Identification of micro satellite markers on chromosomes of bread ...

African Journals Online (AJOL)

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2007-07-18

Jul 18, 2007 ... 2 Department of Biotechnology and Molecular Biology, CCS Haryana Agricultural University, ... markers closely linked to karnal bunt resistance in wheat. ... from leaf tissues using modified CTAB procedure (Saghai-Maroof et.

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Monte Carlo simulations on marker grouping and ordering.

Science.gov (United States)

Wu, J; Jenkins, J; Zhu, J; McCarty, J; Watson, C

2003-08-01

Four global algorithms, maximum likelihood (ML), sum of adjacent LOD score (SALOD), sum of adjacent recombinant fractions (SARF) and product of adjacent recombinant fraction (PARF), and one approximation algorithm, seriation (SER), were used to compare the marker ordering efficiencies for correctly given linkage groups based on doubled haploid (DH) populations. The Monte Carlo simulation results indicated the marker ordering powers for the five methods were almost identical. High correlation coefficients were greater than 0.99 between grouping power and ordering power, indicating that all these methods for marker ordering were reliable. Therefore, the main problem for linkage analysis was how to improve the grouping power. Since the SER approach provided the advantage of speed without losing ordering power, this approach was used for detailed simulations. For more generality, multiple linkage groups were employed, and population size, linkage cutoff criterion, marker spacing pattern (even or uneven), and marker spacing distance (close or loose) were considered for obtaining acceptable grouping powers. Simulation results indicated that the grouping power was related to population size, marker spacing distance, and cutoff criterion. Generally, a large population size provided higher grouping power than small population size, and closely linked markers provided higher grouping power than loosely linked markers. The cutoff criterion range for achieving acceptable grouping power and ordering power differed for varying cases; however, combining all situations in this study, a cutoff criterion ranging from 50 cM to 60 cM was recommended for achieving acceptable grouping power and ordering power for different cases.

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Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ...t_db_link_en.zip (36.3 KB) - 6 Genome analysis methods pgdbj_dna_marker_linkage_map_genome_analysis_methods_... of This Database Site Policy | Contact Us Download - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

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Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods ... QTL list, Plant DB link & Genome analysis methods Alternative name - DOI 10.18908/lsdba.nbdc01194-01-000 Cr...ers and QTLs are curated manually from the published literature. The marker information includes marker sequences, genotyping methods... Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive ...

An AFLP marker linked to the Pm-1 gene that confers resistance to Podosphaera xanthii race 1 in Cucumis melo

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Ana Paula Matoso Teixeira

2008-01-01

Full Text Available Brazil produced 330,000 metric tons of melons in 2005, principally in the Northeast region where one of the most important melon pathogens is the powdery mildew fungus Podosphaera xanthii. The disease is controlled mainly by incorporating single dominant resistance genes into commercial hybrids. We report on linkage analysis of the Pm-1 resistance gene, introgressed from the AF125Pm-1 Cantalupensis Charentais-type breeding line into the yellow-fleshed melon (Group Inodorus breeding line AF426-S by backcrossing to produce the resistant line AF426-R, and the amplified fragment length polymorphism (AFLP marker M75/H35_155 reported to be polymorphic between AF426-S and AF426-R. Segregation analysis of M75/H35_155 using a backcross population of 143 plants derived from [AF426-R x AF426-S] x AF426-S and screened for resistance to P. xanthii race 1 produced a recombination frequency of 4.9%, indicating close linkage between M75/H35_155 and Pm-1. Using the same segregating population, the M75/H35_155 marker had previously been reported to be distantly linked to Prv¹, a gene conferring resistance to papaya ringspot virus-type W. Since M75/H35_155 is linked to Prv¹ at a distance of 40.9 cM it is possible that Pm-1 and Prv¹ are also linked.

Evolution of closely linked gene pairs in vertebrate genomes

NARCIS (Netherlands)

Franck, E.; Hulsen, T.; Huynen, M.A.; Jong, de W.W.; Lunsen, N.H.; Madsen, O.

2008-01-01

The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of

An AFLP marker linked to turnip mosaic virus resistance gene in pak ...

African Journals Online (AJOL)

STORAGESEVER

2009-06-03

Jun 3, 2009 ... polymorphism (AFLP) technique and bulked segregant analysis (BSA) method were used to study the. F2 population. An AFLP marker ... TuRB03 (Hughes et al., 2003), TuRB04-05 (Jenner et al.,. 2002), ConTR01 ... The resistance evaluation was done by visual observation and direct enzyme-linked ...

Development of Molecular Markers Linked to Powdery Mildew Resistance Gene Pm4b by Combining SNP Discovery from Transcriptome Sequencing Data with Bulked Segregant Analysis (BSR-Seq) in Wheat.

Science.gov (United States)

Wu, Peipei; Xie, Jingzhong; Hu, Jinghuang; Qiu, Dan; Liu, Zhiyong; Li, Jingting; Li, Miaomiao; Zhang, Hongjun; Yang, Li; Liu, Hongwei; Zhou, Yang; Zhang, Zhongjun; Li, Hongjie

2018-01-01

Powdery mildew resistance gene Pm4b , originating from Triticum persicum , is effective against the prevalent Blumeria graminis f. sp. tritici ( Bgt ) isolates from certain regions of wheat production in China. The lack of tightly linked molecular markers with the target gene prevents the precise identification of Pm4b during the application of molecular marker-assisted selection (MAS). The strategy that combines the RNA-Seq technique and the bulked segregant analysis (BSR-Seq) was applied in an F 2:3 mapping population (237 families) derived from a pair of isogenic lines VPM1/7 ∗ Bainong 3217 F 4 (carrying Pm4b ) and Bainong 3217 to develop more closely linked molecular markers. RNA-Seq analysis of the two phenotypically contrasting RNA bulks prepared from the representative F 2:3 families generated 20,745,939 and 25,867,480 high-quality read pairs, and 82.8 and 80.2% of them were uniquely mapped to the wheat whole genome draft assembly for the resistant and susceptible RNA bulks, respectively. Variant calling identified 283,866 raw single nucleotide polymorphisms (SNPs) and InDels between the two bulks. The SNPs that were closely associated with the powdery mildew resistance were concentrated on chromosome 2AL. Among the 84 variants that were potentially associated with the disease resistance trait, 46 variants were enriched in an about 25 Mb region at the distal end of chromosome arm 2AL. Four Pm4b -linked SNP markers were developed from these variants. Based on the sequences of Chinese Spring where these polymorphic SNPs were located, 98 SSR primer pairs were designed to develop distal markers flanking the Pm4b gene. Three SSR markers, Xics13 , Xics43 , and Xics76 , were incorporated in the new genetic linkage map, which located Pm4b in a 3.0 cM genetic interval spanning a 6.7 Mb physical genomic region. This region had a collinear relationship with Brachypodium distachyon chromosome 5, rice chromosome 4, and sorghum chromosome 6. Seven genes associated with

Development of Molecular Markers Linked to Powdery Mildew Resistance Gene Pm4b by Combining SNP Discovery from Transcriptome Sequencing Data with Bulked Segregant Analysis (BSR-Seq in Wheat

Directory of Open Access Journals (Sweden)

Peipei Wu

2018-02-01

Full Text Available Powdery mildew resistance gene Pm4b, originating from Triticum persicum, is effective against the prevalent Blumeria graminis f. sp. tritici (Bgt isolates from certain regions of wheat production in China. The lack of tightly linked molecular markers with the target gene prevents the precise identification of Pm4b during the application of molecular marker-assisted selection (MAS. The strategy that combines the RNA-Seq technique and the bulked segregant analysis (BSR-Seq was applied in an F2:3 mapping population (237 families derived from a pair of isogenic lines VPM1/7∗Bainong 3217 F4 (carrying Pm4b and Bainong 3217 to develop more closely linked molecular markers. RNA-Seq analysis of the two phenotypically contrasting RNA bulks prepared from the representative F2:3 families generated 20,745,939 and 25,867,480 high-quality read pairs, and 82.8 and 80.2% of them were uniquely mapped to the wheat whole genome draft assembly for the resistant and susceptible RNA bulks, respectively. Variant calling identified 283,866 raw single nucleotide polymorphisms (SNPs and InDels between the two bulks. The SNPs that were closely associated with the powdery mildew resistance were concentrated on chromosome 2AL. Among the 84 variants that were potentially associated with the disease resistance trait, 46 variants were enriched in an about 25 Mb region at the distal end of chromosome arm 2AL. Four Pm4b-linked SNP markers were developed from these variants. Based on the sequences of Chinese Spring where these polymorphic SNPs were located, 98 SSR primer pairs were designed to develop distal markers flanking the Pm4b gene. Three SSR markers, Xics13, Xics43, and Xics76, were incorporated in the new genetic linkage map, which located Pm4b in a 3.0 cM genetic interval spanning a 6.7 Mb physical genomic region. This region had a collinear relationship with Brachypodium distachyon chromosome 5, rice chromosome 4, and sorghum chromosome 6. Seven genes associated with

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DNA markers linked to the major salinity tolerance locus of traditional rice, Pokkali (abstract)

International Nuclear Information System (INIS)

Rehman, S.; Seraj, Z.I.; Das, D.K.; Salam, M.A.

2005-01-01

The major QTL for salinity tolerance traits, of the traditional rice salt tolerant benchmark Pokkali, referred to as 'Saltol' was located within a large 16cM loci of rice chromosome 1 by previous workers at IRRI. This was done by using a recombinant inbred population between Pokkali and sensitive IR29 (Total RILs=275). These workers had identified the flanking markers, RM23 and RM9, as the limits of 'Saltol'. By designing primers between these two markers, and using a subset of the same RILs, we were able to identify a 5cM region, which was completely linked to the tolerance of seedlings. Further work with a subset of another NIL population raised at IRRI between Pokkali and recurring IR29 at the BC/sub 3/F/sub 2/ stage has narrowed down the linked region to about 0.3cM, each at 4 different locations within the 5cM loc. This was done by scoring the tolerance of the seedlings and determining the percent of progeny that showed the tolerant allele at the specified maker locus. Thirty seedlings from each of 10 BC/sub 3/F/sub 2/ progeny were scored. Only the most tolerant and sensitive seedlings were used for DNA isolation and amplification. The work was derived from complex crosses involving Pokkali as the tolerance donor. Three common loci linked to salinity tolerance were found to be the same in the NILs and the breeding population. DNA markers homologous to these 3 loci will be confirmed for their ability to identify tolerant progeny in breeding populations. (author)

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X linked neonatal centronuclear/myotubular myopathy: evidence for linkage to Xq28 DNA marker loci.

OpenAIRE

Thomas, N S; Williams, H; Cole, G; Roberts, K; Clarke, A; Liechti-Gallati, S; Braga, S; Gerber, A; Meier, C; Moser, H

1990-01-01

We have studied the inheritance of several polymorphic Xq27/28 DNA marker loci in two three generation families with the X linked neonatal lethal form of centronuclear/myotubular myopathy (XL MTM). We found complete linkage of XLMTM to all four informative Xq28 markers analysed, with GCP/RCP (Z = 3.876, theta = 0.00), with DXS15 (Z = 3.737, theta = 0.00), with DXS52 (Z = 2.709, theta = 0.00), and with F8C (Z = 1.020, theta = 0.00). In the absence of any observable recombination, we are unable...

Development of dominant sequence characterized amplified region (SCAR marker linked with plume moth (Exelastis atomosa Walsingham 1886 resistance in pigeon-pea

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Ramya R Mishra

2015-12-01

Full Text Available The mode of gene action governing resistance to plume moth (Exelastis atomosa Walsingham 1886 derived from pigeon-pea (Cajanus scarabaeoides (L. Thouars accession ICPW-94 has been determined and the resistance alleles have been designated as PPM1. The progenies of F2 population and F3 families derived from an interspecific cross C. cajan (L. Huth ('ICP-26' x C. scarabaeoides (accession ICPW-94 revealed monogenic gene action for resistance to plume moth, and the dominant control by single locus or cluster of tightly linked alleles. Bulked segregant analysis (BSA of 116 F2 progenies by using 143 parental polymorphic RAPD primers could identify a fragment OPA09(910 associated with plume moth resistance in coupling phase of linkage. Further single plant analysis of the 116 F2 mapping population revealed OPA09(910 was linked to PPMi locus conferring host resistance to plume moth with recombination fraction (rf value of 0.125 (12.7 cM of Kosambi function. The resistance specific fragment OPA09(910 was cloned, sequenced and converted into a sequence characterized amplified region (SCAR marker, SCOPA09(942, which was also closely associated (10.3 cM with the locus PPMl with rf value 0.102. BLAST analysis with pigeon-pea genome sequence also confirmed its occurrence in CcLG02 (Scafseq.LG_V5.0fa and contig 01597 (AFSP01.fsa1. This SCAR marker showed reasonable screening efficiency in the F2, F3, and BC1F1 lines, thus it can be used as genetic handle in marker-assisted introgression of the genomic fragment conferring plume moth resistance and screening of breeding lines in pigeon-pea.

Marker-trait association study for protein content in chickpea (Cicer

Indian Academy of Sciences (India)

Gene ontology search identified 29 candidate genes in the region of significant MTAs on LG3. The present study will be helpful in concentrating on LG3 and LG5 for identification of closely linked markers for protein content in chickpea and for their use in molecular breeding programme for nutritional quality improvement.

Inheritance patterns and identification of microsatellite markers linked to the rice blast resistance in BC2F1 population of rice breeding

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Gous Miah

2015-03-01

Full Text Available The BC2F1 population was derived from a cross between rice variety, MR219 (susceptible to blast and Pongsu Seribu 1 (resistant to blast. The objectives of this research were to know the inheritance pattern of blast resistance and to identify the linked markers associated with blast resistance in BC2F1 population. Sixteen microsatellite markers were found as polymorphic between the parents related to blast resistant genes (Pi-genes. Among the selected blast resistant linked markers, two markers RM6836 and RM8225 showed expected testcross ratio (1:1 for single-gene model in the BC2F1 population with the association between resistant and susceptible progeny. A total of 333-BC2F1 plants were challenged with the most virulent pathotype P7.2 of Magnaporthe oryzae. Chi-square (χ2 analysis for phenotypic segregation in single-gene model showed goodness of fit (P = 0.4463 to the expected segregation ratio (1:1. In marker segregation analysis, two polymorphic markers (RM6836 and RM8225 clearly showed goodness of fit to the expected segregation testcross ratio (1:1 for the single-gene model. The marker RM8225 and RM6836 showed significant R2 values higher than 10 for the trait of the blast lesions degree (BLD. The positions of RM6836 and RM8225 markers on rice chromosome 6 and the distance between these two markers is 0.2 cM. We conclude that single dominant gene control the blast resistance in Pongsu Seribu 1 located on chromosome 6, which is linked to RM8225 and RM6836 microsatellite markers. This information could be useful in marker-assisted selection for blast resistance in rice breeding involving Pongsu Seribu 1.

AFLP marker linked to water-stress-tolerant bulks in barley (Hordeum vulgare L.

Directory of Open Access Journals (Sweden)

A. Altinkut

2003-01-01

Full Text Available The amplified fragment length polymorphism (AFLP assay is an efficient method for the identification of molecular markers, useful in the improvement of numerous crop species. Bulked Segregant Analysis (BSA was used to identify AFLP markers associated with water-stress tolerance in barley, as this would permit rapid selection of water-stress tolerant genotypes in breeding programs. AFLP markers linked to water-stress tolerance was identified in two DNA pools (tolerant and sensitive, which were established using selected F2 individuals resulting from a cross between water-stress-tolerant and sensitive barley parental genotypes, based on their paraquat (PQ tolerance, leaf size, and relative water content (RWC. All these three traits were previously shown to be associated with water-stress tolerance in segregating F2 progeny of the barley cross used in a previous study. AFLP analysis was then performed on these DNA pools, using 40 primer pairs to detect AFLP fragments that are present/absent, respectively, in the two pools and their parental lines. One separate AFLP fragment, which was present in the tolerant parent and in the tolerant bulk, but absent in the sensitive parent and in the sensitive bulk, was identified. Polymorphism of the AFLP marker was tested among tolerant and sensitive F2 individuals. The presence of this marker that is associated with water-stress tolerance will greatly enhance selection for paraquat and water-stress tolerant genotypes in future breeding programs.

Identification of novel microsatellite markers preimplantation genetic diagnosis of beta-thalassemia.

Science.gov (United States)

Chen, Min; Tan, Arnold S C; Cheah, Felicia S H; Saw, Eugene E L; Chong, Samuel S

2015-12-01

Beta (β)-thalassemia is one of the most common monogenic diseases worldwide. Affected pregnancies can be avoided through preimplantation genetic diagnosis (PGD), which commonly involves customized assays to detect the different combinations of β-globin (HBB) gene mutations present in couples, in conjunction with linkage analysis of flanking microsatellite markers. Currently, the limited number of reported closely linked markers hampers their utility in indirect linkage-based PGD for this disorder. To increase the available markers closely flanking the HBB gene, an in silico search was performed to identify all markers within 1 Mb flanking the HBB gene. Fifteen markers with potentially high polymorphism information content (PIC) and heterozygosity values were selected and optimized into a single-tube pentadecaplex PCR panel. Allele frequencies and polymorphism and heterozygosity indices of each marker were assessed in five populations. A total of 238 alleles were observed from the 15 markers. PIC was >0.7 for all markers, with expected heterozygosity and observed heterozygosity values ranging from 0.74 to 0.90 and 0.72 to 0.88, respectively. Greater than 99% of individuals were heterozygous for at least seven markers, with at least two heterozygous markers on either side of the HBB gene. The pentadecaplex marker assay also performed reliably on single cells either directly or after whole genome amplification, thus validating its use in standalone linkage-based β-thalassemia PGD or in conjunction with HBB mutation detection. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microsatellite markers linked to the locus of the watermelon fruit stripe pattern.

Science.gov (United States)

Gama, R N C S; Santos, C A F; Dias, R C S; Alves, J C S F; Nogueira, T O

2015-01-16

Agronomic performance and external and internal appearance of watermelon (Citrullus lanatus) fruit are important traits that should be taken into consideration during the development of a new cultivar, as well as being the principal identification elements used by the consumer, which are based on the external appearance and quality of the fruit. Externally, the fruit can be characterized in terms of the shape, the color of the lower rind, and the presence of grooves and stripes, the stripes can be classified as clearly defined or diffuse. The objective of this study was to identify microsatellite markers linked to the stripe pattern of watermelon fruit to support watermelon improvement programs, with the selection of this characteristic in the plantlet stage. F1 and F2 populations, result of a cross between the cultivars BRS Opara (clearly defined stripes) and Pérola (diffuse stripes), were phenotyped for their fruit stripe pattern. The CTAB 2X protocol was used for DNA extraction and 116 microsatellite markers were examined in a group of F2 plants that had fruit with well-defined stripes and fruit with diffuse stripes. The microsatellite loci MCPI_05 and MCPI_16 exhibited a linkage to the stripe pattern at a distance of 1.5 and 1.8 cM, respectively, with LOD scores of 39.28 and 38.11, respectively, which were located on chromosome six of the watermelon genome. These markers can be used in marker-assisted selection in watermelon improvement programs, by various research institutions.

Closely linked polymorphic marker: successful application in preimplantation genetic diagnosis for beta-thalassemia%紧密连锁的多态性位点在β地中海贫血植入前遗传学诊断中的应用

Institute of Scientific and Technical Information of China (English)

邓捷; 庄广伦; 彭文林; 周灿权; 李洁; 方丛; 李穗萍; 陈勇; 童大跃

2005-01-01

目的探讨与β珠蛋白基因紧密连锁的多态性位点 HumTH01在β地中海贫血(β地贫)植入前遗传学诊断(preimplantation genetic diagnosis,PGD)中的作用.方法对4例已出生重型β地贫患儿的、双方均为β地贫基因携带者的夫妇进行了6个周期的PGD治疗,应用多重巢式PCR同时检测β珠蛋白基因及 HumTH01基因,选择健康的胚胎移植入子宫.结果 6个周期共活检44个胚胎,获得44个卵裂球,其中41个卵裂球扩增成功,35个胚胎经PCR分析后获得明确诊断,移植了14个胚胎,获得1例临床妊娠.孕17周时经脐带血穿刺,证实为完全正常胚胎,现已出生一正常女婴.单个卵裂球平均扩增效率为89.7%,等位基因脱扣(allele drop-out, ADO)率为14.4%. HumTH01基因可以帮助检测出ADO及污染的发生.结论本研究为国内首次报道应用多重巢式PCR同时检测β珠蛋白基因及 HumTH01基因对β地贫进行植入前遗传学诊断并成功获得临床妊娠.在PGD中同时检测与β珠蛋白基因紧密连锁的多态性位点可以降低PGD中由于ADO及污染造成的误诊的风险.%Objective To evaluate the applicability of the polymorphic marker closely linked with beta-globin gene for the preimplantati on genetic diagnosis (PGD) in couples at risk of having child with beta-thalassemia. Methods Single cell multiplex nested PCR which coamplifies the beta-globin gene and the closely linked polymorphic marker, HumTHO1 gene, was applied in six clinical PGD cycles for four couples with beta-thalassemia. Results In six clinical PGD cycles, a total of 44 embryos were biopsied and 44 blastomeres were obtained. Forty-one blastomeres were amplified and thirty-five embryos were given definite diagnoses. Fourteen embryos were transferred back to the uterus of the patients and one pregnancy went on well and ended with one live healthy birth, which confirmed the results of PGD. The average amplification efficiency of single blastomere was 89.7% and

Automated genotyping of dinucleotide repeat markers

Energy Technology Data Exchange (ETDEWEB)

Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)

1994-09-01

The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

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

Science.gov (United States)

Gholave, Avinash R; Pawar, Kiran D; Yadav, Shrirang R; Bapat, Vishwas A; Jadhav, Jyoti P

2017-01-01

Plastid DNA markers sequencing and DNA fingerprinting approaches were used and compared for resolving molecular phylogeny of closely related, previously unexplored Amorphophallus species of India. The utility of individual plastid markers namely rbcL , matK , trnH - psbA , trnLC - trnLD , their combined dataset and two fingerprinting techniques viz. RAPD and ISSR were tested for their efficacy to resolves Amorphophallus species into three sections specific clades namely Rhaphiophallus , Conophallus and Amorphophallus . In the present study, sequences of these four plastid DNA regions as well as RAPD and ISSR profiles of 16 Amorphophallus species together with six varieties of two species were generated and analyzed. Maximum likelihood and Bayesian Inference based construction of phylogenetic trees indicated that among the four plastid DNA regions tested individually and their combined dataset, rbcL was found best suited for resolving closely related Amorphophallus species into section specific clades. When analyzed individually, rbcL exhibited better discrimination ability than matK , trnH - psbA , trnLC - trnLD and combination of all four tested plastid markers. Among two fingerprinting techniques used, the resolution of Amorphophallus species using RAPD was better than ISSR and combination of RAPD +ISSR and in congruence with resolution based on rbcL .

Affective traits link to reliable neural markers of incentive anticipation.

Science.gov (United States)

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'santicipation 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. © 2013. Published by Elsevier Inc. All rights reserved.

Intelligent DNA-based molecular diagnostics using linked genetic markers

Energy Technology Data Exchange (ETDEWEB)

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.

Development of SSR Markers Linked to Low Hydrocyanic Acid Content in Sorghum-Sudan Grass Hybrid Based on BSA Method.

Science.gov (United States)

Xiao-Xia, Yu; Zhi-Hua, Liu; Zhuo, Yu; Yue, Shi; Xiao-Yu, Li

2016-01-01

Sorghum-Sudan grass hybrid containing high hydrocyanic acid content can cause hydrocyanic acid poisoning to the livestock and limit the popularization of this forage crop. Molecular markers associated with low hydrocyanic acid content can speed up the process of identification of genotypes with low hydrocyanic acid content. In the present study, 11 polymorphic SSR primers were screened and used for bulked segregant analysis and single marker analysis. Three SSR markers Xtxp7230, Xtxp7375 and Bnlg667960 associated with low hydrocyanic acid content were rapidly identified by BSA. In single marker analysis, six markers Xtxp7230, Xtxp7375, Bnlg667960, Xtxp67-11, Xtxp295-7 and Xtxp12-9 were linked to low hydrocyanic acid content, which explained the proportion of phenotypic variation from 7.6 % to 41.2 %. The markers identified by BSA were also verified by single marker analysis. The three SSR marker bands were then cloned and sequenced for sequence homology analysis in NCBI. It is the first report on the development of molecular markers associated with low hydrocyanic acid content in sorghum- Sudan grass hybrid. These markers will be useful for genetic improvement of low hydrocyanic acid sorghum-Sudan grass hybrid by marker-assisted breeding.

Magnetic Resonance Imaging Features as Surrogate Markers of X-Linked Hypophosphatemic Rickets Activity.

Science.gov (United States)

Lempicki, Marta; Rothenbuhler, Anya; Merzoug, Valérie; Franchi-Abella, Stéphanie; Chaussain, Catherine; Adamsbaum, Catherine; Linglart, Agnès

2017-01-01

X-linked hypophosphatemic rickets (XLH) is the most common form of inheritable rickets. Rickets treatment is monitored by assessing alkaline phosphatase (ALP) levels, clinical features, and radiographs. Our objectives were to describe the magnetic resonance imaging (MRI) features of XLH and to assess correlations with disease activity. Twenty-seven XLH patients (median age 9.2 years) were included in this prospective single-center observational study. XLH activity was assessed using height, leg bowing, dental abscess history, and serum ALP levels. We looked for correlations between MRI features and markers of disease activity. On MRI, the median maximum width of the physis was 5.6 mm (range 4.8-7.8; normal 1.5 mm in all of the patients. The appearance of the zone of provisional calcification was abnormal on 21 MRI images (78%), Harris lines were present on 24 (89%), and bone marrow signal abnormalities were present on 16 (59%). ALP levels correlated with the maximum physeal widening and with the transverse extent of the widening. MRI of the knee provides precise rickets patterns that are correlated with ALP, an established biochemical marker of the disease, avoiding X-ray exposure and providing surrogate quantitative markers of disease activity. © 2017 S. Karger AG, Basel.

The likelihood ratio as a random variable for linked markers in kinship analysis.

Science.gov (United States)

Egeland, Thore; Slooten, Klaas

2016-11-01

The likelihood ratio is the fundamental quantity that summarizes the evidence in forensic cases. Therefore, it is important to understand the theoretical properties of this statistic. This paper is the last in a series of three, and the first to study linked markers. We show that for all non-inbred pairwise kinship comparisons, the expected likelihood ratio in favor of a type of relatedness depends on the allele frequencies only via the number of alleles, also for linked markers, and also if the true relationship is another one than is tested for by the likelihood ratio. Exact expressions for the expectation and variance are derived for all these cases. Furthermore, we show that the expected likelihood ratio is a non-increasing function if the recombination rate increases between 0 and 0.5 when the actual relationship is the one investigated by the LR. Besides being of theoretical interest, exact expressions such as obtained here can be used for software validation as they allow to verify the correctness up to arbitrary precision. The paper also presents results and advice of practical importance. For example, we argue that the logarithm of the likelihood ratio behaves in a fundamentally different way than the likelihood ratio itself in terms of expectation and variance, in agreement with its interpretation as weight of evidence. Equipped with the results presented and freely available software, one may check calculations and software and also do power calculations.

X linked neonatal centronuclear/myotubular myopathy: evidence for linkage to Xq28 DNA marker loci.

Science.gov (United States)

Thomas, N S; Williams, H; Cole, G; Roberts, K; Clarke, A; Liechti-Gallati, S; Braga, S; Gerber, A; Meier, C; Moser, H

1990-05-01

We have studied the inheritance of several polymorphic Xq27/28 DNA marker loci in two three generation families with the X linked neonatal lethal form of centronuclear/myotubular myopathy (XL MTM). We found complete linkage of XLMTM to all four informative Xq28 markers analysed, with GCP/RCP (Z = 3.876, theta = 0.00), with DXS15 (Z = 3.737, theta = 0.00), with DXS52 (Z = 2.709, theta = 0.00), and with F8C (Z = 1.020, theta = 0.00). In the absence of any observable recombination, we are unable to sublocalise the XLMTM locus further within the Xq28 region. This evidence for an Xq28 localisation may allow us to carry out useful genetic counselling within such families.

Linkage Map of a Gene Controlling Zero Tannins (zt-1 in Faba Bean (Vicia faba L. with SSR and ISSR Markers

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Wanwei Hou

2018-05-01

Full Text Available Faba bean (Vicia faba L., a partially allogamous species, is rich in protein. Condensed tannins limit the use of faba beans as food and feed. Two recessive genes, zt-1 and zt-2, control the zero tannin content in faba bean and promote a white flower phenotype. To determine the inheritance and develop a linkage map for the zt-1 gene in the faba bean germplasm M3290, F2 and F3 progenies were derived from the purple flower and high tannin content genotypes Qinghai12 and zt-1 line M3290, respectively. Genetic analysis verified a single recessive gene for zero tannin content and flower colour. In total, 596 SSR markers and 100 ISSR markers were used to test the polymorphisms between the parents and bulks for the contrasting flower colour via Bulked Segregant Analysis (BSA. Subsequently, six SSR markers and seven ISSR markers were used to genotype the entire 413 F2 population. Linkage analysis showed that the zt-1 gene was closely linked to the SSR markers SSR84 and M78, with genetic distances of 2.9 and 5.8 cM, respectively. The two flanked SSR markers were used to test 34 faba bean genotypes with different flower colours. The closely linked SSR marker SSR84 predicted the zt-1 genotypes with absolute accuracy. The results from the marker-assisted selection (MAS from this study could provide a solid foundation for further faba bean breeding programmes.

Genetic characterization of Moroccan and the exotic bread wheat cultivars using functional and random DNA markers linked to the agronomic traits for genomics-assisted improvement.

Science.gov (United States)

Henkrar, Fatima; El-Haddoury, Jamal; Ouabbou, Hassan; Bendaou, Najib; Udupa, Sripada M

2016-06-01

Genetic characterization, diversity analysis and estimate of the genetic relationship among varieties using functional and random DNA markers linked to agronomic traits can provide relevant guidelines in selecting parents and designing new breeding strategies for marker-assisted wheat cultivar improvement. Here, we characterize 20 Moroccan and 19 exotic bread wheat (Triticum aestivum L.) cultivars using 47 functional and 7 linked random DNA markers associated with 21 loci of the most important traits for wheat breeding. The functional marker analysis revealed that 35, 45, and 10 % of the Moroccan cultivars, respectively have the rust resistance genes (Lr34/Yr18/Pm38), dwarfing genes (Rht1b or Rht2b alleles) and the leaf rust resistance gene (Lr68). The marker alleles for genes Lr37/Yr17/Sr38, Sr24 and Yr36 were present only in the exotic cultivars and absent in Moroccan cultivars. 25 % of cultivars had 1BL.1RS translocation. 70 % of the wheat cultivars had Ppo-D1a and Ppo-A1b associated with low polyphenol oxidase activity. 10 % of cultivars showed presence of a random DNA marker allele (175 bp) linked to Hessian fly resistance gene H22. The majority of the Moroccan cultivars were carrying alleles that impart good bread making quality. Neighbor joining (NJ) and principal coordinate analysis based on the marker data revealed a clear differentiation between elite Moroccan and exotic wheat cultivars. The results of this study are useful for selecting suitable parents for making targeted crosses in marker-assisted wheat breeding and enhancing genetic diversity in the wheat cultivars.

Nutritional assessment, health markers and lipoprotein profile in postmenopausal women belonging to a closed community.

Science.gov (United States)

Sánchez-Muniz, F J; Carbajal, A; Ródenas, S; Méndez, M T; Bastida, S; Raposo, R; Ruiz, T

2003-09-01

To assess the dietary characteristics of a closed community and their relationship with several health markers and lipid and lipoprotein values in postmenopausal women. Energy and nutrient intake, serum lipids, lipoproteins, antioxidants, peroxides and low-density lipoprotein (LDL) peroxides in addition to several health markers were measured in a closed, postmenopausal female community consuming a diet without meat, meat products and alcoholic beverages. Departamento de Nutrición and Sección Departamental de Química Analítica and Escuela de Especialización de Análisis Clínicos, Universidad Complutense de Madrid, Spain and Lerma, Burgos, Spain. Cereals, vegetables, legumes and fruit, together with milk and eggs, constituted the most important ingredients of the diet consumed. Dietary carbohydrates contributed 42%en and lipids 46.4%en. The SFA/MUFA/PUFA ratio was 1/2/1 and the n-3/n-6 ratio 0.05 (SFA=saturated fatty acids, MUFA=monounsaturated fatty acids, PUFA=polyunsaturated fatty acids). The study community diet was monotonous and made for possible deficiencies of iron, magnesium, zinc, vitamin B(6) and vitamin D, in variable proportions. Routine biochemical and haematological normality markers indicate that only one woman presented hyperglycaemia and hyperuricaemia. Two women had haemoglobin levels 6.21 mmol/l) was 42.8%, while that of high LDL-cholesterol levels (>3.88 mmol/l) was 35.7%, but none of the women displayed levels of high-density lipoprotein (HDL)-cholesterol 1.2 mmol/l or an LDL-cholesterol/HDL-cholesterol ratio>3. Only one woman had apolipoprotein (Apo) B levels >1.5 g/l, while most of the women presented Apo B values <1.2 g/l and an ApoA-1/ApoB ratio &<1.1. Plasma and LDL-peroxide levels, together with the tocopherol and carotene intakes, suggest a good antioxidant status in this population. The diet of the study group seems compatible with a healthy life-profile and permits a more-than-acceptable degree of cardiovascular disease

Tagging microsatellite marker to a blast resistance gene in the irrigated rice cultivar Cica-8

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Thiago Martins Pinheiro

2012-09-01

Full Text Available The rice cultivar Cica-8 exhibit differential reaction to several pathotypes of Magnaporthe oryzae. The objective of the present investigation was to determine the number of alleles involved in the expression of resistance to leaf blast and identify microsatellite markers linked to these alleles. A cross between cultivar Metica-1 and Cica-8 susceptible and resistant, respectively, to pathotype IB-1 (Py1049 was made to obtain F1, F2, BC1:1 and BC1:2 progenies. Greenhouse tests for leaf blast reaction showed that resistance is controlled by a monogenic dominant gene. For testing microsatellite markers, DNA of both resistant and susceptible parents and F1 and F2 populations was extracted. As expected for single dominant gene the F2 populations segregated at a ratio of 3:1. Of the 11 microsatellite markers tested, one marker RM 7102 was found to be closely linked to the resistant allele at a distance of 2.7 cM, in the cultivar Cica-8 to pathotype IB-1.

Markers of human immunodeficiency virus infection in high-risk individuals seronegative by first generation enzyme-linked immunosorbent assay

DEFF Research Database (Denmark)

Pedersen, C; Lindhardt, B O; Lauritzen, E

1989-01-01

-linked immunoassay (ELISA). Seventy-four of the serum samples had been obtained from 40 sexual partners of HIV antibody positive individuals. Two of the samples were reactive for p24 in immunoblot, but no other markers of HIV infection were found. From 80 sexually active male homosexuals, 117 serum samples were...

Identification of SSR and RAPD markers linked to a resistance allele for angular leaf spot in the common bean (Phaseolus vulgaris line ESAL 550

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Gilvan Ferreira da Silva

2003-12-01

Full Text Available The objective of this study was to identify RAPD and SSR markers associated with a resistant allele for angular leaf spot (Phaeoisariopsis griseola from the line 'ESAL 550', derived from the Andean 'Jalo EEP 558' cultivar, to assist selection of resistant genotypes. The resistant line 'ESAL 550' and the susceptible cultivar 'Carioca MG' were crossed to generate F1 and F2 populations. One hundred and twenty F2:3 families were evaluated. The DNA of the 12 most resistant families was bulked and the same was done with the DNA of the 10 most susceptible, generating two contrasting bulks. One RAPD and one SSR marker was found to be linked in coupling phase to the resistant allele. The SSR marker was amplified by the primer PV-atct001(282C, and its distance from the resistant allele was 7.6 cM. This is the most useful marker for indirect selection of resistant plants in segregating populations. The RAPD marker was amplified by the primer OPP07(857C linked in coupling phase to the resistant allele, and distant 24.4 cM. Therefore, this RAPD marker is not so useful in assisting selection because it is too far from the resistant allele.

Identification of a RAPD marker linked to the Co-6 anthracnose resistant gene in common bean cultivar AB 136

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Alzate-Marin Ana Lilia

2000-01-01

Full Text Available The pathogenic variability of the fungus Colletotrichum lindemuthianum represents an obstacle for the creation of resistant common bean (Phaseolus vulgaris L. varieties. Gene pyramiding is an alternative strategy for the development of varieties with durable resistance. RAPD markers have been proposed as a means to facilitate pyramiding of resistance genes without the need for multiple inoculations of the pathogens. The main aims of this work were to define the inheritance pattern of resistance present in common bean cultivar AB 136 in segregating populations derived from crosses with cultivar Rudá (susceptible to most C. lindemuthianum races and to identify RAPD markers linked to anthracnose resistance. The two progenitors, populations F1 and F2, F2:3 families and backcross-derived plants were inoculated with race 89 of C. lindemuthianum under environmentally controlled greenhouse conditions. The results indicate that a single dominant gene, Co-6, controls common bean resistance to this race, giving a segregation ratio between resistant and susceptible plants of 3:1 in the F2, 1:0 in the backcrosses to AB 136 and 1:1 in the backcross to Rudá. The segregation ratio of F2:3 families derived from F2 resistant plants was 1:2 (homozygous to heterozygous resistant. Molecular marker analyses in the F2 population identified a DNA band of approximately 940 base pairs (OPAZ20(940, linked in coupling phase at 7.1 cM of the Co-6 gene. This marker is being used in our backcross breeding program to develop Rudá-derived common bean cultivars resistant to anthracnose and adapted to central Brazil.

Marker-trait association study for protein content in chickpea (Cicer arietinum L.).

Science.gov (United States)

Jadhav, A A; Rayate, S J; Mhase, L B; Thudi, M; Chitikineni, A; Harer, P N; Jadhav, A S; Varshney, R K; Kulwal, P L

2015-06-01

Chickpea (Cicer arietinum L.) is the second most important cool season food legume cultivated in arid and semiarid regions of the world. The objective of the present study was to study variation for protein content in chickpea germplasm, and to find markers associated with it. A set of 187 genotypes comprising both international and exotic collections, and representing both desi and kabuli types with protein content ranging from 13.25% to 26.77% was used. Twenty-three SSR markers representing all eight linkage groups (LG) amplifying 153 loci were used for the analysis. Population structure analysis identified three subpopulations, and corresponding Q values of principal components were used to take care of population structure in the analysis which was performed using general linear and mixed linear models. Marker-trait association (MTA) analysis identified nine significant associations representing four QTLs in the entire population. Subpopulation analyses identified ten significant MTAs representing five QTLs, four of which were common with that of the entire population. Two most significant QTLs linked with markers TR26.205 and CaM1068.195 were present on LG3 and LG5. Gene ontology search identified 29 candidate genes in the region of significant MTAs on LG3. The present study will be helpful in concentrating on LG3 and LG5 for identification of closely linked markers for protein content in chickpea and for their use in molecular breeding programme for nutritional quality improvement.

Linking the potato genome to the conserved ortholog set (COS) markers

Science.gov (United States)

2013-01-01

Background Conserved ortholog set (COS) markers are an important functional genomics resource that has greatly improved orthology detection in Asterid species. A comprehensive list of these markers is available at Sol Genomics Network (http://solgenomics.net/) and many of these have been placed on the genetic maps of a number of solanaceous species. Results We amplified over 300 COS markers from eight potato accessions involving two diploid landraces of Solanum tuberosum Andigenum group (formerly classified as S. goniocalyx, S. phureja), and a dihaploid clone derived from a modern tetraploid cultivar of S. tuberosum and the wild species S. berthaultii, S. chomatophilum, and S. paucissectum. By BLASTn (Basic Local Alignment Search Tool of the NCBI, National Center for Biotechnology Information) algorithm we mapped the DNA sequences of these markers into the potato genome sequence. Additionally, we mapped a subset of these markers genetically in potato and present a comparison between the physical and genetic locations of these markers in potato and in comparison with the genetic location in tomato. We found that most of the COS markers are single-copy in the reference genome of potato and that the genetic location in tomato and physical location in potato sequence are mostly in agreement. However, we did find some COS markers that are present in multiple copies and those that map in unexpected locations. Sequence comparisons between species show that some of these markers may be paralogs. Conclusions The sequence-based physical map becomes helpful in identification of markers for traits of interest thereby reducing the number of markers to be tested for applications like marker assisted selection, diversity, and phylogenetic studies. PMID:23758607

Tunisian Toxoplasma gondii strains genotyping by the use of AK69 marker

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Aoun Karim

2011-08-01

Full Text Available Abstract Background Clinical manifestation due to infection by Toxoplasma gondii is closely linked to the infecting strain of the parasite. Several genetic markers are available to determinate its genotype but few of them are able to discriminate between the three predominant lineages, namely types I, II and III. The number of markers decreases when atypical, recombinant/mixed genotypes need to be identified. Findings In our study, the contribution of sequence polymorphisms in the AK69 gene as typing markers for T. gondii was investigated for the first time in an epidemiological study. The coding region of the marker was amplified, sequenced and aligned for different Toxoplasma strains. The identified nucleotide polymorphism at 12 positions was able to highly discriminate between the different congenital toxoplasmosis Tunisian strains. Moreover the high detection sensitivity level of the marker enabled unambiguous identification of mixed/recombinant genotypes directly. Conclusion It can be, thus, very useful for direct typing in areas where such genotypes are frequently encountered, mainly in the African continent.

Identification and characterization of RAPD-SCAR markers linked to glyphosate-susceptible and -resistant biotypes of Eleusine indica (L.) Gaertn.

Science.gov (United States)

Cha, Thye San; Anne-Marie, Kaben; Chuah, Tse Seng

2014-02-01

Eleusine indica is one of the most common weed species found in agricultural land worldwide. Although herbicide-glyphosate provides good control of the weed, its frequent uses has led to abundant reported cases of resistance. Hence, the development of genetic markers for quick detection of glyphosate-resistance in E. indica population is imperative for the control and management of the weed. In this study, a total of 14 specific random amplified polymorphic DNA (RAPD) markers were identified and two of the markers, namely S4R727 and S26R6976 were further sequence characterized. Sequence alignment revealed that marker S4R727 showing a 12-bp nucleotides deletion in resistant biotypes, while marker S26R6976 contained a 167-bp nucleotides insertion in the resistant biotypes. Based on these sequence differences, three pairs of new sequence characterized amplified region (SCAR) primers were developed. The specificity of these primer pairs were further validated with genomic DNA extracted from ten individual plants of one glyphosate-susceptible and five glyphosate-resistant (R2, R4, R6, R8 and R11) populations. The resulting RAPD-SCAR markers provided the basis for assessing genetic diversity between glyphosate-susceptible and -resistant E. indica biotypes, as well for the identification of genetic locus link to glyphosate-resistance event in the species.

Comparative Analysis of Disease-Linked Single Nucleotide Polymorphic Markers from Brassica rapa for Their Applicability to Brassica oleracea

Science.gov (United States)

Cho, Young-Il; Ahn, Yul-Kyun; Tripathi, Swati; Kim, Jeong-Ho; Lee, Hye-Eun; Kim, Do-Sun

2015-01-01

Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH—developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP—based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS—derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species. PMID:25790283

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

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Yang Huaan

2012-07-01

Full Text Available Abstract Background In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM, and are now replacing the markers previously developed by a traditional DNA

Tagging of blast resistance gene(s) to DNA markers and marker-assisted selection (MAS) in rice improvement

International Nuclear Information System (INIS)

Zhuang, J.Y.; Lu, J.; Qian, H.R.; Lin, H.X.; Zheng, K.L.

1998-01-01

This paper reports progress made on the tagging of blast resistance gene(s) to DNA markers and on the initiation of marker-assisted selection (MAS) for blast resistance in rice improvement. A pair of near isogenic lines, K8OR and K79S, were developed using a Chinese landrace Hong-jiao-zhan as the resistance donor. Ten putatively positive markers were identified by screening 177 mapped DNA markers. Using the F 2 population of 143 plants and the derived F 3 lines, three Restriction Fragment Length Polymorphism (RFLP) markers (RG81, RG869 and RZ397) on chromosome 12 of rice were identified to be closely linked to the blast resistance gene Pi-12(t). The genetic distance between Pi-12(t) and the closest marker RG869 was 5.1 cM. By employing the bulk segregant analysis (BSA) procedure, six of 199 arbitrary primers were found to produce positive Randomly Amplified Polymorphic DNA (RAPD) bands. Tight linkage between Pi-12(t) and three RAPD bands, each from a different primer, was confirmed after amplification of DNA of all F 2 individuals. Two fragments were cloned and sequenced, and two sequence characterised amplified re-ion (SCAR) markers were established. In two other F 3 populations, Xian-feng I/Tetep and Xian-feng, 1/Hong-jiao-zhan, the blast resistance was found to be controlled by interactions of two or more genes. One resistance gene was located in the vicinity of RG81 in both populations. Work to identify other gene(s) is currently under way. Marker assisted selection for blast resistance was initiated. Crosses were made between elite varieties and blast resistance donors to develop populations for DNA marker-assisted selection of blast resistance. In addition, 48 varieties widely used in current rice breeding programs were provided by rice breeders. DNA marker-based polymorphism among, these varieties and resistance donors were analysed to produce a database for future MAS program. (author)

Development and characterization of microsatellite markers for Morus spp. and assessment of their transferability to other closely related species

Science.gov (United States)

2013-01-01

Background Adoption of genomics based breeding has emerged as a promising approach for achieving comprehensive crop improvement. Such an approach is more relevant in the case of perennial species like mulberry. However, unavailability of genomic resources of co-dominant marker systems has been the major constraint for adopting molecular breeding to achieve genetic enhancement of Mulberry. The goal of this study was to develop and characterize a large number of locus specific genic and genomic SSR markers which can be effectively used for molecular characterization of mulberry species/genotypes. Result We analyzed a total of 3485 DNA sequences including genomic and expressed sequences (ESTs) of mulberry (Morus alba L.) genome. We identified 358 sequences to develop appropriate microsatellite primer pairs representing 222 genomic and 136 EST regions. Primers amplifying locus specific regions of Dudia white (a genotype of Morus alba L), were identified and 137 genomic and 51 genic SSR markers were standardized. A two pronged strategy was adopted to assess the applicability of these SSR markers using mulberry species and genotypes along with a few closely related species belonging to the family Moraceae viz., Ficus, Fig and Jackfruit. While 100% of these markers amplified specific loci on the mulberry genome, 79% were transferable to other related species indicating the robustness of these markers and the potential they hold in analyzing the molecular and genetic diversity among mulberry germplasm as well as other related species. The inherent ability of these markers in detecting heterozygosity combined with a high average polymorphic information content (PIC) of 0.559 ranging between 0.076 and 0.943 clearly demonstrates their potential as genomic resources in diversity analysis. The dissimilarity coefficient determined based on Neighbor joining method, revealed that the markers were successful in segregating the mulberry species, genotypes and other related species

Identification of sequence-related amplified polymorphism markers linked to the red leaf trait in ornamental kale (Brassica oleracea L. var. acephala).

Science.gov (United States)

Wang, Y S; Liu, Z Y; Li, Y F; Zhang, Y; Yang, X F; Feng, H

2013-04-02

Artistic diversiform leaf color is an important agronomic trait that affects the market value of ornamental kale. In the present study, genetic analysis showed that a single-dominant gene, Re (red leaf), determines the red leaf trait in ornamental kale. An F2 population consisting of 500 individuals from the cross of a red leaf double-haploid line 'D05' with a white leaf double-haploid line 'D10' was analyzed for the red leaf trait. By combining bulked segregant analysis and sequence-related amplified polymorphism technology, we identified 3 markers linked to the Re/re locus. A genetic map of the Re locus was constructed using these sequence-related amplified polymorphism markers. Two of the markers, Me8Em4 and Me8Em17, were located on one side of Re/re at distances of 2.2 and 6.4 cM, whereas the other marker, Me9Em11, was located on the other side of Re/re at a distance of 3.7 cM. These markers could be helpful for the subsequent cloning of the red trait gene and marker-assisted selection in ornamental kale breeding programs.

Genetic Recombination at the Buff Spore Color Locus in SORDARIA BREVICOLLIS. II. Analysis of Flanking Marker Behavior in Crosses between Buff Mutants

OpenAIRE

Sang, Helen; Whitehouse, Harold L K

1983-01-01

Aberrant asci containing one or more wild-type spores were selected from crosses between pairs of alleles of the buff locus in the presence of closely linked flanking markers. Data were obtained relating to the site of aberrant segregation and the position of any associated crossover giving recombination of flanking markers. Aberrant segregation at a proximal site within the buff gene may be associated with a crossover proximal to the site of aberrant segregation or, with equal frequency, wit...

Enzyme markers in inbred rat strains: genetics of new markers and strain profiles.

Science.gov (United States)

Adams, M; Baverstock, P R; Watts, C H; Gutman, G A

1984-08-01

Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.

BAC-derived markers converted from RFLP linked to Phytophthora capsici resistance in pepper (Capsicum annuum L.).

Science.gov (United States)

Kim, Hyoun-Joung; Nahm, Seok-Hyeon; Lee, Heung-Ryul; Yoon, Gi-Bo; Kim, Ki-Taek; Kang, Byoung-Cheorl; Choi, Doil; Kweon, Oh Yeol; Cho, Myeong-Cheoul; Kwon, Jin-Kyung; Han, Jung-Heon; Kim, Jeong-Ho; Park, Minkyu; Ahn, Jong Hwa; Choi, Soon Ho; Her, Nam Han; Sung, Joo-Hee; Kim, Byung-Dong

2008-12-01

Phytophthora capsici Leonian, an oomycete pathogen, is a serious problem in pepper worldwide. Its resistance in pepper is controlled by quantitative trait loci (QTL). To detect QTL associated with P. capsici resistance, a molecular linkage map was constructed using 100 F(2) individuals from a cross between Capsicum annuum 'CM334' and C. annuum 'Chilsungcho'. This linkage map consisted of 202 restriction fragment length polymorphisms (RFLPs), 6 WRKYs and 1 simple sequence repeat (SSR) covering 1482.3 cM, with an average interval marker distance of 7.09 cM. QTL mapping of Phytophthora root rot and damping-off resistance was performed in F(2:3) originated from a cross between resistant Mexican landrace C. annuum 'CM334' and susceptible Korean landrace C. annuum 'Chilsungcho' using composite interval mapping (CIM) analysis. Four QTL explained 66.3% of the total phenotypic variations for root rot resistance and three 44.9% for damping-off resistance. Of these QTL loci, two were located close to RFLP markers CDI25 on chromosome 5 (P5) and CT211A on P9. A bacterial artificial chromosome (BAC) library from C. annuum 'CM334' was screened with these two RFLP probes to obtain sequence information around the RFLP marker loci for development of PCR-based markers. CDI25 and CT211 probes identified seven and eight BAC clones, respectively. Nine positive BAC clones containing probe regions were sequenced and used for cytogenetic analysis. One single-nucleotide amplified polymorphism (SNAP) for the CDI25 locus, and two SSRs and cleaved amplified polymorphic sequence (CAPS) for CT211 were developed using sequences of the positive BAC clones. These markers will be valuable for rapid selection of genotypes and map-based cloning for resistance genes against P. capsici.

Molecular markers shared by diverse apomictic Pennisetum species.

Science.gov (United States)

Lubbers, E L; Arthur, L; Hanna, W W; Ozias-Akins, P

1994-11-01

Two molecular markers, a RAPD (randomly amplified polymorphic DNA) and a RFLP/STS (restriction fragment length polymorphism/sequence-tagged site), previously were found associated with apomictic reproductive behavior in a backcross population produced to transfer apomixis from Pennisetum squamulatum to pearl millet. The occurrence of these molecular markers in a range of 29 accessions of Pennisetum comprising 11 apomictic and 8 sexual species was investigated. Both markers were specific for apomictic species in Pennisetum. The RFLP/STS marker, UGT 197, was found to be associated with all taxa that displayed apomictic reproductive behavior except those in section Brevivalvula. Neither UGT197 nor the cloned RAPD fragment OPC-04600 hybridized with any sexually reproducing representatives of the genus. The cloned C04600 was associated with 3 of the 11 apomictic species, P. ciliare, P. massaicum, and P. squamulatum. UGT197 was more consistently associated with apomictic reproductive behavior than OPC04600 or cloned C04600, thus it could be inferred that UGT197 is more closely linked to the gene(s) for apomixis than the cloned C04600. The successful use of these probes to survey other Pennisetum species indicates that apomixis is a trait that can be followed across species by using molecular means. This technique of surveying species within a genus will be useful in determining the relative importance of newly isolated markers and may facilitate the identification of the apomixis gene(s).

Molecular Method for Sex Identification of Half-Smooth Tongue Sole (Cynoglossus semilaevis Using a Novel Sex-Linked Microsatellite Marker

Directory of Open Access Journals (Sweden)

Xiaolin Liao

2014-07-01

Full Text Available Half-smooth tongue sole (Cynoglossus semilaevis is one of the most important flatfish species for aquaculture in China. To produce a monosex population, we attempted to develop a marker-assisted sex control technique in this sexually size dimorphic fish. In this study, we identified a co-dominant sex-linked marker (i.e., CyseSLM by screening genomic microsatellites and further developed a novel molecular method for sex identification in the tongue sole. CyseSLM has a sequence similarity of 73%–75% with stickleback, medaka, Fugu and Tetraodon. At this locus, two alleles (i.e., A244 and A234 were amplified from 119 tongue sole individuals with primer pairs CyseSLM-F1 and CyseSLM-R. Allele A244 was present in all individuals, while allele A234 (female-associated allele, FAA was mostly present in females with exceptions in four male individuals. Compared with the sequence of A244, A234 has a 10-bp deletion and 28 SNPs. A specific primer (CyseSLM-F2 was then designed based on the A234 sequence, which amplified a 204 bp fragment in all females and four males with primer CyseSLM-R. A time-efficient multiplex PCR program was developed using primers CyseSLM-F2, CyseSLM-R and the newly designed primer CyseSLM-F3. The multiplex PCR products with co-dominant pattern could be detected by agarose gel electrophoresis, which accurately identified the genetic sex of the tongue sole. Therefore, we have developed a rapid and reliable method for sex identification in tongue sole with a newly identified sex-linked microsatellite marker.

Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids

Directory of Open Access Journals (Sweden)

Annette M. Bartkiewicz

2018-05-01

Full Text Available Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by prickle pollination of two tetraploid cultivars with Solanum phureja and genotyped with the 12.8 k SolCAP single nucleotide polymorphism (SNP array. We show that in a population of monoparental haploids, the number of biallelic SNP markers segregating in linkage to loci from the tetraploid donor genotype is much larger than in putative crosses of this genotype to a diverse selection of 125 tetraploid cultivars. Although this strategy is more laborious than conventional breeding, the generation of haploid progeny for efficient marker analysis is straightforward if morphological markers and flow cytometry are utilized to select true haploid progeny. The level of introgressed fragments from S. phureja, the haploid inducer, is very low, supporting its suitability for genetic analysis. Mapping with single-dose markers allowed the analysis of quantitative trait loci (QTL for four phenotypic traits.

Genetic studies and a search for molecular markers that are linked ...

African Journals Online (AJOL)

SERVER

Instead, linkage analysis resulted in the construction of a molecular marker linkage map consisting of 45 ..... This limits the application of this marker type, particularly in ... primer design when one uses RAPDs. .... Concepts of Genetics. Fourth.

Relocation of a rust resistance gene R 2 and its marker-assisted gene pyramiding in confection sunflower (Helianthus annuus L.).

Science.gov (United States)

Qi, L L; Ma, G J; Long, Y M; Hulke, B S; Gong, L; Markell, S G

2015-03-01

The rust resistance gene R 2 was reassigned to linkage group 14 of the sunflower genome. DNA markers linked to R 2 were identified and used for marker-assisted gene pyramiding in a confection type genetic background. Due to the frequent evolution of new pathogen races, sunflower rust is a recurring threat to sunflower production worldwide. The inbred line Morden Cross 29 (MC29) carries the rust resistance gene, R 2 , conferring resistance to numerous races of rust fungus in the US, Canada, and Australia, and can be used as a broad-spectrum resistance resource. Based on phenotypic assessments and SSR marker analyses on the 117 F2 individuals derived from a cross of HA 89 with MC29 (USDA), R 2 was mapped to linkage group (LG) 14 of the sunflower, and not to the previously reported location on LG9. The closest SSR marker HT567 was located at 4.3 cM distal to R 2 . Furthermore, 36 selected SNP markers from LG14 were used to saturate the R 2 region. Two SNP markers, NSA_002316 and SFW01272, flanked R 2 at a genetic distance of 2.8 and 1.8 cM, respectively. Of the three closely linked markers, SFW00211 amplified an allele specific for the presence of R 2 in a marker validation set of 46 breeding lines, and SFW01272 was also shown to be diagnostic for R 2 . These newly developed markers, together with the previously identified markers linked to the gene R 13a , were used to screen 524 F2 individuals from a cross of a confection R 2 line and HA-R6 carrying R 13a . Eleven homozygous double-resistant F2 plants with the gene combination of R 2 and R 13a were obtained. This double-resistant line will be extremely useful in confection sunflower, where few rust R genes are available, risking evolution of new virulence phenotypes and further disease epidemics.

New distal marker closely linked to the fragile X locus

NARCIS (Netherlands)

Hulsebos, T. J.; Oostra, B. A.; Broersen, S.; Smits, A.; van Oost, B. A.; Westerveld, A.

1991-01-01

We have isolated II-10, a new X-chromosomal probe that identifies a highly informative two-allele TaqI restriction fragment length polymorphism at locus DXS466. Using somatic cell hybrids containing distinct portions of the long arm of the X chromosome, we could localize DXS466 between DXS296 and

Genome analysis methods - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Genome analysis... methods Data detail Data name Genome analysis methods DOI 10.18908/lsdba.nbdc01194-01-005 De...scription of data contents The current status and related information of the genomic analysis about each org...anism (March, 2014). In the case of organisms carried out genomic analysis, the d...e File name: pgdbj_dna_marker_linkage_map_genome_analysis_methods_en.zip File URL: ftp://ftp.biosciencedbc.j

Validation and use of DNA markers for sex determination in papaya (Carica papaya)

International Nuclear Information System (INIS)

Ejaz, M.; Iqbal, M.; Ahmed, I.

