SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays

PubMed Central

Schönherr, Sebastian; Neuner, Mathias; Forer, Lukas; Specht, Günther; Kloss-Brandstätter, Anita; Kronenberg, Florian; Coassin, Stefan

2013-01-01

Single nucleotide polymorphisms (SNPs) play a prominent role in modern genetics. Current genotyping technologies such as Sequenom iPLEX, ABI TaqMan and KBioscience KASPar made the genotyping of huge SNP sets in large populations straightforward and allow the generation of hundreds of thousands of genotypes even in medium sized labs. While data generation is straightforward, the subsequent data conversion, storage and quality control steps are time-consuming, error-prone and require extensive bioinformatic support. In order to ease this tedious process, we developed SNPflow. SNPflow is a lightweight, intuitive and easily deployable application, which processes genotype data from Sequenom MassARRAY (iPLEX) and ABI 7900HT (TaqMan, KASPar) systems and is extendible to other genotyping methods as well. SNPflow automatically converts the raw output files to ready-to-use genotype lists, calculates all standard quality control values such as call rate, expected and real amount of replicates, minor allele frequency, absolute number of discordant replicates, discordance rate and the p-value of the HWE test, checks the plausibility of the observed genotype frequencies by comparing them to HapMap/1000-Genomes, provides a module for the processing of SNPs, which allow sex determination for DNA quality control purposes and, finally, stores all data in a relational database. SNPflow runs on all common operating systems and comes as both stand-alone version and multi-user version for laboratory-wide use. The software, a user manual, screenshots and a screencast illustrating the main features are available at http://genepi-snpflow.i-med.ac.at. PMID:23527209

Who goes, who stays?

PubMed

Light, D A

2001-01-01

The merger announcement between DeWaal Pharmaceuticals and BioHealth Labs was front-page news. Pictures of CEO Steve Lindell and chairman Kaspar van de Velde had appeared in newspapers around the world. Two months later, the press had moved on to a new story, and the hard labor of integration loomed. Steve had worked tirelessly to clear regulatory hurdles, and all signs pointed toward approval in the near future. Now Steve was feeling pressure to attack the real challenge of the merger: bringing together two very different cultures as quickly and efficiently as possible. DeWaal was an established drug-maker based in the Netherlands, and BioHealth, headquartered just north of New York City, had in recent years become competitive at the highest tier of the market. The first step in integrating the two companies was to select the top layers of management for the new company. At the moment, there were some 120 people on two continents for about 65 senior-level jobs. Steve's urgency was not without cause: talented people from both sides were jumping ship, and BioHealth's stock price had dipped 20% after the initial euphoria over the deal had worn off. Complicating matters was confusion over who was really in charge: Steve wanted to take leadership and move ahead rapidly, but he was often disarmed by Kaspar's charming persuasiveness. As the two men attempt to work through the important personnel issues during a lunch meeting, they quickly hit a roadblock. How can they come to agreement about who goes and who stays? Four commentators offer advice in response to this fictional case.

Development of COS-SNP and HRM markers for high-throughput and reliable haplotype-based detection of Lr14a in durum wheat (Triticum durum Desf.).

PubMed

Terracciano, Irma; Maccaferri, Marco; Bassi, Filippo; Mantovani, Paola; Sanguineti, Maria C; Salvi, Silvio; Simková, Hana; Doležel, Jaroslav; Massi, Andrea; Ammar, Karim; Kolmer, James; Tuberosa, Roberto

2013-04-01

Leaf rust (Puccinia triticina Eriks. & Henn.) is a major disease affecting durum wheat production. The Lr14a-resistant gene present in the durum wheat cv. Creso and its derivative cv. Colosseo is one of the best characterized leaf-rust resistance sources deployed in durum wheat breeding. Lr14a has been mapped close to the simple sequence repeat markers gwm146, gwm344 and wmc10 in the distal portion of the chromosome arm 7BL, a gene-dense region. The objectives of this study were: (1) to enrich the Lr14a region with single nucleotide polymorphisms (SNPs) and high-resolution melting (HRM)-based markers developed from conserved ortholog set (COS) genes and from sequenced Diversity Array Technology (DArT(®)) markers; (2) to further investigate the gene content and colinearity of this region with the Brachypodium and rice genomes. Ten new COS-SNP and five HRM markers were mapped within an 8.0 cM interval spanning Lr14a. Two HRM markers pinpointed the locus in an interval of <1.0 cM and eight COS-SNPs were mapped 2.1-4.1 cM distal to Lr14a. Each marker was tested for its capacity to predict the state of Lr14a alleles (in particular, Lr14-Creso associated to resistance) in a panel of durum wheat elite germplasm including 164 accessions. Two of the most informative markers were converted into KASPar(®) markers. Single assay markers ubw14 and wPt-4038-HRM designed for agarose gel electrophoresis/KASPar(®) assays and high-resolution melting analysis, respectively, as well as the double-marker combinations ubw14/ubw18, ubw14/ubw35 and wPt-4038-HRM-ubw35 will be useful for germplasm haplotyping and for molecular-assisted breeding.

