A Genomewide Admixture Mapping Panel for Hispanic/Latino Populations

PubMed Central

Mao, Xianyun ; Bigham, Abigail W. ; Mei, Rui ; Gutierrez, Gerardo ; Weiss, Ken M. ; Brutsaert, Tom D. ; Leon-Velarde, Fabiola ; Moore, Lorna G. ; Vargas, Enrique ; McKeigue, Paul M. ; Shriver, Mark D. ; Parra, Esteban J. 

2007-01-01

Admixture mapping (AM) is a promising method for the identification of genetic risk factors for complex traits and diseases showing prevalence differences among populations. Efficient application of this method requires the use of a genomewide panel of ancestry-informative markers (AIMs) to infer the population of origin of chromosomal regions in admixed individuals. Genomewide AM panels with markers showing high frequency differences between West African and European populations are already available for disease-gene discovery in African Americans. However, no such a map is yet available for Hispanic/Latino populations, which are the result of two-way admixture between Native American and European populations or of three-way admixture of Native American, European, and West African populations. Here, we report a genomewide AM panel with 2,120 AIMs showing high frequency differences between Native American and European populations. The average intermarker genetic distance is ∼1.7 cM. The panel was identified by genotyping, with the Affymetrix GeneChip Human Mapping 500K array, a population sample with European ancestry, a Mesoamerican sample comprising Maya and Nahua from Mexico, and a South American sample comprising Aymara/Quechua from Bolivia and Quechua from Peru. The main criteria for marker selection were both high information content for Native American/European ancestry (measured as the standardized variance of the allele frequencies, also known as “f value”) and small frequency differences between the Mesoamerican and South American samples. This genomewide AM panel will make it possible to apply AM approaches in many admixed populations throughout the Americas. PMID:17503334

Arabidopsis transcriptional responses differentiating closely related chemicals (herbicides) and cross-species extrapolation to Brassica

EPA Science Inventory

Using whole genome Affymetrix ATH1 GeneChips we characterized the transcriptional response of Arabidopsis thaliana Columbia 24 hours after treatment with five different herbicides. Four of them (chloransulam, imazapyr, primisulfuron, sulfometuron) inhibit acetolactate synthase (A...

Mapping MRI/MRS Parameters with Genetic Over-expression Profiles In Human Prostate Cancer: Demonstrating the Potential

PubMed Central

Lenkinski, Robert E.; Bloch, B. Nicholas; Liu, Fangbing; Frangioni, John V.; Perner, Sven; Rubin, Mark A.; Genega, Elizabeth; Rofsky, Neil M.; Gaston, Sandra M.

2009-01-01

Magnetic resonance imaging (MRI) and MR spectroscopy can probe a variety of physiological (e.g. blood vessel permeability) and metabolic characteristics of prostate cancer. However, little is known about the changes in gene expression that underlie the spectral and imaging features observed in prostate cancer. Tumor induced changes in vascular permeability and angiogenesis are thought to contribute to patterns of dynamic contrast enhanced (DCE) MRI images of prostate cancer even though the genetic basis of tumor vasculogenesis is complex and the specific mechanisms underlying these DCEMRI features have not yet been determined. In order to identify the changes in gene expression that correspond to MRS and DCEMRI patterns in human prostate cancers, we have utilized tissue print micropeel techniques to generate “whole mount” molecular maps of radical prostatectomy specimens that correspond to pre-surgical MRI/MRS studies. These molecular maps include RNA expression profiles from both Affymetrix GeneChip microarrays and quantitative reverse transcriptase PCR (qrt-PCR) analysis, as well as immunohistochemical studies. Using these methods on patients with prostate cancer, we found robust over-expression of choline kinase a in the majority of primary tumors. We also observed overexpression of neuropeptide Y (NPY), a newly identified angiogenic factor, in a subset of DCEMRI positive prostate cancers. These studies set the stage for establishing MRI/MRS parameters as validated biomarkers for human prostate cancer. PMID:18752015

Differential gene expression in anterior pituitary glands from anestrous and cycling postpartum beef cows

USDA-ARS?s Scientific Manuscript database

Oligionucleotide microarrays (GeneChip Bovine Genome Arrays, Affymetrix Inc., Santa Clara, CA) were used to evaluate gene expression profiles in anterior pituitary glands collected from 4 anestrous and 4 cycling postpartum primiparous beef cows to provide insight into genes associated with transitio...

Genetic loci associated with delayed clearance of Plasmodium falciparum following artemisinin treatment in Southeast Asia

DTIC Science & Technology

2013-01-02

intensity data from the SNP array were normalized using the Affymetrix GeneChip Targeted Genotyping Analysis Software ( GTGS ). To assess robustness of SNP...calls, genotypes were called using three algorithms: (i) GTGS , (ii) illuminus (27), and (iii) a heuristic algorithm based on discrete cutoffs of

Arabidopsis transcriptional responses differentiate between O3 and herbicides

EPA Science Inventory

Using published data based on Affymetrix ATH1 Gene-Chips we characterized the transcriptional response of Arabidopsis thaliana Columbia to O3 and a few other major environmental stresses including oxidative stress . A set of 101 markers could be extracted which provided a compo...

[Research on the expression of hemolysin genes of Leptospira in vivo by genechip].

PubMed

Zhao, Hui; Bao, Lang

2012-07-01

To explore the expression of hemolysin genes of Leptospira in infected host. Amplified the gene segment of hemolysin genes from the genome of Leptospira by PCR for gene probe. Manufacture genechip by the VersArray Chipwriter systerm. The total RNAs of Leptospira before and after infection host were extracted, reversely transcribed to cDNA, after the random PCR, the products were marked with HEX and CY5 respectively, and hybridized to genechip to demonstrate the expression of hemolysin genes of Leptospira. The hemolysin genes LA1029 (Ratio = 0.65), LA1027 (Ratio = 0.53) were up-regulated after infection of host; LA3540 (Ratio = 1.88), LA3937 (Ratio = 5.58), LA1029 (Ratio = 3.00) were up-regulated and LA4004 (Ratio = 0.67) was down-regulated in live than in blood; LA3937 (Ratio = 2.28), LA1029 (Ratio = 2.20) were up-regulated in kidney than in blood. The expression level of hemolysin genes exist observable differences with inducement in vivo and in different organs. These suggested that these genes are probably involved in the pathogenesis and and disease progression.

Framework for reanalysis of publicly available Affymetrix® GeneChip® data sets based on functional regions of interest.

PubMed

Saka, Ernur; Harrison, Benjamin J; West, Kirk; Petruska, Jeffrey C; Rouchka, Eric C

2017-12-06

Since the introduction of microarrays in 1995, researchers world-wide have used both commercial and custom-designed microarrays for understanding differential expression of transcribed genes. Public databases such as ArrayExpress and the Gene Expression Omnibus (GEO) have made millions of samples readily available. One main drawback to microarray data analysis involves the selection of probes to represent a specific transcript of interest, particularly in light of the fact that transcript-specific knowledge (notably alternative splicing) is dynamic in nature. We therefore developed a framework for reannotating and reassigning probe groups for Affymetrix® GeneChip® technology based on functional regions of interest. This framework addresses three issues of Affymetrix® GeneChip® data analyses: removing nonspecific probes, updating probe target mapping based on the latest genome knowledge and grouping probes into gene, transcript and region-based (UTR, individual exon, CDS) probe sets. Updated gene and transcript probe sets provide more specific analysis results based on current genomic and transcriptomic knowledge. The framework selects unique probes, aligns them to gene annotations and generates a custom Chip Description File (CDF). The analysis reveals only 87% of the Affymetrix® GeneChip® HG-U133 Plus 2 probes uniquely align to the current hg38 human assembly without mismatches. We also tested new mappings on the publicly available data series using rat and human data from GSE48611 and GSE72551 obtained from GEO, and illustrate that functional grouping allows for the subtle detection of regions of interest likely to have phenotypical consequences. Through reanalysis of the publicly available data series GSE48611 and GSE72551, we profiled the contribution of UTR and CDS regions to the gene expression levels globally. The comparison between region and gene based results indicated that the detected expressed genes by gene-based and region-based CDFs show high

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface.

PubMed

Chen, Josephine; Zhao, Po; Massaro, Donald; Clerch, Linda B; Almon, Richard R; DuBois, Debra C; Jusko, William J; Hoffman, Eric P

2004-01-01

Publicly accessible DNA databases (genome browsers) are rapidly accelerating post-genomic research (see http://www.genome.ucsc.edu/), with integrated genomic DNA, gene structure, EST/ splicing and cross-species ortholog data. DNA databases have relatively low dimensionality; the genome is a linear code that anchors all associated data. In contrast, RNA expression and protein databases need to be able to handle very high dimensional data, with time, tissue, cell type and genes, as interrelated variables. The high dimensionality of microarray expression profile data, and the lack of a standard experimental platform have complicated the development of web-accessible databases and analytical tools. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource; PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries. Planned implementations of PEPR will include web-based remote entry of projects adhering to quality control and standard operating procedure (QC/SOP) criteria, and automated output of alternative probe set algorithms for each project (see http://microarray.cnmcresearch.org/pgadatatable.asp).

The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface

PubMed Central

Chen, Josephine; Zhao, Po; Massaro, Donald; Clerch, Linda B.; Almon, Richard R.; DuBois, Debra C.; Jusko, William J.; Hoffman, Eric P.

2004-01-01

Publicly accessible DNA databases (genome browsers) are rapidly accelerating post-genomic research (see http://www.genome.ucsc.edu/), with integrated genomic DNA, gene structure, EST/ splicing and cross-species ortholog data. DNA databases have relatively low dimensionality; the genome is a linear code that anchors all associated data. In contrast, RNA expression and protein databases need to be able to handle very high dimensional data, with time, tissue, cell type and genes, as interrelated variables. The high dimensionality of microarray expression profile data, and the lack of a standard experimental platform have complicated the development of web-accessible databases and analytical tools. We have designed and implemented a public resource of expression profile data containing 1024 human, mouse and rat Affymetrix GeneChip expression profiles, generated in the same laboratory, and subject to the same quality and procedural controls (Public Expression Profiling Resource; PEPR). Our Oracle-based PEPR data warehouse includes a novel time series query analysis tool (SGQT), enabling dynamic generation of graphs and spreadsheets showing the action of any transcript of interest over time. In this report, we demonstrate the utility of this tool using a 27 time point, in vivo muscle regeneration series. This data warehouse and associated analysis tools provides access to multidimensional microarray data through web-based interfaces, both for download of all types of raw data for independent analysis, and also for straightforward gene-based queries. Planned implementations of PEPR will include web-based remote entry of projects adhering to quality control and standard operating procedure (QC/SOP) criteria, and automated output of alternative probe set algorithms for each project (see http://microarray.cnmcresearch.org/pgadatatable.asp). PMID:14681485

Nanobarcode gene expression monitoring system for potential miniaturized space applications

NASA Astrophysics Data System (ADS)

Ruan, Weiming; Eastman, P. Scott; Cooke, Patrick A.; Park, Jennifer S.; Chu, Julia S. F.; Gray, Joe W.; Li, Song; Chen, Fanqing Frank

Manned mission to space has been threatened by various cosmos risks including radiation, mirogravity, vacuum, confinement, etc., which may cause genetic variations of astronauts and eventually lead to damages of their health. Thus, the development of small biomedical devices, which can monitor astronaut gene expression changes, is useful for future long-term space missions. Using magnetic microbeads packed with nanocrystal quantum dots at controlled ratios, we were able to generate highly multiplexed nanobarcodes, which can encode a flexible panel of genes. Also, by using a reporter quantum dot, this nanobarcode platform can monitor and quantify gene expression level with improved speed and sensitivity. As a comparison, we studied TGF-β1 induced transcription changes in human bone marrow mesenchymal stem cells with both the nanobarcode microbead system and the Affymetrix GeneChip ® HTA system, which is currently considered as the industrial standard. Though using only 1/20 of the sample RNA, the nanobarcode system showed sensitivity equivalent to Affymetrix GeneChip ® system. The coefficient of variation, dynamic range, and accuracy of the nanobarcodes measurement is equivalent to that of the GeneChip ® HTA system. Therefore, this newly invented nanobarcode microbead platform is thought to be sensitive, flexible, cost-effective and accurate in a level equivalent to the conventional methods. As an extension of the use of this new platform, spacecrafts may carry this miniaturized system as a diagnostic tool for the astronauts.

DMET-analyzer: automatic analysis of Affymetrix DMET data.

PubMed

Guzzi, Pietro Hiram; Agapito, Giuseppe; Di Martino, Maria Teresa; Arbitrio, Mariamena; Tassone, Pierfrancesco; Tagliaferri, Pierosandro; Cannataro, Mario

2012-10-05

Clinical Bioinformatics is currently growing and is based on the integration of clinical and omics data aiming at the development of personalized medicine. Thus the introduction of novel technologies able to investigate the relationship among clinical states and biological machineries may help the development of this field. For instance the Affymetrix DMET platform (drug metabolism enzymes and transporters) is able to study the relationship among the variation of the genome of patients and drug metabolism, detecting SNPs (Single Nucleotide Polymorphism) on genes related to drug metabolism. This may allow for instance to find genetic variants in patients which present different drug responses, in pharmacogenomics and clinical studies. Despite this, there is currently a lack in the development of open-source algorithms and tools for the analysis of DMET data. Existing software tools for DMET data generally allow only the preprocessing of binary data (e.g. the DMET-Console provided by Affymetrix) and simple data analysis operations, but do not allow to test the association of the presence of SNPs with the response to drugs. We developed DMET-Analyzer a tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The proposed system allows: (i) to automatize the workflow of analysis of DMET-SNP data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaGKB, a major knowledge base for pharmacogenomic studies. DMET-Analyzer has a simple graphical user interface that allows users (doctors/biologists) to upload and analyse DMET files produced by Affymetrix DMET-Console in an interactive way. The effectiveness and easy use of DMET Analyzer is demonstrated through different case studies regarding the analysis of

puma: a Bioconductor package for propagating uncertainty in microarray analysis.

PubMed

Pearson, Richard D; Liu, Xuejun; Sanguinetti, Guido; Milo, Marta; Lawrence, Neil D; Rattray, Magnus

2009-07-09

Most analyses of microarray data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By determining uncertainties from Affymetrix GeneChip data and propagating these uncertainties to downstream analyses it has been shown that we can improve results of differential expression detection, principal component analysis and clustering. Previously, implementations of these uncertainty propagation methods have only been available as separate packages, written in different languages. Previous implementations have also suffered from being very costly to compute, and in the case of differential expression detection, have been limited in the experimental designs to which they can be applied. puma is a Bioconductor package incorporating a suite of analysis methods for use on Affymetrix GeneChip data. puma extends the differential expression detection methods of previous work from the 2-class case to the multi-factorial case. puma can be used to automatically create design and contrast matrices for typical experimental designs, which can be used both within the package itself but also in other Bioconductor packages. The implementation of differential expression detection methods has been parallelised leading to significant decreases in processing time on a range of computer architectures. puma incorporates the first R implementation of an uncertainty propagation version of principal component analysis, and an implementation of a clustering method based on uncertainty propagation. All of these techniques are brought together in a single, easy-to-use package with clear, task-based documentation. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. These methods can be used to improve results from more traditional analyses of microarray data. puma also offers improvements in terms of scope and speed of execution over previously available methods. puma is recommended for

Transcript Profiling of Common Bean (Phaseolus vulgaris) Using the GeneChip Soybean Genome Array: Optimizing Analysis by Masking Biased Probes

USDA-ARS?s Scientific Manuscript database

Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common b...

Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

PubMed

Guzzi, Pietro Hiram; Cannataro, Mario

2013-08-01

A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power

ITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays.

PubMed

Rigaill, Guillem; Hupé, Philippe; Almeida, Anna; La Rosa, Philippe; Meyniel, Jean-Philippe; Decraene, Charles; Barillot, Emmanuel

2008-03-15

Affymetrix SNP arrays can be used to determine the DNA copy number measurement of 11 000-500 000 SNPs along the genome. Their high density facilitates the precise localization of genomic alterations and makes them a powerful tool for studies of cancers and copy number polymorphism. Like other microarray technologies it is influenced by non-relevant sources of variation, requiring correction. Moreover, the amplitude of variation induced by non-relevant effects is similar or greater than the biologically relevant effect (i.e. true copy number), making it difficult to estimate non-relevant effects accurately without including the biologically relevant effect. We addressed this problem by developing ITALICS, a normalization method that estimates both biological and non-relevant effects in an alternate, iterative manner, accurately eliminating irrelevant effects. We compared our normalization method with other existing and available methods, and found that ITALICS outperformed these methods for several in-house datasets and one public dataset. These results were validated biologically by quantitative PCR. The R package ITALICS (ITerative and Alternative normaLIzation and Copy number calling for affymetrix Snp arrays) has been submitted to Bioconductor.

ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs

PubMed Central

2011-01-01

Background Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications. Results ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms. Conclusions ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the

Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment.

PubMed

Severgnini, Marco; Bicciato, Silvio; Mangano, Eleonora; Scarlatti, Francesca; Mezzelani, Alessandra; Mattioli, Michela; Ghidoni, Riccardo; Peano, Clelia; Bonnal, Raoul; Viti, Federica; Milanesi, Luciano; De Bellis, Gianluca; Battaglia, Cristina

2006-06-01

Meta-analysis of microarray data is increasingly important, considering both the availability of multiple platforms using disparate technologies and the accumulation in public repositories of data sets from different laboratories. We addressed the issue of comparing gene expression profiles from two microarray platforms by devising a standardized investigative strategy. We tested this procedure by studying MDA-MB-231 cells, which undergo apoptosis on treatment with resveratrol. Gene expression profiles were obtained using high-density, short-oligonucleotide, single-color microarray platforms: GeneChip (Affymetrix) and CodeLink (Amersham). Interplatform analyses were carried out on 8414 common transcripts represented on both platforms, as identified by LocusLink ID, representing 70.8% and 88.6% of annotated GeneChip and CodeLink features, respectively. We identified 105 differentially expressed genes (DEGs) on CodeLink and 42 DEGs on GeneChip. Among them, only 9 DEGs were commonly identified by both platforms. Multiple analyses (BLAST alignment of probes with target sequences, gene ontology, literature mining, and quantitative real-time PCR) permitted us to investigate the factors contributing to the generation of platform-dependent results in single-color microarray experiments. An effective approach to cross-platform comparison involves microarrays of similar technologies, samples prepared by identical methods, and a standardized battery of bioinformatic and statistical analyses.

Power enhancement via multivariate outlier testing with gene expression arrays.

PubMed

Asare, Adam L; Gao, Zhong; Carey, Vincent J; Wang, Richard; Seyfert-Margolis, Vicki

2009-01-01

As the use of microarrays in human studies continues to increase, stringent quality assurance is necessary to ensure accurate experimental interpretation. We present a formal approach for microarray quality assessment that is based on dimension reduction of established measures of signal and noise components of expression followed by parametric multivariate outlier testing. We applied our approach to several data resources. First, as a negative control, we found that the Affymetrix and Illumina contributions to MAQC data were free from outliers at a nominal outlier flagging rate of alpha=0.01. Second, we created a tunable framework for artificially corrupting intensity data from the Affymetrix Latin Square spike-in experiment to allow investigation of sensitivity and specificity of quality assurance (QA) criteria. Third, we applied the procedure to 507 Affymetrix microarray GeneChips processed with RNA from human peripheral blood samples. We show that exclusion of arrays by this approach substantially increases inferential power, or the ability to detect differential expression, in large clinical studies. http://bioconductor.org/packages/2.3/bioc/html/arrayMvout.html and http://bioconductor.org/packages/2.3/bioc/html/affyContam.html affyContam (credentials: readonly/readonly)

MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data

PubMed Central

2014-01-01

Background Mandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets. Analysis of raw microarray data files (e.g. Affymetrix CEL files) can be time consuming, complex, and requires fundamental computational and bioinformatics skills. The development of analytical workflows to automate these tasks simplifies the processing of, improves the efficiency of, and serves to standardize multiple and sequential analyses. Once installed, workflows facilitate the tedious steps required to run rapid intra- and inter-dataset comparisons. Results We developed a workflow to facilitate and standardize Meta-Analysis of Affymetrix Microarray Data analysis (MAAMD) in Kepler. Two freely available stand-alone software tools, R and AltAnalyze were embedded in MAAMD. The inputs of MAAMD are user-editable csv files, which contain sample information and parameters describing the locations of input files and required tools. MAAMD was tested by analyzing 4 different GEO datasets from mice and drosophila. MAAMD automates data downloading, data organization, data quality control assesment, differential gene expression analysis, clustering analysis, pathway visualization, gene-set enrichment analysis, and cross-species orthologous-gene comparisons. MAAMD was utilized to identify gene orthologues responding to hypoxia or hyperoxia in both mice and drosophila. The entire set of analyses for 4 datasets (34 total microarrays) finished in ~ one hour. Conclusions MAAMD saves time, minimizes the required computer skills, and offers a standardized procedure for users to analyze microarray datasets and make new intra- and inter-dataset comparisons. PMID:24621103

Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

USDA-ARS?s Scientific Manuscript database

Natural antisense transcripts (NATs) are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded) or a different locus (trans-encoded). They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation....

Genome-wide and fine-resolution association analysis of malaria in West Africa.

PubMed

Jallow, Muminatou; Teo, Yik Ying; Small, Kerrin S; Rockett, Kirk A; Deloukas, Panos; Clark, Taane G; Kivinen, Katja; Bojang, Kalifa A; Conway, David J; Pinder, Margaret; Sirugo, Giorgio; Sisay-Joof, Fatou; Usen, Stanley; Auburn, Sarah; Bumpstead, Suzannah J; Campino, Susana; Coffey, Alison; Dunham, Andrew; Fry, Andrew E; Green, Angela; Gwilliam, Rhian; Hunt, Sarah E; Inouye, Michael; Jeffreys, Anna E; Mendy, Alieu; Palotie, Aarno; Potter, Simon; Ragoussis, Jiannis; Rogers, Jane; Rowlands, Kate; Somaskantharajah, Elilan; Whittaker, Pamela; Widden, Claire; Donnelly, Peter; Howie, Bryan; Marchini, Jonathan; Morris, Andrew; SanJoaquin, Miguel; Achidi, Eric Akum; Agbenyega, Tsiri; Allen, Angela; Amodu, Olukemi; Corran, Patrick; Djimde, Abdoulaye; Dolo, Amagana; Doumbo, Ogobara K; Drakeley, Chris; Dunstan, Sarah; Evans, Jennifer; Farrar, Jeremy; Fernando, Deepika; Hien, Tran Tinh; Horstmann, Rolf D; Ibrahim, Muntaser; Karunaweera, Nadira; Kokwaro, Gilbert; Koram, Kwadwo A; Lemnge, Martha; Makani, Julie; Marsh, Kevin; Michon, Pascal; Modiano, David; Molyneux, Malcolm E; Mueller, Ivo; Parker, Michael; Peshu, Norbert; Plowe, Christopher V; Puijalon, Odile; Reeder, John; Reyburn, Hugh; Riley, Eleanor M; Sakuntabhai, Anavaj; Singhasivanon, Pratap; Sirima, Sodiomon; Tall, Adama; Taylor, Terrie E; Thera, Mahamadou; Troye-Blomberg, Marita; Williams, Thomas N; Wilson, Michael; Kwiatkowski, Dominic P

2009-06-01

We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 × 10(-7) to P = 4 × 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations.

A fast boosting-based screening method for large-scale association study in complex traits with genetic heterogeneity.

PubMed

Wang, Lu-Yong; Fasulo, D

2006-01-01

Genome-wide association study for complex diseases will generate massive amount of single nucleotide polymorphisms (SNPs) data. Univariate statistical test (i.e. Fisher exact test) was used to single out non-associated SNPs. However, the disease-susceptible SNPs may have little marginal effects in population and are unlikely to retain after the univariate tests. Also, model-based methods are impractical for large-scale dataset. Moreover, genetic heterogeneity makes the traditional methods harder to identify the genetic causes of diseases. A more recent random forest method provides a more robust method for screening the SNPs in thousands scale. However, for more large-scale data, i.e., Affymetrix Human Mapping 100K GeneChip data, a faster screening method is required to screening SNPs in whole-genome large scale association analysis with genetic heterogeneity. We propose a boosting-based method for rapid screening in large-scale analysis of complex traits in the presence of genetic heterogeneity. It provides a relatively fast and fairly good tool for screening and limiting the candidate SNPs for further more complex computational modeling task.

CGO: utilizing and integrating gene expression microarray data in clinical research and data management.

PubMed

Bumm, Klaus; Zheng, Mingzhong; Bailey, Clyde; Zhan, Fenghuang; Chiriva-Internati, M; Eddlemon, Paul; Terry, Julian; Barlogie, Bart; Shaughnessy, John D

2002-02-01

Clinical GeneOrganizer (CGO) is a novel windows-based archiving, organization and data mining software for the integration of gene expression profiling in clinical medicine. The program implements various user-friendly tools and extracts data for further statistical analysis. This software was written for Affymetrix GeneChip *.txt files, but can also be used for any other microarray-derived data. The MS-SQL server version acts as a data mart and links microarray data with clinical parameters of any other existing database and therefore represents a valuable tool for combining gene expression analysis and clinical disease characteristics.

Questioning the utility of pooling samples in microarray experiments with cell lines.

PubMed

Lusa, L; Cappelletti, V; Gariboldi, M; Ferrario, C; De Cecco, L; Reid, J F; Toffanin, S; Gallus, G; McShane, L M; Daidone, M G; Pierotti, M A

2006-01-01

We describe a microarray experiment using the MCF-7 breast cancer cell line in two different experimental conditions for which the same number of independent pools as the number of individual samples was hybridized on Affymetrix GeneChips. Unexpectedly, when using individual samples, the number of probe sets found to be differentially expressed between treated and untreated cells was about three times greater than that found using pools. These findings indicate that pooling samples in microarray experiments where the biological variability is expected to be small might not be helpful and could even decrease one's ability to identify differentially expressed genes.

Who Are the Okinawans? Ancestry, Genome Diversity, and Implications for the Genetic Study of Human Longevity From a Geographically Isolated Population

PubMed Central

Hsueh, Wen-Chi; He, Qimei; Willcox, D. Craig; Nievergelt, Caroline M.; Donlon, Timothy A.; Kwok, Pui-Yan; Suzuki, Makoto; Willcox, Bradley J.

2014-01-01

Isolated populations have advantages for genetic studies of longevity from decreased haplotype diversity and long-range linkage disequilibrium. This permits smaller sample sizes without loss of power, among other utilities. Little is known about the genome of the Okinawans, a potential population isolate, recognized for longevity. Therefore, we assessed genetic diversity, structure, and admixture in Okinawans, and compared this with Caucasians, Chinese, Japanese, and Africans from HapMap II, genotyped on the same Affymetrix GeneChip Human Mapping 500K array. Principal component analysis, haplotype coverage, and linkage disequilibrium decay revealed a distinct Okinawan genome—more homogeneity, less haplotype diversity, and longer range linkage disequilibrium. Population structure and admixture analyses utilizing 52 global reference populations from the Human Genome Diversity Cell Line Panel demonstrated that Okinawans clustered almost exclusively with East Asians. Sibling relative risk (λs) analysis revealed that siblings of Okinawan centenarians have 3.11 times (females) and 3.77 times (males) more likelihood of centenarianism. These findings suggest that Okinawans are genetically distinct and share several characteristics of a population isolate, which are prone to develop extreme phenotypes (eg, longevity) from genetic drift, natural selection, and population bottlenecks. These data support further exploration of genetic influence on longevity in the Okinawans. PMID:24444611

Estimating the similarity of alternative Affymetrix probe sets using transcriptional networks

PubMed Central

2013-01-01

Background The usefulness of the data from Affymetrix microarray analysis depends largely on the reliability of the files describing the correspondence between probe sets, genes and transcripts. Particularly, when a gene is targeted by several probe sets, these files should give information about the similarity of each alternative probe set pair. Transcriptional networks integrate the multiple correlations that exist between all probe sets and supply much more information than a simple correlation coefficient calculated for two series of signals. In this study, we used the PSAWN (Probe Set Assignment With Networks) programme we developed to investigate whether similarity of alternative probe sets resulted in some specific properties. Findings PSAWNpy delivered a full textual description of each probe set and information on the number and properties of secondary targets. PSAWNml calculated the similarity of each alternative probe set pair and allowed finding relationships between similarity and localisation of probes in common transcripts or exons. Similar alternative probe sets had very low negative correlation, high positive correlation and similar neighbourhood overlap. Using these properties, we devised a test that allowed grouping similar probe sets in a given network. By considering several networks, additional information concerning the similarity reproducibility was obtained, which allowed defining the actual similarity of alternative probe set pairs. In particular, we calculated the common localisation of probes in exons and in known transcripts and we showed that similarity was correctly correlated with them. The information collected on all pairs of alternative probe sets in the most popular 3’ IVT Affymetrix chips is available in tabular form at http://bns.crbm.cnrs.fr/download.html. Conclusions These processed data can be used to obtain a finer interpretation when comparing microarray data between biological conditions. They are particularly well

Gene Profiling in Experimental Models of Eye Growth: Clues to Myopia Pathogenesis

PubMed Central

Stone, Richard A.; Khurana, Tejvir S.

2010-01-01

To understand the complex regulatory pathways that underlie the development of refractive errors, expression profiling has evaluated gene expression in ocular tissues of well-characterized experimental models that alter postnatal eye growth and induce refractive errors. Derived from a variety of platforms (e.g. differential display, spotted microarrays or Affymetrix GeneChips), gene expression patterns are now being identified in species that include chicken, mouse and primate. Reconciling available results is hindered by varied experimental designs and analytical/statistical features. Continued application of these methods offers promise to provide the much-needed mechanistic framework to develop therapies to normalize refractive development in children. PMID:20363242

EzArray: A web-based highly automated Affymetrix expression array data management and analysis system

PubMed Central

Zhu, Yuerong; Zhu, Yuelin; Xu, Wei

2008-01-01

Background Though microarray experiments are very popular in life science research, managing and analyzing microarray data are still challenging tasks for many biologists. Most microarray programs require users to have sophisticated knowledge of mathematics, statistics and computer skills for usage. With accumulating microarray data deposited in public databases, easy-to-use programs to re-analyze previously published microarray data are in high demand. Results EzArray is a web-based Affymetrix expression array data management and analysis system for researchers who need to organize microarray data efficiently and get data analyzed instantly. EzArray organizes microarray data into projects that can be analyzed online with predefined or custom procedures. EzArray performs data preprocessing and detection of differentially expressed genes with statistical methods. All analysis procedures are optimized and highly automated so that even novice users with limited pre-knowledge of microarray data analysis can complete initial analysis quickly. Since all input files, analysis parameters, and executed scripts can be downloaded, EzArray provides maximum reproducibility for each analysis. In addition, EzArray integrates with Gene Expression Omnibus (GEO) and allows instantaneous re-analysis of published array data. Conclusion EzArray is a novel Affymetrix expression array data analysis and sharing system. EzArray provides easy-to-use tools for re-analyzing published microarray data and will help both novice and experienced users perform initial analysis of their microarray data from the location of data storage. We believe EzArray will be a useful system for facilities with microarray services and laboratories with multiple members involved in microarray data analysis. EzArray is freely available from . PMID:18218103

A Transcriptomic Comparison of Two Bambara Groundnut Landraces under Dehydration Stress

PubMed Central

Khan, Faraz; Chai, Hui Hui; Ajmera, Ishan; Hodgman, Charlie; Mayes, Sean; Lu, Chungui

2017-01-01

The ability to grow crops under low-water conditions is a significant advantage in relation to global food security. Bambara groundnut is an underutilised crop grown by subsistence farmers in Africa and is known to survive in regions of water deficit. This study focuses on the analysis of the transcriptomic changes in two bambara groundnut landraces in response to dehydration stress. A cross-species hybridisation approach based on the Soybean Affymetrix GeneChip array has been employed. The differential gene expression analysis of a water-limited treatment, however, showed that the two landraces responded with almost completely different sets of genes. Hence, both landraces with very similar genotypes (as assessed by the hybridisation of genomic DNA onto the Soybean Affymetrix GeneChip) showed contrasting transcriptional behaviour in response to dehydration stress. In addition, both genotypes showed a high expression of dehydration-associated genes, even under water-sufficient conditions. Several gene regulators were identified as potentially important. Some are already known, such as WRKY40, but others may also be considered, namely PRR7, ATAUX2-11, CONSTANS-like 1, MYB60, AGL-83, and a Zinc-finger protein. These data provide a basis for drought trait research in the bambara groundnut, which will facilitate functional genomics studies. An analysis of this dataset has identified that both genotypes appear to be in a dehydration-ready state, even in the absence of dehydration stress, and may have adapted in different ways to achieve drought resistance. This will help in understanding the mechanisms underlying the ability of crops to produce viable yields under drought conditions. In addition, cross-species hybridisation to the soybean microarray has been shown to be informative for investigating the bambara groundnut transcriptome. PMID:28420201

Evaluation of the Affymetrix CytoScan® Dx Assay for Developmental Delay

PubMed Central

Webb, Bryn D.; Scharf, Rebecca J.; Spear, Emily A.; Edelmann, Lisa J.; Stroustrup, Annemarie

2015-01-01

The goal of molecular cytogenetic testing for children presenting with developmental delay is to identify or exclude genetic abnormalities that are associated with cognitive, behavioral, and/or motor symptoms. Until 2010, chromosome analysis was the standard first-line genetic screening test for evaluation of patients with developmental delay when a specific syndrome was not suspected. In 2010, The American College of Medical Genetics and several other groups recommended chromosomal microarray (CMA) as the first-line test in children with developmental delays, multiple congenital anomalies, and/or autism. This test is able to detect regions of genomic imbalances at a much finer resolution than G-banded karyotyping. Until recently, no CMA testing had been approved by the United States Food and Drug Administration (FDA). This review will focus on the use of the Affymetrix CytoScan® Dx Assay, the first CMA to receive FDA approval for the genetic evaluation of individuals with developmental delay. PMID:25350348

Identification of potential biomarkers for post-traumatic complications released after trauma-hemorrhage from murine Kupffer cells and its investigation in lung and liver.

PubMed

Schultze, Cornelia; Hildebrand, Frank; Noack, Sandra; Krettek, Christian; Zeckey, Christian; Neunaber, Claudia

2016-11-01

Early diagnosis of complications after severe trauma by specific biomarkers remains difficult. Identify potential new biomarkers for early diagnosis of post-traumatic complications. Mice underwent pressure-controlled hemorrhage or sham procedure. Four hours later, genome-wide expression of isolated Kupffer cells was compared with controls using Affymetrix-Genechip-Expression-Analysis and real-time-PCR. Expression analysis and real-time-PCR revealed a significant increase of gene expression of Cxcl10, Il4ra, Csf2rb2, Lcn2, and Gbp5. Cxcl10, Il4ra, Csf2rb2, Lcn2, and Gbp5 might represent new biomarkers for early diagnosis of post-traumatic complications, if they are linked to the development of post-traumatic complications.

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce

PubMed Central

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W.

2013-01-01

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa. The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. PMID:23550116

An Ultra-High-Density, Transcript-Based, Genetic Map of Lettuce.

PubMed

Truco, Maria José; Ashrafi, Hamid; Kozik, Alexander; van Leeuwen, Hans; Bowers, John; Wo, Sebastian Reyes Chin; Stoffel, Kevin; Xu, Huaqin; Hill, Theresa; Van Deynze, Allen; Michelmore, Richard W

2013-04-09

We have generated an ultra-high-density genetic map for lettuce, an economically important member of the Compositae, consisting of 12,842 unigenes (13,943 markers) mapped in 3696 genetic bins distributed over nine chromosomal linkage groups. Genomic DNA was hybridized to a custom Affymetrix oligonucleotide array containing 6.4 million features representing 35,628 unigenes of Lactuca spp. Segregation of single-position polymorphisms was analyzed using 213 F 7:8 recombinant inbred lines that had been generated by crossing cultivated Lactuca sativa cv. Salinas and L. serriola acc. US96UC23, the wild progenitor species of L. sativa The high level of replication of each allele in the recombinant inbred lines was exploited to identify single-position polymorphisms that were assigned to parental haplotypes. Marker information has been made available using GBrowse to facilitate access to the map. This map has been anchored to the previously published integrated map of lettuce providing candidate genes for multiple phenotypes. The high density of markers achieved in this ultradense map allowed syntenic studies between lettuce and Vitis vinifera as well as other plant species. Copyright © 2013 Truco et al.

affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling.

PubMed

Hernandez-Ferrer, Carles; Quintela Garcia, Ines; Danielski, Katharina; Carracedo, Ángel; Pérez-Jurado, Luis A; González, Juan R

2015-05-20

The well-known Genome-Wide Association Studies (GWAS) had led to many scientific discoveries using SNP data. Even so, they were not able to explain the full heritability of complex diseases. Now, other structural variants like copy number variants or DNA inversions, either germ-line or in mosaicism events, are being studies. We present the R package affy2sv to pre-process Affymetrix CytoScan HD/750k array (also for Genome-Wide SNP 5.0/6.0 and Axiom) in structural variant studies. We illustrate the capabilities of affy2sv using two different complete pipelines on real data. The first one performing a GWAS and a mosaic alterations detection study, and the other detecting CNVs and performing an inversion calling. Both examples presented in the article show up how affy2sv can be used as part of more complex pipelines aimed to analyze Affymetrix SNP arrays data in genetic association studies, where different types of structural variants are considered.

Analysis of the Metabolic Pathways Affected by Poly(γ-glutamic Acid) in Arabidopsis thaliana Based on GeneChip Microarray.

PubMed

Xu, Zongqi; Lei, Peng; Feng, Xiaohai; Li, Sha; Xu, Hong

2016-08-17

Plant growth is promoted by poly(γ-glutamic acid) (γ-PGA). However, the molecular mechanism underlying such promotion is not yet well understood. Therefore, we used GeneChip microarrays to explore the effects of γ-PGA on gene transcription in Arabidopsis thaliana. Our results revealed 299 genes significantly regulated by γ-PGA. These differently expressed genes participate mainly in metabolic and cellular processes and in stimuli responses. The metabolic pathways linked to these differently expressed genes were also investigated. A total of 64 of the 299 differently expressed genes were shown to be directly involved in 24 pathways such as brassinosteroid biosynthesis, α-linolenic acid metabolism, phenylpropanoid biosynthesis, and nitrogen metabolism, all of which were influenced by γ-PGA. The analysis demonstrated that γ-PGA promoted nitrogen assimilation and biosynthesis of brassinosteroids, jasmonic acid, and lignins, providing a better explanation for why γ-PGA promotes growth and enhances stress tolerance in plants.

Construction and Validation of the Rhodobacter sphaeroides 2.4.1 DNA Microarray: Transcriptome Flexibility at Diverse Growth Modes

PubMed Central

Pappas, Christopher T.; Sram, Jakub; Moskvin, Oleg V.; Ivanov, Pavel S.; Mackenzie, R. Christopher; Choudhary, Madhusudan; Land, Miriam L.; Larimer, Frank W.; Kaplan, Samuel; Gomelsky, Mark

2004-01-01

A high-density oligonucleotide DNA microarray, a genechip, representing the 4.6-Mb genome of the facultative phototrophic proteobacterium, Rhodobacter sphaeroides 2.4.1, was custom-designed and manufactured by Affymetrix, Santa Clara, Calif. The genechip contains probe sets for 4,292 open reading frames (ORFs), 47 rRNA and tRNA genes, and 394 intergenic regions. The probe set sequences were derived from the genome annotation generated by Oak Ridge National Laboratory after extensive revision, which was based primarily upon codon usage characteristic of this GC-rich bacterium. As a result of the revision, numerous missing ORFs were uncovered, nonexistent ORFs were deleted, and misidentified start codons were corrected. To evaluate R. sphaeroides transcriptome flexibility, expression profiles for three diverse growth modes—aerobic respiration, anaerobic respiration in the dark, and anaerobic photosynthesis—were generated. Expression levels of one-fifth to one-third of the R. sphaeroides ORFs were significantly different in cells under any two growth modes. Pathways involved in energy generation and redox balance maintenance under three growth modes were reconstructed. Expression patterns of genes involved in these pathways mirrored known functional changes, suggesting that massive changes in gene expression are the major means used by R. sphaeroides in adaptation to diverse conditions. Differential expression was observed for genes encoding putative new participants in these pathways (additional photosystem genes, duplicate NADH dehydrogenase, ATP synthases), whose functionality has yet to be investigated. The DNA microarray data correlated well with data derived from quantitative reverse transcription-PCR, as well as with data from the literature, thus validating the R. sphaeroides genechip as a powerful and reliable tool for studying unprecedented metabolic versatility of this bacterium. PMID:15231807

Rice-arsenate interactions in hydroponics: whole genome transcriptional analysis.

PubMed

Norton, Gareth J; Lou-Hing, Daniel E; Meharg, Andrew A; Price, Adam H

2008-01-01

Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 muM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the BalaxAzucena mapping population.

Rice–arsenate interactions in hydroponics: whole genome transcriptional analysis

PubMed Central

Norton, Gareth J.; Lou-Hing, Daniel E.; Meharg, Andrew A.; Price, Adam H.

2008-01-01

Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 μM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the Bala×Azucena mapping population. PMID:18453530

Vibration mechanosignals superimposed to resistive exercise result in baseline skeletal muscle transcriptome profiles following chronic disuse in bed rest.

PubMed

Salanova, Michele; Gambara, Guido; Moriggi, Manuela; Vasso, Michele; Ungethuem, Ute; Belavý, Daniel L; Felsenberg, Dieter; Cerretelli, Paolo; Gelfi, Cecilia; Blottner, Dieter

2015-11-24

Disuse-induced muscle atrophy is a major concern in aging, in neuromuscular diseases, post-traumatic injury and in microgravity life sciences affecting health and fitness also of crew members in spaceflight. By using a laboratory analogue to body unloading we perform for the first time global gene expression profiling joined to specific proteomic analysis to map molecular adaptations in disused (60 days of bed rest) human soleus muscle (CTR) and in response to a resistive exercise (RE) countermeasure protocol without and with superimposed vibration mechanosignals (RVE). Adopting Affymetrix GeneChip technology we identified 235 differently transcribed genes in the CTR group (end- vs. pre-bed rest). RE comprised 206 differentially expressed genes, whereas only 51 changed gene transcripts were found in RVE. Most gene transcription and proteomic changes were linked to various key metabolic pathways (glycolysis, oxidative phosphorylation, tricarboxylic acid (TCA) cycle, lipid metabolism) and to functional contractile structures. Gene expression profiling in bed rest identified a novel set of genes explicitly responsive to vibration mechanosignals in human soleus. This new finding highlights the efficacy of RVE protocol in reducing key signs of disuse maladaptation and atrophy, and to maintain a close-to-normal skeletal muscle quality outcome following chronic disuse in bed rest.

Genome-wide single-nucleotide polymorphism arrays demonstrate high fidelity of multiple displacement-based whole-genome amplification.

PubMed

Tzvetkov, Mladen V; Becker, Christian; Kulle, Bettina; Nürnberg, Peter; Brockmöller, Jürgen; Wojnowski, Leszek

2005-02-01

Whole-genome DNA amplification by multiple displacement (MD-WGA) is a promising tool to obtain sufficient DNA amounts from samples of limited quantity. Using Affymetrix' GeneChip Human Mapping 10K Arrays, we investigated the accuracy and allele amplification bias in DNA samples subjected to MD-WGA. We observed an excellent concordance (99.95%) between single-nucleotide polymorphisms (SNPs) called both in the nonamplified and the corresponding amplified DNA. This concordance was only 0.01% lower than the intra-assay reproducibility of the genotyping technique used. However, MD-WGA failed to amplify an estimated 7% of polymorphic loci. Due to the algorithm used to call genotypes, this was detected only for heterozygous loci. We achieved a 4.3-fold reduction of noncalled SNPs by combining the results from two independent MD-WGA reactions. This indicated that inter-reaction variations rather than specific chromosomal loci reduced the efficiency of MD-WGA. Consistently, we detected no regions of reduced amplification, with the exception of several SNPs located near chromosomal ends. Altogether, despite a substantial loss of polymorphic sites, MD-WGA appears to be the current method of choice to amplify genomic DNA for array-based SNP analyses. The number of nonamplified loci can be substantially reduced by amplifying each DNA sample in duplicate.

Cell- and Tissue-Specific Transcriptome Analyses of Medicago truncatula Root Nodules

PubMed Central

Limpens, Erik; Moling, Sjef; Hooiveld, Guido; Pereira, Patrícia A.; Bisseling, Ton; Becker, Jörg D.; Küster, Helge

2013-01-01

Legumes have the unique ability to host nitrogen-fixing Rhizobium bacteria as symbiosomes inside root nodule cells. To get insight into this key process, which forms the heart of the endosymbiosis, we isolated specific cells/tissues at different stages of symbiosome formation from nodules of the model legume Medicago truncatula using laser-capture microdissection. Next, we determined their associated expression profiles using Affymetrix Medicago GeneChips. Cells were collected from the nodule infection zone divided into a distal (where symbiosome formation and division occur) and proximal region (where symbiosomes are mainly differentiating), as well as infected cells from the fixation zone containing mature nitrogen fixing symbiosomes. As non-infected cells/tissue we included nodule meristem cells and uninfected cells from the fixation zone. Here, we present a comprehensive gene expression map of an indeterminate Medicago nodule and selected genes that show specific enriched expression in the different cells or tissues. Validation of the obtained expression profiles, by comparison to published gene expression profiles and experimental verification, indicates that the data can be used as digital “in situ”. This digital “in situ” offers a genome-wide insight into genes specifically associated with subsequent stages of symbiosome and nodule cell development, and can serve to guide future functional studies. PMID:23734198

Uncovering the molecular secrets of inflammatory breast cancer biology: an integrated analysis of three distinct affymetrix gene expression datasets.

PubMed

Van Laere, Steven J; Ueno, Naoto T; Finetti, Pascal; Vermeulen, Peter; Lucci, Anthony; Robertson, Fredika M; Marsan, Melike; Iwamoto, Takayuki; Krishnamurthy, Savitri; Masuda, Hiroko; van Dam, Peter; Woodward, Wendy A; Viens, Patrice; Cristofanilli, Massimo; Birnbaum, Daniel; Dirix, Luc; Reuben, James M; Bertucci, François

2013-09-01

Inflammatory breast cancer (IBC) is a poorly characterized form of breast cancer. So far, the results of expression profiling in IBC are inconclusive due to various reasons including limited sample size. Here, we present the integration of three Affymetrix expression datasets collected through the World IBC Consortium allowing us to interrogate the molecular profile of IBC using the largest series of IBC samples ever reported. Affymetrix profiles (HGU133-series) from 137 patients with IBC and 252 patients with non-IBC (nIBC) were analyzed using unsupervised and supervised techniques. Samples were classified according to the molecular subtypes using the PAM50-algorithm. Regression models were used to delineate IBC-specific and molecular subtype-independent changes in gene expression, pathway, and transcription factor activation. Four robust IBC-sample clusters were identified, associated with the different molecular subtypes (P<0.001), all of which were identified in IBC with a similar prevalence as in nIBC, except for the luminal A subtype (19% vs. 42%; P<0.001) and the HER2-enriched subtype (22% vs. 9%; P<0.001). Supervised analysis identified and validated an IBC-specific, molecular subtype-independent 79-gene signature, which held independent prognostic value in a series of 871 nIBCs. Functional analysis revealed attenuated TGF-β signaling in IBC. We show that IBC is transcriptionally heterogeneous and that all molecular subtypes described in nIBC are detectable in IBC, albeit with a different frequency. The molecular profile of IBC, bearing molecular traits of aggressive breast tumor biology, shows attenuation of TGF-β signaling, potentially explaining the metastatic potential of IBC tumor cells in an unexpected manner. ©2013 AACR.

Autosomal dominant spastic paraplegia with peripheral neuropathy maps to chr12q23-24.

PubMed

Schüle, R; Bonin, M; Dürr, A; Forlani, S; Sperfeld, A D; Klimpe, S; Mueller, J C; Seibel, A; van de Warrenburg, B P; Bauer, P; Schöls, L

2009-06-02

Hereditary spastic paraplegias (HSP) are genetically exceedingly heterogeneous. To date, 37 genetic loci for HSP have been described (SPG1-41), among them 16 loci for autosomal dominant disease. Notwithstanding, further genetic heterogeneity is to be expected in HSP, as various HSP families do not link to any of the known HSP loci. In this study, we aimed to map the disease locus in a German family segregating autosomal dominant complicated HSP. A genome-wide linkage analysis was performed using the GeneChip Mapping 10Kv2.0 Xba Array containing 10,204 SNP markers. Suggestive loci were further analyzed by mapping of microsatellite markers. One locus on chromosome 12q23-24, termed SPG36, was confirmed by high density microsatellite fine mapping with a significant LOD score of 3.2. SPG36 is flanked by markers D12S318 and D12S79. Linkage to SPG36 was excluded in >20 additional autosomal dominant HSP families. Candidate genes were selected and sequenced. No disease-causing mutations were identified in the coding regions of ATXN2, HSPB8, IFT81, Myo1H, UBE3B, and VPS29. SPG36 is complicated by a sensory and motor neuropathy; it is therefore the eighth autosomal dominant subtype of complicated HSP. We report mapping of a new locus for autosomal dominant hereditary spastic paraplegia (HSP) (SPG36) on chromosome 12q23-24 in a German family with autosomal dominant HSP complicated by peripheral neuropathy.

Genomic response to Wnt signalling is highly context-dependent - Evidence from DNA microarray and chromatin immunoprecipitation screens of Wnt/TCF targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Railo, Antti; Pajunen, Antti; Itaeranta, Petri

2009-10-01

Wnt proteins are important regulators of embryonic development, and dysregulated Wnt signalling is involved in the oncogenesis of several human cancers. Our knowledge of the downstream target genes is limited, however. We used a chromatin immunoprecipitation-based assay to isolate and characterize the actual gene segments through which Wnt-activatable transcription factors, TCFs, regulate transcription and an Affymetrix microarray analysis to study the global transcriptional response to the Wnt3a ligand. The anti-{beta}-catenin immunoprecipitation of DNA-protein complexes from mouse NIH3T3 fibroblasts expressing a fusion protein of {beta}-catenin and TCF7 resulted in the identification of 92 genes as putative TCF targets. GeneChip assays ofmore » gene expression performed on NIH3T3 cells and the rat pheochromocytoma cell line PC12 revealed 355 genes in NIH3T3 and 129 genes in the PC12 cells with marked changes in expression after Wnt3a stimulus. Only 2 Wnt-regulated genes were shared by both cell lines. Surprisingly, Disabled-2 was the only gene identified by the chromatin immunoprecipitation approach that displayed a marked change in expression in the GeneChip assay. Taken together, our approaches give an insight into the complex context-dependent nature of Wnt pathway transcriptional responses and identify Disabled-2 as a potential new direct target for Wnt signalling.« less

High-Resolution Maps of Mouse Reference Populations

PubMed Central

Simecek, Petr; Forejt, Jiri; Williams, Robert W.; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E.; Bennett, Beth; Deschepper, Christian F.; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A.

2017-01-01

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. PMID:28839117

High-Resolution Maps of Mouse Reference Populations.

PubMed

Simecek, Petr; Forejt, Jiri; Williams, Robert W; Shiroishi, Toshihiko; Takada, Toyoyuki; Lu, Lu; Johnson, Thomas E; Bennett, Beth; Deschepper, Christian F; Scott-Boyer, Marie-Pier; Pardo-Manuel de Villena, Fernando; Churchill, Gary A

2017-10-05

Genetic reference panels are widely used to map complex, quantitative traits in model organisms. We have generated new high-resolution genetic maps of 259 mouse inbred strains from recombinant inbred strain panels (C57BL/6J × DBA/2J, ILS/IbgTejJ × ISS/IbgTejJ, and C57BL/6J × A/J) and chromosome substitution strain panels (C57BL/6J-Chr#, C57BL/6J-Chr#, and C57BL/6J-Chr#). We genotyped all samples using the Affymetrix Mouse Diversity Array with an average intermarker spacing of 4.3 kb. The new genetic maps provide increased precision in the localization of recombination breakpoints compared to the previous maps. Although the strains were presumed to be fully inbred, we found residual heterozygosity in 40% of individual mice from five of the six panels. We also identified de novo deletions and duplications, in homozygous or heterozygous state, ranging in size from 21 kb to 8.4 Mb. Almost two-thirds (46 out of 76) of these deletions overlap exons of protein coding genes and may have phenotypic consequences. Twenty-nine putative gene conversions were identified in the chromosome substitution strains. We find that gene conversions are more likely to occur in regions where the homologous chromosomes are more similar. The raw genotyping data and genetic maps of these strain panels are available at http://churchill-lab.jax.org/website/MDA. Copyright © 2017 Simecek et al.

An evaluation of the genetic-matched pair study design using genome-wide SNP data from the European population.

PubMed

Lu, Timothy Tehua; Lao, Oscar; Nothnagel, Michael; Junge, Olaf; Freitag-Wolf, Sandra; Caliebe, Amke; Balascakova, Miroslava; Bertranpetit, Jaume; Bindoff, Laurence Albert; Comas, David; Holmlund, Gunilla; Kouvatsi, Anastasia; Macek, Milan; Mollet, Isabelle; Nielsen, Finn; Parson, Walther; Palo, Jukka; Ploski, Rafal; Sajantila, Antti; Tagliabracci, Adriano; Gether, Ulrik; Werge, Thomas; Rivadeneira, Fernando; Hofman, Albert; Uitterlinden, André Gerardus; Gieger, Christian; Wichmann, Heinz-Erich; Ruether, Andreas; Schreiber, Stefan; Becker, Christian; Nürnberg, Peter; Nelson, Matthew Roberts; Kayser, Manfred; Krawczak, Michael

2009-07-01

Genetic matching potentially provides a means to alleviate the effects of incomplete Mendelian randomization in population-based gene-disease association studies. We therefore evaluated the genetic-matched pair study design on the basis of genome-wide SNP data (309,790 markers; Affymetrix GeneChip Human Mapping 500K Array) from 2457 individuals, sampled at 23 different recruitment sites across Europe. Using pair-wise identity-by-state (IBS) as a matching criterion, we tried to derive a subset of markers that would allow identification of the best overall matching (BOM) partner for a given individual, based on the IBS status for the subset alone. However, our results suggest that, by following this approach, the prediction accuracy is only notably improved by the first 20 markers selected, and increases proportionally to the marker number thereafter. Furthermore, in a considerable proportion of cases (76.0%), the BOM of a given individual, based on the complete marker set, came from a different recruitment site than the individual itself. A second marker set, specifically selected for ancestry sensitivity using singular value decomposition, performed even more poorly and was no more capable of predicting the BOM than randomly chosen subsets. This leads us to conclude that, at least in Europe, the utility of the genetic-matched pair study design depends critically on the availability of comprehensive genotype information for both cases and controls.

Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean

PubMed Central

2010-01-01

Background The nutritional and economic value of many crops is effectively a function of seed protein and oil content. Insight into the genetic and molecular control mechanisms involved in the deposition of these constituents in the developing seed is needed to guide crop improvement. A quantitative trait locus (QTL) on Linkage Group I (LG I) of soybean (Glycine max (L.) Merrill) has a striking effect on seed protein content. Results A soybean near-isogenic line (NIL) pair contrasting in seed protein and differing in an introgressed genomic segment containing the LG I protein QTL was used as a resource to demarcate the QTL region and to study variation in transcript abundance in developing seed. The LG I QTL region was delineated to less than 8.4 Mbp of genomic sequence on chromosome 20. Using Affymetrix® Soy GeneChip and high-throughput Illumina® whole transcriptome sequencing platforms, 13 genes displaying significant seed transcript accumulation differences between NILs were identified that mapped to the 8.4 Mbp LG I protein QTL region. Conclusions This study identifies gene candidates at the LG I protein QTL for potential involvement in the regulation of protein content in the soybean seed. The results demonstrate the power of complementary approaches to characterize contrasting NILs and provide genome-wide transcriptome insight towards understanding seed biology and the soybean genome. PMID:20199683

Analysis of the genetic structure of the Malay population: Ancestry-informative marker SNPs in the Malay of Peninsular Malaysia.

PubMed

Yahya, Padillah; Sulong, Sarina; Harun, Azian; Wan Isa, Hatin; Ab Rajab, Nur-Shafawati; Wangkumhang, Pongsakorn; Wilantho, Alisa; Ngamphiw, Chumpol; Tongsima, Sissades; Zilfalil, Bin Alwi

2017-09-01

Malay, the main ethnic group in Peninsular Malaysia, is represented by various sub-ethnic groups such as Melayu Banjar, Melayu Bugis, Melayu Champa, Melayu Java, Melayu Kedah Melayu Kelantan, Melayu Minang and Melayu Patani. Using data retrieved from the MyHVP (Malaysian Human Variome Project) database, a total of 135 individuals from these sub-ethnic groups were profiled using the Affymetrix GeneChip Mapping Xba 50-K single nucleotide polymorphism (SNP) array to identify SNPs that were ancestry-informative markers (AIMs) for Malays of Peninsular Malaysia. Prior to selecting the AIMs, the genetic structure of Malays was explored with reference to 11 other populations obtained from the Pan-Asian SNP Consortium database using principal component analysis (PCA) and ADMIXTURE. Iterative pruning principal component analysis (ipPCA) was further used to identify sub-groups of Malays. Subsequently, we constructed an AIMs panel for Malays using the informativeness for assignment (I n ) of genetic markers, and the K-nearest neighbor classifier (KNN) was used to teach the classification models. A model of 250 SNPs ranked by I n , correctly classified Malay individuals with an accuracy of up to 90%. The identified panel of SNPs could be utilized as a panel of AIMs to ascertain the specific ancestry of Malays, which may be useful in disease association studies, biomedical research or forensic investigation purposes. Copyright © 2017 Elsevier B.V. All rights reserved.

Gain of GRHL2 is associated with early recurrence of hepatocellular carcinoma.

PubMed

Tanaka, Yasuo; Kanai, Fumihiko; Tada, Motohisa; Tateishi, Ryosuke; Sanada, Masashi; Nannya, Yasuhito; Ohta, Miki; Asaoka, Yoshinari; Seto, Motoko; Shiina, Shuichiro; Yoshida, Haruhiko; Kawabe, Takao; Yokosuka, Osamu; Ogawa, Seishi; Omata, Masao

2008-11-01

The aim of this study is to identify genomic changes that might be implicated in hepatocellular carcinoma (HCC) progression, and evaluate the associations with clinico-pathological features. The genomic DNA of 17 hepatoma cell lines was analyzed using Affymetrix GeneChip Human Mapping 50K high-density oligonucleotide arrays. We selected representative genes from recurrent amplified regions and measured the copy number of these genes in 70 HCC clinical samples. We found 10 recurrent high-grade gain regions spanning less than 3 Mb in at least two hepatoma cell lines, and selected 10 representative genes. The copy number was almost normal in non-cancerous tissue and frequently amplified in Edmondson grade II or III HCC compared to Edmondson grade I HCC. Gain of TAX1BP1 in 7p15.2-1 was associated with larger tumor size and positivity of HCV antibody, and gain of CCND1 in 11q13.2-3 was associated with larger tumor size by multivariate analysis. Furthermore, a gain of GRHL2 in 8q22.3 was associated with early recurrence of HCC, controlling for clinical parameters. Decreased GRHL2 expression by RNA interference inhibits the growth of hepatoma cells, suggesting its association with cell proliferation. A gain of GRHL2 might be a predictive marker for HCC recurrence.

Variable hearing impairment in a DFNB2 family with a novel MYO7A missense mutation.

PubMed

Hildebrand, M S; Thorne, N P; Bromhead, C J; Kahrizi, K; Webster, J A; Fattahi, Z; Bataejad, M; Kimberling, W J; Stephan, D; Najmabadi, H; Bahlo, M; Smith, R J H

2010-06-01

Myosin VIIA mutations have been associated with non-syndromic hearing loss (DFNB2; DFNA11) and Usher syndrome type 1B (USH1B). We report clinical and genetic analyses of a consanguineous Iranian family segregating autosomal recessive non-syndromic hearing loss (ARNSHL). The hearing impairment was mapped to the DFNB2 locus using Affymetrix 50K GeneChips; direct sequencing of the MYO7A gene was completed. The Iranian family (L-1419) was shown to segregate a novel homozygous missense mutation (c.1184G>A) that results in a p.R395H amino acid substitution in the motor domain of the myosin VIIA protein. As one affected family member had significantly less severe hearing loss, we used a candidate approach to search for a genetic modifier. This novel MYO7A mutation is the first reported to cause DFNB2 in the Iranian population and this DFNB2 family is the first to be associated with a potential modifier. The absence of vestibular and retinal defects, and less severe low frequency hearing loss, is consistent with the phenotype of a recently reported Pakistani DFNB2 family. Thus, we conclude this family has non-syndromic hearing loss (DFNB2) rather than USH1B, providing further evidence that these two diseases represent discrete disorders.

Isolation of Microarray-Grade Total RNA, MicroRNA, and DNA from a Single PAXgene Blood RNA Tube

PubMed Central

Kruhøffer, Mogens; Dyrskjøt, Lars; Voss, Thorsten; Lindberg, Raija L.P.; Wyrich, Ralf; Thykjaer, Thomas; Orntoft, Torben F.

2007-01-01

We have developed a procedure for isolation of microRNA and genomic DNA in addition to total RNA from whole blood stabilized in PAXgene Blood RNA tubes. The procedure is based on automatic extraction on a BioRobot MDx and includes isolation of DNA from a fraction of the stabilized blood and recovery of small RNA species that are otherwise lost. The procedure presented here is suitable for large-scale experiments and is amenable to further automation. Procured total RNA and DNA was tested using Affymetrix Expression and single-nucleotide polymorphism GeneChips, respectively, and isolated microRNA was tested using spotted locked nucleic acid-based microarrays. We conclude that the yield and quality of total RNA, microRNA, and DNA from a single PAXgene blood RNA tube is sufficient for downstream microarray analysis. PMID:17690207

sscMap: an extensible Java application for connecting small-molecule drugs using gene-expression signatures.

PubMed

Zhang, Shu-Dong; Gant, Timothy W

2009-07-31

Connectivity mapping is a process to recognize novel pharmacological and toxicological properties in small molecules by comparing their gene expression signatures with others in a database. A simple and robust method for connectivity mapping with increased specificity and sensitivity was recently developed, and its utility demonstrated using experimentally derived gene signatures. This paper introduces sscMap (statistically significant connections' map), a Java application designed to undertake connectivity mapping tasks using the recently published method. The software is bundled with a default collection of reference gene-expression profiles based on the publicly available dataset from the Broad Institute Connectivity Map 02, which includes data from over 7000 Affymetrix microarrays, for over 1000 small-molecule compounds, and 6100 treatment instances in 5 human cell lines. In addition, the application allows users to add their custom collections of reference profiles and is applicable to a wide range of other 'omics technologies. The utility of sscMap is two fold. First, it serves to make statistically significant connections between a user-supplied gene signature and the 6100 core reference profiles based on the Broad Institute expanded dataset. Second, it allows users to apply the same improved method to custom-built reference profiles which can be added to the database for future referencing. The software can be freely downloaded from http://purl.oclc.org/NET/sscMap.

Identifier mapping performance for integrating transcriptomics and proteomics experimental results

PubMed Central

2011-01-01

Background Studies integrating transcriptomic data with proteomic data can illuminate the proteome more clearly than either separately. Integromic studies can deepen understanding of the dynamic complex regulatory relationship between the transcriptome and the proteome. Integrating these data dictates a reliable mapping between the identifier nomenclature resultant from the two high-throughput platforms. However, this kind of analysis is well known to be hampered by lack of standardization of identifier nomenclature among proteins, genes, and microarray probe sets. Therefore data integration may also play a role in critiquing the fallible gene identifications that both platforms emit. Results We compared three freely available internet-based identifier mapping resources for mapping UniProt accessions (ACCs) to Affymetrix probesets identifications (IDs): DAVID, EnVision, and NetAffx. Liquid chromatography-tandem mass spectrometry analyses of 91 endometrial cancer and 7 noncancer samples generated 11,879 distinct ACCs. For each ACC, we compared the retrieval sets of probeset IDs from each mapping resource. We confirmed a high level of discrepancy among the mapping resources. On the same samples, mRNA expression was available. Therefore, to evaluate the quality of each ACC-to-probeset match, we calculated proteome-transcriptome correlations, and compared the resources presuming that better mapping of identifiers should generate a higher proportion of mapped pairs with strong inter-platform correlations. A mixture model for the correlations fitted well and supported regression analysis, providing a window into the performance of the mapping resources. The resources have added and dropped matches over two years, but their overall performance has not changed. Conclusions The methods presented here serve to achieve concrete context-specific insight, to support well-informed decisions in choosing an ID mapping strategy for "omic" data merging. PMID:21619611

A model of binding on DNA microarrays: understanding the combined effect of probe synthesis failure, cross-hybridization, DNA fragmentation and other experimental details of affymetrix arrays

PubMed Central

2012-01-01

Background DNA microarrays are used both for research and for diagnostics. In research, Affymetrix arrays are commonly used for genome wide association studies, resequencing, and for gene expression analysis. These arrays provide large amounts of data. This data is analyzed using statistical methods that quite often discard a large portion of the information. Most of the information that is lost comes from probes that systematically fail across chips and from batch effects. The aim of this study was to develop a comprehensive model for hybridization that predicts probe intensities for Affymetrix arrays and that could provide a basis for improved microarray analysis and probe development. The first part of the model calculates probe binding affinities to all the possible targets in the hybridization solution using the Langmuir isotherm. In the second part of the model we integrate details that are specific to each experiment and contribute to the differences between hybridization in solution and on the microarray. These details include fragmentation, wash stringency, temperature, salt concentration, and scanner settings. Furthermore, the model fits probe synthesis efficiency and target concentration parameters directly to the data. All the parameters used in the model have a well-established physical origin. Results For the 302 chips that were analyzed the mean correlation between expected and observed probe intensities was 0.701 with a range of 0.88 to 0.55. All available chips were included in the analysis regardless of the data quality. Our results show that batch effects arise from differences in probe synthesis, scanner settings, wash strength, and target fragmentation. We also show that probe synthesis efficiencies for different nucleotides are not uniform. Conclusions To date this is the most complete model for binding on microarrays. This is the first model that includes both probe synthesis efficiency and hybridization kinetics/cross-hybridization. These

Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip

PubMed Central

Hill, Theresa A.; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W.; Van Deynze, Allen

2013-01-01

The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome

Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30K unigene Pepper GeneChip.