2015-01-01

Profitable papaya production requires female and hermaphrodite plants in higher number than male plants. This is only possible if sex of plants is determined at an early growth stage. The present study was conducted to validate sex-linked DNA markers using plants from two Pakistani papaya varieties and subsequently utilize them for determination of sex in juvenile papaya plants. One hundred and five plants (including 49 male and 56 female) of two Pakistani Papaya varieties at flowering stage were screened with six DNA markers viz., W-11, T12, SDP, Napf-76Napf-76, PKBT4 and PKBT5. All male plants exhibited amplification of sex-linked alleles with markers T12 and W11, whereas, 96% and 95% of female plants showed the absence of sex-linked allele with these markers, respectively. Markers SDP, PKBT5 and Napf-76 showed the presence of sex-linked alleles in 98%, 96% and 93% of male plants, respectively, whereas the same markers showed the absence of sex-linked alleles in 100%, 96% and 94% of female plants. One marker, PKBT4 could not produce expected PCR amplification reported previously. The five DNA markers were further used to screen 171 papaya seedlings. These markers clearly differentiated male and female sex types in the studied papaya plants. Results of our study are likely to facilitate Pakistani papaya breeders and growers to incorporate DNA based screening at juvenile stage to determine sex at early stage and to ensure profitable papaya production. (author)

Identification of new SSR markers linked to leaf chlorophyll content, flag leaf senescence and cell membrane stability traits in wheat under water stressed condition.

Science.gov (United States)

Barakat, Mohamed N; Saleh, Mohamed; Al-Doss, Abdullah A; Moustafa, Khaled A; Elshafei, Adel A; Al-Qurainy, Fahed H

2015-03-01

Segregating F4 families from the cross between drought sensitive (Yecora Rojo) and drought tolerant (Pavon 76) genotypes were made to identify SSR markers linked to leaf chlorophyll content, flag leaf senescence and cell membrane stability traits in wheat (Triticum aestivum L.) under water-stressed condition and to map quantitative trait locus (QTL) for the three physiological traits. The parents and 150 F4 families were evaluated phenotypically for drought tolerance using two irrigation treatments (2500 and 7500 m3/ha). Using 400 SSR primers tested for polymorphism in testing parental and F4 families genotypes, the results revealed that QTL for leaf chlorophyll content, flag leaf senescence and cell membrane stability traits were associated with 12, 5 and 12 SSR markers, respectively and explained phenotypic variation ranged from 6 to 42%. The SSR markers for physiological traits had genetic distances ranged from 12.5 to 25.5 cM. These SSR markers can be further used in breeding programs for drought tolerance in wheat.

Gains following perceptual learning are closely linked to the initial visual acuity.

Science.gov (United States)

Yehezkel, Oren; Sterkin, Anna; Lev, Maria; Levi, Dennis M; Polat, Uri

2016-04-28

The goal of the present study was to evaluate the dependence of perceptual learning gains on initial visual acuity (VA), in a large sample of subjects with a wide range of VAs. A large sample of normally sighted and presbyopic subjects (N = 119; aged 40 to 63) with a wide range of uncorrected near visual acuities (VA, -0.12 to 0.8 LogMAR), underwent perceptual learning. Training consisted of detecting briefly presented Gabor stimuli under spatial and temporal masking conditions. Consistent with previous findings, perceptual learning induced a significant improvement in near VA and reading speed under conditions of limited exposure duration. Our results show that the improvements in VA and reading speed observed following perceptual learning are closely linked to the initial VA, with only a minor fraction of the observed improvement that may be attributed to the additional sessions performed by those with the worse VA.

[Norrie syndrome: identification of carriers by segregation analysis with flanking DNA markers].

Science.gov (United States)

Körner, J; Uhlhaas, S; Neugebauer, M; Gal, A

1989-01-01

Norrie disease is an X-linked recessive disorder. Affected males present with congenital blindness. Additionally, hearing loss and psychotic behavior may occur at any time. Since carriers are clinically healthy, they can only be identified by genetic means. Daughters of carriers or sisters of affected males have an à priori 50% risk of being carriers themselves. Close linkage has been found between the Norrie disease locus (NDP) and the DNA locus DXS7 mapped to Xp11.3. For genetic counselling, this linkage relationship allows carriers of the disease to be identified in informative families. We describe a large pedigree with Norrie disease. Segregation analysis was carried out with DXS7 and a second flanking marker, DXS255, both linked to NDP. In this way, three females at risk were identified who had a high probability of being carriers for Norrie disease.

Dosimetric impact of gold markers implanted closely to lung tumors: a Monte Carlo simulation.

Science.gov (United States)

Shiinoki, Takehiro; Sawada, Akira; Ishihara, Yoshitomo; Miyabe, Yuki; Matsuo, Yukinori; Mizowaki, Takashi; Kokubo, Masaki; Hiraoka, Masahiro

2014-05-08

We are developing an innovative dynamic tumor tracking irradiation technique using gold markers implanted around a tumor as a surrogate signal, a real-time marker detection system, and a gimbaled X-ray head in the Vero4DRT. The gold markers implanted in a normal organ will produce uncertainty in the dose calculation during treatment planning because the photon mass attenuation coefficient of a gold marker is much larger than that of normal tissue. The purpose of this study was to simulate the dose variation near the gold markers in a lung irradiated by a photon beam using the Monte Carlo method. First, the single-beam and the opposing-beam geometries were simulated using both water and lung phantoms. Subsequently, the relative dose profiles were calculated using a stereotactic body radiotherapy (SBRT) treatment plan for a lung cancer patient having gold markers along the anterior-posterior (AP) and right-left (RL) directions. For the single beam, the dose at the gold marker-phantom interface laterally along the perpendicular to the beam axis increased by a factor of 1.35 in the water phantom and 1.58 in the lung phantom, respectively. Furthermore, the entrance dose at the interface along the beam axis increased by a factor of 1.63 in the water phantom and 1.91 in the lung phantom, while the exit dose increased by a factor of 1.00 in the water phantom and 1.12 in the lung phantom, respectively. On the other hand, both dose escalations and dose de-escalations were canceled by each beam for opposing portal beams with the same beam weight. For SBRT patient data, the dose at the gold marker edge located in the tumor increased by a factor of 1.30 in both AP and RL directions. In clinical cases, dose escalations were observed at the small area where the distance between a gold marker and the lung tumor was ≤ 5 mm, and it would be clinically negligible in multibeam treatments, although further investigation may be required.

The marker: A precious link between generations and a part of the long-term safety story

International Nuclear Information System (INIS)

Massart, Cecile

2014-01-01

High-level radioactive waste brings us face to face with a social, emotional, ethical, political and environmental situation at the heart of which lies the security of the living world. From now on, mankind has to make commitments to protect itself. Building an artistic device, a continuous creation that links and reveals the situation will inform and shed some light on the objectives. In co-operation with industries that manage geological repositories, the installation of markers above ground introduces non-technical aspects that can increase safety. In the art world, many works of art produced throughout the 20. century associate art with waste as vestiges for keeping. The use of waste has shaken the nature of art since Marcel Duchamp, the eye of Man Ray as well as the definition of the artist. The waste recycling industry has modified the way we see it. For what is waste? It embodies above all the imperfect and also a 'time capsule'. In the case that concerns us, waste stays buried in our doubt, secured by our current financial means that are substantial. The notion of time for its decay is calculated and, at the end, it vanishes. Its visibility is next to nil, whereas its presence remains very powerful and thrills the imagination. The hosting community is permeated with it. At the same time the laboratory at the disposal facility provides economic dynamism, an analysis of upheavals in this territory, an exhibition of artistic devices and an awareness of danger. The proposals that are described here are the result of a decade of research. It seems that from the beginning there has been negligence on the part of the nuclear industry regarding the storage of high-level radioactive waste. The general public is not very knowledgeable about the subject. Projects for geological disposal often give the local population the feeling of an ablation of a piece of territory. To sum it up, in the long run, we consider the study of two barriers for the safety of high

New Microsatellite Markers for Tricyrtis macrantha (Convallariaceae and Cross-Amplification in Closely Related Species

Directory of Open Access Journals (Sweden)

Noriko Ohki

2013-05-01

Full Text Available Premise of the study: Microsatellite markers were characterized in Tricyrtis macrantha (sect. Brachycyrtis, Convallariaceae, a vulnerable species endemic to Japan, to investigate its genetic diversity and population structure. Methods and Results: Eleven microsatellite markers were developed. The number of alleles per locus ranged from one to seven, and genetic diversity per locus ranged from 0.142 to 0.812. Four markers were successfully amplified in other species of sect. Brachycyrtis (T. ishiiana, T. ishiiana var. surugensis, and T. macranthopsis. Conclusions: The microsatellite markers can be used to investigate the genetic diversity and population structure of the vulnerable and endangered species of Tricyrtis sect. Brachycyrtis, to aid in the development of conservation strategies for each species.

A general model for likelihood computations of genetic marker data accounting for linkage, linkage disequilibrium, and mutations.

Science.gov (United States)

Kling, Daniel; Tillmar, Andreas; Egeland, Thore; Mostad, Petter

2015-09-01

Several applications necessitate an unbiased determination of relatedness, be it in linkage or association studies or in a forensic setting. An appropriate model to compute the joint probability of some genetic data for a set of persons given some hypothesis about the pedigree structure is then required. The increasing number of markers available through high-density SNP microarray typing and NGS technologies intensifies the demand, where using a large number of markers may lead to biased results due to strong dependencies between closely located loci, both within pedigrees (linkage) and in the population (allelic association or linkage disequilibrium (LD)). We present a new general model, based on a Markov chain for inheritance patterns and another Markov chain for founder allele patterns, the latter allowing us to account for LD. We also demonstrate a specific implementation for X chromosomal markers that allows for computation of likelihoods based on hypotheses of alleged relationships and genetic marker data. The algorithm can simultaneously account for linkage, LD, and mutations. We demonstrate its feasibility using simulated examples. The algorithm is implemented in the software FamLinkX, providing a user-friendly GUI for Windows systems (FamLinkX, as well as further usage instructions, is freely available at www.famlink.se ). Our software provides the necessary means to solve cases where no previous implementation exists. In addition, the software has the possibility to perform simulations in order to further study the impact of linkage and LD on computed likelihoods for an arbitrary set of markers.

(SRAP) markers linked to bacterial wilt resistance genes i

African Journals Online (AJOL)

SAM

2014-03-19

Mar 19, 2014 ... Bacterial wilt caused by Ralstonia solanacearum is one of the most economically important diseases affecting potato (Solanum tuberosum). It is necessary to develop more molecular markers for potential use in potato genetic research. A highly resistant primitive cultivated species Solanum phureja was.

Markers for nutrition studies: review of criteria for the evaluation of markers.

Science.gov (United States)

de Vries, Jan; Antoine, Jean-Michel; Burzykowski, Tomasz; Chiodini, Alessandro; Gibney, Mike; Kuhnle, Gunter; Méheust, Agnès; Pijls, Loek; Rowland, Ian

2013-10-01

Markers are important tools to assess the nutrition status and effects of nutrition interventions. There is currently insufficient consensus in nutrition sciences on how to evaluate markers, despite the need for properly evaluating them. To identify the criteria for the evaluation of markers related to nutrition, health and disease and to propose generic criteria for evaluation. The report on "Evaluation of Biomarker and Surrogate Endpoints in Chronic Disease" from the Institute of Medicine was the starting point for the literature search. Additionally, specific search strategies were developed for Pubmed. In nutrition, no set of criteria or systematic approach to evaluate markers is currently available. There is a reliance on the medical area where statistical methods have been developed to quantify the evaluation of markers. Even here, a systematic approach is lacking-markers are still evaluated on a case-by-case basis. The review of publications from the literature search resulted in a database with definitions, criteria for validity and the rationale behind the criteria. It was recognized that, in nutrition, a number of methodological aspects differ from medical research. The following criteria were identified as essential elements in the evaluation of markers: (1) the marker has a causal biological link with the endpoint, (2) there is a significant association between marker and endpoint in the target population, (3) marker changes consistently with the endpoint, e.g., in response to an intervention, and (4) change in the marker explains a substantial proportion of the change in the endpoint in response to the intervention.

Circulating fibrosis markers, eosinophil cationic protein and eosinophil protein X in patients with Wuchereria bancrofti infection: association with clinical status

Directory of Open Access Journals (Sweden)

Esterre P.

2006-06-01

Full Text Available We measured the concentrations of several circulating fibrosis markers (type I collagen I, type III procollagen, hyaluronan and eosinophil granule proteins (ECP and EPX in lymphatic filariasis patients to investigate their relationship with clinical, parasitological and immunological data. This study was conducted in Polynesian patients with various stages of the disease (acute lymphangitis, chyluria, hydrocoele, elephantiasis, a closely related microbial lymphangitis and endemic controls. We observed modifications of the different markers in this pathology. Serum type I collagen and PIIINP were decreased. Serum hyaluronan, linked to perilymphatic granulomatous inflammation, was significantly increased in acute lymphangitis and elephantiasis patients. Serum ECP was also increased, at the limit of significance in our sample, in elephantiasis patients. These two last markers, already validated in another helminth disease, schistosomiasis, have potential interest in terms of follow-up of morbidity in these parasitic diseases.

(SSR) markers for drought tolerance in maize

African Journals Online (AJOL)

use

2011-11-21

Nov 21, 2011 ... and dominance gene effects in inheritance are included in almost all traits related to drought (Shiri et al., 2010a, b). Identifying the complete-linked molecular markers with target gene and mapping its chromosome locus is an important goal in plant breeding for gene cloning and marker-aided selection.

A DArT marker genetic map of perennial ryegrass (Lolium perenne L.) integrated with detailed comparative mapping information; comparison with existing DArT marker genetic maps of Lolium perenne, L. multiflorum and Festuca pratensis.

Science.gov (United States)

King, Julie; Thomas, Ann; James, Caron; King, Ian; Armstead, Ian

2013-07-03

Ryegrasses and fescues (genera, Lolium and Festuca) are species of forage and turf grasses which are used widely in agricultural and amenity situations. They are classified within the sub-family Pooideae and so are closely related to Brachypodium distachyon, wheat, barley, rye and oats. Recently, a DArT array has been developed which can be used in generating marker and mapping information for ryegrasses and fescues. This represents a potential common marker set for ryegrass and fescue researchers which can be linked through to comparative genomic information for the grasses. A F2 perennial ryegrass genetic map was developed consisting of 7 linkage groups defined by 1316 markers and deriving a total map length of 683 cM. The marker set included 866 DArT and 315 gene sequence-based markers. Comparison with previous DArT mapping studies in perennial and Italian ryegrass (L. multiflorum) identified 87 and 105 DArT markers in common, respectively, of which 94% and 87% mapped to homoeologous linkage groups. A similar comparison with meadow fescue (F. pratensis) identified only 28 DArT markers in common, of which c. 50% mapped to non-homoelogous linkage groups. In L. perenne, the genetic distance spanned by the DArT markers encompassed the majority of the regions that could be described in terms of comparative genomic relationships with rice, Brachypodium distachyon, and Sorghum bicolor. DArT markers are likely to be a useful common marker resource for ryegrasses and fescues, though the success in aligning different populations through the mapping of common markers will be influenced by degrees of population interrelatedness. The detailed mapping of DArT and gene-based markers in this study potentially allows comparative relationships to be derived in future mapping populations characterised using solely DArT markers.

Hidden marker position estimation during sit-to-stand with walker.

Science.gov (United States)

Yoon, Sang Ho; Jun, Hong Gul; Dan, Byung Ju; Jo, Byeong Rim; Min, Byung Hoon

2012-01-01

Motion capture analysis of sit-to-stand task with assistive device is hard to achieve due to obstruction on reflective makers. Previously developed robotic system, Smart Mobile Walker, is used as an assistive device to perform motion capture analysis in sit-to-stand task. All lower limb markers except hip markers are invisible through whole session. The link-segment and regression method is applied to estimate the marker position during sit-to-stand. Applying a new method, the lost marker positions are restored and the biomechanical evaluation of the sit-to-stand movement with a Smart Mobile Walker could be carried out. The accuracy of the marker position estimation is verified with normal sit-to-stand data from more than 30 clinical trials. Moreover, further research on improving the link segment and regression method is addressed.

Properties of closed 3-braids and braid representations of links

CERN Document Server

Stoimenow, Alexander

2017-01-01

This book studies diverse aspects of braid representations via knots and links. Complete classification results are illustrated for several properties through Xu’s normal 3-braid form and the Hecke algebra representation theory of link polynomials developed by Jones. Topological link types are identified within closures of 3-braids which have a given Alexander or Jones polynomial. Further classifications of knots and links arising by the closure of 3-braids are given, and new results about 4-braids are part of the work. Written with knot theorists, topologists,and graduate students in mind, this book features the identification and analysis of effective techniques for diagrammatic examples with unexpected properties.

A PCR marker linked to a THCA synthase polymorphism is a reliable tool to discriminate potentially THC-rich plants of Cannabis sativa L.

Science.gov (United States)

Staginnus, Christina; Zörntlein, Siegfried; de Meijer, Etienne

2014-07-01

Neither absolute THC content nor morphology allows the unequivocal discrimination of fiber cultivars and drug strains of Cannabis sativa L. unequivocally. However, the CBD/THC ratio remains constant throughout the plant's life cycle, is independent of environmental factors, and considered to be controlled by a single locus (B) with two codominant alleles (B(T) and B(D)). The homozygous B(T)/B(T) genotype underlies the THC-predominant phenotype, B(D)/B(D) is CBD predominant, and an intermediate phenotype is induced by the heterozygous state (B(T)/B(D)). Using PCR-based markers in two segregating populations, we proved that the THCA synthase gene represents the postulated B locus and that specific sequence polymorphisms are absolutely linked either to the THC-predominant or the THC-intermediate chemotype. The absolute linkage provides an excellent reliability of the marker signal in forensic casework. For validation, the species-specific marker system was applied to a large number of casework samples and fiber hemp cultivars. © 2014 American Academy of Forensic Sciences.

Conservation of Sex-Linked Markers among Conspecific Populations of a Viviparous Skink, Niveoscincus ocellatus, Exhibiting Genetic and Temperature-Dependent Sex Determination

Science.gov (United States)

Burridge, Christopher P; Ezaz, Tariq; Wapstra, Erik

2018-01-01

Abstract Sex determination systems are exceptionally diverse and have undergone multiple and independent evolutionary transitions among species, particularly reptiles. However, the mechanisms underlying these transitions have not been established. Here, we tested for differences in sex-linked markers in the only known reptile that is polymorphic for sex determination system, the spotted snow skink, Niveoscincus ocellatus, to quantify the genomic differences that have accompanied this transition. In a highland population, sex is determined genetically, whereas in a lowland population, offspring sex ratio is influenced by temperature. We found a similar number of sex-linked loci in each population, including shared loci, with genotypes consistent with male heterogamety (XY). However, population-specific linkage disequilibrium suggests greater differentiation of sex chromosomes in the highland population. Our results suggest that transitions between sex determination systems can be facilitated by subtle genetic differences. PMID:29659810

High-resolution mapping of the x-linked hypohidrotic ectodermal dysplasia (EDA) locus

Energy Technology Data Exchange (ETDEWEB)

Zonana, J.; Jones, M.; Litt, M.; Kramer, P.; Browne, D.; Becker, H.W. (Oregon Health Sciences Univ., Portland, OR (United States)); Brockdorff, N.; Rastan, S. (Medical Council Clinical Research Centre, Harrow (United Kingdom)); Davies, K.P.; Clarke, A. (Univ. of Wales College of Medicine, Cardiff (United Kingdom)) (and others)

1992-11-01

The X-linked hypohidrotic ectodermal dysplasia (EDA) locus has been previously localized to the subchromosomal region Xq11-q21.1. The authors have extended previous linkage studies and analyzed linkage between the EDA locus and 10 marker loci, including five new loci, in 41 families. Four of the marker loci showed no recombination with the EDA locus, and six other loci were also linked to the EDA locus with recombination fractions of .009-.075. Multipoint analysis gave support to the placement of the PGK1P1 locus proximal to the EDA locus and the DXS453 and PGK1 loci distal to EDA. Further ordering of the loci could be inferred from a human-rodent somatic cell hybrid derived from an affected female with EDA and an X;9 translocation and from studies of an affected male with EDA and a submicroscopic deletion. Three of the proximal marker loci, which showed no recombination with the EDA locus, when used in combination, were informative in 92% of females. The closely linked flanking polymorphic loci DXS339 and DXS453 had heterozygosites of 72% and 76%, respectively, and when used jointly, they were doubly informative in 52% of females. The human DXS732 locus was defined by a conserved mouse probe pcos169E/4 (DXCrc169 locus) that consegregates with the mouse tabby (Ta) locus, a potential homologue to the EDA locus. The absence of recombination between EDA and the DXSA732 locus lends support to the hypothesis that the DXCrc169 locus in the mouse and the DXS732 locus in humans may contain candidate sequences for the Ta and EDA genes, respectively. 36 refs., 1 fig., 5 tabs.

Genetic localization and phenotypic expression of X-linked cataract (Xcat) in Mus musculus.

Science.gov (United States)

Favor, J; Pretsch, W

1990-01-01

Linkage data relative to the markers tabby and glucose-6-phosphate dehydrogenase are presented to locate X-linked cataract (Xcat) in the distal portion of the mouse X-chromosome between jimpy and hypophosphatemia. The human X-linked cataract-dental syndrome, Nance-Horan Syndrome, also maps closely to human hypophosphatemia and would suggest homology between mouse Xcat and human Nance-Horan Syndrome genes. In hemizygous males and homozygous females penetrance is complete with only slight variation in the degree of expression. Phenotypic expression in Xcat heterozygous females ranges from totally clear to totally opaque lenses. The phenotypic expression between the two lenses of a heterozygous individual could also vary between totally clear and totally opaque lenses. However, a correlation in the degree of expression between the eyes of an individual was observed. A variegated pattern of lens opacity was evident in female heterozygotes. Based on these observations, the site of gene action for the Xcat locus is suggested to be endogenous to the lens cells and the precursor cell population of the lens is concluded to be small. The identification of an X-linked cataract locus is an important contribution to the estimate of the number of mutable loci resulting in cataract, an estimate required so that dominant cataract mutagenesis results may be expressed on a per locus basis. The Xcat mutation may be a useful marker for a distal region of the mouse X-chromosome which is relatively sparsely marked and the X-linked cataract mutation may be employed in gene expression and lens development studies.

Determination of molecular markers associated with anthesis-silking interval in maize

International Nuclear Information System (INIS)

Simpson, J.

1998-01-01

Maize lines contrasting in anthesis-silking, interval (ASI), a trait strongly linked to drought tolerance, have been analyzed under different water stress conditions in the field and with molecular markers. Correlation of marker and field data has revealed molecular markers strongly associated with flowering and yield traits. (author)

Selection Of Drought Resistant Mutants In Rice Using DNA Markers

International Nuclear Information System (INIS)

Nguyen Duc Thanh; Le Thi Bich Thuy; Dang Thi Minh Lua

2008-01-01

In recent years, the marker - assisted selection (MAS) strategy have been used for selection of traits that are difficult and costly performed measurement and score. Selection for a well-developed root system could improve the drought resistance of rice as the plant would avoid water stress by absorbing water from the soil. There were several reports on map construction and identification of the markers tightly linked to morphological and physiological traits related to drought resistance in rice, in particular, root traits in upland and lowland rice (Champoux et al., 1995; Ray et al., 1996; Price et al., 1997, 2000; Yadav et al., 1997). In this report, we present the results on selection of drought resistance mutants in rice using the DNA markers tightly linked to root traits favorable for drought resistance. The mutant rice lines were obtained from irradiated seeds and calluses by gamma ray. The selection was performed at M2 mutants using the DNA markers linked to maximum root length (MRL), root weight to shoot weight ratio (RW/SR), and weight of deep root to shoot weight ratio (DRW/SR). The obtained results showed that there were many lines possessed drought resistant markers. In addition, there is a number of lines have altered genome. Several lines having drought markers proved to be more resistant to drought in green-house test. These lines could be useful for further test and development of drought resistant varieties. (author)

High-Resolution Amplified Fragment Length Polymorphism Typing of Lactococcus lactis Strains Enables Identification of Genetic Markers for Subspecies-Related Phenotypes▿

Science.gov (United States)

Kütahya, Oylum Erkus; Starrenburg, Marjo J. C.; Rademaker, Jan L. W.; Klaassen, Corné H. W.; van Hylckama Vlieg, Johan E. T.; Smid, Eddy J.; Kleerebezem, Michiel

2011-01-01

A high-resolution amplified fragment length polymorphism (AFLP) methodology was developed to achieve the delineation of closely related Lactococcus lactis strains. The differentiation depth of 24 enzyme-primer-nucleotide combinations was experimentally evaluated to maximize the number of polymorphisms. The resolution depth was confirmed by performing diversity analysis on 82 L. lactis strains, including both closely and distantly related strains with dairy and nondairy origins. Strains clustered into two main genomic lineages of L. lactis subsp. lactis and L. lactis subsp. cremoris type-strain-like genotypes and a third novel genomic lineage rooted from the L. lactis subsp. lactis genomic lineage. Cluster differentiation was highly correlated with small-subunit rRNA homology and multilocus sequence analysis (MLSA) studies. Additionally, the selected enzyme-primer combination generated L. lactis subsp. cremoris phenotype-specific fragments irrespective of the genotype. These phenotype-specific markers allowed the differentiation of L. lactis subsp. lactis phenotype from L. lactis subsp. cremoris phenotype strains within the same L. lactis subsp. cremoris type-strain-like genomic lineage, illustrating the potential of AFLP for the generation of phenotype-linked genetic markers. PMID:21666014

Development and dissection of diagnostic SNP markers for the downy mildew resistance genes Pl Arg and Pl 8 and maker-assisted gene pyramiding in sunflower (Helianthus annuus L.).

Science.gov (United States)

Qi, L L; Talukder, Z I; Hulke, B S; Foley, M E

2017-06-01

Diagnostic DNA markers are an invaluable resource in breeding programs for successful introgression and pyramiding of disease resistance genes. Resistance to downy mildew (DM) disease in sunflower is mediated by Pl genes which are known to be effective against the causal fungus, Plasmopara halstedii. Two DM resistance genes, Pl Arg and Pl 8 , are highly effective against P. halstedii races in the USA, and have been previously mapped to the sunflower linkage groups (LGs) 1 and 13, respectively, using simple sequence repeat (SSR) markers. In this study, we developed high-density single nucleotide polymorphism (SNP) maps encompassing the Pl arg and Pl 8 genes and identified diagnostic SNP markers closely linked to these genes. The specificity of the diagnostic markers was validated in a highly diverse panel of 548 sunflower lines. Dissection of a large marker cluster co-segregated with Pl Arg revealed that the closest SNP markers NSA_007595 and NSA_001835 delimited Pl Arg to an interval of 2.83 Mb on the LG1 physical map. The SNP markers SFW01497 and SFW06597 delimited Pl 8 to an interval of 2.85 Mb on the LG13 physical map. We also developed sunflower lines with homozygous, three gene pyramids carrying Pl Arg , Pl 8 , and the sunflower rust resistance gene R 12 using the linked SNP markers from a segregating F 2 population of RHA 340 (carrying Pl 8 )/RHA 464 (carrying Pl Arg and R 12 ). The high-throughput diagnostic SNP markers developed in this study will facilitate marker-assisted selection breeding, and the pyramided sunflower lines will provide durable resistance to downy mildew and rust diseases.

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Application of molecular markers in breeding for bean common ...

African Journals Online (AJOL)

Sequence characterised amplified region (SCAR) markers, linked to four independent quantitative trait loci (QTL) in XAN 159 and GN #1 Nebr. sel. 27, are available for indirect selection of resistance to common bacterial blight in Phaseolus vulgaris. Existing SCAR-markers, SU91, BC420, BC409 and SAP6, were evaluated ...

Identification of AFLP markers linked with cocoon weight genes in ...

African Journals Online (AJOL)

STORAGESEVER

2010-03-08

Mar 8, 2010 ... needful for life. This industry has .... work for anchoring morphological or other molecular markers and identifying of ... An electronic balance was used and .... These QTLs are designated as cw[x/y], where cw is cocoon weight .... silkworm Bombyx mori L., using individual selection in 3P generation. Asian J.

Identification of RAPD markers linked to salinity tolerance in wheat ...

African Journals Online (AJOL)

Genetic diversity can be measured by a number of ways, including pedigree, phenotype and allelic diversity at loci controlling phenotypes of interest. A DNA marker for root length in wheat (Triticum aestivum L.) was identified. The individual plants from F2 population segregation for salinity tolerance and the parents (S-24 ...

Clinical and linkage study of a large family with simple ectopia lentis linked to FBN1

Energy Technology Data Exchange (ETDEWEB)

Edwards, M.J.; Roberts, J.; Partington, M.W. [Newcastle and Northern New South Wales Genetics Service (Australia); Colley, P.W. [John Hunter Hospital, Newcastle (Australia); Hollway, G.E.; Kozman, H.M.; Mulley, J.C. [Adelaide Children`s Hospital, North Adelaide (Australia)

1994-10-15

Simple ectopia lentis (EL) was studied in a large family, by clinical examination and analysis of linkage to markers in the region of FBN1, the gene for fibrillin which causes Marfan syndrome on chromosome 15. No patient had clinical or echocardiographic evidence of Marfan syndrome, although there was a trend towards relatively longer measurements of height; lower segment; arm span; middle finger, hand, and foot length in the affected members of the family, compared with unaffected sibs of the same sex. Analysis of linkage to intragenic FBN1 markers was inconclusive because they were relatively uninformative. Construction of a multipoint background map from the CEPH reference families identified microsatellite markers linked closely to FBN1 which could demonstrate linkage of EL in this family to the FBN1 region. LINKMAP analysis detected a multipoint lod score of 5.68 at D15S119, a marker approximately 6 cM distal to FBN1, and a multipoint lod score of 5.04 at FBN1. The EL gene in this family is likely to be allelic to Marfan syndrome, and molecular characterization of the FBN1 mutation should now be possible. 25 refs., 6 figs., 2 tabs.

Development and mapping of SSR markers linked to resistance-gene homologue clusters in common bean

Institute of Scientific and Technical Information of China (English)

Luz; Nayibe; Garzon; Matthew; Wohlgemuth; Blair

2014-01-01

Common bean is an important but often a disease-susceptible legume crop of temperate,subtropical and tropical regions worldwide. The crop is affected by bacterial, fungal and viral pathogens. The strategy of resistance-gene homologue(RGH) cloning has proven to be an efficient tool for identifying markers and R(resistance) genes associated with resistances to diseases. Microsatellite or SSR markers can be identified by physical association with RGH clones on large-insert DNA clones such as bacterial artificial chromosomes(BACs). Our objectives in this work were to identify RGH-SSR in a BAC library from the Andean genotype G19833 and to test and map any polymorphic markers to identify associations with known positions of disease resistance genes. We developed a set of specific probes designed for clades of common bean RGH genes and then identified positive BAC clones and developed microsatellites from BACs having SSR loci in their end sequences. A total of 629 new RGH-SSRs were identified and named BMr(bean microsatellite RGH-associated markers). A subset of these markers was screened for detecting polymorphism in the genetic mapping population DOR364 × G19833. A genetic map was constructed with a total of 264 markers,among which were 80 RGH loci anchored to single-copy RFLP and SSR markers. Clusters of RGH-SSRs were observed on most of the linkage groups of common bean and in positions associated with R-genes and QTL. The use of these new markers to select for disease resistance is discussed.

Molecular marker-assisted selection for resistance to pathogens in tomato

International Nuclear Information System (INIS)

Barone, A.; Frusciante, L.

2007-01-01

Since the 1980s, the use of molecular markers has been suggested to improve the efficiency of releasing resistant varieties, thus overcoming difficulties met with classical breeding. For tomato, a high-density molecular map is available in which more than 40 resistance genes are localized. Markers linked to these genes can be used to speed up gene transfer and pyramiding. Suitable PCR markers targeting resistance genes were constructed directly on the sequences of resistance genes or on restriction fragment length polymorphisms (RFLPs) tightly linked to them, and used to select resistant genotypes in backcross schemes. In some cases, the BC 5 generation was reached, and genotypes that cumulated two homozygous resistant genes were also obtained. These results supported the feasibility of using marker-assisted selection (MAS) in tomato and reinforcing the potential of this approach for other genes, which is today also driven by the development of new techniques and increasing knowledge about the tomato genome. (author)

Sample positioning in neutron diffraction experiments using a multi-material fiducial marker

Energy Technology Data Exchange (ETDEWEB)

Marais, D., E-mail: Deon.Marais@necsa.co.za [Research and Development Division, South African Nuclear Energy Corporation (Necsa) SOC Limited, PO Box 582, Pretoria 0001 (South Africa); School of Mechanical and Nuclear Engineering, North-West University, Potchefstroom 2520 (South Africa); Venter, A.M., E-mail: Andrew.Venter@necsa.co.za [Research and Development Division, South African Nuclear Energy Corporation (Necsa) SOC Limited, PO Box 582, Pretoria 0001 (South Africa); Faculty of Agriculture Science and Technology, North-West University, Mahikeng 2790 (South Africa); Markgraaff, J., E-mail: Johan.Markgraaff@nwu.ac.za [School of Mechanical and Nuclear Engineering, North-West University, Potchefstroom 2520 (South Africa); James, J., E-mail: Jon.James@open.ac.uk [Faculty of Mathematics, Computing and Technology, The Open University, Milton Keynes, MK76AA England (United Kingdom)

2017-01-01

An alternative sample positioning method is reported for use in conjunction with sample positioning and experiment planning software systems deployed on some neutron diffraction strain scanners. In this approach, the spherical fiducial markers and location trackers used with optical metrology hardware are replaced with a specifically designed multi-material fiducial marker that requires one diffraction measurement. In a blind setting, the marker position can be determined within an accuracy of ±164 µm with respect to the instrument gauge volume. The scheme is based on a pre-determined relationship that links the diffracted peak intensity to the absolute positioning of the fiducial marker with respect to the instrument gauge volume. Two methods for establishing the linking relationship are presented, respectively based on fitting multi-dimensional quadratic functions and a cross-correlation artificial neural network.

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

Science.gov (United States)

Williams, Larry J; O'Boyle, Ernest H

2015-09-01

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

The carboxy-terminal pyridinoline cross-linked telopeptide of type I collagen in serum as a marker of bone resorption

DEFF Research Database (Denmark)

Hassager, C; Jensen, L T; Pødenphant, J

1994-01-01

Carboxy-terminal pyridinoline cross-linked telopeptide of type I collagen (ICTP) in serum has recently been proposed as a new biochemical marker of bone resorption. In the present study we compared serum ICTP with radiopharmaceutical and histomorphometric measurements of bone turnover...... in postmenopausal women with mild osteoporosis, and assessed the effect of hormone replacement therapy (HRT) (2 mg 17 beta-estradiol plus 1 mg norethisterone daily) and anabolic steroid therapy (50 mg nandrolone decanoate (ND) i.m. every 3 weeks) on serum ICTP in two double-blind placebo-controlled studies with 55...... to 75-year-old women. Serum ICTP measured by radioimmunoassay (RIA) correlated significantly with the 24-hour whole body retention of 99m-technetium diphosphonate (Rho = 0.47, P

Links between Adolescents’ Closeness to Adoptive Parents and Attachment Style in Young Adulthood

Science.gov (United States)

Grant-Marsney, Holly A.; Grotevant, Harold D.; Sayer, Aline G.

2014-01-01

This study examined whether adolescents’ closeness to adoptive parents (APs) predicted attachment styles in close relationships outside their family during young adulthood. In a longitudinal study of domestic infant adoptions, closeness to adoptive mother and adoptive father was assessed in 156 adolescents (M = 15.7 years). Approximately nine years later (M = 25.0 years), closeness to parents was assessed again as well as attachment style in their close relationships. Multilevel modeling was used to predict attachment style in young adulthood from the average and discrepancy of closeness to adolescents’ adoptive mothers and fathers and the change over time in closeness to APs. Less avoidant attachment style was predicted by stronger closeness to both APs during adolescence. Increased closeness to APs over time was related to less anxiety in close relationships. Higher closeness over time to either AP was related to less avoidance and anxiety in close relationships. PMID:25859067

Links between Adolescents' Closeness to Adoptive Parents and Attachment Style in Young Adulthood.

Science.gov (United States)

Grant-Marsney, Holly A; Grotevant, Harold D; Sayer, Aline G

2015-04-01

This study examined whether adolescents' closeness to adoptive parents (APs) predicted attachment styles in close relationships outside their family during young adulthood. In a longitudinal study of domestic infant adoptions, closeness to adoptive mother and adoptive father was assessed in 156 adolescents ( M = 15.7 years). Approximately nine years later ( M = 25.0 years), closeness to parents was assessed again as well as attachment style in their close relationships. Multilevel modeling was used to predict attachment style in young adulthood from the average and discrepancy of closeness to adolescents' adoptive mothers and fathers and the change over time in closeness to APs. Less avoidant attachment style was predicted by stronger closeness to both APs during adolescence. Increased closeness to APs over time was related to less anxiety in close relationships. Higher closeness over time to either AP was related to less avoidance and anxiety in close relationships.

Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis

Directory of Open Access Journals (Sweden)

Doerge RW

2003-06-01

Full Text Available Abstract Background It has been reported in the quantitative trait locus (QTL literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases. Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach. We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster. Results Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis. Conclusion We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test.

PAV markers in Sorghum bicolour

DEFF Research Database (Denmark)

Shen, Xin; Liu, Zhiquan; Mocoeur, Anne Raymonde Joelle

2015-01-01

Abstract Genic presence/absence variants (PAVs) correlate closely to the phenotypic variation, impacting plant genome sizes and the adaption to the environment. To shed more light on their genome-wide patterns, functions and to test the possibility of using them as molecular markers, we analyzed...... enriched in stress responses and protein modification. We used 325 polymorphic PAVs in two sorghum inbred lines Ji2731 and E-Tian, together with 49 SSR markers, and constructed a genetic map, which consisted of 10 linkage groups corresponding to the 10 chromosomes of sorghum and spanned 1430.3 cM in length...

Characterisation of Triticum vavilovii-derived stripe rust resistance using genetic, cytogenetic and molecular analyses and its marker-assisted selection.

Science.gov (United States)

Bariana, H. S.; Brown, G. N.; Ahmed, N. U.; Khatkar, S.; Conner, R. L.; Wellings, C. R.; Haley, S.; Sharp, P. J.; Laroche, A.

2002-02-01

Stripe rust resistance was identified in Triticum vavilovii( T. vaviloviiAus22498)-derived Russian wheat aphid (RWA)-resistant germplasm. Inheritance studies indicated monogenic control of resistance. The resistance gene was tentatively designated as Yrvav and was located on chromosome 1B by monosomic analysis. A close association (1.5+/-0.9% recombination) of Yrvav with a T. vavilovii-derived gliadin allele ( Gli-B1vav) placed it in chromosome arm 1BS. Yrvavwas allelic with Yr10. Tests with Yr10 avirulent and virulent pathotypes showed that Yrvav and Yr10 possess identical pathogenic specificity. Yrvav and Yr10 showed close genetic associations with alternate alleles at the Xpsp3000(microsatellite marker), Gli-B1 and Rg1 loci. Based on these observations Yrvav was named as Yr10vav. The close association between Xpsp3000 and Gli-B1 was also confirmed. The Yr10vav-linked Xpsp3000 allele (285 bp) was not present in 65 Australian cultivars, whereas seven Australian wheats lacking Yr10 carried the same Xpsp3000 allele (260 bp) as Yr10carrying wheat cultivar Moro. Xpsp3000 and/or Gli-B1 could be used in marker-assisted selection for pyramiding Yr10vavor Yr10 with other stripe rust resistance genes. Yr10vav was inherited independently of the T. vavilovii-derived RWA resistance.

+2.71 LOD score at zero recombination is not sufficient for establishing linkage between X-linked mental retardation and X-chromosome markers

Energy Technology Data Exchange (ETDEWEB)

Robledo, R.; Melis, P.; Siniscalco, M. [and others

1996-07-12

Nonspecific X-linked mental retardation (MRX) is the denomination attributed to the familial type of mental retardation compatible with X-linked inheritance but lacking specific phenotypic manifestations. It is thus to be expected that families falling under such broad definition are genetically heterogeneous in the sense that they may be due to different types of mutations occurring, most probably, at distinct X-chromosome loci. To facilitate a genetic classification of these conditions, the Nomenclature Committee of the Eleventh Human Gene Mapping Workshop proposed to assign a unique MRX-serial number to each family where evidence of linkage with one or more X-chromosome markers had been established with a LOD score of at least +2 at zero recombination. This letter is meant to emphasize the inadequacy of this criterion for a large pedigree where the segregation of the disease has been evaluated against the haplotype constitution of the entire X-chromosome carrying the mutation in question. 12 refs., 2 figs., 1 tab.

Glyoxylate, a New Marker Metabolite of Type 2 Diabetes

Science.gov (United States)

Nikiforova, Victoria J.; Giesbertz, Pieter; Wiemer, Jan; Bethan, Bianca; Looser, Ralf; Liebenberg, Volker; Ruiz Noppinger, Patricia; Daniel, Hannelore; Rein, Dietrich

2014-01-01

Type 2 diabetes (T2D) is characterized by a variety of metabolic impairments that are closely linked to nonenzymatic glycation reactions of proteins and peptides resulting in advanced glycation end-products (AGEs). Reactive aldehydes derived from sugars play an important role in the generation of AGEs. Using metabolite profiling to characterize human plasma from diabetic versus nondiabetic subjects we observed in a recent study that the reactive aldehyde glyoxylate was increased before high levels of plasma glucose, typical for a diabetic condition, could be measured. Following this observation, we explored the relevance of increased glyoxylate in diabetic subjects and in diabetic C57BLKS/J-Leprdb/db−/− mice in the pathophysiology of diabetes. A retrospective study using samples of long-term blood donors revealed that glyoxylate levels unlike glucose levels became significantly elevated up to 3 years prior to diabetes diagnosis (difference to control P = 0.034). Elevated glyoxylate levels impact on newly identified mechanisms linking hyperglycemia and AGE production with diabetes-associated complications such as diabetic nephropathy. Glyoxylate in its metabolic network may serve as an early marker in diabetes diagnosis with predictive qualities for associated complications and as potential to guide the development of new antidiabetic therapies. PMID:25525609

Co-regulation analysis of closely linked genes identifies a highly recurrent gain on chromosome 17q25.3 in prostate cancer

International Nuclear Information System (INIS)

Bermudo, Raquel; Martínez-A, Carlos; Ortiz, Ángel R; Fernández, Pedro L; Thomson, Timothy M; Abia, David; Ferrer, Berta; Nayach, Iracema; Benguria, Alberto; Zaballos, Ángel; Rey, Javier del; Miró, Rosa; Campo, Elías

2008-01-01

Transcriptional profiling of prostate cancer (PC) has unveiled new markers of neoplasia and allowed insights into mechanisms underlying this disease. Genomewide analyses have also identified new chromosomal abnormalities associated with PC. The combination of both classes of data for the same sample cohort might provide better criteria for identifying relevant factors involved in neoplasia. Here we describe transcriptional signatures identifying distinct normal and tumoral prostate tissue compartments, and the inference and demonstration of a new, highly recurrent copy number gain on chromosome 17q25.3. We have applied transcriptional profiling to tumoral and non-tumoral prostate samples with relatively homogeneous epithelial representations as well as pure stromal tissue from peripheral prostate and cultured cell lines, followed by quantitative RT-PCR validations and immunohistochemical analysis. In addition, we have performed in silico colocalization analysis of co-regulated genes and validation by fluorescent in situ hybridization (FISH). The transcriptomic analysis has allowed us to identify signatures corresponding to non-tumoral luminal and tumoral epithelium, basal epithelial cells, and prostate stromal tissue. In addition, in silico analysis of co-regulated expression of physically linked genes has allowed us to predict the occurrence of a copy number gain at chromosomal region 17q25.3. This computational inference was validated by fluorescent in situ hybridization, which showed gains in this region in over 65% of primary and metastatic tumoral samples. Our approach permits to directly link gene copy number variations with transcript co-regulation in association with neoplastic states. Therefore, transcriptomic studies of carefully selected samples can unveil new diagnostic markers and transcriptional signatures highly specific of PC, and lead to the discovery of novel genomic abnormalities that may provide additional insights into the causes and mechanisms

Identification and Validation of SNP Markers Linked to Dwarf Traits Using SLAF-Seq Technology in Lagerstroemia

Science.gov (United States)

Ju, Yiqian; Jiao, Yao; Feng, Lu; Pan, Huitang; Cheng, Tangren; Zhang, Qixiang

2016-01-01

The genetic control of plant architecture is a promising approach to breed desirable cultivars, particularly in ornamental flowers. In this study, the F1 population (142 seedlings) derived from Lagerstroemia fauriei (non-dwarf) × L. indica ‘Pocomoke’ (dwarf) was phenotyped for six traits (plant height (PH), internode length (IL), internode number, primary lateral branch height (PLBH), secondary lateral branch height and primary branch number), and the IL and PLBH traits were positively correlated with the PH trait and considered representative indexes of PH. Fifty non-dwarf and dwarf seedlings were pooled and subjected to a specific-locus amplified fragment sequencing (SLAF-seq) method, which screened 1221 polymorphic markers. A total of 3 markers segregating between bulks were validated in the F1 population, with the M16337 and M38412 markers highly correlated with the IL trait and the M25207 marker highly correlated with the PLBH trait. These markers provide a predictability of approximately 80% using a single marker (M25207) and a predictability of 90% using marker combinations (M16337 + M25207) in the F1 population, which revealed that the IL and the PLBH traits, especially the PLBH, were the decisive elements for PH in terms of molecular regulation. Further validation was performed in the BC1 population and a set of 28 Lagerstroemia stocks using allele-specific PCR (AS-PCR) technology, and the results showed the stability and reliability of the SNP markers and the co-determination of PH by multiple genes. Our findings provide an important theoretical and practical basis for the early prediction and indirect selection of PH using the IL and the PLBH, and the detected SNPs may be useful for marker-assisted selection (MAS) in crape myrtle. PMID:27404662

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Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations

Directory of Open Access Journals (Sweden)

Yang Hsin-Chou

2012-07-01

Full Text Available Abstract Background Ancestry informative markers (AIMs are a type of genetic marker that is informative for tracing the ancestral ethnicity of individuals. Application of AIMs has gained substantial attention in population genetics, forensic sciences, and medical genetics. Single nucleotide polymorphisms (SNPs, the materials of AIMs, are useful for classifying individuals from distinct continental origins but cannot discriminate individuals with subtle genetic differences from closely related ancestral lineages. Proof-of-principle studies have shown that gene expression (GE also is a heritable human variation that exhibits differential intensity distributions among ethnic groups. GE supplies ethnic information supplemental to SNPs; this motivated us to integrate SNP and GE markers to construct AIM panels with a reduced number of required markers and provide high accuracy in ancestry inference. Few studies in the literature have considered GE in this aspect, and none have integrated SNP and GE markers to aid classification of samples from closely related ethnic populations. Results We integrated a forward variable selection procedure into flexible discriminant analysis to identify key SNP and/or GE markers with the highest cross-validation prediction accuracy. By analyzing genome-wide SNP and/or GE markers in 210 independent samples from four ethnic groups in the HapMap II Project, we found that average testing accuracies for a majority of classification analyses were quite high, except for SNP-only analyses that were performed to discern study samples containing individuals from two close Asian populations. The average testing accuracies ranged from 0.53 to 0.79 for SNP-only analyses and increased to around 0.90 when GE markers were integrated together with SNP markers for the classification of samples from closely related Asian populations. Compared to GE-only analyses, integrative analyses of SNP and GE markers showed comparable testing

Marker-assisted pyramiding of Thinopyrumderived leaf rust ...

Indian Academy of Sciences (India)

2017-03-20

Mar 20, 2017 ... resistance genes Lr19 and Lr24 using marker assisted foreground .... is linked with stem rust resistance gene Sr24(McIntosh et al. 1976). .... Received 29 July 2016, in final revised form 3 March 2017; accepted 16 March 2017.

Serum hepatitis B core-related antigen is a satisfactory surrogate marker of intrahepatic covalently closed circular DNA in chronic hepatitis B.

Science.gov (United States)

Chen, En-Qiang; Feng, Shu; Wang, Meng-Lan; Liang, Ling-Bo; Zhou, Ling-Yun; Du, Ling-Yao; Yan, Li-Bo; Tao, Chuan-Min; Tang, Hong

2017-03-14

Recently, hepatitis B core-related antigen (HBcrAg) has been suggested as an additional marker of hepatitis B virus (HBV) infection. This study aimed to investigate whether serum quantitative HBcrAg (qHBcrAg) was a satisfactory surrogate marker of intrahepatic covalently closed circular DNA (cccDNA). A total of 139 patients with liver biopsy were enrolled, consisting of 59 patients in immune tolerance (IT) phase, 52 patients in immune clearance (IC) phase, 18 patients in low-replication (LR) phase, and 10 patients in reactivation phase. All patients in IC phase have received entecavir (ETV) therapy, and 32 of them undergone a second liver biopsy at 24 months. Among those patients, qHBcrAg was strongly correlated with intrahepatic cccDNA, which is superior to that of qHBsAg and HBV DNA. And similar findings were also observed in patients in IT, IC, LR and reactivation phases. Among the 32 ETV-treated patients with a second liver biopsy in IC phase, the decline of intrahepatic cccDNA was accompanied by changes in both qHBcrAg and qHBsAg. However, as compared to qHBsAg, the change of qHBcrAg was more strongly associated with intrahepatic cccDNA-decline. In summary, serum qHBcrAg should be a satisfactory surrogate of intrahepatic HBV cccDNA in CHB patients.

Genetics Home Reference: X-linked creatine deficiency

Science.gov (United States)

... Health Conditions X-linked creatine deficiency X-linked creatine deficiency Printable PDF Open All Close All Enable ... view the expand/collapse boxes. Description X-linked creatine deficiency is an inherited disorder that primarily affects ...

Genetics Home Reference: X-linked sideroblastic anemia

Science.gov (United States)

... Conditions X-linked sideroblastic anemia X-linked sideroblastic anemia Printable PDF Open All Close All Enable Javascript ... the expand/collapse boxes. Description X-linked sideroblastic anemia is an inherited disorder that prevents developing red ...

Radiographic markers - A reservoir for bacteria?

International Nuclear Information System (INIS)

Tugwell, Jenna; Maddison, Adele

2011-01-01

Introduction: Amongst the most frequently handled objects in the radiology department are radiographic markers. They are personal accessories used with every patient, and are kept in the radiographers pockets when not utilised. Upon enquiry it was discovered that many radiographers disregarded the potential of these accessories to become a vector for cross-contamination thus never or rarely clean them. The aims of this study were therefore to identify if radiographic markers are a reservoir for bacteria and to establish an effective cleaning method for decontaminating them. Methodology: 25 radiographers/student radiographers were selected for this study. Swabbing of their markers prior and post cleaning took place. The microbiology laboratory subsequently analyzed the results by quantifying and identifying the bacteria present. The participants also completed a closed questionnaire regarding their markers (e.g. frequency of cleaning and type of marker) to help specify the results gained from the swabbing procedure. Results: From the sample swabbed, 92% were contaminated with various organisms including Staphylococcus and Bacillus species, the amount of bacteria present ranged from 0 to >50 CFU. There were no significant differences between disinfectant wipes and alcohol gel in decontaminating the markers. Both successfully reduced their bacterial load, with 80% of the markers post cleaning having 0 CFU. Conclusion: The results indicated that radiographic markers can become highly contaminated with various organisms thus serve as a reservoir for bacteria. In addition, the markers need to be cleaned on a regular basis, with either disinfectant wipes or alcohol gel to reduce their bacterial load.

Specific gut microbiota features and metabolic markers in postmenopausal women with obesity

DEFF Research Database (Denmark)

Brahe, Lena Kirchner; Le Chatelier, E; Prifti, E

2015-01-01

BACKGROUND: Gut microbial gene richness and specific bacterial species are associated with metabolic risk markers in humans, but the impact of host physiology and dietary habits on the link between the gut microbiota and metabolic markers remain unclear. The objective of this study was to identify...

Beclin 1 Expression is Closely Linked to Colorectal Carcinogenesis and Distant Metastasis of Colorectal Carcinoma

Directory of Open Access Journals (Sweden)

Mei-Ying Zhang

2014-08-01

Full Text Available Beclin 1 participates in development, autophagy, differentiation, anti- apoptosis, neurodegeneration, tumorigenesis and cancer progression. The roles of Beclin 1 in colorectal carcinogenesis and its subsequent progression are still unclear. Here, the mRNA and protein expression of Beclin 1 were determined in colorectal carcinoma and matched mucosa by Reverse transcriptase-polymerase chain reaction and Western blot. Immunohistochemistry and in situ hybridization (ISH were performed on tissue microarryer with colorectal carcinoma, adenoma and mucosa. The expression of Beclin 1 mRNA and protein was found to be higher in colorectal carcinoma than matched mucosa by real-time PCR and Western blot (p < 0.05. According to the ISH data, Beclin 1 expression was lower in colorectal non-neoplastic mucosa (NNM than adenoma and carcinoma (p < 0.05. Immunohistochemically, primary carcinoma showed stronger Beclin 1 expression than NNM and metastatic carcinoma in the liver (p < 0.05. Beclin 1 protein expression was negatively related to liver and distant metastasis (p < 0.05, but not correlated with age, sex, depth of invasion, lymphatic or venous invasion, lymph node metastasis, tumor-node-metastasis (TNM staging, differentiation or serum carcinoembryonic antigen (CEA concentration (p > 0.05. Survival analysis indicated that Beclin 1 expression was not linked to favorable prognosis of the patients with colorectal carcinoma (p > 0.05. Cox’s model indicated that depth of invasion and distant metastasis were independent prognostic factors for colorectal carcinomas (p < 0.05. It was suggested that Beclin 1 expression is closely linked to colorectal carcinogenesis and distant metastasis of colorectal carcinoma.

Suitability and use of two molecular markers to track race-specific ...

African Journals Online (AJOL)

Molecular markers linked to resistance to different races of S. gesneriodes have been identified. It was desirable to demonstrate the applicability and efficiency for use in ... The two marker data set were significantly correlated with the phenotypic data (r=0.95). Based on the tight linkage with the resistant locus, 61RM2 was ...

Pornography use and closeness with others in women

Directory of Open Access Journals (Sweden)

Popović Miodrag

2011-01-01

Full Text Available Introduction. Closeness/intimacy and pornography are sometimes linked and frequently presented as competing with each other. They have been the subject of some research but many issues in the area remain controversial and indeterminate. Objective. The aim of this pilot study was to establish whether female pornography users and non-users’ ratings in terms of socio-emotional closeness differed, i.e. to examine the association between pornography use and aspects of socio-emotional closeness in a non-clinical sample of females. Methods. Sixty-six females participated in the study. Their actual and ideal socioemotional closeness was measured by the Perceived Interpersonal Closeness Scale/PICS, while their pornography use was examined by the Background and Pornography Use Information Questionnaire. Potential links between the two variables and comparisons with the relevant results obtained by males are presented. Results. The results showed that there were no significant differences between self-reported female pornography users and non-users in terms of total closeness numbers and scores and also in specific socioemotional closeness with the most significant adults in their lives (i.e., partners, closest friends, mothers and fathers. Conclusion. The results confirmed that there were differences between females and males’ approaches to pornography and closeness; females had lower interest in pornography and their use of it had not been associated with higher total closeness numbers and scores. Due to the participant group’s size (N limitations, this sample was rather used for preliminary investigations that would enable some elementary insight into females’ relevant behaviours. Further investigations of pornography’s complex links with socio-emotional and sexual closeness on larger samples may allow more reliable comparisons between gender and pornography users groups.

Analysis of the discriminative methods for diagnosis of benign and malignant solitary pulmonary nodules based on serum markers.

Science.gov (United States)

Wang, Wanping; Liu, Mingyue; Wang, Jing; Tian, Rui; Dong, Junqiang; Liu, Qi; Zhao, Xianping; Wang, Yuanfang

2014-01-01

Screening indexes of tumor serum markers for benign and malignant solitary pulmonary nodules (SPNs) were analyzed to find the optimum method for diagnosis. Enzyme-linked immunosorbent assays, an automatic immune analyzer and radioimmunoassay methods were used to examine the levels of 8 serum markers in 164 SPN patients, and the sensitivity for differential diagnosis of malignant or benign SPN was compared for detection using a single plasma marker or a combination of markers. The results for serological indicators that closely relate to benign and malignant SPNs were screened using the Fisher discriminant analysis and a non-conditional logistic regression analysis method, respectively. The results were then verified by the k-means clustering analysis method. The sensitivity when using a combination of serum markers to detect SPN was higher than that using a single marker. By Fisher discriminant analysis, cytokeratin 19 fragments (CYFRA21-1), carbohydrate antigen 125 (CA125), squamous cell carcinoma antigen (SCC) and breast cancer antigen (CA153), which relate to the benign and malignant SPNs, were screened. Through non-conditional logistic regression analysis, CYFRA21-1, SCC and CA153 were obtained. Using the k-means clustering analysis, the cophenetic correlation coefficient (0.940) obtained by the Fisher discriminant analysis was higher than that obtained with logistic regression analysis (0.875). This study indicated that the Fisher discriminant analysis functioned better in screening out serum markers to recognize the benign and malignant SPN. The combined detection of CYFRA21-1, CA125, SCC and CA153 is an effective way to distinguish benign and malignant SPN, and will find an important clinical application in the early diagnosis of SPN. © 2014 S. Karger GmbH, Freiburg.

Performance Benefits with Scene-Linked HUD Symbology: An Attentional Phenomenon?