Towards a molecular taxonomic key of the Aurantioideae subfamily using chloroplastic SNP diagnostic markers of the main clades genotyped by competitive allele-specific PCR.

PubMed

Oueslati, Amel; Ollitrault, Frederique; Baraket, Ghada; Salhi-Hannachi, Amel; Navarro, Luis; Ollitrault, Patrick

2016-08-18

Chloroplast DNA is a primary source of molecular variations for phylogenetic analysis of photosynthetic eukaryotes. However, the sequencing and analysis of multiple chloroplastic regions is difficult to apply to large collections or large samples of natural populations. The objective of our work was to demonstrate that a molecular taxonomic key based on easy, scalable and low-cost genotyping method should be developed from a set of Single Nucleotide Polymorphisms (SNPs) diagnostic of well-established clades. It was applied to the Aurantioideae subfamily, the largest group of the Rutaceae family that includes the cultivated citrus species. The publicly available nucleotide sequences of eight plastid genomic regions were compared for 79 accessions of the Aurantioideae subfamily to search for SNPs revealing taxonomic differentiation at the inter-tribe, inter-subtribe, inter-genus and interspecific levels. Diagnostic SNPs (DSNPs) were found for 46 of the 54 clade levels analysed. Forty DSNPs were selected to develop KASPar markers and their taxonomic value was tested by genotyping 108 accessions of the Aurantioideae subfamily. Twenty-seven markers diagnostic of 24 clades were validated and they displayed a very high rate of transferability in the Aurantioideae subfamily (only 1.2 % of missing data on average). The UPGMA from the validated markers produced a cladistic organisation that was highly coherent with the previous phylogenetic analysis based on the sequence data of the eight plasmid regions. In particular, the monophyletic origin of the "true citrus" genera plus Oxanthera was validated. However, some clarification remains necessary regarding the organisation of the other wild species of the Citreae tribe. We validated the concept that with well-established clades, DSNPs can be selected and efficiently transformed into competitive allele-specific PCR markers (KASPar method) allowing cost-effective highly efficient cladistic analysis in large collections at

[The proof of paternity. An andrological-forensic challenge in historical perspective].

PubMed

Albrecht, K; Schultheiss, D

2004-10-01

For centuries, difficulties have occurred in determining unresolved paternities. In addition to the modern standard methods, such as the examination of DNA or serological proof, expert opinion on fertility once played an important role. The andrological difference between incapability to fertilise and the inability to participate in sexual intercourse was also distinguished historically. Of special significance was the discovery of spermatozoa by the medical student Johan Ham in 1677 and their further investigation by Antoni van Leeuwenhoek.Recently, modern DNA methods have also been applied for historical investigations. Illustrious examples are the DNA analysis in the case of Kaspar Hauser of Ansbach and the dispute about Thomas Jefferson, President of the U.S., fathering a child by one of his slaves. In this discourse, a medicinal-forensic review of the development of expert opinion, illustrated with historical case studies, is given.

Impact of the Indonesian Throughflow on the Atlantic Meridional Overturning Circulation

NASA Astrophysics Data System (ADS)

Le Bars, Dewi; Dijkstra, Henk

2014-05-01

Understanding the mechanisms controlling the strength and variability of the Atlantic Meridional Overturning Circulation (AMOC) is one of the main topics of climate science and in particular physical oceanography. Current simple representations of the global ocean overturning separates the surface return flow to the Atlantic basin into a cold water path through the Drake Passage and a warm water path through the Indonesian Throughflow and Agulhas leakage. The relative importance of these two paths has been investigated in non-eddying ocean models. In these models the Agulhas retroflection cannot be modelled properly, which leads to an important overestimation of the Agulhas leakage. Furthermore, it seems that the in these models the relation between the meridional density gradient and the overturning strength is greatly simplified and changes significantly when eddies are resolved (Den Toom et al. 2013). As a result, the impact of the Pacific-Indian Oceans exchange through the Indonesian Throughflow on the AMOC is still unknown. To investigate this question we run a state-of-the-art ocean model, the Parallel Ocean Program (POP), globally, at eddy resolving resolution (0.1º). Using climatological forcing from the CORE dataset we perform two simulations of 110 years, a control experiment with realistic coastlines and one in which the Indonesian Passages are closed. Results show that, for a closed Indonesian Throughflow, the Indian Ocean cools down but its salinity increases. The Agulhas leakage reduces also by 3Sv (Le Bars et al. 2013) and the net effect on the south Atlantic is a cooling down and decrease salinity. The anomalies propagate slowly northward and a significant decrease of the AMOC is found at 26ºN after 50 years. This decrease AMOC also leads to reduced northward heat flux in the Atlantic. These processes are investigated with a detailed analysis of the heat and freshwater balances in the Atlantic-Arctic region and in the region south of 34ºS where

Development and validation of a breeder-friendly KASPar marker for wheat leaf rust resistance locus Lr21

USDA-ARS?s Scientific Manuscript database

Development and utilization of genetic markers play a pivotal role in marker assisted breeding of wheat cultivars with pyramids of disease resistance genes. The objective of this study is to develop a closed tube, gel-free assay for high throughput genotyping of leaf rust resistance locus Lr21. Poly...