PubMed

Hill, Theresa A; Ashrafi, Hamid; Reyes-Chin-Wo, Sebastian; Yao, JiQiang; Stoffel, Kevin; Truco, Maria-Jose; Kozik, Alexander; Michelmore, Richard W; Van Deynze, Allen

2013-01-01

The widely cultivated pepper, Capsicum spp., important as a vegetable and spice crop world-wide, is one of the most diverse crops. To enhance breeding programs, a detailed characterization of Capsicum diversity including morphological, geographical and molecular data is required. Currently, molecular data characterizing Capsicum genetic diversity is limited. The development and application of high-throughput genome-wide markers in Capsicum will facilitate more detailed molecular characterization of germplasm collections, genetic relationships, and the generation of ultra-high density maps. We have developed the Pepper GeneChip® array from Affymetrix for polymorphism detection and expression analysis in Capsicum. Probes on the array were designed from 30,815 unigenes assembled from expressed sequence tags (ESTs). Our array design provides a maximum redundancy of 13 probes per base pair position allowing integration of multiple hybridization values per position to detect single position polymorphism (SPP). Hybridization of genomic DNA from 40 diverse C. annuum lines, used in breeding and research programs, and a representative from three additional cultivated species (C. frutescens, C. chinense and C. pubescens) detected 33,401 SPP markers within 13,323 unigenes. Among the C. annuum lines, 6,426 SPPs covering 3,818 unigenes were identified. An estimated three-fold reduction in diversity was detected in non-pungent compared with pungent lines, however, we were able to detect 251 highly informative markers across these C. annuum lines. In addition, an 8.7 cM region without polymorphism was detected around Pun1 in non-pungent C. annuum. An analysis of genetic relatedness and diversity using the software Structure revealed clustering of the germplasm which was confirmed with statistical support by principle components analysis (PCA) and phylogenetic analysis. This research demonstrates the effectiveness of parallel high-throughput discovery and application of genome

An expression database for roots of the model legume Medicago truncatula under salt stress

PubMed Central

2009-01-01

Background Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes. Description The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database. Conclusion MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/. PMID:19906315

An expression database for roots of the model legume Medicago truncatula under salt stress.

PubMed

Li, Daofeng; Su, Zhen; Dong, Jiangli; Wang, Tao

2009-11-11

Medicago truncatula is a model legume whose genome is currently being sequenced by an international consortium. Abiotic stresses such as salt stress limit plant growth and crop productivity, including those of legumes. We anticipate that studies on M. truncatula will shed light on other economically important legumes across the world. Here, we report the development of a database called MtED that contains gene expression profiles of the roots of M. truncatula based on time-course salt stress experiments using the Affymetrix Medicago GeneChip. Our hope is that MtED will provide information to assist in improving abiotic stress resistance in legumes. The results of our microarray experiment with roots of M. truncatula under 180 mM sodium chloride were deposited in the MtED database. Additionally, sequence and annotation information regarding microarray probe sets were included. MtED provides functional category analysis based on Gene and GeneBins Ontology, and other Web-based tools for querying and retrieving query results, browsing pathways and transcription factor families, showing metabolic maps, and comparing and visualizing expression profiles. Utilities like mapping probe sets to genome of M. truncatula and In-Silico PCR were implemented by BLAT software suite, which were also available through MtED database. MtED was built in the PHP script language and as a MySQL relational database system on a Linux server. It has an integrated Web interface, which facilitates ready examination and interpretation of the results of microarray experiments. It is intended to help in selecting gene markers to improve abiotic stress resistance in legumes. MtED is available at http://bioinformatics.cau.edu.cn/MtED/.

A Pilot Proteogenomic Study with Data Integration Identifies MCT1 and GLUT1 as Prognostic Markers in Lung Adenocarcinoma.

PubMed

Stewart, Paul A; Parapatics, Katja; Welsh, Eric A; Müller, André C; Cao, Haoyun; Fang, Bin; Koomen, John M; Eschrich, Steven A; Bennett, Keiryn L; Haura, Eric B

2015-01-01

We performed a pilot proteogenomic study to compare lung adenocarcinoma to lung squamous cell carcinoma using quantitative proteomics (6-plex TMT) combined with a customized Affymetrix GeneChip. Using MaxQuant software, we identified 51,001 unique peptides that mapped to 7,241 unique proteins and from these identified 6,373 genes with matching protein expression for further analysis. We found a minor correlation between gene expression and protein expression; both datasets were able to independently recapitulate known differences between the adenocarcinoma and squamous cell carcinoma subtypes. We found 565 proteins and 629 genes to be differentially expressed between adenocarcinoma and squamous cell carcinoma, with 113 of these consistently differentially expressed at both the gene and protein levels. We then compared our results to published adenocarcinoma versus squamous cell carcinoma proteomic data that we also processed with MaxQuant. We selected two proteins consistently overexpressed in squamous cell carcinoma in all studies, MCT1 (SLC16A1) and GLUT1 (SLC2A1), for further investigation. We found differential expression of these same proteins at the gene level in our study as well as in other public gene expression datasets. These findings combined with survival analysis of public datasets suggest that MCT1 and GLUT1 may be potential prognostic markers in adenocarcinoma and druggable targets in squamous cell carcinoma. Data are available via ProteomeXchange with identifier PXD002622.

Transcriptomic Response of Porcine PBMCs to Vaccination with Tetanus Toxoid as a Model Antigen

PubMed Central

Adler, Marcel; Murani, Eduard; Brunner, Ronald; Ponsuksili, Siriluck; Wimmers, Klaus

2013-01-01

The aim of the present study was to characterize in vivo genome-wide transcriptional responses to immune stimulation in order to get insight into the resulting changes of allocation of resources. Vaccination with tetanus toxoid was used as a model for a mixed Th1 and Th2 immune response in pig. Expression profiles of PBMCs (peripheral blood mononuclear cells) before and at 12 time points over a period of four weeks after initial and booster vaccination at day 14 were studied by use of Affymetrix GeneChip microarrays and Ingenuity Pathway Analysis (IPA). The transcriptome data in total comprised more than 5000 genes with different transcript abundances (DE-genes). Within the single time stages the numbers of DE-genes were between several hundred and more than 1000. Ingenuity Pathway Analysis mainly revealed canonical pathways of cellular immune response and cytokine signaling as well as a broad range of processes in cellular and organismal growth, proliferation and development, cell signaling, biosynthesis and metabolism. Significant changes in the expression profiles of PBMCs already occurred very early after immune stimulation. At two hours after the first vaccination 679 DE-genes corresponding to 110 canonical pathways of cytokine signaling, cellular immune response and other multiple cellular functions were found. Immune competence and global disease resistance are heritable but difficult to measure and to address by breeding. Besides QTL mapping of immune traits gene expression profiling facilitates the detection of functional gene networks and thus functional candidate genes. PMID:23536793

Transcriptomic response of porcine PBMCs to vaccination with tetanus toxoid as a model antigen.

PubMed

Adler, Marcel; Murani, Eduard; Brunner, Ronald; Ponsuksili, Siriluck; Wimmers, Klaus

2013-01-01

The aim of the present study was to characterize in vivo genome-wide transcriptional responses to immune stimulation in order to get insight into the resulting changes of allocation of resources. Vaccination with tetanus toxoid was used as a model for a mixed Th1 and Th2 immune response in pig. Expression profiles of PBMCs (peripheral blood mononuclear cells) before and at 12 time points over a period of four weeks after initial and booster vaccination at day 14 were studied by use of Affymetrix GeneChip microarrays and Ingenuity Pathway Analysis (IPA). The transcriptome data in total comprised more than 5000 genes with different transcript abundances (DE-genes). Within the single time stages the numbers of DE-genes were between several hundred and more than 1000. Ingenuity Pathway Analysis mainly revealed canonical pathways of cellular immune response and cytokine signaling as well as a broad range of processes in cellular and organismal growth, proliferation and development, cell signaling, biosynthesis and metabolism. Significant changes in the expression profiles of PBMCs already occurred very early after immune stimulation. At two hours after the first vaccination 679 DE-genes corresponding to 110 canonical pathways of cytokine signaling, cellular immune response and other multiple cellular functions were found. Immune competence and global disease resistance are heritable but difficult to measure and to address by breeding. Besides QTL mapping of immune traits gene expression profiling facilitates the detection of functional gene networks and thus functional candidate genes.

Comparative transcriptional profiling of two wheat genotypes, with contrasting levels of minerals in grains, shows expression differences during grain filling.

PubMed

Singh, Sudhir P; Jeet, Raja; Kumar, Jitendra; Shukla, Vishnu; Srivastava, Rakesh; Mantri, Shrikant S; Tuli, Rakesh

2014-01-01

Wheat is one of the most important cereal crops in the world. To identify the candidate genes for mineral accumulation, it is important to examine differential transcriptome between wheat genotypes, with contrasting levels of minerals in grains. A transcriptional comparison of developing grains was carried out between two wheat genotypes- Triticum aestivum Cv. WL711 (low grain mineral), and T. aestivum L. IITR26 (high grain mineral), using Affymetrix GeneChip Wheat Genome Array. The study identified a total of 580 probe sets as differentially expressed (with log2 fold change of ≥2 at p≤0.01) between the two genotypes, during grain filling. Transcripts with significant differences in induction or repression between the two genotypes included genes related to metal homeostasis, metal tolerance, lignin and flavonoid biosynthesis, amino acid and protein transport, vacuolar-sorting receptor, aquaporins, and stress responses. Meta-analysis revealed spatial and temporal signatures of a majority of the differentially regulated transcripts.

Effects of Progesterone Treatment on Expression of Genes Involved in Uterine Quiescence

PubMed Central

Jeng, Yow-Jiun; Izban, Michael G.; Sinha, Mala; Luxon, Bruce A.; Stamnes, Susan J.; England, Sarah K.

2011-01-01

An important action of progesterone during pregnancy is to maintain the uterus in a quiescent state and thereby prevent preterm labor. The causes of preterm labor are not well understood, so progesterone action on the myometrium can provide clues about the processes that keep the uterus from contracting prematurely. Accordingly, we have carried out Affymetrix GeneChip analysis of progesterone effects on gene expression in immortalized human myometrial cells cultured from a patient near the end of pregnancy. Progesterone appears to inhibit uterine excitability by a number of mechanisms, including increased expression of calcium and voltage-operated K+ channels, which dampens the electrical activity of the myometrial cell, downregulation of agents, and receptors involved in myometrial contraction, reduction in cell signal components that lead to increased intracellular Ca2+ concentrations in response to contractile stimuli, and downregulation of proteins involved in the cross-linking of actin and myosin filaments to produce uterine contractions. PMID:21795739

Comparative Transcriptional Profiling of Two Wheat Genotypes, with Contrasting Levels of Minerals in Grains, Shows Expression Differences during Grain Filling

PubMed Central

Singh, Sudhir P.; Jeet, Raja; Kumar, Jitendra; Shukla, Vishnu; Srivastava, Rakesh; Mantri, Shrikant S.; Tuli, Rakesh

2014-01-01

Wheat is one of the most important cereal crops in the world. To identify the candidate genes for mineral accumulation, it is important to examine differential transcriptome between wheat genotypes, with contrasting levels of minerals in grains. A transcriptional comparison of developing grains was carried out between two wheat genotypes- Triticum aestivum Cv. WL711 (low grain mineral), and T. aestivum L. IITR26 (high grain mineral), using Affymetrix GeneChip Wheat Genome Array. The study identified a total of 580 probe sets as differentially expressed (with log2 fold change of ≥2 at p≤0.01) between the two genotypes, during grain filling. Transcripts with significant differences in induction or repression between the two genotypes included genes related to metal homeostasis, metal tolerance, lignin and flavonoid biosynthesis, amino acid and protein transport, vacuolar-sorting receptor, aquaporins, and stress responses. Meta-analysis revealed spatial and temporal signatures of a majority of the differentially regulated transcripts. PMID:25364903

A genome wide association study of mathematical ability reveals an association at chromosome 3q29, a locus associated with autism and learning difficulties: a preliminary study.

PubMed

Baron-Cohen, Simon; Murphy, Laura; Chakrabarti, Bhismadev; Craig, Ian; Mallya, Uma; Lakatošová, Silvia; Rehnstrom, Karola; Peltonen, Leena; Wheelwright, Sally; Allison, Carrie; Fisher, Simon E; Warrier, Varun

2014-01-01

Mathematical ability is heritable, but few studies have directly investigated its molecular genetic basis. Here we aimed to identify specific genetic contributions to variation in mathematical ability. We carried out a genome wide association scan using pooled DNA in two groups of U.K. samples, based on end of secondary/high school national academic exam achievement: high (n = 419) versus low (n = 183) mathematical ability while controlling for their verbal ability. Significant differences in allele frequencies between these groups were searched for in 906,600 SNPs using the Affymetrix GeneChip Human Mapping version 6.0 array. After meeting a threshold of p<1.5×10(-5), 12 SNPs from the pooled association analysis were individually genotyped in 542 of the participants and analyzed to validate the initial associations (lowest p-value 1.14 ×10(-6)). In this analysis, one of the SNPs (rs789859) showed significant association after Bonferroni correction, and four (rs10873824, rs4144887, rs12130910 rs2809115) were nominally significant (lowest p-value 3.278 × 10(-4)). Three of the SNPs of interest are located within, or near to, known genes (FAM43A, SFT2D1, C14orf64). The SNP that showed the strongest association, rs789859, is located in a region on chromosome 3q29 that has been previously linked to learning difficulties and autism. rs789859 lies 1.3 kbp downstream of LSG1, and 700 bp upstream of FAM43A, mapping within the potential promoter/regulatory region of the latter. To our knowledge, this is only the second study to investigate the association of genetic variants with mathematical ability, and it highlights a number of interesting markers for future study.

Adaptation of a RAS pathway activation signature from FF to FFPE tissues in colorectal cancer.

PubMed

Omolo, Bernard; Yang, Mingli; Lo, Fang Yin; Schell, Michael J; Austin, Sharon; Howard, Kellie; Madan, Anup; Yeatman, Timothy J

2016-10-19

The KRAS gene is mutated in about 40 % of colorectal cancer (CRC) cases, which has been clinically validated as a predictive mutational marker of intrinsic resistance to anti-EGFR inhibitor (EGFRi) therapy. Since nearly 60 % of patients with a wild type KRAS fail to respond to EGFRi combination therapies, there is a need to develop more reliable molecular signatures to better predict response. Here we address the challenge of adapting a gene expression signature predictive of RAS pathway activation, created using fresh frozen (FF) tissues, for use with more widely available formalin fixed paraffin-embedded (FFPE) tissues. In this study, we evaluated the translation of an 18-gene RAS pathway signature score from FF to FFPE in 54 CRC cases, using a head-to-head comparison of five technology platforms. FFPE-based technologies included the Affymetrix GeneChip (Affy), NanoString nCounter™ (NanoS), Illumina whole genome RNASeq (RNA-Acc), Illumina targeted RNASeq (t-RNA), and Illumina stranded Total RNA-rRNA-depletion (rRNA). Using Affy_FF as the "gold" standard, initial analysis of the 18-gene RAS scores on all 54 samples shows varying pairwise Spearman correlations, with (1) Affy_FFPE (r = 0.233, p = 0.090); (2) NanoS_FFPE (r = 0.608, p < 0.0001); (3) RNA-Acc_FFPE (r = 0.175, p = 0.21); (4) t-RNA_FFPE (r = -0.237, p = 0.085); (5) and t-RNA (r = -0.012, p = 0.93). These results suggest that only NanoString has successful FF to FFPE translation. The subsequent removal of identified "problematic" samples (n = 15) and genes (n = 2) further improves the correlations of Affy_FF with three of the five technologies: Affy_FFPE (r = 0.672, p < 0.0001); NanoS_FFPE (r = 0.738, p < 0.0001); and RNA-Acc_FFPE (r = 0.483, p = 0.002). Of the five technology platforms tested, NanoString technology provides a more faithful translation of the RAS pathway gene expression signature from FF to FFPE than the Affymetrix

Identification of hypertension-related genes through an integrated genomic-transcriptomic approach.

PubMed

Yagil, Chana; Hubner, Norbert; Monti, Jan; Schulz, Herbert; Sapojnikov, Marina; Luft, Friedrich C; Ganten, Detlev; Yagil, Yoram

2005-04-01

In search for the genetic basis of hypertension, we applied an integrated genomic-transcriptomic approach to identify genes involved in the pathogenesis of hypertension in the Sabra rat model of salt-susceptibility. In the genomic arm of the project, we previously detected in male rats two salt-susceptibility QTLs on chromosome 1, SS1a (D1Mgh2-D1Mit11; span 43.1 cM) and SS1b (D1Mit11-D1Mit4; span 18 cM). In the transcriptomic arm, we studied differential gene expression in kidneys of SBH/y and SBN/y rats that had been fed regular diet or salt-loaded. We used the Affymetrix Rat Genome RAE230 GeneChip and probed >30,000 transcripts. The research algorithm called for an initial genome-wide screen for differentially expressed transcripts between the study groups. This step was followed by cluster analysis based on 2x2 ANOVA to identify transcripts that were of relevance specifically to salt-sensitivity and hypertension and to salt-resistance. The two arms of the project were integrated by identifying those differentially expressed transcripts that showed an allele-specific hypertensive effect on salt-loading and that mapped within the defined boundaries of the salt-susceptibility QTLs on chromosome 1. The differentially expressed transcripts were confirmed by RT-PCR. Of the 2933 genes annotated to rat chromosome 1, 1102 genes were identified within the boundaries of the two blood pressure QTLs. The microarray identified 2470 transcripts that were differentially expressed between the study groups. Cluster analysis identified genome-wide 192 genes that were relevant to salt-susceptibility and/or hypertension, 19 of which mapped to chromosome 1. Eight of these genes mapped within the boundaries of QTLs SS1a and SS1b. RT-PCR confirmed 7 genes, leaving TcTex1, Myadm, Lisch7, Axl-like, Fah, PRC1-like, and Serpinh1. None of these genes has been implicated in hypertension before. These genes become henceforth targets for our continuing search for the genetic basis of

A map of copy number variations in Chinese populations.

PubMed

Lou, Haiyi; Li, Shilin; Yang, Yajun; Kang, Longli; Zhang, Xin; Jin, Wenfei; Wu, Bailin; Jin, Li; Xu, Shuhua

2011-01-01

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in

A Map of Copy Number Variations in Chinese Populations

PubMed Central

Yang, Yajun; Kang, Longli; Zhang, Xin; Jin, Wenfei; Wu, Bailin; Jin, Li; Xu, Shuhua

2011-01-01

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in

At what scale should microarray data be analyzed?

PubMed

Huang, Shuguang; Yeo, Adeline A; Gelbert, Lawrence; Lin, Xi; Nisenbaum, Laura; Bemis, Kerry G

2004-01-01

The hybridization intensities derived from microarray experiments, for example Affymetrix's MAS5 signals, are very often transformed in one way or another before statistical models are fitted. The motivation for performing transformation is usually to satisfy the model assumptions such as normality and homogeneity in variance. Generally speaking, two types of strategies are often applied to microarray data depending on the analysis need: correlation analysis where all the gene intensities on the array are considered simultaneously, and gene-by-gene ANOVA where each gene is analyzed individually. We investigate the distributional properties of the Affymetrix GeneChip signal data under the two scenarios, focusing on the impact of analyzing the data at an inappropriate scale. The Box-Cox type of transformation is first investigated for the strategy of pooling genes. The commonly used log-transformation is particularly applied for comparison purposes. For the scenario where analysis is on a gene-by-gene basis, the model assumptions such as normality are explored. The impact of using a wrong scale is illustrated by log-transformation and quartic-root transformation. When all the genes on the array are considered together, the dependent relationship between the expression and its variation level can be satisfactorily removed by Box-Cox transformation. When genes are analyzed individually, the distributional properties of the intensities are shown to be gene dependent. Derivation and simulation show that some loss of power is incurred when a wrong scale is used, but due to the robustness of the t-test, the loss is acceptable when the fold-change is not very large.

Comparative analysis of temporal gene expression patterns in the developing ovary of the embryonic chicken

PubMed Central

YU, Minli; XU, Yali; YU, Defu; YU, Debing; DU, Wenxing

2015-01-01

Many genes participate in the process of ovarian germ cell development, while the combined action mechanisms of these molecular regulators still need clarification. The present study was focused on determination of differentially expressed genes and gene functions at four critical time points in chicken ovarian development. Comparative transcriptional profiling of ovaries from embryonic day 5.5 (E5.5), E12.5, E15.5 and E18.5 was performed using an Affymetrix GeneChip chicken genome microarray. Differential expression patterns for genes specifically depleted and enriched in each stage were identified. The results showed that most of the up- and downregulated genes were involved in the metabolism of retinoic acid (RA) and synthesis of hormones. Among them, a higher number of up- and downregulated genes in the E15.5 ovary were identified as being involved in steroid biosynthesis and retinol metabolism, respectively. To validate gene changes, expressions of twelve candidate genes related to germ cell development were examined by real-time PCR and found to be consistent with the of GeneChip data. Moreover, the immunostaining results suggested that ovarian development during different stages was regulated by different genes. Furthermore, a Raldh2 knockdown chicken model was produced to investigate the fundamental role of Raldh2 in meiosis initiation. It was found that meiosis occurred abnormally in Raldh2 knockdown ovaries, but the inhibitory effect on meiosis was reversed by the addition of exogenous RA. This study offers insights into the profile of gene expression and mechanisms regulating ovarian development, especially the notable role of Raldh2 in meiosis initiation in the chicken. PMID:25736178

Changes in the transcriptome of bovine ovarian cortex during follicle activation in vitro

PubMed Central

Yang, M. Y.

2015-01-01

The signals that regulate activation, a key transition in ovarian follicular development, are still not well understood, especially in nonrodent species. To gain insight into the regulation of this transition in cattle, we combined a microarray approach with an in vitro system in which ovarian cortical pieces cultured in control medium are enriched for primordial follicles, whereas pieces cultured with insulin are enriched for primary follicles. Total RNA was extracted from cultured cortical pieces, and then transcripts were identified and analyzed using the Affymetrix Bovine Genome GeneChip array. Around 65% of the transcripts in the bovine GeneChip were detected in cultured cortical pieces. Comparison between pieces cultured with or without insulin generated 158 differentially expressed transcripts. Compared with controls, 90 transcripts were upregulated and 68 were downregulated by insulin. These transcripts are involved in many biological processes and functions, but most are associated with cellular growth or cell cycle/cell death. The transcript encoding ubiquitin-conjugating enzyme E2C (UBE2C) was significantly upregulated during follicle activation, and Ingenuity Pathways Analysis revealed that UBE2C can interact with the tumor suppressor phosphatase and tensin homolog (PTEN). Both PTEN mRNA and protein were lower in cortical pieces cultured with insulin than in controls. In addition, FOXO3a, a downstream effector of PTEN signaling, underwent nuclear-cytoplasmic shuttling during primordial to primary follicle development in bovine fetal ovaries, further suggesting the involvement of the PTEN pathway in follicle activation in cattle. Genes and pathways identified in this study provide interesting candidates for further investigation of mechanisms underlying follicle activation. PMID:26443523

Dexpanthenol modulates gene expression in skin wound healing in vivo.

PubMed

Heise, R; Skazik, C; Marquardt, Y; Czaja, K; Sebastian, K; Kurschat, P; Gan, L; Denecke, B; Ekanayake-Bohlig, S; Wilhelm, K-P; Merk, H F; Baron, J M

2012-01-01

Topical application of dexpanthenol is widely used in clinical practice for the improvement of wound healing. Previous in vitro experiments identified a stimulatory effect of pantothenate on migration, proliferation and gene regulation in cultured human dermal fibroblasts. To correlate these in vitro findings with the more complex in vivo situation of wound healing, a clinical trial was performed in which the dexpanthenol-induced gene expression profile in punch biopsies of previously injured and dexpanthenol-treated skin in comparison to placebo-treated skin was analyzed at the molecular level by Affymetrix® GeneChip analysis. Upregulation of IL-6, IL-1β, CYP1B1, CXCL1, CCL18 and KAP 4-2 gene expression and downregulation of psorasin mRNA and protein expression were identified in samples treated topically with dexpanthenol. This in vivo study might provide new insight into the molecular mechanisms responsible for the effect of dexpanthenol in wound healing and shows strong correlations to previous in vitro data using cultured dermal fibroblasts. Copyright © 2012 S. Karger AG, Basel.

Identification of long non-coding RNA and mRNA expression in βΒ2-crystallin knockout mice.

PubMed

Jia, Yin; Xiong, Kang; Ren, Han-Xiao; Li, Wen-Jie

2018-05-01

βΒ2-crystallin (CRYBB2) is expressed at an increased level in the postnatal lens cortex and is associated with cataracts. Improved understanding of the underlying biology of cataracts is likely to be critical for the development of early detection strategies and new therapeutics. The present study aimed to identify long non-coding RNAs (lncRNAs) and mRNAs associated with CRYBB2 knockdown (KO)-induced cataracts. RNAs from 3 non-treated mice and 3 CRYBB2 KO mice were analyzed using the Affymetrix GeneChip Mouse Gene 2.0 ST array. A total of 149 lncRNAs and 803 mRNAs were identified to have upregulated expression, including Snora73b, Klk1b22 and Rnu3a, while the expression levels of 180 lncRNAs and 732 mRNAs were downregulated in CRYBB2 KO mice, including Snord82, Snhg9 and Foxn3. This lncRNA and mRNA expression profile of mice with CRYBB2 KO provides a basis for studying the genetic mechanisms of cataract progression.

Impaired revascularization in a mouse model of type 2 diabetes is associated with dysregulation of a complex angiogenic-regulatory network.

PubMed

Schiekofer, Stephan; Galasso, Gennaro; Sato, Kaori; Kraus, Benjamin J; Walsh, Kenneth

2005-08-01

Diabetes is a risk factor for the development of cardiovascular diseases associated with impaired angiogenesis or increased endothelial cell apoptosis. Here it is shown that angiogenic repair of ischemic hindlimbs was impaired in Lepr(db/db) mice, a leptin receptor-deficient model of diabetes, compared with wild-type (WT) C57BL/6 mice, as evaluated by laser Doppler flow and capillary density analyses. To identify molecular targets associated with this disease process, hindlimb cDNA expression profiles were created from adductor muscle of Lepr(db/db) and WT mice before and after hindlimb ischemia using Affymetrix GeneChip Mouse Expression Set microarrays. The expression patterns of numerous angiogenesis-related proteins were altered in Lepr(db/db) versus WT mice after ischemic injury. These transcripts included neuropilin-1, vascular endothelial growth factor-A, placental growth factor, elastin, and matrix metalloproteinases implicated in blood vessel growth and maintenance of vessel wall integrity. These data illustrate that impaired ischemia-induced neovascularization in type 2 diabetes is associated with the dysregulation of a complex angiogenesis-regulatory network.

Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression.

PubMed

Lemieux, Sébastien

2006-08-25

The identification of differentially expressed genes (DEGs) from Affymetrix GeneChips arrays is currently done by first computing expression levels from the low-level probe intensities, then deriving significance by comparing these expression levels between conditions. The proposed PL-LM (Probe-Level Linear Model) method implements a linear model applied on the probe-level data to directly estimate the treatment effect. A finite mixture of Gaussian components is then used to identify DEGs using the coefficients estimated by the linear model. This approach can readily be applied to experimental design with or without replication. On a wholly defined dataset, the PL-LM method was able to identify 75% of the differentially expressed genes within 10% of false positives. This accuracy was achieved both using the three replicates per conditions available in the dataset and using only one replicate per condition. The method achieves, on this dataset, a higher accuracy than the best set of tools identified by the authors of the dataset, and does so using only one replicate per condition.

Wnt/β-catenin signaling pathway inhibits the proliferation and apoptosis of U87 glioma cells via different mechanisms

PubMed Central

Gao, Liyang; Chen, Bing; Li, Jinhong; Yang, Fan; Cen, Xuecheng; Liao, Zhuangbing; Long, Xiao’ao

2017-01-01

The Wnt signaling pathway is necessary for the development of the central nervous system and is associated with tumorigenesis in various cancers. However, the mechanism of the Wnt signaling pathway in glioma cells has yet to be elucidated. Small-molecule Wnt modulators such as ICG-001 and AZD2858 were used to inhibit and stimulate the Wnt/β-catenin signaling pathway. Techniques including cell proliferation assay, colony formation assay, Matrigel cell invasion assay, cell cycle assay and Genechip microarray were used. Gene Ontology Enrichment Analysis and Gene Set Enrichment Analysis have enriched many biological processes and signaling pathways. Both the inhibiting and stimulating Wnt/β-catenin signaling pathways could influence the cell cycle, moreover, reduce the proliferation and survival of U87 glioma cells. However, Affymetrix expression microarray indicated that biological processes and networks of signaling pathways between stimulating and inhibiting the Wnt/β-catenin signaling pathway largely differ. We propose that Wnt/β-catenin signaling pathway might prove to be a valuable therapeutic target for glioma. PMID:28837560

Transcriptomic data analysis and differential gene expression of antioxidant pathways in king penguin juveniles (Aptenodytes patagonicus) before and after acclimatization to marine life.

PubMed

Rey, Benjamin; Dégletagne, Cyril; Duchamp, Claude

2016-12-01

In this article, we present differentially expressed gene profiles in the pectoralis muscle of wild juvenile king penguins that were either naturally acclimated to cold marine environment or experimentally immersed in cold water as compared with penguin juveniles that never experienced cold water immersion. Transcriptomic data were obtained by hybridizing penguins total cDNA on Affymetrix GeneChip Chicken Genome arrays and analyzed using maxRS algorithm , " Transcriptome analysis in non-model species: a new method for the analysis of heterologous hybridization on microarrays " (Dégletagne et al., 2010) [1] . We focused on genes involved in multiple antioxidant pathways. For better clarity, these differentially expressed genes were clustered into six functional groups according to their role in controlling redox homeostasis. The data are related to a comprehensive research study on the ontogeny of antioxidant functions in king penguins, "Hormetic response triggers multifaceted anti-oxidant strategies in immature king penguins (Aptenodytes patagonicus)" (Rey et al., 2016) [2] . The raw microarray dataset supporting the present analyses has been deposited at the Gene Expression Omnibus (GEO) repository under accessions GEO: GSE17725 and GEO: GSE82344.

Mutation spectrum in BBS genes guided by homozygosity mapping in an Indian cohort.

PubMed

Sathya Priya, C; Sen, P; Umashankar, V; Gupta, N; Kabra, M; Kumaramanickavel, G; Stoetzel, C; Dollfus, H; Sripriya, S

2015-02-01

Bardet-Biedl syndrome (BBS), a ciliopathy disorder with pleiotropic effect manifests primarily as retinal degeneration along with renal insufficiency, polydactyly and obesity. In this study, we have performed homozygosity mapping using NspI 250K affymetrix gene chip followed by mutation screening of the candidate genes located in the homozygous blocks. These regions are prioritized based on the block length and candidature of the genes in BBS and other ciliopathies. Gene alterations in known BBS (22) and other ciliopathy genes such as ALMS1 (2) were seen in 24 of 30 families (80%). Mutations in BBS3 gene, inclusive of a novel recurrent mutation (p.I91T) accounted for 18% of the identified variations. Disease associated polymorphisms p.S70N (BBS2), rs1545 and rs1547 (BBS6) were also observed. This is the first study in Indian BBS patients and homozygosity mapping has proved to be an effective tool in prioritizing the candidate genes in consanguineous pedigrees. The study reveals a different mutation profile in the ciliopathy genes in Indian population and implication of novel loci/genes in 20% of the study group. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Gene profile in the spleen under massive partial hepatectomy using complementary DNA microarray and pathway analysis.

PubMed

Arakawa, Yusuke; Shimada, Mitsuo; Utsunomiya, Tohru; Imura, Satoru; Morine, Yuji; Ikemoto, Tetsuya; Mori, Hiroki; Kanamoto, Mami; Iwahashi, Shuichi; Saito, Yu; Takasu, Chie

2014-08-01

In general, the spleen is one of the abdominal organs connected by the portal system, and a splenectomy improves hepatic functions in the settings of partial hepatectomy (Hx) for portal hypertensive cases or living donor liver transplantation with excessive portal vein flow. Those precise mechanisms remain still unclear; therefore, we investigated the DNA expression profile in the spleen after 90% Hx in rats using complementary DNA microarray and pathway analysis. Messenger RNAs (mRNAs) were prepared from three rat spleens at each time point (0, 3, and 6 h after 90% Hx). Using the gene chip, mRNA was hybridized to Affymetrix GeneChip Rat Genome 230 2.0 Array (Affymetrix®) and pathway analysis was done with Ingenuity Pathway Analysis (IPA®). We determined the 3-h or 6-h/0-h ratio to assess the influence of Hx, and cut-off values were set at more than 2.0-fold or less than 1/2 (0.5)-fold. Chemokine activity-related genes including Cxcl1 (GRO1) and Cxcl2 (MIP-2) related pathway were upregulated in the spleen. Also, immediate early response genes including early growth response-1 (EGR1), FBJ murine osteosarcoma (FOS) and activating transcription factor 3 (ATF3) related pathway were upregulated in the spleen. We concluded that in the spleen the expression of numerous inflammatory-related genes would occur after 90% Hx. The spleen could take a harmful role and provide a negative impact during post Hx phase due to the induction of chemokine and transcription factors including GRO1 and EGR1. © 2014 Journal of Gastroenterology and Hepatology Foundation and Wiley Publishing Asia Pty Ltd.

Development of a High-Throughput Resequencing Array for the Detection of Pathogenic Mutations in Osteogenesis Imperfecta

PubMed Central

Wang, Yao; Cui, Yazhou; Zhou, Xiaoyan; Han, Jinxiang

2015-01-01

Objective Osteogenesis imperfecta (OI) is a rare inherited skeletal disease, characterized by bone fragility and low bone density. The mutations in this disorder have been widely reported to be on various exonal hotspots of the candidate genes, including COL1A1, COL1A2, CRTAP, LEPRE1, and FKBP10, thus creating a great demand for precise genetic tests. However, large genome sizes make the process daunting and the analyses, inefficient and expensive. Therefore, we aimed at developing a fast, accurate, efficient, and cheaper sequencing platform for OI diagnosis; and to this end, use of an advanced array-based technique was proposed. Method A CustomSeq Affymetrix Resequencing Array was established for high-throughput sequencing of five genes simultaneously. Genomic DNA extraction from 13 OI patients and 85 normal controls and amplification using long-range PCR (LR-PCR) were followed by DNA fragmentation and chip hybridization, according to standard Affymetrix protocols. Hybridization signals were determined using GeneChip Sequence Analysis Software (GSEQ). To examine the feasibility, the outcome from new resequencing approach was validated by conventional capillary sequencing method. Result Overall call rates using resequencing array was 96–98% and the agreement between microarray and capillary sequencing was 99.99%. 11 out of 13 OI patients with pathogenic mutations were successfully detected by the chip analysis without adjustment, and one mutation could also be identified using manual visual inspection. Conclusion A high-throughput resequencing array was developed that detects the disease-associated mutations in OI, providing a potential tool to facilitate large-scale genetic screening for OI patients. Through this method, a novel mutation was also found. PMID:25742658

Mismatch and G-Stack Modulated Probe Signals on SNP Microarrays

PubMed Central

Binder, Hans; Fasold, Mario; Glomb, Torsten

2009-01-01

Background Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates. Methodology/Principal Findings The probe design of GeneChip SNP arrays enables us to disentangle different sources of intensity modulations such as the number of mismatches per duplex, matched and mismatched base pairings including nearest and next-nearest neighbors and their position along the probe sequence. The effect of probe sequence was estimated in terms of triple-motifs with central matches and mismatches which include all 256 combinations of possible base pairings. The probe/target interactions on the chip can be decomposed into nearest neighbor contributions which correlate well with free energy terms of DNA/DNA-interactions in solution. The effect of mismatches is about twice as large as that of canonical pairings. Runs of guanines (G) and the particular type of mismatched pairings formed in cross-allelic probe/target duplexes constitute sources of systematic biases of the probe signals with consequences for genotyping and copy number estimates. The poly-G effect seems to be related to the crowded arrangement of probes which facilitates complex formation of neighboring probes with at minimum three adjacent G's in their sequence. Conclusions The applied method of “triple-averaging” represents a model-free approach to estimate the mean intensity contributions of different sequence motifs which can be applied in calibration algorithms to correct signal values for sequence effects. Rules for appropriate sequence corrections are suggested. PMID:19924253

GWAS and admixture mapping identify different asthma-associated loci in Latinos: The GALA II Study

PubMed Central

Galanter, Joshua M; Gignoux, Christopher R; Torgerson, Dara G; Roth, Lindsey A; Eng, Celeste; Oh, Sam S; Nguyen, Elizabeth A; Drake, Katherine A; Huntsman, Scott; Hu, Donglei; Sen, Saunak; Davis, Adam; Farber, Harold J.; Avila, Pedro C.; Brigino-Buenaventura, Emerita; LeNoir, Michael A.; Meade, Kelley; Serebrisky, Denise; Borrell, Luisa N; Rodríguez-Cintrón, William; Estrada, Andres Moreno; Mendoza, Karla Sandoval; Winkler, Cheryl A.; Klitz, William; Romieu, Isabelle; London, Stephanie J.; Gilliland, Frank; Martinez, Fernando; Bustamante, Carlos; Williams, L Keoki; Kumar, Rajesh; Rodríguez-Santana, José R.; Burchard, and Esteban G.

2013-01-01

Background Asthma is a complex disease with both genetic and environmental causes. Genome-wide association studies of asthma have mostly involved European populations and replication of positive associations has been inconsistent. Objective To identify asthma-associated genes in a large Latino population with genome-wide association analysis and admixture mapping. Methods Latino children with asthma (n = 1,893) and healthy controls (n = 1,881) were recruited from five sites in the United States: Puerto Rico, New York, Chicago, Houston, and the San Francisco Bay Area. Subjects were genotyped on an Affymetrix World Array IV chip. We performed genome-wide association and admixture mapping to identify asthma-associated loci. Results We identified a significant association between ancestry and asthma at 6p21 (lowest p-value: rs2523924, p < 5 × 10−6). This association replicates in a meta-analysis of the EVE Asthma Consortium (p = 0.01). Fine mapping of the region in this study and the EVE Asthma Consortium suggests an association between PSORS1C1 and asthma. We confirmed the strong allelic association between the 17q21 asthma in Latinos (IKZF3, lowest p-value: rs90792, OR: 0.67, 95% CI 0.61 – 0.75, p = 6 × 10−13) and replicated associations in several genes that had previously been associated with asthma in genome-wide association studies. Conclusions Admixture mapping and genome-wide association are complementary techniques that provide evidence for multiple asthma-associated loci in Latinos. Admixture mapping identifies a novel locus on 6p21 that replicates in a meta-analysis of several Latino populations, while genome-wide association confirms the previously identified locus on 17q21. PMID:24406073

GeneChip Expression Profiling Reveals the Alterations of Energy Metabolism Related Genes in Osteocytes under Large Gradient High Magnetic Fields

PubMed Central

Wang, Yang; Chen, Zhi-Hao; Yin, Chun; Ma, Jian-Hua; Li, Di-Jie; Zhao, Fan; Sun, Yu-Long; Hu, Li-Fang; Shang, Peng; Qian, Ai-Rong

2015-01-01

The diamagnetic levitation as a novel ground-based model for simulating a reduced gravity environment has recently been applied in life science research. In this study a specially designed superconducting magnet with a large gradient high magnetic field (LG-HMF), which can provide three apparent gravity levels (μ-g, 1-g, and 2-g), was used to simulate a space-like gravity environment. Osteocyte, as the most important mechanosensor in bone, takes a pivotal position in mediating the mechano-induced bone remodeling. In this study, the effects of LG-HMF on gene expression profiling of osteocyte-like cell line MLO-Y4 were investigated by Affymetrix DNA microarray. LG-HMF affected osteocyte gene expression profiling. Differentially expressed genes (DEGs) and data mining were further analyzed by using bioinfomatic tools, such as DAVID, iReport. 12 energy metabolism related genes (PFKL, AK4, ALDOC, COX7A1, STC1, ADM, CA9, CA12, P4HA1, APLN, GPR35 and GPR84) were further confirmed by real-time PCR. An integrated gene interaction network of 12 DEGs was constructed. Bio-data mining showed that genes involved in glucose metabolic process and apoptosis changed notablly. Our results demostrated that LG-HMF affected the expression of energy metabolism related genes in osteocyte. The identification of sensitive genes to special environments may provide some potential targets for preventing and treating bone loss or osteoporosis. PMID:25635858

GeneChip expression profiling reveals the alterations of energy metabolism related genes in osteocytes under large gradient high magnetic fields.

PubMed

Wang, Yang; Chen, Zhi-Hao; Yin, Chun; Ma, Jian-Hua; Li, Di-Jie; Zhao, Fan; Sun, Yu-Long; Hu, Li-Fang; Shang, Peng; Qian, Ai-Rong

2015-01-01

The diamagnetic levitation as a novel ground-based model for simulating a reduced gravity environment has recently been applied in life science research. In this study a specially designed superconducting magnet with a large gradient high magnetic field (LG-HMF), which can provide three apparent gravity levels (μ-g, 1-g, and 2-g), was used to simulate a space-like gravity environment. Osteocyte, as the most important mechanosensor in bone, takes a pivotal position in mediating the mechano-induced bone remodeling. In this study, the effects of LG-HMF on gene expression profiling of osteocyte-like cell line MLO-Y4 were investigated by Affymetrix DNA microarray. LG-HMF affected osteocyte gene expression profiling. Differentially expressed genes (DEGs) and data mining were further analyzed by using bioinfomatic tools, such as DAVID, iReport. 12 energy metabolism related genes (PFKL, AK4, ALDOC, COX7A1, STC1, ADM, CA9, CA12, P4HA1, APLN, GPR35 and GPR84) were further confirmed by real-time PCR. An integrated gene interaction network of 12 DEGs was constructed. Bio-data mining showed that genes involved in glucose metabolic process and apoptosis changed notablly. Our results demostrated that LG-HMF affected the expression of energy metabolism related genes in osteocyte. The identification of sensitive genes to special environments may provide some potential targets for preventing and treating bone loss or osteoporosis.

Microarray-assisted fine-mapping of quantitative trait loci for cold tolerance in rice.

PubMed

Liu, Fengxia; Xu, Wenying; Song, Qian; Tan, Lubin; Liu, Jiayong; Zhu, Zuofeng; Fu, Yongcai; Su, Zhen; Sun, Chuanqing

2013-05-01

Many important agronomic traits, including cold stress resistance, are complex and controlled by quantitative trait loci (QTLs). Isolation of these QTLs will greatly benefit the agricultural industry but it is a challenging task. This study explored an integrated strategy by combining microarray with QTL-mapping in order to identify cold-tolerant QTLs from a cold-tolerant variety IL112 at early-seedling stage. All the early seedlings of IL112 survived normally for 9 d at 4-5°C, while Guichao2 (GC2), an indica cultivar, died after 4 d under the same conditions. Using the F2:3 population derived from the progeny of GC2 and IL112, we identified seven QTLs for cold tolerance. Furthermore, we performed Affymetrix rice whole-genome array hybridization and obtained the expression profiles of IL112 and GC2 under both low-temperature and normal conditions. Four genes were selected as cold QTL-related candidates, based on microarray data mining and QTL-mapping. One candidate gene, LOC_Os07g22494, was shown to be highly associated with cold tolerance in a number of rice varieties and in the F2:3 population, and its overexpression transgenic rice plants displayed strong tolerance to low temperature at early-seedling stage. The results indicated that overexpression of this gene (LOC_Os07g22494) could increase cold tolerance in rice seedlings. Therefore, this study provides a promising strategy for identifying candidate genes in defined QTL regions.

Alterations of LKB1 and KRAS and risk of brain metastasis: comprehensive characterization by mutation analysis, copy number, and gene expression in non-small-cell lung carcinoma.

PubMed

Zhao, Ni; Wilkerson, Matthew D; Shah, Usman; Yin, Xiaoying; Wang, Anyou; Hayward, Michele C; Roberts, Patrick; Lee, Carrie B; Parsons, Alden M; Thorne, Leigh B; Haithcock, Benjamin E; Grilley-Olson, Juneko E; Stinchcombe, Thomas E; Funkhouser, William K; Wong, Kwok-Kin; Sharpless, Norman E; Hayes, D Neil

2014-11-01

Brain metastases are one of the most malignant complications of lung cancer and constitute a significant cause of cancer related morbidity and mortality worldwide. Recent years of investigation suggested a role of LKB1 in NSCLC development and progression, in synergy with KRAS alteration. In this study, we systematically analyzed how LKB1 and KRAS alteration, measured by mutation, gene expression (GE) and copy number (CN), are associated with brain metastasis in NSCLC. Patients treated at University of North Carolina Hospital from 1990 to 2009 with NSCLC provided frozen, surgically extracted tumors for analysis. GE was measured using Agilent 44,000 custom-designed arrays, CN was assessed by Affymetrix GeneChip Human Mapping 250K Sty Array or the Genome-Wide Human SNP Array 6.0 and gene mutation was detected using ABI sequencing. Integrated analysis was conducted to assess the relationship between these genetic markers and brain metastasis. A model was proposed for brain metastasis prediction using these genetic measurements. 17 of the 174 patients developed brain metastasis. LKB1 wild type tumors had significantly higher LKB1 CN (p<0.001) and GE (p=0.002) than the LKB1 mutant group. KRAS wild type tumors had significantly lower KRAS GE (p<0.001) and lower CN, although the latter failed to be significant (p=0.295). Lower LKB1 CN (p=0.039) and KRAS mutation (p=0.007) were significantly associated with more brain metastasis. The predictive model based on nodal (N) stage, patient age, LKB1 CN and KRAS mutation had a good prediction accuracy, with area under the ROC curve of 0.832 (p<0.001). LKB1 CN in combination with KRAS mutation predicted brain metastasis in NSCLC. Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Revisiting adverse effects of cross-hybridization in Affymetrix gene expression data: do they matter for correlation analysis?

PubMed

Klebanov, Lev; Chen, Linlin; Yakovlev, Andrei

2007-11-07

This work was undertaken in response to a recently published paper by Okoniewski and Miller (BMC Bioinformatics 2006, 7: Article 276). The authors of that paper came to the conclusion that the process of multiple targeting in short oligonucleotide microarrays induces spurious correlations and this effect may deteriorate the inference on correlation coefficients. The design of their study and supporting simulations cast serious doubt upon the validity of this conclusion. The work by Okoniewski and Miller drove us to revisit the issue by means of experimentation with biological data and probabilistic modeling of cross-hybridization effects. We have identified two serious flaws in the study by Okoniewski and Miller: (1) The data used in their paper are not amenable to correlation analysis; (2) The proposed simulation model is inadequate for studying the effects of cross-hybridization. Using two other data sets, we have shown that removing multiply targeted probe sets does not lead to a shift in the histogram of sample correlation coefficients towards smaller values. A more realistic approach to mathematical modeling of cross-hybridization demonstrates that this process is by far more complex than the simplistic model considered by the authors. A diversity of correlation effects (such as the induction of positive or negative correlations) caused by cross-hybridization can be expected in theory but there are natural limitations on the ability to provide quantitative insights into such effects due to the fact that they are not directly observable. The proposed stochastic model is instrumental in studying general regularities in hybridization interaction between probe sets in microarray data. As the problem stands now, there is no compelling reason to believe that multiple targeting causes a large-scale effect on the correlation structure of Affymetrix gene expression data. Our analysis suggests that the observed long-range correlations in microarray data are of a

Molecular genetic analysis of retinitis pigmentosa in Indonesia using genome-wide homozygosity mapping

PubMed Central

Siemiatkowska, Anna M.; Arimadyo, Kentar; Moruz, Luminita M.; Astuti, Galuh D.N.; de Castro-Miro, Marta; Zonneveld, Marijke N.; Strom, Tim M.; de Wijs, Ilse J.; Hoefsloot, Lies H.; Faradz, Sultana M.H.; Cremers, Frans P.M.; den Hollander, Anneke I.

2011-01-01

Purpose Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous retinal disorder. Despite tremendous knowledge about the genes involved in RP, little is known about the genetic causes of RP in Indonesia. Here, we aim to identify the molecular genetic causes underlying RP in a small cohort of Indonesian patients, using genome-wide homozygosity mapping. Methods DNA samples from affected and healthy individuals from 14 Indonesian families segregating autosomal recessive, X-linked, or isolated RP were collected. Homozygosity mapping was conducted using Illumina 6k or Affymetrix 5.0 single nucleotide polymorphism (SNP) arrays. Known autosomal recessive RP (arRP) genes residing in homozygous regions and X-linked RP genes were sequenced for mutations. Results In ten out of the 14 families, homozygous regions were identified that contained genes known to be involved in the pathogenesis of RP. Sequence analysis of these genes revealed seven novel homozygous mutations in ATP-binding cassette, sub-family A, member 4 (ABCA4), crumbs homolog 1 (CRB1), eyes shut homolog (Drosophila) (EYS), c-mer proto-oncogene tyrosine kinase (MERTK), nuclear receptor subfamily 2, group E, member 3 (NR2E3) and phosphodiesterase 6A, cGMP-specific, rod, alpha (PDE6A), all segregating in the respective families. No mutations were identified in the X-linked genes retinitis pigmentosa GTPase regulator (RPGR) and retinitis pigmentosa 2 (X-linked recessive; RP2). Conclusions Homozygosity mapping is a powerful tool to identify the genetic defects underlying RP in the Indonesian population. Compared to studies involving patients from other populations, the same genes appear to be implicated in the etiology of recessive RP in Indonesia, although all mutations that were discovered are novel and as such may be unique for this population. PMID:22128245

Release of (and lessons learned from mining) a pioneering large toxicogenomics database.

PubMed

Sandhu, Komal S; Veeramachaneni, Vamsi; Yao, Xiang; Nie, Alex; Lord, Peter; Amaratunga, Dhammika; McMillian, Michael K; Verheyen, Geert R

2015-07-01

We release the Janssen Toxicogenomics database. This rat liver gene-expression database was generated using Codelink microarrays, and has been used over the past years within Janssen to derive signatures for multiple end points and to classify proprietary compounds. The release consists of gene-expression responses to 124 compounds, selected to give a broad coverage of liver-active compounds. A selection of the compounds were also analyzed on Affymetrix microarrays. The release includes results of an in-house reannotation pipeline to Entrez gene annotations, to classify probes into different confidence classes. High confidence unambiguously annotated probes were used to create gene-level data which served as starting point for cross-platform comparisons. Connectivity map-based similarity methods show excellent agreement between Codelink and Affymetrix runs of the same samples. We also compared our dataset with the Japanese Toxicogenomics Project and observed reasonable agreement, especially for compounds with stronger gene signatures. We describe an R-package containing the gene-level data and show how it can be used for expression-based similarity searches. Comparing the same biological samples run on the Affymetrix and the Codelink platform, good correspondence is observed using connectivity mapping approaches. As expected, this correspondence is smaller when the data are compared with an independent dataset such as TG-GATE. We hope that this collection of gene-expression profiles will be incorporated in toxicogenomics pipelines of users.

Gene expression profiling during asexual development of the late blight pathogen Phytophthora infestans reveals a highly dynamic transcriptome.

PubMed

Judelson, Howard S; Ah-Fong, Audrey M V; Aux, George; Avrova, Anna O; Bruce, Catherine; Cakir, Cahid; da Cunha, Luis; Grenville-Briggs, Laura; Latijnhouwers, Maita; Ligterink, Wilco; Meijer, Harold J G; Roberts, Samuel; Thurber, Carrie S; Whisson, Stephen C; Birch, Paul R J; Govers, Francine; Kamoun, Sophien; van West, Pieter; Windass, John

2008-04-01

Much of the pathogenic success of Phytophthora infestans, the potato and tomato late blight agent, relies on its ability to generate from mycelia large amounts of sporangia, which release zoospores that encyst and form infection structures. To better understand these stages, Affymetrix GeneChips based on 15,650 unigenes were designed and used to profile the life cycle. Approximately half of P. infestans genes were found to exhibit significant differential expression between developmental transitions, with approximately (1)/(10) being stage-specific and most changes occurring during zoosporogenesis. Quantitative reverse-transcription polymerase chain reaction assays confirmed the robustness of the array results and showed that similar patterns of differential expression were obtained regardless of whether hyphae were from laboratory media or infected tomato. Differentially expressed genes encode potential cellular regulators, especially protein kinases; metabolic enzymes such as those involved in glycolysis, gluconeogenesis, or the biosynthesis of amino acids or lipids; regulators of DNA synthesis; structural proteins, including predicted flagellar proteins; and pathogenicity factors, including cell-wall-degrading enzymes, RXLR effector proteins, and enzymes protecting against plant defense responses. Curiously, some stage-specific transcripts do not appear to encode functional proteins. These findings reveal many new aspects of oomycete biology, as well as potential targets for crop protection chemicals.

Transcriptome analysis reveals that multidrug efflux genes are upregulated to protect Pseudomonas aeruginosa from pentachlorophenol stress.

PubMed

Muller, Jocelyn Fraga; Stevens, Ann M; Craig, Johanna; Love, Nancy G

2007-07-01

Through chemical contamination of natural environments, microbial communities are exposed to many different types of chemical stressors; however, research on whole-genome responses to this contaminant stress is limited. This study examined the transcriptome response of a common soil bacterium, Pseudomonas aeruginosa, to the common environmental contaminant pentachlorophenol (PCP). Cells were grown in chemostats at a low growth rate to obtain substrate-limited, steady-state, balanced-growth conditions. The PCP stress was administered as a continuous increase in concentration, and samples taken over time were examined for physiological function changes with whole-cell acetate uptake rates (WAURs) and cell viability and for gene expression changes by Affymetrix GeneChip technology and real-time reverse transcriptase PCR. Cell viability, measured by heterotrophic plate counts, showed a moderately steady decrease after exposure to the stressor, but WAURs did not change in response to PCP. In contrast to the physiological data, the microarray data showed significant changes in the expression of several genes. In particular, genes coding for multidrug efflux pumps, including MexAB-OprM, were strongly upregulated. The upregulation of these efflux pumps protected the cells from the potentially toxic effects of PCP, allowing the physiological whole-cell function to remain constant.

Transcriptional Profiling of Canker-Resistant Transgenic Sweet Orange (Citrus sinensis Osbeck) Constitutively Overexpressing a Spermidine Synthase Gene

PubMed Central

Fu, Xing-Zheng; Liu, Ji-Hong

2013-01-01

Citrus canker disease caused by Xanthomonas citri subsp. citri (Xcc) is one of the most devastating diseases affecting the citrus industry worldwide. In our previous study, the canker-resistant transgenic sweet orange (Citrus sinensis Osbeck) plants were produced via constitutively overexpressing a spermidine synthase. To unravel the molecular mechanisms underlying Xcc resistance of the transgenic plants, in the present study global transcriptional profiling was compared between untransformed line (WT) and the transgenic line (TG9) by hybridizing with Affymetrix Citrus GeneChip. In total, 666 differentially expressed genes (DEGs) were identified, 448 upregulated, and 218 downregulated. The DEGs were classified into 33 categories after Gene ontology (GO) annotation, in which 68 genes are in response to stimulus and involved in immune system process, 12 genes are related to cell wall, and 13 genes belong to transcription factors. These genes and those related to starch and sucrose metabolism, glutathione metabolism, biosynthesis of phenylpropanoids, and plant hormones were hypothesized to play major roles in the canker resistance of TG9. Semiquantitative RT-PCR analysis showed that the transcript levels of several candidate genes in TG9 were significantly higher than in WT both before and after Xcc inoculation, indicating their potential association with canker disease. PMID:23509803

Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis1[w

PubMed Central

Czechowski, Tomasz; Stitt, Mark; Altmann, Thomas; Udvardi, Michael K.; Scheible, Wolf-Rüdiger

2005-01-01

Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a diverse set of 20 cDNA samples. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future. PMID:16166256

Reverse engineering and analysis of large genome-scale gene networks

PubMed Central

Aluru, Maneesha; Zola, Jaroslaw; Nettleton, Dan; Aluru, Srinivas

2013-01-01

Reverse engineering the whole-genome networks of complex multicellular organisms continues to remain a challenge. While simpler models easily scale to large number of genes and gene expression datasets, more accurate models are compute intensive limiting their scale of applicability. To enable fast and accurate reconstruction of large networks, we developed Tool for Inferring Network of Genes (TINGe), a parallel mutual information (MI)-based program. The novel features of our approach include: (i) B-spline-based formulation for linear-time computation of MI, (ii) a novel algorithm for direct permutation testing and (iii) development of parallel algorithms to reduce run-time and facilitate construction of large networks. We assess the quality of our method by comparison with ARACNe (Algorithm for the Reconstruction of Accurate Cellular Networks) and GeneNet and demonstrate its unique capability by reverse engineering the whole-genome network of Arabidopsis thaliana from 3137 Affymetrix ATH1 GeneChips in just 9 min on a 1024-core cluster. We further report on the development of a new software Gene Network Analyzer (GeNA) for extracting context-specific subnetworks from a given set of seed genes. Using TINGe and GeNA, we performed analysis of 241 Arabidopsis AraCyc 8.0 pathways, and the results are made available through the web. PMID:23042249

Validation of endogenous internal real-time PCR controls in renal tissues.

PubMed

Cui, Xiangqin; Zhou, Juling; Qiu, Jing; Johnson, Martin R; Mrug, Michal

2009-01-01

Endogenous internal controls ('reference' or 'housekeeping' genes) are widely used in real-time PCR (RT-PCR) analyses. Their use relies on the premise of consistently stable expression across studied experimental conditions. Unfortunately, none of these controls fulfills this premise across a wide range of experimental conditions; consequently, none of them can be recommended for universal use. To determine which endogenous RT-PCR controls are suitable for analyses of renal tissues altered by kidney disease, we studied the expression of 16 commonly used 'reference genes' in 7 mildly and 7 severely affected whole kidney tissues from a well-characterized cystic kidney disease model. Expression levels of these 16 genes, determined by TaqMan RT-PCR analyses and Affymetrix GeneChip arrays, were normalized and tested for overall variance and equivalence of the means. Both statistical approaches and both TaqMan- and GeneChip-based methods converged on 3 out of the 4 top-ranked genes (Ppia, Gapdh and Pgk1) that had the most constant expression levels across the studied phenotypes. A combination of the top-ranked genes will provide a suitable endogenous internal control for similar studies of kidney tissues across a wide range of disease severity. Copyright 2009 S. Karger AG, Basel.

Kidney Transplant Rejection and Tissue Injury by Gene Profiling of Biopsies and Peripheral Blood Lymphocytes

PubMed Central

Flechner, Stuart M.; Kurian, Sunil M.; Head, Steven R.; Sharp, Starlette M.; Whisenant, Thomas C.; Zhang, Jie; Chismar, Jeffrey D.; Horvath, Steve; Mondala, Tony; Gilmartin, Timothy; Cook, Daniel J.; Kay, Steven A.; Walker, John R.; Salomon, Daniel R.

2007-01-01

A major challenge for kidney transplantation is balancing the need for immunosuppression to prevent rejection, while minimizing drug-induced toxicities. We used DNA microarrays (HG-U95Av2 GeneChips, Affymetrix) to determine gene expression profiles for kidney biopsies and peripheral blood lymphocytes (PBLs) in transplant patients including normal donor kidneys, well-functioning transplants without rejection, kidneys undergoing acute rejection, and transplants with renal dysfunction without rejection. We developed a data analysis schema based on expression signal determination, class comparison and prediction, hierarchical clustering, statistical power analysis and real-time quantitative PCR validation. We identified distinct gene expression signatures for both biopsies and PBLs that correlated significantly with each of the different classes of transplant patients. This is the most complete report to date using commercial arrays to identify unique expression signatures in transplant biopsies distinguishing acute rejection, acute dysfunction without rejection and well-functioning transplants with no rejection history. We demonstrate for the first time the successful application of high density DNA chip analysis of PBL as a diagnostic tool for transplantation. The significance of these results, if validated in a multicenter prospective trial, would be the establishment of a metric based on gene expression signatures for monitoring the immune status and immunosuppression of transplanted patients. PMID:15307835

Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments.

PubMed

Kitchen, Robert R; Sabine, Vicky S; Simen, Arthur A; Dixon, J Michael; Bartlett, John M S; Sims, Andrew H

2011-12-01

Systematic processing noise, which includes batch effects, is very common in microarray experiments but is often ignored despite its potential to confound or compromise experimental results. Compromised results are most likely when re-analysing or integrating datasets from public repositories due to the different conditions under which each dataset is generated. To better understand the relative noise-contributions of various factors in experimental-design, we assessed several Illumina and Affymetrix datasets for technical variation between replicate hybridisations of Universal Human Reference (UHRR) and individual or pooled breast-tumour RNA. A varying degree of systematic noise was observed in each of the datasets, however in all cases the relative amount of variation between standard control RNA replicates was found to be greatest at earlier points in the sample-preparation workflow. For example, 40.6% of the total variation in reported expressions were attributed to replicate extractions, compared to 13.9% due to amplification/labelling and 10.8% between replicate hybridisations. Deliberate probe-wise batch-correction methods were effective in reducing the magnitude of this variation, although the level of improvement was dependent on the sources of noise included in the model. Systematic noise introduced at the chip, run, and experiment levels of a combined Illumina dataset were found to be highly dependent upon the experimental design. Both UHRR and pools of RNA, which were derived from the samples of interest, modelled technical variation well although the pools were significantly better correlated (4% average improvement) and better emulated the effects of systematic noise, over all probes, than the UHRRs. The effect of this noise was not uniform over all probes, with low GC-content probes found to be more vulnerable to batch variation than probes with a higher GC-content. The magnitude of systematic processing noise in a microarray experiment is variable

Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments

PubMed Central

2011-01-01

Background Systematic processing noise, which includes batch effects, is very common in microarray experiments but is often ignored despite its potential to confound or compromise experimental results. Compromised results are most likely when re-analysing or integrating datasets from public repositories due to the different conditions under which each dataset is generated. To better understand the relative noise-contributions of various factors in experimental-design, we assessed several Illumina and Affymetrix datasets for technical variation between replicate hybridisations of Universal Human Reference (UHRR) and individual or pooled breast-tumour RNA. Results A varying degree of systematic noise was observed in each of the datasets, however in all cases the relative amount of variation between standard control RNA replicates was found to be greatest at earlier points in the sample-preparation workflow. For example, 40.6% of the total variation in reported expressions were attributed to replicate extractions, compared to 13.9% due to amplification/labelling and 10.8% between replicate hybridisations. Deliberate probe-wise batch-correction methods were effective in reducing the magnitude of this variation, although the level of improvement was dependent on the sources of noise included in the model. Systematic noise introduced at the chip, run, and experiment levels of a combined Illumina dataset were found to be highly dependant upon the experimental design. Both UHRR and pools of RNA, which were derived from the samples of interest, modelled technical variation well although the pools were significantly better correlated (4% average improvement) and better emulated the effects of systematic noise, over all probes, than the UHRRs. The effect of this noise was not uniform over all probes, with low GC-content probes found to be more vulnerable to batch variation than probes with a higher GC-content. Conclusions The magnitude of systematic processing noise in a

Too much data, but little inter-changeability: a lesson learned from mining public data on tissue specificity of gene expression.

PubMed

Li, Shuyu; Li, Yiqun Helen; Wei, Tao; Su, Eric Wen; Duffin, Kevin; Liao, Birong

2006-10-25

The tissue expression pattern of a gene often provides an important clue to its potential role in a biological process. A vast amount of gene expression data have been and are being accumulated in public repository through different technology platforms. However, exploitations of these rich data sources remain limited in part due to issues of technology standardization. Our objective is to test the data comparability between SAGE and microarray technologies, through examining the expression pattern of genes under normal physiological states across variety of tissues. There are 42-54% of genes showing significant correlations in tissue expression patterns between SAGE and GeneChip, with 30-40% of genes whose expression patterns are positively correlated and 10-15% of genes whose expression patterns are negatively correlated at a statistically significant level (p = 0.05). Our analysis suggests that the discrepancy on the expression patterns derived from technology platforms is not likely from the heterogeneity of tissues used in these technologies, or other spurious correlations resulting from microarray probe design, abundance of genes, or gene function. The discrepancy can be partially explained by errors in the original assignment of SAGE tags to genes due to the evolution of sequence databases. In addition, sequence analysis has indicated that many SAGE tags and Affymetrix array probe sets are mapped to different splice variants or different sequence regions although they represent the same gene, which also contributes to the observed discrepancies between SAGE and array expression data. To our knowledge, this is the first report attempting to mine gene expression patterns across tissues using public data from different technology platforms. Unlike previous similar studies that only demonstrated the discrepancies between the two gene expression platforms, we carried out in-depth analysis to further investigate the cause for such discrepancies. Our study shows

Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle

PubMed Central

Ron, Micha; Israeli, Galit; Seroussi, Eyal; Weller, Joel I; Gregg, Jeffrey P; Shani, Moshe; Medrano, Juan F

2007-01-01

Background Many studies have found segregating quantitative trait loci (QTL) for milk production traits in different dairy cattle populations. However, even for relatively large effects with a saturated marker map the confidence interval for QTL location by linkage analysis spans tens of map units, or hundreds of genes. Combining mapping and arraying has been suggested as an approach to identify candidate genes. Thus, gene expression analysis in the mammary gland of genes positioned in the confidence interval of the QTL can bridge the gap between fine mapping and quantitative trait nucleotide (QTN) determination. Results We hybridized Affymetrix microarray (MG-U74v2), containing 12,488 murine probes, with RNA derived from mammary gland of virgin, pregnant, lactating and involuting C57BL/6J mice in a total of nine biological replicates. We combined microarray data from two additional studies that used the same design in mice with a total of 75 biological replicates. The same filtering and normalization was applied to each microarray data using GeneSpring software. Analysis of variance identified 249 differentially expressed probe sets common to the three experiments along the four developmental stages of puberty, pregnancy, lactation and involution. 212 genes were assigned to their bovine map positions through comparative mapping, and thus form a list of candidate genes for previously identified QTLs for milk production traits. A total of 82 of the genes showed mammary gland-specific expression with at least 3-fold expression over the median representing all tissues tested in GeneAtlas. Conclusion This work presents a web tool for candidate genes for QTL (cgQTL) that allows navigation between the map of bovine milk production QTL, potential candidate genes and their level of expression in mammary gland arrays and in GeneAtlas. Three out of four confirmed genes that affect QTL in livestock (ABCG2, DGAT1, GDF8, IGF2) were over expressed in the target organ. Thus, cg

Insights into significant pathways and gene interaction networks underlying breast cancer cell line MCF-7 treated with 17β-estradiol (E2).

