. Conclusions Overexpression of proteins related to the complement system and inflammation seems to correlate with oral disease status. Similar bacterial proteomes in healthy and diseased individuals suggests that the salivary microbiota predominantly thrives in a planktonic state expressing no disease-associated characteristics of metabolic activity.

  16. Metaproteomics of saliva identifies human protein markers specific for individuals with periodontitis and dental caries compared to orally healthy controls

    PubMed Central

    Damgaard, Christian; Jensen, Lars J.; Holmstrup, Palle

    2016-01-01

    Background The composition of the salivary microbiota has been reported to differentiate between patients with periodontitis, dental caries and orally healthy individuals. To identify characteristics of diseased and healthy saliva we thus wanted to compare saliva metaproteomes from patients with periodontitis and dental caries to healthy individuals. Methods Stimulated saliva samples were collected from 10 patients with periodontitis, 10 patients with dental caries and 10 orally healthy individuals. The proteins in the saliva samples were subjected to denaturing buffer and digested enzymatically with LysC and trypsin. The resulting peptide mixtures were cleaned up by solid-phase extraction and separated online with 2 h gradients by nano-scale C18 reversed-phase chromatography connected to a mass spectrometer through an electrospray source. The eluting peptides were analyzed on a tandem mass spectrometer operated in data-dependent acquisition mode. Results We identified a total of 35,664 unique peptides from 4,161 different proteins, of which 1,946 and 2,090 were of bacterial and human origin, respectively. The human protein profiles displayed significant overexpression of the complement system and inflammatory markers in periodontitis and dental caries compared to healthy controls. Bacterial proteome profiles and functional annotation were very similar in health and disease. Conclusions Overexpression of proteins related to the complement system and inflammation seems to correlate with oral disease status. Similar bacterial proteomes in healthy and diseased individuals suggests that the salivary microbiota predominantly thrives in a planktonic state expressing no disease-associated characteristics of metabolic activity. PMID:27672500

  17. Dietary carbohydrate restriction improves insulin sensitivity, blood pressure, microvascular function, and cellular adhesion markers in individuals taking statins.

    PubMed

    Ballard, Kevin D; Quann, Erin E; Kupchak, Brian R; Volk, Brittanie M; Kawiecki, Diana M; Fernandez, Maria Luz; Seip, Richard L; Maresh, Carl M; Kraemer, William J; Volek, Jeff S

    2013-11-01

    Statins positively impact plasma low-density lipoprotein cholesterol, inflammation and vascular endothelial function (VEF). Carbohydrate restricted diets (CRD) improve atherogenic dyslipidemia, and similar to statins, have been shown to favorably affect markers of inflammation and VEF. No studies have examined whether a CRD provides additional benefit beyond that achieved by habitual statin use. We hypothesized that a CRD (<50 g carbohydrate/d) for 6 weeks would improve lipid profiles and insulin sensitivity, reduce blood pressure, decrease cellular adhesion and inflammatory biomarkers, and augment VEF (flow-mediated dilation and forearm blood flow) in statin users. Participants (n = 21; 59.3 ± 9.3 y, 29.5 ± 3.0 kg/m(2)) decreased total caloric intake by approximately 415 kcal at 6 weeks (P < .001). Daily nutrient intakes at baseline (46/36/17% carb/fat/pro) and averaged across the intervention (11/58/28% carb/fat/pro) demonstrated dietary compliance, with carbohydrate intake at baseline nearly 5-fold greater than during the intervention (P < .001). Compared to baseline, both systolic and diastolic blood pressure decreased after 3 and 6 weeks (P < .01). Peak forearm blood flow, but not flow-mediated dilation, increased at week 6 compared to baseline and week 3 (P ≤ .03). Serum triglyceride, insulin, soluble E-Selectin and intracellular adhesion molecule-1 decreased (P < .01) from baseline at week 3, and this effect was maintained at week 6. In conclusion, these findings demonstrate that individuals undergoing statin therapy experience additional improvements in metabolic and vascular health from a 6 weeks CRD as evidenced by increased insulin sensitivity and resistance vessel endothelial function, and decreased blood pressure, triglycerides, and adhesion molecules. PMID:24176230

  18. Dietary carbohydrate restriction improves insulin sensitivity, blood pressure, microvascular function, and cellular adhesion markers in individuals taking statins.

    PubMed

    Ballard, Kevin D; Quann, Erin E; Kupchak, Brian R; Volk, Brittanie M; Kawiecki, Diana M; Fernandez, Maria Luz; Seip, Richard L; Maresh, Carl M; Kraemer, William J; Volek, Jeff S

    2013-11-01

    Statins positively impact plasma low-density lipoprotein cholesterol, inflammation and vascular endothelial function (VEF). Carbohydrate restricted diets (CRD) improve atherogenic dyslipidemia, and similar to statins, have been shown to favorably affect markers of inflammation and VEF. No studies have examined whether a CRD provides additional benefit beyond that achieved by habitual statin use. We hypothesized that a CRD (<50 g carbohydrate/d) for 6 weeks would improve lipid profiles and insulin sensitivity, reduce blood pressure, decrease cellular adhesion and inflammatory biomarkers, and augment VEF (flow-mediated dilation and forearm blood flow) in statin users. Participants (n = 21; 59.3 ± 9.3 y, 29.5 ± 3.0 kg/m(2)) decreased total caloric intake by approximately 415 kcal at 6 weeks (P < .001). Daily nutrient intakes at baseline (46/36/17% carb/fat/pro) and averaged across the intervention (11/58/28% carb/fat/pro) demonstrated dietary compliance, with carbohydrate intake at baseline nearly 5-fold greater than during the intervention (P < .001). Compared to baseline, both systolic and diastolic blood pressure decreased after 3 and 6 weeks (P < .01). Peak forearm blood flow, but not flow-mediated dilation, increased at week 6 compared to baseline and week 3 (P ≤ .03). Serum triglyceride, insulin, soluble E-Selectin and intracellular adhesion molecule-1 decreased (P < .01) from baseline at week 3, and this effect was maintained at week 6. In conclusion, these findings demonstrate that individuals undergoing statin therapy experience additional improvements in metabolic and vascular health from a 6 weeks CRD as evidenced by increased insulin sensitivity and resistance vessel endothelial function, and decreased blood pressure, triglycerides, and adhesion molecules.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  1. Intra-individual variation of GH-dependent markers in athletes: comparison of population based and individual thresholds for detection of GH abuse in sports.

    PubMed

    Kniess, Astrid; Ziegler, Eckart; Thieme, Detlef; Müller, R Klaus

    2013-10-01

    The GH-2000 discriminant functions, using insulin-like growth factor I (IGF-I) and the N-terminal propeptide of type III procollagen (PIIINP), enabled the detection of growth hormone (GH) doping despite the broad inter-individual normal range of both peptides. The sensitivity of the discriminant function-based methodology may perhaps be further increased in future by applying individual athlete profiles. The purpose of the present study was to evaluate the intra-individual variability of IGF-I, PIIINP and the GH-2000 scores in athletes. For this purpose a total of eight blood samples were taken from each of fifty male and female elite athletes over a period of up to 18 months. The IGF-I and PIIINP levels, we found, lay predominantly within the reference range for elite athletes. The intra-individual variability for IGF-I ranged between 6 and 26%, while that for PIIINP ranged between 6 and 33%. The intra-individual variations of both parameters were higher in female than in male subjects and were found to be mostly moderate. We found that the intra-individual variations of the GH-2000 test scores, expressed as CV, ranged from 4 to 36% and were in most of the subjects markedly smaller than the inter-individual variation. Individual cut-offs for the GH-2000 scores would be lower than population based ones in most of the cases.

  2. Short-term Effects of Air Temperature on Blood Markers of Coagulation and Inflammation in Potentially Susceptible Individuals

    EPA Science Inventory

    Objectives: Changes in air temperature are associated with an increase in cardiovascular events, but the role of pro-coagulant and pro-inflammatory blood markers is still poorly understood. We investigated the association between air temperature and fibrinogen, plasminogen act...

  3. Body Composition, Soluble Markers of Inflammation, and Bone Mineral Density in Antiretroviral Therapy-Naïve HIV-1 Infected Individuals

    PubMed Central

    Brown, Todd T.; Chen, Yun; Currier, Judith S.; Ribaudo, Heather J.; Rothenberg, Jennifer; Dubé, Michael P.; Murphy, Robert; Stein, James H.; McComsey, Grace A.

    2013-01-01

    Objective To determine the association between bone mineral density (BMD), inflammatory markers, and alterations in fat and lean mass in untreated HIV-infected individuals. Design Cross-sectional analysis of antiretroviral therapy (ART)-naïve persons enrolled into a randomized clinical trial Methods Dual energy x-ray absorptiometry (DXA) for BMD, lean and fat mass, and a laboratory assessment were performed. Soluble biomarkers included adipocytokines (leptin, adiponectin), inflammatory markers (hsCRP, IL-6), and markers related to bone metabolism (osteoprotegerin (OPG)), receptor activator of NFκB Ligand (RANKL)). BMD at the lumbar spine, total hip, and femoral neck was expressed as a Z-score (number of standard deviations away from an age-, race-, sex-matched reference population). Results 331 subjects had a median (Q1, Q3) age of 36 (28,45) years, were 89% male, and 44% white. The prevalence of low BMD (Z-score ≤ −2 at any of the 3 sites) was 10%. No associations were detected between Z-scores and hsCRP, IL-6, or RANKL (P≥0.1). In a linear model adjusting for age, gender, race, and total fat mass, lower lumbar spine Z-scores were associated with lower total lean mass, higher serum adiponectin, and lower OPG. Results at the total hip or femoral neck were similar. Conclusions Among ART-naïve HIV-infected individuals, lower BMD was associated with lower lean mass, higher adiponectin, and lower OPG, but not HIV disease variables or any of the inflammatory markers. These findings may have implications for bone metabolism in untreated HIV, in which hypoadiponectinemia and higher OPG may mitigate bone loss. PMID:23591634

  4. Validating the use of colouration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers.

    PubMed

    Monteiro, N M; Silva, R M; Cunha, M; Antunes, A; Jones, A G; Vieira, M N

    2014-01-01

    In studies of behaviour, ecology and evolution, identification of individual organisms can be an invaluable tool, capable of unravelling otherwise cryptic information regarding group structure, movement patterns, population size and mating strategies. The use of natural markings is arguably the least invasive method for identification. However, to be truly useful natural markings must be sufficiently variable to allow for unique identification, while being stable enough to permit long-term studies. Non-invasive marking techniques are especially important in fishes of the Family Syngnathidae (pipefishes, seahorses and seadragons), as many of these taxa are of conservation concern or used extensively in studies of sexual selection. Here, we assessed the reliability of natural markings as a character for individual identification in a wild population of Nerophis lumbriciformis by comparing results from natural markings to individual genetic assignments based on eight novel microsatellite loci. We also established a minimally invasive method based on epithelial cell swabbing to sample DNA. All pipefish used in the validation of natural markings, independently of sex or time between recaptures, were individually recognized through facial colouration patterns. Their identities were verified by the observation of the same multilocus genotype at every sampling event for each individual that was identified on the basis of natural markings. Successful recaptures of previously swabbed pipefish indicated that this process probably did not induce an elevated rate of mortality. Also, the recapture of newly pregnant males showed that swabbing did not affect reproductive behaviour.

  5. Size-exclusion chromatography as a stand-alone methodology identifies novel markers in mass spectrometry analyses of plasma-derived vesicles from healthy individuals.

    PubMed

    de Menezes-Neto, Armando; Sáez, María José Fidalgo; Lozano-Ramos, Inés; Segui-Barber, Joan; Martin-Jaular, Lorena; Ullate, Josep M Estanyol; Fernandez-Becerra, Carmen; Borrás, Francesc E; Del Portillo, Hernando A

    2015-01-01

    Plasma-derived vesicles hold a promising potential for use in biomedical applications. Two major challenges, however, hinder their implementation into translational tools: (a) the incomplete characterization of the protein composition of plasma-derived vesicles, in the size range of exosomes, as mass spectrometric analysis of plasma sub-components is recognizably troublesome and (b) the limited reach of vesicle-based studies in settings where the infrastructural demand of ultracentrifugation, the most widely used isolation/purification methodology, is not available. In this study, we have addressed both challenges by carrying-out mass spectrometry (MS) analyses of plasma-derived vesicles, in the size range of exosomes, from healthy donors obtained by 2 alternative methodologies: size-exclusion chromatography (SEC) on sepharose columns and Exo-Spin™. No exosome markers, as opposed to the most abundant plasma proteins, were detected by Exo-Spin™. In contrast, exosomal markers were present in the early fractions of SEC where the most abundant plasma proteins have been largely excluded. Noticeably, after a cross-comparative analysis of all published studies using MS to characterize plasma-derived exosomes from healthy individuals, we also observed a paucity of "classical exosome markers." Independent of the isolation method, however, we consistently identified 2 proteins, CD5 antigen-like (CD5L) and galectin-3-binding protein (LGALS3BP), whose presence was validated by a bead-exosome FACS assay. Altogether, our results support the use of SEC as a stand-alone methodology to obtain preparations of extracellular vesicles, in the size range of exosomes, from plasma and suggest the use of CD5L and LGALS3BP as more suitable markers of plasma-derived vesicles in MS.

  6. The dose of hazelnuts influences acceptance and diet quality but not inflammatory markers and body composition in overweight and obese individuals.

    PubMed

    Tey, Siew Ling; Gray, Andrew R; Chisholm, Alexandra W; Delahunty, Conor M; Brown, Rachel C

    2013-08-01

    Regular nut consumption may improve markers of inflammation and endothelial dysfunction. The quantity of nuts required to achieve these health benefits without compromising body weight and acceptance is unknown. This study compared the effects of incorporating hazelnuts at 2 different doses with a diet without nuts on inflammatory markers, cell adhesion molecules, and body composition in 107 overweight and obese individuals. This was a randomized, controlled, parallel 12-wk intervention including 3 treatment arms: no nuts (control group), 30 g/d of hazelnuts, or 60 g/d of hazelnuts. Blood pressure, body composition, plasma high-sensitivity C-reactive protein (hs-CRP), interleukin 6 (IL-6), intercellular adhesion molecule 1 (ICAM-1), vascular cell adhesion molecule 1 (VCAM-1), lipid, and apolipoprotein (apo) profiles were assessed at baseline and at 6 and 12 wk. "Desire" and "liking" for nuts were assessed during the intervention. Results showed no significant differences in follow-up clinical outcomes between groups after adjusting for baseline values, age, sex, and BMI (all P ≥ 0.10), except for a tendency toward improvement in VCAM-1 concentration in the 60-g/d nut group (P = 0.07). Hazelnut consumption significantly improved diet quality in a dose-response manner. Desire and liking for nuts remained stable in the 30-g/d group, whereas these ratings decreased significantly over time in the 60-g/d group (both P < 0.001). In conclusion, 12 wk of hazelnut consumption appears to have minimal effect on inflammatory markers and cell adhesion molecules in this group of healthy, normocholesterolemic overweight and obese individuals. Nut consumption improves diet quality without adversely affecting body composition. Consuming 30 g/d of nuts regularly is achievable, whereas 60 g/d appears to compromise desire and liking.

  7. Sorting single satellite cells from individual myofibers reveals heterogeneity in cell-surface markers and myogenic capacity.

    PubMed

    Chapman, Matthew R; Balakrishnan, Karthik R; Li, Ju; Conboy, Michael J; Huang, Haiyan; Mohanty, Swomitra K; Jabart, Eric; Hack, James; Conboy, Irina M; Sohn, Lydia L

    2013-04-01

    Traditional cell-screening techniques such as FACS and MACS are better suited for large numbers of cells isolated from bulk tissue and cannot easily screen stem or progenitor cells from minute populations found in their physiological niches. Furthermore, these techniques rely upon irreversible antibody binding, potentially altering cell properties, including gene expression and regenerative capacity. To address these challenges, we have developed a novel, label-free stem-cell analysis and sorting platform capable of quantifying cell-surface marker expression of single functional organ stem cells directly isolated from their micro-anatomical niche. Using our unique platform, we have discovered a remarkable heterogeneity in both the regenerative capacity and expression of CXCR4, β1-integrin, Sca-1, M-cadherin, Syndecan-4, and Notch-1 in freshly isolated muscle stem (satellite) cells residing on different, single myofibers and have identified a small population of Sca-1(+)/Myf5(+) myogenic satellite cells. Our results demonstrate the utility of our single-cell platform for uncovering and functionally characterizing stem-cell heterogeneity in the organ microniche.

  8. Magnetic resonance spectroscopy as a prognostic marker in neonatal hypoxic-ischemic encephalopathy: a study protocol for an individual patient data meta-analysis

    PubMed Central

    2013-01-01

    Background The prognostic accuracy of 1H (proton) magnetic resonance spectroscopy (MRS) in neonatal hypoxic-ischemic encephalopathy has been assessed by a criticized study-based meta-analysis. An individual patient data meta-analysis may overcome some of the drawbacks encountered in the aggregate data meta-analysis. Moreover, the prognostic marker can be assessed quantitatively and the effect of covariates can be estimated. Methods Diagnostic accuracy studies relevant to the study topic were retrieved. The primary authors will be invited to share the raw de-identified study data. These individual patient data will be analyzed using logistic regression analysis. A prediction tool calculating the individualized risk of very adverse outcome will be devised. Discussion The proposed individual patient data meta-analysis provides several advantages. Inclusion and exclusion criteria can be applied more uniformly. Furthermore, adjustment is possible for confounding factors and subgroup analyses can be conducted. Our goal is to develop a prediction model for outcome in newborns with hypoxic-ischemic encephalopathy. PMID:24156407

  9. Microsatellite markers isolated in olive ( Olea europaea L.) are suitable for individual fingerprinting and reveal polymorphism within ancient cultivars.

    PubMed

    Cipriani, G.; Marrazzo, M. T.; Marconi, R.; Cimato, A.; Testolin, R.

    2002-02-01

    We have isolated and sequenced 52 microsatellites or simple sequence repeats (SSRs) from nearly 60 positive clones obtained from two 'Frantoio' olive genomic libraries enriched in (AC/GT) and (AG/CT) repeats, respectively. The repeat-containing fragments obtained from genomic DNA restricted with Tsp509I were separated using a biotinylated probe bound to streptavidin-coated paramagnetic beads. Fragments were then cloned into lambda ZAPII vector and sequenced. Thirty of the 36 primer pairs which gave correct re-amplification in the source genome were used to assay the polymorphism of 12 olive cultivars, namely four well-known cultivars ('Coratina', 'Frantoio', 'Leccino', 'Pendolino') and eight ancient cultivars grown locally near Lake Garda ('Casaliva', 'Favarol', 'Fort', 'Grignan', 'Less', 'Raza', 'Rossanel', 'Trep'). The local cultivars were each re- presented by two to four long-lived individuals. The analysis was carried out using (33)P-labelled primers and 6% polyacrylamide sequencing gels. All except two microsatellites showed polymorphism, the number of alleles varying from 1 to 5. The average genetic diversity ( H) was 0.55. The power of discrimination ( PD) was 0.60. All cultivars, including the local ones, were easily separated from each other. Variations in the SSR pattern were observed among individual plants of the same cultivar in four out of the eight local cultivars analysed. Several primer pairs (17%) amplified more than one locus.

  10. The impact of decreases in air temperature and increases in ozone on markers of endothelial function in individuals having type-2 diabetes.

    PubMed

    Lanzinger, Stefanie; Breitner, Susanne; Neas, Lucas; Cascio, Wayne; Diaz-Sanchez, David; Hinderliter, Alan; Peters, Annette; Devlin, Robert B; Schneider, Alexandra

    2014-10-01

    Several studies have reported an association between air pollution and endothelial dysfunction, especially in individuals having diabetes. However, very few studies have examined the impact of air temperature on endothelial function. The objective of this analysis was to investigate short-term effects of temperature and ozone on endothelial function in individuals having diabetes. Moreover, we investigated interactive effects between air temperature and air pollution on markers of endothelial function. Between November 2004 and December 2005 flow-mediated dilatation (FMD), nitroglycerin-mediated dilatation (NTGMD) and several blood markers representing endothelial function were measured using brachial artery ultrasound on four consecutive days in 22 individuals with type-2 diabetes mellitus in Chapel Hill, North Carolina (USA). Daily measurements of meteorological parameters, ozone and particulate matter with an aerodynamic diameter ≤2.5 µm (PM2.5) were obtained from fixed monitoring sites. We used additive mixed-models adjusting for time trend, day of the week, relative humidity and barometric pressure to assess temperature and ozone associations with endothelial function. A 1 °C decrease in the 24-h temperature average was associated with a decrease in mean FMD on the same day (-2.2% (95%-confidence interval:[-4.7;0.3%])) and with a delay of one and four days. A temperature decrement also led to an immediate (-1.7%[-3.3;-0.04]) decrease in NTGMD. Moreover, we observed an immediate (-14.6%[-26.3;-2.9%]) and a one day delayed (-13.5%[-27.0; 0.04%]) decrease in FMD in association with a 0.01 ppm increase in the maximum 8-h moving average of ozone. Temperature effects on FMD strengthened when PM2.5 and ozone concentrations were high. The associations were similar during winter and summer. We detected an association between temperature decreases and ozone increases on endothelial dysfunction in individuals having diabetes. We conclude that endothelial dysfunction

  11. Associations of the Inflammatory Marker YKL-40 with Measures of Obesity and Dyslipidaemia in Individuals at High Risk of Type 2 Diabetes

    PubMed Central

    Thomsen, Stine B.; Gjesing, Anette P.; Rathcke, Camilla N.; Ekstrøm, Claus T.; Eiberg, Hans; Hansen, Torben; Pedersen, Oluf; Vestergaard, Henrik

    2015-01-01

    Introduction Circulating levels of the inflammatory marker YKL-40 are elevated in cardiovascular disease and obesity-related type 2 diabetes (T2D), and serum YKL-40 levels are related to elements of dyslipidaemia. Objective We aimed to investigate the associations between serum YKL-40 and obesity-related traits in a Danish sample of non-diabetic relatives to T2D patients and, furthermore, to estimate the heritability of YKL-40. Research Design and Methods 324 non-diabetic individuals with family relation to a T2D patient were included in the study. The participants underwent oral- and intravenous glucose tolerance tests for estimation of glucose tolerance and surrogate measures of insulin sensitivity. Anthropometric measures were retrieved and biochemical measures of the plasma lipid profile and serum YKL-40 levels were obtained. Association-analyses between serum YKL-40 and obesity-related traits and estimates of the narrow sense heritability of YKL-40 were based on a polygenic variance component model. Results Fasting serum levels of YKL-40 were positively associated with waist-hip-ratio (p<0.001) and fasting plasma triglyceride levels (p<0.001). None of the insulin sensitivity indexes were significantly associated with YKL-40. According to the AE model, the familiality-estimate h2 of YKL-40 was 0.45 (SE 0.13). When the ACE-model was applied, the heritability-estimate h2 of YKL-40 did not reach statistical significance. Conclusions Our results suggest a role of serum YKL-40 in obesity-related low grade inflammation, but do not indicate that YKL-40 is directly involved in the development of T2D. PMID:26197239

  12. Markers of Serotonergic Function in the Orbitofrontal Cortex and Dorsal Raphé Nucleus Predict Individual Variation in Spatial-Discrimination Serial Reversal Learning

    PubMed Central

    Barlow, Rebecca L; Alsiö, Johan; Jupp, Bianca; Rabinovich, Rebecca; Shrestha, Saurav; Roberts, Angela C; Robbins, Trevor W; Dalley, Jeffrey W

    2015-01-01

    Dysfunction of the orbitofrontal cortex (OFC) impairs the ability of individuals to flexibly adapt behavior to changing stimulus-reward (S-R) contingencies. Impaired flexibility also results from interventions that alter serotonin (5-HT) and dopamine (DA) transmission in the OFC and dorsomedial striatum (DMS). However, it is unclear whether similar mechanisms underpin naturally occurring variations in behavioral flexibility. In the present study, we used a spatial-discrimination serial reversal procedure to investigate interindividual variability in behavioral flexibility in rats. We show that flexibility on this task is improved following systemic administration of the 5-HT reuptake inhibitor citalopram and by low doses of the DA reuptake inhibitor GBR12909. Rats in the upper quintile of the distribution of perseverative responses during repeated S-R reversals showed significantly reduced levels of the 5-HT metabolite, 5-hydroxy-indoleacetic acid, in the OFC. Additionally, 5-HT2A receptor binding in the OFC of mid- and high-quintile rats was significantly reduced compared with rats in the low-quintile group. These perturbations were accompanied by an increase in the expression of monoamine oxidase-A (MAO-A) and MAO-B in the lateral OFC and by a decrease in the expression of MAO-A, MAO-B, and tryptophan hydroxylase in the dorsal raphé nucleus of highly perseverative rats. We found no evidence of significant differences in markers of DA and 5-HT function in the DMS or MAO expression in the ventral tegmental area of low- vs high-perseverative rats. These findings indicate that diminished serotonergic tone in the OFC may be an endophenotype that predisposes to behavioral inflexibility and other forms of compulsive behavior. PMID:25567428

  13. Markers of serotonergic function in the orbitofrontal cortex and dorsal raphé nucleus predict individual variation in spatial-discrimination serial reversal learning.

    PubMed

    Barlow, Rebecca L; Alsiö, Johan; Jupp, Bianca; Rabinovich, Rebecca; Shrestha, Saurav; Roberts, Angela C; Robbins, Trevor W; Dalley, Jeffrey W

    2015-06-01

    Dysfunction of the orbitofrontal cortex (OFC) impairs the ability of individuals to flexibly adapt behavior to changing stimulus-reward (S-R) contingencies. Impaired flexibility also results from interventions that alter serotonin (5-HT) and dopamine (DA) transmission in the OFC and dorsomedial striatum (DMS). However, it is unclear whether similar mechanisms underpin naturally occurring variations in behavioral flexibility. In the present study, we used a spatial-discrimination serial reversal procedure to investigate interindividual variability in behavioral flexibility in rats. We show that flexibility on this task is improved following systemic administration of the 5-HT reuptake inhibitor citalopram and by low doses of the DA reuptake inhibitor GBR12909. Rats in the upper quintile of the distribution of perseverative responses during repeated S-R reversals showed significantly reduced levels of the 5-HT metabolite, 5-hydroxy-indoleacetic acid, in the OFC. Additionally, 5-HT2A receptor binding in the OFC of mid- and high-quintile rats was significantly reduced compared with rats in the low-quintile group. These perturbations were accompanied by an increase in the expression of monoamine oxidase-A (MAO-A) and MAO-B in the lateral OFC and by a decrease in the expression of MAO-A, MAO-B, and tryptophan hydroxylase in the dorsal raphé nucleus of highly perseverative rats. We found no evidence of significant differences in markers of DA and 5-HT function in the DMS or MAO expression in the ventral tegmental area of low- vs high-perseverative rats. These findings indicate that diminished serotonergic tone in the OFC may be an endophenotype that predisposes to behavioral inflexibility and other forms of compulsive behavior.

  14. Markers of serotonergic function in the orbitofrontal cortex and dorsal raphé nucleus predict individual variation in spatial-discrimination serial reversal learning.

    PubMed

    Barlow, Rebecca L; Alsiö, Johan; Jupp, Bianca; Rabinovich, Rebecca; Shrestha, Saurav; Roberts, Angela C; Robbins, Trevor W; Dalley, Jeffrey W

    2015-06-01

    Dysfunction of the orbitofrontal cortex (OFC) impairs the ability of individuals to flexibly adapt behavior to changing stimulus-reward (S-R) contingencies. Impaired flexibility also results from interventions that alter serotonin (5-HT) and dopamine (DA) transmission in the OFC and dorsomedial striatum (DMS). However, it is unclear whether similar mechanisms underpin naturally occurring variations in behavioral flexibility. In the present study, we used a spatial-discrimination serial reversal procedure to investigate interindividual variability in behavioral flexibility in rats. We show that flexibility on this task is improved following systemic administration of the 5-HT reuptake inhibitor citalopram and by low doses of the DA reuptake inhibitor GBR12909. Rats in the upper quintile of the distribution of perseverative responses during repeated S-R reversals showed significantly reduced levels of the 5-HT metabolite, 5-hydroxy-indoleacetic acid, in the OFC. Additionally, 5-HT2A receptor binding in the OFC of mid- and high-quintile rats was significantly reduced compared with rats in the low-quintile group. These perturbations were accompanied by an increase in the expression of monoamine oxidase-A (MAO-A) and MAO-B in the lateral OFC and by a decrease in the expression of MAO-A, MAO-B, and tryptophan hydroxylase in the dorsal raphé nucleus of highly perseverative rats. We found no evidence of significant differences in markers of DA and 5-HT function in the DMS or MAO expression in the ventral tegmental area of low- vs high-perseverative rats. These findings indicate that diminished serotonergic tone in the OFC may be an endophenotype that predisposes to behavioral inflexibility and other forms of compulsive behavior. PMID:25567428

  15. Marker development

    SciTech Connect

    Adams, M.R.

    1987-05-01

    This report is to discuss the marker development for radioactive waste disposal sites. The markers must be designed to last 10,000 years, and place no undue burdens on the future generations. Barriers cannot be constructed that preclude human intrusion. Design specifications for surface markers will be discussed, also marker pictograms will also be covered.

  16. Assessing Cortisol Reactivity to a Linguistic Task as a Marker of Stress in Individuals with Left-Hemisphere Stroke and Aphasia

    ERIC Educational Resources Information Center

    Laures-Gore, Jacqueline; Heim, Christine M.; Hsu, Yu-Sheng

    2007-01-01

    Purpose: In this study, the authors explore a method of measuring physiologic and perceived stress in individuals with aphasia by investigating salivary cortisol reactivity and subjectively perceived stress in response to a standardized linguistic task. Method: Fifteen individuals with aphasia and 15 age-matched healthy controls participated in a…

  17. Do glycemic marker levels vary by race? Differing results from a cross-sectional analysis of individuals with and without diagnosed diabetes

    PubMed Central

    Carson, April P; Muntner, Paul; Selvin, Elizabeth; Carnethon, Mercedes R; Li, Xuelin; Gross, Myron D; Garvey, W Timothy; Lewis, Cora E

    2016-01-01

    Objective It is well known that A1c varies by race. However, racial differences in other biomarkers of hyperglycemia are less well characterized. The objective of this study was to determine whether average levels of glycemic markers differ by race in adults with and without diagnosed diabetes, before and after accounting for postchallenge glucose. Research design and methods This cross-sectional study included 2692 middle-aged men and women (5.5% with diagnosed diabetes; 44% African-American; and 56% white) from the Coronary Artery Risk Development in Young Adults Study (2005–2006) who had fasting glucose, 2-hour postchallenge glucose, A1c, glycated albumin, fructosamine, and 1,5-anhydroglucitol (1,5-AG) measured. Multiple linear regression was used to evaluate racial differences in mean levels of each glycemic marker stratified by the diabetes status and adjusted for sociodemographics, cardiovascular factors, and postchallenge glucose. Results Among those with diagnosed diabetes, racial differences were not observed for any of the glycemic markers. In contrast, among those without diagnosed diabetes, African-Americans had higher mean levels than whites of A1c (β=0.19% points; 95% CI 0.14 to 0.24), glycated albumin (β=0.82% points; 95% CI 0.68 to 0.97), fructosamine (β=8.68 μmol/L; 95% CI 6.68 to 10.68), and 2-hour glucose (β=3.50 mg/dL; 95% CI 0.10 to 6.90) after multivariable adjustment, whereas there were no statistically significant racial difference in 1,5-AG. The racial differences observed for A1c, glycated albumin, and fructosamine persisted after further adjustment for fasting and 2-hour glucose and were of similar magnitude (SD units). Conclusions Racial differences in glycemic marker levels were evident among middle-aged adults without diagnosed diabetes even after adjustment for postchallenge glucose. Whether these racial differences in biomarkers of hyperglycemia affect the risk of complications warrants additional study. PMID:27335652

  18. Bone Markers

    MedlinePlus

    ... Alkaline Phosphatase; Osteocalcin; P1NP; Procollagen Type 1 N-Terminal Propeptide Formal name: Biochemical Markers of Bone Remodeling ... tests for evaluating bone turnover: C-telopeptide (C-terminal telopeptide of type 1 collagen (CTx)) – a marker ...

  19. The impact of decreases in air temperature and increases in ozone on markers of endothelial function in individuals having type-2 diabetes

    EPA Science Inventory

    Several studies have reported an association between air pollution and endothelial dysfunction, especially in individuals having diabetes. However, very few studies have examined the impact of air temperature on endothelial function. The objective of this analysis was to investig...

  20. Dopamine and the Management of Attentional Resources: Genetic Markers of Striatal D2 Dopamine Predict Individual Differences in the Attentional Blink

    ERIC Educational Resources Information Center

    Colzato, Lorenza S.; Slagter, Heleen A.; de Rover, Mischa; Hommel, Bernhard

    2011-01-01

    The attentional blink (AB)--a deficit in reporting the second of two target stimuli presented in close succession in a rapid sequence of distracters--has been related to processing limitations in working memory. Given that dopamine (DA) plays a crucial role working memory, the present study tested whether individual differences in the size of the…

  1. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 1 2011-01-01 2011-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  2. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 1 2010-01-01 2010-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  3. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 1 2013-01-01 2013-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  4. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 1 2014-01-01 2014-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  5. 10 CFR 39.47 - Radioactive markers.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 1 2012-01-01 2012-01-01 false Radioactive markers. 39.47 Section 39.47 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY REQUIREMENTS FOR WELL LOGGING Equipment § 39.47 Radioactive markers. The licensee may use radioactive markers in wells only if the individual markers...

  6. Three-dimensional morphometric analysis of craniofacial shape in the unaffected relatives of individuals with nonsyndromic orofacial clefts: a possible marker for genetic susceptibility.

    PubMed

    Weinberg, Seth M; Neiswanger, Katherine; Richtsmeier, Joan T; Maher, Brion S; Mooney, Mark P; Siegel, Michael I; Marazita, Mary L

    2008-02-15

    Numerous studies have described altered patterns of craniofacial form in the unaffected relatives of individuals with nonsyndromic clefts. Unfortunately, results from such studies have been highly variable and have failed to provide a reliable method for differentiating "at-risk" relatives from controls. In the present study, we compared craniofacial shape between a sample of unaffected relatives (33 females; 14 males) from cleft multiplex families and an equal number of age/sex/ethnicity-matched controls. Sixteen x,y,z facial landmark coordinates derived from 3D photogrammetry were analyzed via Euclidean Distance Matrix Analysis, while 14 additional linear distances were analyzed via t tests. A subset of variables was then entered into a discriminant function analysis (DFA). Compared to controls, female unaffected relatives demonstrated increased upper facial width, midface reduction and lateral displacement of the alar cartilage. DFA correctly classified 70% of female unaffected relatives and 73% of female controls. Male unaffected relatives demonstrated increased upper facial and cranial base width, increased lower facial height and decreased upper facial height compared with controls. DFA correctly classified 86% of male unaffected relatives and 93% of male controls. In both sexes, upper facial width contributed most to group discrimination. Following DFA, unaffected relatives were assigned to risk/liability classes based on the degree of phenotypic divergence from controls. Results indicate that craniofacial shape differences characterizing unaffected relatives are partly sex-specific and are in broad agreement with previous reports. These findings further suggest that a quantitative assessment of the craniofacial phenotype may allow for the identification of susceptible individuals within nonsyndromic cleft families.

  7. Magnesium supplementation, metabolic and inflammatory markers, and global genomic and proteomic profiling: a randomized, double-blind, controlled, crossover trial in overweight individuals123

    PubMed Central

    Chacko, Sara A; Sul, James; Song, Yiqing; Li, Xinmin; LeBlanc, James; You, Yuko; Butch, Anthony; Liu, Simin

    2011-01-01

    Background: Dietary magnesium intake has been favorably associated with reduced risk of metabolic outcomes in observational studies; however, few randomized trials have introduced a systems-biology approach to explore molecular mechanisms of pleiotropic metabolic actions of magnesium supplementation. Objective: We examined the effects of oral magnesium supplementation on metabolic biomarkers and global genomic and proteomic profiling in overweight individuals. Design: We undertook this randomized, crossover, pilot trial in 14 healthy, overweight volunteers [body mass index (in kg/m2) ≥25] who were randomly assigned to receive magnesium citrate (500 mg elemental Mg/d) or a placebo for 4 wk with a 1-mo washout period. Fasting blood and urine specimens were collected according to standardized protocols. Biochemical assays were conducted on blood specimens. RNA was extracted and subsequently hybridized with the Human Gene ST 1.0 array (Affymetrix, Santa Clara, CA). Urine proteomic profiling was analyzed with the CM10 ProteinChip array (Bio-Rad Laboratories, Hercules, CA). Results: We observed that magnesium treatment significantly decreased fasting C-peptide concentrations (change: −0.4 ng/mL after magnesium treatment compared with +0.05 ng/mL after placebo treatment; P = 0.004) and appeared to decrease fasting insulin concentrations (change: −2.2 μU/mL after magnesium treatment compared with 0.0 μU/mL after placebo treatment; P = 0.25). No consistent patterns were observed across inflammatory biomarkers. Gene expression profiling revealed up-regulation of 24 genes and down-regulation of 36 genes including genes related to metabolic and inflammatory pathways such as C1q and tumor necrosis factor–related protein 9 (C1QTNF9) and pro-platelet basic protein (PPBP). Urine proteomic profiling showed significant differences in the expression amounts of several peptides and proteins after treatment. Conclusion: Magnesium supplementation for 4 wk in overweight

  8. Learned Irrelevance and Associative Learning Is Attenuated in Individuals at Risk for Psychosis but not in Asymptomatic First-Degree Relatives of Schizophrenia Patients: Translational State Markers of Psychosis?

    PubMed Central

    Orosz, Ariane T.; Feldon, Joram; Simon, Andor E.; Hilti, Leonie M.; Gruber, Kerstin; Yee, Benjamin K.; Cattapan-Ludewig, Katja

    2011-01-01

    Learned irrelevance (LIrr) refers to a form of selective learning that develops as a result of prior noncorrelated exposures of the predicted and predictor stimuli. In learning situations that depend on the associative link between the predicted and predictor stimuli, LIrr is expressed as a retardation of learning. It represents a form of modulation of learning by selective attention. Given the relevance of selective attention impairment to both positive and cognitive schizophrenia symptoms, the question remains whether LIrr impairment represents a state (relating to symptom manifestation) or trait (relating to schizophrenia endophenotypes) marker of human psychosis. We examined this by evaluating the expression of LIrr in an associative learning paradigm in (1) asymptomatic first-degree relatives of schizophrenia patients (SZ-relatives) and in (2) individuals exhibiting prodromal signs of psychosis (“ultrahigh risk” [UHR] patients) in each case relative to demographically matched healthy control subjects. There was no evidence for aberrant LIrr in SZ-relatives, but LIrr as well as associative learning were attenuated in UHR patients. It is concluded that LIrr deficiency in conjunction with a learning impairment might be a useful state marker predictive of psychotic state but a relatively weak link to a potential schizophrenia endophenotype. PMID:20080901

  9. DNA isolation from teeth by organic extraction and identification of sex of the individual by analyzing the AMEL gene marker using PCR

    PubMed Central

    Praveen Kumar, Subramanian Thangaraj; Aswath, Nalini

    2016-01-01

    Background: To identify the sex of the deceased individual from dental hard tissue such as enamel and dentine. Objective: To isolate the DNA from dental hard tissue (enamel and dentin) from teeth extracted for prophylactic purpose, to assess the quality and purity of DNA and to identify the sex using polymerized chain reactor (PCR). Materials and Methods: DNA was extracted following phenol/chloroform (organic) extraction from 20 male and 20 female teeth. The samples that contain the amelogenin gene (amel) were amplified by PCR. The products of the PCR were run on agarose gel with ethidium bromide staining on gel documentation system. Results: The results on the gel showed the presence of X-specific bands at 212 bp and Y-specific bands at 218 bp. Males were distinguished from females by the presence of two bands whereas female samples showed only one, that is, X-specific band on the gel. The gender from the known samples was determined with complete accuracy, and the results were analyzed statistically by the Chi-square test. Conclusion: In our study, the PCR-based method showed 100% specificity and sensitivity. PMID:27051218

  10. Grave Markers.

    ERIC Educational Resources Information Center

    DeMuro, Ted

    1985-01-01

    Junior high school students studied the cultural uses, symbolic meanings, and general physical forms of tombs and tombstones and then used basic slab building techniques to construct large clay grave markers. (RM)

  11. [Serological markers of fibrosis].

    PubMed

    Fernández-Varo, Guillermo

    2012-12-01

    Liver biopsy has classically been considered the gold standard to evaluate the degree of fibrosis, since it allows direct measurement of this entity. However, this technique carries an inherent risk of complications and observer variability and technical limitations can provoke sampling errors, all of which has prompted the search for alternative, noninvasive methods. The use of routine clinical laboratory tests has been investigated and various indexes that combine indirect serological markers have been developed and validated. These indexes are useful, low-cost, noninvasive tests to detect significant fibrosis or cirrhosis. Direct serological markers are those that reflect changes in the composition of the extracellular matrix. Several studies have analyzed the utility of these markers (either individually or combined with other direct and indirect markers) in the detection of the severity and progression of liver fibrosis and in the follow-up of changes related to antiviral therapy. In the last few years, imaging tests based on the measurement of liver stiffness, such as FibroScan or acoustic radiation force impulse (ARFI), have been found to be rapid and reproducible methods to evaluate liver fibrosis. Recently, the results obtained by combining distinct serological markers and imaging techniques have shown a higher diagnostic yield and this strategy seems promising. The present article reviews the most widely discussed noninvasive markers, the most recent alternatives, and the perspectives for their use in clinical practice. PMID:23298654

  12. Markers of vulnerability in schizophrenia

    PubMed Central

    Prelipceanu, D

    2009-01-01

    Vulnerability in schizophrenia is an integrative concept, which tries to explain the development of schizophrenia as an interaction between different individual susceptibility factors and environmental risk factors. Vulnerability markers used in genetic studies include biochemical indicators, neuroanatomical, neurophysiologic, and cognitive abnormalities. Among those, the most extensive studied markers were: evoked potentials, smooth pursuit eye movements, and attentional deficits. Some of the potential indicators presented in this paper satisfy most of the criteria necessary for a vulnerability marker, but none meets all of them. Nevertheless, they represent important markers of risk to schizophrenia. Key words: vulnerability, evoked potentials, eye movements, attentional deficits PMID:20108534

  13. A multi-nutrient supplement reduced markers of inflammation and improved physical performance in active individuals of middle to older age: a randomized, double-blind, placebo-controlled study

    PubMed Central

    2011-01-01

    grip strength (from 42.1 ± 5.9 to 48.5 ± 4.9 kg). Conclusions A multi-nutrient supplement is effective in improving inflammatory status in both men and women, markers of pain, joint pain, strength, and power in men only, and both anxiety and balance (a risk factor for hip fracture) in women. Therefore, a multi-nutrient supplement may help middle-aged individuals to prolong physical function and maintain a healthy, active lifestyle. PMID:21899733

  14. Effects of D-003, a mixture of high-molecular-weight sugar cane wax acids, on lipid peroxidation markers in older individuals: A randomized, double-blind, placebo-controlled study

    PubMed Central

    Pérez, Yohani; Menéndez, Roberto; Ferrer, José I.; Lopez, Ernesto; Castaño, Gladys; Fernández, Julio; Ferreiro, Rosa M.; Fernández, Lilia; Mendoza, Sarahí; González, Rosa; Mesa, Melbis

    2008-01-01

    Background: Aging is associated with increased lipid peroxidation (LP). D-003, a mixture of long-chain aliphatic primary acids purified from sugar cane wax, has been found to inhibit LP in experimental models and in healthy subjects. Objectives: The aim of this study was to assess the effects of D-003 on LP markers and the lipid profile of older individuals. Methods: This randomized, double-blind, placebo-controlled study was conducted at the Plaza Veterans' House, Havana City, Cuba. Male and female patients aged ≥60 years with total cholesterol values of <6.1 mmol/L were eligible for inclusion in the study. After a 3-week lead-in and baseline assessment period, patients were randomized to receive PO D-003 5 mg/d, D-003 10 mg/d, or placebo for 8 weeks. The effect on copper-induced LP of low-density lipoprotein (LDL) particles was the primary variable, and the effects on plasma total antioxidant status (TAS), plasma malondialdehyde (MDA) concentration, plasma antioxidant enzyme (superoxide dismutase and glutathione peroxidase) activities, and the lipid profile were secondary variables. A clinical examination was performed at each visit (baseline, weeks 4 and 8). A clinical examination, LP, and blood tests (lipid profile, hematologic, and blood biochemistry safety indicators) were performed at baseline and after 8 weeks of treatment. Compliance and adverse events (AEs) were assessed at weeks 4 and 8. A 2-tailed P < 0.05 was considered statistically significant for comparisons of both continuous and categoric variables. Results: Fifty-four patients aged ≥60 years were assessed for inclusion in the study, and 51 patients (40 women, 11 men; mean [SD] age, 67 [6] years) were included in the study. The lag phase of conjugated diene formation increased significantly and in a dose-dependent manner in the group treated with D-003 5 mg (24.7%; P < 0.01) and in the group treated with D-003 10 mg (29.3%; P < 0.01) compared with placebo. The maximal rate of conjugated diene

  15. Tumour marker detection in oesophageal carcinoma.

    PubMed

    Mealy, K; Feely, J; Reid, I; McSweeney, J; Walsh, T; Hennessy, T P

    1996-10-01

    Levels of the tumour markers CEA, CA 19-9, CA 125 and SCC were measured in 58 patients presenting with oesophageal carcinoma and compared with levels in patients with benign oesophageal disease and levels in normal volunteers. CEA and CA 19-9 were significantly increased in the patients with oesophageal cancer, however, individual sensitivity for CEA, CA 19-9, CA 125 and SCC was only 28, 34, 10, and 32%, respectively. The combined sensitivity of all markers was 64% and specificity was 80%. There was no difference in combined tumour marker sensitivity between squamous or adenocarcinomas of the oesophagus. No consistent change in marker levels occurred with treatment, and tumour marker levels could not be significantly correlated with stage of disease or short-term survival. These results indicate that tumour marker sensitivity is too low for oesophageal cancer screening and has poor prognostic significance in those undergoing treatment.

  16. Ceramic subsurface marker prototypes

    SciTech Connect

    Lukens, C.E.

    1985-05-02

    The client submitted 5 sets of porcelain and stoneware subsurface (radioactive site) marker prototypes (31 markers each set). The following were determined: compressive strength, thermal shock resistance, thermal crazing resistance, alkali resistance, color retention, and chemical resistance.

  17. Social Individualism.

    ERIC Educational Resources Information Center

    Cornille, Thomas A.; Harrigan, John

    Relationships between individuals and society have often been presented from the perspective of the social institution. Social psychology has addressed the variables that affect the individual in relationships with larger groups. Social individualism is a conceptual framework that explores the relationship of the individual and society from the…

  18. Cross-species amplification of microsatellite markers in the Great Horned Owl Bubo virginianus, Short-eared Owl Asio flammeus and Snowy Owl B. scandiacus for use in population genetics, individual identification and parentage studies

    USGS Publications Warehouse

    Dial, Cody R.; Talbot, Sandra L.; Sage, George K.; Seidensticker, M.T.; Holt, D.W.

    2012-01-01

    Using DNA from blood and feathers, we screened twenty-four microsatellite primer pairs initially developed for six strigid owls, and four primer pairs shown to be polymorphic across avian taxa, for their utility in Great Horned Owl (Bubo virginianus), Short-eared Owl (Asio flammeus), and Snowy Owl (Bubo scandiacus). Eight of these primers reliably amplified polymorphic fragments in Great Horned Owl, eleven in Short-eared owl, and ten in Snowy Owl. Analyses of results from presumably unrelated owls demonstrate the utility of these loci for individual identification, parentage assignment, and population genetics studies.

  19. Tumor markers for hepatocellular carcinoma

    PubMed Central

    ZHAO, YAN-JIE; JU, QIANG; LI, GUAN-CHENG

    2013-01-01

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors with a high rate of morbidity and mortality. HCC affects approximately one million individuals annually worldwide, with the incidence equal to the mortality rate. In 2008, HCC was listed as the third most lethal cancer. Thus, early diagnosis is crucial for improving the survival rate for patients. α-fetoprotein (AFP) together with iconography and pathology detection are commonly used in the clinical early diagnosis of liver cancer. However, the specificity and sensitivity of AFP used in screening for liver cancer are not satisfactory. Athough the development of molecular biology has led to the identification of new tumor markers, including proteantigens, cytokines, enzymes and isoenzymes, as well as related genes that can be used in the treatment and prognosis of liver cancer, more tumor markers are required for effective early diagnosis of diseases and monitoring of the curative effect. PMID:24649215

  20. A Subgroup of First-Degree Relatives of Crohn's Disease Patients Shows a Profile of Inflammatory Markers in the Blood Which Is More Typical of Crohn's Disease Patients Than of Normal Individuals

    PubMed Central

    Efrat, Broide; Iris, Goren; Wang, Hongbin; Eitan, Scapa; Yona, Keisari

    2006-01-01

    Introduction. Family member with IBD is the greatest risk factor for developing the disease. The hematological profile of first-degree relatives (FDRs) of Crohn's disease (CD) patients was studied in order to identify healthy FDRs at risk to develop disease. Materials and methods. Thirty CD patients, 90 FDRs, and 28 non-related individuals (controls) were enrolled. Hematological profile and C-reactive protein were determined. Results. All hematological parameters were significantly different in CD patients compared to controls, with significantly higher levels of CRP, WBC, PMN, MONO, and PLT and lower Hb and lymphocyte count. The hematological profile of FDRs showed values between the controls and CD patients with ten FDRs that their parameters matched those of CD patients and significantly different from other FDRs. This group was defined as high-risk relatives (HRRs). Conclusions. Analysis of the hematological profile and CRP level might be proven as a fast, reliable, and less money-consuming tool to identify FDRs with a probable increased risk to develop the disease. PMID:16883067

  1. Biological markers in reproductive epidemiology: prospects and precautions

    SciTech Connect

    Stein, Z.; Hatch, M.

    1987-10-01

    We begin by defining ''biological markers'' for the purposes of the present review, distinguishing markers from other types of information, such as subject reports or conventional clinical data. We find the distinctions to be hazy. Next, from the standpoint of epidemiologists, we set out circumstances in which exposure markers might be needed, suggesting requirements for useful markers. We give two instances (lead, PCB), drawn from studies of female reproduction, where the use of exposure markers is compared to environmental or anamnestic data. Effect markers are considered in turn. It is argued that their usefulness (if they are to be more informative than exposure markers) depends on their sensitivity and specificity in relation to the disease outcome. Also, their timeliness, and the use that can be made of the gain in time, for individuals and populations is discussed. In this context, we consider markers of events before and around fertilization; more specifically, we consider those events that precede the clinical marker of the first missed period. In returning to the potential uses of biological markers in discovering or interpreting female reproductive disorders that might be owed to environmental causes, we compare markers of the pre- and peri-implantation phases with markers of the postimplantation phase, drawing on experience with studies of chromosome anomaly in spontaneous abortion. Finally, we suggest other sensitive reproductive processes for which biological markers might usefully be developed. 30 references.

  2. Individual Education.

    ERIC Educational Resources Information Center

    Corsini, Raymond

    1981-01-01

    Paper presented at the 66th Convention of the International Association of Pupil Personnel Workers, October 20, 1980, Baltimore, Maryland, describes individual education based on the principles of Alfred Adler. Defines six advantages of individual education, emphasizing student responsibility, mutual respect, and allowing students to progress at…

  3. Paternity and Nested-within-Family Marker Assisted Selection in Space Planted Red Clover Nurseries

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Presented is a cost effective marker assisted selection methodology that utilizes individual plant phenotypes, seed production based knowledge of maternity, molecular marker determined paternity, and nested within halfsib family linkage relationships. Combining all above listed components, selection...

  4. Today's oxidative stress markers.

    PubMed

    Czerska, Marta; Mikołajewska, Karolina; Zieliński, Marek; Gromadzińska, Jolanta; Wąsowicz, Wojciech

    2015-01-01

    Oxidative stress represents a situation where there is an imbalance between the reactive oxygen species (ROS) and the availability and the activity of antioxidants. This balance is disturbed by increased generation of free radicals or decreased antioxidant activity. It is very important to develop methods and find appropriate biomarkers that may be used to assess oxidative stress in vivo. It is significant because appropriate measurement of such stress is necessary in identifying its role in lifestyle-related diseases. Previously used markers of oxidative stress, such as thiobarbituric acid reactive substances (TBARS) or malondialdehyde (MDA), are progressively being supplemented by new ones, such as isoprostanes (IsoPs) and their metabolites or allantoin. This paper is focusing on the presentation of new ones, promising markers of oxidative stress (IsoPs, their metabolites and allantoin), taking into account the advantage of those markers over markers used previously. PMID:26325052

  5. [Biological markers of alcoholism].