[BIOLOGICALLY ACTIVE ALKALOIDS FROM RHIZOMES WITH ROOTS OF VINCA HERBACEA WALDST. ET KIT, GROWING IN GEORGIA].

PubMed

Vachnadze, V; Vachnadze, N; Gogitidze, N; Mushkiashvili, N; Mchedlidze, K

2017-10-01

Roots and rhizomes of Vinca herbacea Waldst. et Kit, were collected during early flowering and fruiting. Рhenophases biologically active substances I and II were obtained by liquid-liquid extraction. Dominant alkaloids: tabersonin, reserpine, maidine, norfluorocurarin and copsinin were obtained after the dispertion in citrare-phosfhate buffer and subsequent TLC. Accelerated restitution of granulocytopoiesis was observed in mice during both irradiation and myelotoxic drug-induced acute leucopenia. Increase in total WBC over 200% was observed after treatment by substance I in drug-induced leucopenia model (fivefold oral administration) and over 130% after treatment by substance I in irradiate mice (fivefold intraperitoneal administration). Morphological and anatomical structures of the underground organs of V. herbacea have been studied. The main microstructural characteristics are revealed - Rhizomes are characterized by coutinized epidermis, lamellar collenchyma, fibers and the texture of the vascular system of a monocyclic structure. The root system shows the whole cortex, the endoderm with Kaspar spots; the outer, radially continuous phloem tissue is located in the conducting system and distinguishes the cylindrical xylem tissue with annular and spiral-circular blood vessels.

Development and validation of breeder-friendly KASPar markers for er1, a powdery mildew resistance gene in pea (Pisum sativum L.)

USDA-ARS?s Scientific Manuscript database

Powdery mildew of pea is caused by Erysiphe pisi DC and is a serious threat to pea (Pisum sativum L.) production throughout much of the world. Development and utilization of genetic resistance to powdery mildew is considered an effective and sustainable strategy to manage this disease. One gene, er1...

Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean

PubMed Central

Patil, Gunvant; Do, Tuyen; Vuong, Tri D.; Valliyodan, Babu; Lee, Jeong-Dong; Chaudhary, Juhi; Shannon, J. Grover; Nguyen, Henry T.

2016-01-01

Soil salinity is a limiting factor of crop yield. The soybean is sensitive to soil salinity, and a dominant gene, Glyma03g32900 is primarily responsible for salt-tolerance. The identification of high throughput and robust markers as well as the deployment of salt-tolerant cultivars are effective approaches to minimize yield loss under saline conditions. We utilized high quality (15x) whole-genome resequencing (WGRS) on 106 diverse soybean lines and identified three major structural variants and allelic variation in the promoter and genic regions of the GmCHX1 gene. The discovery of single nucleotide polymorphisms (SNPs) associated with structural variants facilitated the design of six KASPar assays. Additionally, haplotype analysis and pedigree tracking of 93 U.S. ancestral lines were performed using publically available WGRS datasets. Identified SNP markers were validated, and a strong correlation was observed between the genotype and salt treatment phenotype (leaf scorch, chlorophyll content and Na+ accumulation) using a panel of 104 soybean lines and, an interspecific bi-parental population (F8) from PI483463 x Hutcheson. These markers precisely identified salt-tolerant/sensitive genotypes (>91%), and different structural-variants (>98%). These SNP assays, supported by accurate phenotyping, haplotype analyses and pedigree tracking information, will accelerate marker-assisted selection programs to enhance the development of salt-tolerant soybean cultivars. PMID:26781337

Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs

PubMed Central

Saxena, Rachit K.; von Wettberg, Eric; Upadhyaya, Hari D.; Sanchez, Vanessa; Songok, Serah; Saxena, Kulbhushan; Kimurto, Paul; Varshney, Rajeev K.

2014-01-01

Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively. PMID:24533111

SNP discovery in the bovine milk transcriptome using RNA-Seq technology.