PubMed

Huan, Jinliang; Wang, Lishan; Xing, Li; Qin, Xianju; Feng, Lingbin; Pan, Xiaofeng; Zhu, Ling

2014-01-01

Estrogens are known to regulate the proliferation of breast cancer cells and to alter their cytoarchitectural and phenotypic properties, but the gene networks and pathways by which estrogenic hormones regulate these events are only partially understood. We used global gene expression profiling by Affymetrix GeneChip microarray analysis, with KEGG pathway enrichment, PPI network construction, module analysis and text mining methods to identify patterns and time courses of genes that are either stimulated or inhibited by estradiol (E2) in estrogen receptor (ER)-positive MCF-7 human breast cancer cells. Of the genes queried on the Affymetrix Human Genome U133 plus 2.0 microarray, we identified 628 (12h), 852 (24h) and 880 (48 h) differentially expressed genes (DEGs) that showed a robust pattern of regulation by E2. From pathway enrichment analysis, we found out the changes of metabolic pathways of E2 treated samples at each time point. At 12h time point, the changes of metabolic pathways were mainly focused on pathways in cancer, focal adhesion, and chemokine signaling pathway. At 24h time point, the changes were mainly enriched in neuroactive ligand-receptor interaction, cytokine-cytokine receptor interaction and calcium signaling pathway. At 48 h time point, the significant pathways were pathways in cancer, regulation of actin cytoskeleton, cell adhesion molecules (CAMs), axon guidance and ErbB signaling pathway. Of interest, our PPI network analysis and module analysis found that E2 treatment induced enhancement of PRSS23 at the three time points and PRSS23 was in the central position of each module. Text mining results showed that the important genes of DEGs have relationship with signal pathways, such as ERbB pathway (AREG), Wnt pathway (NDP), MAPK pathway (NTRK3, TH), IP3 pathway (TRA@) and some transcript factors (TCF4, MAF). Our studies highlight the diverse gene networks and metabolic and cell regulatory pathways through which E2 operates to achieve its

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine).

PubMed

Wong, Darren C J; Sweetman, Crystal; Drew, Damian P; Ford, Christopher M

2013-12-16

Gene expression datasets in model plants such as Arabidopsis have contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine, Vitis vinifera. The new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the Affymetrix Vitis vinifera GeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and flavonoid biosynthesis

Transcriptional responses in thyroid tissues from rats treated with a tumorigenic and a non-tumorigenic triazole conazole fungicide.

PubMed

Hester, Susan D; Nesnow, Stephen

2008-03-15

Conazoles are azole-containing fungicides that are used in agriculture and medicine. Conazoles can induce follicular cell adenomas of the thyroid in rats after chronic bioassay. The goal of this study was to identify pathways and networks of genes that were associated with thyroid tumorigenesis through transcriptional analyses. To this end, we compared transcriptional profiles from tissues of rats treated with a tumorigenic and a non-tumorigenic conazole. Triadimefon, a rat thyroid tumorigen, and myclobutanil, which was not tumorigenic in rats after a 2-year bioassay, were administered in the feed to male Wistar/Han rats for 30 or 90 days similar to the treatment conditions previously used in their chronic bioassays. Thyroid gene expression was determined using high density Affymetrix GeneChips (Rat 230_2). Gene expression was analyzed by the Gene Set Expression Analyses method which clearly separated the tumorigenic treatments (tumorigenic response group (TRG)) from the non-tumorigenic treatments (non-tumorigenic response group (NRG)). Core genes from these gene sets were mapped to canonical, metabolic, and GeneGo processes and these processes compared across group and treatment time. Extensive analyses were performed on the 30-day gene sets as they represented the major perturbations. Gene sets in the 30-day TRG group had over representation of fatty acid metabolism, oxidation, and degradation processes (including PPARgamma and CYP involvement), and of cell proliferation responses. Core genes from these gene sets were combined into networks and found to possess signaling interactions. In addition, the core genes in each gene set were compared with genes known to be associated with human thyroid cancer. Among the genes that appeared in both rat and human data sets were: Acaca, Asns, Cebpg, Crem, Ddit3, Gja1, Grn, Jun, Junb, and Vegf. These genes were major contributors in the previously developed network from triadimefon-treated rat thyroids. It is postulated that

Prenatal stress-induced programming of genome-wide promoter DNA methylation in 5-HTT-deficient mice.

PubMed

Schraut, K G; Jakob, S B; Weidner, M T; Schmitt, A G; Scholz, C J; Strekalova, T; El Hajj, N; Eijssen, L M T; Domschke, K; Reif, A; Haaf, T; Ortega, G; Steinbusch, H W M; Lesch, K P; Van den Hove, D L

2014-10-21

The serotonin transporter gene (5-HTT/SLC6A4)-linked polymorphic region has been suggested to have a modulatory role in mediating effects of early-life stress exposure on psychopathology rendering carriers of the low-expression short (s)-variant more vulnerable to environmental adversity in later life. The underlying molecular mechanisms of this gene-by-environment interaction are not well understood, but epigenetic regulation including differential DNA methylation has been postulated to have a critical role. Recently, we used a maternal restraint stress paradigm of prenatal stress (PS) in 5-HTT-deficient mice and showed that the effects on behavior and gene expression were particularly marked in the hippocampus of female 5-Htt+/- offspring. Here, we examined to which extent these effects are mediated by differential methylation of DNA. For this purpose, we performed a genome-wide hippocampal DNA methylation screening using methylated-DNA immunoprecipitation (MeDIP) on Affymetrix GeneChip Mouse Promoter 1.0 R arrays. Using hippocampal DNA from the same mice as assessed before enabled us to correlate gene-specific DNA methylation, mRNA expression and behavior. We found that 5-Htt genotype, PS and their interaction differentially affected the DNA methylation signature of numerous genes, a subset of which showed overlap with the expression profiles of the corresponding transcripts. For example, a differentially methylated region in the gene encoding myelin basic protein (Mbp) was associated with its expression in a 5-Htt-, PS- and 5-Htt × PS-dependent manner. Subsequent fine-mapping of this Mbp locus linked the methylation status of two specific CpG sites to Mbp expression and anxiety-related behavior. In conclusion, hippocampal DNA methylation patterns and expression profiles of female prenatally stressed 5-Htt+/- mice suggest that distinct molecular mechanisms, some of which are promoter methylation-dependent, contribute to the behavioral effects of the 5-Htt

Changes in global gene expression profiles induced by HPV 16 E6 oncoprotein variants in cervical carcinoma C33-A cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zacapala-Gómez, Ana Elvira, E-mail: zak_ana@yahoo.com.mx; Del Moral-Hernández, Oscar, E-mail: odelmoralh@gmail.com; Villegas-Sepúlveda, Nicolás, E-mail: nvillega@cinvestav.mx

We analyzed the effects of the expression of HPV 16 E6 oncoprotein variants (AA-a, AA-c, E-A176/G350, E-C188/G350, E-G350), and the E-Prototype in global gene expression profiles in an in vitro model. E6 gene was cloned into an expression vector fused to GFP and was transfected in C33-A cells. Affymetrix GeneChip Human Transcriptome Array 2.0 platform was used to analyze the expression of over 245,000 coding transcripts. We found that HPV16 E6 variants altered the expression of 387 different genes in comparison with E-Prototype. The altered genes are involved in cellular processes related to the development of cervical carcinoma, such asmore » adhesion, angiogenesis, apoptosis, differentiation, cell cycle, proliferation, transcription and protein translation. Our results show that polymorphic changes in HPV16 E6 natural variants are sufficient to alter the overall gene expression profile in C33-A cells, explaining in part the observed differences in oncogenic potential of HPV16 variants. - Highlights: • Amino acid changes in HPV16 E6 variants modulate the transciption of specific genes. • This is the first comparison of global gene expression profile of HPV 16 E6 variants. • Each HPV 16 E6 variant appears to have its own molecular signature.« less

Similar Response Patterns to 5%Topical Minoxidil Foam in Frontal and Vertex Scalp of Men with Androgenetic Alopecia: A Microarray Analysis

PubMed Central

Mirmirani, P.; Consolo, M.; Oyetakin-White, P.; Baron, E.; Leahy, P.; Karnik, P.

2014-01-01

Summary Background There are regional variations in scalp hair miniaturization seen in androgenetic alopecia (AGA). Use of topical minoxidil can lead to reversal of miniaturization in the vertex scalp. However, its effects on other scalp regions are less well studied. Methods A placebo controlled double-blinded prospective pilot study of minoxidil topical foam 5% (MTF) vs placebo was conducted in sixteen healthy men ages 18-49 with Hamilton-Norwood type IV-V thinning. The subjects were asked to apply the treatment (active drug or placebo) to the scalp twice daily for eight weeks. Stereotactic scalp photographs were taken at the baseline and final visits to monitor global hair growth. Scalp biopsies were done at the leading edge of hair loss from the frontal and vertex scalp before and after treatment with MTF and placebo and microarray analysis was done using the Affymetrix GeneChip HG U133 Plus 2.0. Results Global stereotactic photographs showed that MTF induced hair growth in both the frontal and vertex scalp of AGA patients. Regional differences in gene expression profiles were observed before treatment. However, MTF treatment induced the expression of hair keratin associated genes and decreased the expression of epidermal differentiation complex (EDC) and inflammatory genes in both scalp regions. Conclusions These data suggest that MTF is effective in the treatment of both the frontal and vertex scalp of AGA patients. PMID:25204361

Molecular pathology of acute kidney injury in a choline-deficient model and fish oil protective effect.

PubMed

Denninghoff, Valeria; Ossani, Georgina; Uceda, Ana; Rugnone, Matias; Fernández, Elmer; Fresno, Cristóbal; González, German; Díaz, Maria Luisa; Avagnina, Alejandra; Elsner, Boris; Monserrat, Alberto

2014-04-01

The aim of this work was to investigate the potential protective effects of fish oil on the basis of kidney transcriptomic data on a nutritional experimental model. Male weanling Wistar rats were divided into four groups and fed choline-deficient (CD) and choline-supplemented (CS) diets with vegetable oil (VO) and menhaden oil (MO): CSVO, CDVO, CSMO and CDMO. Animals were killed after receiving the diets for 6 days. Total RNA was purified from the right kidney and hybridized to Affymetrix GeneChip Rat Gene 1.0 ST Array. Differentially expressed genes were analyzed. All CSVO, CSMO and CDMO rats showed no renal alterations, while all CDVO rats showed renal cortical necrosis. A thorough analysis of the differential expression between groups CSMO and CDMO was carried out. There were no differential genes for p < 0.01. The analysis of the differential expression between groups CSVO and CSMO revealed 32 genes, 11 were over-expressed and 21 were under-expressed in CSMO rats. This work was part of a large set of experiments and was used in a hypothesis-generating manner. The comprehensive analysis of genetic expression allowed confirming that menhaden oil has a protective effect on this nutritional experimental model and identifying 32 genes that could be responsible for that protection, including Gstp1. These results reveal that gene changes could play a role in renal injury.

Whole-genome transcriptional analysis of heavy metal stresses inCaulobacter crescentus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hu, Ping; Brodie, Eoin L.; Suzuki, Yohey

2005-09-21

The bacterium Caulobacter crescentus and related stalkbacterial species are known for their distinctive ability to live in lownutrient environments, a characteristic of most heavy metal contaminatedsites. Caulobacter crescentus is a model organism for studying cell cycleregulation with well developed genetics. We have identified the pathwaysresponding to heavy metal toxicity in C. crescentus to provide insightsfor possible application of Caulobacter to environmental restoration. Weexposed C. crescentus cells to four heavy metals (chromium, cadmium,selenium and uranium) and analyzed genome wide transcriptional activitiespost exposure using a Affymetrix GeneChip microarray. C. crescentusshowed surprisingly high tolerance to uranium, a possible mechanism forwhich may be formationmore » of extracellular calcium-uranium-phosphateprecipitates. The principal response to these metals was protectionagainst oxidative stress (up-regulation of manganese-dependent superoxidedismutase, sodA). Glutathione S-transferase, thioredoxin, glutaredoxinsand DNA repair enzymes responded most strongly to cadmium and chromate.The cadmium and chromium stress response also focused on reducing theintracellular metal concentration, with multiple efflux pumps employed toremove cadmium while a sulfate transporter was down-regulated to reducenon-specific uptake of chromium. Membrane proteins were also up-regulatedin response to most of the metals tested. A two-component signaltransduction system involved in the uranium response was identified.Several differentially regulated transcripts from regions previously notknown to encode proteins were identified, demonstrating the advantage ofevaluating the transcriptome using whole genome microarrays.« less

Water deficit modulates the response of Vitis vinifera to the Pierce's disease pathogen Xylella fastidiosa.

PubMed

Choi, Hong-Kyu; Iandolino, Alberto; da Silva, Francisco Goes; Cook, Douglas R

2013-06-01

Pierce's disease, caused by the bacterium Xylella fastidiosa, is one of the most devastating diseases of cultivated grape, currently restricted to the Americas. To test the long-standing hypothesis that Pierce's disease results from pathogen-induced drought stress, we used the Affymetrix Vitis GeneChip to compare the transcriptional response of Vitis vinifera to Xylella infection, water deficit, or a combination of the two stresses. The results reveal a redirection of gene transcription involving 822 genes with a minimum twofold change (P < 0.05), including the upregulation of transcripts for phenylpropanoid and flavonoid biosynthesis, pathogenesis-related proteins, abscisic acid- and jasmonic acid-responsive biosynthesis, and downregulation of transcripts related to photosynthesis, growth, and nutrition. Although the transcriptional response of plants to Xylella infection was largely distinct from the response of healthy plants to water stress, we find that 138 of the pathogen-induced genes exhibited a significantly stronger transcriptional response when plants were simultaneously exposed to infection and drought stress, suggesting a strong interaction between disease and water deficit. This interaction between drought stress and disease was mirrored in planta at the physiological level for aspects of water relations and photosynthesis and in terms of the severity of disease symptoms and the extent of pathogen colonization, providing a molecular correlate of the classical concept of the disease triangle in which environment impacts disease severity.

Characterization of visceral and subcutaneous adipose tissue transcriptome in pregnant women with and without spontaneous labor at term: implication of alternative splicing in the metabolic adaptations of adipose tissue to parturition.

PubMed

Mazaki-Tovi, Shali; Tarca, Adi L; Vaisbuch, Edi; Kusanovic, Juan Pedro; Than, Nandor Gabor; Chaiworapongsa, Tinnakorn; Dong, Zhong; Hassan, Sonia S; Romero, Roberto

2016-10-01

The aim of this study was to determine gene expression and splicing changes associated with parturition and regions (visceral vs. subcutaneous) of the adipose tissue of pregnant women. The transcriptome of visceral and abdominal subcutaneous adipose tissue from pregnant women at term with (n=15) and without (n=25) spontaneous labor was profiled with the Affymetrix GeneChip Human Exon 1.0 ST array. Overall gene expression changes and the differential exon usage rate were compared between patient groups (unpaired analyses) and adipose tissue regions (paired analyses). Selected genes were tested by quantitative reverse transcription-polymerase chain reaction. Four hundred and eighty-two genes were differentially expressed between visceral and subcutaneous fat of pregnant women with spontaneous labor at term (q-value <0.1; fold change >1.5). Biological processes enriched in this comparison included tissue and vasculature development as well as inflammatory and metabolic pathways. Differential splicing was found for 42 genes [q-value <0.1; differences in Finding Isoforms using Robust Multichip Analysis scores >2] between adipose tissue regions of women not in labor. Differential exon usage associated with parturition was found for three genes (LIMS1, HSPA5, and GSTK1) in subcutaneous tissues. We show for the first time evidence of implication of mRNA splicing and processing machinery in the subcutaneous adipose tissue of women in labor compared to those without labor.

BCL6 mediates the effects of Gastrodin on promoting M2-like macrophage polarization and protecting against oxidative stress-induced apoptosis and cell death in macrophages.

PubMed

Jia, Jing; Shi, Xiaojie; Jing, Xiaoqian; Li, Jianguo; Gao, Jie; Liu, Mengya; Lin, Chi-Iou; Guo, Xinzhi; Hua, Qian

2017-04-29

Cerebral palsy (CP) is the most common childhood disability worldwide, yet biomarkers for predicting CP are lacking. By subjecting peripheral blood samples from 62 CP patients and 30 healthy controls to Affymetrix GeneChip ® PrimeView™ HumanGene Expression Microarray analysis, we identified the novel biomarker B-cell lymphoma 6 (BCL6) as the most upregulated gene in the CP samples. Gastrodin is a traditional Chinese medicine and bioactive compound that promotes adductor angle release, as well as gross and fine motor performance by increasing Gross Motor Function Measure-66 and Fine Motor Function Measure-45 scores. Gastrodin upregulates the mRNA expression of Mgl2 and Mrc1, M2 macrophage markers, and arginase activity, an M2 polarization indicator, in murine RAW264.7 macrophages. Moreover, these effects were blocked by BCL6 siRNA, which also abrogated the protective effects of Gastrodin against hydrogen peroxide-induced apoptosis and death in RAW264.7 cells. Our work identified BCL6 as a novel biomarker for early prediction of CP. Moreover, we demonstrated that Gastrodin not only stimulated polarization toward M2-like macrophages, which promote tissue repair, but also rescued macrophages from oxidative stress, apoptosis and death by inducing BCL6 expression. BCL6-targeted therapeutic strategies have promise for improving motor performance in CP patients. Copyright © 2017 Elsevier Inc. All rights reserved.

Characterization of visceral and subcutaneous adipose tissue transcriptome in pregnant women with and without spontaneous labor at term: Implication of alternative splicing in the metabolic adaptations of adipose tissue to parturition

PubMed Central

Mazaki-Tovi, Shali; Tarca, Adi L.; Vaisbuch, Edi; Kusanovic, Juan Pedro; Than, Nandor Gabor; Chaiworapongsa, Tinnakorn; Dong, Zhong; Hassan, Sonia S; Romero, Roberto

2018-01-01

OBJECTIVE The aim of this study was to determine gene expression and splicing changes associated with parturition and regions (visceral vs subcutaneous) of the adipose tissue of pregnant women. STUDY DESIGN The transcriptome of visceral and abdominal subcutaneous adipose tissue from pregnant women at term with (n=15) and without (n=25) spontaneous labor was profiled with Affymetrix GeneChip Human Exon 1.0 ST array. Overall gene expression changes and differential exon usage rate were compared between patient groups and adipose tissue regions (paired analyses). Selected genes were tested by quantitative reverse transcription–polymerase chain reaction. RESULTS Four hundred eighty-two genes were differentially expressed between visceral and subcutaneous fat of pregnant women with spontaneous labor at term (q-value <0.1; fold change >1.5). Biological processes enriched in this comparison included tissue and vasculature development, inflammatory and metabolic pathways. Differential splicing was found for 42 genes (q-value <0.1; difference FIRMA scores >2) between adipose tissue regions of women not in labor. Differential exon usage associated with parturition was found for three genes (LIMS1, HSPA5 and GSTK1) in subcutaneous tissues. CONCLUSION We show for the first time evidence of implication of mRNA splicing and processing machinery in the subcutaneous adipose tissue of women in labor compared to those without labor. PMID:26994472

Revisiting the Evolution of Mycobacterium bovis

PubMed Central

Mostowy, Serge; Inwald, Jackie; Gordon, Steve; Martin, Carlos; Warren, Rob; Kremer, Kristin; Cousins, Debby; Behr, Marcel A.

2005-01-01

Though careful consideration has been placed towards genetic characterization of tubercle bacillus isolates causing disease in humans, those causing disease predominantly among wild and domesticated mammals have received less attention. In contrast to Mycobacterium tuberculosis, whose host range is largely specific to humans, M. bovis and “M bovis-like” organisms infect a broad range of animal species beyond their most prominent host in cattle. To determine whether strains of variable genomic content are associated with distinct distributions of disease, the DNA contents of M. bovis or M. bovis-like isolates from a variety of hosts were investigated via Affymetrix GeneChip. Consistent with previous genomic analysis of the M. tuberculosis complex (MTC), large sequence polymorphisms of putative diagnostic and biological consequence were able to unambiguously distinguish interrogated isolates. The distribution of deleted regions indicates organisms genomically removed from M. bovis and also points to structured genomic variability within M. bovis. Certain genomic profiles spanned a variety of hosts but were clustered by geography, while others associated primarily with host type. In contrast to the prevailing assumption that M. bovis has broad host capacity, genomic profiles suggest that distinct MTC lineages differentially infect a variety of mammals. From this, a phylogenetic stratification of genotypes offers a predictive framework upon which to base future genetic and phenotypic studies of the MTC. PMID:16159772

Respiratory chain complex I deficiency due to NDUFA12 mutations as a new cause of Leigh syndrome.

PubMed

Ostergaard, Elsebet; Rodenburg, Richard J; van den Brand, Mariël; Thomsen, Lise Lykke; Duno, Morten; Batbayli, Mustafa; Wibrand, Flemming; Nijtmans, Leo

2011-11-01

This study investigated a girl with Leigh syndrome born to first-cousin parents of Pakistani descent with an isolated respiratory chain complex I deficiency in muscle and fibroblasts. Her early development was delayed, and from age 2 years she started losing motor abilities. Cerebral MRI showed basal ganglia lesions typical of Leigh syndrome. A genome-wide search for homozygosity was performed with the Affymetrix GeneChip 50K Xba array. The analysis revealed several homozygous regions. Three candidate genes were identified, and in one of the genes, NDUFA12, a homozygous c.178C→T mutation leading to a premature stop codon (p.Arg60X) was found. Western blot analysis showed absence of NDUFA12 protein in patient fibroblasts and functional complementation by a baculovirus system showed restoration of complex I activity. NDUFA12 mutations are apparently not a frequent cause of complex I deficiency, since mutations were not found by screening altogether 122 complex I deficient patients in two different studies. NDUFA12 encodes an accessory subunit of complex I and is a paralogue of NDUFAF2. Despite the complete absence of NDUFA12 protein, a fully assembled and enzymatically active complex I could be found, albeit in reduced amounts. This suggests that NDUFA12 is required either at a late step in the assembly of complex I, or in the stability of complex I.

Phycocyanobilin promotes PC12 cell survival and modulates immune and inflammatory genes and oxidative stress markers in acute cerebral hypoperfusion in rats.

PubMed

Marín-Prida, Javier; Pavón-Fuentes, Nancy; Llópiz-Arzuaga, Alexey; Fernández-Massó, Julio R; Delgado-Roche, Liván; Mendoza-Marí, Yssel; Santana, Seydi Pedroso; Cruz-Ramírez, Alieski; Valenzuela-Silva, Carmen; Nazábal-Gálvez, Marcelo; Cintado-Benítez, Alberto; Pardo-Andreu, Gilberto L; Polentarutti, Nadia; Riva, Federica; Pentón-Arias, Eduardo; Pentón-Rol, Giselle

2013-10-01

Since the inflammatory response and oxidative stress are involved in the stroke cascade, we evaluated here the effects of Phycocyanobilin (PCB, the C-Phycocyanin linked tetrapyrrole) on PC12 cell survival, the gene expression and the oxidative status of hypoperfused rat brain. After the permanent bilateral common carotid arteries occlusion (BCCAo), the animals were treated with saline or PCB, taking samples 24h post-surgery. Global gene expression was analyzed with GeneChip Rat Gene ST 1.1 from Affymetrix; the expression of particular genes was assessed by the Fast SYBR Green RT-PCR Master Mix and Bioplex methods; and redox markers (MDA, PP, CAT, SOD) were evaluated spectrophotometrically. The PCB treatment prevented the H2O2 and glutamate induced PC12 cell injury assessed by the MTT assay, and modulated 190 genes (93 up- and 97 down-regulated) associated to several immunological and inflammatory processes in BCCAo rats. Furthermore, PCB positively modulated 19 genes mostly related to a detrimental pro-inflammatory environment and counteracted the oxidative imbalance in the treated BCCAo animals. Our results support the view of an effective influence of PCB on major inflammatory mediators in acute cerebral hypoperfusion. These results suggest that PCB has a potential to be a treatment for ischemic stroke for which further studies are needed. Copyright © 2013 Elsevier Inc. All rights reserved.

Effects of dietary supplementation with EPA and/or α-lipoic acid on adipose tissue transcriptomic profile of healthy overweight/obese women following a hypocaloric diet.

PubMed

Huerta, Ana E; Prieto-Hontoria, Pedro L; Fernández-Galilea, Marta; Escoté, Xavier; Martínez, J Alfredo; Moreno-Aliaga, María J

2017-01-02

In obesity, the increment of adiposity levels disrupts the whole body homeostasis, promoting an over production of oxidants and inflammatory mediators. The current study aimed to characterize the transcriptomic changes promoted by supplementation with eicosapentaenoic acid (EPA, 1.3 g/day), α-lipoic acid (0.3 g/day), or both (EPA + α-lipoic acid, 1.3 g/day + 0.3 g/day) in subcutaneous abdominal adipose tissue from overweight/obese healthy women, who followed a hypocaloric diet (30% of total energy expenditure) during ten weeks, by using a microarray approach. At the end of the intervention, a total of 33,297 genes were analyzed using Affymetrix GeneChip arrays. EPA promoted changes in extracellular matrix remodeling gene expression, besides a rise of genes associated with either chemotaxis or wound repair. α-Lipoic acid decreased expression of genes related with cell adhesion and inflammation. Furthermore, α-lipoic acid, especially in combination with EPA, upregulated the expression of genes associated with lipid catabolism while downregulated genes involved in lipids storage. Together, all these data suggest that some of the metabolic effects of EPA and α-lipoic acid could be related to their regulatory actions on adipose tissue metabolism. © 2016 BioFactors, 43(1):117-131, 2017. © 2016 International Union of Biochemistry and Molecular Biology.

Genotype imputation for African Americans using data from HapMap phase II versus 1000 genomes projects.

PubMed

Sung, Yun J; Gu, C Charles; Tiwari, Hemant K; Arnett, Donna K; Broeckel, Ulrich; Rao, Dabeeru C

2012-07-01

Genotype imputation provides imputation of untyped single nucleotide polymorphisms (SNPs) that are present on a reference panel such as those from the HapMap Project. It is popular for increasing statistical power and comparing results across studies using different platforms. Imputation for African American populations is challenging because their linkage disequilibrium blocks are shorter and also because no ideal reference panel is available due to admixture. In this paper, we evaluated three imputation strategies for African Americans. The intersection strategy used a combined panel consisting of SNPs polymorphic in both CEU and YRI. The union strategy used a panel consisting of SNPs polymorphic in either CEU or YRI. The merge strategy merged results from two separate imputations, one using CEU and the other using YRI. Because recent investigators are increasingly using the data from the 1000 Genomes (1KG) Project for genotype imputation, we evaluated both 1KG-based imputations and HapMap-based imputations. We used 23,707 SNPs from chromosomes 21 and 22 on Affymetrix SNP Array 6.0 genotyped for 1,075 HyperGEN African Americans. We found that 1KG-based imputations provided a substantially larger number of variants than HapMap-based imputations, about three times as many common variants and eight times as many rare and low-frequency variants. This higher yield is expected because the 1KG panel includes more SNPs. Accuracy rates using 1KG data were slightly lower than those using HapMap data before filtering, but slightly higher after filtering. The union strategy provided the highest imputation yield with next highest accuracy. The intersection strategy provided the lowest imputation yield but the highest accuracy. The merge strategy provided the lowest imputation accuracy. We observed that SNPs polymorphic only in CEU had much lower accuracy, reducing the accuracy of the union strategy. Our findings suggest that 1KG-based imputations can facilitate discovery of

Intrahepatic Cholestasis of Pregnancy (ICP) in U.S. Latinas and Chileans: Clinical features, Ancestry Analysis, and Admixture Mapping.

PubMed

Bull, Laura N; Hu, Donglei; Shah, Sohela; Temple, Luisa; Silva, Karla; Huntsman, Scott; Melgar, Jennifer; Geiser, Mary T; Sanford, Ukina; Ortiz, Juan A; Lee, Richard H; Kusanovic, Juan P; Ziv, Elad; Vargas, Juan E

2015-01-01

In the Americas, women with Indigenous American ancestry are at increased risk of intrahepatic cholestasis of pregnancy (ICP), relative to women of other ethnicities. We hypothesized that ancestry-related genetic factors contribute to this increased risk. We collected clinical and laboratory data, and performed biochemical assays on samples from U.S. Latinas and Chilean women, with and without ICP. The study sample included 198 women with ICP (90 from California, U.S., and 108 from Chile) and 174 pregnant control women (69 from California, U.S., and 105 from Chile). SNP genotyping was performed using Affymetrix arrays. We compared overall genetic ancestry between cases and controls, and used a genome-wide admixture mapping approach to screen for ICP susceptibility loci. We identified commonalities and differences in features of ICP between the 2 countries and determined that cases had a greater proportion of Indigenous American ancestry than did controls (p = 0.034). We performed admixture mapping, taking country of origin into account, and identified one locus for which Native American ancestry was associated with increased risk of ICP at a genome-wide level of significance (P = 3.1 x 10(-5), Pcorrected = 0.035). This locus has an odds ratio of 4.48 (95% CI: 2.21-9.06) for 2 versus zero Indigenous American chromosomes. This locus lies on chromosome 2, with a 10 Mb 95% confidence interval which does not contain any previously identified hereditary 'cholestasis genes.' Our results indicate that genetic factors contribute to the risk of developing ICP in the Americas, and support the utility of clinical and genetic studies of ethnically mixed populations for increasing our understanding of ICP.

Genome-Wide Mapping of Copy Number Variation in Humans: Comparative Analysis of High Resolution Array Platforms

PubMed Central

Haraksingh, Rajini R.; Abyzov, Alexej; Gerstein, Mark; Urban, Alexander E.; Snyder, Michael

2011-01-01

Accurate and efficient genome-wide detection of copy number variants (CNVs) is essential for understanding human genomic variation, genome-wide CNV association type studies, cytogenetics research and diagnostics, and independent validation of CNVs identified from sequencing based technologies. Numerous, array-based platforms for CNV detection exist utilizing array Comparative Genome Hybridization (aCGH), Single Nucleotide Polymorphism (SNP) genotyping or both. We have quantitatively assessed the abilities of twelve leading genome-wide CNV detection platforms to accurately detect Gold Standard sets of CNVs in the genome of HapMap CEU sample NA12878, and found significant differences in performance. The technologies analyzed were the NimbleGen 4.2 M, 2.1 M and 3×720 K Whole Genome and CNV focused arrays, the Agilent 1×1 M CGH and High Resolution and 2×400 K CNV and SNP+CGH arrays, the Illumina Human Omni1Quad array and the Affymetrix SNP 6.0 array. The Gold Standards used were a 1000 Genomes Project sequencing-based set of 3997 validated CNVs and an ultra high-resolution aCGH-based set of 756 validated CNVs. We found that sensitivity, total number, size range and breakpoint resolution of CNV calls were highest for CNV focused arrays. Our results are important for cost effective CNV detection and validation for both basic and clinical applications. PMID:22140474

Mapping autism risk loci using genetic linkage and chromosomal rearrangements

PubMed Central

Szatmari, Peter; Paterson, Andrew; Zwaigenbaum, Lonnie; Roberts, Wendy; Brian, Jessica; Liu, Xiao-Qing; Vincent, John; Skaug, Jennifer; Thompson, Ann; Senman, Lili; Feuk, Lars; Qian, Cheng; Bryson, Susan; Jones, Marshall; Marshall, Christian; Scherer, Stephen; Vieland, Veronica; Bartlett, Christopher; Mangin, La Vonne; Goedken, Rhinda; Segre, Alberto; Pericak-Vance, Margaret; Cuccaro, Michael; Gilbert, John; Wright, Harry; Abramson, Ruth; Betancur, Catalina; Bourgeron, Thomas; Gillberg, Christopher; Leboyer, Marion; Buxbaum, Joseph; Davis, Kenneth; Hollander, Eric; Silverman, Jeremy; Hallmayer, Joachim; Lotspeich, Linda; Sutcliffe, James; Haines, Jonathan; Folstein, Susan; Piven, Joseph; Wassink, Thomas; Sheffield, Val; Geschwind, Daniel; Bucan, Maja; Brown, Ted; Cantor, Rita; Constantino, John; Gilliam, Conrad; Herbert, Martha; Lajonchere, Clara; Ledbetter, David; Lese-Martin, Christa; Miller, Janet; Nelson, Stan; Samango-Sprouse, Carol; Spence, Sarah; State, Matthew; Tanzi, Rudolph; Coon, Hilary; Dawson, Geraldine; Devlin, Bernie; Estes, Annette; Flodman, Pamela; Klei, Lambertus; Mcmahon, William; Minshew, Nancy; Munson, Jeff; Korvatska, Elena; Rodier, Patricia; Schellenberg, Gerard; Smith, Moyra; Spence, Anne; Stodgell, Chris; Tepper, Ping Guo; Wijsman, Ellen; Yu, Chang-En; Rogé, Bernadette; Mantoulan, Carine; Wittemeyer, Kerstin; Poustka, Annemarie; Felder, Bärbel; Klauck, Sabine; Schuster, Claudia; Poustka, Fritz; Bölte, Sven; Feineis-Matthews, Sabine; Herbrecht, Evelyn; Schmötzer, Gabi; Tsiantis, John; Papanikolaou, Katerina; Maestrini, Elena; Bacchelli, Elena; Blasi, Francesca; Carone, Simona; Toma, Claudio; Van Engeland, Herman; De Jonge, Maretha; Kemner, Chantal; Koop, Frederieke; Langemeijer, Marjolein; Hijmans, Channa; Staal, Wouter; Baird, Gillian; Bolton, Patrick; Rutter, Michael; Weisblatt, Emma; Green, Jonathan; Aldred, Catherine; Wilkinson, Julie-Anne; Pickles, Andrew; Le Couteur, Ann; Berney, Tom; Mcconachie, Helen; Bailey, Anthony; Francis, Kostas; Honeyman, Gemma; Hutchinson, Aislinn; Parr, Jeremy; Wallace, Simon; Monaco, Anthony; Barnby, Gabrielle; Kobayashi, Kazuhiro; Lamb, Janine; Sousa, Ines; Sykes, Nuala; Cook, Edwin; Guter, Stephen; Leventhal, Bennett; Salt, Jeff; Lord, Catherine; Corsello, Christina; Hus, Vanessa; Weeks, Daniel; Volkmar, Fred; Tauber, Maïté; Fombonne, Eric; Shih, Andy; Meyer, Kacie

2007-01-01

Autism spectrum disorders (ASD) are common, heritable neurodevelopmental conditions. The genetic architecture of ASD is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASD by using Affymetrix 10K single nucleotide polymorphism (SNP) arrays and 1168 families with ≥ 2 affected individuals to perform the largest linkage scan to date, while also analyzing copy number variation (CNV) in these families. Linkage and CNV analyses implicate chromosome 11p12-p13 and neurexins, respectively, amongst other candidate loci. Neurexins team with previously-implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for ASD. PMID:17322880

Interference of peritoneal dialysis fluids with cell cycle mechanisms.

PubMed

Büchel, Janine; Bartosova, Maria; Eich, Gwendolyn; Wittenberger, Timo; Klein-Hitpass, Ludger; Steppan, Sonja; Hackert, Thilo; Schaefer, Franz; Passlick-Deetjen, Jutta; Schmitt, Claus P

2015-01-01

Peritoneal dialysis fluids (PDF) differ with respect to osmotic and buffer compound, and pH and glucose degradation products (GDP) content. The impact on peritoneal membrane integrity is still insufficiently described. We assessed global genomic effects of PDF in primary human peritoneal mesothelial cells (PMC) by whole genome analyses, quantitative real-time polymerase chain reaction (RT-PCR) and functional measurements. PMC isolated from omentum of non-uremic patients were incubated with conventional single chamber PDF (CPDF), lactate- (LPDF), bicarbonate- (BPDF) and bicarbonate/lactate-buffered double-chamber PDF (BLPDF), icodextrin (IPDF) and amino acid PDF (APDF), diluted 1:1 with medium. Affymetrix GeneChip U133Plus2.0 (Affymetrix, CA, USA) and quantitative RT-PCR were applied; cell viability was assessed by proliferation assays. The number of differentially expressed genes compared to medium was 464 with APDF, 208 with CPDF, 169 with IPDF, 71 with LPDF, 45 with BPDF and 42 with BLPDF. Out of these genes 74%, 73%, 79%, 72%, 47% and 57% were downregulated. Gene Ontology (GO) term annotations mainly revealed associations with cell cycle (p = 10(-35)), cell division, mitosis, and DNA replication. One hundred and eighteen out of 249 probe sets detecting genes involved in cell cycle/division were suppressed, with APDF-treated PMC being affected the most regarding absolute number and degree, followed by CPDF and IPDF. Bicarbonate-containing PDF and BLPDF-treated PMC were affected the least. Quantitative RT-PCR measurements confirmed microarray findings for key cell cycle genes (CDK1/CCNB1/CCNE2/AURKA/KIF11/KIF14). Suppression was lowest for BPDF and BLPDF, they upregulated CCNE2 and SMC4. All PDF upregulated 3 out of 4 assessed cell cycle repressors (p53/BAX/p21). Cell viability scores confirmed gene expression results, being 79% of medium for LPDF, 101% for BLPDF, 51% for CPDF and 23% for IPDF. Amino acid-containing PDF (84%) incubated cells were as viable as BPDF

Interference of Peritoneal Dialysis Fluids with Cell Cycle Mechanisms

PubMed Central

Büchel, Janine; Bartosova, Maria; Eich, Gwendolyn; Wittenberger, Timo; Klein-Hitpass, Ludger; Steppan, Sonja; Hackert, Thilo; Schaefer, Franz; Passlick-Deetjen, Jutta; Schmitt, Claus P.

2015-01-01

♦ Introduction: Peritoneal dialysis fluids (PDF) differ with respect to osmotic and buffer compound, and pH and glucose degradation products (GDP) content. The impact on peritoneal membrane integrity is still insufficiently described. We assessed global genomic effects of PDF in primary human peritoneal mesothelial cells (PMC) by whole genome analyses, quantitative real-time polymerase chain reaction (RT-PCR) and functional measurements. ♦ Methods: PMC isolated from omentum of non-uremic patients were incubated with conventional single chamber PDF (CPDF), lactate- (LPDF), bicarbonate- (BPDF) and bicarbonate/lactate-buffered double-chamber PDF (BLPDF), icodextrin (IPDF) and amino acid PDF (APDF), diluted 1:1 with medium. Affymetrix GeneChip U133Plus2.0 (Affymetrix, CA, USA) and quantitative RT-PCR were applied; cell viability was assessed by proliferation assays. ♦ Results: The number of differentially expressed genes compared to medium was 464 with APDF, 208 with CPDF, 169 with IPDF, 71 with LPDF, 45 with BPDF and 42 with BLPDF. Out of these genes 74%, 73%, 79%, 72%, 47% and 57% were downregulated. Gene Ontology (GO) term annotations mainly revealed associations with cell cycle (p = 10-35), cell division, mitosis, and DNA replication. One hundred and eighteen out of 249 probe sets detecting genes involved in cell cycle/division were suppressed, with APDF-treated PMC being affected the most regarding absolute number and degree, followed by CPDF and IPDF. Bicarbonate-containing PDF and BLPDF-treated PMC were affected the least. Quantitative RT-PCR measurements confirmed microarray findings for key cell cycle genes (CDK1/CCNB1/CCNE2/AURKA/KIF11/KIF14). Suppression was lowest for BPDF and BLPDF, they upregulated CCNE2 and SMC4. All PDF upregulated 3 out of 4 assessed cell cycle repressors (p53/BAX/p21). Cell viability scores confirmed gene expression results, being 79% of medium for LPDF, 101% for BLPDF, 51% for CPDF and 23% for IPDF. Amino acid-containing PDF

In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis.

PubMed

Lim, Daniel A; Suárez-Fariñas, Mayte; Naef, Felix; Hacker, Coleen R; Menn, Benedicte; Takebayashi, Hirohide; Magnasco, Marcelo; Patil, Nila; Alvarez-Buylla, Arturo

2006-01-01

Neural stem cells and neurogenesis persist in the adult mammalian brain subventricular zone (SVZ). Cells born in the rodent SVZ migrate to the olfactory bulb (Ob) where they differentiate into interneurons. To determine the gene expression and functional profile of SVZ neurogenesis, we performed three complementary sets of transcriptional analysis experiments using Affymetrix GeneChips: (1) comparison of adult mouse SVZ and Ob gene expression profiles with those of the striatum, cerebral cortex, and hippocampus; (2) profiling of SVZ stem cells and ependyma isolated by fluorescent-activated cell sorting (FACS); and (3) analysis of gene expression changes during in vivo SVZ regeneration after anti-mitotic treatment. Gene Ontology (GO) analysis of data from these three separate approaches showed that in adult SVZ neurogenesis, RNA splicing and chromatin remodeling are biological processes as statistically significant as cell proliferation, transcription, and neurogenesis. In non-neurogenic brain regions, RNA splicing and chromatin remodeling were not prominent processes. Fourteen mRNA splicing factors including Sf3b1, Sfrs2, Lsm4, and Khdrbs1/Sam68 were detected along with 9 chromatin remodeling genes including Mll, Bmi1, Smarcad1, Baf53a, and Hat1. We validated the transcriptional profile data with Northern blot analysis and in situ hybridization. The data greatly expand the catalogue of cell cycle components, transcription factors, and migration genes for adult SVZ neurogenesis and reveal RNA splicing and chromatin remodeling as prominent biological processes for these germinal cells.

Different Transcriptional Response to Xanthomonas citri subsp. citri between Kumquat and Sweet Orange with Contrasting Canker Tolerance

PubMed Central

Fu, Xing-Zheng; Gong, Xiao-Qing; Zhang, Yue-Xin; Wang, Yin; Liu, Ji-Hong

2012-01-01

Citrus canker disease caused by Xanthomonas citri subsp. citri (Xcc) is one of the most devastating biotic stresses affecting the citrus industry. Meiwa kumquat (Fortunella crassifolia) is canker-resistant, while Newhall navel orange (Citrus sinensis Osbeck) is canker-sensitive. To understand the molecular mechanisms underlying the differences in responses to Xcc, transcriptomic profiles of these two genotypes following Xcc attack were compared by using the Affymetrix citrus genome GeneChip. A total of 794 and 1324 differentially expressed genes (DEGs) were identified as canker-responsive genes in Meiwa and Newhall, respectively. Of these, 230 genes were expressed in common between both genotypes, while 564 and 1094 genes were only significantly expressed in either Meiwa or Newhall. Gene ontology (GO) annotation and Singular Enrichment Analysis (SEA) of the DEGs showed that genes related to the cell wall and polysaccharide metabolism were induced for basic defense in both Meiwa and Newhall, such as chitinase, glucanase and thaumatin-like protein. Moreover, apart from inducing basic defense, Meiwa showed specially upregulated expression of several genes involved in the response to biotic stimulus, defense response, and cation binding as comparing with Newhall. And in Newhall, abundant photosynthesis-related genes were significantly down-regulated, which may be in order to ensure the basic defense. This study revealed different molecular responses to canker disease in Meiwa and Newhall, affording insight into the response to canker and providing valuable information for the identification of potential genes for engineering canker tolerance in the future. PMID:22848606

Bone-related gene profiles in developing calvaria.

PubMed

Cho, Je-Yoel; Lee, Won-Bong; Kim, Hyun-Jung; Mi Woo, Kyung; Baek, Jeong-Hwa; Choi, Je-Yong; Hur, Cheol-Gu; Ryoo, Hyun-Mo

2006-05-10

Generating a comprehensive understanding of osteogenesis-related gene profiles is very important in the development of new treatments for osteopenic conditions. Developing calvaria undergoes a typical intramembranous bone-forming process. To identify genes associated with osteoblast differentiation, we isolated total RNAs from parietal bones, that represent active osteoblasts, and sutural mesenchyme, that represents osteoprogenitor cells, and comprehensively analyzed their gene expression profiles using an oligo-based Affymetrix microarray chip containing 22,690 probes. About 2100 genes with "Present" calls had more than 2-fold higher expression in bone compared to sutures while 73 of these genes had more than 8-fold expression. Some of these genes are already known to be bone-related biomarkers: VitD receptor, bone sialoprotein, osteocalcin, osteopontin, MMP13, etc. Eight genes were selected and subjected to confirmation by quantitative real-time RT-PCR analyses. All the genes tested showed higher expression in bones, ranging from 5- to 140-fold. Several of these genes are ESTs while others are already known but their functions in osteogenesis were not previously known. Most genes of the BMP and FGF families probed in the Genechip analysis were more highly expressed in bone tissues compared to suture. All differentially-expressed Runx and Dlx family genes also showed higher expression in bone. These results imply that our data is valid and can be used as a good standard for the mining of osteogenesis-related genes.

Molecular defense mechanisms of Barrett's metaplasia estimated by an integrative genomics.

PubMed

Ostrowski, Jerzy; Mikula, Michal; Karczmarski, Jakub; Rubel, Tymon; Wyrwicz, Lucjan S; Bragoszewski, Piotr; Gaj, Pawel; Dadlez, Michal; Butruk, Eugeniusz; Regula, Jaroslaw

2007-07-01

Barrett's esophagus is characterized by the replacement of squamous epithelium with specialized intestinal metaplastic mucosa. The exact mechanisms of initiation and development of Barrett's metaplasia remain unknown, but a hypothesis of "successful adaptation" against noxious reflux components has been proposed. To search for the repertoire of adaptation mechanisms of Barrett's metaplasia, we employed high-throughput functional genomic and proteomic methods that defined the molecular background of metaplastic mucosa resistance to reflux. Transcriptional profiling was established for 23 pairs of esophageal squamous epithelium and Barrett's metaplasia tissue samples using Affymetrix U133A 2.0 GeneChips and validated by quantitative real-time polymerase chain reaction. Differences in protein composition were assessed by electrophoretic and mass-spectrometry-based methods. Among 2,822 genes differentially expressed between Barrett's metaplasia and squamous epithelium, we observed significantly overexpressed metaplastic mucosa genes that encode cytokines and growth factors, constituents of extracellular matrix, basement membrane and tight junctions, and proteins involved in prostaglandin and phosphoinositol metabolism, nitric oxide production, and bioenergetics. Their expression likely reflects defense and repair responses of metaplastic mucosa, whereas overexpression of genes encoding heat shock proteins and several protein kinases in squamous epithelium may reflect lower resistance of normal esophageal epithelium than Barrett's metaplasia to reflux components. Despite the methodological and interpretative difficulties in data analyses discussed in this paper, our studies confirm that Barrett's metaplasia may be regarded as a specific microevolution allowing for accumulation of mucosal morphological and physiological changes that better protect against reflux injury.

Dose response evaluation of gene expression profiles in the skin of K6/ODC mice exposed to sodium arsenite.

PubMed

Ahlborn, Gene J; Nelson, Gail M; Ward, William O; Knapp, Geremy; Allen, James W; Ouyang, Ming; Roop, Barbara C; Chen, Yan; O'Brien, Thomas; Kitchin, Kirk T; Delker, Don A

2008-03-15

Chronic drinking water exposure to inorganic arsenic and its metabolites increases tumor frequency in the skin of K6/ODC transgenic mice. To identify potential biomarkers and modes of action for this skin tumorigenicity, we characterized gene expression profiles from analysis of K6/ODC mice administered 0, 0.05, 0.25, 1.0 and 10 ppm sodium arsenite in their drinking water for 4 weeks. Following exposure, total RNA was isolated from mouse skin and processed to biotin-labeled cRNA for microarray analyses. Skin gene expression was analyzed with Affymetrix Mouse Genome 430A 2.0 GeneChips, and pathway analysis was conducted with DAVID (NIH), Ingenuity Systems and MetaCore's GeneGo. Differential expression of several key genes was verified through qPCR. Only the highest dose (10 ppm) resulted in significantly altered KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, including MAPK, regulation of actin cytoskeleton, Wnt, Jak-Stat, Tight junction, Toll-like, phosphatidylinositol and insulin signaling pathways. Approximately 20 genes exhibited a dose response, including several genes known to be associated with carcinogenesis or tumor progression including cyclin D1, CLIC4, Ephrin A1, STAT3 and DNA methyltransferase 3a. Although transcription changes in all identified genes have not previously been linked to arsenic carcinogenesis, their association with carcinogenesis in other systems suggests that these genes may play a role in the early stages of arsenic-induced skin carcinogenesis and can be considered potential biomarkers.

Analysis of global and absorption, distribution, metabolism, and elimination gene expression in the progressive stages of human nonalcoholic fatty liver disease.

PubMed

Lake, April D; Novak, Petr; Fisher, Craig D; Jackson, Jonathan P; Hardwick, Rhiannon N; Billheimer, D Dean; Klimecki, Walter T; Cherrington, Nathan J

2011-10-01

Nonalcoholic fatty liver disease (NAFLD) is characterized by a series of pathological changes that range from simple fatty liver to nonalcoholic steatohepatitis (NASH). The objective of this study is to describe changes in global gene expression associated with the progression of human NAFLD. This study is focused on the expression levels of genes responsible for the absorption, distribution, metabolism, and elimination (ADME) of drugs. Differential gene expression between three clinically defined pathological groups-normal, steatosis, and NASH-was analyzed. Genome-wide mRNA levels in samples of human liver tissue were assayed with Affymetrix GeneChip Human 1.0ST arrays. A total of 11,633 genes exhibited altered expression out of 33,252 genes at a 5% false discovery rate. Most gene expression changes occurred in the progression from steatosis to NASH. Principal component analysis revealed that hepatic disease status was the major determinant of differential ADME gene expression rather than age or sex of sample donors. Among the 515 drug transporters and 258 drug-metabolizing enzymes (DMEs) examined, uptake transporters but not efflux transporters or DMEs were significantly over-represented in the number of genes down-regulated. These results suggest that uptake transporter genes are coordinately targeted for down-regulation at the global level during the pathological development of NASH and that these patients may have decreased drug uptake capacity. This coordinated regulation of uptake transporter genes is indicative of a hepatoprotective mechanism acting to prevent accumulation of toxic intermediates in disease-compromised hepatocytes.

A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians

PubMed Central

2012-01-01

Background There is reason to expect strong genetic influences on the risk of developing active pulmonary tuberculosis (TB) among latently infected individuals. Many of the genome wide linkage and association studies (GWAS) to date have been conducted on African populations. In order to identify additional targets in genetically dissimilar populations, and to enhance our understanding of this disease, we performed a multi-stage GWAS in a Southeast Asian cohort from Indonesia. Methods In stage 1, we used the Affymetrix 100 K SNP GeneChip marker set to genotype 259 Indonesian samples. After quality control filtering, 108 cases and 115 controls were analyzed for association of 95,207 SNPs. In stage 2, we attempted validation of 2,453 SNPs with promising associations from the first stage, in 1,189 individuals from the same Indonesian cohort, and finally in stage 3 we selected 251 SNPs from this stage to test TB association in an independent Caucasian cohort (n = 3,760) from Russia. Results Our study suggests evidence of association (P = 0.0004-0.0067) for 8 independent loci (nominal significance P < 0.05), which are located within or near the following genes involved in immune signaling: JAG1, DYNLRB2, EBF1, TMEFF2, CCL17, HAUS6, PENK and TXNDC4. Conclusions Mechanisms of immune defense suggested by some of the identified genes exhibit biological plausibility and may suggest novel pathways involved in the host containment of infection with TB. PMID:22239941

A genome wide association study of pulmonary tuberculosis susceptibility in Indonesians.

PubMed

Png, Eileen; Alisjahbana, Bachti; Sahiratmadja, Edhyana; Marzuki, Sangkot; Nelwan, Ron; Balabanova, Yanina; Nikolayevskyy, Vladyslav; Drobniewski, Francis; Nejentsev, Sergey; Adnan, Iskandar; van de Vosse, Esther; Hibberd, Martin L; van Crevel, Reinout; Ottenhoff, Tom H M; Seielstad, Mark

2012-01-13

There is reason to expect strong genetic influences on the risk of developing active pulmonary tuberculosis (TB) among latently infected individuals. Many of the genome wide linkage and association studies (GWAS) to date have been conducted on African populations. In order to identify additional targets in genetically dissimilar populations, and to enhance our understanding of this disease, we performed a multi-stage GWAS in a Southeast Asian cohort from Indonesia. In stage 1, we used the Affymetrix 100 K SNP GeneChip marker set to genotype 259 Indonesian samples. After quality control filtering, 108 cases and 115 controls were analyzed for association of 95,207 SNPs. In stage 2, we attempted validation of 2,453 SNPs with promising associations from the first stage, in 1,189 individuals from the same Indonesian cohort, and finally in stage 3 we selected 251 SNPs from this stage to test TB association in an independent Caucasian cohort (n = 3,760) from Russia. Our study suggests evidence of association (P = 0.0004-0.0067) for 8 independent loci (nominal significance P < 0.05), which are located within or near the following genes involved in immune signaling: JAG1, DYNLRB2, EBF1, TMEFF2, CCL17, HAUS6, PENK and TXNDC4. Mechanisms of immune defense suggested by some of the identified genes exhibit biological plausibility and may suggest novel pathways involved in the host containment of infection with TB.

The effect of maternal chromium status on lipid metabolism in female elderly mice offspring and involved molecular mechanism

PubMed Central

Zhang, Qian; Sun, Xiaofang; Zheng, Jia; Li, Ming; Yu, Miao; Ping, Fan; Wang, Zhixin; Qi, Cuijuan; Wang, Tong; Wang, Xiaojing

2017-01-01

Maternal malnutrition leads to the incidence of metabolic diseases in offspring. The purpose of this project was to examine whether maternal low chromium could disturb normal lipid metabolism in offspring, altering adipose cell differentiation and leading to the incidence of lipid metabolism diseases, including metabolic syndrome and obesity. Female C57BL mice were given a control diet (CD) or a low chromium diet (LCD) during the gestational and lactation periods. After weaning, offspring was fed with CD or LCD. The female offspring were assessed at 32 weeks of age. Fresh adipose samples from CD–CD group and LCD–CD group were collected. Genome mRNA were analysed using Affymetrix GeneChip Mouse Gene 2.0 ST Whole Transcript-based array. Differentially expressed genes (DEGs) were analysed based on gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis database. Maternal low chromium irreversibly increased offspring body weight, fat-pad weight, serum triglyceride (TG) and TNF-α. Eighty five genes increased and 109 genes reduced in the offspring adipose of the maternal low chromium group. According to KEGG pathway and String analyses, the PPAR signalling pathway may be the key controlled pathway related to the effect of maternal low chromium on female offspring. Maternal chromium status have long-term effects of lipid metabolism in female mice offspring. Normalizing offspring diet can not reverse these effects. The potential underlying mechanisms are the disturbance of the PPAR signalling pathway in adipose tissue. PMID:28320771

Stage-specific differential gene expression profiling and functional network analysis during morphogenesis of diphyodont dentition in miniature pigs, Sus Scrofa

PubMed Central

2014-01-01

Background Our current knowledge of tooth development derives mainly from studies in mice, which have only one set of non-replaced teeth, compared with the diphyodont dentition in humans. The miniature pig is also diphyodont, making it a valuable alternative model for understanding human tooth development and replacement. However, little is known about gene expression and function during swine odontogenesis. The goal of this study is to undertake the survey of differential gene expression profiling and functional network analysis during morphogenesis of diphyodont dentition in miniature pigs. The identification of genes related to diphyodont development should lead to a better understanding of morphogenetic patterns and the mechanisms of diphyodont replacement in large animal models and humans. Results The temporal gene expression profiles during early diphyodont development in miniature pigs were detected with the Affymetrix Porcine GeneChip. The gene expression data were further evaluated by ANOVA as well as pathway and STC analyses. A total of 2,053 genes were detected with differential expression. Several signal pathways and 151 genes were then identified through the construction of pathway and signal networks. Conclusions The gene expression profiles indicated that spatio-temporal down-regulation patterns of gene expression were predominant; while, both dynamic activation and inhibition of pathways occurred during the morphogenesis of diphyodont dentition. Our study offers a mechanistic framework for understanding dynamic gene regulation of early diphyodont development and provides a molecular basis for studying teeth development, replacement, and regeneration in miniature pigs. PMID:24498892

Whole blood miRNA expression analysis reveals miR-3613-3p as a potential biomarker for dedifferentiated liposarcoma.

PubMed

Fricke, A; Cimniak, A F V; Ullrich, P V; Becherer, C; Bickert, C; Pfeifer, D; Heinz, J; Stark, G B; Bannasch, H; Braig, D; Eisenhardt, S U

2018-04-09

Liposarcoma constitute about 13% of all soft tissue sarcoma and are associated with a high risk of metastases. As the preoperative differentiation between benign and malign lipomatous tumors is restricted to magnetic resonance imaging, computed tomography and biopsy, we performed a miRNA array to distinguish dedifferentiated liposarcoma patients from healthy controls and lipoma patients. Blood samples of patients with dedifferentiated liposarcoma, healthy controls and lipoma patients were collected. Whole blood RNA was extracted and samples of patients with dedifferentiated liposarcoma (n= 6) and of healthy donors (n= 4) were analyzed using an Affymetrix GeneChip miRNA Array v. 4.0. qRT-PCR was carried out to confirm the most differentially expressed miRNA; being further analyzed in an independent cohort of healthy controls as well as in lipoma patients. As shown by the microarray, two miRNAs (miR-3613-3p, miR-4668-5p) were shown to be significantly upregulated (fold change: > 2.5; p< 0.05) in patients with dedifferentiated liposarcoma (n= 6) as compared to healthy controls (n= 4). miR-3613-3p was further validated by qRT-PCR to be significantly upregulated in dedifferentiated liposarcoma patients compared to an independent cohort of healthy controls (n= 3) and lipoma patients (n= 5). We identified a specific whole blood miRNA (miR-3613-3p) that may serve to distinguish between dedifferentiated liposarcoma patients and healthy controls, thus potentially serving as a specific biomarker for dedifferentiated liposarcoma.

Over-expression of the miRNA cluster at chromosome 14q32 in the alcoholic brain correlates with suppression of predicted target mRNA required for oligodendrocyte proliferation.

PubMed

Manzardo, A M; Gunewardena, S; Butler, M G

2013-09-10

We examined miRNA expression from RNA isolated from the frontal cortex (Broadman area 9) of 9 alcoholics (6 males, 3 females, mean age 48 years) and 9 matched controls using both the Affymetrix GeneChip miRNA 2.0 and Human Exon 1.0 ST Arrays to further characterize genetic influences in alcoholism and the effects of alcohol consumption on predicted target mRNA expression. A total of 12 human miRNAs were significantly up-regulated in alcohol dependent subjects (fold change≥1.5, false discovery rate (FDR)≤0.3; p<0.05) compared with controls including a cluster of 4 miRNAs (e.g., miR-377, miR-379) from the maternally expressed 14q32 chromosome region. The status of the up-regulated miRNAs was supported using the high-throughput method of exon microarrays showing decreased predicted mRNA gene target expression as anticipated from the same RNA aliquot. Predicted mRNA targets were involved in cellular adhesion (e.g., THBS2), tissue differentiation (e.g., CHN2), neuronal migration (e.g., NDE1), myelination (e.g., UGT8, CNP) and oligodendrocyte proliferation (e.g., ENPP2, SEMA4D1). Our data support an association of alcoholism with up-regulation of a cluster of miRNAs located in the genomic imprinted domain on chromosome 14q32 with their predicted gene targets involved with oligodendrocyte growth, differentiation and signaling. Copyright © 2013 Elsevier B.V. All rights reserved.

A microarray analysis of potential genes underlying the neurosensitivity of mice to propofol.

PubMed

Lowes, Damon A; Galley, Helen F; Lowe, Peter R; Rikke, Brad A; Johnson, Thomas E; Webster, Nigel R

2005-09-01

Establishing the mechanism of action of general anesthetics at the molecular level is difficult because of the multiple targets with which these drugs are associated. Inbred short sleep (ISS) and long sleep (ILS) mice are differentially sensitive in response to ethanol and other sedative hypnotics and contain a single quantitative trait locus (Lorp1) that accounts for the genetic variance of loss-of-righting reflex in response to propofol (LORP). In this study, we used high-density oligonucleotide microarrays to identify global gene expression and candidate genes differentially expressed within the Lorp1 region that may give insight into the molecular mechanism underlying LORP. Microarray analysis was performed using Affymetrix MG-U74Av2 Genechips and a selection of differentially expressed genes was confirmed by semiquantitative reverse transcription-polymerase chain reaction. Global expression in the brains of ILS and ISS mice revealed 3423 genes that were significantly expressed, of which 139 (4%) were differentially expressed. Analysis of genes located within the Lorp1 region showed that 26 genes were significantly expressed and that just 2 genes (7%) were differentially expressed. These genes encoded for the proteins AWP1 (associated with protein kinase 1) and "BTB (POZ) domain containing 1," whose functions are largely uncharacterized. Genes differentially expressed outside Lorp1 included seven genes with previously characterized neuronal functions and thus stand out as additional candidate genes that may be involved in mediating the neurosensitivity differences between ISS and ILS.

miR-151-5p, targeting chromatin remodeler SMARCA5, as a marker for the BRCAness phenotype

PubMed Central

Tommasi, Stefania; Pinto, Rosamaria; Danza, Katia; Pilato, Brunella; Palumbo, Orazio; Micale, Lucia; Summa, Simona De

2016-01-01

In recent years, the assessment of biomarkers useful for “precision medicine” has been a hot topic in research. The involvement of microRNAs in the pathogenesis of breast cancer has been highly investigated with the aim of being able to molecularly stratify this highly heterogeneous disease. Our aim was to identify microRNAs targeting DNA repair machinery, through Affymetrix GeneChip miRNA Arrays, in a cohort of BRCA-related and sporadic breast cancers. Moreover, we analyzed microRNA expression taking into account our previous results on the expression of PARP1, because of its importance in targeted therapy. miR-361-5p and miR-151-5p were found to be overexpressed in PARP1-upregulating BRCA-germline mutated and sporadic breast tumors. Pathway enrichment analysis was performed to identify potential target genes to be analyzed in the validation step in an independent cohort. Our results confirmed the overexpression of miR-151-5p and, interestingly, its role in the targeting of SMARCA5, a chromatin remodeler. This result was also confirmed in vitro, both through luciferase assay and by analyzing endogenous levels of SMARCA5 in MCF-7 cell lines using miR-151-5p mimic and inhibitor. In conclusion, our data showed the possibility of considering the overexpression of PARP1 and miR-151-5p as biomarkers useful to correctly treat sporadic breast cancers, which eventually could be considered as BRCAness tumors, with PARP-inhibitors. PMID:27385001

Patterns of gene expression reveal a temporally orchestrated wound healing response in the injured spinal cord.

PubMed

Velardo, Margaret J; Burger, Corinna; Williams, Philip R; Baker, Henry V; López, M Cecilia; Mareci, Thomas H; White, Todd E; Muzyczka, Nicholas; Reier, Paul J

2004-09-29

Spinal cord injury (SCI) induces a progressive pathophysiology affecting cell survival and neurological integrity via complex and evolving molecular cascades whose interrelationships are not fully understood. The present experiments were designed to: (1) determine potential functional interactions within transcriptional expression profiles obtained after a clinically relevant SCI and (2) test the consistency of transcript expression after SCI in two genetically and immunologically diverse rat strains characterized by differences in T cell competence and associated inflammatory responses. By interrogating Affymetrix U34A rat genome GeneChip microarrays, we defined the transcriptional expression patterns in midcervical contusion lesion sites between 1 and 90 d postinjury of athymic nude (AN) and Sprague Dawley (SD) strains. Stringent statistical analyses detected significant changes in 3638 probe sets, with 80 genes differing between the AN and SD groups. Subsequent detailed functional categorization of these transcripts unveiled an overall tissue remodeling response that was common to both strains. The functionally organized gene profiles were temporally distinct and correlated with repair indices observed microscopically and by magnetic resonance microimaging. Our molecular and anatomical observations have identified a novel, longitudinal perspective of the post-SCI response, namely, that of a highly orchestrated tissue repair and remodeling repertoire with a prominent cutaneous wound healing signature that is conserved between two widely differing rat strains. These results have significant bearing on the continuing development of cellular and pharmacological therapeutics directed at tissue rescue and neuronal regeneration in the injured spinal cord.

Arabidopsis gene expression patterns during spaceflight

NASA Astrophysics Data System (ADS)

Paul, A.-L.; Ferl, R. J.