Science.gov (United States)

Levy, Jonathan L.; Foyle, David C.; McCann, Robert S.; Null, Cynthia H. (Technical Monitor)

1999-01-01

Previous research has shown that in a simulated flight task, navigating a path defined by ground markers while maintaining a target altitude is more accurate when an altitude indicator appears in a virtual "scenelinked" format (projected symbology moving as if it were part of the out-the-window environment) compared to the fixed-location, superimposed format found on present-day HUDs (Foyle, McCann & Shelden, 1995). One explanation of the scene-linked performance advantage is that attention can be divided between scene-linked symbology and the outside world more efficiently than between standard (fixed-position) HUD symbology and the outside world. The present study tested two alternative explanations by manipulating the location of the scene-linked HUD symbology relative to the ground path markers. Scene-linked symbology yielded better ground path-following performance than standard fixed-location superimposed symbology regardless of whether the scene-linked symbology appeared directly along the ground path or at various distances off the path. The results support the explanation that the performance benefits found with scene-linked symbology are attentional.

Molecular markers of neuropsychological functioning and Alzheimer's disease.

Science.gov (United States)

Edwards, Melissa; Balldin, Valerie Hobson; Hall, James; O'Bryant, Sid

2015-03-01

The current project sought to examine molecular markers of neuropsychological functioning among elders with and without Alzheimer's disease (AD) and determine the predictive ability of combined molecular markers and select neuropsychological tests in detecting disease presence. Data were analyzed from 300 participants (n = 150, AD and n = 150, controls) enrolled in the Texas Alzheimer's Research and Care Consortium. Linear regression models were created to examine the link between the top five molecular markers from our AD blood profile and neuropsychological test scores. Logistical regressions were used to predict AD presence using serum biomarkers in combination with select neuropsychological measures. Using the neuropsychological test with the least amount of variance overlap with the molecular markers, the combined neuropsychological test and molecular markers was highly accurate in detecting AD presence. This work provides the foundation for the generation of a point-of-care device that can be used to screen for AD.

Collagen derived serum markers in carcinoma of the prostate

DEFF Research Database (Denmark)

Rudnicki, M; Jensen, L T; Iversen, P

1995-01-01

Three new collagen markers deriving from the collagenous matrix, e.g. carboxyterminal propeptide of type I procollagen (PICP), carboxy-terminal pyridinoline cross-linked telopeptide of type I collagen (ICTP), and aminoterminal propeptide of type III procollagen (PIIINP) were used for the diagnose......, ICTP, and PICP did not differ between these two groups. In patients with metastatic prostatic cancer all five markers were increased compared to the level measured in patients with localized cancer (p

Prenatal exclusion of Norrie disease with flanking DNA markers.

Science.gov (United States)

Gal, A; Uhlhaas, S; Glaser, D; Grimm, T

1988-10-01

Three polymorphic DNA markers linked to the locus of Norrie disease were used for indirect genotype analysis in a ten-wk-old fetus at risk for the disease. When haplotypes of the family members and the estimated recombination frequency between Norrie gene and each of the DNA marker loci DXS7, DXS84, and DXS146 were taken into account, the risk that the fetus had inherited the mutation was about 1%.

A new nonsyndromic X-linked sensorineural hearing impairment linked to Xp21.2

Energy Technology Data Exchange (ETDEWEB)

Lalwani, A.K.; Brister, J.R.; Fex, J.; Grundfast, K.M.; Pikus, A.T.; Ploplis, B.; San Agustin, T.; Skarka, H.; Wilcox, E.R. [National Institutes of Health, Bethesda, MD (United States)

1994-10-01

X-linked deafness is a rare cause of hereditary hearing impairment. We have identified a family with X-linked dominant sensorineural hearing impairment, characterized by incomplete penetrance and variable expressivity in carrier females, that is linked to the Xp21.2, which contains the Duchenne muscular dystrophy (DMD) locus. The auditory impairment in affected males was congenital, bilateral, profound, sensorineural, affecting all frequencies, and without evidence of radiographic abnormality of the temporal bone. Adult carrier females manifested bilateral, mild-to-moderate high-frequency sensorineural hearing impairment of delayed onset during adulthood. Eighteen commercially available polymorphic markers from the X chromosome, generating a 10-15-cM map, were initially used for identification of a candidate region. DXS997, located within the DMD gene, generated a two-point LOD score of 2.91 at {theta} = 0, with every carrier mother heterozygous at this locus. Recombination events at DXS992 (located within the DMD locus, 3{prime} to exon 50 of the dystrophin gene) and at DXS1068 (5{prime} to the brain promoter of the dystrophin gene) were observed. No recombination events were noted with the following markers within the DMD locus: 5{prime}DYS II, intron 44, DXS997, and intron 50. There was no clinical evidence of Duchenne or Becker muscular dystrophy in any family member. It is likely that this family represents a new locus on the X chromosome, which when mutated results in nonsyndromic sensorineural hearing loss and is distinct from the heterogeneous group of X-linked hearing losses that have been previously described. 57 refs., 6 figs., 1 tab.

Preliminary Research on Discourse Markers and Politeness in the Spanish of the United States

Directory of Open Access Journals (Sweden)

Tania Constanza Gómez Ríos

2016-07-01

Full Text Available This preliminary study determines the dynamics of the discourse markers and politeness in sociolinguistic interviews among Spanish speakers living in the Chicago area. The analysis is based on theories of social relations and politeness strategies (Brown and Levinson, 1987 and Bravo, 1999. By analyzing the markers within the turn organization (i.e. beginning of the turn and during the turn development, this study revealed that speakers make use of three main types of markers: connectors, modals, and appellatives. The findings suggest that the selection of a marker maintains a close relationship with the speaker’s main goal in the conversation. Either, the speaker detaches himself/herself from the interlocutor or he/she gets close to him/her. Thus, the speaker employs mitigation or intensification strategies through various linguistic forms or pauses that appear with the marker or within the turn. This study with Spanish speakers living in the area of Chicago confirms, as other studies in Spanish, that the interaction between markers and politeness is conditioned to the context and the role of the speakers.

Mapping the x-linked lymphoproliferative syndrome

International Nuclear Information System (INIS)

Skare, J.C.; Milunsky, A.; Byron, K.S.; Sullivan, J.L.

1987-01-01

The X-linked lymphoproliferative syndrome is triggered by Epstein-Barr virus infection and results in fatal mononucleosis, immunodeficiency, and lymphoproliferative disorders. This study shows that the mutation responsible for X-linked lymphoproliferative syndrome is genetically linked to a restriction fragment length polymorphism detected with the DXS42 probe (from Xq24-q27). The most likely recombination frequency between the loci is 4%, and the associated logarithm of the odds is 5.26. Haplotype analysis using flanking restriction fragment length polymorphism markers indicates that the locus for X-linked lymphoproliferative syndrome is distal to probe DXS42 but proximal to probe DXS99 (from Xq26-q27). It is now possible to predict which members of a family with X-linked lymphoproliferative syndrome are carrier females and to diagnose the syndrome prenatally

Mapping the x-linked lymphoproliferative syndrome

Energy Technology Data Exchange (ETDEWEB)

Skare, J.C.; Milunsky, A.; Byron, K.S.; Sullivan, J.L.

1987-04-01

The X-linked lymphoproliferative syndrome is triggered by Epstein-Barr virus infection and results in fatal mononucleosis, immunodeficiency, and lymphoproliferative disorders. This study shows that the mutation responsible for X-linked lymphoproliferative syndrome is genetically linked to a restriction fragment length polymorphism detected with the DXS42 probe (from Xq24-q27). The most likely recombination frequency between the loci is 4%, and the associated logarithm of the odds is 5.26. Haplotype analysis using flanking restriction fragment length polymorphism markers indicates that the locus for X-linked lymphoproliferative syndrome is distal to probe DXS42 but proximal to probe DXS99 (from Xq26-q27). It is now possible to predict which members of a family with X-linked lymphoproliferative syndrome are carrier females and to diagnose the syndrome prenatally.

Genetic mapping, marker assisted selection and allelic relationships for the Pu 6 gene conferring rust resistance in sunflower.

Science.gov (United States)

Bulos, Mariano; Vergani, Pablo Nicolas; Altieri, Emiliano

2014-09-01

Rust resistance in the sunflower line P386 is controlled by Pu 6 , a gene which was reported to segregate independently from other rust resistant genes, such as R 4 . The objectives of this work were to map Pu 6 , to provide and validate molecular tools for its identification, and to determine the linkage relationship of Pu 6 and R 4 . Genetic mapping of Pu 6 with six markers covered 24.8 cM of genetic distance on the lower end of linkage Group 13 of the sunflower consensus map. The marker most closely linked to Pu 6 was ORS316 at 2.5 cM in the distal position. ORS316 presented five alleles when was assayed with a representative set of resistant and susceptible lines. Allelism test between Pu 6 and R 4 indicated that both genes are linked at a genetic distance of 6.25 cM. This is the first confirmation based on an allelism test that at least two members of the R adv /R 4 /R 11 / R 13a /R 13b /Pu 6 cluster of genes are at different loci. A fine elucidation of the architecture of this complex locus will allow designing and constructing completely new genomic regions combining genes from different resistant sources and the elimination of the linkage drag around each resistant gene.

Identificação e validação de marcadores microssatélites ligados ao gene Rpp5 de resistência à ferrugem-asiática-da-soja Identification and validation of microsatellite markers linked to the Rpp5 gene conferring resistance to Asian soybean rust

Directory of Open Access Journals (Sweden)

Thaiza Galhardo Silva Morceli

2008-11-01

Full Text Available O objetivo deste trabalho foi identificar novos marcadores microssatélites, ligados ao gene Rpp5 de resistência à ferrugem-da-soja, e validar os marcadores previamente mapeados, para que possam ser utilizados em programas de seleção assistida por marcadores moleculares (SAM. Para tanto, uma população F2 com 100 indivíduos, derivada do cruzamento entre a PI 200526 e a cultivar Coodetec 208, suscetível à ferrugem, foi artificialmente infectada e avaliada quanto à sua reação de resistência à ferrugem. Marcadores microssatélites foram testados nos genitores e em dois "bulks" contrastantes, para a identificação de marcadores ligados. Dois novos marcadores, potencialmente associados à resistência, foram testados em plantas individuais, e se constatou que eles estão ligados ao gene Rpp5 e estão presentes no grupo de ligação N da soja. A eficiência de seleção foi determinada em relação a todos os marcadores ligados ao gene Rpp5, e a combinação entre os marcadores Sat_275+Sat_280 foi de 100%.The main objective of this work was to identify new microsatellite markers, linked to the Rpp5 resistance gene to Asian soybean rust, and to validate previously mapped markers for use in marker-assisted selection (MAS programs. To this end, a F2 population with 100 individuals, derived from crossing between PI 200526 and cultivar Coodetec 208, susceptible to rust, was artificially infected and evaluated for its reaction of resistance to rust. Microsatellite markers were tested on parents and in the two contrasting bulks to identifying linked markers. Two new markers, potentially associated with resistance, were tested in individual plants, and they were found to be linked to gene Rpp5 and to be present in the N linkage group of soybean. The selection efficiencies were determined for all markers linked to gene Rpp5, and the combination of the markers Sat_275+Sat_280 was 100%.

Can bone metabolism markers be adopted as an alternative to scintigraphic imaging in monitoring bone metastases from breast cancer?

International Nuclear Information System (INIS)

Bombardieri, E.; Martinetti, A.; Castellani, M.R.; Seregni, E.; Miceli, R.; Mariani, L.

1997-01-01

Bone scintigraphy plays a major role in the diagnosis of bone metastases. The clinical utility of new biochemical markers of bone metabolism has recently been investigated in various bone diseases. This study evaluated the role of some bone metabolism markers in comparison with bone scan in the follow-up of breast cancer patients. We studied 149 patients with breast cancer, 33 (22%) of whom had bone metastases. IRMAs were used for the evaluation of blood levels of osteocalcin, bone alkaline phosphatase (BAP), the C-terminal propeptide of type I procollagen and the C-terminal cross-linked telopeptide of type I collagen (ICTP). Multivariate regression analysis showed that menopausal status (P=0.007) and metastatic bone lesions (P=0.001) affected bone marker levels. When considering post-menopausal women, the only subset in which bone metabolism marker behaviour could be reliably investigated, we found a high degree of overlap in marker distribution for scan-positive and scan-negative patients. Discrimination between scan-negative and scan-positive patients based on the above markers, taken singly or jointly, was assessed by means of logistic discriminant analysis. The best discrimination was achieved with BAP, closely followed by ICTP. BAP and ICTP together gave a slight improvement over the use of the two markers separately. However, even in this case the degree of discrimination was poor and its clinical utility was limited. In fact, to achieve a specificity of 95%, the sensitivity of the test was about 20%; conversely, with a sensitivity of 95%, the specificity was below 10%. In conclusion, based on our findings, we believe that blood levels of the investigated markers cannot replace bone scintigraphy in the follow-up of breast cancer patients for the early detection of bone metastases. (orig.)

Decouplink: Dynamic Links for Java

DEFF Research Database (Denmark)

Jensen, Martin Lykke Rytter; Jørgensen, Bo Nørregaard

2011-01-01

of dimensions of extension that can be exploited without performing modification of existing types. Thus, dynamic links make it possible to enforce the open/closed principle in situations where it would otherwise not be possible. We present Decouplink – a library-based implementation of dynamic links for Java...

Advances in plant gene-targeted and functional markers: a review

Directory of Open Access Journals (Sweden)

Poczai Péter

2013-02-01

Full Text Available Abstract Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information

Advances in plant gene-targeted and functional markers: a review

Science.gov (United States)

2013-01-01

Public genomic databases have provided new directions for molecular marker development and initiated a shift in the types of PCR-based techniques commonly used in plant science. Alongside commonly used arbitrarily amplified DNA markers, other methods have been developed. Targeted fingerprinting marker techniques are based on the well-established practices of arbitrarily amplified DNA methods, but employ novel methodological innovations such as the incorporation of gene or promoter elements in the primers. These markers provide good reproducibility and increased resolution by the concurrent incidence of dominant and co-dominant bands. Despite their promising features, these semi-random markers suffer from possible problems of collision and non-homology analogous to those found with randomly generated fingerprints. Transposable elements, present in abundance in plant genomes, may also be used to generate fingerprints. These markers provide increased genomic coverage by utilizing specific targeted sites and produce bands that mostly seem to be homologous. The biggest drawback with most of these techniques is that prior genomic information about retrotransposons is needed for primer design, prohibiting universal applications. Another class of recently developed methods exploits length polymorphism present in arrays of multi-copy gene families such as cytochrome P450 and β-tubulin genes to provide cross-species amplification and transferability. A specific class of marker makes use of common features of plant resistance genes to generate bands linked to a given phenotype, or to reveal genetic diversity. Conserved DNA-based strategies have limited genome coverage and may fail to reveal genetic diversity, while resistance genes may be under specific evolutionary selection. Markers may also be generated from functional and/or transcribed regions of the genome using different gene-targeting approaches coupled with the use of RNA information. Such techniques have the

Analytical characterisation of glutardialdehyde cross-linking products in gelatine-gum arabic complex coacervates

Energy Technology Data Exchange (ETDEWEB)

Fuguet, Elisabet [Advanced Measurement and Imaging, Unilever Food and Health Research Institute, Olivier van Noortlaan 120, 3133 AT Vlaardingen (Netherlands)], E-mail: eli.fuguet@gmail.com; Platerink, Chris van [Advanced Measurement and Imaging, Unilever Food and Health Research Institute, Olivier van Noortlaan 120, 3133 AT Vlaardingen (Netherlands); Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht (Netherlands); Janssen, Hans-Gerd [Advanced Measurement and Imaging, Unilever Food and Health Research Institute, Olivier van Noortlaan 120, 3133 AT Vlaardingen (Netherlands); van' t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam (Netherlands)

2007-11-26

Encapsulates having shells of cross-linked mixtures of proteins and polysaccharides are widely used in the food and pharmaceutical industry for controlled release of actives and flavour compounds. In order to be able to predict the behaviour and the release characteristics of the microcapsules, a better understanding of the nature and extent of the cross-linking reaction is needed. Several analytical techniques were applied for the characterisation of glutardialdehyde (GDA) cross-linked encapsulates made of gelatine and gum arabic. To allow the use of sensitive, high-resolution methods such as chromatography and mass spectrometry, the sample first had to be hydrolysed. In this way, a mixture of amino acids, small peptides and the cross-link moieties was obtained. High-resolution liquid chromatography coupled to high-resolution mass spectrometry (HPLC-MS) was applied to detect possible cross-link markers through a comparison of HPLC-MS mass-chromatograms obtained for cross-linked and non-cross-linked coacervates. HPLC-MS/MS was used to identify the species responsible for the differences. Cross-linking occurred between GDA molecules and lysine and hydroxylysine {epsilon}-amino groups, and up to eight cross-link products of different nature could be identified. They included pyridinium ions and Schiff bases, and also unreacted GDA condensation products. Next, based on the insight gained in the possible chemical structures present in the cross-link markers, methods for selective labelling of these functionalities were employed to allow easier detection of related reaction products. Both liquid chromatography (LC) and gas chromatography (GC) were used in these experiments. Unfortunately, these approaches failed to detect new cross-link markers, most likely as a result of the low levels at which these are present.

Analytical characterisation of glutardialdehyde cross-linking products in gelatine-gum arabic complex coacervates

International Nuclear Information System (INIS)

Fuguet, Elisabet; Platerink, Chris van; Janssen, Hans-Gerd

2007-01-01

Encapsulates having shells of cross-linked mixtures of proteins and polysaccharides are widely used in the food and pharmaceutical industry for controlled release of actives and flavour compounds. In order to be able to predict the behaviour and the release characteristics of the microcapsules, a better understanding of the nature and extent of the cross-linking reaction is needed. Several analytical techniques were applied for the characterisation of glutardialdehyde (GDA) cross-linked encapsulates made of gelatine and gum arabic. To allow the use of sensitive, high-resolution methods such as chromatography and mass spectrometry, the sample first had to be hydrolysed. In this way, a mixture of amino acids, small peptides and the cross-link moieties was obtained. High-resolution liquid chromatography coupled to high-resolution mass spectrometry (HPLC-MS) was applied to detect possible cross-link markers through a comparison of HPLC-MS mass-chromatograms obtained for cross-linked and non-cross-linked coacervates. HPLC-MS/MS was used to identify the species responsible for the differences. Cross-linking occurred between GDA molecules and lysine and hydroxylysine ε-amino groups, and up to eight cross-link products of different nature could be identified. They included pyridinium ions and Schiff bases, and also unreacted GDA condensation products. Next, based on the insight gained in the possible chemical structures present in the cross-link markers, methods for selective labelling of these functionalities were employed to allow easier detection of related reaction products. Both liquid chromatography (LC) and gas chromatography (GC) were used in these experiments. Unfortunately, these approaches failed to detect new cross-link markers, most likely as a result of the low levels at which these are present

Scandinavian links

DEFF Research Database (Denmark)

Matthiessen, Christian Wichmann; Knowles, Richard D.

2014-01-01

are impressive mega structures spanning international waterways. These waterways between the Baltic Sea and the North Sea have played major roles in history. The length of each of the crossings are around 20 km. The fixed links closes gaps between the Scandinavian and European motorway and rail networks...

Novel Technique for Hepatic Fiducial Marker Placement for Stereotactic Body Radiation Therapy

International Nuclear Information System (INIS)

Jarraya, Hajer; Chalayer, Chloé; Tresch, Emmanuelle; Bonodeau, Francois; Lacornerie, Thomas; Mirabel, Xavier; Boulanger, Thomas; Taieb, Sophie; Kramar, Andrew; Lartigau, Eric; Ceugnart, Luc

2014-01-01

Purpose: To report experience with fiducial marker insertion and describe an advantageous, novel technique for fiducial placement in the liver for stereotactic body radiation therapy with respiratory tracking. Methods and Materials: We implanted 1444 fiducials (single: 834; linked: 610) in 328 patients with 424 hepatic lesions. Two methods of implantation were compared: the standard method (631 single fiducials) performed on 153 patients from May 2007 to May 2010, and the cube method (813 fiducials: 610 linked/203 single) applied to 175 patients from April 2010 to March 2013. The standard method involved implanting a single marker at a time. The novel technique entailed implanting 2 pairs of linked markers when possible in a way to occupy the perpendicular edges of a cube containing the tumor inside. Results: Mean duration of the cube method was shorter than the standard method (46 vs 61 minutes; P<.0001). Median numbers of skin and subcapsular entries were significantly smaller with the cube method (2 vs 4, P<.0001, and 2 vs 4, P<.0001, respectively). The rate of overall complications (total, major, and minor) was significantly lower in the cube method group compared with the standard method group (5.7% vs 13.7%; P=.013). Major complications occurred while using single markers only. The success rate was 98.9% for the cube method and 99.3% for the standard method. Conclusions: We propose a new technique of hepatic fiducial implantation that makes use of linked fiducials and involves fewer skin entries and shorter time of implantation. The technique is less complication-prone and is migration-resistant

Shuttle Planning for Link Closures in Urban Public Transport Networks

NARCIS (Netherlands)

van der Hurk, E.; Koutsopoulos, H.; Wilson, N.H.M.; Kroon, L.G.; Maroti, G.

2016-01-01

Urban public transport systems must periodically close certain links for maintenance, which can have significant effects on the service provided to passengers. In practice, the effects of closures are mitigated by replacing the closed links with a simple shuttle service. However, alternative shuttle

Marker assisted characterization of chickpea genotypes for wilt ...

African Journals Online (AJOL)

Further, the sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) analysis of seed storage protein showed a difference in protein profile among studied genotypes but none of polypeptide fragment was specific to wilt resistance or susceptibility. In present study, the reported markers linked to susceptibility ...

Analysis of fourth-grade flat machines with movable close-cycle formed by the rods and two complex links

Directory of Open Access Journals (Sweden)

S.О. Koshel

2016-09-01

Full Text Available Complex multielement mechanisms are increasingly used in the technical equipment of consumer industry. The lack of a universal method of kinematic research of these mechanisms asserts the relevance of work on the kinematic analysis of multielement mechanisms. Aim: The aim of this research is to develop an algorithm kinetic research of velocities of the points that coincide with geometric centers kinematic pairs of structure group of the 4th class and 3rd order with movable close-cycle formed by connecting rod and two complex links. Materials and Methods: The graphic-analytical method of a kinematic research will be used to achieve the goals of research. Development of an algorithm is based on provisions of the theory of mechanisms and engines about property of high classes mechanisms to change its class depending on another possible initial mechanism chosen conditionally which comes to structure of the conducted structural groups of the mechanism links and provisions of theoretical mechanics relatively to instantaneous center of speeds. Results: Velocity vectors of points of Assur group links of the 4th class and 3rd order of the composite flat mechanism are determined by a graphic-analytical method, where the initial mechanism speeds that led to decrease of a class of the mechanism and allowed to investigate it. Unlike the known erroneous statements method which is applied to research the structural groups of the 3rd class, the offered algorithm of the kinematic analysis allows to investigate mechanisms of the 4th class without need to rebuild the plan which was constructed in a uncertain scale, with the subsequent calculation of the real scale parameter of provided plotting of a graph.

Screening and identification of a microsatellite marker associated with sex in Wami tilapia, Oreochromis urolepis hornorum.

Science.gov (United States)

Zhu, Huaping; Liu, Zhigang; Lu, Maixin; Gao, Fengying; Ke, Xiaoli; Ma, Dongmei; Huang, Zhanghan; Cao, Jianmeng; Wang, Miao

2016-06-01

In this study, primer pairs of 15 microsatellite markers associated with sex determination of tilapia were selected and amplified in Wami tilapia, Oreochromis urolepis hornorum. While one marker, UNH168, on linkage group 3 (LG3) was associated (P tilapia chromosome pair (chromosome 1, equivalent to LG3). This sex-linked microsatellite marker could potentially be used for marker-assisted selection in tilapia breeding programmes to produce monosex male tilapia.

Screening and characterization a RAPD marker of tobacco brown ...

African Journals Online (AJOL)

RAPD) methods were used to analyze F2 individuals of 82-3041 × Yunyan 84 to screen and characterize the molecular marker linked to brown-spot resistant gene. A total of 800 arbitrary decamer oligonucleotide primers were used for RAPD ...

Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks.

Science.gov (United States)

Billiard, Sylvain; Ferrière, Régis; Méléard, Sylvie; Tran, Viet Chi

2015-11-01

How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.

Enzyme-linked immunosorbent assay (ELISA) for the anthropogenic marker isolithocholic acid in water.

Science.gov (United States)

Baldofski, Stefanie; Hoffmann, Holger; Lehmann, Andreas; Breitfeld, Stefan; Garbe, Leif-Alexander; Schneider, Rudolf J

2016-11-01

Bile acids are promising chemical markers to assess the pollution of water samples with fecal material. This study describes the optimization and validation of a direct competitive enzyme-linked immunosorbent assay for the bile acid isolithocholic acid (ILA). The quantification range of the optimized assay was between 0.09 and 15 μg/L. The assay was applied to environmental water samples. Most studies until now were focused on bile acid fractions in the particulate phase of water samples. In order to avoid tedious sample preparation, we undertook to evaluate the dynamics and significance of ILA levels in the aqueous phase. Very low concentrations in tap and surface water samples made a pre-concentration step necessary for this matrix as well as for wastewater treatment plant (WWTP) effluent. Mean recoveries for spiked water samples were between 97% and 109% for tap water and WWTP influent samples and between 102% and 136% for WWTP effluent samples. 90th percentiles of intra-plate and inter-plate coefficients of variation were below 10% for influents and below 20% for effluents and surface water. ILA concentrations were quantified in the range of 33-72 μg/L in influent, 21-49 ng/L in effluent and 18-48 ng/L in surface water samples. During wastewater treatment the ILA levels were reduced by more than 99%. ILA concentrations of influents determined by ELISA and LC-MS/MS were in good agreement. However, findings in LC-ELISA experiments suggest that the true ILA levels in concentrated samples are lower due to interfering effects of matrix compounds and/or cross-reactants. Yet, the ELISA will be a valuable tool for the performance check and comparison of WWTPs and the localization of fecal matter input into surface waters. Copyright © 2016 Elsevier Ltd. All rights reserved.

Gender Identification in Date Palm Using Molecular Markers.

Science.gov (United States)

Awan, Faisal Saeed; Maryam; Jaskani, Muhammad J; Sadia, Bushra

2017-01-01

Breeding of date palm is complicated because of its long life cycle and heterozygous nature. Sexual propagation of date palm does not produce true-to-type plants. Sex of date palms cannot be identified until the first flowering stage. Molecular markers such as random amplified polymorphic DNA (RAPD), sequence-characterized amplified regions (SCAR), and simple sequence repeats (SSR) have successfully been used to identify the sex-linked loci in the plant genome and to isolate the corresponding genes. This chapter highlights the use of three molecular markers including RAPD, SCAR, and SSR to identify the gender of date palm seedlings.

Genetics Home Reference: X-linked sideroblastic anemia and ataxia

Science.gov (United States)

... linked sideroblastic anemia and ataxia X-linked sideroblastic anemia and ataxia Printable PDF Open All Close All ... the expand/collapse boxes. Description X-linked sideroblastic anemia and ataxia is a rare condition characterized by ...

Collagen derived serum markers in carcinoma of the prostate

DEFF Research Database (Denmark)

Rudnicki, M; Jensen, L T; Iversen, P

1995-01-01

Three new collagen markers deriving from the collagenous matrix, e.g. carboxyterminal propeptide of type I procollagen (PICP), carboxy-terminal pyridinoline cross-linked telopeptide of type I collagen (ICTP), and aminoterminal propeptide of type III procollagen (PIIINP) were used for the diagnose...

Genetic Recombination at the Buff Spore Color Locus in SORDARIA BREVICOLLIS. II. Analysis of Flanking Marker Behavior in Crosses between Buff Mutants.

Science.gov (United States)

Sang, H; Whitehouse, H L

1983-02-01

Aberrant asci containing one or more wild-type spores were selected from crosses between pairs of alleles of the buff locus in the presence of closely linked flanking markers. Data were obtained relating to the site of aberrant segregation and the position of any associated crossover giving recombination of flanking markers. Aberrant segregation at a proximal site within the buff gene may be associated with a crossover proximal to the site of aberrant segregation or, with equal frequency, with a crossover distal to the site of the second mutant present in the cross. Similarly, segregation at a distal site may be associated with a crossover distal to the site or, with lower frequency, with a crossover proximal to the site of the proximal mutant present in the cross. Crossovers between the alleles were rare. This evidence for the relationship between hybrid DNA and crossing over is discussed in terms of current models for the mechanism of recombination.

A prosthesis-specific multi-link segment model of lower-limb amputee sprinting.

Science.gov (United States)

Rigney, Stacey M; Simmons, Anne; Kark, Lauren

2016-10-03

Lower-limb amputees commonly utilize non-articulating energy storage and return (ESAR) prostheses for high impact activities such as sprinting. Despite these prostheses lacking an articulating ankle joint, amputee gait analysis conventionally features a two-link segment model of the prosthetic foot. This paper investigated the effects of the selected link segment model׳s marker-set and geometry on a unilateral amputee sprinter׳s calculated lower-limb kinematics, kinetics and energetics. A total of five lower-limb models of the Ottobock ® 1E90 Sprinter were developed, including two conventional shank-foot models that each used a different version of the Plug-in-Gait (PiG) marker-set to test the effect of prosthesis ankle marker location. Two Hybrid prosthesis-specific models were then developed, also using the PiG marker-sets, with the anatomical shank and foot replaced by prosthesis-specific geometry separated into two segments. Finally, a Multi-link segment (MLS) model was developed, consisting of six segments for the prosthesis as defined by a custom marker-set. All full-body musculoskeletal models were tested using four trials of experimental marker trajectories within OpenSim 3.2 (Stanford, California, USA) to find the affected and unaffected hip, knee and ankle kinematics, kinetics and energetics. The geometry of the selected lower-limb prosthesis model was found to significantly affect all variables on the affected leg (p prosthesis-specific spatial, inertial and elastic properties from full-body models significantly affects the calculated amputee gait characteristics, and we therefore recommend the implementation of a MLS model. Copyright © 2016 Elsevier Ltd. All rights reserved.

Digital Discourse Markers in an ESL Learning Setting: The Case of Socialisation Forums

Directory of Open Access Journals (Sweden)

Alireza Shakarami

2016-08-01

Full Text Available Analysis of the linguistic discourse plays an important role in the social, cultural, ethnographic, and comparative studies of languages. Discourse markers as indispensable parts of this analysis are reportedly more common in informal speech than in written language. They could be used at different levels, i.e. as „linking words‟, „linking phrases‟, or „sentence connectors‟ to bind together pieces of a text like „glue‟. The objective of the study is to ascertain the discourse markers employed in synchronous online interactions and networking through constant comparison of discourse markers used in the discussion forums (DF with the discourse markers already reported in the literature. The study maintains discourse markers (DMs used in the formal written discourse in order to identify any probable pragmatic, or discoursal level differences in the DMs used in the two modes of writing (formal writing and typing in online communication. The findings indicate that the written language that students use in their electronic posts is to a great extent similar to that of the process view of writing. Specifically, the written language used in a digital socialisation forum is at times, monitored, reviewed, revised, and corrected by the students themselves and their peers.

Population Structure, Diversity and Trait Association Analysis in Rice (Oryza sativa L. Germplasm for Early Seedling Vigor (ESV Using Trait Linked SSR Markers.

Directory of Open Access Journals (Sweden)

Annamalai Anandan

Full Text Available Early seedling vigor (ESV is the essential trait for direct seeded rice to dominate and smother the weed growth. In this regard, 629 rice genotypes were studied for their morphological and physiological responses in the field under direct seeded aerobic situation on 14th, 28th and 56th days after sowing (DAS. It was determined that the early observations taken on 14th and 28th DAS were reliable estimators to study ESV as compared to 56th DAS. Further, 96 were selected from 629 genotypes by principal component (PCA and discriminate function analyses. The selected genotypes were subjected to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic by using ESV QTL linked simple sequence repeat (SSR markers. To assess the genetic structure, model and distance based approaches were used. Genotyping of 96 rice lines using 39 polymorphic SSRs produced a total of 128 alleles with the phenotypic information content (PIC value of 0.24. The model based population structure approach grouped the accession into two distinct populations, whereas unrooted tree grouped the genotypes into three clusters. Both model based and structure based approach had clearly distinguished the early vigor genotypes from non-early vigor genotypes. Association analysis revealed that 16 and 10 SSRs showed significant association with ESV traits by general linear model (GLM and mixed linear model (MLM approaches respectively. Marker alleles on chromosome 2 were associated with shoot dry weight on 28 DAS, vigor index on 14 and 28 DAS. Improvement in the rate of seedling growth will be useful for identifying rice genotypes acquiescent to direct seeded conditions through marker-assisted selection.

Identification of a rice gene (Bph 1) conferring resistance to brown planthopper (Nilaparvata lugens Stal) using STS markers.

Science.gov (United States)

Kim, Suk-Man; Sohn, Jae-Keun

2005-08-31

This study was carried out to identify a high-resolution marker for a gene conferring resistance to brown planthopper (BPH) biotype 1, using japonica type resistant lines. Bulked segregant analyses were conducted using 520 RAPD primers to identify RAPD fragments linked to the BPH resistance gene. Eleven RAPDs were shown to be polymorphic amplicons between resistant and susceptible progeny. One of these primers, OPE 18, which amplified a 923 bp band tightly linked to resistance, was converted into a sequence-tagged-site (STS) marker. The STS marker, BpE18-3, was easily detectable as a dominant band with tight linkage (3.9cM) to Bph1. It promises to be useful as a marker for assisted selection of resistant progeny in backcross breeding programs to introgress the resistance gene into elite japonica cultivars.

Inheritance of blast resistance and identification of SSR marker ...

Indian Academy of Sciences (India)

2013-08-02

Aug 2, 2013 ... arm of chromosome 6 and in close proximity of blast resis- ... resistance to a M. oryzae race in a gene-for-gene manner. DNA markers have been ... order to identify the new sources of resistance against blast, there is need for ...

Empirical psychology, common sense, and Kant's empirical markers for moral responsibility.

Science.gov (United States)

Frierson, Patrick

2008-12-01

This paper explains the empirical markers by which Kant thinks that one can identify moral responsibility. After explaining the problem of discerning such markers within a Kantian framework I briefly explain Kant's empirical psychology. I then argue that Kant's empirical markers for moral responsibility--linked to higher faculties of cognition--are not sufficient conditions for moral responsibility, primarily because they are empirical characteristics subject to natural laws. Next. I argue that these markers are not necessary conditions of moral responsibility. Given Kant's transcendental idealism, even an entity that lacks these markers could be free and morally responsible, although as a matter of fact Kant thinks that none are. Given that they are neither necessary nor sufficient conditions, I discuss the status of Kant's claim that higher faculties are empirical markers of moral responsibility. Drawing on connections between Kant's ethical theory and 'common rational cognition' (4:393), I suggest that Kant's theory of empirical markers can be traced to ordinary common sense beliefs about responsibility. This suggestion helps explain both why empirical markers are important and what the limits of empirical psychology are within Kant's account of moral responsibility.

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

Science.gov (United States)

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. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

Detecting a cortical fingerprint of Parkinson’s disease for closed-loop neuromodulation

Directory of Open Access Journals (Sweden)

Kevin eKern

2016-03-01

Full Text Available Recent evidence suggests that deep brain stimulation (DBS of the subthalamic nucleus (STN in Parkinson’s disease (PD mediates its clinical effects by modulating cortical oscillatory activity, presumably via a direct cortico-subthalamic connection. This observation might pave the way for novel closed-loop approaches comprising a cortical sensor. Enhanced beta oscillations (13-35 Hz have been linked to the pathophysiology of PD and may serve as such a candidate marker to localize a cortical area reliably modulated by DBS. However, beta-oscillations are widely distributed over the cortical surface, necessitating an additional signal source for spotting the cortical area linked to the pathologically synchronized cortico-subcortical motor network.In this context, both cortico-subthalamic coherence and cortico-muscular coherence (CMC have been studied in PD patients. Whereas the former requires invasive recordings, the latter allows for non-invasive detection, but displays a rather distributed cortical synchronization pattern in motor tasks. This distributed cortical representation may conflict with the goal of detecting a cortical localization with robust biomarker properties which is detectable on a single subject basis. We propose that this limitation could be overcome when recording CMC at rest. We hypothesized that – unlike healthy subjects – PD would show CMC at rest owing to the enhanced beta oscillations observed in PD. By performing source space analysis of beta CMC recorded during resting-state magnetoencephalography, we provide preliminary evidence in one patient for a cortical hot spot that is modulated most strongly by subthalamic DBS. Such a spot would provide a prominent target region either for direct neuromodulation or for placing a potential sensor in closed-loop DBS approaches, a proposal that requires investigation in a larger cohort of PD patients.

Generation and application of SSR markers in avocado

International Nuclear Information System (INIS)

Sharon, D.; Lavi, U.; Cregan, P.B.; Hillel, J.

1998-01-01

Simple Sequence Repeat (SSR) DNA markers were generated and applied to avocado. An SSR marker is based on a pair of primers which are synthesized on the basis of DNA sequences flanking a micro satellite. These markers are PCR based, quite polymorphic and abundant in several species. These are the markers, of choice in the human genome. The number of SSR markers in the avocado genome was calculated to be about 45,000, with the A/T micro satellite being the most frequent (1 in 40 kb). SSR markers are quite expensive to generate due to the required multi-step procedure; Screening a genomic library, about 66% of the positive clones turned out after sequencing to be SSR containing clones. In only about 55% of these, was it possible to synthesize primers and, of this group, only about 50% of the markers were useful for typing a specific family. Typing of five avocado cultivars using 59 SSR markers results in one to eight alleles per locus, mean heterozygosity ranging between 0.51 and 0.66 and gene diversity ranging between 0.42 and 0.66. The SSR markers were used to estimate the genetic relationships between various Persea species. The number of alleles in these species ranged between five and twelve with heterozygosity levels between 0.11-0.78 and gene diversity between 0.69-0.89. A preliminary genetic map, based on these SSR markers together with some DNA fingerprints (DFP) and randomly amplified polymorphic DNA (RAPD) markers, was drawn. The map consists of 12 linkage group having two to five markers each. Linkage analysis with several quantitative trait loci (QTLs) was performed by genetic typing and phenotypic assessment of the progeny of a controlled cross. The results of the interval mapping suggest that the gene(s) coding for the existence of fibers in the flesh, are probably linked to linkage group 3. (author)

Generation and application of SSR markers in avocado

Energy Technology Data Exchange (ETDEWEB)

Sharon, D; Lavi, U [Institute of Horticulture, ARO Volcani Center, Bet-Dagan (Israel); Cregan, P B [United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland (United States); Hillel, J [Faculty of Agriculture, Hebrew University of Jerusalem, Rehovot (Israel)

1998-10-01

Simple Sequence Repeat (SSR) DNA markers were generated and applied to avocado. An SSR marker is based on a pair of primers which are synthesized on the basis of DNA sequences flanking a micro satellite. These markers are PCR based, quite polymorphic and abundant in several species. These are the markers, of choice in the human genome. The number of SSR markers in the avocado genome was calculated to be about 45,000, with the A/T micro satellite being the most frequent (1 in 40 kb). SSR markers are quite expensive to generate due to the required multi-step procedure; Screening a genomic library, about 66% of the positive clones turned out after sequencing to be SSR containing clones. In only about 55% of these, was it possible to synthesize primers and, of this group, only about 50% of the markers were useful for typing a specific family. Typing of five avocado cultivars using 59 SSR markers results in one to eight alleles per locus, mean heterozygosity ranging between 0.51 and 0.66 and gene diversity ranging between 0.42 and 0.66. The SSR markers were used to estimate the genetic relationships between various Persea species. The number of alleles in these species ranged between five and twelve with heterozygosity levels between 0.11-0.78 and gene diversity between 0.69-0.89. A preliminary genetic map, based on these SSR markers together with some DNA fingerprints (DFP) and randomly amplified polymorphic DNA (RAPD) markers, was drawn. The map consists of 12 linkage group having two to five markers each. Linkage analysis with several quantitative trait loci (QTLs) was performed by genetic typing and phenotypic assessment of the progeny of a controlled cross. The results of the interval mapping suggest that the gene(s) coding for the existence of fibers in the flesh, are probably linked to linkage group 3. (author) 20 refs, 3 figs, 8 tabs

Measurement of some tumor markers by IRMA in vietnam

International Nuclear Information System (INIS)

Tran Xuan Truong

2004-01-01

As we known that a perfect tumor markers could be used in five different ways : for population screening, for diagnose, for monitoring therapy and for follow-up early evidence of cancer recurrence. In order to achieve perfect status a tumor markers would require total negativity in healthy subject, total positivity for single tumor type and close correlation between plasma tumor marker concentration and tumor size . The advance of monoclonal antibodies has had dramatic impact in oncology, where new tumor markers have been discovered and assay methods for all tumor markers have been improved commercially . Analytical performance of these new methods are potentially as good as that of the best Immunoradiometric assay for others analytes. In Vietnam, the first time we use immunoradiometric assay (IRMA) for the measurement of some tumor markers in normal subject and cancer diseases. These are Thyroglobulin (TG) of thyroid cancer, cancer-antigen 15-3 (CA15-3) of breast cancer and cancer-antigen 72-4 (CA72-4) of stomach cancer. We would like applying the CA72-4 in the indication of stomach cancer, CA15-3 in the differential diagnosis of breast cancer, and TG in the differential diagnosis of thyroid cancer. And all of these tumor markers were also used in the clinical follow-up and early detection of recurrence and metastatic Cancer of them. We could try researching on them much more. (authors)

Identification and evaluation of two diagnostic markers linked to Fusarium wilt resistance (race 4) in banana (Musa spp.).

Science.gov (United States)

Wang, Wei; Hu, Yulin; Sun, Dequan; Staehelin, Christian; Xin, Dawei; Xie, Jianghui

2012-01-01

Fusarium wilt caused by the fungus Fusarium oxysporum f. sp. cubense race 4 (FOC4) results in vascular tissue damage and ultimately death of banana (Musa spp.) plants. Somaclonal variants of in vitro micropropagated banana can hamper success in propagation of genotypes resistant to FOC4. Early identification of FOC4 resistance in micropropagated banana plantlets is difficult, however. In this study, we identified sequence-characterized amplified region (SCAR) markers of banana associated with resistance to FOC4. Using pooled DNA from resistant or susceptible genotypes and 500 arbitrary 10-mer oligonucleotide primers, 24 random amplified polymorphic DNA (RAPD) products were identified. Two of these RAPD markers were successfully converted to SCAR markers, called ScaU1001 (GenBank accession number HQ613949) and ScaS0901 (GenBank accession number HQ613950). ScaS0901 and ScaU1001 could be amplified in FOC4-resistant banana genotypes ("Williams 8818-1" and Goldfinger), but not in five tested banana cultivars susceptible to FOC4. The two SCAR markers were then used to identify a somaclonal variant of the genotype "Williams 8818-1", which lost resistance to FOC4. Hence, the identified SCAR markers can be applied for a rapid quality control of FOC4-resistant banana plantlets immediately after the in vitro micropropagation stage. Furthermore, ScaU1001 and ScaS0901 will facilitate marker-assisted selection of new banana cultivars resistant to FOC4.

[Gender differences in the use of tumour markers].

Science.gov (United States)

Moreno-Campoy, E E; Mérida-De la Torre, F J; Martos-Crespo, F; Plebani, M

2015-01-01

Gender is one of the factors that can influence the use of health resources. The use of tumour markers is widespread, due to the importance of these in monitoring cancer development. The aim of this study is to analyse the influence of gender on the use of tumour markers, and to investigate whether there are differences in their use. A longitudinal, retrospective and descriptive study, with a 2-year follow-up, was conducted in the catchment area of the University Hospital of Padua. An analysis was performed on 23,059 analytical requests for tumour markers. A descriptive and frequency analysis was performed on all variables. The statistical analysis was performed using Chi squared, Student t and Mann-Whitney U to test for significance. The number of requests for women (1.5) was lower than men (1.6). In patients with tumour pathology, the number of requests was higher than in patients without tumour disease. In the analysis by disease and gender, the difference remained significant. As regards the number of tumour markers per request, the difference between genders was also significant: 2.13 in males versus 2.85 in women. Similar results were obtained when requests for tumour markers linked to gender-related diseases were eliminated. There are differences in the use of tumour markers by gender with the number of requests for male patients being higher than for females. However, the number of tumour markers per request is greater in women than in men. Copyright © 2015 SECA. Published by Elsevier Espana. All rights reserved.

Genetic structure and inter-generic relationship of closed colony of laboratory rodents based on RAPD markers.

Science.gov (United States)

Kumar, Mahadeo; Kumar, Sharad

2014-11-01

Molecular genetic analysis was performed using random amplified polymorphic DNA (RAPD) on three commonly used laboratory bred rodent genera viz. mouse (Mus musculus), rat (Rattus norvegicus) and guinea pig (Cavia porcellus) as sampled from the breeding colony maintained at the Animal Facility, CSIR-Indian Institute of Toxicology Research, Lucknow. In this study, 60 samples, 20 from each genus, were analyzed for evaluation of genetic structure of rodent stocks based on polymorphic bands using RAPD markers. Thirty five random primers were assessed for RAPD analysis. Out of 35, only 20 primers generated a total of 56.88% polymorphic bands among mice, rats and guinea pigs. The results revealed significantly variant and distinct fingerprint patterns specific to each of the genus. Within-genera analysis, the highest (89.0%) amount of genetic homogeneity was observed in mice samples and the least (79.3%) were observed in guinea pig samples. The amount of genetic homogeneity was observed very high within all genera. The average genetic diversity index observed was low (0.045) for mice and high (0.094) for guinea pigs. The inter-generic distances were maximum (0.8775) between mice and guinea pigs; and the minimum (0.5143) between rats and mice. The study proved that the RAPD markers are useful as genetic markers for assessment of genetic structure as well as inter-generic variability assessments.

Minding the close relationship.

Science.gov (United States)

Harvey, J H; Omarzu, J

1997-01-01

In this theoretical analysis, we argue that a process referred to as minding is essential for a couple to feel mutually close and satisfied in a close relationship over a long period Minding represents a package of mutual self-disclosure, other forms of goal-oriented behavior aimed at facilitating the relationship, and attributions about self's and other's motivations, intentions, and Mort in the relationship. Self-disclosure and attribution activities in minding are aimed at getting to know the other, trying to understand the other's motivations and deeper disposition as they pertain to the relationship, and showing respect and acceptance for knowledge gained about other. We link the concept of minding to other major ideas and literatures about how couples achieve closeness: self-disclosure and social penetration, intimacy, empathy and empathic accuracy, and love and self-expansion. We argue that the minding process articulated here has not previously been delineated and that it is a useful composite notion about essential steps in bonding among humans. We also argue that the minding concept stretches our understanding of the interface of attribution and close relationships. We present research possibilities and implications and consider possible alternative positions and counter arguments about the merits of the minding idea for close relationship satisfaction.

Use of multiple genetic markers in prediction of breeding values.

NARCIS (Netherlands)

Arendonk, van J.A.M.; Tier, B.; Kinghorn, B.P.

1994-01-01

Genotypes at a marker locus give information on transmission of genes from parents to offspring and that information can be used in predicting the individuals' additive genetic value at a linked quantitative trait locus (MQTL). In this paper a recursive method is presented to build the gametic

Biochemical Markers in Neurocritical Care

Directory of Open Access Journals (Sweden)

Omidvar Rezae

2016-07-01

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

Comparison between low-cost marker-less and high-end marker-based motion capture systems for the computer-aided assessment of working ergonomics.

Science.gov (United States)

Patrizi, Alfredo; Pennestrì, Ettore; Valentini, Pier Paolo

2016-01-01

The paper deals with the comparison between a high-end marker-based acquisition system and a low-cost marker-less methodology for the assessment of the human posture during working tasks. The low-cost methodology is based on the use of a single Microsoft Kinect V1 device. The high-end acquisition system is the BTS SMART that requires the use of reflective markers to be placed on the subject's body. Three practical working activities involving object lifting and displacement have been investigated. The operational risk has been evaluated according to the lifting equation proposed by the American National Institute for Occupational Safety and Health. The results of the study show that the risk multipliers computed from the two acquisition methodologies are very close for all the analysed activities. In agreement to this outcome, the marker-less methodology based on the Microsoft Kinect V1 device seems very promising to promote the dissemination of computer-aided assessment of ergonomics while maintaining good accuracy and affordable costs. PRACTITIONER’S SUMMARY: The study is motivated by the increasing interest for on-site working ergonomics assessment. We compared a low-cost marker-less methodology with a high-end marker-based system. We tested them on three different working tasks, assessing the working risk of lifting loads. The two methodologies showed comparable precision in all the investigations.

Can microsatellite markers resolve phylogenetic relationships between closely related crested newt species (Triturus cristatus superspecies)?

Czech Academy of Sciences Publication Activity Database

Mikulíček, P.; Crnobrnja-Isailović, J.; Piálek, Jaroslav

2007-01-01

Roč. 28, č. 4 (2007), s. 467-474 ISSN 0173-5373 R&D Projects: GA ČR GA206/01/0695; GA MŠk LC06073 Institutional research plan: CEZ:AV0Z60930519 Keywords : crested newt * microsatelitte markers Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.929, year: 2007

Genetic analysis of autoimmune gld mice. I. Identification of a restriction fragment length polymorphism closely linked to the gld mutation within a conserved linkage group

Science.gov (United States)

1988-01-01

A linkage map of distal mouse chromosome 1 was generated using restriction fragment length polymorphism (RFLP) analysis of DNA prepared from 95 [C3H-gld/gld X Mus spretus)F1 X C3H-gld/gld] backcross mice. The gene order was: (centromere) C4bp, Ren-1,2, Ly-5, [At-3/gld], Apoa-2/Ly-17, Spna-1 (telomere). All mice expressing the phenotype of gld homozygotes were homozygous for the At-3 RFLP characteristic of C3H mice and none of the mice heterozygous for At-3 RFLPs had characteristics of gld homozygotes, demonstrating close linkage between these genes. The identification of an RFLP closely linked to the gld gene provides a starting point for the identification of a genetic defect that results in abnormal T cells and autoimmune disease. PMID:2894402

A new approach to chromosome-wide analysis of X-linked markers identifies new associations in Asian and European case-parent triads of orofacial clefts.

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Øivind Skare

Full Text Available GWAS discoveries on the X-chromosome are underrepresented in the literature primarily because the analytical tools that have been applied were originally designed for autosomal markers. Our objective here is to employ a new robust and flexible tool for chromosome-wide analysis of X-linked markers in complex traits. Orofacial clefts are good candidates for such analysis because of the consistently observed excess of females with cleft palate only (CPO and excess of males with cleft lip with or without cleft palate (CL/P.Genotypes for 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European isolated cleft triads were available from a previously published GWAS. The R-package HAPLIN enables genome-wide-level analyses as well as statistical power simulations for a range of biologic scenarios. We analyzed isolated CL/P and isolated CPO for each ethnicity in HAPLIN, using a sliding-window approach to haplotype analysis and two different statistical models, with and without X-inactivation in females.There was a larger number of associations in the Asian versus the European sample, and similar to previous reports that have analyzed the same GWAS dataset using different methods, we identified associations with EFNB1/PJA1 and DMD. In addition, new associations were detected with several other genes, among which KLHL4, TBX22, CPXCR1 and BCOR were noteworthy because of their roles in clefting syndromes. A few of the associations were only detected by one particular X-inactivation model, whereas a few others were only detected in one sex.We found new support for the involvement of X-linked variants in isolated clefts. The associations were specific for ethnicity, sex and model parameterization, highlighting the need for flexible tools that are capable of detecting and estimating such effects. Further efforts are needed to verify and elucidate the potential roles of EFNB1/PJA1, KLHL4, TBX22, CPXCR1 and BCOR in isolated clefts.

Using SNP markers to dissect linkage disequilibrium at a major quantitative trait locus for resistance to the potato cyst nematode Globodera pallida on potato chromosome V.

Science.gov (United States)

Achenbach, Ute; Paulo, Joao; Ilarionova, Evgenyia; Lübeck, Jens; Strahwald, Josef; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Gebhardt, Christiane

2009-02-01

The damage caused by the parasitic root cyst nematode Globodera pallida is a major yield-limiting factor in potato cultivation . Breeding for resistance is facilitated by the PCR-based marker 'HC', which is diagnostic for an allele conferring high resistance against G. pallida pathotype Pa2/3 that has been introgressed from the wild potato species Solanum vernei into the Solanum tuberosum tetraploid breeding pool. The major quantitative trait locus (QTL) controlling this nematode resistance maps on potato chromosome V in a hot spot for resistance to various pathogens including nematodes and the oomycete Phytophthora infestans. An unstructured sample of 79 tetraploid, highly heterozygous varieties and breeding clones was selected based on presence (41 genotypes) or absence (38 genotypes) of the HC marker. Testing the clones for resistance to G. pallida confirmed the diagnostic power of the HC marker. The 79 individuals were genotyped for 100 single nucleotide polymorphisms (SNPs) at 10 loci distributed over 38 cM on chromosome V. Forty-five SNPs at six loci spanning 2 cM in the interval between markers GP21-GP179 were associated with resistance to G. pallida. Based on linkage disequilibrium (LD) between SNP markers, six LD groups comprising between 2 and 18 SNPs were identified. The LD groups indicated the existence of multiple alleles at a single resistance locus or at several, physically linked resistance loci. LD group C comprising 18 SNPs corresponded to the 'HC' marker. LD group E included 16 SNPs and showed an association peak, which positioned one nematode resistance locus physically close to the R1 gene family.

Pea Marker Database (PMD) - A new online database combining known pea (Pisum sativum L.) gene-based markers.

Science.gov (United States)

Kulaeva, Olga A; Zhernakov, Aleksandr I; Afonin, Alexey M; Boikov, Sergei S; Sulima, Anton S; Tikhonovich, Igor A; Zhukov, Vladimir A

2017-01-01

Pea (Pisum sativum L.) is the oldest model object of plant genetics and one of the most agriculturally important legumes in the world. Since the pea genome has not been sequenced yet, identification of genes responsible for mutant phenotypes or desirable agricultural traits is usually performed via genetic mapping followed by candidate gene search. Such mapping is best carried out using gene-based molecular markers, as it opens the possibility for exploiting genome synteny between pea and its close relative Medicago truncatula Gaertn., possessing sequenced and annotated genome. In the last 5 years, a large number of pea gene-based molecular markers have been designed and mapped owing to the rapid evolution of "next-generation sequencing" technologies. However, the access to the complete set of markers designed worldwide is limited because the data are not uniformed and therefore hard to use. The Pea Marker Database was designed to combine the information about pea markers in a form of user-friendly and practical online tool. Version 1 (PMD1) comprises information about 2484 genic markers, including their locations in linkage groups, the sequences of corresponding pea transcripts and the names of related genes in M. truncatula. Version 2 (PMD2) is an updated version comprising 15944 pea markers in the same format with several advanced features. To test the performance of the PMD, fine mapping of pea symbiotic genes Sym13 and Sym27 in linkage groups VII and V, respectively, was carried out. The results of mapping allowed us to propose the Sen1 gene (a homologue of SEN1 gene of Lotus japonicus (Regel) K. Larsen) as the best candidate gene for Sym13, and to narrow the list of possible candidate genes for Sym27 to ten, thus proving PMD to be useful for pea gene mapping and cloning. All information contained in PMD1 and PMD2 is available at www.peamarker.arriam.ru.

Low intensity aerobic exercise and oxidative stress markers in older adults.

Science.gov (United States)

Bouzid, Mohamed A; Hammouda, Omar; Matran, Régis; Robin, Sophie; Fabre, Claudine

2014-10-01

This comparative study examined the effects of regular low intensity aerobic exercise on oxidative stress markers in older adults. The study was carried out on 15 sedentary subjects (age: 65.1 ± 3.5 years) versus 18 subjects performing fitness exercises (age: 65.8 ± 3.3 years). Before and after an incremental exercise test, oxidative stress markers were assessed. Superoxide dismutase was higher at rest and at the recovery for the physically active subjects compared with sedentary subjects (p aerobic exercise may be useful to prevent the decline of antioxidants linked with aging.

Analysis of cold resistance and identification of SSR markers linked to cold resistance genes in Brassica rapa L.

Science.gov (United States)

Huang, Zhen; Zhang, Xuexian; Jiang, Shouhua; Qin, Mengfan; Zhao, Na; Lang, Lina; Liu, Yaping; Tian, Zhengshu; Liu, Xia; Wang, Yang; Zhang, Binbin; Xu, Aixia

2017-06-01

Currently, cold temperatures are one of the main factors threatening rapeseed production worldwide; thus, it is imperative to identify cold-resistant germplasm and to cultivate cold-resistant rapeseed varieties. In this study, the cold resistance of four Brassica rapa varieties was analyzed. The cold resistance of Longyou6 and Longyou7 was better than that of Tianyou2 and Tianyou4. Thus, an F 2 population derived from Longyou6 and Tianyou4 was used to study the correlation of cold resistance and physiological indexes. Our results showed that the degree of frost damage was related to the relative conductivity and MDA content (r1 = 0.558 and r2 = 0.447, respectively). In order to identify the markers related to cold resistance, 504 pairs of SSR (simple sequence repeats) primers were used to screen the two parents and F 2 population. Four and five SSR markers had highly significant positive correlation to relative conductivity and MDA, respectively. In addition, three of these SSR markers had a highly significant positive correlation to both of these two indexes. These three SSR markers were subsequently confirmed to be used to distinguish between cold-resistant and non-cold-resistant varieties. The results of this study will lay a solid foundation for the mapping of cold-resistant genes and molecular markers assisted selection for the cold-resistance.