PubMed

Cánovas, Angela; Rincon, Gonzalo; Islas-Trejo, Alma; Wickramasinghe, Saumya; Medrano, Juan F

2010-12-01

High-throughput sequencing of RNA (RNA-Seq) was developed primarily to analyze global gene expression in different tissues. However, it also is an efficient way to discover coding SNPs. The objective of this study was to perform a SNP discovery analysis in the milk transcriptome using RNA-Seq. Seven milk samples from Holstein cows were analyzed by sequencing cDNAs using the Illumina Genome Analyzer system. We detected 19,175 genes expressed in milk samples corresponding to approximately 70% of the total number of genes analyzed. The SNP detection analysis revealed 100,734 SNPs in Holstein samples, and a large number of those corresponded to differences between the Holstein breed and the Hereford bovine genome assembly Btau4.0. The number of polymorphic SNPs within Holstein cows was 33,045. The accuracy of RNA-Seq SNP discovery was tested by comparing SNPs detected in a set of 42 candidate genes expressed in milk that had been resequenced earlier using Sanger sequencing technology. Seventy of 86 SNPs were detected using both RNA-Seq and Sanger sequencing technologies. The KASPar Genotyping System was used to validate unique SNPs found by RNA-Seq but not observed by Sanger technology. Our results confirm that analyzing the transcriptome using RNA-Seq technology is an efficient and cost-effective method to identify SNPs in transcribed regions. This study creates guidelines to maximize the accuracy of SNP discovery and prevention of false-positive SNP detection, and provides more than 33,000 SNPs located in coding regions of genes expressed during lactation that can be used to develop genotyping platforms to perform marker-trait association studies in Holstein cattle.

IRF6 rs2235375 single nucleotide polymorphism is associated with isolated non-syndromic cleft palate but not with cleft lip with or without palate in south Indian population.

PubMed

Gurramkonda, Venkatesh Babu; Syed, Altaf Hussain; Murthy, Jyotsna; Lakkakula, Bhaskar V K S

2017-06-26

Transcription factors are very diverse family of proteins involved in activating or repressing the transcription of a gene at a given time. Several studies using animal models demonstrated the role of transcription factor genes in craniofacial development. We aimed to investigate the association of IRF6 intron-6 polymorphism in the non-syndromic cleft lip with or without Palate in a south Indian population. 173 unrelated nonsyndromic cleft lip with or without Palate patients and 176 controls without clefts patients were genotyped for IRF6 rs2235375 variant by allele-specific amplification using the KASPar single nucleotide polymorphism genotyping system. The association between interferon regulatory factor-6 gene intron-6 dbSNP208032210:g.G>C (rs2235375) single nucleotide polymorphism and non-syndromic cleft lip with or without palate risk was investigated by chi-square test. There were significant differences in genotype or allele frequencies of rs2235375 single nucleotide polymorphism between controls and cases with non-syndromic cleft lip with or without palate. IRF6 rs2235375 variant was significantly associated with increased risk of non-syndromic cleft lip with or without palate in co-dominant, dominant (OR: 1.19; 95% CI 1.03-2.51; p=0.034) and allelic models (OR: 1.40; 95% CI 1.04-1.90; p=0.028). When subset analysis was applied significantly increased risk was observed in cleft palate only group (OR dominant: 4.33; 95% CI 1.44-12.97; p=0.005). These results suggest that IRF6 rs2235375 SNP play a major role in the pathogenesis and risk of developing non-syndromic cleft lip with or without palate. Copyright © 2017 Associação Brasileira de Otorrinolaringologia e Cirurgia Cérvico-Facial. Published by Elsevier Editora Ltda. All rights reserved.

Paraoxonase promoter and intronic variants modify risk of sporadic amyotrophic lateral sclerosis

PubMed Central

Cronin, Simon; Greenway, Matthew J; Prehn, Jochen H M; Hardiman, Orla

2007-01-01

Background The paraoxonases, PON1–3, play a major protective role both against environmental toxins and as part of the antioxidant defence system. Recently, non‐synonymous coding single nucleotide polymorphisms (SNPs), known to lower serum PON activity, have been associated with sporadic ALS (SALS) in a Polish population. A separate trio based study described a detrimental allele at the PON3 intronic variant INS2+3651 (rs10487132). Association between PON gene cluster variants and SALS requires external validation in an independent dataset. Aims To examine the association of the promoter SNPs PON1−162G>A and PON1−108T>C; the non‐synonymous functional SNPs PON1Q192R and L55M and PON2C311S and A148G; and the intronic marker PON3INS2+3651A>G, with SALS in a genetically homogenous population. Methods 221 Irish patients with SALS and 202 unrelated control subjects were genotyped using KASPar chemistries. Statistical analyses and haplotype estimations were conducted using Haploview and Unphased software. Multiple permutation testing, as implemented in Unphased, was applied to haplotype p values to correct for multiple hypotheses. Results Two of the seven SNPs were associated with SALS in the Irish population: PON155M (OR 1.52, p = 0.006) and PON3INS2+3651 G (OR 1.36, p = 0.03). Two locus haplotype analysis showed association only when both of these risk alleles were present (OR 1.7, p = 0.005), suggesting a potential effect modification. Low functioning promoter variants were observed to influence this effect when compared with wild‐type. Conclusions These data provide additional evidence that genetic variation across the paroxanase loci may be common susceptibility factors for SALS. PMID:17702780

Influence of angiotensin converting enzyme (ACE) gene rs4362 polymorphism on the progression of kidney failure in patients with autosomal dominant polycystic kidney disease (ADPKD).