The exposure of Arabidopsis thaliana (Arabidopsis) plants to spaceflight environments resulted in the differential expression of hundreds of genes. A 5 day mission on orbiter Columbia in 1999 (STS-93) carried transgenic Arabidopsis plants engineered with a transgene composed of the alcohol dehydrogenase (Adh) gene promoter linked to the β -Glucuronidase (GUS) reporter gene. The plants were used to evaluate the effects of spaceflight on two fronts. First, expression patterns visualized with the Adh/GUS transgene were used to address specifically the possibility that spaceflight induces a hypoxic stress response, and to assess whether any spaceflight response was similar to control terrestrial hypoxia-induced gene expression patterns. (Paul et al., Plant Physiol. 2001, 126:613). Second, genome-wide patterns of native gene expression were evaluated utilizing the Affymetrix ATH1 GeneChip? array of 8,000 Arabidopsis genes. As a control for the veracity of the array analyses, a selection of genes identified with the arrays was further characterized with quantitative Real-Time RT PCR (ABI - TaqmanTM). Comparison of the patterns of expression for arrays of hybridized with RNA isolated from plants exposed to spaceflight compared to the control arrays revealed hundreds of genes that were differentially expressed in response to spaceflight, yet most genes that are hallmarks of hypoxic stress were unaffected. These results will be discussed in light of current models for plant responses to the spaceflight environment, and with regard to potential future flight opportunities.

Elucidation of the ‘Honeycrisp’ pedigree through haplotype analysis with a multi-family integrated SNP linkage map and a large apple (Malus×domestica) pedigree-connected SNP data set

PubMed Central

Howard, Nicholas P; van de Weg, Eric; Bedford, David S; Peace, Cameron P; Vanderzande, Stijn; Clark, Matthew D; Teh, Soon Li; Cai, Lichun; Luby, James J

2017-01-01

The apple (Malus×domestica) cultivar Honeycrisp has become important economically and as a breeding parent. An earlier study with SSR markers indicated the original recorded pedigree of ‘Honeycrisp’ was incorrect and ‘Keepsake’ was identified as one putative parent, the other being unknown. The objective of this study was to verify ‘Keepsake’ as a parent and identify and genetically describe the unknown parent and its grandparents. A multi-family based dense and high-quality integrated SNP map was created using the apple 8 K Illumina Infinium SNP array. This map was used alongside a large pedigree-connected data set from the RosBREED project to build extended SNP haplotypes and to identify pedigree relationships. ‘Keepsake’ was verified as one parent of ‘Honeycrisp’ and ‘Duchess of Oldenburg’ and ‘Golden Delicious’ were identified as grandparents through the unknown parent. Following this finding, siblings of ‘Honeycrisp’ were identified using the SNP data. Breeding records from several of these siblings suggested that the previously unreported parent is a University of Minnesota selection, MN1627. This selection is no longer available, but now is genetically described through imputed SNP haplotypes. We also present the mosaic grandparental composition of ‘Honeycrisp’ for each of its 17 chromosome pairs. This new pedigree and genetic information will be useful in future pedigree-based genetic studies to connect ‘Honeycrisp’ with other cultivars used widely in apple breeding programs. The created SNP linkage map will benefit future research using the data from the Illumina apple 8 and 20 K and Affymetrix 480 K SNP arrays. PMID:28243452

Map Downloads | USDA Plant Hardiness Zone Map

Science.gov Websites

formats. National, regional, and state maps are available under the View Maps section. Print Quality Maps dpi Graphic TIF 222 MB US Map 300 dpi Adobe Photoshop PS 25 MB *Print quality maps are very large | Non-Discrimination Statement | Information Quality | USA.gov | Whitehouse.gov

Site Map | USDA Plant Hardiness Zone Map

Science.gov Websites

Acknowledgments & Citation Copyright Map & Data Downloads Map Downloads Geography (GIS) Downloads Multi ; Citation Copyright Map & Data Downloads Map Downloads Geography (GIS) Downloads Multi-ZIP Code Finder

Parallel mRNA, proteomics and miRNA expression analysis in cell line models of the intestine.

PubMed

O'Sullivan, Finbarr; Keenan, Joanne; Aherne, Sinead; O'Neill, Fiona; Clarke, Colin; Henry, Michael; Meleady, Paula; Breen, Laura; Barron, Niall; Clynes, Martin; Horgan, Karina; Doolan, Padraig; Murphy, Richard

2017-11-07

To identify miRNA-regulated proteins differentially expressed between Caco2 and HT-29: two principal cell line models of the intestine. Exponentially growing Caco-2 and HT-29 cells were harvested and prepared for mRNA, miRNA and proteomic profiling. mRNA microarray profiling analysis was carried out using the Affymetrix GeneChip Human Gene 1.0 ST array. miRNA microarray profiling analysis was carried out using the Affymetrix Genechip miRNA 3.0 array. Quantitative Label-free LC-MS/MS proteomic analysis was performed using a Dionex Ultimate 3000 RSLCnano system coupled to a hybrid linear ion trap/Orbitrap mass spectrometer. Peptide identities were validated in Proteome Discoverer 2.1 and were subsequently imported into Progenesis QI software for further analysis. Hierarchical cluster analysis for all three parallel datasets (miRNA, proteomics, mRNA) was conducted in the R software environment using the Euclidean distance measure and Ward's clustering algorithm. The prediction of miRNA and oppositely correlated protein/mRNA interactions was performed using TargetScan 6.1. GO biological process, molecular function and cellular component enrichment analysis was carried out for the DE miRNA, protein and mRNA lists via the Pathway Studio 11.3 Web interface using their Mammalian database. Differential expression (DE) profiling comparing the intestinal cell lines HT-29 and Caco-2 identified 1795 Genes, 168 Proteins and 160 miRNAs as DE between the two cell lines. At the gene level, 1084 genes were upregulated and 711 were downregulated in the Caco-2 cell line relative to the HT-29 cell line. At the protein level, 57 proteins were found to be upregulated and 111 downregulated in the Caco-2 cell line relative to the HT-29 cell line. Finally, at the miRNAs level, 104 were upregulated and 56 downregulated in the Caco-2 cell line relative to the HT-29 cell line. Gene ontology (GO) analysis of the DE mRNA identified cell adhesion, migration and ECM organization, cellular lipid

Parallel mRNA, proteomics and miRNA expression analysis in cell line models of the intestine

PubMed Central

O’Sullivan, Finbarr; Keenan, Joanne; Aherne, Sinead; O’Neill, Fiona; Clarke, Colin; Henry, Michael; Meleady, Paula; Breen, Laura; Barron, Niall; Clynes, Martin; Horgan, Karina; Doolan, Padraig; Murphy, Richard

2017-01-01

AIM To identify miRNA-regulated proteins differentially expressed between Caco2 and HT-29: two principal cell line models of the intestine. METHODS Exponentially growing Caco-2 and HT-29 cells were harvested and prepared for mRNA, miRNA and proteomic profiling. mRNA microarray profiling analysis was carried out using the Affymetrix GeneChip Human Gene 1.0 ST array. miRNA microarray profiling analysis was carried out using the Affymetrix Genechip miRNA 3.0 array. Quantitative Label-free LC-MS/MS proteomic analysis was performed using a Dionex Ultimate 3000 RSLCnano system coupled to a hybrid linear ion trap/Orbitrap mass spectrometer. Peptide identities were validated in Proteome Discoverer 2.1 and were subsequently imported into Progenesis QI software for further analysis. Hierarchical cluster analysis for all three parallel datasets (miRNA, proteomics, mRNA) was conducted in the R software environment using the Euclidean distance measure and Ward’s clustering algorithm. The prediction of miRNA and oppositely correlated protein/mRNA interactions was performed using TargetScan 6.1. GO biological process, molecular function and cellular component enrichment analysis was carried out for the DE miRNA, protein and mRNA lists via the Pathway Studio 11.3 Web interface using their Mammalian database. RESULTS Differential expression (DE) profiling comparing the intestinal cell lines HT-29 and Caco-2 identified 1795 Genes, 168 Proteins and 160 miRNAs as DE between the two cell lines. At the gene level, 1084 genes were upregulated and 711 were downregulated in the Caco-2 cell line relative to the HT-29 cell line. At the protein level, 57 proteins were found to be upregulated and 111 downregulated in the Caco-2 cell line relative to the HT-29 cell line. Finally, at the miRNAs level, 104 were upregulated and 56 downregulated in the Caco-2 cell line relative to the HT-29 cell line. Gene ontology (GO) analysis of the DE mRNA identified cell adhesion, migration and ECM

Maps & minds : mapping through the ages

USGS Publications Warehouse

,

1984-01-01

Throughout time, maps have expressed our understanding of our world. Human affairs have been influenced strongly by the quality of maps available to us at the major turning points in our history. "Maps & Minds" traces the ebb and flow of a few central ideas in the mainstream of mapping. Our expanding knowledge of our cosmic neighborhood stems largely from a small number of simple but grand ideas, vigorously pursued.

MapEdit: solution to continuous raster map creation

NASA Astrophysics Data System (ADS)

Rančić, Dejan; Djordjevi-Kajan, Slobodanka

2003-03-01

The paper describes MapEdit, MS Windows TM software for georeferencing and rectification of scanned paper maps. The software produces continuous raster maps which can be used as background in geographical information systems. Process of continuous raster map creation using MapEdit "mosaicking" function is also described as well as the georeferencing and rectification algorithms which are used in MapEdit. Our approach for georeferencing and rectification using four control points and two linear transformations for each scanned map part, together with nearest neighbor resampling method, represents low cost—high speed solution that produce continuous raster maps with satisfactory quality for many purposes (±1 pixel). Quality assessment of several continuous raster maps at different scales that have been created using our software and methodology, has been undertaken and results are presented in the paper. For the quality control of the produced raster maps we referred to three wide adopted standards: US Standard for Digital Cartographic Data, National Standard for Spatial Data Accuracy and US National Map Accuracy Standard. The results obtained during the quality assessment process are given in the paper and show that our maps meat all three standards.

Planetary maps

USGS Publications Warehouse

,

1992-01-01

An important goal of the USGS planetary mapping program is to systematically map the geology of the Moon, Mars, Venus, and Mercury, and the satellites of the outer planets. These geologic maps are published in the USGS Miscellaneous Investigations (I) Series. Planetary maps on sale at the USGS include shaded-relief maps, topographic maps, geologic maps, and controlled photomosaics. Controlled photomosaics are assembled from two or more photographs or images using a network of points of known latitude and longitude. The images used for most of these planetary maps are electronic images, obtained from orbiting television cameras, various optical-mechanical systems. Photographic film was only used to map Earth's Moon.

YouGenMap: a web platform for dynamic multi-comparative mapping and visualization of genetic maps

Treesearch

Keith Batesole; Kokulapalan Wimalanathan; Lin Liu; Fan Zhang; Craig S. Echt; Chun Liang

2014-01-01

Comparative genetic maps are used in examination of genome organization, detection of conserved gene order, and exploration of marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability of users' own genetic mapping between 2 or more map sets. Users' genetic map data and optional gene annotations are...

Mapping Children--Mapping Space.

ERIC Educational Resources Information Center

Pick, Herbert L., Jr.

Research is underway concerning the way the perception, conception, and representation of spatial layout develops. Three concepts are important here--space itself, frame of reference, and cognitive map. Cognitive map refers to a form of representation of the behavioral space, not paired associate or serial response learning. Other criteria…

Maps for the nation: The current federal mapping establishment

USGS Publications Warehouse

North, G.W.

1983-01-01

The U.S. Government annually produces an estimated 53,000 new maps and charts and distributes about 160 million copies. A large number of these maps are produced under the national mapping program, a decentralized Federal/State cooperative approach to mapping the country at standard scales. Circular A-16, issued by the Office of Management and Budget in 1953 and revised in 1967, delegates the mapping responsibilities to various federal agencies. The U.S. Department of the Interior's Geological Survey is the principal federal agency responsible for implementing the national mapping program. Other major federal map producing agencies include the Departments of Agriculture, Commerce, Defense, Housing and Urban Development, and Transportation, and the Tennessee Valley Authority. To make maps and mapping information more readily available, the National Cartographic Information Center was established in 1974 and an expanded National Map Library Depository Program in 1981. The most recent of many technological advances made under the mapping program are in the areas of digital cartography and video disc and optical disc information storage systems. Future trends and changes in the federal mapping program will involve expanded information and customer service operations, further developments in the production and use of digital cartographic data, and consideration of a Federal Mapping Agency. ?? 1983.

Map reading tools for map libraries.

USGS Publications Warehouse

Greenberg, G.L.

1982-01-01

Engineers, navigators and military strategists employ a broad array of mechanical devices to facilitate map use. A larger number of map users such as educators, students, tourists, journalists, historians, politicians, economists and librarians are unaware of the available variety of tools which can be used with maps to increase the speed and efficiency of their application and interpretation. This paper identifies map reading tools such as coordinate readers, protractors, dividers, planimeters, and symbol-templets according to a functional classification. Particularly, arrays of tools are suggested for use in determining position, direction, distance, area and form (perimeter-shape-pattern-relief). -from Author

Gene expression from plants grown on the International Space Station

NASA Astrophysics Data System (ADS)

Stimpson, Alexander; Pereira, Rhea; Kiss, John Z.; Correll, Melanie

Three experiments were performed on the International Space Station (ISS) in 2006 as part of the TROPI experiments. These experiments were performed to study graviTROPIsm and photoTROPIsm responses of Arabidopsis in microgravity (µg). Seedlings were grown with a variety of light and gravitational treatments for approximately five days. The frozen samples were returned to Earth during three space shuttle missions in 2007 and stored at -80° C. Due to the limited amount of plant biomass returned, new protocols were developed to minimize the amount of material needed for RNA extraction as a preparation for microarray analysis. Using these new protocols, RNA was extracted from several sets of seedlings grown in red light followed by blue light with one sample from 1.0g treatment and the other at µg. Using a 2-fold change criterion, microarray (Affymetrix, GeneChip) results showed that 613 genes were upregulated in the µg sample while 757 genes were downregulated. Upregulated genes in response to µg included transcription factors from the WRKY (15 genes), MYB (3) and ZF (8) families as well as those that are involved in auxin responses (10). Downregulated genes also included transcription factors such as MYB (5) and Zinc finger (10) but interestingly only two WRKY family genes were down-regulated during the µg treatment. Studies are underway to compare these results with other samples to identify the genes involved in the gravity and light signal transduction pathways (this project is Supported By: NASA NCC2-1200).

GbTCP, a cotton TCP transcription factor, confers fibre elongation and root hair development by a complex regulating system.

PubMed

Hao, Juan; Tu, Lili; Hu, Haiyan; Tan, Jiafu; Deng, Fenglin; Tang, Wenxin; Nie, Yichun; Zhang, Xianlong

2012-10-01

As the most important natural raw material for textile industry, cotton fibres are an excellent model for studying single-cell development. Although expression profiling and functional genomics have provided some data, the mechanism of fibre development is still not well known. A class I TCP transcription factor (designated GbTCP), encoding 344 amino acids, was isolated from the normalized cDNA library of sea-island cotton fibre (from -2 to 25 days post anthesis). GbTCP was preferentially expressed in the elongating cotton fibre from 5 to 15 days post anthesis. Some expression was also observed in stems, apical buds, and petals. RNAi silencing of GbTCP produced shorter fibre, a reduced lint percentage, and a lower fibre quality than the wild-type plants. Overexpression of GbTCP enhanced root hair initiation and elongation in Arabidopsis and regulated branching. Solexa sequencing and Affymetrix GeneChip analysis indicated that GbTCP positively regulates the level of jasmonic acid (JA) and, as a result, activates downstream genes (reactive oxygen species, calcium signalling, ethylene biosynthesis and response, and several NAC and WRKY transcription factors) necessary for elongation of fibres and root hairs. JA content analysis in cotton also confirmed that GbTCP has a profound effect on JA biosynthesis. In vitro ovule culture showed that an appropriate concentration of JA promoted fibre elongation. The results suggest that GbTCP is an important transcription factor for fibre and root hair development by regulating JA biosynthesis and response and other pathways, including reactive oxygen species, calcium channel and ethylene signalling.

GbTCP, a cotton TCP transcription factor, confers fibre elongation and root hair development by a complex regulating system

PubMed Central

Zhang, Xianlong

2012-01-01

As the most important natural raw material for textile industry, cotton fibres are an excellent model for studying single-cell development. Although expression profiling and functional genomics have provided some data, the mechanism of fibre development is still not well known. A class I TCP transcription factor (designated GbTCP), encoding 344 amino acids, was isolated from the normalized cDNA library of sea-island cotton fibre (from –2 to 25 days post anthesis). GbTCP was preferentially expressed in the elongating cotton fibre from 5 to 15 days post anthesis. Some expression was also observed in stems, apical buds, and petals. RNAi silencing of GbTCP produced shorter fibre, a reduced lint percentage, and a lower fibre quality than the wild-type plants. Overexpression of GbTCP enhanced root hair initiation and elongation in Arabidopsis and regulated branching. Solexa sequencing and Affymetrix GeneChip analysis indicated that GbTCP positively regulates the level of jasmonic acid (JA) and, as a result, activates downstream genes (reactive oxygen species, calcium signalling, ethylene biosynthesis and response, and several NAC and WRKY transcription factors) necessary for elongation of fibres and root hairs. JA content analysis in cotton also confirmed that GbTCP has a profound effect on JA biosynthesis. In vitro ovule culture showed that an appropriate concentration of JA promoted fibre elongation. The results suggest that GbTCP is an important transcription factor for fibre and root hair development by regulating JA biosynthesis and response and other pathways, including reactive oxygen species, calcium channel and ethylene signalling. PMID:23105133

IL-17A Mediates a Selective Gene Expression Profile in Asthmatic Human Airway Smooth Muscle Cells

PubMed Central

Dragon, Stéphane; Hirst, Stuart J.; Lee, Tak H.

2014-01-01

Airway smooth muscle (ASM) cells are thought to contribute to the pathogenesis of allergic asthma by orchestrating and perpetuating airway inflammation and remodeling responses. In this study, we evaluated the IL-17RA signal transduction and gene expression profile in ASM cells from subjects with mild asthma and healthy individuals. Human primary ASM cells were treated with IL-17A and probed by the Affymetrix GeneChip array, and gene targets were validated by real-time quantitative RT-PCR. Genomic analysis underlined the proinflammatory nature of IL-17A, as multiple NF-κB regulatory factors and chemokines were induced in ASM cells. Transcriptional regulators consisting of primary response genes were overrepresented and displayed dynamic expression profiles. IL-17A poorly enhanced IL-1β or IL-22 gene responses in ASM cells from both subjects with mild asthma and healthy donors. Interestingly, protein modifications to the NF-κB regulatory network were not observed after IL-17A stimulation, although oscillations in IκBε expression were detected. ASM cells from subjects with mild asthma up-regulated more genes with greater overall variability in response to IL-17A than from healthy donors. Finally, in response to IL-17A, ASM cells displayed rapid activation of the extracellular signal–regulated kinase/ribosomal S6 kinase signaling pathway and increased nuclear levels of phosphorylated extracellular signal–regulated kinase. Taken together, our results suggest that IL-17A mediated modest gene expression response, which, in cooperation with the NF-κB signaling network, may regulate the gene expression profile in ASM cells. PMID:24393021

Amelioration of hypertensive heart failure by amlodipine may occur via antioxidative effects.

PubMed

Hasegawa, Hiroshi; Takano, Hiroyuki; Kohro, Takahide; Ueda, Kazutaka; Niitsuma, Yuriko; Aburatani, Hiroyuki; Komuro, Issei

2006-09-01

Although recent clinical studies have suggested that long-acting calcium channel blockers (CCBs) have beneficial effects on heart failure, the precise mechanism is unknown. In this study, Dahl salt-sensitive rats fed a high salt diet were treated with the long-acting CCB amlodipine, the low-molecular-weight membrane permeable superoxide dismutase mimetic 4-hydroxy-2,2,6,6-tetramethyl piperidinoxyl (Tempol), or saline from 11 weeks after birth. The cardiac geometry and function, and gene expression profiles were determined at 17 weeks. Dahl salt-sensitive rats fed a high salt diet followed by saline as a non-treatment control (HS group) showed a marked increase in blood pressure and developed concentric hypertrophy at 11 weeks, followed by left ventricular (LV) dilation and congestive heart failure by 17 weeks. The treatment with amlodipine (AMLO group) or Tempol (TEMP group) significantly inhibited the development of LV hypertrophy and cardiac dysfunction. Analysis using an Affymetrix GeneChip U34 revealed that the expression levels of 195 genes were changed by the treatment with amlodipine. Among these 195 genes, 110 genes were increased in HS rats and decreased in AMLO rats. And of these 110 genes, 54 genes were also decreased in TEMP rats. In contrast, 85 genes were decreased in HS rats and increased in AMLO rats. Of these 85 genes, 38 genes were also increased in TEMP rats. Approximately 48% of the genes were changed in similar fashion in AMLO and TEMP rats, suggesting that amlodipine shows beneficial effects on heart failure mainly via antioxidative mechanisms.

Similar response patterns to topical minoxidil foam 5% in frontal and vertex scalp of men with androgenetic alopecia: a microarray analysis.

PubMed

Mirmirani, P; Consolo, M; Oyetakin-White, P; Baron, E; Leahy, P; Karnik, P

2015-06-01

There are regional variations in the scalp hair miniaturization seen in androgenetic alopecia (AGA). Use of topical minoxidil can lead to reversal of miniaturization in the vertex scalp. However, its effects on other scalp regions have been less well studied. To determine whether scalp biopsies from men with AGA show variable gene expression before and after 8 weeks of treatment with minoxidil topical foam 5% (MTF) vs. placebo. A placebo-controlled double-blinded prospective pilot study of MTF vs. placebo was conducted in 16 healthy men aged 18-49 years with Hamilton-Norwood type IV-V thinning. The subjects were asked to apply the treatment (active drug or placebo) to the scalp twice daily for 8 weeks. Stereotactic scalp photographs were taken at the baseline and final visits, to monitor global hair growth. Scalp biopsies were taken at the leading edge of hair loss from the frontal and vertex scalp before and after treatment with MTF and placebo, and microarray analysis was performed using the Affymetrix GeneChip HG U133 Plus 2.0. Global stereotactic photographs showed that MTF induced hair growth in both the frontal and vertex scalp of patients with AGA. Regional differences in gene expression profiles were observed before treatment. However, MTF treatment induced the expression of hair keratin-associated genes and decreased the expression of epidermal differentiation complex and inflammatory genes in both scalp regions. These data suggest that MTF is effective in the treatment of both the frontal and vertex scalp of patients with AGA. © 2014 British Association of Dermatologists.

Inhibiting glycogen synthase kinase-3 and transforming growth factor-β signaling to promote epithelial transition of human adipose mesenchymal stem cells.

PubMed

Setiawan, Melina; Tan, Xiao-Wei; Goh, Tze-Wei; Hin-Fai Yam, Gary; Mehta, Jodhbir S

2017-09-02

This study was aimed to investigate the epithelial differentiation of human adipose-derived mesenchymal stem cells (ADSCs) by inhibiting glycogen synthase kinase-3 (GSK3) and transforming growth factor β (TGFβ) signaling. STEMPRO human ADSCs at passage 2 were treated with CHIR99021 (GSK3 inhibitor), E-616452 (TGFβ1 receptor kinase inhibitor), A-83-01 (TGFβ type 1 receptor inhibitor), valproic acid (histone deacetylase inhibitor), tranylcypromine (monoamine oxidase inhibitor) and all-trans retinoic acid for 72 h. The mesenchymal-epithelial transition was shown by down-regulation of mesenchymal genes (Slug, Zinc Finger E-box Binding Homeobox 1 ZEB1, integrin α5 ITGA5 and vimentin VIM) and up-regulation of epithelial genes (E-cadherin, Epithelial Cell Adhesion Molecule EpCAM, Zonula Occludens-1 ZO-1, occludin, deltaN p63 δNp63, Transcription Factor 4 TCF4 and Twist Family bHLH Transcription Factor TWIST), compared to untreated ADSCs. Cell morphology and stress fiber pattern were examined and the treated cells became less migratory in scratch wound closure assay. The formation of cell junction complexes was observed under transmission electron microscopy. Global gene expression using GeneChip ® Human Genome U133 Array (Affymetrix) showed that the treatment up-regulated 540 genes (containing genes for cell cycle, cytoskeleton reorganization, chemotaxis, epithelium development and regulation of cell migration) and down-regulated 483 genes. Human ADSCs were transited to epithelial lineage by inhibiting GSK3 and TGFβ signaling. It can be an adult stem cell source for epithelial cell-based therapy. Copyright © 2017 Elsevier Inc. All rights reserved.

Transcriptional profiling of root-knot nematode induced feeding sites in cowpea (Vigna unguiculata L. Walp.) using a soybean genome array.

PubMed

Das, Sayan; Ehlers, Jeffrey D; Close, Timothy J; Roberts, Philip A

2010-08-19

The locus Rk confers resistance against several species of root-knot nematodes (Meloidogyne spp., RKN) in cowpea (Vigna unguiculata). Based on histological and reactive oxygen species (ROS) profiles, Rk confers a delayed but strong resistance mechanism without a hypersensitive reaction-mediated cell death process, which allows nematode development but blocks reproduction. Responses to M. incognita infection in roots of resistant genotype CB46 and a susceptible near-isogenic line (null-Rk) were investigated using a soybean Affymetrix GeneChip expression array at 3 and 9 days post-inoculation (dpi). At 9 dpi 552 genes were differentially expressed in incompatible interactions (infected resistant tissue compared with non-infected resistant tissue) and 1,060 genes were differentially expressed in compatible interactions (infected susceptible tissue compared with non-infected susceptible tissue). At 3 dpi the differentially expressed genes were 746 for the incompatible and 623 for the compatible interactions. When expression between infected resistant and susceptible genotypes was compared, 638 and 197 genes were differentially expressed at 9 and 3 dpi, respectively. In comparing the differentially expressed genes in response to nematode infection, a greater number and proportion of genes were down-regulated in the resistant than in the susceptible genotype, whereas more genes were up-regulated in the susceptible than in the resistant genotype. Gene ontology based functional categorization revealed that the typical defense response was partially suppressed in resistant roots, even at 9 dpi, allowing nematode juvenile development. Differences in ROS concentrations, induction of toxins and other defense related genes seem to play a role in this unique resistance mechanism.

Effect of the difference in vehicles on gene expression in the rat liver--analysis of the control data in the Toxicogenomics Project Database.

PubMed

Takashima, Kayoko; Mizukawa, Yumiko; Morishita, Katsumi; Okuyama, Manabu; Kasahara, Toshihiko; Toritsuka, Naoki; Miyagishima, Toshikazu; Nagao, Taku; Urushidani, Tetsuro

2006-05-08

The Toxicogenomics Project is a 5-year collaborative project by the Japanese government and pharmaceutical companies in 2002. Its aim is to construct a large-scale toxicology database of 150 compounds orally administered to rats. The test consists of a single administration test (3, 6, 9 and 24 h) and a repeated administration test (3, 7, 14 and 28 days), and the conventional toxicology data together with the gene expression data in liver as analyzed by using Affymetrix GeneChip are being accumulated. In the project, either methylcellulose or corn oil is employed as vehicle. We examined whether the vehicle itself affects the analysis of gene expression and found that corn oil alone affected the food consumption and biochemical parameters mainly related to lipid metabolism, and this accompanied typical changes in the gene expression. Most of the genes modulated by corn oil were related to cholesterol or fatty acid metabolism (e.g., CYP7A1, CYP8B1, 3-hydroxy-3-methylglutaryl-Coenzyme A reductase, squalene epoxidase, angiopoietin-like protein 4, fatty acid synthase, fatty acid binding proteins), suggesting that the response was physiologic to the oil intake. Many of the lipid-related genes showed circadian rhythm within a day, but the expression pattern of general clock genes (e.g., period 2, arylhydrocarbon nuclear receptor translocator-like, D site albumin promoter binding protein) were unaffected by corn oil, suggesting that the effects are specific for lipid metabolism. These results would be useful for usage of the database especially when drugs with different vehicle control are compared.

Transcriptome profiling of visceral adipose tissue in a novel obese rat model, WNIN/Ob & its comparison with other animal models.

PubMed

Sakamuri, Siva Sankara Vara Prasad; Putcha, Uday Kumar; Veettil, Giridharan Nappan; Ayyalasomayajula, Vajreswari

2016-09-01

Adipose tissue dysfunction in obesity is linked to the development of type 2 diabetes and cardiovascular diseases. We studied the differential gene expression in retroperitoneal adipose tissue of a novel obese rat model, WNIN/Ob, to understand the possible underlying transcriptional changes involved in the development of obesity and associatedcomorbidities in this model. Four month old, male WNIN/Ob lean and obese rats were taken, blood was collected and tissues were dissected. Body composition analysis and adipose tissue histology were performed. Global gene expression in retroperitoneal adipose tissue of lean and obese rats was studied by microarray using Affymetrix GeneChips. One thousand and seventeen probe sets were downregulated and 963 probe sets were upregulated (more than two-fold) in adipose tissue of WNIN/Ob obese rats when compared to that of lean rats. Small nucleolar RNA (SnoRNA) made most of the underexpressed probe sets, whereas immune system-related genes werethe most overexpressed in the adipose tissues of obese rats. Genes coding for cytoskeletal proteinswere downregulated, whereas genes related to lipid biosynthesis were elevated in the adipose tissue of obese rats. Majority of the altered genes and pathways in adipose tissue of WNIN/Ob obese rats were similar to the observations in other obese animal models and human obesity. Based on these observations, it is proposed that WNIN/Ob obese rat model may be a good model to study the mechanisms involved in the development of obesity and its comorbidities. Downregulation of SnoRNA appears to be a novel feature in this obese rat model.

The BCL2 antagonist of cell death pathway influences endometrial cancer cell sensitivity to cisplatin.

PubMed

Chon, Hye Sook; Marchion, Douglas C; Xiong, Yin; Chen, Ning; Bicaku, Elona; Stickles, Xiaomang Ba; Bou Zgheib, Nadim; Judson, Patricia L; Hakam, Ardeshir; Gonzalez-Bosquet, Jesus; Wenham, Robert M; Apte, Sachin M; Lancaster, Johnathan M

2012-01-01

To identify pathways that influence endometrial cancer (EC) cell sensitivity to cisplatin and to characterize the BCL2 antagonist of cell death (BAD) pathway as a therapeutic target to increase cisplatin sensitivity. Eight EC cell lines (Ishikawa, MFE296, RL 95-2, AN3CA, KLE, MFE280, MFE319, HEC-1-A) were subjected to Affymetrix Human U133A GeneChip expression analysis of approximately 22,000 probe sets. In parallel, endometrial cell line sensitivity to cisplatin was quantified by MTS assay, and IC(50) values were calculated. Pearson's correlation test was used to identify genes associated with response to cisplatin. Genes associated with cisplatin responsiveness were subjected to pathway analysis. The BAD pathway was identified and subjected to targeted modulation, and the effect on cisplatin sensitivity was evaluated. Pearson's correlation analysis identified 1443 genes associated with cisplatin resistance (P<0.05), which included representation of the BAD-apoptosis pathway. Small interfering RNA (siRNA) knockdown of BAD pathway protein phosphatase PP2C expression was associated with increased phosphorylated BAD (serine-155) levels and a parallel increase in cisplatin resistance in Ishikawa (P=0.004) and HEC-1-A (P=0.02) cell lines. In contrast, siRNA knockdown of protein kinase A expression increased cisplatin sensitivity in the Ishikawa (P=0.02) cell line. The BAD pathway influences EC cell sensitivity to cisplatin, likely via modulation of the phosphorylation status of the BAD protein. The BAD pathway represents an appealing therapeutic target to increase EC cell sensitivity to cisplatin. Copyright © 2011 Elsevier Inc. All rights reserved.

Genetically Determined Susceptibility to Tuberculosis in Mice Causally Involves Accelerated and Enhanced Recruitment of Granulocytes

PubMed Central

Keller, Christine; Hoffmann, Reinhard; Lang, Roland; Brandau, Sven; Hermann, Corinna; Ehlers, Stefan

2006-01-01

Classical twin studies and recent linkage analyses of African populations have revealed a potential involvement of host genetic factors in susceptibility or resistance to Mycobacterium tuberculosis infection. In order to identify the candidate genes involved and test their causal implication, we capitalized on the mouse model of tuberculosis, since inbred mouse strains also differ substantially in their susceptibility to infection. Two susceptible and two resistant mouse strains were aerogenically infected with 1,000 CFU of M. tuberculosis, and the regulation of gene expression was examined by Affymetrix GeneChip U74A array with total lung RNA 2 and 4 weeks postinfection. Four weeks after infection, 96 genes, many of which are involved in inflammatory cell recruitment and activation, were regulated in common. One hundred seven genes were differentially regulated in susceptible mouse strains, whereas 43 genes were differentially expressed only in resistant mice. Data mining revealed a bias towards the expression of genes involved in granulocyte pathophysiology in susceptible mice, such as an upregulation of those for the neutrophil chemoattractant LIX (CXCL5), interleukin 17 receptor, phosphoinositide kinase 3 delta, or gamma interferon-inducible protein 10. Following M. tuberculosis challenge in both airways or peritoneum, granulocytes were recruited significantly faster and at higher numbers in susceptible than in resistant mice. When granulocytes were efficiently depleted by either of two regimens at the onset of infection, only susceptible mice survived aerosol challenge with M. tuberculosis significantly longer than control mice. We conclude that initially enhanced recruitment of granulocytes contributes to susceptibility to tuberculosis. PMID:16790804

The effect of maternal chromium status on lipid metabolism in female elderly mice offspring and involved molecular mechanism.

PubMed

Zhang, Qian; Sun, Xiaofang; Xiao, Xinhua; Zheng, Jia; Li, Ming; Yu, Miao; Ping, Fan; Wang, Zhixin; Qi, Cuijuan; Wang, Tong; Wang, Xiaojing

2017-04-30

Maternal malnutrition leads to the incidence of metabolic diseases in offspring. The purpose of this project was to examine whether maternal low chromium could disturb normal lipid metabolism in offspring, altering adipose cell differentiation and leading to the incidence of lipid metabolism diseases, including metabolic syndrome and obesity. Female C57BL mice were given a control diet (CD) or a low chromium diet (LCD) during the gestational and lactation periods. After weaning, offspring was fed with CD or LCD. The female offspring were assessed at 32 weeks of age. Fresh adipose samples from CD-CD group and LCD-CD group were collected. Genome mRNA were analysed using Affymetrix GeneChip Mouse Gene 2.0 ST Whole Transcript-based array. Differentially expressed genes (DEGs) were analysed based on gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis database. Maternal low chromium irreversibly increased offspring body weight, fat-pad weight, serum triglyceride (TG) and TNF-α. Eighty five genes increased and 109 genes reduced in the offspring adipose of the maternal low chromium group. According to KEGG pathway and String analyses, the PPAR signalling pathway may be the key controlled pathway related to the effect of maternal low chromium on female offspring. Maternal chromium status have long-term effects of lipid metabolism in female mice offspring. Normalizing offspring diet can not reverse these effects. The potential underlying mechanisms are the disturbance of the PPAR signalling pathway in adipose tissue. © 2017 The Author(s).

Gene expression profiles characterize early graft response in living donor small bowel transplantation: a case report.

PubMed

Bradley, S P; Pahari, M; Uknis, M E; Rastellini, C; Cicalese, L

2006-01-01

The cellular and histological events that occur during the regeneration process in invertebrates have been studied in the field of visceral regeneration. We would like to explore the molecular aspects of the regeneration process in the small intestine. The aim of this study was to characterize the gene expression profiles of the intestinal graft to identify which genes may have a role in regeneration of graft tissue posttransplant. In a patient undergoing living related small bowel transplantation (LRSBTx) in our institution, mucosal biopsies were obtained from the recipient intestine and donor graft at the time of transplant and at weeks 1, 2, 3, and 6 posttransplant. Total RNA was isolated from sample biopsies followed by gene expression profiles determined from the replicate samples (n = 3) for each biopsy using the Affymetrix U133 Plus 2.0 Human GeneChip set. Two profiles were obtained from the data. One profile showed rapid increase of 45 genes immediately after transplant by week 1 with significant changes (P < .05) greater than threefold including the chemokine CXC9 and glutathione-related stress factors, GPX2 and GSTA4. The second profile identified 133 genes that were significantly decreased by threefold or greater immediately after transplant week 1, including UCC1, the human homolog of the Ependymin gene. We have identified two gene expression profiles representing early graft responses to small bowel transplantation. These profiles will serve to identify and study those genes whose products may play a role in accelerating tissue regeneration following segmental LRSBTx.

Genetic Diversity of the Q Fever Agent, Coxiella burnetii, Assessed by Microarray-Based Whole-Genome Comparisons†

PubMed Central

Beare, Paul A.; Samuel, James E.; Howe, Dale; Virtaneva, Kimmo; Porcella, Stephen F.; Heinzen, Robert A.

2006-01-01

Coxiella burnetii, a gram-negative obligate intracellular bacterium, causes human Q fever and is considered a potential agent of bioterrorism. Distinct genomic groups of C. burnetii are revealed by restriction fragment-length polymorphisms (RFLP). Here we comprehensively define the genetic diversity of C. burnetii by hybridizing the genomes of 20 RFLP-grouped and four ungrouped isolates from disparate sources to a high-density custom Affymetrix GeneChip containing all open reading frames (ORFs) of the Nine Mile phase I (NMI) reference isolate. We confirmed the relatedness of RFLP-grouped isolates and showed that two ungrouped isolates represent distinct genomic groups. Isolates contained up to 20 genomic polymorphisms consisting of 1 to 18 ORFs each. These were mostly complete ORF deletions, although partial deletions, point mutations, and insertions were also identified. A total of 139 chromosomal and plasmid ORFs were polymorphic among all C. burnetii isolates, representing ca. 7% of the NMI coding capacity. Approximately 67% of all deleted ORFs were hypothetical, while 9% were annotated in NMI as nonfunctional (e.g., frameshifted). The remaining deleted ORFs were associated with diverse cellular functions. The only deletions associated with isogenic NMI variants of attenuated virulence were previously described large deletions containing genes involved in lipopolysaccharide (LPS) biosynthesis, suggesting that these polymorphisms alone are responsible for the lower virulence of these variants. Interestingly, a variant of the Australia QD isolate producing truncated LPS had no detectable deletions, indicating LPS truncation can occur via small genetic changes. Our results provide new insight into the genetic diversity and virulence potential of Coxiella species. PMID:16547017

TGFbeta and miRNA regulation in familial and sporadic breast cancer

PubMed Central

Pinto, Rosamaria; Pilato, Brunella; Palumbo, Orazio; Carella, Massimo; Popescu, Ondina; Digennaro, Maria; Lacalamita, Rosanna; Tommasi, Stefania

2017-01-01

The term ‘BRCAness’ was introduced to identify sporadic malignant tumors sharing characteristics similar to those germline BRCA-related. Among all mechanisms attributable to BRCA1 expression silencing, a major role has been assigned to microRNAs. MicroRNAs role in familial and sporadic breast cancer has been explored but few data are available about microRNAs involvement in homologous recombination repair control in these breast cancer subgroups. Our aim was to seek microRNAs associated to pathways underlying DNA repair dysfunction in breast cancer according to a family history of the disease. Affymetrix GeneChip microRNA Arrays were used to perform microRNA expression analysis in familial and sporadic breast cancer. Pathway enrichment analysis and microRNA target prediction was carried out using DIANA miRPath v.3 web-based computational tool and miRWalk v.2 database. We analyzed an external gene expression dataset (E-GEOD-49481), including both familial and sporadic breast cancers. For microRNA validation, an independent set of 19 familial and 10 sporadic breast cancers was used. Microarray analysis identified a signature of 28 deregulated miRNAs. For our validation analyses by real time PCR, we focused on miR-92a-1*, miR-1184 and miR-943 because associated to TGF-β signalling pathway, ATM and BRCA1 genes expression. Our results highlighted alterations in miR-92a-1*, miR-1184 and miR-943 expression levels suggesting their involvement in repair of DNA double-strand breaks through TGF-beta pathway control. PMID:28881597

Form-Deprivation Myopia in Chick Induces Limited Changes in Retinal Gene Expression

PubMed Central

McGlinn, Alice M.; Baldwin, Donald A.; Tobias, John W.; Budak, Murat T.; Khurana, Tejvir S.; Stone, Richard A.

2007-01-01

Purpose Evidence has implicated the retina as a principal controller of refractive development. In the present study, the retinal transcriptome was analyzed to identify alterations in gene expression and potential signaling pathways involved in form-deprivation myopia of the chick. Methods One-week-old white Leghorn chicks wore a unilateral image-degrading goggle for 6 hours or 3 days (n = 6 at each time). Total RNA from the retina/(retinal pigment epithelium) was used for expression profiling with chicken gene microarrays (Chicken GeneChips; Affymetrix, Santa Clara, CA). To identify gene expression level differences between goggled and contralateral nongoggled eyes, normalized microarray signal intensities were analyzed by the significance analysis of microarrays (SAM) approach. Differentially expressed genes were validated by real-time quantitative reverse transcription–polymerase chain reaction (qPCR) in independent biological replicates. Results Small changes were detected in differentially expressed genes in form-deprived eyes. In chickens that had 6 hours of goggle wear, downregulation of bone morphogenetic protein 2 and connective tissue growth factor was validated. In those with 3 days of goggle wear, downregulation of bone morphogenetic protein 2, vasoactive intestinal peptide, preopro-urotensin II–related peptide and mitogen-activated protein kinase phosphatase 2 was validated, and upregulation of endothelin receptor type B and interleukin-18 was validated. Conclusions Form-deprivation myopia, in its early stages, is associated with only minimal changes in retinal gene expression at the level of the transcriptome. While the list of validated genes is short, each merits further study for potential involvement in the signaling cascade mediating myopia development. PMID:17652709

F-box protein DOR functions as a novel inhibitory factor for abscisic acid-induced stomatal closure under drought stress in Arabidopsis,.

PubMed

Zhang, Yu'e; Xu, Wenying; Li, Zhonghui; Deng, Xing Wang; Wu, Weihua; Xue, Yongbiao

2008-12-01

Guard cells, which form stoma in leaf epidermis, sense and integrate environmental signals to modulate stomatal aperture in response to diverse conditions. Under drought stress, plants synthesize abscisic acid (ABA), which in turn induces a rapid closing of stoma, to prevent water loss by transpiration. However, many aspects of the molecular mechanism for ABA-mediated stomatal closure are still not understood. Here, we report a novel negative regulator of guard cell ABA signaling, DOR, in Arabidopsis (Arabidopsis thaliana). The DOR gene encodes a putative F-box protein, a member of the S-locus F-box-like family related to AhSLF-S(2) and specifically interacting with ASK14 and CUL1. A null mutation in DOR resulted in a hypersensitive ABA response of stomatal closing and a substantial increase of drought tolerance; in contrast, the transgenic plants overexpressing DOR were more susceptible to the drought stress. DOR is strongly expressed in guard cells and suppressed by ABA treatment, suggesting a negative feedback loop of DOR in ABA responses. Double-mutant analyses of dor with ABA-insensitive mutant abi1-1 showed that abi1-1 is epistatic to dor, but no apparent change of phospholipase Dalpha1 was detected between the wild type and dor. Affymetrix GeneChip analysis showed that DOR likely regulates ABA biosynthesis under drought stress. Taken together, our results demonstrate that DOR acts independent of phospholipase Dalpha1 in an ABA signaling pathway to inhibit the ABA-induced stomatal closure under drought stress.

Comparison of Two Methods for Detecting Alternative Splice Variants Using GeneChip® Exon Arrays

PubMed Central

Fan, Wenhong; Stirewalt, Derek L.; Radich, Jerald P.; Zhao, Lueping

2011-01-01

The Affymetrix GeneChip Exon Array can be used to detect alternative splice variants. Microarray Detection of Alternative Splicing (MIDAS) and Partek® Genomics Suite (Partek® GS) are among the most popular analytical methods used to analyze exon array data. While both methods utilize statistical significance for testing, MIDAS and Partek® GS could produce somewhat different results due to different underlying assumptions. Comparing MIDAS and Partek® GS is quite difficult due to their substantially different mathematical formulations and assumptions regarding alternative splice variants. For meaningful comparison, we have used the previously published generalized probe model (GPM) which encompasses both MIDAS and Partek® GS under different assumptions. We analyzed a colon cancer exon array data set using MIDAS, Partek® GS and GPM. MIDAS and Partek® GS produced quite different sets of genes that are considered to have alternative splice variants. Further, we found that GPM produced results similar to MIDAS as well as to Partek® GS under their respective assumptions. Within the GPM, we show how discoveries relating to alternative variants can be quite different due to different assumptions. MIDAS focuses on relative changes in expression values across different exons within genes and tends to be robust but less efficient. Partek® GS, however, uses absolute expression values of individual exons within genes and tends to be more efficient but more sensitive to the presence of outliers. From our observations, we conclude that MIDAS and Partek® GS produce complementary results, and discoveries from both analyses should be considered. PMID:23675234

IL-17/Th17 Pathway Is Activated in Acne Lesions

PubMed Central

Kelhälä, Hanna-Leena; Palatsi, Riitta; Fyhrquist, Nanna; Lehtimäki, Sari; Väyrynen, Juha P.; Kallioinen, Matti; Kubin, Minna E.; Greco, Dario; Tasanen, Kaisa; Alenius, Harri; Bertino, Beatrice; Carlavan, Isabelle; Mehul, Bruno; Déret, Sophie; Reiniche, Pascale; Martel, Philippe; Marty, Carine; Blume-Peytavi, Ulrike; Voegel, Johannes J.; Lauerma, Antti

2014-01-01

The mechanisms of inflammation in acne are currently subject of intense investigation. This study focused on the activation of adaptive and innate immunity in clinically early visible inflamed acne lesions and was performed in two independent patient populations. Biopsies were collected from lesional and non-lesional skin of acne patients. Using Affymetrix Genechips, we observed significant elevation of the signature cytokines of the Th17 lineage in acne lesions compared to non-lesional skin. The increased expression of IL-17 was confirmed at the RNA and also protein level with real-time PCR (RT-PCR) and Luminex technology. Cytokines involved in Th17 lineage differentiation (IL-1β, IL-6, TGF-β, IL23p19) were remarkably induced at the RNA level. In addition, proinflammatory cytokines and chemokines (TNF-α, IL-8, CSF2 and CCL20), Th1 markers (IL12p40, CXCR3, T-bet, IFN-γ), T regulatory cell markers (Foxp3, IL-10, TGF-β) and IL-17 related antimicrobial peptides (S100A7, S100A9, lipocalin, hBD2, hBD3, hCAP18) were induced. Importantly, immunohistochemistry revealed significantly increased numbers of IL-17A positive T cells and CD83 dendritic cells in the acne lesions. In summary our results demonstrate the presence of IL-17A positive T cells and the activation of Th17-related cytokines in acne lesions, indicating that the Th17 pathway is activated and may play a pivotal role in the disease process, possibly offering new targets of therapy. PMID:25153527

Oxygen and tissue culture affect placental gene expression.

PubMed

Brew, O; Sullivan, M H F

2017-07-01

Placental explant culture is an important model for studying placental development and functions. We investigated the differences in placental gene expression in response to tissue culture, atmospheric and physiologic oxygen concentrations. Placental explants were collected from normal term (38-39 weeks of gestation) placentae with no previous uterine contractile activity. Placental transcriptomic expressions were evaluated with GeneChip ® Human Genome U133 Plus 2.0 arrays (Affymetrix). We uncovered sub-sets of genes that regulate response to stress, induction of apoptosis programmed cell death, mis-regulation of cell growth, proliferation, cell morphogenesis, tissue viability, and protection from apoptosis in cultured placental explants. We also identified a sub-set of genes with highly unstable pattern of expression after exposure to tissue culture. Tissue culture irrespective of oxygen concentration induced dichotomous increase in significant gene expression and increased enrichment of significant pathways and transcription factor targets (TFTs) including HIF1A. The effect was exacerbated by culture at atmospheric oxygen concentration, where further up-regulation of TFTs including PPARA, CEBPD, HOXA9 and down-regulated TFTs such as JUND/FOS suggest intrinsic heightened key biological and metabolic mechanisms such as glucose use, lipid biosynthesis, protein metabolism; apoptosis, inflammatory responses; and diminished trophoblast proliferation, differentiation, invasion, regeneration, and viability. These findings demonstrate that gene expression patterns differ between pre-culture and cultured explants, and the gene expression of explants cultured at atmospheric oxygen concentration favours stressed, pro-inflammatory and increased apoptotic transcriptomic response. Copyright © 2017 Elsevier Ltd. All rights reserved.

Generalized Smooth Transition Map Between Tent and Logistic Maps

NASA Astrophysics Data System (ADS)

Sayed, Wafaa S.; Fahmy, Hossam A. H.; Rezk, Ahmed A.; Radwan, Ahmed G.

There is a continuous demand on novel chaotic generators to be employed in various modeling and pseudo-random number generation applications. This paper proposes a new chaotic map which is a general form for one-dimensional discrete-time maps employing the power function with the tent and logistic maps as special cases. The proposed map uses extra parameters to provide responses that fit multiple applications for which conventional maps were not enough. The proposed generalization covers also maps whose iterative relations are not based on polynomials, i.e. with fractional powers. We introduce a framework for analyzing the proposed map mathematically and predicting its behavior for various combinations of its parameters. In addition, we present and explain the transition map which results in intermediate responses as the parameters vary from their values corresponding to tent map to those corresponding to logistic map case. We study the properties of the proposed map including graph of the map equation, general bifurcation diagram and its key-points, output sequences, and maximum Lyapunov exponent. We present further explorations such as effects of scaling, system response with respect to the new parameters, and operating ranges other than transition region. Finally, a stream cipher system based on the generalized transition map validates its utility for image encryption applications. The system allows the construction of more efficient encryption keys which enhances its sensitivity and other cryptographic properties.

Story Map Instruction: A Road Map for Reading Comprehension.

ERIC Educational Resources Information Center

Davis, Zephaniah, T.; McPherson, Michael D.

1989-01-01

Introduces teachers to the development and use of story maps as a tool for promoting reading comprehension. Presents a definition and review of story map research. Explains how to construct story maps, and offers suggestions for starting story map instruction. Provides variations on the use of story maps. (MG)

Contour Mapping

NASA Technical Reports Server (NTRS)

1995-01-01

In the early 1990s, the Ohio State University Center for Mapping, a NASA Center for the Commercial Development of Space (CCDS), developed a system for mobile mapping called the GPSVan. While driving, the users can map an area from the sophisticated mapping van equipped with satellite signal receivers, video cameras and computer systems for collecting and storing mapping data. George J. Igel and Company and the Ohio State University Center for Mapping advanced the technology for use in determining the contours of a construction site. The new system reduces the time required for mapping and staking, and can monitor the amount of soil moved.

Topographic mapping

USGS Publications Warehouse

,

2008-01-01

The U.S. Geological Survey (USGS) produced its first topographic map in 1879, the same year it was established. Today, more than 100 years and millions of map copies later, topographic mapping is still a central activity for the USGS. The topographic map remains an indispensable tool for government, science, industry, and leisure. Much has changed since early topographers traveled the unsettled West and carefully plotted the first USGS maps by hand. Advances in survey techniques, instrumentation, and design and printing technologies, as well as the use of aerial photography and satellite data, have dramatically improved mapping coverage, accuracy, and efficiency. Yet cartography, the art and science of mapping, may never before have undergone change more profound than today.

African Ancestry Analysis and Admixture Genetic Mapping for Proliferative Diabetic Retinopathy in African Americans.

PubMed

Tandon, Arti; Chen, Ching J; Penman, Alan; Hancock, Heather; James, Maurice; Husain, Deeba; Andreoli, Christopher; Li, Xiaohui; Kuo, Jane Z; Idowu, Omolola; Riche, Daniel; Papavasilieou, Evangelia; Brauner, Stacey; Smith, Sataria O; Hoadley, Suzanne; Richardson, Cole; Kieser, Troy; Vazquez, Vanessa; Chi, Cheryl; Fernandez, Marlene; Harden, Maegan; Cotch, Mary Frances; Siscovick, David; Taylor, Herman A; Wilson, James G; Reich, David; Wong, Tien Y; Klein, Ronald; Klein, Barbara E K; Rotter, Jerome I; Patterson, Nick; Sobrin, Lucia

2015-06-01

To examine the relationship between proportion of African ancestry (PAA) and proliferative diabetic retinopathy (PDR) and to identify genetic loci associated with PDR using admixture mapping in African Americans with type 2 diabetes (T2D). Between 1993 and 2013, 1440 participants enrolled in four different studies had fundus photographs graded using the Early Treatment Diabetic Retinopathy Study scale. Cases (n = 305) had PDR while controls (n = 1135) had nonproliferative diabetic retinopathy (DR) or no DR. Covariates included diabetes duration, hemoglobin A1C, systolic blood pressure, income, and education. Genotyping was performed on the Affymetrix platform. The association between PAA and PDR was evaluated using logistic regression. Genome-wide admixture scanning was performed using ANCESTRYMAP software. In the univariate analysis, PDR was associated with increased PAA (odds ratio [OR] = 1.36, 95% confidence interval [CI] = 1.16-1.59, P = 0.0002). In multivariate regression adjusting for traditional DR risk factors, income and education, the association between PAA and PDR was attenuated and no longer significant (OR = 1.21, 95% CI = 0.59-2.47, P = 0.61). For the admixture analyses, the maximum genome-wide score was 1.44 on chromosome 1. In this largest study of PDR in African Americans with T2D to date, an association between PAA and PDR is not present after adjustment for clinical, demographic, and socioeconomic factors. No genome-wide significant locus (defined as having a locus-genome statistic > 5) was identified with admixture analysis. Further analyses with even larger sample sizes are needed to definitively assess if any admixture signal for DR is present.

African Ancestry Analysis and Admixture Genetic Mapping for Proliferative Diabetic Retinopathy in African Americans

PubMed Central

Tandon, Arti; Chen, Ching J.; Penman, Alan; Hancock, Heather; James, Maurice; Husain, Deeba; Andreoli, Christopher; Li, Xiaohui; Kuo, Jane Z.; Idowu, Omolola; Riche, Daniel; Papavasilieou, Evangelia; Brauner, Stacey; Smith, Sataria O.; Hoadley, Suzanne; Richardson, Cole; Kieser, Troy; Vazquez, Vanessa; Chi, Cheryl; Fernandez, Marlene; Harden, Maegan; Cotch, Mary Frances; Siscovick, David; Taylor, Herman A.; Wilson, James G.; Reich, David; Wong, Tien Y.; Klein, Ronald; Klein, Barbara E. K.; Rotter, Jerome I.; Patterson, Nick; Sobrin, Lucia

2015-01-01

Purpose. To examine the relationship between proportion of African ancestry (PAA) and proliferative diabetic retinopathy (PDR) and to identify genetic loci associated with PDR using admixture mapping in African Americans with type 2 diabetes (T2D). Methods. Between 1993 and 2013, 1440 participants enrolled in four different studies had fundus photographs graded using the Early Treatment Diabetic Retinopathy Study scale. Cases (n = 305) had PDR while controls (n = 1135) had nonproliferative diabetic retinopathy (DR) or no DR. Covariates included diabetes duration, hemoglobin A1C, systolic blood pressure, income, and education. Genotyping was performed on the Affymetrix platform. The association between PAA and PDR was evaluated using logistic regression. Genome-wide admixture scanning was performed using ANCESTRYMAP software. Results. In the univariate analysis, PDR was associated with increased PAA (odds ratio [OR] = 1.36, 95% confidence interval [CI] = 1.16–1.59, P = 0.0002). In multivariate regression adjusting for traditional DR risk factors, income and education, the association between PAA and PDR was attenuated and no longer significant (OR = 1.21, 95% CI = 0.59–2.47, P = 0.61). For the admixture analyses, the maximum genome-wide score was 1.44 on chromosome 1. Conclusions. In this largest study of PDR in African Americans with T2D to date, an association between PAA and PDR is not present after adjustment for clinical, demographic, and socioeconomic factors. No genome-wide significant locus (defined as having a locus-genome statistic > 5) was identified with admixture analysis. Further analyses with even larger sample sizes are needed to definitively assess if any admixture signal for DR is present. PMID:26098467

Mapping Variables.

ERIC Educational Resources Information Center

Stone, Mark H.; Wright, Benjamin D.; Stenner, A. Jackson

1999-01-01

Describes mapping variables, the principal technique for planning and constructing a test or rating instrument. A variable map is also useful for interpreting results. Provides several maps to show the importance and value of mapping a variable by person and item data. (Author/SLD)

USGS maps

USGS Publications Warehouse

,

2005-01-01

Discover a small sample of the millions of maps produced by the U.S. Geological Survey (USGS) in its mission to map the Nation and survey its resources. This booklet gives a brief overview of the types of maps sold and distributed by the USGS through its Earth Science Information Centers (ESIC) and also available from business partners located in most States. The USGS provides a wide variety of maps, from topographic maps showing the geographic relief and thematic maps displaying the geology and water resources of the United States, to special studies of the moon and planets.

Enhancements to Demilitarization Process Maps Program (ProMap)

DTIC Science & Technology

2016-10-14

map tool, ProMap, was improved by implementing new features, and sharing data with MIDAS and AMDIT databases . Specifically, process efficiency was...improved by 1) providing access to APE information contained in the AMDIT database directly from inside ProMap when constructing a process map, 2...what equipment can be efficiently used to demil a particular munition. Associated with this task was the upgrade of the AMDIT database so that

Molecular genetic responses to lysergic acid diethylamide include transcriptional activation of MAP kinase phosphatase-1, C/EBP-beta and ILAD-1, a novel gene with homology to arrestins.

PubMed

Nichols, Charles D; Sanders-Bush, Elaine

2004-08-01

We recently demonstrated that the potent hallucinogenic drug lysergic acid diethylamide (LSD) dynamically influences the expression of a small collection of genes within the mammalian prefrontal cortex. Towards generating a greater understanding of the molecular genetic effects of hallucinogens and how they may relate to alterations in behavior, we have identified and characterized expression patterns of a new collection of three genes increased in expression by acute LSD administration. These genes were identified through additional screens of Affymetrix DNA microarrays and examined in experiments to assess dose-response, time course and the receptor mediating the expression changes. The first induced gene, C/EBP-beta, is a transcription factor. The second gene, MKP-1, suggests that LSD activates the MAP (mitogen activated protein) kinase pathway. The third gene, ILAD-1, demonstrates sequence similarity to the arrestins. The increase in expression of each gene was partially mediated through LSD interactions at 5-HT2A (serotonin) receptors. There is evidence of alternative splicing at the ILAD-1 locus. Furthermore, data suggests that various splice isoforms of ILAD-1 respond differently at the transcriptional level to LSD. The genes thus far found to be responsive to LSD are beginning to give a more complete picture of the complex intracellular events initiated by hallucinogens.

ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

PubMed

Fooshee, David; Andronico, Alessio; Baldi, Pierre

2013-11-25

Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon's AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu .

Genome-Wide Mapping of Cystitis Due to Streptococcus agalactiae and Escherichia coli in Mice Identifies a Unique Bladder Transcriptome That Signifies Pathogen-Specific Antimicrobial Defense against Urinary Tract Infection

PubMed Central

Tan, Chee K.; Carey, Alison J.; Cui, Xiangqin; Webb, Richard I.; Ipe, Deepak; Crowley, Michael; Cripps, Allan W.; Benjamin, William H.; Ulett, Kimberly B.; Schembri, Mark A.

2012-01-01

The most common causes of urinary tract infections (UTIs) are Gram-negative pathogens such as Escherichia coli; however, Gram-positive organisms, including Streptococcus agalactiae, or group B streptococcus (GBS), also cause UTI. In GBS infection, UTI progresses to cystitis once the bacteria colonize the bladder, but the host responses triggered in the bladder immediately following infection are largely unknown. Here, we used genome-wide expression profiling to map the bladder transcriptome of GBS UTI in mice infected transurethrally with uropathogenic GBS that was cultured from a 35-year-old women with cystitis. RNA from bladders was applied to Affymetrix Gene-1.0ST microarrays; quantitative reverse transcriptase PCR (qRT-PCR) was used to analyze selected gene responses identified in array data sets. A surprisingly small significant-gene list of 172 genes was identified at 24 h; this compared to 2,507 genes identified in a side-by-side comparison with uropathogenic E. coli (UPEC). No genes exhibited significantly altered expression at 2 h in GBS-infected mice according to arrays despite high bladder bacterial loads at this early time point. The absence of a marked early host response to GBS juxtaposed with broad-based bladder responses activated by UPEC at 2 h. Bioinformatics analyses, including integrative system-level network mapping, revealed multiple activated biological pathways in the GBS bladder transcriptome that regulate leukocyte activation, inflammation, apoptosis, and cytokine-chemokine biosynthesis. These findings define a novel, minimalistic type of bladder host response triggered by GBS UTI, which comprises collective antimicrobial pathways that differ dramatically from those activated by UPEC. Overall, this study emphasizes the unique nature of bladder immune activation mechanisms triggered by distinct uropathogens. PMID:22733575

IntegratedMap: a Web interface for integrating genetic map data.

PubMed

Yang, Hongyu; Wang, Hongyu; Gingle, Alan R

2005-05-01

IntegratedMap is a Web application and database schema for storing and interactively displaying genetic map data. Its Web interface includes a menu for direct chromosome/linkage group selection, a search form for selection based on mapped object location and linkage group displays. An overview display provides convenient access to the full range of mapped and anchored object types with genetic locus details, such as numbers, types and names of mapped/anchored objects displayed in a compact scrollable list box that automatically updates based on selected map location and object type. Also, multilinkage group and localized map views are available along with links that can be configured for integration with other Web resources. IntegratedMap is implemented in C#/ASP.NET and the package, including a MySQL schema creation script, is available from http://cggc.agtec.uga.edu/Data/download.asp

Occupancy Grid Map Merging Using Feature Maps

DTIC Science & Technology

2010-11-01

each robot begins exploring at different starting points, once two robots can communicate, they send their odometry data, LIDAR observations, and maps...robots [11]. Moreover, it is relevant to mention that significant success has been achieved in solving SLAM problems when using hybrid maps [12...represents the environment by parametric features. Our method is capable of representing a LIDAR scanned environment map in a parametric fashion. In general

The World Karst Aquifer Mapping project: concept, mapping procedure and map of Europe

NASA Astrophysics Data System (ADS)

Chen, Zhao; Auler, Augusto S.; Bakalowicz, Michel; Drew, David; Griger, Franziska; Hartmann, Jens; Jiang, Guanghui; Moosdorf, Nils; Richts, Andrea; Stevanovic, Zoran; Veni, George; Goldscheider, Nico

2017-05-01

Karst aquifers contribute substantially to freshwater supplies in many regions of the world, but are vulnerable to contamination and difficult to manage because of their unique hydrogeological characteristics. Many karst systems are hydraulically connected over wide areas and require transboundary exploration, protection and management. In order to obtain a better global overview of karst aquifers, to create a basis for sustainable international water-resources management, and to increase the awareness in the public and among decision makers, the World Karst Aquifer Mapping (WOKAM) project was established. The goal is to create a world map and database of karst aquifers, as a further development of earlier maps. This paper presents the basic concepts and the detailed mapping procedure, using France as an example to illustrate the step-by-step workflow, which includes generalization, differentiation of continuous and discontinuous carbonate and evaporite rock areas, and the identification of non-exposed karst aquifers. The map also shows selected caves and karst springs, which are collected in an associated global database. The draft karst aquifer map of Europe shows that 21.6% of the European land surface is characterized by the presence of (continuous or discontinuous) carbonate rocks; about 13.8% of the land surface is carbonate rock outcrop.

NeatMap--non-clustering heat map alternatives in R.

PubMed

Rajaram, Satwik; Oono, Yoshi

2010-01-22

The clustered heat map is the most popular means of visualizing genomic data. It compactly displays a large amount of data in an intuitive format that facilitates the detection of hidden structures and relations in the data. However, it is hampered by its use of cluster analysis which does not always respect the intrinsic relations in the data, often requiring non-standardized reordering of rows/columns to be performed post-clustering. This sometimes leads to uninformative and/or misleading conclusions. Often it is more informative to use dimension-reduction algorithms (such as Principal Component Analysis and Multi-Dimensional Scaling) which respect the topology inherent in the data. Yet, despite their proven utility in the analysis of biological data, they are not as widely used. This is at least partially due to the lack of user-friendly visualization methods with the visceral impact of the heat map. NeatMap is an R package designed to meet this need. NeatMap offers a variety of novel plots (in 2 and 3 dimensions) to be used in conjunction with these dimension-reduction techniques. Like the heat map, but unlike traditional displays of such results, it allows the entire dataset to be displayed while visualizing relations between elements. It also allows superimposition of cluster analysis results for mutual validation. NeatMap is shown to be more informative than the traditional heat map with the help of two well-known microarray datasets. NeatMap thus preserves many of the strengths of the clustered heat map while addressing some of its deficiencies. It is hoped that NeatMap will spur the adoption of non-clustering dimension-reduction algorithms.

Human Mind Maps

ERIC Educational Resources Information Center

Glass, Tom

2016-01-01

When students generate mind maps, or concept maps, the maps are usually on paper, computer screens, or a blackboard. Human Mind Maps require few resources and little preparation. The main requirements are space where students can move around and a little creativity and imagination. Mind maps can be used for a variety of purposes, and Human Mind…

CrowdMapping: A Crowdsourcing-Based Terminology Mapping Method for Medical Data Standardization.

PubMed

Mao, Huajian; Chi, Chenyang; Huang, Boyu; Meng, Haibin; Yu, Jinghui; Zhao, Dongsheng

2017-01-01

Standardized terminology is the prerequisite of data exchange in analysis of clinical processes. However, data from different electronic health record systems are based on idiosyncratic terminology systems, especially when the data is from different hospitals and healthcare organizations. Terminology standardization is necessary for the medical data analysis. We propose a crowdsourcing-based terminology mapping method, CrowdMapping, to standardize the terminology in medical data. CrowdMapping uses a confidential model to determine how terminologies are mapped to a standard system, like ICD-10. The model uses mappings from different health care organizations and evaluates the diversity of the mapping to determine a more sophisticated mapping rule. Further, the CrowdMapping model enables users to rate the mapping result and interact with the model evaluation. CrowdMapping is a work-in-progress system, we present initial results mapping terminologies.