    PubMed

    Marcos Martín, M; Pastor Encinas, I; Laso Guzmán, F J

    2005-09-01

    Diagnosis of alcoholism is very important, given its high prevalence and possibility of influencing the disease course. For this reason, the so-called biological markers of alcoholism are useful. These are analytic parameters that alter in the presence of excessive alcohol consumption. The two most relevant markers are the gamma-glutamyltranspeptidase and carbohydrate deficient transferrin. With this clinical comment, we aim to contribute to the knowledge of these tests and promote its use in the clinical practice. PMID:16194480

  6. Markers predicting progression of human immunodeficiency virus-related disease.

    PubMed Central

    Tsoukas, C M; Bernard, N F

    1994-01-01

    Human immunodeficiency virus (HIV) interacts with the immune system throughout the course of infection. For most of the disease process, HIV activates the immune system, and the degree of activation can be assessed by measuring serum levels of molecules such as beta 2-microglobulin and neopterin, as well as other serum and cell surface phenotype markers. The levels of some of these markers correlate with clinical progression of HIV disease, and these markers may be useful as surrogate markers for development of clinical AIDS. Because the likelihood and timing of development of clinical AIDS following seroconversion, for any particular individual, are not readily predictable, the use of nonclinical disease markers has become critically important to patient management. Surrogate markers of HIV infection are, by definition, measurable traits that correlate with disease progression. An ideal marker should identify patients at highest risk of disease progression, provide information on how long an individual has been infected, help in staging HIV disease, predict development of opportunistic infections associated with AIDS, monitor the therapeutic efficacy of immunomodulating or antiviral treatments, and the easily quantifiable, reliable, clinically available, and affordable. This review examines the current state of knowledge and the role of surrogate markers in the natural history and treatment of HIV infection. The clinical usefulness of each marker is assessed with respect to the criteria outlined for the ideal surrogate marker for HIV disease progression. PMID:8118788

  7. DEVELOPMENT OF CODOMINANT MARKERS FOR IDENTIFYING SPECIES HYBRIDS

    EPA Science Inventory

    Herein we describe a simple method for developing species-diagnostic markers that would permit the rapid identification of hybrid individuals. Our method relies on amplified length polymorphism (AFLP) and single strand conformation polymorphism (SSCP) technologies, both of which...

  8. Markers for Detection of Prostate Cancer

    PubMed Central

    Clarke, Raymond A.; Schirra, Horst J.; Catto, James W.; Lavin, Martin F.; Gardiner, Robert A.

    2010-01-01

    Early detection of prostate cancer is problematic, not just because of uncertainly whether a diagnosis will benefit an individual patient, but also as a result of the imprecise and invasive nature of establishing a diagnosis by biopsy. Despite its low sensitivity and specificity for identifying patients harbouring prostate cancer, serum prostate specific antigen (PSA) has become established as the most reliable and widely-used diagnostic marker for this condition. In its wake, many other markers have been described and evaluated. This review focuses on the supporting evidence for the most prominent of these for detection and also for predicting outcome in prostate cancer. PMID:24281110

  9. Individualizing Medicare.

    PubMed

    Chollet, D J

    1999-05-01

    Despite the enactment of significant changes to the Medicare program in 1997, Medicare's Hospital Insurance trust fund is projected to be exhausted just as the baby boom enters retirement. To address Medicare's financial difficulties, a number of reform proposals have been offered, including several to individualize Medicare financing and benefits. These proposals would attempt to increase Medicare revenues and reduce Medicare expenditures by having individuals bear risk--investment market risk before retirement and insurance market risk after retirement. Many fundamental aspects of these proposals have yet to be worked out, including how to guarantee a baseline level of saving for health insurance after retirement, how retirees might finance unanticipated health insurance price increases after retirement, the potential implications for Medicaid of inadequate individual saving, and whether the administrative cost of making the system fair and adequate ultimately would eliminate any rate-of-return advantages from allowing workers to invest their Medicare contributions in corporate stocks and bonds.

  10. Individualizing Medicare.

    PubMed

    Chollet, D J

    1999-05-01

    Despite the enactment of significant changes to the Medicare program in 1997, Medicare's Hospital Insurance trust fund is projected to be exhausted just as the baby boom enters retirement. To address Medicare's financial difficulties, a number of reform proposals have been offered, including several to individualize Medicare financing and benefits. These proposals would attempt to increase Medicare revenues and reduce Medicare expenditures by having individuals bear risk--investment market risk before retirement and insurance market risk after retirement. Many fundamental aspects of these proposals have yet to be worked out, including how to guarantee a baseline level of saving for health insurance after retirement, how retirees might finance unanticipated health insurance price increases after retirement, the potential implications for Medicaid of inadequate individual saving, and whether the administrative cost of making the system fair and adequate ultimately would eliminate any rate-of-return advantages from allowing workers to invest their Medicare contributions in corporate stocks and bonds. PMID:10915458

  11. Glycomics and Disease Markers

    PubMed Central

    An, Hyun Joo; Kronewitter, Scott R.; de Leoz, Maria Lorna A.; Lebrilla, Carlito B.

    2009-01-01

    Summary of Recent Advances Glycomics is the comprehensive study of all glycans expressed in biological systems. The biosynthesis of glycan relies on a number of highly competitive processes involving glycosyl transferase. Glycosylation is therefore highly sensitive to the biochemical environment and has been implicated in many diseases including cancer. Recently, interest in profiling the glycome has increased due to the potential of glycans for disease markers. In this regard, mass spectrometry is emerging as a powerful technique for profiling the glycome. Global glycan profiling of human serum based on mass spectrometry has already led to several potentially promising markers for several types of cancer and diseases. PMID:19775929

  12. [Individualizing Education.

    ERIC Educational Resources Information Center

    Horrigan, William J.

    The individually guided education (IGE) program developed by the Kettering Foundation was implemented in September of 1973 at the John F. Kennedy Memorial Junior High School in Woburn, Massachusetts. The components of the program described in this speech include pupil and teacher scheduling, physical layout, pupil selection and adjustment,…

  13. The Swift Turbidity Marker

    ERIC Educational Resources Information Center

    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…

  14. Individualized Communications

    NASA Technical Reports Server (NTRS)

    1997-01-01

    IntelliWeb and IntelliPrint, products from MicroMass Communications, utilize C Language Integrated Production System (CLIPS), a development and delivery expert systems tool developed at Johnson Space Center. IntelliWeb delivers personalized messages by dynamically creating single web pages or entire web sites based on information provided by each website visitor. IntelliPrint is a product designed to create tailored, individualized messages via printed media. The software uses proprietary technology to generate printed messages that are personally relevant and tailored to meet each individual's needs. Intelliprint is in use in many operations including Brystol-Myers Squibb's personalized newsletter, "Living at Your Best," geared to each recipient based on a health and lifestyle survey taken earlier; and SmithKline Beecham's "Nicorette Committed Quitters Program," in which customized motivational materials support participants in their attempt to quit smoking.

  15. Metabolic markers in sports medicine.

    PubMed

    Banfi, Giuseppe; Colombini, Alessandra; Lombardi, Giovanni; Lubkowska, Anna

    2012-01-01

    Physical exercise induces adaptations in metabolism considered beneficial for health. Athletic performance is linked to adaptations, training, and correct nutrition in individuals with genetic traits that can facilitate such adaptations. Intense and continuous exercise, training, and competitions, however, can induce changes in the serum concentrations of numerous laboratory parameters. When these modifications, especially elevated laboratory levels, result outside the reference range, further examinations are ordered or participation in training and competition is discontinued or sports practice loses its appeal. In order to correctly interpret commonly used laboratory data, laboratory professionals and sport physicians need to know the behavior of laboratory parameters during and after practice and competition. We reviewed the literature on liver, kidney, muscle, heart, energy, and bone parameters in athletes with a view to increase the knowledge about clinical chemistry applied to sport and to stimulate studies in this field. In liver metabolism, the interpretation of serum aminotransferases concentration in athletes should consider the release of aspartate aminotransferase (AST) from muscle and of alanine aminotransferase (ALT) mainly from the liver, when bilirubin can be elevated because of continuous hemolysis, which is typical of exercise. Muscle metabolism parameters such as creatine kinase (CK) are typically increased after exercise. This parameter can be used to interpret the physiological release of CK from muscle, its altered release due to rhabdomyolysis, or incomplete recovery due to overreaching or trauma. Cardiac markers are released during exercise, and especially endurance training. Increases in these markers should not simply be interpreted as a signal of cardiac damage or wall stress but rather as a sign of regulation of myocardial adaptation. Renal function can be followed in athletes by measuring serum creatinine concentration, but it should

  16. Prognostic molecular markers in early breast cancer

    PubMed Central

    Esteva, Francisco J; Hortobagyi, Gabriel N

    2004-01-01

    A multitude of molecules involved in breast cancer biology have been studied as potential prognostic markers. In the present review we discuss the role of established molecular markers, as well as potential applications of emerging new technologies. Those molecules used routinely to make treatment decisions in patients with early-stage breast cancer include markers of proliferation (e.g. Ki-67), hormone receptors, and the human epidermal growth factor receptor 2. Tumor markers shown to have prognostic value but not used routinely include cyclin D1 and cyclin E, urokinase-like plasminogen activator/plasminogen activator inhibitor, and cathepsin D. The level of evidence for other molecular markers is lower, in part because most studies were retrospective and not adequately powered, making their findings unsuitable for choosing treatments for individual patients. Gene microarrays have been successfuly used to classify breast cancers into subtypes with specific gene expression profiles and to evaluate prognosis. RT-PCR has also been used to evaluate expression of multiple genes in archival tissue. Proteomics technologies are in development. PMID:15084231

  17. The impact of genetic markers on selection.

    PubMed

    Davis, G P; DeNise, S K

    1998-09-01

    Genetic marker technologies, such as marker-assisted selection, parentage identification, and gene introgression can be applied to livestock selection programs. Highly saturated genetic maps are now available for cattle, swine, and sheep to provide the genetic framework for developing MAS programs. These programs rely on three phases for commercialization of the technology: the detection phase, in which quantitative trait loci are located and their effects on the phenotype measured; the evaluation phase, in which the markers are evaluated in commercial populations; and the implementation phase, in which markers are combined with phenotypic and pedigree information in genetic evaluation for predicting the genetic merit of individuals within the population. Predicting the economic impact of genetic technologies is a complex process that requires quantitative prediction and economic analysis. Evaluating the impact of these benefits across an industry can be achieved through a process in which gains from implementation of a genetic technology are assessed at the individual, enterprise, and industry levels. A pattern of annual benefits and costs can be predicted using gene flows that can be evaluated by conventional economic analysis.

  18. Microsatellite DNA markers in Populus tremuloides.

    PubMed

    Rahman, M H; Dayanandan, S; Rajora, O P

    2000-04-01

    Markers for eight new microsatellite DNA or simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides) from a partial genomic library. Informativeness of these microsatellite DNA markers was examined by determining polymorphisms in 38 P. tremuloides individuals. Inheritance of selected markers was tested in progenies of controlled crosses. Six characterized SSR loci were of dinucleotide repeats (two perfect and four imperfect), and one each of trinucleotide and tetranucleotide repeats. The monomorphic SSR locus (PTR15) was of a compound imperfect dinucleotide repeat. The primers of one highly polymorphic SSR locus (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. At the other six polymorphic loci, 25 alleles were detected in 38 P. tremuloides individuals; the number of alleles ranged from 2 to 7, with an average of 4.2 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.61, with an average of 0.36 per locus. The two perfect dinucleotide and one trinucleotide microsatellite DNA loci were the most informative. Microsatellite DNA variants of four SSR loci characterized previously followed a single-locus Mendelian inheritance pattern, whereas those of PTR7 from the present study showed a two-locus Mendelian inheritance pattern in controlled crosses. The microsatellite DNA markers developed and reported here could be used for assisting various genetic, breeding, biotechnology, genome mapping, conservation, and sustainable forest management programs in poplars. PMID:10791817

  19. Associations between STR autosomal markers and longevity.

    PubMed

    Bediaga, N G; Aznar, J M; Elcoroaristizabal, X; Albóniga, O; Gómez-Busto, F; Artaza Artabe, I; Rocandio, Ana; de Pancorbo, M M

    2015-10-01

    Life span is a complex and multifactorial trait, which is shaped by genetic, epigenetic, environmental, and stochastic factors. The possibility that highly hypervariable short tandem repeats (STRs) associated with longevity has been largely explored by comparing the genotypic pools of long lived and younger individuals, but results so far have been contradictory. In view of these contradictory findings, the present study aims to investigate whether HUMTHO1 and HUMCSF1PO STRs, previously associated with longevity, exert a role as a modulator of life expectancy, as well as to assess the extent to which other autosomal STR markers are associated with human longevity in population from northern Spain. To that end, 21 autosomal microsatellite markers have been studied in 304 nonagenarian individuals (more than 90 years old) and 516 younger controls of European descent. Our results do not confirm the association found in previous studies between longevity and THO1 and CSF1PO loci. However, significant association between longevity and autosomal STR markers D12S391, D22S1045, and DS441 was observed. Even more, when we compared allelic frequency distribution of the 21 STR markers between cases and controls, we found that 6 out of the 21 STRs studied showed different allelic frequencies, thus suggesting that the genomic portrait of the human longevity is far complex and probably shaped by a high number of genomic loci. PMID:26335621

  20. Referential Markers and Agreement Markers in Functional Discourse Grammar

    ERIC Educational Resources Information Center

    Hengeveld, Kees

    2012-01-01

    It follows from the ordering principles that are applied in Functional Discourse Grammar that the positional possibilities of markers of agreement and those of cross-reference are different. Markers of cross reference are predicted to occur closer to the verb stem, while markers of agreement would occupy peripheral positions. This paper tests…

  1. Lipoprotein marker for hypertriglyceridemia

    DOEpatents

    Cubicciotti, Roger S.; Karu, Alexander E.; Krauss, Ronald M.

    1986-01-01

    Methods and compositions are provided for the detection of a particular low density lipoprotein which has been found to be a marker for patients suffering from type IV hypertriglyceridemia. A monoclonal antibody capable of specifically binding to a characteristic epitopic site on this LDL subspecies can be utilized in a wide variety of immunoassays. Hybridoma cell line SPL.IVA5A1 was deposited at the American Type Culture Collection on Mar. 29, 1984, and granted accession no. HB 8535.

  2. MACD: an imaging marker for cardiovascular disease

    NASA Astrophysics Data System (ADS)

    Ganz, Melanie; de Bruijne, Marleen; Nielsen, Mads

    2010-03-01

    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 with coronary artery calcifications. Hence an early detection of aortic calcified plaques helps to predict the risk of related coronary diseases. Also since two thirds of the adverse events have no prior symptoms, possibilities to screen for risk in low cost imaging are important. To this end the Morphological Atherosclerotic Calcification Distribution (MACD) index was developed. In the following several potential severity scores relating to the geometrical outline of the calcified deposits in the lumbar aortic region are introduced. Their individual as well as their combined predictive power is examined and a combined marker, MACD, is constructed. This is done using a Cox regression analysis, also known as survival analysis. Furthermore we show how a Cox regression yields MACD to be the most efficient marker. We also demonstrate that MACD has a larger individual predictive power than any of the other individual imaging markers described. Finally we present that the MACD index predicts cardiovascular death with a hazard ratio of approximately four.

  3. [Tumor markers in gastric cancer].

    PubMed

    Ohkura, Hisanao

    2002-04-01

    There are two markers, pepsinogen isoenzymes and antibody against Helicobactor pyroli, for screening of high-risk group for gastric cancer. Most of markers are used in diagnosis, staging, monitoring and differentiating subgroups of gastric cancer. Markers in ascitic fluid are used for diagnosing peritoneal invasion of gastric cancer. PMID:11977555

  4. Individualization of antiretroviral therapy

    PubMed Central

    Pavlos, Rebecca; Phillips, Elizabeth J

    2012-01-01

    Antiretroviral therapy (ART) has evolved considerably over the last three decades. From the early days of monotherapy with high toxicities and pill burdens, through to larger pill burdens and more potent combination therapies, and finally, from 2005 and beyond where we now have the choice of low pill burdens and once-daily therapies. More convenient and less toxic regimens are also becoming available, even in resource-poor settings. An understanding of the individual variation in response to ART, both efficacy and toxicity, has evolved over this time. The strong association of the major histocompatibility class I allele HLA-B*5701 and abacavir hypersensitivity, and its translation and use in routine HIV clinical practice as a predictive marker with 100% negative predictive value, has been a success story and a notable example of the challenges and triumphs in bringing pharmacogenetics to the clinic. In real clinical practice, however, it is going to be the exception rather than the rule that individual biomarkers will definitively guide patient therapy. The need for individualized approaches to ART has been further increased by the importance of non-AIDS comorbidities in HIV clinical practice. In the future, the ideal utilization of the individualized approach to ART will likely consist of a combined approach using a combination of knowledge of drug, virus, and host (pharmacogenetic and pharmacoecologic [factors in the individual’s environment that may be dynamic over time]) information to guide the truly personalized prescription. This review will focus on our knowledge of the pharmacogenetics of the efficacy and toxicity of currently available antiretroviral agents and the current and potential utility of such information and approaches in present and future HIV clinical care. PMID:23226059

  5. Antibody markers in the diagnosis of inflammatory bowel disease

    PubMed Central

    Mitsuyama, Keiichi; Niwa, Mikio; Takedatsu, Hidetoshi; Yamasaki, Hiroshi; Kuwaki, Kotaro; Yoshioka, Shinichiro; Yamauchi, Ryosuke; Fukunaga, Shuhei; Torimura, Takuji

    2016-01-01

    Inflammatory bowel disease (IBD), including Crohn’s disease and ulcerative colitis, is a chronic intestinal inflammation of unknown etiology. The diagnosis of IBD is based on endoscopic, radiologic and histopathologic criteria. Recently, the search for a noninvasive marker that could augment or replace part of this diagnostic process has become a focus of IBD research. In this review, antibody markers, including microbial antibodies, autoantibodies and peptide antibodies, will be described, focusing on their common features. At present, no single marker with qualities that are satisfactory for the diagnosis and treatment of IBD has been identified, although panels of some antibodies are being evaluated with keen interest. The discovery of novel IBD-specific and sensitive markers is anticipated. Such markers could minimize the use of endoscopic and radiologic examinations and could enable clinicians to implement individualized treatment plans designed to improve the long-term prognosis of patients with IBD. PMID:26811667

  6. [Markers of hepatitis virus].

    PubMed

    Suzuki, Fumitaka

    2008-11-01

    Hepatitis B virus (HBV) and hepatitis C virus (HCV) are the major viruses known to cause viral hepatitis. Serological markers are commonly used as diagnostic and/or prognostic indicators of acute or chronic HBV or HCV infection. The ability to detect HBV DNA in serum has been reported to have prognostic value for the outcome of chronic HBV infection. A rapid and sustained drop in HBV DNA or HCV RNA levels in patients under therapy has been shown to be a predictive factor for a favourable treatment outcome. Various techniques for detecting HBV DNA or HCV RNA have already been described; however, there are various problems with the sensitivity or detection range of those methods. New virus measuring methods have recently been reported and used. The Cobas Taq Man HCV Test is a new method to detect HBV DNA and HCV RNA with higher sensitivity and a broader range of quantitation than conventional methods. Some reports have shown that these methods improve therapy monitoring and the management of HBV or HCV infection. Moreover, hepatitis E virus (HEV) infection has been reported in Japan. The clinical features and viral markers of HEV have also been described. PMID:19086457

  7. Polymorphic microsatellite markers in Euryale ferox Salisb. (Nymphaeaceae).

    PubMed

    Quan, Zhiwu; Pan, Lei; Ke, Weidong; Ding, Yi

    2009-01-01

    Eleven polymorphic microsatellite markers were isolated and identified in the aquatic plant Euryale ferox Salisb. (Nymphaeaceae). This species, which belongs to basal Magnoliophyta, reproduces sexually. All of these 11 microsatellite markers yielded 25 alleles in a survey of a wild population of 34 individuals. Two or three alleles per locus were detected, with expected heterozygosity ranging from 0.056 to 0.634 and observed heterozygosity from 0.000 to 0.088. These simple sequence repeat markers will be useful for evaluating the genetic structure of the E. ferox population in the future.

  8. Polymorphic microsatellite markers in Euryale ferox Salisb. (Nymphaeaceae).

    PubMed

    Quan, Zhiwu; Pan, Lei; Ke, Weidong; Ding, Yi

    2009-01-01

    Eleven polymorphic microsatellite markers were isolated and identified in the aquatic plant Euryale ferox Salisb. (Nymphaeaceae). This species, which belongs to basal Magnoliophyta, reproduces sexually. All of these 11 microsatellite markers yielded 25 alleles in a survey of a wild population of 34 individuals. Two or three alleles per locus were detected, with expected heterozygosity ranging from 0.056 to 0.634 and observed heterozygosity from 0.000 to 0.088. These simple sequence repeat markers will be useful for evaluating the genetic structure of the E. ferox population in the future. PMID:21564641

  9. Automated fiducial marker planning for thoracic stereotactic body radiation therapy

    NASA Astrophysics Data System (ADS)

    Gibbs, Jason D.; Rai, Lav; Wibowo, Henky; Tsalyuk, Serge; Anderson, Eric D.

    2012-02-01

    Stereotactic body-radiation therapy (SBRT) has gained acceptance in treating lung cancer. Localization of a thoracic lesion is challenging as tumors can move significantly with breathing. Some SBRT systems compensate for tumor motion with the intrafraction tracking of targets by two stereo fluoroscopy cameras. However, many lung tumors lack a fluoroscopic signature and cannot be directly tracked. Small radiopaque fiducial markers, acting as fluoroscopically visible surrogates, are instead implanted nearby. The spacing and configuration of the fiducial markers is important to the success of the therapy as SBRT systems impose constraints on the geometry of a fiducial-marker constellation. It is difficult even for experienced physicians mentally assess the validity of a constellation a priori. To address this challenge, we present the first automated planning system for bronchoscopic fiducial-marker placement. Fiducial-marker planning is posed as a constrained combinatoric optimization problem. Constraints include requiring access from a navigable airway, having sufficient separation in the fluoroscopic imaging planes to resolve each individual marker, and avoidance of major blood vessels. Automated fiducial-marker planning takes approximately fifteen seconds, fitting within the clinical workflow. The resulting locations are integrated into a virtual bronchoscopic planning system, which provides guidance to each location during the implantation procedure. To date, we have retrospectively planned over 50 targets for treatment, and have implanted markers according to the automated plan in one patient who then underwent SBRT treatment. To our knowledge, this approach is the first to address automated bronchoscopic fiducialmarker planning for SBRT.

  10. Predictive Markers of Honey Bee Colony Collapse

    PubMed Central

    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. PMID:22384162

  11. Predictive markers of honey bee colony collapse.

    PubMed

    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.

  12. [Biochemical and immunological markers of autoimmune thyroiditis].

    PubMed

    Biktagirova, E M; Sattarova, L I; Vagapova, G R; Skibo, Y V; Chuhlovina, E N; Kravtsova, O A; Abramova, Z I

    2016-05-01

    Correlations between biochemical and immunological markers of programmed cell death (apoptosis), and the functional state of the thyroid gland (hyperthyroidism, euthyroidism, hypothyroidism) have been investigated in autoimmune thyroiditis (AT) (also known as chronic autoimmune thyroiditis). Annexin V, TRAIL and TNF-a, as well as DNA-hydrolyzing antibodies were used as the main markers. Increased levels of TRAIL were found in the serum of AT patients (hyperthyroidism>hypothyroidism>euthyroidism) compared with healthy individuals. The highest frequency of antibodies to denatured DNA (Abs-dDNA) had the highest frequency in AT patients (97%) compared with healthy controls. Among these patients, 75% had hyperthyroidism, 85% had hypothyroidism, and 84.7% had euthyroidism. Abs hydrolyzing activity demonstrated correlation dependence with symptoms of the thyroid dysfunction. PMID:27563001

  13. Marker evaluation of human breast and bladder cancers

    SciTech Connect

    Mayall, B.H.; Carroll, P.R.; Chen, Ling-Chun; Cohen, M.B.; Goodson, W.H. III; Smith, H.S.; Waldman, F.M. )

    1990-11-02

    We are investigating multiple markers in human breast and bladder cancers. Our aim is to identify markers that are clinically relevant and that contribute to our understanding of the disease process in individual patients. Good markers accurately assess the malignant potential of a cancer in an individual patient. Thus, they help identify those cancers that will recur, and they may be used to predict more accurately time to recurrence, response to treatment, and overall prognosis. Therapy and patient management may then be optimized to the individual patient. Relevant markers reflect the underlying pathobiology of individual tumors. As a tissue undergoes transformation from benign to malignant, the cells lose their differentiated phenotype. As a generalization, the more the cellular phenotype, cellular proliferation and cellular genotype depart from normal, the more advanced is the tumor in its biological evolution and the more likely it is that the patient has a poor prognosis. We use three studies to illustrate our investigation of potential tumor markers. Breast cancers are labeled in vivo with 5-bromodeoxyuridine (BrdUrd) to give a direct measure of the tumor labeling index. Bladder cancers are analyzed immunocytochemically using an antibody against proliferation. Finally, the techniques of molecular genetics are used to detect allelic loss in breast cancers. 6 refs., 3 figs.

  14. Urinary markers for bladder cancer

    PubMed Central

    Smith, Zachary L.

    2013-01-01

    Bladder cancer has the fifth highest incidence of all malignancies in the United States, with a propensity to recur, requiring lifelong surveillance after diagnosis. Urinary markers of disease have been of extreme interest in this field in an effort to simplify surveillance schedules and improve early detection of tumors. Many markers have been described, but most remain investigational. However, some markers have undergone clinical trials and are approved for clinical use. In this review, urinary markers and their application for screening and surveillance of bladder cancer are discussed. PMID:23864929

  15. Occurrence of bacteria and biochemical markers on public surfaces.

    PubMed

    Reynolds, Kelly A; Watt, Pamela M; Boone, Stephanie A; Gerba, Charles P

    2005-06-01

    From 1999-2003, the hygiene of 1061 environmental surfaces from shopping, daycare, and office environments, personal items, and miscellaneous activities (i.e., gymnasiums, airports, movie theaters, restaurants, etc.), in four US cities, was monitored. Samples were analyzed for fecal and total coliform bacteria, protein, and biochemical markers. Biochemical markers, i.e., hemoglobin (blood marker), amylase (mucus, saliva, sweat, and urine marker), and urea (urine and sweat marker) were detected on 3% (26/801); 15% (120/801), and 6% (48/801) of the surfaces, respectively. Protein (general hygiene marker) levels > or = 200 microg/10 cm2 were present on 26% (200/801) of the surfaces tested. Surfaces from children's playground equipment and daycare centers were the most frequently contaminated (biochemical markers on 36%; 15/42 and 46%; 25/54, respectively). Surfaces from the shopping, miscellaneous activities, and office environments were positive for biochemical markers with a frequency of 21% (69/333), 21% (66/308), and 11% (12/105), respectively). Sixty samples were analyzed for biochemical markers and bacteria. Total and fecal coliforms were detected on 20% (12/60) and 7% (4/ 60) of the surfaces, respectively. Half and one-third of the sites positive for biochemical markers were also positive for total and fecal coliforms, respectively. Artificial contamination of public surfaces with an invisible fluorescent tracer showed that contamination from outside surfaces was transferred to 86% (30/ 35) of exposed individual's hands and 82% (29/35) tracked the tracer to their home or personal belongings hours later. Results provide information on the relative hygiene of commonly encountered public surfaces and aid in the identification of priority environments where contaminant occurrence and risk of exposure may be greatest. Children's playground equipment is identified as a priority surface for additional research on the occurrence of and potential exposure to infectious

  16. Analysis of genetic diversity in earthworms using DNA markers.

    PubMed

    Sharma, Anshul; Sonah, Humira; Deshmukh, Rupesh K; Gupta, Navneet K; Singh, Nagendra K; Sharma, Tilak R

    2011-01-01

    Earthworms are one of the most important and beneficial macrofauna, and are used extensively in organic farming. Earthworms mediate soil biological regulation systems, and produce biogenic structures. They help to maintain soil structure, water infiltration, and regulate the availability of nutrients assimilated by plants. The objectives of this study were to perform morphological and molecular characterizations of 24 earthworm individuals collected from geographically diverse locations to assess the level of genetic variation. For molecular analysis, the effectiveness of RAPD, ISSR, and Universal rice primers (URPs) markers was investigated to identify polymorphism among 24 isolates of earthworms. A total of 62 molecular markers were used for amplification of genomic DNA of earthworms. Of these, 10 RAPD, 10 ISSR, and 10 URPs markers were used for characterization, which showed 95.7%, 96.7% and 98.3% polymorphism, respectively. The dendrogram, generated from the DNA markers by the unweighted pair group method using arithmetic averages, grouped all the isolates into two main clusters. All Eisenia fetida isolates were clustered in group A, whereas group B included three isolates belonging to Eudrilus eugeniae. Molecular markers allowed a rapid assessment of genetic variation among these closely related isolates of earthworms. These results suggest that molecular markers are a good choice for diversity analysis of earthworm individuals. PMID:21186943

  17. Genetic markers: Potential candidates for cardiovascular disease.

    PubMed

    Rather, Riyaz Ahmad; Dhawan, Veena

    2016-10-01

    The effective prevention of cardiovascular disease depends upon the ability to recognize the high-risk individuals at an early stage of the disease or long before the development of adverse events. Evolving technologies in the fields of proteomics, metabolomics, and genomics have played a significant role in the discovery of cardiovascular biomarkers, but so far these methods have achieved the modest success. Hence, there is a crucial need for more reliable, suitable, and lasting diagnostic and therapeutic markers to screen the disease well in time to start the clinical aid to the patients. Gene polymorphisms associated with the cardiovascular disease play a decisive role in the disease onset. Therefore, the genetic marker evaluation to classify high-risk patients from low-risk patients trends an effective approach to patient management and care. Currently, there are no genetic markers available for extensive adoption as risk factors for coronary vascular disease, yet, there are numerous promising, biologically acceptable candidates. Many of these gene biomarkers, alone or in combination, can play an essential role in the prediction of cardiovascular risk. The present review highlights some putative emerging genetic biomarkers that could facilitate more authentic and fast diagnosis of CVD. This review also briefly describes few technological approaches employed in the biomarker search. PMID:27416153

  18. Genetic markers: Potential candidates for cardiovascular disease.

    PubMed

    Rather, Riyaz Ahmad; Dhawan, Veena

    2016-10-01

    The effective prevention of cardiovascular disease depends upon the ability to recognize the high-risk individuals at an early stage of the disease or long before the development of adverse events. Evolving technologies in the fields of proteomics, metabolomics, and genomics have played a significant role in the discovery of cardiovascular biomarkers, but so far these methods have achieved the modest success. Hence, there is a crucial need for more reliable, suitable, and lasting diagnostic and therapeutic markers to screen the disease well in time to start the clinical aid to the patients. Gene polymorphisms associated with the cardiovascular disease play a decisive role in the disease onset. Therefore, the genetic marker evaluation to classify high-risk patients from low-risk patients trends an effective approach to patient management and care. Currently, there are no genetic markers available for extensive adoption as risk factors for coronary vascular disease, yet, there are numerous promising, biologically acceptable candidates. Many of these gene biomarkers, alone or in combination, can play an essential role in the prediction of cardiovascular risk. The present review highlights some putative emerging genetic biomarkers that could facilitate more authentic and fast diagnosis of CVD. This review also briefly describes few technological approaches employed in the biomarker search.

  19. Development of microsatellite markers for Crepis mollis (Asteraceae)1

    PubMed Central

    Duwe, Virginia K.; Muller, Ludo A. H.; Borsch, Thomas; Ismail, Sascha A.

    2016-01-01

    Premise of the study: Polymorphic microsatellite markers were developed for the threatened species Crepis mollis (Asteraceae) to investigate population and conservation genetics. Methods and Results: Illumina sequencing was conducted on pooled genomic DNA from 10 individuals of two populations. Ten polymorphic and 10 monomorphic microsatellite loci with di-, tri-, tetra-, penta-, and hexanucleotide repeat motifs were developed and characterized in C. mollis. In the polymorphic markers, up to 17 alleles per locus were detected with an observed and expected heterozygosity ranging from 0.120 to 0.780 and 0.102 to 0.834, respectively. Furthermore, the polymorphic markers were tested for cross-amplification in three congeneric species (C. biennis, C. foetida, and C. sancta) and amplified in up to three loci. Conclusions: The markers developed in this study are the first microsatellites tested on C. mollis and will be useful for performing population and conservation genetic studies in this threatened species. PMID:27437177

  20. SNP marker detection and genotyping in tilapia.

    PubMed

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

    2012-09-01

    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 SNPs by genotyping tilapia individuals from different strains and different geographical locations. In all strains and species tested (O. niloticus, O. aureus and O. mossambicus), the genotyping assay was working for a similar number of SNPs (288-305 SNPs). The actual number of polymorphic SNPs was, as expected, highest for individuals from the GIFT population (255 SNPs). In the individuals from an Egyptian strain and in individuals caught in the wild in the basin of the river Volta, 197 and 163 SNPs were polymorphic, respectively. A pairwise calculation of Nei's genetic distance allowed the discrimination of the individual strains and species based on the genotypes determined with the SNP set. We expect that this set will be widely applicable for use in tilapia aquaculture, e.g. for pedigree reconstruction. In addition, this set is currently used for assaying the genetic diversity of native Nile tilapia in areas where tilapia is, or will be, introduced in aquaculture projects. This allows the tracing of escapees from aquaculture and the monitoring of effects of introgression and hybridization. PMID:22524158

  1. SNP marker detection and genotyping in tilapia.

    PubMed

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

    2012-09-01

    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 SNPs by genotyping tilapia individuals from different strains and different geographical locations. In all strains and species tested (O. niloticus, O. aureus and O. mossambicus), the genotyping assay was working for a similar number of SNPs (288-305 SNPs). The actual number of polymorphic SNPs was, as expected, highest for individuals from the GIFT population (255 SNPs). In the individuals from an Egyptian strain and in individuals caught in the wild in the basin of the river Volta, 197 and 163 SNPs were polymorphic, respectively. A pairwise calculation of Nei's genetic distance allowed the discrimination of the individual strains and species based on the genotypes determined with the SNP set. We expect that this set will be widely applicable for use in tilapia aquaculture, e.g. for pedigree reconstruction. In addition, this set is currently used for assaying the genetic diversity of native Nile tilapia in areas where tilapia is, or will be, introduced in aquaculture projects. This allows the tracing of escapees from aquaculture and the monitoring of effects of introgression and hybridization.

  2. [Tumor markers for hepatocellular carcinoma].

    PubMed

    Tateishi, Ryosuke; Enooku, Kenichiro; Shiina, Shuichiro; Koike, Kazuhiko

    2012-05-01

    Three tumor markers for hepatocellular carcinoma (HCC) are available in Japan: alpha-fetoprotein (AFP), protein induced by vitamin K absence or antagonists-II (PIVKA-II), and Lens culinaris agglutinin-reactive fraction of alpha-fetoprotein (AFP-L3). Although AFP has drawbacks in its specificity, it is widely utilized in treatment evaluation and prognosis prediction. PIVKA-II is a unique marker that does not correlate with AFP value and can predict microvascular invasion. AFP-L3 is a highly specific marker and strong predictor of poor prognosis. These three markers are indispensable in every aspect of clinical practice of hepatocellular carcinoma including surveillance, diagnosis, treatment evaluation, and prognosis prediction.

  3. Beta-2 Microglobulin Tumor Marker

    MedlinePlus

    ... limited. Home Visit Global Sites Search Help? Beta-2 Microglobulin Tumor Marker Share this page: Was this page helpful? Also known as: B2M; B 2 M; β2-Microglobulin; Thymotaxin Formal name: Beta 2 ...

  4. Use of microsatellite markers to assign goats to their breeds.

    PubMed

    Aljumaah, R S; Alobre, M M; Al-Atiyat, R M

    2015-08-07

    We investigated the potential of 17 microsatellite markers for assigning Saudi goat individuals to their breeds. Three local breeds, Bishi, Jabali, and Tohami were genotyped using these markers, and Somali goats were used as a reference breed. The majority of alleles were shared between the breeds, except for some that were specific to each breed. The Garza-Williamson index was lowest in the Bishi breed, indicating that a recent bottleneck event occurred. The overall results assigned the goat individuals (based on their genotypes) to the same breeds from which they were sampled, except in a few cases. The individuals' genotypes were sufficient to provide a clear distinction between the Somali goat breed and the others. In three factorial dimensions, the results of a correspondence analysis indicated that the total variation for the first and second factors was 48.85 and 31.43%, respectively. Consequently, Jabali, Bishi, and Tohami goats were in separate groups. The Jabali goat was closely related to the Bishi goat. Somali goats were distinguished from each other and from individuals of the other three goat breeds. The markers were successful in assigning individual goats to their breeds, based on the likelihood of a given individual's genotype.

  5. [Laboratory markers of melanoma progression].

    PubMed

    Bánfalvi, Teodóra; Edesné, Mariann B; Gergye, Mária; Udvarhelyi, Nóra; Orosz, Zsolt; Gilde, Katalin; Kremmer, Tibor; Ottó, Szabolcs; Tímár, József

    2003-01-01

    Extracellular tumour markers may have potential role in the follow-up of patients with malignant melanoma, in therapy monitoring and in prediction of prognosis. In our article circulating tumour markers in melanoma (melanoma inhibitory activity, lipid bound sialic acid, neuron specific enolase, TA90 immune complex, S-100B protein, 5-S-cysteinyldopa, tyrosinase, cytokines, metalloproteinases, LDH) were reviewed. Among laboratory melanoma markers the S-100B protein is the most investigated. S-100B protein has high specificity, appropriate sensitivity and proved to be significant prognostic factor independent from stages. High serum values are associated with shorter survival. However, before S-100B monitoring immunohistochemistry for the detection of S-100B is required. In the case of malignant melanomas with low expression serum S-100B monitoring may not be sensitive enough to follow disease progression. Although the serum concentration of 5-S-cysteinyldopa did not prove to be independent prognostic factor in our previous studies comprising the highest patient number in the literature, the marker was suggested for therapy monitoring. The survival analysis indicated that the elevated 5-S-cysteinyldopa level predicts shorter survival. In spite of the calculated low correlation between the two markers, parallel elevation of S-100B protein and 5-S-cysteinyldopa indicated shorter survival. On the basis of the literature LDH is the most appropriate tumour marker in stage IV to predict prognosis, but its sensitivity and specificity could not achieve that of S-100B protein. S-100B and LDH proved to be similarly reliable in respect to the clinical outcome. Determination of serum concentration of MIA and tyrosinase are also reliable markers in malignant melanoma. The other investigated markers are not well known yet or do not provide useful information to the clinicians. PMID:12704461

  6. Breast cancer statistics and markers.

    PubMed

    Donepudi, Mallika Siva; Kondapalli, Kasturi; Amos, Seelam Jeevan; Venkanteshan, Pavithra

    2014-01-01

    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.

  7. Evaluation of algorithms used to order markers on genetic maps.

    PubMed

    Mollinari, M; Margarido, G R A; Vencovsky, R; Garcia, A A F

    2009-12-01

    When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results.

  8. Excap: maximization of haplotypic diversity of linked markers.

    PubMed

    Kahles, André; Sarqume, Fahad; Savolainen, Peter; Arvestad, Lars

    2013-01-01

    Genetic markers, defined as variable regions of DNA, can be utilized for distinguishing individuals or populations. As long as markers are independent, it is easy to combine the information they provide. For nonrecombinant sequences like mtDNA, choosing the right set of markers for forensic applications can be difficult and requires careful consideration. In particular, one wants to maximize the utility of the markers. Until now, this has mainly been done by hand. We propose an algorithm that finds the most informative subset of a set of markers. The algorithm uses a depth first search combined with a branch-and-bound approach. Since the worst case complexity is exponential, we also propose some data-reduction techniques and a heuristic. We implemented the algorithm and applied it to two forensic caseworks using mitochondrial DNA, which resulted in marker sets with significantly improved haplotypic diversity compared to previous suggestions. Additionally, we evaluated the quality of the estimation with an artificial dataset of mtDNA. The heuristic is shown to provide extensive speedup at little cost in accuracy.

  9. Salivary markers of oxidative stress in oral diseases

    PubMed Central

    Tóthová, L'ubomíra; Kamodyová, Natália; Červenka, Tomáš; Celec, Peter

    2015-01-01

    Saliva is an interesting alternative diagnostic body fluid with several specific advantages over blood. These include non-invasive and easy collection and related possibility to do repeated sampling. One of the obstacles that hinders the wider use of saliva for diagnosis and monitoring of systemic diseases is its composition, which is affected by local oral status. However, this issue makes saliva very interesting for clinical biochemistry of oral diseases. Periodontitis, caries, oral precancerosis, and other local oral pathologies are associated with oxidative stress. Several markers of lipid peroxidation, protein oxidation and DNA damage induced by reactive oxygen species can be measured in saliva. Clinical studies have shown an association with oral pathologies at least for some of the established salivary markers of oxidative stress. This association is currently limited to the population level and none of the widely used markers can be applied for individual diagnostics. Oxidative stress seems to be of local oral origin, but it is currently unclear whether it is caused by an overproduction of reactive oxygen species due to inflammation or by the lack of antioxidants. Interventional studies, both, in experimental animals as well as humans indicate that antioxidant treatment could prevent or slow-down the progress of periodontitis. This makes the potential clinical use of salivary markers of oxidative stress even more attractive. This review summarizes basic information on the most commonly used salivary markers of oxidative damage, antioxidant status, and carbonyl stress and the studies analyzing these markers in patients with caries or periodontitis. PMID:26539412

  10. Biochemical Markers of Myocardial Damage

    PubMed Central

    2016-01-01

    Heart diseases, especially coronary artery diseases (CAD), are the leading causes of morbidity and mortality in developed countries. Effective therapy is available to ensure patient survival and to prevent long term sequelae after an acute ischemic event caused by CAD, but appropriate therapy requires rapid and accurate diagnosis. Research into the pathology of CAD have demonstrated the usefulness of measuring concentrations of chemicals released from the injured cardiac muscle can aid the diagnosis of diseases caused by myocardial ischemia. Since the mid-1950s successively better biochemical markers have been described in research publications and applied for the clinical diagnosis of acute ischemic myocardial injury. Aspartate aminotransferase of the 1950s was replaced by other cytosolic enzymes such as lactate dehydrogenase, creatine kinase and their isoenzymes that exhibited better cardiac specificity. With the availability of immunoassays, other muscle proteins, that had no enzymatic activity, were also added to the diagnostic arsenal but their limited tissue specificity and sensitivity lead to suboptimal diagnostic performance. After the discovery that cardiac troponins I and T have the desired specificity, they have replaced the cytosolic enzymes in the role of diagnosing myocardial ischemia and infarction. The use of the troponins provided new knowledge that led to revision and redefinition of ischemic myocardial injury as well as the introduction of biochemicals for estimation of the probability of future ischemic myocardial events. These markers, known as cardiac risk markers, evolved from the diagnostic markers such as CK-MB or troponins, but markers of inflammation also belong to these groups of diagnostic chemicals. This review article presents a brief summary of the most significant developments in the field of biochemical markers of cardiac injury and summarizes the most recent significant recommendations regarding the use of the cardiac markers in

  11. Biochemical Markers of Myocardial Damage.

    PubMed

    Bodor, Geza S

    2016-04-01

    Heart diseases, especially coronary artery diseases (CAD), are the leading causes of morbidity and mortality in developed countries. Effective therapy is available to ensure patient survival and to prevent long term sequelae after an acute ischemic event caused by CAD, but appropriate therapy requires rapid and accurate diagnosis. Research into the pathology of CAD have demonstrated the usefulness of measuring concentrations of chemicals released from the injured cardiac muscle can aid the diagnosis of diseases caused by myocardial ischemia. Since the mid-1950s successively better biochemical markers have been described in research publications and applied for the clinical diagnosis of acute ischemic myocardial injury. Aspartate aminotransferase of the 1950s was replaced by other cytosolic enzymes such as lactate dehydrogenase, creatine kinase and their isoenzymes that exhibited better cardiac specificity. With the availability of immunoassays, other muscle proteins, that had no enzymatic activity, were also added to the diagnostic arsenal but their limited tissue specificity and sensitivity lead to suboptimal diagnostic performance. After the discovery that cardiac troponins I and T have the desired specificity, they have replaced the cytosolic enzymes in the role of diagnosing myocardial ischemia and infarction. The use of the troponins provided new knowledge that led to revision and redefinition of ischemic myocardial injury as well as the introduction of biochemicals for estimation of the probability of future ischemic myocardial events. These markers, known as cardiac risk markers, evolved from the diagnostic markers such as CK-MB or troponins, but markers of inflammation also belong to these groups of diagnostic chemicals. This review article presents a brief summary of the most significant developments in the field of biochemical markers of cardiac injury and summarizes the most recent significant recommendations regarding the use of the cardiac markers in

  12. Alterations in phenotypic biochemical markers in bladder epithelium during tumorigenesis.

    PubMed

    Rao, J Y; Hemstreet, G P; Hurst, R E; Bonner, R B; Jones, P L; Min, K W; Fradet, Y

    1993-09-01

    Phenotypic biochemical markers of oncogenesis and differentiation were mapped in bladder biopsies to investigate changes that occur in bladder tumorigenesis and to identify markers for increased bladder cancer risk. Touch preparations from biopsy specimens from 30 patients were obtained from tumors, the adjacent bladder epithelium, and random distant bladder epithelium. Markers, including DNA ploidy, epidermal growth factor receptor (EGFR), and oncoproteins, were quantified in individual cells by using quantitative fluorescence image analysis. Cluster analysis revealed the markers fell into three independent groups: (i) G-actin and EGFR; (ii) ploidy, cytology, and p185 (HER-2/neu oncoprotein) (ERBB2); and (iii) p300, a low-grade tumor antigen. Each marker displayed a gradient of abnormality from distant field to adjacent field to tumor. Different patterns for each marker suggested a developmental sequence of bladder cancer oncogenesis; G-actin was altered in 58% of distant biopsies (vs. 0/6 normals, P < 0.001), ploidy and cytology were altered in < 20% of distant fields and approximately 80% of tumors, and the other markers were intermediate. Patterns of EGFR and p185 suggest low-and high-grade tracks diverge early (P < 0.05 by Mann-Whitney U test for EGFR and ANOVA for p185). In conclusion, this study shows that a sequence of phenotypic changes accompanies development and progression of bladder cancers. Biochemical alterations in cells of the bladder field are often detectable before abnormal pathology, and markers previously thought to be limited to tumors were found in the field. The hierarchy of expression may be useful in identifying high-risk patients, assessing completeness of response to therapy, and monitoring and predicting recurrence. PMID:8367495

  13. New sequence-tagged site molecular markers for identification of sex in Distichlis spicata.

    PubMed

    Eppley, Sarah M; O'Quinn, Robin; Brown, Anna L

    2009-09-01

    Sex-linked molecular markers have become valuable tools for understanding sex ratio evolution and sex-specific physiology in pre-reproductive plants. To develop new accurate methods for sexing Distichlis spicata juveniles and nonflowering individuals, we converted a random amplified polymorphic DNA-polymerase chain reaction marker that co-segregated with the female phenotype into a set of sequence-tagged site markers. We tested the marker pair on known males and females from populations in Oregon and California. A single band was obtained for all female samples but never for males.

  14. Development of nuclear and chloroplast microsatellite markers for the endangered conifer Callitris sulcata (Cupressaceae)1

    PubMed Central

    Sakaguchi, Shota; Lannuzel, Guillaume; Fogliani, Bruno; Wulff, Adrien S.; L’Huillier, Laurent; Kurata, Seikan; Ueno, Saneyoshi; Isagi, Yuji; Tsumura, Yoshihiko; Ito, Motomi

    2015-01-01

    Premise of the study: Microsatellite markers were developed for Callitris sulcata (Cupressaceae), an endangered conifer species in New Caledonia. Methods and Results: Using sequencing by synthesis (SBS) of an RNA-Seq library, 15 polymorphic nuclear and chloroplast microsatellite markers were developed. When evaluated with 48 individuals, these markers showed genetic variations ranging from two to 15 alleles and expected heterozygosity ranging from 0 to 0.881. Conclusions: These markers will be useful for examining the genetic diversity and structure of remaining wild populations and improving the genetic status of ex situ populations. PMID:26312198

  15. Marker imputation in barley association studies

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Association mapping requires higher marker density than linkage mapping, potentially leading to more missing marker data and to higher genotyping costs. In human genetics, methods exist to impute missing marker data and whole markers that were typed in a reference panel but not in the experimental d...

  16. Markers of bile duct tumors

    PubMed Central

    Malaguarnera, Giulia; Giordano, Maria; Paladina, Isabella; Rando, Alessandra; Uccello, Mario; Basile, Francesco; Biondi, Antonio; Carnazzo, Santo; Alessandria, Innocenza; Mazzarino, Clorinda

    2011-01-01

    Biliary tract carcinomas are relatively rare, representing less than 1% of cancers. However, their incidence has increased in Japan and in industrialized countries like the USA. Biliary tract tumors have a poor prognosis and a high mortality rate because they are usually detected late in the course of the disease; therapeutic treatment options are often limited and of minimal utility. Recent studies have shown the importance of serum and molecular markers in the diagnosis and follow up of biliary tract tumors. This review aims to introduce the main features of the most important serum and molecular markers of biliary tree tumors. Some considerable tumor markers are cancer antigen 125, carbohydrate antigen 19-9, carcinoembryonic antigen, chromogranin A, mucin 1, mucin 5, alpha-fetoprotein, claudins and cytokeratins. PMID:21528090

  17. Urine markers of interstitial cystitis.

    PubMed

    Erickson, D R

    2001-06-01

    This article describes the current state of the art with regard to urine markers of interstitial cystitis (IC), and describes the areas that need continuing research. Articles referenced in MEDLINE that describe urine alterations in IC were reviewed. Additional articles were identified by cross-referencing. The different marker alterations were tabulated. The relevant articles were discussed, considering different purposes for urine markers including: (1) diagnosing IC; (2) confirming a specific pathophysiology for IC; and (3) predicting or following response to a specific treatment. Currently, 2 markers (glycoprotein-51 and antiproliferative factor [APF]) clearly separate IC and control subjects, with minimal overlap. Markers that correlate with specific bladder biopsy features include 1,4-methylimidazole acetic acid and eosinophil cationic protein (ECP), which correlate with mast cell density, and interleukin (IL)-6, which correlates with mononuclear inflammation. Markers that changed after treatment were as follows: (1) nitric oxide synthase and cyclic guanosine monophosphate increased with oral L-arginine; (2) ECP decreased with subcutaneous heparin; (3) prostaglandin E(2) and kallikrein decreased after bladder distention; (4) neutrophil chemotactic activity decreased after dimethyl sulfoxide; (5) IL-2 inhibitor decreased after oral nifedipine; (6) IL-2, IL-6, and IL-8 decreased after bacille Calmette-Guérin (BCG) vaccine; and (7) APF and heparin-binding epidermal growth factor changed to or toward normal levels after bladder distention or sacral nerve stimulation. A larger number of urine alterations have been reported, and a few are being pursued further by correlating with bladder biopsy findings or treatment responses. Further research is needed.

  18. Uniparental genetic markers in South Amerindians

    PubMed Central

    Bisso-Machado, Rafael; Bortolini, Maria Cátira; Salzano, Francisco Mauro

    2012-01-01

    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. PMID:22888284

  19. Useful Immunohistochemical Markers of Tumor Differentiation

    PubMed Central

    Painter, J. T.; Clayton, N. P.; Herbert, R. A.