PubMed

Ramanathan, Gnanasambandan; Ghosh, Santu; Elumalai, Ramprasad; Periyasamy, Soundararajan; Lakkakula, Bhaskar V K S

2016-06-01

Autosomal dominant polycystic kidney disease (ADPKD) is an inherited systemic disorder, characterized by the fluid filled cysts in the kidneys leading to end stage renal failure in later years of life. Hypertension is one of the major factors independently contributing to the chronic kidney disease (CKD) progression. The renin-angiotensin aldosterone system (RAAS) genes have been extensively studied as hypertension candidate genes. The aim of the present study was to investigate the role of angiotensin converting enzyme tagging - single nucleotide polymorphisms (ACE tag-SNPs) in progression of CKD in patients with ADPKD. m0 ethods: In the present study six ACE tagSNPs (angiotensin converting enzyme tag single nucleotide polymorphisms) and insertion/deletion (I/D) in 102 ADPKD patients and 106 control subjects were investigated. The tagSNPs were genotyped using FRET-based KASPar method and ACE ID by polymerase chain reaction (PCR) and electrophoresis. Genotypes and haplotypes were compared between ADPKD patients and controls. Univariate and multivariate logistic regression analyses were performed to assess the effect of genotypes and hypertension on CKD advancement. Mantel-Haenszel (M-H) stratified analysis was performed to study the relationship between different CKD stages and hypertension and their interaction. All loci were polymorphic and except rs4293 SNP the remaining loci followed Hardy-Weinberg equilibrium. Distribution of ACE genotypes and haplotypes in controls and ADPKD patients was not significant. A significant linkage disequilibrium (LD) was observed between SNPs forming two LD blocks. The univariate analysis revealed that the age, hypertension, family history of diabetes and ACE rs4362 contributed to the advancement of CKD. The results suggest that the ACE genotypes are effect modifiers of the relationship between hypertension and CKD advancement among the ADPKD patients.

J. W. Goethe - poet engaged in Earth sciences

NASA Astrophysics Data System (ADS)

Nemec, Vaclav

2014-05-01

The famous German poet Johann Wolfgang Goethe (1749 - 1832) was a man of an outstanding interest for the Earth sciences. In the Czech geological dictionary his own biography remembers his frequent visits to the famous West Bohemian health resorts. In this region he was focusing his attention to the geological history, petrography and mineralogy, genesis of mineral water springs etc. Some of his studies were published. His geological points of view were not always correct (as seen from a recent knowledge) but his efforts to deepen studies of this territory cannot be forgotten. - In his rich correspondence with the count Kaspar Maria Sternberg (1761 - 1838) - founder of the (nowadays) National Museum in Prague - the author of this article has recently discovered in the Prague archives a letter written just one week before the death of the poet. It is a confession of his deep relation especially to the region if West Bohemia where he found lot of enjoyment and new knowledge in the course of numerous visits and stays. - Goethe had the largest private collection of minerals in all of Europe (17800 rock samples). A mineral goethite has been named after him. - The Czech composer Václav Jan Tomášek (1774 - 1850) describing his visit paid to Goethe in Cheb (Eger) in 1822 remembers also mineralogical interest of the poet and his excursions to the region for collecting local minerals. The main reason for personal contact in this case was the art (Tomášek composed songs using Goethe's poems). But Tomášek described also his frequent talks on science with the famous Swedish chemist Jöns Jacob Berzelius (1779 - 1848) in Karlsbad (1822). From other sources a common stay of Berzelius, Goethe and Sternberg in Marienbad (also 1822) is reported.

LINGO1 rs9652490 and rs11856808 polymorphisms are not associated with risk for multiple sclerosis

PubMed Central

2013-01-01

Background Some recent experimental data suggest a possible role of LINGO-1 in the pathogenesis of multiple sclerosis (MS). In an attempt to identify genetic biomarkers related to MS susceptibility, we genotyped two common SNPs in the LINGO1 gene which have been associated to other neurological conditions, in patients with MS and in healthy subjects. These SNPs are linked to several SNPs within the LINGO1 gene, especially in individuals of Oriental or Caucasian descent. Methods We analyzed the allelic and genotype frequency of two LINGO1 variants (rs9652490 and rs11856808) in 293 patients with MS and 318 healthy controls, using KASPar assays. Results LINGO1 rs9652490 and rs11856808 allelic and genotype frequencies did not differ significantly between MS patients and controls. The minor allele frequencies for rs9652490 were 0.171 (95% CI = 0.140-0.201) and 0.167 (95% CI = 0.138-0.196 for cases and controls respectively (p = 0.853). For rs11856808 the minor allele frequencies were 0.317 (95% CI = 0.280-0.355) and 0.310 (95% CI = 0.274-0.346) for cases and controls, respectively (p = 0.773). Allele and genotype frequencies were unrelated with the age of onset of MS, gender, and clinical course of MS. In addition, haplotype analyses did not reveal any putative risk related to haplotypes. Conclusions These results suggest that LINGO1 rs9652490 and rs11856808 polymorphisms are not related with risk for MS. This study adds to other published evidence indicating that, to date, the LINGO1 SNPs studied here could be useful risk biomarkers of developing essential tremor, but not other movement disorders. PMID:23574883

The Arctic Boreal Vulnerability Experiment (ABoVE) 2017 Airborne Campaign

NASA Astrophysics Data System (ADS)

Miller, C. E.; Goetz, S. J.; Griffith, P. C.; Hoy, E.; Larson, E. K.; Hodkinson, D. J.; Hansen, C.; Woods, J.; Kasischke, E. S.; Margolis, H. A.