Accurate Mobile Urban Mapping via Digital Map-Based SLAM †

PubMed Central

Roh, Hyunchul; Jeong, Jinyong; Cho, Younggun; Kim, Ayoung

2016-01-01

This paper presents accurate urban map generation using digital map-based Simultaneous Localization and Mapping (SLAM). Throughout this work, our main objective is generating a 3D and lane map aiming for sub-meter accuracy. In conventional mapping approaches, achieving extremely high accuracy was performed by either (i) exploiting costly airborne sensors or (ii) surveying with a static mapping system in a stationary platform. Mobile scanning systems recently have gathered popularity but are mostly limited by the availability of the Global Positioning System (GPS). We focus on the fact that the availability of GPS and urban structures are both sporadic but complementary. By modeling both GPS and digital map data as measurements and integrating them with other sensor measurements, we leverage SLAM for an accurate mobile mapping system. Our proposed algorithm generates an efficient graph SLAM and achieves a framework running in real-time and targeting sub-meter accuracy with a mobile platform. Integrated with the SLAM framework, we implement a motion-adaptive model for the Inverse Perspective Mapping (IPM). Using motion estimation derived from SLAM, the experimental results show that the proposed approaches provide stable bird’s-eye view images, even with significant motion during the drive. Our real-time map generation framework is validated via a long-distance urban test and evaluated at randomly sampled points using Real-Time Kinematic (RTK)-GPS. PMID:27548175

USGS Maps

USGS Publications Warehouse

,

1994-01-01

Most USGS topographic maps use brown contours to show the shape and elevation of the terrain. Elevations are usually shown in feet, but on some maps they are in meters. Contour intervals vary, depending mainly on the scale of the map and the type of terrain.

Polder maps: Improving OMIT maps by excluding bulk solvent

DOE PAGES

Liebschner, Dorothee; Afonine, Pavel V.; Moriarty, Nigel W.; ...

2017-02-01

The crystallographic maps that are routinely used during the structure-solution workflow are almost always model-biased because model information is used for their calculation. As these maps are also used to validate the atomic models that result from model building and refinement, this constitutes an immediate problem: anything added to the model will manifest itself in the map and thus hinder the validation. OMIT maps are a common tool to verify the presence of atoms in the model. The simplest way to compute an OMIT map is to exclude the atoms in question from the structure, update the corresponding structure factorsmore » and compute a residual map. It is then expected that if these atoms are present in the crystal structure, the electron density for the omitted atoms will be seen as positive features in this map. This, however, is complicated by the flat bulk-solvent model which is almost universally used in modern crystallographic refinement programs. This model postulates constant electron density at any voxel of the unit-cell volume that is not occupied by the atomic model. Consequently, if the density arising from the omitted atoms is weak then the bulk-solvent model may obscure it further. A possible solution to this problem is to prevent bulk solvent from entering the selected OMIT regions, which may improve the interpretative power of residual maps. This approach is called a polder (OMIT) map. Polder OMIT maps can be particularly useful for displaying weak densities of ligands, solvent molecules, side chains, alternative conformations and residues both in terminal regions and in loops. As a result, the tools described in this manuscript have been implemented and are available in PHENIX.« less

Integrating Databases with Maps: The Delivery of Cultural Data through TimeMap.

ERIC Educational Resources Information Center

Johnson, Ian

TimeMap is a unique integration of database management, metadata and interactive maps, designed to contextualise and deliver cultural data through maps. TimeMap extends conventional maps with the time dimension, creating and animating maps "on-the-fly"; delivers them as a kiosk application or embedded in Web pages; links flexibly to…

Mapping Van

NASA Technical Reports Server (NTRS)

1994-01-01

A NASA Center for the Commercial Development of Space (CCDS) - developed system for satellite mapping has been commercialized for the first time. Global Visions, Inc. maps an area while driving along a road in a sophisticated mapping van equipped with satellite signal receivers, video cameras and computer systems for collecting and storing mapping data. Data is fed into a computerized geographic information system (GIS). The resulting amps can be used for tax assessment purposes, emergency dispatch vehicles and fleet delivery companies as well as other applications.

Creation of a Human Secretome: A Novel Composite Library of Human Secreted Proteins: Validation Using Ovarian Cancer Gene Expression Data and a Virtual Secretome Array.

PubMed

Vathipadiekal, Vinod; Wang, Victoria; Wei, Wei; Waldron, Levi; Drapkin, Ronny; Gillette, Michael; Skates, Steven; Birrer, Michael

2015-11-01

To generate a comprehensive "Secretome" of proteins potentially found in the blood and derive a virtual Affymetrix array. To validate the utility of this database for the discovery of novel serum-based biomarkers using ovarian cancer transcriptomic data. The secretome was constructed by aggregating the data from databases of known secreted proteins, transmembrane or membrane proteins, signal peptides, G-protein coupled receptors, or proteins existing in the extracellular region, and the virtual array was generated by mapping them to Affymetrix probeset identifiers. Whole-genome microarray data from ovarian cancer, normal ovarian surface epithelium, and fallopian tube epithelium were used to identify transcripts upregulated in ovarian cancer. We established the secretome from eight public databases and a virtual array consisting of 16,521 Affymetrix U133 Plus 2.0 probesets. Using ovarian cancer transcriptomic data, we identified candidate blood-based biomarkers for ovarian cancer and performed bioinformatic validation by demonstrating rediscovery of known biomarkers including CA125 and HE4. Two novel top biomarkers (FGF18 and GPR172A) were validated in serum samples from an independent patient cohort. We present the secretome, comprising the most comprehensive resource available for protein products that are potentially found in the blood. The associated virtual array can be used to translate gene-expression data into cancer biomarker discovery. A list of blood-based biomarkers for ovarian cancer detection is reported and includes CA125 and HE4. FGF18 and GPR172A were identified and validated by ELISA as being differentially expressed in the serum of ovarian cancer patients compared with controls. ©2015 American Association for Cancer Research.

Smart "geomorphological" map browsing - a tale about geomorphological maps and the internet

NASA Astrophysics Data System (ADS)

Geilhausen, M.; Otto, J.-C.

2012-04-01

With the digital production of geomorphological maps, the dissemination of research outputs now extends beyond simple paper products. Internet technologies can contribute to both, the dissemination of geomorphological maps and access to geomorphologic data and help to make geomorphological knowledge available to a greater public. Indeed, many national geological surveys employ end-to-end digital workflows from data capture in the field to final map production and dissemination. This paper deals with the potential of web mapping applications and interactive, portable georeferenced PDF maps for the distribution of geomorphological information. Web mapping applications such as Google Maps have become very popular and widespread and increased the interest and access to mapping. They link the Internet with GIS technology and are a common way of presenting dynamic maps online. The GIS processing is performed online and maps are visualised in interactive web viewers characterised by different capabilities such as zooming, panning or adding further thematic layers, with the map refreshed after each task. Depending on the system architecture and the components used, advanced symbology, map overlays from different applications and sources and their integration into a Desktop GIS are possible. This interoperability is achieved through the use of international open standards that include mechanisms for the integration and visualisation of information from multiple sources. The portable document format (PDF) is commonly used for printing and is a standard format that can be processed by many graphic software and printers without loss of information. A GeoPDF enables the sharing of geospatial maps and data in PDF documents. Multiple, independent map frames with individual spatial reference systems are possible within a GeoPDF, for example, for map overlays or insets. Geospatial functionality of a GeoPDF includes scalable map display, layer visibility control, access to attribute

BOREAS Hardcopy Maps

NASA Technical Reports Server (NTRS)

Hall, Forrest G. (Editor); Nelson, Elizabeth; Newcomer, Jeffrey A.

2000-01-01

Boreal Ecosystem-Atmospheric Study (BOREAS) hardcopy maps are a collection of approximately 1,000 hardcopy maps representing the physical, climatological, and historical attributes of areas covering primarily the Manitoba and Saskatchewan provinces of Canada. These maps were collected by BOREAS Information System (BORIS) and Canada for Remote Sensing (CCRS) staff to provide basic information about site positions, manmade features, topography, geology, hydrology, land cover types, fire history, climate, and soils of the BOREAS study region. These maps are not available for distribution through the BOREAS project but may be used as an on-site resource. Information is provided within this document for individuals who want to order copies of these maps from the original map source. Note that the maps are not contained on the BOREAS CD-ROM set. An inventory listing file is supplied on the CD-ROM to inform users of the maps that are available. This inventory listing is available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). For hardcopies of the individual maps, contact the sources provided.

Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa.

PubMed

Bassil, Nahla V; Davis, Thomas M; Zhang, Hailong; Ficklin, Stephen; Mittmann, Mike; Webster, Teresa; Mahoney, Lise; Wood, David; Alperin, Elisabeth S; Rosyara, Umesh R; Koehorst-Vanc Putten, Herma; Monfort, Amparo; Sargent, Daniel J; Amaya, Iraida; Denoyes, Beatrice; Bianco, Luca; van Dijk, Thijs; Pirani, Ali; Iezzoni, Amy; Main, Dorrie; Peace, Cameron; Yang, Yilong; Whitaker, Vance; Verma, Sujeet; Bellon, Laurent; Brew, Fiona; Herrera, Raul; van de Weg, Eric

2015-03-07

A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing "haploSNPs" (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative "codon-based" SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix's "SNPolisher" R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family 'Holiday' × 'Korona' with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array's high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses

ActionMap: A web-based software that automates loci assignments to framework maps.

PubMed

Albini, Guillaume; Falque, Matthieu; Joets, Johann

2003-07-01

Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/).

ActionMap: a web-based software that automates loci assignments to framework maps

PubMed Central

Albini, Guillaume; Falque, Matthieu; Joets, Johann

2003-01-01

Genetic linkage computation may be a repetitive and time consuming task, especially when numerous loci are assigned to a framework map. We thus developed ActionMap, a web-based software that automates genetic mapping on a fixed framework map without adding the new markers to the map. Using this tool, hundreds of loci may be automatically assigned to the framework in a single process. ActionMap was initially developed to map numerous ESTs with a small plant mapping population and is limited to inbred lines and backcrosses. ActionMap is highly configurable and consists of Perl and PHP scripts that automate command steps for the MapMaker program. A set of web forms were designed for data import and mapping settings. Results of automatic mapping can be displayed as tables or drawings of maps and may be exported. The user may create personal access-restricted projects to store raw data, settings and mapping results. All data may be edited, updated or deleted. ActionMap may be used either online or downloaded for free (http://moulon.inra.fr/~bioinfo/). PMID:12824426

Cartographic mapping study

NASA Technical Reports Server (NTRS)

Wilson, C.; Dye, R.; Reed, L.

1982-01-01

The errors associated with planimetric mapping of the United States using satellite remote sensing techniques are analyzed. Assumptions concerning the state of the art achievable for satellite mapping systems and platforms in the 1995 time frame are made. An analysis of these performance parameters is made using an interactive cartographic satellite computer model, after first validating the model using LANDSAT 1 through 3 performance parameters. An investigation of current large scale (1:24,000) US National mapping techniques is made. Using the results of this investigation, and current national mapping accuracy standards, the 1995 satellite mapping system is evaluated for its ability to meet US mapping standards for planimetric and topographic mapping at scales of 1:24,000 and smaller.

Mapping Applications Center, National Mapping Division, U.S. Geological Survey

USGS Publications Warehouse

,

1996-01-01

The Mapping Applications Center (MAC), National Mapping Division (NMD), is the eastern regional center for coordinating the production, distribution, and sale of maps and digital products of the U.S. Geological Survey (USGS). It is located in the John Wesley Powell Federal Building in Reston, Va. The MAC's major functions are to (1) establish and manage cooperative mapping programs with State and Federal agencies; (2) perform new research in preparing and applying geospatial information; (3) prepare digital cartographic data, special purpose maps, and standard maps from traditional and classified source materials; (4) maintain the domestic names program of the United States; (5) manage the National Aerial Photography Program (NAPP); (6) coordinate the NMD's publications and outreach programs; and (7) direct the USGS mapprinting operations.

Functional genomic responses to cystic fibrosis transmembrane conductance regulator (CFTR) and CFTR(delta508) in the lung.

PubMed

Xu, Yan; Liu, Cong; Clark, Jean C; Whitsett, Jeffrey A

2006-04-21

Cystic fibrosis (CF), a common lethal pulmonary disorder in Caucasians, is caused by mutations in the cystic fibrosis transmembrane conductance regulator gene (CFTR) that disturbs fluid homeostasis and host defense in target organs. The effects of CFTR and delta508-CFTR were assessed in transgenic mice that 1) lack CFTR expression (Cftr-/-); 2) express the human delta508 CFTR (CFTR(delta508)); 3) overexpress the normal human CFTR (CFTR(tg)) in respiratory epithelial cells. Genes were selected from Affymetrix Murine Gene-Chips analysis and subjected to functional classification, k-means clustering, promoter cis-elements/modules searching, literature mining, and pathway exploring. Genomic responses to Cftr-/- were not corrected by expression of CFTR(delta508). Genes regulating host defense, inflammation, fluid and electrolyte transport were similarly altered in Cftr-/- and CFTR(delta508) mice. CFTR(delta508) induced a primary disturbance in expression of genes regulating redox and antioxidant systems. Genomic responses to CFTR(tg) were modest and were not associated with lung pathology. CFTR(tg) and CFTR(delta508) induced genes encoding heat shock proteins and other chaperones but did not activate the endoplasmic reticulum-associated degradation pathway. RNAs encoding proteins that directly interact with CFTR were identified in each of the CFTR mouse models, supporting the hypothesis that CFTR functions within a multiprotein complex whose members interact at the level of protein-protein interactions and gene expression. Promoters of genes influenced by CFTR shared common regulatory elements, suggesting that their co-expression may be mediated by shared regulatory mechanisms. Genes and pathways involved in the response to CFTR may be of interest as modifiers of CF.

Inflammatory and Repair Pathways Induced in Human Bronchoalveolar Lavage Cells with Ozone Inhalation

PubMed Central

Wong, Hofer; Tenney, Rachel; Chen, Chun; Stiner, Rachel; Balmes, John R.; Paquet, Agnès C.; Arjomandi, Mehrdad

2015-01-01

Background Inhalation of ambient levels of ozone causes airway inflammation and epithelial injury. Methods To examine the responses of airway cells to ozone-induced oxidative injury, 19 subjects (7 with asthma) were exposed to clean air (0ppb), medium (100ppb), and high (200ppb) ambient levels of ozone for 4h on three separate occasions in a climate-controlled chamber followed by bronchoscopy with bronchoalveolar lavage (BAL) 24h later. BAL cell mRNA expression was examined using Affymetrix GeneChip Microarray. The role of a differentially expressed gene (DEG) in epithelial injury was evaluated in an in vitro model of injury [16HBE14o- cell line scratch assay]. Results Ozone exposure caused a dose-dependent up-regulation of several biologic pathways involved in inflammation and repair including chemokine and cytokine secretion, activity, and receptor binding; metalloproteinase and endopeptidase activity; adhesion, locomotion, and migration; and cell growth and tumorigenesis regulation. Asthmatic subjects had 1.7- to 3.8-fold higher expression of many DEGs suggestive of increased proinflammatory and matrix degradation and remodeling signals. The most highly up-regulated gene was osteopontin, the protein level of which in BAL fluid increased in a dose-dependent manner after ozone exposure. Asthmatic subjects had a disproportionate increase in non-polymerized osteopontin with increasing exposure to ozone. Treatment with polymeric, but not monomeric, osteopontin enhanced the migration of epithelial cells and wound closure in an α9β1 integrin-dependent manner. Conclusions Expression profiling of BAL cells after ozone exposure reveals potential regulatory genes and pathways activated by oxidative stress. One DEG, osteopontin, promotes epithelial wound healing in an in vitro model of injury. PMID:26035830

Molecular classification of gastric cancer: a new paradigm.

PubMed

Shah, Manish A; Khanin, Raya; Tang, Laura; Janjigian, Yelena Y; Klimstra, David S; Gerdes, Hans; Kelsen, David P

2011-05-01

Gastric cancer may be subdivided into 3 distinct subtypes--proximal, diffuse, and distal gastric cancer--based on histopathologic and anatomic criteria. Each subtype is associated with unique epidemiology. Our aim is to test the hypothesis that these distinct gastric cancer subtypes may also be distinguished by gene expression analysis. Patients with localized gastric adenocarcinoma being screened for a phase II preoperative clinical trial (National Cancer Institute, NCI #5917) underwent endoscopic biopsy for fresh tumor procurement. Four to 6 targeted biopsies of the primary tumor were obtained. Macrodissection was carried out to ensure more than 80% carcinoma in the sample. HG-U133A GeneChip (Affymetrix) was used for cDNA expression analysis, and all arrays were processed and analyzed using the Bioconductor R-package. Between November 2003 and January 2006, 57 patients were screened to identify 36 patients with localized gastric cancer who had adequate RNA for expression analysis. Using supervised analysis, we built a classifier to distinguish the 3 gastric cancer subtypes, successfully classifying each into tightly grouped clusters. Leave-one-out cross-validation error was 0.14, suggesting that more than 85% of samples were classified correctly. Gene set analysis with the false discovery rate set at 0.25 identified several pathways that were differentially regulated when comparing each gastric cancer subtype to adjacent normal stomach. Subtypes of gastric cancer that have epidemiologic and histologic distinctions are also distinguished by gene expression data. These preliminary data suggest a new classification of gastric cancer with implications for improving our understanding of disease biology and identification of unique molecular drivers for each gastric cancer subtype. ©2011 AACR.

Molecular Classification of Gastric Cancer: A new paradigm

PubMed Central

Shah, Manish A.; Khanin, Raya; Tang, Laura; Janjigian, Yelena Y.; Klimstra, David S.; Gerdes, Hans; Kelsen, David P.

2011-01-01

Purpose Gastric cancer may be subdivided into three distinct subtypes –proximal, diffuse, and distal gastric cancer– based on histopathologic and anatomic criteria. Each subtype is associated with unique epidemiology. Our aim is to test the hypothesis that these distinct gastric cancer subtypes may also be distinguished by gene expression analysis. Experimental Design Patients with localized gastric adenocarcinoma being screened for a phase II preoperative clinical trial (NCI 5917) underwent endoscopic biopsy for fresh tumor procurement. 4–6 targeted biopsies of the primary tumor were obtained. Macrodissection was performed to ensure >80% carcinoma in the sample. HG-U133A GeneChip (Affymetrix) was used for cDNA expression analysis, and all arrays were processed and analyzed using the Bioconductor R-package. Results Between November 2003 and January 2006, 57 patients were screened to identify 36 patients with localized gastric cancer who had adequate RNA for expression analysis. Using supervised analysis, we built a classifier to distinguish the three gastric cancer subtypes, successfully classifying each into tightly grouped clusters. Leave-one-out cross validation error was 0.14, suggesting that >85% of samples were classified correctly. Gene set analysis with the False Discovery Rate set at 0.25 identified several pathways that were differentially regulated when comparing each gastric cancer subtype to adjacent normal stomach. Conclusions Subtypes of gastric cancer that have epidemiologic and histologic distinction are also distinguished by gene expression data. These preliminary data suggest a new classification of gastric cancer with implications for improving our understanding of disease biology and identification of unique molecular drivers for each gastric cancer subtype. PMID:21430069

Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines

PubMed Central

Elling, Axel A; Mitreva, Makedonka; Recknor, Justin; Gai, Xiaowu; Martin, John; Maier, Thomas R; McDermott, Jeffrey P; Hewezi, Tarek; McK Bird, David; Davis, Eric L; Hussey, Richard S; Nettleton, Dan; McCarter, James P; Baum, Thomas J

2007-01-01

Background The soybean cyst nematode Heterodera glycines is the most important parasite in soybean production worldwide. A comprehensive analysis of large-scale gene expression changes throughout the development of plant-parasitic nematodes has been lacking to date. Results We report an extensive genomic analysis of H. glycines, beginning with the generation of 20,100 expressed sequence tags (ESTs). In-depth analysis of these ESTs plus approximately 1,900 previously published sequences predicted 6,860 unique H. glycines genes and allowed a classification by function using InterProScan. Expression profiling of all 6,860 genes throughout the H. glycines life cycle was undertaken using the Affymetrix Soybean Genome Array GeneChip. Our data sets and results represent a comprehensive resource for molecular studies of H. glycines. Demonstrating the power of this resource, we were able to address whether arrested development in the Caenorhabditis elegans dauer larva and the H. glycines infective second-stage juvenile (J2) exhibits shared gene expression profiles. We determined that the gene expression profiles associated with the C. elegans dauer pathway are not uniformly conserved in H. glycines and that the expression profiles of genes for metabolic enzymes of C. elegans dauer larvae and H. glycines infective J2 are dissimilar. Conclusion Our results indicate that hallmark gene expression patterns and metabolism features are not shared in the developmentally arrested life stages of C. elegans and H. glycines, suggesting that developmental arrest in these two nematode species has undergone more divergent evolution than previously thought and pointing to the need for detailed genomic analyses of individual parasite species. PMID:17919324

The Regulation of Cytokine Networks in Hippocampal CA1 Differentiates Extinction from Those Required for the Maintenance of Contextual Fear Memory after Recall

PubMed Central

Scholz, Birger; Doidge, Amie N.; Barnes, Philip; Hall, Jeremy; Wilkinson, Lawrence S.; Thomas, Kerrie L.

2016-01-01

We investigated the distinctiveness of gene regulatory networks in CA1 associated with the extinction of contextual fear memory (CFM) after recall using Affymetrix GeneChip Rat Genome 230 2.0 Arrays. These data were compared to previously published retrieval and reconsolidation-attributed, and consolidation datasets. A stringent dual normalization and pareto-scaled orthogonal partial least-square discriminant multivariate analysis together with a jack-knifing-based cross-validation approach was used on all datasets to reduce false positives. Consolidation, retrieval and extinction were correlated with distinct patterns of gene expression 2 hours later. Extinction-related gene expression was most distinct from the profile accompanying consolidation. A highly specific feature was the discrete regulation of neuroimmunological gene expression associated with retrieval and extinction. Immunity–associated genes of the tyrosine kinase receptor TGFβ and PDGF, and TNF families’ characterized extinction. Cytokines and proinflammatory interleukins of the IL-1 and IL-6 families were enriched with the no-extinction retrieval condition. We used comparative genomics to predict transcription factor binding sites in proximal promoter regions of the retrieval-regulated genes. Retrieval that does not lead to extinction was associated with NF-κB-mediated gene expression. We confirmed differential NF-κBp65 expression, and activity in all of a representative sample of our candidate genes in the no-extinction condition. The differential regulation of cytokine networks after the acquisition and retrieval of CFM identifies the important contribution that neuroimmune signalling plays in normal hippocampal function. Further, targeting cytokine signalling upon retrieval offers a therapeutic strategy to promote extinction mechanisms in human disorders characterised by dysregulation of associative memory. PMID:27224427

An eleven gene molecular signature for extra-capsular spread in oral squamous cell carcinoma serves as a prognosticator of outcome in patients without nodal metastases.

PubMed

Wang, Weining; Lim, Weng Khong; Leong, Hui Sun; Chong, Fui Teen; Lim, Tony K H; Tan, Daniel S W; Teh, Bin Tean; Iyer, N Gopalakrishna

2015-04-01

Extracapsular spread (ECS) is an important prognostic factor for oral squamous cell carcinoma (OSCC) and is used to guide management. In this study, we aimed to identify an expression profile signature for ECS in node-positive OSCC using data derived from two different sources: a cohort of OSCC patients from our institution (National Cancer Centre Singapore) and The Cancer Genome Atlas (TCGA) head and neck squamous cell carcinoma (HNSCC) cohort. We also sought to determine if this signature could serve as a prognostic factor in node negative cancers. Patients with a histological diagnosis of OSCC were identified from an institutional database and fresh tumor samples were retrieved. RNA was extracted and gene expression profiling was performed using the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarray platform. RNA sequence data and corresponding clinical data for the TCGA HNSCC cohort were downloaded from the TCGA Data Portal. All data analyses were conducted using R package and SPSS. We identified an 11 gene signature (GGH, MTFR1, CDKN3, PSRC1, SMIM3, CA9, IRX4, CPA3, ZSCAN16, CBX7 and ZFP3) which was robust in segregating tumors by ECS status. In node negative patients, patients harboring this ECS signature had a significantly worse overall survival (p=0.04). An eleven gene signature for ECS was derived. Our results also suggest that this signature is prognostic in a separate subset of patients with no nodal metastasis Further validation of this signature on other datasets and immunohistochemical studies are required to establish utility of this signature in stratifying early stage OSCC patients. Copyright © 2014 Elsevier Ltd. All rights reserved.

Microarray analysis of laser capture microdissected-anulus cells from the human intervertebral disc.

PubMed

Gruber, Helen E; Mougeot, Jean-Luc; Hoelscher, Gretchen; Ingram, Jane A; Hanley, Edward N

2007-05-15

Five Thompson Grade I/II discs (Group 1), 7 Grade III discs (Group 2), and 3 Grade IV discs (Group IV) were studied here in a project approved by the authors' Human Subjects Institutional Review Board. Our objective was to use laser capture microdissection (LCM) to harvest cells from the human anulus and to derive gene expression profiles using microarray analysis. Appropriate gene expression is essential in the intervertebral disc for maintenance of extracellular matrix (ECM), ECM remodeling, and maintenance of a viable disc cell population. During disc degeneration, cell numbers drop, making gene expression studies challenging. LCM was used to harvest cells from paraffin-embedded sections of human anulus tissue. Gene profiling used Affymetrix GeneChip Human X3P arrays. ANOVA and SAM permutation analysis were applied to dCHIP normalized, filtered, and log-transformed gene expression data ( approximately 33,500 probes), and data analyzed to identify genes that were significantly differentially expressed between the 3 groups. We identified 47 genes that were significantly differentially expressed between the 3 groups (P < 0.001 and lowest q values). Compared with the healthiest discs (Grade I/II), 13 genes were up-regulated and 19 down-regulated in both the Grade III and the Grade IV discs. Genes with biologic significance regulated during degeneration involved cell senescence, low cell division rates, hypoxia-related genes, heat-shock protein 70 interacting protein, neuropilin 2, and interleukin-23p19 (interleukin-12 family). Results expand our understanding of disc aging and degeneration and show that LCM is a valuable technique that can be used to collect mRNA amounts adequate for microarray analysis from the sparse cell population of the human anulus.

Downstream effects of ROCK signaling in cultured human corneal stromal cells: microarray analysis of gene expression.

PubMed

Harvey, Stephen A K; Anderson, Susan C; SundarRaj, Nirmala

2004-07-01

Rho-associated coiled-coil-containing protein kinase (ROCK) is a downstream target of Rho GTPase signaling and regulates the assembly of stress fibers. Previous reports indicate that Rho/ROCK signaling is involved in the regulation of several cellular processes, some of which may be cell-type specific and are probably critical to corneal stromal cell activation. The present study identified ROCK-regulated gene expression in corneal stromal cells. Corneal stromal cells derived from eyes of three different donors were cultured to yield the following designated phenotypes: baseline fibroblasts (DMEM with 10% serum), activated fibroblasts (10% serum+bFGF+heparin), and myofibroblasts (1% serum+TGF-beta 1). Cells were exposed to the ROCK inhibitor Y-27632 or vehicle for 12 hours, and transcript levels altered by ROCK inhibition were identified with oligonucleotide microarrays (GeneChips; Affymetrix, Santa Clara, CA). In these phenotypes, Y-27632 caused marked (twofold or more) increases or decreases in 14/4, 12/3, and 15/10 transcripts. In both fibroblast groups Y-27632-treatment increased expression of endothelin receptors and of parathyroid hormone-like hormone. The upregulation of alpha-smooth muscle actin in myofibroblasts was attenuated by Y-27632. Combining data from all groups identified ROCK-supported (Y-27632 inhibitable) expression of 10 transcripts, including ribonucleotide reductase M2, the cyclin B1-CDC2-CKS2 system, and four mitotic spindle-associated proteins. ROCK inhibition causes broad inhibition of DNA synthesis and mitosis and causes changes that are different between (bFGF-activated) fibroblasts and (TGF-beta 1-induced) myofibroblasts. Thus, Rho/ROCK signaling regulates both common and distinct downstream events in corneal stromal cells activated (differentiated) to fibroblast or myofibroblast phenotype.

Expression of HOXB2, a retinoic acid signaling target in pancreatic cancer and pancreatic intraepithelial neoplasia.

PubMed

Segara, Davendra; Biankin, Andrew V; Kench, James G; Langusch, Catherine C; Dawson, Amanda C; Skalicky, David A; Gotley, David C; Coleman, Maxwell J; Sutherland, Robert L; Henshall, Susan M

2005-05-01

Despite significant progress in understanding the molecular pathology of pancreatic cancer and its precursor lesion: pancreatic intraepithelial neoplasia (PanIN), there remain no molecules with proven clinical utility as prognostic or therapeutic markers. Here, we used oligonucleotide microarrays to interrogate mRNA expression of pancreatic cancer tissue and normal pancreas to identify novel molecular pathways dysregulated in the development and progression of pancreatic cancer. RNA was hybridized to Affymetrix Genechip HG-U133 oligonucleotide microarrays. A relational database integrating data from publicly available resources was created to identify candidate genes potentially relevant to pancreatic cancer. The protein expression of one candidate, homeobox B2 (HOXB2), in PanIN and pancreatic cancer was assessed using immunohistochemistry. We identified aberrant expression of several components of the retinoic acid (RA) signaling pathway (RARalpha, MUC4, Id-1, MMP9, uPAR, HB-EGF, HOXB6, and HOXB2), many of which are known to be aberrantly expressed in pancreatic cancer and PanIN. HOXB2, a downstream target of RA, was up-regulated 6.7-fold in pancreatic cancer compared with normal pancreas. Immunohistochemistry revealed ectopic expression of HOXB2 in 15% of early PanIN lesions and 48 of 128 (38%) pancreatic cancer specimens. Expression of HOXB2 was associated with nonresectable tumors and was an independent predictor of poor survival in resected tumors. We identified aberrant expression of RA signaling components in pancreatic cancer, including HOXB2, which was expressed in a proportion of PanIN lesions. Ectopic expression of HOXB2 was associated with a poor prognosis for all patients with pancreatic cancer and was an independent predictor of survival in patients who underwent resection.

Microarray-based analysis of the lung recovery process after stainless-steel welding fume exposure in Sprague-Dawley rats.

PubMed

Oh, Jung-Hwa; Yang, Mi-jin; Yang, Young-Su; Park, Han-Jin; Heo, Sun Hee; Lee, Eun-Hee; Song, Chang-Woo; Yoon, Seokjoo

2009-02-01

Repeated exposure to welding fumes promotes a reversible increase in pulmonary disease risk, but the molecular mechanisms by which welding fumes induce lung injury and how the lung recovers from such insults are unclear. In the present study, pulmonary function and gene-expression profiles in the lung were analyzed by Affymetrix GeneChip microarray after 30 days of consecutive exposure to manual metal arc welding combined with stainless-steel (MMA-SS) welding fumes, and again after 30 days of recovery from MMA-SS fume exposure. In total, 577 genes were identified as being either up-regulated or down-regulated (over twofold changes, p < 0.05) in the lungs of low-dose or high-dose groups. Differentially expressed genes were classified based on a k-means clustering algorithm and biological functions and molecular networks were further analyzed using Ingenuity Pathways Analysis. Among the genes affected by exposure to or recovery from MMA-SS fumes, the transcriptional changes of 13 genes that were highly altered by treatment were confirmed by quantitative real-time PCR. Notably, Mmp12, Cd5l, Ccl7, Cxcl5, and Spp1 related to the immune response were up-regulated only in the exposure group, whereas Trem2, IgG-2a, Igh-1a, and Igh were persistently up-regulated in both the exposure and recovery groups. In addition, several genes that might play a role in the repair process of the lung were up-regulated exclusively in the recovery group. Collectively, these data may help elucidate the molecular mechanism of the recovery process of the lung after welding fume exposure.

Growth hormone regulation of metabolic gene expression in muscle: a microarray study in hypopituitary men.

PubMed

Sjögren, Klara; Leung, Kin-Chuen; Kaplan, Warren; Gardiner-Garden, Margaret; Gibney, James; Ho, Ken K Y

2007-07-01

Muscle is a target of growth hormone (GH) action and a major contributor to whole body metabolism. Little is known about how GH regulates metabolic processes in muscle or the extent to which muscle contributes to changes in whole body substrate metabolism during GH treatment. To identify GH-responsive genes that regulate substrate metabolism in muscle, we studied six hypopituitary men who underwent whole body metabolic measurement and skeletal muscle biopsies before and after 2 wk of GH treatment (0.5 mg/day). Transcript profiles of four subjects were analyzed using Affymetrix GeneChips. Serum insulin-like growth factor I (IGF-I) and procollagens I and III were measured by RIA. GH increased serum IGF-I and procollagens I and III, enhanced whole body lipid oxidation, reduced carbohydrate oxidation, and stimulated protein synthesis. It induced gene expression of IGF-I and collagens in muscle. GH reduced expression of several enzymes regulating lipid oxidation and energy production. It reduced calpain 3, increased ribosomal protein L38 expression, and displayed mixed effects on genes encoding myofibrillar proteins. It increased expression of circadian gene CLOCK, and reduced that of PERIOD. In summary, GH exerted concordant effects on muscle expression and blood levels of IGF-I and collagens. It induced changes in genes regulating protein metabolism in parallel with a whole body anabolic effect. The discordance between muscle gene expression profiles and metabolic responses suggests that muscle is unlikely to contribute to GH-induced stimulation of whole body energy and lipid metabolism. GH may regulate circadian function in skeletal muscle by modulating circadian gene expression with possible metabolic consequences.

Using gene chips to identify organ-specific, smooth muscle responses to experimental diabetes: potential applications to urological diseases.

PubMed

Hipp, Jason D; Davies, Kelvin P; Tar, Moses; Valcic, Mira; Knoll, Abraham; Melman, Arnold; Christ, George J

2007-02-01

To identify early diabetes-related alterations in gene expression in bladder and erectile tissue that would provide novel diagnostic and therapeutic treatment targets to prevent, delay or ameliorate the ensuing bladder and erectile dysfunction. The RG-U34A rat GeneChip (Affymetrix Inc., Sunnyvale, CA, USA) oligonucleotide microarray (containing approximately 8799 genes) was used to evaluate gene expression in corporal and male bladder tissue excised from rats 1 week after confirmation of a diabetic state, but before demonstrable changes in organ function in vivo. A conservative analytical approach was used to detect alterations in gene expression, and gene ontology (GO) classifications were used to identify biological themes/pathways involved in the aetiology of the organ dysfunction. In all, 320 and 313 genes were differentially expressed in bladder and corporal tissue, respectively. GO analysis in bladder tissue showed prominent increases in biological pathways involved in cell proliferation, metabolism, actin cytoskeleton and myosin, as well as decreases in cell motility, and regulation of muscle contraction. GO analysis in corpora showed increases in pathways related to ion channel transport and ion channel activity, while there were decreases in collagen I and actin genes. The changes in gene expression in these initial experiments are consistent with the pathophysiological characteristics of the bladder and erectile dysfunction seen later in the diabetic disease process. Thus, the observed changes in gene expression might be harbingers or biomarkers of impending organ dysfunction, and could provide useful diagnostic and therapeutic targets for a variety of progressive urological diseases/conditions (i.e. lower urinary tract symptoms related to benign prostatic hyperplasia, erectile dysfunction, etc.).

MiR-578 and miR-573 as potential players in BRCA-related breast cancer angiogenesis

PubMed Central

Danza, Katia; Summa, Simona De; Pinto, Rosamaria; Pilato, Brunella; Palumbo, Orazio; Merla, Giuseppe; Simone, Gianni; Tommasi, Stefania

2015-01-01

The involvement of microRNA (miRNAs), a new class of small RNA molecules, in governing angiogenesis has been well described. Our aim was to investigate miRNA-mediated regulation of angiogenesis in a series of familial breast cancers stratified by BRCA1/2 mutational status in BRCA carriers and BRCA non-carriers (BRCAX). Affymetrix GeneChip miRNA Arrays were used to perform miRNA expression analysis on 43 formalin-fixed paraffin-embedded (FFPE) tumour tissue familial breast cancers (22 BRCA 1/2-related and 21 BRCAX). Pathway enrichment analysis was carried out with the DIANA miRPath v2.0 web-based computational tool, and the miRWalk database was used to identify target genes of deregulated miRNAs. An independent set of 8 BRCA 1/2-related and 11 BRCAX breast tumors was used for validation by Real-Time PCR. In vitro analysis on HEK293, MCF-7 and SUM149PT cells were performed to best-clarify miR-573 and miR-578 role. A set of 16 miRNAs differentially expressed between BRCA 1/2-related and BRCAX breast tumors emerged from the profile analysis. Among these, miR-578 and miR-573 were found to be down-regulated in BRCA 1/2-related breast cancer and associated to the Focal adhesion, Vascular Endothelial Growth Factor (VEGF) and Hypoxia Inducible Factor-1 (HIF-1) signaling pathways. Our data highlight the role of miR-578 and miR-573 in controlling BRCA 1/2-related angiogenesis by targeting key regulators of Focal adhesion, VEGF and HIF-1 signaling pathways. PMID:25333258

Transcriptional changes in porcine skin at 7 days following sulfur mustard and thermal burn injury.

PubMed

Price, Jennifer A; Rogers, James V; McDougal, James N; Shaw, Morgan Q; Reid, Frances M; Graham, John S

2009-01-01

Severe cutaneous injuries continue to result from exposure to sulfur mustard [bis(2-chloroethyl)sulfide; HD] and thermal burns. Microarray analysis was utilized in this study to evaluate transcriptional changes in porcine skin assessing the underlying repair mechanisms of HD and thermal injury involved in wound healing. Four ventral abdominal sites on each of 4 weanling swine were exposed to 400 microL undiluted HD or a heated brass rod (70 degrees C) for 8 minutes and 45-60 seconds, respectively. At 7 days postexposure, skin samples were excised and total RNA was isolated, labeled, and hybridized to Affymetrix GeneChip (Santa Clara, CA, USA) Porcine Genome Arrays (containing 20,201 genes). Based on the gene expression patterns in HD- and thermal-exposed skin at 7 days, the transcriptional profiles do not differ greatly. HD and thermal exposures promoted similar changes in transcription, where 270 and 283 transcripts were increased with HD and thermal exposures, respectively. Both exposures promoted decreases in 317 and 414 transcripts, respectively. Of the significantly increased transcripts, at least 77% were commonly expressed in both HD- and thermal-exposed skin, whereas at least 67% of decreased transcripts were common between both exposure types. Six of the top 10 biological functions were common to HD and thermal injury in which 9 canonical pathways were shared. The present study illustrates the similarities found between HD and thermal injury with respect to transcriptional response and wound healing and identifies specific genes (CXCL2, CXCR4, FGFR2, HMOX1, IGF1, PF4, PLAU, PLAUR, S100A8, SPP1, and TNC) that may be useful as potential therapeutic targets to promote improved wound healing.

Microarray-based comparison of three amplification methods for nanogram amounts of total RNA

PubMed Central

Singh, Ruchira; Maganti, Rajanikanth J.; Jabba, Sairam V.; Wang, Martin; Deng, Glenn; Heath, Joe Don; Kurn, Nurith; Wangemann, Philine

2007-01-01

Gene expression profiling using microarrays requires microgram amounts of RNA, which limits its direct application for the study of nanogram RNA samples obtained using microdissection, laser capture microscopy, or needle biopsy. A novel system based on Ribo-SPIA technology (RS, Ovation-Biotin amplification and labeling system) was recently introduced. The utility of the RS system, an optimized prototype system for picogram RNA samples (pRS), and two T7-based systems involving one or two rounds of amplification (OneRA, Standard Protocol, or TwoRA, Small Sample Prototcol, version II) were evaluated in the present study. Mouse kidney (MK) and mouse universal reference (MUR) RNA samples, 0.3 ng to 10 μg, were analyzed using high-density Affymetrix Mouse Genome 430 2.0 GeneChip arrays. Call concordance between replicates, correlations of signal intensity, signal intensity ratios, and minimal fold increase necessary for significance were determined. All systems amplified partially overlapping sets of genes with similar signal intensity correlations. pRS amplified the highest number of genes from 10-ng RNA samples. We detected 24 of 26 genes verified by RT-PCR in samples prepared using pRS. TwoRA yielded somewhat higher call concordances than did RS and pRS (91.8% vs. 89.3% and 88.1%, respectively). Although all target preparation methods were suitable, pRS amplified the highest number of targets and was found to be suitable for amplification of as little as 0.3 ng of total RNA. In addition, RS and pRS were faster and simpler to use than the T7-based methods and resulted in the generation of cDNA, which is more stable than cRNA. PMID:15613496

Exercise-driven metabolic pathways in healthy cartilage.

PubMed

Blazek, A D; Nam, J; Gupta, R; Pradhan, M; Perera, P; Weisleder, N L; Hewett, T E; Chaudhari, A M; Lee, B S; Leblebicioglu, B; Butterfield, T A; Agarwal, S

2016-07-01

Exercise is vital for maintaining cartilage integrity in healthy joints. Here we examined the exercise-driven transcriptional regulation of genes in healthy rat articular cartilage to dissect the metabolic pathways responsible for the potential benefits of exercise. Transcriptome-wide gene expression in the articular cartilage of healthy Sprague-Dawley female rats exercised daily (low intensity treadmill walking) for 2, 5, or 15 days was compared to that of non-exercised rats, using Affymetrix GeneChip arrays. Database for Annotation, Visualization and Integrated Discovery (DAVID) was used for Gene Ontology (GO)-term enrichment and Functional Annotation analysis of differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genome (KEGG) pathway mapper was used to identify the metabolic pathways regulated by exercise. Microarray analysis revealed that exercise-induced 644 DEGs in healthy articular cartilage. The DAVID bioinformatics tool demonstrated high prevalence of functional annotation clusters with greater enrichment scores and GO-terms associated with extracellular matrix (ECM) biosynthesis/remodeling and inflammation/immune response. The KEGG database revealed that exercise regulates 147 metabolic pathways representing molecular interaction networks for Metabolism, Genetic Information Processing, Environmental Information Processing, Cellular Processes, Organismal Systems, and Diseases. These pathways collectively supported the complex regulation of the beneficial effects of exercise on the cartilage. Overall, the findings highlight that exercise is a robust transcriptional regulator of a wide array of metabolic pathways in healthy cartilage. The major actions of exercise involve ECM biosynthesis/cartilage strengthening and attenuation of inflammatory pathways to provide prophylaxis against onset of arthritic diseases in healthy cartilage. Copyright © 2016 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights

Genome-wide methylation analysis identifies genes silenced in non-seminoma cell lines

PubMed Central

Noor, Dzul Azri Mohamed; Jeyapalan, Jennie N; Alhazmi, Safiah; Carr, Matthew; Squibb, Benjamin; Wallace, Claire; Tan, Christopher; Cusack, Martin; Hughes, Jaime; Reader, Tom; Shipley, Janet; Sheer, Denise; Scotting, Paul J

2016-01-01

Silencing of genes by DNA methylation is a common phenomenon in many types of cancer. However, the genome-wide effect of DNA methylation on gene expression has been analysed in relatively few cancers. Germ cell tumours (GCTs) are a complex group of malignancies. They are unique in developing from a pluripotent progenitor cell. Previous analyses have suggested that non-seminomas exhibit much higher levels of DNA methylation than seminomas. The genomic targets that are methylated, the extent to which this results in gene silencing and the identity of the silenced genes most likely to play a role in the tumours’ biology have not yet been established. In this study, genome-wide methylation and expression analysis of GCT cell lines was combined with gene expression data from primary tumours to address this question. Genome methylation was analysed using the Illumina infinium HumanMethylome450 bead chip system and gene expression was analysed using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Regulation by methylation was confirmed by demethylation using 5-aza-2-deoxycytidine and reverse transcription–quantitative PCR. Large differences in the level of methylation of the CpG islands of individual genes between tumour cell lines correlated well with differential gene expression. Treatment of non-seminoma cells with 5-aza-2-deoxycytidine verified that methylation of all genes tested played a role in their silencing in yolk sac tumour cells and many of these genes were also differentially expressed in primary tumours. Genes silenced by methylation in the various GCT cell lines were identified. Several pluripotency-associated genes were identified as a major functional group of silenced genes. PMID:29263807

Genome-wide methylation analysis identifies genes silenced in non-seminoma cell lines.

PubMed

Noor, Dzul Azri Mohamed; Jeyapalan, Jennie N; Alhazmi, Safiah; Carr, Matthew; Squibb, Benjamin; Wallace, Claire; Tan, Christopher; Cusack, Martin; Hughes, Jaime; Reader, Tom; Shipley, Janet; Sheer, Denise; Scotting, Paul J

2016-01-01

Silencing of genes by DNA methylation is a common phenomenon in many types of cancer. However, the genome-wide effect of DNA methylation on gene expression has been analysed in relatively few cancers. Germ cell tumours (GCTs) are a complex group of malignancies. They are unique in developing from a pluripotent progenitor cell. Previous analyses have suggested that non-seminomas exhibit much higher levels of DNA methylation than seminomas. The genomic targets that are methylated, the extent to which this results in gene silencing and the identity of the silenced genes most likely to play a role in the tumours' biology have not yet been established. In this study, genome-wide methylation and expression analysis of GCT cell lines was combined with gene expression data from primary tumours to address this question. Genome methylation was analysed using the Illumina infinium HumanMethylome450 bead chip system and gene expression was analysed using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Regulation by methylation was confirmed by demethylation using 5-aza-2-deoxycytidine and reverse transcription-quantitative PCR. Large differences in the level of methylation of the CpG islands of individual genes between tumour cell lines correlated well with differential gene expression. Treatment of non-seminoma cells with 5-aza-2-deoxycytidine verified that methylation of all genes tested played a role in their silencing in yolk sac tumour cells and many of these genes were also differentially expressed in primary tumours. Genes silenced by methylation in the various GCT cell lines were identified. Several pluripotency-associated genes were identified as a major functional group of silenced genes.

Mapping or Tracing? Rethinking Curriculum Mapping in Higher Education

ERIC Educational Resources Information Center

Wang, Chia-Ling

2015-01-01

Curriculum mapping has been emphasized in recent curriculum innovations in higher education in the drive for global competitiveness. This paper begins by providing an outline of current discourses of curriculum mapping in higher education. Curriculum mapping is frequently associated with outcome-based learning and work readiness, and guiding the…

Map Separates

USGS Publications Warehouse

,

2001-01-01

U.S. Geological Survey (USGS) topographic maps are printed using up to six colors (black, blue, green, red, brown, and purple). To prepare your own maps or artwork based on maps, you can order separate black-and-white film positives or negatives for any color printed on a USGS topographic map, or for one or more of the groups of related features printed in the same color on the map (such as drainage and drainage names from the blue plate.) In this document, examples are shown with appropriate ink color to illustrate the various separates. When purchased, separates are black-and-white film negatives or positives. After you receive a film separate or composite from the USGS, you can crop, enlarge or reduce, and edit to add or remove details to suit your special needs. For example, you can adapt the separates for making regional and local planning maps or for doing many kinds of studies or promotions by using the features you select and then printing them in colors of your choice.

Genetic Risk Score for Essential Hypertension and Risk of Preeclampsia.

PubMed

Smith, Caitlin J; Saftlas, Audrey F; Spracklen, Cassandra N; Triche, Elizabeth W; Bjonnes, Andrew; Keating, Brendan; Saxena, Richa; Breheny, Patrick J; Dewan, Andrew T; Robinson, Jennifer G; Hoh, Josephine; Ryckman, Kelli K

2016-01-01

Preeclampsia is a hypertensive complication of pregnancy characterized by novel onset of hypertension after 20 weeks gestation, accompanied by proteinuria. Epidemiological evidence suggests that genetic susceptibility exists for preeclampsia; however, whether preeclampsia is the result of underlying genetic risk for essential hypertension has yet to be investigated. Based on the hypertensive state that is characteristic of preeclampsia, we aimed to determine if established genetic risk scores (GRSs) for hypertension and blood pressure are associated with preeclampsia. Subjects consisted of 162 preeclamptic cases and 108 normotensive pregnant controls, all of Iowa residence. Subjects' DNA was extracted from buccal swab samples and genotyped on the Affymetrix Genome-wide Human SNP Array 6.0 (Affymetrix, Santa Clara, CA). Missing genotypes were imputed using MaCH and Minimac software. GRSs were calculated for hypertension, systolic blood pressure (SBP), diastolic blood pressure (DBP), and mean arterial pressure (MAP) using established genetic risk loci for each outcome. Regression analyses were performed to determine the association between GRS and risk of preeclampsia. These analyses were replicated in an independent US population of 516 cases and 1,097 controls of European ancestry. GRSs for hypertension, SBP, DBP, and MAP were not significantly associated with risk for preeclampsia (P > 0.189). The results of the replication analysis also yielded nonsignificant associations. GRSs for hypertension and blood pressure are not associated with preeclampsia, suggesting that an underlying predisposition to essential hypertension is not on the causal pathway of preeclampsia. © American Journal of Hypertension, Ltd 2015. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Validation of a novel mapping system and utility for mapping complex atrial tachycardias.

PubMed

Honarbakhsh, S; Hunter, R J; Dhillon, G; Ullah, W; Keating, E; Providencia, R; Chow, A; Earley, M J; Schilling, R J

2018-03-01

This study sought to validate a novel wavefront mapping system utilizing whole-chamber basket catheters (CARTOFINDER, Biosense Webster). The system was validated in terms of (1) mapping atrial-paced beats and (2) mapping complex wavefront patterns in atrial tachycardia (AT). Patients undergoing catheter ablation for AT and persistent AF were included. A 64-pole-basket catheter was used to acquire unipolar signals that were processed by CARTOFINDER mapping system to generate dynamic wavefront propagation maps. The left atrium was paced from four sites to demonstrate focal activation. ATs were mapped with the mechanism confirmed by conventional mapping, entrainment, and response to ablation. Twenty-two patients were included in the study (16 with AT and 6 with AF initially who terminated to AT during ablation). In total, 172 maps were created with the mapping system. It correctly identified atrial-pacing sites in all paced maps. It accurately mapped 9 focal/microreentrant and 18 macroreentrant ATs both in the left and right atrium. A third and fourth observer independently identified the sites of atrial pacing and the AT mechanism from the CARTOFINDER maps, while being blinded to the conventional activation maps. This novel mapping system was effectively validated by mapping focal activation patterns from atrial-paced beats. The system was also effective in mapping complex wavefront patterns in a range of ATs in patients with scarred atria. The system may therefore be of practical use in the mapping and ablation of AT and could have potential for mapping wavefront activations in AF. © 2018 Wiley Periodicals, Inc.

Venus mapping

NASA Technical Reports Server (NTRS)

Batson, R. M.; Morgan, H. F.; Sucharski, Robert

1991-01-01

Semicontrolled image mosaics of Venus, based on Magellan data, are being compiled at 1:50,000,000, 1:10,000,000, 1:5,000,000, and 1:1,000,000 scales to support the Magellan Radar Investigator (RADIG) team. The mosaics are semicontrolled in the sense that data gaps were not filled and significant cosmetic inconsistencies exist. Contours are based on preliminary radar altimetry data that is subjected to revision and improvement. Final maps to support geologic mapping and other scientific investigations, to be compiled as the dataset becomes complete, will be sponsored by the Planetary Geology and Geophysics Program and/or the Venus Data Analysis Program. All maps, both semicontrolled and final, will be published as I-maps by the United States Geological Survey. All of the mapping is based on existing knowledge of the spacecraft orbit; photogrammetric triangulation, a traditional basis for geodetic control on planets where framing cameras were used, is not feasible with the radar images of Venus, although an eventual shift of coordinate system to a revised spin-axis location is anticipated. This is expected to be small enough that it will affect only large-scale maps.

Comparing the Performance of Japan's Earthquake Hazard Maps to Uniform and Randomized Maps

NASA Astrophysics Data System (ADS)

Brooks, E. M.; Stein, S. A.; Spencer, B. D.

2015-12-01

The devastating 2011 magnitude 9.1 Tohoku earthquake and the resulting shaking and tsunami were much larger than anticipated in earthquake hazard maps. Because this and all other earthquakes that caused ten or more fatalities in Japan since 1979 occurred in places assigned a relatively low hazard, Geller (2011) argued that "all of Japan is at risk from earthquakes, and the present state of seismological science does not allow us to reliably differentiate the risk level in particular geographic areas," so a map showing uniform hazard would be preferable to the existing map. Defenders of the maps countered by arguing that these earthquakes are low-probability events allowed by the maps, which predict the levels of shaking that should expected with a certain probability over a given time. Although such maps are used worldwide in making costly policy decisions for earthquake-resistant construction, how well these maps actually perform is unknown. We explore this hotly-contested issue by comparing how well a 510-year-long record of earthquake shaking in Japan is described by the Japanese national hazard (JNH) maps, uniform maps, and randomized maps. Surprisingly, as measured by the metric implicit in the JNH maps, i.e. that during the chosen time interval the predicted ground motion should be exceeded only at a specific fraction of the sites, both uniform and randomized maps do better than the actual maps. However, using as a metric the squared misfit between maximum observed shaking and that predicted, the JNH maps do better than uniform or randomized maps. These results indicate that the JNH maps are not performing as well as expected, that what factors control map performance is complicated, and that learning more about how maps perform and why would be valuable in making more effective policy.

MapFactory - Towards a mapping design pattern for big geospatial data

NASA Astrophysics Data System (ADS)

Rautenbach, Victoria; Coetzee, Serena

2018-05-01

With big geospatial data emerging, cartographers and geographic information scientists have to find new ways of dealing with the volume, variety, velocity, and veracity (4Vs) of the data. This requires the development of tools that allow processing, filtering, analysing, and visualising of big data through multidisciplinary collaboration. In this paper, we present the MapFactory design pattern that will be used for the creation of different maps according to the (input) design specification for big geospatial data. The design specification is based on elements from ISO19115-1:2014 Geographic information - Metadata - Part 1: Fundamentals that would guide the design and development of the map or set of maps to be produced. The results of the exploratory research suggest that the MapFactory design pattern will help with software reuse and communication. The MapFactory design pattern will aid software developers to build the tools that are required to automate map making with big geospatial data. The resulting maps would assist cartographers and others to make sense of big geospatial data.

Mapping the Heart

ERIC Educational Resources Information Center

Hulse, Grace

2012-01-01

In this article, the author describes how her fourth graders made ceramic heart maps. The impetus for this project came from reading "My Map Book" by Sara Fanelli. This book is a collection of quirky, hand-drawn and collaged maps that diagram a child's world. There are maps of her stomach, her day, her family, and her heart, among others. The…

Open Land-Use Map: A Regional Land-Use Mapping Strategy for Incorporating OpenStreetMap with Earth Observations

NASA Astrophysics Data System (ADS)

Yang, D.; Fu, C. S.; Binford, M. W.

2017-12-01

The southeastern United States has high landscape heterogeneity, withheavily managed forestlands, highly developed agriculture lands, and multiple metropolitan areas. Human activities are transforming and altering land patterns and structures in both negative and positive manners. A land-use map for at the greater scale is a heavy computation task but is critical to most landowners, researchers, and decision makers, enabling them to make informed decisions for varying objectives. There are two major difficulties in generating the classification maps at the regional scale: the necessity of large training point sets and the expensive computation cost-in terms of both money and time-in classifier modeling. Volunteered Geographic Information (VGI) opens a new era in mapping and visualizing our world, where the platform is open for collecting valuable georeferenced information by volunteer citizens, and the data is freely available to the public. As one of the most well-known VGI initiatives, OpenStreetMap (OSM) contributes not only road network distribution, but also the potential for using this data to justify land cover and land use classifications. Google Earth Engine (GEE) is a platform designed for cloud-based mapping with a robust and fast computing power. Most large scale and national mapping approaches confuse "land cover" and "land-use", or build up the land-use database based on modeled land cover datasets. Unlike most other large-scale approaches, we distinguish and differentiate land-use from land cover. By focusing our prime objective of mapping land-use and management practices, a robust regional land-use mapping approach is developed by incorporating the OpenstreepMap dataset into Earth observation remote sensing imageries instead of the often-used land cover base maps.

Geologic Map and Map Database of Eastern Sonoma and Western Napa Counties, California

USGS Publications Warehouse

Graymer, R.W.; Brabb, E.E.; Jones, D.L.; Barnes, J.; Nicholson, R.S.; Stamski, R.E.

2007-01-01

Introduction This report contains a new 1:100,000-scale geologic map, derived from a set of geologic map databases (Arc-Info coverages) containing information at 1:62,500-scale resolution, and a new description of the geologic map units and structural relations in the map area. Prepared as part of the San Francisco Bay Region Mapping Project, the study area includes the north-central part of the San Francisco Bay region, and forms the final piece of the effort to generate new, digital geologic maps and map databases for an area which includes Alameda, Contra Costa, Marin, Napa, San Francisco, San Mateo, Santa Clara, Santa Cruz, Solano, and Sonoma Counties. Geologic mapping in Lake County in the north-central part of the map extent was not within the scope of the Project. The map and map database integrates both previously published reports and new geologic mapping and field checking by the authors (see Sources of Data index map on the map sheet or the Arc-Info coverage eswn-so and the textfile eswn-so.txt). This report contains new ideas about the geologic structures in the map area, including the active San Andreas Fault system, as well as the geologic units and their relations. Together, the map (or map database) and the unit descriptions in this report describe the composition, distribution, and orientation of geologic materials and structures within the study area at regional scale. Regional geologic information is important for analysis of earthquake shaking, liquifaction susceptibility, landslide susceptibility, engineering materials properties, mineral resources and hazards, as well as groundwater resources and hazards. These data also assist in answering questions about the geologic history and development of the California Coast Ranges.

DistMap: a toolkit for distributed short read mapping on a Hadoop cluster.

PubMed

Pandey, Ram Vinay; Schlötterer, Christian

2013-01-01

With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework. DistMap is easy to use, currently supports nine different short read mapping tools and can be run on all Unix-based operating systems. It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms. DistMap is available from http://code.google.com/p/distmap/

Computer-composite mapping for geologists

USGS Publications Warehouse

van Driel, J.N.

1980-01-01

A computer program for overlaying maps has been tested and evaluated as a means for producing geologic derivative maps. Four maps of the Sugar House Quadrangle, Utah, were combined, using the Multi-Scale Data Analysis and Mapping Program, in a single composite map that shows the relative stability of the land surface during earthquakes. Computer-composite mapping can provide geologists with a powerful analytical tool and a flexible graphic display technique. Digitized map units can be shown singly, grouped with different units from the same map, or combined with units from other source maps to produce composite maps. The mapping program permits the user to assign various values to the map units and to specify symbology for the final map. Because of its flexible storage, easy manipulation, and capabilities of graphic output, the composite-mapping technique can readily be applied to mapping projects in sedimentary and crystalline terranes, as well as to maps showing mineral resource potential. ?? 1980 Springer-Verlag New York Inc.

EnGeoMAP - geological applications within the EnMAP hyperspectral satellite science program

NASA Astrophysics Data System (ADS)

Boesche, N. K.; Mielke, C.; Rogass, C.; Guanter, L.

2016-12-01

Hyperspectral investigations from near field to space substantially contribute to geological exploration and mining monitoring of raw material and mineral deposits. Due to their spectral characteristics, large mineral occurrences and minefields can be identified from space and the spatial distribution of distinct proxy minerals be mapped. In the frame of the EnMAP hyperspectral satellite science program a mineral and elemental mapping tool was developed - the EnGeoMAP. It contains a basic mineral mapping and a rare earth element mapping approach. This study shows the performance of EnGeoMAP based on simulated EnMAP data of the rare earth element bearing Mountain Pass Carbonatite Complex, USA, and the Rodalquilar and Lomilla Calderas, Spain, which host the economically relevant gold-silver, lead-zinc-silver-gold and alunite deposits. The mountain pass image data was simulated on the basis of AVIRIS Next Generation images, while the Rodalquilar data is based on HyMap images. The EnGeoMAP - Base approach was applied to both images, while the mountain pass image data were additionally analysed using the EnGeoMAP - REE software tool. The results are mineral and elemental maps that serve as proxies for the regional lithology and deposit types. The validation of the maps is based on chemical analyses of field samples. Current airborne sensors meet the spatial and spectral requirements for detailed mineral mapping and future hyperspectral space borne missions will additionally provide a large coverage. For those hyperspectral missions, EnGeoMAP is a rapid data analysis tool that is provided to spectral geologists working in mineral exploration.

Symplectic Propagation of the Map, Tangent Map and Tangent Map Derivative through Quadrupole and Combined-Function Dipole Magnets without Truncation

NASA Astrophysics Data System (ADS)

Bruhwiler, D. L.; Cary, J. R.; Shasharina, S.

1998-04-01

The MAPA accelerator modeling code symplectically advances the full nonlinear map, tangent map and tangent map derivative through all accelerator elements. The tangent map and its derivative are nonlinear generalizations of Browns first- and second-order matrices(K. Brown, SLAC-75, Rev. 4 (1982), pp. 107-118.), and they are valid even near the edges of the dynamic aperture, which may be beyond the radius of convergence for a truncated Taylor series. In order to avoid truncation of the map and its derivatives, the Hamiltonian is split into pieces for which the map can be obtained analytically. Yoshidas method(H. Yoshida, Phys. Lett. A 150 (1990), pp. 262-268.) is then used to obtain a symplectic approximation to the map, while the tangent map and its derivative are appropriately composed at each step to obtain them with equal accuracy. We discuss our splitting of the quadrupole and combined-function dipole Hamiltonians and show that typically few steps are required for a high-energy accelerator.

Toward a national fuels mapping strategy: Lessons from selected mapping programs

USGS Publications Warehouse

Loveland, Thomas R.

2001-01-01

The establishment of a robust national fuels mapping program must be based on pertinent lessons from relevant national mapping programs. Many large-area mapping programs are under way in numerous Federal agencies. Each of these programs follows unique strategies to achieve mapping goals and objectives. Implementation approaches range from highly centralized programs that use tightly integrated standards and dedicated staff, to dispersed programs that permit considerable flexibility. One model facilitates national consistency, while the other allows accommodation of locally relevant conditions and issues. An examination of the programmatic strategies of four national vegetation and land cover mapping initiatives can identify the unique approaches, accomplishments, and lessons of each that should be considered in the design of a national fuel mapping program. The first three programs are the U.S. Geological Survey Gap Analysis Program, the U.S. Geological Survey National Land Cover Characterization Program, and the U.S. Fish and Wildlife Survey National Wetlands Inventory. A fourth program, the interagency Multiresolution Land Characterization Program, offers insights in the use of partnerships to accomplish mapping goals. Collectively, the programs provide lessons, guiding principles, and other basic concepts that can be used to design a successful national fuels mapping initiative.

DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster

PubMed Central

Pandey, Ram Vinay; Schlötterer, Christian

2013-01-01

With the rapid and steady increase of next generation sequencing data output, the mapping of short reads has become a major data analysis bottleneck. On a single computer, it can take several days to map the vast quantity of reads produced from a single Illumina HiSeq lane. In an attempt to ameliorate this bottleneck we present a new tool, DistMap - a modular, scalable and integrated workflow to map reads in the Hadoop distributed computing framework. DistMap is easy to use, currently supports nine different short read mapping tools and can be run on all Unix-based operating systems. It accepts reads in FASTQ format as input and provides mapped reads in a SAM/BAM format. DistMap supports both paired-end and single-end reads thereby allowing the mapping of read data produced by different sequencing platforms. DistMap is available from http://code.google.com/p/distmap/ PMID:24009693

FEM: Feature-enhanced map

DOE Office of Scientific and Technical Information (OSTI.GOV)

Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat

A method is presented that modifies a 2 m F obs- D F modelσ A-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretabilitymore » and decreased model bias compared with the starting 2 m F obs- D F modelσ A-weighted map.« less

FEM: Feature-enhanced map

DOE PAGES

Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat; ...

2015-02-26

A method is presented that modifies a 2 m F obs- D F modelσ A-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretabilitymore » and decreased model bias compared with the starting 2 m F obs- D F modelσ A-weighted map.« less

FEM: feature-enhanced map

PubMed Central

Afonine, Pavel V.; Moriarty, Nigel W.; Mustyakimov, Marat; Sobolev, Oleg V.; Terwilliger, Thomas C.; Turk, Dusan; Urzhumtsev, Alexandre; Adams, Paul D.

2015-01-01

A method is presented that modifies a 2m F obs − D F model σA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2m F obs − D F model σA-weighted map. PMID:25760612

Google Maps: You Are Here

ERIC Educational Resources Information Center

Jacobsen, Mikael

2008-01-01

Librarians use online mapping services such as Google Maps, MapQuest, Yahoo Maps, and others to check traffic conditions, find local businesses, and provide directions. However, few libraries are using one of Google Maps most outstanding applications, My Maps, for the creation of enhanced and interactive multimedia maps. My Maps is a simple and…

Interactive Map | USDA Plant Hardiness Zone Map

Science.gov Websites

Choose Basemap: Terrain Road Map Satellite Image Turn on Basemap Roads and Labels Zone Color Transparency menu to switch between Terrain, Road Map, and Satellite Image. Turn on Basemap Roads and Labels Click option is available only for Terrain and Satellite Image basemap choices. Zone Color Transparency The

Cat-Map: putting cataract on the map

PubMed Central

Bennett, Thomas M.; Hejtmancik, J. Fielding

2010-01-01

Lens opacities, or cataract(s), may be inherited as a classic Mendelian disorder usually with early-onset or, more commonly, acquired with age as a multi-factorial or complex trait. Many genetic forms of cataract have been described in mice and other animal models. Considerable progress has been made in mapping and identifying the genes and mutations responsible for inherited forms of cataract, and genetic determinants of age-related cataract are beginning to be discovered. To provide a convenient and accurate summary of current information focused on the increasing genetic complexity of Mendelian and age-related cataract we have created an online chromosome map and reference database for cataract in humans and mice (Cat-Map). PMID:21042563

183. Photocopy of map (Twin Falls Canal Company). TOPOGRAPHICAL MAP ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

183. Photocopy of map (Twin Falls Canal Company). TOPOGRAPHICAL MAP OF MILNER DAM SITE, TWIN FALLS COUNTY, MILNER, IDAHO; MAP, LEFT SIDE ONLY. CROSS REFERENCE: ID-15-192. - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID

Baby Brain Map

MedlinePlus

... a Member Home Resources & Services Professional Resource Baby Brain Map Mar 17, 2016 The Brain Map was adapted in 2006 by ZERO TO ... supports Adobe Flash Player. To view the Baby Brain Map, please visit this page on a browser ...