    2011-01-01

    Immunohistochemistry (IHC) has been somewhat underutilized in the practice of toxicological pathology but can be a valuable tool for the evaluation of rodent neoplasms, both in a diagnostic and an investigational role. Determining an exact tumor type using standard hematoxylin and eosin (H&E) staining of formalin-fixed tissues can be challenging, especially with metastatic and/or poorly differentiated tumors. Successful IHC is dependent on many factors, including species and tissue type, type and duration of fixation, quality fresh or frozen sectioning, and antibody specificity. The initial approach of most tumor diagnosis IHC applications is distinguishing epithelial from mesenchymal differentiation using vimentin and cytokeratin markers, although false-negative and/or false-positive results may occur. Experimentally, IHC can be employed to investigate the earliest changes in transformed tissues, identifying cellular changes not normally visible with H&E. Individual markers for proliferation, apoptosis, and specific tumor proteins can be used to help distinguish hyperplasia from neoplasia and determine specific tumor origin/type. IHC provides a relatively rapid and simple method to better determine the origin of neoplastic tissue or investigate the behavior or progression of a given neoplasm. Several experimental and diagnostic examples will be presented to illustrate the utility of IHC as a supplement to standard staining techniques. PMID:20028992

  20. Uniparental genetic markers in South Amerindians.

    PubMed

    Bisso-Machado, Rafael; Bortolini, Maria Cátira; Salzano, Francisco Mauro

    2012-04-01

    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. PMID:22888284

  1. Marker-trait association analysis of functional gene markers for provitamin A levels across diverse tropical yellow maize inbred lines

    PubMed Central

    2013-01-01

    Background Biofortification of staple crops is a cost effective and sustainable approach that can help combat vitamin A and other micronutrient deficiencies in developing countries. PCR -based DNA markers distinguishing alleles of three key genes of maize endosperm carotenoid biosynthesis (PSY1, lcyE and crtRB1) have been developed to facilitate maize provitamin A biofortification via marker assisted selection. Previous studies of these functional DNA markers revealed inconsistent effects. The germplasm previously employed for discovering and validating these functional markers was mainly of temperate origin containing low frequencies of the favourable allele of the most significant polymorphism, crtRB1-5′TE. Here, we investigate the vitamin A biofortification potential of these DNA markers in a germplasm panel of diverse tropical yellow maize inbred lines, with mixed genetic backgrounds of temperate and tropical germplasm to identify the most effective diagnostic markers for vitamin A biofortification. Results The functional DNA markers crtRB1-5′TE and crtRB1-3′TE were consistently and strongly associated with provitamin A content across the tropical maize inbred lines tested. The alleles detected by these two functional markers were in high linkage disequilibrium (R2 = 0.75) and occurred in relatively high frequency (18%). Genotypes combining the favourable alleles at the two loci (N = 20) displayed a 3.22 fold average increase in β-carotene content compared to those genotypes lacking the favourable alleles (N = 106). The PSY1 markers were monomorphic across all of the inbred lines. The functional DNA markers for lcyE were associated with lutein, and with the ratio of carotenoids in the alpha and beta branches, but not with provitamin A levels. However, the combined effects of the two genes were stronger than their individual effects on all carotenoids. Conclusions Tropical maize inbred lines harbouring the favourable alleles of the crtRB1-5

  2. Expert judgment on markers to deter inadvertent human intrusion into the Waste Isolation Pilot Plant

    SciTech Connect

    Trauth, K.M.; Hora, S.C.; Guzowski, R.V.

    1993-11-01

    The expert panel identified basic principles to guide current and future marker development efforts: (1) the site must be marked, (2) message(s) must be truthful and informative, (3) multiple components within a marker system, (4) multiple means of communication (e.g., language, pictographs, scientific diagrams), (5) multiple levels of complexity within individual messages on individual marker system elements, (6) use of materials with little recycle value, and (7) international effort to maintain knowledge of the locations and contents of nuclear waste repositories. The efficacy of the markers in deterring inadvertent human intrusion was estimated to decrease with time, with the probability function varying with the mode of intrusion (who is intruding and for what purpose) and the level of technological development of the society. The development of a permanent, passive marker system capable of surviving and remaining interpretable for 10,000 years will require further study prior to implementation.

  3. An update of biochemical markers of hepatocellular carcinoma

    PubMed Central

    AlSalloom, Abdulaziz Ajlan M.

    2016-01-01

    The definition of a tumor marker is broad, which covers a wide spectrum of biomacromolecules synthesized in excess concentration by a wide variety of neoplastic cells. Tumor markers can be normal endogenous products that are produced at a greater rate in cancer cells or the products of newly switched on genes that remained inactive in the normal cells. These markers consist of any products of either tumor itself or the host in reaction to tumor’s presence that distinguishes malignant tissues from benign and is measurable in body fluids or tissues. They increase with progressive or recurrent disease, decrease with response to treatment, and normalize with remission. Clinical applications include screening in asymptomatic individuals, confirming a suspected diagnosis, assisting in tumor classification and staging, prognosis, monitoring treatment response, surveillance for residual disease, and early detection of recurrent disease. PMID:27004063

  4. Characterization of new microsatellite markers of Siganus fuscescens (Siganidae).

    PubMed

    Li, Q H; Li, Z B; Dai, G; Chen, X J; Chen, L N; Cao, Y Y; Shangguan, J B; Ning, Y F

    2013-07-30

    Siganus fuscescens, which is a small commercially important marine fish, is wildly distributed in shallow waters throughout the tropical and subtropical Indo-Pacific and Eastern Mediterranean regions. It is part of a group known as rabbitfish. Fifteen new polymorphic microsatellite markers for S. fuscescens were identified, and 32 wild individuals were used to evaluate the degree of polymorphism of these markers. The number of alleles per locus ranged from 2 to 12, and the polymorphism information content ranged from 0.210 to 0.849. The observed and expected heterozygosities were 0.142-0.808 and 0.225-0.853, respectively. Although significant deviations from Hardy-Weinberg equilibrium were detected at 2 loci (Sf1-37-2 and Sf1-47), no significant deviations were detected at the other 13 loci. These microsatellite markers will provide a useful tool for studies on genetic diversity and differentiation of S. fuscescens.

  5. Isolation of nuclear microsatellite markers for Cyperus fuscus (Cyperaceae)1

    PubMed Central

    Böckelmann, Jörg; Wieser, David; Tremetsberger, Karin; Šumberová, Kateřina; Bernhardt, Karl-Georg

    2015-01-01

    Premise of the study: Microsatellite markers were characterized in the extremely specialized ephemeral wetland plant species Cyperus fuscus (Cyperaceae). The markers will be used for studying population genetics in natural vs. anthropogenic habitats, on a European scale, and the role of the soil seed bank in the life cycle of this ephemeral species. Methods and Results: Twenty-one microsatellite loci were established and scored in two populations, with mean number of alleles of 2.6 and 2.9 and mean expected heterozygosity of 0.405 and 0.470, respectively. Forty-four additional loci with the number of alleles ranging from one to four (mean = 2.1) were successfully amplified in seven individuals. Conclusions: The novel microsatellite markers will be useful for studying the genetic structure of populations of this ephemeral plant as well as their seed bank. PMID:26649269

  6. [CA 125--a tumor marker?].

    PubMed

    Pabst, T; Ludwig, C

    1995-06-17

    Tumor markers are useful tools in monitoring malignancies postoperatively or under hormone-/chemotherapy. In contrast, they usually lack diagnostic relevance and uncritical use may result in confusing situations. We describe three cases of diagnostic determinations of the tumor marker CA 125 resulting in subsequent partially invasive procedures. Based on these three cases, serum CA 125 levels were examined in 49 patients with abdominal diseases. We found CA 125 to be less a tumor product than an unspecific expression of stimulated mesothelial cells of the peritoneum. CA 125 was a marker for ascites (16 of 16 patients) and an indicator of infra-diaphragmatic involvement in non-Hodgkin's lymphoma (11 of 12 patients). Furthermore, 5 of 6 patients with inflammatory abdominal diseases showed elevated CA 125 levels, as did 13 of 15 patients with solid abdominal tumors of different histology (all non-ovarian cancer, no ascites). In conclusion, CA 125 remains a good marker for follow-up of ovarian cancer, but should not be used for diagnosis of abdominal processes.

  7. Neuroinflammation in treated HIV-positive individuals

    PubMed Central

    Guo, Qi; Cole, James H.; Boasso, Adriano; Greathead, Louise; Kelleher, Peter; Rabiner, Eugenii A; Kalk, Nicola; Bishop, Courtney; Gunn, Roger N.; Matthews, Paul M.; Winston, Alan

    2016-01-01

    Objective: To explore the effects of microglial activation on brain function and structure, and its relationship with peripheral inflammatory markers, in treated, HIV-positive individuals, using in vivo [11C]PBR28 PET (to measure the 18 kDa translocator protein [TSPO]). Methods: Cognitively healthy HIV-positive individuals on suppressive antiretroviral therapy and HIV-negative individuals (controls) underwent brain [11C]PBR28 PET and MRI. HIV-positive patients completed neuropsychological testing and CSF testing for chemokines. The concentration of bacterial ribosomal 16sDNA in plasma was measured as a marker of microbial translocation. Results: HIV-positive individuals showed global increases in TSPO expression compared to controls (corrected p < 0.01), with significant regional increases in the parietal (p = 0.001) and occipital (p = 0.046) lobes and in the globus pallidus (p = 0.035). TSPO binding in the hippocampus, amygdala, and thalamus were associated with poorer global cognitive performance in tasks assessing verbal and visual memory (p < 0.05). Increased TSPO binding was associated with increased brain white matter diffusion MRI mean diffusivity in HIV-positive individuals, a lower CD4/CD8 ratio, and both high pretreatment HIV RNA and plasma concentration ribosomal 16s DNA (p < 0.05). Conclusions: Cognitively healthy HIV-positive individuals show evidence for a chronically activated brain innate immune response and elevated blood markers of microbial translocation despite effective control of plasma viremia. Increased brain inflammation is associated with poorer cognitive performance and white matter microstructural pathology, suggesting a possible role in cognitive impairments found in some HIV-positive patients despite effective treatment. PMID:26911637

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

    PubMed Central

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

    2015-01-01

    Coffea canephora exhibit poor root system and are very sensitive to drought stress that affects growth and production. Deeper root system has been largely empirical as better avoidance to soil water limitation in drought condition. The present study aimed to identify molecular markers linked to high root types in Coffea canephora using molecular markers. Contrasting parents, L1 valley with low root and S.3334 with high root type, were crossed, and 134 F1 individuals were phenotyped for root and associated physiological traits (29 traits) and genotyped with 41 of the 320 RAPD and 9 of the 55 SSR polymorphic primers. Single marker analysis was deployed for detecting the association of markers linked to root associated traits by SAS software. There were 13 putative RAPD markers associated with root traits such as root length, secondary roots, root dry weight, and root to shoot ratio, in which root length associated marker OPS1850 showed high phenotypic variance of 6.86%. Two microsatellite markers linked to root length (CPCM13400) and root to shoot ratio (CM211300). Besides, 25 markers were associated with more than one trait and few of the markers were associated with positively related physiological traits and can be used in marker assisted trait selection. PMID:25821599

  9. Cranial muscle markers: a preliminary examination of size, sex, and age effects.

    PubMed

    Weiss, Elizabeth

    2010-02-01

    Most muscle marker research consists of post-cranial analyses, but some researchers examine crania to reconstruct activities. Regardless of bones examined, anthropologists know of some of the complexities surrounding muscle marker development. Here, posterior cranial muscle markers are analyzed to determine whether they are useful in reconstructing activities by examining effects that may hinder reconstructions. Additionally, upper limb muscle markers and humeral cross-sectional robusticity variables are correlated with cranial muscle markers to determine if robust individuals are generally robust due to the synergistic effects of muscle use. Cranial muscle markers of 65 prehistoric California Amerinds are scored using a five-point observer rating scale. Body mass is calculated from femoral head size; maximum cranial length and breadth are measured with a spreading caliper; and age and sex are determined through standard procedures. Upper limb muscle markers are scored on seven sites using two dimensions within a seven-point scale. Cross-sectional properties are calculated from biplanar humeral radiographs. Aggregates are created for cranial muscle markers, upper limb muscle markers, and cross-sectional robusticity. Cranial muscle markers correlate significantly with cranial length, r=0.25 and cross-sectional robusticity of humerus, r=0.29; P's<0.05. All variables differed between sexes (Mann-Whitney=31.00-307.50, P's<0.01). Results imply that some differences in cranial muscle markers are related to size; however, individuals with well-developed cranial muscle markers have greater upper limb robusticity possibly due to activity patterns. Sex differences remained after size controls and may relate to activity differences.

  10. Pancreatic cancer stem cell markers and exosomes - the incentive push.

    PubMed

    Heiler, Sarah; Wang, Zhe; Zöller, Margot

    2016-07-14

    Pancreatic cancer (PaCa) has the highest death rate and incidence is increasing. Poor prognosis is due to late diagnosis and early metastatic spread, which is ascribed to a minor population of so called cancer stem cells (CSC) within the mass of the primary tumor. CSC are defined by biological features, which they share with adult stem cells like longevity, rare cell division, the capacity for self renewal, differentiation, drug resistance and the requirement for a niche. CSC can also be identified by sets of markers, which for pancreatic CSC (Pa-CSC) include CD44v6, c-Met, Tspan8, alpha6beta4, CXCR4, CD133, EpCAM and claudin7. The functional relevance of CSC markers is still disputed. We hypothesize that Pa-CSC markers play a decisive role in tumor progression. This is fostered by the location in glycolipid-enriched membrane domains, which function as signaling platform and support connectivity of the individual Pa-CSC markers. Outside-in signaling supports apoptosis resistance, stem cell gene expression and tumor suppressor gene repression as well as miRNA transcription and silencing. Pa-CSC markers also contribute to motility and invasiveness. By ligand binding host cells are triggered towards creating a milieu supporting Pa-CSC maintenance. Furthermore, CSC markers contribute to the generation, loading and delivery of exosomes, whereby CSC gain the capacity for a cell-cell contact independent crosstalk with the host and neighboring non-CSC. This allows Pa-CSC exosomes (TEX) to reprogram neighboring non-CSC towards epithelial mesenchymal transition and to stimulate host cells towards preparing a niche for metastasizing tumor cells. Finally, TEX communicate with the matrix to support tumor cell motility, invasion and homing. We will discuss the possibility that CSC markers are the initial trigger for these processes and what is the special contribution of CSC-TEX. PMID:27468191

  11. Pancreatic cancer stem cell markers and exosomes - the incentive push

    PubMed Central

    Heiler, Sarah; Wang, Zhe; Zöller, Margot

    2016-01-01

    Pancreatic cancer (PaCa) has the highest death rate and incidence is increasing. Poor prognosis is due to late diagnosis and early metastatic spread, which is ascribed to a minor population of so called cancer stem cells (CSC) within the mass of the primary tumor. CSC are defined by biological features, which they share with adult stem cells like longevity, rare cell division, the capacity for self renewal, differentiation, drug resistance and the requirement for a niche. CSC can also be identified by sets of markers, which for pancreatic CSC (Pa-CSC) include CD44v6, c-Met, Tspan8, alpha6beta4, CXCR4, CD133, EpCAM and claudin7. The functional relevance of CSC markers is still disputed. We hypothesize that Pa-CSC markers play a decisive role in tumor progression. This is fostered by the location in glycolipid-enriched membrane domains, which function as signaling platform and support connectivity of the individual Pa-CSC markers. Outside-in signaling supports apoptosis resistance, stem cell gene expression and tumor suppressor gene repression as well as miRNA transcription and silencing. Pa-CSC markers also contribute to motility and invasiveness. By ligand binding host cells are triggered towards creating a milieu supporting Pa-CSC maintenance. Furthermore, CSC markers contribute to the generation, loading and delivery of exosomes, whereby CSC gain the capacity for a cell-cell contact independent crosstalk with the host and neighboring non-CSC. This allows Pa-CSC exosomes (TEX) to reprogram neighboring non-CSC towards epithelial mesenchymal transition and to stimulate host cells towards preparing a niche for metastasizing tumor cells. Finally, TEX communicate with the matrix to support tumor cell motility, invasion and homing. We will discuss the possibility that CSC markers are the initial trigger for these processes and what is the special contribution of CSC-TEX. PMID:27468191

  12. Integrating objective gene-brain-behavior markers of psychiatric disorders.

    PubMed

    Gordon, Evian; Liddell, Belinda J; Brown, Kerri J; Bryant, Richard; Clark, C Richard; DAS, Pritha; Dobson-Stone, Carol; Falconer, Erin; Felmingham, Kim; Flynn, Gary; Gatt, Justine M; Harris, Anthony; Hermens, Daniel F; Hopkinson, Patrick J; Kemp, Andrew H; Kuan, Stacey A; Lazzaro, Illario; Moyle, Jonson; Paul, Robert H; Rennie, Chris J; Schofield, Peter; Whitford, Thomas; Williams, Leanne M

    2007-03-01

    There is little consensus about which objective markers should be used to assess major psychiatric disorders, and predict/evaluate treatment response for these disorders. Clinical practice relies instead on subjective signs and symptoms, such that there is a "translational gap" between research findings and clinical practice. This gap arises from: a) a lack of integrative theoretical models which provide a basis for understanding links between gene-brain-behavior mechanisms and clinical entities; b) the reliance on studying one measure at a time so that linkages between markers are their specificity are not established; and c) the lack of a definitive understanding of what constitutes normative function. Here, we draw on a standardized methodology for acquiring multiple sources of genomic, brain and behavioral data in the same subjects, to propose candidate markers of selected psychiatric disorders: depression, post-traumatic stress disorder, schizophrenia, attention-deficit/hyperactivity disorder and dementia disorders. This methodology has been used to establish a standardized international database which provides a comprehensive framework and the basis for testing hypotheses derived from an integrative theoretical model of the brain. Using this normative base, we present preliminary findings for a number of disorders in relation to the proposed markers. Establishing these objective markers will be the first step towards determining their sensitivity, specificity and treatment prediction in individual patients.

  13. [New biological and radiological markers in amyotrophic lateral sclerosis].

    PubMed

    Pradat, Pierre-François

    2009-12-01

    The only specific marker of sporadic amyotrophic lateral sclerosis (ALS), that represent about 90% of all cases, is neuropathological and based on the demonstration of motoneuronal degeneration associated with typical inclusions positive for ubiquitine and TDP-43. The gene encoding the superoxide dismutase 1 (SOD1) is implicated in about 10-20% of familial ALS. A mutation in the SOD1 gene can be considered as a genetic marker of ALS, and not a polymorphism, if the mutation has been shown to be pathogenic or to segregate to the disease in familial cases. Studies in blood or cerebral spinal fluid have shown biological changes involving different physiopathological pathways (oxidative stress, inflammation, excitotoxicity...). These abnormalities are neither sensitive nor specific enough to provide a diagnostic tool. The ectopic expression of Nogo-A in muscle biopsy is a promising marker but further studies are needed to demonstrate its value as a diagnostic tool in ALS. Studies in series of ALS patients have shown that MR-spectroscopy and diffusion tensor imaging can detect cortico-spinal degeneration. However, because of an overlap between patients and normal subjects, spectroscopic and DTI-parameters cannot be used as diagnostic tool in individual patients. In the future, a combination of biological, radiological and electrophysiological markers, rather than a single marker, may provide diagnostic tool for the diagnosis and follow-up of ALS patients.

  14. SSR markers: a tool for species identification in Psidium (Myrtaceae).

    PubMed

    Tuler, A C; Carrijo, T T; Nóia, L R; Ferreira, A; Peixoto, A L; da Silva Ferreira, M F

    2015-11-01

    Molecular DNA markers are used for detection of polymorphisms in individuals. As they are independent of developmental stage of the plant and environmental influences, they can be useful tools in taxonomy. The alleles of simple sequence repeat (SSR) markers (or microsatellites) are traditionally used to identify taxonomic units. This application demands the laborious and costly delimitation of exclusive alleles in order to avoid homoplasy. Here, we propose a method for identification of species based on the amplification profile of groups of SSR markers obtained by a transferability study. The approach considers that the SSR are conserved among related species. In this context, using Psidium as a model, 141 SSR markers developed for Psidium guajava were transferred to 13 indigenous species of Psidium from the Atlantic Rainforest. Transferability of the markers was high and 28 SSR were conserved in all species. Four SSR groups were defined and they can help in the identification of all 13 Psidium species studied. A group of 31 SSR was genotyped, with one to six alleles each. The H0 varied from 0.0 to 0.46, and PIC from 0.0 to 0.74. Cluster analysis revealed shared alleles among species. The high percentage of SSR transferability found in Psidium evidences the narrow phylogenetic relationship existing among these species since transferability occurs by the preservation of the microsatellites and anchoring regions. The proposed method was useful for distinguishing the species of Psidium, being useful in taxonomic studies.

  15. SSR markers: a tool for species identification in Psidium (Myrtaceae).

    PubMed

    Tuler, A C; Carrijo, T T; Nóia, L R; Ferreira, A; Peixoto, A L; da Silva Ferreira, M F

    2015-11-01

    Molecular DNA markers are used for detection of polymorphisms in individuals. As they are independent of developmental stage of the plant and environmental influences, they can be useful tools in taxonomy. The alleles of simple sequence repeat (SSR) markers (or microsatellites) are traditionally used to identify taxonomic units. This application demands the laborious and costly delimitation of exclusive alleles in order to avoid homoplasy. Here, we propose a method for identification of species based on the amplification profile of groups of SSR markers obtained by a transferability study. The approach considers that the SSR are conserved among related species. In this context, using Psidium as a model, 141 SSR markers developed for Psidium guajava were transferred to 13 indigenous species of Psidium from the Atlantic Rainforest. Transferability of the markers was high and 28 SSR were conserved in all species. Four SSR groups were defined and they can help in the identification of all 13 Psidium species studied. A group of 31 SSR was genotyped, with one to six alleles each. The H0 varied from 0.0 to 0.46, and PIC from 0.0 to 0.74. Cluster analysis revealed shared alleles among species. The high percentage of SSR transferability found in Psidium evidences the narrow phylogenetic relationship existing among these species since transferability occurs by the preservation of the microsatellites and anchoring regions. The proposed method was useful for distinguishing the species of Psidium, being useful in taxonomic studies. PMID:26476530

  16. [Biochemical markers for acute and chronic alcohol consumption].

    PubMed

    Geppert, Bogna; Tezyk, Artur; Zaba, Czesław

    2012-01-01

    In spite of the fact, that ethyl alcohol is a legal and socially accepted recreational drug its abuse may cause numerous problems for the individual and society. Casualties of car accidents caused by drunk drivers, aggressive behavior, family problems and effective less work are the main problems connected with alcohol abuse. The easiest and most effective way of proving recent alcohol consumption is confirming its presence in biological samples taken from the individual. However, the main disadvantage of this method is a short window detection for ethanol, because of its high speed of elimination process. Nowadays, in order to prevent and have a better control of alcohol abuse, markers that could provide a better view of short and long term ethanol consumption are in frequent use. Ethyl alcohol present in the body cause many qualitative and quantitative disturbances in biochemical metabolites that could be used as markers of its consumption. In practice markers of ethanol consumption are usually divided into acute (tests confirm single alcohol intake) and chronic (confirm long term alcohol consumption or lack of teetotalism). Markers of ethanol consumption are valuable alternative and complementation to customary examinations performed in medical practice and forensic medicine.

  17. Demonstrating Cost-Effective Marker Assisted Selection for Biomass Yield in Red Clover (Trifolium pratense L.) – Part 1: Paternity Testing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many methods have been proposed to incorporate molecular markers into breeding programs. Presented is a cost effective marker assisted selection (MAS) methodology that utilizes individual plant phenotypes, seed production-based knowledge of maternity, and molecular marker-determined paternity. Proge...

  18. Validation of candidate gene markers for marker-assisted selection of potato cultivars with improved tuber quality.

    PubMed

    Li, Li; Tacke, Eckhard; Hofferbert, Hans-Reinhardt; Lübeck, Jens; Strahwald, Josef; Draffehn, Astrid M; Walkemeier, Birgit; Gebhardt, Christiane

    2013-04-01

    Tuber yield, starch content, starch yield and chip color are complex traits that are important for industrial uses and food processing of potato. Chip color depends on the quantity of reducing sugars glucose and fructose in the tubers, which are generated by starch degradation. Reducing sugars accumulate when tubers are stored at low temperatures. Early and efficient selection of cultivars with superior yield, starch yield and chip color is hampered by the fact that reliable phenotypic selection requires multiple year and location trials. Application of DNA-based markers early in the breeding cycle, which are diagnostic for superior alleles of genes that control natural variation of tuber quality, will reduce the number of clones to be evaluated in field trials. Association mapping using genes functional in carbohydrate metabolism as markers has discovered alleles of invertases and starch phosphorylases that are associated with tuber quality traits. Here, we report on new DNA variants at loci encoding ADP-glucose pyrophosphorylase and the invertase Pain-1, which are associated with positive or negative effect with chip color, tuber starch content and starch yield. Marker-assisted selection (MAS) and marker validation were performed in tetraploid breeding populations, using various combinations of 11 allele-specific markers associated with tuber quality traits. To facilitate MAS, user-friendly PCR assays were developed for specific candidate gene alleles. In a multi-parental population of advanced breeding clones, genotypes were selected for having different combinations of five positive and the corresponding negative marker alleles. Genotypes combining five positive marker alleles performed on average better than genotypes with four negative alleles and one positive allele. When tested individually, seven of eight markers showed an effect on at least one quality trait. The direction of effect was as expected. Combinations of two to three marker alleles were

  19. Predictive testing for Huntington's disease with linked DNA markers.

    PubMed

    Brock, D J; Mennie, M; Curtis, A; Millan, F A; Barron, L; Raeburn, J A; Dinwoodie, D; Holloway, S; Crosbie, A; Wright, A

    1989-08-26

    Availability of new DNA markers, more tightly linked to the Huntington's disease (HD) locus than the original G8 (D4S10) probes, has improved predictive accuracy for both presymptomatic and prenatal exclusion testing. 50 predictive tests were carried out on high-risk individuals. 6 of these were on first-trimester chorionic villus biopsy specimens; in 2 cases the HD gene was not transmitted to the fetus while in 4 cases no exclusion could be made. The remaining 44 tests were on adults with either 25 or 50% risk of manifesting the disease; 19 had a greatly increased risk and 25 a substantially decreased risk of HD. Family structures in Scotland are suitable for testing about 75% of potentially affected individuals, and the new generation of DNA markers makes virtually all families fully informative.

  20. Biochemical markers of acute pancreatitis.

    PubMed

    Matull, W R; Pereira, S P; O'Donohue, J W

    2006-04-01

    Serum amylase remains the most commonly used biochemical marker for the diagnosis of acute pancreatitis, but its sensitivity can be reduced by late presentation, hypertriglyceridaemia, and chronic alcoholism. Urinary trypsinogen-2 is convenient, of comparable diagnostic accuracy, and provides greater (99%) negative predictive value. Early prediction of the severity of acute pancreatitis can be made by well validated scoring systems at 48 hours, but the novel serum markers procalcitonin and interleukin 6 allow earlier prediction (12 to 24 hours after admission). Serum alanine transaminase >150 IU/l and jaundice suggest a gallstone aetiology, requiring endoscopic retrograde cholangiopancreatography. For obscure aetiologies, serum calcium and triglycerides should be measured. Genetic polymorphisms may play an important role in "idiopathic" acute recurrent pancreatitis.

  1. Allelic association between marker loci.

    PubMed

    Lonjou, C; Collins, A; Morton, N E

    1999-02-16

    Allelic association has proven useful to refine the location of major genes prior to positional cloning, but it is of uncertain value for genome scans in complex inheritance. We have extended kinship theory to give information content for linkage and allelic association. Application to pairs of closely linked markers as a surrogate for marker x oligogene pairs indicates that association is largely determined by regional founders, with little effect of subsequent demography. Sub-Saharan Africa has the least allelic association, consistent with settlement of other regions by small numbers of founders. Recent speculation about substantial advantages of isolates over large populations, of constant size over expansion, and of F1 hybrids over incrosses is not supported by theory or data. On the contrary, fewer affected cases, less opportunity for replication, and more stochastic variation tend to make isolates less informative for allelic association, as they are for linkage.

  2. Lessons from mouse chimaera experiments with a reiterated transgene marker: revised marker criteria and a review of chimaera markers.

    PubMed

    Keighren, Margaret A; Flockhart, Jean; Hodson, Benjamin A; Shen, Guan-Yi; Birtley, James R; Notarnicola-Harwood, Antonio; West, John D

    2015-08-01

    Recent reports of a new generation of ubiquitous transgenic chimaera markers prompted us to consider the criteria used to evaluate new chimaera markers and develop more objective assessment methods. To investigate this experimentally we used several series of fetal and adult chimaeras, carrying an older, multi-copy transgenic marker. We used two additional independent markers and objective, quantitative criteria for cell selection and cell mixing to investigate quantitative and spatial aspects of developmental neutrality. We also suggest how the quantitative analysis we used could be simplified for future use with other markers. As a result, we recommend a five-step procedure for investigators to evaluate new chimaera markers based partly on criteria proposed previously but with a greater emphasis on examining the developmental neutrality of prospective new markers. These five steps comprise (1) review of published information, (2) evaluation of marker detection, (3) genetic crosses to check for effects on viability and growth, (4) comparisons of chimaeras with and without the marker and (5) analysis of chimaeras with both cell populations labelled. Finally, we review a number of different chimaera markers and evaluate them using the extended set of criteria. These comparisons indicate that, although the new generation of ubiquitous fluorescent markers are the best of those currently available and fulfil most of the criteria required of a chimaera marker, further work is required to determine whether they are developmentally neutral.

  3. Cutaneous Markers of Internal Disease

    PubMed Central

    Forsey, R. R.; Reardon, P. Michael

    1982-01-01

    Cutaneous markers of internal disease are legion. This article discusses the pigmentary disorders, acanthosis nigricans, pruritus, the xanthomas and problems of photosensitivity, outlining the appropriate procedures to establish a definite diagnosis, and in some cases the management of such patients. ImagesFig. 1Fig. 2Fig. 3Fig. 4Fig. 5Fig. 6Fig. 7Fig. 8Fig. 9Fig. 10Fig. 11 PMID:21286147

  4. Serotonin, neural markers, and memory

    PubMed Central

    Meneses, Alfredo

    2015-01-01

    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. PMID:26257650

  5. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this... the following: (1) Markers must be located at each public road crossing, at each railroad...

  6. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this... the following: (1) Markers must be located at each public road crossing, at each railroad...

  7. Molecular Marker Systems for Oenothera Genetics

    PubMed Central

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

    2008-01-01

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

  8. Identifying marker typing incompatibilities in linkage analysis

    SciTech Connect

    Stringham, H.M.; Boehnke, M.

    1996-10-01

    A common problem encountered in linkage analyses is that execution of the computer program is halted because of genotypes in the data that are inconsistent with Mendelian inheritance. Such inconsistencies may arise because of pedigree errors or errors in typing. In some cases, the source of the inconsistencies is easily identified by examining the pedigree. In others, the error is not obvious, and substantial time and effort are required to identify the responsible genotypes. We have developed two methods for automatically identifying those individuals whose genotypes are most likely the cause of the inconsistencies. First, we calculate the posterior probability of genotyping error for each member of the pedigree, given the marker data on all pedigree members and allowing anyone in the pedigree to have an error. Second, we identify those individuals whose genotypes could be solely responsible for the inconsistency in the pedigree. We illustrate these methods with two examples: one a pedigree error, the second a genotyping error. These methods have been implemented as a module of the pedigree analysis program package MENDEL. 9 refs., 2 figs., 2 tabs.

  9. Circulating serum markers and QRS scar score in Chagas cardiomyopathy.

    PubMed

    Clark, Eva H; Marks, Morgan A; Gilman, Robert H; Fernandez, Antonio B; Crawford, Thomas C; Samuels, Aaron M; Hidron, Alicia I; Galdos-Cardenas, Gerson; Menacho-Mendez, Gilberto Silvio; Bozo-Gutierrez, Ricardo W; Martin, Diana L; Bern, Caryn

    2015-01-01

    Approximately 8 million people have Trypanosoma cruzi infection, and nearly 30% will manifest Chagas cardiomyopathy (CC). Identification of reliable early indicators of CC risk would enable prioritization of treatment to those with the highest probability of future disease. Serum markers and electrocardiogram (EKG) changes were measured in 68 T. cruzi-infected individuals in various stages of cardiac disease and 17 individuals without T. cruzi infection or cardiac disease. T. cruzi-infected individuals were assigned to stage A (normal EKG/chest x-ray [CXR]), B (abnormal EKG/normal CXR), or C (abnormal EKG/cardiac structural changes). Ten serum markers were measured using enzyme-linked immunosorbent assay (ELISA)/Luminex, and QRS scores were calculated. Higher concentrations of transforming growth factor-β1 (TGFβ1), and TGFβ2 were associated with stage B compared with stage A. Matrix Metalloproteinase 2 (MMP2), Tissue Inhibitors of MMP 1, QRS score, and Brain Natriuretic Protein rose progressively with increasing CC severity. Elevated levels of several markers of cardiac damage and inflammation are seen in early CC and warrant additional evaluation in longitudinal studies.

  10. Circulating Serum Markers and QRS Scar Score in Chagas Cardiomyopathy

    PubMed Central

    Clark, Eva H.; Marks, Morgan A.; Gilman, Robert H.; Fernandez, Antonio B.; Crawford, Thomas C.; Samuels, Aaron M.; Hidron, Alicia I.; Galdos-Cardenas, Gerson; Menacho-Mendez, Gilberto Silvio; Bozo-Gutierrez, Ricardo W.; Martin, Diana L.; Bern, Caryn

    2015-01-01

    Approximately 8 million people have Trypanosoma cruzi infection, and nearly 30% will manifest Chagas cardiomyopathy (CC). Identification of reliable early indicators of CC risk would enable prioritization of treatment to those with the highest probability of future disease. Serum markers and electrocardiogram (EKG) changes were measured in 68 T. cruzi-infected individuals in various stages of cardiac disease and 17 individuals without T. cruzi infection or cardiac disease. T. cruzi-infected individuals were assigned to stage A (normal EKG/chest x-ray [CXR]), B (abnormal EKG/normal CXR), or C (abnormal EKG/cardiac structural changes). Ten serum markers were measured using enzyme-linked immunosorbent assay (ELISA)/Luminex, and QRS scores were calculated. Higher concentrations of transforming growth factor-β1 (TGFβ1), and TGFβ2 were associated with stage B compared with stage A. Matrix Metalloproteinase 2 (MMP2), Tissue Inhibitors of MMP 1, QRS score, and Brain Natriuretic Protein rose progressively with increasing CC severity. Elevated levels of several markers of cardiac damage and inflammation are seen in early CC and warrant additional evaluation in longitudinal studies. PMID:25385865

  11. Quality Control of Genotypes Using Heritability Estimates of Gene Content at the Marker

    PubMed Central

    Forneris, Natalia S.; Legarra, Andres; Vitezica, Zulma G.; Tsuruta, Shogo; Aguilar, Ignacio; Misztal, Ignacy; Cantet, Rodolfo J. C.

    2015-01-01

    Quality control filtering of single-nucleotide polymorphisms (SNPs) is a key step when analyzing genomic data. Here we present a practical method to identify low-quality SNPs, meaning markers whose genotypes are wrongly assigned for a large proportion of individuals, by estimating the heritability of gene content at each marker, where gene content is the number of copies of a particular reference allele in a genotype of an animal (0, 1, or 2). If there is no mutation at the marker, gene content has an additive heritability of 1 by construction. The method uses restricted maximum likelihood (REML) to estimate heritability of gene content at each SNP and also builds a likelihood-ratio test statistic to test for zero error variance in genotyping. As a by-product, estimates of the allele frequencies of markers at the base population are obtained. Using simulated data with 10% permutation error (4% actual error) in genotyping, the method had a specificity of 0.96 (4% of correct markers are rejected) and a sensitivity of 0.99 (1% of wrong markers are accepted) if markers with heritability lower than 0.975 are discarded. Checking of Mendelian errors resulted in a lower sensitivity (0.84) for the same simulation. The proposed method is further illustrated with a real data set with genotypes from 3534 animals genotyped for 50,433 markers from the Illumina PorcineSNP60 chip and a pedigree of 6473 individuals; those markers underwent very little quality control. A total of 4099 markers with P-values lower than 0.01 were discarded based on our method, with associated estimates of heritability as low as 0.12. Contrary to other techniques, our method uses all information in the population simultaneously, can be used in any population with markers and pedigree recordings, and is simple to implement using standard software for REML estimation. Scripts for its use are provided. PMID:25567991

  12. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 49 Transportation 3 2011-10-01 2011-10-01 false Line markers. 195.410 Section 195.410... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this section, each operator shall place and maintain line markers over each buried pipeline in accordance...

  13. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 49 Transportation 3 2012-10-01 2012-10-01 false Line markers. 195.410 Section 195.410... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this section, each operator shall place and maintain line markers over each buried pipeline in accordance...

  14. Judging Quality through Substantive Conversations between Markers

    ERIC Educational Resources Information Center

    Grainger, Peter; Purnell, Ken; Zipf, Reyna

    2008-01-01

    Decisions by markers about quality in student work remain confusing to most students and markers. This may in part be due to the relatively subjective nature of what constitutes a quality response to an assessment task. This paper reports on an experiment that documented the process of decision-making by multiple markers at a university who…

  15. 49 CFR 195.410 - Line markers.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 49 Transportation 3 2014-10-01 2014-10-01 false Line markers. 195.410 Section 195.410... PIPELINE Operation and Maintenance § 195.410 Line markers. (a) Except as provided in paragraph (b) of this section, each operator shall place and maintain line markers over each buried pipeline in accordance...

  16. Mixtures with relatives and linked markers.

    PubMed

    Dørum, Guro; Kling, Daniel; Tillmar, Andreas; Vigeland, Magnus Dehli; Egeland, Thore

    2016-05-01

    Mixture DNA profiles commonly appear in forensic genetics, and a large number of statistical methods and software are available for such cases. However, most of the literature concerns mixtures where the contributors are assumed unrelated and the genetic markers are unlinked. In this paper, we consider mixtures of linked markers and related contributors. If no relationships are involved, linkage can be ignored. While unlinked markers can be treated independently, linkage introduces dependencies. The use of linked markers presents statistical and computational challenges, but may also lead to a considerable increase in power since the number of markers available is much larger if we do not require the markers to be unlinked. In addition, some cases that cannot be solved with an unlimited number of unlinked autosomal markers can be solved with linked markers. We focus on two special cases of linked markers: pairs of linked autosomal markers and X-chromosomal markers. A framework is presented for calculation of likelihood ratios for mixtures with general relationships and with linkage between any number of markers. Finally, we explore the effect of linkage disequilibrium, also called allelic association, on the likelihood ratio.

  17. Rethinking evolutionary individuality

    PubMed Central

    Ereshefsky, Marc; Pedroso, Makmiller

    2015-01-01

    This paper considers whether multispecies biofilms are evolutionary individuals. Numerous multispecies biofilms have characteristics associated with individuality, such as internal integrity, division of labor, coordination among parts, and heritable adaptive traits. However, such multispecies biofilms often fail standard reproductive criteria for individuality: they lack reproductive bottlenecks, are comprised of multiple species, do not form unified reproductive lineages, and fail to have a significant division of reproductive labor among their parts. If such biofilms are good candidates for evolutionary individuals, then evolutionary individuality is achieved through other means than frequently cited reproductive processes. The case of multispecies biofilms suggests that standard reproductive requirements placed on individuality should be reconsidered. More generally, the case of multispecies biofilms indicates that accounts of individuality that focus on single-species eukaryotes are too restrictive and that a pluralistic and open-ended account of evolutionary individuality is needed. PMID:26039982

  18. Explicating Individual Training Decisions

    ERIC Educational Resources Information Center

    Walter, Marcel; Mueller, Normann

    2015-01-01

    In this paper, we explicate individual training decisions. For this purpose, we propose a framework based on instrumentality theory, a psychological theory of motivation that has frequently been applied to individual occupational behavior. To test this framework, we employ novel German individual data and estimate the effect of subjective expected…

  19. The neurobiology of individuality

    NASA Astrophysics Data System (ADS)

    de Bivort, Benjamin

    2015-03-01

    Individuals often display conspicuously different patterns of behavior, even when they are very closely related genetically. These differences give rise to our sense of individuality, but what is their molecular and neurobiological basis? Individuals that are nominally genetically identical differ at various molecular and neurobiological levels: cell-to-cell variation in somatic genomes, cell-to-cell variation in expression patterns, individual-to-individual variation in neuronal morphology and physiology, and individual-to-individual variation in patterns of brain activity. It is unknown which of these levels is fundamentally causal of behavioral differences. To investigate this problem, we use the fruit fly Drosophila melanogaster, whose genetic toolkit allows the manipulation of each of these mechanistic levels, and whose rapid lifecycle and small size allows for high-throughput automation of behavioral assays. This latter point is crucial; identifying inter-individual behavioral differences requires high sample sizes both within and across individual animals. Automated behavioral characterization is at the heart of our research strategy. In every behavior examined, individual flies have individual behavioral preferences, and we have begun to identify both neural genes and circuits that control the degree of behavioral variability between individuals.

  20. Models for Individualized Instruction.

    ERIC Educational Resources Information Center

    Georgiades, William, Ed.; Clark, Donald C., Ed.

    This book, consisting of five parts, provides a collection of source materials that will assist in implementing individualized instruction; provides examples of interrelated systems for individualizing instruction; and describes the components of individualized instructional systems, including flexible use of time, differentiated staffing, new…

  1. [Neuropathologic markers in degenerative dementias].

    PubMed

    Hauw, J J; Seilhean, D; Colle, M A; Hogenhuys, J; Duyckaerts, C

    1998-01-01

    The number of neuropathological markers used for the diagnosis of degenerative dementias is rapidly increasing, and this is somewhat confusing: some lesions described a long time ago, such as ballooned cells, proved to be less specific than they were supposed to be; this is also the case for Lewy bodies, that have been recognised in a larger spectrum of disorders than thought a few years ago. On the contrary, for an increasing number of neuropathologists, Pick bodies are now mandatory for the diagnosis of Pick disease, and this contrasts with the prevalent opinions of the late sixties or seventies. There are a number of reasons for the changing significance of neuropathological markers. Three of them can be easily identified: 1) the burst of immunohistochemistry into neuropathology allowed an easier recognition, a better delineation and new pathophysiological approaches to old lesions, and a dramatic increase in the description of new markers, especially in glial cells; 2) in some conditions characterized by the number and distribution of some lesions rather than by their mere presence, such as aging and Alzheimer disease, a better neuroanatomical point of view permitted new insights into the concept of disease versus age-related changes; 3) more accurate clinicopathologic correlations showed clearly the need of grouping or lumping together some entities: for example, obvious relationship aroused between progressive supranuclear palsy and corticobasal degeneration; in contrast, distinguishing different disorders in the frontal lobe dementias grouped together into "Pick disease" was felt necessary. This review summarizes the main criteria for identification, and the presumed meaning of the chief markers indicating the presence of abnormally phosphorylated tau proteins, A beta peptides, and PrP proteins. Abnormally phosphorylated tau proteins can be stored in the neurons, and participate in the constitution of many lesions (neurofibrillary tangles, neuropil threads

  2. [Immunological markers of rheumatoid arthritis].

    PubMed

    Matuszewska, Agnieszka; Madej, Marta; Wiland, Piotr

    2016-03-25

    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.

  3. Genic Microsatellite Markers in Brassica rapa: Development, Characterization, Mapping, and Their Utility in Other Cultivated and Wild Brassica Relatives

    PubMed Central

    Ramchiary, Nirala; Nguyen, Van Dan; Li, Xiaonan; Hong, Chang Pyo; Dhandapani, Vignesh; Choi, Su Ryun; Yu, Ge; Piao, Zhong Yun; Lim, Yong Pyo

    2011-01-01

    Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species. PMID:21768136

  4. Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives.

    PubMed

    Ramchiary, Nirala; Nguyen, Van Dan; Li, Xiaonan; Hong, Chang Pyo; Dhandapani, Vignesh; Choi, Su Ryun; Yu, Ge; Piao, Zhong Yun; Lim, Yong Pyo

    2011-10-01

    Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species.

  5. A novel set of single-copy nuclear DNA markers for the genetic study of Salicaceae.

    PubMed

    Du, S H; Wang, Z S; Zhang, J G

    2014-07-04

    Species of Populus are widely distributed worldwide, playing a significant role in both ecology and economy. However, the lack of single-copy nuclear markers limits knowledge about the phylogeny and population genetics of this genus. In the present study, primer pairs of 15 single-copy nuclear markers were developed through bioinformatic methods based on complete genomic sequences of Populus trichocarpa and Salix arbutifolia. Twenty individuals of Populus davidiana Dode and Salix matsudana Koidz were used to evaluate the basic application of these markers with respect to marker length and diversity indices, respectively. The utility of single-copy nuclear markers is anticipated to facilitate further studies about the phylogeny, population genetics, and phylogeography of this genus, in addition to providing information about the evolutionary dynamics of Salicaceae.

  6. Genetic markers as instrumental variables

    PubMed Central

    von Hinke, Stephanie; Davey Smith, George; Lawlor, Debbie A.; Propper, Carol; Windmeijer, Frank

    2016-01-01

    The use of genetic markers as instrumental variables (IV) is receiving increasing attention from economists, statisticians, epidemiologists and social scientists. Although IV is commonly used in economics, the appropriate conditions for the use of genetic variants as instruments have not been well defined. The increasing availability of biomedical data, however, makes understanding of these conditions crucial to the successful use of genotypes as instruments. We combine the econometric IV literature with that from genetic epidemiology, and discuss the biological conditions and IV assumptions within the statistical potential outcomes framework. We review this in the context of two illustrative applications. PMID:26614692

  7. One hundred fifty-four genetic markers for the turkey (Meleagris gallopavo).

    PubMed

    Knutson, Todd P; Chaves, Lee D; Hall, Majken K; Reed, Kent M

    2004-12-01

    Identifying and selectively breeding for improved traits is one of the ultimate goals of genetic research in agriculturally important species. Genome characterization and analysis are important first steps in this process. Genetic linkage maps based on the linear order of polymorphic DNA markers are typically developed through statistical analysis of inheritance patterns in pedigreed families. To develop microsatellite markers for further improvement of the turkey genetic linkage map, small-insert genomic libraries were screened for tandem repeats. Oligonuclotide primers were designed to amplify 164 microsatellite-containing fragments from genomic DNA. Genetic polymorphisms at 154 markers were determined by genotyping the F(1) individuals of two resource populations. Markers determined as segregating in the University of Minnesota/Nicholas Turkey Breeding Farms (UMN/NTBF) reference population were used to genotype F(2) individuals and a two-point linkage analysis was performed.

  8. Increased homozygosity at four microsatellite marker loci in Pima Indian DNA

    SciTech Connect

    Sell, S.M.; Knowler, W.C.; Bogardus, C.

    1994-09-01

    Using 100 Marshfield-derived (MFD) microsatellite markers (screening set v.2) and DNA from 13 Pima Indians, none of whom were first degree relatives, we observed 4 marker loci on 3 different chromosomes which showed marked deviation from the reported heterozygosities for the Caucasian CEPH families. These 4 markers were also tested in 60 individuals from 8 different multigenerational pedigrees. For the marker MFD77, only a single allele was observed for all individuals tested. Our results indicate that a high degree of genetic homogeneity occurs in limited regions of the genome in the Pima Indian population. We are investigating the possibility that these regions of homogeneity might be associated with disease susceptibility in this population with a high prevalence of obesity, gallstones and diabetes mellitus.

  9. Analysis of chromosome 22 markers in nine schizophrenia pedigrees

    SciTech Connect

    Coon, H.; Holik, J.; Reimherr, F.

    1994-03-15

    Previous results of a genome-wide survey for schizophrenia susceptibility genes in nine multiplex families indicated a possible region of linkage on chromosome 22. We therefore tested for linkage using ten highly polymorphic chromosome 22 DNA markers. Lod score analyses were suggestive of linkage for several markers on the distal end of the chromosome; however, no lod score exceeded 3 assuming either autosomal dominant or autosomal recessive transmission. The highest lod score was 2.09 (theta = 0.10) for marker D22S276 assuming autosomal recessive inheritance. Based on simulation analyses, this result is unlikely to represent a false positive. Analyses using information from affected individuals only resulted in reduced lod scores, with a maximum of 1.40 (theta = 0.05) for D22S276 assuming autosomal recessive inheritance. Two nonparametric methods, sib pair analysis and the Affected-Pedigree-Member method, also yielded suggestive but inconclusive findings; results were positive, but strict thresholds of significance were not met. Additionally, we tested one candidate gene, the Arylsulfatase A gene, located in the region of 22q13.31-qter. Results were again inconclusive, though the DNA marker available for this gene was a 2-allele RFLP with heterozygosity of 0.5, and therefore not maximally informative. Further investigation of this chromosomal region and this and other candidate genes may be warranted. 37 refs., 2 figs., 5 tabs.

  10. Short communication: Imputation of markers on the bovine X chromosome.

    PubMed

    Mao, Xiaowei; Johansson, Anna Maria; Sahana, Goutam; Guldbrandtsen, Bernt; De Koning, Dirk-Jan

    2016-09-01

    Imputation is a cost-effective approach to augment marker data for genomic selection and genome-wide association studies. However, most imputation studies have focused on autosomes. Here, we assessed the imputation of markers on the X chromosome in Holstein cattle for nongenotyped animals and animals genotyped with low-density (Illumina BovineLD, Illumina Inc., San Diego, CA) chips, using animals genotyped with medium-density (Illumina BovineSNP50) chips. A total of 26,884 genotyped Holstein individuals genotyped with medium-density chips were used in this study. Imputation was carried out using FImpute V2.2. The following parameters were examined: treating the pseudoautosomal region as autosomal or as X specific, different sizes of reference groups, different male/female proportions in the reference group, and cumulated degree of relationship between the reference group and target group. The imputation accuracy of markers on the X chromosome was improved if the pseudoautosomal region was treated as autosomal. Increasing the proportion of females in the reference group improved the imputation accuracy for the X chromosome. Imputation for nongenotyped animals in general had lower accuracy compared with animals genotyped with the low-density single nucleotide polymorphism array. In addition, higher cumulative pedigree relationships between the reference group and the target animal led to higher imputation accuracy. In the future, better marker coverage of the X chromosome should be developed to facilitate genomic studies involving the X chromosome.

  11. Ventricular repolarization markers for predicting malignant arrhythmias in clinical practice

    PubMed Central

    Castro-Torres, Yaniel; Carmona-Puerta, Raimundo; Katholi, Richard E

    2015-01-01

    Malignant cardiac arrhythmias which result in sudden cardiac death may be present in individuals apparently healthy or be associated with other medical conditions. The way to predict their appearance represents a challenge for the medical community due to the tragic outcomes in most cases. In the last two decades some ventricular repolarization (VR) markers have been found to be useful to predict malignant cardiac arrhythmias in several clinical conditions. The corrected QT, QT dispersion, Tpeak-Tend, Tpeak-Tend dispersion and Tp-e/QT have been studied and implemented in clinical practice for this purpose. These markers are obtained from 12 lead surface electrocardiogram. In this review we discuss how these markers have demonstrated to be effective to predict malignant arrhythmias in medical conditions such as long and short QT syndromes, Brugada syndrome, early repolarization syndrome, acute myocardial ischemia, heart failure, hypertension, diabetes mellitus, obesity and highly trained athletes. Also the main pathophysiological mechanisms that explain the arrhythmogenic predisposition in these diseases and the basis for the VR markers are discussed. However, the same results have not been found in all conditions. Further studies are needed to reach a global consensus in order to incorporate these VR parameters in risk stratification of these patients. PMID:26301231

  12. Isolation of polymorphic microsatellite markers for the tetraploid Dipteryx odorata, an intensely exploited Amazonian tree species.

    PubMed

    Vinson, C C; Ribeiro, D O; Harris, S A; Sampaio, I; Ciampi, A Y

    2009-11-01

    Dipteryx odorata is an intensely exploited Amazonian tree legume. Microsatellite markers were developed to study the genetic structure, gene flow and reproductive biology of D. odorata. Eight highly polymorphic microsatellite markers were isolated from enriched repeat libraries screened for microsatellite repeats. An average of 16 alleles and 0.964 phenotype diversity per locus were found in 76 individuals from the Tapajos National Forest, in the state of Pará in the Brazilian Amazon.