The Immature Fiber Mutant Phenotype of Cotton (Gossypium hirsutum Is Linked to a 22-bp Frame-Shift Deletion in a Mitochondria Targeted Pentatricopeptide Repeat Gene

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Gregory N. Thyssen

2016-06-01

Full Text Available Cotton seed trichomes are the most important source of natural fibers globally. The major fiber thickness properties influence the price of the raw material, and the quality of the finished product. The recessive immature fiber (im gene reduces the degree of fiber cell wall thickening by a process that was previously shown to involve mitochondrial function in allotetraploid Gossypium hirsutum. Here, we present the fine genetic mapping of the im locus, gene expression analysis of annotated proteins near the locus, and association analysis of the linked markers. Mapping-by-sequencing identified a 22-bp deletion in a pentatricopeptide repeat (PPR gene that is completely linked to the immature fiber phenotype in 2837 F2 plants, and is absent from all 163 cultivated varieties tested, although other closely linked marker polymorphisms are prevalent in the diversity panel. This frame-shift mutation results in a transcript with two long open reading frames: one containing the N-terminal transit peptide that targets mitochondria, the other containing only the RNA-binding PPR domains, suggesting that a functional PPR protein cannot be targeted to mitochondria in the im mutant. Taken together, these results suggest that PPR gene Gh_A03G0489 is involved in the cotton fiber wall thickening process, and is a promising candidate gene at the im locus. Our findings expand our understanding of the molecular mechanisms that modulate cotton fiber fineness and maturity, and may facilitate the development of cotton varieties with superior fiber attributes.

Information Theoretical Limits of Free-Space Optical Links

KAUST Repository

Ansari, Imran Shafique

2016-08-25

Generalized fading has been an imminent part and parcel of wireless communications. It not only characterizes the wireless channel appropriately but also allows its utilization for further performance analysis of various types of wireless communication systems. Under the umbrella of generalized fading channels, a unified ergodic capacity analysis of a free-space optical (FSO) link under both types of detection techniques (i.e., intensity modulation/direct detection (IM/DD) as well as heterodyne detection) over generalized atmospheric turbulence channels that account for generalized pointing errors is presented. Specifically, unified exact closed-form expressions for the moments of the end-to-end signal-to-noise ratio (SNR) of a single link FSO transmission system are presented. Subsequently, capitalizing on these unified statistics, unified exact closed-form expressions for ergodic capacity performance metric of FSO link transmission systems is offered. Additionally, for scenarios wherein the exact closed-form solution is not possible to obtain, some asymptotic results are derived in the high SNR regime. All the presented results are verified via computer-based Monte-Carlo simulations.

MCM - 2 and Ki - 67 as proliferation markers in renal cell carcinoma: A quantitative and semi - quantitative analysis.

Science.gov (United States)

Mehdi, Muhammad Zain; Nagi, Abdul Hanan; Naseem, Nadia

2016-01-01

Fuhrman nuclear grade is the most important histological parameter to predict prognosis in a patient of renal cell carcinoma (RCC). However, it suffers from inter-observer and intra-observer variation giving rise to need of a parameter that not only correlates with nuclear grade but is also objective and reproducible. Proliferation is the measure of aggressiveness of a tumour and it is strongly correlated with Fuhrman nuclear grade, clinical survival and recurrence in RCC. Ki-67 is conventionally used to assess proliferation. Mini-chromosome maintenance 2 (MCM-2) is a lesser known marker of proliferation and identifies a greater proliferation faction. This study was designed to assess the prognostic significance of MCM-2 by comparing it with Fuhrman nuclear grade and Ki-67. n=50 cases of various ages, stages, histological subtypes and grades of RCC were selected for this study. Immunohistochemical staining using Ki-67(MIB-1, Mouse monoclonal antibody, Dako) and MCM-2 (Mouse monoclonal antibody, Thermo) was performed on the paraffin embedded blocks in the department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore. Labeling indices (LI) were determined by two pathologists independently using quantitative and semi-quantitative analysis. Statistical analysis was carried out using SPSS 20.0. Kruskall-Wallis test was used to determine a correlation of proliferation markers with grade, and Pearson's correlate was used to determine correlation between the two proliferation markers. Labeling index of MCM-2 (median=24.29%) was found to be much higher than Ki-67(median=13.05%). Both markers were significantly related with grade (p=0.00; Kruskall-Wallis test). LI of MCM-2 was found to correlate significantly with LI of Ki-67(r=0.0934;p=0.01 with Pearson's correlate). Results of semi-quantitative analysis correlated well with quantitative analysis. Both Ki-67 and MCM-2 are markers of proliferation which are closely linked to grade. Therefore, they

Identification of ISSR and RAPD markers linked to yield traits in bread wheat under normal and drought conditions

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A.G.A. Khaled

2015-12-01

Full Text Available Genetic variability and identification of some molecular markers were studied in twenty promising lines of wheat using agronomic traits, ISSR (inter simple sequences repeats and RAPD (random amplified polymorphic DNA markers. Significant variation was evidenced in all agronomic traits. The lines proved to be superior to the check cultivar Sahel1 in yield and its component traits. Lines L2, L7 and L8 were the best in most yield component traits in both seasons. Moreover, Lines L2, L4, L5, L7 and L8 showed drought tolerance by which they displayed high performance in agronomic traits as well as a low drought susceptibility index. The percentage of polymorphism was 39.3% and 53.2% for ISSRs and RAPDs, respectively. UBC-881 belonged to penta-nucleotide repeat sequences (GGGTG that produced the highest level of polymorphism, while UBC-846 belonged to di-nucleotide repeat sequences (CA that produced the lowest level of polymorphism. Genetic similarities among wheat lines based on ISSR and RAPD markers ranged from 0.81 to 1.00 and from 0.86 to 0.98, respectively. There was a low average of PIC (polymorphism information content values which were 0.10 (ISSR and 0.15 (RAPD. The RAPD technique exhibited a higher marker index (MI = 0.69 compared to ISSR (MI = 0.43. There was insignificant correlation between ISSR and RAPD data (0.168, p > 0.05. There were two markers (UBC-881450bp and OPF-10540bp, on each of which two traits regressed significantly. The associated markers each explained a maximum regression of 18.92–34.95% of the total available variation for individual associated traits.

Mapping Late Leaf Spot Resistance in Peanut (Arachis hypogaea Using QTL-seq Reveals Markers for Marker-Assisted Selection

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Josh Clevenger

2018-02-01

Full Text Available Late leaf spot (LLS; Cercosporidium personatum is a major fungal disease of cultivated peanut (Arachis hypogaea. A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools.Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping.

Fatty acid trophic markers and trophic links among seston, crustacean zooplankton and the siphonophore Nanomia cara in Georges Basin and Oceanographer Canyon (NW Atlantic

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Sergio Rossi

2008-06-01

Full Text Available Fatty acid concentrations expressed as percentages of total fatty acid pools in seston, stage V copepodites of Calanus finmarchicus, adults of the euphausiid Meganyctiphanes norvegica, and the physonect siphonophore Nanomia cara were used to elucidate trophic links in Georges Basin and Oceanographer Canyon in September 2003. Seston at both locations was refractory and comprised mainly of saturated fatty acids. Phytoplankton did not contribute significantly to the fatty acid composition of seston or higher trophic levels. Only four fatty acids, i.e. 14:0, 16:0, 16:1 (n–7 and 18:1 (n–7, were transferred from seston to C. finmarchicus or M. norvegica, which suggested weak trophic interactions. Fatty acids transferred from the two species of crustaceans to N. cara included the same four fatty acids, along with three polyunsaturated fatty acids found in relatively high concentrations in both crustaceans, i.e. 20:3 (n–6, 20:5 (n–3 and 22:6 (n–3. In addition, 18:1 (n–9, which occurred in relatively high concentrations only in M. norvegica, and 18:0 and 18:2 (n–6, which were found in low concentrations in both crustaceans, also appeared to be transferred to N. cara. Overall, fatty acid trophic markers proved useful for identifying trophic links to N. cara.

Tagging genes for drought resistance by DNA markers in wheat (abstract)

International Nuclear Information System (INIS)

Malik, T.A.; Rahman, S.; Zafar, Y.

2005-01-01

Wheat families (F/sub 3) raised from the seed of drought resistant and susceptible F/sub 2/ plants developed from the cross of drought resistant and susceptible parents were grown under greenhouse conditions in polyethylene tubes filled with soil and sand mixture. Drought stress was imposed and monitored at the seedling stage. The relative water content and net photosynthesis was recorded with increasing drought stress until a significant part of the seedling population had zero or negative net photosynthesis. The seedling with zero or negative net photosynthesis were named as drought susceptible and the seedlings at the same drought stress showing net photosynthesis were named as drought resistance. Twenty each of the most susceptible and resistant seedlings were selected for DNA extraction. Random Amplified Polymorphic DNA (RAPD) technique using bulked segregant analysis was used to identify DNA markers linked to drought resistance. The primers OPJ-05, OPJ-14, OPI-20 and OPA-19 produced polymorphic DNA fragments between the contrasting bulks. The polymorphic DNA fragment of 1.55kb produced by the primer OPA-19 was found linked to drought resistance. This DNA marker can be used in markers-assisted selection for drought resistance or to clone drought resistance gene. (author)

Identify super quality markers from prototype-based pharmacokinetic markers of Tangzhiqing tablet (TZQ) based on in vitro dissolution/ permeation and in vivo absorption correlations.

Science.gov (United States)

Li, Ziqiang; Liu, Jia; Li, Yazhuo; Du, Xi; Li, Yanfen; Wang, Ruihua; Lv, Chunxiao; He, Xin; Wang, Baohe; Huang, Yuhong; Zhang, Deqin

2018-06-01

A quality marker (Q-marker) is defined as an inherent chemical compound that is used for the quality control of a drug. Its biological activities are closely related to safety and therapeutic effects. Generally, a multiple-component herbal medicine may have many Q-markers. We therefore proposed a concept of "super Q-marker" satisfying both the criterion of Q-markers and PK-markers to be used in more effective quality control of herbal medicine. The first aim was to find suitable prototype-based PK-markers from Tangzhiqing tablets (TZQ), a Chinese patent medicine. Then super Q-markers were expected to be identified from the prototype-based PK-markers based on an in vitro-in vivo correlation study. Potentially eligible prototype-based PK-markers were identified in a single- and multiple-dose pharmacokinetic study on TZQ in 30 healthy volunteers. The in vitro dissolution and permeation profiles of the prototype-based PK-markers of TZQ were evaluated by the physiologically-based drug dissolution/absorption simulating system (DDASS). An in vitro-in vivo correlation analysis was conducted between the dissolution/permeation behaviors in DDASS and the actual absorption profiles in human to test the transferability and traceability of the promising super Q-markers for TZQ. In human, plasma paeoniflorin and nuciferine as prototype-based PK-markers exhibited the appropriate pharmacokinetic properties, including dose-dependent systemic exposure (AUC, C max ) and a proper elimination half-life (1∼3h). In DDASS, it was predicted that paeoniflorin and nuciferine are highly permeable but the absorption rates are primarily limited by the dissolution rates. Moreover, the established in vitro-in vivo correlations of paeoniflorin and nuciferine were in support of the super Q-markers features. Paeoniflorin and nuciferine are identified as the super Q-markers from the prototype-based PK-markers of TZQ based on findings from a combination of in vitro, in vivo, and in vitro-in vivo

Incorporation of Bacterial Blight Resistance Genes Into Lowland Rice Cultivar Through Marker-Assisted Backcross Breeding.

Science.gov (United States)

Pradhan, Sharat Kumar; Nayak, Deepak Kumar; Pandit, Elssa; Behera, Lambodar; Anandan, Annamalai; Mukherjee, Arup Kumar; Lenka, Srikanta; Barik, Durga Prasad

2016-07-01

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae is a major disease of rice in many rice growing countries. Pyramided lines carrying two BB resistance gene combinations (Xa21+xa13 and Xa21+xa5) were developed in a lowland cultivar Jalmagna background through backcross breeding by integrating molecular markers. In each backcross generation, markers closely linked to the disease resistance genes were used to select plants possessing the target genes. Background selection was continued in those plants carrying resistant genes until BC(3) generation. Plants having the maximum contribution from the recurrent parent genome were selected in each generation and hybridized with the recipient parent. The BB-pyramided line having the maximum recipient parent genome recovery of 95% was selected among BC3F1 plants and selfed to isolate homozygous BC(3)F(2) plants with different combinations of BB resistance genes. Twenty pyramided lines with two resistance gene combinations exhibited high levels of tolerance against the BB pathogen. In order to confirm the resistance, the pyramided lines were inoculated with different X. oryzae pv. oryzae strains of Odisha for bioassay. The genotypes with combination of two BB resistance genes conferred high levels of resistance to the predominant X. oryzae pv. oryzae isolates prevalent in the region. The pyramided lines showed similarity with the recipient parent with respect to major agro-morphologic traits.

[Studies of marker screening efficiency and corresponding influencing factors in QTL composite interval mapping].

Science.gov (United States)

Gao, Yong-Ming; Wan, Ping

2002-06-01

Screening markers efficiently is the foundation of mapping QTLs by composite interval mapping. Main and interaction markers distinguished, besides using background control for genetic variation, could also be used to construct intervals of two-way searching for mapping QTLs with epistasis, which can save a lot of calculation time. Therefore, the efficiency of marker screening would affect power and precision of QTL mapping. A doubled haploid population with 200 individuals and 5 chromosomes was constructed, with 50 markers evenly distributed at 10 cM space. Among a total of 6 QTLs, one was placed on chromosome I, two linked on chromosome II, and the other three linked on chromosome IV. QTL setting included additive effects and epistatic effects of additive x additive, the corresponding QTL interaction effects were set if data were collected under multiple environments. The heritability was assumed to be 0.5 if no special declaration. The power of marker screening by stepwise regression, forward regression, and three methods for random effect prediction, e.g. best linear unbiased prediction (BLUP), linear unbiased prediction (LUP) and adjusted unbiased prediction (AUP), was studied and compared through 100 Monte Carlo simulations. The results indicated that the marker screening power by stepwise regression at 0.1, 0.05 and 0.01 significant level changed from 2% to 68%, the power changed from 2% to 72% by forward regression. The larger the QTL effects, the higher the marker screening power. While the power of marker screening by three random effect prediction was very low, the maximum was only 13%. That suggested that regression methods were much better than those by using the approaches of random effect prediction to identify efficient markers flanking QTLs, and forward selection method was more simple and efficient. The results of simulation study on heritability showed that heightening of both general heritability and interaction heritability of genotype x

Marital Quality and Spouses' Marriage Work with Close Friends and Each Other.

Science.gov (United States)

Helms, Heather M.; Crouter, Ann C.; McHale, Susan M.

2003-01-01

Explores how husbands' and wives' marriage work with close friends and one another was linked to their perceptions of marital quality. Results showed that husbands engaged in more marriage work with their wives than with close friends, whereas wives engaged in similar levels of marriage work with their close friends and husbands. (Contains 58…

Sex linked versus autosomal inbreeding coefficient in close consanguineous marriages in the Basque country and Castile (Spain): genetic implications.

Science.gov (United States)

Calderón, R; Morales, B; Peña, J A; Delgado, J

1995-10-01

Pedigree structures of 161 uncle/niece-aunt/nephew and 4420 first cousin consanguineous marriages registered during the 19th and 20th centuries in two large and very different Spanish regions have been analysed and their genetic consequences evaluated. The frequencies of the different pedigree subtypes within each degree of relationship were quite similar in both populations despite significant heterogeneity in inbreeding patterns. The mean X-linked inbreeding coefficient (Fx) for each type of cousin mating was calculated and compared to that expected for autosomal genes (F). The effect of genealogical structure on the Fx/F ratio was compared to different cultural populations worldwide. Preferentiality and avoidance of close consanguinity along with specific types of pedigrees are discussed on the basis of premarital migration and sociocultural rules still deeply rooted in certain human groups. By admitting that the observed Fx coefficient is usually higher than F in most human populations some remarks have been made in terms of population genetic risk.

Development of DArT-based PCR markers for selecting drought-tolerant spring barley.

Science.gov (United States)

Fiust, Anna; Rapacz, Marcin; Wójcik-Jagła, Magdalena; Tyrka, Mirosław

2015-08-01

The tolerance of spring barley (Hordeum vulgare L.) cultivars to spring drought is an important agronomic trait affecting crop yield and quality in Poland. Therefore, breeders require new molecular markers to select plants with lower spring drought susceptibility. With the advent of genomic selection technology, simple molecular tools may still be applicable to screen material for markers of the most important traits and in-depth genome scanning. In previous studies, diversity arrays technology (DArT)-based genetic maps were constructed for F2 populations of Polish fodder and malt barley elite breeding lines, and 15 and 18 quantitative trait loci (QTLs) related to spring drought tolerance were identified, respectively. In this paper, we show the results of a conversion of 30 DArT markers corresponding to 11 QTLs into simple sequence repeat (SSR) and sequence tagged site (STS) markers. Twenty-two polymorphic markers were obtained, including 13 DArT-based SSRs. Additionally, 31 SSR markers, located in close proximity to the DArT markers, were selected from the GrainGenes database and tested. Further analyses of 24 advanced breeding lines with different drought tolerances confirmed that five out of the 30 converted markers, as well as three out of the 31 additional SSR markers, were effective in marker-assisted selection for drought tolerance. The possible function of clones related to these markers in drought tolerance is discussed.

Anthropomorphiс formidentinents-markers of significative field of catholic ethnoreligious space

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V. I. Kryachko

2014-12-01

Anthropomorphic significative subsystem with its formidentinents­markers of the significative field of Catholic ethnoreligious space includes visualized in space anthropomorphic and personificated symbolic constructions and formelements, that are explicated via objective­material patterns: paintings, architecture, etc., and are often linked with various religious and ethnic symbolic systems.

Candidacy of a chitin-inducible gibberellin-responsive gene for a major locus affecting plant height in rice that is closely linked to Green Revolution gene sd1.

Science.gov (United States)

Kovi, Mallikarjuna Rao; Zhang, Yushan; Yu, Sibin; Yang, Gaiyu; Yan, Wenhao; Xing, Yongzhong

2011-09-01

Appropriate plant height is crucial for lodging resistance to improve the rice crop yield. The application of semi-dwarf 1 led to the green revolution in the 1960s, by predominantly increasing the rice yield. However, the frequent use of single sd1 gene sources may cause genetic vulnerability to pests and diseases. Identifying useful novel semi-dwarf genes is important for the genetic manipulation of plant architecture in practical rice breeding. In this study, introgression lines derived from two parents contrasting in plant height, Zhenshan 97 and Pokkali were employed to locate a gene with a large effect on plant height by the bulk segregant analysis method. A major gene, ph1, was mapped to a region closely linked to sd1 on chromosome 1; the additive effects of ph1 were more than 50 cm on the plant height and 2 days on the heading date in a BC(4)F(2) population and its progeny. ph1 was then fine mapped to BAC AP003227. Gene annotation indicated that LOC_OS01g65990 encoding a chitin-inducible gibberellin-responsive protein (CIGR), which belongs to the GRAS family, might be the right candidate gene of ph1. Co-segregation analysis of the candidate gene-derived marker finally confirmed its identity as the candidate gene. A higher expression level of the CIGR was detected in all the tested tissues in tall plants compared to those of short plants, especially in the young leaf sheath containing elongating tissues, which indicated its importance role in regulating plant height. ph1 showed a tremendous genetic effect on plant height, which is distinct from sd1 and could be a new resource for breeding semi-dwarf varieties.

Genetic markers, translocations and sexing genes on chromosome 2 of Ceratitis capitata

International Nuclear Information System (INIS)

Cladera, J.L.

1997-01-01

A review is presented of results obtained in a search for genetic markers, translocations and selectable genes obtained at the Instituto de Genetica, Castelar, Argentina, with special reference to chromosome 2 linked mutations and genes useful for developing self-sexing strains in Ceratitis capitata. (author)

Analysis of the association between spawning time QTL markers and the biannual spawning behavior in rainbow trout (Oncorhynchus mykiss

Directory of Open Access Journals (Sweden)

Nelson Colihueque

2010-01-01

Full Text Available The rainbow trout is a salmonid fish that occasionally exhibits broodstocks with biannual spawning behavior, a phenomenon known as a double annual reproductive cycle (DARC. Spawning time quantitative trait loci (SPT-QTLs affect the time of the year that female rainbow trout spawn and may influence expression of the DARC trait. In this study, microsatellite markers linked and unlinked to SPT-QTLs were genotyped to investigate the underlying genetics of this trait. SPT-QTLs influenced the DARC trait since in two case-control comparisons three linked markers (OmyFGT12TUF, One3ASC and One19ASC had significant levels of allelic frequency differentiation and marker-character association. Furthermore, alleles of One3ASC and One19ASC had significantly higher frequencies in populations that carried the DARC trait.

Are the metabolomic responses to folivory of closely related plant species linked to macroevolutionary and plant-folivore coevolutionary processes?

Energy Technology Data Exchange (ETDEWEB)

Rivas-Ubach, Albert [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland Washington 99354 USA; CREAF, Cerdanyola del Vallès 08913 Catalonia Spain; Hódar, José A. [Grupo de Ecología Terrestre, Departamento de Biología Animal y Ecología, Facultad de Ciencias, Universidad de Granada, 18071 Granada Spain; Sardans, Jordi [CREAF, Cerdanyola del Vallès 08913 Catalonia Spain; CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès 08913 Catalonia Spain; Kyle, Jennifer E. [Biological Sciences Division, Pacific Northwest National Laboratory, Richland Washington 99354 USA; Kim, Young-Mo [Biological Sciences Division, Pacific Northwest National Laboratory, Richland Washington 99354 USA; Oravec, Michal [Global Change Research Centre, Academy of Sciences of the Czech Republic, Bĕlidla 4a CZ-603 00 Brno Czech Republic; Urban, Otmar [Global Change Research Centre, Academy of Sciences of the Czech Republic, Bĕlidla 4a CZ-603 00 Brno Czech Republic; Guenther, Alex [Department of Earth System Science, University of California, Irvine California 92697 USA; Peñuelas, Josep [CREAF, Cerdanyola del Vallès 08913 Catalonia Spain; CSIC, Global Ecology Unit CREAF-CEAB-CSIC-UAB, Cerdanyola del Vallès 08913 Catalonia Spain

2016-06-02

The debate whether the coevolution of plants and insects or macroevolutionary processes (phylogeny) is the main driver determining the arsenal of molecular defensive compounds of plants remains unresolved. Attacks by herbivorous insects affect not only the composition of defensive compounds in plants but the entire metabolome (the set of molecular metabolites), including defensive compounds. Metabolomes are the final products of genotypes and are directly affected by macroevolutionary processes, so closely related species should have similar metabolomic compositions and may respond in similar ways to attacks by folivores. We analyzed the elemental compositions and metabolomes of needles from Pinus pinaster, P. nigra and P. sylvestris to determine if these closely related Pinus species with different coevolutionary histories with the caterpillars of the processionary moth respond similarly to attacks by this lepidopteran. All pines had different metabolomes and metabolic responses to herbivorous attack. The metabolomic variation among the pine species and the responses to folivory reflected their macroevolutionary relationships, with P. pinaster having the most divergent metabolome. The concentrations of phenolic metabolites were generally not higher in the attacked trees, which had lower concentrations of terpenes, suggesting that herbivores avoid individuals with high concentrations of terpenes. Our results suggest that macroevolutionary history plays important roles in the metabolomic responses of these pine species to folivory, but plant-insect coevolution probably constrains those responses. Combinations of different evolutionary factors and trade-offs are likely responsible for the different responses of each species to folivory, which is not necessarily exclusively linked to plant-insect coevolution.

A study of autoimmune markers in hepatitis C infection.

Science.gov (United States)

Agarwal, N; Handa, R; Acharya, S K; Wali, J P; Dinda, A K; Aggarwal, P

2001-05-01

Hepatitis C virus (HCV) infection is associated with several autoimmune markers. Despite HCV being common in India, no information on this aspect is available. This study was undertaken to ascertain the frequency and clinical significance of autoimmune markers like rheumatoid factor (RF), antinuclear antibodies (ANA), antibodies to double stranded deoxyribonucleic acid (dsDNA), anti neutrophil cytoplasmic antibody (ANCA), anti smooth muscle antibodies (ASMA), anti liver kidney microsomal 1 antibodies (anti LKM1), anti gastric parietal cell antibodies (anti GPCA), anti mitochondrial antibodies (AMA), anti cardiolipin antibodies (ACL) and cryoglobulins in HCV infection and to determine the effect of treatment on these markers. Twenty five patients with chronic hepatitis C and 25 healthy controls were studied. Cryoglobulins were detected by cryoprecipitation, RF by latex agglutination, anti dsDNA and ACL by ELISA while indirect immunofluorescence was used to detect all other autoantibodies. Eighteen patients (72%) demonstrated autoimmune markers. RF, cryoglobulins and anti LKM1 antibodies were the most frequently detected markers (in 32% patients each). ASMA, perinuclear ANCA (pANCA), ANA and anti GPCA were seen in 24, 20, 12 and 4 per cent patients respectively. None of the patients exhibited ACL, AMA or antibodies to dsDNA. No antibodies were detected in healthy controls. Sixty per cent of the patients had rheumatological symptoms. Of the seven patients followed up after treatment with alpha interferon, only two exhibited persistence of RF, while symptoms and other markers disappeared. Rheumatological symptoms and autoimmune markers are common in HCV infection and are usually overlooked. Patients with unexplained joint pains and/or palpable purpura should be screened for HCV. Further studies are needed to delineate fully the link between infection and autoimmunity.

A proof-of-principle simulation for closed-loop control based on preexisting experimental thalamic DBS-enhanced instrumental learning.

Science.gov (United States)

Wang, Ching-Fu; Yang, Shih-Hung; Lin, Sheng-Huang; Chen, Po-Chuan; Lo, Yu-Chun; Pan, Han-Chi; Lai, Hsin-Yi; Liao, Lun-De; Lin, Hui-Ching; Chen, Hsu-Yan; Huang, Wei-Chen; Huang, Wun-Jhu; Chen, You-Yin

Deep brain stimulation (DBS) has been applied as an effective therapy for treating Parkinson's disease or essential tremor. Several open-loop DBS control strategies have been developed for clinical experiments, but they are limited by short battery life and inefficient therapy. Therefore, many closed-loop DBS control systems have been designed to tackle these problems by automatically adjusting the stimulation parameters via feedback from neural signals, which has been reported to reduce the power consumption. However, when the association between the biomarkers of the model and stimulation is unclear, it is difficult to develop an optimal control scheme for other DBS applications, i.e., DBS-enhanced instrumental learning. Furthermore, few studies have investigated the effect of closed-loop DBS control for cognition function, such as instrumental skill learning, and have been implemented in simulation environments. In this paper, we proposed a proof-of-principle design for a closed-loop DBS system, cognitive-enhancing DBS (ceDBS), which enhanced skill learning based on in vivo experimental data. The ceDBS acquired local field potential (LFP) signal from the thalamic central lateral (CL) nuclei of animals through a neural signal processing system. A strong coupling of the theta oscillation (4-7 Hz) and the learning period was found in the water reward-related lever-pressing learning task. Therefore, the theta-band power ratio, which was the averaged theta band to averaged total band (1-55 Hz) power ratio, could be used as a physiological marker for enhancement of instrumental skill learning. The on-line extraction of the theta-band power ratio was implemented on a field-programmable gate array (FPGA). An autoregressive with exogenous inputs (ARX)-based predictor was designed to construct a CL-thalamic DBS model and forecast the future physiological marker according to the past physiological marker and applied DBS. The prediction could further assist the design of

Decoupling Identification for Serial Two-Link Two-Inertia System

Science.gov (United States)

Oaki, Junji; Adachi, Shuichi

The purpose of our study is to develop a precise model by applying the technique of system identification for the model-based control of a nonlinear robot arm, under taking joint-elasticity into consideration. We previously proposed a systematic identification method, called “decoupling identification,” for a “SCARA-type” planar two-link robot arm with elastic joints caused by the Harmonic-drive® reduction gears. The proposed method serves as an extension of the conventional rigid-joint-model-based identification. The robot arm is treated as a serial two-link two-inertia system with nonlinearity. The decoupling identification method using link-accelerometer signals enables the serial two-link two-inertia system to be divided into two linear one-link two-inertia systems. The MATLAB®'s commands for state-space model estimation are utilized in the proposed method. Physical parameters such as motor inertias, link inertias, joint-friction coefficients, and joint-spring coefficients are estimated through the identified one-link two-inertia systems using a gray-box approach. This paper describes accuracy evaluations using the two-link arm for the decoupling identification method under introducing closed-loop-controlled elements and varying amplitude-setup of identification-input. Experimental results show that the identification method also works with closed-loop-controlled elements. Therefore, the identification method is applicable to a “PUMA-type” vertical robot arm under gravity.

A case against bio markers as they are currently used in radioecological risk analyses: a problem of linkage

International Nuclear Information System (INIS)

Hinton, T.G.; Brechignac, F.

2005-01-01

Bio-markers are successfully used in human risk analyses as early indicators of contaminant exposure and predictors of deleterious effects. This has boosted the search for bio-markers in determining ecological risks to non-human biota, and particularly for assessments related to radioactive contaminants. There are difficulties, however, that prevent an easy transfer of the bio-marker concept from humans to non-human biota, as there are significant differences in endpoints of concern, units of observation and dose response relationships between human and ecological risk analyses. The use of bio-markers in ecological risk analyses currently lacks a linkage between molecular-level effects and quantifiable impacts observed in individuals and populations. This is important because ecological risk analyses generally target the population level of biological organisation. We highlight various examples that demonstrate the difficulties of linking individual responses to population-level impacts, such as indirect effects and compensatory interactions. Eco-toxicologists cope with such difficulties through the use of uncertainty or extrapolation factors. Extrapolation factors (EF) typically range from 1 to 1000 when linking effects observed in individuals to those predicted to occur in populations. We question what magnitude of EF will be required when going from a molecular level effect, measured by a bio-marker, all the way up to the population level of biological organisation. Particularly, we stress that a successful application of bio-markers to radioecological risk assessment can only be achieved once the connection has been made between changes in individual resource allocation-based life histories and population dynamics. This clearly emphasises the need to quantify the propagation of molecular and cellular level effects to higher levels of biological organisation, especially in the long-term via several generations of exposure. Finally, we identify pertinent research

NABIC marker database: A molecular markers information network of agricultural crops.

Science.gov (United States)

Kim, Chang-Kug; Seol, Young-Joo; Lee, Dong-Jun; Jeong, In-Seon; Yoon, Ung-Han; Lee, Gang-Seob; Hahn, Jang-Ho; Park, Dong-Suk

2013-01-01

In 2013, National Agricultural Biotechnology Information Center (NABIC) reconstructs a molecular marker database for useful genetic resources. The web-based marker database consists of three major functional categories: map viewer, RSN marker and gene annotation. It provides 7250 marker locations, 3301 RSN marker property, 3280 molecular marker annotation information in agricultural plants. The individual molecular marker provides information such as marker name, expressed sequence tag number, gene definition and general marker information. This updated marker-based database provides useful information through a user-friendly web interface that assisted in tracing any new structures of the chromosomes and gene positional functions using specific molecular markers. The database is available for free at http://nabic.rda.go.kr/gere/rice/molecularMarkers/

Shuttle Planning for Link Closures in Urban Public Transport Networks

DEFF Research Database (Denmark)

van der Hurk, Evelien; Koutsopoulos, Haris N.; Wilson, Nigel

2016-01-01

Urban public transport systems must periodically close certain links for maintenance, which can have significant effects on the service provided to passengers. In practice, the effects of closures are mitigated by replacing the closed links with a simple shuttle service. However, alternative...... cost, which includes transfers and frequency-dependent waiting time costs. This model is applied to a shuttle design problem based on a real-world case study of the Massachusetts Bay Transportation Authority network of Boston, Massachusetts. The results show that additional shuttle routes can reduce...

Marker Assisted Transfer of Two Powdery Mildew Resistance Genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss.) to Triticum aestivum (L.).

Science.gov (United States)

Elkot, Ahmed Fawzy Abdelnaby; Chhuneja, Parveen; Kaur, Satinder; Saluja, Manny; Keller, Beat; Singh, Kuldeep

2015-01-01

Powdery mildew (PM), caused by Blumeria graminis f. sp. tritici, is one of the important wheat diseases, worldwide. Two PM resistance genes, designated as PmTb7A.1 and PmTb7A.2, were identified in T. boeoticum acc. pau5088 and mapped on chromosome 7AL approximately 48cM apart. Two resistance gene analogue (RGA)-STS markers Ta7AL-4556232 and 7AL-4426363 were identified to be linked to the PmTb7A.1 and PmTb7A.2, at a distance of 0.6cM and 6.0cM, respectively. In the present study, following marker assisted selection (MAS), the two genes were transferred to T. aestivum using T. durum as bridging species. As many as 12,317 florets of F1 of the cross T. durum /T. boeoticum were pollinated with T. aestivum lines PBW343-IL and PBW621 to produce 61 and 65 seeds, respectively, of three-way F1. The resulting F1s of the cross T. durum/T. boeoticum//T. aestivum were screened with marker flanking both the PM resistance genes PmTb7A.1 and PmTb7A.2 (foreground selection) and the selected plants were backcrossed to generate BC1F1. Marker assisted selection was carried both in BC1F1 and the BC2F1 generations. Introgression of alien chromatin in BC2F1 plants varied from 15.4-62.9 percent. Out of more than 110 BC2F1 plants showing introgression for markers linked to the two PM resistance genes, 40 agronomically desirable plants were selected for background selection for the carrier chromosome to identify the plants with minimum of the alien introgression. Cytological analysis showed that most plants have chromosome number ranging from 40-42. The BC2F2 plants homozygous for the two genes have been identified. These will be crossed to generate lines combining both the PM resistance genes but with minimal of the alien introgression. The PM resistance gene PmTb7A.1 maps in a region very close to Sr22, a stem rust resistance gene effective against the race Ug99. Analysis of selected plants with markers linked to Sr22 showed introgression of Sr22 from T. boeoticum in several BC2F1 plants

Marker Assisted Transfer of Two Powdery Mildew Resistance Genes PmTb7A.1 and PmTb7A.2 from Triticum boeoticum (Boiss. to Triticum aestivum (L..

Directory of Open Access Journals (Sweden)

Ahmed Fawzy Abdelnaby Elkot

Full Text Available Powdery mildew (PM, caused by Blumeria graminis f. sp. tritici, is one of the important wheat diseases, worldwide. Two PM resistance genes, designated as PmTb7A.1 and PmTb7A.2, were identified in T. boeoticum acc. pau5088 and mapped on chromosome 7AL approximately 48cM apart. Two resistance gene analogue (RGA-STS markers Ta7AL-4556232 and 7AL-4426363 were identified to be linked to the PmTb7A.1 and PmTb7A.2, at a distance of 0.6cM and 6.0cM, respectively. In the present study, following marker assisted selection (MAS, the two genes were transferred to T. aestivum using T. durum as bridging species. As many as 12,317 florets of F1 of the cross T. durum /T. boeoticum were pollinated with T. aestivum lines PBW343-IL and PBW621 to produce 61 and 65 seeds, respectively, of three-way F1. The resulting F1s of the cross T. durum/T. boeoticum//T. aestivum were screened with marker flanking both the PM resistance genes PmTb7A.1 and PmTb7A.2 (foreground selection and the selected plants were backcrossed to generate BC1F1. Marker assisted selection was carried both in BC1F1 and the BC2F1 generations. Introgression of alien chromatin in BC2F1 plants varied from 15.4-62.9 percent. Out of more than 110 BC2F1 plants showing introgression for markers linked to the two PM resistance genes, 40 agronomically desirable plants were selected for background selection for the carrier chromosome to identify the plants with minimum of the alien introgression. Cytological analysis showed that most plants have chromosome number ranging from 40-42. The BC2F2 plants homozygous for the two genes have been identified. These will be crossed to generate lines combining both the PM resistance genes but with minimal of the alien introgression. The PM resistance gene PmTb7A.1 maps in a region very close to Sr22, a stem rust resistance gene effective against the race Ug99. Analysis of selected plants with markers linked to Sr22 showed introgression of Sr22 from T. boeoticum in

LEOPARD syndrome is not linked to the Marfan syndrome and the Watson syndrome loci

Energy Technology Data Exchange (ETDEWEB)

Rass-Rothchild, A.: Abeliovitch, D.; Kornstein, A. [Tel Aviv Univ. (Israel)]|[Hebrew Univ., Jerusalem (Israel)

1994-09-01

The acronym LEOPARD stands for a syndromic association of Lentigines, Eletrocardiographic changes, Ocular hypertelorism, Pulmonic stenosis, Abnormal genitalia, Retardation of growth and sensorineural Deafness. Inheritance is autosomal dominant with high penetrance and variable expressivity. In 1990 Torok et al. reported on the association of LEOPARD and Marfan syndrome. In addition a clinical similarity (cardiac and cutaneous involvement) exists with the Watson syndrome (neurofibromatosis and pulmonic stenosis) which is linked to the marker D17S33 on chromosome 17. We studied possible linkage of LEOPARD syndrome to the Marfan syndrome locus on chromosome 15 (D15S1, MF13, and (TAAAA)n repeats) and to the NF-1 locus on chromosome 17 in a family with 9 cases of LEOPARD syndrome. Close linkage between LEOPARD syndrome and both the Marfan locus on chromosome 15 and the NF-1 locus on chromosome 17 was excluded (lod score <-2.0 through {theta} = 0.1).

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

Directory of Open Access Journals (Sweden)

Y. H. Li

2014-05-01

Full Text Available 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

Phylogeny Inference of Closely Related Bacterial Genomes: Combining the Features of Both Overlapping Genes and Collinear Genomic Regions

Science.gov (United States)

Zhang, Yan-Cong; Lin, Kui

2015-01-01

Overlapping genes (OGs) represent one type of widespread genomic feature in bacterial genomes and have been used as rare genomic markers in phylogeny inference of closely related bacterial species. However, the inference may experience a decrease in performance for phylogenomic analysis of too closely or too distantly related genomes. Another drawback of OGs as phylogenetic markers is that they usually take little account of the effects of genomic rearrangement on the similarity estimation, such as intra-chromosome/genome translocations, horizontal gene transfer, and gene losses. To explore such effects on the accuracy of phylogeny reconstruction, we combine phylogenetic signals of OGs with collinear genomic regions, here called locally collinear blocks (LCBs). By putting these together, we refine our previous metric of pairwise similarity between two closely related bacterial genomes. As a case study, we used this new method to reconstruct the phylogenies of 88 Enterobacteriale genomes of the class Gammaproteobacteria. Our results demonstrated that the topological accuracy of the inferred phylogeny was improved when both OGs and LCBs were simultaneously considered, suggesting that combining these two phylogenetic markers may reduce, to some extent, the influence of gene loss on phylogeny inference. Such phylogenomic studies, we believe, will help us to explore a more effective approach to increasing the robustness of phylogeny reconstruction of closely related bacterial organisms. PMID:26715828

Performance Analysis of ARQ-Based RF-FSO Links

KAUST Repository

Makki, Behrooz

2017-02-22

We study the performance of hybrid radio-frequency (RF) and free-space optical (FSO) links using automatic repeat request (ARQ). We derive closed-form expressions for the throughput and outage probability with different channel models. We also evaluate the effect of adaptive power allocation between the ARQ retransmissions on the system performance. The results show that joint implementation of the RF and FSO links leads to substantial performance improvement, compared to the cases with only the RF or the FSO link.

Single-tube tetradecaplex panel of highly polymorphic microsatellite markers hemophilia A.

Science.gov (United States)

Zhao, M; Chen, M; Tan, A S C; Cheah, F S H; Mathew, J; Wong, P C; Chong, S S

2017-07-01

Essentials Preimplantation genetic diagnosis (PGD) of severe hemophilia A relies on linkage analysis. Simultaneous multi-marker screening can simplify selection of informative markers in a couple. We developed a single-tube tetradecaplex panel of polymorphic markers for hemophilia A PGD use. Informative markers can be used for linkage analysis alone or combined with mutation detection. Background It is currently not possible to perform single-cell preimplantation genetic diagnosis (PGD) to directly detect the common inversion mutations of the factor VIII (F8) gene responsible for severe hemophilia A (HEMA). As such, PGD for such inversion carriers relies on indirect analysis of linked polymorphic markers. Objectives To simplify linkage-based PGD of HEMA, we aimed to develop a panel of highly polymorphic microsatellite markers located near the F8 gene that could be simultaneously genotyped in a multiplex-PCR reaction. Methods We assessed the polymorphism of various microsatellite markers located ≤ 1 Mb from F8 in 177 female subjects. Highly polymorphic markers were selected for co-amplification with the AMELX/Y indel dimorphism in a single-tube reaction. Results Thirteen microsatellite markers located within 0.6 Mb of F8 were successfully co-amplified with AMELX/Y in a single-tube reaction. Observed heterozygosities of component markers ranged from 0.43 to 0.84, and ∼70-80% of individuals were heterozygous for ≥ 5 markers. The tetradecaplex panel successfully identified fully informative markers in a couple interested in PGD for HEMA because of an intragenic F8 point mutation, with haplotype phasing established through a carrier daughter. In-vitro fertilization (IVF)-PGD involved single-tube co-amplification of fully informative markers with AMELX/Y and the mutation-containing F8 amplicon, followed by microsatellite analysis and amplicon mutation-site minisequencing analysis. Conclusions The single-tube multiplex-PCR format of this highly polymorphic

miR-21 Is Linked to Glioma Angiogenesis

DEFF Research Database (Denmark)

Hermansen, Simon Kjær; Nielsen, Boye Schnack; Aaberg-Jessen, Charlotte

2016-01-01

MicroRNA-21 (miR-21) is the most consistently over-expressed microRNA (miRNA) in malignant gliomas. We have previously reported that miR-21 is upregulated in glioma vessels and subsets of glioma cells. To better understand the role of miR-21 in glioma angiogenesis and to characterize miR-21......-localized with the hypoxia- and angiogenesis-associated markers HIF-1α (p=0.0020) and VEGF (p=0.0096), whereas the putative miR-21 target, PTEN, was expressed independently of miR-21. Expression of stem cell markers Oct4, Sox2 and CD133 was not associated with miR-21. In six glioblastoma cultures, miR-21 did not correlate...... with the six markers. These findings suggest that miR-21 is linked to glioma angiogenesis, that miR-21 is unlikely to regulate PTEN, and that miR-21-positive tumor cells do not possess stem cell characteristics....

[18F]-FMISO PET study of hypoxia in gliomas before surgery: correlation with molecular markers of hypoxia and angiogenesis

Energy Technology Data Exchange (ETDEWEB)

Bekaert, Lien [CHU de Caen, Department of Neurology, Caen (France); Normandie Univ, UNICAEN, CEA, CNRS, ISTCT/CERVOxy Group, Caen (France); CHU de Caen, Department of Neurosurgery, Caen (France); CHU de Caen, Service de Neurochirurgie, Caen (France); Valable, Samuel; Collet, Solene; Bordji, Karim; Petit, Edwige; Bernaudin, Myriam [Normandie Univ, UNICAEN, CEA, CNRS, ISTCT/CERVOxy Group, Caen (France); Lechapt-Zalcman, Emmanuele [Normandie Univ, UNICAEN, CEA, CNRS, ISTCT/CERVOxy Group, Caen (France); CHU de Caen, Department of Pathology, Caen (France); Ponte, Keven [CHU de Caen, Department of Neurosurgery, Caen (France); Normandie Univ, UNICAEN, CEA, CNRS, ISTCT/CERVOxy Group, Caen (France); Constans, Jean-Marc [Normandie Univ, UNICAEN, CEA, CNRS, ISTCT/CERVOxy Group, Caen (France); CHU de Caen, Department of Neuroradiology, Caen (France); Levallet, Guenaelle [CHU de Caen, Department of Pathology, Caen (France); Branger, Pierre [CHU de Caen, Department of Neurology, Caen (France); Emery, Evelyne [CHU de Caen, Department of Neurosurgery, Caen (France); Manrique, Alain [CHU de Caen, Department of Nuclear Medicine, Caen (France); Barre, Louisa [Normandie Univ, UNICAEN, CEA, CNRS, ISTCT/LDM-TEP group, Caen (France); Guillamo, Jean-Sebastien [CHU de Caen, Department of Neurology, Caen (France); Normandie Univ, UNICAEN, CEA, CNRS, ISTCT/CERVOxy Group, Caen (France); CHU de Nimes, Department of Neurology, Nimes (France)

2017-08-15

Hypoxia in gliomas is associated with tumor resistance to radio- and chemotherapy. However, positron emission tomography (PET) imaging of hypoxia remains challenging, and the validation of biological markers is, therefore, of great importance. We investigated the relationship between uptake of the PET hypoxia tracer [18F]-FMISO and other markers of hypoxia and angiogenesis and with patient survival. In this prospective single center clinical study, 33 glioma patients (grade IV: n = 24, III: n = 3, and II: n = 6) underwent [18F]-FMISO PET and MRI including relative cerebral blood volume (rCBV) maps before surgery. Maximum standardized uptake values (SUVmax) and hypoxic volume were calculated, defining two groups of patients based on the presence or absence of [18F]-FMISO uptake. After surgery, molecular quantification of CAIX, VEGF, Ang2 (rt-qPCR), and HIF-1α (immunohistochemistry) were performed on tumor specimens. [18F]-FMISO PET uptake was closely linked to tumor grade, with high uptake in glioblastomas (GB, grade IV). Expression of biomarkers of hypoxia (CAIX, HIF-1α), and angiogenesis markers (VEGF, Ang2, rCBV) were significantly higher in the [18F]-FMISO uptake group. We found correlations between the degree of hypoxia (hypoxic volume and SUVmax) and expression of HIF-1α, CAIX, VEGF, Ang2, and rCBV (p < 0.01). Patients without [18F]-FMISO uptake had a longer survival time than uptake positive patients (log-rank, p < 0.005). Tumor hypoxia as evaluated by [18F]-FMISO PET is associated with the expression of hypoxia markers on a molecular level and is related to angiogenesis. [18F]-FMISO uptake is a mark of an aggressive tumor, almost always a glioblastoma. Our results underline that [18F]-FMISO PET could be useful to guide glioma treatment, and in particular radiotherapy, since hypoxia is a well-known factor of resistance. (orig.)

Demographic changes and marker properties affect detection of human population differentiation

Directory of Open Access Journals (Sweden)

Sanichwankul Kittipong

2007-05-01

Full Text Available Abstract Background Differentiating genetically between populations is valuable for admixture and population stratification detection and in understanding population history. This is easy to achieve for major continental populations, but not for closely related populations. It has been claimed that a large marker panel is necessary to reliably distinguish populations within a continent. We investigated whether empirical genetic differentiation could be accomplished efficiently among three Asian populations (Hmong, Thai, and Chinese using a small set of highly variable markers (15 tetranucleotide and 17 dinucleotide repeats. Results Hmong could be differentiated from Thai and Chinese based on multi-locus genotypes, but Thai and Chinese were indistinguishable from each other. We found significant evidence for a recent population bottleneck followed by expansion in the Hmong that was not present in the Thai or Chinese. Tetranucleotide repeats were less useful than dinucleotide repeat markers in distinguishing between major continental populations (Asian, European, and African while both successfully distinguished Hmong from Thai and Chinese. Conclusion Demographic history contributes significantly to robust detection of intracontinental population structure. Populations having experienced a rapid size reduction may be reliably distinguished as a result of a genetic drift -driven redistribution of population allele frequencies. Tetranucleotide markers, which differ from dinucleotide markers in mutation mechanism and rate, are similar in information content to dinucleotide markers in this situation. These factors should be considered when identifying populations suitable for gene mapping studies and when interpreting interpopulation relationships based on microsatellite markers.

Development of marker-free transgenic Jatropha curcas producing curcin-deficient seeds through endosperm-specific RNAi-mediated gene silencing.

Science.gov (United States)

Gu, Keyu; Tian, Dongsheng; Mao, Huizhu; Wu, Lifang; Yin, Zhongchao

2015-10-08

Jatropha curcas L. is a potential biofuel plant and its seed oil is suitable for biodiesel production. Despite this promising application, jatropha seeds contain two major toxic components, namely phorbol esters and curcins. These compounds would reduce commercial value of seed cake and raise safety and environment concerns on jatropha plantation and processing. Curcins are Type I ribosome inactivating proteins. Several curcin genes have been identified in the jatropha genome. Among which, the Curcin 1 (C1) gene is identified to be specifically expressed in endosperm, whereas the Curcin 2A (C2A) is mainly expressed in young leaves. A marker-free RNAi construct carrying a β-estradiol-regulated Cre/loxP system and a C1 promoter-driven RNAi cassette for C1 gene was made and used to generate marker-free transgenic RNAi plants to specifically silence the C1 gene in the endosperm of J. curcas. Plants of transgenic line L1, derived from T0-1, carry two copies of marker-free RNAi cassette, whereas plants of L35, derived from T0-35, harbored one copy of marker-free RNAi cassette and three copies of closely linked and yet truncated Hpt genes. The C1 protein content in endosperm of L1 and L35 seeds was greatly reduced or undetectable, while the C2A proteins in young leaves of T0-1 and T0-35 plants were unaffected. In addition, the C1 mRNA transcripts were undetectable in the endosperm of T3 seeds of L1 and L35. The results demonstrated that the expression of the C1 gene was specifically down-regulated or silenced by the double-stranded RNA-mediated RNA interference generated from the RNAi cassette. The C1 promoter-driven RNAi cassette for the C1 gene in transgenic plants was functional and heritable. Both C1 transcripts and C1 proteins were greatly down-regulated or silenced in the endosperm of transgenic J. curcas. The marker-free transgenic plants and curcin-deficient seeds developed in this study provided a solution for the toxicity of curcins in jatropha seeds and

Ascorbic acid: Nonradioactive extracellular space marker in canine heart

International Nuclear Information System (INIS)

Reil, G.H.; Frombach, R.; Kownatzki, R.; Quante, W.; Lichtlen, P.R.

1987-01-01

The distribution pattern of ascorbic acid and L-[ 14 C]ascorbic acid in myocardial tissue was compared with those of the classical radioactive extracellular space markers [ 3 H]-inulin, [ 3 H]sucrose, and Na 82 Br. A new polarographic techniques was developed for analogue registration of ascorbic acid concentration in coronary venous blood. The kinetic data of the markers were studied in an open-chest canine heart preparation during a constant tracer infusion of up to 9 min. Distribution volumes were calculated based on the mean transit time method of Zierler. The distribution volume of ascorbic acid as well as of L-[ 14 C]ascorbic acid in myocardial tissue agreed closely with those of [ 3 H]inulin and [ 3 H]sucrose as well as 82 Br. The obtained kinetic data confirmed that ascorbic acid exhibits the physicochemical properties of an extracellular space marker, though this compound was shown to leak slowly into myocardial cells. Favorable attributes of this indicator are its low molecular weight, high diffusibility in interstitial fluid, low binding affinity to macromolecules, and high transcapillary as well as low transplasmalemmal penetration rate. Therefore, this nonradioactive marker can be applied in a safe and simple fashion, and without untoward side effects in experimental animals as well as in patients

Characterization of Fungus-Specific Microsatellite Markers in the Lichen Fungus Usnea subfloridana (Parmeliaceae

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Tiiu Tõrra

2014-07-01

Full Text Available Premise of the study: Microsatellite loci were developed for the haploid lichenized fungal species Usnea subfloridana to study its population subdivision and the species' response to forest disturbance, fragmentation, and environmental pollution. Methods and Results: We developed 14 polymorphic microsatellite markers using 454 pyrosequencing data of U. subfloridana. The number of alleles per locus ranged from three to 15, and Nei's unbiased gene diversity averaged over nine markers without null alleles ranged from 0.64 to 0.67. Evaluation of the cross-species amplification in U. glabrescens and U. wasmuthii indicates that these markers are also informative in other Usnea species. Conclusions: These markers will allow us to investigate the effects of forest management and environmental pollution on genetic population structure of U. subfloridana and closely related species. Moreover, they will help facilitate phylogeographic studies of U. subfloridana across the species' distribution area in Europe.

Genetics and mapping of the R₁₁ gene conferring resistance to recently emerged rust races, tightly linked to male fertility restoration, in sunflower (Helianthus annuus L.).

Science.gov (United States)

Qi, L L; Seiler, G J; Vick, B A; Gulya, T J

2012-09-01

Sunflower oil is one of the major sources of edible oil. As the second largest hybrid crop in the world, hybrid sunflowers are developed by using the PET1 cytoplasmic male sterility system that contributes to a 20 % yield advantage over the open-pollinated varieties. However, sunflower production in North America has recently been threatened by the evolution of new virulent pathotypes of sunflower rust caused by the fungus Puccinia helianthi Schwein. Rf ANN-1742, an 'HA 89' backcross restorer line derived from wild annual sunflower (Helianthus annuus L.), was identified as resistant to the newly emerged rust races. The aim of this study was to elucidate the inheritance of rust resistance and male fertility restoration and identify the chromosome location of the underlying genes in Rf ANN-1742. Chi-squared analysis of the segregation of rust response and male fertility in F(2) and F(3) populations revealed that both traits are controlled by single dominant genes, and that the rust resistance gene is closely linked to the restorer gene in the coupling phase. The two genes were designated as R ( 11 ) and Rf5, respectively. A set of 723 mapped SSR markers of sunflower was used to screen the polymorphism between HA 89 and the resistant plant. Bulked segregant analysis subsequently located R ( 11 ) on linkage group (LG) 13 of sunflower. Based on the SSR analyses of 192 F(2) individuals, R ( 11 ) and Rf5 both mapped to the lower end of LG13 at a genetic distance of 1.6 cM, and shared a common marker, ORS728, which was mapped 1.3 cM proximal to Rf5 and 0.3 cM distal to R ( 11 ) (Rf5/ORS728/R ( 11 )). Two additional SSRs were linked to Rf5 and R ( 11 ): ORS995 was 4.5 cM distal to Rf5 and ORS45 was 1.0 cM proximal to R ( 11 ). The advantage of such an introduced alien segment harboring two genes is its large phenotypic effect and simple inheritance, thereby facilitating their rapid deployment in sunflower breeding programs. Suppressed recombination was observed in LGs 2, 9

TIMP-1 as a tumor marker in breast cancer - an update

DEFF Research Database (Denmark)

Würtz, Sidse Ørnbjerg; Rasmussen, Anne-Sofie Schrohl; Mouridsen, Henning

2008-01-01

. This review gives an update on the ongoing investigation of the potential role of TIMP-1 as a tumor marker in breast cancer. Furthermore, we link the clinical findings with studies of the molecular actions of the TIMP-1 protein, raising hypotheses that may explain why TIMP-1 could play an important role...... opportunities emerge in the future this need will continue to grow. Thus, the search for molecular markers of prognosis and prediction is ongoing. Tissue Inhibitor of Metalloproteinases-1 (TIMP-1) has been suggested as a marker of both prognosis and response to treatment. Several studies have demonstrated...... the association between TIMP-1 and prognosis in breast cancer and new studies within this area have focused on the possibility of using blood samples or paraffin embedded tissue instead of tumor tissue extracts for measurements of TIMP-1. Interestingly, recent studies have investigated the association between...

Malformation/dysplasia syndrome (neural tube defect, hypospadias neuroblastoma) associated with an extra dicentric marker chromosome 15 ({open_quotes}inversion duplication 15{close_quotes})

Energy Technology Data Exchange (ETDEWEB)

Reitnauer, P.J.; Rao, K.W.; Tepperberg, J.H. [Univ. of North Carolina, Chapel Hill, NC (United States)

1994-09-01

Extra dicentric 15 marker chromosomes are associated with variable degrees of mental retardation but not major structural birth defects. We have studied a unique patient, a male infant who was prenatally diagnosed with lumbar meningomyelocele and an extra pseudodicentric marker chromosome: 47,XY,+psu dic(15)t(15;15)(?q12,?q12)mat. Hairy ears and a coronal hypospadias were noted at birth. At three months of age, a stage I thoracic neuroblastoma was primarily resected. Tumor cells, skin fibroblasts and peripheral blood lymphocytes contained the dicentric 15. The mother is mosaic for the marker chromosome. Fluorescence in situ hybridization (FISH) studies using a classic 15 satellite probe (D15Z1 [Oncor]) confirmed the presence of 2 number 15 centromeres in the marker. The marker is felt to be the result of a translocation rather than an inverted duplication because the G-band morphology of the short arm/satellite complexes differ from one another, implying that the arms originate from 2 different number 15s. FISH analysis using cosmid probes for the Prader-Willi/Angelman critical region (D15S11 and GABRB3 [Oncor]) revealed 2 copies of this region, indicating that these loci are duplicated in the marker. Although some features of the patient`s phenotype such as developmental delay and hypotonia have been associated with dicentric chromosome 15 markers, this is the first malformation/dysplasia syndrome or neuroblastoma reported to our knowledge. The association of neuroblastoma with chromosome 15 aberrations in this case provides speculation as to the role of chromosome 15 loci in cell division control.

Estimation of genetic parameters and detection of quantitative trait loci for minerals in Danish Holstein and Danish Jersey milk

DEFF Research Database (Denmark)

Buitenhuis, Albert Johannes; Poulsen, Nina Aagaard; Sehested, Jakob

2015-01-01

of significant markers between DH and DJ revealed that the SNP ARS-BFGL-NGS-4939 was common in both breeds for Zn. This SNP marker is closely linked to the DGAT1 gene. Even though we found significant SNP markers on BTA14 in both DH and DJ for Ca, and Fe these significant SNPs did not overlap. Conclusion...

APPLICATION OF RYE SSR MARKERS FOR DETECTION OF GENETIC DIVERSITY IN TRITICALE

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Želmíra Balážová

2016-06-01

Full Text Available Present study aims to testify usefulness of particular rye SSR markers for the detection of genetic diversity degree in the set of 20 triticale cultivars coming from different European countries. For this purpose, a set of six rye SSR markers were used. The set of six polymorphic markers provided 22 alleles with an average frequency of 3.67 alleles per locus. The number of alleles ranged between 2 (SCM43 and 5 (SCM28, SCM86. Resulting from the number and frequency of alleles diversity index (DI, polymorphic information content (PIC and probability of identity (PI were calculated. An average value of PIC for 6 SSR markers was 0.505, the highest value was calculated for rye SSR marker SCM86 (0.706. Based on UPGMA algorithm, a dendrogram was constructed. In dendrogram cultivars were divided into two main clusters. The first cluster contained two cultivars, Russian cultivar Greneder and Slovak cultivar Largus, and second included 18 cultivars. Genetically the closest were two Greek cultivars (Niobi and Thisbi and were close to other Greek cultivar Vrodi. It was possible to separate triticale cultivars of spring and winter form in dendrogram. Results showed the utility of rye microsatellite markers for estimation of genetic diversity of European triticale genotypes leading to genotype identification.

Identifying Quantitative Trait Loci (QTLs) and Developing Diagnostic Markers Linked to Orange Rust Resistance in Sugarcane (Saccharum spp.).