2017-12-01

The 2017 ABoVE Airborne Campaign (AAC) was one of the largest airborne experiments ever conducted by NASA's Earth Science Division. It involved nine aircraft in 17 deployments - more than 100 flights - between April and October and sampled over 4 million km2in Alaska and northwestern Canada. Many of these flights were coordinated with detailed, same-day ground-based measurements to link field-based, process-level studies with geospatial data products derived from satellite remote sensing. A major goal of the 2017 AAC was to collect data that spanned the critical intermediate space and time scales that are essential for a comprehensive understanding of scaling issues across the ABoVE Study Domain and extrapolation to the pan-Arctic. Additionally, the 2017 AAC provided unique opportunities to validate satellite and airborne remote sensing data for northern high latitude ecosystems, develop and advance fundamental remote sensing science, and explore scientific insights from innovative sensor combinations. The 2017 AAC science strategy coupled domain-wide sampling with L-band and P-band synthetic aperture radar (SAR), imaging spectroscopy (AVIRIS-NG), full waveform lidar (LVIS) and atmospheric carbon dioxide and methane with more spatially and temporally focused studies using Ka-band SAR (Ka-SPAR) and solar induced chlorophyll fluorescence (CFIS). Additional measurements were coordinated with the NEON Airborne Observing Platform, the ASCENDS instrument development suite, and the ATOM EV-S2 investigation. Targets of interest included the array of field sites operated by the ABoVE Science Team as well as the intensive sites operated by the DOE NGEE-Arctic team on the Seward Peninsula and in Barrow, NSF's LTER sites at Toolik Lake (North Slope) and Bonanza Creek (Interior Alaska), the Canadian Cold Regions Hydrology sites in the Arctic tundra near Trail Valley Creek NT, the Government of the Northwest Territories Slave River/Slave Delta watershed time series and numerous

Genetic risk analysis of coronary artery disease in Pakistani subjects using a genetic risk score of 21 variants.

PubMed

Shahid, Saleem Ullah; Shabana; Cooper, Jackie A; Beaney, Katherine E; Li, Kawah; Rehman, Abdul; Humphries, Steve E

2017-03-01

Conventional coronary artery disease (CAD) risk factors like age, gender, blood lipids, hypertension and smoking have been the basis of CAD risk prediction algorithms, but provide only modest discrimination. Genetic risk score (GRS) may provide improved discrimination over and above conventional risk factors. Here we analyzed the genetic risk of CAD in subjects from Pakistan, using a GRS of 21 variants in 18 genes and examined whether the GRS is associated with blood lipid levels. 625 (405 cases and 220 controls) subjects were genotyped for variants, NOS3 rs1799983, SMAD3 rs17228212, APOB rs1042031, LPA rs3798220, LPA rs10455872, SORT1 rs646776, APOE rs429358, GLUL rs10911021, FTO rs9939609, MIA3 rs17465637, CDKN2Ars10757274, DAB2IP rs7025486, CXCL12 rs1746048, ACE rs4341, APOA5 rs662799, CETP rs708272, MRAS rs9818870, LPL rs328, LPL rs1801177, PCSK9 rs11591147 and APOE rs7412 by TaqMan and KASPar allele discrimination techniques. Individually, the single SNPs were not associated with CAD except APOB rs1042031 and FTO rs993969 (p = 0.01 and 0.009 respectively). However, the combined GRS of 21 SNPs was significantly higher in cases than controls (19.37 ± 2.56 vs. 18.47 ± 2.45, p = 2.9 × 10 -5 ), and compared to the bottom quintile, CAD risk in the top quintile of the GRS was 2.96 (95% CI 1.71-5.13). Atherogenic blood lipids showed significant positive association with GRS. The GRS was quantitatively associated with CAD risk and showed association with blood lipid levels, suggesting that the mechanism of these variants is likely to be, in part at least, through creating an atherogenic lipid profile in subjects carrying high numbers of risk alleles. Copyright © 2017 Elsevier B.V. All rights reserved.