  13. Characterization of 10 microsatellite markers for the understorey Amazonian herb Heliconia acuminata.

    PubMed

    Côrtes, M C; Gowda, V; Kress, W J; Bruna, E M; Uriarte, M

    2009-07-01

    We characterized 10 microsatellite loci for the plant Heliconia acuminata from the Biological Dynamics of Forest Fragments Project (Manaus, Brazil). Markers were screened in 61 individuals from one population and were found to be polymorphic with an average of eight alleles per locus. We found moderate to high levels of polymorphic information content, and observed and expected heterozygosities. All 10 markers are suitable for spatial genetic structure and parentage analyses and will be used for understanding H. acuminata dynamics across a fragmented landscape.

  14. Isolation and characterization of polymorphic microsatellite markers from the velvet tree, Miconia calvescens DC. (Melastomataceae).

    PubMed

    LE Roux, Johannes J; Wieczorek, Ania M

    2008-09-01

    Nine polymorphic microsatellite loci were isolated and characterized from the invasive velvet tree (Miconia calvescens DC.), a serious forest invader in tropical Pacific oceanic islands. These loci provided markers with polymorphism of three to 10 alleles per locus within 95 individuals. The expected and observed heterozygosities ranged from 0.0367 to 0.5053 and from 0.0370 to 0.2473, respectively. These markers should be useful to study dispersal and the invasion genetics of the velvet tree. PMID:21585941

  15. PERMANENT GENETIC RESOURCES: Development of polymorphic microsatellite markers in Acer mono Maxim.

    PubMed

    Kikuchi, S; Shibata, M

    2008-03-01

    Thirteen polymorphic microsatellite markers were developed for Acer mono Maxim., one of the major components of deciduous forests in Japan. An average of 13.8 alleles were found, with expected heterozygosity ranging from 0.140 to 0.945 in 34 A. mono individuals from the Ogawa Forest Reserve in Ibaraki Prefecture, Japan. This set of microsatellite markers can be used to analyse mating patterns and gene flow in A. mono populations.

  16. Qualitative and Quantitative Requirements for Assessing Prognostic Markers in Prostate Cancer

    PubMed Central

    Burdelski, Christoph; Matuszewska, Aleksandra; Kluth, Martina; Koop, Christina; Grupp, Katharina; Steurer, Stefan; Wittmer, Corinna; Minner, Sarah; Tsourlakis, Maria Christina; Sauter, Guido; Schlomm, Thorsten; Simon, Ronald

    2014-01-01

    Molecular prognostic markers are urgently needed in order to improve therapy decisions in prostate cancer. To better understand the requirements for biomarker studies, we re-analyzed prostate cancer tissue microarray immunohistochemistry (IHC) data from 39 prognosis markers in subsets of 50 – >10,000 tumors. We found a strong association between the “prognostic power” of individual markers and the number of tissues that should be minimally included in such studies. The prognostic relevance of more than 90% of the 39 IHC markers could be detected if ≥6400 tissue samples were analyzed. Studying markers of tissue quality, including immunohistochemistry of ets-related gene (ERG) and vimentin, and fluorescence in-situ hybridization analysis of human epidermal growth factor receptor 2 (HER2), we found that 18% of tissues in our tissue microarray (TMA) showed signs of reduced tissue preservation and limited immunoreactivity. Comparing the results of Kaplan-Meier survival analyses or associations to ERG immunohistochemistry in subsets of tumors with and without exclusion of these defective tissues did not reveal statistically relevant differences. In summary, our study demonstrates that TMA-based marker validation studies using biochemical recurrence as an endpoint require at least 6400 individual tissue samples for establishing statistically relevant associations between the expression of molecular markers and patient outcome if weak to moderate prognosticators should also be reliably identified.

  17. Systematic Review of Anthocyanins and Markers of Cardiovascular Disease

    PubMed Central

    Wallace, Taylor C.; Slavin, Margaret; Frankenfeld, Cara L.

    2016-01-01

    Anthocyanins are dietary flavonoids commonly consumed in the diet, which have been suggested to have a preventative effect on cardiovascular disease (CVD) development among epidemiological studies. We systematically reviewed randomized controlled trials (RCTs) testing the effects of purified anthocyanins and anthocyanin-rich extracts on markers of CVD (triglycerides, total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and blood pressure) in both healthy and diseased populations. Eligible studies included RCTs of adults published in English. We searched PubMed, Web of Science Core Collection, and BIOSIS Previews for relevant articles from inception until 1 July 2014. Twelve RCTs representing 10 studies were included in this review. Supplementation with anthocyanins significantly improved LDL cholesterol among diseased individuals or those with elevated biomarkers. Supplementation did not significantly affect other markers of CVD in either healthy individuals or those with elevated markers. No adverse effects of anthocyanins were reported across studies at levels up to 640 mg/day. Limitations of trials in the qualitative analyses include short trial duration and large variability in the dose administered within the trials. Longer-duration trials assessing dose response are needed to adequately determine whether an effect of supplementation exists. PMID:26761031

  18. Systematic Review of Anthocyanins and Markers of Cardiovascular Disease.

    PubMed

    Wallace, Taylor C; Slavin, Margaret; Frankenfeld, Cara L

    2016-01-01

    Anthocyanins are dietary flavonoids commonly consumed in the diet, which have been suggested to have a preventative effect on cardiovascular disease (CVD) development among epidemiological studies. We systematically reviewed randomized controlled trials (RCTs) testing the effects of purified anthocyanins and anthocyanin-rich extracts on markers of CVD (triglycerides, total cholesterol, low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and blood pressure) in both healthy and diseased populations. Eligible studies included RCTs of adults published in English. We searched PubMed, Web of Science Core Collection, and BIOSIS Previews for relevant articles from inception until 1 July 2014. Twelve RCTs representing 10 studies were included in this review. Supplementation with anthocyanins significantly improved LDL cholesterol among diseased individuals or those with elevated biomarkers. Supplementation did not significantly affect other markers of CVD in either healthy individuals or those with elevated markers. No adverse effects of anthocyanins were reported across studies at levels up to 640 mg/day. Limitations of trials in the qualitative analyses include short trial duration and large variability in the dose administered within the trials. Longer-duration trials assessing dose response are needed to adequately determine whether an effect of supplementation exists. PMID:26761031

  19. A Somatic Marker Perspective of Immoral and Corrupt Behavior

    PubMed Central

    Sobhani, Mona; Bechara, Antoine

    2012-01-01

    Individuals who engage in corrupt and immoral behavior are in some ways similar to psychopaths. Normal people refrain from engaging in such behaviors because they tie together the moral value of society and the risk for punishment when they violate social rules. What is it, then, that allows these immoral individuals to behave in this manner, and in some situations to even prosper? When there is a dysfunction of somatic markers, specific disadvantageous impairments in decision-making arise, for example in moral judgment, but paradoxically, under some circumstances, the damage can cause the patient to make optimal financial investment decisions. Interestingly, individuals with psychopathy, a personality disorder, share many of these same behavioral characteristics as those seen in VMPFC and amygdala lesion patients, suggesting that defective somatic markers may serve as a neural framework for explaining immoral and corrupt behaviors. While these sociopathic behaviors of sometimes famous and powerful individuals have long been discussed primarily within the realm of social science and psychology, here we offer a neurocognitive perspective on possible neural roots for immoral and corrupt behaviors. PMID:21919563

  20. Development of a SCAR marker for the analysis of B chromosome presence in Partamona helleri (Hymenoptera, Apidae).

    PubMed

    Tosta, V C; Tavares, M G; Fernandes-Salomão, T M; Barros, E G; Campos, L A O; Camacho, J P M

    2007-01-01

    Chromosomes in hymenopteran insects cannot currently be analysed in adult individuals. The only available cytogenetic techniques need to be performed in larvae. Here we develop and implement a SCAR (Sequence Characterized Amplified Region) marker, associated with B chromosomes in the bee Partamona helleri, which has proven to be very useful to reveal B chromosome presence in adults from natural populations. The marker was tested in ten different colonies simultaneously analysed by both molecular (ten adults per colony) and cytogenetic (20 larvae per colony) techniques. The presence of the SCAR marker always showed the same pattern as B chromosome presence: both were present or absent in all individuals from a same colony, or both were present in only part of the individuals from a same colony. This molecular marker is thus a useful tool for analysing new aspects of this B chromosome system such as B frequency and geographical distribution, B transmission, or B effects in adult individuals.

  1. Comparison of the effects of maximal dose atorvastatin and rosuvastatin therapy on cholesterol synthesis and absorption markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We measured plasma markers of cholesterol synthesis (lathosterol) and absorption (campesterol, sitosterol, and cholestanol) in order to compare the effects of maximal doses of rosuvastatin with atorvastatin and investigate the basis for the significant individual variation in lipid lowering response...

  2. Agriculture increases individual fitness.

    PubMed

    Kovaka, Karen; Santana, Carlos; Patel, Raj; Akçay, Erol; Weisberg, Michael

    2016-01-01

    We question the need to explain the onset of agriculture by appealing to the second type of multilevel selection (MLS2). Unlike eusocial insect colonies, human societies do not exhibit key features of evolutionary individuals. If we avoid the mistake of equating Darwinian fitness with health and quality of life, the adoption of agriculture is almost certainly explicable in terms of individual-level selection and individual rationality. PMID:27561384

  3. Biochemical markers of bone metabolism in growing thoroughbreds: a longitudinal study.

    PubMed

    Price, J S; Jackson, B F; Gray, J A; Harris, P A; Wright, I M; Pfeiffer, D U; Robins, S P; Eastell, R; Ricketts, S W

    2001-08-01

    This study describes longitudinal changes in serum levels of biochemical markers of bone cell activity in a group of 24 thoroughbred foals from birth to 18 months of age. The markers of bone formation included the type I collagen carboxy-terminal propeptide (PICP), the bone-specific isoenzyme of alkaline phosphatase (BAP), and osteocalcin (OC). Levels of the cross-linked telopeptide of type I collagen (ICTP), a marker of bone resorption, and the N-terminal propeptide of type III collagen (PNIIIP), a marker of soft tissue turnover, were also measured. Levels of all markers fell significantly between birth and 18 months of age (70-80 per cent); this decrease being most marked between 0 and 6 months. However, a transient increase in levels of the markers then occurred between 6 and 14 months of age. The timing of this increase was specific for each parameter. ICTP and OC concentrations increased between October and December. PICP concentrations increased between December and April whereas the increase in PIIINP was coincident with the peak in weight gain between April and June. Changes in BAP concentration were less distinct at this time. Season was shown to have significant effects on the biochemical markers independent from the effect of age. Concentrations of all markers decreased with increasing body weight and at any given age heavier horses had lower marker levels. These results show that biochemical markers of bone cell activity and soft tissue turnover follow characteristic patterns of change in growing thoroughbreds influenced by age, season and bodyweight. The demonstration that the reference ranges for the biochemical markers change from month to month means that single samples from individuals are of little value for monitoring bone cell activity in growing thoroughbreds.

  4. Isolation and characterization of new highly polymorphic DNA markers from the Huntington disease region

    SciTech Connect

    Weber, B.; Hedrick, A.; Andrew, S.; Riess, O.; Collins, C.; Kowbel, D.; Hayden, M.R. )

    1992-02-01

    The defect causing Huntington disease (HD) has been mapped to 4p16.3, distal to the DNA marker D4S10. Subsequently, additional polymorphic markers closer to the HD gene have been isolated, which has led to the establishment of predictive testing programs for individuals at risk for HD. Approximately 17% of persons presenting to the Canadian collaborative study for predictive testing for HD have not received any modification of risk, in part because of limited informativeness of currently available DNA markers. Therefore, more highly polymorphic DNA markers are needed, which well further increase the accuracy and availability of predictive testing, specifically for families with complex or incomplete pedigree structures. In addition, new markers are urgently needed in order to refine the breakpoints in the few known recombinant HD chromosomes, which could allow a more accurate localization of the HD gene within 4p16.3 and, therefore, accelerate the cloning of the disease gene. In this study, the authors present the identification and characterization of nine new polymorphic DNA markers, including three markers which detect highly informative multiallelic VNTR-like polymorphisms with PIC values of up to .84. These markers have been isolated from a cloned region of DNA which has been previously mapped approximately 1,000 kb from the 4p telomere.

  5. 75 FR 59620 - Natchez Fireworks Safety Zone; Lower Mississippi River, Mile Marker 365.5 to Mile Marker 363...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-28

    ..., Mile Marker 365.5 to Mile Marker 363, Natchez, MS AGENCY: Coast Guard, DHS. ACTION: Temporary final...; Lower Mississippi River, Mile Marker 365.5 to Mile Marker 363, Natchez, MS (a) Location. The...

  6. Consistent-handed individuals are more authoritarian.

    PubMed

    Lyle, Keith B; Grillo, Michael C

    2014-01-01

    Individuals differ in the consistency with which they use one hand over the other to perform everyday activities. Some individuals are very consistent, habitually using a single hand to perform most tasks. Others are relatively inconsistent, and hence make greater use of both hands. More- versus less-consistent individuals have been shown to differ in numerous aspects of personality and cognition. In several respects consistent-handed individuals resemble authoritarian individuals. For example, both consistent-handedness and authoritarianism have been linked to cognitive inflexibility. Therefore we hypothesised that consistent-handedness is an external marker for authoritarianism. Confirming our hypothesis, we found that consistent-handers scored higher than inconsistent-handers on a measure of submission to authority, were more likely to identify with a conservative political party (Republican), and expressed less-positive attitudes towards out-groups. We propose that authoritarianism may be influenced by the degree of interaction between the left and right brain hemispheres, which has been found to differ between consistent- and inconsistent-handed individuals. PMID:23586369

  7. Eryptosis as a marker of Parkinson's disease

    PubMed Central

    Pretorius, Etheresia; Swanepoel, Albe C; Buys, Antoinette V; Vermeulen, Natasha; Duim, Wiebren; Kell, Douglas B

    2014-01-01

    A major trend in recent Parkinson's disease (PD) research is the investigation of biological markers that could help in identifying at-risk individuals or to track disease progression and response to therapies. Central to this is the knowledge that inflammation is a known hallmark of PD and of many other degenerative diseases. In the current work, we focus on inflammatory signalling in PD, using a systems approach that allows us to look at the disease in a more holistic way. We discuss cyclooxygenases, prostaglandins, thromboxanes and also iron in PD. These particular signalling molecules are involved in PD pathophysiology, but are also very important in an aberrant coagulation/hematology system. We present and discuss a hypothesis regarding the possible interaction of these aberrant signalling molecules implicated in PD, and suggest that these molecules may affect the erythrocytes of PD patients. This would be observable as changes in the morphology of the RBCs and of PD patients relative to healthy controls. We then show that the RBCs of PD patients are indeed rather dramatically deranged in their morphology, exhibiting eryptosis (a kind of programmed cell death). This morphological indicator may have useful diagnostic and prognostic significance. PMID:25411230

  8. Development of novel chloroplast microsatellite markers for Ginkgo biloba.

    PubMed

    Xu, M; Xu, L A; Cao, F L; Zhang, H J; Yu, F X

    2015-07-13

    Ginkgo biloba is considered to be a living fossil that can be used to understand the ancient evolutionary history of gymnosperms, but little attention has been given to the study of its population genetics, molecular phylogeography, and genetic resources assessment. Chloroplast simple sequence repeat (cpSSR) markers are powerful tools for genetic studies of plants. In this study, a total of 30 perfect cpSSRs of Ginkgo were identified and characterized, including di-, tri, tetra-, penta-, and hexanucleotide repeats. Fifteen of 21 designed primer pairs were successfully amplified to yield specific polymerase chain reaction products from 16 Ginkgo cultivars. Polymorphic cpSSRs were further applied to determine the genetic variation of 116 individuals in 5 populations of G. biloba. The results showed that 24 and 76% genetic variation existed within and among populations of this species, respectively. These polymorphic and monomorphic cpSSR markers can be used to trace the origin and evolutionary history of Ginkgo.

  9. Nineteen polymorphic microsatellite markers developed for Trachinotus ovatus.

    PubMed

    Xie, Z Z; Huang, M W; Xu, W; Peng, C; He, J N; Meng, Z N; Zhang, Y; Li, S S; Lin, H R

    2014-12-12

    To evaluate the population genetic diversity of the ovate pompano, we isolated and characterized 19 microsatellite markers using a (CA)13-enriched genomic library. Polymorphism was assessed in 30 individuals from a single population collected from the Daya Bay Aquaculture Center, Guangdong, China. The number of alleles per locus ranged from 2 to 18 with an average of 7.8. The observed and expected heterozygosities varied from 0.2667 to 1.000 and from 0.3960 to 0.9435, respectively. Sixteen of 19 loci conformed to Hardy-Weinberg equilibrium, and no significant linkage disequilibrium was detected between any locus pairs. Our study supplies candidate microsatellite markers that can be useful for studying the population genetic structure of ovate pompano.

  10. Can volatile organic compounds be markers of sea salt?

    PubMed

    Silva, Isabel; Coimbra, Manuel A; Barros, António S; Marriott, Philip J; Rocha, Sílvia M

    2015-02-15

    Sea salt is a handmade food product that is obtained by evaporation of seawater in saltpans. During the crystallisation process, organic compounds from surroundings can be incorporated into sea salt crystals. The aim of this study is to search for potential volatile markers of sea salt. Thus, sea salts from seven north-east Atlantic Ocean locations (France, Portugal, Continental Spain, Canary Islands, and Cape Verde) were analysed by headspace solid-phase microextraction combined with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry. A total of 165 compounds were detected, ranging from 32 to 71 compounds per salt. The volatile composition revealed the variability and individuality of each salt, and a set of ten compounds were detected in all samples. From these, seven are carotenoid-derived compounds that can be associated with the typical natural surroundings of ocean hypersaline environment. These ten compounds are proposed as potential volatile markers of sea salt. PMID:25236204

  11. Can volatile organic compounds be markers of sea salt?

    PubMed

    Silva, Isabel; Coimbra, Manuel A; Barros, António S; Marriott, Philip J; Rocha, Sílvia M

    2015-02-15

    Sea salt is a handmade food product that is obtained by evaporation of seawater in saltpans. During the crystallisation process, organic compounds from surroundings can be incorporated into sea salt crystals. The aim of this study is to search for potential volatile markers of sea salt. Thus, sea salts from seven north-east Atlantic Ocean locations (France, Portugal, Continental Spain, Canary Islands, and Cape Verde) were analysed by headspace solid-phase microextraction combined with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry. A total of 165 compounds were detected, ranging from 32 to 71 compounds per salt. The volatile composition revealed the variability and individuality of each salt, and a set of ten compounds were detected in all samples. From these, seven are carotenoid-derived compounds that can be associated with the typical natural surroundings of ocean hypersaline environment. These ten compounds are proposed as potential volatile markers of sea salt.

  12. Mentoring Emotionally Sensitive Individuals.

    ERIC Educational Resources Information Center

    Shaughnessy, Michael F.; Self, Elizabeth

    Mentoring individuals who are gifted, talented, and creative, but somewhat emotionally sensitive is a challenging and provocative arena. Several reasons individuals experience heightened sensitivity include: lack of nurturing, abuse, alcoholism in the family, low self-esteem, unrealistic parental expectations, and parental pressure to achieve.…

  13. Problems of Individualization.

    ERIC Educational Resources Information Center

    Anderson, Clarence

    Due in part to the open enrollment policy in junior colleges, there is a great diversity in student reading ability that dictates a need to individualize reading instruction. Individualization, defined as personalized instruction, may be accomplished through helping the student to read course materials, helping him to read special materials, or…

  14. Elements of Individualized Instruction.

    ERIC Educational Resources Information Center

    Svara, Ronald

    Although many schools claim to make use of individualized instruction, no common definition of this term has been agreed on. The author reviewed definitions of "individualized instruction" in five studies and then surveyed 30 community and junior colleges who claimed to be using this method of instruction to learn what their programs consisted of.…

  15. Individualizing the Mainstream Classroom.

    ERIC Educational Resources Information Center

    Munroe, Mary Jeanne

    The Education for All Handicapped Children Act requires an individualized education plan for all students identified as handicapped. While computer technology has application for greater individualization, no single method makes a perfect "fit" for all students. Social survival skills are vital elements of mainstreaming as well as academics.…

  16. Technology and Individual Differences.

    ERIC Educational Resources Information Center

    Cavalier, Albert R.; And Others

    1994-01-01

    Six papers on special education technology and individual differences are introduced. The papers illustrate the growing influence of constructivist perspectives on the use of technology to accommodate individual differences among people. The papers recognize the importance of using technology to scaffold the client's construction of different…

  17. Transcending Cognitive Individualism

    ERIC Educational Resources Information Center

    Zerubavel, Eviatar; Smith, Eliot R.

    2010-01-01

    Advancing knowledge in many areas of psychology and neuroscience, underlined by dazzling images of brain scans, appear to many professionals and to the public to show that people are on the way to explaining cognition purely in terms of processes within the individual's head. Yet while such cognitive individualism still dominates the popular…

  18. Classroom Demonstrations: Individual Differences.

    ERIC Educational Resources Information Center

    Singer, Sandra M.

    These demonstrations stress individual differences, a concept becoming increasingly important in psychological research. Intended for use in undergraduate psychology courses, four demonstrations that illustrate common examples of human variation are described. The demonstrations deal with the following individual differences: taste blindness,…

  19. [Breast cancer. Individualized therapy concepts].

    PubMed

    Harbeck, N; Wuerstlein, R

    2013-02-01

    Personalized medicine in the sense of individualized therapy concepts plays an important role in breast cancer. In early breast cancer the molecular subtypes luminal A and B and basal-like are important for planning adjuvant systemic therapy. Prognostic and predictive markers, such as hormone receptor status, HER2, Ki-67, uPA/PAI-1 or multiple gene tests, such as Oncotype DX® currently allow avoidance of an over therapy or under therapy. In early and also advanced breast cancer there are an increasing number of new targeted therapies which represent an augmentation of standard endocrine and chemotherapy and in the future could at least partially replace them. As a whole the therapy regimens for breast cancer have become more complex due to the inclusion of molecular information, new therapies and the withdrawal of conventional treatment concepts. Decisive for the future will be the confirmation of this development by modern study concepts contemporarily with adequate evidence. It could then be expected that a personalized therapy for early breast cancer and in particular adjuvant chemotherapy would only be used for those patients for whom it is really necessary. In advanced stage disease there is justified hope that the survival time in the sense of a chronic disease can be improved by the use of targeted therapy.

  20. Optimizing reproducibility evaluation for random amplified polymorphic DNA markers.

    PubMed

    Ramos, J R; Telles, M P C; Diniz-Filho, J A F; Soares, T N; Melo, D B; Oliveira, G

    2008-01-01

    The random amplified polymorphic DNA (RAPD) technique is often criticized because it usually shows low levels of repeatability; thus it can generate spurious bands. These problems can be partially overcome by rigid laboratory protocols and by performing repeatability tests. However, because it is expensive and time-consuming to obtain genetic data twice for all individuals, a few randomly chosen individuals are usually selected for a priori repeatability analysis, introducing a potential bias in genetic parameter estimates. We developed a procedure to optimize repeatability analysis based on RAPD data, which was applied to evaluate genetic variability in three local populations of Tibochina papyrus, an endemic Cerrado plant found in elevated rocky fields in Brazil. We used a simulated annealing procedure to select the smallest number of individuals that contain all bands and repeated the analyses only for those bands that were reproduced in these individuals. We compared genetic parameter estimates using HICKORY and POPGENE softwares on an unreduced data set and on data sets in which we eliminated bands based on repeatability of individuals selected by simulated annealing and based on three randomly selected individuals. Genetic parameter estimates were very similar when we used the optimization procedure to reduce the number of bands analyzed, but as expected, selecting only three individuals to evaluate the repeatability of bands produced very different estimates. We conclude that the problems of repeatability attributed to RAPD markers could be due to bias in the selection of loci and primers and not necessarily to the RAPD technique per se. PMID:19065774

  1. Newer markers for hepatocellular carcinoma.

    PubMed

    Marrero, Jorge A; Lok, Anna S F

    2004-11-01

    The incidence of hepatocellular carcinoma (HCC) is increasing worldwide; the overall survival of patients with HCC is grim because most patients are diagnosed late, when curative treatment is not possible. Cirrhosis is the strongest risk factor for the development of HCC. HCC surveillance with alpha-fetoprotein (AFP) and ultrasonography has been recommended for persons with cirrhosis. However, AFP level is insensitive for the early detection of HCC, and ultrasonography is expensive and operator dependent. Clearly, there is a need for novel strategies for the early detection of HCC. The ideal biomarker assay for HCC would be sensitive, specific, noninvasive, reproducible, inexpensive, and acceptable to patients. The Early Detection Research Network of the National Cancer Institute has proposed 5 phases for biomarker validation: preclinical exploratory studies, clinical assay development for disease, retrospective longitudinal study to detect preclinical disease, prospective screening study, and cancer control studies. Several biomarkers, such as des-gamma carboxyprothrombin, lens culinaris agglutinin-reactive AFP, human hepatocyte growth factor, and insulin-like growth factor-1, are promising, but none of these markers has been validated for clinical use. Limitations of the current literature include inadequate sample size, heterogeneity in biomarker assay methods and result reporting, limited analysis of demographics and cause of liver disease as covariates in the expression of these markers, and a scarcity of longitudinal studies evaluating the ability of biomarkers to detect preclinical disease. There is an urgent need for novel biomarkers for the detection of early HCC; the National Cancer Institute proposal provides a framework for future validation studies. PMID:15508074

  2. Immunohistochemical diagnostic and prognostic markers for melanoma.

    PubMed

    Nosrati, Mehdi; Kashani-Sabet, Mohammed

    2014-01-01

    Recent studies in our laboratory have identified novel molecular diagnostic and prognostic markers based on analyses in large cohorts of melanoma patients. These markers were initially derived from gene expression profiling analyses of distinct stages of melanoma progression. Immunohistochemical analyses confirmed the differential expression of these markers, and immunohistochemistry-based multimarker assays were developed to assess melanoma diagnosis and prognosis at the molecular level. In this chapter we review the development of these assays and the methodologies used to assess marker expression in both nevi and primary melanomas. PMID:24258983

  3. Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna.

    PubMed

    Nikolic, Natacha; Duthoy, Stéphanie; Destombes, Antoine; Bodin, Nathalie; West, Wendy; Puech, Alexis; Bourjea, Jérôme

    2015-01-01

    Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87-90%), and assignment index. ThuAla-Hki-01

  4. Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna

    PubMed Central

    Nikolic, Natacha; Duthoy, Stéphanie; Destombes, Antoine; Bodin, Nathalie; West, Wendy; Puech, Alexis; Bourjea, Jérôme

    2015-01-01

    Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87–90%), and assignment index. ThuAla-Hki-01

  5. Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna.

    PubMed

    Nikolic, Natacha; Duthoy, Stéphanie; Destombes, Antoine; Bodin, Nathalie; West, Wendy; Puech, Alexis; Bourjea, Jérôme

    2015-01-01

    Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87-90%), and assignment index. ThuAla-Hki-01

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-06-01

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

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

    PubMed

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

    2016-06-01

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

  9. Altering Visual Perception Abnormalities: A Marker for Body Image Concern

    PubMed Central

    Duncum, Anna J. F.; Mundy, Matthew E.

    2016-01-01

    The body image concern (BIC) continuum ranges from a healthy and positive body image, to clinical diagnoses of abnormal body image, like body dysmorphic disorder (BDD). BDD and non-clinical, yet high-BIC participants have demonstrated a local visual processing bias, characterised by reduced inversion effects. To examine whether this bias is a potential marker of BDD, the visual processing of individuals across the entire BIC continuum was examined. Dysmorphic Concern Questionnaire (DCQ; quantified BIC) scores were expected to correlate with higher discrimination accuracy and faster reaction times of inverted stimuli, indicating reduced inversion effects (occurring due to increased local visual processing). Additionally, an induced global or local processing bias via Navon stimulus presentation was expected to alter these associations. Seventy-four participants completed the DCQ and upright-inverted face and body stimulus discrimination task. Moderate positive associations were revealed between DCQ scores and accuracy rates for inverted face and body stimuli, indicating a graded local bias accompanying increases in BIC. This relationship supports a local processing bias as a marker for BDD, which has significant assessment implications. Furthermore, a moderate negative relationship was found between DCQ score and inverted face accuracy after inducing global processing, indicating the processing bias can temporarily be reversed in high BIC individuals. Navon stimuli were successfully able to alter the visual processing of individuals across the BIC continuum, which has important implications for treating BDD. PMID:27003715

  10. Audio Indexing for Individualization

    ERIC Educational Resources Information Center

    Rahmlow, Harold F.; And Others

    1973-01-01

    Article describes a new development in indexing audiotapes called Zimdex. The system was developed in response to the problem of individualizing review materials for candidates studying the mathematics of life insurance. (Author/HB)

  11. The decisionalization of individualization.

    PubMed

    Biedermann, A; Bozza, S; Taroni, F

    2016-09-01

    Throughout forensic science and adjacent branches, academic researchers and practitioners continue to diverge in their perception and understanding of the notion of 'individualization', that is the claim to reduce a pool of potential donors of a forensic trace to a single source. In particular, recent shifts to refer to the practice of individualization as a decision have been revealed as being a mere change of label [1], leaving fundamental changes in thought and understanding still pending. What is more, professional associations and practitioners shy away from embracing the notion of decision in terms of the formal theory of decision in which individualization may be framed, mainly because of difficulties to deal with the measurement of desirability or undesirability of the consequences of decisions (e.g., using utility functions). Building on existing research in the area, this paper presents and discusses fundamental concepts of utilities and losses with particular reference to their application to forensic individualization. The paper emphasizes that a proper appreciation of decision tools not only reduces the number of individual assignments that the application of decision theory requires, but also shows how such assignments can be meaningfully related to constituting features of the real-world decision problem to which the theory is applied. It is argued that the decisonalization of individualization requires such fundamental insight to initiate changes in the fields' underlying understandings, not merely in their label. PMID:27196399

  12. Conservation of spermatogonial stem cell marker expression in undifferentiated felid spermatogonia.

    PubMed

    Vansandt, Lindsey M; Livesay, Janelle L; Dickson, Melissa Joy; Li, Lei; Pukazhenthi, Budhan S; Keefer, Carol L

    2016-09-01

    Spermatogonial stem cells (SSCs) are distinct in their ability to self-renew, transmit genetic information, and persist throughout the life of an individual. These characteristics make SSCs a useful tool for addressing diverse challenges such as efficient transgenic production in nonrodent, biomedical animal models, or preservation of the male genome for species in which survival of frozen-thawed sperm is low. A requisite first step to access this technology in felids is the establishment of molecular markers. This study was designed to evaluate, in the domestic cat (Felis catus), the expression both in situ and following enrichment in vitro of six genes (GFRA1, GPR125, ZBTB16, POU5F1, THY1, and UCHL1) that had been previously identified as SSC markers in other species. Antibodies for surface markers glial cell line-derived neurotrophic factor family receptor alpha 1, G protein-coupled receptor 125, and thymus cell antigen 1 could not be validated, whereas Western blot analysis of prepubertal, peripubertal, and adult cat testis confirmed protein expression for the intracellular markers ubiquitin carboxy-terminal hydrolase 1, zinc finger and BTB domain-containing protein 16, and POU domain, class 5, transcription factor 1. Colocalization of the markers by immunohistochemistry revealed that several cells within the subpopulation adjacent to the basement membrane of the seminiferous tubules and identified morphologically as spermatogonia, expressed all three intracellular markers. Studies performed on cheetah (Acinonyx jubatus) and Amur leopard (Panthera pardus orientalis) testis exhibited a conserved expression pattern in protein molecular weights, relative abundance, and localization of positive cells within the testis. The expression of the three intracellular SSC marker proteins in domestic and wild cat testes confirms conservation of these markers in felids. Enrichment of marker transcripts after differential plating was also observed. These markers will

  13. Marker-Assisted Selection in Soybean Breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In the late 1990's Nevin Young expressed a cautious optimism for the future of marker-assisted breeding. Although marker-assisted selection (MAS) for soybean cyst nematode (SCN; Heterodera glycines) was offered as a case study on how genotype-based selection could be useful and cost-effective to a p...

  14. Discourse Markers in Second Language Research.

    ERIC Educational Resources Information Center

    Demirci, Mahide; Kleiner, Brian

    1997-01-01

    Investigates the use of discourse markers by advanced Turkish learners of English. The research discussed here aims to make an initial contribution to the study of how discourse markers are used by second-language learners, and to illustrate why such research should be valuable and necessary component of interlanguage pragmatics. (Author/VWL)

  15. Smart magnetic markers use in hydraulic fracturing.

    PubMed

    Zawadzki, Jarosław; Bogacki, Jan

    2016-11-01

    One of the main challenges and unknowns during shale gas exploration is to assess the range and efficiency of hydraulic fracturing. It is also essential to assess the distribution of proppant, which keeps the fracture pathways open. Solving these problems may considerably increase the efficiency of the shale gas extraction. Because of that, the idea of smart magnetic marker, which can be detected when added to fracturing fluid, has been considered for a long time. This study provides overview of the possibilities of magnetic marker application for shale gas extraction. The imaging methods using electromagnetic markers, are considered or developed in two directions. The first possibility is the markers' electromagnetic activity throughout the whole volume of the fracturing fluid. Thus, it can be assumed that the whole fracturing fluid is the marker. Among these type of hydraulic fracturing solutions, ferrofluid could be considered. The second possibility is marker, which is just one of many components of the fracturing fluid. In this case feedstock magnetic materials, ferrites and nanomaterials could be considered. Magnetic properties of magnetite could be too low and ferrofluids' or nanomaterials' price is unacceptably high. Because of that, ferrites, especially ZnMn ferrites seems to be the best material for magnetic marker. Because of the numerous applications in electronics, it is cheap and easily available, although the price is higher, then that of magnetite. The disadvantage of using ferrite, could be too small mechanical strength. It creates an essential need for combining magnetic marker with proppant into magnetic-ceramic composite. PMID:27475294

  16. 43 CFR 15.6 - Markers.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Markers. 15.6 Section 15.6 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.6 Markers. No person shall willfully mark, deface or injure in any way, or displace, remove or tamper with any Preserve...

  17. 43 CFR 15.6 - Markers.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 1 2013-10-01 2013-10-01 false Markers. 15.6 Section 15.6 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.6 Markers. No person shall willfully mark, deface or injure in any way, or displace, remove or tamper with any Preserve...

  18. 43 CFR 15.6 - Markers.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 43 Public Lands: Interior 1 2012-10-01 2011-10-01 true Markers. 15.6 Section 15.6 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.6 Markers. No person shall willfully mark, deface or injure in any way, or displace, remove or tamper with any Preserve...

  19. 43 CFR 15.6 - Markers.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Markers. 15.6 Section 15.6 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.6 Markers. No person shall willfully mark, deface or injure in any way, or displace, remove or tamper with any Preserve...

  20. Characterizing Safflower Germplasm with AFLP Molecular Markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  1. 21 CFR 878.4660 - Skin marker.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Skin marker. 878.4660 Section 878.4660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GENERAL AND PLASTIC SURGERY DEVICES Surgical Devices § 878.4660 Skin marker. (a) Identification. A...

  2. 21 CFR 878.4660 - Skin marker.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Skin marker. 878.4660 Section 878.4660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GENERAL AND PLASTIC SURGERY DEVICES Surgical Devices § 878.4660 Skin marker. (a) Identification. A...

  3. 21 CFR 878.4660 - Skin marker.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Skin marker. 878.4660 Section 878.4660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GENERAL AND PLASTIC SURGERY DEVICES Surgical Devices § 878.4660 Skin marker. (a) Identification. A...

  4. 21 CFR 878.4660 - Skin marker.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Skin marker. 878.4660 Section 878.4660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GENERAL AND PLASTIC SURGERY DEVICES Surgical Devices § 878.4660 Skin marker. (a) Identification. A...

  5. 21 CFR 878.4660 - Skin marker.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Skin marker. 878.4660 Section 878.4660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES GENERAL AND PLASTIC SURGERY DEVICES Surgical Devices § 878.4660 Skin marker. (a) Identification. A...

  6. Bilingual Discourse Markers in Indigenous Languages

    ERIC Educational Resources Information Center

    Torres, Lourdes

    2006-01-01

    This review of research considers the occurrence and function of Spanish discourse markers and other particles in indigenous speech. I discuss important research that has examined these phenomena and refer to studies of bilingual discourse markers in other non-indigenous language contact situations to address unresolved issues concerning the form…

  7. Smart magnetic markers use in hydraulic fracturing.

    PubMed

    Zawadzki, Jarosław; Bogacki, Jan

    2016-11-01

    One of the main challenges and unknowns during shale gas exploration is to assess the range and efficiency of hydraulic fracturing. It is also essential to assess the distribution of proppant, which keeps the fracture pathways open. Solving these problems may considerably increase the efficiency of the shale gas extraction. Because of that, the idea of smart magnetic marker, which can be detected when added to fracturing fluid, has been considered for a long time. This study provides overview of the possibilities of magnetic marker application for shale gas extraction. The imaging methods using electromagnetic markers, are considered or developed in two directions. The first possibility is the markers' electromagnetic activity throughout the whole volume of the fracturing fluid. Thus, it can be assumed that the whole fracturing fluid is the marker. Among these type of hydraulic fracturing solutions, ferrofluid could be considered. The second possibility is marker, which is just one of many components of the fracturing fluid. In this case feedstock magnetic materials, ferrites and nanomaterials could be considered. Magnetic properties of magnetite could be too low and ferrofluids' or nanomaterials' price is unacceptably high. Because of that, ferrites, especially ZnMn ferrites seems to be the best material for magnetic marker. Because of the numerous applications in electronics, it is cheap and easily available, although the price is higher, then that of magnetite. The disadvantage of using ferrite, could be too small mechanical strength. It creates an essential need for combining magnetic marker with proppant into magnetic-ceramic composite.

  8. 43 CFR 15.6 - Markers.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 43 Public Lands: Interior 1 2014-10-01 2014-10-01 false Markers. 15.6 Section 15.6 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.6 Markers. No person shall willfully mark, deface or injure in any way, or displace, remove or tamper with any Preserve...

  9. [Myoepithelial differentiation markers in salivary gland neoplasia].

    PubMed

    Scarpellini, F; Marucci, G; Foschini, M P

    2001-12-01

    Salivary gland tumors frequently present myoepithelial cell differentiation that is not always easily identified on routinely stained sections. Recently novel markers of myoepithelium have been studied, such as calponin (CALP), caldesmon (CALD), and smooth muscle myosin heavy chain. These markers, together with smooth muscle actin may be useful tools for identifying myoepithelial cells. We immunohistochemically studied a series of 23 benign and malignant salivary gland tumors using antibodies to these four markers. The tumors were classified as follows: pleomorphic adenoma (n = 8), basal cell adenoma (n = 3), myoepithelioma with plasmacytoid cells (n = 2), epithelial-myoepithelial cell carcinoma (n = 6) and adenoid cystic carcinoma (n = 4). All tumors were positive for at least one of the four markers. CALP and smooth muscle actin were the markers more frequently expressed. Positivity was mostly located in the myoepithelial cells that constitute the external layer of the glandular or tubular neoplastic structures. In poorly differentiated epithelial myoepithelial carcinomas, composed of solid sheets of neoplastic cells and sometimes of clear cells, immunohistochemical staining for myoepithelial markers evidenced rudimentary glandular structures. CALP and smooth muscle actin were positive in the two cases of myoepithelioma with plasmacytoid cells. In conclusion, the combined staining with four markers helps to disclose myoepithelial cell differentiation and can be a useful tool for the correct histopathological diagnosis of salivary gland tumors. Among the four markers studied, CALP and smooth muscle actin were the most useful to identify myoepithelial cell differentiation.

  10. Fiducial marker for correlating images

    DOEpatents

    Miller, Lisa Marie; Smith, Randy J.; Warren, John B.; Elliott, Donald

    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.

  11. Prevalence and putative risk markers of challenging behavior in students with intellectual disabilities.

    PubMed

    Dworschak, Wolfgang; Ratz, Christoph; Wagner, Michael

    2016-11-01

    Numerous studies have reported a high prevalence of challenging behavior among students with intellectual disabilities (ID). They discuss different putative risk markers as well as their influence on the occurrence of challenging behavior. The study investigates the prevalence of challenging behavior and evaluates in terms of a replication study well-known putative risk markers among a representative sample of students with ID (N=1629) in Bavaria, one of the largest regions in Germany. The research is based on a modified version of the Developmental Behavior Checklist (DBC). Findings indicate a prevalence rate of 52% for challenging behavior. The following putative risk markers are associated with challenging behavior: intense need for care, male gender, lack of communication skills, and residential setting. These risk markers explain 8.4% of the variance concerning challenging behavior. These results reveal that challenging behavior either is to a large extent determined by situations and interactions between individuals and environment and cannot be explained by the measured individual and social risk markers alone, or it is determined by further risk markers that were not measured. PMID:27608371

  12. Efficiency of Marker-Assisted Selection in the Improvement of Quantitative Traits

    PubMed Central

    Lande, R.; Thompson, R.

    1990-01-01

    Molecular genetics can be integrated with traditional methods of artificial selection on phenotypes by applying marker-assisted selection (MAS). We derive selection indices that maximize the rate of improvement in quantitative characters under different schemes of MAS combining information on molecular genetic polymorphisms (marker loci) with data on phenotypic variation among individuals (and their relatives). We also analyze statistical limitations on the efficiency of MAS, including the detectability of associations between marker loci and quantitative trait loci, and sampling errors in estimating the weighting coefficients in the selection index. The efficiency of artifical selection can be increased substantially using MAS following hybridization of selected lines. This requires initially scoring genotypes at a few hundred molecular marker loci, as well as phenotypic traits, on a few hundred to a few thousand individuals; the number of marker loci scored can be greatly reduced in later generations. The increase in selection efficiency from the use of marker loci, and the sample sizes necessary to achieve them, depend on the genetic parameters and the selection scheme. PMID:1968875

  13. Nanometer scale marker for fluorescent microscopy

    SciTech Connect

    Hiraga, Takashi; Iketaki, Yoshinori; Watanabe, Takeshi; Ohyi, Hideyuki; Kobayashi, Kazumasa; Yamamoto, Noritaka; Mizokuro, Toshiko; Fujii, Masaaki

    2005-07-15

    To establish a calibration method of optical performance in fluorescence microscopy, we fabricated a fluorescent nanometer-scale marker by combining a dry dye method for polymer film and fine lithography. The marker has a 50 nm line-and-space fluorescent pattern, finer than the optical diffraction limit. A spin-coated poly(methyl methacrylate) thin film on a silicon wafer was densely doped with Rhodamine 6G using a simple vacuum process, named the vapor-transportation method, and then the pattern was formed on the film using electron-beam lithography. The figure accuracy of the fabricated marker was calibrated by electron microscopes. Using this marker, one can quantitatively evaluate the optical properties; i.e., the contrast-transfer function, the point-spread function, magnification, and so on. To show practical use of the marker, we demonstrated the evaluation of a fluorescent microscope system.

  14. Development of new PCR-based markers specific for chromosome arms of rye (Secale cereale L.).

    PubMed

    Qiu, Ling; Tang, Zong-xiang; Li, Meng; Fu, Shu-lan

    2016-03-01

    PCR-based rye (Secale cereale L.) chromosome-specific markers can contribute to the effective utilization of elite genes of rye in wheat (Triticum aestivum L.) breeding programs. In the present study, 578 new PCR-based rye-specific markers have been developed by using specific length amplified fragment sequencing (SLAF-seq) technology, and 76 markers displayed different polymorphism among rye Kustro, Imperial, and King II. A total of 427 and 387 markers were, respectively, located on individual chromosomes and chromosome arms of Kustro by using a set of wheat-rye monosomic addition lines and 13 monotelosomic addition lines, which were derived from T. aestivum L. 'Mianyang11' × S. cereale L. 'Kustro'. In addition, two sets of wheat-rye disomic addition lines, which were derived from T. aestivum L. var. Chinese Spring × S. cereale L. var. Imperial and T. aestivum L. 'Holdfast' × S. cereale L. var. King II, were used to test the chromosomal specificity of the 427 markers. The chromosomal locations of 281 markers were consistent among the three sets of wheat-rye addition lines. The markers developed in this study can be used to identify a given segment of rye chromosomes in wheat background and accelerate the utilization of elite genes on rye chromosomes in wheat breeding programs.

  15. The first genetic linkage map of Luohanguo (Siraitia grosvenorii ) based on ISSR and SRAP markers.

    PubMed

    Liu, Lihua; Ma, Xiaojun; Wei, Jianhe; Qin, Jiaming; Mo, Changming

    2011-01-01

    In this study, the first genetic map of Luohanguo (Siraitia grosvenorii (Swingle) C. Jeffrey) was constructed with 150 F₂ population individuals using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. A total of 100 ISSRs and 196 SRAP primer combinations generated 51 and 222 polymorphic markers, respectively. Among the 273 markers obtained, 199 markers (29 ISSRs and 170 SRAPs) were mapped to 25 linkage groups. The map covered 1463.3 cM with a mean map distance of 7.35 cM between adjacent markers and a maximum map distance of 52.6 cM between two markers. The markers were distributed randomly in 25 groups except for minor clusters in the distal region of linkage groups. All 25 linkage groups consisted of 2-36 loci ranging in length from 19.5 to 152.6 cM and accounted for 59.8% of the total map distance. This map provides reference information for future molecular breeding work on Luohanguo.

  16. Development of Genetic Markers for Triploid Verification of the Pacific Oyster, Crassostrea gigas

    PubMed Central

    Kang, Jung-Ha; Lim, Hyun Jeong; Kang, Hyun-Soek; Lee, Jung-Mee; Baby, Sumy; Kim, Jong-Joo

    2013-01-01

    The triploid Pacific oyster, which is produced by mating tetraploid and diploid oysters, is favored by the aquaculture industry because of its better flavor and firmer texture, particularly during the summer. However, tetraploid oyster production is not feasible in all oysters; the development of tetraploid oysters is ongoing in some oyster species. Thus, a method for ploidy verification is necessary for this endeavor, in addition to ploidy verification in aquaculture farms and in the natural environment. In this study, a method for ploidy verification of triploid and diploid oysters was developed using multiplex polymerase chain reaction (PCR) panels containing primers for molecular microsatellite markers. Two microsatellite multiplex PCR panels consisting of three markers each were developed using previously developed microsatellite markers that were optimized for performance. Both panels were able to verify the ploidy levels of 30 triploid oysters with 100% accuracy, illustrating the utility of microsatellite markers as a tool for verifying the ploidy of individual oysters. PMID:25049868

  17. Development of chloroplast microsatellite markers for the endangered Maianthemum bicolor (Asparagaceae s.l.)1

    PubMed Central

    Park, Hana; Kim, Changkyun; Lee, You-Mi; Kim, Joo-Hwan

    2016-01-01

    Premise of the study: Ten polymorphic chloroplast microsatellite (cpSSR) markers were developed and characterized in an endemic and endangered herb, Maianthemum bicolor (Asparagaceae s.l.), for use in conservation genetics. Methods and Results: Primer sets flanking each of the 10 cpSSR loci in noncoding regions of the chloroplast genome of M. bicolor were designed. These cpSSR markers were tested on a total of 33 adult individuals from three natural populations in South Korea. The number of alleles per locus ranged from two to three. The unbiased haplotype diversity per locus ranged from 0.061 to 0.682. All markers were successfully transferred to the congeneric species M. japonicum, M. bifolium, and M. dilatatum with polymorphisms among the species. Conclusions: The developed cpSSR markers will be useful in assessing the genetic diversity and population structure of M. bicolor and will help to infer its molecular identification, thereby providing a basis for conservation.

  18. Microsatellite DNA markers for delineating population structure and kinship among the endangered Kirtland's warbler (Dendroica kirtlandii)

    USGS Publications Warehouse

    King, T.L.; Eackles, M.S.; Henderson, A.P.; Bocetti, C.I.; Currie, D.; Wunderle, J.M.

    2005-01-01

    We document the isolation and characterization of 23 microsatellite DNA markers for the endangered Kirtland's warbler (Dendroica kirtlandii), a Nearctic/Neotropical migrant passerine. This suite of markers revealed moderate to high levels of allelic diversity (averaging 7.7 alleles per locus) and heterozygosity (averaging 72%). Genotypic frequencies at 22 of 23 (95%) markers conformed to Hardy-Weinberg equilibrium expectations, and no linkage disequilibrium was observed in blood samples taken from 14 warblers found on the wintering grounds in the Bahamas archipelago. Multilocus genotypes resulting from this suite of markers should reduce the amount of resources required for initiating new genetic studies assessing breeding structure, parentage, demographics, and individual-level ecological interactions for D. kirtlandii. ?? 2005 Blackwell Publishing Ltd.

  19. cpDNA microsatellite markers for Lemna minor (Araceae): Phylogeographic implications1

    PubMed Central

    Wani, Gowher A.; Shah, Manzoor A.; Reshi, Zafar A.; Atangana, Alain R.; Khasa, Damase P.

    2014-01-01

    • Premise of the study: A lack of genetic markers impedes our understanding of the population biology of Lemna minor. Thus, the development of appropriate genetic markers for L. minor promises to be highly useful for population genetic studies and for addressing other life history questions regarding the species. • Methods and Results: For the first time, we characterized nine polymorphic and 24 monomorphic chloroplast microsatellite markers in L. minor using DNA samples of 26 individuals sampled from five populations in Kashmir and of 17 individuals from three populations in Quebec. Initially, we designed 33 primer pairs, which were tested on genomic DNA from natural populations. Nine loci provided markers with two alleles. Based on genotyping of the chloroplast DNA fragments from 43 sampled individuals, we identified one haplotype in Quebec and 11 haplotypes in Kashmir, of which one occurs in 56% of the genotypes, one in 8%, and nine in 4%, respectively. There was a maximum of two alleles per locus. • Conclusions: These new chloroplast microsatellite markers for L. minor and haplotype distribution patterns indicate a complex phylogeographic history that merits further investigation. PMID:25202636

  20. Individual Hearing Loss

    PubMed Central

    Dau, Torsten; Christensen-Dalsgaard, Jakob; Tranebjærg, Lisbeth; Andersen, Ture; Poulsen, Torben

    2016-01-01

    It is well-established that hearing loss does not only lead to a reduction of hearing sensitivity. Large individual differences are typically observed among listeners with hearing impairment in a wide range of suprathreshold auditory measures. In many cases, audiometric thresholds cannot fully account for such individual differences, which make it challenging to find adequate compensation strategies in hearing devices. How to characterize, model, and compensate for individual hearing loss were the main topics of the fifth International Symposium on Auditory and Audiological Research (ISAAR), held in Nyborg, Denmark, in August 2015. The following collection of papers results from some of the work that was presented and discussed at the symposium. PMID:27566802

  1. Optimal marker-strategy clinical trial design to detect predictive markers for targeted therapy.

    PubMed

    Zang, Yong; Liu, Suyu; Yuan, Ying

    2016-07-01

    In developing targeted therapy, the marker-strategy design (MSD) provides an important approach to evaluate the predictive marker effect. This design first randomizes patients into non-marker-based or marker-based strategies. Patients allocated to the non-marker-based strategy are then further randomized to receive either the standard or targeted treatments, while patients allocated to the marker-based strategy receive treatments based on their marker statuses. Little research has been done on the statistical properties of the MSD, which has led to some widespread misconceptions and placed clinical researchers at high risk of using inefficient designs. In this article, we show that the commonly used between-strategy comparison has low power to detect the predictive effect and is valid only under a restrictive condition that the randomization ratio within the non-marker-based strategy matches the marker prevalence. We propose a Wald test that is generally valid and also uniformly more powerful than the between-strategy comparison. Based on that, we derive an optimal MSD that maximizes the power to detect the predictive marker effect by choosing the optimal randomization ratios between the two strategies and treatments. Our numerical study shows that using the proposed optimal designs can substantially improve the power of the MSD to detect the predictive marker effect. We use a lung cancer trial to illustrate the proposed optimal designs. PMID:26951724

  2. Optimal marker-strategy clinical trial design to detect predictive markers for targeted therapy.

    PubMed

    Zang, Yong; Liu, Suyu; Yuan, Ying

    2016-07-01

    In developing targeted therapy, the marker-strategy design (MSD) provides an important approach to evaluate the predictive marker effect. This design first randomizes patients into non-marker-based or marker-based strategies. Patients allocated to the non-marker-based strategy are then further randomized to receive either the standard or targeted treatments, while patients allocated to the marker-based strategy receive treatments based on their marker statuses. Little research has been done on the statistical properties of the MSD, which has led to some widespread misconceptions and placed clinical researchers at high risk of using inefficient designs. In this article, we show that the commonly used between-strategy comparison has low power to detect the predictive effect and is valid only under a restrictive condition that the randomization ratio within the non-marker-based strategy matches the marker prevalence. We propose a Wald test that is generally valid and also uniformly more powerful than the between-strategy comparison. Based on that, we derive an optimal MSD that maximizes the power to detect the predictive marker effect by choosing the optimal randomization ratios between the two strategies and treatments. Our numerical study shows that using the proposed optimal designs can substantially improve the power of the MSD to detect the predictive marker effect. We use a lung cancer trial to illustrate the proposed optimal designs.