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Yang, Xiping; Islam, Md S; Sood, Sushma; Maya, Stephanie; Hanson, Erik A; Comstock, Jack; Wang, Jianping

2018-01-01

Sugarcane ( Saccharum spp.) is an important economic crop, contributing up to 80% of table sugar used in the world and has become a promising feedstock for biofuel production. Sugarcane production has been threatened by many diseases, and fungicide applications for disease control have been opted out for sustainable agriculture. Orange rust is one of the major diseases impacting sugarcane production worldwide. Identifying quantitative trait loci (QTLs) and developing diagnostic markers are valuable for breeding programs to expedite release of superior sugarcane cultivars for disease control. In this study, an F 1 segregating population derived from a cross between two hybrid sugarcane clones, CP95-1039 and CP88-1762, was evaluated for orange rust resistance in replicated trails. Three QTLs controlling orange rust resistance in sugarcane (qORR109, qORR4 and qORR102) were identified for the first time ever, which can explain 58, 12 and 8% of the phenotypic variation, separately. We also characterized 1,574 sugarcane putative resistance ( R ) genes. These sugarcane putative R genes and simple sequence repeats in the QTL intervals were further used to develop diagnostic markers for marker-assisted selection of orange rust resistance. A PCR-based Resistance gene-derived maker, G1 was developed, which showed significant association with orange rust resistance. The putative QTLs and marker developed in this study can be effectively utilized in sugarcane breeding programs to facilitate the selection process, thus contributing to the sustainable agriculture for orange rust disease control.

Molecular markers associated with aluminium tolerance in Sorghum bicolor.

Science.gov (United States)

Too, Emily Jepkosgei; Onkware, Augustino Osoro; Were, Beatrice Ang'iyo; Gudu, Samuel; Carlsson, Anders; Geleta, Mulatu

2018-01-01

Sorghum ( Sorghum bicolor , L. Moench) production in many agro-ecologies is constrained by a variety of stresses, including high levels of aluminium (Al) commonly found in acid soils. Therefore, for such soils, growing Al tolerant cultivars is imperative for high productivity. In this study, molecular markers associated with Al tolerance were identified using a mapping population developed by crossing two contrasting genotypes for this trait. Four SSR ( Xtxp34 , Sb5_236 , Sb6_34 , and Sb6_342 ), one STS ( CTG29_3b ) and three ISSR ( 811_1400 , 835_200 and 884_200 ) markers produced alleles that showed significant association with Al tolerance. CTG29_3b, 811_1400 , Xtxp34 and Sb5_ 236 are located on chromosome 3 with the first two markers located close to Alt SB , a locus that underlie the Al tolerance gene ( SbMATE ) implying that their association with Al tolerance is due to their linkage to this gene. Although CTG29_3b and 811_ 1400 are located closer to Alt SB , Xtxp34 and Sb5_236 explained higher phenotypic variance of Al tolerance indices. Markers 835_200 , 884_200 , Sb6_34 and Sb6_342 are located on different chromosomes, which implies the presence of several genes involved in Al tolerance in addition to S bMATE in sorghum. These molecular markers have a high potential for use in breeding for Al tolerance in sorghum.

Performance Analysis of FSO Links over Unified Gamma-Gamma Turbulence Channels

KAUST Repository

Ansari, Imran Shafique; Yilmaz, Ferkan; Alouini, Mohamed-Slim

2015-01-01

, then, present unified exact closed-form expressions for various statistical characteristics of the end-to-end signal-to-noise ratio (SNR) of a single link FSO transmission system. We capitalize on these unified results to offer unified exact closed

Soluble Endoglin as a new marker for prediction of pre-eclampsia in early pregnancy

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Khaled Gaber

2010-01-01

Conclusion: Pregnant women who are at risk of developing pre-eclampsia can be offered measuring these markers as a screening method to point out those who are more likely to develop pre-eclampsia and warrant close observation and intervention.

A Three Level Framework for Closed-Loop Supply Chain Management—Linking Society, Chain and Actor Level

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Stefan Seuring

2011-04-01

Full Text Available Supply chain management and closed-loop supply chain management (CLSCM have developed into established concepts in recent years. The related material cycles and product returns form an important part of all related processes with high potential for reducing environmental burden. The paper proposes a framework for (environmentally triggered closed-loop supply chain management, spanning three different levels: the societal or governance, the chain and the actor level. Within each level, a set of activities or processes can be identified. Taken together, the levels allow a comprehensive analysis of a closed-loop supply chain system. This is illustrated building on two case studies in the textile and apparel industry, where closed-loop supply chains have been designed to take specific apparel products back. The case studies are analyzed against all three levels and allow exemplification of related challenges and interrelations among the three levels. The three levels contribute to the further comprehension of the multiple issues having to be taken into account for successfully implementing closed-loop supply chains.

A novel male-associated marker for sex identification in Ussuri catfish Pseudobagrus ussuriensis

Science.gov (United States)

Zhu, Chuankun; Pan, Zhengjun; Wang, Hui; Chang, Guoliang; Ding, Huaiyu

2017-08-01

The Ussuri catfish Pseudobagrus ussuriensis is a promising aquaculture fish with sexual dimorphism that males grow 2-3 times faster than females. Therefore, all-male breeding could increase production of this fish, and sex-linked markers would be useful during the breeding process. In this study, a male-associated marker named PuGT54 was isolated in P. ussuriensis from a previously constructed microsatellite library. A total of 185 P. ussuriensis individuals containing 95 females and 90 males were used to test the usage of this maker. And results showed that sexes of all individuals were successfully identified, indicating the high reliability and accuracy of this marker for sex identification. Furthermore, the male-specific fragment amplified by this maker was cloned and sequenced, which was 118 base pairs in length. As homologous genes of this fragment was not found through BLASTn, detailed information of the male-specific fragment is unknown presently. Nevertheless, this marker would be helpful in conservation, breeding and ecological study of P. ussuriensis.

Structural Diversity and Close Interracial Relationships in College

Science.gov (United States)

Bowman, Nicholas A.

2012-01-01

Recent legal and political actions have challenged the use of race-conscious college admissions policies. Earlier research offers mixed evidence about the link between an institution's racial/ethnic composition (i.e., structural diversity) and the formation of close interracial relationships, so the present study examines this topic directly for…

An index formula for the self-linking number of a space curve

DEFF Research Database (Denmark)

Røgen, Peter

2008-01-01

Given an embedded closed space curve with non-vanishing curvature, its self-linking number is defined as the linking number between the original curve and a curve pushed slightly off in the direction of its principal normals. We present an index formula for the self-linking number in terms of the...

Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis for Crossbreeding

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Yueting Dai

2017-11-01

Full Text Available Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu. However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation. Results showed that 39, 43 and 34 novel EST-SSR markers successfully identified monokaryons from their parent dikaryons, differentiated two different mating types and discriminated F1 and F2 hybrid offspring, respectively. Furthermore, a total of 86 alleles were detected in 37 monokaryons using 18 highly informative EST-SSRs. The observed number of alleles per locus ranged from three to seven. Cluster analysis revealed that these monokaryons have a relatively high level of genetic diversity. Transfer rates of the EST-SSRs in the monokaryons of closely-related species Pleurotus eryngii var. ferulae and Pleurotus ostreatus were 72% and 64%, respectively. Therefore, our study provides new SSR markers and an efficient method to enhance the crossbreeding of Bailinggu and closely-related species.

Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis) for Crossbreeding

Science.gov (United States)

Dai, Yueting; Su, Wenying; Song, Bing; Li, Yu; Fu, Yongping

2017-01-01

Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation. Results showed that 39, 43 and 34 novel EST-SSR markers successfully identified monokaryons from their parent dikaryons, differentiated two different mating types and discriminated F1 and F2 hybrid offspring, respectively. Furthermore, a total of 86 alleles were detected in 37 monokaryons using 18 highly informative EST-SSRs. The observed number of alleles per locus ranged from three to seven. Cluster analysis revealed that these monokaryons have a relatively high level of genetic diversity. Transfer rates of the EST-SSRs in the monokaryons of closely-related species Pleurotus eryngii var. ferulae and Pleurotus ostreatus were 72% and 64%, respectively. Therefore, our study provides new SSR markers and an efficient method to enhance the crossbreeding of Bailinggu and closely-related species. PMID:29149037

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

Science.gov (United States)

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

EarthCube GeoLink: Semantics and Linked Data for the Geosciences

Science.gov (United States)

Arko, R. A.; Carbotte, S. M.; Chandler, C. L.; Cheatham, M.; Fils, D.; Hitzler, P.; Janowicz, K.; Ji, P.; Jones, M. B.; Krisnadhi, A.; Lehnert, K. A.; Mickle, A.; Narock, T.; O'Brien, M.; Raymond, L. M.; Schildhauer, M.; Shepherd, A.; Wiebe, P. H.

2015-12-01

The NSF EarthCube initiative is building next-generation cyberinfrastructure to aid geoscientists in collecting, accessing, analyzing, sharing, and visualizing their data and knowledge. The EarthCube GeoLink Building Block project focuses on a specific set of software protocols and vocabularies, often characterized as the Semantic Web and "Linked Data", to publish data online in a way that is easily discoverable, accessible, and interoperable. GeoLink brings together specialists from the computer science, geoscience, and library science domains, and includes data from a network of NSF-funded repositories that support scientific studies in marine geology, marine ecosystems, biogeochemistry, and paleoclimatology. We are working collaboratively with closely-related Building Block projects including EarthCollab and CINERGI, and solicit feedback from RCN projects including Cyberinfrastructure for Paleogeosciences (C4P) and iSamples. GeoLink has developed a modular ontology that describes essential geoscience research concepts; published data from seven collections (to date) on the Web as geospatially-enabled Linked Data using this ontology; matched and mapped data between collections using shared identifiers for investigators, repositories, datasets, funding awards, platforms, research cruises, physical specimens, and gazetteer features; and aggregated the results in a shared knowledgebase that can be queried via a standard SPARQL endpoint. Client applications have been built around the knowledgebase, including a Web/map-based data browser using the Leaflet JavaScript library and a simple query service using the OpenSearch format. Future development will include extending and refining the GeoLink ontology, adding content from additional repositories, developing semi-automated algorithms to enhance metadata, and further work on client applications.

A simple chromosomal marker can reliably distinguishes Poncirus from Citrus species.

Science.gov (United States)

Brasileiro-Vidal, A C; Dos Santos-Serejo, J A; Soares Filho, W Dos S; Guerra, M

2007-03-01

Several chromosome types have been recognized in Citrus and related genera by chromomycin A(3 )(CMA) banding patterns and fluorescent in situ hybridization (FISH). They can be used to characterize cultivars and species or as markers in hybridization and backcrossing experiments. In the present work, characterization of six cultivars of P. trifoliata ("Barnes", "Fawcett", "Flying Dragon", "Pomeroy", "Rubidoux", "USDA") and one P. trifoliata x C. limonia hybrid was performed by sequential analyses of CMA banding and FISH using 5S and 45S rDNA as probes. All six cultivars showed a similar CMA(+) banding pattern with the karyotype formula 4B + 8D + 6F. The capital letters indicate chromosomal types: B, a chromosome with one telomeric and one proximal band; D, with only one telomeric band; F, without bands. In situ hybridization labeling was also similar among cultivars. Three chromosome pairs displayed a closely linked set of 5S and 45S rDNA sites, two of them co-located with the proximal band of the B type chromosomes (B/5S-45S) and the third one co-located with the terminal band of a D pair (D/5S-45S). The B/5S-45S chromosome has never been found in any citrus accessions investigated so far. Therefore, this B chromosome can be used as a marker to recognize the intergeneric Poncirus x Citrus hybrids. The intergeneric hybrid analyzed here displayed the karyotype formula 4B + 8D + 6F, with two chromosome types B/5S-45S and two D/5S-45S. The karyotype formula and the presence of two B/5S-45S chromosomes clearly indicate that the plant investigated is a symmetric hybrid. It also demonstrates the suitability of karyotype analyses to differentiate zygotic embryos or somatic cell fusions involving trifoliate orange germplasm.

Tagging and mapping of SSR marker for rust resistance gene in lentil (Lens culinaris Medikus subsp. culinaris).

Science.gov (United States)

Dikshit, H K; Singh, Akanksha; Singh, D; Aski, M; Jain, Neelu; Hegde, V S; Basandrai, A K; Basandrai, D; Sharma, T R

2016-06-01

Lentil, as an economical source of protein, minerals and vitamins, plays important role in nutritional security of the common man. Grown mainly in West Asia, North Africa (WANA) region and South Asia, it suffers from several biotic stresses such as wilt, rust, blight and broomrape. Lentil rust caused by autoecious fungus Uromyces viciae fabae (Pers.) Schroet is a serious lentil disease in Algeria, Bangladesh, Ethiopia, India, Italy, Morocco, Pakistan and Nepal. The disease symptoms are observed during flowering and early podding stages. Rust causes severe yield losses in lentil. It can only be effectively controlled by identifying the resistant source, understanding its inheritance and breeding for host resistance. The obligate parasitic nature of pathogen makes it difficult to maintain the pathogen in culture and to apply it to screen segregating progenies under controlled growth conditions. Hence, the use of molecular markers will compliment in identification of resistant types in different breeding programs. Here, we studied the inheritance of resistance to rust in lentil using F₁, F₂ and F₂:₃ from cross PL 8 (susceptible) x L 4149 (resistant) varieties. The phenotyping of lentil population was carried out at Sirmour, India. The result of genetic analysis revealed that a single dominant gene controls rust resistance in lentil genotype L 4149. The F2 population from this cross was used to tag and map the rust resistance gene using SSR and SRAP markers. Markers such as 270 SRAP and 162 SSR were studied for polymorphism and 101 SRAP and 33 SSRs were found to be polymorphic between the parents. Two SRAP and two SSR markers differentiated the resistant and susceptible bulks. SSR marker Gllc 527 was estimated to be linked to rust resistant locus at a distance of 5.9 cM. The Gllc 527 marker can be used for marker assisted selection for rust resistance; however, additional markers closer to rust resistant locus are required. The markers linked to the rust

CEA A BIOCHEMICAL MARKER FOR DIAGNOSIS AND PROGNOSIS OF GASTROINTESTINAL CANCER

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Prathibha

2016-02-01

Full Text Available Serum tumor markers (TM are widely used for diagnosis and monitoring of treatment of cancer. Carcinoembryonic Antigen (CEA is one of the most widely investigated tumor markers in gastrointestinal (GI cancers. Estimation of circulating tumor markers is a non- invasive quantitative method. Serum levels of CEA were studied for diagnosis and prognosis of gastrointestinal malignancies. 140 subjects were undertaken out of which 35 normal and remaining 105 were GI cancer patients. Serum levels of CEA were analyzed by Enzyme Linked Immunosorbent Assay (ELISA. Result of serum CEA levels of the GI cancer patients and normal subjects were analyzed statistically. It was observed that there was significant increase in (P <0.01 in CEA levels of oesophagus, stomach and colon cancer patients as compared to normal subjects. The levels of CEA decreased significantly after the surgery but the decrease in levels of CEA was not up to the levels as normal control subjects.

Isolation and Characterization of Microsatellite Markers for Canavalia cathartica and C. lineata (Fabaceae

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Asuka Yamashiro

2013-01-01

Full Text Available Premise of the study: Microsatellite markers were developed for the sea-dispersed legume Canavalia cathartica to investigate its genetic diversity and population structure. We also applied these microsatellite markers to the closely related species C. lineata. Methods and Results: Ten primer sets were developed for C. cathartica, and all of the primers were amplified in C. lineata. The number of alleles per locus ranged from two to 13 and one to 10 for C. cathartica and C. lineata, respectively. The expected heterozygosity ranged from 0.375 to 0.870 and from 0.071 to 0.877 for C. cathartica and C. lineata, respectively. Conclusions: The 10 microsatellite markers developed in this study can be used to analyze the population genetic structure of C. cathartica and other related taxa.

Helically linked mirror arrangement

International Nuclear Information System (INIS)

Ranjan, P.

1986-08-01

A scheme is described for helical linking of mirror sections, which endeavors to combine the better features of toroidal and mirror devices by eliminating the longitudinal loss of mirror machines, having moderately high average β and steady state operation. This scheme is aimed at a device, with closed magnetic surfaces having rotational transform for equilibrium, one or more axisymmetric straight sections for reduced radial loss, a simple geometrical axis for the links and an overall positive magnetic well depth for stability. We start by describing several other attempts at linking of mirror sections, made both in the past and the present. Then a description of our helically linked mirror scheme is given. This example has three identical straight sections connected by three sections having helical geometric axes. A theoretical analysis of the magnetic field and single-particle orbits in them leads to the conclusion that most of the passing particles would be confined in the device and they would have orbits independent of pitch angle under certain conditions. Numerical results are presented, which agree well with the theoretical results as far as passing particle orbits are concerned

Digital Discourse Markers in an ESL Learning Setting: The Case of Socialisation Forums

Science.gov (United States)

Shakarami, Alireza; Hajhashemi, Karim; Caltabiano, Nerina

2016-01-01

Analysis of the linguistic discourse plays an important role in the social, cultural, ethnographic, and comparative studies of languages. Discourse markers as indispensable parts of this analysis are reportedly more common in informal speech than in written language. They could be used at different levels, i.e. as "linking words,"…

Tumor-associated auto-antibodies as early detection markers for ovarian cancer?

DEFF Research Database (Denmark)

Kaaks, Rudolf; Fortner, Renée Turzanski; Hüsing, Anika

2018-01-01

.08-0.40] for CTAG1A, CTAG2 and NUDT1 to 0.23 [0.10-0.44] for P53 (0.33 [0.11-0.68] for high-grade serous tumors). However, at longer lead-times the ability of these AAb markers to distinguish future ovarian cancer cases from controls declined rapidly; at lead times >1 year, SE98 estimates were close to zero (all...... invasive cases, range: 0.01-0.11). Compared to CA125 alone, combined logistic regression scores of AAbs and CA125 did not improve detection sensitivity at equal level of specificity. The added value of these selected AAbs as markers for ovarian cancer beyond CA125 for early detection is therefore limited...

The isolated perfused human skin flap model: A missing link in skin penetration studies?

Science.gov (United States)

Ternullo, Selenia; de Weerd, Louis; Flaten, Gøril Eide; Holsæter, Ann Mari; Škalko-Basnet, Nataša

2017-01-01

Development of effective (trans)dermal drug delivery systems requires reliable skin models to evaluate skin drug penetration. The isolated perfused human skin flap remains metabolically active tissue for up to 6h during in vitro perfusion. We introduce the isolated perfused human skin flap as a close-to-in vivo skin penetration model. To validate the model's ability to evaluate skin drug penetration the solutions of a hydrophilic (calcein) and a lipophilic (rhodamine) fluorescence marker were applied. The skin flaps were perfused with modified Krebs-Henseleit buffer (pH7.4). Infrared technology was used to monitor perfusion and to select a well-perfused skin area for administration of the markers. Flap perfusion and physiological parameters were maintained constant during the 6h experiments and the amount of markers in the perfusate was determined. Calcein was detected in the perfusate, whereas rhodamine was not detectable. Confocal images of skin cross-sections shoved that calcein was uniformly distributed through the skin, whereas rhodamine accumulated in the stratum corneum. For comparison, the penetration of both markers was evaluated on ex vivo human skin, pig skin and cellophane membrane. The proposed perfused flap model enabled us to distinguish between the penetrations of the two markers and could be a promising close-to-in vivo tool in skin penetration studies and optimization of formulations destined for skin administration. Copyright © 2016 Elsevier B.V. All rights reserved.

Fecal markers of intestinal inflammation and intestinal permeability are elevated in Parkinson's disease.

Science.gov (United States)

Schwiertz, Andreas; Spiegel, Jörg; Dillmann, Ulrich; Grundmann, David; Bürmann, Jan; Faßbender, Klaus; Schäfer, Karl-Herbert; Unger, Marcus M

2018-02-12

Intestinal inflammation and increased intestinal permeability (both possibly fueled by dysbiosis) have been suggested to be implicated in the multifactorial pathogenesis of Parkinson's disease (PD). The objective of the current study was to investigate whether fecal markers of inflammation and impaired intestinal barrier function corroborate this pathogenic aspect of PD. In a case-control study, we quantitatively analyzed established fecal markers of intestinal inflammation (calprotectin and lactoferrin) and fecal markers of intestinal permeability (alpha-1-antitrypsin and zonulin) in PD patients (n = 34) and controls (n = 28, group-matched for age) by enzyme-linked immunosorbent assay. The study design controlled for potential confounding factors. Calprotectin, a fecal marker of intestinal inflammation, and two fecal markers of increased intestinal permeability (alpha-1-antitrypsin and zonulin) were significantly elevated in PD patients compared to age-matched controls. Lactoferrin, as a second fecal marker of intestinal inflammation, showed a non-significant trend towards elevated concentrations in PD patients. None of the four fecal markers correlated with disease severity, PD subtype, dopaminergic therapy, or presence of constipation. Fecal markers reflecting intestinal inflammation and increased intestinal permeability have been primarily investigated in inflammatory bowel disease so far. Our data indicate that calprotectin, alpha-1-antitrypsin and zonulin could be useful non-invasive markers in PD as well. Even though these markers are not disease-specific, they corroborate the hypothesis of an intestinal inflammation as contributing factor in the pathogenesis of PD. Further investigations are needed to determine whether calprotectin, alpha-1-antitrypsin and zonulin can be used to define PD subgroups and to monitor the effect of interventions in PD. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bone markers during acute burn care: Relevance to clinical practice?

Science.gov (United States)

Rousseau, Anne-Françoise; Damas, Pierre; Delanaye, Pierre; Cavalier, Etienne

2017-02-01

Bone changes are increasingly described after burn. How bone markers could help to detect early bone changes or to screen burn patients at higher risk of demineralization is still not made clear. We performed an observational study assessing the changes in serum bone markers after moderate burn. Adults admitted in the first 24h following burn extended on >10% body surface area were included. Serum levels of collagen type 1 cross-linked C-telopeptide (CTX), tartrate-resistant acid phosphatase 5b (TRAP), type 1 procollagen N-terminal (P1NP) and bone alkaline phosphatase (b-ALP) were measured at admission and every week during the first month. Data are expressed as median [min-max]. Bone markers were measured in 20 patients: 18 men, 2 women (including one post-menopausal). Age was 46 [19-86] years old, burn surface area reached 15 [7-85] %. Twelve patients completed the study. All biomarkers mainly remained into normal ranges during evolution. A huge variability was observed regarding biomarkers evolution. Patient's evolution was not linear and could fluctuate from a decrease to an increase of blood concentrations. There was not necessarily a consistency between the two formation or the two resorption markers. Variations observed between two consecutive measurements were lesser than the accepted critical difference in almost one third of the cases. Considering available data, role and interest of bone markers in management of burn related bone disease remain unclear. Copyright © 2016 Elsevier Ltd and ISBI. All rights reserved.

A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis.

Directory of Open Access Journals (Sweden)

Dunja K Lamatsch

Full Text Available Sex-specific markers are a prerequisite for understanding reproductive biology, genetic factors involved in sex differences, mechanisms of sex determination, and ultimately the evolution of sex chromosomes. The Western mosquitofish, Gambusia affinis, may be considered a model species for sex-chromosome evolution, as it displays female heterogamety (ZW/ZZ, and is also ecologically interesting as a worldwide invasive species. Here, de novo RNA-sequencing on the gonads of sexually mature G. affinis was used to identify contigs that were highly transcribed in females but not in males (i.e., transcripts with ovary-specific expression. Subsequently, 129 primer pairs spanning 79 contigs were tested by PCR to identify sex-specific transcripts. Of those primer pairs, one female-specific DNA marker was identified, Sanger sequenced and subsequently validated in 115 fish. Sequence analyses revealed a high similarity between the identified sex-specific marker and the 3´ UTR of the aminomethyl transferase (amt gene of the closely related platyfish (Xiphophorus maculatus. This is the first time that RNA-seq has been used to successfully characterize a sex-specific marker in a fish species in the absence of a genome map. Additionally, the identified sex-specific marker represents one of only a handful of such markers in fishes.

Markers of inflammation and hemodynamic measurements in obesity: Copenhagen City Heart Study

DEFF Research Database (Denmark)

Asferg, Camilla; Jensen, Jan S; Marott, Jacob L

2009-01-01

BACKGROUND: Low-grade chronic inflammation has been proposed to play a major role in the pathogenesis of hypertension. Low-grade chronic inflammation is also closely associated with obesity, an established causative factor in the development of hypertension. The purpose of this study was to inves......BACKGROUND: Low-grade chronic inflammation has been proposed to play a major role in the pathogenesis of hypertension. Low-grade chronic inflammation is also closely associated with obesity, an established causative factor in the development of hypertension. The purpose of this study...... was to investigate the relationship between two markers of inflammation, C-reactive protein (CRP) and fibrinogen, and blood pressure (BP) and other hemodynamic variables in obese subjects. METHODS: From a large cardiovascular study based in the general population, we selected subjects with a body mass index (BMI...... index (rho: -0.057 to 0.068; P > 0.13). However, fibrinogen and CRP were found to be significantly related to heart rate (rho: 0.127-0.169; P obese subjects from the general population, we found no significant relationships between markers...

Fine mapping of the rice Bph1 gene, which confers resistance to the brown planthopper (Nilaparvata lugens stal), and development of STS markers for marker-assisted selection.

Science.gov (United States)

Cha, Young-Soon; Ji, Hyeonso; Yun, Doh-Won; Ahn, Byoung-Ohg; Lee, Myung Chul; Suh, Seok-Cheol; Lee, Chun Seok; Ahn, Eok Keun; Jeon, Yong-Hee; Jin, Il-Doo; Sohn, Jae-Keun; Koh, Hee-Jong; Eun, Moo-Young

2008-08-31

The brown planthopper (BPH) is a major insect pest in rice, and damages these plants by sucking phloem-sap and transmitting viral diseases. Many BPH resistance genes have been identified in indica varieties and wild rice accessions, but none has yet been cloned. In the present study we report fine mapping of the region containing the Bph1 locus, which enabled us to perform marker-aided selection (MAS). We used 273 F8 recombinant inbred lines (RILs) derived from a cross between Cheongcheongbyeo, an indica type variety harboring Bph1 from Mudgo, and Hwayeongbyeo, a BPH susceptible japonica variety. By random amplification of polymorphic DNA (RAPD) analysis using 656 random 10-mer primers, three RAPD markers (OPH09, OPA10 and OPA15) linked to Bph1 were identified and converted to SCAR (sequence characterized amplified region) markers. These markers were found to be contained in two BAC clones derived from chromosome 12: OPH09 on OSJNBa0011B18, and both OPA10 and OPA15 on OSJNBa0040E10. By sequence analysis of ten additional BAC clones evenly distributed between OSJNBa0011B18 and OSJNBa0040E10, we developed 15 STS markers. Of these, pBPH4 and pBPH14 flanked Bph1 at distances of 0.2 cM and 0.8 cM, respectively. The STS markers pBPH9, pBPH19, pBPH20, and pBPH21 co-segregated with Bph1. These markers were shown to be very useful for marker-assisted selection (MAS) in breeding populations of 32 F6 RILs from a cross between Andabyeo and IR71190, and 32 F5 RILs from a cross between Andabyeo and Suwon452.

Diversity in 113 cowpea [Vigna unguiculata (L) Walp] accessions assessed with 458 SNP markers.

Science.gov (United States)

Egbadzor, Kenneth F; Ofori, Kwadwo; Yeboah, Martin; Aboagye, Lawrence M; Opoku-Agyeman, Michael O; Danquah, Eric Y; Offei, Samuel K

2014-01-01

Single Nucleotide Polymorphism (SNP) markers were used in characterization of 113 cowpea accessions comprising of 108 from Ghana and 5 from abroad. Leaf tissues from plants cultivated at the University of Ghana were genotyped at KBioscience in the United Kingdom. Data was generated for 477 SNPs, out of which 458 revealed polymorphism. The results were used to analyze genetic dissimilarity among the accessions using Darwin 5 software. The markers discriminated among all of the cowpea accessions and the dissimilarity values which ranged from 0.006 to 0.63 were used for factorial plot. Unexpected high levels of heterozygosity were observed on some of the accessions. Accessions known to be closely related clustered together in a dendrogram drawn with WPGMA method. A maximum length sub-tree which comprised of 48 core accessions was constructed. The software package structure was used to separate accessions into three groups, and the programme correctly identified varieties that were known hybrids. The hybrids were those accessions with numerous heterozygous loci. The structure plot showed closely related accessions with similar genome patterns. The SNP markers were more efficient in discriminating among the cowpea germplasm than morphological, seed protein polymorphism and simple sequence repeat studies reported earlier on the same collection.

Toward fully automated genotyping: Genotyping microsatellite markers by deconvolution

Energy Technology Data Exchange (ETDEWEB)

Perlin, M.W.; Lancia, G.; See-Kiong, Ng [Carnegie Mellon Univ., Pittsburgh, PA (United States)

1995-11-01

Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA){sub n} repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces additional stutter bands. With two (or more) closely spaced alleles, the stutter bands overlap, and it is difficult to accurately determine the correct alleles; this stutter phenomenon has all but precluded full automation, since a human must visually inspect the allele data. We describe here novel deconvolution methods for accurate genotyping that mathematically remove PCR stutter artifact from microsatellite markers. These methods overcome the manual interpretation bottleneck and thereby enable full automation of genetic map construction and use. New functionalities, including the pooling of DNAs and the pooling of markers, are described that may greatly reduce the associated experimentation requirements. 32 refs., 5 figs., 3 tabs.

A recoding scheme for X-linked and pseudoautosomal loci to be used with computer programs for autosomal LOD-score analysis.

Science.gov (United States)

Strauch, Konstantin; Baur, Max P; Wienker, Thomas F

2004-01-01

We present a recoding scheme that allows for a parametric multipoint X-chromosomal linkage analysis of dichotomous traits in the context of a computer program for autosomes that can use trait models with imprinting. Furthermore, with this scheme, it is possible to perform a joint multipoint analysis of X-linked and pseudoautosomal loci. It is required that (1) the marker genotypes of all female nonfounders are available and that (2) there are no male nonfounders who have daughters in the pedigree. The second requirement does not apply if the trait locus is pseudoautosomal. The X-linked marker loci are recorded by adding a dummy allele to the males' hemizygous genotypes. For modelling an X-linked trait locus, five different liability classes are defined, in conjunction with a paternal imprinting model for male nonfounders. The formulation aims at the mapping of a diallelic trait locus relative to an arbitrary number of codominant markers with known genetic distances, in cases where a program for a genuine X-chromosomal analysis is not available. 2004 S. Karger AG, Basel.

A systematic review of secondhand smoke exposure in a car: Attributable changes in atmospheric and biological markers.

Science.gov (United States)

Raoof, Sana A; Agaku, Israel T; Vardavas, Constantine I

2015-05-01

Exposure to secondhand smoke (SHS) has been linked to disease, disability, and premature death. While several countries have enacted smoke-free legislations, exposure to SHS may still occur in unregulated private environments, such as in the family car. We performed a systematic review of peer-reviewed literature in PubMed and Web of Science up to May 2013. Articles were selected if they provided a quantitative measure of SHS exposure (biological or atmospheric markers); the study was conducted inside a car; and the assessed exposure was attributable to cigarette combustion. From 202 articles identified, 12 met the inclusion criteria. Among all studies that assessed smoking in cars with at least one window partially open, the particulate matter 2.5 μm or less in diameter (PM2.5) concentrations ranged from 47 μg/m(3) to 12,150 μg/m(3). For studies with all windows closed, PM2.5 ranged from 203.6 μg/m(3) to 13,150 μg/m(3). SHS concentration in a car was mediated by air-conditioning status, extent of airflow, and driving speed. Smoking in cars leads to extremely high exposure to SHS and increased concentration of atmospheric markers of exposure-even in the presence of air-conditioning or increased airflow from open windows. This clearly shows that the only way to protect nonsmokers, especially children, from SHS within cars is by eliminating tobacco smoking. © The Author(s) 2015.

Markers

Science.gov (United States)

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…

DNA sequences from two SSRs (CIR316 and MUCS088) linked to root-knot nematode resistance genes from diverse cottons (Gossypium spp).

Science.gov (United States)

We investigated DNA sequencing information from alleles (DNA amplified fragments) of two previously reported SSR markers (CIR316 and MUCS088) linked to root-knot nematode (RKN) resistance genes. Markers based on electrophoretic differences, including RFLPs, AFLPs and SSRs can sometimes mask underlyi...

Spatio-kinematic modelling: Testing the link between planetary nebulae and close binaries

OpenAIRE

Jones, David; Tyndall, Amy A.; Huckvale, Leo; Prouse, Barnabas; Lloyd, Myfanwy

2011-01-01

It is widely believed that central star binarity plays an important role in the formation and evolution of aspherical planetary nebulae, however observational support for this hypothesis is lacking. Here, we present the most recent results of a continuing programme to model the morphologies of all planetary nebulae known to host a close binary central star. Initially, this programme allows us to compare the inclination of the nebular symmetry axis to that of the binary plane, testing the theo...

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

Science.gov (United States)

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

2017-03-01

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

Manifold-splitting regularization, self-linking, twisting, writhing numbers of space-time ribbons

International Nuclear Information System (INIS)

Tze, C.H.

1988-01-01

The authors present an alternative formulation of Polyakov's regularization of Gauss' integral formula for a single closed Feynman path. A key element in his proof of the D = 3 fermi-bose transmutations induced by topological gauge fields, this regularization is linked here with the existence and properties of a nontrivial topological invariant for a closed space ribbon. This self-linking coefficient, an integer, is the sum of two differential characteristics of the ribbon, its twisting and writhing numbers. These invariants form the basis for a physical interpretation of our regularization. Their connection to Polyakov's spinorization is discussed. The authors further generalize their construction to the self-linking, twisting and writhing of higher dimensional d = eta(odd) submanifolds in D = (2eta + 1) space-time

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

Science.gov (United States)

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. © 2016 John Wiley & Sons Ltd.

Denitrification activity is closely linked to the total ambient Fe concentration in mangrove sediments of Goa, India

Science.gov (United States)

Fernandes, Sheryl Oliveira; Gonsalves, Maria-Judith; Michotey, Valérie D.; Bonin, Patricia C.; Loka, A.; Bharathi, P.

2013-10-01

Denitrification activity (DNT) and associated environmental parameters were examined in two mangrove ecosystems of Goa, India - the relatively unimpacted Tuvem and the anthropogenically-influenced Divar. Sampling was carried out at every 2 cm interval within the 0-10 cm depth range to determine (1) seasonal (pre-monsoon, monsoon and post-monsoon) down-core variation in DNT (2) assess the environmental factors influencing the DNT and (3) to build predictive models for benthic DNT. Denitrification generally decreased with depth and showed marked seasonal variation at both the locations. Denitrification peaked during the pre-monsoon occurring at a rate of up to 21.00 ± 12.84 nmol N2O g-1 h-1 within 0-4 cm at both the locations. Further, DNT at pre-monsoon was significantly influenced by Fe content at Tuvem and Divar suggesting Fe-mediated nitrate respiration. The influence of other limiting substrates such as NO3- and NO2- was most important during the monsoon and post-monsoon especially at Divar. The multiple regression models developed could predict 67-98% of the observed variability in DNT through the seasons. About 6-9 environmental variables were required to relatively well-predict DNT in these sediments with the complexity governing DNT decreasing from pre-monsoon to post-monsoon. Our results reveal that seasonal dynamics of DNT in tropical mangrove sediments are closely linked to the total Fe at the prevailing ambient concentration in both the systems.

Linking of uniform random polygons in confined spaces

International Nuclear Information System (INIS)

Arsuaga, J; Blackstone, T; Diao, Y; Karadayi, E; Saito, M

2007-01-01

In this paper, we study the topological entanglement of uniform random polygons in a confined space. We derive the formula for the mean squared linking number of such polygons. For a fixed simple closed curve in the confined space, we rigorously show that the linking probability between this curve and a uniform random polygon of n vertices is at least 1-O(1/√n). Our numerical study also indicates that the linking probability between two uniform random polygons (in a confined space), of m and n vertices respectively, is bounded below by 1-O(1/√(mn)). In particular, the linking probability between two uniform random polygons, both of n vertices, is bounded below by 1-O(1/n)

Information Theoretical Limits of Free-Space Optical Links

KAUST Repository

Ansari, Imran Shafique; Al-Quwaiee, Hessa; Zedini, Emna; Alouini, Mohamed-Slim

2016-01-01

detection) over generalized atmospheric turbulence channels that account for generalized pointing errors is presented. Specifically, unified exact closed-form expressions for the moments of the end-to-end signal-to-noise ratio (SNR) of a single link FSO

Species delineation and hybrid identification using diagnostic nuclear markers for Plectropomus leopardus and Plectropomus maculatus

KAUST Repository

He, Song

2018-06-01

Diagnostic molecular markers are an essential tool in the study of species’ ecology and evolution, particularly in closely related and sympatric species. Furthermore, the increasing awareness of wild-hybrids has led to a renewed interest in rapid diagnostic assays. Here, we test the ability of two mitochondrial (Cytb and COI) and two nuclear markers (ETS2 and TMO-4c4) to confidently discriminate purebred P. leopardus and P. maculatus and their first-generation hybrids. A sample of 48 purebred individuals and 91 interspecific hybrids were used in this study and their delineation confirmed using a set of microsatellite markers. Our results indicate mitochondrial markers could not distinguish even between species but both nuclear markers confidently identified species and first-generation hybrids. However, later-generation hybrids could not always be confidently identified due to on-going introgression between species. Our findings provide a robust tool to distinguish purebred individuals and interspecific hybrids in a pair of species with an unexpectedly high incidence of hybridization. The quick species discrimination abilities provided by these diagnostic markers are important for stock assessment and recruitment studies of these important fishery species.

Species delineation and hybrid identification using diagnostic nuclear markers for Plectropomus leopardus and Plectropomus maculatus

KAUST Repository

He, Song; Harrison, Hugo B.; Berumen, Michael L.

2018-01-01

Diagnostic molecular markers are an essential tool in the study of species’ ecology and evolution, particularly in closely related and sympatric species. Furthermore, the increasing awareness of wild-hybrids has led to a renewed interest in rapid diagnostic assays. Here, we test the ability of two mitochondrial (Cytb and COI) and two nuclear markers (ETS2 and TMO-4c4) to confidently discriminate purebred P. leopardus and P. maculatus and their first-generation hybrids. A sample of 48 purebred individuals and 91 interspecific hybrids were used in this study and their delineation confirmed using a set of microsatellite markers. Our results indicate mitochondrial markers could not distinguish even between species but both nuclear markers confidently identified species and first-generation hybrids. However, later-generation hybrids could not always be confidently identified due to on-going introgression between species. Our findings provide a robust tool to distinguish purebred individuals and interspecific hybrids in a pair of species with an unexpectedly high incidence of hybridization. The quick species discrimination abilities provided by these diagnostic markers are important for stock assessment and recruitment studies of these important fishery species.

A study of the relationships between Parkinson's disease and markers of traffic-derived and environmental manganese air pollution in two Canadian cities.

Science.gov (United States)

Finkelstein, Murray M; Jerrett, Michael

2007-07-01

There is concern that industrial emissions of manganese (Mn) and the use of Mn-containing compounds as fuel additives might increase the population risk of Parkinson's disease (PD)-like disorders. We investigated associations between the diagnosis and treatment of PD and markers of exposure to vehicle exhaust and industrial emissions of Mn within a cohort of 110,000 subjects in the cities of Toronto and Hamilton, Canada. Methylcyclopentadienyl manganese tricarbonyl (MMT) has been added to Canadian gasoline since 1976 and steelmaking in Hamilton emits Mn to the air. Using residential postal codes, subjects were mapped to: (1) residence locations close to traffic and to neighbourhood levels of NO2, as markers of traffic-generated air pollution (TGAP); and, (2) neighbourhood levels of ambient Mn in Hamilton, as measured by the Mn fraction of total suspended particulate. Subjects were linked to Ministry of Health administrative databases, 1992-1999, to identify physicians' diagnoses of PD and prescriptions for l-Dopa containing medications. In Toronto, we found no association between PD and the markers of TGAP. In Hamilton, the odds ratio for a physician's diagnosis of PD was 1.034 (1.00-1.07) per 10 ng/m3 increase in Mn in TSP. The estimate of the "doubling exposure" for physician-diagnosed PD was about 150 ng/m3 Mn in TSP. Examination of prevalence curves suggested that exposure to ambient Mn advances the age of diagnosis of PD, consistent with the theory that exposure to Mn adds to the natural loss of neurons attributable to the aging process.

Phosphoproteins in extracellular vesicles as candidate markers for breast cancer

OpenAIRE

Chen, I-Hsuan; Xue, Liang; Hsu, Chuan-Chih; Paez, Juan Sebastian Paez; Pan, Li; Andaluz, Hillary; Wendt, Michael K.; Iliuk, Anton B.; Zhu, Jian-Kang; Tao, W. Andy

2017-01-01

Protein phosphorylation is a major regulatory mechanism for many cellular functions, but no phosphoprotein in biofluids has been developed for disease diagnosis because of the presence of active phosphatases. This study presents a general strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs from small volumes of plasma sam...

Collagen derived serum markers in carcinoma of the prostate

DEFF Research Database (Denmark)

Rudnicki, M; Jensen, L T; Iversen, P

1995-01-01

Three new collagen markers deriving from the collagenous matrix, e.g. carboxyterminal propeptide of type I procollagen (PICP), carboxy-terminal pyridinoline cross-linked telopeptide of type I collagen (ICTP), and aminoterminal propeptide of type III procollagen (PIIINP) were used for the diagnose...... of prostatic bone metastases. Blood samples were obtained prior to biopsy or TURP. Serum PICP, PIIINP and ICTP were measured with commercial available RIAs and PSA by IRMA. Serum PSA was increased in patients with local prostatic cancer compared with patients with hyperplasia (p

Site-directed cross-linking: establishing the dimeric structure of the aspartate receptor of bacterial chemotaxis

International Nuclear Information System (INIS)

Milligan, D.L.; Koshland, D.E. Jr.

1988-01-01

Cysteine residues introduced at specific locations in the aspartate receptor of Salmonella typhimurium provide anchor points for cross-linking and serve as chemical markers for structural studies of this oligomeric receptor. These markers have been used to measure the rate of subunit exchange between oligomeric receptors and to show that ligand binding inhibits this exchange. The cysteine-containing receptors can be oxidatively cross-linked to completion within the oligomeric receptor, indicating that the receptor has an even number of subunits. Based on this observation, a technique has been developed that can be used to determine the oligomeric structure of proteins under a variety of experimental conditions. The technique involves the measurement of the effect of dilution by cysteineless receptor subunits on cross-linking and reveals that the aspartate receptor is dimeric in detergent solution, in a mixed-micelle system, and in reconstituted membrane vesicles. Binding of aspartate does not change the oligomeric structure of the receptor, indicating that transmembrane signaling occurs within an oligomeric receptor of constant size

Relationship between heart rate recovery and inflammatory markers in patients with polycystic ovary syndrome: a cross-sectional study

Directory of Open Access Journals (Sweden)

Giallauria Francesco

2009-02-01

Full Text Available Abstract Background Polycystic ovary syndrome (PCOS is an endocrine disease closely related to several risk factors for cardiovascular disease. An abnormal heart rate recovery (HRR, an easily-obtained measure derived from exercise stress test and closely related to an increased risk for cardiovascular mortality, has been recently described in PCOS women. A subclinical increase of the inflammation markers has been also observed in the PCOS. This study was designed to study the relationships between HRR and inflammatory markers in PCOS women. Methods Two-hundred forty-three young PCOS patients without known risk factors for cardiovascular risk were enrolled. All patients underwent hormonal and metabolic profile, white blood cells (WBCs count and C-reactive protein (CRP. HRR was calculated as the difference between heart rate at peak exercise and heart rate at first minute of the cool-down period. Abnormal HRR was defined as ≤18 beats/min for standard exercise testing. Results Eighty-nine out of 243 patients presented abnormal HRR. Serum CRP (1.8 ± 0.7 vs. 1.1 ± 0.4 mg/dl, p 9 cells/l, p versus normal HRR. HRR was significantly associated with both CRP (r = -0.33, p p Conclusion Abnormal HRR and inflammatory markers are closely associated in PCOS women acting probably in concert to increase the cardiovascular risk profile of these patients.

Association Analysis of SSR Markers with Phenology, Grain, and Stover-Yield Related Traits in Pearl Millet (Pennisetum glaucum (L. R. Br.

Directory of Open Access Journals (Sweden)

Baskaran Kannan

2014-01-01

Full Text Available Pearl millet is a staple food crop for millions of people living in the arid and semi-arid tropics. Molecular markers have been used to identify genomic regions linked to traits of interest by conventional QTL mapping and association analysis. Phenotypic recurrent selection is known to increase frequencies of favorable alleles and decrease those unfavorable for the traits under selection. This study was undertaken (i to quantify the response to recurrent selection for phenotypic traits during breeding of the pearl millet open-pollinated cultivar “CO (Cu 9” and its four immediate progenitor populations and (ii to assess the ability of simple sequence repeat (SSR marker alleles to identify genomic regions linked to grain and stover yield-related traits in these populations by association analysis. A total of 159 SSR alleles were detected across 34 selected single-copy SSR loci. SSR marker data revealed presence of subpopulations. Association analysis identified genomic regions associated with flowering time located on linkage group (LG 6 and plant height on LG4, LG6, and LG7. Marker alleles on LG6 were associated with stover yield, and those on LG7 were associated with grain yield. Findings of this study would give an opportunity to develop marker-assisted recurrent selection (MARS or marker-assisted population improvement (MAPI strategies to increase the rate of gain for pearl millet populations undergoing recurrent selection.

Locating inefficient links in a large-scale transportation network

Science.gov (United States)

Sun, Li; Liu, Like; Xu, Zhongzhi; Jie, Yang; Wei, Dong; Wang, Pu

2015-02-01

Based on data from geographical information system (GIS) and daily commuting origin destination (OD) matrices, we estimated the distribution of traffic flow in the San Francisco road network and studied Braess's paradox in a large-scale transportation network with realistic travel demand. We measured the variation of total travel time Δ T when a road segment is closed, and found that | Δ T | follows a power-law distribution if Δ T 0. This implies that most roads have a negligible effect on the efficiency of the road network, while the failure of a few crucial links would result in severe travel delays, and closure of a few inefficient links would counter-intuitively reduce travel costs considerably. Generating three theoretical networks, we discovered that the heterogeneously distributed travel demand may be the origin of the observed power-law distributions of | Δ T | . Finally, a genetic algorithm was used to pinpoint inefficient link clusters in the road network. We found that closing specific road clusters would further improve the transportation efficiency.

Rich, poor share stake in poverty, pollution link

International Nuclear Information System (INIS)

DeCanio, S.J.

1993-01-01

A dirty environment and poverty go together, and this link between environmental protection and economic development is creating a new basis for international cooperation, says Stephen J. DeCanio of the University of California at Santa Barbara. open-quotes Both developed and developing countries have a stake in solving the development/environment impasse,close quotes DeCanio adds. open-quotes Furthermore, the link between these problems offers a fresh opportunity to make progress on both fronts.close quotes He says environmental protection expenditures by developed countries can be used to promote the sustainable economic growth of those countries struggling to escape from poverty. The money could be collected in several ways, he notes: from various types of environmental taxes, such as a carbon tax; from environmental user fees; from open-quotes debt-for natureclose quotes swaps; and from tradable emissions permits. Such mechanisms transfer resources to developing countries, where they can be applied to economic development-a desired objective, according to DeCanio. open-quotes The benefits of equitable worldwide growth and development outweigh any temporary loss of wealth developed countries may experience as a result of environmental transfers,close quotes he asserts

Detection of multiple tumor markers using ultra-long carbon nanotube devices

Science.gov (United States)

So, Hye-Mi; Park, Dong-Won; Kim, Beom Soo; Kong, Ki-Jeong; Buh, Gyoung-Ho; Chang, Hyunju; Lee, Jeong-O.; Kong, Jing

2008-03-01

For the simultaneous detection of multiple tumor markers, we have fabricated ultra-long carbon nanotube sensors that can detect carcinoembryonic antigen (CEA) and prostate specific antigen (PSA), simultaneously. Ultra-long carbon nanotubes, several millimeters long, were grown by ethanol CVD, and fabricated as FET sensors by using conventional photolithography. To functionalize each segment of a single ultra-long nanotube device with multiple-tumor markers, we first functionalize the entire device with CDI-Tween 20 linking molecules, and then immobilized CEA and PSA antibodies using the microfluidic channel. The electrical conductance from CEA-antibody functionalized and PSA-antibody functionalized segment of a ultra-long carbon nanotube device was monitored simultaneously with Ag/AgCl reference electrode as a liquid gate. We will discuss the advantages of long-nanotube device in detail.

Application of in silico bulked segregant analysis for rapid development of markers linked to Bean common mosaic virus resistance in common bean

Science.gov (United States)

Common bean was one of the first crops that benefited from the development and utilization of molecular markers in tagging major disease resistance genes for marker-assisted selection (MAS). Efficiency of MAS breeding in common bean is still hampered; however, due to the dominance, linkage phase, an...

Isolation and Characterization of Microsatellite Markers for the Cleistogamous Species Lamium amplexicaule (Lamiaceae

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Bojana Stojanova

2013-02-01

Full Text Available Premise of the study: Lamium amplexicaule is a cleistogamous plant that produces both closed flowers (obligately self-pollinated and open flowers (potentially outcrossed. The conditions for the maintenance of such a mating system depend on the outcrossing rate of the open flowers, which can be estimated using neutral microsatellite markers. Methods and Results: Forty primer pairs corresponding to microsatellite motifs obtained by coupling multiplex microsatellite enrichment and next-generation sequencing were tested. Thirteen primers amplified with satisfying results. The polymorphism of these markers was studied in four French populations. Allele number varied from one to eight per locus and per population. Heterozygosity levels were significantly lower than those expected under Hardy-Weinberg equilibrium. Conclusions: Our results are consistent with a partial self-fertilization pattern. These markers will be used to estimate the outcrossing rate as well as population differentiation in L. amplexicaule.

Atrial fibrillation and bleeding complication - risk factors and risk marker

NARCIS (Netherlands)

Breithardt, G.; Ravens, U.; Kirchhof, P.; van Gelder, I. C.

2012-01-01

The development of atrial fibrillation (AF) is closely linked to risk factors like hypertension and heart failure, diabetes mellitus, myocardial infarction and valvular heart disease. These factors partly overlap with those which determine the progression of atrial fibrillation and the incidence of

Development and evaluation of microsatellite markers for Acer miyabei (Sapindaceae), a threatened maple species in East Asia.

Science.gov (United States)

Saeki, Ikuyo; Hirao, Akira S; Kenta, Tanaka

2015-06-01

Twelve microsatellite markers were developed and characterized in a threatened maple species, Acer miyabei (Sapindaceae), for use in population genetic analyses. Using Ion Personal Genome Machine (PGM) sequencing, we developed microsatellite markers with perfect di- and trinucleotide repeats. These markers were tested on a total of 44 individuals from two natural populations of A. miyabei subsp. miyabei f. miyabei in Hokkaido Island, Japan. The number of alleles per locus ranged from two to eight. The observed and expected heterozygosities per locus ranged from 0.05 to 0.75 and from 0.05 to 0.79, respectively. Some of the markers were successfully transferred to the closely related species A. campestre, A. platanoides, and A. pictum. The developed markers will be useful in characterizing the genetic structure and diversity of A. miyabei and will help to understand its spatial genetic variation, levels of inbreeding, and patterns of gene flow, thereby providing a basis for conservation.

Efficient dynamic modeling of manipulators containing closed kinematic loops

Science.gov (United States)

Ferretti, Gianni; Rocco, Paolo

An approach to efficiently solve the forward dynamics problem for manipulators containing closed chains is proposed. The two main distinctive features of this approach are: the dynamics of the equivalent open loop tree structures (any closed loop can be in general modeled by imposing some additional kinematic constraints to a suitable tree structure) is computed through an efficient Newton Euler formulation; the constraint equations relative to the most commonly adopted closed chains in industrial manipulators are explicitly solved, thus, overcoming the redundancy of Lagrange's multipliers method while avoiding the inefficiency due to a numerical solution of the implicit constraint equations. The constraint equations considered for an explicit solution are those imposed by articulated gear mechanisms and planar closed chains (pantograph type structures). Articulated gear mechanisms are actually used in all industrial robots to transmit motion from actuators to links, while planar closed chains are usefully employed to increase the stiffness of the manipulators and their load capacity, as well to reduce the kinematic coupling of joint axes. The accuracy and the efficiency of the proposed approach are shown through a simulation test.

Genetic Diversity Analysis of South and East Asian Duck Populations Using Highly Polymorphic Microsatellite Markers

Directory of Open Access Journals (Sweden)

Dongwon Seo

2016-04-01

Full Text Available Native duck populations have lower productivity, and have not been developed as much as commercials duck breeds. However, native ducks have more importance in terms of genetic diversity and potentially valuable economic traits. For this reason, population discriminable genetic markers are needed for conservation and development of native ducks. In this study, 24 highly polymorphic microsatellite (MS markers were investigated using commercial ducks and native East and South Asian ducks. The average polymorphic information content (PIC value for all MS markers was 0.584, indicating high discrimination power. All populations were discriminated using 14 highly polymorphic MS markers by genetic distance and phylogenetic analysis. The results indicated that there were close genetic relationships among populations. In the structure analysis, East Asian ducks shared more haplotypes with commercial ducks than South Asian ducks, and they had more independent haplotypes than others did. These results will provide useful information for genetic diversity studies in ducks and for the development of duck traceability systems in the market.

Linking of uniform random polygons in confined spaces

Science.gov (United States)

Arsuaga, J.; Blackstone, T.; Diao, Y.; Karadayi, E.; Saito, M.

2007-03-01

In this paper, we study the topological entanglement of uniform random polygons in a confined space. We derive the formula for the mean squared linking number of such polygons. For a fixed simple closed curve in the confined space, we rigorously show that the linking probability between this curve and a uniform random polygon of n vertices is at least 1-O\\big(\\frac{1}{\\sqrt{n}}\\big) . Our numerical study also indicates that the linking probability between two uniform random polygons (in a confined space), of m and n vertices respectively, is bounded below by 1-O\\big(\\frac{1}{\\sqrt{mn}}\\big) . In particular, the linking probability between two uniform random polygons, both of n vertices, is bounded below by 1-O\\big(\\frac{1}{n}\\big) .

Molecular markers to assess genetic diversity and mutant identifications in Jatropha curcas

International Nuclear Information System (INIS)

Azhar Mohamad; Yie Min Kwan; Fatin Mastura Derani; Abdul Rahim Harun

2010-01-01

Jatropha curcas (Linnaeus) belongs to the Euphorbiaceae family, is a multipurpose use, drought resistant and perennial plant. It is an economic important crop, which generates wide interest in understanding the genetic diversity of the species towards selection and breeding of superior genotypes. Jatropha accessions are closely related family species. Thus, better understanding of the effectiveness of the different DNA-based markers is an important step towards plant germplasm characterization and evaluation. It is becoming a prerequisite for more effective application of marker techniques in breeding programs. Inter-simple sequence repeats (ISSRs) has shown rapid, simple, reproducible and inexpensive means in molecular taxonomy, conservation breeding and genetic diversity analysis. These markers were used to understand diversity and differentiate amongst accessions of Jatropha population and mutant lines generated by acute gamma radiation. The ISSR for marker applications are essential to facilitate management, conservation and genetic improvement programs towards improvement of bio-diesel production and medication substances. A total of 62 ISSR primers were optimized for polymorphism evaluations on five foreign accessions (Africa, India, Myanmar, Indonesia, Thailand), nine local accessions and two mutants of Jatropha. Optimization was resulted 54 ISSR primers affirmative for the polymorphism evaluation study, which encountered 12 ISSR primers, showed significance polymorphism amongst the accessions and mutants. Marker derived from ISSR profiling is a powerful method for identification and molecular classification of Jatropha from accession to generated mutant varieties. (author)

Population genetic study of 34 X-Chromosome markers in 5 main ethnic groups of China.

Science.gov (United States)

Zhang, Suhua; Bian, Yingnan; Li, Li; Sun, Kuan; Wang, Zheng; Zhao, Qi; Zha, Lagabaiyila; Cai, Jifeng; Gao, Yuzhen; Ji, Chaoneng; Li, Chengtao

2015-12-04

As a multi-ethnic country, China has some indigenous population groups which vary in culture and social customs, perhaps as a result of geographic isolation and different traditions. However, upon close interactions and intermarriage, admixture of different gene pools among these ethnic groups may occur. In order to gain more insight on the genetic background of X-Chromosome from these ethnic groups, a set of X-markers (18 X-STRs and 16 X-Indels) was genotyped in 5 main ethnic groups of China (HAN, HUI, Uygur, Mongolian, Tibetan). Twenty-three private alleles were detected in HAN, Uygur, Tibetan and Mongolian. Significant differences (p population differentiation of HUI and Uygur. However, the HAN, Tibetan and Mongolian ethnic groups were closely clustered. Eighteen X-Indels exhibited in general congruent phylogenetic signal and similar cluster among the 5 ethnic groups compared with 16 X-STRs. Aforementioned results proved the genetic polymorphism and potential of the 34 X-markers in the 5 ethnic groups.

Gc globulin as a diagnostic and prognostic marker in horses

DEFF Research Database (Denmark)

Pihl, Tina Holberg

can prevent development of shock and thereby increase survival chances. The in vivo toxicity of Gc-globulin infusion is currently being investigated in horses and other species. Gc-globulin has been demonstrated in horse plasma and its structure closely resembles that of human Gc-globulin. Gc......-globulin concentrations in horses under clinical conditions have never previously been investigated. The Ph.D. project focuses on Gc-globulin as a prognostic marker in horses with acute abdominal pain....

The use of bone turnover markers in chronic kidney disease-mineral and bone disorders.