Gene-Based Single Nucleotide Polymorphism Markers for Genetic and Association Mapping in Common Bean

PubMed Central

2012-01-01

Background In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic mapping and association studies. Results In this study, a total of 313 new gene-based markers were developed at target genes. Intronic variation was deeply explored in order to capture more polymorphism. Introns were putatively identified after comparing the common bean ESTs with the soybean genome, and the primers were designed over intron-flanking regions. The intronic regions were evaluated for parental polymorphisms using the single strand conformational polymorphism (SSCP) technique and Sequenom MassARRAY system. A total of 53 new marker loci were placed on an integrated molecular map in the DOR364 × G19833 recombinant inbred line (RIL) population. The new linkage map was used to build a consensus map, merging the linkage maps of the BAT93 × JALO EEP558 and DOR364 × BAT477 populations. A total of 1,060 markers were mapped, with a total map length of 2,041 cM across 11 linkage groups. As a second application of the generated resource, a diversity panel with 93 genotypes was evaluated with 173 SNP markers using the MassARRAY-platform and KASPar technology. These results were coupled with previous SSR evaluations and drought tolerance assays carried out on the same individuals. This agglomerative dataset was examined, in order to discover marker-trait associations, using general linear model (GLM) and mixed linear model (MLM). Some significant associations with yield components were identified, and were consistent with previous findings. Conclusions In short, this study illustrates the power of intron

SNP Discovery for mapping alien introgressions in wheat

PubMed Central

2014-01-01

Background Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L). Results The short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes. Conclusion This approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and

Lithospheric heterogeneity beneath the EARS interpreted from major and trace element analyses of mafic rocks

NASA Astrophysics Data System (ADS)

Hamblock, J.; Anthony, E.; Omenda, P.; Chesley, J.

2003-04-01

We report chemical analyses for tholeiites from the axial region of the EARS and tholeiites and basanites from the Chyulu Hills Volcanic Province (CHVP), located on the SE flank of the Kenya Rift. The purpose of the study is to: i) explore contrasts in lithospheric composition from the axial region, where seismic velocities imply high temperatures and presence of melt at shallow depths, to the flanks, where geophysical studies indicate thick lithosphere and a zone of partial melt centered under the CHVP (Ritter and Kaspar, 1997, Tectonophysics 278, 149-169). ii) investigate plume components and plume-lithosphere interactions in the different settings. This study complements the characterization of lithosphere along the axis of the Rift by MacDonald et al. (2001, J. Petrol. 42, 877-900) and the study of temporal evolution of the CHVP by Späth et al. (2001, J. Petrol. 42, 765-787). Basanites within the CHVP are similar to OIB in their trace-element patterns, but with a pronounced negative K-anomaly. Späth et al. attribute this anomaly to melting of a lithospheric mantle source containing amphibole. They postulate, based on radiogenic isotopes (Sr, Pb, Nd), recent metasomatism due to interaction of the lithosphere with the EARS plume. High La/Yb suggests a source within the garnet-peridotite field. Tholeiites from the CHVP are distinct in trace-element chemistry from basanites, with flatter multi-element patterns and generally lower elemental concentrations. The CHVP tholeiites have La/Yb indicative of a spinel peridotite source. The role of crustal contamination for tholeiites remains open; however, substantial evidence exists for lithospheric heterogeneity beneath the CHVP. Axial lavas show similar elemental behavior as the CHVP: basanites have negative K-anomalies (MacDonald et al., 2001), whereas tholeiites do not. Tholeiites have flat multi-element patterns with low overall concentrations, similar to those from the CHVP, with one significant difference

Modeling spatially- and temporally-explicit water stress indices for use in life cycle assessment

NASA Astrophysics Data System (ADS)

Scherer, L.; Venkatesh, A.; Karuppiah, R.; Usadi, A.; Pfister, S.; Hellweg, S.

2013-12-01

model regions (including Africa and North America). These WSIs were used to estimate revised CFs for freshwater consumption to be used in LCAs. Future work will extend results to a global scale. References 1. Brown, A., Matlock, M., 2011. A Review of Water Scarcity Indices and Methodologies, University of Kansas, The Sustainability Consortium, White Paper #106. 2. Pfister, S., Koehler, A., Hellweg, S., 2009. Assessing the Environmental Impacts of Freshwater Consumption in LCA. Environ. Sci. Technol. 43 (11), 4098-4104. 3. Alcamo, J.; Doll, P.; Henrichs, T.; Kaspar, F.; Lehner, B.; Rosch, T.; Siebert, S. Development and testing of the WaterGAP 2 global model of water use and availability Hydrol. Sci. J. 2003, 48 (3) 317- 337. 4. Arnold, J.G., Srinivasan, R., Muttiah, R.S., Allen, P.M., 1999. Continental scale simulation of the hydrologic balance. J. Am.Water Resour. Assoc. 35 (5), 1037-1051. 5. Pfister, S., Bayer, P., Koehler, A., Hellweg, S., 2011. Environmental Impacts of Water Use in Global Crop Production: Hotspots and Trade-Offs with Land Use. Environ. Sci. Technol. 45 (13), 5761- 5768.