  3. Individualizing anaemia therapy.

    PubMed

    de Francisco, Angel L M

    2010-12-01

    Individualized strategies for managing renal anaemia with erythropoiesis-stimulating agents (ESAs) need to be advanced. Recent outcomes from clinical studies prompted a narrowing of the guideline-recommended haemoglobin target (11-12 g/dL) due to increased mortality and morbidity when targeting higher haemoglobin concentrations. Maintaining a narrow target is a clinical challenge, as haemoglobin concentration tends to fluctuate. The goal of individualized treatment is to achieve the haemoglobin target at the lowest ESA dose while avoiding significant fluctuations in haemoglobin concentrations and persistently low or high concentrations. This may require changes to the ESA dose and dosing frequency over the course of treatment.

  4. Micro- and minisatellite-expressed sequence tag (EST) markers discriminate between populations of Rhipicephalus appendiculatus.

    PubMed

    Kanduma, Esther G; Mwacharo, Joram M; Sunter, Jack D; Nzuki, Inosters; Mwaura, Stephen; Kinyanjui, Peter W; Kibe, Michael; Heyne, Heloise; Hanotte, Olivier; Skilton, Robert A; Bishop, Richard P

    2012-06-01

    Biological differences, including vector competence for the protozoan parasite Theileria parva have been reported among populations of Rhipicephalus appendiculatus (Acari: Ixodidae) from different geographic regions. However, the genetic diversity and population structure of this important tick vector remain unknown due to the absence of appropriate genetic markers. Here, we describe the development and evaluation of a panel of EST micro- and minisatellite markers to characterize the genetic diversity within and between populations of R. appendiculatus and other rhipicephaline species. Sixty-six micro- and minisatellite markers were identified through analysis of the R. appendiculatus Gene Index (RaGI) EST database and selected bacterial artificial chromosome (BAC) sequences. These were used to genotype 979 individual ticks from 10 field populations, 10 laboratory-bred stocks, and 5 additional Rhipicephalus species. Twenty-nine markers were polymorphic and therefore informative for genetic studies while 6 were monomorphic. Primers designed from the remaining 31 loci did not reliably generate amplicons. The 29 polymorphic markers discriminated populations of R. appendiculatus and also 4 other Rhipicephalus species, but not R. zambeziensis. The percentage Principal Component Analysis (PCA) implemented using Multiple Co-inertia Analysis (MCoA) clustered populations of R. appendiculatus into 2 groups. Individual markers however differed in their ability to generate the reference typology using the MCoA approach. This indicates that different panels of markers may be required for different applications. The 29 informative polymorphic micro- and minisatellite markers are the first available tools for the analysis of the phylogeography and population genetics of R. appendiculatus. PMID:22789728

  5. Inflammatory markers in relation to long-term air pollution.

    PubMed

    Mostafavi, Nahid; Vlaanderen, Jelle; Chadeau-Hyam, Marc; Beelen, Rob; Modig, Lars; Palli, Domenico; Bergdahl, Ingvar A; Vineis, Paolo; Hoek, Gerard; Kyrtopoulos, Soterios Α; Vermeulen, Roel

    2015-08-01

    Long-term exposure to ambient air pollution can lead to chronic health effects such as cancer, cardiovascular and respiratory disease. Systemic inflammation has been hypothesized as a putative biological mechanism contributing to these adverse health effects. We evaluated the effect of long-term exposure to air pollution on blood markers of systemic inflammation. We measured a panel of 28 inflammatory markers in peripheral blood samples from 587 individuals that were biobanked as part of a prospective study. Participants were from Varese and Turin (Italy) and Umea (Sweden). Long-term air pollution estimates of nitrogen oxides (NOx) were available from the European Study of Cohorts for Air Pollution Effects (ESCAPE). Linear mixed models adjusted for potential confounders were applied to assess the association between NOx and the markers of inflammation. Long-term exposure to NOx was associated with decreased levels of interleukin (IL)-2, IL-8, IL-10 and tumor necrosis factor-α in Italy, but not in Sweden. NOx exposure levels were considerably lower in Sweden than in Italy (Sweden: median (5th, 95th percentiles) 6.65 μg/m(3) (4.8, 19.7); Italy: median (5th, 95th percentiles) 94.2 μg/m(3) (7.8, 124.5)). Combining data from Italy and Sweden we only observed a significant association between long-term exposure to NOx and decreased levels of circulating IL-8. We observed some indication for perturbations in the inflammatory markers due to long-term exposure to NOx. Effects were stronger in Italy than in Sweden, potentially reflecting the difference in air pollution levels between the two cohorts.

  6. Microsatellite markers for identification and parentage analysis in the European wild boar (Sus scrofa)

    PubMed Central

    2012-01-01

    Background The wild boar (Sus scrofa) is among the most widespread mammal species throughout the old world. Presently, studies concerning microsatellites in domestic pigs and wild boars have been carried out in order to investigate domestication, social behavior and general diversity patterns among either populations or breeds. The purpose of the current study is to develop a robust set of microsatellites markers for parentage analyses and individual identification. Findings A set of 14 previously reported microsatellites markers have been optimized and tested in three populations from Hungary, Portugal and Spain, in a total of 167 samples. The results indicate high probabilities of exclusion (0.99999), low probability of identity (2.0E-13 – 2.5E-9) and a parentage assignment of 100%. Conclusions Our results demonstrate that this set of markers is a useful and efficient tool for the individual identification and parentage assignment in wild boars. PMID:22943565

  7. Breakpoint analysis: Precise localization of genetic markers by means of nonstatistical computation using relatively few genotypes

    SciTech Connect

    Elsner, T.I.; Albertsen, H.; Gerken, S.C.; Cartwright, P.; White, R.

    1995-02-01

    Placing new markers on a previously existing genetic map by using conventional methods of multilocus linkage analysis requires that a large number of reference families be genotyped. This paper presents a methodology for placing new markers on existing genetic maps by genotyping only a few individuals in a selected subset of the reference panel. We show that by identifying meiotic breakpoint events within existing genetic maps and genotyping individuals who exhibit these events, along with one nonrecombinant sibling and their parents, we can determine precise locations for new markers even within subcentimorgan chromosomal regions. This method also improves detection of errors in genotyping and assists in the observation of chromosome behavior in specific regions. 31 refs., 9 figs.

  8. Family/Individual Health.

    ERIC Educational Resources Information Center

    Texas Tech Univ., Lubbock. Home Economics Curriculum Center.

    This curriculum guide consists of materials for use in planning and delivering junior high school homemaking courses focusing on individual and family health. Discussed first are program and curriculum planning. The next chapter focuses on the special needs of handicapped and disadvantaged learners and details strategies for addressing these…

  9. Applied Music (Individual Study).

    ERIC Educational Resources Information Center

    Texas Education Agency, Austin.

    Background information and resources to help students in grades 9-12 in Texas pursue an individual study contract in applied music is presented. To fulfill a contract students must publicly perform from memory, with accompaniment as specified, three selections from a list of approved music for their chosen field (instrument or voice). Material…

  10. Individualized Instruction and Unipacs.

    ERIC Educational Resources Information Center

    Kohut, Sylvester, Jr.

    Individualized instruction is an educational program in which grade levels and time units are designed to permit the student to work at his own pace and level with the use of unipacs. The unipac, a "unique package," is a specially designed group of learning activities based on specific behavioral objectives chosen by the student. Unipacs consist…

  11. Individual Learning Issues.

    ERIC Educational Resources Information Center

    1997

    This document contains three papers from a symposium on individual learning issues in human resource development (HRD). "Bringing Cross-Cultural Sensitivity to Human Resource Development: An Example from the Classroom" (Robert L. Dilworth) reports on a classroom-based case study in curriculum design for global HRD that emphasizes the importance of…

  12. Individual Folk Anthology.

    ERIC Educational Resources Information Center

    Griffin, Jean L.

    An individual folk anthology unit covering eight topics is described in this paper. The eight topics include (1) I have an identity, (2) my interesting name, (3) mandalas and sentences, (4) rhythms and rhymes of old times, (5) myths of my childhood, (6) folk legends/old and new, (7) aspects of folklore, and (8) slang. The activities accompanying…

  13. Perspectives in Individualized Learning.

    ERIC Educational Resources Information Center

    Weisgerber, Robert A.

    The readings presented here are an analysis of selected factors underlying the process of individualized learning. The book is organized topically and moves from theoretical considerations toward an analysis of important educational components. The readings come from a cross section of experts representing the areas of learning theory, individual…

  14. AN INDIVIDUALIZED SCIENCE LABORATORY.

    ERIC Educational Resources Information Center

    LIPSON, JOSEPH I.

    THE LEARNING RESEARCH AND DEVELOPMENT CENTER AT THE UNIVERSITY OF PITTSBURGH IS WORKING ON AN EXPERIMENTAL PROJECT TO EXAMINE METHODS OF INDIVIDUALIZED INSTRUCTION IN SCIENCE AT THE ELEMENTARY SCHOOL LEVEL. AT THIS TIME, THE EXPERIMENT IS FOCUSED UPON NON-READERS IN GRADES K-3. EACH STUDENT RECEIVES A TAPE CARTRIDGE AND A PLASTIC BOX CONTAINING…

  15. Enhancing Individual Readiness.

    ERIC Educational Resources Information Center

    1997

    This document contains three papers from a symposium on enhancing individual readiness through human resource development (HRD). "Secondary School Administrator's Perception of Enhancing Self-Worth through Service" (Thomas Li-Ping Tang, Emily James Weatherford) presents results of a study to examine secondary school administrators' endorsement of…

  16. Individual Differences in Learning.

    ERIC Educational Resources Information Center

    1999

    This document contains three symposium papers on individual differences in learning. "Creek Women's Perceptions of Work: A Qualitative Study" (Barbara Bussell Kawulich, Carol D. Hansen), which is an ethnographic study, discusses differences between the value systems held by Creek women and those of the mainstream population. "Subordinates'…

  17. Responding to Individual Needs.

    ERIC Educational Resources Information Center

    Ainscow, Mel

    1990-01-01

    Effective teachers of students with disabilities respond successfully to students' individual needs by ensuring that students understand the purpose of their activities, by presenting students with variety and choice, by encouraging them to reflect upon and review their learning, by making flexible use of time and resources, and by implementing…

  18. Enhancing Individuality in Learning.

    ERIC Educational Resources Information Center

    Fountain Valley School District, CA.

    The Curriculum Materials Center is described as a service agency cooperating with teachers to make learning more effective by way of the multi-media approach. The center promotes the concept of individualized instruction which is said to increase learning efficiency by means of--(1) materials selection, (2) curriculum flexibility, (3) valid…

  19. Individualized Education Programs.

    ERIC Educational Resources Information Center

    National Information Center for Handicapped Children and Youth, Washington, DC.

    The monograph interprets individualized education program (IEP) requirements of Part B of Public Law 94-142, the Education for All Handicapped Children Act. After introductory information outlining the purpose of the IEP and basic IEP requirements, a question and answer format of 60 questions provides specific details. Nine inserts highlight major…

  20. Virulence markers of opportunistic black yeast in Exophiala.

    PubMed

    Sav, Hafize; Ozakkas, Fatma; Altınbas, Rabiye; Kiraz, Nuri; Tümgör, Ayşegül; Gümral, Ramazan; Döğen, Aylin; Ilkit, Macit; de Hoog, G Sybren

    2016-06-01

    The black yeast genus Exophiala is known to cause a wide variety of diseases in severely ill individuals but can also affect immunocompetent individuals. Virulence markers and other physiological parameters were tested in eight clinical and 218 environmental strains, with a specific focus on human-dominated habitats for the latter. Urease and catalase were consistently present in all samples; four strains expressed proteinase and three strains expressed DNase, whereas none of the strains showed phospholipase, haemolysis, or co-haemolysis activities. Biofilm formation was identified in 30 (13.8%) of the environmental isolates, particularly in strains from dishwashers, and was noted in only two (25%) of the clinical strains. These results indicate that virulence factors are inconsistently present in the investigated Exophiala species, suggesting opportunism rather than pathogenicity. PMID:26857806

  1. Salivary Markers for Periodontal and General Diseases

    PubMed Central

    Podzimek, Stepan; Vondrackova, Lucie; Duskova, Jana; Janatova, Tatjana; Broukal, Zdenek

    2016-01-01

    The determination of biomarkers in saliva is becoming an important part of laboratory diagnostics and the prediction of not only periodontal, but also other tissue and organ diseases. Biomarkers in saliva (e.g., enzymes, protein markers, or oxidative stress markers) can be used for activity determination and for periodontal disease prognosis. Saliva also contains many markers which can predict the risk of certain diseases (e.g., diabetes mellitus, cardiovascular, oncology, endocrinology, and psychiatric diseases). The study of salivary components proteomics clearly shows the relationship of periodontal diseases and diseases of distant systems, organs, or tissues. PMID:27143814

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

    PubMed

    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.

  3. Genetic Linkage Maps of Eucalyptus Grandis and Eucalyptus Urophylla Using a Pseudo-Testcross: Mapping Strategy and Rapd Markers

    PubMed Central

    Grattapaglia, D.; Sederoff, R.

    1994-01-01

    We have used a ``two-way pseudo-testcross'' mapping strategy in combination with the random amplified polymorhic DNA (RAPD) assay to construct two moderate density genetic linkage maps for species of Eucalyptus. In the cross between two heterozygous individuals many single-dose RAPD markers will be heterozygous in one parent, null in the other and therefore segregate 1:1 in their F(1) progeny following a testcross configuration. Meiosis and gametic segregation in each individual can be directly and efficiently analyzed using RAPD markers. We screened 305 primers of arbitrary sequence, and selected 151 to amplify a total of 558 markers. These markers were grouped at LOD 5.0, θ = 0.25, resulting in the maternal Eucalyptus grandis map having a total of 240 markers into 14 linkage groups (1552 cM) and the paternal Eucalyptus urophylla map with 251 markers in 11 linkage groups (1101 cM) (n = 11 in Eucalyptus). Framework maps ordered with a likelihood support >/=1000:1 were assembled covering 95% of the estimated genome size in both individuals. Characterization of genome complexity of a sample of 48 mapped random amplified polymorphic DNA (RAPD) markers indicate that 53% amplify from low copy regions. These are the first reported high coverage linkage maps for any species of Eucalyptus and among the first for any hardwood tree species. We propose the combined use of RAPD markers and the pseudo-testcross configuration as a general strategy for the construction of single individual genetic linkage maps in outbred forest trees as well as in any highly heterozygous sexually reproducing living organism. A survey of the occurrence of RAPD markers in different individuals suggests that the pseudo-testcross/RAPD mapping strategy should also be efficient at the intraspecific level and increasingly so with crosses of genetically divergent individuals. The ability to quickly construct single-tree genetic linkage maps in any forest species opens the way for a shift from the

  4. Using RAD-seq to recognize sex-specific markers and sex chromosome systems.

    PubMed

    Gamble, Tony

    2016-05-01

    Next-generation sequencing methods have initiated a revolution in molecular ecology and evolution (Tautz et al. ). Among the most impressive of these sequencing innovations is restriction site-associated DNA sequencing or RAD-seq (Baird et al. ; Andrews et al. ). RAD-seq uses the Illumina sequencing platform to sequence fragments of DNA cut by a specific restriction enzyme and can generate tens of thousands of molecular genetic markers for analysis. One of the many uses of RAD-seq data has been to identify sex-specific genetic markers, markers found in one sex but not the other (Baxter et al. ; Gamble & Zarkower ). Sex-specific markers are a powerful tool for biologists. At their most basic, they can be used to identify the sex of an individual via PCR. This is useful in cases where a species lacks obvious sexual dimorphism at some or all life history stages. For example, such tests have been important for studying sex differences in life history (Sheldon ; Mossman & Waser ), the management and breeding of endangered species (Taberlet et al. ; Griffiths & Tiwari ; Robertson et al. ) and sexing embryonic material (Hacker et al. ; Smith et al. ). Furthermore, sex-specific markers allow recognition of the sex chromosome system in cases where standard cytogenetic methods fail (Charlesworth & Mank ; Gamble & Zarkower ). Thus, species with male-specific markers have male heterogamety (XY) while species with female-specific markers have female heterogamety (ZW). In this issue, Fowler & Buonaccorsi () illustrate the ease by which RAD-seq data can generate sex-specific genetic markers in rockfish (Sebastes). Moreover, by examining RAD-seq data from two closely related rockfish species, Sebastes chrysomelas and Sebastes carnatus (Fig. ), Fowler & Buonaccorsi () uncover shared sex-specific markers and a conserved sex chromosome system. PMID:27213697

  5. Development of a core set of single-locus SSR markers for allotetraploid rapeseed (Brassica napus L.).

    PubMed

    Li, Haitao; Younas, Muhammad; Wang, Xiaofeng; Li, Xuemin; Chen, Lin; Zhao, Bo; Chen, Xun; Xu, Jinsong; Hou, Fan; Hong, Baohua; Liu, Gang; Zhao, Hongyang; Wu, Xueli; Du, Hongzhi; Wu, Jiangsheng; Liu, Kede

    2013-04-01

    Brassica napus (AACC) is a recent allotetraploid species evolved through hybridization between two diploids, B. rapa (AA) and B. oleracea (CC). Due to extensive genome duplication and homoeology within and between the A and C genomes of B. napus, most SSR markers display multiple fragments or loci, which limit their application in genetics and breeding studies of this economically important crop. In this study, we collected 3,890 SSR markers from previous studies and also developed 5,968 SSR markers from genomic sequences of B. rapa, B. oleracea and B. napus. Of these, 2,701 markers that produced single amplicons were putative single-locus markers in the B. napus genome. Finally, a set of 230 high-quality single-locus SSR markers were established and assigned to the 19 linkage groups of B. napus using a segregating population with 154 DH individuals. A subset of 78 selected single-locus SSR markers was proved to be highly stable and could successfully discriminate each of the 45 inbred lines and hybrids. In addition, most of the 230 SSR markers showed the single-locus nature in at least one of the Brassica species of the U's triangle besides B. napus. These results indicated that this set of single-locus SSR markers has a wide range of coverage with excellent stability and would be useful for gene tagging, sequence scaffold assignment, comparative mapping, diversity analysis, variety identification and association mapping in Brassica species.

  6. Construction of an integrated map of rose with AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers.

    PubMed

    Yan, Z; Denneboom, C; Hattendorf, A; Dolstra, O; Debener, T; Stam, P; Visser, P B

    2005-02-01

    A high-density genetic map with a number of anchor markers has been created to be used as a tool to dissect genetic variation in rose. Linkage maps for the diploid 94/1 population consisting of 88 individuals were constructed using a total of 520 molecular markers including AFLP, SSR, PK, RGA, RFLP, SCAR and morphological markers. Seven linkage groups, putatively corresponding to the seven haploid rose chromosomes, were identified for each parent, spanning 487 cM and 490 cM, respectively. The average length of 70 cM may cover more than 90% of the rose genome. An integrated map was constructed by incorporating the homologous parental linkage groups, resulting in seven linkage groups with a total length of 545 cM. The present linkage map is currently the most advanced map in rose with regard to marker density, genome coverage and with robust markers, giving good perspectives for QTL mapping and marker-assisted breeding in rose. The SSR markers, together with RFLP markers, provide good anchor points for future map alignment studies in rose and related species. Codominantly scored AFLP markers were helpful in the integration of the parental maps.

  7. Methylation markers: a potential force driving cancer diagnostics forward.

    PubMed

    Khandige, Surabhi; Shanbhogue, Vikram V; Chakrabarty, Sanjiban; Kapettu, Satyamoorthy

    2011-01-01

    Epigenetics, transcending genetics, genomics, and molecular biology, is now poised to be the avant-garde beacon of biological science. The rise of DNA methylation studies marks a new dawn in the field of epigenetics, which only a few decades ago was largely underestimated, but is now a dynamic area of research challenging and revising traditional paradigms of gene expression and behavior. Cancer research enjoys a major share of this attention to DNA methylation and it has been widely accepted for some time now that cancer is as much an epigenetic phenomenon as it is genetic. Epigenetic lesions and perturbations are acquired during the life of an individual and accumulate with aging and represent the flip side of the same coin that bears genetic mutations. Both events, either individually or in cooperation, result in the development and progression of cancer. Epigenetic research and the hunt for strong methylation markers has been ably mitigated by new and improved high throughput technology that has improved the efficacy and enabled the rapid progress of biomarker evaluation and validation. This review looks into some of the recent strides in biomarker research dealing exclusively with methylation markers and the potential key they may hold to the resilient door shut tight on cancer diagnostics and treatment.

  8. A case of Cryptococcus neoformans meningitis in a patient with abnormal levels of isolated immunological markers.

    PubMed

    Simsek, B; Guven, E; Gumral, R; Mert, G; Saracli, M A; Besirbellioglu, B; Yildiran, S T

    2016-09-01

    Cryptococcal meningitis is considered rare in immunocompetent patients and is mainly a disease of immunocompromised patients. We report a case of cryptococcal meningitis, due to Cryptococcus neoformans, in an apparently healthy individual with abnormal levels of isolated immunological markers. Regardless of the patient's immune status, the result of the disease can be serious unless the disease is diagnosed early. PMID:27402508

  9. An improved consensus linkage map of barley based on flow-sorted chromosomes and SNP markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Recent advances in high-throughput genotyping have made it easier to combine information from different mapping populations into consensus genetic maps, which provide increased marker density and genome coverage compared to individual maps. Previously, a SNP-based genotyping platform was developed a...

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

    SciTech Connect

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

    1994-07-01

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

  11. A Study of the Acquisition of Discourse Markers by Chinese Learners of English

    ERIC Educational Resources Information Center

    Bu, Jiemin

    2013-01-01

    This study investigates the acquisition of discourse markers by Chinese learners of English in terms of gender, style and individual identity. The subjects of the study are 15 female university students and 15 male university students. The data is collected by means of audio recording in the classroom discussion and in the interviews. The examined…

  12. Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Accurate identification of individual genotypes is important for cacao (Theobroma cacao L.) breeding, germplasm conservation and seed propagation. The development of single nucleotide polymorphism (SNP) markers in cacao offers an effective way to use a high-throughput genotyping system for cacao gen...

  13. MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES

    EPA Science Inventory

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

  14. (ISEA) MOLECULAR MARKER ANALYSIS OF DEARS SAMPLES

    EPA Science Inventory

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

  15. Sarcoidosis: Immunopathogenesis and Immunological Markers

    PubMed Central

    Loke, Wei Sheng Joshua; Herbert, Cristan; Thomas, Paul S.

    2013-01-01

    Sarcoidosis is a multisystem granulomatous disorder invariably affecting the lungs. It is a disease with noteworthy variations in clinical manifestation and disease outcome and has been described as an “immune paradox” with peripheral anergy despite exaggerated inflammation at disease sites. Despite extensive research, sarcoidosis remains a disease with undetermined aetiology. Current evidence supports the notion that the immune response in sarcoidosis is driven by a putative antigen in a genetically susceptible individual. Unfortunately, there currently exists no reliable biomarker to delineate the disease severity and prognosis. As such, the diagnosis of sarcoidosis remains a vexing clinical challenge. In this review, we outline the immunological features of sarcoidosis, discuss the evidence for and against various candidate etiological agents (infective and noninfective), describe the exhaled breath condensate, a novel method of identifying immunological biomarkers, and suggest other possible immunological biomarkers to better characterise the immunopathogenesis of sarcoidosis. PMID:26464848

  16. Understanding individual routing behaviour.

    PubMed

    Lima, Antonio; Stanojevic, Rade; Papagiannaki, Dina; Rodriguez, Pablo; González, Marta C

    2016-03-01

    Knowing how individuals move between places is fundamental to advance our understanding of human mobility (González et al. 2008 Nature 453, 779-782. (doi:10.1038/nature06958)), improve our urban infrastructure (Prato 2009 J. Choice Model. 2, 65-100. (doi:10.1016/S1755-5345(13)70005-8)) and drive the development of transportation systems. Current route-choice models that are used in transportation planning are based on the widely accepted assumption that people follow the minimum cost path (Wardrop 1952 Proc. Inst. Civ. Eng. 1, 325-362. (doi:10.1680/ipeds.1952.11362)), despite little empirical support. Fine-grained location traces collected by smart devices give us today an unprecedented opportunity to learn how citizens organize their travel plans into a set of routes, and how similar behaviour patterns emerge among distinct individual choices. Here we study 92 419 anonymized GPS trajectories describing the movement of personal cars over an 18-month period. We group user trips by origin-destination and we find that most drivers use a small number of routes for their routine journeys, and tend to have a preferred route for frequent trips. In contrast to the cost minimization assumption, we also find that a significant fraction of drivers' routes are not optimal. We present a spatial probability distribution that bounds the route selection space within an ellipse, having the origin and the destination as focal points, characterized by high eccentricity independent of the scale. While individual routing choices are not captured by path optimization, their spatial bounds are similar, even for trips performed by distinct individuals and at various scales. These basic discoveries can inform realistic route-choice models that are not based on optimization, having an impact on several applications, such as infrastructure planning, routing recommendation systems and new mobility solutions. PMID:26962031

  17. Understanding individual routing behaviour.

    PubMed

    Lima, Antonio; Stanojevic, Rade; Papagiannaki, Dina; Rodriguez, Pablo; González, Marta C

    2016-03-01

    Knowing how individuals move between places is fundamental to advance our understanding of human mobility (González et al. 2008 Nature 453, 779-782. (doi:10.1038/nature06958)), improve our urban infrastructure (Prato 2009 J. Choice Model. 2, 65-100. (doi:10.1016/S1755-5345(13)70005-8)) and drive the development of transportation systems. Current route-choice models that are used in transportation planning are based on the widely accepted assumption that people follow the minimum cost path (Wardrop 1952 Proc. Inst. Civ. Eng. 1, 325-362. (doi:10.1680/ipeds.1952.11362)), despite little empirical support. Fine-grained location traces collected by smart devices give us today an unprecedented opportunity to learn how citizens organize their travel plans into a set of routes, and how similar behaviour patterns emerge among distinct individual choices. Here we study 92 419 anonymized GPS trajectories describing the movement of personal cars over an 18-month period. We group user trips by origin-destination and we find that most drivers use a small number of routes for their routine journeys, and tend to have a preferred route for frequent trips. In contrast to the cost minimization assumption, we also find that a significant fraction of drivers' routes are not optimal. We present a spatial probability distribution that bounds the route selection space within an ellipse, having the origin and the destination as focal points, characterized by high eccentricity independent of the scale. While individual routing choices are not captured by path optimization, their spatial bounds are similar, even for trips performed by distinct individuals and at various scales. These basic discoveries can inform realistic route-choice models that are not based on optimization, having an impact on several applications, such as infrastructure planning, routing recommendation systems and new mobility solutions.

  18. Predicting Individual Fuel Economy

    SciTech Connect

    Lin, Zhenhong; Greene, David L

    2011-01-01

    To make informed decisions about travel and vehicle purchase, consumers need unbiased and accurate information of the fuel economy they will actually obtain. In the past, the EPA fuel economy estimates based on its 1984 rules have been widely criticized for overestimating on-road fuel economy. In 2008, EPA adopted a new estimation rule. This study compares the usefulness of the EPA's 1984 and 2008 estimates based on their prediction bias and accuracy and attempts to improve the prediction of on-road fuel economies based on consumer and vehicle attributes. We examine the usefulness of the EPA fuel economy estimates using a large sample of self-reported on-road fuel economy data and develop an Individualized Model for more accurately predicting an individual driver's on-road fuel economy based on easily determined vehicle and driver attributes. Accuracy rather than bias appears to have limited the usefulness of the EPA 1984 estimates in predicting on-road MPG. The EPA 2008 estimates appear to be equally inaccurate and substantially more biased relative to the self-reported data. Furthermore, the 2008 estimates exhibit an underestimation bias that increases with increasing fuel economy, suggesting that the new numbers will tend to underestimate the real-world benefits of fuel economy and emissions standards. By including several simple driver and vehicle attributes, the Individualized Model reduces the unexplained variance by over 55% and the standard error by 33% based on an independent test sample. The additional explanatory variables can be easily provided by the individuals.

  19. Genetics and biological markers in urachal cancer

    PubMed Central

    van Rhijn, Bas W. G.

    2016-01-01

    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. PMID:27785422

  20. Individuality of handwriting.

    PubMed

    Srihari, Sargur N; Cha, Sung-Hyuk; Arora, Hina; Lee, Sangjik

    2002-07-01

    Motivated by several rulings in United States courts concerning expert testimony in general, and handwriting testimony in particular, we undertook a study to objectively validate the hypothesis that handwriting is individual. Handwriting samples of 1,500 individuals, representative of the U.S. population with respect to gender, age, ethnic groups, etc., were obtained. Analyzing differences in handwriting was done by using computer algorithms for extracting features from scanned images of handwriting. Attributes characteristic of the handwriting were obtained, e.g., line separation, slant, character shapes, etc. These attributes, which are a subset of attributes used by forensic document examiners (FDEs), were used to quantitatively establish individuality by using machine learning approaches. Using global attributes of handwriting and very few characters in the writing, the ability to determine the writer with a high degree of confidence was established. The work is a step towards providing scientific support for admitting handwriting evidence in court. The mathematical approach and the resulting software also have the promise of aiding the FDE.

  1. Detection of immunocytological markers in photomicroscopic images

    NASA Astrophysics Data System (ADS)

    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.

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

    SciTech Connect

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

    1994-12-31

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

  3. Development of diagnostic microsatellite markers from whole-genome sequences of Ammodramus sparrows for assessing admixture in a hybrid zone

    PubMed Central

    Kovach, Adrienne I; Walsh, Jennifer; Ramsdell, Jordan; Kelley Thomas, W

    2015-01-01

    Studies of hybridization and introgression and, in particular, the identification of admixed individuals in natural populations benefit from the use of diagnostic genetic markers that reliably differentiate pure species from each other and their hybrid forms. Such diagnostic markers are often infrequent in the genomes of closely related species, and genomewide data facilitate their discovery. We used whole-genome data from Illumina HiSeqS2000 sequencing of two recently diverged (600,000 years) and hybridizing, avian, sister species, the Saltmarsh (Ammodramus caudacutus) and Nelson's (A. nelsoni) Sparrow, to develop a suite of diagnostic markers for high-resolution identification of pure and admixed individuals. We compared the microsatellite repeat regions identified in the genomes of the two species and selected a subset of 37 loci that differed between the species in repeat number. We screened these loci on 12 pure individuals of each species and report on the 34 that successfully amplified. From these, we developed a panel of the 12 most diagnostic loci, which we evaluated on 96 individuals, including individuals from both allopatric populations and sympatric individuals from the hybrid zone. Using simulations, we evaluated the power of the marker panel for accurate assignments of individuals to their appropriate pure species and hybrid genotypic classes (F1, F2, and backcrosses). The markers proved highly informative for species discrimination and had high accuracy for classifying admixed individuals into their genotypic classes. These markers will aid future investigations of introgressive hybridization in this system and aid conservation efforts aimed at monitoring and preserving pure species. Our approach is transferable to other study systems consisting of closely related and incipient species. PMID:26078861

  4. On the Additive and Dominant Variance and Covariance of Individuals Within the Genomic Selection Scope

    PubMed Central

    Vitezica, Zulma G.; Varona, Luis; Legarra, Andres

    2013-01-01

    Genomic evaluation models can fit additive and dominant SNP effects. Under quantitative genetics theory, additive or “breeding” values of individuals are generated by substitution effects, which involve both “biological” additive and dominant effects of the markers. Dominance deviations include only a portion of the biological dominant effects of the markers. Additive variance includes variation due to the additive and dominant effects of the markers. We describe a matrix of dominant genomic relationships across individuals, D, which is similar to the G matrix used in genomic best linear unbiased prediction. This matrix can be used in a mixed-model context for genomic evaluations or to estimate dominant and additive variances in the population. From the “genotypic” value of individuals, an alternative parameterization defines additive and dominance as the parts attributable to the additive and dominant effect of the markers. This approach underestimates the additive genetic variance and overestimates the dominance variance. Transforming the variances from one model into the other is trivial if the distribution of allelic frequencies is known. We illustrate these results with mouse data (four traits, 1884 mice, and 10,946 markers) and simulated data (2100 individuals and 10,000 markers). Variance components were estimated correctly in the model, considering breeding values and dominance deviations. For the model considering genotypic values, the inclusion of dominant effects biased the estimate of additive variance. Genomic models were more accurate for the estimation of variance components than their pedigree-based counterparts. PMID:24121775

  5. Self-Injurious Behaviour in Individuals with Autism Spectrum Disorder and Intellectual Disability

    ERIC Educational Resources Information Center

    Richards, C.; Oliver, C.; Nelson, L.; Moss, J.

    2012-01-01

    Background: Autism spectrum disorder (ASD) has been identified as a risk marker for self-injurious behaviour. In this study we aimed to describe the prevalence, topography and correlates of self-injury in individuals with ASD in contrast to individuals with Fragile X and Down syndromes and examine person characteristics associated with self-injury…

  6. Paternal isodisomy of chromosome 6 in association with a maternal supernumerary marker chromosome (6)

    SciTech Connect

    James, R.S.; Crolla, J.A.; Sitch, F.L.

    1994-09-01

    Uniparental disomy may arise by a number of different mechanisms of aneuploidy correction. A population that has been identified as being at increased risk of aneuploidy are those individuals bearing supernumerary marker chromosomes (SMCs). There have been a number of cases reported of trisomy 21 in association with bi-satellited marker chromosomes have described two individuals with small inv dup (15) markers. One had paternal isodisomy of chromosome 15 and Angelman syndrome. The other had maternal heterodisomy (15) and Prader-Willi syndrome. At the Wessex Regional Genetics Laboratory we have conducted a search for uniparental disomy of the normal homologues of the chromosomes from which SMCs originated. Our study population consists of 39 probands with SMCs originating from a number of different autosomes, including 17 with SMCs of chromosome 15 origin. Using PCR amplification of microsatellite repeat sequences located distal to the regions included in the SMCs we have determined the parental origin of the two normal homologues in each case. We have identified paternal isodisomy of chromosome 6 in a female child with a supernumerary marker ring chromosome 6 in approximately 70% of peripheral blood lymphocytes. The marker was found to be of maternal origin. This is the second case of paternal isodisomy of chromosome 6 to be reported, and the first in association with a SMC resulting in a partial trisomy for a portion of the short arm of chromosome 6. In spite of this, the patient appears to be functioning appropriately for her age.

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

    PubMed

    Khadivi-Khub, Abdollah; Soorni, Aboozar

    2014-06-01

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

  8. Distribution of Genetic Marker Concentrations for Fecal Indicator Bacteria in Sewage and Animal Feces

    PubMed Central

    Kelty, Catherine A.; Varma, Manju; Sivaganesan, Mano; Haugland, Richard A.

    2012-01-01

    Very little is known about the density and distribution of fecal indicator bacteria (FIB) genetic markers measured by quantitative real-time PCR (qPCR) in fecal pollution sources. Before qPCR-based FIB technologies can be applied to waste management and public health risk applications, it is vital to characterize the concentrations of these genetic markers in pollution sources (i.e., untreated wastewater and animal feces). We report the distribution of rRNA genetic markers for several general FIB groups, including Clostridium spp., Escherichia coli, enterococci, and Bacteroidales, as determined by qPCR on reference collections consisting of 54 primary influent sewage samples collected from treatment facilities across the United States and fecal samples representing 20 different animal species. Based on raw sewage sample collection data, individual FIB genetic markers exhibited a remarkable similarity in concentration estimates from locations across the United States ranging from Hawaii to Florida. However, there was no significant correlation between genetic markers for most FIB combinations (P > 0.05). In addition, large differences (up to 5 log10 copies) in the abundance of FIB genetic markers were observed between animal species, emphasizing the importance of indicator microorganism selection and animal source contribution for future FIB applications. PMID:22504809

  9. Multi-Marker Strategy in Heart Failure: Combination of ST2 and CRP Predicts Poor Outcome

    PubMed Central

    Dupuy, Anne Marie; Curinier, Corentin; Kuster, Nils; Huet, Fabien; Leclercq, Florence; Davy, Jean Marc; Cristol, Jean Paul; Roubille, François

    2016-01-01

    Natriuretic peptides (BNP and NT-proBNP) are recognized as gold-standard predictive markers in Heart Failure (HF). However, currently ST2 (member of the interleukin 1 receptor family) has emerged as marker of inflammation, fibrosis and cardiac stress. We evaluated ST2 and CRP as prognostic markers in 178 patients with chronic heart failure in comparison with other classical markers such as clinical established parameters but also biological markers: NT-proBNP, hs-cTnT alone or in combination. In multivariate analysis, subsequent addition of ST2 led to age, CRP and ST2 as the only remaining predictors of all-cause mortality (HR 1.03, HR 1.61 and HR 2.75, respectively) as well as of cardiovascular mortality (HR 1.00, HR 2.27 and HR 3.78, respectively). The combined increase of ST2 and CRP was significant for predicting worsened outcomes leading to identify a high risk subgroup that individual assessment of either marker. The same analysis was performed with ST2 in combination with Barcelona score. Overall, our findings extend previous data demonstrating that ST2 in combination with CRP as a valuable tool for identifying patients at risk of death. PMID:27311068

  10. Large-scale development of PIP and SSR markers and their complementary applied in Nicotiana.

    PubMed

    Huang, L; Cao, H; Yang, L; Yu, Yu; Wang, Yu

    2013-08-01

    PIP (Potential Intron Polymorphism) and SSR (Simple Sequence Repeats) were used in many species, but large-scale development and combined use of these two markers have not been reported in tobacco. In this study, a total of 12,388 PIP and 76,848 SSR markers were designed and uploaded to a web-accessible database (http://yancao.sdau.edu.cn/tgb/). E-PCR analysis showed that PIP and SSR rarely overlapped and were strongly complementary in the tobacco genome. The density was 3.07 PIP and 1.72 SSR markers per 10 kb of the known sequences. A total of 153 and 166 alleles were detectedby 22 PIP and 22 SSR markers in 64 Nicotiana accessions. SSR produced higher PIC (polymorphism information content) values and identified more alleles than PIP, whereas PIP could identify larger numbers of rare alleles. Mantel testing demonstrated a high correlation coefficient (r = 0.949, P < 0.001) between PIP and SSR. The UPGMA dendrogram created from the combined PIP and SSR markers was clearer and more reliable than the individual PIP or SSR dendrograms. It suggested that PIP and SSR can make up the deficiency of molecular markers not only in tobacco but other plant.

  11. A comparison of single-sample estimators of effective population sizes from genetic marker data.

    PubMed

    Wang, Jinliang

    2016-10-01

    In molecular ecology and conservation genetics studies, the important parameter of effective population size (Ne ) is increasingly estimated from a single sample of individuals taken at random from a population and genotyped at a number of marker loci. Several estimators are developed, based on the information of linkage disequilibrium (LD), heterozygote excess (HE), molecular coancestry (MC) and sibship frequency (SF) in marker data. The most popular is the LD estimator, because it is more accurate than HE and MC estimators and is simpler to calculate than SF estimator. However, little is known about the accuracy of LD estimator relative to that of SF and about the robustness of all single-sample estimators when some simplifying assumptions (e.g. random mating, no linkage, no genotyping errors) are violated. This study fills the gaps and uses extensive simulations to compare the biases and accuracies of the four estimators for different population properties (e.g. bottlenecks, nonrandom mating, haplodiploid), marker properties (e.g. linkage, polymorphisms) and sample properties (e.g. numbers of individuals and markers) and to compare the robustness of the four estimators when marker data are imperfect (with allelic dropouts). Extensive simulations show that SF estimator is more accurate, has a much wider application scope (e.g. suitable to nonrandom mating such as selfing, haplodiploid species, dominant markers) and is more robust (e.g. to the presence of linkage and genotyping errors of markers) than the other estimators. An empirical data set from a Yellowstone grizzly bear population was analysed to demonstrate the use of the SF estimator in practice.

  12. A comparison of single-sample estimators of effective population sizes from genetic marker data.

    PubMed

    Wang, Jinliang

    2016-10-01

    In molecular ecology and conservation genetics studies, the important parameter of effective population size (Ne ) is increasingly estimated from a single sample of individuals taken at random from a population and genotyped at a number of marker loci. Several estimators are developed, based on the information of linkage disequilibrium (LD), heterozygote excess (HE), molecular coancestry (MC) and sibship frequency (SF) in marker data. The most popular is the LD estimator, because it is more accurate than HE and MC estimators and is simpler to calculate than SF estimator. However, little is known about the accuracy of LD estimator relative to that of SF and about the robustness of all single-sample estimators when some simplifying assumptions (e.g. random mating, no linkage, no genotyping errors) are violated. This study fills the gaps and uses extensive simulations to compare the biases and accuracies of the four estimators for different population properties (e.g. bottlenecks, nonrandom mating, haplodiploid), marker properties (e.g. linkage, polymorphisms) and sample properties (e.g. numbers of individuals and markers) and to compare the robustness of the four estimators when marker data are imperfect (with allelic dropouts). Extensive simulations show that SF estimator is more accurate, has a much wider application scope (e.g. suitable to nonrandom mating such as selfing, haplodiploid species, dominant markers) and is more robust (e.g. to the presence of linkage and genotyping errors of markers) than the other estimators. An empirical data set from a Yellowstone grizzly bear population was analysed to demonstrate the use of the SF estimator in practice. PMID:27288989

  13. Evaluation of Colon Cancer – Specific Antigen 2 as a Potential Serum Marker for Colorectal Cancer

    PubMed Central

    Leman, Eddy S.; Schoen, Robert E.; Magheli, Ahmed; Sokoll, Lori J.; Chan, Daniel W.; Getzenberg, Robert H.

    2015-01-01

    Purpose A blood test to detect colon cancer at a preventable stage would represent a major advancement. We have previously identified colon cancer – specific markers using focused proteomics analysis of nuclear structural proteins. Two of these markers, colon cancer – specific antigen (CCSA)-3 and CCSA-4, have been developed into blood-based markers that are able to distinguish individuals with colorectal cancer from those without. CCSA-2 is a distinct novel colon cancer marker identified using focused proteomics. Experimental Design Using an indirect ELISA on serum samples obtained from two institutions, we evaluated CCSA-2 as a serum-based colon cancer marker. A total of111serumsamples from individuals who underwent colonoscopy and were subsequently diagnosed as either being normal or having hyperplastic polyps, nonadvanced adenomas, advanced adenomas, and colorectal cancer were evaluated. A diverse control population that consisted of 125 serum samples was also included in this study. Results Receiver operating characteristic analyses were used to measure the sensitivity and specificity of CCSA-2. CCSA-2 at a cutoff of 10.8 µg/mL has overall specificity of 78.4% [95% confidence interval (95% CI), 67.3–87.1%] and sensitivity of 97.3% (95% CI, 85.8–99.5%) in separating individuals with advanced adenomas and colorectal cancer from normal, hyperplastic, and nonadvanced adenoma populations. The receiver operating characteristic curve for CCSA-2 has an area under the curve of 0.90 (95% CI, 0.83–0.95). Conclusion Our initial study shows that CCSA-2 is a potential serum-based marker for colon cancer detection with high sensitivity and specificity. PMID:18316554

  14. From Individuals to Epidemics

    NASA Technical Reports Server (NTRS)

    Levin, Simon A.; Durrett, R.

    1996-01-01

    Heterogeneous mixing fundamentally changes the dynamics of infectious diseases; finding ways to incorporate it into models represents a critical challenge. Phenomenological approaches are deficient in their lack of attention to underlying processes; individual-based models, on the other hand, may obscure the essential interactions in a sea of detail. The challenge then is to find ways to bridge these levels of description, starting from individual-based models and deriving macroscopic descriptions from them that retain essential detail, and filter out the rest. In this paper, attempts to achieve this transformation are described for a class of models where non-random mixing arises from the spatial localization of interactions. In general, the epidemic threshold is found to be larger owing to spatial localization than for a homogeneous mixing population. An improved estimate of the dynamics is developed by the use of moment equations, and a simple estimate of the threshold in terms of a 'dyad heuristic'. For more general models in which local infection is not described by mass action, the connection with related partial differential equations is investigated.

  15. Individual Genetic Susceptibility

    SciTech Connect

    Eric J. Hall

    2008-12-08

    Risk estimates derived from epidemiological studies of exposed populations, as well as the maximum permissible doses allowed for occupational exposure and exposure of the public to ionizing radiation are all based on the assumption that the human population is uniform in its radiosensitivity, except for a small number of individuals, such as ATM homozygotes who are easily identified by their clinical symptoms. The hypothesis upon which this proposal is based is that the human population is not homogeneous in radiosensitiviry, but that radiosensitive sub-groups exist which are not easy to identify. These individuals would suffer an increased incidence of detrimental radiation effects, and distort the shape of the dose response relationship. The radiosensitivity of these groups depend on the expression levels of specific proteins. The plan was to investigate the effect of 3 relatively rare, high penetrate genes available in mice, namely Atm, mRad9 & Brca1. The purpose of radiation protection is to prevent! deterministic effects of clinical significance and limit stochastic effects to acceptable levels. We plan, therefore to compare with wild type animals the radiosensitivity of mice heterozygous for each of the genes mentioned above, as well as double heterozygotes for pairs of genes, using two biological endpoints: a) Ocular cataracts as an important and relevant deterministic effect, and b) Oncogenic transformation in cultured embryo fibroblasts, as a surrogate for carcinogenesis, the most relevant stochastic effect.

  16. Individual Colorimetric Observer Model

    PubMed Central

    Asano, Yuta; Fairchild, Mark D.; Blondé, Laurent

    2016-01-01

    This study proposes a vision model for individual colorimetric observers. The proposed model can be beneficial in many color-critical applications such as color grading and soft proofing to assess ranges of color matches instead of a single average match. We extended the CIE 2006 physiological observer by adding eight additional physiological parameters to model individual color-normal observers. These eight parameters control lens pigment density, macular pigment density, optical densities of L-, M-, and S-cone photopigments, and λmax shifts of L-, M-, and S-cone photopigments. By identifying the variability of each physiological parameter, the model can simulate color matching functions among color-normal populations using Monte Carlo simulation. The variabilities of the eight parameters were identified through two steps. In the first step, extensive reviews of past studies were performed for each of the eight physiological parameters. In the second step, the obtained variabilities were scaled to fit a color matching dataset. The model was validated using three different datasets: traditional color matching, applied color matching, and Rayleigh matches. PMID:26862905

  17. Individual recovery profiles in basketball players.

    PubMed

    Moreno, Jordi; Ramos-Castro, Juan; Rodas, Gil; Tarragó, Joan R; Capdevila, Lluís

    2015-01-01

    In the sport context, recovery has been characterized as a multifactor process (physiological, psychological, behavioral, social, etc.). This study takes a multidisciplinary approach to find psychophysiological markers of the stress-recovery process. It aims to determine how athletes' specific recovery actions relate to their perceptions of recovery, and Heart Rate Variability (HRV). A total of 196 assessments were analyzed from 6 players on a men's professional basketball team within the Liga LEB Oro basketball federation (2012/2013 season). Perceptions of recovery, recovery strategies, and HRV were recorded. The results show a pattern of individual differences in behavior related to athletes' recovery actions and HRV profiles throughout the season (p < .05). Moreover, we observed that each player had different recovery needs. In light of these results, we suggest an individualistic approach to evaluating and monitoring recovery to attend more accurately to each player's recovery needs.

  18. SSR and SRAP marker-based linkage map of Vitis vinifera L.

    PubMed Central

    Guo, Yinshan; Lin, Hong; Liu, Zhendong; Zhao, Yuhui; Guo, Xiuwu; Li, Kun

    2014-01-01

    An F1 population was created by the cross ‘87-1’ × ‘9-22’. The female parent ‘87-1’ was an extremely early maturing cultivar with strong flavour. The male parent was an excellent breeding line producing large berries maturing late. The mapping population included 149 randomly chosen individuals. Molecular genetic map for each parent and the consensus map were constructed using simple sequence repeat and sequence-related amplified polymorphism markers by software JoinMap 3.0. The ‘87-1’ map covers a total length of 1272.9 cM distributed in 21 linkage groups and consists of 163 molecular markers with an average distance between adjacent markers of 8.9 cM. The ‘9-22’ map covers a total length of 1267.4 cM distributed in 20 linkage groups and consists of 158 molecular markers with an average distance between adjacent markers of 9.1 cM. The consensus map covers a total length of 1537.1 cM distributed in 21 linkage groups and one doublet and consists of 217 molecular markers with an average distance of 7.8 cM between adjacent markers. The length of the linkage groups is 69.8 cM on average. The map covers the 19 chromosomes of the Vitis genome and can lay a solid foundation for further studies such as quantative trait loci (QTL) mapping of correlated traits and marker-assisted selection. PMID:26019507

  19. Identification and assessment of markers of biotin status in healthy adults.

    PubMed

    Eng, Wei Kay; Giraud, David; Schlegel, Vicki L; Wang, Dong; Lee, Bo Hyun; Zempleni, Janos

    2013-07-28

    Human biotin requirements are unknown and the identification of reliable markers of biotin status is necessary to fill this knowledge gap. Here, we used an outpatient feeding protocol to create states of biotin deficiency, sufficiency and supplementation in sixteen healthy men and women. A total of twenty possible markers of biotin status were assessed, including the abundance of biotinylated carboxylases in lymphocytes, the expression of genes from biotin metabolism and the urinary excretion of biotin and organic acids. Only the abundance of biotinylated 3-methylcrotonyl-CoA carboxylase (holo-MCC) and propionyl-CoA carboxylase (holo-PCC) allowed for distinguishing biotin-deficient and biotin-sufficient individuals. The urinary excretion of biotin reliably identified biotin-supplemented subjects, but did not distinguish between biotin-depleted and biotin-sufficient individuals. The urinary excretion of 3-hydroxyisovaleric acid detected some biotin-deficient subjects, but produced a meaningful number of false-negative results and did not distinguish between biotin-sufficient and biotin-supplemented individuals. None of the other organic acids that were tested were useful markers of biotin status. Likewise, the abundance of mRNA coding for biotin transporters, holocarboxylase synthetase and biotin-dependent carboxylases in lymphocytes were not different among the treatment groups. Generally, datasets were characterised by variations that exceeded those seen in studies in cell cultures. We conclude that holo-MCC and holo-PCC are the most reliable, single markers of biotin status tested in the present study.