Science.gov (United States)

Chiang, Cherie

2017-03-01

Bone turnover markers assist in fracture risk prediction, management and monitoring of osteoporosis in patients without chronic kidney disease (CKD). The use in CKD-mineral bone disorder (MBD) has been limited as many of these markers and breakdown products are renally excreted, including the most commonly used and well standardized procollagen type I N propeptide and C-terminal cross-linking telopeptide of type I collagen. Of the markers unaffected by renal function, bone specific alkaline phosphatase is associated with mortality and fracture rate in CKD subjects and is now available on several automated analysers. When used in combination with PTH, bone specific alkaline phosphatase as a bone formation marker correlated well with bone biopsy histomorphometry in predicting adynamic bone disease. Tartrate-resistant acid phosphatase 5b is a resorption marker that is under development for automation. Both high and low bone turnover in CKD-MBD patients are associated with increased fracture and mortality risk. Bone biopsy as the gold standard to differentiate between adynamic bone disease and osteitis fibrosa is limited by availability and cost. Appropriate use of bone turnover markers is vital in the decision to commence anti-resorptive agents, and to monitor efficacy in order to avoid over suppression of bone turnover, which may lead to stress fractures. Further efforts are required to develop markers unaffected by renal function with standardized cut-off values and fracture as well as vascular calcification end-points. © 2017 Asian Pacific Society of Nephrology.

Development of novel low-copy nuclear markers for Hieraciinae (Asteraceae) and their perspective for other tribes.

Science.gov (United States)

Krak, Karol; Alvarez, Inés; Caklová, Petra; Costa, Andrea; Chrtek, Jindrich; Fehrer, Judith

2012-02-01

The development of three low-copy nuclear markers for low taxonomic level phylogenies in Asteraceae with emphasis on the subtribe Hieraciinae is reported. Marker candidates were selected by comparing a Lactuca complementary DNA (cDNA) library with public DNA sequence databases. Interspecific variation and phylogenetic signal of the selected genes were investigated for diploid taxa from the subtribe Hieraciinae and compared to a reference phylogeny. Their ability to cross-amplify was assessed for other Asteraceae tribes. All three markers had higher variation (2.1-4.5 times) than the internal transcribed spacer (ITS) in Hieraciinae. Cross-amplification was successful in at least seven other tribes of the Asteraceae. Only three cases indicating the presence of paralogs or pseudogenes were detected. The results demonstrate the potential of these markers for phylogeny reconstruction in the Hieraciinae as well as in other Asteraceae tribes, especially for very closely related species.

Implications of Artefacts Reduction in the Planning CT Originating from Implanted Fiducial Markers

International Nuclear Information System (INIS)

Kassim, Iskandar; Joosten, Hans; Barnhoorn, Jaco C.; Heijmen, Ben J.M.; Dirkx, Maarten L.P.

2011-01-01

The efficacy of metal artefact reduction (MAR) software to suppress artefacts in reconstructed computed tomography (CT) images originating from small metal objects, like tumor markers and surgical clips, was evaluated. In addition, possible implications of using digital reconstructed radiographs (DRRs), based on the MAR CT images, for setup verification were analyzed. A phantom and 15 patients with different tumor sites and implanted markers were imaged with a multislice CT scanner. The raw image data was reconstructed both with the clinically used filtered-backprojection (FBP) and with the MAR software. Using the MAR software, improvements in image quality were often observed in CT slices with markers or clips. Especially when several markers were located near to each other, fewer streak artefacts were observed than with the FBP algorithm. In addition, the shape and size of markers could be identified more accurately, reducing the contoured marker volumes by a factor of 2. For the phantom study, the CT numbers measured near to the markers corresponded more closely to the expected values. However, the MAR images were slightly more smoothed compared with the images reconstructed with FBP. For 8 prostate cancer patients in this study, the interobserver variation in 3D marker definition was similar (<0.4 mm) when using DRRs based on either FBP or MAR CT scans. Automatic marker matches also showed a similar success rate. However, differences in automatic match results up to 1 mm, caused by differences in the marker definition, were observed, which turned out to be (borderline) statistically significant (p = 0.06) for 2 patients. In conclusion, the MAR software might improve image quality by suppressing metal artefacts, probably allowing for a more reliable delineation of structures. When implanted markers or clips are used for setup verification, the accuracy may slightly be improved as well, which is relevant when using very tight clinical target volume (CTV) to

Identification of genomic regions conferring drought tolerance in bread wheat using ISSR markers

International Nuclear Information System (INIS)

Maqsood, R.; Khaliq, I.; Amjid, M.W.

2017-01-01

Drought stress is one of ever escalating and disastrous situation for plantadaptations under changing climate. Quantitative Trait Loci (QTL) analysis was done to identify chromosomal locations containing QTLs for photosynthetic rate, relative water content and cell membrane stability under drought stress conditions. An F2 population was developed from an intraspecific cross between a drought tolerant genotype (Chakawal-50) and a drought susceptible genotype (9436) of Triticum aestivum. A total of 30 ISSR markers were used to screen both parents. Only 4 ISSR markers were found polymorphic which were used to score 180 F2 plants. A total of 73 bands produced were found polymorphic from these 4 markers using capillary electrophoresis. One QTL was found linked to Photosynthetic rate on chromosome 3A, one to relative water contents on chromosome 4D and one to cell membrane thermo-stability on chromosome 2B, respectively. As these traits were also positively correlated with thousand grain weight, so indirectly these QTLs might improve plant yield under limited water conditions. Therefore, these QTLs may be used through marker assisted selection while breeding wheat under limited water conditions. (author)

Wireless Energy and Information Transmission in FSO and RF-FSO Links

KAUST Repository

Makki, Behrooz

2017-09-22

We propose and analyze a wireless energy and information transmission scheme in free-space optical (FSO) links. The results are presented for both quasi-static and fast-fading conditions. We derive closed-form expressions for throughput, outage probability and optimal power allocation optimizing the system throughput/outage probability. Finally, we complement the FSO link with an additional radio frequency (RF) link to create a hybrid RF-FSO system and reduce the system outage probability. The results show that joint implementation of the RF and FSO links leads to considerable performance improvement, compared to the cases with only FSO-based communication.

ISSR markers for gender identification and genetic diagnosis of Hippophae rhamnoides ssp. turkestanica growing at high altitudes in Ladakh region (Jammu and Kashmir).

Science.gov (United States)

Das, Kamal; Ganie, Showkat Hussain; Mangla, Yash; Dar, Tanvir-Ul-Hassan; Chaudhary, Manju; Thakur, Rakesh Kumar; Tandon, Rajesh; Raina, S N; Goel, Shailendra

2017-03-01

Hippophae rhamnoides L. ssp. turkestanica (Elaeagnaceae) is a predominantly dioecious and wind-pollinated medicinal plant species. The mature fruits of the species possess antioxidative, anti-inflammatory, antimicrobial, anticancerous, and antistimulatory properties that are believed to improve the immune system. The identification of male and female plants in H. rhamnoides ssp. turkestanica is quite difficult until flowering which usually takes 3-4 years or more. A sex-linked marker can be helpful in establishing the orchards through identification of genders at an early stage of development. Therefore, we studied the genetic diversity of populations in Ladakh with the aim to identify a gender-specific marker using ISSR markers. Fifty-eight ISSR primers were used to characterize the genome of H. rhamnoides ssp. turkestanica, of which eight primers generated 12 sex-specific fragments specific to one or more populations. The ISSR primer (P-45) produced a fragment which faithfully segregates all the males from the female plants across all the three valleys surveyed. This male-specific locus was converted into a SCAR. Forward and reverse primers designed from this fragment amplified a 750-bp sequence in males only, thus specifying it as an informative male-specific sex-linked marker. This SCAR marker was further validated for its capability to differentiate gender on an additional collection of plants, representing three geographically isolated valleys (Nubra, Suru, and Indus) from Ladakh region of India. The results confirmed sex-linked specificity of the marker suggesting that this conserved sequence at the Y chromosome is well preserved through the populations in Ladakh region. At present, there are no reliable markers which can differentiate male from female plants across all the three valleys of Ladakh region at an early stage of plant development. It is therefore envisaged that the developed SCAR marker shall provide a reliable molecular tool for early

The development of retrosynthetic glycan libraries to profile and classify the human serum N-linked glycome.

Science.gov (United States)

Kronewitter, Scott R; An, Hyun Joo; de Leoz, Maria Lorna; Lebrilla, Carlito B; Miyamoto, Suzanne; Leiserowitz, Gary S

2009-06-01

Annotation of the human serum N-linked glycome is a formidable challenge but is necessary for disease marker discovery. A new theoretical glycan library was constructed and proposed to provide all possible glycan compositions in serum. It was developed based on established glycobiology and retrosynthetic state-transition networks. We find that at least 331 compositions are possible in the serum N-linked glycome. By pairing the theoretical glycan mass library with a high mass accuracy and high-resolution MS, human serum glycans were effectively profiled. Correct isotopic envelope deconvolution to monoisotopic masses and the high mass accuracy instruments drastically reduced the amount of false composition assignments. The high throughput capacity enabled by this library permitted the rapid glycan profiling of large control populations. With the use of the library, a human serum glycan mass profile was developed from 46 healthy individuals. This paper presents a theoretical N-linked glycan mass library that was used for accurate high-throughput human serum glycan profiling. Rapid methods for evaluating a patient's glycome are instrumental for studying glycan-based markers.

Results for five sets of forensic genetic markers studied in a Greek population sample

DEFF Research Database (Denmark)

Tomas Mas, Carmen; Skitsa, I; Steinmeier, E

2015-01-01

A population sample of 223 Greek individuals was typed for five sets of forensic genetic markers with the kits NGM SElect™, SNPforID 49plex, DIPplex(®), Argus X-12 and PowerPlex(®) Y23. No significant deviation from Hardy-Weinberg expectations was observed for any of the studied markers after Holm...... origin. The Greek population grouped closely to the other European populations measured by FST(*) distances. The match probability ranged from a value of 1 in 2×10(7) males by using haplotype frequencies of four X-chromosome haplogroups in males to 1 in 1.73×10(21) individuals for 16 autosomal STRs....

Genomic markers for decision making: what is preventing us from using markers?

Science.gov (United States)

Coyle, Vicky M; Johnston, Patrick G

2010-02-01

The advent of novel genomic technologies that enable the evaluation of genomic alterations on a genome-wide scale has significantly altered the field of genomic marker research in solid tumors. Researchers have moved away from the traditional model of identifying a particular genomic alteration and evaluating the association between this finding and a clinical outcome measure to a new approach involving the identification and measurement of multiple genomic markers simultaneously within clinical studies. This in turn has presented additional challenges in considering the use of genomic markers in oncology, such as clinical study design, reproducibility and interpretation and reporting of results. This Review will explore these challenges, focusing on microarray-based gene-expression profiling, and highlights some common failings in study design that have impacted on the use of putative genomic markers in the clinic. Despite these rapid technological advances there is still a paucity of genomic markers in routine clinical use at present. A rational and focused approach to the evaluation and validation of genomic markers is needed, whereby analytically validated markers are investigated in clinical studies that are adequately powered and have pre-defined patient populations and study endpoints. Furthermore, novel adaptive clinical trial designs, incorporating putative genomic markers into prospective clinical trials, will enable the evaluation of these markers in a rigorous and timely fashion. Such approaches have the potential to facilitate the implementation of such markers into routine clinical practice and consequently enable the rational and tailored use of cancer therapies for individual patients.

The macrophage low-grade inflammation marker sCD163 is modulated by exogenous sex steroids

DEFF Research Database (Denmark)

Thomsen, Henrik Holm; Møller, Holger Jon; Trolle, Christian

2013-01-01

Soluble CD163 (sCD163) is a novel marker linked to states of low grade inflammation such as diabetes, obesity, liver disease and atherosclerosis, all prevalent in subjects with Turner and Klinefelter Syndromes. We aimed to assess the levels of sCD163 and the regulation of sCD163 in regards...

Characterization and comparison of EST-SSR and TRAP markers for genetic analysis of the Japanese persimmon Diospyros kaki.

Science.gov (United States)

Luo, C; Zhang, F; Zhang, Q L; Guo, D Y; Luo, Z R

2013-01-09

We developed and characterized expressed sequence tags (ESTs)-simple sequence repeats (SSRs) and targeted region amplified polymorphism (TRAP) markers to examine genetic relationships in the persimmon genus Diospyros gene pool. In total, we characterized 14 EST-SSR primer pairs and 36 TRAP primer combinations, which were amplified across 20 germplasms of 4 species in the genus Diospyros. We used various genetic parameters, including effective multiplex ratio (EMR), diversity index (DI), and marker index (MI), to test the utility of these markers. TRAP markers gave higher EMR (24.85) but lower DI (0.33), compared to EST-SSRs (EMR = 3.65, DI = 0.34). TRAP gave a very high MI (8.08), which was about 8 times than the MI of EST-SSR (1.25). These markers were utilized for phylogenetic inference of 20 genotypes of Diospyros kaki Thunb. and allied species, with a result that all kaki genotypes clustered closely and 3 allied species formed an independent group. These markers could be further exploited for large-scale genetic relationship inference.

Cultivar identification and genetic relationship of pineapple (Ananas comosus) cultivars using SSR markers.

Science.gov (United States)

Lin, Y S; Kuan, C S; Weng, I S; Tsai, C C

2015-11-25

The genetic relationships among 27 pineapple [Ananas comosus (L.) Merr.] cultivars and lines were examined using 16 simple sequence repeat (SSR) markers. The number of alleles per locus of the SSR markers ranged from 2 to 6 (average 3.19), for a total of 51 alleles. Similarity coefficients were calculated on the basis of 51 amplified bands. A dendrogram was created according to the 16 SSR markers by the unweighted pair-group method. The banding patterns obtained from the SSR primers allowed most of the cultivars and lines to be distinguished, with the exception of vegetative clones. According to the dendrogram, the 27 pineapple cultivars and lines were clustered into three main clusters and four individual clusters. As expected, the dendrogram showed that derived cultivars and lines are closely related to their parental cultivars; the genetic relationships between pineapple cultivars agree with the genealogy of their breeding history. In addition, the analysis showed that there is no obvious correlation between SSR markers and morphological characters. In conclusion, SSR analysis is an efficient method for pineapple cultivar identification and can offer valuable informative characters to identify pineapple cultivars in Taiwan.

Markers, Models, and Measurement Error: Exploring the Links between Attention Deficits and Language Impairments

Science.gov (United States)

Redmond, Sean M.

2016-01-01

Purpose: The empirical record regarding the expected co-occurrence of attention-deficit/hyperactivity disorder (ADHD) and specific language impairment is confusing and contradictory. A research plan is presented that has the potential to untangle links between these 2 common neurodevelopmental disorders. Method: Data from completed and ongoing…

Reconstructing the phylogeny of Scolytinae and close allies: Major obstacles and prospects for a solution

Science.gov (United States)

Bjarte H. Jordal

2007-01-01

To enable the resolution of deep phylogenetic divergence in Scolytinae and closely related weevils, several new molecular markers were screened for their phylogenetic potential. The nuclear protein encoding genes, CAD and Arginine Kinase, were particularly promising and will be added to future phylogenetic studies in combination with 28S, COI, and Elongation Factor 1...

Integrating Multiple Data Sources for Combinatorial Marker Discovery: A Study in Tumorigenesis.

Science.gov (United States)

Bandyopadhyay, Sanghamitra; Mallik, Saurav

2018-01-01

Identification of combinatorial markers from multiple data sources is a challenging task in bioinformatics. Here, we propose a novel computational framework for identifying significant combinatorial markers ( s) using both gene expression and methylation data. The gene expression and methylation data are integrated into a single continuous data as well as a (post-discretized) boolean data based on their intrinsic (i.e., inverse) relationship. A novel combined score of methylation and expression data (viz., ) is introduced which is computed on the integrated continuous data for identifying initial non-redundant set of genes. Thereafter, (maximal) frequent closed homogeneous genesets are identified using a well-known biclustering algorithm applied on the integrated boolean data of the determined non-redundant set of genes. A novel sample-based weighted support ( ) is then proposed that is consecutively calculated on the integrated boolean data of the determined non-redundant set of genes in order to identify the non-redundant significant genesets. The top few resulting genesets are identified as potential s. Since our proposed method generates a smaller number of significant non-redundant genesets than those by other popular methods, the method is much faster than the others. Application of the proposed technique on an expression and a methylation data for Uterine tumor or Prostate Carcinoma produces a set of significant combination of markers. We expect that such a combination of markers will produce lower false positives than individual markers.

Relationship between heart rate recovery and inflammatory markers in patients with polycystic ovary syndrome: a cross-sectional study

OpenAIRE

Giallauria Francesco; Orio Francesco; Lombardi Gaetano; Colao Annamaria; Vigorito Carlo; Tafuri Maria; Palomba Stefano

2009-01-01

Abstract Background Polycystic ovary syndrome (PCOS) is an endocrine disease closely related to several risk factors for cardiovascular disease. An abnormal heart rate recovery (HRR), an easily-obtained measure derived from exercise stress test and closely related to an increased risk for cardiovascular mortality, has been recently described in PCOS women. A subclinical increase of the inflammation markers has been also observed in the PCOS. This study was designed to study the relationships ...

Genetics Home Reference: X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia

Science.gov (United States)

... Conditions XMEN X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia Printable PDF Open All Close ... boxes. Description X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia (typically known by the acronym ...

X-linked recessive panhypopituitarism associated with a regional duplication in Xq25-q26.

Science.gov (United States)

Lagerström-Fermér, M; Sundvall, M; Johnsen, E; Warne, G L; Forrest, S M; Zajac, J D; Rickards, A; Ravine, D; Landegren, U; Pettersson, U

1997-01-01

We present a linkage analysis and a clinical update on a previously reported family with X-linked recessive panhypopituitarism, now in its fourth generation. Affected members exhibit variable degrees of hypopituitarism and mental retardation. The markers DXS737 and DXS1187 in the q25-q26 region of the X chromosome showed evidence for linkage with a peak LOD score (Zmax) of 4.12 at zero recombination fraction (theta(max) = 0). An apparent extra copy of the marker DXS102, observed in the region of the disease gene in affected males and heterozygous carrier females, suggests that a segment including this marker is duplicated. The gene causing this disorder appears to code for a dosage-sensitive protein central to development of the pituitary. Images Figure 2 PMID:9106538

Application of microsatellite markers as potential tools for traceability of Girgentana goat breed dairy products.

Science.gov (United States)

Sardina, Maria Teresa; Tortorici, Lina; Mastrangelo, Salvatore; Di Gerlando, Rosalia; Tolone, Marco; Portolano, Baldassare

2015-08-01

In livestock, breed assignment may play a key role in the certification of products linked to specific breeds. Traceability of farm animals and authentication of their products can contribute to improve breed profitability and sustainability of animal productions with significant impact on the rural economy of particular geographic areas and on breed and biodiversity conservation. With the goal of developing a breed genetic traceability system for Girgentana dairy products, the aim of this study was to identify specific microsatellite markers able to discriminate among the most important Sicilian dairy goat breeds, in order to detect possible adulteration in Girgentana dairy products. A total of 20 microsatellite markers were analyzed on 338 individual samples from Girgentana, Maltese, and Derivata di Siria goat breeds. Specific microsatellite markers useful for traceability of dairy products were identified. Eight microsatellite markers showed alleles present at the same time in Maltese and Derivata di Siria and absent in Girgentana and, therefore, they were tested on DNA pools of the three breeds. Considering the electropherograms' results, only FCB20, SRCRSP5, and TGLA122 markers were tested on DNA samples extracted from cheeses of Girgentana goat breed. These three microsatellite markers could be applied in a breed genetic traceability system of Girgentana dairy products in order to detect adulteration due to Maltese and Derivata di Siria goat breeds. Copyright © 2015 Elsevier Ltd. All rights reserved.

Development of functional markers associated with phenotypic characteristics for identification of soy variety

International Nuclear Information System (INIS)

Ibarra, M.; Castro, A; Capdevielle, F.

2013-01-01

The organization of agricultural systems requires the verification of the genetic identity and purity of cultivars. The increase in the number of soy varieties to be evaluated, and the narrow genetic base of soybean cultivars, make the identification using phenotypic descriptors very difficult. The International Union for the Protection of New Varieties of Plants (UPOV) has recognized the utility of molecular markers associated with descriptive phenotypic characteristics. With the goal of developing this kind of markers, six genic or genomic S SR were selected in silico (Sat286, Satt229, GmPrx1, GMES1173, Satt571 and Gm Hi), plus two previously reported markers (GmF35H and SoyF3H). All were evaluated in 35 soybean cultivars. The SSRs GmPrx1 and Gm Hi selected for seed coat peroxidase and hilum color respectively were monomorphic. The mean Polymorphism Information Content (PI C) value within the selected group of polymorphic markers was 0.48 with an average of 3.12 allele per locus. GmF35H discriminated the soybean varieties according to the flower color (white and purple). Discrimination tests showed a high percentage of accurate classification of growth habit (95.8%) and pubescence color (80.6%) with Sat286 and Soy F3H, respectively. The classification values for pod color (74.2%) and leaflet size (73.5%) were intermediate using GMES1173 and Satt571, respectively. The marker Satt229 was not discriminating for flowering time (50%) and maturity (42.8%). Molecular markers selected in or close to sequences of interest can be integrated into a genetic identification system as complementary markers to the classic phenotypic descriptors of soybean varieties

Elimination of ghost markers during dual sensor-based infrared tracking of multiple individual reflective markers

International Nuclear Information System (INIS)

Stroian, G.; Falco, T.; Seuntjens, J.P.

2004-01-01

The accuracy of dose delivery in radiotherapy is affected by the uncertainty in tumor localization. Motion of internal anatomy due to physiological processes such as respiration may lead to significant displacements which compromise tumor coverage and generate irradiation of healthy tissue. Real-time tracking with infrared-based systems is often used for tracking thoracic motion in radiation therapy. We studied the origin of ghost markers ('crosstalk') which may appear during dual sensor-based infrared tracking of independent reflective markers. Ghost markers occur when two or more reflective markers are coplanar with each other and with the sensors of the two camera-based infrared tracking system. Analysis shows that sensors are not points but they have a finite extent and this extent determines for each marker a 'ghost volume'. If one reflective marker enters the ghost volume of another marker, ghost markers will be reported by the tracking system; if the reflective markers belong to a surface their 'ghost volume' is reduced to a 'ghost surface' (ghost zone). Appearance of ghost markers is predicted for markers taped on the torso of an anthropomorphic phantom. This study illustrates the dependence of the shape, extent, and location of the ghost zones on the shape of the anthropomorphic phantom, the angle of view of the tracking system, and the distance between the tracking system and the anthropomorphic phantom. It is concluded that the appearance of ghost markers can be avoided by positioning the markers outside the ghost zones of the other markers. However, if this is not possible and the initial marker configuration is ghost marker-free, ghost markers can be eliminated during real-time tracking by virtue of the fact that they appear in the coordinate data sequence only temporarily

Multipoint linkage analysis and homogeneity tests in 15 Dutch X-linked retinitis pigmentosa families

NARCIS (Netherlands)

Bergen, A. A.; van den Born, L. I.; Schuurman, E. J.; Pinckers, A. J.; van Ommen, G. J.; Bleekers-Wagemakers, E. M.; Sandkuijl, L. A.

1995-01-01

Linkage analysis and homogeneity tests were carried out in 15 Dutch families segregating X-linked retinitis pigmentosa (X L R P). The study included segregation data for eight polymorphic DNA markers from the short arm of the human X chromosome. The results of both multipoint linkage analysis in

Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5’ accessions

Science.gov (United States)

2012-01-01

Background Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for fire blight resistance has been reported on linkage group 3 of Malus ‘Robusta 5’. In this study we identified markers derived from putative fire blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. Results When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand ‘Malling 9’ X ‘Robusta 5’ population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German ‘Idared’ X ‘Robusta 5’ population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6 cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90). In the US ‘Otawa3’ X ‘Robusta5’ population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in fire blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor

Identification and Validation of a New Male Sex-Specific ISSR Marker in Pointed Gourd (Trichosanthes dioica Roxb.

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Sinchan Adhikari

2014-01-01

Full Text Available The aim of the present study was to develop a genetic sex marker for the pointed gourd (Trichosanthes dioica Roxb. to allow gender determination at any stage in the life cycle. Screening of genomic DNA with intersimple sequence repeat (ISSR primers was used to discover sex-specific touch-down polymerase chain reaction (Td-PCR amplification products. Using pooled DNA from male and female genotypes and 42 ISSR primers, a putative male specific marker (~550 bp was identified. DNA marker specific to male is an indication of existence of nonepigenetic factors involved in gender development in pointed gourd. The ISSR technique has proved to be a reliable technique in gender determination of pointed gourd genotypes at the seedling phenophase. The sex marker developed here could also be used as a starting material towards sequence characterization of sex linked genes for better understanding the developmental as well as evolutionary pathways in sexual dimorphism.

Lung tumor tracking during stereotactic radiotherapy treatment with the CyberKnife: Marker placement and early results

International Nuclear Information System (INIS)

Nuyttens, J.J.; Prevost, J.B.; Praag, J.; Hoogeman, M.; Levendag, P.C.; Klaveren, R.J. van; Pattynama, P.M.T.

2006-01-01

Lung tumor tracking during stereotactic radiotherapy with the CyberKnife requires the insertion of markers in or close to the tumor. To reduce the risk of pneumothorax, three methods of marker placement were used: 1) intravascular coil placement, 2) percutaneous intrathoracal, and 3) percutaneous extrathoracal placement. We investigated the toxicity of marker placement and the tumor response of the lung tumor tracking treatment. Markers were placed in 20 patients with 22 tumors: 13 patients received a curative treatment, seven a palliative. The median Charlson Comorbidity Score was 4 (range: 1-8). Platinum fiducials and intravascular embolisation coils were used as markers. In total, 78 markers were placed: 34 intrathoracal, 23 intravascular and 21 extrathoracal. The PTV equaled the GTV + 5 mm. A median dose of 45 Gy (range: 30-60 Gy, in 3 fractions) was prescribed to the 70-85% isodose. The response was evaluated with a CTscan performed 6-8 weeks after the last treatment and routinely thereafter. The median follow-up was 4 months (range: 2-11). No severe toxicity due to the marker placement was seen. Pneumothorax was not seen. The local control was 100%. Four tumors in four patients showed a complete response, 15 tumors in 14 patients a partial response, and three tumors in two patients with metastatic disease had stable disease. No severe toxicity of marker placement was seen due to the appropriate choice of one of the three methods. CyberKnife tumor tracking with markers is feasible and resulted in excellent tumor response. Longer follow-up is needed to validate the local control

Cyanobacteria to Link Closed Ecological Systems and In-Situ Resources Utilization Processes

Science.gov (United States)

Brown, Igor

production), require significant power (tens of kWh/kg), and in many processes requires high temperatures ( 1000o C) to be effec-tive; therefore they are not compatible with closed life support systems such as MELiSSA. With the release of the NASA Lunar Architecture Team's latest Lunar Mission Strategy, the investigation of more efficient air bioregeneration techniques based on the metabolism of lower order photosynthetic organisms with ability to leach (weather) in situ rocks appears to be very timely and relevant. Cyanobacteria (CB) are known as very effective producers of O2, proteins, vitamins, immunomodulators (Brown et al., 2006) and as mineral destroyers (Friedmann, 1980; Gorbushina and Palinska, 1999) to supply themselves with different elements. Results: As a result of pilot studies, we propose, therefore, to develop a concept for semi-closed integrated system that uses CB to extract useful elements for their sustaining, to revitalize air and produce valuable biomolecules. Such a system could be the foundation of a self-sustaining extraterrestrial outpost (Hendrickx, De Wever et al., 2005; Handford, 2006). A potential advantage of a cyanobacterial photoreactor placed between LSS and ISRU loops is the possibility of supplying these systems with extracted elements and compounds from the regolith. In addition, waste regolith may be transformed into additional products such as methane, biomass, and organic and inorganic soil enrichment for the cultivation of high plants. We have used several species of siderophilic CB isolated from iron-depositing hot springs in Yellowstone Na-tional Park (Brown et al., 2007) to characterize their ability to utilize terrestrial analogs of lunar and martian rocks. Severe dilution of a rich medium for the cultivation of CB with deionized water did not lead to the growth repression of the cyanobacterium JSC-12. It was found that the suspension of JSC Mars-1 soil stimulant in deionized water sup-ports the proliferation of several

Tantalum markers in radiography

International Nuclear Information System (INIS)

Aronson, A.S.; Jonsson, N.; Alberius, P.

1985-01-01

The biocompatibility of two types of radiopaque tantalum markers was evaluated histologically. Reactions to pin markers (99.9% purity) and spherical markers (95.2% purity) were investigated after 3-6 weeks in rabbits and 5-48 weeks in children with abnormal growth. Both marker types were firmly attached to bone trabeculae; this was most pronounced in rabbit bone, and no adverse macroscopic reactions were observed. Microscopically, no reactions or only slight fibrosis of bone tissue were detected, while soft tissues only demonstrated a minor inflammatory reaction. Nevertheless, the need for careful preparation and execution of marker implantations is stressed, and particularly avoidance iof the use of emery in sharpening of cannulae. The bioinertness of tantalum was reconfirmed as was its suitability for use as skeletal and soft tissue radiographic markers. (orig.)

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

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Briggs, M.D.; Rasmussen, M.; Garber, P.; Rimoin, D.L.; Cohn, D.H. (Steven Spielberg Pediatric Research Center, Los Angeles, CA (United States)); Weber, J.L. (Marshfield Medical Research Foundation, WI (United States)); Yuen, J.; Reinker, K. (Univ. of Hawaii, Honolulu, HI (United States))

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.

Gastric emptying of solid radiopaque markers: studies in healthy subjects and diabetic patients

International Nuclear Information System (INIS)

Feldman, M.; Smith, H.J.; Simon, T.R.

1984-01-01

The purpose of these studies was to develop a radiologic method for assessing gastric emptying of an indigestible solid in humans and to apply this technique to the evaluation of patients with diabetes mellitus. Thirty healthy subjects ingested 10 solid radiopaque markers (small pieces of nasogastric tubing) together with a standard meal (donuts and 7-Up). Radiographs of the upper abdomen were obtained hourly for up to 6 h until all markers had emptied from the stomach. In some experiments, 99mTc-labeled scrambled eggs were added to the meal so that emptying of this digestible solid, assessed by scintigraphy, could be compared with emptying of liquids and solid radiopaque markers. In healthy subjects, the digestible solid emptied more slowly than the liquid (t 1/2 . 154 +/- 11 min vs. 30 +/- 3 min, p less than 0.001), but emptying of digestible solid was significantly faster than the emptying of the indigestible solid radiopaque markers. In diabetics, emptying rates for the digestible solid and liquid were close to normal (t 1/2 . 178 +/- 5 min and 40 +/- 3 min, respectively), whereas indigestible solid markers were retained in the stomach 6 h after the meal in 50% of the patients. Radiopaque markers proved to be a simple method for measuring gastric emptying of indigestible solids in humans. Using this technique, patients with insulin-dependent diabetes mellitus had a high incidence of abnormally slow gastric emptying of indigestible solids; the method may be a more sensitive indicator of gastric motor dysfunction than radionuclide scintigraphy

Gastric emptying of solid radiopaque markers: studies in healthy subjects and diabetic patients

Energy Technology Data Exchange (ETDEWEB)

Feldman, M.; Smith, H.J.; Simon, T.R.

1984-10-01

The purpose of these studies was to develop a radiologic method for assessing gastric emptying of an indigestible solid in humans and to apply this technique to the evaluation of patients with diabetes mellitus. Thirty healthy subjects ingested 10 solid radiopaque markers (small pieces of nasogastric tubing) together with a standard meal (donuts and 7-Up). Radiographs of the upper abdomen were obtained hourly for up to 6 h until all markers had emptied from the stomach. In some experiments, 99mTc-labeled scrambled eggs were added to the meal so that emptying of this digestible solid, assessed by scintigraphy, could be compared with emptying of liquids and solid radiopaque markers. In healthy subjects, the digestible solid emptied more slowly than the liquid (t 1/2 . 154 +/- 11 min vs. 30 +/- 3 min, p less than 0.001), but emptying of digestible solid was significantly faster than the emptying of the indigestible solid radiopaque markers. In diabetics, emptying rates for the digestible solid and liquid were close to normal (t 1/2 . 178 +/- 5 min and 40 +/- 3 min, respectively), whereas indigestible solid markers were retained in the stomach 6 h after the meal in 50% of the patients. Radiopaque markers proved to be a simple method for measuring gastric emptying of indigestible solids in humans. Using this technique, patients with insulin-dependent diabetes mellitus had a high incidence of abnormally slow gastric emptying of indigestible solids; the method may be a more sensitive indicator of gastric motor dysfunction than radionuclide scintigraphy.

Distinctive mitochondrial genome of Calanoid copepod Calanus sinicus with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phylogenetic and population studies

Science.gov (United States)

2011-01-01

Background Copepods are highly diverse and abundant, resulting in extensive ecological radiation in marine ecosystems. Calanus sinicus dominates continental shelf waters in the northwest Pacific Ocean and plays an important role in the local ecosystem by linking primary production to higher trophic levels. A lack of effective molecular markers has hindered phylogenetic and population genetic studies concerning copepods. As they are genome-level informative, mitochondrial DNA sequences can be used as markers for population genetic studies and phylogenetic studies. Results The mitochondrial genome of C. sinicus is distinct from other arthropods owing to the concurrence of multiple non-coding regions and a reshuffled gene arrangement. Further particularities in the mitogenome of C. sinicus include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes atp6 and atp8 relative to other copepods. The monophyletic Copepoda should be placed within the Vericrustacea. The close affinity between Cyclopoida and Poecilostomatoida suggests reassigning the latter as subordinate to the former. Monophyly of Maxillopoda is rejected. Within the alignment of 11 C. sinicus mitogenomes, there are 397 variable sites harbouring three 'hotspot' variable sites and three microsatellite loci. Conclusion The occurrence of the circular subgenomic fragment during laboratory assays suggests that special caution should be taken when sequencing mitogenomes using long PCR. Such a phenomenon may provide additional evidence of mitochondrial DNA recombination, which appears to have been a prerequisite for shaping the present mitochondrial profile of C. sinicus during its evolution. The lack of synapomorphic gene arrangements among copepods has cast doubt on the utility of gene order as a useful molecular marker for deep phylogenetic analysis. However, mitochondrial genomic sequences have been valuable markers for

Assessment of genetic diversity and relationships among Egyptian mango (Mangifera indica L.) cultivers grown in Suez Canal and Sinai region using RAPD markers.

Science.gov (United States)

Mansour, Hassan; Mekki, Laila E; Hussein, Mohammed A

2014-01-01

DNA-based RAPD (Random Amplification of Polymorphic DNA) markers have been used extensively to study genetic diversity and relationships in a number of fruit crops. In this study, 10 (7 commercial mango cultivars and 3 accessions) mango genotypes traditionally grown in Suez Canal and Sinai region of Egypt, were selected to assess genetic diversity and relatedness. Total genomic DNA was extracted and subjected to RAPD analysis using 30 arbitrary 10-mer primers. Of these, eleven primers were selected which gave 92 clear and bright fragments. A total of 72 polymorphic RAPD bands were detected out of 92 bands, generating 78% polymorphisms. The mean PIC values scores for all loci were of 0.85. This reflects a high level of discriminatory power of a marker and most of these primers produced unique band pattern for each cultivar. A dendrogram based on Nei's Genetic distance co-efficient implied a moderate degree of genetic diversity among the cultivars used for experimentation, with some differences. The hybrid which had derived from cultivar as female parent was placed together. In the cluster, the cultivars and accessions formed separate groups according to bearing habit and type of embryo and the members in each group were very closely linked. Cluster analysis clearly showed two main groups, the first consisting of indigenous to the Delta of Egypt cultivars and the second consisting of indigenous to the Suez Canal and Sinai region. From the analysis of results, it appears the majority of mango cultivars originated from a local mango genepool and were domesticated later. The results indicated the potential of RAPD markers for the identification and management of mango germplasm for breeding purposes.

Bladder tumor markers beyond cytology: International Consensus Panel on bladder tumor markers.

NARCIS (Netherlands)

Lokeshwar, V.B.; Habuchi, T.; Grossman, H.B.; Murphy, W.M.; Hautmann, S.H.; Hemstreet, G.P.; Bono, A.V.; Getzenberg, R.H.; Goebell, P.; Schmitz-Drager, B.J.; Schalken, J.A.; Fradet, Y.; Marberger, M.; Messing, E.; Droller, M.J.

2005-01-01

This is the first of 2 articles that summarize the findings of the International Consensus Panel on cytology and bladder tumor markers. The objectives of our panel were to reach a consensus on the areas where markers are needed, to define the attributes of an ideal tumor marker, and to identify

Autosomal and sex-linked microsatellite loci in the green oak leaf roller Tortrix viridana L.

NARCIS (Netherlands)

Schroeder, H.C.; Arens, P.F.P.; Smulders, M.J.M.

2009-01-01

Eight microsatellite markers were developed for the lepidopteran species Tortrix viridana using an enrichment protocol. The loci were highly variable with number of alleles ranging from four to 38. Six of the eight loci were in Hardy¿Weinberg equilibrium. The other two were linked to the

Rust resistance evaluation of advanced wheat (triticum aestivum l.) genotypes using pcr-based dna markers

International Nuclear Information System (INIS)

Rahman, S.U.; Younis, M.; Iqbal, M.Z.; Nawaz, M.

2014-01-01

The most effective and environmental friendly approach for the control of wheat rust disease is the use of resistant genotypes. The present study was conducted to explore rust resistance potential of 85 elite wheat genotypes (36 varieties and 49 advanced lines) using various types of DNA markers like STS, SCAR and SSR. DNA markers linked with different genes conferring resistance to rusts (Leaf rust=Lr, Yellow rust=Yr and Stem rust=Sr) were employed in this study. A total of 18 genes, consisting of eleven Lr (lr1, lr10, lr19, lr21, lr28, lr34, lr39, lr46, lr47, lr51 and lr52), four Yr (yr5, yr18, yr26 and yr29) and three Sr genes (sr2, sr29, and sr36) were studied through linked DNA markers. Maximum number of Lr genes was found in 17 advanced lines and 9 varieties, Yr genes in 26 advanced lines and 20 wheat varieties, and Sr genes in 43 advanced lines and 27 varieties. Minimum number of Lr genes was found in advanced line D-97 and variety Kohinoor-83, Yr genes in wheat variety Bwp-97 and Sr genes in 6 advanced lines and 8 varieties. Molecular data revealed that genotypes having same origin, from a specified area showed resistance for similar type of genes. In this study, an average similarity of 84% was recorded among wheat genotypes. Out of 18 loci, 15 were found to be polymorphic. (author)

Tenascin-C is not a useful marker for disease activity in psoriasis.

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Latijnhouwers, M A; Bergers, M; Kuijpers, A L; van der Vleuten, C J; Dijkman, H; van de Kerkhof, P C; Schalkwijk, J

1998-09-01

Tenascin-C is an extracellular matrix glycoprotein that is markedly upregulated in the dermis of psoriatic skin. In this study, we have addressed the question whether the presence of tenascin-C in the lesion or in serum is a marker for disease activity. Immunohistochemical staining of tenascin-C before and after treatment with different topical and systemic medication showed that tenascin-C remained abundant after clinical remission of lesions, indicating that downregulation of tenascin-C to normal values is a slow process. By using a sensitive enzyme-linked immunosorbent assay to measure levels of serum tenascin-C in psoriatic patients and unaffected individuals, we found that tenascin-C levels in most patients were within the normal range. Moreover, tenascin-C values did not correlate with disease activity. We conclude that tenascin-C is not useful as a marker for disease activity in psoriasis.

Diagnostic significance of combined detention of multiple tumour markers in lung cancer

International Nuclear Information System (INIS)

Chen Yanming; Qiu Jianming

2003-01-01

Objective: To explore the diagnostic value of combined detection of multiple markers in the determination of lung cancer. Methods: Using enzyme-linked immunosorbent assay (ELISA), the serum CEA, CA19-9, CA125, CA15-3 was determined in eighty-six lung cancer patients, thirty benign lung disease patients and thirty healthy persons. Results; Serum concentrations of CEA, CA19-9, CA125 and CA15-3 were significantly higher in patents with lung cancer than that in the patients with benign lung disease patients and healthy persons. The single test sensitivity of CEA, CA19-9, CA125 and CA15-3 for diagnosis of lung cancer is 41.9%, 37.2%, 48.9%, 36% respectively; the combined test sensitivity is 94.2%. Conclusions: Assessing several tumour markers can help differentiating various histological type of lung cancer and increase the sensitivity

Tumor markers in clinical oncology

International Nuclear Information System (INIS)

Novakovic, S.

2004-01-01

The subtle differences between normal and tumor cells are exploited in the detection and treatment of cancer. These differences are designated as tumor markers and can be either qualitative or quantitative in their nature. That means that both the structures that are produced by tumor cells as well as the structures that are produced in excessive amounts by host tissues under the influence of tumor cells can function as tumor markers. Speaking in general, the tumor markers are the specific molecules appearing in the blood or tissues and the occurrence of which is associated with cancer. According to their application, tumor markers can be roughly divided as markers in clinical oncology and markers in pathology. In this review, only tumor markers in clinical oncology are going to be discussed. Current tumor markers in clinical oncology include (i) oncofetal antigens, (ii) placental proteins, (iii) hormones, (iv) enzymes, (v) tumor-associated antigens, (vi) special serum proteins, (vii) catecholamine metabolites, and (viii) miscellaneous markers. As to the literature, an ideal tumor marker should fulfil certain criteria - when using it as a test for detection of cancer disease: (1) positive results should occur in the early stages of the disease, (2) positive results should occur only in the patients with a specific type of malignancy, (3) positive results should occur in all patients with the same malignancy, (4) the measured values should correlate with the stage of the disease, (5) the measured values should correlate to the response to treatment, (6) the marker should be easy to measure. Most tumor markers available today meet several, but not all criteria. As a consequence of that, some criteria were chosen for the validation and proper selection of the most appropriate marker in a particular malignancy, and these are: (1) markers' sensitivity, (2) specificity, and (3) predictive values. Sensitivity expresses the mean probability of determining an elevated tumor

Expression of Lymphatic Markers in the Adult Rat Spinal Cord.

Science.gov (United States)

Kaser-Eichberger, Alexandra; Schroedl, Falk; Bieler, Lara; Trost, Andrea; Bogner, Barbara; Runge, Christian; Tempfer, Herbert; Zaunmair, Pia; Kreutzer, Christina; Traweger, Andreas; Reitsamer, Herbert A; Couillard-Despres, Sebastien

2016-01-01

Under physiological conditions, lymphatic vessels are thought to be absent from the central nervous system (CNS), although they are widely distributed within the rest of the body. Recent work in the eye, i.e., another organ regarded as alymphatic, revealed numerous cells expressing lymphatic markers. As the latter can be involved in the response to pathological conditions, we addressed the presence of cells expressing lymphatic markers within the spinal cord by immunohistochemistry. Spinal cord of young adult Fisher rats was scrutinized for the co-expression of the lymphatic markers PROX1 and LYVE-1 with the cell type markers Iba1, CD68, PGP9.5, OLIG2. Rat skin served as positive control for the lymphatic markers. PROX1-immunoreactivity was detected in many nuclei throughout the spinal cord white and gray matter. These nuclei showed no association with LYVE-1. Expression of LYVE-1 could only be detected in cells at the spinal cord surface and in cells closely associated with blood vessels. These cells were found to co-express Iba1, a macrophage and microglia marker. Further, double labeling experiments using CD68, another marker found in microglia and macrophages, also displayed co-localization in the Iba1+ cells located at the spinal cord surface and those apposed to blood vessels. On the other hand, PROX1-expressing cells found in the parenchyma were lacking Iba1 or PGP9.5, but a significant fraction of those cells showed co-expression of the oligodendrocyte lineage marker OLIG2. Intriguingly, following spinal cord injury, LYVE-1-expressing cells assembled and reorganized into putative pre-vessel structures. As expected, the rat skin used as positive controls revealed classical lymphatic vessels, displaying PROX1+ nuclei surrounded by LYVE-1-immunoreactivity. Classical lymphatics were not detected in adult rat spinal cord. Nevertheless, numerous cells expressing either LYVE-1 or PROX1 were identified. Based on their localization and overlapping expression with

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

Science.gov (United States)

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

2017-11-01

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

Preoperative values of inflammatory markers predict clinical outcomes in patients after CABG, regardless of the use of cardiopulmonary bypass

Directory of Open Access Journals (Sweden)

Dariusz Plicner

2016-12-01

Conclusion: Links between preoperative 8-iso-PGF2α, ADMA and β-TG and unfavorable early post-CABG outcomes suggest that these markers could be useful in identifying patients with increased risk of LCOS, PMI and in-hospital cardiovascular death following elective CABG.

Dependency of the regio- and stereoselectivity of intramolecular, ring-closing glycosylations upon the ring size

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Patrick Claude

2011-12-01

Full Text Available Phenyl 3,4,6-tri-O-benzyl-2-O-(3-carboxypropionyl-1-thio-β-D-galactopyranoside (1 was condensed via its pentafluorophenyl ester 2 with 5-aminopentyl (4a, 4-aminobutyl (4b, 3-aminopropyl (4c and 2-aminoethyl 4,6-O-benzylidene-β-D-glucopyranoside (4d, prepared from the corresponding N-Cbz protected glucosides 3a–d, to give the corresponding 2-[3-(alkylcarbamoylpropionyl] tethered saccharides 5a–d. Intramolecular, ring closing glycosylation of the saccharides with NIS and TMSOTf afforded the tethered β(1→3 linked disaccharides 6a–c, the α(1→3 linked disaccharides 7a–d and the α(1→2 linked disaccharide 8d in ratios depending upon the ring size formed during glycosylation. No β(1→2 linked disaccharides were formed. Molecular modeling of saccharides 6–8 revealed that a strong aromatic stacking interaction between the aromatic parts of the benzyl and benzylidene protecting groups in the galactosyl and glucosyl moieties was mainly responsible for the observed regioselectivity and anomeric selectivity of the ring-closing glycosylation step.

The interest of gait markers in the identification of subgroups among fibromyalgia patients

OpenAIRE

Auvinet, Bernard; Chaleil, Denis; Cabane, Jean; Dumolard, Anne; Hatron, Pierre; Juvin, Robert; Lanteri-Minet, Michel; Mainguy, Yves; Negre-Pages, Laurence; Pillard, Fabien; Riviere, Daniel; Maugars, Yves-Michel

2011-01-01

Abstract Background Fibromyalgia (FM) is a heterogeneous syndrome and its classification into subgroups calls for broad-based discussion. FM subgrouping, which aims to adapt treatment according to different subgroups, relies in part, on psychological and cognitive dysfunctions. Since motor control of gait is closely related to cognitive function, we hypothesized that gait markers could be of interest in the identification of FM patients' subgroups. This controlled study aimed at characterizin...

On the Performance of HARQ-Based RF-FSO Links

KAUST Repository

Makki, Behrooz

2016-03-28

© 2015 IEEE. This paper studies the performance of the hybrid radio-frequency (RF) and free-space optical (FSO) links assuming perfect channel state information (CSI) at the receiver. Considering the cases with and without hybrid automatic repeat request (HARQ), we derive closed-form expressions for the message decoding probabilities as well as the throughput and the outage probability of the RF- FSO setups. We also evaluate the effect of different channel conditions on the throughput and the outage probability. The results show the efficiency of the RF-FSO links in different conditions.

Validation of bio markers for diagnosis of Hepatocellular Carcinoma (H and c) in Egyptian patients suffering from hepatitis - C virus

International Nuclear Information System (INIS)

Moawed, F.S.M.

2013-01-01

The differential diagnosis between chronic liver diseases (CLD) and hepatocellular carcinoma (HCC) is a challenge. The aim of this study is to identify new bio markers related to HCV metabolic changes, which are altered during tumorigenesis, and combine them with tumor specific markers in order to improve HCC surveillance among patients with chronic hepatitis C (CHC). Methods: This study included 137 patients with CHC, 107 of them with proven diagnosis of HCC with no metastasis. The tumor markers studied included AFP and AGP. Fibrosis markers, liver function tests, oxidative stress, antioxidant enzymes, Cu, and zinc serum levels were determined as transition markers. Results: We were able to differentiate 100% between CLD and HCC by applying a new marker “[(log_1_0 AFP x zinc + log_1_0 AGP) / SOD] x100 ” “AZAS”, with a cut-off value of 9.2. The results were applicable for both genders with or without bilharzia. Conclusion: We were able to discriminate between HCC and CLD by combining their markers simultaneously. We suggest that in cancer validation studies, it is imperative to search for markers that link to the preneoplastic process, and to determine what type of mechanism is active in each stage albumin (C), and bilirubin (D)

Modelling and Intelligent Control of an Elastic Link Robot Manipulator

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Malik Loudini

2013-01-01

Full Text Available In this paper, precise control of the end-point position of a planar single-link elastic manipulator robot is discussed. The Timoshenko beam theory (TBT has been used to characterize the structural link elasticity including important damping mechanisms. A suitable nonlinear model is derived based on the Lagrangian assumed modes method. Elastic link manipulators are classified as systems possessing highly complex dynamics. In addition, the environment in which they operate may have a lot of disturbances. These give rise to special problems that may be solved using intelligent control techniques. The application of two advanced control strategies based on fuzzy set theory is investigated. The first closed-loop control scheme to be applied is the standard Proportional-Derivative (PD type fuzzy logic controller (FLC, also known as PD-type Mamdani's FLC (MPDFLC. Then, a genetic algorithm (GA is used to optimize the MPDFLC parameters with innovative tuning procedures. Both the MPDFLC and the GA optimized FLC (GAOFLC are implemented and tested to achieve a precise control of the manipulator end-point. The performances of the adopted closed-loop intelligent control strategies are examined via simulation experiments.

Gastric emptying of solid radiopaque markers: studies in healthy subjects and diabetic patients.

Science.gov (United States)

Feldman, M; Smith, H J; Simon, T R

1984-10-01

The purpose of these studies was to develop a radiologic method for assessing gastric emptying of an indigestible solid in humans and to apply this technique to the evaluation of patients with diabetes mellitus. Thirty healthy subjects ingested 10 solid radiopaque markers (small pieces of nasogastric tubing) together with a standard meal (donuts and 7-Up). Radiographs of the upper abdomen were obtained hourly for up to 6 h until all markers had emptied from the stomach. Although most of the liquid component of the meal, labeled with 111In, emptied during the first hour (as assessed simultaneously by radionuclide scintigraphy), few radiopaque markers emptied from the stomach during the first 2 h after the meal. Most markers emptied during the fourth postprandial hour, and all 10 markers had emptied by 6 h in 45 of 46 experiments. In contrast, not all of the solid radiopaque markers emptied from the stomach by 6 h in 16 of 26 experiments in patients with diabetes mellitus (p less than 0.001 vs. healthy controls). In some experiments, 99mTc-labeled scrambled eggs were added to the meal so that emptying of this digestible solid, assessed by scintigraphy, could be compared with emptying of liquids and solid radiopaque markers. In healthy subjects, the digestible solid emptied more slowly than the liquid (t 1/2 = 154 +/- 11 min vs. 30 +/- 3 min, p less than 0.001), but emptying of digestible solid was significantly faster than the emptying of the indigestible solid radiopaque markers. In diabetics, emptying rates for the digestible solid and liquid were close to normal (t 1/2 = 178 +/- 5 min and 40 +/- 3 min, respectively), whereas indigestible solid markers were retained in the stomach 6 h after the meal in 50% of the patients. Radiopaque markers proved to be a simple method for measuring gastric emptying of indigestible solids in humans. Using this technique, patients with insulin-dependent diabetes mellitus had a high incidence of abnormally slow gastric emptying of

The ways of controlling microbiota of the higher plant link in LSS

Science.gov (United States)

Tirranen, L. S.; Gitelson, I. I.

The ways of controlling microbiota of the higher plant link have been considered, as the sterile plant growth in closed ecological human life support systems is impossible. One of the ways of controlling the link microbial community - building sterile intrasystem barriers between the system links - is problematic and dangerous. An accidental breach of microorganisms through the barrier can lead to disastrous consequences - either unrestrained reproduction of microbes including pathogenic and conditionally pathogenic species or, on the contrary, elimination of species most valuable for the given microbial community. Another way of control is maintaining suitable conditions for human and plant habitat, creating some constructive system properties directed at microbial exchange weakening. The use of catalytic furnace for oxidizing organic impurities in system atmosphere, UV processing of air and plants in the phytotron before and in the beginning of the experiments promoted decrease of microorganism amount in the link. To restrict the distribution of microorganisms of the higher plant link in other system links the module for yield processing being under constant suction was isolated. To prevent the introduction of microorganisms into the system we applied the UV processing of all objects transferred to the system and continuous atmosphere overpressure inside the system. It is important to detect the ultimate amount of microorganism indicator groups in the higher plant link biocenosis. It would indicate the microbial pollution of the link and be the signal for regulation of its microbial population or processing technologies in the studied objects. There were two 4-month experiments with the "human - higher plants" closed ecosystem carried out. There was no progressive deterioration for plants, decrease of wheat yield to zero and rapid growth of microorganisms in the higher plant link after making all listed arrangements. Microbiological analyses of the studied

Simultaneous control and piezoelectric insert optimization for manipulators with flexible link

OpenAIRE

Bottega, Valdecir; Pergher, Rejane; Fonseca, Jun S. O.

2009-01-01

This work proposes a tracking control model for a flexible link robotic manipulator using simultaneously motor torques and piezoelectric actuators. The dynamic model of manipulator is obtained in a closed form through the Lagrangian approach. The control uses the motor torques for the tracking control of the joints and also to reduce the low frequency vibration induced in the manipulator links. The stability of this control is guaranteed by the Lyapunov stability theory. Piezoelectric actuato...

Allele-specific marker generation and linkage mapping on the Xiphophorus sex chromosomes.

Science.gov (United States)

Woolcock, B; Kazianis, S; Lucito, R; Walter, R B; Kallman, K D; Morizot, D C; Vielkind, J R

2006-01-01

There is great interest in the sex chromosomes of Xiphophorus fishes because both WY/YY and XX/XY sex-determining mechanisms function in these species, with at least one taxon possessing all three types of sex chromosomes, and because in certain interspecific hybrids melanoma arises as a consequence of inheritance of the sex-linked macromelanophore determining locus (MDL). Representational difference analysis (RDA) has been used to clone two sequences from the sex-determining region of X. maculatus, including a cholinergic receptor, nicotinic, delta polypeptide (CHRND) orthologue. Allele-specific assays for these sequences, as well as for the sex-linked XMRK1 and XMRK2 genes, were developed to distinguish W, X, and Y chromosomes derived from a X. maculatus (XX/XY) strain and a X. helleri (WY/YY) strain. Linkage mapping localized these markers to linkage group (LG) 24. No recombinants were observed between XMRK2 and MDL, confirming a role for XMRK2 in macromelanophore development. Although the master sex-determining (SD) locus certainly resides on Xiphophorus LG 24, autosomal loci are probably involved in sex determination as well, as indicated by the abnormal sex ratios in the backcross hybrids that contrast theoretical predictions based on LG 24 genotyping. Marker development and allelic discrimination on the Xiphophorus sex chromosomes should prove highly useful for studies that utilize this genus as an animal model.

The Y chromosome as the most popular marker in genetic genealogy benefits interdisciplinary research.

Science.gov (United States)

Calafell, Francesc; Larmuseau, Maarten H D

2017-05-01

The Y chromosome is currently by far the most popular marker in genetic genealogy that combines genetic data and family history. This popularity is based on its haploid character and its close association with the patrilineage and paternal inherited surname. Other markers have not been found (yet) to overrule this status due to the low sensitivity and precision of autosomal DNA for genetic genealogical applications, given the vagaries of recombination, and the lower capacities of mitochondrial DNA combined with an in general much lower interest in maternal lineages. The current knowledge about the Y chromosome and the availability of markers with divergent mutation rates make it possible to answer questions on relatedness levels which differ in time depth; from the individual and familial level to the surnames, clan and population level. The use of the Y chromosome in genetic genealogy has led to applications in several well-established research disciplines; namely in, e.g., family history, demography, anthropology, forensic sciences, population genetics and sex chromosome evolution. The information obtained from analysing this chromosome is not only interesting for academic scientists but also for the huge and lively community of amateur genealogists and citizen-scientists, fascinated in analysing their own genealogy or surname. This popularity, however, has also some drawbacks, mainly for privacy reasons related to the DNA donor, his close family and far-related namesakes. In this review paper we argue why Y-chromosomal analysis and its genetic genealogical applications will still perform an important role in future interdisciplinary research.

On the capacity of FSO links under lognormal and Rician-lognormal turbulences

KAUST Repository

Ansari, Imran Shafique

2014-09-01

A unified capacity analysis under weak and composite turbulences of a free-space optical (FSO) link that accounts for pointing errors and both types of detection techniques (i.e. intensity modulation/direct detection as well as heterodyne detection) is addressed in this work. More specifically, a unified exact closed-form expression for the moments of the end-to-end signal-to-noise ratio (SNR) of a single link FSO transmission system is presented in terms of well-known elementary functions. Capitalizing on these new moments expressions, unified approximate and simple closed- form results are offered for the ergodic capacity at high SNR regime as well as at low SNR regime. All the presented results are verified via computer- based Monte-Carlo simulations.

A closed-loop anesthetic delivery system for real-time control of burst suppression

Science.gov (United States)

Liberman, Max Y.; Ching, ShiNung; Chemali, Jessica; Brown, Emery N.