Topographical Hill Shading Map Production Based Tianditu (map World)

NASA Astrophysics Data System (ADS)

Wang, C.; Zha, Z.; Tang, D.; Yang, J.

2018-04-01

TIANDITU (Map World) is the public version of National Platform for Common Geospatial Information Service, and the terrain service is an important channel for users on the platform. With the development of TIANDITU, topographical hill shading map production for providing and updating global terrain map on line becomes necessary for the characters of strong intuition, three-dimensional sense and aesthetic effect. As such, the terrain service of TIANDITU focuses on displaying the different scales of topographical data globally. And this paper mainly aims to research the method of topographical hill shading map production globally using DEM (Digital Elevation Model) data between the displaying scales about 1 : 140,000,000 to 1 : 4,000,000, corresponded the display level from 2 to 7 on TIANDITU website.

Single-edition quadrangle maps

USGS Publications Warehouse

,

1998-01-01

In August 1993, the U.S. Geological Survey's (USGS) National Mapping Division and the U.S. Department of Agriculture's Forest Service signed an Interagency Agreement to begin a single-edition joint mapping program. This agreement established the coordination for producing and maintaining single-edition primary series topographic maps for quadrangles containing National Forest System lands. The joint mapping program saves money by eliminating duplication of effort by the agencies and results in a more frequent revision cycle for quadrangles containing national forests. Maps are revised on the basis of jointly developed standards and contain normal features mapped by the USGS, as well as additional features required for efficient management of National Forest System lands. Single-edition maps look slightly different but meet the content, accuracy, and quality criteria of other USGS products. The Forest Service is responsible for the land management of more than 191 million acres of land throughout the continental United States, Alaska, and Puerto Rico, including 155 national forests and 20 national grasslands. These areas make up the National Forest System lands and comprise more than 10,600 of the 56,000 primary series 7.5-minute quadrangle maps (15-minute in Alaska) covering the United States. The Forest Service has assumed responsibility for maintaining these maps, and the USGS remains responsible for printing and distributing them. Before the agreement, both agencies published similar maps of the same areas. The maps were used for different purposes, but had comparable types of features that were revised at different times. Now, the two products have been combined into one so that the revision cycle is stabilized and only one agency revises the maps, thus increasing the number of current maps available for National Forest System lands. This agreement has improved service to the public by requiring that the agencies share the same maps and that the maps meet a

Mapping landscape corridors

Treesearch

Peter Vogt; Kurt H. Riitters; Marcin Iwanowski; Christine Estreguil; Jacek Kozak; Pierre Soille

2007-01-01

Corridors are important geographic features for biological conservation and biodiversity assessment. The identification and mapping of corridors is usually based on visual interpretations of movement patterns (functional corridors) or habitat maps (structural corridors). We present a method for automated corridor mapping with morphological image processing, and...

cudaMap: a GPU accelerated program for gene expression connectivity mapping

PubMed Central

2013-01-01

Background Modern cancer research often involves large datasets and the use of sophisticated statistical techniques. Together these add a heavy computational load to the analysis, which is often coupled with issues surrounding data accessibility. Connectivity mapping is an advanced bioinformatic and computational technique dedicated to therapeutics discovery and drug re-purposing around differential gene expression analysis. On a normal desktop PC, it is common for the connectivity mapping task with a single gene signature to take > 2h to complete using sscMap, a popular Java application that runs on standard CPUs (Central Processing Units). Here, we describe new software, cudaMap, which has been implemented using CUDA C/C++ to harness the computational power of NVIDIA GPUs (Graphics Processing Units) to greatly reduce processing times for connectivity mapping. Results cudaMap can identify candidate therapeutics from the same signature in just over thirty seconds when using an NVIDIA Tesla C2050 GPU. Results from the analysis of multiple gene signatures, which would previously have taken several days, can now be obtained in as little as 10 minutes, greatly facilitating candidate therapeutics discovery with high throughput. We are able to demonstrate dramatic speed differentials between GPU assisted performance and CPU executions as the computational load increases for high accuracy evaluation of statistical significance. Conclusion Emerging ‘omics’ technologies are constantly increasing the volume of data and information to be processed in all areas of biomedical research. Embracing the multicore functionality of GPUs represents a major avenue of local accelerated computing. cudaMap will make a strong contribution in the discovery of candidate therapeutics by enabling speedy execution of heavy duty connectivity mapping tasks, which are increasingly required in modern cancer research. cudaMap is open source and can be freely downloaded from http://purl.oclc.org/NET/cudaMap

cudaMap: a GPU accelerated program for gene expression connectivity mapping.

PubMed

McArt, Darragh G; Bankhead, Peter; Dunne, Philip D; Salto-Tellez, Manuel; Hamilton, Peter; Zhang, Shu-Dong

2013-10-11

Modern cancer research often involves large datasets and the use of sophisticated statistical techniques. Together these add a heavy computational load to the analysis, which is often coupled with issues surrounding data accessibility. Connectivity mapping is an advanced bioinformatic and computational technique dedicated to therapeutics discovery and drug re-purposing around differential gene expression analysis. On a normal desktop PC, it is common for the connectivity mapping task with a single gene signature to take > 2h to complete using sscMap, a popular Java application that runs on standard CPUs (Central Processing Units). Here, we describe new software, cudaMap, which has been implemented using CUDA C/C++ to harness the computational power of NVIDIA GPUs (Graphics Processing Units) to greatly reduce processing times for connectivity mapping. cudaMap can identify candidate therapeutics from the same signature in just over thirty seconds when using an NVIDIA Tesla C2050 GPU. Results from the analysis of multiple gene signatures, which would previously have taken several days, can now be obtained in as little as 10 minutes, greatly facilitating candidate therapeutics discovery with high throughput. We are able to demonstrate dramatic speed differentials between GPU assisted performance and CPU executions as the computational load increases for high accuracy evaluation of statistical significance. Emerging 'omics' technologies are constantly increasing the volume of data and information to be processed in all areas of biomedical research. Embracing the multicore functionality of GPUs represents a major avenue of local accelerated computing. cudaMap will make a strong contribution in the discovery of candidate therapeutics by enabling speedy execution of heavy duty connectivity mapping tasks, which are increasingly required in modern cancer research. cudaMap is open source and can be freely downloaded from http://purl.oclc.org/NET/cudaMap.

MAPS of Cancer

NASA Technical Reports Server (NTRS)

Gray, Lincoln

1998-01-01

Our goal was to produce an interactive visualization from a mathematical model that successfully predicts metastases from head and neck cancer. We met this goal early in the project. The visualization is available for the public to view. Our work appears to fill a need for more information about this deadly disease. The idea of this project was to make an easily interpretable visualization based on what we call "functional maps" of disease. A functional map is a graphic summary of medical data, where distances between parts of the body are determined by the probability of disease, not by anatomical distances. Functional maps often beat little resemblance to anatomical maps, but they can be used to predict the spread of disease. The idea of modeling the spread of disease in an abstract multidimensional space is difficult for many people. Our goal was to make the important predictions easy to see. NASA must face this problem frequently: how to help laypersons and professionals see important trends in abstract, complex data. We took advantage of concepts perfected in NASA's graphics libraries. As an analogy, consider a functional map of early America. Suppose we choose travel times, rather than miles, as our measures of inter-city distances. For Abraham Lincoln, travel times would have been the more meaningful measure of separation between cities. In such a map New Orleans would be close to Memphis because of the Mississippi River. St. Louis would be close to Portland because of the Oregon Trail. Oklahoma City would be far from Little Rock because of the Cheyenne. Such a map would look puzzling to those of us who have always seen physical maps, but the functional map would be more useful in predicting the probabilities of inter-site transit. Continuing the analogy, we could predict the spread of social diseases such as gambling along the rivers and cattle rustling along the trails. We could simply print the functional map of America, but it would be more interesting

Mapping Inner Space: Learning and Teaching Visual Mapping. Second Edition.

ERIC Educational Resources Information Center

Margulies, Nancy

More than 10 years ago, when "Mapping Inner Space" was first published, a few teachers were using this creative technique and teaching it to their students. Today mapping is widely used in schools, universities, and the corporate world, as well. This second edition of the book explores a variety of mapping styles and also takes a fresh look at the…

Adventures with Maps.

ERIC Educational Resources Information Center

Hofferber, Michael

1989-01-01

Orienteering--the game of following a map to find predetermined locations--can spark interest and develop skills in map making and map reading. This article gives background on orienteering; describes indoor and outdoor orienteering activities; offers suggestions for incorporating orienteering into science, math, and language arts; and provides a…

Application of OpenStreetMap (OSM) to Support the Mapping Village in Indonesia

NASA Astrophysics Data System (ADS)

Swasti Kanthi, Nurin; Hery Purwanto, Taufik

2016-11-01

Geospatial Information is a important thing in this era, because the need for location information is needed to know the condition of a region. In 2015 the Indonesian government release detailed mapping in village level and their Parent maps Indonesian state regulatory standards set forth in Rule form Norm Standards, Procedures and Criteria for Mapping Village (NSPK). Over time Web and Mobile GIS was developed with a wide range of applications. The merger between detailed mapping and Web GIS is still rarely performed and not used optimally. OpenStreetMap (OSM) is a WebGIS which can be utilized as Mobile GIS providing sufficient information to the representative levels of the building and can be used for mapping the village.Mapping Village using OSM was conducted using remote sensing approach and Geographical Information Systems (GIS), which's to interpret remote sensing imagery from OSM. The study was conducted to analyzed how far the role of OSM to support the mapping of the village, it's done by entering the house number data, administrative boundaries, public facilities and land use into OSM with reference data and data image Village Plan. The results of the mapping portion villages in OSM as a reference map-making village and analyzed in accordance with NSPK for detailed mapping Rukun Warga (RW) is part of the village mapping. The use of OSM greatly assists the process of mapping the details of the region with data sources in the form of images and can be accessed for Open Source. But still need their care and updating the data source to maintain the validity of the data.

RadMap

EPA Pesticide Factsheets

RadMap is an interactive desktop tool featuring a nationwide geographic information systems (GIS) map of long-term radiation monitoring locations across the United States with access to key information about the monitor and the area surrounding it.

Use of sentinel node mapping for cancer of the colon: 'to map or not to map".

PubMed

Thomas, Kristen A; Lechner, Jonathan; Shen, Perry; Waters, Gregory S; Geisinger, Kim R; Levine, Edward A

2006-07-01

Sentinel lymph node (SLN) mapping has become a cornerstone of oncologic surgery because it is a proven method for identifying nodal disease in melanoma and breast cancer. In addition, it can ameliorate the surgical morbidity secondary to lymphadenectomy. However, experience with SLN mapping for carcinoma of the colon and other visceral malignancies is limited. This study represents an update to our initial pilot experience with SLN mapping for carcinoma of the colon. Consenting patients over the age of 18 diagnosed with adenocarcinoma of the colon were included in this study. At the time of operation, 1 to 2 mL of isosulfan blue was injected with a 25-gauge needle into the subserosa at 4 sites around the edge of the palpable tumor. The SLN was identified visually and excised followed by a standard lymphadenectomy and surgical resection. SLNs were evaluated by standard hematoxylin and eosin (H&E) evaluation as well as immunohistochemical (IHC) techniques for carcinoembryonic antigen and cytokeratin if the H&E was negative. Sixty-nine patients underwent SLN mapping. A SLN was identified in 93 per cent (64 of 69) of patients. Nodal metastases were identified in 38 per cent (26 of 69) of patients overall. In 5 patients, the only positive node identified was the SLN, 2 of which were positive by IHC criteria alone. Therefore, 3 per cent (2 of 69) of patients were upstaged by SLN mapping. This technique was 100 per cent specific while being 46 per cent sensitive. Fourteen patients had false-negative SLNs. Metastasis to regional lymph nodes remains the key prognostic factor for colon cancer. SLN mapping is feasible for colon cancer and can identify a subset of patients who could benefit from adjuvant chemotherapy. Although SLN mapping did not alter the surgical management of colon cancer, it does make possible a more focused and cost-effective pathologic evaluation of nodal disease. We do not suggest routine utilization of SLN mapping for colon cancer, but we believe that

Saturation of an Intra-Gene Pool Linkage Map: Towards a Unified Consensus Linkage Map for Fine Mapping and Synteny Analysis in Common Bean

PubMed Central

Galeano, Carlos H.; Fernandez, Andrea C.; Franco-Herrera, Natalia; Cichy, Karen A.; McClean, Phillip E.; Vanderleyden, Jos; Blair, Matthew W.

2011-01-01

Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364×BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364×G19833 (DG) and BAT93×JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning. PMID:22174773

Exon-Specific QTLs Skew the Inferred Distribution of Expression QTLs Detected Using Gene Expression Array Data

PubMed Central

Veyrieras, Jean-Baptiste; Gaffney, Daniel J.; Pickrell, Joseph K.; Gilad, Yoav; Stephens, Matthew; Pritchard, Jonathan K.

2012-01-01

Mapping of expression quantitative trait loci (eQTLs) is an important technique for studying how genetic variation affects gene regulation in natural populations. In a previous study using Illumina expression data from human lymphoblastoid cell lines, we reported that cis-eQTLs are especially enriched around transcription start sites (TSSs) and immediately upstream of transcription end sites (TESs). In this paper, we revisit the distribution of eQTLs using additional data from Affymetrix exon arrays and from RNA sequencing. We confirm that most eQTLs lie close to the target genes; that transcribed regions are generally enriched for eQTLs; that eQTLs are more abundant in exons than introns; and that the peak density of eQTLs occurs at the TSS. However, we find that the intriguing TES peak is greatly reduced or absent in the Affymetrix and RNA-seq data. Instead our data suggest that the TES peak observed in the Illumina data is mainly due to exon-specific QTLs that affect 3′ untranslated regions, where most of the Illumina probes are positioned. Nonetheless, we do observe an overall enrichment of eQTLs in exons versus introns in all three data sets, consistent with an important role for exonic sequences in gene regulation. PMID:22359548

Engineering With Nature Geographic Project Mapping Tool (EWN ProMap)

DTIC Science & Technology

2015-07-01

EWN ProMap database provides numerous case studies for infrastructure projects such as breakwaters, river engineering dikes, and seawalls that have...the EWN Project Mapping Tool (EWN ProMap) is to assist users in their search for case study information that can be valuable for developing EWN ideas...Essential elements of EWN include: (1) using science and engineering to produce operational efficiencies supporting sustainable delivery of

Oil Exploration Mapping

NASA Technical Reports Server (NTRS)

1994-01-01

After concluding an oil exploration agreement with the Republic of Yemen, Chevron International needed detailed geologic and topographic maps of the area. Chevron's remote sensing team used imagery from Landsat and SPOT, combining images into composite views. The project was successfully concluded and resulted in greatly improved base maps and unique topographic maps.

RICH MAPS

EPA Science Inventory

Michael Goodchild recently gave eight reasons why traditional maps are limited as communication devices, and how interactive internet mapping can overcome these limitations. In the past, many authorities in cartography, from Jenks to Bertin, have emphasized the importance of sim...

Coastal mapping handbook

USGS Publications Warehouse

,; ,; Ellis, Melvin Y.

1978-01-01

Passage of the Coastal Zone Management Act of 1972 focused attention on the Nation's coastal land and water areas. As plans for more effective management of the coastal zone evolved, it soon became apparent that improved maps and charts of these areas were needed. This handbook was prepared with the requirements of the entire coastal community in mind, giving greatest attention to the needs of coastal zone managers and planners at the State and local levels. Its principal objective is to provide general information and guidance; it is neither a textbook nor a technical manual, but rather a primer on coastal mapping. This handbook should help planners and managers of coastal programs to determine their mapping requirements, select the best maps and charts for their particular needs, and to deal effectively with personnel who gather data and prepare maps. The sections on "Sources of Assistance and Advice" and "Product and Data Sources" should be especially useful to all involved in mapping the coastal zone. Brief summaries of the mapping efforts of several State coastal zone management programs are included. "Future outlook" discusses anticipated progress and changes in mapping procedures and techniques. Illustrations are inserted, where appropriate, to illustrate the products and equipment discussed. Because of printing restrictions, the colors in map illustrations may vary from those in the original publication. The appendixes include substantial material which also should be of interest. In addition a glossary and an index are included to provide easy and quick access to the terms and concepts used in the text. For those interested in more technical detail than is provided in this handbook, the "Selected references" will be useful. Also, the publications of the professional societies listed in appendix 4 will provide technical information in detail.

The National Map: from geography to mapping and back again

USGS Publications Warehouse

Kelmelis, John A.; DeMulder, Mark L.; Ogrosky, Charles E.; Van Driel, J. Nicholas; Ryan, Barbara J.

2003-01-01

When the means of production for national base mapping were capital intensive, required large production facilities, and had ill-defined markets, Federal Government mapping agencies were the primary providers of the spatial data needed for economic development, environmental management, and national defense. With desktop geographic information systems now ubiquitous, source data available as a commodity from private industry, and the realization that many complex problems faced by society need far more and different kinds of spatial data for their solutions, national mapping organizations must realign their business strategies to meet growing demand and anticipate the needs of a rapidly changing geographic information environment. The National Map of the United States builds on a sound historic foundation of describing and monitoring the land surface and adds a focused effort to produce improved understanding, modeling, and prediction of land-surface change. These added dimensions bring to bear a broader spectrum of geographic science to address extant and emerging issues. Within the overarching construct of The National Map, the U.S. Geological Survey (USGS) is making a transition from data collector to guarantor of national data completeness; from producing paper maps to supporting an online, seamless, integrated database; and from simply describing the Nation’s landscape to linking these descriptions with increased scientific understanding. Implementing the full spectrum of geographic science addresses a myriad of public policy issues, including land and natural resource management, recreation, urban growth, human health, and emergency planning, response, and recovery. Neither these issues nor the science and technologies needed to deal with them are static. A robust research agenda is needed to understand these changes and realize The National Map vision. Initial successes have been achieved. These accomplishments demonstrate the utility of

Knowledge Maps for E-Learning

ERIC Educational Resources Information Center

Lee, Jae Hwa; Segev, Aviv

2012-01-01

Maps such as concept maps and knowledge maps are often used as learning materials. These maps have nodes and links, nodes as key concepts and links as relationships between key concepts. From a map, the user can recognize the important concepts and the relationships between them. To build concept or knowledge maps, domain experts are needed.…

Comparison of Comparative Genomic Hybridization Technologies across Microarray Platforms

EPA Science Inventory

In the 2007 Association of Biomolecular Resource Facilities (ABRF) Microarray Research Group (MARG) project, we analyzed HL-60 DNA with five platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation (CNV) was analyzed ...

Preferred reporting items for studies mapping onto preference-based outcome measures: The MAPS statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-01-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. The primary audiences for the MAPS statement are researchers reporting mapping studies, the funders of the research, and peer reviewers and editors involved in assessing mapping studies for publication. A de novo list of 29 candidate reporting items and accompanying explanations was created by a working group comprised of six health economists and one Delphi methodologist. Following a two-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community, a final set of 23 items deemed essential for transparent reporting, and accompanying explanations, was developed. The items are contained in a user friendly 23 item checklist. They are presented numerically and categorised within six sections, namely: (i) title and abstract; (ii) introduction; (iii) methods; (iv) results; (v) discussion; and (vi) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document. It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by seven health economics and quality of life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in five years' time.

Preferred Reporting Items for Studies Mapping onto Preference-Based Outcome Measures: The MAPS Statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-10-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite the publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. The primary audiences for the MAPS statement are researchers reporting mapping studies, the funders of the research, and peer reviewers and editors involved in assessing mapping studies for publication. A de novo list of 29 candidate reporting items and accompanying explanations was created by a working group comprising six health economists and one Delphi methodologist. Following a two-round modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community, a final set of 23 items deemed essential for transparent reporting, and accompanying explanations, was developed. The items are contained in a user-friendly 23-item checklist. They are presented numerically and categorised within six sections, namely: (1) title and abstract; (2) introduction; (3) methods; (4) results; (5) discussion; and (6) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document. It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by seven health economics and quality-of-life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years' time.

The Mapping X-ray Fluorescence Spectrometer (MapX)

NASA Astrophysics Data System (ADS)

Sarrazin, P.; Blake, D. F.; Marchis, F.; Bristow, T.; Thompson, K.

2017-12-01

Many planetary surface processes leave traces of their actions as features in the size range 10s to 100s of microns. The Mapping X-ray Fluorescence Spectrometer (MapX) will provide elemental imaging at 100 micron spatial resolution, yielding elemental chemistry at a scale where many relict physical, chemical, or biological features can be imaged and interpreted in ancient rocks on planetary bodies and planetesimals. MapX is an arm-based instrument positioned on a rock or regolith with touch sensors. During an analysis, an X-ray source (tube or radioisotope) bombards the sample with X-rays or alpha-particles / gamma-rays, resulting in sample X-ray Fluorescence (XRF). X-rays emitted in the direction of an X-ray sensitive CCD imager pass through a 1:1 focusing lens (X-ray micro-pore Optic (MPO)) that projects a spatially resolved image of the X-rays onto the CCD. The CCD is operated in single photon counting mode so that the energies and positions of individual X-ray photons are recorded. In a single analysis, several thousand frames are both stored and processed in real-time. Higher level data products include single-element maps with a lateral spatial resolution of 100 microns and quantitative XRF spectra from ground- or instrument- selected Regions of Interest (ROI). XRF spectra from ROI are compared with known rock and mineral compositions to extrapolate the data to rock types and putative mineralogies. When applied to airless bodies and implemented with an appropriate radioisotope source for alpha-particle excitation, MapX will be able to analyze biogenic elements C, N, O, P, S, in addition to the cations of the rock-forming elements >Na, accessible with either X-ray or gamma-ray excitation. The MapX concept has been demonstrated with a series of lab-based prototypes and is currently under refinement and TRL maturation.

Map of Nasca Geoglyphs

NASA Astrophysics Data System (ADS)

Hanzalová, K.; Pavelka, K.

2013-07-01

The Czech Technical University in Prague in the cooperation with the University of Applied Sciences in Dresden (Germany) work on the Nasca Project. The cooperation started in 2004 and much work has been done since then. All work is connected with Nasca lines in southern Peru. The Nasca project started in 1995 and its main target is documentation and conservation of the Nasca lines. Most of the project results are presented as WebGIS application via Internet. In the face of the impending destruction of the soil drawings, it is possible to preserve this world cultural heritage for the posterity at least in a digital form. Creating of Nasca lines map is very useful. The map is in a digital form and it is also available as a paper map. The map contains planimetric component of the map, map lettering and altimetry. Thematic folder in this map is a vector layer of the geoglyphs in Nasca/Peru. Basis for planimetry are georeferenced satellite images, altimetry is created from digital elevation model. This map was created in ArcGis software.

SLAMM: Visual monocular SLAM with continuous mapping using multiple maps

PubMed Central

Md. Sabri, Aznul Qalid; Loo, Chu Kiong; Mansoor, Ali Mohammed

2018-01-01

This paper presents the concept of Simultaneous Localization and Multi-Mapping (SLAMM). It is a system that ensures continuous mapping and information preservation despite failures in tracking due to corrupted frames or sensor’s malfunction; making it suitable for real-world applications. It works with single or multiple robots. In a single robot scenario the algorithm generates a new map at the time of tracking failure, and later it merges maps at the event of loop closure. Similarly, maps generated from multiple robots are merged without prior knowledge of their relative poses; which makes this algorithm flexible. The system works in real time at frame-rate speed. The proposed approach was tested on the KITTI and TUM RGB-D public datasets and it showed superior results compared to the state-of-the-arts in calibrated visual monocular keyframe-based SLAM. The mean tracking time is around 22 milliseconds. The initialization is twice as fast as it is in ORB-SLAM, and the retrieved map can reach up to 90 percent more in terms of information preservation depending on tracking loss and loop closure events. For the benefit of the community, the source code along with a framework to be run with Bebop drone are made available at https://github.com/hdaoud/ORBSLAMM. PMID:29702697

An Affymetrix Microarray Design for Microbial Genotyping

DTIC Science & Technology

2009-10-01

sanguinis SK36 232 Streptococcus sanguinis HPT sanguinis 5 Streptococcus suis 05ZYH33 138 Streptococcus suis 98 HAH33 65 Streptococcus thermophilus...Rickettsia species, plasmids pBC16 and pLS1. Sequences representing bacterial toxins and antimicrobial resistance (e.g. antibiotic markers) were also...Also included were regions that were constant within a species but differed between species, virulence genes, and antibiotic resistance genes. 2.3

BikeMaps.org: A Global Tool for Collision and Near Miss Mapping

PubMed Central

Nelson, Trisalyn A.; Denouden, Taylor; Jestico, Benjamin; Laberee, Karen; Winters, Meghan

2015-01-01

There are many public health benefits to cycling, such as chronic disease reduction and improved air quality. Real and perceived concerns about safety are primary barriers to new ridership. Due to limited forums for official reporting of cycling incidents, lack of comprehensive data is limiting our ability to study cycling safety and conduct surveillance. Our goal is to introduce BikeMaps.org, a new website developed by the authors for crowd-source mapping of cycling collisions and near misses. BikeMaps.org is a global mapping system that allows citizens to map locations of cycling incidents and report on the nature of the event. Attributes collected are designed for spatial modeling research on predictors of safety and risk, and to aid surveillance and planning. Released in October 2014, within 2 months the website had more than 14,000 visitors and mapping in 14 countries. Collisions represent 38% of reports (134/356) and near misses 62% (222/356). In our pilot city, Victoria, Canada, citizens mapped data equivalent to about 1 year of official cycling collision reports within 2 months via BikeMaps.org. Using report completeness as an indicator, early reports indicate that data are of high quality with 50% being fully attributed and another 10% having only one missing attribute. We are advancing this technology, with the development of a mobile App, improved data visualization, real-time altering of hazard reports, and automated open-source tools for data sharing. Researchers and citizens interested in utilizing the BikeMaps.org technology can get involved by encouraging citizen mapping in their region. PMID:25870852

BikeMaps.org: A Global Tool for Collision and Near Miss Mapping.

PubMed

Nelson, Trisalyn A; Denouden, Taylor; Jestico, Benjamin; Laberee, Karen; Winters, Meghan

2015-01-01

There are many public health benefits to cycling, such as chronic disease reduction and improved air quality. Real and perceived concerns about safety are primary barriers to new ridership. Due to limited forums for official reporting of cycling incidents, lack of comprehensive data is limiting our ability to study cycling safety and conduct surveillance. Our goal is to introduce BikeMaps.org, a new website developed by the authors for crowd-source mapping of cycling collisions and near misses. BikeMaps.org is a global mapping system that allows citizens to map locations of cycling incidents and report on the nature of the event. Attributes collected are designed for spatial modeling research on predictors of safety and risk, and to aid surveillance and planning. Released in October 2014, within 2 months the website had more than 14,000 visitors and mapping in 14 countries. Collisions represent 38% of reports (134/356) and near misses 62% (222/356). In our pilot city, Victoria, Canada, citizens mapped data equivalent to about 1 year of official cycling collision reports within 2 months via BikeMaps.org. Using report completeness as an indicator, early reports indicate that data are of high quality with 50% being fully attributed and another 10% having only one missing attribute. We are advancing this technology, with the development of a mobile App, improved data visualization, real-time altering of hazard reports, and automated open-source tools for data sharing. Researchers and citizens interested in utilizing the BikeMaps.org technology can get involved by encouraging citizen mapping in their region.

Coastal habitat mapping in the Aegean Sea using high resolution orthophoto maps

NASA Astrophysics Data System (ADS)

Topouzelis, Konstantinos; Papakonstantinou, Apostolos; Doukari, Michaela; Stamatis, Panagiotis; Makri, Despina; Katsanevakis, Stelios

2017-09-01

The significance of coastal habitat mapping lies in the need to prevent from anthropogenic interventions and other factors. Until 2015, Landsat-8 (30m) imagery were used as medium spatial resolution satellite imagery. So far, Sentinel-2 satellite imagery is very useful for more detailed regional scale mapping. However, the use of high resolution orthophoto maps, which are determined from UAV data, is expected to improve the mapping accuracy. This is due to small spatial resolution of the orthophoto maps (30 cm). This paper outlines the integration of UAS for data acquisition and Structure from Motion (SfM) pipeline for the visualization of selected coastal areas in the Aegean Sea. Additionally, the produced orthophoto maps analyzed through an object-based image analysis (OBIA) and nearest-neighbor classification for mapping the coastal habitats. Classification classes included the main general habitat types, i.e. seagrass, soft bottom, and hard bottom The developed methodology applied at the Koumbara beach (Ios Island - Greece). Results showed that UAS's data revealed the sub-bottom complexity in large shallow areas since they provide such information in the spatial resolution that permits the mapping of seagrass meadows with extreme detail. The produced habitat vectors are ideal as reference data for studies with satellite data of lower spatial resolution.

Generating Multi-Destination Maps.

PubMed

Zhang, Junsong; Fan, Jiepeng; Luo, Zhenshan

2017-08-01

Multi-destination maps are a kind of navigation maps aimed to guide visitors to multiple destinations within a region, which can be of great help to urban visitors. However, they have not been developed in the current online map service. To address this issue, we introduce a novel layout model designed especially for generating multi-destination maps, which considers the global and local layout of a multi-destination map. We model the layout problem as a graph drawing that satisfies a set of hard and soft constraints. In the global layout phase, we balance the scale factor between ROIs. In the local layout phase, we make all edges have good visibility and optimize the map layout to preserve the relative length and angle of roads. We also propose a perturbation-based optimization method to find an optimal layout in the complex solution space. The multi-destination maps generated by our system are potential feasible on the modern mobile devices and our result can show an overview and a detail view of the whole map at the same time. In addition, we perform a user study to evaluate the effectiveness of our method, and the results prove that the multi-destination maps achieve our goals well.

Bedrock geologic map of Vermont

USGS Publications Warehouse

Ratcliffe, Nicholas M.; Stanley, Rolfe S.; Gale, Marjorie H.; Thompson, Peter J.; Walsh, Gregory J.; With contributions by Hatch, Norman L.; Rankin, Douglas W.; Doolan, Barry L.; Kim, Jonathan; Mehrtens, Charlotte J.; Aleinikoff, John N.; McHone, J. Gregory; Cartography by Masonic, Linda M.

2011-01-01

The Bedrock Geologic Map of Vermont is the result of a cooperative agreement between the U.S. Geological Survey (USGS) and the State of Vermont. The State's complex geology spans 1.4 billion years of Earth's history. The new map comes 50 years after the most recent map of the State by Charles G. Doll and others in 1961 and a full 150 years since the publication of the first geologic map of Vermont by Edward Hitchcock and others in 1861. At a scale of 1:100,000, the map shows an uncommon level of detail for State geologic maps. Mapped rock units are primarily based on lithology, or rock type, to facilitate derivative studies in multiple disciplines. The 1961 map was compiled from 1:62,500-scale or smaller maps. The current map was created to integrate more detailed (1:12,000- to 1:24,000-scale) modern and older (1:62,500-scale) mapping with the theory of plate tectonics to provide a framework for geologic, tectonic, economic, hydrogeologic, and environmental characterization of the bedrock of Vermont. The printed map consists of three oversize sheets (52 x 76 inches). Sheets 1 and 2 show the southern and northern halves of Vermont, respectively, and can be trimmed and joined so that the entire State can be displayed as a single entity. These sheets also include 10 cross sections and a geologic structure map. Sheet 3 on the front consists of descriptions of 486 map units, a correlation of map units, and references cited. Sheet 3 on the back features a list of the 195 sources of geologic map data keyed to an index map of 7.5-minute quadrangles in Vermont, as well as a table identifying ages of rocks dated by uranium-lead zircon geochronology.

Surface Chemistry Maps

NASA Image and Video Library

2015-03-13

Maps of magnesium/silicon (left) and thermal neutron absorption (right) across Mercury's surface (red indicates high values, blue low) are shown. These maps, together with maps of other elemental abundances, reveal the presence of distinct geochemical terranes. Volcanic smooth plains deposits are outlined in white. Read the mission news story to learn more! http://photojournal.jpl.nasa.gov/catalog/PIA19242

National Park Service Vegetation Mapping Inventory Program: Appalachian National Scenic Trail vegetation mapping project

USGS Publications Warehouse

Hop, Kevin D.; Strassman, Andrew C.; Hall, Mark; Menard, Shannon; Largay, Ery; Sattler, Stephanie; Hoy, Erin E.; Ruhser, Janis; Hlavacek, Enrika; Dieck, Jennifer

2017-01-01

The National Park Service (NPS) Vegetation Mapping Inventory (VMI) Program classifies, describes, and maps existing vegetation of national park units for the NPS Natural Resource Inventory and Monitoring (I&M) Program. The NPS VMI Program is managed by the NPS I&M Division and provides baseline vegetation information to the NPS Natural Resource I&M Program. The U.S. Geological Survey Upper Midwest Environmental Sciences Center, NatureServe, NPS Northeast Temperate Network, and NPS Appalachian National Scenic Trail (APPA) have completed vegetation classification and mapping of APPA for the NPS VMI Program.Mappers, ecologists, and botanists collaborated to affirm vegetation types within the U.S. National Vegetation Classification (USNVC) of APPA and to determine how best to map the vegetation types by using aerial imagery. Analyses of data from 1,618 vegetation plots were used to describe USNVC associations of APPA. Data from 289 verification sites were collected to test the field key to vegetation associations and the application of vegetation associations to a sample set of map polygons. Data from 269 validation sites were collected to assess vegetation mapping prior to submitting the vegetation map for accuracy assessment (AA). Data from 3,265 AA sites were collected, of which 3,204 were used to test accuracy of the vegetation map layer. The collective of these datasets affirmed 280 USNVC associations for the APPA vegetation mapping project.To map the vegetation and land cover of APPA, 169 map classes were developed. The 169 map classes consist of 150 that represent natural (including ruderal) vegetation types in the USNVC, 11 that represent cultural (agricultural and developed) vegetation types in the USNVC, 5 that represent natural landscapes with catastrophic disturbance or some other modification to natural vegetation preventing accurate classification in the USNVC, and 3 that represent nonvegetated water (non-USNVC). Features were interpreted from viewing 4

Multitissue Transcriptomics Delineates the Diversity of Airway T Cell Functions in Asthma.

PubMed

Singhania, Akul; Wallington, Joshua C; Smith, Caroline G; Horowitz, Daniel; Staples, Karl J; Howarth, Peter H; Gadola, Stephan D; Djukanović, Ratko; Woelk, Christopher H; Hinks, Timothy S C

2018-02-01

Asthma arises from the complex interplay of inflammatory pathways in diverse cell types and tissues. We sought to undertake a comprehensive transcriptomic assessment of the epithelium and airway T cells that remain understudied in asthma and investigate interactions between multiple cells and tissues. Epithelial brushings and flow-sorted CD3 + T cells from sputum and BAL were obtained from healthy subjects (n = 19) and patients with asthma (mild, moderate, and severe asthma; n = 46). Gene expression was assessed using Affymetrix HT HG-U133 + PM GeneChips, and results were validated by real-time quantitative PCR. In the epithelium, IL-13 response genes (POSTN, SERPINB2, and CLCA1), mast cell mediators (CPA3 and TPSAB1), inducible nitric oxide synthase, and cystatins (CST1, CST2, and CST4) were upregulated in mild asthma, but, except for cystatins, were suppressed by corticosteroids in moderate asthma. In severe asthma-with predominantly neutrophilic phenotype-several distinct processes were upregulated, including neutrophilia (TCN1 and MMP9), mucins, and oxidative stress responses. The majority of the disease signature was evident in sputum T cells in severe asthma, where 267 genes were differentially regulated compared with health, highlighting compartmentalization of inflammation. This signature included IL-17-inducible chemokines (CXCL1, CXCL2, CXCL3, IL8, and CSF3) and chemoattractants for neutrophils (IL8, CCL3, and LGALS3), T cells, and monocytes. A protein interaction network in severe asthma highlighted signatures of responses to bacterial infections across tissues (CEACAM5, CD14, and TLR2), including Toll-like receptor signaling. In conclusion, the activation of innate immune pathways in the airways suggests that activated T cells may be driving neutrophilic inflammation and steroid-insensitive IL-17 response in severe asthma.

Gene expression profiling of immunomagnetically separated cells directly from stabilized whole blood for multicenter clinical trials

PubMed Central

2014-01-01

Background Clinically useful biomarkers for patient stratification and monitoring of disease progression and drug response are in big demand in drug development and for addressing potential safety concerns. Many diseases influence the frequency and phenotype of cells found in the peripheral blood and the transcriptome of blood cells. Changes in cell type composition influence whole blood gene expression analysis results and thus the discovery of true transcript level changes remains a challenge. We propose a robust and reproducible procedure, which includes whole transcriptome gene expression profiling of major subsets of immune cell cells directly sorted from whole blood. Methods Target cells were enriched using magnetic microbeads and an autoMACS® Pro Separator (Miltenyi Biotec). Flow cytometric analysis for purity was performed before and after magnetic cell sorting. Total RNA was hybridized on HGU133 Plus 2.0 expression microarrays (Affymetrix, USA). CEL files signal intensity values were condensed using RMA and a custom CDF file (EntrezGene-based). Results Positive selection by use of MACS® Technology coupled to transcriptomics was assessed for eight different peripheral blood cell types, CD14+ monocytes, CD3+, CD4+, or CD8+ T cells, CD15+ granulocytes, CD19+ B cells, CD56+ NK cells, and CD45+ pan leukocytes. RNA quality from enriched cells was above a RIN of eight. GeneChip analysis confirmed cell type specific transcriptome profiles. Storing whole blood collected in an EDTA Vacutainer® tube at 4°C followed by MACS does not activate sorted cells. Gene expression analysis supports cell enrichment measurements by MACS. Conclusions The proposed workflow generates reproducible cell-type specific transcriptome data which can be translated to clinical settings and used to identify clinically relevant gene expression biomarkers from whole blood samples. This procedure enables the integration of transcriptomics of relevant immune cell subsets sorted directly from

Phycocyanobilin promotes PC12 cell survival and modulates immune and inflammatory genes and oxidative stress markers in acute cerebral hypoperfusion in rats

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marín-Prida, Javier; Pavón-Fuentes, Nancy; Llópiz-Arzuaga, Alexey

2013-10-01

Since the inflammatory response and oxidative stress are involved in the stroke cascade, we evaluated here the effects of Phycocyanobilin (PCB, the C-Phycocyanin linked tetrapyrrole) on PC12 cell survival, the gene expression and the oxidative status of hypoperfused rat brain. After the permanent bilateral common carotid arteries occlusion (BCCAo), the animals were treated with saline or PCB, taking samples 24 h post-surgery. Global gene expression was analyzed with GeneChip Rat Gene ST 1.1 from Affymetrix; the expression of particular genes was assessed by the Fast SYBR Green RT-PCR Master Mix and Bioplex methods; and redox markers (MDA, PP, CAT, SOD)more » were evaluated spectrophotometrically. The PCB treatment prevented the H{sub 2}O{sub 2} and glutamate induced PC12 cell injury assessed by the MTT assay, and modulated 190 genes (93 up- and 97 down-regulated) associated to several immunological and inflammatory processes in BCCAo rats. Furthermore, PCB positively modulated 19 genes mostly related to a detrimental pro-inflammatory environment and counteracted the oxidative imbalance in the treated BCCAo animals. Our results support the view of an effective influence of PCB on major inflammatory mediators in acute cerebral hypoperfusion. These results suggest that PCB has a potential to be a treatment for ischemic stroke for which further studies are needed. - Highlights: • Phycocyanobilin (PCB) prevents H{sub 2}O{sub 2} and glutamate induced PC12 cell viability loss. • Anterior cortex and striatum are highly vulnerable to cerebral hypoperfusion (CH). • PCB modulates 190 genes associated to inflammation in acute CH. • PCB regulates 19 genes mostly related to a detrimental pro-inflammatory environment. • PCB restores redox and immune balances showing promise as potential stroke therapy.« less

Characterization of 1,577 Primary Prostate Cancers Reveals Novel Biological and Clinicopathological Insights into Molecular Subtypes

PubMed Central

Tomlins, Scott A.; Alshalalfa, Mohammed; Davicioni, Elai; Erho, Nicholas; Yousefi, Kasra; Zhao, Shuang; Haddad, Zaid; Den, Robert B.; Dicker, Adam P.; Trock, Bruce; DeMarzo, Angelo; Ross, Ashley; Schaeffer, Edward M.; Klein, Eric A.; Magi-Galluzzi, Cristina; Karnes, Jeffery R.; Jenkins, Robert B.; Feng, Felix Y.

2015-01-01

Background Prostate cancer (PCa) molecular subtypes have been defined by essentially mutually exclusive events, including ETS gene fusions (most commonly involving ERG) and SPINK1 over-expression. Clinical assessment may aid in disease stratification, complementing available prognostic tests. Objective To determine the analytical validity and clinicopatholgical associations of microarray-based molecular subtyping. Design, Setting and Participants We analyzed Affymetrix GeneChip expression profiles for 1,577 patients from eight radical prostatectomy (RP) cohorts, including 1,351 cases assessed using the Decipher prognostic assay (performed in a CLIA-certified laboratory). A microarray-based (m-) random forest ERG classification model was trained and validated. Outlier expression analysis was used to predict other mutually exclusive non-ERG ETS gene rearrangements (ETS+) or SPINK1 over-expression (SPINK1+). Outcome Measurements Associations with clinical features and outcomes by multivariable logistic regression analysis and receiver operating curves. Results and Limitations The m-ERG classifier showed 95% accuracy in an independent validation subset (n=155 samples). Across cohorts, 45%, 9%, 8% and 38% of PCa were classified as m-ERG+, m-ETS+, m-SPINK1+, and triple negative (m-ERG−/m-ETS−/m-SPINK1−), respectively. Gene expression profiling supports three underlying molecularly defined groups (m-ERG+, m-ETS+ and m-SPINK1+/triple negative). On multivariable analysis, m-ERG+ tumors were associated with lower preoperative serum PSA and Gleason scores, but enriched for extraprostatic extension (p<0.001). m-ETS+ tumors were associated with seminal vesicle invasion (p=0.01), while m-SPINK1+/triple negative tumors had higher Gleason scores and were more frequent in Black/African American patients (p<0.001). Clinical outcomes were not significantly different between subtypes. Conclusions A clinically available prognostic test (Decipher) can also assess PCa molecular

The carbon starvation response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome

PubMed Central

2012-01-01

Background Filamentous fungi are confronted with changes and limitations of their carbon source during growth in their natural habitats and during industrial applications. To survive life-threatening starvation conditions, carbon from endogenous resources becomes mobilized to fuel maintenance and self-propagation. Key to understand the underlying cellular processes is the system-wide analysis of fungal starvation responses in a temporal and spatial resolution. The knowledge deduced is important for the development of optimized industrial production processes. Results This study describes the physiological, morphological and genome-wide transcriptional changes caused by prolonged carbon starvation during submerged batch cultivation of the filamentous fungus Aspergillus niger. Bioreactor cultivation supported highly reproducible growth conditions and monitoring of physiological parameters. Changes in hyphal growth and morphology were analyzed at distinct cultivation phases using automated image analysis. The Affymetrix GeneChip platform was used to establish genome-wide transcriptional profiles for three selected time points during prolonged carbon starvation. Compared to the exponential growth transcriptome, about 50% (7,292) of all genes displayed differential gene expression during at least one of the starvation time points. Enrichment analysis of Gene Ontology, Pfam domain and KEGG pathway annotations uncovered autophagy and asexual reproduction as major global transcriptional trends. Induced transcription of genes encoding hydrolytic enzymes was accompanied by increased secretion of hydrolases including chitinases, glucanases, proteases and phospholipases as identified by mass spectrometry. Conclusions This study is the first system-wide analysis of the carbon starvation response in a filamentous fungus. Morphological, transcriptomic and secretomic analyses identified key events important for fungal survival and their chronology. The dataset obtained forms a

Organic trace mineral levels in the first 96-h post-hatch impact growth performance and intestinal gene expression in broiler chicks.

PubMed

Brennan, K M; Samuel, R S; Graugnard, T Ao; Xiao, R; Cantor, A H; Pescatore, A J

2013-12-01

Alterations in nutrient intake in the avian neonatal posthatch period can impact development, performance, and metabolism in adulthood. Very little is known about how mineral levels during the post-hatch period affect or “program” gene expression patterns later in life. The objective of this study was to determine the effect of post-hatch (0 to 96 h) dietary mineral supplementation on performance, tissue mineral content, and intestinal gene expression profiles in 21-day-old broiler chicks. One-day-old chicks were randomly assigned to one of two treatment groups consisting of N (organic Zn, Cu, and Mn provided at 100 % of recommendations (National Research Council 1994)) and/or L (organic Zn, Cu, and Mn provided at 20 % of recommendations (National Research Council 1994)) diets fed in two intervals (days 1–4, days 5–21) as follows: (1)N–Lor (2)L–L. Performance parameters did not differ between treatments except that body weight gain was greater (P < 0.05) in L–L birds than N–L birds over the experimental period. Bone mineral content was similar for both treatments at day 21. Intestinal gene expression profiling was examined using the Affymetrix GeneChip Chicken genome array. Ingenuity pathway analysis revealed differences in gene expression profiles between N and L treatments at day 5. At day 21, profiles were unique between N–L and L–L, suggesting that the diet fed until day 4 had an impact on gene expression patterns at day 21 even when birds were fed the same diets day 5–day 21. In this study, we demonstrated that diets fed for the 96 h post-hatch had long-term effects on gene expression, providing unique information as to why post-hatch diets are so important for the longterm bird health and productivity.

Effects of ADMA upon Gene Expression: An Insight into the Pathophysiological Significance of Raised Plasma ADMA

PubMed Central

Smith, Caroline L; Anthony, Shelagh; Hubank, Mike; Leiper, James M; Vallance, Patrick

2005-01-01

Background Asymmetric dimethylarginine (ADMA) is a naturally occurring inhibitor of nitric oxide synthesis that accumulates in a wide range of diseases associated with endothelial dysfunction and enhanced atherosclerosis. Clinical studies implicate plasma ADMA as a major novel cardiovascular risk factor, but the mechanisms by which low concentrations of ADMA produce adverse effects on the cardiovascular system are unclear. Methods and Findings We treated human coronary artery endothelial cells with pathophysiological concentrations of ADMA and assessed the effects on gene expression using U133A GeneChips (Affymetrix). Changes in several genes, including bone morphogenetic protein 2 inducible kinase (BMP2K), SMA-related protein 5 (Smad5), bone morphogenetic protein receptor 1A, and protein arginine methyltransferase 3 (PRMT3; also known as HRMT1L3), were confirmed by Northern blotting, quantitative PCR, and in some instances Western blotting analysis to detect changes in protein expression. To determine whether these changes also occurred in vivo, tissue from gene deletion mice with raised ADMA levels was examined. More than 50 genes were significantly altered in endothelial cells after treatment with pathophysiological concentrations of ADMA (2 μM). We detected specific patterns of changes that identify pathways involved in processes relevant to cardiovascular risk and pulmonary hypertension. Changes in BMP2K and PRMT3 were confirmed at mRNA and protein levels, in vitro and in vivo. Conclusion Pathophysiological concentrations of ADMA are sufficient to elicit significant changes in coronary artery endothelial cell gene expression. Changes in bone morphogenetic protein signalling, and in enzymes involved in arginine methylation, may be particularly relevant to understanding the pathophysiological significance of raised ADMA levels. This study identifies the mechanisms by which increased ADMA may contribute to common cardiovascular diseases and thereby indicates

Identification of diagnostic markers in colorectal cancer via integrative epigenomics and genomics data

PubMed Central

KOK-SIN, TEOW; MOKHTAR, NORFILZA MOHD; HASSAN, NUR ZARINA ALI; SAGAP, ISMAIL; ROSE, ISA MOHAMED; HARUN, ROSLAN; JAMAL, RAHMAN

2015-01-01

Apart from genetic mutations, epigenetic alteration is a common phenomenon that contributes to neoplastic transformation in colorectal cancer. Transcriptional silencing of tumor-suppressor genes without changes in the DNA sequence is explained by the existence of promoter hypermethylation. To test this hypothesis, we integrated the epigenome and transcriptome data from a similar set of colorectal tissue samples. Methylation profiling was performed using the Illumina InfiniumHumanMethylation27 BeadChip on 55 paired cancer and adjacent normal epithelial cells. Fifteen of the 55 paired tissues were used for gene expression profiling using the Affymetrix GeneChip Human Gene 1.0 ST array. Validation was carried out on 150 colorectal tissues using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) technique. PCA and supervised hierarchical clustering in the two microarray datasets showed good separation between cancer and normal samples. Significant genes from the two analyses were obtained based on a ≥2-fold change and a false discovery rate (FDR) P-value of <0.05. We identified 1,081 differentially hypermethylated CpG sites and 36 hypomethylated CpG sites. We also found 709 upregulated and 699 downregulated genes from the gene expression profiling. A comparison of the two datasets revealed 32 overlapping genes with 27 being hypermethylated with downregulated expression and 4 hypermethylated with upregulated expression. One gene was found to be hypomethylated and downregulated. The most enriched molecular pathway identified was cell adhesion molecules that involved 4 overlapped genes, JAM2, NCAM1, ITGA8 and CNTN1. In the present study, we successfully identified a group of genes that showed methylation and gene expression changes in well-defined colorectal cancer tissues with high purity. The integrated analysis gives additional insight regarding the regulation of colorectal cancer-associated genes and their underlying mechanisms that

Altered Global Gene Expression in First Trimester Placentas of Women Destined to Develop Preeclampsia

PubMed Central

Founds, Sandra A.; Conley, Yvette P.; Lyons-Weiler, James F.; Jeyabalan, Arun; Hogge, W. Allen; Conrad, Kirk P.

2009-01-01

Background Preeclampsia is a pregnancy-specific disorder that remains a leading cause of maternal, fetal and neonatal morbidity and mortality, and is associated with risk for future cardiovascular disease. There are no reliable predictors, specific preventative measures or treatments other than delivery. A widely-held view is that the antecedents of preeclampsia lie with impaired placentation in early pregnancy. Accordingly, we hypothesized dysregulation of global gene expression in first trimester placentas of women who later manifested preeclampsia. Methods Surplus chorionic villus sampling (CVS) tissues were collected at 10–12 weeks gestation in 160 patients with singleton fetuses. Four patients developed preeclampsia, and their banked CVS specimens were matched to 8 control samples from patients with unaffected pregnancies. Affymetrix HG-U133 Plus 2.0 GeneChips were utilized for microarray analysis. Naïve Bayes prediction modeling and pathway analysis were conducted. qRT-PCR examined three of the dysregulated genes. Results Thirty-six differentially expressed genes were identified in the preeclampsia placentas. qRT-PCR verified the microarray analysis. Thirty-one genes were down-regulated. Many were related to inflammation/immunoregulation and cell motility. Decidual gene dysregulation was prominent. No evidence was found for alterations in hypoxia and oxidative stress regulated genes. Conclusions To our knowledge, this is the first study to show dysregulation of gene expression in the early placentas of women ~6 months before developing preeclampsia, thereby reinforcing a placental origin of the disorder. We hypothesize that placentation in preeclampsia is compromised in the first trimester by maternal and fetal immune dysregulation, abnormal decidualization, or both, thereby impairing trophoblast invasion. Several of the genes provide potential targets for the development of clinical biomarkers in maternal blood during the first trimester. Supplementary

Differentially expressed microRNAs in the corpus cavernosum from a murine model with type 2 diabetes mellitus-associated erectile dysfunction.

PubMed

Pan, Feng; You, Jinwei; Liu, Yuan; Qiu, Xuefeng; Yu, Wen; Ma, Jiehua; Pan, Lianjun; Zhang, Aixia; Zhang, Qipeng

2016-12-01

To better understand the molecular aetiology of type 2 diabetes mellitus-associated erectile dysfunction (T2DMED) and to provide candidates for further study of its diagnosis and treatment, this study was designed to investigate differentially expressed microRNAs (miRNAs) in the corpus cavernosum (CC) of mice with T2DMED using GeneChip array techniques (Affymetrix miRNA 4.0 Array) and to predict target genes and signalling pathways regulated by these miRNAs based on bioinformatic analysis using TargetScan, the DAIAN web platform and DAVID. In the initial screening, 21 miRNAs appeared distinctly expressed in the T2DMED group (fold change ≥3, p ≤ 0.01). Among them, the differential expression of miR-18a, miR-206, miR-122, and miR-133 were confirmed by qRT-PCR (p < 0.05 and FDR <5 %). According to bioinformatic analysis, the four miRNAs were speculated to play potential roles in the mechanisms of T2DMED via regulating 28 different genes and several pathways, including apoptosis, fibrosis, eNOS/cGMP/PKG, and vascular smooth muscle contraction processes, which mainly focused on influencing the functions of the endothelium and smooth muscle in the CC. IGF-1, as one of the target genes, was verified to decrease in the CCs of T2DMED animals via ELISA and was confirmed as the target of miR-18a or miR-206 via luciferase assay. Finally, these four miRNAs deserve further confirmation as biomarkers of T2DMED in larger studies. Additionally, miR-18a and/or miR-206 may provide new preventive/therapeutic targets for ED management by targeting IGF-1.

Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization.

PubMed

Schaarschmidt, Sara; Gresshoff, Peter M; Hause, Bettina

2013-06-18

Similarly to the legume-rhizobia symbiosis, the arbuscular mycorrhiza interaction is controlled by autoregulation representing a feedback inhibition involving the CLAVATA1-like receptor kinase NARK in shoots. However, little is known about signals and targets down-stream of NARK. To find NARK-related transcriptional changes in mycorrhizal soybean (Glycine max) plants, we analyzed wild-type and two nark mutant lines interacting with the arbuscular mycorrhiza fungus Rhizophagus irregularis. Affymetrix GeneChip analysis of non-inoculated and partially inoculated plants in a split-root system identified genes with potential regulation by arbuscular mycorrhiza or NARK. Most transcriptional changes occur locally during arbuscular mycorrhiza symbiosis and independently of NARK. RT-qPCR analysis verified nine genes as NARK-dependently regulated. Most of them have lower expression in roots or shoots of wild type compared to nark mutants, including genes encoding the receptor kinase GmSIK1, proteins with putative function as ornithine acetyl transferase, and a DEAD box RNA helicase. A predicted annexin named GmAnnx1a is differentially regulated by NARK and arbuscular mycorrhiza in distinct plant organs. Two putative CCAAT-binding transcription factor genes named GmNF-YA1a and GmNF-YA1b are down-regulated NARK-dependently in non-infected roots of mycorrhizal wild-type plants and functional gene analysis confirmed a positive role for these genes in the development of an arbuscular mycorrhiza symbiosis. Our results indicate GmNF-YA1a/b as positive regulators in arbuscular mycorrhiza establishment, whose expression is down-regulated by NARK in the autoregulated root tissue thereby diminishing subsequent infections. Genes regulated independently of arbuscular mycorrhization by NARK support an additional function of NARK in symbioses-independent mechanisms.

In Vivo Genome-Wide Expression Study on Human Circulating B Cells Suggests a Novel ESR1 and MAPK3 Network for Postmenopausal Osteoporosis

PubMed Central

Xiao, Peng; Chen, Yuan; Jiang, Hui; Liu, Yao-Zhong; Pan, Feng; Yang, Tie-Lin; Tang, Zi-Hui; Larsen, Jennifer A; Lappe, Joan M; Recker, Robert R; Deng, Hong-Wen

2008-01-01

Introduction Osteoporosis is characterized by low BMD. Studies have shown that B cells may participate in osteoclastogenesis through expression of osteoclast-related factors, such as RANKL, transforming growth factor β (TGFB), and osteoprotegerin (OPG). However, the in vivo significance of B cells in human bone metabolism and osteoporosis is still largely unknown, particularly at the systematic gene expression level. Materials and Methods In this study, Affymetrix HG-U133A GeneChip arrays were used to identify genes differentially expressed in B cells between 10 low and 10 high BMD postmenopausal women. Significance of differential expression was tested by t-test and adjusted for multiple testing with the Benjamini and Hochberg (BH) procedure (adjusted p ≤ 0.05). Results Twenty-nine genes were downregulated in the low versus high BMD group. These genes were further analyzed using Ingenuity Pathways Analysis (Ingenuity Systems). A network involving estrogen receptor 1 (ESR1) and mitogen activated protein kinase 3 (MAPK3) was identified. Real-time RT-PCR confirmed differential expression of eight genes, including ESR1, MAPK3, methyl CpG binding protein 2 (MECP2), proline-serine-threonine phosphatase interacting protein 1 (PSTPIP1), Scr-like-adaptor (SLA), serine/threonine kinase 11 (STK11), WNK lysine-deficient protein kinase 1 (WNK1), and zinc finger protein 446 (ZNF446). Conclusions This is the first in vivo genome-wide expression study on human B cells in relation to osteoporosis. Our results highlight the significance of B cells in the etiology of osteoporosis and suggest a novel mechanism for postmenopausal osteoporosis (i.e., that downregulation of ESR1 and MAPK3 in B cells regulates secretion of factors, leading to increased osteoclastogenesis or decreased osteoblastogenesis). PMID:18433299

Zinc Replenishment Reverses Overexpression of the Proinflammatory Mediator S100A8 and Esophageal Preneoplasia in the Rat

PubMed Central

Taccioli, Cristian; Wan, Shao-Gui; Liu, Chang-Gong; Alder, Hansjuerg; Volinia, Stefano; Farber, John L.; Croce, Carlo M.

2009-01-01

Background & Aims Zinc-deficiency is implicated in the pathogenesis of human esophageal cancer. In the rat esophagus, it induces cell proliferation, modulates genetic expression, and enhances carcinogenesis. Zinc-replenishment reverses proliferation and inhibits carcinogenesis. The zinc-deficient rat model allows the identification of biological differences affected by zinc during early esophageal carcinogenesis. Methods We evaluated gene expression profiles of esophageal epithelia from zinc-deficient and replenished rats versus sufficient rats using Affymetrix Rat Genome GeneChip. We characterized the role of the top-upregulated gene S100A8 in esophageal hyperplasia/reversal and in chemically-induced esophageal carcinogenesis in zinc-modulated animals by immunohistochemistry and real-time quantitative polymerase chain reaction. Results The hyperplastic deficient esophagus has a distinct expression signature with the proinflammation-gene S100A8 and S100A9 upregulated 57- and 5-fold. “Response to external stimulus” comprising S100A8 was the only significantly overrepresented biological pathway among the upregulated genes. Zinc-replenishment rapidly restored to control levels the expression of S100A8/A9 and 27 other genes and reversed the hyperplastic phenotype. With its receptor RAGE, co-localization and overexpression of S100A8 protein occurred in the deficient esophagus that overexpressed NF-κB p65 and COX-2 protein. Zinc-replenishment but not by a COX-2 inhibitor reduced the overexpression of these 4 proteins. Additionally, esophageal S100A8/A9 mRNA levels were directly associated with the diverse tumorigenic outcome in zinc-deficient and zinc-replenished rats. Conclusions In vivo zinc regulates S100A8 expression and modulates the link between S100A8-RAGE interaction and downstream NF-κB/COX-2 signaling. The finding that zinc regulates an inflammatory pathway in esophageal carcinogenesis may lead to prevention and therapy for this cancer. PMID:19111725

A Gestational High Protein Diet Affects the Abundance of Muscle Transcripts Related to Cell Cycle Regulation throughout Development in Porcine Progeny

PubMed Central

Oster, Michael; Murani, Eduard; Metges, Cornelia C.; Ponsuksili, Siriluck; Wimmers, Klaus

2012-01-01

Background In various animal models pregnancy diets have been shown to affect offspring phenotype. Indeed, the underlying programming of development is associated with modulations in birth weight, body composition, and continual diet-dependent modifications of offspring metabolism until adulthood, producing the hypothesis that the offspring's transcriptome is permanently altered depending on maternal diet. Methodology/Principal Findings To assess alterations of the offspring's transcriptome due to gestational protein supply, German Landrace sows were fed isoenergetic diets containing protein levels of either 30% (high protein - HP) or 12% (adequate protein - AP) throughout their pregnancy. Offspring muscle tissue (M. longissimus dorsi) was collected at 94 days post conception (dpc), and 1, 28, and 188 days post natum (dpn) for use with Affymetrix GeneChip Porcine Genome Arrays and subsequent statistical and Ingenuity pathway analyses. Numerous transcripts were found to have altered abundance at 94 dpc and 1 dpn; at 28 dpn no transcripts were altered, and at 188 dpn only a few transcripts showed a different abundance between diet groups. However, when assessing transcriptional changes across developmental time points, marked differences were obvious among the dietary groups. Depending on the gestational dietary exposure, short- and long-term effects were observed for mRNA expression of genes related to cell cycle regulation, energy metabolism, growth factor signaling pathways, and nucleic acid metabolism. In particular, the abundance of transcripts related to cell cycle remained divergent among the groups during development. Conclusion Expression analysis indicates that maternal protein supply induced programming of the offspring's genome; early postnatal compensation of the slight growth retardation obvious at birth in HP piglets resulted, as did a permanently different developmental alteration and responsiveness to the common environment of the transcriptome. The

GSTA1 Expression Is Correlated With Aldosterone Level in KCNJ5-Mutated Adrenal Aldosterone-Producing Adenoma.

PubMed

Li, Xintao; Wang, Baojun; Tang, Lu; Zhang, Yu; Chen, Luyao; Gu, Liangyou; Zhang, Fan; Ouyang, Jinzhi; Zhang, Xu

2018-03-01

KCNJ5 mutation is a major cause of aldosterone-producing adenomas (APAs). The development of APA apart from KCNJ5 mutation is less investigated. To investigate other mechanisms affecting aldosterone secretion apart from KCNJ5. Six pairs of KCNJ5-mutated, high and low aldosterone-secreting APAs, five non-KCNJ5-mutated APAs, and four normal adrenal glands were assayed by Affymetrix GeneChip Human Transcriptome Array 2.0. A total of 113 APA samples were investigated to explore the expression of glutathione-S-transferase A1 (GSTA1). H295R cells were used to verify the function of GSTA1. GSTA1 was the top gene downregulated in high-aldosterone KCNJ5-mutated APAs. GSTA1 was also downregulated in KCNJ5-mutated APAs compared with wild-type KCNJ5 APAs. Accordingly, mutant KCNJ5 decreased GSTA1 messenger RNA and protein expression levels. GSTA1 overexpression suppressed aldosterone secretion whether in wild-type or mutant KCNJ5 H295R cells. Adding ethacrynic acid or silencing of GSTA1 increased aldosterone secretion by increasing reactive oxygen species (ROS), superoxide, H2O2 levels, and Ca2+ influx. The expression of the transcription factors NR4A1, NR4A2, and CAMK1 and intracellular Ca2+ were significantly upregulated by GSTA1 inhibition. The reduced form of NAD phosphate oxidase inhibitor or H2O2 scavenger or blocking calmodulin or calcium channels could significantly reduce aldosterone secretion in GSTA1-inhibited cells. (1) GSTA1 expression is reversely correlated with aldosterone level in KCNJ5-mutated APAs, (2) GSTA1 regulates aldosterone secretion by ROS and Ca2+ signaling, and (3) KCNJ5 mutation downregulates GSTA1 expression, and overexpression of GSTA1 reverses increased aldosterone in KCNJ5-mutated adrenal cells.

Case report: value of gene expression profiling in the diagnosis of atypical neuroblastoma.

PubMed

Harttrampf, Anne C; Chen, Qingrong; Jüttner, Eva; Geiger, Julia; Vansant, Gordon; Khan, Javed; Kontny, Udo

2017-08-17

Nephroblastoma and neuroblastoma belong to the most common abdominal malignancies in childhood. Similarities in the initial presentation may provide difficulties in distinguishing between these two entities, especially if unusual variations to prevalent patterns of disease manifestation occur. Because of the risk of tumor rupture, European protocols do not require biopsy for diagnosis, which leads to misdiagnosis in some cases. We report on a 4½-year-old girl with a renal tumor displaying radiological and laboratory characteristics supporting the diagnosis of nephroblastoma. Imaging studies showed tumor extension into the inferior vena cava and bilateral lung metastases while urine catecholamines and MIBG-scintigraphy were negative. Preoperative chemotherapy with vincristine, actinomycine D and adriamycin according to the SIOP2001/GPOH protocol for the treatment of nephroblastoma was initiated and followed by surgical tumor resection. Histopathology revealed an undifferentiated tumor with expression of neuronal markers, suggestive of neuroblastoma. MYCN amplification could not be detected. DNA-microarray analysis was performed using Affymetrix genechip human genome U133 plus 2.0 and artificial neural network analysis. Results were confirmed by multiplex RT-PCR. Principal component analysis using 84 genes showed that the patient sample was clearly clustering with neuroblastoma tumors. This was confirmed by hierarchical clustering of the multiplex RT-PCR data. The patient underwent treatment for high-risk neuroblastoma comprising chemotherapy including cisplatin, etoposide, vindesine, dacarbacine, ifosfamide, vincristine, adriamycine and autologous stem cell transplantation followed by maintenance therapy with 13-cis retinoic acid (GPOH NB2004 High Risk Trial Protocol) and is in complete long-term remission. The use of gene expression profiling in an individual patient strongly contributed to clarification in a diagnostic dilemma which finally led to a change of

The Rice B-Box Zinc Finger Gene Family: Genomic Identification, Characterization, Expression Profiling and Diurnal Analysis

PubMed Central

Huang, Jianyan; Zhao, Xiaobo; Weng, Xiaoyu; Wang, Lei; Xie, Weibo

2012-01-01

Background The B-box (BBX) -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX) gene family until now. Methodology/Principal Findings In this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97). In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern. Conclusions/Significance The combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the OsBBX genes. PMID:23118960

Prior to extension, Transcriptomes of fibroblast-like Synoviocytes from extended and Polyarticular juvenile idiopathic arthritis are indistinguishable.