  20. Identification and assessment of markers of biotin status in healthy adults

    PubMed Central

    Eng, Wei Kay; Giraud, David; Schlegel, Vicki L.; Wang, Dong; Lee, Bo Hyun; Zempleni, Janos

    2016-01-01

    Human biotin requirements are unknown and the identification of reliable markers of biotin status is necessary to fill this knowledge gap. Here, we used an outpatient feeding protocol to create states of biotin deficiency, sufficiency and supplementation in sixteen healthy men and women. A total of twenty possible markers of biotin status were assessed, including the abundance of biotinylated carboxylases in lymphocytes, the expression of genes from biotin metabolism and the urinary excretion of biotin and organic acids. Only the abundance of biotinylated 3-methylcrotonyl-CoA carboxylase (holo-MCC) and propionyl-CoA carboxylase (holo-PCC) allowed for distinguishing biotin-deficient and biotin-sufficient individuals. The urinary excretion of biotin reliably identified biotin-supplemented subjects, but did not distinguish between biotin-depleted and biotin-sufficient individuals. The urinary excretion of 3-hydroxyisovaleric acid detected some biotin-deficient subjects, but produced a meaningful number of false-negative results and did not distinguish between biotin-sufficient and biotin-supplemented individuals. None of the other organic acids that were tested were useful markers of biotin status. Likewise, the abundance of mRNA coding for biotin transporters, holocarboxylase synthetase and biotin-dependent carboxylases in lymphocytes were not different among the treatment groups. Generally, datasets were characterised by variations that exceeded those seen in studies in cell cultures. We conclude that holo-MCC and holo-PCC are the most reliable, single markers of biotin status tested in the present study. PMID:23302490

  1. Use of SSR markers to determine the anther-derived homozygous lines in coconut.

    PubMed

    Perera, P I P; Perera, L; Hocher, V; Verdeil, J-L; Yakandawala, D M D; Weerakoon, L K

    2008-11-01

    Anther culture was used to obtain dihaploid (DH) coconut plants and their ploidy level was determined by flow cytometric analysis. Simple sequence repeat (SSR) marker analysis was conducted to identify the homozygous diploid individuals. Ploidy analysis showed that 50% of the tested plantlets were haploid and 50% were diploid. Polymorphic fragments of the mother palm and their segregation patterns in anther-derived plantlets were used to determine the origin of the diploid plantlets. Using a diagnostic SSR marker (CNZ43), all the diploid plantlets tested were identified as being derived from microspores (i.e. were homozygous) and were thus candidates for use in coconut breeding programs. PMID:18712524

  2. Newborn with Supernumerary Marker Chromosome Derived from Chromosomes 11 And 22- A Case Report

    PubMed Central

    VAHIDI MEHRJARDI, Mohammad Yahya; DEHGHAN TEZERJANI, Masoud; NORI-SHADKAM, Mahmoud; KALANTAR, Seyed Mehdi; DEHGHANI, Mohammadreza

    2016-01-01

    The interpretation of supernumerary chromosome is important for genetic counseling and prognosis. Here, we used SNP array and conventional karyotyping method to identify a denovo marker chromosome originated from chromosome 22 and 11 in a newborn transferred to the Neonatal Intensive Care Unit of Shahid Sadoughi Hospital in 2015. Clinical abnormalities identified in the newborn were dysmorphic face, intrauterine growth retardation, atrial septal defect (ASD), the hypoplasia of corpus callosum and septum pellucidum. These clinical abnormalities can be related to this marker, and it may help genetic counselor for predicting abnormality risk in susceptible individuals as well as prenatal diagnosis. PMID:27141501

  3. Newborn with Supernumerary Marker Chromosome Derived from Chromosomes 11 And 22- A Case Report.

    PubMed

    Vahidi Mehrjardi, Mohammad Yahya; Dehghan Tezerjani, Masoud; Nori-Shadkam, Mahmoud; Kalantar, Seyed Mehdi; Dehghani, Mohammadreza

    2016-03-01

    The interpretation of supernumerary chromosome is important for genetic counseling and prognosis. Here, we used SNP array and conventional karyotyping method to identify a denovo marker chromosome originated from chromosome 22 and 11 in a newborn transferred to the Neonatal Intensive Care Unit of Shahid Sadoughi Hospital in 2015. Clinical abnormalities identified in the newborn were dysmorphic face, intrauterine growth retardation, atrial septal defect (ASD), the hypoplasia of corpus callosum and septum pellucidum. These clinical abnormalities can be related to this marker, and it may help genetic counselor for predicting abnormality risk in susceptible individuals as well as prenatal diagnosis. PMID:27141501

  4. Isolation and development of microsatellite markers for the Japanese dormouse, Glirulus japonicus.

    PubMed

    Yasuda, S P; Nakayama, A A; Iwabuchi, M; Minato, S; Tsuchiya, K; Suzuki, H

    2009-03-01

    Eight microsatellite markers were developed for the Japanese dormouse (Glirulus japonicus), a natural monument and near-threatened species in Japan. The markers amplify in individuals from all of the mitochondrial lineages detected in a previous study. Numerous polymorphisms were detected in specimens from a local population in central Honshu (11-21 alleles per locus; n = 31) and from the entire distribution range of the species (19-41 alleles per locus; n = 152). These microsatellites will be useful in conservation genetic studies of G. japonicus.

  5. Newborn with Supernumerary Marker Chromosome Derived from Chromosomes 11 And 22- A Case Report.

    PubMed

    Vahidi Mehrjardi, Mohammad Yahya; Dehghan Tezerjani, Masoud; Nori-Shadkam, Mahmoud; Kalantar, Seyed Mehdi; Dehghani, Mohammadreza

    2016-03-01

    The interpretation of supernumerary chromosome is important for genetic counseling and prognosis. Here, we used SNP array and conventional karyotyping method to identify a denovo marker chromosome originated from chromosome 22 and 11 in a newborn transferred to the Neonatal Intensive Care Unit of Shahid Sadoughi Hospital in 2015. Clinical abnormalities identified in the newborn were dysmorphic face, intrauterine growth retardation, atrial septal defect (ASD), the hypoplasia of corpus callosum and septum pellucidum. These clinical abnormalities can be related to this marker, and it may help genetic counselor for predicting abnormality risk in susceptible individuals as well as prenatal diagnosis.

  6. Somatic markers, working memory, and decision making.

    PubMed

    Hinson, John M; Jameson, Tina L; Whitney, Paul

    2002-12-01

    The somatic marker hypothesis formulated by Damasio (e.g., 1994; Damasio, Tranel, & Damasio, 1991) argues that affective reactions ordinarily guide and simplify decision making. Although originally intended to explain decision-making deficits in people with specific frontal lobe damage, the hypothesis also applies to decision-making problems in populations without brain injury. Subsequently, the gambling task was developed by Bechara (Bechara, Damasio, Damasio, & Anderson, 1994) as a diagnostic test of decision-making deficit in neurological populations. More recently, the gambling task has been used to explore implications of the somatic marker hypothesis, as well as to study suboptimal decision making in a variety of domains. We examined relations among gambling task decision making, working memory (WM) load, and somatic markers in a modified version of the gambling task. Increased WM load produced by secondary tasks led to poorer gambling performance. Declines in gambling performance were associated with the absence of the affective reactions that anticipate choice outcomes and guide future decision making. Our experiments provide evidence that WM processes contribute to the development of somatic markers. If WM functioning is taxed, somatic markers may not develop, and decision making may thereby suffer. PMID:12641178

  7. Individualizing justice after Atkins.

    PubMed

    Brakel, S Jan

    2006-01-01

    On August 6, 2005, newspapers and other media outlets reported that Daryl Atkins had been determined by a Virginia jury not to be retarded and therefore was mentally competent to receive the death penalty. A judge immediately scheduled his execution for December. Atkins, of course, is the convicted murderer whose case three years earlier had led the U.S. Supreme Court, in a landmark ruling, to declare that mentally retarded offenders are constitutionally exempt from the death penalty. While a bitter irony for Atkins, his family, and supporters, the Virginia jury's finding suggests that the practical effects of the Supreme Court's decision are less dramatic than many had anticipated. It shows that mere labels need not be determinative and that judges and juries as well as mental health experts called to assist them in capital cases can continue to work toward an individualized brand of justice.

  8. CA 72-4 compared with CEA and CA 19-9 as a marker of some gastrointestinal malignancies.

    PubMed

    Lopez, J B; Royan, G P; Lakhwani, M N; Mahadaven, M; Timor, J

    1999-01-01

    The objective of this study was to compare CA 72-4 with CEA and CA 19-9 in gastrointestinal malignancies. CA 72-4 was assayed by radioimmunoassay and CEA and CA 19-9 with the Abbott IMx analyser. The study included 52 patients with gastrointestinal cancer and 20 controls with benign gastrointestinal diseases. The 52 cases showed marker sensitivities of 39%, 49% and 35% for CA 72-4, CEA and CA 19-9, respectively, and 64% when the markers were combined. Marker expression in serum was highest in colorectal carcinoma followed by gastric and esophageal carcinoma. The sensitivities of the individual markers in colorectal, gastric and esophageal carcinomas, respectively, were: CA 72-4, 56%, 32% and 18%; CEA, 83%, 33% and 18%; CA 19-9, 53%, 25% and 18%. The sensitivity of the three markers in combination was 89%, 50% and 46% in colorectal, gastric and esophageal cancer, respectively. The specificity of CA 72-4, CEA and CA 19-9 was 100%, 72% and 86%, respectively. However, CA 72-4 is not a useful a marker for gastrointestinal cancers because of its poor sensitivity. CEA, which had the best overall sensitivity and a reasonable specificity, was the most useful single marker, especially for colorectal cancer. Whereas the single markers were not useful in gastric and esophageal cancer, the combination of the three may be.

  9. Consensus mapping and identification of markers for marker-assisted selection of Wsm2 in wheat

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A recently identified Wheat streak mosaic virus (WSMV) resistance gene Wsm2 confers a high level of resistance. Objective of this study was to identify closely linked DNA markers for Wsm2 for use in marker-assisted selection (MAS) in wheat. Two segregating populations (CO960293-2/’TAM 111’ and CO96...

  10. 36 CFR 12.7 - Headstones and markers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 1 2012-07-01 2012-07-01 false Headstones and markers. 12.7... NATIONAL CEMETERY REGULATIONS § 12.7 Headstones and markers. (a) Government headstones and markers...) The erection of a marker or monument at private expense to mark a grave in lieu of a...

  11. 30 CFR 816.11 - Signs and markers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 3 2014-07-01 2014-07-01 false Signs and markers. 816.11 Section 816.11... § 816.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall— (1) Be...) Conform to local ordinances and codes. (b) Duration of maintenance. Signs and markers shall be...

  12. 30 CFR 817.11 - Signs and markers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Signs and markers. 817.11 Section 817.11... ACTIVITIES § 817.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall... markers shall be maintained during all activities to which they pertain. (c) Mine and...

  13. 30 CFR 816.11 - Signs and markers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 3 2013-07-01 2013-07-01 false Signs and markers. 816.11 Section 816.11... § 816.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall— (1) Be...) Conform to local ordinances and codes. (b) Duration of maintenance. Signs and markers shall be...

  14. 36 CFR 12.7 - Headstones and markers.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 36 Parks, Forests, and Public Property 1 2011-07-01 2011-07-01 false Headstones and markers. 12.7... NATIONAL CEMETERY REGULATIONS § 12.7 Headstones and markers. (a) Government headstones and markers...) The erection of a marker or monument at private expense to mark a grave in lieu of a...

  15. 36 CFR 12.7 - Headstones and markers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 36 Parks, Forests, and Public Property 1 2013-07-01 2013-07-01 false Headstones and markers. 12.7... NATIONAL CEMETERY REGULATIONS § 12.7 Headstones and markers. (a) Government headstones and markers...) The erection of a marker or monument at private expense to mark a grave in lieu of a...

  16. 30 CFR 817.11 - Signs and markers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 3 2013-07-01 2013-07-01 false Signs and markers. 817.11 Section 817.11... ACTIVITIES § 817.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall... markers shall be maintained during all activities to which they pertain. (c) Mine and...

  17. 36 CFR 12.7 - Headstones and markers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 1 2014-07-01 2014-07-01 false Headstones and markers. 12.7... NATIONAL CEMETERY REGULATIONS § 12.7 Headstones and markers. (a) Government headstones and markers...) The erection of a marker or monument at private expense to mark a grave in lieu of a...

  18. 30 CFR 816.11 - Signs and markers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Signs and markers. 816.11 Section 816.11... § 816.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall— (1) Be...) Conform to local ordinances and codes. (b) Duration of maintenance. Signs and markers shall be...

  19. 36 CFR 12.7 - Headstones and markers.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Headstones and markers. 12.7... NATIONAL CEMETERY REGULATIONS § 12.7 Headstones and markers. (a) Government headstones and markers...) The erection of a marker or monument at private expense to mark a grave in lieu of a...

  20. 30 CFR 817.11 - Signs and markers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 3 2014-07-01 2014-07-01 false Signs and markers. 817.11 Section 817.11... ACTIVITIES § 817.11 Signs and markers. (a) Specifications. Signs and markers required under this part shall... markers shall be maintained during all activities to which they pertain. (c) Mine and...

  1. Salivary Markers of Inflammation in Response to Acute Stress

    PubMed Central

    Slavish, Danica C.; Graham-Engeland, Jennifer E.; Smyth, Joshua M.; Engeland, Christopher G.

    2014-01-01

    There is burgeoning interest in the ability to detect inflammatory markers in response to stress within naturally occurring social contexts and/or across multiple time points per day within individuals. Salivary collection is a less invasive process than current methods of blood collection and enables intensive naturalistic methodologies, such as those involving extensive repeated measures per day over time. Yet the reliability and validity of saliva-based to blood-based inflammatory biomarkers in response to stress remains unclear. We review and synthesize the published studies that have examined salivary markers of inflammation following exposure to an acute laboratory stressor. Results from each study are reviewed by analyte (IL-1β, TNF-α, IL-6, IL-2, IL-4, IL-10, IL-12, CRP) and stress type (social-cognitive and exercise-physical), after which methodological issues and limitations are addressed. Although the literature is limited, several inflammatory markers (including IL-1β, TNF-α, and IL-6) have been reliably determined from saliva and have increased significantly in response to stress across multiple studies, with effect sizes ranging from very small to very large. Although CRP from saliva has been associated with CRP in circulating blood more consistently than other biomarkers have been associated with their counterparts in blood, evidence demonstrating it reliably responds to acute stress is absent. Although the current literature is presently too limited to allow broad assertion that inflammatory biomarkers determined from saliva are valuable for examining acute stress responses, this review suggests that specific targets may be valid and highlights specific areas of need for future research. PMID:25205395

  2. Forensic performance of two insertion-deletion marker assays.

    PubMed

    Fondevila, M; Phillips, C; Santos, C; Pereira, R; Gusmão, L; Carracedo, A; Butler, J M; Lareu, M V; Vallone, P M

    2012-09-01

    Improving the amplification and analysis of highly degraded DNA extracts has been a longstanding area of research in forensic genetics. One of the most promising recent developments in analysis of degraded DNA is the availability of short, biallelic insertion-deletion length polymorphisms (InDels) in highly multiplexed assays. InDels share many of the favourable characteristics of single-nucleotide polymorphisms (SNPs) that make them ideal markers for analysis of degraded DNA, including: analysis in short amplicon size ranges, high multiplexing capability and low mutation rates. In addition, as length-based polymorphisms, InDels can be analysed with the same simple dye-labelled PCR primer methods as standard forensic short tandem repeats. Separation and detection of fluorescently dye-labelled PCR products by capillary electrophoresis eliminate the multiple step protocols required by SNP typing with single-base extension assays and provide a closer relationship between the input DNA and the profile peak height ratios. Therefore InDel genotyping represents an effective new approach for human identification that adds informative new loci to the existing battery of forensic markers. To assess the utility of InDels for forensic analysis, we characterised population variation with two InDel identification assays: the 30-plex Qiagen DIPplex panel and a 38-plex panel developed by Pereira et al. in 2009. Allele frequencies were generated for the 68 markers in US African American, Caucasian, East Asian and Hispanic samples. We made a thorough assessment of the individual and combined performance of the InDel sets, as well as characterising profile artifacts and other issues related to the routine use of these newly developed forensic assays based on artificially degraded DNA and mixed source samples.

  3. Late positive slow waves as markers of chunking during encoding

    PubMed Central

    Nogueira, Ana M. L.; Bueno, Orlando F. A.; Manzano, Gilberto M.; Kohn, André F.; Pompéia, Sabine

    2015-01-01

    Electrophysiological markers of chunking of words during encoding have mostly been shown in studies that present pairs of related stimuli. In these cases it is difficult to disentangle cognitive processes that reflect distinctiveness (i.e., conspicuous items because they are related), perceived association between related items and unified representations of various items, or chunking. Here, we propose a paradigm that enables the determination of a separate Event-related Potential (ERP) marker of these cognitive processes using sequentially related word triads. Twenty-three young healthy individuals viewed 80 15-word lists composed of unrelated items except for the three words in the middle serial positions (triads), which could be either unrelated (control list), related perceptually, phonetically or semantically. ERP amplitudes were measured at encoding of each one of the words in the triads. We analyzed two latency intervals (350–400 and 400–800 ms) at midline locations. Behaviorally, we observed a progressive facilitation in the immediate free recall of the words in the triads depending on the relations between their items (control < perceptual < phonetic < semantic), but only semantically related items were recalled as chunks. P300-like deflections were observed for perceptually deviant stimuli. A reduction of amplitude of a component akin to the N400 was found for words that were phonetically and semantically associated with prior items and therefore were not associated to chunking. Positive slow wave (PSW) amplitudes increased as successive phonetically and semantically related items were presented, but they were observed earlier and were more prominent at Fz for semantic associates. PSWs at Fz and Cz also correlated with recall of semantic word chunks. This confirms prior claims that PSWs at Fz are potential markers of chunking which, in the proposed paradigm, were modulated differently from the detection of deviant stimuli and of relations between

  4. Liver fibrosis markers in alcoholic liver disease.

    PubMed

    Chrostek, Lech; Panasiuk, Anatol

    2014-07-01

    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. PMID:25009372

  5. [Study of genetic markers of duodenal ulcer].

    PubMed

    Tsimmerman, Ia S; Onosova, E A; Tsimmerman, I Ia

    1989-05-01

    The results of determination of various hereditary predisposition markers in peptic ulcer are given: in the population, in patients with duodenal ulcer and in their siblings (risk group). Of importance for revealing subjects with hereditary predisposition to duodenal ulcer are the clinico-genealogical analysis, determination of the blood group, especially in simultaneous determination of a "secretory status" ("status of non-secretion" of the ABH blood system agglutinogen in the saliva), increase in the mass of parietal cells and, to some extent, of the distinguishing features of dermatoglyphics (in combination with the above markers). Determination of taste sensitivity to phenylthiocarbamide is non-informative. PMID:2770215

  6. Surrogate Markers of Abdominal Aortic Aneurysm Progression.

    PubMed

    Wanhainen, Anders; Mani, Kevin; Golledge, Jonathan

    2016-02-01

    The natural course of many abdominal aortic aneurysms (AAA) is to gradually expand and eventually rupture and monitoring the disease progression is essential to their management. In this publication, we review surrogate markers of AAA progression. AAA diameter remains the most widely used and important marker of AAA growth. Standardized reporting of reproducible methods of measuring AAA diameter is essential. Newer imaging assessments, such as volume measurements, biomechanical analyses, and functional and molecular imaging, as well as circulating biomarkers, have potential to add important information about AAA progression. Currently, however, there is insufficient evidence to recommend their routine use in clinical practice. PMID:26715680

  7. Home care safety markers: a scoping review.

    PubMed

    Macdonald, Marilyn; Lang, Ariella; Storch, Jan; Stevenson, Lynn; Donaldson, Susan; Barber, Tanya; Iaboni, Kristine

    2013-01-01

    Safety in home care is a new research frontier, and one in which demand for services continues to rise. A scoping review of the home care literature on chronic obstructive pulmonary disease and congestive heart failure was thus completed to identify safety markers that could serve to develop our understanding of safety in this sector. Results generated seven safety markers: (a) Home alone; (b) A fixed agenda in a foreign language; (c) Strangers in the home; (d) The butcher, the baker, the candlestick maker; (e) Medication mania; (f) Out of pocket: The cost of caring at home; and (g) My health for yours: Declining caregiver health. PMID:23679662

  8. Molecular marker technologies for plant improvement.

    PubMed

    Winter, P; Kahl, G

    1995-07-01

    The exploitation of DNA polymorphisms by an ever-increasing number of molecular marker technologies has begun to have an impact on plant genome research and breeding. Restriction fragment length polymorphisms, micro- and mini-satellites and PCR-based approaches are used to determine inter- and intra-specific genetic diversity and construct molecular maps of crops using specially designed mapping populations. Resistance genes and other agronomically important loci are tagged with tightly linked DNA markers and the genes isolated by magabase DNA technology and cloning into yeast artificial chromosomes (YAC). This review discusses some recent developments and results in this field.

  9. Urinary 5-hydroxytryptophol: a possible marker of recent alcohol consumption.

    PubMed

    Voltaire, A; Beck, O; Borg, S

    1992-04-01

    Urinary 5-hydroxytryptophol (5-HTOL) is currently being evaluated as a marker of recent alcohol consumption. To compensate for urinary dilution, the molar ratio between 5-HTOL and 5-hydroxyindole-3-acetic acid (5-HIAA) is used. The 5-HTOL/5-HIAA ratio showed a satisfactory degree of individual stability when it was followed in a group of teetotallers for 1 month. The mean value of 5-HTOL/5-HIAA in a group of 69 persons abstaining from alcohol was 7.6 (pmoles 5-HTOL/nmoles 5-HIAA). Ninety-seven percent had values ranging from 4 to 17, with no value exceeding 20. A group of healthy volunteers were tested 12 hr after alcohol consumption and showed a dose-dependent and statistically significant elevation in the 5-HTOL/5-HIAA ratio. Four regular alcohol consumers who were followed during a period of 3 months of drinking had elevated values of the 5-HTOL/5-HIAA ratio in 60% of their urine samples. The present study indicates that urinary 5-HTOL/5-HIAA is a sensitive and reliable marker of recent alcohol consumption. We propose that a 5-HTOL/5-HIAA ratio greater than 20 (pmoles/nmoles) can be used to indicate recent alcohol consumption. This limit gives a low frequency of false positives; the statistical probability of having a value greater than 20 during abstinence from alcohol was calculated to be less than 0.001. PMID:1375446

  10. DNA Methylation as Surrogate Marker For Gastric Cancer

    PubMed Central

    Oh, Jung-Hwan; Jung, Sung-Hoon; Hong, Seung-Jin; Rhyu, Mun-Gan

    2015-01-01

    Stomach cancer remains, stubbornly, highly prevalent in East Asia. Still, stomach cancer has few biomarkers by which it can be predicted. Helicobacter pylori infection, a known carcinogen of stomach cancer, usually goes undetected prior to cancer diagnosis, due to the poor mucosal environments that its related gastric atrophy causes. We propose, herein, an endoscopic-biopsy-based cancer-predicting DNA methylation marker. We semi-quantitatively examined the methylation-variable sites near the CpG-island margins by radioisotope-labeling methylation-specific polymerase chain reaction in association with H. pylori, which increases age-related over-methylation in CpG islands of gastric mucosa. These age-related methylation patterns of the transitional-CpG sites are proposed as useful surrogate markers for stomach cancer. It would be helpful for setting the optimal screening interval for high-risk subjects as well as for estimating the prognosis and the predictability for recurrence of early gastric cancer in patients having undergone endoscopic submucosal dissection. New screening-interval guidelines for gastric cancer should be suggested considering individual risk based on age, severity of atrophy, H. pylori status, and DNA methylation pattern. PMID:26473155

  11. Distribution of forensic marker allelic frequencies in Pernambuco, Northestern Brazil.

    PubMed

    Santos, S M; Souza, C A; Rabelo, K C N; Souza, P R E; Moura, R R; Oliveira, T C; Crovella, S

    2015-04-30

    Pernambuco is one of the 27 federal units of Brazil, ranking seventh in the number of inhabitants. We examined the allele frequencies of 13 short tandem repeat loci (CFS1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, vWA, and TPOX), the minimum recommended by the Federal Bureau of Investigation and commonly used in forensic genetics laboratories in Brazil, in a sample of 609 unrelated individuals from all geographic regions of Pernambuco. The allele frequencies ranged from 5 to 47.2%. No significant differences for any loci analyzed were observed compared with other publications in other various regions of Brazil. Most of the markers observed were in Hardy-Weinberg equilibrium. The occurrence of the allele 47.2 (locus FGA) and alleles 35.1 and 39 (locus D21S11), also described in a single study of the Brazilian population, was observed. The other forensic parameters analyzed (matching probability, power of discrimination, polymorphic information content, paternity exclusion, complement factor I, observed heterozygosity, expected heterozygosity) indicated that the studied markers are very informative for human forensic identification purposes in the Pernambuco population.

  12. A test of mink microsatellite markers in the ferret: amplification and sequence comparisons.

    PubMed

    Anistoroaei, R; Christensen, K

    2006-12-01

    Short tandem repeats are a source of highly polymorphic markers in mammalian genomes. Genetic variation at these hypervariable loci is extensively used for linkage analysis and to identify individuals, and is very useful for interpopulation and interspecies studies. Fifty-nine microsatellite markers from American mink were tested in the ferret, under the same conditions as for the mink. Of the 59, 43 of them (73.5%) amplified a ferret sequence; 5 amplification products differed in size from the respective mink sequences. Ten amplified fragments from ferret were sequenced. The sequences that were identical in size to those from mink displayed a high degree of conservation, with some differences at the repeat motif sites. These results could aid cross-utilization of markers between these two species. PMID:17362355

  13. Genetic variability in wild genotypes of Passiflora cincinnata based on RAPD markers.

    PubMed

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

    2010-12-21

    The genetic diversity and characteristics of commercial interest of Passiflora species make it useful to characterize wild germplasm, because of their potential use for fruit, ornamental and medicinal purposes. We evaluated genetic diversity, using RAPD markers, of 32 genotypes of Passiflora cincinnata collected from the wild in the region of Vitória da Conquista, Bahia, Brazil. Thirteen primers generated 95 polymorphic markers and only one monomorphic marker. The mean genetic distance between the genotypes estimated by the complement of the Dice index was 0.51 (ranging from 0.20-0.85), and genotype grouping based on the UPGMA algorithm showed wide variability among the genotypes. This type of information contributes to identification and conservation of the biodiversity of this species and for the identification of pairs of divergent individuals for maximum exploitation of existing variability.

  14. With current gene markers, presymptomatic diagnosis of heritable disease is still a family affair

    SciTech Connect

    Not Available

    1987-09-04

    In the last four years, genes or genetic markers have been identified for a host of disorders including Huntington's disease, cystic fibrosis, Duchenne muscular dystrophy, polycystic kidney disease, bipolar depressive disorder, retinoblastoma, Alzheimer's disease, and schizophrenia. Such discoveries have made it possible to diagnose in utero some 30 genetic diseases during the first trimester of pregnancy. Yet, while these newly discovered gene markers may be revolutionizing prenatal and presymptomatic diagnosis, they are in many respects halfway technology. Such was the opinion of several speakers at a conference sponsored by the American Medical Association in Washington, DC. At the conference, entitled DNA Probes in the Practice of Medicine, geneticists emphasized that gene markers - stretches of DNA that are usually inherited in tandem with a disease gene - are usually not sufficient for presymptomatic diagnosis of genetic disease in an individual.

  15. Multiple congenital abnormalities in a newborn with two supernumerary marker chromosomes derived from chromosome 14.

    PubMed

    Faas, B H W; Van Der Deure, J; Wunderink, M I; Merkx, G; Brunner, H G

    2006-01-01

    Pure partial duplication or triplication of the proximal part of chromosome 14 has been reported in only 4 patients. Other individuals with a duplication or triplication of this region have additional chromosome imbalances. We present a new case with a supernumerary marker chromosome in all blood cells and in 35% of the cells an additional smaller marker chromosome. Both markers appeared to be derived from chromosome 14 (del(14)(q21.2) in all cells and del(14)(q11.2) in 35% of the cells). This results in a partial duplication of the proximal region of chromosome 14, combined with a mosaic partial triplication of a smaller segment of the same region. In this paper, we compare the clinical features of this case to those of cases from the literature. Although most of the patients from literature were unbalanced translocation carriers, their clinical features were comparable, except from renal abnormalities.

  16. Stability of Palatal Rugae as a Forensic Marker in Orthodontically Treated Cases.

    PubMed

    Ali, Batool; Shaikh, Attiya; Fida, Mubassar

    2016-09-01

    The palatal rugae have been used as a reference landmark and identification marker by orthodontists and forensic analysts. However, the reliability of palatal rugae as a forensic marker remains questionable once an individual is subjected to orthodontic treatment. This study aimed at evaluating the changes in the rugae pattern after nonextraction, extraction, and maxillary expansion orthodontic treatment. The lengths and shapes of palatal rugae were evaluated on the pretreatment and post-treatment dental casts of 168 subjects using the Thomas and Kotze classification. Extraction treatment significantly reduced the second and third rugae lengths (p < 0.05), whereas the third rugae length was significantly increased after palatal expansion (p < 0.05). The shape of rugae remained consistent in all the study groups which may be used as a reliable forensic marker in subjects undergoing orthodontic treatment. However, the use of the lengths of palatal rugae in forensic odontology must be made with caution.

  17. Fourteen polymorphic microsatellite markers for the threatened Arnica montana (Asteraceae)1

    PubMed Central

    Duwe, Virginia K.; Ismail, Sascha A.; Buser, Andres; Sossai, Esther; Borsch, Thomas; Muller, Ludo A. H.

    2015-01-01

    • Premise of the study: Microsatellite markers were developed to investigate population genetic structure in the threatened species Arnica montana. • Methods and Results: Fourteen microsatellite markers with di-, tetra-, and hexanucleotide repeat motifs were developed for A. montana using 454 pyrosequencing without and with library-enrichment methods, resulting in 56,545 sequence reads and 14,467 sequence reads, respectively. All loci showed a high level of polymorphism, with allele numbers ranging from four to 11 in five individuals from five populations (25 samples) and an expected heterozygosity ranging from 0.192 to 0.648 across the loci. • Conclusions: This set of microsatellite markers is the first one described for A. montana and will facilitate conservation genetic applications as well as the understanding of phylogeographic patterns in this species. PMID:25606354

  18. Genetic linkage of mild pseudoachondroplasia (PSACH) to markers in the pericentromeric region of chromosome 19

    SciTech Connect

    Briggs, M.D.; Rasmussen, M.; Garber, P.; Rimoin, D.L.; Cohn, D.H. ); Weber, J.L. ); Yuen, J.; Reinker, K. )

    1993-12-01

    Pseudoachondroplasia (PSACH) is a dominantly inherited form of short-limb dwarfism characterized by dysplastic changes in the spine, epiphyses, and metaphyses and early onset osteoarthropathy. Chondrocytes from affected individuals accumulate an unusual appearing material in the rough endoplasmic reticulum, which has led to the hypothesis that a structural abnormality in a cartilage-specific protein produces the phenotype. The authors recently identified a large family with a mild form of pseudoachondroplasia. By genetic linkage to a dinucleotide repeat polymorphic marker (D19S199), they have localized the disease gene to chromosome 19 (maximum lod score of 7.09 at a recombination fraction of 0.03). Analysis of additional markers and recombinations between the linked markers and the phenotype suggests that the disease gene resides within a 6.3-cM interval in the immediate pericentromeric region of the chromosome. 39 refs., 2 figs., 1 tab.

  19. The use of fecal markers to facilitate sample collection in group-housed cats.

    PubMed

    Griffin, Brenda

    2002-03-01

    The provision of proper social housing is a priority when designing an experiment using domestic cats as laboratory animals. When animals are group-housed, studies requiring analysis of stool samples from individual subjects pose difficulty in sample collection and identification. In this study, commercially available concentrated food colorings (known as bakers pastes) were used as fecal markers in group-housed cats. Cats readily consumed 0.5 ml of bakers paste food coloring once daily in canned cat food. Colorings served as fecal markers by imparting a distinct color to each cat s feces, allowing identification in the litter box. In addition, colored glitter (1/8 teaspoon in canned food) was fed to cats and found to be a reliable fecal marker. Long-term feeding of colorings and glitter was found to be safe and effective at yielding readily identifiable stools. PMID:11958604

  20. The first genetic linkage map of Primulina eburnea (Gesneriaceae) based on EST-derived SNP markers.

    PubMed

    Feng, Chen; Feng, Chao; Kang, Ming

    2016-06-01

    Primulina eburnea is a promising candidate for domestication and floriculture, since it is easy to culture and has beautiful flowers. An F₂ population of 189 individuals was established for the construction of first-generation linkage maps based on expressed sequence tags-derived single-nucleotide polymorphism markers using the massARRAY genotyping platform. Of the 232 screened markers, 215 were assigned to 18 LG according to the haploid number of chromosomes in the species. The linkage map spanned a total of 3774.7 cM with an average distance of 17.6 cM between adjacent markers. This linkage map provides a framework for identification of important genes in breeding programmes. PMID:27350682

  1. Autonomic patterns during respiratory suspensions: possible markers of Transcendental Consciousness.

    PubMed

    Travis, F; Wallace, R K

    1997-01-01

    In two experiments, we investigated physiological correlates of transcendental consciousness during Transcendental Meditation sessions. In the first, experimenter-initiated bells, based on observed physiological patterns, marked three phases during a Transcendental Meditation session in 16 individuals. Interrater reliability between participant and experimenter classification of experiences at each bell was quite good. During phases including transcendental consciousness experiences, skin conductance responses and heart rate deceleration occurred at the onset of respiratory suspensions or reductions in breath volume. In the second experiment, this autonomic pattern was compared with that during forced breath holding. Phasic autonomic activity was significantly higher at respiratory suspension onset than at breath holding onset. These easily measured markers could help focus research on the existence and characteristics of transcendental consciousness.

  2. Characterization of microsatellite markers for Baccharis dracunculifolia (Asteraceae)1

    PubMed Central

    Belini, Camila M. B.; Marques, Marcia O. M.; Figueira, Glyn M.; Bajay, Miklos M.; Campos, Jaqueline B.; Viana, João P. G.; Pinheiro, José B.; Zucchi, Maria I.

    2016-01-01

    Premise of the study: Baccharis dracunculifolia (Asteraceae) is a native plant of the Atlantic Forest that is used for the production of essential oil. Microsatellite markers were developed for this species to investigate the genetic diversity of three natural populations. Methods and Results: Seventeen out of 27 microsatellite loci identified in a genomic library used for the characterization of 315 individuals derived from three natural populations of B. dracunculifolia resulted in successful amplifications. Eleven polymorphic loci, ranging from two to seven alleles per locus, were obtained with expected and observed heterozygosity values ranging between 0.068 and 0.775 and 0.046 and 0.667, respectively. Conclusions: The microsatellite loci described in this study are tools that can be used for further studies of population genetics of B. dracunculifolia with a focus on deforested areas and conservation of natural populations. PMID:27011894

  3. Microsatellite markers for Senna spectabilis var. excelsa (Caesalpinioideae, Fabaceae)1

    PubMed Central

    López-Roberts, M. Cristina; Barbosa, Ariane R.; Paganucci de Queiroz, Luciano; van den Berg, Cássio

    2016-01-01

    Premise of the study: Senna spectabilis var. excelsa (Fabaceae) is a South and Central American tree of great ecological importance and one of the most common species in several sites of seasonally dry forests. Our goal was to develop microsatellite markers to assess the genetic diversity and structure of this species. Methods and Results: We designed and assessed 53 loci obtained from a microsatellite-enriched library and an intersimple sequence repeat library. Fourteen loci were polymorphic, and they presented a total of 39 alleles in a sample of 61 individuals from six populations. The mean values of observed and expected heterozygosities were 0.355 and 0.479, respectively. Polymorphism information content was 0.390 and the Shannon index was 0.778. Conclusions: Polymorphism information content and Shannon index indicate that at least nine of the 14 microsatellite loci developed are moderate to highly informative, and potentially useful for population genetic studies in this species. PMID:26819856

  4. Retinal vascular changes are a marker for cerebral vascular diseases

    PubMed Central

    Moss, Heather E.

    2016-01-01

    The retinal circulation is a potential marker of cerebral vascular disease because it shares origin and drainage with the intracranial circulation and because it can be directly visualized using ophthalmoscopy. Cross sectional and cohort studies have demonstrated associations between chronic retinal and cerebral vascular disease, acute retinal and cerebral vascular disease and chronic retinal vascular disease and acute cerebral vascular disease. In particular, certain qualitative features of retinopathy, retinal artery occlusion and increased retinal vein caliber are associated with concurrent and future cerebrovascular events. These associations persist after accounting for confounding variables known to be disease-causing in both circulations, which supports the potential use of retinal vasculature findings to stratify individuals with regards to cerebral vascular disease risk. PMID:26008809

  5. Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)

    PubMed Central

    2013-01-01

    Background Amorphophallus is a genus of perennial plants widely distributed in the tropics or subtropics of West Africa and South Asia. Its corms contain a high level of water-soluble glucomannan; therefore, it has long been used as a medicinal herb and food source. Genetic studies of Amorphophallus have been hindered by a lack of genetic markers. A large number of molecular markers are required for genetic diversity study and improving disease resistance in Amorphophallus. Here, we report large scale of transcriptome sequencing of two species: Amorphophallus konjac and Amorphophallus bulbifer using deep sequencing technology, and microsatellite (SSR) markers were identified based on these transcriptome sequences. Results cDNAs of A. konjac and A. bulbifer were sequenced using Illumina HiSeq™ 2000 sequencing technology. A total of 135,822 non-redundant unigenes were assembled from about 9.66 gigabases, and 19,596 SSRs were identified in 16,027 non-redundant unigenes. Di-nucleotide SSRs were the most abundant motif (61.6%), followed by tri- (30.3%), tetra- (5.6%), penta- (1.5%), and hexa-nucleotides (1%) repeats. The top di- and tri-nucleotide repeat motifs included AG/CT (45.2%) and AGG/CCT (7.1%), respectively. A total of 10,754 primer pairs were designed for marker development. Of these, 320 primers were synthesized and used for validation of amplification and assessment of polymorphisms in 25 individual plants. The total of 275 primer pairs yielded PCR amplification products, of which 205 were polymorphic. The number of alleles ranged from 2 to 14 and the polymorphism information content valued ranged from 0.10 to 0.90. Genetic diversity analysis was done using 177 highly polymorphic SSR markers. A phenogram based on Jaccard’s similarity coefficients was constructed, which showed a distinct cluster of 25 Amorphophallus individuals. Conclusion A total of 10,754 SSR markers have been identified in Amorphophallus using transcriptome sequencing. One hundred and

  6. A novel marker design for magnetic marker monitoring in the human gastrointestinal tract.

    PubMed

    Biller, Sebastian; Baumgarten, Daniel; Haueisen, Jens

    2011-12-01

    Magnetic marker monitoring (MMM) is a technique to determine the motility of the gastrointestinal tract and to observe the dissolution of pharmaceutical compounds. Today's magnetic markers usually consist of magnetized magnetite. Because of their weak magnetic fields, highly sensitive sensor systems are required. For a wider class of applications, stronger markers and more flexible measurement setups are necessary. In this paper, a novel marker design is introduced. This marker comprises one permanent magnet and a compartment of iron powder in a magnetically unstable configuration. During dissolution of the pharmaceuticals, the powder is redistributed around the magnet, thereby altering the externally measured magnetic induction. Based on this design, magnetically marked tablets and capsules were prepared and their magnetic field during dissolution was observed. Magnetic induction values were between 16 and 0.2  μT at distances of 5-30  cm, which is considerably higher compared to the pico-Tesla range of conventional markers. During dissolution, the magnetic induction decreased by between 14% and 27%. These values could be confirmed in detailed finite element method simulations. In conclusion, the present results indicate that our novel marker design is well suited for MMM with more flexible sensor technologies, such as magnetoresistive sensors.

  7. Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform

    PubMed Central

    Wielstra, B; Duijm, E; Lagler, P; Lammers, Y; Meilink, W R M; Ziermann, J M; Arntzen, J W

    2014-01-01

    Next-generation sequencing is a fast and cost-effective way to obtain sequence data for nonmodel organisms for many markers and for many individuals. We describe a protocol through which we obtain orthologous markers for the crested newts (Amphibia: Salamandridae: Triturus), suitable for analysis of interspecific hybridization. We use transcriptome data of a single Triturus species and design 96 primer pairs that amplify c. 180 bp fragments positioned in 3-prime untranslated regions. Next, these markers are tested with uniplex PCR for a set of species spanning the taxonomical width of the genus Triturus. The 52 markers that consistently show a single band of expected length at gel electrophoreses for all tested crested newt species are then amplified in five multiplex PCRs (with a plexity of ten or eleven) for 132 individual newts: a set of 84 representing the seven (candidate) species and a set of 48 from a presumed hybrid population. After pooling multiplexes per individual, unique tags are ligated to link amplicons to individuals. Subsequently, individuals are pooled equimolar and sequenced on the Ion Torrent next-generation sequencing platform. A bioinformatics pipeline identifies the alleles and recodes these to a genotypic format. Next, we test the utility of our markers. baps allocates the 84 crested newt individuals representing (candidate) species to their expected (candidate) species, confirming the markers are suitable for species delineation. newhybrids, a hybrid index and hiest confirm the 48 individuals from the presumed hybrid population to be genetically admixed, illustrating the potential of the markers to identify interspecific hybridization. We expect the set of markers we designed to provide a high resolving power for analysis of hybridization in Triturus. PMID:24571307

  8. Parallel tagged amplicon sequencing of transcriptome-based genetic markers for Triturus newts with the Ion Torrent next-generation sequencing platform.

    PubMed

    Wielstra, B; Duijm, E; Lagler, P; Lammers, Y; Meilink, W R M; Ziermann, J M; Arntzen, J W

    2014-09-01

    Next-generation sequencing is a fast and cost-effective way to obtain sequence data for nonmodel organisms for many markers and for many individuals. We describe a protocol through which we obtain orthologous markers for the crested newts (Amphibia: Salamandridae: Triturus), suitable for analysis of interspecific hybridization. We use transcriptome data of a single Triturus species and design 96 primer pairs that amplify c. 180 bp fragments positioned in 3-prime untranslated regions. Next, these markers are tested with uniplex PCR for a set of species spanning the taxonomical width of the genus Triturus. The 52 markers that consistently show a single band of expected length at gel electrophoreses for all tested crested newt species are then amplified in five multiplex PCRs (with a plexity of ten or eleven) for 132 individual newts: a set of 84 representing the seven (candidate) species and a set of 48 from a presumed hybrid population. After pooling multiplexes per individual, unique tags are ligated to link amplicons to individuals. Subsequently, individuals are pooled equimolar and sequenced on the Ion Torrent next-generation sequencing platform. A bioinformatics pipeline identifies the alleles and recodes these to a genotypic format. Next, we test the utility of our markers. baps allocates the 84 crested newt individuals representing (candidate) species to their expected (candidate) species, confirming the markers are suitable for species delineation. newhybrids, a hybrid index and hiest confirm the 48 individuals from the presumed hybrid population to be genetically admixed, illustrating the potential of the markers to identify interspecific hybridization. We expect the set of markers we designed to provide a high resolving power for analysis of hybridization in Triturus.

  9. RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout

    PubMed Central

    Salem, Mohamed; Vallejo, Roger L.; Leeds, Timothy D.; Palti, Yniv; Liu, Sixin; Sabbagh, Annas; Rexroad, Caird E.; Yao, Jianbo

    2012-01-01

    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 suitable for marker

  10. Shape and size of the body vs. musculoskeletal stress markers.

    PubMed

    Myszka, Anna; Piontek, Janusz

    2010-01-01

    The objective of this paper is to assess the relationship between the degree of development of muscle attachment sites (musculoskeletal stress markers - MSM1) and the length and circumference measurements of long bones and the body build expressed with the reconstructed values of body height (BH) and body mass (BM). The bone material (102 male and 99 female skeletons) used in the study was collected in the medieval burial ground in Cedynia, Poland. The authors analyzed 10 musculoskeletal stress markers located on the scapula (2), humerus (2), radius (2), femur (2) and tibia (2). The frequency and the degree of expression of muscle attachment size was carried out using the scale prepared by Myszka (2007). The scale encompassed three degrees of expression of muscle attachment size. Only changes of robusticity type (nonpathological changes) were taken into account. The assessment of body build of individuals was carried out according to the method proposed by Vancata & Charvátová (2001). Body height was reconstructed from the length of the humerus and femur using eight equations. Body mass was reconstructed from the measurements of the breadth of the proximal and distal sections of the femur and tibia (mechanical method) using twenty one equations. The equations were developed for different reference populations. The same equations were used for men and women. The correlation between the MSM and the length and circumference measurements of the bones was analyzed using the principal components analysis and the Gamma correlation coefficient. The strength of the correlation between the reconstructed body build traits (BH, BM) and the moderate degree of musculoskeletal stress markers expression was studied based on the principal components method and the Pearson correlation coefficient. A linear correlation was found between musculoskeletal stress markers and the circumference measurements and the reconstructed body mass, but no relationship with body height and the

  11. Thalassemic osteopathy: a new marker of bone deposition.

    PubMed

    Baldini, M; Forti, S; Orsatti, A; Marcon, A; Ulivieri, F M; Airaghi, L; Zanaboni, L; Cappellini, M D

    2014-01-01

    show good precision and low analytical CV, and, compared to other markers, they can acceptably reflect bone metabolic processes and promptly respond to antiosteoporotic treatments. We trust that this sensitive marker can be useful in the assessment of treatment efficacy and can overcome the pitfalls due to wide variability in the normal values of most BTMs that create difficulty in pinpointing the individual patient's response.

  12. Multiplexed microsatellite markers for seven Metarhizium species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cross-species transferability of 41 previously published simple sequence repeat (SSR) markers was assessed for 11 species of the entomopathogenic fungus Metarhizium. A collection of 65 Metarhizium isolates including all 54 used in a recent phylogenetic revision of the genus were characterized. Betwe...

  13. New softwares for automated microsatellite marker development.

    PubMed

    Martins, Wellington; de Sousa, Daniel; Proite, Karina; Guimarães, Patrícia; Moretzsohn, Marcio; Bertioli, David

    2006-01-01

    Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence 'experiment file' format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut. PMID:16493138

  14. Linguistic Markers of Inference Generation While Reading

    ERIC Educational Resources Information Center

    Clinton, Virginia; Carlson, Sarah E.; Seipel, Ben

    2016-01-01

    Words can be informative linguistic markers of psychological constructs. The purpose of this study is to examine associations between word use and the process of making meaningful connections to a text while reading (i.e., inference generation). To achieve this purpose, think-aloud data from third-fifth grade students (N = 218) reading narrative…

  15. Discourse Markers in Chinese Conversational Narrative

    ERIC Educational Resources Information Center

    Xiao, Yang

    2010-01-01

    This study examines the indexicality of discourse markers (DMs) in Chinese conversational narrative. Drawing upon theoretical and methodological principles related to narrative dimensions (Ochs & Capps, 2001), narrative desires (Ochs, 1997, 2004), and narrative positioning (Bamberg, 1997), this work proposes an integrated analytical framework for…

  16. [Tumor markers of urinary tract carcinoma].

    PubMed

    Kikuchi, Haruhito

    2004-04-01

    The tumor markers for malignant tumors arisen from urinary system including prostate cancer were reviewed. As for renal cell carcinoma there was no good marker used in routine test level at present. In the diagnosis of urothelial (transitional cell) carcinoma, mainly bladder cancer, 3 methods (urinary BTA, NMP22 and BFP) are used now in Japan. They all seem to be not fully sufficient in respect of the specificity. In foreign countries, new tests such as urinary telomerase and BLCA-4 are used and have been evaluated. On the diagnosis of prostate cancer, serum total PSA is well established and used. Various PSA relation markers have been advocated for the differentiation between benign prostate hypertrophy and carcinoma in so called "gray zone" level of total PSA. In methods based on the molecular forms of PSA, the ratio of free PSA to total PSA (f/T) is widely use, and proPSA is a test that is expected. Other approaches such as volume of index PSA, age specific PSA reference range and PSA velocity are also in practical application. Human glandular kallikrein 2, which belong to the human kallikrein family as well as PSA, is expected as a tumor specific marker.

  17. [Urinary tumor marker for urothelial cancer].

    PubMed

    Ohtani, M; Iwasaki, A; Shiraiwa, H

    2001-11-01

    The urinary tumor markers BTA, BFP and NMP22 used for urothelial cancer in Japan are reviewed briefly. We also evaluate and compare the sensitivity and specificity of BTA, BFP and NMP22 with urine cytology in detecting bladder cancer in 24 of our patients. The results showed that the sensitivity with urine cytology, BTA, BFP and NMP22 was 37, 54, 66 and 62% respectively. The specificity of BTA, BFP and NMP22 with urine cytology was 100, 65, 60 and 70% respectively. The sensitivity with BTA, BFP and NMP22 for urothelial cancer was higher than that with urine cytology. However, all except for urine cytology showed high false positive rates (83-90%) for urinary tract infection. These markers may thus complement urine cytology, which has a low sensitivity for urothelial cancer. Quite possibly they could act as low-cost and useful tumor markers, which could in turn reduce the number of invasive cystoscopic examinations. However, considering their high false positive rates for benign disease such as urinary tract infection, we must acknowledge that an ideal urothelial tumor marker, which is simple, non-invasive, inexpensive and accurate with high sensitivity and specificity has yet to be developed.