2013-08-01

Objective. There is growing interest in using closed-loop anesthetic delivery (CLAD) systems to automate control of brain states (sedation, unconsciousness and antinociception) in patients receiving anesthesia care. The accuracy and reliability of these systems can be improved by using as control signals electroencephalogram (EEG) markers for which the neurophysiological links to the anesthetic-induced brain states are well established. Burst suppression, in which bursts of electrical activity alternate with periods of quiescence or suppression, is a well-known, readily discernible EEG marker of profound brain inactivation and unconsciousness. This pattern is commonly maintained when anesthetics are administered to produce a medically-induced coma for cerebral protection in patients suffering from brain injuries or to arrest brain activity in patients having uncontrollable seizures. Although the coma may be required for several hours or days, drug infusion rates are managed inefficiently by manual adjustment. Our objective is to design a CLAD system for burst suppression control to automate management of medically-induced coma. Approach. We establish a CLAD system to control burst suppression consisting of: a two-dimensional linear system model relating the anesthetic brain level to the EEG dynamics; a new control signal, the burst suppression probability (BSP) defining the instantaneous probability of suppression; the BSP filter, a state-space algorithm to estimate the BSP from EEG recordings; a proportional-integral controller; and a system identification procedure to estimate the model and controller parameters. Main results. We demonstrate reliable performance of our system in simulation studies of burst suppression control using both propofol and etomidate in rodent experiments based on Vijn and Sneyd, and in human experiments based on the Schnider pharmacokinetic model for propofol. Using propofol, we further demonstrate that our control system reliably

Closed Loop Experiment Manager (CLEM—An Open and Inexpensive Solution for Multichannel Electrophysiological Recordings and Closed Loop Experiments

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Hananel Hazan

2017-10-01

Full Text Available There is growing need for multichannel electrophysiological systems that record from and interact with neuronal systems in near real-time. Such systems are needed, for example, for closed loop, multichannel electrophysiological/optogenetic experimentation in vivo and in a variety of other neuronal preparations, or for developing and testing neuro-prosthetic devices, to name a few. Furthermore, there is a need for such systems to be inexpensive, reliable, user friendly, easy to set-up, open and expandable, and possess long life cycles in face of rapidly changing computing environments. Finally, they should provide powerful, yet reasonably easy to implement facilities for developing closed-loop protocols for interacting with neuronal systems. Here, we survey commercial and open source systems that address these needs to varying degrees. We then present our own solution, which we refer to as Closed Loop Experiments Manager (CLEM. CLEM is an open source, soft real-time, Microsoft Windows desktop application that is based on a single generic personal computer (PC and an inexpensive, general-purpose data acquisition board. CLEM provides a fully functional, user-friendly graphical interface, possesses facilities for recording, presenting and logging electrophysiological data from up to 64 analog channels, and facilities for controlling external devices, such as stimulators, through digital and analog interfaces. Importantly, it includes facilities for running closed-loop protocols written in any programming language that can generate dynamic link libraries (DLLs. We describe the application, its architecture and facilities. We then demonstrate, using networks of cortical neurons growing on multielectrode arrays (MEA that despite its reliance on generic hardware, its performance is appropriate for flexible, closed-loop experimentation at the neuronal network level.

AUTOANTIBODIES TO GLUTAMIC ACID DECARBOXYLASE AS A PATHOGENETIC MARKER OF TYPE I DIABETES MELLITUS

OpenAIRE

N. V. Piven; L. N. Lukhverchyk; A. I. Burakovsky; N. V. Polegenkaya; M. V. Karpovich

2011-01-01

Abstract. A new method of enzyme-linked immunosorbent assay (in solid-phase ELISA format) has been developed to determine concentrations of autoantibodies to glutamic acid decarboxylase, as well as an evidencebased methodology is proposed for its medical implications, as a quantitative pathogenetic predictive marker of autoimmune diagnostics in type 1 diabetes mellitus. This technique could be implied for serial production of diagnostic reagent kits, aimed for detection of autoantibodies to g...

Meerkat close calling patterns are linked to sex, social category, season and wind, but not fecal glucocorticoid metabolite concentrations.

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Jelena Mausbach

Full Text Available It is well established that animal vocalizations can encode information regarding a sender's identity, sex, age, body size, social rank and group membership. However, the association between physiological parameters, particularly stress hormone levels, and vocal behavior is still not well understood. The cooperatively breeding African meerkats (Suricata suricatta live in family groups with despotic social hierarchies. During foraging, individuals emit close calls that help maintain group cohesion. These contact calls are acoustically distinctive and variable in rate across individuals, yet, information on which factors influence close calling behavior is missing. The aim of this study was to identify proximate factors that influence variation in call rate and acoustic structure of meerkat close calls. Specifically, we investigated whether close calling behavior is associated with sex, age and rank, or stress hormone output (i.e., measured as fecal glucocorticoid metabolite (fGCM concentrations as individual traits of the caller, as well as with environmental conditions (weather and reproductive seasonality. To disentangle the effects of these factors on vocal behavior, we analyzed sound recordings and assessed fGCM concentrations in 64 wild but habituated meerkats from 9 groups during the reproductive and non-reproductive seasons. Dominant females and one-year old males called at significantly higher rates compared to other social categories during the reproductive season. Additionally, dominant females produced close calls with the lowest mean fundamental frequencies (F0 and the longest mean pulse durations. Windy conditions were associated with significantly higher call rates during the non-reproductive season. Fecal GCM concentrations were unrelated to close calling behavior. Our findings suggest that meerkat close calling behavior conveys information regarding the sex and social category of the caller, but shows no association with f

Wireless Energy and Information Transmission in FSO and RF-FSO Links

KAUST Repository

Makki, Behrooz; Svensson, Tommy; Buisman, Koen; Perez, Joaquin; Alouini, Mohamed-Slim

2017-01-01

We propose and analyze a wireless energy and information transmission scheme in free-space optical (FSO) links. The results are presented for both quasi-static and fast-fading conditions. We derive closed-form expressions for throughput, outage

Genetic markers for western corn rootworm resistance to Bt toxin.

Science.gov (United States)

Flagel, Lex E; Swarup, Shilpa; Chen, Mao; Bauer, Christopher; Wanjugi, Humphrey; Carroll, Matthew; Hill, Patrick; Tuscan, Meghan; Bansal, Raman; Flannagan, Ronald; Clark, Thomas L; Michel, Andrew P; Head, Graham P; Goldman, Barry S

2015-01-07

Western corn rootworm (WCR) is a major maize (Zea mays L.) pest leading to annual economic losses of more than 1 billion dollars in the United States. Transgenic maize expressing insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt) are widely used for the management of WCR. However, cultivation of Bt-expressing maize places intense selection pressure on pest populations to evolve resistance. Instances of resistance to Bt toxins have been reported in WCR. Developing genetic markers for resistance will help in characterizing the extent of existing issues, predicting where future field failures may occur, improving insect resistance management strategies, and in designing and sustainably implementing forthcoming WCR control products. Here, we discover and validate genetic markers in WCR that are associated with resistance to the Cry3Bb1 Bt toxin. A field-derived WCR population known to be resistant to the Cry3Bb1 Bt toxin was used to generate a genetic map and to identify a genomic region associated with Cry3Bb1 resistance. Our results indicate that resistance is inherited in a nearly recessive manner and associated with a single autosomal linkage group. Markers tightly linked with resistance were validated using WCR populations collected from Cry3Bb1 maize fields showing significant WCR damage from across the US Corn Belt. Two markers were found to be correlated with both diet (R2 = 0.14) and plant (R2 = 0.23) bioassays for resistance. These results will assist in assessing resistance risk for different WCR populations, and can be used to improve insect resistance management strategies. Copyright © 2015 Flagel et al.

Biochemical bone turnover markers in diabetes mellitus - A systematic review.

Science.gov (United States)

Starup-Linde, Jakob; Vestergaard, Peter

2016-01-01

Diabetes mellitus is associated with an increased risk of fractures, which is not explained by bone mineral density. Other markers as bone turnover markers (BTMs) may be useful. To assess the relationship between BTMs, diabetes, and fractures. A systematic literature search was conducted in August 2014. The databases searched were Medline at Pubmed and Embase. Medline at Pubmed was searched by "Diabetes Mellitus" (MESH) and "bone turnover markers" and Embase was searched using the Emtree by "Diabetes Mellitus" and "bone turnover", resulting in 611 studies. The eligibility criteria for the studies were to assess BTM in either type 1 diabetes (T1D) or type 2 diabetes (T2D) patients. Of the 611 eligible studies, removal of duplicates and screening by title and abstract lead to 114 potential studies for full-text review. All these studies were full-text screened for eligibility and 45 studies were included. Two additional studies were added from other sources. Among the 47 studies included there were 1 meta-analysis, 29 cross-sectional studies, 13 randomized controlled trials, and 4 longitudinal studies. Both T1D and T2D were studied. Most studies reported fasting BTM and excluded renal disease. Markers of bone resorption and formation seem to be lower in diabetes patients. Bone specific alkaline phosphatase is normal or increased, which suggests that the matrix becomes hypermineralized in diabetes patients. The BTMs: C-terminal cross-link of collagen, insulin-like growth factor-1, and sclerostin may potentially predict fractures, but longitudinal trials are needed. This article is part of a Special Issue entitled Bone and diabetes. Copyright © 2015 Elsevier Inc. All rights reserved.

A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance.

Science.gov (United States)

Miah, Gous; Rafii, Mohd Y; Ismail, Mohd R; Puteh, Adam B; Rahim, Harun A; Islam, Kh Nurul; Latif, Mohammad Abdul

2013-11-14

Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR), and they are typically composed of 1-6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS) can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS in rice breeding

A Review of Microsatellite Markers and Their Applications in Rice Breeding Programs to Improve Blast Disease Resistance

Directory of Open Access Journals (Sweden)

Mohammad Abdul Latif

2013-11-01

Full Text Available Over the last few decades, the use of molecular markers has played an increasing role in rice breeding and genetics. Of the different types of molecular markers, microsatellites have been utilized most extensively, because they can be readily amplified by PCR and the large amount of allelic variation at each locus. Microsatellites are also known as simple sequence repeats (SSR, and they are typically composed of 1–6 nucleotide repeats. These markers are abundant, distributed throughout the genome and are highly polymorphic compared with other genetic markers, as well as being species-specific and co-dominant. For these reasons, they have become increasingly important genetic markers in rice breeding programs. The evolution of new biotypes of pests and diseases as well as the pressures of climate change pose serious challenges to rice breeders, who would like to increase rice production by introducing resistance to multiple biotic and abiotic stresses. Recent advances in rice genomics have now made it possible to identify and map a number of genes through linkage to existing DNA markers. Among the more noteworthy examples of genes that have been tightly linked to molecular markers in rice are those that confer resistance or tolerance to blast. Therefore, in combination with conventional breeding approaches, marker-assisted selection (MAS can be used to monitor the presence or lack of these genes in breeding populations. For example, marker-assisted backcross breeding has been used to integrate important genes with significant biological effects into a number of commonly grown rice varieties. The use of cost-effective, finely mapped microsatellite markers and MAS strategies should provide opportunities for breeders to develop high-yield, blast resistance rice cultivars. The aim of this review is to summarize the current knowledge concerning the linkage of microsatellite markers to rice blast resistance genes, as well as to explore the use of MAS

Relationship between Inflammation markers, Coagulation Activation and Impaired Insulin Sensitivity in Obese Healthy Women

International Nuclear Information System (INIS)

Soliman, S.Et; Shousha, M.A.

2011-01-01

Obesity, insulin resistance syndrome, and atherosclerosis are closely linked phenomena, often connected with a chronic low grade inflammatory state and pro thrombotic hypo fibrinolytic condition. This study investigated the relationship between impaired insulin sensitivity and selected markers of inflammation and thrombin generation in obese healthy women. The study included 36 healthy obese women (body mass index ≥ 30), with normal insulin sensitivity (NIS, n = 18) or impaired insulin sensitivity (IIS, n 18), and 10 non obese women (body mass index < 25).Impaired insulin sensitivity patients had significantly higher levels of high sensitivity C-reactive protein (hs-CRP), transforming growth factor -β1(TGF-β1), plasminogen activator inhibitor-1 (PAI-1), activated factor VII (VIIa), and prothrombin fragments 1 + 2 (F1 + 2) compared with either control subjects or normal insulin sensitivity patients. On the other hand, NIS patients had higher hs-CRP, TGF-β1, PAI-1, and factor VIIa, but not F1 + 2, levels than controls. Significant inverse correlations were observed between the insulin sensitivity index and TGF-β1, hs-CRP, PAI-1; factor VIIa, and F1 + 2 levels. Moreover, significant direct correlations were noted between TGF-β1 and CRP, PAI-1, factor VIIa, and F1 + 2 concentrations. Finally, multiple regressions revealed that TGF-β1 and the insulin sensitivity index were independently related to F1 + 2. These results document an in vivo relationship between insulin sensitivity and coagulation activation in obesity. Here we report that obesity is associated with higher TGF-β, PAI-1, prothrombin fragments 1 and 2 (F1 + 2), and activated factor VII (VIIa) plasma levels, and that insulin resistance exacerbates these alterations. The elevated TGF-β1 levels detected in the obese population may provide a biochemical link between insulin resistance and an increased risk for cardiovascular disease

Development of SSR markers for a Tibetan medicinal plant, Lancea tibetica (Phrymaceae), based on RAD sequencing.

Science.gov (United States)

Tian, Zunzhe; Zhang, Faqi; Liu, Hairui; Gao, Qingbo; Chen, Shilong

2016-11-01

Lancea tibetica (Phrymaceae), a Tibetan medicinal plant, is endemic to the Qinghai-Tibet Plateau. The over-exploitation of wild L. tibetica has led to the destruction of many populations. To enhance protection and management, biological research, especially population genetic studies, should be carried out on L. tibetica . Simple sequence repeat (SSR) markers of L. tibetica were developed to analyze population diversity. Four thousand four hundred and forty-one SSR loci were identified for L. tibetica based on restriction-site associated DNA (RAD) sequencing on the Illumina HiSeq platform. One hundred SSR loci were arbitrarily selected for primer design, and 38 of them were successfully amplified. These markers were tested on 56 individuals from three populations of L. tibetica , and 10 markers displayed polymorphisms. The total number of alleles per locus ranged from three to eight, and observed and expected heterozygosities ranged from 0.200 to 1.000 and 0.683 to 0.879, respectively. We tested for cross-amplification of these 10 markers in the related species L. hirsuta and found that nine could be successfully amplified. The SSR markers characterized here are the first to be developed and tested in L. tibetica . They will be useful for future population genetic studies on L. tibetica and closely related species.

Behavioral and TMS Markers of Action Observation Might Reflect Distinct Neuronal Processes.

Science.gov (United States)

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.

Behavioral and TMS markers of action observation might reflect distinct neuronal processes

Directory of Open Access Journals (Sweden)

Sébastien Hétu

2016-09-01

Full Text Available 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, fourteen 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 predominant 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.

Development of Microsatellite Markers for a Tropical Seagrass, Syringodium filiforme (Cymodoceaceae

Directory of Open Access Journals (Sweden)

Alexandra L. Bijak

2014-10-01

Full Text Available Premise of the study: A total of 17 polymorphic microsatellite markers were developed for the tropical Atlantic seagrass Syringodium filiforme (Cymodoceaceae, enabling analysis of population genetic structure in this species for the first time. Methods and Results: The 17 primers amplified di- and trinucleotide repeats revealing two to eight alleles per locus among the South Florida populations tested. In the analysis of two populations from the Florida Keys (Florida, USA, observed heterozygosity ranged from 0.063 to 0.905, although sampling was from relatively closely located populations so heterozygosity is expected to be higher across larger spatial scales. Multiplex PCRs consisting of two 6-plex and one 5-plex reactions were developed to maximize genotyping efficiency. Conclusions: We present here 17 polymorphic markers that will be useful for the study of clonality and population structure of S. filiforme, a marine plant that forms extensive habitat throughout the tropical Atlantic and Caribbean.

Identification of cancer stem cell markers in human malignant mesothelioma cells

Energy Technology Data Exchange (ETDEWEB)

Ghani, Farhana Ishrat; Yamazaki, Hiroto; Iwata, Satoshi; Okamoto, Toshihiro [Division of Clinical Immunology, Institute of Medical Science, University of Tokyo, Tokyo (Japan); Aoe, Keisuke; Okabe, Kazunori; Mimura, Yusuke [Departments of Medical Oncology, Yamaguchi-Ube Medical Center, Yamaguchi (Japan); Fujimoto, Nobukazu; Kishimoto, Takumi [Department of Respiratory Medicine, Okayama Rosai Hospital, Okayama (Japan); Yamada, Taketo [Department of Pathology, Keio University School of Medicine, Tokyo (Japan); Xu, C. Wilson [Drug Development Program, Nevada Cancer Institute, Las Vegas, NV (United States); Morimoto, Chikao, E-mail: morimoto@ims.u-tokyo.ac.jp [Division of Clinical Immunology, Institute of Medical Science, University of Tokyo, Tokyo (Japan); Drug Development Program, Nevada Cancer Institute, Las Vegas, NV (United States)

2011-01-14

Research highlights: {yields} We performed serial transplantation of surgical samples and established new cell lines of malignant mesothelioma. {yields} SP cell and expressions of CD9/CD24/CD26 were often observed in mesothelioma cell lines. {yields} SP and CD24{sup +} cells proliferated by asymmetric cell division-like manner. CD9{sup +} and CD24{sup +} cells have higher potential to generate spheroid colony. {yields} The marker-positive cells have clear tendency to generate larger tumors in mice. -- Abstract: Malignant mesothelioma (MM) is an aggressive and therapy-resistant neoplasm arising from the pleural mesothelial cells and usually associated with long-term asbestos exposure. Recent studies suggest that tumors contain cancer stem cells (CSCs) and their stem cell characteristics are thought to confer therapy-resistance. However, whether MM cell has any stem cell characteristics is not known. To understand the molecular basis of MM, we first performed serial transplantation of surgical samples into NOD/SCID mice and established new cell lines. Next, we performed marker analysis of the MM cell lines and found that many of them contain SP cells and expressed several putative CSC markers such as CD9, CD24, and CD26. Interestingly, expression of CD26 closely correlated with that of CD24 in some cases. Sorting and culture assay revealed that SP and CD24{sup +} cells proliferated by asymmetric cell division-like manner. In addition, CD9{sup +} and CD24{sup +} cells have higher potential to generate spheroid colony than negative cells in the stem cell medium. Moreover, these marker-positive cells have clear tendency to generate larger tumors in mouse transplantation assay. Taken together, our data suggest that SP, CD9, CD24, and CD26 are CSC markers of MM and could be used as novel therapeutic targets.

Soluble hemoglobin-haptoglobin scavenger receptor CD163 as a lineage-specific marker in the reactive hemophagocytic syndrome

DEFF Research Database (Denmark)

Schaer, Dominik J; Schleiffenbaum, Boris; Kurrer, Michael

2005-01-01

.1 mg/L), acute mononucleosis (median 8.2 mg/L), Leishmania infection (median 6.7 mg/L) and healthy controls (median 1.8 mg/L). Follow-up of patients with a relapsing course of the disease revealed close correlations of sCD163 with clinical disease activity, serum ferritin and other markers...

Marker Registration Technique for Handwritten Text Marker in Augmented Reality Applications

Science.gov (United States)

Thanaborvornwiwat, N.; Patanukhom, K.

2018-04-01

Marker registration is a fundamental process to estimate camera poses in marker-based Augmented Reality (AR) systems. We developed AR system that creates correspondence virtual objects on handwritten text markers. This paper presents a new method for registration that is robust for low-content text markers, variation of camera poses, and variation of handwritten styles. The proposed method uses Maximally Stable Extremal Regions (MSER) and polygon simplification for a feature point extraction. The experiment shows that we need to extract only five feature points per image which can provide the best registration results. An exhaustive search is used to find the best matching pattern of the feature points in two images. We also compared performance of the proposed method to some existing registration methods and found that the proposed method can provide better accuracy and time efficiency.

Molecular mapping of the Pinus monticola Cr2 gene using AFLP and SCAR markers

Directory of Open Access Journals (Sweden)

A.K.M. Ekramoddoullah

2013-12-01

Full Text Available White pine blister rust (WPBR, caused by Cronartium ribicola, is a devastating disease in five-needle pines. Genetic resistance is an important component of integrated strategies to control WPBR. The major resistance gene Cr2, discovered by Kinloch etal.(1999, is also effective against British Columbia (BC isolates of WPBR (Hunt et al. 2004. Pyramiding Cr2 gene with other resistancegenes is being pursued as a strategy in BC white pine breeding. To facilitate this strategy, we have recently identified a few RAPD markerslinked to Cr2 at one side (Liu et al. 2006. The objective of the present study was to identify amplified fragment length polymorphism(AFLP markers linked to both sides of Cr2 for its more precise apping. Use of the AFLP technique combined with bulked segregant analysis (BSA and haploid segregation analysis allowed the identification of five AFLP markers. Of these five AFLP markers in the Cr2 linkage, markers EacccMccgat-365, EactgMcccac- 290, and EacagEacag-750 werelinked in coupling and EacagMcccag-160r and EacccMccgat-180r in repulsion. Following cloning and sequencing of the AFLP andRAPD markers, specific PCR primers were designed and used in the amplification of sequence characterized amplified region(SCAR markers at both sides of Cr2. EacccMccgat- 365 and RAPD marker U570-843 reported previously were converted into SCARmarkers. These two SCARs segregated in a 1:1 (presence:absence ratio and the scoring cosegregated with their respective AFLP orRAPD marker. The SCAR marker EacccMccgat- 365-scar was positioned at 3.1 Kosambi cM from one side of Cr2 and U570-843-scarlocalized at 1.4 Kosambi cM from other side. Both SCAR markers can be useful in breeding programs with marker-assisted selection procedureto screen for resistance. This study represents the first report of the development of PCR-based sequence-specific markers linkedto blister rust resistance in five-needle pines. These findings may

Ghost marker detection and elimination in marker-based optical tracking systems for real-time tracking in stereotactic body radiotherapy

International Nuclear Information System (INIS)

Yan, Guanghua; Li, Jonathan; Huang, Yin; Mittauer, Kathryn; Lu, Bo; Liu, Chihray

2014-01-01

Purpose: To propose a simple model to explain the origin of ghost markers in marker-based optical tracking systems (OTS) and to develop retrospective strategies to detect and eliminate ghost markers. Methods: In marker-based OTS, ghost markers are virtual markers created due to the cross-talk between the two camera sensors, which can lead to system execution failure or inaccuracy in patient tracking. As a result, the users have to limit the number of markers and avoid certain marker configurations to reduce the chances of ghost markers. In this work, the authors propose retrospective strategies to detect and eliminate ghost markers. The two camera sensors were treated as mathematical points in space. The authors identified the coplanar within limit (CWL) condition as the necessary condition for ghost marker occurrence. A simple ghost marker detection method was proposed based on the model. Ghost marker elimination was achieved through pattern matching: a ghost marker-free reference set was matched with the optical marker set observed by the OTS; unmatched optical markers were eliminated as either ghost markers or misplaced markers. The pattern matching problem was formulated as a constraint satisfaction problem (using pairwise distances as constraints) and solved with an iterative backtracking algorithm. Wildcard markers were introduced to address missing or misplaced markers. An experiment was designed to measure the sensor positions and the limit for the CWL condition. The ghost marker detection and elimination algorithms were verified with samples collected from a five-marker jig and a nine-marker anthropomorphic phantom, rotated with the treatment couch from −60° to +60°. The accuracy of the pattern matching algorithm was further validated with marker patterns from 40 patients who underwent stereotactic body radiotherapy (SBRT). For this purpose, a synthetic optical marker pattern was created for each patient by introducing ghost markers, marker position

Ghost marker detection and elimination in marker-based optical tracking systems for real-time tracking in stereotactic body radiotherapy

Energy Technology Data Exchange (ETDEWEB)

Yan, Guanghua, E-mail: yan@ufl.edu; Li, Jonathan; Huang, Yin; Mittauer, Kathryn; Lu, Bo; Liu, Chihray [Department of Radiation Oncology, University of Florida, Gainesville, Florida 32610 (United States)

2014-10-15

Purpose: To propose a simple model to explain the origin of ghost markers in marker-based optical tracking systems (OTS) and to develop retrospective strategies to detect and eliminate ghost markers. Methods: In marker-based OTS, ghost markers are virtual markers created due to the cross-talk between the two camera sensors, which can lead to system execution failure or inaccuracy in patient tracking. As a result, the users have to limit the number of markers and avoid certain marker configurations to reduce the chances of ghost markers. In this work, the authors propose retrospective strategies to detect and eliminate ghost markers. The two camera sensors were treated as mathematical points in space. The authors identified the coplanar within limit (CWL) condition as the necessary condition for ghost marker occurrence. A simple ghost marker detection method was proposed based on the model. Ghost marker elimination was achieved through pattern matching: a ghost marker-free reference set was matched with the optical marker set observed by the OTS; unmatched optical markers were eliminated as either ghost markers or misplaced markers. The pattern matching problem was formulated as a constraint satisfaction problem (using pairwise distances as constraints) and solved with an iterative backtracking algorithm. Wildcard markers were introduced to address missing or misplaced markers. An experiment was designed to measure the sensor positions and the limit for the CWL condition. The ghost marker detection and elimination algorithms were verified with samples collected from a five-marker jig and a nine-marker anthropomorphic phantom, rotated with the treatment couch from −60° to +60°. The accuracy of the pattern matching algorithm was further validated with marker patterns from 40 patients who underwent stereotactic body radiotherapy (SBRT). For this purpose, a synthetic optical marker pattern was created for each patient by introducing ghost markers, marker position

QTL Mapping of Adult-Plant Resistance to Leaf Rust in the Wheat Cross Zhou 8425B/Chinese Spring Using High-Density SNP Markers

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Peipei Zhang

2017-05-01

Full Text Available Wheat leaf rust is an important disease worldwide. Growing resistant cultivars is an effective means to control the disease. In the present study, 244 recombinant inbred lines from Zhou 8425B/Chinese Spring cross were phenotyped for leaf rust severities during the 2011–2012, 2012–2013, 2013–2014, and 2014–2015 cropping seasons at Baoding, Hebei province, and 2012–2013 and 2013–2014 cropping seasons in Zhoukou, Henan province. The population was genotyped using the high-density Illumina iSelect 90K SNP assay and SSR markers. Inclusive composite interval mapping identified eight QTL, designated as QLr.hebau-2AL, QLr.hebau-2BS, QLr.hebau-3A, QLr.hebau-3BS, QLr.hebau-4AL, QLr.hebau-4B, QLr.hebau-5BL, and QLr.hebau-7DS, respectively. QLr.hebau-2BS, QLr.hebau-3A, QLr.hebau-3BS, and QLr.hebau-5BL were derived from Zhou 8425B, whereas the other four were from Chinese Spring. Three stable QTL on chromosomes 2BS, 4B and 7DS explained 7.5–10.6%, 5.5–24.4%, and 11.2–20.9% of the phenotypic variance, respectively. QLr.hebau-2BS in Zhou 8425B might be the same as LrZH22 in Zhoumai 22; QLr.hebau-4B might be the residual resistance of Lr12, and QLr.hebau-7DS is Lr34. QLr.hebau-2AL, QLr.hebau-3BS, QLr.hebau-4AL, and QLr.hebau-5BL are likely to be novel QTL for leaf rust. These QTL and their closely linked SNP and SSR markers can be used for fine mapping, candidate gene discovery, and marker-assisted selection in wheat breeding.

Lightweight Biometric Sensing for Walker Classification Using Narrowband RF Links

Directory of Open Access Journals (Sweden)

Tong Liu

2017-12-01

Full Text Available This article proposes a lightweight biometric sensing system using ubiquitous narrowband radio frequency (RF links for path-dependent walker classification. The fluctuated received signal strength (RSS sequence generated by human motion is used for feature representation. To capture the most discriminative characteristics of individuals, a three-layer RF sensing network is organized for building multiple sampling links at the most common heights of upper limbs, thighs, and lower legs. The optimal parameters of sensing configuration, such as the height of link location and number of fused links, are investigated to improve sensory data distinctions among subjects, and the experimental results suggest that the synergistic sensing by using multiple links can contribute a better performance. This is the new consideration of using RF links in building a biometric sensing system. In addition, two types of classification methods involving vector quantization (VQ and hidden Markov models (HMMs are developed and compared for closed-set walker recognition and verification. Experimental studies in indoor line-of-sight (LOS and non-line-of-sight (NLOS scenarios are conducted to validate the proposed method.

Lightweight Biometric Sensing for Walker Classification Using Narrowband RF Links.

Science.gov (United States)

Liu, Tong; Liang, Zhuo-Qian

2017-12-05

This article proposes a lightweight biometric sensing system using ubiquitous narrowband radio frequency (RF) links for path-dependent walker classification. The fluctuated received signal strength (RSS) sequence generated by human motion is used for feature representation. To capture the most discriminative characteristics of individuals, a three-layer RF sensing network is organized for building multiple sampling links at the most common heights of upper limbs, thighs, and lower legs. The optimal parameters of sensing configuration, such as the height of link location and number of fused links, are investigated to improve sensory data distinctions among subjects, and the experimental results suggest that the synergistic sensing by using multiple links can contribute a better performance. This is the new consideration of using RF links in building a biometric sensing system. In addition, two types of classification methods involving vector quantization (VQ) and hidden Markov models (HMMs) are developed and compared for closed-set walker recognition and verification. Experimental studies in indoor line-of-sight (LOS) and non-line-of-sight (NLOS) scenarios are conducted to validate the proposed method.

Lightweight Biometric Sensing for Walker Classification Using Narrowband RF Links

Science.gov (United States)

Liang, Zhuo-qian

2017-01-01

This article proposes a lightweight biometric sensing system using ubiquitous narrowband radio frequency (RF) links for path-dependent walker classification. The fluctuated received signal strength (RSS) sequence generated by human motion is used for feature representation. To capture the most discriminative characteristics of individuals, a three-layer RF sensing network is organized for building multiple sampling links at the most common heights of upper limbs, thighs, and lower legs. The optimal parameters of sensing configuration, such as the height of link location and number of fused links, are investigated to improve sensory data distinctions among subjects, and the experimental results suggest that the synergistic sensing by using multiple links can contribute a better performance. This is the new consideration of using RF links in building a biometric sensing system. In addition, two types of classification methods involving vector quantization (VQ) and hidden Markov models (HMMs) are developed and compared for closed-set walker recognition and verification. Experimental studies in indoor line-of-sight (LOS) and non-line-of-sight (NLOS) scenarios are conducted to validate the proposed method. PMID:29206188

Identification and characterization of microsatellite markers in Pinus kesiya var. langbianensis (Pinaceae).

Science.gov (United States)

Cai, Nian-Hui; Xu, Yu-Lan; Wang, Da-Wei; Chen, Shi; Li, Gen-Qian

2017-02-01

Microsatellite primers were developed in Pinus kesiya var. langbianensis (Pinaceae), a species native to southwestern China, to investigate its genetic diversity and population structure in order to provide information for the conservation and management of this species. Using next-generation sequencing, a total of 2349 putative simple sequence repeat primer pairs were designed. Eighteen polymorphic markers in 60 individuals belonging to four populations of P. kesiya var. langbianensis were identified and characterized with two to 11 alleles per locus. The observed and expected heterozygosity ranged from 0.000 to 0.800 and 0.000 to 0.840, respectively. Each of these loci cross-amplified in the closely related species P. massoniana , P. densata , P. tabuliformis , and P. yunnanensis , with one to seven alleles per locus. The new markers are promising tools to study the population genetics of P. kesiya var. langbianensis and related species.

On the performance of millimeter wave-based RF-FSO links with HARQ feedback

KAUST Repository

Makki, Behrooz

2016-12-24

This paper studies the performance of hybrid radio-frequency (RF) and free-space optical (FSO) links in the cases with and without hybrid automatic repeat request (HARQ). Considering millimeter wave (mmwave) characteristics in the RF link and pointing errors in the FSO link, we derive closed-form expressions for the message decoding probabilities as well as the throughput and the outage probability of the RF-FSO setups. We also evaluate the effect of various parameters such as power amplifiers efficiency, different transmission techniques in the FSO link, pointing errors in the FSO link as well as different coherence times/symbol rates of the RF and the FSO links on the throughput and outage probability. The results show the efficiency of the RF-FSO links in different conditions. Moreover, the HARQ can effectively improve the outage probability/energy efficiency, and compensate the effect of hardware impairments in RF-FSO links.

A deterministic simulation study of embryo marker-assisted selection for age at first calving in Nellore ( Bos indicus) beef cattle

NARCIS (Netherlands)

Rosa, A.J.M.; Bijma, P.; Oliveira, H.N.; Lobo, R.B.; Arendonk, van J.A.M.

2007-01-01

We used deterministic simulation of four alternative multiple ovulation and embryo manipulation (MOET) closed nucleus schemes to investigate the benefits of using marker-assisted selection (MAS) of Nellore (Bos indicus) beef cattle embryos prior to transplantation to reduce the age at first calving

Biochemical markers of bone turnover

International Nuclear Information System (INIS)

Kim, Deog Yoon

1999-01-01

Biochemical markers of bone turnover has received increasing attention over the past few years, because of the need for sensitivity and specific tool in the clinical investigation of osteoporosis. Bone markers should be unique to bone, reflect changes of bone less, and should be correlated with radiocalcium kinetics, histomorphometry, or changes in bone mass. The markers also should be useful in monitoring treatment efficacy. Although no bone marker has been established to meet all these criteria, currently osteocalcin and pyridinium crosslinks are the most efficient markers to assess the level of bone turnover in the menopausal and senile osteoporosis. Recently, N-terminal telopeptide (NTX), C-terminal telopeptide (CTX) and bone specific alkaline phosphatase are considered as new valid markers of bone turnover. Recent data suggest that CTX and free deoxypyridinoline could predict the subsequent risk of hip fracture of elderly women. Treatment of postmenopausal women with estrogen, calcitonin and bisphosphonates demonstrated rapid decrease of the levels of bone markers that correlated with the long-term increase of bone mass. Factors such as circadian rhythms, diet, age, sex, bone mass and renal function affect the results of biochemical markers and should be appropriately adjusted whenever possible. Each biochemical markers of bone turnover may have its own specific advantages and limitations. Recent advances in research will provide more sensitive and specific assays

Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers.

Science.gov (United States)

Li, Faji; Wen, Weie; He, Zhonghu; Liu, Jindong; Jin, Hui; Cao, Shuanghe; Geng, Hongwei; Yan, Jun; Zhang, Pingzhi; Wan, Yingxiu; Xia, Xianchun

2018-06-01

We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay. Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5-32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.

Molecular mapping and genetic analysis of a rice brown planthopper (Nilaparvata lugens Stål) resistance gene.

Science.gov (United States)

Yang, Haiyuan; Ren, Xiang; Weng, Qingmei; Zhu, Lili; He, Guangcun

2002-01-01

The brown planthopper (BPH), Nilaparvata lugens Stål, is a serious insect pest of rice (Oryza saliva L.). We have determined the chromosomal location of a BPH resistance gene in rice using SSR and RFLP techniques. A rice line 'B14', derived from the wild rice Oryza latifolia, showed high resistance to BPH. For tagging the resistance gene in 'B14X', an F2 population and a recombinant inbred (RI) population from a cross between Taichung Native 1 and 'B14' were developed and evaluated for BPH resistance. The results showed that a single dominant gene controlled the resistance of 'B14' to BPH. Bulked segregant SSR analysis was employed for identification of DNA markers linked to the resistance gene. From the survey of 302 SSR primer pairs, three SSR (RM335, RM261, RM185) markers linked to the resistance gene were identified. The closest SSR marker RM261 was linked to the resistance gene at a distance of 1.8 cM. Regions surrounding the resistance gene and the SSR markers were examined with additional RFLP markers on chromosome 4 to define the location of the resistance gene. Linkage of RFLP markers C820, R288, C946 with the resistance gene further confirmed its location on the short arm of chromosome 4. Closely linked DNA markers will facilitate selection for resistant lines in breeding programs and provide the basis for map-based cloning of this resistance gene.

Development of Insertion and Deletion Markers based on Biparental Resequencing for Fine Mapping Seed Weight in Soybean

Directory of Open Access Journals (Sweden)

Ying-hui Li

2014-11-01

Full Text Available As a complement to single nucleotide polymorphisms (SNPs and simple sequence repeats (SSRs, biallelic insertions and deletions (InDels represent powerful molecular markers with desirable features for filling the gap in current genetic linkage maps. In this study, 28,908 small InDel polymorphisms (1–5 base pair, bp distributed genome-wide were identified and annotated by comparison of a whole-genome resequencing data set from two soybean [ (L. Merr.] genotypes, cultivar Zhonghunag13 (ZH and line Zhongpin03-5373 (ZP. The physical distribution of InDel polymorphisms in soybean genome was uneven, and matched closely with the distribution of previously annotated genes. The average density of InDel in the arm region was significantly higher than that in the pericentromeric region. The genomic regions that were fixed between the two elites were elucidated. With this information, five InDel markers within a putative quantitative trait locus (QTL for seed weight (SW, , were developed and used to genotype 254 recombinant inbred lines (RILs derived from the cross of ZP × ZH. Adding these five InDel markers to previously used SNP and SSR markers facilitated the discovery of further recombination events allowing fine-mapping the QTL to a 0.5 Mbp region. Our study clearly underlines the high value of InDel markers for map-based cloning and marker-assisted selection in soybean.

Marker Detection in Aerial Images

KAUST Repository

Alharbi, Yazeed

2017-04-09

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

The dual challenges of generality and specificity when developing environmental DNA markers for species and subspecies of Oncorhynchus

Science.gov (United States)

Taylor M. Wilcox; Kellie J. Carim; Kevin S. McKelvey; Michael Young; Michael K. Schwartz

2015-01-01

Environmental DNA (eDNA) sampling is a powerful tool for detecting invasive and native aquatic species. Often, species of conservation interest co-occur with other, closely related taxa. Here, we developed qPCR (quantitative PCR) markers which distinguish westslope cutthroat trout (Oncorhynchus clarkii lewsi), Yellowstone cutthroat trout (O. clarkii bouvieri...

Macdonald operators and homological invariants of the colored Hopf link

International Nuclear Information System (INIS)

Awata, Hidetoshi; Kanno, Hiroaki

2011-01-01

Using a power sum (boson) realization for the Macdonald operators, we investigate the Gukov, Iqbal, Kozcaz and Vafa (GIKV) proposal for the homological invariants of the colored Hopf link, which include Khovanov-Rozansky homology as a special case. We prove the polynomiality of the invariants obtained by GIKV's proposal for arbitrary representations. We derive a closed formula of the invariants of the colored Hopf link for antisymmetric representations. We argue that a little amendment of GIKV's proposal is required to make all the coefficients of the polynomial non-negative integers. (paper)

The Macrophage Inflammatory Proteins MIP1α (CCL3 and MIP2α (CXCL2 in Implant-Associated Osteomyelitis: Linking Inflammation to Bone Degradation

Directory of Open Access Journals (Sweden)

Ulrike Dapunt

2014-01-01

Full Text Available Bacterial infections of bones remain a serious complication of endoprosthetic surgery. These infections are difficult to treat, because many bacterial species form biofilms on implants, which are relatively resistant towards antibiotics. Bacterial biofilms elicit a progressive local inflammatory response, resulting in tissue damage and bone degradation. In the majority of patients, replacement of the prosthesis is required. To address the question of how the local inflammatory response is linked to bone degradation, tissue samples were taken during surgery and gene expression of the macrophage inflammatory proteins MIP1α (CCL3 and MIP2α (CXCL2 was assessed by quantitative RT-PCR. MIPs were expressed predominantly at osteolytic sites, in close correlation with CD14 which was used as marker for monocytes/macrophages. Colocalisation of MIPs with monocytic cells could be confirmed by histology. In vitro experiments revealed that, aside from monocytic cells, also osteoblasts were capable of MIP production when stimulated with bacteria; moreover, CCL3 induced the differentiation of monocytes to osteoclasts. In conclusion, the multifunctional chemokines CCL3 and CXCL2 are produced locally in response to bacterial infection of bones. In addition to their well described chemokine activity, these cytokines can induce generation of bone resorbing osteoclasts, thus providing a link between bacterial infection and osteolysis.

Language development in the early school years: The importance of close relationships with teachers

NARCIS (Netherlands)

Spilt, J.L.; Koomen, H.M.Y.; Harrison, L.J.

2015-01-01

This longitudinal study examined developmental links between closeness in teacher-child relationships and children’s receptive language ability from the end of the preschool years into the early elementary years, while controlling for changes in peer interaction quality and child behavioral

Genetic analysis and location of gene for resistance to stripe rust in ...

Indian Academy of Sciences (India)

2013-08-06

Aug 6, 2013 ... Institute of Plant Protection, Chinese Academy of Agriculture Science, No 2, West ... The molecular marker Xbarc59 closely linked to the gene YrSD could be ... and a minor resistance gene postulated in it (Calonnec et al.

Application of fluorescence-based semi-automated AFLP analysis in barley and wheat

DEFF Research Database (Denmark)

Schwarz, G.; Herz, M.; Huang, X.Q.

2000-01-01

of semi-automated codominant analysis for hemizygous AFLP markers in an F-2 population was too low, proposing the use of dominant allele-typing defaults. Nevertheless, the efficiency of genetic mapping, especially of complex plant genomes, will be accelerated by combining the presented genotyping......Genetic mapping and the selection of closely linked molecular markers for important agronomic traits require efficient, large-scale genotyping methods. A semi-automated multifluorophore technique was applied for genotyping AFLP marker loci in barley and wheat. In comparison to conventional P-33...

Incorporation of conventional genetic markers and RAPD markers into an RFLP based map in maize

International Nuclear Information System (INIS)

Coe, E.H. Jr.; McMullen, M.D.; Polacco, M.; Davis, G.L.; Chao, S.

1998-01-01

Integration of classical genetic markers, in particular mutants, onto the maize Restriction Fragment Length Polymorphism (RFLP) map will provide the tools necessary to further our understanding of plant development and of complex traits. Initially integration was accomplished by visual alignment of common markers and sometimes involved the use of information from several different molecular maps to determine the relative placement of a single mutant. The maize core marker set was designed to provide a common set of markers which could be used for integration of map data. We have completed the mapping, of 56 mutants on chromosome one relative to the core marker set. Phenotypes included whole plant, seedling, and kernel effects and represented a variety of biological processes. Since these mutants were previously located to chromosome arm, mapping required the use of only seven markers per mutant to define the correct bin location. Two mistakes in marker order relative to the classical map were identified, as well as, six groups of mutants which require allelism testing. Placement of mutants and cDNAs into bins using, the core markers provides a necessary resource for identification of gene function in maize. (author)

Serum Bone Resorption Markers after Parathyroidectomy for Renal Hyperparathyroidism: Correlation Analyses for the Cross-Linked N-telopeptide of Collagen I and Tartrate-Resistant Acid Phosphatase

Directory of Open Access Journals (Sweden)

Kuo-Chin Hung

2012-01-01

Full Text Available Patients on long-term dialysis may develop secondary hyperparathyroidism (SHPT with increased serum concentrations of bone resorption markers such as the cross-linked N-telopeptide of type I collagen (NTX and type-5b tartrate-resistant acid phosphatase (TRAP. When SHPT proves refractory to treatment, parathyroidectomy (PTX may be needed. Renal patients on maintenance HD who received PTX for refractory SHPT (n=23 or who did not develop refractory SHPT (control subjects; n=25 were followed prospectively for 4 weeks. Serum intact parathyroid hormone (iPTH, NTX, TRAP, and bone alkaline phosphatase (BAP concentrations were measured serially and correlation analyses were performed. iPTH values decreased rapidly and dramatically. BAP values increased progressively with peak increases observed at 2 weeks after surgery. NTX and TRAP values decreased concurrently and progressively through 4 weeks following PTX. A significant correlation between TRAP and NTX values was observed before PTX but not at 4 weeks after PTX. Additionally, the fractional changes in serum TRAP were larger than those in serum NTX at all times examined after PTX. Serum iPTH, TRAP, and NTX values declined rapidly following PTX for SHPT. Serum TRAP values declined to greater degrees than serum NTX values throughout the 4-week period following PTX.

Periodontal disease level-butyric acid putatively contributes to the ageing blood: A proposed link between periodontal diseases and the ageing process.

Science.gov (United States)

Cueno, Marni E; Seki, Keisuke; Ochiai, Kuniyasu; Imai, Kenichi

2017-03-01

Periodontal diseases are partly attributable to periodontopathic bacteria found in the host, whereas, butyric acid (BA) is a common secondary metabolite produced by periodontopathic bacterial pathogens. BA has been linked to oxidative stress induction while oxidative stress has long been associated with the ageing process. However, the possible link between BA-induced oxidative stress and the ageing process has never been elucidated. Here, we attempted to show the possible role of periodontal diseaselevel-BA (PDL-BA) in influencing the rat blood ageing process. We injected PDL-BA into the young rat gingiva and, after 24h, heart blood extraction was performed. Blood obtained from PDL-BA-treated young rats was compared to untreated young and middle-aged rats. We found that cytosolic, but not mitochondrial, heme was affected 24h post-injection. In addition, we observed that PDL-BA treatment altered blood NOX activation, NADPH-related oxidative stress components (H 2 O 2 and GR), calcium homeostasis, cell death signals (CASP3 and CASP1), and age-related markers (SIRT1 and mTOR) in young rats, with some components more closely mimicking levels found in middle-aged rats. In this regard, we propose that PDL-BA may play a role in contributing to the rat blood ageing process. Copyright © 2017 Elsevier B.V. All rights reserved.

High diversity in neuropeptide immunoreactivity patterns among three closely related species of Dinophilidae (Annelida)

DEFF Research Database (Denmark)

Kerbl, Alexandra; Conzelmann, Markus; Jékely, Gáspár

2017-01-01

Neuropeptides are conserved metazoan signaling molecules, and represent useful markers for comparative investigations on the morphology and function of the nervous system. However, little is known about the variation of neuropeptide expression patterns across closely related species in invertebrate...... groups other than insects. In this study, we compare the immunoreactivity patterns of 14 neuropeptides in three closely related microscopic dinophilid annelids (Dinophilus gyrociliatus, D. taeniatus and Trilobodrilus axi). The brains of all three species were found to consist of around 700 somata...... species. FMRFamide, MLD/pedal peptide, allatotropin, RNamide, excitatory peptide, and FVRIamide showed a broad localization within the brain, while calcitonin, SIFamide, vasotocin, RGWamide, DLamide, FLamide, FVamide, MIP, and serotonin were present in fewer cells in demarcated regions. The different...

Personality, tobacco consumption, physical inactivity, obesity markers, and metabolic components as risk factors for cardiovascular disease in the general population.

Science.gov (United States)

Pocnet, Cornelia; Antonietti, Jean-Philippe; Strippoli, Marie-Pierre F; Glaus, Jennifer; Rossier, Jérôme; Preisig, Martin

2017-09-01

The aim of this study was to investigate the relationship between personality traits, tobacco consumption, physical inactivity, obesity markers and metabolic components as cardiovascular risk factors (CVRFs). A total of 2543 participants from the general population (CoLaus|PsyCoLaus) had provided complete information on physical health and unhealthy behaviors and completed the Revised NEO Five-Factor Inventory. Our results show a strong cross-correlation between obesity markers and metabolic components suggesting that their combination could represent an important CVRF. Moreover, socio-demographic characteristics, tobacco consumption, and physical inactivity were associated with both obesity markers and metabolic components latent traits. The conscientiousness personality trait was significantly associated with obesity markers, but played a modest role. Indeed, higher conscientiousness was associated with lower level of obesity indicators. However, no link between personality and metabolic components were found. In sum, our data suggest that health related behaviours have more effect on the development of cardiovascular diseases than personality traits.

Performance Analysis of FSO Links over Unified Gamma-Gamma Turbulence Channels

KAUST Repository

Ansari, Imran Shafique

2015-05-01

In this work, we present a unified performance analysis of a free-space optical (FSO) link that accounts for pointing errors and both types of detection techniques (i.e. intensity modulation/direct detection as well as heterodyne detection). We, then, present unified exact closed-form expressions for various statistical characteristics of the end-to-end signal-to-noise ratio (SNR) of a single link FSO transmission system. We capitalize on these unified results to offer unified exact closed-form expressions for various performance metrics. Additionally, we derive the asymptotic results for all the expressions derived earlier in the high SNR regime in terms of simple elementary functions. We also derive new asymptotic expressions for the ergodic capacity in the low as well as high SNR regimes in terms of simple elementary functions via utilizing moments. All the presented results are verified via computer-based Monte-Carlo simulations. © 2015 IEEE.

Thermodynamic Analysis of Closed Steady or Cyclic Systems

Directory of Open Access Journals (Sweden)

Jim McGovern

2015-09-01

Full Text Available Closed, steady or cyclic thermodynamic systems, which have temperature variations over their boundaries, can represent an extremely large range of plants, devices or natural objects, such as combined heating, cooling and power plants, computers and data centres, and planets. Energy transfer rates can occur across the boundary, which are characterized as heat or work. We focus on the finite time thermodynamics aspects, on energy-based performance parameters, on rational efficiency and on the environmental reference temperature. To do this, we examine the net work rate of a closed, steady or cyclic system bounded by thermal resistances linked to isothermal reservoirs in terms of the first and second laws of thermodynamics. Citing relevant references from the literature, we propose a methodology that can improve the thermodynamic analysis of an energy-transforming or an exergy-destroying plant. Through the reflections and analysis presented, we have found an explanation of the second law that clarifies the link between the Clausius integral of heat over temperature and the reference temperature of the Gouy–Stodola theorem. With this insight and approach, the specification of the environmental reference temperature in exergy analysis becomes more solid. We have explained the relationship between the Curzon Ahlborn heat engine and an irreversible Carnot heat engine. We have outlined the nature of subsystem rational efficiencies and have found Rant’s anergy to play an important role. We postulate that heat transfer through thermal resistance is the sole basis of irreversibility.

X linked exudative vitreoretinopathy: clinical features and genetic linkage analysis.

Science.gov (United States)

Fullwood, P; Jones, J; Bundey, S; Dudgeon, J; Fielder, A R; Kilpatrick, M W

1993-03-01

A four generation family in which familial exudative vitreoretinopathy is inherited as an X linked condition is described. Essentially the condition is one of abnormal vascularisation and signs at birth are those of a retinopathy superficially resembling retinopathy of prematurity, retinal folds, or, in advanced cases, enophthalmos or even phthisis. Prognosis depends on the progression of the retinal changes. The family members, including seven affected males and five obligate carrier females, have been types for 20 DNA markers, and linkage analysis suggests a gene locus either at Xq21.3 or at Xp11. As the latter region includes the locus for the gene for Norrie disease, it is possible that this and X linked vitreoretinopathy are allelic. We can further speculate that the differences in severity of the clinical manifestations are dependent only upon the timing of the insult.

Identification of QTLs for resistance to powdery mildew and SSR markers diagnostic for powdery mildew resistance genes in melon (Cucumis melo L.).

Science.gov (United States)

Fukino, Nobuko; Ohara, Takayoshi; Monforte, Antonio J; Sugiyama, Mitsuhiro; Sakata, Yoshiteru; Kunihisa, Miyuki; Matsumoto, Satoru

2008-12-01

Powdery mildew caused by Podosphaera xanthii is an important foliar disease in melon. To find molecular markers for marker-assisted selection, we constructed a genetic linkage map of melon based on a population of 93 recombinant inbred lines derived from crosses between highly resistant AR 5 and susceptible 'Earl's Favourite (Harukei 3)'. The map spans 877 cM and consists of 167 markers, comprising 157 simple sequence repeats (SSRs), 7 sequence characterized amplified region/cleavage amplified polymorphic sequence markers and 3 phenotypic markers segregating into 20 linkage groups. Among them, 37 SSRs and 6 other markers were common to previous maps. Quantitative trait locus (QTL) analysis identified two loci for resistance to powdery mildew. The effects of these QTLs varied depending on strain and plant stage. The percentage of phenotypic variance explained for resistance to the pxA strain was similar between QTLs (R (2) = 22-28%). For resistance to pxB strain, the QTL on linkage group (LG) XII was responsible for much more of the variance (41-46%) than that on LG IIA (12-13%). The QTL on LG IIA was located between two SSR markers. Using an independent population, we demonstrated the effectiveness of these markers. This is the first report of universal and effective markers linked to a gene for powdery mildew resistance in melon.

Closing yield gaps: perils and possibilities for biodiversity conservation.

Science.gov (United States)

Phalan, Ben; Green, Rhys; Balmford, Andrew

2014-04-05

Increasing agricultural productivity to 'close yield gaps' creates both perils and possibilities for biodiversity conservation. Yield increases often have negative impacts on species within farmland, but at the same time could potentially make it more feasible to minimize further cropland expansion into natural habitats. We combine global data on yield gaps, projected future production of maize, rice and wheat, the distributions of birds and their estimated sensitivity to changes in crop yields to map where it might be most beneficial for bird conservation to close yield gaps as part of a land-sparing strategy, and where doing so might be most damaging. Closing yield gaps to attainable levels to meet projected demand in 2050 could potentially help spare an area equivalent to that of the Indian subcontinent. Increasing yields this much on existing farmland would inevitably reduce its biodiversity, and therefore we advocate efforts both to constrain further increases in global food demand, and to identify the least harmful ways of increasing yields. The land-sparing potential of closing yield gaps will not be realized without specific mechanisms to link yield increases to habitat protection (and restoration), and therefore we suggest that conservationists, farmers, crop scientists and policy-makers collaborate to explore promising mechanisms.

Performance test of the CMS link alignment system

CERN Document Server

Arce, P; Calvo, E; Fernández, M G; Ferrando, A; Figueroa, C F; García, N; Josa-Mutuberria, I; Molinero, A; Oller, J C; Rodrigo, T; Vila, I; Virto, A L

2002-01-01

A first global test of the CMS Alignment System was performed at the I4 hall of the CERN ISR tunnel. Positions of the network, reproducing a set of points in the CMS detector monitored by the Link System, were reconstructed and compared to survey measurements. Spatial and angular reconstruction precisions reached in the present experimental set-up are already close to the CMS requirements.

Genetic analysis and identification of SSR markers associated with rice blast disease in a BC2F1 backcross population.

Science.gov (United States)

Hasan, N; Rafii, M Y; Abdul Rahim, H; Nusaibah, S A; Mazlan, N; Abdullah, S

2017-01-23

Rice (Oryza sativa L.) blast disease is one of the most destructive rice diseases in the world. The fungal pathogen, Magnaporthe oryzae, is the causal agent of rice blast disease. Development of resistant cultivars is the most preferred method to achieve sustainable rice production. However, the effectiveness of resistant cultivars is hindered by the genetic plasticity of the pathogen genome. Therefore, information on genetic resistance and virulence stability are vital to increase our understanding of the molecular basis of blast disease resistance. The present study set out to elucidate the resistance pattern and identify potential simple sequence repeat markers linked with rice blast disease. A backcross population (BC 2 F 1 ), derived from crossing MR264 and Pongsu Seribu 2 (PS2), was developed using marker-assisted backcross breeding. Twelve microsatellite markers carrying the blast resistance gene clearly demonstrated a polymorphic pattern between both parental lines. Among these, two markers, RM206 and RM5961, located on chromosome 11 exhibited the expected 1:1 testcross ratio in the BC 2 F 1 population. The 195 BC 2 F 1 plants inoculated against M. oryzae pathotype P7.2 showed a significantly different distribution in the backcrossed generation and followed Mendelian segregation based on a single-gene model. This indicates that blast resistance in PS2 is governed by a single dominant gene, which is linked to RM206 and RM5961 on chromosome 11. The findings presented in this study could be useful for future blast resistance studies in rice breeding programs.

Elucidating polyploidization of bermudagrasses as assessed by organelle and nuclear DNA markers.

Science.gov (United States)

Gulsen, Osman; Ceylan, Ahmet

2011-12-01

Clarification of relationships among ploidy series of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to elucidate polyploidization among Cynodon accessions with different ploidy series collected from Turkey based on chloroplast and nuclear DNA. Forty Cynodon accessions including 7 diploids, 3 triploids, 10 tetraploids, 11 pentaploids, and 9 hexaploids were analyzed using chloroplast DNA restriction fragment-length polymorphism (cpDNA RFLP), chloroplast DNA simple sequence repeat (cpDNA SSR), and nuclear DNA markers based on neighbor-joining (NJ) and principle component analyses (PCA). All three-marker systems with two statistical algorithms clustered the diploids apart from the other ploidy levels. Assuming autopolyploidy, spontaneous polyploidization followed by rapid diversification among the higher ploidy levels than the diploids is likely in Cynodon's evolution. Few tetraploid and hexaploid accessions were clustered with or closely to the group of diploids, supporting the hypothesis above. Eleven haplotypes as estimated by cpDNA RFLP and SSR markers were detected. This study indicated that the diploids had different organelle genome from the rest of the ploidy series and provided valuable insight into relationships among ploidy series of Cynodon accessions based on cp and nuclear DNAs.

Utility of MRI versus tumor markers for post-treatment surveillance of marker-positive CNS germ cell tumors.

Science.gov (United States)

Cheung, Victoria; Segal, Devorah; Gardner, Sharon L; Zagzag, David; Wisoff, Jeffrey H; Allen, Jeffrey C; Karajannis, Matthias A

2016-09-01

Patients with marker-positive central nervous system (CNS) germ cell tumors are typically monitored for tumor recurrence with both tumor markers (AFP and b-hCG) and MRI. We hypothesize that the recurrence of these tumors will always be accompanied by an elevation in tumor markers, and that surveillance MRI may not be necessary. We retrospectively identified 28 patients with CNS germ cell tumors treated at our institution that presented with an elevated serum or cerebrospinal fluid (CSF) tumor marker at the time of diagnosis. We then identified those who had a tumor recurrence after having been in remission and whether each recurrence was detected via MRI changes, elevated tumor markers, or both. Four patients suffered a tumor recurrence. Only one patient had simultaneously elevated tumor markers and MRI evidence of recurrence. Two patients had evidence of recurrence on MRI without corresponding elevations in serum or CSF tumor markers. One patient had abnormal tumor markers with no evidence of recurrence on MRI until 6 months later. We conclude that in patients with marker-positive CNS germ cell tumors who achieve complete remission, continued surveillance imaging in addition to measurement of tumor markers is indicated to detect recurrences.

Identification of Quantitative Trait Loci for Resistance to RSIVD in Red Sea Bream (Pagrus major).