PubMed

Brescia, AnneMarie C; Simonds, Megan M; McCahan, Suzanne M; Sullivan, Kathleen E; Rose, Carlos D

2018-01-08

Our intent was to identify differences between the transcriptome of fibroblast-like synoviocytes (FLS) in oligoarticular juvenile idiopathic arthritis (JIA) before extension when compared to persistent subtype of JIA, when the two are clinically indistinguishable. Additionally, we sought to determine if differences between the transcriptomes of FLS from extended-to-be and polyarticular course JIA could be detected. Our hypothesis was that intrinsic differences in the transcriptome of the FLS from extended-to-be JIA would distinguish them from persistent oligoarticular JIA, before the course is clinically apparent. Global gene expression was defined in cultured FLS from 6 controls, 12 JIA with persistent course, 7 JIA prior to extension (extended-to-be), 4 JIA with extended course and 6 polyarticular onset, using Affymetrix Human GeneChips 133plus2.0. Bioconductor Linear Models for Microarray Analysis revealed 22 probesets with differential expression between persistent and extended-to-be FLS at 15% FDR, however only 2 probesets distinguished extended-to-be from extended and none distinguished extended-to-be and polyarticular at 15% FDR. Differences in extended and polyarticular gene expression profiles were not detected. Confirmation of select genes was done on the RNA level by RT-qPCR and on the protein level in synovial fluid by ELISA. The transcriptome of FLS from extended-to-be juvenile idiopathic arthritis is distinct from persistent course before a clinical distinction can be made. Additionally, the transcriptome of extended-to-be and polyarticular course, including those who have already extended, are indistinguishable. These gene expression data suggest that FLS already reflect a polyarticular behavior early in disease course, suggesting that extended-to-be may be "latent polyarticular" at onset. These differences can be used to develop early biomarkers of disease course, allowing for better-informed treatment decisions.

Effect of ovarian steroids on gene expression related to synapse assembly in serotonin neurons of macaques.

PubMed

Bethea, Cynthia L; Reddy, Arubala P

2012-07-01

Dendritic spines are the elementary structural units of neural plasticity. In a model of hormone replacement therapy (HT), we sought to determine the effect of estradiol (E) and progesterone (P) on gene expression related to synapse assembly in a laser-captured preparation enriched for serotonin neurons from rhesus macaques. Microarray analysis was conducted (n = 2 animals/treatment), and the results were confirmed for pivotal genes with qRT-PCR on additional laser-captured material (n = 3 animals/treatment). Ovariectomized rhesus macaques were treated with placebo, E, or E + P via Silastic implants for 1 month. The midbrain was obtained, sectioned, and immunostained for tryptophan hydroxylase (TPH). TPH-positive neurons were laser captured using an arcturus laser dissection microscope (Pixel II). RNA from laser-captured serotonin neurons was hybridized to Rhesus Affymetrix GeneChips for screening purposes. There was a twofold or greater change in the expression of 63 probe sets in the cell adhesion molecule (CAM) category, and 31 probe sets in the synapse assembly category were similarly altered in E- and E + P-treated animals. qRT-PCR assays showed that E treatment induced a significant increase in ephrin receptor A4 (EPHA4) and in integrin A8 (ITGA8) but not in ephrin receptor B4 (EPHB4) or integrin B8 (ITGB8) expression. E also increased expression of cadherin 11 (CDH11), neuroligin 3 (NLGN3), neurexin 3 (NRXN3), syndecan 2 (SCD2), and neural cell adhesion molecule (NCAM) compared with placebo. Supplemental P treatment suppressed E-induced gene expression. In summary, ovarian steroids target gene expression of adhesion molecules in serotonin neurons that are important for synapse assembly. Copyright © 2012 Wiley Periodicals, Inc.

Determining miRNA Expression Levels in Degraded RNA Samples Using Real-Time RT-qPCR and Microarray Technologies

PubMed Central

Tighe, S.; Holbrook, J.; Nadella, V.; Carmical, R.; Sol-Church, K.; Yueng, A.T.; Chittur, S.

2011-01-01

The Nucleic Acid Research Group (NARG) has previously conducted studies evaluating the impact of RNA integrity and priming strategies on cDNA synthesis and real-time RT-qPCR. The results of last year's field study as it relates to degraded RNA will be presented. In continuation of the RNA integrity theme, this year's study was designed to evaluate the impact of RNA integrity on the analysis of miRNA expression using real-time RT-qPCR. Target section was based on data obtained by the Microarray Research Group (MARG) and other published data from next gen sequencing. These 9 miRNAs represent three groups of miRNA that are expressed at low, medium or high levels in the First Choice human brain reference RNA sample. Two popular RT priming strategies tested in this study include the Megaplex miRNA TaqMan assay (ABI) and the RT2 miRNA qPCR assay (Qiagen/SA Biosciences). The basis for the ABI assay design is a target-specific stem-loop structure and reverse-transcription primer, while the Qiagen design combines poly(A) tailing and a universal reverse transcription in one cDNA synthesis reaction. For this study, the human brain reference RNA was subject to controlled degradation using RNase A to RIN (RNA Integrity Number) values of 7 (good), 4 (moderately degraded), and 2 (severely degraded).These templates were then used to assess both RT methods. In addition to this real-time RT-qPCR data, the same RNA templates were further analyzed using universal poly(A) tailing and hybridization to Affymetrix miRNA GeneChips. This talk will provide insights into RT priming strategies for miRNA and contrast the qPCR results obtained using different technologies.

Identification of molecular pathways affected by pterostilbene, a natural dimethylether analog of resveratrol

PubMed Central

Pan, Zhiqiang; Agarwal, Ameeta K; Xu, Tao; Feng, Qin; Baerson, Scott R; Duke, Stephen O; Rimando, Agnes M

2008-01-01

Background Pterostilbene, a naturally occurring phenolic compound produced by agronomically important plant genera such as Vitis and Vacciunium, is a phytoalexin exhibiting potent antifungal activity. Additionally, recent studies have demonstrated several important pharmacological properties associated with pterostilbene. Despite this, a systematic study of the effects of pterostilbene on eukaryotic cells at the molecular level has not been previously reported. Thus, the aim of the present study was to identify the cellular pathways affected by pterostilbene by performing transcript profiling studies, employing the model yeast Saccharomyces cerevisiae. Methods S. cerevisiae strain S288C was exposed to pterostilbene at the IC50 concentration (70 μM) for one generation (3 h). Transcript profiling experiments were performed on three biological replicate samples using the Affymetrix GeneChip Yeast Genome S98 Array. The data were analyzed using the statistical methods available in the GeneSifter microarray data analysis system. To validate the results, eleven differentially expressed genes were further examined by quantitative real-time RT-PCR, and S. cerevisiae mutant strains with deletions in these genes were analyzed for altered sensitivity to pterostilbene. Results Transcript profiling studies revealed that pterostilbene exposure significantly down-regulated the expression of genes involved in methionine metabolism, while the expression of genes involved in mitochondrial functions, drug detoxification, and transcription factor activity were significantly up-regulated. Additional analyses revealed that a large number of genes involved in lipid metabolism were also affected by pterostilbene treatment. Conclusion Using transcript profiling, we have identified the cellular pathways targeted by pterostilbene, an analog of resveratrol. The observed response in lipid metabolism genes is consistent with its known hypolipidemic properties, and the induction of mitochondrial

Transcriptional profiles in liver from mice treated with hepatotumorigenic and nonhepatotumorigenic triazole conazole fungicides: Propiconazole, triadimefon, and myclobutanil.

PubMed

Ward, William O; Delker, Don A; Hester, Susan D; Thai, Sheau-Fung; Wolf, Douglas C; Allen, James W; Nesnow, Stephen

2006-01-01

Conazoles are environmental and pharmaceutical fungicides. The present study relates the toxicological effects of conazoles to alterations of gene and pathway transcription and identifies potential modes of tumorigenic action. In a companion study employing conventional toxicological bioassays (Allen et al., 2006), male CD-1 mice were fed triadimefon, propiconazole, or myclobutanil in a continuous oral-dose regimen for 4, 30, or 90 days. These conazoles were found to induce hepatomegaly, to induce high levels of hepatic pentoxyresorufin-O-dealkylase activity, to increase hepatic cell proliferation, to decrease serum cholesterol, and to increase serum triglycerides. Differentially expressed genes and pathways were identified using Affymetrix GeneChips. Gene-pathway associations were obtained from the Kyoto Encyclopedia of Genes and Genomes, Biocarta, and MetaCore compendia. The pathway profiles of each conazole were different at each time point. In general, the number of altered metabolism, signaling, and growth pathways increased with time and dose and were greatest with propiconazole. All conazoles had effects on nuclear receptors as evidenced by increased expression and enzymatic activities of a series of related cytochrome P450s (CYP). A subset of altered genes and pathways distinguished the three conazoles from each other. Triadimefon and propiconazole both altered apoptosis, cell cycle, adherens junction, calcium signaling, and EGFR signaling pathways. Triadimefon produced greater changes in cholesterol biosynthesis and retinoic acid metabolism genes and in selected signaling pathways. Propiconazole had greater effects on genes responding to oxidative stress and on the IGF/P13K/AKt/PTEN/mTor and Wnt-beta-catenin pathways. In conclusion, while triadimefon, propiconazole, and myclobutanil had similar effects in mouse liver on hepatomegaly, histology, CYP activities, cell proliferation, and serum cholesterol, genomic analyses revealed major differences in their

Transcriptional responses associated with sulfur mustard and thermal burns in porcine skin.

PubMed

Rogers, James V; McDougal, James N; Price, Jennifer A; Reid, Frances M; Graham, John S

2008-01-01

In military and civilian environments, serious cutaneous damage can result from thermal burns or exposure to the blistering agent sulfur mustard [bis (2-chloroethyl) sulfide; HD]. Similar therapies have historically been used to treat cutaneous thermal and HD injuries; however, the underlying molecular mechanisms of tissue damage and wound healing may differ between the types of burns. Using microarray analysis, this study assessed the transcriptional responses to cutaneous HD and thermal injury at 48 hours post-exposure to identify molecular networks and genes associated with each type of skin injury. Ventral abdominal sites on each of 4 weanling swine were exposed to 400 mul of undiluted HD or a heated brass rod (70 degrees C) for 8 minutes and 45-60 seconds, respectively. At 48 hours post-exposure, total RNA was isolated from excised skin samples and hybridized to Affymetrix GeneChip Porcine Genome Arrays (containing 20,201 genes). Both HD and thermal exposure promoted significant transcriptional changes where 290 and 267 transcripts were increased and 197 and 707 transcripts were decreased with HD and thermal exposure, respectively. HD- and thermal-injured skin expressed 149 increased and 148 decreased common transcripts. Comparison of the 10 most significantly changed biological functions for HD and thermal exposures identified 7 overlapping functional groups. Canonical pathways analysis revealed 15 separate signaling pathways containing transcripts associated with both HD and thermal exposure. Within these pathways, 5 transcripts (CXCR4, FGFR2, HMOX1, IL1R1, and TLR4) were identified as known targets for existing phase II/III clinical trial or Food and Drug Administration (FDA)-approved drugs. This study is the first to directly assess transcriptional changes in porcine skin subjected to HD or thermal injury over the same time period.

Oral administration of pentachlorophenol induces interferon signaling mRNAs in C57BL/6 male mouse liver.

PubMed

Kanno, Jun; Aisaki, Ken-ichi; Igarashi, Katsuhide; Kitajima, Satoshi; Matsuda, Nae; Morita, Koichi; Tsuji, Masaki; Moriyama, Noriko; Furukawa, Yusuke; Otsuka, Maki; Tachihara, Erika; Nakatsu, Noriyuki; Kodama, Yukio

2013-01-01

Pentachlorophenol (PCP) was monitored for transcriptome responses in adult mouse liver at 2, 4, 8 and 24 hr after a single oral administration at four dose levels, 0, 10, 30 and 100 mg/kg. The expression data obtained using Affymetrix GeneChip MOE430 2.0 were absolutized by the Percellome method and expressed as three dimensional (3D) surface graphs with axes of time, dose and copy numbers of mRNA per cell. We developed the programs RSort, for comprehensive screening of the 3D surface data and PercellomeExploror for cross-referencing and confirmed the significant responses by visual inspection. In the first 8 hr, approximately 100 probe sets (PSs) related to PXR/SXR and Cyp2a4 and other metabolic enzymes were induced whereas Fos and JunB were suppressed. At 24 hr, about 1,200 PSs were strongly induced. We cross-referenced the Percellome database consisting of 111 chemicals on the liver transcriptome and found that about half of the PSs belonged to the metabolic pathways including Nrf2-mediated oxidative stress response networks shared with some of the 111 chemicals. The other half of the induced genes were interferon signaling network genes (ISG) and their induction was unique to PCP. Toll like receptors and other pattern recognition receptors, interferon regulatory factors and interferon alpha itself were included but inflammatory cytokines were not induced. In summary, these data indicated that functional symptoms of PCP treatment, such as hyperthermia and profuse sweating might be mediated by the ISG rather than the previously documented mitochondrial uncoupling mechanism. PCP might become a hint for developing low molecular weight orally available interferon mimetic drugs following imiquimod and RO4948191 as agonists of toll-like receptor and interferon receptor.

Different DNA damage and cell cycle checkpoint control in low- and high-risk human papillomavirus infections of the vulva.

PubMed

Santegoets, Lindy A M; van Baars, Romy; Terlou, Annelinde; Heijmans-Antonissen, Claudia; Swagemakers, Sigrid M A; van der Spek, Peter J; Ewing, Patricia C; van Beurden, Marc; van der Meijden, Willem I; Helmerhorst, Theo J M; Blok, Leen J

2012-06-15

Human papillomavirus (HPV) infections may result in benign hyperplasia, caused by low-risk HPV types, or (pre)malignant lesions caused by high-risk HPV types. The molecular basis of this difference in malignant potential is not completely understood. Here, we performed gene profiling of different HPV infected vulvar tissues (condylomata acuminata (n = 5), usual type vulvar intraepithelial neoplasia (uVIN) (n = 9)) and control samples (n = 14) using Affymetrix Human U133A plus 2 GeneChips. Data were analyzed using OmniViz®, Partek® and Ingenuity® Software. Results were validated by real-time RT-PCR and immunostaining. Although similarities were observed between gene expression profiles of low- and high-risk HPV infected tissues (e.g., absence of estrogen receptor in condylomata and uVIN), high-risk HPV infected tissues showed more proliferation and displayed more DNA damage than tissues infected with low-risk HPV. These observations were confirmed by differential regulation of cell cycle checkpoints and by increased expression of DNA damage-biomarkers p53 and γH2AX. Furthermore, FANCA, FANCD2, BRCA1 and RAD51, key players in the DNA damage response, were significantly upregulated (p < 0.05). In addition, we compared our results with publicly available gene expression profiles of various other HPV-induced cancers (vulva, cervix and head-and-neck). This showed p16(INK4a) was the most significant marker to detect a high-risk HPV infection, but no other markers could be found. In conclusion, this study provides insight into the molecular basis of low- and high-risk HPV infections and indicates two main pathways (cell cycle and DNA damage response) that are much stronger affected by high-risk HPV as compared to low-risk HPV. Copyright © 2011 UICC.

Stable RNA markers for identification of blood and saliva stains revealed from whole genome expression analysis of time-wise degraded samples

PubMed Central

Zubakov, Dmitry; Hanekamp, Eline; Kokshoorn, Mieke; van IJcken, Wilfred

2007-01-01

Human body fluids such as blood and saliva represent the most common source of biological material found at a crime scene. Reliable tissue identification in forensic science can reveal significant insights into crime scene reconstruction and can thus contribute toward solving crimes. Limitations of existing presumptive tests for body fluid identification in forensics, which are usually based on chemoluminescence or protein analysis, are expected to be overcome by RNA-based methods, provided that stable RNA markers with tissue-specific expression patterns are available. To generate sets of stable RNA markers for reliable identification of blood and saliva stains we (1) performed whole-genome gene expression analyses on a series of time-wise degraded blood and saliva stain samples using the Affymetrix U133 plus2 GeneChip, (2) consulted expression databases to obtain additional information on tissue specificity, and (3) confirmed expression patterns of the most promising candidate genes by quantitative real-time polymerase chain reaction including additional forensically relevant tissues such as semen and vaginal secretion. Overall, we identified nine stable mRNA markers for blood and five stable mRNA markers for saliva detection showing tissue-specific expression signals in stains aged up to 180 days of age, expectedly older. Although, all of the markers were able to differentiate blood/saliva from semen samples, none of them could differentiate vaginal secretion because of the complex nature of vaginal secretion and the biological similarity of buccal and vaginal mucosa. We propose the use of these 14 stable mRNA markers for identification of blood and saliva stains in future forensic practice. Electronic supplementary material The online version of this article (doi:10.1007/s00414-007-0182-6) contains supplementary material, which is available to authorized users. PMID:17579879

Concept Mapping

ERIC Educational Resources Information Center

Technology & Learning, 2005

2005-01-01

Concept maps are graphical ways of working with ideas and presenting information. They reveal patterns and relationships and help students to clarify their thinking, and to process, organize and prioritize. Displaying information visually--in concept maps, word webs, or diagrams--stimulates creativity. Being able to think logically teaches…

Topographic Maps from a Kiosk

USGS Publications Warehouse

,

2001-01-01

In April 2000, the U.S. Geological Survey (USGS) and National Geographic (NG) TOPO entered into a cooperative research and development agreement (CRADA) to explore a new technology that would allow a person to walk into a map retail store and print a personalized topographic map, vending machine style, from a self-service kiosk. Work began to develop systems that offer seamless, digitally stored USGS topographic maps using map-on-demand software from NG TOPO. The vending machine approach ensures that maps are never out of stock, allows customers to define their own map boundaries, and gives customers choices regarding shaded relief and the grids to be printed on the maps to get the exact maps they need.

Preferred reporting items for studies mapping onto preference-based outcome measures: The MAPS statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-08-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. The primary audiences for the MAPS statement are researchers reporting mapping studies, the funders of the research, and peer reviewers and editors involved in assessing mapping studies for publication.A de novo list of 29 candidate reporting items and accompanying explanations was created by a working group comprised of six health economists and one Delphi methodologist. Following a two-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community, a final set of 23 items deemed essential for transparent reporting, and accompanying explanations, was developed. The items are contained in a user friendly 23 item checklist. They are presented numerically and categorised within six sections, namely: (i) title and abstract; (ii) introduction; (iii) methods; (iv) results; (v) discussion; and (vi) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document.It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by eight health economics and quality of life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in five years' time.This statement was published jointly in Applied Health Economics

Mapping racism.

PubMed

Moss, Donald B

2006-01-01

The author uses the metaphor of mapping to illuminate a structural feature of racist thought, locating the degraded object along vertical and horizontal axes. These axes establish coordinates of hierarchy and of distance. With the coordinates in place, racist thought begins to seem grounded in natural processes. The other's identity becomes consolidated, and parochialism results. The use of this kind of mapping is illustrated via two patient vignettes. The author presents Freud's (1905, 1927) views in relation to such a "mapping" process, as well as Adorno's (1951) and Baldwin's (1965). Finally, the author conceptualizes the crucial status of primitivity in the workings of racist thought.

USGS US topo maps for Alaska

USGS Publications Warehouse

Anderson, Becci; Fuller, Tracy

2014-01-01

In July 2013, the USGS National Geospatial Program began producing new topographic maps for Alaska, providing a new map series for the state known as US Topo. Prior to the start of US Topo map production in Alaska, the most detailed statewide USGS topographic maps were 15-minute 1:63,360-scale maps, with their original production often dating back nearly fifty years. The new 7.5-minute digital maps are created at 1:25,000 map scale, and show greatly increased topographic detail when compared to the older maps. The map scale and data specifications were selected based on significant outreach to various map user groups in Alaska. This multi-year mapping initiative will vastly enhance the base topographic maps for Alaska and is possible because of improvements to key digital map datasets in the state. The new maps and data are beneficial in high priority applications such as safety, planning, research and resource management. New mapping will support science applications throughout the state and provide updated maps for parks, recreation lands and villages.

Global Map of Pluto

NASA Image and Video Library

2015-07-27

The science team of NASA's New Horizons mission has produced an updated global map of the dwarf planet Pluto. The map includes all resolved images of the surface acquired between July 7-14, 2015, at pixel resolutions ranging from 40 kilometers (24 miles) on the Charon-facing hemisphere (left and right sides of the map) to 400 meters (1,250 feet) on the anti-Charon facing hemisphere (map center). Many additional images are expected in fall of 2015 and these will be used to complete the global map. http://photojournal.jpl.nasa.gov/catalog/PIA19858

Genome mapping

USDA-ARS?s Scientific Manuscript database

Genome maps can be thought of much like road maps except that, instead of traversing across land, they traverse across the chromosomes of an organism. Genetic markers serve as landmarks along the chromosome and provide researchers information as to how close they may be to a gene or region of inter...

Assessing map accuracy in a remotely sensed, ecoregion-scale cover map

USGS Publications Warehouse

Edwards, T.C.; Moisen, Gretchen G.; Cutler, D.R.

1998-01-01

Landscape- and ecoregion-based conservation efforts increasingly use a spatial component to organize data for analysis and interpretation. A challenge particular to remotely sensed cover maps generated from these efforts is how best to assess the accuracy of the cover maps, especially when they can exceed 1000 s/km2 in size. Here we develop and describe a methodological approach for assessing the accuracy of large-area cover maps, using as a test case the 21.9 million ha cover map developed for Utah Gap Analysis. As part of our design process, we first reviewed the effect of intracluster correlation and a simple cost function on the relative efficiency of cluster sample designs to simple random designs. Our design ultimately combined clustered and subsampled field data stratified by ecological modeling unit and accessibility (hereafter a mixed design). We next outline estimation formulas for simple map accuracy measures under our mixed design and report results for eight major cover types and the three ecoregions mapped as part of the Utah Gap Analysis. Overall accuracy of the map was 83.2% (SE=1.4). Within ecoregions, accuracy ranged from 78.9% to 85.0%. Accuracy by cover type varied, ranging from a low of 50.4% for barren to a high of 90.6% for man modified. In addition, we examined gains in efficiency of our mixed design compared with a simple random sample approach. In regard to precision, our mixed design was more precise than a simple random design, given fixed sample costs. We close with a discussion of the logistical constraints facing attempts to assess the accuracy of large-area, remotely sensed cover maps.

Maps | Geospatial Data Science | NREL

Science.gov Websites

Maps Maps NREL develops an array of maps to support renewable energy development and generation resource in the United States by county Geothermal Maps of geothermal power plants, resources for enhanced geothermal systems, and hydrothermal sites in the United States Hydrogen Maps of hydrogen production

BM-Map: Bayesian Mapping of Multireads for Next-Generation Sequencing Data

PubMed Central

Ji, Yuan; Xu, Yanxun; Zhang, Qiong; Tsui, Kam-Wah; Yuan, Yuan; Norris, Clift; Liang, Shoudan; Liang, Han

2011-01-01

Summary Next-generation sequencing (NGS) technology generates millions of short reads, which provide valuable information for various aspects of cellular activities and biological functions. A key step in NGS applications (e.g., RNA-Seq) is to map short reads to correct genomic locations within the source genome. While most reads are mapped to a unique location, a significant proportion of reads align to multiple genomic locations with equal or similar numbers of mismatches; these are called multireads. The ambiguity in mapping the multireads may lead to bias in downstream analyses. Currently, most practitioners discard the multireads in their analysis, resulting in a loss of valuable information, especially for the genes with similar sequences. To refine the read mapping, we develop a Bayesian model that computes the posterior probability of mapping a multiread to each competing location. The probabilities are used for downstream analyses, such as the quantification of gene expression. We show through simulation studies and RNA-Seq analysis of real life data that the Bayesian method yields better mapping than the current leading methods. We provide a C++ program for downloading that is being packaged into a user-friendly software. PMID:21517792

Mapping Potassium

NASA Image and Video Library

2015-04-16

During the first year of NASA MESSENGER orbital mission, the spacecraft GRS instrument measured the elemental composition of Mercury surface materials. mong the most important discoveries from the GRS was the observation of higher abundances of the moderately volatile elements potassium, sodium, and chlorine than expected from previous scientific models and theories. Particularly high concentrations of these elements were observed at high northern latitudes, as illustrated in this potassium abundance map, which provides a view of the surface centered at 60° N latitude and 120° E longitude. This map was the first elemental map ever made of Mercury's surface and is to-date the only map to report absolute elemental concentrations, in comparison to element ratios. Prior to MESSENGER's arrival at Mercury, scientists expected that the planet would be depleted in moderately volatile elements, as is the case for our Moon. The unexpectedly high abundances observed with the GRS have forced a reevaluation of our understanding of the formation and evolution of Mercury. In addition, the K map provided the first evidence for distinct geochemical terranes on Mercury, as the high-potassium region was later found to also be distinct in its low Mg/Si, Ca/Si, S/Si, and high Na/Si and Cl/Si abundances. Instrument: Gamma-Ray Spectrometer (GRS) http://photojournal.jpl.nasa.gov/catalog/PIA19414

Planetary Geologic Mapping Handbook - 2009

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Skinner, J. A.; Hare, T. M.

2009-01-01

Geologic maps present, in an historical context, fundamental syntheses of interpretations of the materials, landforms, structures, and processes that characterize planetary surfaces and shallow subsurfaces (e.g., Varnes, 1974). Such maps also provide a contextual framework for summarizing and evaluating thematic research for a given region or body. In planetary exploration, for example, geologic maps are used for specialized investigations such as targeting regions of interest for data collection and for characterizing sites for landed missions. Whereas most modern terrestrial geologic maps are constructed from regional views provided by remote sensing data and supplemented in detail by field-based observations and measurements, planetary maps have been largely based on analyses of orbital photography. For planetary bodies in particular, geologic maps commonly represent a snapshot of a surface, because they are based on available information at a time when new data are still being acquired. Thus the field of planetary geologic mapping has been evolving rapidly to embrace the use of new data and modern technology and to accommodate the growing needs of planetary exploration. Planetary geologic maps have been published by the U.S. Geological Survey (USGS) since 1962 (Hackman, 1962). Over this time, numerous maps of several planetary bodies have been prepared at a variety of scales and projections using the best available image and topographic bases. Early geologic map bases commonly consisted of hand-mosaicked photographs or airbrushed shaded-relief views and geologic linework was manually drafted using mylar bases and ink drafting pens. Map publishing required a tedious process of scribing, color peel-coat preparation, typesetting, and photo-laboratory work. Beginning in the 1990s, inexpensive computing, display capability and user-friendly illustration software allowed maps to be drawn using digital tools rather than pen and ink, and mylar bases became obsolete

Geologic Maps as the Foundation of Mineral-Hazards Maps in California

NASA Astrophysics Data System (ADS)

Higgins, C. T.; Churchill, R. K.; Downey, C. I.; Clinkenbeard, J. P.; Fonseca, M. C.

2010-12-01

The basic geologic map is essential to the development of products that help planners, engineers, government officials, and the general public make decisions concerning natural hazards. Such maps are the primary foundation that the California Geological Survey (CGS) uses to prepare maps that show potential for mineral-hazards. Examples of clients that request these maps are the California Department of Transportation (Caltrans) and California Department of Public Health (CDPH). Largely because of their non-catastrophic nature, mineral hazards have received much less public attention compared to earthquakes, landslides, volcanic eruptions, and floods. Nonetheless, mineral hazards can be a major concern locally when considering human health and safety and potential contamination of the environment by human activities such as disposal of earth materials. To address some of these concerns, the CGS has focused its mineral-hazards maps on naturally occurring asbestos (NOA), radon, and various potentially toxic metals as well as certain artificial features such as mines and oil and gas wells. The maps range in scope from statewide to counties and Caltrans districts to segments of selected highways. To develop the hazard maps, the CGS begins with traditional paper and digital versions of basic geologic maps, which are obtained from many sources such as its own files, the USGS, USDA Forest Service, California Department of Water Resources, and counties. For each study area, these maps present many challenges of compilation related to vintage, scale, definition of units, and edge-matching across map boundaries. The result of each CGS compilation is a digital geologic layer that is subsequently reinterpreted and transformed into new digital layers (e.g., lithologic) that focus on the geochemical and mineralogical properties of the area’s earth materials and structures. These intermediate layers are then integrated with other technical data to derive final digital layers

Historical Topographic Map Collection bookmark

USGS Publications Warehouse

Fishburn, Kristin A.; Allord, Gregory J.

2017-06-29

The U.S. Geological Survey (USGS) National Geospatial Program is scanning published USGS 1:250,000-scale and larger topographic maps printed between 1884, the inception of the topographic mapping program, and 2006. The goal of this project, which began publishing the historical scanned maps in 2011, is to provide a digital repository of USGS topographic maps, available to the public at no cost. For more than 125 years, USGS topographic maps have accurately portrayed the complex geography of the Nation. The USGS is the Nation’s largest producer of printed topographic maps, and prior to 2006, USGS topographic maps were created using traditional cartographic methods and printed using a lithographic printing process. As the USGS continues the release of a new generation of topographic maps (US Topo) in electronic form, the topographic map remains an indispensable tool for government, science, industry, land management planning, and leisure.

Hydrologic unit maps

USGS Publications Warehouse

Seaber, Paul R.; Kapinos, F. Paul; Knapp, George L.

1987-01-01

A set of maps depicting approved boundaries of, and numerical codes for, river-basin units of the United States has been developed by the U.S . Geological Survey. These 'Hydrologic Unit Maps' are four-color maps that present information on drainage, culture, hydrography, and hydrologic boundaries and codes of (1) the 21 major water-resources regions and the 222 subregions designated by the U.S . Water Resources Council, (2) the 352 accounting units of the U.S. Geological Survey's National Water Data Network, and (3) the 2,149 cataloging units of the U.S . Geological Survey's 'Catalog of information on Water Data:' The maps are plotted on the Geological Survey State base-map series at a scale of 1 :500,000 and, except for Alaska, depict hydrologic unit boundaries for all drainage basins greater than 700 square miles (1,813 square kilometers). A complete list of all the hydrologic units, along with their drainage areas, their names, and the names of the States or outlying areas in which they reside, is contained in the report. These maps and associated codes provide a standardized base for use by water-resources organizations in locating, storing, retrieving, and exchanging hydrologic data, in indexing and inventorying hydrologic data and information, in cataloging water-data acquisition activities, and in a variety of other applications. Because the maps have undergone extensive review by all principal Federal, regional, and State water-resource agencies, they are widely accepted for use in planning and describing water-use and related land-use activities, and in geographically organizing hydrologic data . Examples of these uses are given in the report . The hydrologic unit codes shown on the maps have been approved as a Federal Information Processing Standard for use by the Federal establishment.

A new catalog of planetary maps

NASA Technical Reports Server (NTRS)

Batson, R. M.; Inge, J. L.

1991-01-01

A single, concise reference to all existing planetary maps, including lunar ones, is being prepared that will allow map users to identify and locate maps of their areas of interest. This will be the first such comprehensive listing of planetary maps. Although the USGS shows index maps on the collar of each map sheet, periodically publishes index maps of Mars, and provides informal listings of the USGS map database, no tabulation exists that identifies all planetary maps, including those published by DMA and other organizations. The catalog will consist of a booklet containing small-scale image maps with superimposed quadrangle boundaries and map data tabulations.

Hybrid optical acoustic seafloor mapping

NASA Astrophysics Data System (ADS)

Inglis, Gabrielle

The oceanographic research and industrial communities have a persistent demand for detailed three dimensional sea floor maps which convey both shape and texture. Such data products are used for archeology, geology, ship inspection, biology, and habitat classification. There are a variety of sensing modalities and processing techniques available to produce these maps and each have their own potential benefits and related challenges. Multibeam sonar and stereo vision are such two sensors with complementary strengths making them ideally suited for data fusion. Data fusion approaches however, have seen only limited application to underwater mapping and there are no established methods for creating hybrid, 3D reconstructions from two underwater sensing modalities. This thesis develops a processing pipeline to synthesize hybrid maps from multi-modal survey data. It is helpful to think of this processing pipeline as having two distinct phases: Navigation Refinement and Map Construction. This thesis extends existing work in underwater navigation refinement by incorporating methods which increase measurement consistency between both multibeam and camera. The result is a self consistent 3D point cloud comprised of camera and multibeam measurements. In map construction phase, a subset of the multi-modal point cloud retaining the best characteristics of each sensor is selected to be part of the final map. To quantify the desired traits of a map several characteristics of a useful map are distilled into specific criteria. The different ways that hybrid maps can address these criteria provides justification for producing them as an alternative to current methodologies. The processing pipeline implements multi-modal data fusion and outlier rejection with emphasis on different aspects of map fidelity. The resulting point cloud is evaluated in terms of how well it addresses the map criteria. The final hybrid maps retain the strengths of both sensors and show significant improvement

Karst map of Puerto Rico

USGS Publications Warehouse

Alemán González, Wilma B.

2010-01-01

This map is a digital compilation, combining the mapping of earlier geologists. Their work, cited on the map, contains more detailed descriptions of karst areas and landforms in Puerto Rico. This map is the basis for the Puerto Rico part of a new national karst map currently being compiled by the U.S. Geological Survey. In addition, this product is a standalone, citable source of digital karst data for Puerto Rico. Nearly 25 percent of the United States is underlain by karst terrain, and a large part of that area is undergoing urban and industrial development. Accurate delineations of karstic rocks are needed at scales suitable for national, State, and local maps. The data on this map contribute to a better understanding of subsidence hazards, groundwater contamination potential, and cave resources as well as serve as a guide to topical research on karst. Because the karst data were digitized from maps having a different scale and projection from those on the base map used for this publication, some karst features may not coincide perfectly with physiographic features portrayed on the base map.

Genetic map of artichoke × wild cardoon: toward a consensus map for Cynara cardunculus.

PubMed

Sonnante, Gabriella; Gatto, Angela; Morgese, Anita; Montemurro, Francesco; Sarli, Giulio; Blanco, Emanuela; Pignone, Domenico

2011-11-01

An integrated consensus linkage map is proposed for globe artichoke. Maternal and paternal genetic maps were constructed on the basis of an F(1) progeny derived from crossing an artichoke genotype (Mola) with its progenitor, the wild cardoon (Tolfa), using EST-derived SSRs, genomic SSRs, AFLPs, ten genes, and two morphological traits. For most genes, mainly belonging to the chlorogenic acid pathway, new markers were developed. Five of these were SNP markers analyzed through high-resolution melt technology. From the maternal (Mola) and paternal (Tolfa) maps, an integrated map was obtained, containing 337 molecular and one morphological markers ordered in 17 linkage groups (LGs), linked between Mola and Tolfa. The integrated map covers 1,488.8 cM, with an average distance of 4.4 cM between markers. The map was aligned with already existing maps for artichoke, and 12 LGs were linked via 31 bridge markers. LG numbering has been proposed. A total of 124 EST-SSRs and two genes were mapped here for the first time, providing a framework for the construction of a functional map in artichoke. The establishment of a consensus map represents a necessary condition to plan a complete sequencing of the globe artichoke genome.

Going beyond the flood insurance rate map: insights from flood hazard map co-production

NASA Astrophysics Data System (ADS)

Luke, Adam; Sanders, Brett F.; Goodrich, Kristen A.; Feldman, David L.; Boudreau, Danielle; Eguiarte, Ana; Serrano, Kimberly; Reyes, Abigail; Schubert, Jochen E.; AghaKouchak, Amir; Basolo, Victoria; Matthew, Richard A.

2018-04-01

Flood hazard mapping in the United States (US) is deeply tied to the National Flood Insurance Program (NFIP). Consequently, publicly available flood maps provide essential information for insurance purposes, but they do not necessarily provide relevant information for non-insurance aspects of flood risk management (FRM) such as public education and emergency planning. Recent calls for flood hazard maps that support a wider variety of FRM tasks highlight the need to deepen our understanding about the factors that make flood maps useful and understandable for local end users. In this study, social scientists and engineers explore opportunities for improving the utility and relevance of flood hazard maps through the co-production of maps responsive to end users' FRM needs. Specifically, two-dimensional flood modeling produced a set of baseline hazard maps for stakeholders of the Tijuana River valley, US, and Los Laureles Canyon in Tijuana, Mexico. Focus groups with natural resource managers, city planners, emergency managers, academia, non-profit, and community leaders refined the baseline hazard maps by triggering additional modeling scenarios and map revisions. Several important end user preferences emerged, such as (1) legends that frame flood intensity both qualitatively and quantitatively, and (2) flood scenario descriptions that report flood magnitude in terms of rainfall, streamflow, and its relation to an historic event. Regarding desired hazard map content, end users' requests revealed general consistency with mapping needs reported in European studies and guidelines published in Australia. However, requested map content that is not commonly produced included (1) standing water depths following the flood, (2) the erosive potential of flowing water, and (3) pluvial flood hazards, or flooding caused directly by rainfall. We conclude that the relevance and utility of commonly produced flood hazard maps can be most improved by illustrating pluvial flood hazards

MAPPING IN MICRONESIA.

USGS Publications Warehouse

Olsen, Randle W.; Swinnerton, J.R.

1984-01-01

The U. S. Geological Survey has recently completed a series of new topographic maps of Micronesia in cooperation with the Trust Territory of the Pacific Islands, the Federal agency administering the islands. Monocolor 1:10,000-scale manuscripts were compiled, from which 1:25,000-scale metric quadrangles were derived with symbology consistent with USGS quadrangle mapping. The publication of these new maps coincides with the impending political changes resulting from self-determination referendums held in Micronesia. Local sources have helped considerably with field logistics and resolution of geographic name controversies. Technical aspects of this project included development of tropical feature symbology, location of cadastral subdivisions and associated boundaries and mapping of many outlying coral reefs.

Geologic mapping of Argyre Planitia

NASA Technical Reports Server (NTRS)

Gorsline, Donn S.; Parker, Timothy J.

1995-01-01

This report describes the results from the geologic mapping of the central and southern Argyre basin of Mars. At the Mars Geologic Mapper's Meeting in Flagstaff during July, 1993, Dave Scott (United States Geological Survey, Mars Geologic Mapping Steering Committee Chair) recommended that all four quadrangles be combined into a single 1:1,000,000 scale map for publication. It was agreed that this would be cost-effective and that the decrease in scale would not compromise the original science goals of the mapping. Tim Parker completed mapping on the 1:500,000 scale base maps, for which all the necessary materials had already been produced, and included the work as a chapter in his dissertation, which was completed in the fall of 1994. Geologic mapping of the two southernmost quadrangles (MTM -55036 and MTM -55043; MTM=Mars Transverse Mercator) was completed as planned during the first year of work. These maps and a detailed draft of the map text were given a preliminary review by Dave Scott during summer, 1993. Geologic mapping of the remaining two quadrangles (MTM -50036 and MTM -50043) was completed by summer, 1994. Results were described at the Mars Geologic Mappers Meeting, held in Pocatello, Idaho, during July, 1994. Funds for the third and final year of the project have been transferred to the Jet Propulsion Laboratory, where Tim Parker will revise and finalize all maps and map text for publication by the United States Geological Survey at the 1:1,000,000 map scale.

Preferred Reporting Items for Studies Mapping onto Preference-Based Outcome Measures: The MAPS Statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-10-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprising six health economists and one Delphi methodologist. A two-round, modified Delphi survey, with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community, was used to identify a list of essential reporting items from this larger list. From the initial de novo list of 29 candidate items, a set of 23 essential reporting items was developed. The items are presented numerically and categorized within six sections: (1) title and abstract; (2) introduction; (3) methods; (4) results; (5) discussion; and (6) other. The MAPS statement is best applied in conjunction with the accompanying MAPS Explanation and Elaboration paper. It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of the reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by seven health economics and quality-of-life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years' time.

Preferred reporting items for studies mapping onto preference-based outcome measures: the MAPS statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2016-02-01

'Mapping' onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MApping onto Preference-based measures reporting Standards (MAPS) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprised of six health economists and one Delphi methodologist. A two-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies and the biomedical journal editorial community was used to identify a list of essential reporting items from this larger list. From the initial de novo list of 29 candidate items, a set of 23 essential reporting items was developed. The items are presented numerically and categorised within six sections, namely (1) title and abstract; (2) introduction; (3) methods; (4) results; (5) discussion; and (6) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document. It is anticipated that the MAPS statement will improve the clarity, transparency and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by seven health economics and quality of life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years' time.

PREFERRED REPORTING ITEMS FOR STUDIES MAPPING ONTO PREFERENCE-BASED OUTCOME MEASURES: THE MAPS STATEMENT.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-01-01

"Mapping" onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist, which aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprised of six health economists and one Delphi methodologist. A two-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies, and the biomedical journal editorial community was used to identify a list of essential reporting items from this larger list. From the initial de novo list of twenty-nine candidate items, a set of twenty-three essential reporting items was developed. The items are presented numerically and categorized within six sections, namely: (i) title and abstract, (ii) introduction, (iii) methods, (iv) results, (v) discussion, and (vi) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document. It is anticipated that the MAPS statement will improve the clarity, transparency. and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by seven health economics and quality of life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in five years' time.

Preferred Reporting Items for Studies Mapping onto Preference-Based Outcome Measures: The MAPS Statement.

PubMed

Petrou, Stavros; Rivero-Arias, Oliver; Dakin, Helen; Longworth, Louise; Oppe, Mark; Froud, Robert; Gray, Alastair

2015-08-01

"Mapping" onto generic preference-based outcome measures is increasingly being used as a means of generating health utilities for use within health economic evaluations. Despite the publication of technical guides for the conduct of mapping research, guidance for the reporting of mapping studies is currently lacking. The MAPS (MApping onto Preference-based measures reporting Standards) statement is a new checklist that aims to promote complete and transparent reporting of mapping studies. In the absence of previously published reporting checklists or reporting guidance documents, a de novo list of reporting items was created by a working group comprised of 6 health economists and 1 Delphi methodologist. A 2-round, modified Delphi survey with representatives from academia, consultancy, health technology assessment agencies, and the biomedical journal editorial community was used to identify a list of essential reporting items from this larger list. From the initial de novo list of 29 candidate items, a set of 23 essential reporting items was developed. The items are presented numerically and categorized within 6 sections, namely: (i) title and abstract; (ii) introduction; (iii) methods; (iv) results; (v) discussion; and (vi) other. The MAPS statement is best applied in conjunction with the accompanying MAPS explanation and elaboration document. It is anticipated that the MAPS statement will improve the clarity, transparency, and completeness of reporting of mapping studies. To facilitate dissemination and uptake, the MAPS statement is being co-published by 7 health economics and quality-of-life journals, and broader endorsement is encouraged. The MAPS working group plans to assess the need for an update of the reporting checklist in 5 years.

Development of predictive mapping techniques for soil survey and salinity mapping

NASA Astrophysics Data System (ADS)

Elnaggar, Abdelhamid A.

Conventional soil maps represent a valuable source of information about soil characteristics, however they are subjective, very expensive, and time-consuming to prepare. Also, they do not include explicit information about the conceptual mental model used in developing them nor information about their accuracy, in addition to the error associated with them. Decision tree analysis (DTA) was successfully used in retrieving the expert knowledge embedded in old soil survey data. This knowledge was efficiently used in developing predictive soil maps for the study areas in Benton and Malheur Counties, Oregon and accessing their consistency. A retrieved soil-landscape model from a reference area in Harney County was extrapolated to develop a preliminary soil map for the neighboring unmapped part of Malheur County. The developed map had a low prediction accuracy and only a few soil map units (SMUs) were predicted with significant accuracy, mostly those shallow SMUs that have either a lithic contact with the bedrock or developed on a duripan. On the other hand, the developed soil map based on field data was predicted with very high accuracy (overall was about 97%). Salt-affected areas of the Malheur County study area are indicated by their high spectral reflectance and they are easily discriminated from the remote sensing data. However, remote sensing data fails to distinguish between the different classes of soil salinity. Using the DTA method, five classes of soil salinity were successfully predicted with an overall accuracy of about 99%. Moreover, the calculated area of salt-affected soil was overestimated when mapped using remote sensing data compared to that predicted by using DTA. Hence, DTA could be a very helpful approach in developing soil survey and soil salinity maps in more objective, effective, less-expensive and quicker ways based on field data.

Drawing Road Networks with Mental Maps.

PubMed

Lin, Shih-Syun; Lin, Chao-Hung; Hu, Yan-Jhang; Lee, Tong-Yee

2014-09-01

Tourist and destination maps are thematic maps designed to represent specific themes in maps. The road network topologies in these maps are generally more important than the geometric accuracy of roads. A road network warping method is proposed to facilitate map generation and improve theme representation in maps. The basic idea is deforming a road network to meet a user-specified mental map while an optimization process is performed to propagate distortions originating from road network warping. To generate a map, the proposed method includes algorithms for estimating road significance and for deforming a road network according to various geometric and aesthetic constraints. The proposed method can produce an iconic mark of a theme from a road network and meet a user-specified mental map. Therefore, the resulting map can serve as a tourist or destination map that not only provides visual aids for route planning and navigation tasks, but also visually emphasizes the presentation of a theme in a map for the purpose of advertising. In the experiments, the demonstrations of map generations show that our method enables map generation systems to generate deformed tourist and destination maps efficiently.

National Park Service Vegetation Mapping Inventory Program: Natchez Trace Parkway vegetation mapping project report

USGS Publications Warehouse

Hop, Kevin D.; Strassman, Andrew C.; Nordman, Carl; Pyne, Milo; White, Rickie; Jakusz, Joseph; Hoy, Erin E.; Dieck, Jennifer

2016-01-01

The National Park Service (NPS) Vegetation Mapping Inventory (VMI) Program is an effort to classify, describe, and map existing vegetation of national park units for the NPS Natural Resource Inventory and Monitoring (I&M) Program. The NPS VMI Program is managed by the NPS I&M Division and provides baseline vegetation information to the NPS Natural Resource I&M Program. The U.S. Geological Survey Upper Midwest Environmental Sciences Center, NatureServe, NPS Gulf Coast Network, and NPS Natchez Trace Parkway (NATR; also referred to as Parkway) have completed vegetation classification and mapping of NATR for the NPS VMI Program.Mappers, ecologists, and botanists collaborated to affirm vegetation types within the U.S. National Vegetation Classification (USNVC) of NATR and to determine how best to map them by using aerial imagery. Analyses of data from 589 vegetation plots had been used to describe an initial 99 USNVC associations in the Parkway; this classification work was completed prior to beginning this NATR vegetation mapping project. Data were collected during this project from another eight quick plots to support new vegetation types not previously identified at the Parkway. Data from 120 verification sites were collected to test the field key to vegetation associations and the application of vegetation associations to a sample set of map polygons. Furthermore, data from 900 accuracy assessment (AA) sites were collected (of which 894 were used to test accuracy of the vegetation map layer). The collective of all these datasets resulted in affirming 122 USNVC associations at NATR.To map the vegetation and open water of NATR, 63 map classes were developed. including the following: 54 map classes represent natural (including ruderal) vegetation types in the USNVC, 5 map classes represent cultural (agricultural and developed) vegetation types in the USNVC, 3 map classes represent nonvegetation open-water bodies (non-USNVC), and 1 map class represents landscapes that

Map Adventures.

ERIC Educational Resources Information Center

Geological Survey (Dept. of Interior), Reston, VA.

This curriculum packet about maps, with seven accompanying lessons, is appropriate for students in grades K-3. Students learn basic concepts for visualizing objects from different perspectives and how to understand and use maps. Lessons in the packet center on a story about a little girl, Nikki, who rides in a hot-air balloon that gives her, and…

Looking for an old map

USGS Publications Warehouse

,

1996-01-01

Many people want maps that show an area of the United States as it existed many years ago. These are called historical maps, and there are two types. The most common type consists of special maps prepared by commercial firms to show such historical features as battle-fields, military routes, or the paths taken by famous travelers. Typically, these maps are for sale to tourists at the sites of historical events. The other type is the truly old map--one compiled by a surveyor or cartographer many years ago. Lewis and Clark, for example, made maps of their journeys into the Northwest Territories in 1803-6, and originals of some of these maps still exist.

Labeling Projections on Published Maps

USGS Publications Warehouse

Snyder, John P.

1987-01-01

To permit accurate scaling on a map, and to use the map as a source of accurate positions in the transfer of data, certain parameters - such as the standard parallels selected for a conic projection - must be stated on the map. This information is often missing on published maps. Three current major world atlases are evaluated with respect to map projection identification. The parameters essential for the projections used in these three atlases are discussed and listed. These parameters should be stated on any map based on the same projection.

MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes

PubMed Central

Mok, Calvin A.; Au, Vinci; Thompson, Owen A.; Edgley, Mark L.; Gevirtzman, Louis; Yochem, John; Lowry, Joshua; Memar, Nadin; Wallenfang, Matthew R.; Rasoloson, Dominique; Bowerman, Bruce; Schnabel, Ralf; Seydoux, Geraldine; Moerman, Donald G.; Waterston, Robert H.

2017-01-01

Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans. Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C. elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2. We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures. PMID:28827289

Beyond data collection in digital mapping: interpretation, sketching and thought process elements in geological map making

NASA Astrophysics Data System (ADS)

Watkins, Hannah; Bond, Clare; Butler, Rob

2016-04-01

Geological mapping techniques have advanced significantly in recent years from paper fieldslips to Toughbook, smartphone and tablet mapping; but how do the methods used to create a geological map affect the thought processes that result in the final map interpretation? Geological maps have many key roles in the field of geosciences including understanding geological processes and geometries in 3D, interpreting geological histories and understanding stratigraphic relationships in 2D and 3D. Here we consider the impact of the methods used to create a map on the thought processes that result in the final geological map interpretation. As mapping technology has advanced in recent years, the way in which we produce geological maps has also changed. Traditional geological mapping is undertaken using paper fieldslips, pencils and compass clinometers. The map interpretation evolves through time as data is collected. This interpretive process that results in the final geological map is often supported by recording in a field notebook, observations, ideas and alternative geological models explored with the use of sketches and evolutionary diagrams. In combination the field map and notebook can be used to challenge the map interpretation and consider its uncertainties. These uncertainties and the balance of data to interpretation are often lost in the creation of published 'fair' copy geological maps. The advent of Toughbooks, smartphones and tablets in the production of geological maps has changed the process of map creation. Digital data collection, particularly through the use of inbuilt gyrometers in phones and tablets, has changed smartphones into geological mapping tools that can be used to collect lots of geological data quickly. With GPS functionality this data is also geospatially located, assuming good GPS connectivity, and can be linked to georeferenced infield photography. In contrast line drawing, for example for lithological boundary interpretation and sketching

A reference linkage map for Eucalyptus

PubMed Central

2012-01-01

Background Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. Results The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. Conclusion The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for

mapKITE: a New Paradigm for Simultaneous Aerial and Terrestrial Geodata Acquisition and Mapping

NASA Astrophysics Data System (ADS)

Molina, P.; Blázquez, M.; Sastre, J.; Colomina, I.

2016-06-01

We introduce a new mobile, simultaneous terrestrial and aerial, geodata collection and post-processing method: mapKITE. By combining two mapping technologies such as terrestrial mobile mapping and unmanned aircraft aerial mapping, geodata are simultaneously acquired from air and ground. More in detail, a mapKITE geodata acquisition system consists on an unmanned aircraft and a terrestrial vehicle, which hosts the ground control station. By means of a real-time navigation system on the terrestrial vehicle, real-time waypoints are sent to the aircraft from the ground. By doing so, the aircraft is linked to the terrestrial vehicle through a "virtual tether," acting as a "mapping kite." In the article, we entail the concept of mapKITE as well as the various technologies and techniques involved, from aircraft guidance and navigation based on IMU and GNSS, optical cameras for mapping and tracking, sensor orientation and calibration, etc. Moreover, we report of a new measurement introduced in mapKITE, that is, point-and-scale photogrammetric measurements [of image coordinates and scale] for optical targets of known size installed on the ground vehicle roof. By means of accurate posteriori trajectory determination of the terrestrial vehicle, mapKITE benefits then from kinematic ground control points which are photogrametrically observed by point-and-scale measures. Initial results for simulated configurations show that these measurements added to the usual Integrated Sensor Orientation ones reduce or even eliminate the need of conventional ground control points -therefore, lowering mission costs- and enable selfcalibration of the unmanned aircraft interior orientation parameters in corridor configurations, in contrast to the situation of traditional corridor configurations. Finally, we report about current developments of the first mapKITE prototype, developed under the European Union Research and Innovation programme Horizon 2020. The first mapKITE mission will be held at

Revision of Primary Series Maps

USGS Publications Warehouse

,

2000-01-01

In 1992, the U.S. Geological Survey (USGS) completed a 50-year effort to provide primary series map coverage of the United States. Many of these maps now need to be updated to reflect the construction of new roads and highways and other changes that have taken place over time. The USGS has formulated a graphic revision plan to help keep the primary series maps current. Primary series maps include 1:20,000-scale quadrangles of Puerto Rico, 1:24,000- or 1:25,000-scale quadrangles of the conterminous United States, Hawaii, and U.S. Territories, and 1:63,360-scale quadrangles of Alaska. The revision of primary series maps from new collection sources is accomplished using a variety of processes. The raster revision process combines the scanned content of paper maps with raster updating technologies. The vector revision process involves the automated plotting of updated vector files. Traditional processes use analog stereoplotters and manual scribing instruments on specially coated map separates. The ability to select from or combine these processes increases the efficiency of the National Mapping Division map revision program.

CAFÉ-Map: Context Aware Feature Mapping for mining high dimensional biomedical data.

PubMed

Minhas, Fayyaz Ul Amir Afsar; Asif, Amina; Arif, Muhammad

2016-12-01

Feature selection and ranking is of great importance in the analysis of biomedical data. In addition to reducing the number of features used in classification or other machine learning tasks, it allows us to extract meaningful biological and medical information from a machine learning model. Most existing approaches in this domain do not directly model the fact that the relative importance of features can be different in different regions of the feature space. In this work, we present a context aware feature ranking algorithm called CAFÉ-Map. CAFÉ-Map is a locally linear feature ranking framework that allows recognition of important features in any given region of the feature space or for any individual example. This allows for simultaneous classification and feature ranking in an interpretable manner. We have benchmarked CAFÉ-Map on a number of toy and real world biomedical data sets. Our comparative study with a number of published methods shows that CAFÉ-Map achieves better accuracies on these data sets. The top ranking features obtained through CAFÉ-Map in a gene profiling study correlate very well with the importance of different genes reported in the literature. Furthermore, CAFÉ-Map provides a more in-depth analysis of feature ranking at the level of individual examples. CAFÉ-Map Python code is available at: http://faculty.pieas.edu.pk/fayyaz/software.html#cafemap . The CAFÉ-Map package supports parallelization and sparse data and provides example scripts for classification. This code can be used to reconstruct the results given in this paper. Copyright © 2016 Elsevier Ltd. All rights reserved.

Self Consistent Bathymetric Mapping Using Sub-maps: Survey Results From the TAG Hydrothermal Structure

NASA Astrophysics Data System (ADS)

Roman, C. N.; Reves-Sohn, R.; Singh, H.; Humphris, S.

2005-12-01

The spatial resolution of microbathymetry maps created using robotic vehicles such as ROVs, AUVs and manned submersibles in the deep ocean is currently limited by the accuracy of the vehicle navigation data. Errors in the vehicle position estimate commonly exceed the ranging errors of the acoustic mapping sensor itself, which creates inconsistency in the map making process and produces artifacts that lower resolution and distort map integrity. We present a methodology for producing self-consistent maps and improving vehicle position estimation by exploiting accurate local navigation and utilizing terrain relative measurements. The complete map is broken down into individual "sub-maps'', which are generated using short term Doppler based navigation. The sub-maps are pairwise registered to constrain the vehicle position estimates by matching terrain that has been imaged multiple times. This procedure is implemented using a delayed state Kalman filter to incorporate the sub-map registrations as relative position measurements between previously visited vehicle locations. Archiving of previous positions in a filter state vector allows for continual adjustment of the sub-map locations. The terrain registration is accomplished using a two dimensional correlation and a six degree of freedom point cloud alignment method tailored to bathymetric data. This registration procedure is applicable to fully 3 dimensional complex underwater environments. The complete bathymetric map is then created from the union of all sub-maps that have been aligned in a consistent manner. The method is applied to an SM2000 multibeam survey of the TAG hydrothermal structure on the Mid-Atlantic Ridge at 26(°)N using the Jason II ROV. The survey included numerous crossing tracklines designed to test this algorithm, and the final gridded bathymetry data is sub-meter accurate. The high-resolution map has allowed for the identification of previously unrecognized fracture patterns associated with flow

The evolving Alaska mapping program.

USGS Publications Warehouse

Brooks, P.D.; O'Brien, T. J.

1986-01-01

This paper describes the development of mapping in Alaska, the current status of the National Mapping Program, and future plans for expanding and improving the mapping coverage. Research projects with Landsat Multispectral Scanner and Return Vidicon imagery and real- and synthetic-aperture radar; image mapping programs; digital mapping; remote sensing projects; the Alaska National Interest Lands Conservation Act; and the Alaska High-Altitude Aerial Photography Program are also discussed.-from Authors

An Inquiry-Oriented Curriculum in Map Making and Map Interpretation for the Intermediate Grades.

ERIC Educational Resources Information Center

Janeway, W. Whitney

This publication contains class activities and provocative inquiry questions for intermediate-grade teachers to use to involve students in map making and map interpretation. The author believes that the only things that are needed to develop an inquiry-oriented unit on mapping are a good map, a small group of students, and a perceptive teacher who…

MAP - a mapping and analysis program for harvest planning

Treesearch

Robert N. Eli; Chris B. LeDoux; Penn A. Peters

1984-01-01

The Northeastern Forest Experiment Station and the Department of Civil Engineering at West Virginia University are cooperating in the development of a Mapping and Analysis Program, to be named MAP. The goal of this computer software package is to significantly improve the planning and harvest efficiency of small to moderately sized harvest units located in mountainous...

Dynamic map labeling.

PubMed

Been, Ken; Daiches, Eli; Yap, Chee

2006-01-01

We address the problem of filtering, selecting and placing labels on a dynamic map, which is characterized by continuous zooming and panning capabilities. This consists of two interrelated issues. The first is to avoid label popping and other artifacts that cause confusion and interrupt navigation, and the second is to label at interactive speed. In most formulations the static map labeling problem is NP-hard, and a fast approximation might have O(nlogn) complexity. Even this is too slow during interaction, when the number of labels shown can be several orders of magnitude less than the number in the map. In this paper we introduce a set of desiderata for "consistent" dynamic map labeling, which has qualities desirable for navigation. We develop a new framework for dynamic labeling that achieves the desiderata and allows for fast interactive display by moving all of the selection and placement decisions into the preprocessing phase. This framework is general enough to accommodate a variety of selection and placement algorithms. It does not appear possible to achieve our desiderata using previous frameworks. Prior to this paper, there were no formal models of dynamic maps or of dynamic labels; our paper introduces both. We formulate a general optimization problem for dynamic map labeling and give a solution to a simple version of the problem. The simple version is based on label priorities and a versatile and intuitive class of dynamic label placements we call "invariant point placements". Despite these restrictions, our approach gives a useful and practical solution. Our implementation is incorporated into the G-Vis system which is a full-detail dynamic map of the continental USA. This demo is available through any browser.

MIP-MAP: High-Throughput Mapping of Caenorhabditis elegans Temperature-Sensitive Mutants via Molecular Inversion Probes.

PubMed

Mok, Calvin A; Au, Vinci; Thompson, Owen A; Edgley, Mark L; Gevirtzman, Louis; Yochem, John; Lowry, Joshua; Memar, Nadin; Wallenfang, Matthew R; Rasoloson, Dominique; Bowerman, Bruce; Schnabel, Ralf; Seydoux, Geraldine; Moerman, Donald G; Waterston, Robert H

2017-10-01

Mutants remain a powerful means for dissecting gene function in model organisms such as Caenorhabditis elegans Massively parallel sequencing has simplified the detection of variants after mutagenesis but determining precisely which change is responsible for phenotypic perturbation remains a key step. Genetic mapping paradigms in C . elegans rely on bulk segregant populations produced by crosses with the problematic Hawaiian wild isolate and an excess of redundant information from whole-genome sequencing (WGS). To increase the repertoire of available mutants and to simplify identification of the causal change, we performed WGS on 173 temperature-sensitive (TS) lethal mutants and devised a novel mapping method. The mapping method uses molecular inversion probes (MIP-MAP) in a targeted sequencing approach to genetic mapping, and replaces the Hawaiian strain with a Million Mutation Project strain with high genomic and phenotypic similarity to the laboratory wild-type strain N2 We validated MIP-MAP on a subset of the TS mutants using a competitive selection approach to produce TS candidate mapping intervals with a mean size < 3 Mb. MIP-MAP successfully uses a non-Hawaiian mapping strain and multiplexed libraries are sequenced at a fraction of the cost of WGS mapping approaches. Our mapping results suggest that the collection of TS mutants contains a diverse library of TS alleles for genes essential to development and reproduction. MIP-MAP is a robust method to genetically map mutations in both viable and essential genes and should be adaptable to other organisms. It may also simplify tracking of individual genotypes within population mixtures. Copyright © 2017 by the Genetics Society of America.

Creative Concept Mapping.

ERIC Educational Resources Information Center

Brown, David S.

2002-01-01

Recommends the use of concept mapping in science teaching and proposes that it be presented as a creative activity. Includes a sample lesson plan of a potato stamp concept mapping activity for astronomy. (DDR)

Elementary maps on nest algebras

NASA Astrophysics Data System (ADS)

Li, Pengtong

2006-08-01

Let , be algebras and let , be maps. An elementary map of is an ordered pair (M,M*) such that for all , . In this paper, the general form of surjective elementary maps on standard subalgebras of nest algebras is described. In particular, such maps are automatically additive.

46. GENERAL MAP OF SANTA ANA NO. 3 PROJECT MAP ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

46. GENERAL MAP OF SANTA ANA NO. 3 PROJECT MAP OF ALL THREE POWER HOUSE SYSTEMS, EXHIBIT J, JAN. 25, 1956. SCE drawing no. 535041 (sheet no. 1; for filing with Federal Power Commission). - Santa Ana River Hydroelectric System, Redlands, San Bernardino County, CA

Using Web Maps to Analyze the Construction of Global Scale Cognitive Maps

ERIC Educational Resources Information Center

Pingel, Thomas J.

2018-01-01

Game-based Web sites and applications are changing the ways in which students learn the world map. In this study, a Web map-based digital learning tool was used as a study aid for a university-level geography course in order to examine the way in which global scale cognitive maps are constructed. A network analysis revealed that clicks were…

Comparing physiographic maps with different categorisations

NASA Astrophysics Data System (ADS)

Zawadzka, J.; Mayr, T.; Bellamy, P.; Corstanje, R.

2015-02-01

This paper addresses the need for a robust map comparison method suitable for finding similarities between thematic maps with different forms of categorisations. In our case, the requirement was to establish the information content of newly derived physiographic maps with regards to set of reference maps for a study area in England and Wales. Physiographic maps were derived from the 90 m resolution SRTM DEM, using a suite of existing and new digital landform mapping methods with the overarching purpose of enhancing the physiographic unit component of the Soil and Terrain database (SOTER). Reference maps were seven soil and landscape datasets mapped at scales ranging from 1:200,000 to 1:5,000,000. A review of commonly used statistical methods for categorical comparisons was performed and of these, the Cramer's V statistic was identified as the most appropriate for comparison of maps with different legends. Interpretation of multiple Cramer's V values resulting from one-by-one comparisons of the physiographic and baseline maps was facilitated by multi-dimensional scaling and calculation of average distances between the maps. The method allowed for finding similarities and dissimilarities amongst physiographic maps and baseline maps and informed the recommendation of the most suitable methodology for terrain analysis in the context of soil mapping.

StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes.

PubMed

Sanchez Sorzano, Carlos Oscar; Alvarez-Cabrera, Ana Lucia; Kazemi, Mohsen; Carazo, Jose María; Jonić, Slavica

2016-04-26

Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Using maps in genealogy

USGS Publications Warehouse

,

1999-01-01

Maps are one of many sources you may need to complete a family tree. In genealogical research, maps can provide clues to where our ancestors may have lived and where to look for written records about them. Beginners should master basic genealogical research techniques before starting to use topographic maps.

Mapping with Young Children.

ERIC Educational Resources Information Center

Sunal, Cynthia Szymanski; Warash, Bobbi Gibson

Techniques for encouraging young children to discover the purpose and use of maps are discussed. Motor activity and topological studies form a base from which the teacher and children can build a mapping program of progressive sophistication. Concepts important to mapping include boundaries, regions, exteriors, interiors, holes, order, point of…

A Lithology Based Map Unit Schema For Onegeology Regional Geologic Map Integration

NASA Astrophysics Data System (ADS)

Moosdorf, N.; Richard, S. M.

2012-12-01

A system of lithogenetic categories for a global lithological map (GLiM, http://www.ifbm.zmaw.de/index.php?id=6460&L=3) has been compiled based on analysis of lithology/genesis categories for regional geologic maps for the entire globe. The scheme is presented for discussion and comment. Analysis of units on a variety of regional geologic maps indicates that units are defined based on assemblages of rock types, as well as their genetic type. In this compilation of continental geology, outcropping surface materials are dominantly sediment/sedimentary rock; major subdivisions of the sedimentary category include clastic sediment, carbonate sedimentary rocks, clastic sedimentary rocks, mixed carbonate and clastic sedimentary rock, colluvium and residuum. Significant areas of mixed igneous and metamorphic rock are also present. A system of global categories to characterize the lithology of regional geologic units is important for Earth System models of matter fluxes to soils, ecosystems, rivers and oceans, and for regional analysis of Earth surface processes at global scale. Because different applications of the classification scheme will focus on different lithologic constituents in mixed units, an ontology-type representation of the scheme that assigns properties to the units in an analyzable manner will be pursued. The OneGeology project is promoting deployment of geologic map services at million scale for all nations. Although initial efforts are commonly simple scanned map WMS services, the intention is to move towards data-based map services that categorize map units with standard vocabularies to allow use of a common map legend for better visual integration of the maps (e.g. see OneGeology Europe, http://onegeology-europe.brgm.fr/ geoportal/ viewer.jsp). Current categorization of regional units with a single lithology from the CGI SimpleLithology (http://resource.geosciml.org/201202/ Vocab2012html/ SimpleLithology201012.html) vocabulary poorly captures the

Role of post-mapping computed tomography in virtual-assisted lung mapping.