  18. A visible dominant marker for insect transgenesis.

    PubMed

    Osanai-Futahashi, Mizuko; Ohde, Takahiro; Hirata, Junya; Uchino, Keiro; Futahashi, Ryo; Tamura, Toshiki; Niimi, Teruyuki; Sezutsu, Hideki

    2012-01-01

    Transgenesis of most insects currently relies on fluorescence markers. Here we establish a transformation marker system causing phenotypes visible to the naked eye due to changes in the color of melanin pigments, which are widespread in animals. Ubiquitous overexpression of arylalkylamine-N-acetyl transferase in the silkworm, Bombyx mori, changes the color of newly hatched first-instar larvae from black to a distinctive light brown color, and can be used as a molecular marker by directly connecting to baculovirus immediate early 1 gene promoter. Suppression of black pigmentation by Bm-arylalkylamine-N-acetyl transferase can be observed throughout the larval stages and in adult animals. Alternatively, overexpression in another gene, B. mori β-alanyl-dopamine synthetase (Bm-ebony), changes the larval body color of older instars, although first-instar larvae had normal dark coloration. We further show that ectopic Bm-arylalkylamine-N-acetyl transferase expression lightens coloration in ladybird beetle Harmonia axyridis and fruit fly Drosophila melanogaster, highlighting the potential usefulness of this marker for transgenesis in diverse insect taxa. PMID:23250425

  19. Comprehension of Discourse Markers and Reading Comprehension

    ERIC Educational Resources Information Center

    Khatib, Mohamad

    2011-01-01

    According to many research findings, the presence of discourse markers (DMs) enhances readers' comprehension of the texts they read. However, there is a paucity of research on the relationship between knowledge of DMs and reading comprehension (RC) and the present study explores the relationship between them. Knowledge of DMs is measured through…

  20. Multiplexed Detection of Epigenetic Markers Using Quantum Dot (QD)-Encoded Hydrogel Microparticles.

    PubMed

    Yeom, Sang Yun; Son, Choong Hyun; Kim, Byung Sun; Tag, Sung Hyun; Nam, Eunjoo; Shin, Hyogeun; Kim, So Hyun; Gang, Haemin; Lee, Hyunjoo J; Choi, Jungkyu; Im, Heh-In; Cho, Il-Joo; Choi, Nakwon

    2016-04-19

    Epigenetic alterations in gene expression are influenced by experiences and environment, resulting in significant variation of epigenetic markers from individual to individual. Therefore, it is imperative to measure various epigenetic markers simultaneously from samples of individual subjects to accurately analyze the epigenetic markers in biological samples. Moreover, the individualized genome-wide analysis has become a critical technology for recent trends in clinical applications such as early diagnosis and personalized medicine screening of numerous diseases. The array-based detection of modified histones, conventionally used for multiplexed analysis of epigenetic changes, requires pooling of samples from many subjects to analyze population-wise differences in the expression of histone markers and does not permit individualized analysis. Here, we report multiplexed detection of genome-wide changes in various histone modifications at a single-residue resolution using quantum dot (QD)-encoded polyethylene glycol diacrylate (PEGDA) hydrogel microparticles. To demonstrate the potential of our methodology, we present the simultaneous detection of (1) acetylation of lysine 9 of histone 3 (Ac-H3K9), (2) dimethylation of H3K9 (2Me-H3K9), and (3) trimethylation of H3K9 (3Me-H3K9) from three distinct regions in the brain [nucleus accumbens (NAc), dorsal striatum (DSt), and cerebellum (Cbl)] of cocaine-exposed mice. Our hydrogel-based epigenetic assay enabled relative quantification of the three histone variants from only 10 μL of each brain lysate (protein content = ∼ 1 μg/μL) per mouse. We verified that the exposure to cocaine induced a significant increase of acetylation while a notable decrease in methylation in NAc. PMID:26974493

  1. Genetic Map of Triticale Integrating Microsatellite, DArT and SNP Markers

    PubMed Central

    Tyrka, Mirosław; Tyrka, Dorota; Wędzony, Maria

    2015-01-01

    Triticale (×Triticosecale Wittm) is an economically important crop for fodder and biomass production. To facilitate the identification of markers for agronomically important traits and for genetic and genomic characteristics of this species, a new high-density genetic linkage map of triticale was constructed using doubled haploid (DH) population derived from a cross between cultivars ‘Hewo’ and ‘Magnat’. The map consists of 1615 bin markers, that represent 50 simple sequence repeat (SSR), 842 diversity array technology (DArT), and 16888 DArTseq markers mapped onto 20 linkage groups assigned to the A, B, and R genomes of triticale. No markers specific to chromosome 7R were found, instead mosaic linkage group composed of 1880 highly distorted markers (116 bins) from 10 wheat chromosomes was identified. The genetic map covers 4907 cM with a mean distance between two bins of 3.0 cM. Comparative analysis in respect to published maps of wheat, rye and triticale revealed possible deletions in chromosomes 4B, 5A, and 6A, as well as inversion in chromosome 7B. The number of bin markers in each chromosome varied from 24 in chromosome 3R to 147 in chromosome 6R. The length of individual chromosomes ranged between 50.7 cM for chromosome 2R and 386.2 cM for chromosome 7B. A total of 512 (31.7%) bin markers showed significant (P < 0.05) segregation distortion across all chromosomes. The number of 8 the segregation distorted regions (SDRs) were identified on 1A, 7A, 1B, 2B, 7B (2 SDRs), 5R and 6R chromosomes. The high-density genetic map of triticale will facilitate fine mapping of quantitative trait loci, the identification of candidate genes and map-based cloning. PMID:26717308

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

    PubMed

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

    2014-11-01

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

  3. Genetic Map of Triticale Integrating Microsatellite, DArT and SNP Markers.

    PubMed

    Tyrka, Mirosław; Tyrka, Dorota; Wędzony, Maria

    2015-01-01

    Triticale (×Triticosecale Wittm) is an economically important crop for fodder and biomass production. To facilitate the identification of markers for agronomically important traits and for genetic and genomic characteristics of this species, a new high-density genetic linkage map of triticale was constructed using doubled haploid (DH) population derived from a cross between cultivars 'Hewo' and 'Magnat'. The map consists of 1615 bin markers, that represent 50 simple sequence repeat (SSR), 842 diversity array technology (DArT), and 16888 DArTseq markers mapped onto 20 linkage groups assigned to the A, B, and R genomes of triticale. No markers specific to chromosome 7R were found, instead mosaic linkage group composed of 1880 highly distorted markers (116 bins) from 10 wheat chromosomes was identified. The genetic map covers 4907 cM with a mean distance between two bins of 3.0 cM. Comparative analysis in respect to published maps of wheat, rye and triticale revealed possible deletions in chromosomes 4B, 5A, and 6A, as well as inversion in chromosome 7B. The number of bin markers in each chromosome varied from 24 in chromosome 3R to 147 in chromosome 6R. The length of individual chromosomes ranged between 50.7 cM for chromosome 2R and 386.2 cM for chromosome 7B. A total of 512 (31.7%) bin markers showed significant (P < 0.05) segregation distortion across all chromosomes. The number of 8 the segregation distorted regions (SDRs) were identified on 1A, 7A, 1B, 2B, 7B (2 SDRs), 5R and 6R chromosomes. The high-density genetic map of triticale will facilitate fine mapping of quantitative trait loci, the identification of candidate genes and map-based cloning. PMID:26717308

  4. Genetic marker anchoring by six-dimensional pools for development of a soybean physical map

    PubMed Central

    Wu, Xiaolei; Zhong, Guohua; Findley, Seth D; Cregan, Perry; Stacey, Gary; Nguyen, Henry T

    2008-01-01

    Background Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genome. Molecular markers provide anchor points for integration of genetic and physical maps and also validate BAC contigs assembled based solely on BAC fingerprints. We employed a six-dimensional BAC pooling strategy and an in silico approach to anchor molecular markers onto the soybean physical map. Results A total of 1,470 markers (580 SSRs and 890 STSs) were anchored by PCR on a subset of a Williams 82 BstY I BAC library pooled into 208 pools in six dimensions. This resulted in 7,463 clones (~1× genome equivalent) associated with 1470 markers, of which the majority of clones (6,157, 82.5%) were anchored by one marker and 1106 (17.5%) individual clones contained two or more markers. This contributed to 1184 contigs having anchor points through this 6-D pool screening effort. In parallel, the 21,700 soybean Unigene set from NCBI was used to perform in silico mapping on 80,700 Williams 82 BAC end sequences (BES). This in silico analysis yielded 9,835 positive results anchored by 4152 unigenes that contributed to 1305 contigs and 1624 singletons. Among the 1305 contigs, 305 have not been previously anchored by PCR. Therefore, 1489 (78.8%) of 1893 contigs are anchored with molecular markers. These results are being integrated with BAC fingerprints to assemble the BAC contigs. Ultimately, these efforts will lead to an integrated physical and genetic map resource. Conclusion We demonstrated that the six-dimensional soybean BAC pools can be efficiently used to anchor markers to soybean BACs despite the complexity of the soybean genome. In addition to anchoring markers, the 6-D pooling method was also effective for targeting BAC clones for investigating gene families and

  5. Cancers Screening in an Asymptomatic Population by Using Multiple Tumour Markers

    PubMed Central

    Wang, Hsin-Yao; Hsieh, Chia-Hsun; Wen, Chiao-Ni; Wen, Ying-Hao

    2016-01-01

    Background Analytic measurement of serum tumour markers is one of commonly used methods for cancer risk management in certain areas of the world (e.g. Taiwan). Recently, cancer screening based on multiple serum tumour markers has been frequently discussed. However, the risk–benefit outcomes appear to be unfavourable for patients because of the low sensitivity and specificity. In this study, cancer screening models based on multiple serum tumour markers were designed using machine learning methods, namely support vector machine (SVM), k-nearest neighbour (KNN), and logistic regression, to improve the screening performance for multiple cancers in a large asymptomatic population. Methods AFP, CEA, CA19-9, CYFRA21-1, and SCC were determined for 20 696 eligible individuals. PSA was measured in men and CA15-3 and CA125 in women. A variable selection process was applied to select robust variables from these serum tumour markers to design cancer detection models. The sensitivity, specificity, positive predictive value (PPV), negative predictive value, area under the curve, and Youden index of the models based on single tumour markers, combined test, and machine learning methods were compared. Moreover, relative risk reduction, absolute risk reduction (ARR), and absolute risk increase (ARI) were evaluated. Results To design cancer detection models using machine learning methods, CYFRA21-1 and SCC were selected for women, and all tumour markers were selected for men. SVM and KNN models significantly outperformed the single tumour markers and the combined test for men. All 3 studied machine learning methods outperformed single tumour markers and the combined test for women. For either men or women, the ARRs were between 0.003–0.008; the ARIs were between 0.119–0.306. Conclusion Machine learning methods outperformed the combined test in analysing multiple tumour markers for cancer detection. However, cancer screening based solely on the application of multiple tumour

  6. Development of novel tetra- and trinucleotide microsatellite markers for giant grouper Epinephelus lanceolatus using 454 pyrosequencing.

    PubMed

    Kim, Keun-Sik; Noh, Choong Hwan; Moon, Shin-Joo; Han, Seung-Hee; Bang, In-Chul

    2016-06-01

    Giant grouper (Epinephelus lanceolatus) is a commercially important species, but its wild population has recently been classified as vulnerable. This species has significant potential for use in aquaculture, though a greater understanding of population genetics is necessary for selective breeding programs to minimize kinship for genetically healthy individuals. High-throughput pyrosequencing of genomic DNA was used to identify and characterize novel tetra- and trinucleotide microsatellite markers in giant grouper from Sabah, Malaysia. In total, of 62,763 sequences containing simple sequence repeats (SSRs) were obtained, and 78 SSR loci were selected to possibly contain tetra- and trinucleotide repeats. Of these loci, 16 had tetra- and 8 had trinucleotide repeats, all of which exhibited polymorphisms within easily genotyped regions. A total of 143 alleles were identified with an average of 5.94 alleles per locus, with mean observed and expected heterozygosities of 0.648 and 0.620, respectively. Among of them, 15 microsatellite markers were identified without null alleles and with Hardy-Weinberg equilibrium. These alleles showed a combined non-exclusion probability of 0.01138. The probability of individual identification (PID) value combined with in descending order 12 microsatellite markers was 0.00008, which strongly suggests that the use of the microsatellite markers developed in this study in various combinations would result in a high resolution method for parentage analysis and individual identification. These markers could be used to establish a broodstock management program for giant grouper and to provide a foundation for genetic studies such as population structure, parentage analysis, and kinship selection. PMID:27059503

  7. Biochemical markers of ongoing joint damage in rheumatoid arthritis - current and future applications, limitations and opportunities

    PubMed Central

    2011-01-01

    Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease associated with potentially debilitating joint inflammation, as well as altered skeletal bone metabolism and co-morbid conditions. Early diagnosis and aggressive treatment to control disease activity offers the highest likelihood of preserving function and preventing disability. Joint inflammation is characterized by synovitis, osteitis, and/or peri-articular osteopenia, often accompanied by development of subchondral bone erosions, as well as progressive joint space narrowing. Biochemical markers of joint cartilage and bone degradation may enable timely detection and assessment of ongoing joint damage, and their use in facilitating treatment strategies is under investigation. Early detection of joint damage may be assisted by the characterization of biochemical markers that identify patients whose joint damage is progressing rapidly and who are thus most in need of aggressive treatment, and that, alone or in combination, identify those individuals who are likely to respond best to a potential treatment, both in terms of limiting joint damage and relieving symptoms. The aims of this review are to describe currently available biochemical markers of joint metabolism in relation to the pathobiology of joint damage and systemic bone loss in RA; to assess the limitations of, and need for additional, novel biochemical markers in RA and other rheumatic diseases, and the strategies used for assay development; and to examine the feasibility of advancement of personalized health care using biochemical markers to select therapeutic agents to which a patient is most likely to respond. PMID:21539724

  8. Development and characterization of novel EST-SSR markers for Speranskia tuberculata (Euphorbiaceae)1

    PubMed Central

    Fu, Yi; Ju, Miao-Miao; Ma, Huan-Cheng; Xin, Pei-Yao; He, Cheng-Zhong; Jia, Dong-Rui; Tian, Bin

    2016-01-01

    Premise of the study: The first set of expressed sequence tag–simple sequence repeat (EST-SSR) markers were developed and characterized for Speranskia tuberculata (Euphorbiaceae), a traditional medicinal plant endemic to northern China, to explore the effects of recent habitat fragmentation on the genetic diversity and structure of this species. Methods and Results: In this study, a total of 18 novel polymorphic microsatellite (EST-SSR) markers were developed for S. tuberculata using high-throughput transcriptome sequencing. Analysis of 24 individuals of S. tuberculata from four natural populations revealed their robust polymorphic reliability. The number of alleles per locus ranged from two to 11, while the expected and observed heterozygosity per marker varied from 0.187 to 0.827 and 0.042 to 0.917, respectively. Of these markers, 13 showed good amplification results in the closely related species S. cantonensis. Conclusions: These newly generated SSR markers are expected to provide novel tools for genetic studies of S. tuberculata, which will contribute to the conservation and sustainable use of the species’ wild genetic resources. PMID:27785384

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

    PubMed

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

    2002-01-01

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

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

    PubMed

    Hunt, G J; Page, R E

    1992-10-01

    The polymerase chain reaction (PCR) was used to generate random amplified polymorphic DNA (RAPD) from honey bee DNA samples in order to follow the patterns of inheritance of RAPD markers in a haplodiploid insect. The genomic DNA samples from two parental bees, a haploid drone and a diploid queen, were screened for polymorphism with 68 different tennucleotide primers of random sequence. Parents were scored for the presence or absence of individual bands. An average of 6.3 bands and 1.3 polymorphisms for presence/absence were observed per primer between the parents. Thirteen of these primers were used to determine the inheritance of RAPD marker alleles in the resulting progeny and in haploid drones from a daughter queen. Four types of polymorphisms were observed. Polymorphisms for band presence/absence as well as for band brightness were inherited as dominant markers, meeting Mendelian expectations in haploid and diploid progeny. Polymorphisms for fragment-length were also observed. These segregated in a near 1∶1 ratio in drone progeny. The last type of polymorphism was manifested as a diploid-specific band. Mixing of amplification products after PCR showed that the diploid-specific band was the result of heteroduplex formation from the DNA of alternate alleles in heterozygotes. In two of the four cases of heteroduplex formation, the alternative alleles were manifested as small fragment-length polymorphisms, resulting in co-dominant markers. This is the first demonstration that a proportion of RAPD markers are not inherited in a dominant fashion.

  11. Neural, psychophysiological, and behavioral markers of fear processing in PTSD: a review of the literature.

    PubMed

    Shvil, Erel; Rusch, Heather L; Sullivan, Gregory M; Neria, Yuval

    2013-05-01

    As presently defined, post-traumatic stress disorder (PTSD) is an amalgam of symptoms falling into: re-experiencing of the trauma, avoidance of reminders of it, emotional numbing and hyperarousal. PTSD has a well-known proximate cause, commonly occurring after a life-threatening event that induces a response of intense fear, horror, and helplessness. Much of the advancement in understanding of the neurobiology of PTSD has emerged from conceptualizing the disorder as one that involves substantial dysfunction in fear processing. This article reviews recent knowledge of fear processing markers in PTSD. A systematic search was performed of reports within the specific three-year publication time period of January 2010 to December 2012. We identified a total of 31 studies reporting fear processing markers in PTSD. We further categorized them according to the following classification: (1) neural-activation markers (n=10), (2) psychophysiological markers (n=14), and (3) behavioral markers (n=7). Across most studies reviewed here, significant differences between individuals with PTSD and healthy controls were shown. Methodological, theoretical and clinical implications were discussed. PMID:23619614

  12. Estimating genome-wide heterozygosity: effects of demographic history and marker type

    PubMed Central

    Miller, J M; Malenfant, R M; David, P; Davis, C S; Poissant, J; Hogg, J T; Festa-Bianchet, M; Coltman, D W

    2014-01-01

    Heterozygosity–fitness correlations (HFCs) are often used to link individual genetic variation to differences in fitness. However, most studies examining HFCs find weak or no correlations. Here, we derive broad theoretical predictions about how many loci are needed to adequately measure genomic heterozygosity assuming different levels of identity disequilibrium (ID), a proxy for inbreeding. We then evaluate the expected ability to detect HFCs using an empirical data set of 200 microsatellites and 412 single nucleotide polymorphisms (SNPs) genotyped in two populations of bighorn sheep (Ovis canadensis), with different demographic histories. In both populations, heterozygosity was significantly correlated across marker types, although the strength of the correlation was weaker in a native population compared with one founded via translocation and later supplemented with additional individuals. Despite being bi-allelic, SNPs had similar correlations to genome-wide heterozygosity as microsatellites in both populations. For both marker types, this association became stronger and less variable as more markers were considered. Both populations had significant levels of ID; however, estimates were an order of magnitude lower in the native population. As with heterozygosity, SNPs performed similarly to microsatellites, and precision and accuracy of the estimates of ID increased as more loci were considered. Although dependent on the demographic history of the population considered, these results illustrate that genome-wide heterozygosity, and therefore HFCs, are best measured by a large number of markers, a feat now more realistically accomplished with SNPs than microsatellites. PMID:24149650

  13. Have we made progress in pharmacogenomics? The implementation of molecular markers in colon cancer.

    PubMed

    Allen, Wendy L; Johnston, Patrick G

    2005-09-01

    For the last 40 years, 5-fluorouracil (5-FU) has remained the treatment of choice in both the adjuvant and advanced treatment of colorectal cancer (CRC). However, 5-FU monotherapy produces response rates of only 10-20% in the advanced setting. 5-FU has been combined with newer agents, such as oxaliplatin and irinotecan, and this has significantly increased response rates to 40-50% in the advanced setting. More recently, novel biological agents, such as the monoclonal antibodies targeting either the epidermal growth factor receptor or vascular endothelial growth factor, have shown to provide additional clinical benefit for patients with metastatic CRC. A number of predictive markers have been identified for CRC to date. However, their usefulness as individual markers of response has led to somewhat inconclusive results. Therefore, there is a need to identify panels of predictive markers of response to therapy for advanced CRC, in order to improve these disappointing response rates. The advent of high-throughput methodologies, such as microarrays, enables tumor samples to be profiled on a global scale. This technology has been utilized to develop predictive markers for a wide range of tumor types to date, and hopefully this technology can be translated into the CRC setting with the hope of predicting the response of each individual tumor to chemotherapy.

  14. Integrating microsatellite DNA markers and otolith geochemistry to assess population structure of European hake (Merluccius merluccius)

    NASA Astrophysics Data System (ADS)

    Tanner, Susanne E.; Pérez, Montse; Presa, Pablo; Thorrold, Simon R.; Cabral, Henrique N.

    2014-04-01

    Population structure and natal origins of European hake were investigated using microsatellite DNA markers and otolith geochemistry data. Five microsatellites were sequenced and otolith core geochemical composition was determined from age-1 hake collected in the northeast Atlantic Ocean and the Mediterranean Sea. Microsatellites provided evidence of a major genetic split in the vicinity of the Strait of Gibraltar, separating the Atlantic and the Mediterranean populations, with the exception of the Gulf of Cádiz. Based on classification models using otolith core geochemical values, individual natal origins were identified, although with an increased error rate. Coupling genotype and otolith data increased the classification accuracy of individuals to their potential natal origins while providing evidence of movement between the northern and southern stock units in the Atlantic Ocean. Information obtained by the two natural markers on population structure of European hake was complementary as the two markers act at different spatio-temporal scales. Otolith geochemistry provides information over an ecological time frame and on a fine spatial scale, while microsatellite DNA markers report on gene flow over evolutionary time scales and therefore act on a broader spatio-temporal resolution. Thus, this study confirmed the value of otolith geochemistry to complement the assessment of early life stage dispersal in populations with high gene flow and low genetic divergence.

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

    PubMed

    Patzak, Josef; Vrba, Lukás; Matousek, Jaroslav

    2007-01-01

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

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

    PubMed

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

    2014-01-01

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

  17. Identification of Molecular Markers Associated with Verticillium Wilt Resistance in Alfalfa (Medicago Sativa L.) Using High-Resolution Melting

    PubMed Central

    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. PMID:25536106

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

    PubMed

    Patzak, Josef; Vrba, Lukás; Matousek, Jaroslav

    2007-01-01

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

  19. Marker-dependent associations among oxidative stress, growth and survival during early life in a wild mammal

    PubMed Central

    Selman, Colin; Blount, Jonathan D.; Pilkington, Jill G.; Watt, Kathryn A.; Pemberton, Josephine M.; Reid, Jane M.

    2016-01-01

    Oxidative stress (OS) is hypothesized to be a key physiological mechanism mediating life-history trade-offs, but evidence from wild populations experiencing natural environmental variation is limited. We tested the hypotheses that increased early life growth rate increases OS, and that increased OS reduces first-winter survival, in wild Soay sheep (Ovis aries) lambs. We measured growth rate and first-winter survival for four consecutive cohorts, and measured two markers of oxidative damage (malondialdehyde (MDA), protein carbonyls (PC)) and two markers of antioxidant (AOX) protection (total AOX capacity (TAC), superoxide dismutase (SOD)) from blood samples. Faster lamb growth was weakly associated with increased MDA, but not associated with variation in the other three markers. Lambs with higher SOD activity were more likely to survive their first winter, as were male but not female lambs with lower PC concentrations. Survival did not vary with MDA or total TAC. Key predictions relating OS to growth and survival were therefore supported in some OS markers, but not others. This suggests that different markers capture different aspects of the complex relationships between individual oxidative state, physiology and fitness, and that overarching hypotheses relating OS to life-history variation cannot be supported or refuted by studying individual markers. PMID:27733545

  20. A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine.

    PubMed

    Yang, Shanshan; Fresnedo-Ramírez, Jonathan; Wang, Minghui; Cote, Linda; Schweitzer, Peter; Barba, Paola; Takacs, Elizabeth M; Clark, Matthew; Luby, James; Manns, David C; Sacks, Gavin; Mansfield, Anna Katharine; Londo, Jason; Fennell, Anne; Gadoury, David; Reisch, Bruce; Cadle-Davidson, Lance; Sun, Qi

    2016-01-01

    Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220-244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis. PMID:27257505

  1. A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine.

    PubMed

    Yang, Shanshan; Fresnedo-Ramírez, Jonathan; Wang, Minghui; Cote, Linda; Schweitzer, Peter; Barba, Paola; Takacs, Elizabeth M; Clark, Matthew; Luby, James; Manns, David C; Sacks, Gavin; Mansfield, Anna Katharine; Londo, Jason; Fennell, Anne; Gadoury, David; Reisch, Bruce; Cadle-Davidson, Lance; Sun, Qi

    2016-01-01

    Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220-244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis.

  2. A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine

    PubMed Central

    Yang, Shanshan; Fresnedo-Ramírez, Jonathan; Wang, Minghui; Cote, Linda; Schweitzer, Peter; Barba, Paola; Takacs, Elizabeth M; Clark, Matthew; Luby, James; Manns, David C; Sacks, Gavin; Mansfield, Anna Katharine; Londo, Jason; Fennell, Anne; Gadoury, David; Reisch, Bruce; Cadle-Davidson, Lance; Sun, Qi

    2016-01-01

    Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220–244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis. PMID:27257505

  3. Individualizing Instruction: Promise Versus Reality.

    ERIC Educational Resources Information Center

    Stewart, Norman L., Ed.

    1975-01-01

    This issue of the "Illinois English Bulletin" is divided into 30 sections which discuss individualizing instruction. Some of the topics included are: the advantages of individualizing instruction in general, the writing of daily learning objectives for use by the classroom teacher, individualizing instruction at Lincolnland Community College,…

  4. The Science of the Individual

    ERIC Educational Resources Information Center

    Rose, L. Todd; Rouhani, Parisa; Fischer, Kurt W.

    2013-01-01

    Our goal is to establish a science of the individual, grounded in dynamic systems, and focused on the analysis of individual variability. Our argument is that individuals behave, learn, and develop in distinctive ways, showing patterns of variability that are not captured by models based on statistical averages. As such, any meaningful attempt to…

  5. Widespread detection of human- and ruminant-origin Bacteroidales markers in subtidal waters of the Salish Sea in Washington State.

    PubMed

    Oyafuso, Zack S; Baxter, Anne E; Hall, Jason E; Naman, Sean M; Greene, Correigh M; Rhodes, Linda D

    2015-09-01

    Rising populations around coastal systems are increasing the threats to marine water quality. To assess anthropogenic fecal influence, subtidal waters were examined monthly for human- and ruminant-sourced Bacteroidales markers at 80 sites across six oceanographic basins of the Salish Sea (Washington State) from April through October, 2011. In the basins containing cities with individual populations>190,000, >50% of sites were positive for the human marker, while in the basins with high densities of dairy and cattle operations, ∼30% of sites were positive for the ruminant marker. Marker prevalence was elevated in spring (April and May) and fall (October) and reduced during summer (June through September), corresponding with seasonal precipitation. By logistic regression, the odds of human marker detection increased with percentage of adjacent catchment impervious surface, dissolved nitrate concentration, and abundance of low nucleic acid bacteria, but decreased with salinity and chlorophyll fluorescence. The odds of ruminant marker detection increased with dissolved ammonium concentration, mean flow rate for the nearest river, and adjacent shoreline length. These relationships are consistent with terrestrial to marine water flow as a transport mechanism. Thus, Bacteroidales markers traditionally used for identifying nearby sources can be used for assessing anthropogenic fecal inputs to regional marine ecosystems. PMID:26322768

  6. Construction of a genetic linkage map of black gram, Vigna mungo (L.) Hepper, based on molecular markers and comparative studies.

    PubMed

    Gupta, S K; Souframanien, J; Gopalakrishna, T

    2008-08-01

    A genetic linkage map of black gram, Vigna mungo (L.) Hepper, was constructed with 428 molecular markers using an F9 recombinant inbred population of 104 individuals. The population was derived from an inter-subspecific cross between a black gram cultivar, TU94-2, and a wild genotype, V. mungo var. silvestris. The linkage analysis at a LOD score of 5.0 distributed all 428 markers (254 AFLP, 47 SSR, 86 RAPD, and 41 ISSR) into 11 linkage groups. The map spanned a total distance of 865.1 cM with an average marker density of 2 cM. The largest linkage group spanned 115 cM and the smallest linkage group was of 44.9 cM. The number of markers per linkage group ranged from 11 to 86 and the average distance between markers varied from 1.1 to 5.6 cM. Comparison of the map with other published azuki bean and black gram maps showed high colinearity of markers, with some inversions. The current map is the most saturated map for black gram to date and will provide a useful tool for identification of QTLs and for marker-assisted selection of agronomically important characters in black gram.

  7. [Construction of the first genetic linkage map of Salvia miltiorrhiza Bge. using SSR, SRAP and ISSR markers].

    PubMed

    Zong Cheng-kun; Song, Zhen-qiao; Chen, Hai-mei; Liu, Chang; Wang, Jian-hua; Guo, Lin-lin; Liu, Tian; Pan, Yu-ling

    2015-03-01

    The first genetic linkage map of Salvia miltiorrhiza was constructed in 94 F1 individuals from an intraspecific cross by using simple sequence repeat (SSR), sequence-related amplified polymorphism (SRAP) and inter-simple sequence repeat (ISSR) markers. A total of 93 marker loci in the linkage map, consisting of 53 SSR, 38 SRAP and 2 ISSR locus were made up of eight linkage groups, covered a total length of 400.1 cm with an average distance of 4.3 cm per marker. The length of linkage groups varied from 3.3 -132 cm and each of them included 2-23 markers, separately. The result will provide important basis for QTL mapping, map-based cloning and association studies for commercially important traits in S. miltiorrhiza.

  8. Effect of ageing and μ-calpain markers on meat quality from Brangus steers finished on pasture.

    PubMed

    Mazzucco, Juliana Papaleo; Melucci, Lilia M; Villarreal, Edgardo L; Mezzadra, Carlos A; Soria, Liliana; Corva, Pablo; Motter, Mariana M; Schor, Alejandro; Miquel, María C

    2010-11-01

    Brangus steers (n=247) finished on pasture were used to evaluate the effects of post-mortem ageing and polymorphism CAPN1 316 and CAPN1 4751 markers on meat tenderness and objective colour measurements (CIEL*a*b*) of m. Longissimus dorsi. Ageing meat for 7 days decreased shear force (SF) by 13.7% and improved a* (8.4%) and b* (10%) compared to ageing for 1 day. No difference between 7 and 14 days of ageing was found for SF, a* and b*. However, L* increased markedly with ageing. Fitting both markers simultaneously, CAPN1 316 showed association with SF and L* and CAPN1 4751 with a* and b*. Fitting the markers individually, CAPN1 4751 affected all traits and CAPN1 316 showed association with SF and L*. Post-mortem ageing and the use of markers represent two independent and alternative tools that could be used for improving quality of meat from Brangus cattle. PMID:20709460

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

    PubMed Central

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

    2016-01-01

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

  10. Persistence of host-associated Bacteroidales gene markers and their quantitative detection in an urban and agricultural mixed prairie watershed.

    PubMed

    Tambalo, Dinah D; Fremaux, Bastien; Boa, Tyler; Yost, Christopher K

    2012-06-01

    Microbial source tracking is an emerging tool developed to protect water sources from faecal pollution. In this study, we evaluated the suitability of real time-quantitative PCR (qPCR) Taqman assays developed for detection of host-associated Bacteroidales markers in a prairie watershed. The qPCR primers and probes used in this study exhibited high accuracy (88-96% sensitivity and ≥ 99% host specificity) in detecting Bacteroidales spp. that are associated with faeces from humans, ruminants, bovines, and horses. The ruminant- and human-associated markers were also found in high concentrations within individual faecal samples, ranging from 3.4 to 7.3 log(10) marker copy numberg(-1) of individual host faeces. Following validation of host sensitivity and specificity, the host-associated Bacteroidales markers were detected in the Qu'Appelle Valley watershed of Saskatchewan, Canada which experiences a diversity of anthropogenic inputs. Concentrations of the ruminant marker were well-correlated with proximity to cattle operations and there was a correlation between the marker and Escherichia coli concentrations at these sites. Low concentrations of the human faecal marker were measured throughout the sampling sites, and may indicate a consistent influx of human faecal pollution into the watershed area. Persistence of each of the Bacteroidales host-associated marker was also studied in situ. The results indicated that the markers persist for shorter periods of time (99% decay in <8 days) compared with the conventional E. coli marker (99% decay in >15 days), suggesting they are effective at detecting recent faecal contamination events. The levels of Bacteroidales markers and E. coli counts did not correlate with the presence of the pathogenic bacteria, Salmonella spp. or Campylobacter spp. detected in the Qu'Appelle Valley. Collectively, the results obtained in this study demonstrated that the qPCR approach for detecting host-associated Bacteroidales spp. markers can be a

  11. An application of control region sequence as a matrilineage marker for Elliot's pheasant of a zoo population.

    PubMed

    Jiang, Ping-Ping; Fang, Sheng-Gou; Ding, Ping

    2005-01-01

    Control region sequence, an mtDNA marker, was usually used in phylogenesis analysis in species level or genetic structure study among populations. In this study, enlightened by its character of maternal heredity in vertebrates, we used control region sequence as a matrilineage marker for Elliot's pheasant (Syrmaticus ellioti) of Ningbo Zoo population. In Ningbo Zoo, 36 individuals of Elliot's pheasant were descendants from three female founders introduced in 1988. Three control region haplotypes (Ha, Hb, Hc) were identified by six variable nucleotide positions among the control region sequences over 36 individuals. The number of haplotypes was accorded with the number of female founders. Total 20 individuals (C04, C06, C08-11, C14, C20, C21, C23-29, C32, C34-36) shared haplotype a, while 12 individuals (C01, C05, C07, C12, C13, C16-19, C22, C30, C33) shared haplotype b and 4 individuals (C02, C03, C15, C31) shared haplotype c. Those individuals sharing the same haplotype were offspring from one female founder. In other words, there were three maternal lineages and the simple relationship among individuals was indicated. As a result, it seemed that the control region sequence was a useful marker for identification of matrilineage in this study. Meanwhile, the matrilineage information may be compensatory data if there were no any pedigree records in captive species for breeding management.

  12. Improved age determination of blood and teeth samples using a selected set of DNA methylation markers

    PubMed Central

    Kamalandua, Aubeline

    2015-01-01

    Age estimation from DNA methylation markers has seen an exponential growth of interest, not in the least from forensic scientists. The current published assays, however, can still be improved by lowering the number of markers in the assay and by providing more accurate models to predict chronological age. From the published literature we selected 4 age-associated genes (ASPA, PDE4C, ELOVL2, and EDARADD) and determined CpG methylation levels from 206 blood samples of both deceased and living individuals (age range: 0–91 years). This data was subsequently used to compare prediction accuracy with both linear and non-linear regression models. A quadratic regression model in which the methylation levels of ELOVL2 were squared showed the highest accuracy with a Mean Absolute Deviation (MAD) between chronological age and predicted age of 3.75 years and an adjusted R2 of 0.95. No difference in accuracy was observed for samples obtained either from living and deceased individuals or between the 2 genders. In addition, 29 teeth from different individuals (age range: 19–70 years) were analyzed using the same set of markers resulting in a MAD of 4.86 years and an adjusted R2 of 0.74. Cross validation of the results obtained from blood samples demonstrated the robustness and reproducibility of the assay. In conclusion, the set of 4 CpG DNA methylation markers is capable of producing highly accurate age predictions for blood samples from deceased and living individuals PMID:26280308

  13. Linkage and association to genetic markers.

    PubMed

    Elston, R C

    1995-01-01

    Genetic markers that are sufficiently polymorphic (as measured by their heterozygosities) can be used in linkage and association analyses to detect Mendelian segregation underlying disease phenotypes. Each type of analysis can either be based on a specific genetic model or not make any assumptions about the mode of inheritance of the disease. Principles underlying these methods are reviewed, and the assumptions underlying them stressed. Association analyses are more powerful, provided there is linkage disequilibrium between the marker and disease loci; however, only linkage analyses have power in the absence of such disequilibrium. For this reason, models that allow for both kinds of tests are preferred, and such models must adequately approximate the complexity of the disease being studied.

  14. [Genetic virulence markers of opportunistic bacteria].

    PubMed

    Bondarenko, V M

    2011-01-01

    The analysis of opportunistic bacteria phenotypic and genetic virulence markers indicates that pathogenicity formation is based on a structural modification of bacterial DNA which is linked with migration of interbacterial pathogenicity "islands" genetic determinants. Structural organization features of these mobile genetic elements determine high expression probability, and PCR detection of pathogenicity "islands" determinants that control adhesins, invasins, cytotoxic and cytolitic toxines synthesis may indicate etiopathogenetic significance of clinical isolates.

  15. Laboratory markers predicting severity of acute pancreatitis.

    PubMed

    Staubli, Sebastian Manuel; Oertli, Daniel; Nebiker, Christian Andreas

    2015-01-01

    Acute pancreatitis (AP) is an inflammatory disease of highly variable severity, ranging from mild cases with low mortality to severe cases with high mortality. Numerous biomarkers have been studied as potential early predictors of the severity of this disease so that treatment can be optimally tailored to prevent complications. We aim to present and discuss the most relevant biomarkers for early severity assessment in AP that have been studied to date. We review the current literature on biomarkers that have been used to predict the severity in AP. C-reactive protein (CRP) is still considered to be the gold standard, with a cut-off value of 150 mg/ml 48 h after disease onset. Other markers, including procalcitonin (PCT) and interleukin 6 (IL-6) have been implemented in some hospitals, but are not used on a routine basis. Most other markers, including acute phase proteins (LBP, SAA, PTX3), cytokines (Il-8, TNF-a, MIF), activation peptides of pancreatic proteases (TAP, CAPAP, PLAP), antiproteases (AAT, a2M), adhesion molecules (ICAM-1, selectins, E-cadherin) and leukocyte-derived enzymes (PA2, PMN-E) have shown some promising results but have not been routinely implemented. Furthermore, new and interesting biomarkers (Copeptin, TRX-1, Ang-2, E-2) have shown good results, but more research is needed to determine if they could play a role in the future. Various reasons why new markers for disease severity have not been adopted in daily routine include low accuracy, cumbersome laboratory techniques and high cost. Despite these difficulties, research is still very active in finding new markers to predict the severity of AP.

  16. Automated genotyping of dinucleotide repeat markers

    SciTech Connect

    Perlin, M.W.; Hoffman, E.P. |

    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.

  17. Gemini 4 Recovery with Green Marker Dye

    NASA Technical Reports Server (NTRS)

    1965-01-01

    Overhead view of the Gemini 4 spacecraft showing the yellow flotation collar used to stabilize the spacecraft in choppy seas. The green marker dye is highly visible from the air and is used as a locating aid. A crewmember is being hoisted aboard a U.S. Navy helicopter during recovery operations following the successful four-day, 62 revolution mission highlighted by Ed White's space walk.

  18. Functional molecular markers for crop improvement.

    PubMed

    Kage, Udaykumar; Kumar, Arun; Dhokane, Dhananjay; Karre, Shailesh; Kushalappa, Ajjamada C

    2016-10-01

    A tremendous decline in cultivable land and resources and a huge increase in food demand calls for immediate attention to crop improvement. Though molecular plant breeding serves as a viable solution and is considered as "foundation for twenty-first century crop improvement", a major stumbling block for crop improvement is the availability of a limited functional gene pool for cereal crops. Advancement in the next generation sequencing (NGS) technologies integrated with tools like metabolomics, proteomics and association mapping studies have facilitated the identification of candidate genes, their allelic variants and opened new avenues to accelerate crop improvement through development and use of functional molecular markers (FMMs). The FMMs are developed from the sequence polymorphisms present within functional gene(s) which are associated with phenotypic trait variations. Since FMMs obviate the problems associated with random DNA markers, these are considered as "the holy grail" of plant breeders who employ targeted marker assisted selections (MAS) for crop improvement. This review article attempts to consider the current resources and novel methods such as metabolomics, proteomics and association studies for the identification of candidate genes and their validation through virus-induced gene silencing (VIGS) for the development of FMMs. A number of examples where the FMMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance and abiotic stress tolerance traits have been considered. PMID:26171816

  19. Transcriptome marker diagnostics using big data.

    PubMed

    Han, Henry; Liu, Ying

    2016-02-01

    The big omics data are challenging translational bioinformatics in an unprecedented way for its complexities and volumes. How to employ big omics data to achieve a rivalling-clinical, reproducible disease diagnosis from a systems approach is an urgent problem to be solved in translational bioinformatics and machine learning. In this study, the authors propose a novel transcriptome marker diagnosis to tackle this problem using big RNA-seq data by viewing whole transcriptome as a profile marker systematically. The systems diagnosis not only avoids the reproducibility issue of the existing gene-/network-marker-based diagnostic methods, but also achieves rivalling-clinical diagnostic results by extracting true signals from big RNA-seq data. Their method demonstrates a better fit for personalised diagnostics by attaining exceptional diagnostic performance via using systems information than its competitive methods and prepares itself as a good candidate for clinical usage. To the best of their knowledge, it is the first study on this topic and will inspire the more investigations in big omics data diagnostics.

  20. Early markers of adult obesity: a review.

    PubMed

    Brisbois, T D; Farmer, A P; McCargar, L J

    2012-04-01

    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.

  1. [THE EVOLUTION OF MARKERS OF PROSTATE CANCER].

    PubMed

    Peshkov, M N; Generozov, E V; Kostryukova, E S

    2016-03-01

    The implementation of biochemical laboratory tests in oncology practice increased exponentially during last decades and continues to be in progress nowadays. The application of modern molecular genetic technologies permits using diagnostic systems with greater diagnostic sensitivity and specificity. The new tests are actively implemented permitting to diagnose physical presence of tumor systemic manifestations of malignant neoplasm (cachexia, pyrexia), paraneoplastic syndromes and also to detect tumor markers. The oncomarker permits to differentiate malignant from benign tumor on the basis of quantitative differences in content of corresponding antigene-tumor marker in blood serum independently of localization of tumor nidus. The prostate cancer is a medical social problem of male population. On initial stages, this disease can take its course asymptomatically or with symptomatic conditioned by such concomitant and more prevalent pathologies as chronic prostatitis and prostate benign hyperplasia. The early diagnostic ofprostate cancer permits implementing timely radical treatment frequently contributing to total recovery of patients. The article presents detailed description of evolutionary conception of markers using in diagnostic, staging and prognostication of course of prostate cancer. The acid phosphatase was applied for the first time in early diagnostic of staging of prostate cancer in 1974. Nowadays, in century of "OMX"-technologies, in common clinical practice detection of RNA in urine of patient is used for staging diagnostic and prognostication of progression of process of tissue neotransformation. PMID:27506103

  2. Bone turnover markers: use in osteoporosis.

    PubMed

    Naylor, Kim; Eastell, Richard

    2012-07-01

    Biochemical markers of bone turnover (bone turnover markers, BTMs) can be used to study changes in bone remodelling in osteoporosis. Investigators and clinicians should be aware of the appropriate sample collection and storage conditions for optimum measurements of these markers. Improvements in the variability of BTM measurements have resulted from the development of assays for automated analysers, and from international consensus regarding their use. Appropriate reference intervals should be used for the optimum interpretation of results. BTMs can provide information that is useful for the management of patients with osteoporosis, for both the initial clinical assessment and for guiding and monitoring of treatment. BTMs are clinically useful to determine possible causes of secondary osteoporosis by identifying patients with high bone turnover and rapid bone loss. In the follow-up of treatment response, BTM levels respond rapidly to both anabolic and antiresorptive treatments. BTM changes can also be used for understanding the mechanism of action of drugs in development and identifying the correct dose; they are also potentially useful as surrogate biomarkers for fracture.

  3. Microsatellite genotyping of individual abalone larvae: parentage assignment in aquaculture.

    PubMed

    Selvamani, M J; Degnan, S M; Degnan, B M

    2001-09-01

    In aquaculture, microsatellite DNA markers are used to genotype parental broodstock, to assess fertilization success, and to maintain pedigree information for selective breeding. In this study we genotyped individual Haliotis asinina larvae by analyzing a suit of polymorphic microsatellite loci. At least 10 loci can be analyzed from a single abalone veliger larva. We assayed 5 polymorphic loci to identify the parents of individual larvae produced in 3 separate crosses. In all cases, the parents of an individual veliger could be determined from as few as 3 loci. The microsatellite analysis revealed that, in each of our crosses, a single male fathered most of the veligers, despite efforts to normalize the amount of sperm contributed by competing males. These observations suggest that highly controlled breeding practices may be required to ensure that the genetic diversity of an abalone population produced for aquaculture is maintained at the level of diversity of the original broodstock.

  4. Biogeography and individuality shape function in the human skin metagenome.

    PubMed

    Oh, Julia; Byrd, Allyson L; Deming, Clay; Conlan, Sean; Kong, Heidi H; Segre, Julia A

    2014-10-01

    The varied topography of human skin offers a unique opportunity to study how the body's microenvironments influence the functional and taxonomic composition of microbial communities. Phylogenetic marker gene-based studies have identified many bacteria and fungi that colonize distinct skin niches. Here metagenomic analyses of diverse body sites in healthy humans demonstrate that local biogeography and strong individuality define the skin microbiome. We developed a relational analysis of bacterial, fungal and viral communities, which showed not only site specificity but also individual signatures. We further identified strain-level variation of dominant species as heterogeneous and multiphyletic. Reference-free analyses captured the uncharacterized metagenome through the development of a multi-kingdom gene catalogue, which was used to uncover genetic signatures of species lacking reference genomes. This work is foundational for human disease studies investigating inter-kingdom interactions, metabolic changes and strain tracking, and defines the dual influence of biogeography and individuality on microbial composition and function. PMID:25279917

  5. CGMD: An integrated database of cancer genes and markers

    PubMed Central

    Pradeepkiran, Jangampalli Adi; Sainath, Sri Bhashyam; Kramthi Kumar, Konidala; Balasubramanyam, Lokanada; Vidya Prabhakar, Kodali; Bhaskar, Matcha

    2015-01-01

    Integrating cancer genes and markers with experimental evidence might provide valuable information for the further investigation of crosstalk between tumor genes and markers in cancer biology. To achieve this objective, we developed a database known as the Cancer Gene Marker Database (CGMD), which integrates data on tumor genes and markers based on experimental evidence. The major goal of CGMD is to provide the following: 1) current systematic treatment approaches and recent advances in different cancer treatments; 2) the aggregation of different genes and markers by their molecular characteristics and pathway associations; and 3) free access to the data compiled by CGMD at http://cgmd.in/. The database consists of 309 genes and 206 markers, as well as a list of 40 different human cancers, with detailed descriptions of all characterized markers. CGMD provides complete cancer annotations and molecular descriptions of cancer genes and markers such as CpG islands, promoters, exons, PDB structures, active sites and domains. PMID:26160459

  6. Sea dye marker provides visibility for 20 hours

    NASA Technical Reports Server (NTRS)

    De Laat, F.

    1966-01-01

    Sea dye marker block releases a visible slick which lasts at least twelve hours. The dye marker uses a fluorescent dye in a heat cured binder which, when immersed in seawater, releases the dye at a controlled rate.

  7. Quantitative proteomics reveals novel therapeutic and diagnostic markers in hypertension.

    PubMed

    Matafora, Vittoria; Zagato, Laura; Ferrandi, Mara; Molinari, Isabella; Zerbini, Gianpaolo; Casamassima, Nunzia; Lanzani, Chiara; Delli Carpini, Simona; Trepiccione, Francesco; Manunta, Paolo; Bachi, Angela; Capasso, Giovambattista

    2014-12-01

    Hypertension is a prevalent disorder in the world representing one of the major risk factors for heart attack and stroke. These risks are increased in salt sensitive individuals. Hypertension and salt sensitivity are complex phenotypes whose pathophysiology remains poorly understood and, remarkably, salt sensitivity is still laborious to diagnose. Here we present a urinary proteomic study specifically designed to identify urinary proteins relevant for the pathogenesis of hypertension and salt sensitivity. Despite previous studies that underlined the association of UMOD gene variants with hypertension, this work provides novel evidence showing different uromodulin protein level in the urine of hypertensive patients compared to healthy individuals. Notably, we also show that patients with higher level of uromodulin are homozygous for UMOD risk variant and display a decreased level of salt excretion, highlighting the essential role of UMOD in the regulation of salt reabsorption in hypertension. Additionally, we found that urinary nephrin 1, a marker of glomerular slit diaphragm, may predict a salt sensitive phenotype and positively correlate with increased albuminuria associated with this type of hypertension. PMID:26672470

  8. Affective traits link to reliable neural markers of incentive anticipation

    PubMed Central

    Wu, Charlene C.; Samanez-Larkin, Gregory R.; Katovich, Kiefer; Knutson, Brian

    2013-01-01

    While theorists have speculated that different affective traits are linked to reliable brain activity during anticipation of gains and losses, few have directly tested this prediction. We examined these associations in a community sample of healthy human adults (n = 52) as they played a Monetary Incentive Delay Task while undergoing functional magnetic resonance imaging (FMRI). Factor analysis of personality measures revealed that subjects independently varied in trait Positive Arousal and Negative Arousal. In a subsample (n = 14) retested over 2.5 years later, left nucleus accumbens (NAcc) activity during anticipation of large gains (+$5.00) and right anterior insula activity during anticipation of large losses (−$5.00) showed significant test-retest reliability (intraclass correlations > 0.50, p’s < 0.01). In the full sample (n = 52), trait Positive Arousal correlated with individual differences in left NAcc activity during anticipation of large gains, while trait Negative Arousal correlated with individual differences in right anterior insula activity during anticipation of large losses. Associations of affective traits with neural activity were not attributable to the influence of other potential confounds (including sex, age, wealth, and motion). Together, these results demonstrate selective links between distinct affective traits and reliably-elicited activity in neural circuits associated with anticipation of gain versus loss. The findings thus reveal neural markers for affective dimensions of healthy personality, and potentially for related psychiatric symptoms. PMID:24001457

  9. Affective traits link to reliable neural markers of incentive anticipation.

    PubMed

    Wu, Charlene C; Samanez-Larkin, Gregory R; Katovich, Kiefer; Knutson, Brian

    2014-01-01

    While theorists have speculated that different affective traits are linked to reliable brain activity during anticipation of gains and losses, few have directly tested this prediction. We examined these associations in a community sample of healthy human adults (n=52) as they played a Monetary Incentive Delay task while undergoing functional magnetic resonance imaging (FMRI). Factor analysis of personality measures revealed that subjects independently varied in trait Positive Arousal and trait Negative Arousal. In a subsample (n=14) retested over 2.5years later, left nucleus accumbens (NAcc) activity during anticipation of large gains (+$5.00) and right anterior insula activity during anticipation of large losses (-$5.00) showed significant test-retest reliability (intraclass correlations>0.50, p's<0.01). In the full sample (n=52), trait Positive Arousal correlated with individual differences in left NAcc activity during anticipation of large gains, while trait Negative Arousal correlated with individual differences in right anterior insula activity during anticipation of large losses. Associations of affective traits with neural activity were not attributable to the influence of other potential confounds (including sex, age, wealth, and motion). Together, these results demonstrate selective links between distinct affective traits and reliably-elicited activity in neural circuits associated with anticipation of gain versus loss. The findings thus reveal neural markers for affective dimensions of healthy personality, and potentially for related psychiatric symptoms.

  10. Selective DNA Pooling for Determination of Linkage between a Molecular Marker and a Quantitative Trait Locus

    PubMed Central

    Darvasi, A.; Soller, M.

    1994-01-01

    Selective genotyping is a method to reduce costs in marker-quantitative trait locus (QTL) linkage determination by genotyping only those individuals with extreme, and hence most informative, quantitative trait values. The DNA pooling strategy (termed: ``selective DNA pooling'') takes this one step further by pooling DNA from the selected individuals at each of the two phenotypic extremes, and basing the test for linkage on marker allele frequencies as estimated from the pooled samples only. This can reduce genotyping costs of marker-QTL linkage determination by up to two orders of magnitude. Theoretical analysis of selective DNA pooling shows that for experiments involving backcross, F(2) and half-sib designs, the power of selective DNA pooling for detecting genes with large effect, can be the same as that obtained by individual selective genotyping. Power for detecting genes with small effect, however, was found to decrease strongly with increase in the technical error of estimating allele frequencies in the pooled samples. The effect of technical error, however, can be markedly reduced by replication of technical procedures. It is also shown that a proportion selected of 0.1 at each tail will be appropriate for a wide range of experimental conditions. PMID:7896115

  11. POLYMORPHIC CHLOROPLAST MICROSATELLITE MARKERS IN THE OCTOPLOID LEPIDIUM MEYENII (BRASSICACEAE) AND CROSS-SPECIES AMPLIFICATION IN LEPIDIUM

    PubMed Central

    Hasan, Nabeeh A.; Mummenhoff, Klaus; Quiros, Carlos F.; Tay, C. David; Bailey, C. Donovan

    2013-01-01

    Premise of the study As a crop and medicinal plant, the octoploid Andean endemic Lepidium meyenii suffers from taxonomic uncertainty. Few molecular markers are available to genotype individuals or track gene flow in wild and cultivated material. Methods and Results Using available sequence data, eight cpSSR primer pairs were developed for L. meyenii. Levels of polymorphism checked in 56 individual L. meyenii, including cultivated and wild material, revealed that the number of alleles per locus ranged from three to five, and intrapopulation allele frequencies ranged from 0.071 to 1.0. Polymerase-chain-reaction screens using our cpSSR primers in 27 other Lepidium species and three Coronopus species suggested a high degree of interspecific amplification. Conclusions These polymorphic cpSSR markers should prove useful in characterizing genetic variation among cultivated and wild L. meyenii. Additionally, interspecific amplifications suggest that these markers will be useful for the study of related taxa. PMID:21616787

  12. Model-independent evaluation of tumor markers and a logistic-tree approach to diagnostic decision support.

    PubMed

    Ni, Weizeng; Huang, Samuel H; Su, Qiang; Shi, Jinghua

    2014-01-01

    Sensitivity and specificity of using individual tumor markers hardly meet the clinical requirement. This challenge gave rise to many efforts, e.g., combing multiple tumor markers and employing machine learning algorithms. However, results from different studies are often inconsistent, which are partially attributed to the use of different evaluation criteria. Also, the wide use of model-dependent validation leads to high possibility of data overfitting when complex models are used for diagnosis. We propose two model-independent criteria, namely, area under the curve (AUC) and Relief to evaluate the diagnostic values of individual and multiple tumor markers, respectively. For diagnostic decision support, we propose the use of logistic-tree which combines decision tree and logistic regression. Application on a colorectal cancer dataset shows that the proposed evaluation criteria produce results that are consistent with current knowledge. Furthermore, the simple and highly interpretable logistic-tree has diagnostic performance that is competitive with other complex models. PMID:25516124

  13. Identification of RFLP and NBS/PK profiling markers for disease resistance loci in genetic maps of oats.

    PubMed

    Sanz, M J; Loarce, Y; Fominaya, A; Vossen, J H; Ferrer, E

    2013-01-01

    Two of the domains most widely shared among R genes are the nucleotide binding site (NBS) and protein kinase (PK) domains. The present study describes and maps a number of new oat resistance gene analogues (RGAs) with two purposes in mind: (1) to identify genetic regions that contain R genes and (2) to determine whether RGAs can be used as molecular markers for qualitative loci and for QTLs affording resistance to Puccinia coronata. Such genes have been mapped in the diploid A. strigosa × A. wiestii (Asw map) and the hexaploid MN841801-1 × Noble-2 (MN map). Genomic and cDNA NBS-RGA probes from oat, barley and wheat were used to produce RFLPs and to obtain markers by motif-directed profiling based on the NBS (NBS profiling) and PK (PK profiling) domains. The efficiency of primers used in NBS/PK profiling to amplify RGA fragments was assessed by sequencing individual marker bands derived from genomic and cDNA fragments. The positions of 184 markers were identified in the Asw map, while those for 99 were identified in the MN map. Large numbers of NBS and PK profiling markers were found in clusters across different linkage groups, with the PK profiling markers more evenly distributed. The location of markers throughout the genetic maps and the composition of marker clusters indicate that NBS- and PK-based markers cover partly complementary regions of oat genomes. Markers of the different classes obtained were found associated with the two resistance loci, PcA and R-284B-2, mapped on Asw, and with five out of eight QTLs for partial resistance in the MN map. 53 RGA-RFLPs and 187 NBS/PK profiling markers were also mapped on the hexaploid map A. byzantina cv. Kanota × A. sativa cv. Ogle. Significant co-localization was seen between the RGA markers in the KO map and other markers closely linked to resistance loci, such as those for P. coronata and barley yellow dwarf virus (Bydv) that were previously mapped in other segregating populations.