Science.gov (United States)

Sawayama, Eitaro; Tanizawa, Shiho; Kitamura, Shin-Ichi; Nakayama, Kei; Ohta, Kohei; Ozaki, Akiyuki; Takagi, Motohiro

2017-12-01

Red sea bream iridoviral disease (RSIVD) is a major viral disease in red sea bream farming in Japan. Previously, we identified one candidate male individual of red sea bream that was significantly associated with convalescent individuals after RSIVD. The purpose of this study is to identify the quantitative trait loci (QTL) linked to the RSIVD-resistant trait for future marker-assisted selection (MAS). Two test families were developed using the candidate male in 2014 (Fam-2014) and 2015 (Fam-2015). These test families were challenged with RSIV, and phenotypes were evaluated. Then, de novo genome sequences of red sea bream were obtained through next-generation sequencing, and microsatellite markers were searched and selected for linkage map construction. One immune-related gene, MHC class IIβ, was also used for linkage map construction. Of the microsatellite markers searched, 148 and 197 were mapped on 23 and 27 linkage groups in the female and male linkage maps, respectively, covering approximately 65% of genomes in both sexes. One QTL linked to an RSIVD-resistant trait was found in linkage group 2 of the candidate male in Fam-2014, and the phenotypic variance of the QTL was 31.1%. The QTL was closely linked to MHC class IIβ. Moreover, the QTL observed in Fam-2014 was also significantly linked to an RSIVD-resistant trait in the candidate male of Fam-2015. Our results suggest that the RSIVD-resistant trait in the candidate male was controlled by one major QTL closely linked to the MHC class IIβ gene and could be useful for MAS of red sea bream.

Association mapping of agro-morphological characters among the global collection of finger millet genotypes using genomic SSR markers.

Science.gov (United States)

Kalyana Babu, B; Agrawal, P K; Pandey, Dinesh; Jaiswal, J P; Kumar, Anil

2014-08-01

Identification of alleles responsible for various agro-morphological characters is a major concern to further improve the finger millet germplasm. Forty-six genomic SSRs were used for genetic analysis and population structure analysis of a global collection of 190 finger millet genotypes and fifteen agro-morphological characters were evaluated. The overall results showed that Asian genotypes were smaller in height, smaller flag leaf length, less basal tiller number, early flowering and early maturity nature, small ear head length, and smaller in length of longest finger. The 46 SSRs yielded 90 scorable alleles and the polymorphism information content values varied from 0.292 to 0.703 at an average of 0.442. The gene diversity was in the range of 0.355 to 0.750 with an average value of 0.528. The 46 genomic SSR loci grouped the 190 finger millet genotypes into two major clusters based on their geographical origin by the both phylogenetic clustering and population structure analysis by STRUCTURE software. Association mapping of QTLs for 15 agro-morphological characters with 46 genomic SSRs resulted in identification of five markers were linked to QTLs of four traits at a significant threshold (P) level of ≤ 0.01 and ≤ 0.001. The QTL for basal tiller number was strongly associated with the locus UGEP81 at a P value of 0.001 by explaining the phenotypic variance (R (2)) of 10.8%. The QTL for days to 50% flowering was linked by two SSR loci UGEP77 and UGEP90, explained 10 and 8.7% of R (2) respectively at a P value of 0.01. The SSR marker, FM9 found to have strong association to two agro-morphological traits, flag leaf width (P-0.001, R(2)-14.1 %) and plant height (P-0.001, R(2)-11.2%). The markers linked to the QTLs for above agro-morphological characters found in the present study can be further used for cloning of the full length gene, fine mapping and their further use in the marker assisted breeding programmes for introgression of alleles into locally well

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

Science.gov (United States)

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

2014-01-01

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

Development of CACTA transposon derived SCAR markers and their use in population structure analysis in Zea mays.

Science.gov (United States)

Roy, Neha Samir; Park, Kyong-Cheul; Lee, Sung-Il; Im, Min-Ji; Ramekar, Rahul Vasudeo; Kim, Nam-Soo

2018-02-01

Molecular marker technologies have proven to be an important breakthrough for genetic studies, construction of linkage maps and population genetics analysis. Transposable elements (TEs) constitute major fractions of repetitive sequences in plants and offer a wide range of possible areas to be explored as molecular markers. Sequence characterized amplified region (SCAR) marker development provides us with a simple and time saving alternative approach for marker development. We employed the CACTA-TD to develop SCARs and then integrated them into linkage map and used them for population structure and genetic diversity analysis of corn inbred population. A total of 108 dominant SCAR markers were designed out of which, 32 were successfully integrated in to the linkage map of maize RIL population and the remaining were added to a physical map for references to check the distribution throughout all chromosomes. Moreover, 76 polymorphic SCARs were used for diversity analysis of corn accessions being used in Korean corn breeding program. The overall average polymorphic information content (PIC) was 0.34, expected heterozygosity was 0.324 and Shannon's information index was 0.491 with a percentage of polymorphism of 98.67%. Further analysis by associating with desirable traits may also provide some accurate trait specific tagged SCAR markers. TE linked SCARs can provide an added level of polymorphism as well as improved discriminating ability and therefore can be useful in further breeding programs to develop high yielding germplasm.

Identification of SSR and retrotransposon-based molecular markers linked to morphological characters in oily sunfl ower (Helianthus annuus L.) under natural and water-limited states.

Science.gov (United States)

Ali, Soleimani Gezeljeh; Darvishzadeh, Reza; Ebrahimi, Asa; Bihamta, Mohammad Reza

2018-03-01

Sunflower is an important source of edible oil. Drought is known as an important factor limiting the growth and productivity of field crops in most parts of the world. Agricultural biotechnology mainly aims at developing crops with higher tolerance to the challenging environmental conditions, such as drought. This study examined a number of morphological characters, along with relative water content (RWC) in 100 inbred sunflower lines. A 10 × 10 simple lattice design with two replications was employed to measure the mentioned parameters under natural and water-limited states during two successive years. In molecular trial, 30 simple sequence repeat (SSR) primer pairs, as well as 14 inter-retrotransposon amplified polymorphism (IRAP) and 14 retrotransposon-microsatellite amplified polymorphism (REMAP) primer combinations were used for DNA fingerprinting of the lines. Most of the examined characters had lower average values under water-limited than natural states. Maximum and minimum reductions were observed in the cases of yield and oil percentage, respectively. The broad-sense heritabilities for all the examined characters were 0.20-0.73 and 0.10-0.34 under natural and water-limited states, respectively. In the studied samples, 8.97% of the 435 possible locus pairs of the SSRs represented significant linkage disequilibrium (LD) levels. In the association analysis using SSR markers, 22 and 21 markers were identified (P ≤ 0.05) for the studied characters under natural and water-limited states, respectively. The corresponding values were 50 and 37 using retrotransposon-based molecular markers. Some detected markers were communal between the characters under water-limited and natural states. This was in line with the phenotypic correlations detected between the characters. Communal markers facilitate the simultaneous selection of several characters and can thus improve the efficacy of selection based on markers in the plant-breeding activities.

Development of cost-effective Hordeum chilense DNA markers: molecular aids for marker-assisted cereal breeding.

Science.gov (United States)

Hernández, P; Dorado, G; Ramírez, M C; Laurie, D A; Snape, J W; Martín, A

2003-01-01

Hordeum chilense is a potential source of useful genes for wheat breeding. The use of this wild species to increase genetic variation in wheat will be greatly facilitated by marker-assisted introgression. In recent years, the search for the most suitable DNA marker system for tagging H. chilense genomic regions in a wheat background has lead to the development of RAPD and SCAR markers for this species. RAPDs represent an easy way of quickly generating suitable introgression markers, but their use is limited in heterogeneous wheat genetic backgrounds. SCARs are more specific assays, suitable for automatation or multiplexing. Direct sequencing of RAPD products is a cost-effective approach that reduces labour and costs for SCAR development. The use of SSR and STS primers originally developed for wheat and barley are additional sources of genetic markers. Practical applications of the different marker approaches for obtaining derived introgression products are described.

Genetic diversity, identification, and certification of Chilean rice varieties using molecular markers

Directory of Open Access Journals (Sweden)

Viviana Becerra

2015-09-01

Full Text Available It takes approximately 14 yr to produce a new rice (Oryza sativa L. variety, that is, from initial hybridization to its commercial release. Currently, new varieties are identified based on morphological descriptors, which have been efficient over time. However, due to the main constraints on seed type impose to other breeding objectives and the pressure of continuous release of varieties, high degree of parentage, and genetic and morphological uniformity has been observed in the breeding populations. The objectives of this study were: to determine the genetic variability of Chilean and foreign commercial rice varieties, and determine, identify, and certify the genetic relationships among varieties, using simple sequence repeat (SSR markers. A total of 16 commercial varieties, some of them closely related, were included in the study, which were genétically analyzed using 54 microsatellites. The 54 microsatellite loci allowed the discrimination among the 16 varieties. The number of alleles ranged between 2 and 8 with a mean of 3.54 alleles per locus, while the polymorphism information content (PIC presented a mean of 0.44. The genetic distance and diversity parameters between pairs of varieties indicate a limited diversity among these genotypes. The cluster analysis indicated that varieties were grouped according to their grain type and pedigree. Results demonstrate that the identification and certification of varieties using microsatellite markers could be a good complement to existing agro-morphological data when varieties are closed related.

Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.

Science.gov (United States)

Phung, Tanya N; Huber, Christian D; Lohmueller, Kirk E

2016-08-01

A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only

Relationship between heart rate recovery and inflammatory markers in patients with polycystic ovary syndrome: a cross-sectional study.

Science.gov (United States)

Giallauria, Francesco; Orio, Francesco; Lombardi, Gaetano; Colao, Annamaria; Vigorito, Carlo; Tafuri, Maria Giovanna; Palomba, Stefano

2009-02-02

Polycystic ovary syndrome (PCOS) is an endocrine disease closely related to several risk factors for cardiovascular disease. An abnormal heart rate recovery (HRR), an easily-obtained measure derived from exercise stress test and closely related to an increased risk for cardiovascular mortality, has been recently described in PCOS women. A subclinical increase of the inflammation markers has been also observed in the PCOS. This study was designed to study the relationships between HRR and inflammatory markers in PCOS women. Two-hundred forty-three young PCOS patients without known risk factors for cardiovascular risk were enrolled. All patients underwent hormonal and metabolic profile, white blood cells (WBCs) count and C-reactive protein (CRP). HRR was calculated as the difference between heart rate at peak exercise and heart rate at first minute of the cool-down period. Abnormal HRR was defined as PCOS patients with abnormal versus normal HRR. HRR was significantly associated with both CRP (r = -0.33, p PCOS women acting probably in concert to increase the cardiovascular risk profile of these patients.

Assessment of genome origins and genetic diversity in the genus Eleusine with DNA markers.

Science.gov (United States)

Salimath, S S; de Oliveira, A C; Godwin, I D; Bennetzen, J L

1995-08-01

Finger millet (Eleusine coracana), an allotetraploid cereal, is widely cultivated in the arid and semiarid regions of the world. Three DNA marker techniques, restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA (RAPD), and inter simple sequence repeat amplification (ISSR), were employed to analyze 22 accessions belonging to 5 species of Eleusine. An 8 probe--3 enzyme RFLP combination, 18 RAPD primers, and 6 ISSR primers, respectively, revealed 14, 10, and 26% polymorphism in 17 accessions of E. coracana from Africa and Asia. These results indicated a very low level of DNA sequence variability in the finger millets but did allow each line to be distinguished. The different Eleusine species could be easily identified by DNA marker technology and the 16% intraspecific polymorphism exhibited by the two analyzed accessions of E. floccifolia suggested a much higher level of diversity in this species than in E. coracana. Between species, E. coracana and E. indica shared the most markers, while E. indica and E. tristachya shared a considerable number of markers, indicating that these three species form a close genetic assemblage within the Eleusine. Eleusine floccifolia and E. compressa were found to be the most divergent among the species examined. Comparison of RFLP, RAPD, and ISSR technologies, in terms of the quantity and quality of data output, indicated that ISSRs are particularly promising for the analysis of plant genome diversity.

Genetic molecular analysis of Coffea arabica (Rubiaceae hybrids using SRAP markers

Directory of Open Access Journals (Sweden)

Manoj Kumar Mishra

2011-06-01

Full Text Available In Coffea arabica (arabica coffee, the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. Rev. Biol. Trop. 59 (2: 607-617. Epub 2011 June 01.

Fiducial marker guided stereotactic liver radiotherapy: Is a time delay between marker implantation and planning CT needed?

DEFF Research Database (Denmark)

Worm, Esben S; Bertholet, Jenny; Høyer, Morten

2016-01-01

To minimize the risk of marker migration in fiducial marker guided liver SBRT it is common to add a delay of a week between marker implantation and planning CT. This study found that such a delay is unnecessary and could be avoided to minimize the treatment preparation time.......To minimize the risk of marker migration in fiducial marker guided liver SBRT it is common to add a delay of a week between marker implantation and planning CT. This study found that such a delay is unnecessary and could be avoided to minimize the treatment preparation time....

Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus) in China with multiple gene markers.

Science.gov (United States)

Dai, Qing-Yan; Gao, Qiang; Wu, Chun-Sheng; Chesters, Douglas; Zhu, Chao-Dong; Zhang, Ai-Bing

2012-01-01

Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI) gene and two alternative internal transcribed spacer (ITS) genes (ITS1 and ITS2). Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML)/Neighbor-joining (NJ), "best close match" (BCM), Minimum distance (MD), and BP-based method (BP)), representing commonly used methodology (tree-based and non-tree based) in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In addition, our

Phylogenetic reconstruction and DNA barcoding for closely related pine moth species (Dendrolimus in China with multiple gene markers.

Directory of Open Access Journals (Sweden)

Qing-Yan Dai

Full Text Available Unlike distinct species, closely related species offer a great challenge for phylogeny reconstruction and species identification with DNA barcoding due to their often overlapping genetic variation. We tested a sibling species group of pine moth pests in China with a standard cytochrome c oxidase subunit I (COI gene and two alternative internal transcribed spacer (ITS genes (ITS1 and ITS2. Five different phylogenetic/DNA barcoding analysis methods (Maximum likelihood (ML/Neighbor-joining (NJ, "best close match" (BCM, Minimum distance (MD, and BP-based method (BP, representing commonly used methodology (tree-based and non-tree based in the field, were applied to both single-gene and multiple-gene analyses. Our results demonstrated clear reciprocal species monophyly for three relatively distant related species, Dendrolimus superans, D. houi, D. kikuchii, as recovered by both single and multiple genes while the phylogenetic relationship of three closely related species, D. punctatus, D. tabulaeformis, D. spectabilis, could not be resolved with the traditional tree-building methods. Additionally, we find the standard COI barcode outperforms two nuclear ITS genes, whatever the methods used. On average, the COI barcode achieved a success rate of 94.10-97.40%, while ITS1 and ITS2 obtained a success rate of 64.70-81.60%, indicating ITS genes are less suitable for species identification in this case. We propose the use of an overall success rate of species identification that takes both sequencing success and assignation success into account, since species identification success rates with multiple-gene barcoding system were generally overestimated, especially by tree-based methods, where only successfully sequenced DNA sequences were used to construct a phylogenetic tree. Non-tree based methods, such as MD, BCM, and BP approaches, presented advantages over tree-based methods by reporting the overall success rates with statistical significance. In

Linkage of familial Alzheimer disease to chromosome 14 in two large early-onset pedigrees: effects of marker allele frequencies on lod scores.

Science.gov (United States)

Nechiporuk, A; Fain, P; Kort, E; Nee, L E; Frommelt, E; Polinsky, R J; Korenberg, J R; Pulst, S M

1993-05-01

Alzheimer disease (AD) is a devastating neurodegenerative disease leading to global dementia. In addition to sporadic forms of AD, familial forms (FAD) have been recognized. Mutations in the amyloid precursor protein (APP) gene on chromosome (CHR) 21 have been shown to cause early-onset AD in a small number of pedigrees. Recently, linkage to markers on CHR 14 has been established in several early-onset FAD pedigrees. We now report lod scores for CHR 14 markers in two large early-onset FAD pedigrees. Pairwise linkage analysis suggested that in these pedigrees the mutation is tightly linked to the loci D14S43 and D14S53. However, assumptions regarding marker allele frequencies had a major and often unpredictable effect on calculated lod scores. Therefore, caution needs to be exercised when single pedigrees are analyzed with marker allele frequencies determined from the literature or from a pool of spouses.

The diagnostic value of preoperative inflammatory markers in craniopharyngioma: a multicenter cohort study.

Science.gov (United States)

Chen, Ming; Zheng, Shi-Hao; Yang, Min; Chen, Zhi-Hua; Li, Shi-Ting

2018-05-01

To compare the different levels of preoperative inflammatory markers in peripheral blood samples between craniopharyngioma (CP) and other sellar region tumors so as to explore their differential diagnostic value. The level of white blood cell (WBC), neutrophil, lymphocyte, monocyte, platelet, albumin, neutrophil lymphocyte ratio (NLR), derived NLR (dNLR), platelet lymphocyte ratio (PLR), monocyte lymphocyte ratio (MLR) and prognostic nutritional index (PNI) were compared between the CP and other sellar region tumors. A receiver operating characteristics (ROC) curve analysis was performed to evaluate the diagnostic significance of the peripheral blood inflammatory markers and their paired combinations for CP including its pathological types. Patients with CP had higher levels of pre-operative WBC, lymphocyte and PNI. The papillary craniopharyngioma (PCP) group had higher neutrophil count and NLR than the adamantinomatous craniopharyngioma (ACP) and healthy control groups whereas the ACP group had higher platelet count and PNI than the PCP and healthy control groups. There were not any significant differences in preoperative inflammatory markers between the primary and recurrent CP groups. The AUC values of WBC, neutrophil, NLR + PLR and dNLR + PLR in PCP were all higher than 0.7. Inflammation seems to be closely correlated with CP's development. The preoperative inflammatory markers including WBC, neutrophil, NLR + PLR and dNLR + PLR may differentially diagnose PCP, pituitary tumor (PT) and Rathke cleft cyst (RCC). In addition, some statistical results in this study indirectly proved previous experimental conclusions and strictly matched CP's biological features.

The mechanism of collagen cross-linking in diabetes: a puzzle nearing resolution.

Science.gov (United States)

Monnier, V M; Glomb, M; Elgawish, A; Sell, D R

1996-07-01

Considerable interest has been focused in recent years on the mechanism of collagen cross-linking by high glucose in vitro and in vivo. Experiments in both diabetic humans and in animals have shown that over time collagen becomes less soluble, less digestible by collagenase, more stable to heat-induced denaturation, and more glycated. In addition, collagen becomes more modified by advanced products of the Maillard reaction, i.e., immunoreactive advanced glycation end products and the glycoxidation markers carboxymethyllysine and pentosidine. Mechanistic studies have shown that collagen cross-linking in vitro can be uncoupled from glycation by the use of antioxidants and chelating agents. Experiments in the authors' laboratory revealed that approximately 50% of carboxymethyllysine formed in vitro originates from pathways other than oxidation of Amadori products, i.e., most likely the oxidation of Schiff base-linked glucose. In addition, the increase in thermal stability of rat tail tendons exposed to high glucose in vitro or in vivo was found to strongly depend on H2O2 formation. The final missing piece of the puzzle is that of the structure of the major cross-link. We speculate that it is a nonfluorescent nonultraviolet active cross-link between two lysine residues, which includes a fragmentation product of glucose linked in a nonreducible bond labile to both strong acids and bases.

Hypothyroidism and depression: Are cytokines the link?

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Parimal S Tayde

2017-01-01

Full Text Available Context: Primary hypothyroidism has been thought of as an inflammatory condition characterized by raised levels of cytokines such as C-reactive protein (CRP, interleukin-6 (IL-6, and tumor necrosis factor-alpha (TNF-α. Depression is also well known to occur in hypothyroidism. Depression is also characterized by elevated inflammatory cytokines. We planned to study whether cytokines play an important part in linking these two conditions. Objectives: (1 To know the prevalence of depression in overt hypothyroidism due to autoimmune thyroid disease. (2 To correlate the levels of inflammatory markers with the occurrence of depression. (3 To study the effect of levothyroxine on inflammatory markers and depression. Materials and Methods: In this longitudinal, case–controlled study, 33 patients with autoimmune hypothyroidism (thyroid-stimulating hormone >10 uIU/ml were included with 33 age-, sex-, and body max index-matched healthy controls. Individuals were tested for Serum TNF-α, IL-6, high-sensitivity-CRP (hs-CRP. They were assessed for depression using Montgomery Asberg Depression Rating Scale (MADRS and World Health Organization Quality of Life (QOL Scale. Patients received L Thyroxine titrated to achieve euthyroidism and were reassessed for inflammatory markers and cognitive dysfunction. Results: Nineteen patients (57% had mild to moderate depression (MADRS >11. After 6 months of treatment, eight patients (42% had remission of depression with significant improvement in QOL scores (P < 0.05. TNF-α, IL-6, and hs-CRP were significantly elevated in patients compared with controls and reduced with therapy but did not reach baseline as controls. The change in inflammatory markers correlated with improvement in QOL scores in social and environmental domains (P < 0.01. Conclusions: Primary autoimmune hypothyroidism is an inflammatory state characterized by elevated cytokines which decline with LT4 therapy. It is associated with depression and poor

Radiopaque anastomosis marker

International Nuclear Information System (INIS)

Elliott, D.P.; Halseth, W.L.

1977-01-01

This invention relates to split ring markers fabricated in whole or in part from a radiopaque material, usually metal, having the terminal ends thereof and a medial portion formed to define eyelets by means of which said marker can be sutured to the tissue at the site of an anastomosis to provide a visual indication of its location when examined fluoroscopically

The discovery of putative urine markers for the specific detection of prostate tumor by integrative mining of public genomic profiles.

Directory of Open Access Journals (Sweden)

Min Chen

Full Text Available Urine has emerged as an attractive biofluid for the noninvasive detection of prostate cancer (PCa. There is a strong imperative to discover candidate urinary markers for the clinical diagnosis and prognosis of PCa. The rising flood of various omics profiles presents immense opportunities for the identification of prospective biomarkers. Here we present a simple and efficient strategy to derive candidate urine markers for prostate tumor by mining cancer genomic profiles from public databases. Prostate, bladder and kidney are three major tissues from which cellular matters could be released into urine. To identify urinary markers specific for PCa, upregulated entities that might be shed in exosomes of bladder cancer and kidney cancer are first excluded. Through the ontology-based filtering and further assessment, a reduced list of 19 entities encoding urinary proteins was derived as putative PCa markers. Among them, we have found 10 entities closely associated with the process of tumor cell growth and development by pathway enrichment analysis. Further, using the 10 entities as seeds, we have constructed a protein-protein interaction (PPI subnetwork and suggested a few urine markers as preferred prognostic markers to monitor the invasion and progression of PCa. Our approach is amenable to discover and prioritize potential markers present in a variety of body fluids for a spectrum of human diseases.

Lagrangian numerical techniques for modelling multicomponent flow in the presence of large viscosity contrasts: Markers-in-bulk versus Markers-in-chain

Science.gov (United States)

Mulyukova, Elvira; Dabrowski, Marcin; Steinberger, Bernhard

2015-04-01

avoided when using interface tracking methods for advection. Marker-chain method is one such approach, where rather than discretizing the volume of each material, only their interface is discretized by a connected set of markers. Together with the boundary of the domain, the marker-chain constitutes closed polygon-boundaries which enclose the regions spanned by each material. Communicating material properties to the static grid can be done by determining which polygon each grid-node (or integration point) falls into, eliminating the need for interpolation. In our chosen implementation, an efficient parallelized algorithm for the point-in-polygon location is used, so this part of the code takes up only a small fraction of the CPU-time spent on each time step, and allows for spatial resolution of the compositional field beyond that which is practical with markers-in-bulk methods. An additional advantage of using marker-chains for material advection is that it offers a possibility to use some of its markers, or even edges, to generate a FEM grid. One can tailor a grid for obtaining a Stokes solution with optimal accuracy, while controlling the quality and size of its elements. Where geometry of the interface allows - element-edges may be aligned with it, which is known to significantly improve the quality of Stokes solution, compared to when the interface cuts through the elements (Moresi et al., 1996; Deubelbeiss and Kaus, 2008). In more geometrically complex interface-regions, the grid may simply be refined to reduce the error. As materials get deformed in the course of a simulation, the interface may get stretched and entangled. Addition of new markers along the chain may be required in order to properly resolve the increasingly complicated geometry. Conversely, some markers may be removed from regions where they get clustered. Such resampling of the interface requires additional computational effort (although small compared to other parts of the code), and introduces an

Frameworking memory and serotonergic markers.

Science.gov (United States)

Meneses, Alfredo

2017-07-26

The evidence for neural markers and memory is continuously being revised, and as evidence continues to accumulate, herein, we frame earlier and new evidence. Hence, in this work, the aim is to provide an appropriate conceptual framework of serotonergic markers associated with neural activity and memory. Serotonin (5-hydroxytryptamine [5-HT]) has multiple pharmacological tools, well-characterized downstream signaling in mammals' species, and established 5-HT neural markers showing new insights about memory functions and dysfunctions, including receptors (5-HT1A/1B/1D, 5-HT2A/2B/2C, and 5-HT3-7), transporter (serotonin transporter [SERT]) and volume transmission present in brain areas involved in memory. Bidirectional influence occurs between 5-HT markers and memory/amnesia. A growing number of researchers report that memory, amnesia, or forgetting modifies neural markers. Diverse approaches support the translatability of using neural markers and cerebral functions/dysfunctions, including memory formation and amnesia. At least, 5-HT1A, 5-HT4, 5-HT6, and 5-HT7 receptors and SERT seem to be useful neural markers and therapeutic targets. Hence, several mechanisms cooperate to achieve synaptic plasticity or memory, including changes in the expression of neurotransmitter receptors and transporters.

Analysis of a closed-kinematic chain robot manipulator

Science.gov (United States)

Nguyen, Charles C.; Pooran, Farhad J.

1988-01-01

Presented are the research results from the research grant entitled: Active Control of Robot Manipulators, sponsored by the Goddard Space Flight Center (NASA) under grant number NAG-780. This report considers a class of robot manipulators based on the closed-kinematic chain mechanism (CKCM). This type of robot manipulators mainly consists of two platforms, one is stationary and the other moving, and they are coupled together through a number of in-parallel actuators. Using spatial geometry and homogeneous transformation, a closed-form solution is derived for the inverse kinematic problem of the six-degree-of-freedom manipulator, built to study robotic assembly in space. Iterative Newton Raphson method is employed to solve the forward kinematic problem. Finally, the equations of motion of the above manipulators are obtained by employing the Lagrangian method. Study of the manipulator dynamics is performed using computer simulation whose results show that the robot actuating forces are strongly dependent on the mass and centroid locations of the robot links.

Language Development in the Early School Years: The Importance of Close Relationships with Teachers

Science.gov (United States)

Spilt, Jantine L.; Koomen, Helma M. Y.; Harrison, Linda J.

2015-01-01

This longitudinal study examined developmental links between closeness in teacher-child relationships and children's receptive language ability from the end of the preschool years into the early elementary years, while controlling for changes in peer interaction quality and child behavioral functioning. The sample included children and their…

Emotional closeness to parents and grandparents: A moderated mediation model predicting adolescent adjustment.

Science.gov (United States)

Attar-Schwartz, Shalhevet

2015-09-01

Warm and emotionally close relationships with parents and grandparents have been found in previous studies to be linked with better adolescent adjustment. The present study, informed by Family Systems Theory and Intergenerational Solidarity Theory, uses a moderated mediation model analyzing the contribution of the dynamics of these intergenerational relationships to adolescent adjustment. Specifically, it examines the mediating role of emotional closeness to the closest grandparent in the relationship between emotional closeness to a parent (the offspring of the closest grandparent) and adolescent adjustment difficulties. The model also examines the moderating role of emotional closeness to parents in the relationship between emotional closeness to grandparents and adjustment difficulties. The study was based on a sample of 1,405 Jewish Israeli secondary school students (ages 12-18) who completed a structured questionnaire. It was found that emotional closeness to the closest grandparent was more strongly associated with reduced adjustment difficulties among adolescents with higher levels of emotional closeness to their parents. In addition, adolescent adjustment and emotional closeness to parents was partially mediated by emotional closeness to grandparents. Examining the family conditions under which adolescents' relationships with grandparents is stronger and more beneficial for them can help elucidate variations in grandparent-grandchild ties and expand our understanding of the mechanisms that shape child outcomes. (c) 2015 APA, all rights reserved).

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

DEFF Research Database (Denmark)

Poulsen, Henrik E.; Loft, Steffen

1995-01-01

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

Sleep and inflammatory markers in different psychiatric disorders.

Science.gov (United States)

Krysta, Krzysztof; Krzystanek, Marek; Bratek, Agnieszka; Krupka-Matuszczyk, Irena

2017-02-01

Many psychiatric disorders, like schizophrenia, affective disorders, addictions and different forms of dementia are associated with sleep disturbances. In the etiology and course of those diseases inflammatory processes are regarded to be an increasingly important factor. They are also a frequently discussed element of the pathology of sleep. In this literature review reports on correlations between poor sleep and inflammatory responses in various psychiatric conditions are discussed. The link between schizophrenia, affective disorders and inflammatory cytokines is a complex phenomenon, which has been already confirmed in a number of studies. However, the presence of sleep deficits in those conditions, being a common symptom of depression and psychoses, can be an additional factor having a considerable impact on the immunological processes in mental illnesses. In the analyzed data, a number of studies are presented describing the role of inflammatory markers in sleep disturbances and psychopathological symptoms of affective, psychotic, neurogenerative and other disorders. Also attention is drawn to possible implications for their treatment. Efforts to use, e.g., anti-inflammatory agents in psychiatry in the context of their impact on sleep are reported. The aspect of inflammatory markers in the role of sleep deprivation as the treatment method in major depressive disorder is also discussed. A general conclusion is drawn that the improvement of sleep quality plays a crucial role in the care for psychiatric patients.

Effects of alginate hydrogel cross-linking density on mechanical and biological behaviors for tissue engineering.

Science.gov (United States)

Jang, Jinah; Seol, Young-Joon; Kim, Hyeon Ji; Kundu, Joydip; Kim, Sung Won; Cho, Dong-Woo

2014-09-01

An effective cross-linking of alginate gel was made through reaction with calcium carbonate (CaCO3). We used human chondrocytes as a model cell to study the effects of cross-linking density. Three different pore size ranges of cross-linked alginate hydrogels were fabricated. The morphological, mechanical, and rheological properties of various alginate hydrogels were characterized and responses of biosynthesis of cells encapsulated in each gel to the variation in cross-linking density were investigated. Desired outer shape of structure was maintained when the alginate solution was cross-linked with the applied method. The properties of alginate hydrogel could be tailored through applying various concentrations of CaCO3. The rate of synthesized GAGs and collagens was significantly higher in human chondrocytes encapsulated in the smaller pore structure than that in the larger pore structure. The expression of chondrogenic markers, including collagen type II and aggrecan, was enhanced in the smaller pore structure. It was found that proper structural morphology is a critical factor to enhance the performance and tissue regeneration. Copyright © 2014 Elsevier Ltd. All rights reserved.

Linked-cluster perturbation theory for closed and open-shell systems: derivation of effective π-electron hamiltonians

International Nuclear Information System (INIS)

Brandow, B.H.

1977-01-01

The Brueckner--Goldstone form of linked-cluster perturbation theory is derived, together with its open-shell analog, by an elementary time-independent approach. This serves to focus attention on the physical interpretation of the results. The open-shell expansion is used to provide a straightforward justification for the effective π-electron Hamiltonians of planar organic molecules

On the capacity of FSO links under lognormal and Rician-lognormal turbulences

KAUST Repository

Ansari, Imran Shafique; Alouini, Mohamed-Slim; Cheng, Julian

2014-01-01

) is addressed in this work. More specifically, a unified exact closed-form expression for the moments of the end-to-end signal-to-noise ratio (SNR) of a single link FSO transmission system is presented in terms of well-known elementary functions. Capitalizing

On H-closed and U-closed functions | Cammaroto | Quaestiones ...

African Journals Online (AJOL)

In this article, we extend the work on H-closed functions started by Cammaroto, Fedorchuk and Porter in 1998. Also, U-closed functions are introduced and characterized in terms of filters and adherence. The hereditary and productivity properties are examined and developed for both H-closed and U-closed functions.

Marker-assisted identification of restorer gene(s) in iso-cytoplasmic restorer lines of WA cytoplasm in rice and assessment of their fertility restoration potential across environments.

Science.gov (United States)

Kumar, Amit; Bhowmick, Prolay Kumar; Singh, Vikram Jeet; Malik, Manoj; Gupta, Ashish Kumar; Seth, R; Nagarajan, M; Krishnan, S Gopala; Singh, Ashok Kumar

2017-10-01

Iso-cytoplasmic restorers possess the same male sterile cytoplasm as the cytoplasmic male sterile (CMS) lines, thereby minimizing the potential cyto-nuclear conflict in the hybrids. Restoration of fertility of the wild abortive CMS is governed by two major genes namely, Rf3 and Rf4 . Therefore, assessing the allelic status of these restorer genes in the iso-cytoplasmic restorers using molecular markers will not only help in estimating the efficiency of these genes either alone or in combination, in fertility restoration in the hybrids in different environments, but will also be useful in determining the efficacy of these markers. In the present study, the efficiency of molecular markers in identifying genotypes carrying restorer allele of the gene(s) Rf3 and Rf4, restoring male fertility of WA cytoplasm in rice was assessed in a set of 100 iso-cytoplasmic rice restorers using gene linked as well as candidate gene based markers. In order to validate the efficacy of markers in identifying the restorers, a sub-set of selected 25 iso-cytoplasmic rice restorers were crossed with four different cytoplasmic male sterile lines namely, IR 79156A, IR 58025A, Pusa 6A and RTN 12A, and the pollen and spikelet fertility of the F 1 s were evaluated at three different locations. Marker analysis showed that Rf4 was the predominant fertility restorer gene in the iso-cytoplasmic restorers and Rf3 had a synergistic effect on fertility restoration. The efficiency of gene based markers, DRCG-RF4-14 and DRRM-RF3-10 for Rf4 (87%) and Rf3 (84%) genes was higher than respective gene-linked SSR markers RM6100 (80%) and RM3873 (82%). It is concluded that the gene based markers can be effectively used in identifying fertility restorer lines obviating the need for making crosses and evaluating the F 1 s. Though gene based markers are more efficient, there is a need to identify functional polymorphisms which can provide 100% efficiency. Three iso-cytoplasmic restorers namely, PRR 300, PRR 363

X-chromosome STR markers data in a Cabo Verde immigrant population of Lisboa.

Science.gov (United States)

Afonso Costa, Heloísa; Morais, Paulo; Vieira da Silva, Cláudia; Matos, Sara; Marques Santos, Rodolfo; Espinheira, Rosa; Costa Santos, Jorge; Amorim, António

2014-01-01

Population genetic data of 12 X chromosomal short tandem repeats markers (DXS10074, DXS10079, DXS10101, DXS10103, DXS10134, DXS10135, DXS10146, DXS10148, DXS7132, DXS7423, DXS8378 and HPRTB) were analysed in 54 females and 95 males of an immigrant population from Cabo Verde living in Lisboa. The obtained results for forensic statistical parameters such as observed heterozigosity, polymorphism information content, power of discrimination and mean exclusion chance, based on single allele frequencies, reveal that this multiplex system is highly informative and can represent an important tool for genetic identification purposes in the immigrant population of Cabo Verde. Since the studied short tandem repeats genetic markers are distributed on four linkage groups, that can provide independent genotype information, we studied those groups as haploytes. The forensic efficiency parameters for the linked groups were all higher than 0.97, with linkage group I being the most polymorphic and linkage group III the less informative.

Experimental gingivitis induces systemic inflammatory markers in young healthy individuals: a single-subject interventional study.

Science.gov (United States)

Eberhard, Jörg; Grote, Karsten; Luchtefeld, Maren; Heuer, Wieland; Schuett, Harald; Divchev, Dimitar; Scherer, Ralph; Schmitz-Streit, Ruth; Langfeldt, Daniela; Stumpp, Nico; Staufenbiel, Ingmar; Schieffer, Bernhard; Stiesch, Meike

2013-01-01

We here investigated whether experimental gingivitis enhances systemic markers of inflammation which are also known as surrogate markers of atherosclerotic plaque development. Gingivitis is a low-level oral infection induced by bacterial deposits with a high prevalence within Western populations. A potential link between the more severe oral disease periodontitis and cardiovascular disease has already been shown. 37 non-smoking young volunteers with no inflammatory disease or any cardiovascular risk factors participated in this single-subject interventional study with an intra-individual control. Intentionally experimental oral inflammation was induced by the interruption of oral hygiene for 21 days, followed by a 21-days resolving phase after reinitiation of oral hygiene. Primary outcome measures at baseline, day 21 and 42 were concentrations of hsCRP, IL-6, and MCP-1, as well as adhesion capacity and oxLDL uptake of isolated blood monocytes. The partial cessation of oral hygiene procedures was followed by the significant increase of gingival bleeding (34.0%, Pgingivitis. Bacterial-induced gingival low-level inflammation induced a systemic increase in inflammatory markers. Dental hygiene almost completely reversed this experimental inflammatory process, suggesting that appropriate dental prophylaxis may also limit systemic markers of inflammation in subjects with natural gingivitis. International Clinical Trials Register Platform of the World Health Organization, registry number: DRKS00003366, URL: http://apps.who.int/trialsearch/Default.aspx.

Differences in mating strategies in two closely related small ermine moth species (Lepidoptera: Yponomeutidae)

NARCIS (Netherlands)

Bakker, A.C.; van Ginkel, W.E.; Roessingh, P.; Menken, S.B.J.

2008-01-01

The degree of polyandry in a species is linked to other life history traits such as egg maturation, life span, and male ejaculate size and quality. The study of differences in mating strategies between closely related species can provide a better understanding of the evolution of these strategies

Mutation Analysis in Classical Phenylketonuria Patients Followed by Detecting Haplotypes Linked to Some PAH Mutations.

Science.gov (United States)

Dehghanian, Fatemeh; Silawi, Mohammad; Tabei, Seyed M B

2017-02-01

Deficiency of phenylalanine hydroxylase (PAH) enzyme and elevation of phenylalanine in body fluids cause phenylketonuria (PKU). The gold standard for confirming PKU and PAH deficiency is detecting causal mutations by direct sequencing of the coding exons and splicing involved sequences of the PAH gene. Furthermore, haplotype analysis could be considered as an auxiliary approach for detecting PKU causative mutations before direct sequencing of the PAH gene by making comparisons between prior detected mutation linked-haplotypes and new PKU case haplotypes with undetermined mutations. In this study, 13 unrelated classical PKU patients took part in the study detecting causative mutations. Mutations were identified by polymerase chain reaction (PCR) and direct sequencing in all patients. After that, haplotype analysis was performed by studying VNTR and PAHSTR markers (linked genetic markers of the PAH gene) through application of PCR and capillary electrophoresis (CE). Mutation analysis was performed successfully and the detected mutations were as follows: c.782G>A, c.754C>T, c.842C>G, c.113-115delTCT, c.688G>A, and c.696A>G. Additionally, PAHSTR/VNTR haplotypes were detected to discover haplotypes linked to each mutation. Mutation detection is the best approach for confirming PAH enzyme deficiency in PKU patients. Due to the relatively large size of the PAH gene and high cost of the direct sequencing in developing countries, haplotype analysis could be used before DNA sequencing and mutation detection for a faster and cheaper way via identifying probable mutated exons.

No Robust Association between Static Markers of Testosterone and Facets of Socio-Economic Decision Making

OpenAIRE

Kaltwasser, Laura; Mikac, Una; Buško, Vesna; Hildebrandt, Andrea

2017-01-01

Digit ratio (2D:4D) and facial width-to-height ratio (WHR) are supposedly static indicators of testosterone exposition during prenatal and pubertal lifetime, respectively. Both measures have been linked to aggressive and assertive behavior in laboratory economic games, as well as in real world scenarios. Most of the research—often limited to male subjects—considers the associations between these behaviors, traits, and hormonal markers separately for 2D:4D and WHR. Reported associations are we...

Dosing related effects of zoledronic acid on bone markers and creatinine clearance in patients with multiple myeloma and metastatic breast cancer

DEFF Research Database (Denmark)

Søe, Kent; Delaissé, Jean-Marie; Jakobsen, Erik H

2014-01-01

phase II clinical trial we investigated the effect of Zol treatment on the serum levels of the bone markers collagen type 1 cross-linked C-telopeptide (CTX) and bone specific alkaline phosphatase (bALP) as well as on creatinine clearance (kidney function) in response to dosing and duration of treatment...

Microsatellite marker development by partial sequencing of the sour passion fruit genome (Passiflora edulis Sims).

Science.gov (United States)

Araya, Susan; Martins, Alexandre M; Junqueira, Nilton T V; Costa, Ana Maria; Faleiro, Fábio G; Ferreira, Márcio E

2017-07-21

The Passiflora genus comprises hundreds of wild and cultivated species of passion fruit used for food, industrial, ornamental and medicinal purposes. Efforts to develop genomic tools for genetic analysis of P. edulis, the most important commercial Passiflora species, are still incipient. In spite of many recognized applications of microsatellite markers in genetics and breeding, their availability for passion fruit research remains restricted. Microsatellite markers in P. edulis are usually limited in number, show reduced polymorphism, and are mostly based on compound or imperfect repeats. Furthermore, they are confined to only a few Passiflora species. We describe the use of NGS technology to partially assemble the P. edulis genome in order to develop hundreds of new microsatellite markers. A total of 14.11 Gbp of Illumina paired-end sequence reads were analyzed to detect simple sequence repeat sites in the sour passion fruit genome. A sample of 1300 contigs containing perfect repeat microsatellite sequences was selected for PCR primer development. Panels of di- and tri-nucleotide repeat markers were then tested in P. edulis germplasm accessions for validation. DNA polymorphism was detected in 74% of the markers (PIC = 0.16 to 0.77; number of alleles/locus = 2 to 7). A core panel of highly polymorphic markers (PIC = 0.46 to 0.77) was used to cross-amplify PCR products in 79 species of Passiflora (including P. edulis), belonging to four subgenera (Astrophea, Decaloba, Distephana and Passiflora). Approximately 71% of the marker/species combinations resulted in positive amplicons in all species tested. DNA polymorphism was detected in germplasm accessions of six closely related Passiflora species (P. edulis, P. alata, P. maliformis, P. nitida, P. quadrangularis and P. setacea) and the data used for accession discrimination and species assignment. A database of P. edulis DNA sequences obtained by NGS technology was examined to identify microsatellite repeats in

Finger-Based Numerical Skills Link Fine Motor Skills to Numerical Development in Preschoolers.

Science.gov (United States)

Suggate, Sebastian; Stoeger, Heidrun; Fischer, Ursula

2017-12-01

Previous studies investigating the association between fine-motor skills (FMS) and mathematical skills have lacked specificity. In this study, we test whether an FMS link to numerical skills is due to the involvement of finger representations in early mathematics. We gave 81 pre-schoolers (mean age of 4 years, 9 months) a set of FMS measures and numerical tasks with and without a specific finger focus. Additionally, we used receptive vocabulary and chronological age as control measures. FMS linked more closely to finger-based than to nonfinger-based numerical skills even after accounting for the control variables. Moreover, the relationship between FMS and numerical skill was entirely mediated by finger-based numerical skills. We concluded that FMS are closely related to early numerical skill development through finger-based numerical counting that aids the acquisition of mathematical mental representations.

Marker traits association of agronomical traits correlated with stagnant flooding tolerance in rice

Science.gov (United States)

Sitaresmi, T.; Utami, D. W.; Suwarno, W. B.; Ardie, S. W.; Susanto, U.; Aswidinnoor, H.

2017-05-01

In deep-water areas, the water depth increases gradually throughout the year and maintains up to more than 50 cm of deep of water for long period. In these situations, elongation ability is necessary to allow the plants to keep up with rising floodwater. The elongation of internode during submergence is regulated by environmental and hormonal factors. The objective of this study was aimed to identify the SNP markers on 384 SNPs linked with agronomical and morphological traits related to stagnant flooding tolerance. The research were conducted at Indonesian Center for Rice Research and Indonesian Centre for Agricultural Biotechnology and Genetic Resources Research and Development. The phenotypical data was collected from F2 from bi-parental crossing of IR 42 and IRRI 119. IR 42 was sensitive parent, and IRRI 119 was tolerant. DNA extraction for rice was using a modified version of Murray and Thompson method using cetyl tri-methyl-ammonium bromide (CTAB). The genotyping was carried out using 384 SNPs Golden Gate Illumina assay. Association analysis between SNP markers and phenotypical data was performed using General Linear Model in Tassel versus 5.0 software program. Based on GLM analysis, the significant marker for plant height with P value < 0.05 are TBGI275345, TBGI275367, and TBGI424383. The significant marker for number of tiller are TBGI000722, TBGI258600, TBGI270843, TBGI271066, TBGI271076, TBGI272122, TBGI272241, and TBGI327790. Two of them, TBGI424383 and TBGI271066 were expected associated with family of protein kinase which play role in plant stress signalling.

Marker traits association of agronomical traits correlated with stagnant flooding tolerance in rice

International Nuclear Information System (INIS)

Sitaresmi, T; Utami, D W; Suwarno, W B; Ardie, S W; Aswidinnoor, H; Susanto, U

2017-01-01

In deep-water areas, the water depth increases gradually throughout the year and maintains up to more than 50 cm of deep of water for long period. In these situations, elongation ability is necessary to allow the plants to keep up with rising floodwater. The elongation of internode during submergence is regulated by environmental and hormonal factors. The objective of this study was aimed to identify the SNP markers on 384 SNPs linked with agronomical and morphological traits related to stagnant flooding tolerance. The research were conducted at Indonesian Center for Rice Research and Indonesian Centre for Agricultural Biotechnology and Genetic Resources Research and Development. The phenotypical data was collected from F2 from bi-parental crossing of IR 42 and IRRI 119. IR 42 was sensitive parent, and IRRI 119 was tolerant. DNA extraction for rice was using a modified version of Murray and Thompson method using cetyl tri-methyl-ammonium bromide (CTAB). The genotyping was carried out using 384 SNPs Golden Gate Illumina assay. Association analysis between SNP markers and phenotypical data was performed using General Linear Model in Tassel versus 5.0 software program. Based on GLM analysis, the significant marker for plant height with P value < 0.05 are TBGI275345, TBGI275367, and TBGI424383. The significant marker for number of tiller are TBGI000722, TBGI258600, TBGI270843, TBGI271066, TBGI271076, TBGI272122, TBGI272241, and TBGI327790. Two of them, TBGI424383 and TBGI271066 were expected associated with family of protein kinase which play role in plant stress signalling. (paper)

Long-term and short-term action-effect links and their impact on effect monitoring.

Science.gov (United States)

Wirth, Robert; Steinhauser, Robert; Janczyk, Markus; Steinhauser, Marco; Kunde, Wilfried

2018-04-23

People aim to produce effects in the environment, and according to ideomotor theory, actions are selected and executed via anticipations of their effects. Further, to ensure that an action has been successful and an effect has been realized, we must be able to monitor the consequences of our actions. However, action-effect links might vary between situations, some might apply for a majority of situations, while others might only apply to special occasions. With a combination of behavioral and electrophysiological markers, we show that monitoring of self-produced action effects interferes with other tasks, and that the length of effect monitoring is determined by both, long-term action-effect links that hold for most situations, and short-term action-effect links that emerge from a current setting. Effect monitoring is fast and frugal when these action-effect links allow for valid anticipation of action effects, but otherwise effect monitoring takes longer and delays a subsequent task. Specific influences of long-term and short-term links on the P1/N1 and P3a further allow to dissect the temporal dynamics of when these links interact for the purpose of effect monitoring. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper.

Science.gov (United States)

Manivannan, Abinaya; Kim, Jin-Hee; Yang, Eun-Young; Ahn, Yul-Kyun; Lee, Eun-Su; Choi, Sena; Kim, Do-Sun

2018-01-01

Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS) approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding. The availability of genomic information aids in the deeper understanding of several molecular mechanisms behind the vital physiological processes. In addition, the NGS methods facilitate the genome-wide discovery of DNA based markers linked to key genes involved in important biological phenomenon. Among the molecular markers, single nucleotide polymorphism (SNP) indulges various benefits in comparison with other existing DNA based markers. The present review concentrates on the impact of NGS approaches in the discovery of useful SNP markers associated with pungency and disease resistance in pepper. The information provided in the current endeavor can be utilized for the betterment of pepper breeding in future.

Next-Generation Sequencing Approaches in Genome-Wide Discovery of Single Nucleotide Polymorphism Markers Associated with Pungency and Disease Resistance in Pepper

Directory of Open Access Journals (Sweden)

Abinaya Manivannan

2018-01-01

Full Text Available Pepper is an economically important horticultural plant that has been widely used for its pungency and spicy taste in worldwide cuisines. Therefore, the domestication of pepper has been carried out since antiquity. Owing to meet the growing demand for pepper with high quality, organoleptic property, nutraceutical contents, and disease tolerance, genomics assisted breeding techniques can be incorporated to develop novel pepper varieties with desired traits. The application of next-generation sequencing (NGS approaches has reformed the plant breeding technology especially in the area of molecular marker assisted breeding. The availability of genomic information aids in the deeper understanding of several molecular mechanisms behind the vital physiological processes. In addition, the NGS methods facilitate the genome-wide discovery of DNA based markers linked to key genes involved in important biological phenomenon. Among the molecular markers, single nucleotide polymorphism (SNP indulges various benefits in comparison with other existing DNA based markers. The present review concentrates on the impact of NGS approaches in the discovery of useful SNP markers associated with pungency and disease resistance in pepper. The information provided in the current endeavor can be utilized for the betterment of pepper breeding in future.

Accuracy of localizing radiopaque markers by abdominal radiography and correlation between their gastric emptying rate and that of a canned food in dogs

International Nuclear Information System (INIS)

Guilford, W.G.; Lawoko, C.R.O.; Allen, F.J.

1997-01-01

Objectives: To determine accuracy of abdominal radiography in locating radiopaque markers in the gastrointestinal tract and to assess correlation between gastric emptying rate of radiopaque markers and that of canned food. Animals: 17 healthy dogs. Procedure: Dogs were fed thirty 1.5-mm markers and ten 5-mm markers mixed in sufficient food to meet 25% of their daily caloric intake. They were then euthanatized by administration of an overdose of barbiturate at 1, 2, 5, 8, or 12 hours after eating and the abdomen was radiographed. The stomach, small intestine, and large intestine were then separated and radiographed in isolation. The wet and dry weights of the stomach contents were determined. The apparent and actual locations of the markers and the gastric emptying rates of markers, wet matter, and dry matter were compared, using rank correlation. Results: All comparisons indicated significant (P 0.92). The mean difference between the apparent and actual locations of the markers was < 3% for all comparisons. The mean difference between the percentage of small markers and large markers retained in the stomach and that of dry matter was 7.8 (SD, 6.2; range, 0 to 18)% and 11.9 (SD, 12.5; range, 0 to 44)%, respectively. Conclusions: The gastric emptying and orocolic transit rates of the markers were accurately predicted by abdominal radiography. The gastric emptying rate of the diet and the small markers and, to a lesser extent, the large markers was closely correlated. Clinical Relevance: When fed with a special canned food diet, radiopaque markers can be used to assess the gastric emptying rate of food with sufficient accuracy for clinical purposes

Development of SCAR (sequence-characterized amplified region) markers as a complementary tool for identification of ginger (Zingiber officinale Roscoe) from crude drugs and multicomponent formulations.

Science.gov (United States)

Chavan, Preeti; Warude, Dnyaneshwar; Joshi, Kalpana; Patwardhan, Bhushan

2008-05-01

Zingiber officinale Roscoe (common or culinary ginger) is an official drug in Ayurvedic, Indian herbal, Chinese, Japanese, African and British Pharmacopoeias. The objective of the present study was to develop DNA-based markers that can be applied for the identification and differentiation of the commercially important plant Z. officinale Roscoe from the closely related species Zingiber zerumbet (pinecone, bitter or 'shampoo' ginger) and Zingiber cassumunar [cassumunar or plai (Thai) ginger]. The rhizomes of the other two Zingiber species used in the present study are morphologically similar to that of Z. officinale Roscoe and can be used as its adulterants or contaminants. Various methods, including macroscopy, microscopy and chemoprofiling, have been reported for the quality control of crude ginger and its products. These methods are reported to have limitations in distinguishing Z. officinale from closely related species. Hence, newer complementary methods for correct identification of ginger are useful. In the present study, RAPD (random amplification of polymorphic DNA) analysis was used to identify putative species-specific amplicons for Z. officinale. These were further cloned and sequenced to develop SCAR (sequence-characterized amplified region) markers. The developed SCAR markers were tested in several non-Zingiber species commonly used in ginger-containing formulations. One of the markers, P3, was found to be specific for Z. officinale and was successfully applied for detection of Z. officinale from Trikatu, a multicomponent formulation.

Results from the European Prospective Investigation into Cancer and Nutrition Link Vitamin B6 Catabolism and Lung Cancer Risk.

NARCIS (Netherlands)

Zuo, Hui; Ueland, Per M; Midttun, Øivind; Vollset, Stein E; Tell, Grethe S; Theofylaktopoulou, Despoina; Travis, Ruth C; Boutron-Ruault, Marie-Christine; Fournier, Agnès; Severi, Gianluca; Kvaskoff, Marina; Boeing, Heiner; Bergmann, Manuela M; Fortner, Renée T; Kaaks, Rudolf; Trichopoulou, Antonia; Kotanidou, Anastasia; Lagiou, Pagona; Palli, Domenico; Sieri, Sabina; Panico, Salvatore; Bueno-de-Mesquita, H Bas; Peeters, Petra H; Grankvist, Kjell; Johansson, Mikael; Agudo, Antonio; Garcia, Jose Ramon Quiros; Larranaga, Nerea; Sanchez, Maria-Jose; Chirlaque, Maria Dolores; Ardanaz, Eva; Chuang, Shu-Chun; Gallo, Valentina; Brennan, Paul; Johansson, Mattias; Ulvik, Arve

2018-01-01

Circulating pyridoxal-5'-phosphate (PLP) has been linked to lung cancer risk. The PAr index, defined as the ratio 4-pyridoxic acid/(pyridoxal + PLP), reflects increased vitamin B6 catabolism during inflammation. PAr has been defined as a marker of lung cancer risk in a prospective cohort study, but

Re-Examination of Mixed Media Communication: The Impact of Voice, Data Link, and Mixed Air Traffic Control Environments on the Flight Deck

Science.gov (United States)

Dunbar, Melisa; McGann, Alison; Mackintosh, Margaret-Anne; Lozito, Sandra; Ashford, Rose (Technical Monitor)

2001-01-01

A simulation in the B747-400 was conducted at NASA Ames Research Center that compared how crews handled voice and data link air traffic control (ATC) messages in a single medium versus a mixed voice and data link ATC environment The interval between ATC messages was also varied to examine the influence of time pressure in voice, data link, and mixed ATC environments. For messages sent via voice, transaction times were lengthened in the mixed media environment for closely spaced messages. The type of environment did not affect data link times. However, messages times were lengthened in both single and mixed-modality environments under time pressure. Closely spaced messages also increased the number of requests for clarification for voice messages in the mixed environment and review menu use for data link messages. Results indicated that when time pressure is introduced, the mix of voice and data link does not necessarily capitalize on the advantages of both media. These findings emphasize the need to develop procedures for managing communication in mixed voice and data link environments.

X-linked ichthyosis associated with psychosis and behavioral abnormalities: a case report.

Science.gov (United States)

Malik, Amna; Amer, Ahmed Bait; Salama, Mohammed; Haddad, Bander; Alrifai, Muhammad T; Balwi, Mohammed Al; Davies, William; Eyaid, Wafaa

2017-09-22

X-linked ichthyosis is a dermatological condition caused by deficiency for the enzyme steroid sulfatase. Previously, X-linked ichthyosis/steroid sulfatase deficiency has been associated with developmental and neurological phenotypes. Here, we show for the first time, that X-linked ichthyosis may be comorbid with an additional psychiatric phenotype (psychosis). We report the case of an 11-year-old Saudi Arabian boy with X-linked ichthyosis associated with psychosis, mental retardation, autism spectrum disorder, inattentive attention deficit hyperactivity disorder, and epilepsy. Genetic analysis revealed a 1.68 Mb deletion encompassing STS in 95% of cells while biochemical analysis revealed correspondingly low steroid sulfatase activity consistent with a diagnosis of X-linked ichthyosis. The psychotic symptoms could be reasonably well controlled by administration of an atypical antipsychotic. This report describes a case of comorbid X-linked ichthyosis and psychosis (most closely corresponding to early-onset schizophrenia) for the first time, and suggests that deficiency for steroid sulfatase and contiguous genes may increase vulnerability to psychosis as well as other psychological disorders.

Targeting the Sources of Fecal Contamination using Dog-, Human-, and Ruminant- Specific Markers in the Lake Herrick Watershed, Georgia.

Science.gov (United States)

Saintil, T.; Radcliffe, D. E.; Rasmussen, T. C.; Habteselassie, M.; Sowah, R.; Kannan, A.

2016-12-01

The Lake Herrick Watershed is about 1.5 km2 and covers portions of the University of Georgia's East campus, the Oconee Forest, residential and commercial landuse. Lake Herrick, a recreational site on the University of Georgia campus, was closed in 2002 due to fecal contamination. Subsequent monitoring confirmed persistent contamination, which led to a permanent closure to swimming, boating, and fishing. While fecal coliform abundance is a standard metric for determining human health risks, Geldreich (1970) showed that fecal abundance does not necessarily correlate with the presence of pathogens. Nor does it identify pollution sources, which are needed to mitigate health risks. Two inflow tributaries and the outlet stream were monitored for discharge, fecal coliform, forms of nitrogen and phosphorus and other water-quality data to quantify lake influent and effluent bacteria loads. Fecal sources were identified using the human HF183 genetic marker (Seurinck et al., 2005), the ruminant BacR marker (Reischer et al., 2006), and the dog mitochondrial DNA (mtDNA) marker (Tambalo et al., 2012). Preliminary results confirm high concentrations of E. coli and Enterococci, above the State's limit of 124 MPN/100 mL, in both baseflows and stormflows. The findings also suggest that the E. coli and Enterococci loads from the inlet tributaries are on average higher compared to the bacteria loads coming out of the outlet stream. The human markers were detectable at all three sites but most of the samples were not quantifiable. The ruminant markers were quantifiable at both inlets but no ruminant markers were found at the outlet. The dog markers were detectable but not quantifiable at both inlets and no dog markers were detected at the outlet. Statistical analyses will be used to establish relationships between the nutrients data, the fecal concentrations, and the gene-specific markers.