Comparing a simple methodology to evaluate hydrodynamic parameters with rainfall simulation experiments

NASA Astrophysics Data System (ADS)

Di Prima, Simone; Bagarello, Vincenzo; Bautista, Inmaculada; Burguet, Maria; Cerdà, Artemi; Iovino, Massimo; Prosdocimi, Massimo

2016-04-01

., Haverkamp, R., 2006. Beerkan Estimation of Soil Transfer Parameters through Infiltration Experiments - BEST. Soil Science Society of America Journal 70, 521. doi:10.2136/sssaj2005.0026 Liu, H., Lei, T.W., Zhao, J., Yuan, C.P., Fan, Y.T., Qu, L.Q., 2011. Effects of rainfall intensity and antecedent soil water content on soil infiltrability under rainfall conditions using the run off-on-out method. Journal of Hydrology 396, 24-32. doi:10.1016/j.jhydrol.2010.10.028 Logsdon, S.D., Jaynes, D.B., 1996. Spatial Variability of Hydraulic Conductivity in a Cultivated Field at Different Times. Soil Science Society of America Journal 60, 703. doi:10.2136/sssaj1996.03615995006000030003x Prieksat, M.A., Kaspar, T.C., Ankeny, M.D., 1994. Positional and Temporal Changes in Ponded Infiltration in a Corn Field. Soil Science Society of America Journal 58, 181. doi:10.2136/sssaj1994.03615995005800010026x Tricker, A.S., 1979. The design of a portable rainfall simulator infiltrometer. Journal of Hydrology 41, 143-147. doi:10.1016/0022-1694(79)90111-2 van De Giesen, N.C., Stomph, T.J., de Ridder, N., 2000. Scale effects of Hortonian overland flow and rainfall-runoff dynamics in a West African catena landscape. Hydrol. Process. 14, 165-175. doi:10.1002/(SICI)1099-1085(200001)14:1<165::AID-HYP920>3.0.CO;2-1 Zimmermann, A., Schinn, D.S., Francke, T., Elsenbeer, H., Zimmermann, B., 2013. Uncovering patterns of near-surface saturated hydraulic conductivity in an overland flow-controlled landscape. Geoderma 195-196, 1-11. doi:10.1016/j.geoderma.2012.11.002

EDITORIAL: Focus on Dilute Magnetic Semiconductors FOCUS ON DILUTE MAGNETIC SEMICONDUCTORS

NASA Astrophysics Data System (ADS)

Chambers, Scott A.; Gallagher, Bryan

2008-05-01

Chisholm, J D Budai and D P Norton Role of charge carriers for ferromagnetism in cobalt-doped rutile TiO2 T Fukumura, H Toyosaki, K Ueno, M Nakano and M Kawasaki Ab-initio study of exchange constants and electronic structure in diluted magnetic group-IV semiconductors Silvia Picozzi and Marjana Ležaić Phase coherent transport in (Ga,Mn)As D Neumaier, K Wagner, U Wurstbauer, M Reinwald, W Wegscheider and D Weiss Hydrogen interstitials-mediated ferromagnetism in MnxGe1-x magnetic semiconductors Xin-Xin Yao, Shi-Shen Yan, Shu-Jun Hu, Xue-Ling Lin, Chong Han, Yan-Xue Chen, Guo-Lei Liu and Liang-Mo Mei Electronic structures of magnetic semiconductors FeCr2Se4 and Fe0.5Cu0.5Cr2Se4 B I Min, Seung Su Baik, H C Choi, S K Kwon and J-S Kang Investigation of pure and Co2+-doped ZnO quantum dot electronic structures using the density functional theory: choosing the right functional Ekaterina Badaeva, Yong Feng, Daniel R Gamelin and Xiaosong Li Magnetic properties of sol-gel-derived doped ZnO as a potential ferromagnetic semiconductor: a synchrotron-based study N R S Farley, K W Edmonds, A A Freeman, G van der Laan, C R Staddon, D H Gregory and B L Gallagher Local electronic structure of Cr in the II-VI diluted ferromagnetic semiconductor Zn1-xCrxTe M Kobayashi, Y Ishida, J I Hwang, G S Song, A Fujimori, C S Yang, L Lee, H-J Lin, D J Huang, C T Chen, Y Takeda, K Terai, S-I Fujimori, T Okane, Y Saitoh, H Yamagami, K Kobayashi, A Tanaka, H Saito and K Ando Lack of ferromagnetism in n-type cobalt-doped ZnO epitaxial thin films T C Kaspar, T Droubay, S M Heald, P Nachimuthu, C M Wang, V Shutthanandan, C A Johnson, D R Gamelin and S A Chambers XMCD studies on Co and Li doped ZnO magnetic semiconductors Thomas Tietze, Milan Gacic, Gisela Schütz, Gerhard Jakob, Sebastian Brück and Eberhard Goering Ferromagnetic semiconductors and the role of disorder B W Wessels An extensive comparison of anisotropies in MBE grown (Ga,Mn)As material C Gould, S Mark, K Pappert, R G Dengel, J Wenisch, R P