  14. A marker chromosome in post-transplant bone marrow.

    PubMed

    Morsberger, Laura; Powell, Kerry; Ning, Yi

    2016-01-01

    Detection of small supernumerary marker chromosomes in karyotype analysis represents a diagnostic challenge. While such markers are usually detected during cytogenetic studies of constitutional chromosome abnormalities, they have also been found in specimens submitted from patients with acquired malignancies. We report here the detection of a marker chromosome in a bone marrow specimen from a patient who received a bone marrow transplantation. We discuss the importance of proper characterization and interpretation of marker chromosomes in clinical practice. PMID:27252781

  15. Effect of diversity and missing data on genetic assignment with RAD-Seq markers.

    PubMed

    Chattopadhyay, Balaji; Garg, Kritika M; Ramakrishnan, Uma

    2014-11-25

    Reduced representation libraries are being used as a preferred source of markers to address population genetic questions. However, libraries of RAD-Seq variants often suffer from significant percentage of missing data. In addition, algorithms used to mine SNPs from the raw data may also underscore biological variation. We investigate the effect of biological diversity in mining SNPs from the program STACKS and the effect of missing data on individual assignment implemented in STRUCTURE. We observed that changing diversity parameters in STACKS significantly alters the number of SNPs discovered and allowing for higher percentage of missing data retrieves more loci and possibly more power for individual assignment.

  16. Microsatellite marker isolation and development for the giant Pacific Octopus (Enteroctopus dofleini)

    USGS Publications Warehouse

    Toussaint, Rebecca K.; Sage, G. Kevin; Talbot, Sandra L.; Scheel, David

    2012-01-01

    We isolated and developed 18 novel microsatellite markers for the giant Pacific octopus (Enteroctopus dofleini) and examined them for 31 individuals from Prince William Sound (PWS), Alaska. These loci displayed moderate levels of allelic diversity (averaging 11 alleles per locus) and heterozygosity (averaging 65%). Seven loci deviated from Hardy–Weinberg Equilibrium (HWE) due to heterozygote deficiency for the PWS population, although deviations were not observed for all these loci in other populations, suggesting the PWS population is not in mutation-drift equilibrium. These novel microsatellite loci yielded sufficient genetic diversity for potential use in population genetics, individual identification, and parentage studies.

  17. Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

    PubMed Central

    Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R. K.; Singh, N. K.; Singh, Rakesh

    2013-01-01

    Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis. PMID:24367635

  18. L-split marker for augmented reality in aircraft assembly

    NASA Astrophysics Data System (ADS)

    Han, Pengfei; Zhao, Gang

    2016-04-01

    In order to improve the performance of conventional square markers widely used by marker-based augmented reality systems in aircraft assembly environments, an L-split marker is proposed. Every marker consists of four separate L-shaped parts and each of them contains partial information about the marker. Geometric features of the L-shape, which are more discriminate than the symmetrical square shape adopted by conventional markers, are used to detect proposed markers from the camera images effectively. The marker is split into four separate parts in order to improve the robustness to occlusion and curvature to some extent. The registration process can be successfully completed as long as three parts are detected (up to about 80% of the area could be occluded). Moreover, when we attach the marker on nonplanar surfaces, the curvature status of the marker can be roughly analyzed with every part's normal direction, which can be obtained since their six corners have been explicitly determined in the previous detection process. And based on the marker design, new detection and recognition algorithms are proposed and detailed. The experimental results show that the marker and the algorithms are effective.

  19. 21 CFR 500.86 - Marker residue and target tissue.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 6 2011-04-01 2011-04-01 false Marker residue and target tissue. 500.86 Section...-Producing Animals § 500.86 Marker residue and target tissue. (a) For each edible tissue, the sponsor shall...) From these data, FDA will select a target tissue and a marker residue and designate the...

  20. 14 CFR 171.269 - Marker beacon performance requirements.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 14 Aeronautics and Space 3 2014-01-01 2014-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon...

  1. 14 CFR 171.269 - Marker beacon performance requirements.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 14 Aeronautics and Space 3 2011-01-01 2011-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon...

  2. 14 CFR 171.269 - Marker beacon performance requirements.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 14 Aeronautics and Space 3 2010-01-01 2010-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon...

  3. 14 CFR 171.269 - Marker beacon performance requirements.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 14 Aeronautics and Space 3 2013-01-01 2013-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon...

  4. 14 CFR 171.269 - Marker beacon performance requirements.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 14 Aeronautics and Space 3 2012-01-01 2012-01-01 false Marker beacon performance requirements. 171.269 Section 171.269 Aeronautics and Space FEDERAL AVIATION ADMINISTRATION, DEPARTMENT OF... Landing System (ISMLS) § 171.269 Marker beacon performance requirements. ISMLS marker beacon...

  5. Genetic and biological markers in drug abuse and alcoholism

    SciTech Connect

    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.

  6. Integration of DNA marker information into breeding value predictions

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Calves from seven breeds including 20 herds were genotyped with a reduced DNA marker panel for weaning weight. The marker panel used was derived using USMARC Cycle VII animals. The results from the current study suggest marker effects are not robust across breeds and that methodology exists to integ...

  7. 30 CFR 817.11 - Signs and markers.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Signs and markers. 817.11 Section 817.11... PERMANENT PROGRAM PERFORMANCE STANDARDS PERMANENT PROGRAM PERFORMANCE STANDARDS-UNDERGROUND MINING ACTIVITIES § 817.11 Signs and markers. (a) Specifications. Signs and markers required under this part...

  8. 30 CFR 817.11 - Signs and markers.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 3 2010-07-01 2010-07-01 false Signs and markers. 817.11 Section 817.11... PERMANENT PROGRAM PERFORMANCE STANDARDS PERMANENT PROGRAM PERFORMANCE STANDARDS-UNDERGROUND MINING ACTIVITIES § 817.11 Signs and markers. (a) Specifications. Signs and markers required under this part...

  9. Discourse Markers in EFL Setting: Perceptions of Turkish EFL Teachers

    ERIC Educational Resources Information Center

    Asik, Asuman

    2015-01-01

    Discourse markers are seen as one of the fundamental units in spoken discourse due to their frequent and multifunctional use by native speakers of English. Discourse markers also have significance in foreign language instruction. In this respect, this study explored the perceptions of Turkish EFL teachers towards the use of discourse markers in…

  10. 36 CFR 12.8 - Memorial headstones and markers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... markers. 12.8 Section 12.8 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL CEMETERY REGULATIONS § 12.8 Memorial headstones and markers. (a) Who may be memorialized... a memorial headstone or marker of an eligible person provided that no more than one...

  11. 30 CFR 717.12 - Signs and markers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 30 Mineral Resources 3 2012-07-01 2012-07-01 false Signs and markers. 717.12 Section 717.12... PROGRAM REGULATIONS UNDERGROUND MINING GENERAL PERFORMANCE STANDARDS § 717.12 Signs and markers. (a... other markers shall be maintained during all operations to which they pertain. (b) Mine and...

  12. 30 CFR 717.12 - Signs and markers.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 3 2011-07-01 2011-07-01 false Signs and markers. 717.12 Section 717.12... PROGRAM REGULATIONS UNDERGROUND MINING GENERAL PERFORMANCE STANDARDS § 717.12 Signs and markers. (a... other markers shall be maintained during all operations to which they pertain. (b) Mine and...

  13. 38 CFR 38.630 - Headstones and markers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2013-07-01 2013-07-01 false Headstones and markers... (CONTINUED) NATIONAL CEMETERIES OF THE DEPARTMENT OF VETERANS AFFAIRS § 38.630 Headstones and markers. (a) Types of Government headstones and markers and inscriptions will be in accordance with policies...

  14. 30 CFR 717.12 - Signs and markers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 30 Mineral Resources 3 2014-07-01 2014-07-01 false Signs and markers. 717.12 Section 717.12... PROGRAM REGULATIONS UNDERGROUND MINING GENERAL PERFORMANCE STANDARDS § 717.12 Signs and markers. (a... other markers shall be maintained during all operations to which they pertain. (b) Mine and...

  15. 36 CFR 12.8 - Memorial headstones and markers.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... markers. 12.8 Section 12.8 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL CEMETERY REGULATIONS § 12.8 Memorial headstones and markers. (a) Who may be memorialized... a memorial headstone or marker of an eligible person provided that no more than one...

  16. 38 CFR 38.630 - Headstones and markers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2012-07-01 2012-07-01 false Headstones and markers... (CONTINUED) NATIONAL CEMETERIES OF THE DEPARTMENT OF VETERANS AFFAIRS § 38.630 Headstones and markers. (a) Types of Government headstones and markers and inscriptions will be in accordance with policies...

  17. 36 CFR 12.8 - Memorial headstones and markers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... markers. 12.8 Section 12.8 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL CEMETERY REGULATIONS § 12.8 Memorial headstones and markers. (a) Who may be memorialized... a memorial headstone or marker of an eligible person provided that no more than one...

  18. 38 CFR 38.630 - Headstones and markers.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2014-07-01 2014-07-01 false Headstones and markers... (CONTINUED) NATIONAL CEMETERIES OF THE DEPARTMENT OF VETERANS AFFAIRS § 38.630 Headstones and markers. (a) Types of Government headstones and markers and inscriptions will be in accordance with policies...

  19. 30 CFR 717.12 - Signs and markers.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 3 2010-07-01 2010-07-01 false Signs and markers. 717.12 Section 717.12... PROGRAM REGULATIONS UNDERGROUND MINING GENERAL PERFORMANCE STANDARDS § 717.12 Signs and markers. (a... other markers shall be maintained during all operations to which they pertain. (b) Mine and...

  20. 36 CFR 12.8 - Memorial headstones and markers.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... markers. 12.8 Section 12.8 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL CEMETERY REGULATIONS § 12.8 Memorial headstones and markers. (a) Who may be memorialized... a memorial headstone or marker of an eligible person provided that no more than one...

  1. 36 CFR 12.8 - Memorial headstones and markers.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... markers. 12.8 Section 12.8 Parks, Forests, and Public Property NATIONAL PARK SERVICE, DEPARTMENT OF THE INTERIOR NATIONAL CEMETERY REGULATIONS § 12.8 Memorial headstones and markers. (a) Who may be memorialized... a memorial headstone or marker of an eligible person provided that no more than one...

  2. 30 CFR 717.12 - Signs and markers.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 30 Mineral Resources 3 2013-07-01 2013-07-01 false Signs and markers. 717.12 Section 717.12... PROGRAM REGULATIONS UNDERGROUND MINING GENERAL PERFORMANCE STANDARDS § 717.12 Signs and markers. (a... other markers shall be maintained during all operations to which they pertain. (b) Mine and...

  3. Behavioral and TMS Markers of Action Observation Might Reflect Distinct Neuronal Processes.

    PubMed

    Hétu, Sébastien; Taschereau-Dumouchel, Vincent; Meziane, Hadj Boumediene; Jackson, Philip L; Mercier, Catherine

    2016-01-01

    Transcranial magnetic stimulation (TMS) studies have shown that observing an action induces muscle-specific changes in corticospinal excitability. From a signal detection theory standpoint, this pattern can be related to sensitivity, which here would measure the capacity to distinguish between two action observation conditions. In parallel to these TMS studies, action observation has also been linked to behavioral effects such as motor priming and interference. It has been hypothesized that behavioral markers of action observation could be related to TMS markers and thus represent a potentially cost-effective mean of assessing the functioning of the action-perception system. However, very few studies have looked at possible relationships between these two measures. The aim of this study was to investigate if individual differences in sensitivity to action observation could be related to the behavioral motor priming and interference effects produced by action observation. To this end, 14 healthy participants observed index and little finger movements during a TMS task and a stimulus-response compatibility task. Index muscle displayed sensitivity to action observation, and action observation resulted in significant motor priming+interference, while no significant effect was observed for the little finger in both task. Nevertheless, our results indicate that the sensitivity measured in TMS was not related to the behavioral changes measured in the stimulus-response compatibility task. Contrary to a widespread assumption, the current results indicate that individual differences in physiological and behavioral markers of action observation may be unrelated. This could have important impacts on the potential use of behavioral markers in place of more costly physiological markers of action observation in clinical settings.

  4. The use and abuse of genetic marker-based estimates of relatedness and inbreeding

    PubMed Central

    Taylor, Helen R

    2015-01-01

    Genetic marker-based estimators remain a popular tool for measuring relatedness (rxy) and inbreeding (F) coefficients at both the population and individual level. The performance of these estimators fluctuates with the number and variability of markers available, and the relatedness composition and demographic history of a population. Several methods are available to evaluate the reliability of the estimates of rxy and F, some of which are implemented in the program COANCESTRY. I used the simulation module in COANCESTRY since assess the performance of marker-based estimators of rxy and F in a species with very low genetic diversity, New Zealand’s little spotted kiwi (Apteryx owenii). I also conducted a review of published papers that have used COANCESTRY as its release to assess whether and how the reliability of the estimates of rxy and F produced by genetic markers are being measured and reported in published studies. My simulation results show that even when the correlation between true (simulated) and estimated rxy or F is relatively high (Pearson’s r = 0.66–0.72 and 0.81–0.85, respectively) the imprecision of the estimates renders them highly unreliable on an individual basis. The literature review demonstrates that the majority of studies do not report the reliability of marker-based estimates of rxy and F. There is currently no standard practice for selecting the best estimator for a given data set or reporting an estimator’s performance. This could lead to experimental results being interpreted out of context and render the robustness of conclusions based on measures of rxy and F debatable. PMID:26357542

  5. Behavioral and TMS Markers of Action Observation Might Reflect Distinct Neuronal Processes.

    PubMed

    Hétu, Sébastien; Taschereau-Dumouchel, Vincent; Meziane, Hadj Boumediene; Jackson, Philip L; Mercier, Catherine

    2016-01-01

    Transcranial magnetic stimulation (TMS) studies have shown that observing an action induces muscle-specific changes in corticospinal excitability. From a signal detection theory standpoint, this pattern can be related to sensitivity, which here would measure the capacity to distinguish between two action observation conditions. In parallel to these TMS studies, action observation has also been linked to behavioral effects such as motor priming and interference. It has been hypothesized that behavioral markers of action observation could be related to TMS markers and thus represent a potentially cost-effective mean of assessing the functioning of the action-perception system. However, very few studies have looked at possible relationships between these two measures. The aim of this study was to investigate if individual differences in sensitivity to action observation could be related to the behavioral motor priming and interference effects produced by action observation. To this end, 14 healthy participants observed index and little finger movements during a TMS task and a stimulus-response compatibility task. Index muscle displayed sensitivity to action observation, and action observation resulted in significant motor priming+interference, while no significant effect was observed for the little finger in both task. Nevertheless, our results indicate that the sensitivity measured in TMS was not related to the behavioral changes measured in the stimulus-response compatibility task. Contrary to a widespread assumption, the current results indicate that individual differences in physiological and behavioral markers of action observation may be unrelated. This could have important impacts on the potential use of behavioral markers in place of more costly physiological markers of action observation in clinical settings. PMID:27683548

  6. Behavioral and TMS Markers of Action Observation Might Reflect Distinct Neuronal Processes

    PubMed Central

    Hétu, Sébastien; Taschereau-Dumouchel, Vincent; Meziane, Hadj Boumediene; Jackson, Philip L.; Mercier, Catherine

    2016-01-01

    Transcranial magnetic stimulation (TMS) studies have shown that observing an action induces muscle-specific changes in corticospinal excitability. From a signal detection theory standpoint, this pattern can be related to sensitivity, which here would measure the capacity to distinguish between two action observation conditions. In parallel to these TMS studies, action observation has also been linked to behavioral effects such as motor priming and interference. It has been hypothesized that behavioral markers of action observation could be related to TMS markers and thus represent a potentially cost-effective mean of assessing the functioning of the action-perception system. However, very few studies have looked at possible relationships between these two measures. The aim of this study was to investigate if individual differences in sensitivity to action observation could be related to the behavioral motor priming and interference effects produced by action observation. To this end, 14 healthy participants observed index and little finger movements during a TMS task and a stimulus–response compatibility task. Index muscle displayed sensitivity to action observation, and action observation resulted in significant motor priming+interference, while no significant effect was observed for the little finger in both task. Nevertheless, our results indicate that the sensitivity measured in TMS was not related to the behavioral changes measured in the stimulus–response compatibility task. Contrary to a widespread assumption, the current results indicate that individual differences in physiological and behavioral markers of action observation may be unrelated. This could have important impacts on the potential use of behavioral markers in place of more costly physiological markers of action observation in clinical settings. PMID:27683548

  7. Behavioral and TMS Markers of Action Observation Might Reflect Distinct Neuronal Processes

    PubMed Central

    Hétu, Sébastien; Taschereau-Dumouchel, Vincent; Meziane, Hadj Boumediene; Jackson, Philip L.; Mercier, Catherine

    2016-01-01

    Transcranial magnetic stimulation (TMS) studies have shown that observing an action induces muscle-specific changes in corticospinal excitability. From a signal detection theory standpoint, this pattern can be related to sensitivity, which here would measure the capacity to distinguish between two action observation conditions. In parallel to these TMS studies, action observation has also been linked to behavioral effects such as motor priming and interference. It has been hypothesized that behavioral markers of action observation could be related to TMS markers and thus represent a potentially cost-effective mean of assessing the functioning of the action-perception system. However, very few studies have looked at possible relationships between these two measures. The aim of this study was to investigate if individual differences in sensitivity to action observation could be related to the behavioral motor priming and interference effects produced by action observation. To this end, 14 healthy participants observed index and little finger movements during a TMS task and a stimulus–response compatibility task. Index muscle displayed sensitivity to action observation, and action observation resulted in significant motor priming+interference, while no significant effect was observed for the little finger in both task. Nevertheless, our results indicate that the sensitivity measured in TMS was not related to the behavioral changes measured in the stimulus–response compatibility task. Contrary to a widespread assumption, the current results indicate that individual differences in physiological and behavioral markers of action observation may be unrelated. This could have important impacts on the potential use of behavioral markers in place of more costly physiological markers of action observation in clinical settings.

  8. The ecology of individuals: incidence and implications of individual specialization.

    PubMed

    Bolnick, Daniel I; Svanbäck, Richard; Fordyce, James A; Yang, Louie H; Davis, Jeremy M; Hulsey, C Darrin; Forister, Matthew L

    2003-01-01

    Most empirical and theoretical studies of resource use and population dynamics treat conspecific individuals as ecologically equivalent. This simplification is only justified if interindividual niche variation is rare, weak, or has a trivial effect on ecological processes. This article reviews the incidence, degree, causes, and implications of individual-level niche variation to challenge these simplifications. Evidence for individual specialization is available for 93 species distributed across a broad range of taxonomic groups. Although few studies have quantified the degree to which individuals are specialized relative to their population, between-individual variation can sometimes comprise the majority of the population's niche width. The degree of individual specialization varies widely among species and among populations, reflecting a diverse array of physiological, behavioral, and ecological mechanisms that can generate intrapopulation variation. Finally, individual specialization has potentially important ecological, evolutionary, and conservation implications. Theory suggests that niche variation facilitates frequency-dependent interactions that can profoundly affect the population's stability, the amount of intraspecific competition, fitness-function shapes, and the population's capacity to diversify and speciate rapidly. Our collection of case studies suggests that individual specialization is a widespread but underappreciated phenomenon that poses many important but unanswered questions.

  9. Expression of squamous cell carcinoma markers and adenocarcinoma markers in primary pulmonary neuroendocrine carcinomas.

    PubMed

    Masai, Kyohei; Tsuta, Koji; Kawago, Mitsumasa; Tatsumori, Takahiro; Kinno, Tomoaki; Taniyama, Tomoko; Yoshida, Akihiko; Asamura, Hisao; Tsuda, Hitoshi

    2013-07-01

    Recent clinical trials have revealed that accurate histologic typing of non-small cell lung cancer is essential. Until now, squamous cell carcinoma (SQC) and adenocarcinoma (ADC) markers have not been thoroughly analyzed for pulmonary neuroendocrine carcinomas (NECs). We analyzed the expression of 8 markers [p63, cytokeratin (CK) 5/6, SOX2, CK7, desmocollin 3, thyroid transcription factor-1 (8G7G3/1 and SPT24), and napsin A] in 224 NECs. SOX2 (76.2%) had the greatest expression for NECs. CK5/6 (1.4%), desmocollin 3 (0.5%), and napsin A (0%) were expressed less or not at all in NECs. Although our investigated markers have been reported useful for differentiating between SQC and ADC, some of them were also present in a portion of pulmonary NECs. In our study, CK5/6 and desmocollin 3 were highly specific markers for SQC, and napsin A was highly specific for ADC. These markers are recommended for diagnosis of poorly differentiated non-small cell lung cancer.

  10. Novelty Seeking as a Phenotypic Marker of Adolescent Substance Use

    PubMed Central

    Bidwell, L Cinnamon; Knopik, Valerie S; Audrain-McGovern, Janet; Glynn, Tiffany R; Spillane, Nichea S; Ray, Lara A; Riggs, Nathaniel R; Guillot, Casey R; Pang, Raina D; Leventhal, Adam M

    2015-01-01

    Trait novelty seeking has been consistently implicated in substance use, yet the origins and mechanisms of novelty seeking in substance use proneness are unclear. We aimed to characterize novelty seeking as a phenotypic marker of substance use proneness in adolescence, a critical period for drug use experimentation. To this end, we parsed novelty seeking’s two constituent subdimensions – exploratory excitability (drive for novel experience) and impulsiveness (careless decision-making) – and explored the individual relations of these dimensions to: (1) the use of a variety of licit and illicit substances, (2) family history of substance use, and (3) subjective drug effects. Five hundred eighty five adolescents (mean age = 14.5 years) completed surveys of key variables. Results indicated that, when accounting for the covariation among exploratory excitability and impulsiveness, impulsiveness emerged as the more salient correlate of substance use and was independently associated with initiation of nearly all drug classes. Mediation analyses of the mechanisms of novelty seeking-related risk illustrated that impulsiveness mediated the association of family history of substance use with both initiation and past 30-day frequency of use. Both impulsiveness and exploratory excitability were associated with increased positive and negative subjective drug effects, and the analyses supported a significant indirect pathway from impulsiveness to a more frequent use via positive subjective effects. Although limited by a cross-sectional design, these findings suggest that impulsiveness-like aspects of the novelty seeking construct may represent a useful phenotypic marker for early substance use proneness that potentially (1) increases initiation risk, (2) has familial origins, and (3) promotes more frequent use by altering subjective drug response. PMID:26106262

  11. Prognostic laboratory markers of joint damage in rheumatoid arthritis

    PubMed Central

    Lindqvist, E; Eberhardt, K; Bendtzen, K; Heinegard, D; Saxne, T

    2005-01-01

    Objective: To investigate whether determination of a set of laboratory markers at baseline provides prognostic information on joint damage in hands and feet in rheumatoid arthritis. Methods: 183 patients with early rheumatoid arthritis included in a prospective study were examined. Radiographic changes in hands and feet at 5 and 10 years after inclusion were evaluated (Larsen). The markers analysed were: erythrocyte sedimentation rate (ESR); HLA-DRB alleles typed by restriction fragment length polymorphism; and C reactive protein, cartilage oligomeric matrix protein (COMP), rheumatoid factor (RF) (IgG, IgA, and IgM subtypes), antibodies against cyclic citrullinated peptide (anti-CCP), and antibodies against interleukin 1α (anti-IL1α), analysed by immunoassays. Multiple linear regression with backward elimination was used to determine the prognostic value of the variables. Results: 117/176 patients were positive for IgG RF, 138/176 for IgA RF, 139/176 for IgM RF, 140/176 for anti-CCP, and 40/182 for anti-IL1α. After five years, ESR, the presence of IgA RF, serum COMP, and the presence of anti-CCP were significantly associated with more severe joint damage, and the presence of anti-IL1α with less severe joint damage. Baseline C reactive protein and anti-CCP predicted radiographic outcome after 10 years. A stronger prediction was obtained by combining the prognostic factors. Conclusions: Early determination of anti-CCP, IgA RF, anti-IL-1α, ESR, C reactive protein, and COMP predicted the development of joint damage in hands and feet in this cohort. A combination of these measures reflecting different aspects of the disease process should be useful for evaluating prognosis in individual patients with early rheumatoid arthritis. PMID:15458956

  12. Rapid detection of autosomal aneuploidy using microsatellite markers

    SciTech Connect

    Ray, P.N.; Teshima, I.E.; Winsor, E.J.T.

    1994-09-01

    Trisomy occurs in at least 4% of all clinically recognized pregnancies, making it the most common type of chromosome abnormality in humans. The most commonly occurring trisomies are those of chromosomes 13, 18, 21 and aneuploidy of X and Y, accounting for about 0.3% of all newborns and a much higher percentage of conceptuses. In Canada, prenatal chromosome analysis by amniocentesis is offered to those women {ge} 35 years of age at the time of delivery or equivalent risk by maternal serum screen. We are developing a rapid molecular diagnostic test to detect the most common autosomal aneuploidies in prenatal and neonatal samples. The tests makes use of highly polymorphic short tandem repeat markers labeled with fluorescent tags which allow analysis on a GENESCANNER automated fragment analyzer (ABI). Multiple polymorphic markers have been selected on each of chromosomes 13, 18 and 21. At a given locus, trisomic fetuses/neonates will have either three alleles or two alleles with one allele having twice the intensity of the other. Unaffected individuals have two equal intensity alleles. We are conducting a blind study that will compare the detection efficiencies of FISH analysis on uncultured cells and the molecular method on confirmation amniotic fluid samples collected at the time of termination of affected fetuses. Results on cultured amniocytes from one such patient confirmed that trisomy 21 can be detected. FISH was not done on this sample. In addition, detection efficiency of the molecular method in whole blood samples from affected neonates is also being studied. To date, two such samples have been tested, one with trisomy 13 and one with trisomy 18, and both samples were diagnosed correctly. Preliminary results suggest that this method may provide a valuable tool for the rapid diagnosis of aneuploidy.

  13. A Novel Approach for Mining Polymorphic Microsatellite Markers In Silico

    PubMed Central

    Hoffman, Joseph I.; Nichols, Hazel J.

    2011-01-01

    An important emerging application of high-throughput 454 sequencing is the isolation of molecular markers such as microsatellites from genomic DNA. However, few studies have developed microsatellites from cDNA despite the added potential for targeting candidate genes. Moreover, to develop microsatellites usually requires the evaluation of numerous primer pairs for polymorphism in the focal species. This can be time-consuming and wasteful, particularly for taxa with low genetic diversity where the majority of primers often yield monomorphic polymerase chain reaction (PCR) products. Transcriptome assemblies provide a convenient solution, functional annotation of transcripts allowing markers to be targeted towards candidate genes, while high sequence coverage in principle permits the assessment of variability in silico. Consequently, we evaluated fifty primer pairs designed to amplify microsatellites, primarily residing within transcripts related to immunity and growth, identified from an Antarctic fur seal (Arctocephalus gazella) transcriptome assembly. In silico visualization was used to classify each microsatellite as being either polymorphic or monomorphic and to quantify the number of distinct length variants, each taken to represent a different allele. The majority of loci (n = 36, 76.0%) yielded interpretable PCR products, 23 of which were polymorphic in a sample of 24 fur seal individuals. Loci that appeared variable in silico were significantly more likely to yield polymorphic PCR products, even after controlling for microsatellite length measured in silico. We also found a significant positive relationship between inferred and observed allele number. This study not only demonstrates the feasibility of generating modest panels of microsatellites targeted towards specific classes of gene, but also suggests that in silico microsatellite variability may provide a useful proxy for PCR product polymorphism. PMID:21853104

  14. SNP markers-based map construction and genome-wide linkage analysis in Brassica napus.

    PubMed

    Raman, Harsh; Dalton-Morgan, Jessica; Diffey, Simon; Raman, Rosy; Alamery, Salman; Edwards, David; Batley, Jacqueline

    2014-09-01

    An Illumina Infinium array comprising 5306 single nucleotide polymorphism (SNP) markers was used to genotype 175 individuals of a doubled haploid population derived from a cross between Skipton and Ag-Spectrum, two Australian cultivars of rapeseed (Brassica napus L.). A genetic linkage map based on 613 SNP and 228 non-SNP (DArT, SSR, SRAP and candidate gene markers) covering 2514.8 cM was constructed and further utilized to identify loci associated with flowering time and resistance to blackleg, a disease caused by the fungus Leptosphaeria maculans. Comparison between genetic map positions of SNP markers and the sequenced Brassica rapa (A) and Brassica oleracea (C) genome scaffolds showed several genomic rearrangements in the B. napus genome. A major locus controlling resistance to L. maculans was identified at both seedling and adult plant stages on chromosome A07. QTL analyses revealed that up to 40.2% of genetic variation for flowering time was accounted for by loci having quantitative effects. Comparative mapping showed Arabidopsis and Brassica flowering genes such as Phytochrome A/D, Flowering Locus C and agamous-Like MADS box gene AGL1 map within marker intervals associated with flowering time in a DH population from Skipton/Ag-Spectrum. Genomic regions associated with flowering time and resistance to L. maculans had several SNP markers mapped within 10 cM. Our results suggest that SNP markers will be suitable for various applications such as trait introgression, comparative mapping and high-resolution mapping of loci in B. napus.

  15. Production and processing studies on calpain-system gene markers for tenderness in Brahman cattle: 2. Objective meat quality.

    PubMed

    Cafe, L M; McIntyre, B L; Robinson, D L; Geesink, G H; Barendse, W; Pethick, D W; Thompson, J M; Greenwood, P L

    2010-09-01

    Effects and interactions of calpain-system tenderness gene markers on objective meat quality traits of Brahman (Bos indicus) cattle were quantified within 2 concurrent experiments at different locations. Cattle were selected for study from commercial and research herds at weaning based on their genotype for calpastatin (CAST) and calpain 3 (CAPN3) gene markers for beef tenderness. Gene marker status for mu-calpain (CAPN1-4751 and CAPN1-316) was also determined for inclusion in statistical analyses. Eighty-two heifer and 82 castrated male cattle with 0 or 2 favorable alleles for CAST and CAPN3 were studied in New South Wales (NSW), and 143 castrated male cattle with 0, 1, or 2 favorable alleles for CAST and CAPN3 were studied in Western Australia (WA). The cattle were backgrounded for 6 to 8 mo and grain-fed for 117 d (NSW) or 80 d (WA) before slaughter. One-half the cattle in each experiment were implanted with a hormonal growth promotant during feedlotting. One side of each carcass was suspended from the Achilles tendon (AT) and the other from the pelvis (tenderstretch). The M. longissimus lumborum from both sides and the M. semitendinosus from the AT side were collected; then samples of each were aged at 1 degrees C for 1 or 7 d. Favorable alleles for one or more markers reduced shear force, with little effect on other meat quality traits. The size of effects of individual markers varied with site, muscle, method of carcass suspension, and aging period. Individual marker effects were additive as evident in cattle with 4 favorable alleles for CAST and CAPN3 markers, which had shear force reductions of 12.2 N (P < 0.001, NSW) and 9.3 N (P = 0.002, WA) in AT 7 d aged M. longissimus lumborum compared with those with no favorable alleles. There was no evidence (all P > 0.05) of interactions between the gene markers, or between the hormonal growth promotant and gene markers for any meat quality traits. This study provides further evidence that selection based on the

  16. Production and processing studies on calpain-system gene markers for tenderness in Brahman cattle: 2. Objective meat quality.

    PubMed

    Cafe, L M; McIntyre, B L; Robinson, D L; Geesink, G H; Barendse, W; Pethick, D W; Thompson, J M; Greenwood, P L

    2010-09-01

    Effects and interactions of calpain-system tenderness gene markers on objective meat quality traits of Brahman (Bos indicus) cattle were quantified within 2 concurrent experiments at different locations. Cattle were selected for study from commercial and research herds at weaning based on their genotype for calpastatin (CAST) and calpain 3 (CAPN3) gene markers for beef tenderness. Gene marker status for mu-calpain (CAPN1-4751 and CAPN1-316) was also determined for inclusion in statistical analyses. Eighty-two heifer and 82 castrated male cattle with 0 or 2 favorable alleles for CAST and CAPN3 were studied in New South Wales (NSW), and 143 castrated male cattle with 0, 1, or 2 favorable alleles for CAST and CAPN3 were studied in Western Australia (WA). The cattle were backgrounded for 6 to 8 mo and grain-fed for 117 d (NSW) or 80 d (WA) before slaughter. One-half the cattle in each experiment were implanted with a hormonal growth promotant during feedlotting. One side of each carcass was suspended from the Achilles tendon (AT) and the other from the pelvis (tenderstretch). The M. longissimus lumborum from both sides and the M. semitendinosus from the AT side were collected; then samples of each were aged at 1 degrees C for 1 or 7 d. Favorable alleles for one or more markers reduced shear force, with little effect on other meat quality traits. The size of effects of individual markers varied with site, muscle, method of carcass suspension, and aging period. Individual marker effects were additive as evident in cattle with 4 favorable alleles for CAST and CAPN3 markers, which had shear force reductions of 12.2 N (P < 0.001, NSW) and 9.3 N (P = 0.002, WA) in AT 7 d aged M. longissimus lumborum compared with those with no favorable alleles. There was no evidence (all P > 0.05) of interactions between the gene markers, or between the hormonal growth promotant and gene markers for any meat quality traits. This study provides further evidence that selection based on the

  17. Divergence of East Asians and Europeans Estimated Using Male- and Female-Specific Genetic Markers

    PubMed Central

    Tateno, Yoshio; Komiyama, Tomoyoshi; Katoh, Toru; Munkhbat, Batmunkh; Oka, Akira; Haida, Yuko; Kobayashi, Hiroyuki; Tamiya, Gen; Inoko, Hidetoshi

    2014-01-01

    To study the male and female lineages of East Asian and European humans, we have sequenced 25 short tandem repeat markers on 453 Y-chromosomes and collected sequences of 72 complete mitochondrial genomes to construct independent phylogenetic trees for male and female lineages. The results indicate that East Asian individuals fall into two clades, one that includes East Asian individuals only and a second that contains East Asian and European individuals. Surprisingly, the European individuals did not form an independent clade, but branched within in the East Asians. We then estimated the divergence time of the root of the European clade as ∼41,000 years ago. These data indicate that, contrary to traditional views, Europeans diverged from East Asians around that time. We also address the origin of the Ainu lineage in northern Japan. PMID:24589501

  18. Differentially expressed protein markers in human submandibular and sublingual secretions.

    PubMed

    Hu, Shen; Denny, Patricia; Denny, Paul; Xie, Yongming; Loo, Joseph A; Wolinsky, Lawrence E; Li, Yang; McBride, Jim; Ogorzalek Loo, Rachel R; Navazesh, Mavash; Wong, David T

    2004-11-01

    Proteome analysis of secretions from individual salivary glands is important for understanding the health of the oral cavity and pathogenesis of certain diseases. However, cross-contamination of submandibular (SM) and sublingual (SL) glandular secretions can occur. The close anatomic relationship of the SM and SL ductal orifices can lead to such contamination. Additionally, these glands may share common ducts. To insure the purity of SM/SL secretions for proteomic analysis, it is important to develop unique biomarkers which could be used to verify the integrity of the individual glandular saliva. In this study, a proteomics approach based on mass spectrometry and gel electrophoresis techniques was utilized to identify and verify a set of proteins (cystatin C, calgranulin B and MUC5B mucin), which are differentially expressed in SM/SL secretions. SM/SL fluids were obtained from nine healthy subjects. Cystatin C was found to be an SM-selective protein as it was found in all SM fluids but not detected in two SL fluids. MUC5B mucin and calgranulin B, on the other hand, were found to be SL-selective proteins. All SL samples contained MUC5B mucin, whereas MUC5B mucin was not detected in four SM samples. Eight of the SL samples contained calgranulin B; however, calgranulin B was absent in eight SM samples. This set of protein markers, especially calgranulin B, can be used to determine the purity of SM/SL samples, and therefore identify potential individuals who do not exhibit cross-contaminated SM/SL secretions, an important requirement for subsequent proteome analysis of pure SM and SL secretions.

  19. Surface markers. [Quarterly report, January 1--June 30, 1995

    SciTech Connect

    Andrews, W.B.

    1995-08-01

    This research examined information on natural phenomena and human activities to ultimately recommend specific sites for surface markers to warn future generations of the potential hazards of disposed waste. Literature pertaining to previous marker designs was reviewed and summarized. This literature primarily addressed the recommendations of a consultant team for developing a marker system to warn future generations about radioactive waste (WIPP, New Mexico). Literature on archeological markers (e.g., Nazca lines in Peru, pyramids) and their durability was also covered. Application to Yucca Mountain is discussed; sites for possible placement of surface markers are considered.

  20. Individualized medicine, health medicine, and constitutional theory in Chinese medicine.

    PubMed

    Wang, Qi

    2012-03-01

    The patterns of modern science and changes in the medical model can result in the transformation of the current state of individualized and health medicines into being the primary trend in medical development. Chinese and Western medical systems are dissimilar in terms of value orientations, thinking style, and research directions because of their different historical and cultural backgrounds. Individualized treatment in modern medicine is mainly established based on individual genome information and the differences in mononucleotide polymorphisms. However, such treatment method is expensive, creates an uncertain genetic marker, and leads to different result interpretations, among other problems. The Chinese constitutional theory developed in the 1970s expresses the principle behind Chinese health medicine and individual treatment and provides the corresponding methods. The Chinese constitutional theory divides the constitution of the Chinese population into nine categories based on established classification criteria. It promotes the study of the relationship of each constitution to diseases and Chinese medicine preparation toward adjusting the constitution and preventing diseases. The theory also provides methods and tools for individualized treatment. Constitution identification shows the direction and provides the core technology for the evaluation of the health status. By combining the developments in modern biotechnology, new diagnostic techniques and treatment models of constitution-differentiation, disease-differentiation, and syndrome-differentiation can be established for the development of individualized Chinese medicine treatment and health medicine for the international medical community.

  1. Automatic Identification of Web-Based Risk Markers for Health Events

    PubMed Central

    Borsa, Diana; Hayward, Andrew C; McKendry, Rachel A; Cox, Ingemar J

    2015-01-01

    Background The escalating cost of global health care is driving the development of new technologies to identify early indicators of an individual’s risk of disease. Traditionally, epidemiologists have identified such risk factors using medical databases and lengthy clinical studies but these are often limited in size and cost and can fail to take full account of diseases where there are social stigmas or to identify transient acute risk factors. Objective Here we report that Web search engine queries coupled with information on Wikipedia access patterns can be used to infer health events associated with an individual user and automatically generate Web-based risk markers for some of the common medical conditions worldwide, from cardiovascular disease to sexually transmitted infections and mental health conditions, as well as pregnancy. Methods Using anonymized datasets, we present methods to first distinguish individuals likely to have experienced specific health events, and classify them into distinct categories. We then use the self-controlled case series method to find the incidence of health events in risk periods directly following a user’s search for a query category, and compare to the incidence during other periods for the same individuals. Results Searches for pet stores were risk markers for allergy. We also identified some possible new risk markers; for example: searching for fast food and theme restaurants was associated with a transient increase in risk of myocardial infarction, suggesting this exposure goes beyond a long-term risk factor but may also act as an acute trigger of myocardial infarction. Dating and adult content websites were risk markers for sexually transmitted infections, such as human immunodeficiency virus (HIV). Conclusions Web-based methods provide a powerful, low-cost approach to automatically identify risk factors, and support more timely and personalized public health efforts to bring human and economic benefits. PMID

  2. Promoting the use of BaP as a marker for PAH exposure in UK soils.

    PubMed

    Bull, Sarah; Collins, Chris

    2013-02-01

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants that frequently accumulate in soils. There is therefore a requirement to determine their levels in contaminated environments for the purposes of determining impacts on human health. PAHs are a suite of individual chemicals, and there is an ongoing debate as to the most appropriate method for assessing the risk to humans from them. Two methods predominate: the surrogate marker approach and the toxic equivalency factor. The former assumes that all chemicals in a mixture have an equivalent toxicity. The toxic equivalency approach estimates the potency of individual chemicals relative to the usually most toxic Benzo(a)pyrene. The surrogate marker approach is believed to overestimate risk and the toxic equivalency factor to underestimate risk. When analysing the risks from soils, the surrogate marker approach is preferred due to its simplicity, but there are concerns because of the potential diversity of the PAH profile across the range of impacted soils. Using two independent data sets containing soils from 274 sites across a diverse range of locations, statistical analysis was undertaken to determine the differences in the composition of carcinogenic PAH between site locations, for example, rural versus industrial. Following principal components analysis, distinct population differences were not seen between site locations in spite of large differences in the total PAH burden between individual sites. Using all data, highly significant correlations were seen between BaP and other carcinogenic PAH with the majority of r (2) values > 0.8. Correlations with the European Food Standards Agency (EFSA) summed groups, that is, EFSA2, EFSA4 and EFSA8 had even higher correlations (r (2) > 0.95). We therefore conclude that BaP is a suitable surrogate marker to represent mixtures of PAH in soil during risk assessments.

  3. Individual Differences in Equity Models

    ERIC Educational Resources Information Center

    Hofmans, Joeri

    2012-01-01

    In the present paper, we (1) study whether people differ in the equity models they use, and (2) test whether individual differences in equity models relate to individual differences in equity sensitivity. To achieve this goal, an Information Integration experiment was performed in which participants were given information on the performance of two…

  4. INDIVIDUALIZING INSTRUCTION IN SMALL SCHOOLS.

    ERIC Educational Resources Information Center

    Western States Small Schools Project, Salt Lake City, UT.

    THIS DOCUMENT DISCUSSES PROCEDURES AND POTENTIALS FOR INDIVIDUALIZING INSTRUCTIONAL PROGRAMS IN SMALL RURAL SCHOOLS. FOUR FACTORS ARE SEEN TO BE OPERANT IN THE INDIVIDUALIZATION PROCESS. THESE ARE THE INSTRUCTOR, THE CURRICULUM AND SUPPLEMENTARY MATERIALS, ADMINISTRATIVE PRACTICE, AND PHYSICAL FACILITIES. NEW INSTRUCTIONAL PROCEDURES SHOULD BE…

  5. INDIVIDUALIZED READING AND PROGRAMED INSTRUCTION.

    ERIC Educational Resources Information Center

    COHEN, S. ALAN

    A MODEL READING APPROACH TO INCREASE THE QUALITY AND QUANTITY OF READING INSTRUCTION IN THE CLASSROOM IS PRESENTED. THE CRITERIA OF GOOD TEACHING METHODOLOGY ARE THAT PROGRAMS SHOULD MEET INDIVIDUAL STUDENT NEEDS, THAT A PROGRAM'S LEVEL OF CONTENT SHOULD BE TAILORED TO THE INDIVIDUAL STUDENT'S LEVEL OF CAPACITY AND ACHIEVEMENT, THAT THE SPEED OF…

  6. Individual Learner Differences in SLA

    ERIC Educational Resources Information Center

    Arabski, Janusz; Wojtaszek, Adam

    2011-01-01

    "Individual Learner Differences in SLA" addresses the apparently insoluble conflict between the unquestionably individual character of the process of second language acquisition/foreign language learning and the institutionalised, often inflexible character of formal instruction in which it takes place. How, then, is success in SLA so prevalent?

  7. Readability of Individualized Education Programs

    ERIC Educational Resources Information Center

    Lo, Lusa

    2014-01-01

    An individualized education program is a legal document that details information regarding the special education program of a student with a disability. For parents to determine whether they agree with the individualized education program that is proposed by the school, they must first be able to read and comprehend the document. This study aimed…

  8. Individualizing Reading Instruction: A Reader.

    ERIC Educational Resources Information Center

    Harris, Larry A.; Smith, Carl B.

    The articles contained in this volume were selected to support and strengthen the concept of individualized instruction through diagnostic teaching. The book is divided into six major parts, each of which is preceded by a brief overview that emphasizes the main tenets advanced by the authors of the individual articles. The six major divisions of…

  9. [Biochemical markers of bone remodeling: pre-analytical variations and guidelines for their use. SFBC (Société Française de Biologie Clinique) Work Group. Biochemical markers of bone remodeling].

    PubMed

    Garnero, P; Bianchi, F; Carlier, M C; Genty, V; Jacob, N; Kamel, S; Kindermans, C; Plouvier, E; Pressac, M; Souberbielle, J C

    2000-01-01

    Biochemical markers of bone turnover have been developed over the past 20 years that are more specific for bone tissue than conventional ones such as total alkaline phosphatase and urinary hydroxyproline. They have been widely used in clinical research and in clinical trials of new therapies as secondary end points of treatment efficacy. Most of the interest has been devoted to their use in postmenopausal osteoporosis, a condition characterized by subtle modifications of bone metabolism that cannot be detected readily by conventional markers of bone turnover. Although several recent studies have suggested that biochemical markers may be used for the management of the individual patient in routine clinical practice, this has not been clearly defined and is a matter of debate. Because of the crucial importance to clarify this issue, the Société Francaise de Biologie Clinique prompted an expert committee to summarize the available data and to make recommendations. The following paper includes a review on the biochemical and analytical aspects of the markers of bone formation and resorption and on the sources of variability such as sex, age, menstrual cycle, pregnancy and lactation, physical activity, seasonal variation and effects of diseases and treatments. We will also describe the effects of pre-analytical factors on the measurements of the different markers. Finally based on that review, we will make practical recommendations for the use of these markers in order to minimize the variability of the measurements and improve the clinical interpretation of the data.

  10. Markers and mapping revisited: finding your gene.

    PubMed

    Jones, Neil; Ougham, Helen; Thomas, Howard; Pasakinskiene, Izolda

    2009-01-01

    This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of

  11. A SOMATIC-MARKER THEORY OF ADDICTION

    PubMed Central

    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

  12. Barcoding markers for Pneumocystis species in wildlife.

    PubMed

    Danesi, Patrizia; da Rold, Graziana; Rizzoli, Annapaola; Hauffe, Heidi C; Marangon, Stefano; Samerpitak, Kittipan; Demanche, Cristine; Guillot, Jacques; Capelli, Gioia; de Hoog, Sybren G

    2016-02-01

    Lung specimens (n = 216) from six wildlife species were examined for occurrence of Pneumocystis species in pulmonary tissues. Among small mammals the shrew Sorex antinorii (80 %) were most frequently colonized. In contrast, foxes and badgers did not yield positive amplification. Host-specificity was noted, at least at the level of the host genus. Phylogenetic trees based on partial mtLSU and mtSSU showed high diversity of species corresponding to animal host diversity. Nuclear rDNA ITS data confirmed unambiguous separation of species. In conclusion, ITS is an excellent marker to distinguish species of the genus Pneumocystis. PMID:26781376

  13. Endometriosis in adolescence: predictive markers and management.

    PubMed

    Steenberg, Christine K; Tanbo, Tom G; Qvigstad, Erik

    2013-05-01

    Endometriosis has long been thought mostly to affect the adult female population. However, awareness of possible endometriosis already in adolescence is now receiving increasing attention. It seems that certain markers in adolescence are associated with a subsequent diagnosis of the disease. These include chronic pelvic pain, severe dysmenorrhea, dysmenorrhea resistant to non-steroidal anti-inflammatory drugs and oral contraceptive pills, and pain interfering with daily activity. Based on current knowledge, it should be possible to diagnose endometriosis before adulthood, thereby alleviating symptoms and possibly limiting sequelae. To do so, knowledge of adolescent endometriosis has to be improved among both health professionals and the public. PMID:23506249

  14. Collective Functionality through Bacterial Individuality

    NASA Astrophysics Data System (ADS)

    Ackermann, Martin

    According to the conventional view, the properties of an organism are a product of nature and nurture - of its genes and the environment it lives in. Recent experiments with unicellular organisms have challenged this view: several molecular mechanisms generate phenotypic variation independently of environmental signals, leading to variation in clonal groups. My presentation will focus on the causes and consequences of this microbial individuality. Using examples from bacterial genetic model systems, I will first discuss different molecular and cellular mechanisms that give rise to bacterial individuality. Then, I will discuss the consequences of individuality, and focus on how phenotypic variation in clonal populations of bacteria can promote interactions between individuals, lead to the division of labor, and allow clonal groups of bacteria to cope with environmental uncertainty. Variation between individuals thus provides clonal groups with collective functionality.

  15. Genetic Fingerprints for Individually Quick Frozen 'Marion' Whole Berries and Puree

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A forensic-type approach was proposed to identify ‘Marion’ type blackberry from Individually Quick Frozen (IQF) whole berries and puree using DNA-based simple sequence repeat (SSR) markers. This approach is useful for quality control and to detect contamination from other berry products. A reliable ...

  16. Assessing the reproductive competence of individual embryos: a proposal for the validation of new "-omics" technologies.

    PubMed

    Scott, Richard T; Treff, Nathan R

    2010-08-01

    Rapid technological advances now provide the tools needed to evaluate the molecular genetics, proteomics, and microenvironment of an individual embryo in an effort to predict its reproductive competence. Rigorous criteria for accepting any test as a validated marker of embryonic reproductive competence should be established, and practitioners should be cautious about applying these tests clinically before the availability of comprehensive and convincing evidence.

  17. A panel of polymorphic bovine, ovine and caprine microsatellite markers.

    PubMed

    Kemp, S J; Hishida, O; Wambugu, J; Rink, A; Longeri, M L; Ma, R Z; Da, Y; Lewin, H A; Barendse, W; Teale, A J

    1995-10-01

    A panel of 81 new polymorphic bovine microsatellite markers is described, together with further information on a previously reported group of 16 markers. The mean polymorphism information content of the 97 markers determined in 20 cattle was 0.66. Seventy-three of these markers have been assigned to chromosomes by either linkage analysis or use of hybrid cell panels. Thirty-nine of the markers were polymorphic in sheep, and 32 were polymorphic in goat. This study identified a set of 18 robust markers that were polymorphic in all three species and that covered 14 bovine chromosomes. This provides a single group of markers, which would be suited to genetic distance analysis and parentage control in cattle, sheep and goat. PMID:7486246

  18. An apricot (Prunus armeniaca L.) F2 progeny linkage map based on SSR and AFLP markers, mapping plum pox virus resistance and self-incompatibility traits.

    PubMed

    Vilanova, S; Romero, C; Abbott, A G; Llácer, G; Badenes, M L

    2003-07-01

    A genetic linkage map of apricot ( Prunus armeniaca L.) was constructed using AFLP and SSR markers. The map is based on an F(2) population (76 individuals) derived from self-pollination of an F(1) individual ('Lito') originated from a cross between 'Stark Early Orange' and 'Tyrinthos'. This family, designated as 'Lito' x 'Lito', segregated for two important agronomical traits: plum pox virus resistance (PPV) and self-incompatibility. A total of 211 markers (180 AFLPs, 29 SSRs and two agronomic traits) were assigned to 11 linkage groups covering 602 cM of the apricot genome. The average distance (cM/marker) between adjacent markers is 3.84 cM. The PPV resistance trait was mapped on linkage group G1 and the self-incompatibility trait was mapped on linkage group G6. Twenty two loci held in common with other Prunus maps allowed us to compare and establish homologies among the respective linkage groups.

  19. Respiratory symptoms in households as an effective marker for influenza-like illness surveillance in the community.

    PubMed

    Lee, Shui Shan; Wong, Ngai Sze

    2014-06-01

    To effectively track the growth of influenza, we piloted an online system to monitor influenza-like illness (ILI) in the community in one district of Hong Kong. Four syndromic markers, namely fever, respiratory symptoms, fever with respiratory symptoms, fever and/or respiratory symptoms, either of the individual or of the household, were collected during the study period from June 2012 to October 2013. A total of 132 residents of Tuen Mun District reported syndromic markers at the individual and household levels on a weekly basis. Temporal patterns of these markers were compared with data derived from laboratory surveillance by dynamic linear regression. Household respiratory symptoms were found to be an effective syndromic marker, pre-dating overall laboratory virus surveillance results on influenza diseases in two influenza seasons by 3-4 weeks. To conclude, respiratory symptoms can be a good marker predicting the onset of the influenza season in the community, and is particularly useful with regard to data from households, even if the sample size may not be a large one.

  20. Respiratory symptoms in households as an effective marker for influenza-like illness surveillance in the community.

    PubMed

    Lee, Shui Shan; Wong, Ngai Sze

    2014-06-01

    To effectively track the growth of influenza, we piloted an online system to monitor influenza-like illness (ILI) in the community in one district of Hong Kong. Four syndromic markers, namely fever, respiratory symptoms, fever with respiratory symptoms, fever and/or respiratory symptoms, either of the individual or of the household, were collected during the study period from June 2012 to October 2013. A total of 132 residents of Tuen Mun District reported syndromic markers at the individual and household levels on a weekly basis. Temporal patterns of these markers were compared with data derived from laboratory surveillance by dynamic linear regression. Household respiratory symptoms were found to be an effective syndromic marker, pre-dating overall laboratory virus surveillance results on influenza diseases in two influenza seasons by 3-4 weeks. To conclude, respiratory symptoms can be a good marker predicting the onset of the influenza season in the community, and is particularly useful with regard to data from households, even if the sample size may not be a large one. PMID:24680819