PubMed

Sato, Masaaki; Nagayama, Kazuhiro; Kuwano, Hideki; Nitadori, Jun-Ichi; Anraku, Masaki; Nakajima, Jun

2017-02-01

Background Virtual-assisted lung mapping is a novel bronchoscopic preoperative lung marking technique in which virtual bronchoscopy is used to predict the locations of multiple dye markings. Post-mapping computed tomography is performed to confirm the locations of the actual markings. This study aimed to examine the accuracy of marking locations predicted by virtual bronchoscopy and elucidate the role of post-mapping computed tomography. Methods Automated and manual virtual bronchoscopy was used to predict marking locations. After bronchoscopic dye marking under local anesthesia, computed tomography was performed to confirm the actual marking locations before surgery. Discrepancies between marking locations predicted by the different methods and the actual markings were examined on computed tomography images. Forty-three markings in 11 patients were analyzed. Results The average difference between the predicted and actual marking locations was 30 mm. There was no significant difference between the latest version of the automated virtual bronchoscopy system (30.7 ± 17.2 mm) and manual virtual bronchoscopy (29.8 ± 19.1 mm). The difference was significantly greater in the upper vs. lower lobes (37.1 ± 20.1 vs. 23.0 ± 6.8 mm, for automated virtual bronchoscopy; p < 0.01). Despite this discrepancy, all targeted lesions were successfully resected using 3-dimensional image guidance based on post-mapping computed tomography reflecting the actual marking locations. Conclusions Markings predicted by virtual bronchoscopy were dislocated from the actual markings by an average of 3 cm. However, surgery was accurately performed using post-mapping computed tomography guidance, demonstrating the indispensable role of post-mapping computed tomography in virtual-assisted lung mapping.

One map policy (OMP) implementation strategy to accelerate mapping of regional spatial planing (RTRW) in Indonesia

NASA Astrophysics Data System (ADS)

Hasyim, Fuad; Subagio, Habib; Darmawan, Mulyanto

2016-06-01

A preparation of spatial planning documents require basic geospatial information and thematic accuracies. Recently these issues become important because spatial planning maps are impartial attachment of the regional act draft on spatial planning (PERDA). The needs of geospatial information in the preparation of spatial planning maps preparation can be divided into two major groups: (i). basic geospatial information (IGD), consist of of Indonesia Topographic maps (RBI), coastal and marine environmental maps (LPI), and geodetic control network and (ii). Thematic Geospatial Information (IGT). Currently, mostly local goverment in Indonesia have not finished their regulation draft on spatial planning due to some constrain including technical aspect. Some constrain in mapping of spatial planning are as follows: the availability of large scale ofbasic geospatial information, the availability of mapping guidelines, and human resources. Ideal conditions to be achieved for spatial planning maps are: (i) the availability of updated geospatial information in accordance with the scale needed for spatial planning maps, (ii) the guideline of mapping for spatial planning to support local government in completion their PERDA, and (iii) capacity building of local goverment human resources to completed spatial planning maps. The OMP strategies formulated to achieve these conditions are: (i) accelerating of IGD at scale of 1:50,000, 1: 25,000 and 1: 5,000, (ii) to accelerate mapping and integration of Thematic Geospatial Information (IGT) through stocktaking availability and mapping guidelines, (iii) the development of mapping guidelines and dissemination of spatial utilization and (iv) training of human resource on mapping technology.

Titan Polar Maps - 2015

NASA Image and Video Library

2015-10-09

The northern and southern hemispheres of Titan are seen in these polar stereographic maps, assembled in 2015 using the best-available images of the giant Saturnian moon from NASA's Cassini mission. The images were taken by Cassini's imaging cameras using a spectral filter centered at 938 nanometers, allowing researchers to examine variations in albedo (or inherent brightness) across the surface of Titan. These maps utilize imaging data collected through Cassini's flyby on April 7, 2014, known as "T100." Titan's north pole was not well illuminated early in Cassini's mission, because it was winter in the northern hemisphere when the spacecraft arrived at Saturn. Cassini has been better able to observe northern latitudes in more recent years due to seasonal changes in solar illumination. Compared to the previous version of Cassini's north polar map (see PIA11146), this map provides much more detail and fills in a large area of missing data. The imaging data in these maps complement Cassini synthetic aperture radar (SAR) mapping of Titan's north pole (see PIA17655). The uniform gray area in the northern hemisphere indicates a gap in the imaging coverage of Titan's surface, to date. The missing data will be imaged by Cassini during flybys on December 15, 2016 and March 5, 2017. Lakes are also seen in the southern hemisphere map, but they are much less common than in the north polar region. Only a lakes have been confirmed in the south. The dark, footprint-shaped feature at 180 degrees west is Ontario Lacus; a smaller lake named Crveno Lacus can be seen as a very dark spot just above Ontario. The dark-albedo area seen at the top of the southern hemisphere map (at 0 degrees west) is an area called Mezzoramia. Each map is centered on one of the poles, and surface coverage extends southward to 60 degrees latitude. Grid lines indicate latitude in 10-degree increments and longitude in 30-degree increments. The scale in the full-size versions of these maps is 4,600 feet (1

Preliminary northeast Asia geodynamics map

USGS Publications Warehouse

Parfenov, Leonid M.; Khanchuk, Alexander I.; Badarch, Gombosuren; Miller, Robert J.; Naumova, Vera V.; Nokleberg, Warren J.; Ogasawara, Masatsugu; Prokopiev, Andrei V.; Yan, Hongquan

2003-01-01

This map portrays the geodynamics of Northeast Asia at a scale of 1:5,000,000 using the concepts of plate tectonics and analysis of terranes and overlap assemblages. The map is the result of a detailed compilation and synthesis at 5 million scale and is part of a major international collaborative study of the Mineral Resources, Metallogenesis, and Tectonics of Northeast Asia conducted from 1997 through 2002 by geologists from earth science agencies and universities in Russia, Mongolia, Northeastern China, South Korea, Japan, and the USA. This map is the result of extensive geologic mapping and associated tectonic studies in Northeast Asia in the last few decades and is the first collaborative compilation of the geology of the region at a scale of 1:5,000,000 by geologists from Russia, Mongolia, Northeastern China, South Korea, Japan, and the USA. The map was compiled by a large group of international geologists using the below concepts and definitions during collaborative workshops over a six-year period. The map is a major new compilation and re-interpretation of pre-existing geologic maps of the region. The map is designed to be used for several purposes, including regional tectonic analyses, mineral resource and metallogenic analysis, petroleum resource analysis, neotectonic analysis, and analysis of seismic hazards and volcanic hazards. The map consists of two sheets. Sheet 1 displays the map at a scale of 1:5,000,000, explanation. Sheet 2 displays the introduction, list of map units, and source references. Detailed descriptions of map units and stratigraphic columns are being published separately. This map is one of a series of publications on the mineral resources, metallogenesis, and geodynamics,of Northeast Asia. Companion studies and other articles and maps , and various detailed reports are: (1) a compilation of major mineral deposit models (Rodionov and Nokleberg, 2000; Rodionov and others, 2000; Obolenskiy and others, in press a); (2) a series of

The National Map 2.0 Tactical Plan: "Toward the (Integrated) National Map"

USGS Publications Warehouse

Zulick, Carl A.

2008-01-01

The National Map's 2-year goal, as described in this plan, is to provide a range of geospatial products and services that meet the basic goals of the original vision for The National Map while furthering the National Spatial Data Infrastructure that underpins U.S. Geological Survey (USGS) science. To accomplish this goal, the National Geospatial Program (NGP) will acquire, store, maintain, and distribute base map data. The management team for the NGP sets priorities for The National Map in three areas: Data and Products, Services, and Management. Priorities for fiscal years 2008 and 2009 (October 1, 2007 through September 30, 2009), involving the current data inventory, data acquisition, and the integration of data, are (1) incorporating current data from Federal, State, and local organizations into The National Map to the degree possible, given data availability and program resources; (2) collaborating with other USGS programs to incorporate data that support the USGS Science Strategy; (3) supporting the Department of the Interior (DOI) high-priority geospatial information needs; (4) emergency response; (5) homeland security, natural hazards; and (6) graphics products delivery. The management team identified known constraints, enablers, and drivers for the acquisition and integration of data. The NGP management team also identified customer-focused products and services of The National Map. Ongoing planning and management activities direct the development and delivery of these products and services. Management of work flow processes to support The National Map priorities are identified and established through a business-driven prioritization process. This tactical plan is primarily for use as a document to guide The National Map program for the next two fiscal years. The document is available to the public because of widespread interest in The National Map. The USGS collaborates with a broad range of customers and partners who are essential to the success of The

Quantitative DNA fiber mapping

DOEpatents

Gray, Joe W.; Weier, Heinz-Ulrich G.

1998-01-01

The present invention relates generally to the DNA mapping and sequencing technologies. In particular, the present invention provides enhanced methods and compositions for the physical mapping and positional cloning of genomic DNA. The present invention also provides a useful analytical technique to directly map cloned DNA sequences onto individual stretched DNA molecules.

Geologic map and map database of the Palo Alto 30' x 60' quadrangle, California

USGS Publications Warehouse

Brabb, E.E.; Jones, D.L.; Graymer, R.W.

2000-01-01

This digital map database, compiled from previously published and unpublished data, and new mapping by the authors, represents the general distribution of bedrock and surficial deposits in the mapped area. Together with the accompanying text file (pamf.ps, pamf.pdf, pamf.txt), it provides current information on the geologic structure and stratigraphy of the area covered. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:62,500 or smaller.

Accuracy, resolution, and cost comparisons between small format and mapping cameras for environmental mapping

NASA Technical Reports Server (NTRS)

Clegg, R. H.; Scherz, J. P.

1975-01-01

Successful aerial photography depends on aerial cameras providing acceptable photographs within cost restrictions of the job. For topographic mapping where ultimate accuracy is required only large format mapping cameras will suffice. For mapping environmental patterns of vegetation, soils, or water pollution, 9-inch cameras often exceed accuracy and cost requirements, and small formats may be better. In choosing the best camera for environmental mapping, relative capabilities and costs must be understood. This study compares resolution, photo interpretation potential, metric accuracy, and cost of 9-inch, 70mm, and 35mm cameras for obtaining simultaneous color and color infrared photography for environmental mapping purposes.

Effect of Map-vaccination in ewes on body condition score, weight and Map-shedding.

PubMed

Hüttner, Klim; Krämer, Ulla; Kleist, Petra

2012-01-01

Vaccination against Mycobacterium avium subspecies paratuberculosis (Map) in sheep receives growing attention worldwide, particularly in countries with national Map control strategies. A field study was conducted, investigating the effect of GUDAIR on body condition, weight and Map-shedding in a professionally managed but largely Map-affected suffolk flock prior and after vaccination. For this, 80 ewes out of 1000 animals were randomly sampled. In the univariate analysis body condition scores of ewes twelve months after vaccination improved significantly compared to those sampled prior to vaccination. At the same time the rate of ewes shedding Map was reduced by 37%.

Riparian Wetlands: Mapping

EPA Science Inventory

Riparian wetlands are critical systems that perform functions and provide services disproportionate to their extent in the landscape. Mapping wetlands allows for better planning, management, and modeling, but riparian wetlands present several challenges to effective mapping due t...

BenMAP Downloads

EPA Pesticide Factsheets

Download the current and legacy versions of the BenMAP program. Download configuration and aggregation/pooling/valuation files to estimate benefits. BenMAP-CE is free and open source software, and the source code is available upon request.

From Open Geographical Data to Tangible Maps: Improving the Accessibility of Maps for Visually Impaired People

NASA Astrophysics Data System (ADS)

Ducasse, J.; Macé, M.; Jouffrais, C.

2015-08-01

Visual maps must be transcribed into (interactive) raised-line maps to be accessible for visually impaired people. However, these tactile maps suffer from several shortcomings: they are long and expensive to produce, they cannot display a large amount of information, and they are not dynamically modifiable. A number of methods have been developed to automate the production of raised-line maps, but there is not yet any tactile map editor on the market. Tangible interactions proved to be an efficient way to help a visually impaired user manipulate spatial representations. Contrary to raised-line maps, tangible maps can be autonomously constructed and edited. In this paper, we present the scenarios and the main expected contributions of the AccessiMap project, which is based on the availability of many sources of open spatial data: 1/ facilitating the production of interactive tactile maps with the development of an open-source web-based editor; 2/ investigating the use of tangible interfaces for the autonomous construction and exploration of a map by a visually impaired user.

Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations.

PubMed

Wong, Gerard; Leckie, Christopher; Gorringe, Kylie L; Haviv, Izhak; Campbell, Ian G; Kowalczyk, Adam

2010-04-15

High-density single nucleotide polymorphism (SNP) genotyping arrays are efficient and cost effective platforms for the detection of copy number variation (CNV). To ensure accuracy in probe synthesis and to minimize production costs, short oligonucleotide probe sequences are used. The use of short probe sequences limits the specificity of binding targets in the human genome. The specificity of these short probeset sequences has yet to be fully analysed against a normal reference human genome. Sequence similarity can artificially elevate or suppress copy number measurements, and hence reduce the reliability of affected probe readings. For the purpose of detecting narrow CNVs reliably down to the width of a single probeset, sequence similarity is an important issue that needs to be addressed. We surveyed the Affymetrix Human Mapping SNP arrays for probeset sequence similarity against the reference human genome. Utilizing sequence similarity results, we identified a collection of fine-scaled putative CNVs between gender from autosomal probesets whose sequence matches various loci on the sex chromosomes. To detect these variations, we utilized our statistical approach, Detecting REcurrent Copy number change using rank-order Statistics (DRECS), and showed that its performance was superior and more stable than the t-test in detecting CNVs. Through the application of DRECS on the HapMap population datasets with multi-matching probesets filtered, we identified biologically relevant SNPs in aberrant regions across populations with known association to physical traits, such as height, covered by the span of a single probe. This provided empirical confirmation of the existence of naturally occurring narrow CNVs as well as the sensitivity of the Affymetrix SNP array technology in detecting them. The MATLAB implementation of DRECS is available at http://ww2.cs.mu.oz.au/ approximately gwong/DRECS/index.html.

Correlation mapping microscopy

NASA Astrophysics Data System (ADS)

McGrath, James; Alexandrov, Sergey; Owens, Peter; Subhash, Hrebesh M.; Leahy, Martin J.

2015-03-01

Changes in the microcirculation are associated with conditions such as Raynauds disease. Current modalities used to assess the microcirculation such as nailfold capillaroscopy are limited due to their depth ambiguity. A correlation mapping technique was recently developed to extend the capabilities of Optical Coherence Tomography to generate depth resolved images of the microcirculation. Here we present the extension of this technique to microscopy modalities, including confocal microscopy. It is shown that this correlation mapping microscopy technique can extend the capabilities of conventional microscopy to enable mapping of vascular networks in vivo with high spatial resolution.

The Circumpolar Arctic vegetation map

USGS Publications Warehouse

Walker, Donald A.; Raynolds, Martha K.; Daniels, F.J.A.; Einarsson, E.; Elvebakk, A.; Gould, W.A.; Katenin, A.E.; Kholod, S.S.; Markon, C.J.; Melnikov, E.S.; Moskalenko, N.G.; Talbot, S. S.; Yurtsev, B.A.; Bliss, L.C.; Edlund, S.A.; Zoltai, S.C.; Wilhelm, M.; Bay, C.; Gudjonsson, G.; Ananjeva, G.V.; Drozdov, D.S.; Konchenko, L.A.; Korostelev, Y.V.; Ponomareva, O.E.; Matveyeva, N.V.; Safranova, I.N.; Shelkunova, R.; Polezhaev, A.N.; Johansen, B.E.; Maier, H.A.; Murray, D.F.; Fleming, Michael D.; Trahan, N.G.; Charron, T.M.; Lauritzen, S.M.; Vairin, B.A.

2005-01-01

Question: What are the major vegetation units in the Arctic, what is their composition, and how are they distributed among major bioclimate subzones and countries? Location: The Arctic tundra region, north of the tree line. Methods: A photo-interpretive approach was used to delineate the vegetation onto an Advanced Very High Resolution Radiometer (AVHRR) base image. Mapping experts within nine Arctic regions prepared draft maps using geographic information technology (ArcInfo) of their portion of the Arctic, and these were later synthesized to make the final map. Area analysis of the map was done according to bioclimate subzones, and country. The integrated mapping procedures resulted in other maps of vegetation, topography, soils, landscapes, lake cover, substrate pH, and above-ground biomass. Results: The final map was published at 1:7 500 000 scale map. Within the Arctic (total area = 7.11 x 106 km 2), about 5.05 ?? 106 km2 is vegetated. The remainder is ice covered. The map legend generally portrays the zonal vegetation within each map polygon. About 26% of the vegetated area is erect shrublands, 18% peaty graminoid tundras, 13% mountain complexes, 12% barrens, 11% mineral graminoid tundras, 11% prostrate-shrub tundras, and 7% wetlands. Canada has by far the most terrain in the High Arctic mostly associated with abundant barren types and prostrate dwarf-shrub tundra, whereas Russia has the largest area in the Low Arctic, predominantly low-shrub tundra. Conclusions: The CAVM is the first vegetation map of an entire global biome at a comparable resolution. The consistent treatment of the vegetation across the circumpolar Arctic, abundant ancillary material, and digital database should promote the application to numerous land-use, and climate-change applications and will make updating the map relatively easy. ?? IAVS; Opulus Press.

Mapping the Natchez Trace Parkway

USGS Publications Warehouse

Rangoonwala, Amina; Bannister, Terri; Ramsey, Elijah W.

2011-01-01

Based on a National Park Service (NPS) landcover classification, a landcover map of the 715-km (444-mile) NPS Natchez Trace Parkway (hereafter referred to as the "Parkway") was created. The NPS landcover classification followed National Vegetation Classification (NVC) protocols. The landcover map, which extended the initial landcover classification to the entire Parkway, was based on color-infrared photography converted to 1-m raster-based digital orthophoto quarter quadrangles, according to U.S. Geological Survey mapping standards. Our goal was to include as many alliance classes as possible in the Parkway landcover map. To reach this goal while maintaining a consistent and quantifiable map product throughout the Parkway extent, a mapping strategy was implemented based on the migration of class-based spectral textural signatures and the congruent progressive refinement of those class signatures along the Parkway. Progressive refinement provided consistent mapping by evaluating the spectral textural distinctiveness of the alliance-association classes, and where necessary, introducing new map classes along the Parkway. By following this mapping strategy, the use of raster-based image processing and geographic information system analyses for the map production provided a quantitative and reproducible product. Although field-site classification data were severely limited, the combination of spectral migration of class membership along the Parkway and the progressive classification strategy produced an organization of alliances that was internally highly consistent. The organization resulted from the natural patterns or alignments of spectral variance and the determination of those spectral patterns that were compositionally similar in the dominant species as NVC alliances. Overall, the mapped landcovers represented the existent spectral textural patterns that defined and encompassed the complex variety of compositional alliances and associations of the Parkway. Based

Linkage Map of Escherichia coli K-12, Edition 10: The Traditional Map

PubMed Central

Berlyn, Mary K. B.

1998-01-01

This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715–1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included. PMID:9729611

Analyzing thematic maps and mapping for accuracy

USGS Publications Warehouse

Rosenfield, G.H.

1982-01-01

Two problems which exist while attempting to test the accuracy of thematic maps and mapping are: (1) evaluating the accuracy of thematic content, and (2) evaluating the effects of the variables on thematic mapping. Statistical analysis techniques are applicable to both these problems and include techniques for sampling the data and determining their accuracy. In addition, techniques for hypothesis testing, or inferential statistics, are used when comparing the effects of variables. A comprehensive and valid accuracy test of a classification project, such as thematic mapping from remotely sensed data, includes the following components of statistical analysis: (1) sample design, including the sample distribution, sample size, size of the sample unit, and sampling procedure; and (2) accuracy estimation, including estimation of the variance and confidence limits. Careful consideration must be given to the minimum sample size necessary to validate the accuracy of a given. classification category. The results of an accuracy test are presented in a contingency table sometimes called a classification error matrix. Usually the rows represent the interpretation, and the columns represent the verification. The diagonal elements represent the correct classifications. The remaining elements of the rows represent errors by commission, and the remaining elements of the columns represent the errors of omission. For tests of hypothesis that compare variables, the general practice has been to use only the diagonal elements from several related classification error matrices. These data are arranged in the form of another contingency table. The columns of the table represent the different variables being compared, such as different scales of mapping. The rows represent the blocking characteristics, such as the various categories of classification. The values in the cells of the tables might be the counts of correct classification or the binomial proportions of these counts divided by

Reading Angles in Maps

ERIC Educational Resources Information Center

Izard, Véronique; O'Donnell, Evan; Spelke, Elizabeth S.

2014-01-01

Preschool children can navigate by simple geometric maps of the environment, but the nature of the geometric relations they use in map reading remains unclear. Here, children were tested specifically on their sensitivity to angle. Forty-eight children (age 47:15-53:30 months) were presented with fragments of geometric maps, in which angle sections…

Derivation of the dipole map

NASA Astrophysics Data System (ADS)

Ali, Halima; Punjabi, Alkesh; Boozer, Allen

2004-09-01

In our method of maps [Punjabi et al., Phy. Rev. Lett. 69, 3322 (1992), and Punjabi et al., J. Plasma Phys. 52, 91 (1994)], symplectic maps are used to calculate the trajectories of magnetic field lines in divertor tokamaks. Effects of the magnetic perturbations are calculated using the low MN map [Ali et al., Phys. Plasmas 11, 1908 (2004)] and the dipole map [Punjabi et al., Phys. Plasmas 10, 3992 (2003)]. The dipole map is used to calculate the effects of externally located current carrying coils on the trajectories of the field lines, the stochastic layer, the magnetic footprint, and the heat load distribution on the collector plates in divertor tokamaks [Punjabi et al., Phys. Plasmas 10, 3992 (2003)]. Symplectic maps are general, efficient, and preserve and respect the Hamiltonian nature of the dynamics. In this brief communication, a rigorous mathematical derivation of the dipole map is given.

Chinese Mapped America Before 1430

NASA Astrophysics Data System (ADS)

Lee, Siu-Leung

2018-05-01

Qualitative and quantitative comparison of Kunyu Wanguo Quantu (the 1602 Chinese world map) and contemporaneous world maps by Mercator (1569), Ortelius (1570) , Mercator's Arctic map (1595), and Plancius (1594) in particular, reveals that the Chinese map is not an adapted copy from European maps. The Chinese world map includes geography of a pre-Renaissance Europe and American geography unknown to Europeans until more than 200 years after Ricci's death. Approximately 50 % of the place names, including those of America, have no equivalents on European maps. Chinese names descriptive of the geographic feature of California peninsula, Mount Ranier, the fjords of Alaska, Mount Denali, tidal bore near Anchorage are all accurate by latitudes. Chile and Peru are correct by relative longitude. Contrarily, the maps by Plancius and Mercator are erroneous and ambiguous on the geography of North and South America. The geography and text of the Chinese world map are consistent with a completion date of 1430, some sixty years before Christopher Columbus' first voyage. Martino Martini's Novus Atlas Sinensis (1655) is not a survey of his own but translated from Chinese sources, revealing that Ming China was capable of determining longitude/latitude on land and ocean, as well as spherical projection. In conclusion, information about American geography was transferred from China to Europe, not the reverse. The Chinese world map Kunyu Wanguo Quantu is the result of Chinese circumnavigation and survey, pioneering the Age of Exploration, overturning 600 years of misinterpreted history.

Historical shoreline mapping (II): Application of the Digital Shoreline Mapping and Analysis Systems (DSMS/DSAS) to shoreline change mapping in Puerto Rico

USGS Publications Warehouse

Thieler, E. Robert; Danforth, William W.

1994-01-01

A new, state-of-the-art method for mapping historical shorelines from maps and aerial photographs, the Digital Shoreline Mapping System (DSMS), has been developed. The DSMS is a freely available, public domain software package that meets the cartographic and photogrammetric requirements of precise coastal mapping, and provides a means to quantify and analyze different sources of error in the mapping process. The DSMS is also capable of resolving imperfections in aerial photography that commonly are assumed to be nonexistent. The DSMS utilizes commonly available computer hardware and software, and permits the entire shoreline mapping process to be executed rapidly by a single person in a small lab. The DSMS generates output shoreline position data that are compatible with a variety of Geographic Information Systems (GIS). A second suite of programs, the Digital Shoreline Analysis System (DSAS) has been developed to calculate shoreline rates-of-change from a series of shoreline data residing in a GIS. Four rate-of-change statistics are calculated simultaneously (end-point rate, average of rates, linear regression and jackknife) at a user-specified interval along the shoreline using a measurement baseline approach. An example of DSMS and DSAS application using historical maps and air photos of Punta Uvero, Puerto Rico provides a basis for assessing the errors associated with the source materials as well as the accuracy of computed shoreline positions and erosion rates. The maps and photos used here represent a common situation in shoreline mapping: marginal-quality source materials. The maps and photos are near the usable upper limit of scale and accuracy, yet the shoreline positions are still accurate ±9.25 m when all sources of error are considered. This level of accuracy yields a resolution of ±0.51 m/yr for shoreline rates-of-change in this example, and is sufficient to identify the short-term trend (36 years) of shoreline change in the study area.

Geologic map of Mars

USGS Publications Warehouse

Tanaka, Kenneth L.; Skinner, James A.; Dohm, James M.; Irwin, Rossman P.; Kolb, Eric J.; Fortezzo, Corey M.; Platz, Thomas; Michael, Gregory G.; Hare, Trent M.

2014-01-01

This global geologic map of Mars, which records the distribution of geologic units and landforms on the planet's surface through time, is based on unprecedented variety, quality, and quantity of remotely sensed data acquired since the Viking Orbiters. These data have provided morphologic, topographic, spectral, thermophysical, radar sounding, and other observations for integration, analysis, and interpretation in support of geologic mapping. In particular, the precise topographic mapping now available has enabled consistent morphologic portrayal of the surface for global mapping (whereas previously used visual-range image bases were less effective, because they combined morphologic and albedo information and, locally, atmospheric haze). Also, thermal infrared image bases used for this map tended to be less affected by atmospheric haze and thus are reliable for analysis of surface morphology and texture at even higher resolution than the topographic products.

Algebraic-geometry approach to integrability of birational plane mappings. Integrable birational quadratic reversible mappings. I

NASA Astrophysics Data System (ADS)

Rerikh, K. V.

1998-02-01

Using classic results of algebraic geometry for birational plane mappings in plane CP 2 we present a general approach to algebraic integrability of autonomous dynamical systems in C 2 with discrete time and systems of two autonomous functional equations for meromorphic functions in one complex variable defined by birational maps in C 2. General theorems defining the invariant curves, the dynamics of a birational mapping and a general theorem about necessary and sufficient conditions for integrability of birational plane mappings are proved on the basis of a new idea — a decomposition of the orbit set of indeterminacy points of direct maps relative to the action of the inverse mappings. A general method of generating integrable mappings and their rational integrals (invariants) I is proposed. Numerical characteristics Nk of intersections of the orbits Φn- kOi of fundamental or indeterminacy points Oi ɛ O ∩ S, of mapping Φn, where O = { O i} is the set of indeterminacy points of Φn and S is a similar set for invariant I, with the corresponding set O' ∩ S, where O' = { O' i} is the set of indeterminacy points of inverse mapping Φn-1, are introduced. Using the method proposed we obtain all nine integrable multiparameter quadratic birational reversible mappings with the zero fixed point and linear projective symmetry S = CΛC-1, Λ = diag(±1), with rational invariants generated by invariant straight lines and conics. The relations of numbers Nk with such numerical characteristics of discrete dynamical systems as the Arnold complexity and their integrability are established for the integrable mappings obtained. The Arnold complexities of integrable mappings obtained are determined. The main results are presented in Theorems 2-5, in Tables 1 and 2, and in Appendix A.

Planetary Geologic Mapping Handbook - 2010. Appendix

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Skinner, J. A., Jr.; Hare, T. M.

2010-01-01

Geologic maps present, in an historical context, fundamental syntheses of interpretations of the materials, landforms, structures, and processes that characterize planetary surfaces and shallow subsurfaces. Such maps also provide a contextual framework for summarizing and evaluating thematic research for a given region or body. In planetary exploration, for example, geologic maps are used for specialized investigations such as targeting regions of interest for data collection and for characterizing sites for landed missions. Whereas most modern terrestrial geologic maps are constructed from regional views provided by remote sensing data and supplemented in detail by field-based observations and measurements, planetary maps have been largely based on analyses of orbital photography. For planetary bodies in particular, geologic maps commonly represent a snapshot of a surface, because they are based on available information at a time when new data are still being acquired. Thus the field of planetary geologic mapping has been evolving rapidly to embrace the use of new data and modern technology and to accommodate the growing needs of planetary exploration. Planetary geologic maps have been published by the U.S. Geological Survey (USGS) since 1962. Over this time, numerous maps of several planetary bodies have been prepared at a variety of scales and projections using the best available image and topographic bases. Early geologic map bases commonly consisted of hand-mosaicked photographs or airbrushed shaded-relief views and geologic linework was manually drafted using mylar bases and ink drafting pens. Map publishing required a tedious process of scribing, color peel-coat preparation, typesetting, and photo-laboratory work. Beginning in the 1990s, inexpensive computing, display capability and user-friendly illustration software allowed maps to be drawn using digital tools rather than pen and ink, and mylar bases became obsolete. Terrestrial geologic maps published by

Vision-based mapping with cooperative robots

NASA Astrophysics Data System (ADS)

Little, James J.; Jennings, Cullen; Murray, Don

1998-10-01

Two stereo-vision-based mobile robots navigate and autonomously explore their environment safely while building occupancy grid maps of the environment. The robots maintain position estimates within a global coordinate frame using landmark recognition. This allows them to build a common map by sharing position information and stereo data. Stereo vision processing and map updates are done at 3 Hz and the robots move at speeds of 200 cm/s. Cooperative mapping is achieved through autonomous exploration of unstructured and dynamic environments. The map is constructed conservatively, so as to be useful for collision-free path planning. Each robot maintains a separate copy of a shared map, and then posts updates to the common map when it returns to observe a landmark at home base. Issues include synchronization, mutual localization, navigation, exploration, registration of maps, merging repeated views (fusion), centralized vs decentralized maps.

User Preferences in Image Map Using

NASA Astrophysics Data System (ADS)

Vondráková, A.; Vozenilek, V.

2016-06-01

In the process of map making, the attention is given to the resulting image map (to be accurate, readable, and suit the primary purpose) and its user aspects. Current cartography understands the user issues as all matters relating to user perception, map use and also user preferences. Most commercial cartographic production is strongly connected to economic circumstances. Companies are discovering user's interests and market demands. However, is it sufficient to focus just on the user's preferences? Recent research on user aspects at Palacký University Olomouc addresses a much wider scope of user aspects. The user's preferences are very often distorting - the users think that the particular image map is kind, beautiful, and useful and they wants to buy it (or use it - it depends on the form of the map production). But when the same user gets the task to use practically this particular map (such as finding the shortest way), so the user concludes that initially preferred map is useless, and uses a map, that was worse evaluated according to his preferences. It is, therefore, necessary to evaluate not only the correctness of image maps and their aesthetics but also to assess the user perception and other user issues. For the accomplishment of such testing, eye-tracking technology is a useful tool. The research analysed how users read image maps, or if they prefer image maps over traditional maps. The eye tracking experiment on the comparison of the conventional and image map reading was conducted. The map readers were asked to solve few simple tasks with either conventional or image map. The readers' choice of the map to solve the task was one of investigated aspect of user preferences. Results demonstrate that the user preferences and user needs are often quite different issues. The research outcomes show that it is crucial to implement map user testing into the cartographic production process.

Piri Reis and the Columbus Map.

ERIC Educational Resources Information Center

Lunde, Paul

1993-01-01

Discusses the origins and impact of the Piri Reis map, an early world map based on the voyages of Columbus and 20 other source maps. Maintains that evidence exists that Christopher Columbus may have drawn part of the map. Includes lengthy quotes from the map's legend written by Reis. (CFR)

USGS Map-on-Demand Printing

USGS Publications Warehouse

,

1999-01-01

Currently, the U.S. Geological Survey (USGS) uses conventional lithographic printing techniques to produce paper copies of most of its mapping products. This practice is not economical for those products that are in low demand. With the advent of newer technologies, high-speed, large-format printers have been coupled with innovative computer software to turn digital map data into a printed map. It is now possible to store and retrieve data from vast geospatial data bases and print a map on an as-needed basis; that is, print on demand, thereby eliminating the need to warehouse an inventory of paper maps for which there is low demand. Using print-on-demand technology, the USGS is implementing map-on-demand (MOD) printing for certain infrequently requested maps. By providing MOD, the USGS can offer an alternative to traditional, large-volume printing and can improve its responsiveness to customers by giving them greater access to USGS scientific data in a format that otherwise might not be available.

Handmade Multitextured Maps.

ERIC Educational Resources Information Center

Trevelyan, Simon

1984-01-01

Tactile maps for visually impaired persons can be made by drawing lines with an aqueous adhesive solution, dusting with thermoengraving powder, and exposing the card to a source of intense heat (such as a heat gun or microwave oven). A raised line map results. (CL)

Construction of a BAC library and mapping BAC clones to the linkage map of Barramundi, Lates calcarifer.

PubMed

Wang, Chun Ming; Lo, Loong Chueng; Feng, Felicia; Gong, Ping; Li, Jian; Zhu, Ze Yuan; Lin, Grace; Yue, Gen Hua

2008-03-25

Barramundi (Lates calcarifer) is an important farmed marine food fish species. Its first generation linkage map has been applied to map QTL for growth traits. To identify genes located in QTL responsible for specific traits, genomic large insert libraries are of crucial importance. We reported herein a bacterial artificial chromosome (BAC) library and the mapping of BAC clones to the linkage map. This BAC library consisted of 49,152 clones with an average insert size of 98 kb, representing 6.9-fold haploid genome coverage. Screening the library with 24 microsatellites and 15 ESTs/genes demonstrated that the library had good genome coverage. In addition, 62 novel microsatellites each isolated from 62 BAC clones were mapped onto the first generation linkage map. A total of 86 BAC clones were anchored on the linkage map with at least one BAC clone on each linkage group. We have constructed the first BAC library for L. calcarifer and mapped 86 BAC clones to the first generation linkage map. This BAC library and the improved linkage map with 302 DNA markers not only supply an indispensable tool to the integration of physical and linkage maps, the fine mapping of QTL and map based cloning genes located in QTL of commercial importance, but also contribute to comparative genomic studies and eventually whole genome sequencing.

Global transcriptional analysis of psoriatic skin and blood confirms known disease-associated pathways and highlights novel genomic "hot spots" for differentially expressed genes.

PubMed

Coda, Alvin B; Icen, Murat; Smith, Jason R; Sinha, Animesh A

2012-07-01

There are major gaps in our knowledge regarding the exact mechanisms and genetic basis of psoriasis. To investigate the pathogenesis of psoriasis, gene expression in 10 skin (5 lesional, 5 nonlesional) and 11 blood (6 psoriatic, 5 nonpsoriatic) samples were examined using Affymetrix HG-U95A microarrays. We detected 535 (425 upregulated, 110 downregulated) DEGs in lesional skin at 1% false discovery rate (FDR). Combining nine microarray studies comparing lesional and nonlesional psoriatic skin, 34.5% of dysregulated genes were overlapped in multiple studies. We further identified 20 skin and 2 blood associated transcriptional "hot spots" at specified genomic locations. At 5% FDR, 11.8% skin and 10.4% blood DEGs in our study mapped to one of the 12 PSORS loci. DEGs that overlap with PSORS loci may offer prioritized targets for downstream genetic fine mapping studies. Novel DEG "hot spots" may provide new targets for defining susceptibility loci in future studies. Copyright © 2012 Elsevier Inc. All rights reserved.

Map projections and the Internet: Chapter 4

USGS Publications Warehouse

Kessler, Fritz; Battersby, Sarah E.; Finn, Michael P.; Clarke, Keith

2017-01-01

The field of map projections can be described as mathematical, static, and challenging. However, this description is evolving in concert with the development of the Internet. The Internet has enabled new outlets for software applications, learning, and interaction with and about map projections . This chapter examines specific ways in which the Internet has moved map projections from a relatively obscure paper-based setting to a more engaging and accessible online environment. After a brief overview of map projections, this chapter discusses four perspectives on how map projections have been integrated into the Internet. First, map projections and their role in web maps and mapping services is examined. Second, an overview of online atlases and the map projections chosen for their maps is presented. Third, new programming languages and code libraries that enable map projections to be included in mapping applications are reviewed. Fourth, the Internet has facilitated map projection education and research especially with the map reader’s comprehension and understanding of complex topics like map projection distortion is discussed.

Bodily maps of emotions

PubMed Central

Nummenmaa, Lauri; Glerean, Enrico; Hari, Riitta; Hietanen, Jari K.

2014-01-01

Emotions are often felt in the body, and somatosensory feedback has been proposed to trigger conscious emotional experiences. Here we reveal maps of bodily sensations associated with different emotions using a unique topographical self-report method. In five experiments, participants (n = 701) were shown two silhouettes of bodies alongside emotional words, stories, movies, or facial expressions. They were asked to color the bodily regions whose activity they felt increasing or decreasing while viewing each stimulus. Different emotions were consistently associated with statistically separable bodily sensation maps across experiments. These maps were concordant across West European and East Asian samples. Statistical classifiers distinguished emotion-specific activation maps accurately, confirming independence of topographies across emotions. We propose that emotions are represented in the somatosensory system as culturally universal categorical somatotopic maps. Perception of these emotion-triggered bodily changes may play a key role in generating consciously felt emotions. PMID:24379370

Bodily maps of emotions.

PubMed

Nummenmaa, Lauri; Glerean, Enrico; Hari, Riitta; Hietanen, Jari K

2014-01-14

Emotions are often felt in the body, and somatosensory feedback has been proposed to trigger conscious emotional experiences. Here we reveal maps of bodily sensations associated with different emotions using a unique topographical self-report method. In five experiments, participants (n = 701) were shown two silhouettes of bodies alongside emotional words, stories, movies, or facial expressions. They were asked to color the bodily regions whose activity they felt increasing or decreasing while viewing each stimulus. Different emotions were consistently associated with statistically separable bodily sensation maps across experiments. These maps were concordant across West European and East Asian samples. Statistical classifiers distinguished emotion-specific activation maps accurately, confirming independence of topographies across emotions. We propose that emotions are represented in the somatosensory system as culturally universal categorical somatotopic maps. Perception of these emotion-triggered bodily changes may play a key role in generating consciously felt emotions.

Construction of Ultradense Linkage Maps with Lep-MAP2: Stickleback F2 Recombinant Crosses as an Example

PubMed Central

Rastas, Pasi; Calboli, Federico C. F.; Guo, Baocheng; Shikano, Takahito; Merilä, Juha

2016-01-01

High-density linkage maps are important tools for genome biology and evolutionary genetics by quantifying the extent of recombination, linkage disequilibrium, and chromosomal rearrangements across chromosomes, sexes, and populations. They provide one of the best ways to validate and refine de novo genome assemblies, with the power to identify errors in assemblies increasing with marker density. However, assembly of high-density linkage maps is still challenging due to software limitations. We describe Lep-MAP2, a software for ultradense genome-wide linkage map construction. Lep-MAP2 can handle various family structures and can account for achiasmatic meiosis to gain linkage map accuracy. Simulations show that Lep-MAP2 outperforms other available mapping software both in computational efficiency and accuracy. When applied to two large F2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (∼6 markers/cM) linkage maps containing 18,691 and 20,054 single nucleotide polymorphisms. The two maps showed a high degree of synteny, but female maps were 1.5–2 times longer than male maps in all linkage groups, suggesting genome-wide recombination suppression in males. Comparison with the genome sequence of the three-spined stickleback (Gasterosteus aculeatus) revealed a high degree of interspecific synteny with a low frequency (<5%) of interchromosomal rearrangements. However, a fairly large (ca. 10 Mb) translocation from autosome to sex chromosome was detected in both maps. These results illustrate the utility and novel features of Lep-MAP2 in assembling high-density linkage maps, and their usefulness in revealing evolutionarily interesting properties of genomes, such as strong genome-wide sex bias in recombination rates. PMID:26668116

OdorMapComparer: an application for quantitative analyses and comparisons of fMRI brain odor maps.

PubMed

Liu, Nian; Xu, Fuqiang; Miller, Perry L; Shepherd, Gordon M

2007-01-01

Brain odor maps are reconstructed flat images that describe the spatial activity patterns in the glomerular layer of the olfactory bulbs in animals exposed to different odor stimuli. We have developed a software application, OdorMapComparer, to carry out quantitative analyses and comparisons of the fMRI odor maps. This application is an open-source window program that first loads two odor map images being compared. It allows image transformations including scaling, flipping, rotating, and warping so that the two images can be appropriately aligned to each other. It performs simple subtraction, addition, and average of signals in the two images. It also provides comparative statistics including the normalized correlation (NC) and spatial correlation coefficient. Experimental studies showed that the rodent fMRI odor maps for aliphatic aldehydes displayed spatial activity patterns that are similar in gross outlines but somewhat different in specific subregions. Analyses with OdorMapComparer indicate that the similarity between odor maps decreases with increasing difference in the length of carbon chains. For example, the map of butanal is more closely related to that of pentanal (with a NC = 0.617) than to that of octanal (NC = 0.082), which is consistent with animal behavioral studies. The study also indicates that fMRI odor maps are statistically odor-specific and repeatable across both the intra- and intersubject trials. OdorMapComparer thus provides a tool for quantitative, statistical analyses and comparisons of fMRI odor maps in a fashion that is integrated with the overall odor mapping techniques.

Image processing for optical mapping.

PubMed

Ravindran, Prabu; Gupta, Aditya

2015-01-01

Optical Mapping is an established single-molecule, whole-genome analysis system, which has been used to gain a comprehensive understanding of genomic structure and to study structural variation of complex genomes. A critical component of Optical Mapping system is the image processing module, which extracts single molecule restriction maps from image datasets of immobilized, restriction digested and fluorescently stained large DNA molecules. In this review, we describe robust and efficient image processing techniques to process these massive datasets and extract accurate restriction maps in the presence of noise, ambiguity and confounding artifacts. We also highlight a few applications of the Optical Mapping system.

Maps of the United States

USGS Publications Warehouse

,

2005-01-01

The U.S. Geological Survey (USGS) sells a variety of maps of the United States. Who needs these maps? Students, land planners, politicians, teachers, marketing specialists, delivery companies, authors and illustrators, attorneys, railroad enthusiasts, travelers, Government agencies, military recruiters, newspapers, map collectors, truckers, boaters, hikers, sales representatives, communication specialists. Everybody. Users of these maps range from a corporation planning a regional expansion or a national marketing campaign, to a person who wants a decoration to hang on the wall. If you are not sure which map best meets your needs, call the Earth Science Information Center for assistance.

Constructing Maps Collaboratively.

ERIC Educational Resources Information Center

Leinhardt, Gaea; Stainton, Catherine; Bausmith, Jennifer Merriman

1998-01-01

Summarizes a study that maintains that students who work together in small groups had a better understanding of map concepts. Discusses why making maps in groups can enhance students' conceptual geographic understanding and offers suggestions for improving geography instructions using small group configurations. Includes statistical and graphic…

Soil maps as data input for soil erosion models: errors related to map scales

NASA Astrophysics Data System (ADS)

van Dijk, Paul; Sauter, Joëlle; Hofstetter, Elodie

2010-05-01

Soil erosion rates depend in many ways on soil and soil surface characteristics which vary in space and in time. To account for spatial variations of soil features, most distributed soil erosion models require data input derived from soil maps. Ideally, the level of spatial detail contained in the applied soil map should correspond to the objective of the modelling study. However, often the model user has only one soil map available which is then applied without questioning its suitability. The present study seeks to determine in how far soil map scale can be a source of error in erosion model output. The study was conducted on two different spatial scales, with for each of them a convenient soil erosion model: a) the catchment scale using the physically-based Limbourg Soil Erosion Model (LISEM), and b) the regional scale using the decision-tree expert model MESALES. The suitability of the applied soil map was evaluated with respect to an imaginary though realistic study objective for both models: the definition of erosion control measures at strategic locations at the catchment scale; the identification of target areas for the definition of control measures strategies at the regional scale. Two catchments were selected to test the sensitivity of LISEM to the spatial detail contained in soil maps: one catchment with relatively little contrast in soil texture, dominated by loess-derived soil (south of the Alsace), and one catchment with strongly contrasted soils at the limit between the Alsatian piedmont and the loess-covered hills of the Kochersberg. LISEM was run for both catchments using different soil maps ranging in scale from 1/25 000 to 1/100 000 to derive soil related input parameters. The comparison of the output differences was used to quantify the map scale impact on the quality of the model output. The sensitivity of MESALES was tested on the Haut-Rhin county for which two soil maps are available for comparison: 1/50 000 and 1/100 000. The order of

Development and evaluation of a specialized task taxonomy for spatial planning - A map literacy experiment with topographic maps

NASA Astrophysics Data System (ADS)

Rautenbach, Victoria; Coetzee, Serena; Çöltekin, Arzu

2017-05-01

Topographic maps are among the most commonly used map types, however, their complex and information-rich designs depicting natural, human-made and cultural features make them difficult to read. Regardless of their complexity, spatial planners make extensive use of topographic maps in their work. On the other hand, various studies suggest that map literacy among the development planning professionals in South Africa is not very high. The widespread use of topographic maps combined with the low levels of map literacy presents challenges for effective development planning. In this paper we address some of these challenges by developing a specialized task taxonomy based on systematically assessed map literacy levels; and conducting an empirical experiment with topographic maps to evaluate our task taxonomy. In such empirical studies if non-realistic tasks are used, the results of map literacy tests may be skewed. Furthermore, experience and familiarity with the studied map type play a role in map literacy. There is thus a need to develop map literacy tests aimed at planners specifically. We developed a taxonomy of realistic map reading tasks typically executed during the planning process. The taxonomy defines six levels tasks of increasing difficulty and complexity, ranging from recognising symbols to extracting knowledge. We hypothesized that competence in the first four levels indicates functional map literacy. In this paper, we present results from an empirical experiment with 49 map literate participants solving a subset of tasks from the first four levels of the taxonomy with a topographic map. Our findings suggest that the proposed taxonomy is a good reference for evaluating topographic map literacy. Participants solved the tasks on all four levels as expected and we therefore conclude that the experiment based on the first four levels of the taxonomy successfully determined the functional map literacy of the participants. We plan to continue the study for the

Cognitive maps and attention.

PubMed

Hardt, Oliver; Nadel, Lynn

2009-01-01

Cognitive map theory suggested that exploring an environment and attending to a stimulus should lead to its integration into an allocentric environmental representation. We here report that directed attention in the form of exploration serves to gather information needed to determine an optimal spatial strategy, given task demands and characteristics of the environment. Attended environmental features may integrate into spatial representations if they meet the requirements of the optimal spatial strategy: when learning involves a cognitive mapping strategy, cues with high codability (e.g., concrete objects) will be incorporated into a map, but cues with low codability (e.g., abstract paintings) will not. However, instructions encouraging map learning can lead to the incorporation of cues with low codability. On the other hand, if spatial learning is not map-based, abstract cues can and will be used to encode locations. Since exploration appears to determine what strategy to apply and whether or not to encode a cue, recognition memory for environmental features is independent of whether or not a cue is part of a spatial representation. In fact, when abstract cues were used in a way that was not map-based, or when they were not used for spatial navigation at all, they were nevertheless recognized as familiar. Thus, the relation between exploratory activity on the one hand and spatial strategy and memory on the other appears more complex than initially suggested by cognitive map theory.

Color on emergency mapping

NASA Astrophysics Data System (ADS)

Jiang, Lili; Qi, Qingwen; Zhang, An

2007-06-01

There are so many emergency issues in our daily life. Such as typhoons, tsunamis, earthquake, fires, floods, epidemics, etc. These emergencies made people lose their lives and their belongings. Every day, every hour, even every minute people probably face the emergency, so how to handle it and how to decrease its hurt are the matters people care most. If we can map it exactly before or after the emergencies; it will be helpful to the emergency researchers and people who live in the emergency place. So , through the emergency map, before emergency is occurring we can predict the situation, such as when and where the emergency will be happen; where people can refuge, etc. After disaster, we can also easily assess the lost, discuss the cause and make the lost less. The primary effect of mapping is offering information to the people who care about the emergency and the researcher who want to study it. Mapping allows the viewers to get a spatial sense of hazard. It can also provide the clues to study the relationship of the phenomenon in emergency. Color, as the basic element of the map, it can simplify and clarify the phenomenon. Color can also affects the general perceptibility of the map, and elicits subjective reactions to the map. It is to say, structure, readability, and the reader's psychological reactions can be affected by the use of color.

Mapping flood hazards under uncertainty through probabilistic flood inundation maps

NASA Astrophysics Data System (ADS)

Stephens, T.; Bledsoe, B. P.; Miller, A. J.; Lee, G.

2017-12-01

Changing precipitation, rapid urbanization, and population growth interact to create unprecedented challenges for flood mitigation and management. Standard methods for estimating risk from flood inundation maps generally involve simulations of floodplain hydraulics for an established regulatory discharge of specified frequency. Hydraulic model results are then geospatially mapped and depicted as a discrete boundary of flood extents and a binary representation of the probability of inundation (in or out) that is assumed constant over a project's lifetime. Consequently, existing methods utilized to define flood hazards and assess risk management are hindered by deterministic approaches that assume stationarity in a nonstationary world, failing to account for spatio-temporal variability of climate and land use as they translate to hydraulic models. This presentation outlines novel techniques for portraying flood hazards and the results of multiple flood inundation maps spanning hydroclimatic regions. Flood inundation maps generated through modeling of floodplain hydraulics are probabilistic reflecting uncertainty quantified through Monte-Carlo analyses of model inputs and parameters under current and future scenarios. The likelihood of inundation and range of variability in flood extents resulting from Monte-Carlo simulations are then compared with deterministic evaluations of flood hazards from current regulatory flood hazard maps. By facilitating alternative approaches of portraying flood hazards, the novel techniques described in this presentation can contribute to a shifting paradigm in flood management that acknowledges the inherent uncertainty in model estimates and the nonstationary behavior of land use and climate.

BowMapCL: Burrows-Wheeler Mapping on Multiple Heterogeneous Accelerators.

PubMed

Nogueira, David; Tomas, Pedro; Roma, Nuno

2016-01-01

The computational demand of exact-search procedures has pressed the exploitation of parallel processing accelerators to reduce the execution time of many applications. However, this often imposes strict restrictions in terms of the problem size and implementation efforts, mainly due to their possibly distinct architectures. To circumvent this limitation, a new exact-search alignment tool (BowMapCL) based on the Burrows-Wheeler Transform and FM-Index is presented. Contrasting to other alternatives, BowMapCL is based on a unified implementation using OpenCL, allowing the exploitation of multiple and possibly different devices (e.g., NVIDIA, AMD/ATI, and Intel GPUs/APUs). Furthermore, to efficiently exploit such heterogeneous architectures, BowMapCL incorporates several techniques to promote its performance and scalability, including multiple buffering, work-queue task-distribution, and dynamic load-balancing, together with index partitioning, bit-encoding, and sampling. When compared with state-of-the-art tools, the attained results showed that BowMapCL (using a single GPU) is 2 × to 7.5 × faster than mainstream multi-threaded CPU BWT-based aligners, like Bowtie, BWA, and SOAP2; and up to 4 × faster than the best performing state-of-the-art GPU implementations (namely, SOAP3 and HPG-BWT). When multiple and completely distinct devices are considered, BowMapCL efficiently scales the offered throughput, ensuring a convenient load-balance of the involved processing in the several distinct devices.

GIS-based realization of international standards for digital geological mapping - developments in planetary mapping

NASA Astrophysics Data System (ADS)

Nass, Andrea; van Gasselt, Stephan; Jaumann, Ralf

2010-05-01

The Helmholtz Alliance and the European Planetary Network are research communities with different main topics. One of the main research topics which are shared by these communities is the question about the geomorphological evolutions of planetary surfaces as well as the geological context of life. This research contains questions like "Is there volcanic activity on a planet?" or "Where are possible landing sites?". In order to help answering such questions, analyses of surface features and morphometric measurements need to be performed. This ultimately leads to the generation of thematic maps (e.g. geological and geomorphologic maps) as a basis for the further studies. By using modern GIS techniques the comparative work and generalisation during mapping processes results in new information. These insights are crucial for subsequent investigations. Therefore, the aim is to make these results available to the research community as a secondary data basis. In order to obtain a common and interoperable data collection results of different mapping projects have to follow a standardised data-infrastructure, metadata definition and map layout. Therefore, we are currently focussing on the generation of a database model arranging all data and processes in a uniform mapping schema. With the help of such a schema, the mapper will be able to utilise a predefined (but customisable) GIS environment with individual tool items as well as a standardised symbolisation and a metadata environment. This environment is based on a data model which is currently on a conceptual level and provides the layout of the data infrastructure including relations and topologies. One of the first tasks towards this data model is the definition of a consistent basis of symbolisation standards developed for planetary mapping. The mapper/geologist will be able to access the pre-built signatures and utilise these in scale dependence within the mapping project. The symbolisation will be related to the

Geologic map and map database of western Sonoma, northernmost Marin, and southernmost Mendocino counties, California

USGS Publications Warehouse

Blake, M.C.; Graymer, R.W.; Stamski, R.E.

2002-01-01

This digital map database, compiled from previously published and unpublished data, and new mapping by the authors, represents the general distribution of bedrock and surficial deposits in the mapped area. Together with the accompanying text file (wsomf.ps, wsomf.pdf, wsomf.txt), it provides current information on the geologic structure and stratigraphy of the area covered. The database delineates map units that are identified by general age and lithology following the stratigraphic nomenclature of the U.S. Geological Survey. The scale of the source maps limits the spatial resolution (scale) of the database to 1:62,500 or smaller.

Geothermal Maps | Geospatial Data Science | NREL

Science.gov Websites

presented in these maps was aggregated from the Geothermal Energy Association 2014 Annual U.S. and Global Geothermal Maps Geothermal Maps Our geothermal map collection covers U.S. geothermal power plants , geothermal resource potential, and geothermal power generation. If you have difficulty accessing these maps

Iconicity as structure mapping

PubMed Central

Emmorey, Karen

2014-01-01

Linguistic and psycholinguistic evidence is presented to support the use of structure-mapping theory as a framework for understanding effects of iconicity on sign language grammar and processing. The existence of structured mappings between phonological form and semantic mental representations has been shown to explain the nature of metaphor and pronominal anaphora in sign languages. With respect to processing, it is argued that psycholinguistic effects of iconicity may only be observed when the task specifically taps into such structured mappings. In addition, language acquisition effects may only be observed when the relevant cognitive abilities are in place (e.g. the ability to make structural comparisons) and when the relevant conceptual knowledge has been acquired (i.e. information key to processing the iconic mapping). Finally, it is suggested that iconicity is better understood as a structured mapping between two mental representations than as a link between linguistic form and human experience. PMID:25092669

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

PubMed

Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert; Tanyolac, Bahattin

2018-01-01

Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39). The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

Harvesting geographic features from heterogeneous raster maps

NASA Astrophysics Data System (ADS)

Chiang, Yao-Yi

2010-11-01

Raster maps offer a great deal of geospatial information and are easily accessible compared to other geospatial data. However, harvesting geographic features locked in heterogeneous raster maps to obtain the geospatial information is challenging. This is because of the varying image quality of raster maps (e.g., scanned maps with poor image quality and computer-generated maps with good image quality), the overlapping geographic features in maps, and the typical lack of metadata (e.g., map geocoordinates, map source, and original vector data). Previous work on map processing is typically limited to a specific type of map and often relies on intensive manual work. In contrast, this thesis investigates a general approach that does not rely on any prior knowledge and requires minimal user effort to process heterogeneous raster maps. This approach includes automatic and supervised techniques to process raster maps for separating individual layers of geographic features from the maps and recognizing geographic features in the separated layers (i.e., detecting road intersections, generating and vectorizing road geometry, and recognizing text labels). The automatic technique eliminates user intervention by exploiting common map properties of how road lines and text labels are drawn in raster maps. For example, the road lines are elongated linear objects and the characters are small connected-objects. The supervised technique utilizes labels of road and text areas to handle complex raster maps, or maps with poor image quality, and can process a variety of raster maps with minimal user input. The results show that the general approach can handle raster maps with varying map complexity, color usage, and image quality. By matching extracted road intersections to another geospatial dataset, we can identify the geocoordinates of a raster map and further align the raster map, separated feature layers from the map, and recognized features from the layers with the geospatial

A Watered-Down Topographic Map. Submarine Ring of Fire--Grades 6-8. Topographic and Bathymetric Maps.

ERIC Educational Resources Information Center

National Oceanic and Atmospheric Administration (DOC), Rockville, MD.

This activity is designed to teach about topographic maps and bathymetric charts. Students are expected to create a topographic map from a model landform, interpret a simple topographic map, and explain the difference between topographic and bathymetric maps. The activity provides learning objectives, a list of needed materials, key vocabulary…

Surface mineral maps of Afghanistan derived from HyMap imaging spectrometer data, version 2

USGS Publications Warehouse

Kokaly, Raymond F.; King, Trude V.V.; Hoefen, Todd M.

2013-01-01

This report presents a new version of surface mineral maps derived from HyMap imaging spectrometer data collected over Afghanistan in the fall of 2007. This report also describes the processing steps applied to the imaging spectrometer data. The 218 individual flight lines composing the Afghanistan dataset, covering more than 438,000 square kilometers, were georeferenced to a mosaic of orthorectified Landsat images. The HyMap data were converted from radiance to reflectance using a radiative transfer program in combination with ground-calibration sites and a network of cross-cutting calibration flight lines. The U.S. Geological Survey Material Identification and Characterization Algorithm (MICA) was used to generate two thematic maps of surface minerals: a map of iron-bearing minerals and other materials, which have their primary absorption features at the shorter wavelengths of the reflected solar wavelength range, and a map of carbonates, phyllosilicates, sulfates, altered minerals, and other materials, which have their primary absorption features at the longer wavelengths of the reflected solar wavelength range. In contrast to the original version, version 2 of these maps is provided at full resolution of 23-meter pixel size. The thematic maps, MICA summary images, and the material fit and depth images are distributed in digital files linked to this report, in a format readable by remote sensing software and Geographic Information Systems (GIS). The digital files can be downloaded from http://pubs.usgs.gov/ds/787/downloads/.

Metrics for comparison of crystallographic maps

DOE PAGES

Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; ...

2014-10-01

Numerical comparison of crystallographic contour maps is used extensively in structure solution and model refinement, analysis and validation. However, traditional metrics such as the map correlation coefficient (map CC, real-space CC or RSCC) sometimes contradict the results of visual assessment of the corresponding maps. This article explains such apparent contradictions and suggests new metrics and tools to compare crystallographic contour maps. The key to the new methods is rank scaling of the Fourier syntheses. The new metrics are complementary to the usual map CC and can be more helpful in map comparison, in particular when only some of their aspects,more » such as regions of high density, are of interest.« less

Probabilistic drug connectivity mapping

PubMed Central

2014-01-01

Background The aim of connectivity mapping is to match drugs using drug-treatment gene expression profiles from multiple cell lines. This can be viewed as an information retrieval task, with the goal of finding the most relevant profiles for a given query drug. We infer the relevance for retrieval by data-driven probabilistic modeling of the drug responses, resulting in probabilistic connectivity mapping, and further consider the available cell lines as different data sources. We use a special type of probabilistic model to separate what is shared and specific between the sources, in contrast to earlier connectivity mapping methods that have intentionally aggregated all available data, neglecting information about the differences between the cell lines. Results We show that the probabilistic multi-source connectivity mapping method is superior to alternatives in finding functionally and chemically similar drugs from the Connectivity Map data set. We also demonstrate that an extension of the method is capable of retrieving combinations of drugs that match different relevant parts of the query drug response profile. Conclusions The probabilistic modeling-based connectivity mapping method provides a promising alternative to earlier methods. Principled integration of data from different cell lines helps to identify relevant responses for specific drug repositioning applications. PMID:24742351

The National Map - Orthoimagery

USGS Publications Warehouse

Mauck, James; Brown, Kim; Carswell, William J.

2009-01-01

Orthorectified digital aerial photographs and satellite images of 1-meter (m) pixel resolution or finer make up the orthoimagery component of The National Map. The process of orthorectification removes feature displacements and scale variations caused by terrain relief and sensor geometry. The result is a combination of the image characteristics of an aerial photograph or satellite image and the geometric qualities of a map. These attributes allow users to: *Measure distance *Calculate areas *Determine shapes of features *Calculate directions *Determine accurate coordinates *Determine land cover and use *Perform change detection *Update maps The standard digital orthoimage is a 1-m or finer resolution, natural color or color infra-red product. Most are now produced as GeoTIFFs and accompanied by a Federal Geographic Data Committee (FGDC)-compliant metadata file. The primary source for 1-m data is the National Agriculture Imagery Program (NAIP) leaf-on imagery. The U.S. Geological Survey (USGS) utilizes NAIP imagery as the image layer on its 'Digital- Map' - a new generation of USGS topographic maps (http://nationalmap.gov/digital_map). However, many Federal, State, and local governments and organizations require finer resolutions to meet a myriad of needs. Most of these images are leaf-off, natural-color products at resolutions of 1-foot (ft) or finer.

Comparative performance of high-density oligonucleotide sequencing and dideoxynucleotide sequencing of HIV type 1 pol from clinical samples.

PubMed

Günthard, H F; Wong, J K; Ignacio, C C; Havlir, D V; Richman, D D

1998-07-01

The performance of the high-density oligonucleotide array methodology (GeneChip) in detecting drug resistance mutations in HIV-1 pol was compared with that of automated dideoxynucleotide sequencing (ABI) of clinical samples, viral stocks, and plasmid-derived NL4-3 clones. Sequences from 29 clinical samples (plasma RNA, n = 17; lymph node RNA, n = 5; lymph node DNA, n = 7) from 12 patients, from 6 viral stock RNA samples, and from 13 NL4-3 clones were generated by both methods. Editing was done independently by a different investigator for each method before comparing the sequences. In addition, NL4-3 wild type (WT) and mutants were mixed in varying concentrations and sequenced by both methods. Overall, a concordance of 99.1% was found for a total of 30,865 bases compared. The comparison of clinical samples (plasma RNA and lymph node RNA and DNA) showed a slightly lower match of base calls, 98.8% for 19,831 nucleotides compared (protease region, 99.5%, n = 8272; RT region, 98.3%, n = 11,316), than for viral stocks and NL4-3 clones (protease region, 99.8%; RT region, 99.5%). Artificial mixing experiments showed a bias toward calling wild-type bases by GeneChip. Discordant base calls are most likely due to differential detection of mixtures. The concordance between GeneChip and ABI was high and appeared dependent on the nature of the templates (directly amplified versus cloned) and the complexity of mixes.

A statistical approach for validating eSOTER and digital soil maps in front of traditional soil maps

NASA Astrophysics Data System (ADS)

Bock, Michael; Baritz, Rainer; Köthe, Rüdiger; Melms, Stephan; Günther, Susann

2015-04-01

During the European research project eSOTER, three different Digital Soil Maps (DSM) were developed for the pilot area Chemnitz 1:250,000 (FP7 eSOTER project, grant agreement nr. 211578). The core task of the project was to revise the SOTER method for the interpretation of soil and terrain data. It was one of the working hypothesis that eSOTER does not only provide terrain data with typical soil profiles, but that the new products actually perform like a conceptual soil map. The three eSOTER maps for the pilot area considerably differed in spatial representation and content of soil classes. In this study we compare the three eSOTER maps against existing reconnaissance soil maps keeping in mind that traditional soil maps have many subjective issues and intended bias regarding the overestimation and emphasize of certain features. Hence, a true validation of the proper representation of modeled soil maps is hardly possible; rather a statistical comparison between modeled and empirical approaches is possible. If eSOTER data represent conceptual soil maps, then different eSOTER, DSM and conventional maps from various sources and different regions could be harmonized towards consistent new data sets for large areas including the whole European continent. One of the eSOTER maps has been developed closely to the traditional SOTER method: terrain classification data (derived from SRTM DEM) were combined with lithology data (re-interpreted geological map); the corresponding terrain units were then extended with soil information: a very dense regional soil profile data set was used to define soil mapping units based on a statistical grouping of terrain units. The second map is a pure DSM map using continuous terrain parameters instead of terrain classification; radiospectrometric data were used to supplement parent material information from geology maps. The classification method Random Forest was used. The third approach predicts soil diagnostic properties based on

Prototype of Partial Cutting Tool of Geological Map Images Distributed by Geological Web Map Service

NASA Astrophysics Data System (ADS)

Nonogaki, S.; Nemoto, T.

2014-12-01

Geological maps and topographical maps play an important role in disaster assessment, resource management, and environmental preservation. These map information have been distributed in accordance with Web services standards such as Web Map Service (WMS) and Web Map Tile Service (WMTS) recently. In this study, a partial cutting tool of geological map images distributed by geological WMTS was implemented with Free and Open Source Software. The tool mainly consists of two functions: display function and cutting function. The former function was implemented using OpenLayers. The latter function was implemented using Geospatial Data Abstraction Library (GDAL). All other small functions were implemented by PHP and Python. As a result, this tool allows not only displaying WMTS layer on web browser but also generating a geological map image of intended area and zoom level. At this moment, available WTMS layers are limited to the ones distributed by WMTS for the Seamless Digital Geological Map of Japan. The geological map image can be saved as GeoTIFF format and WebGL format. GeoTIFF is one of the georeferenced raster formats that is available in many kinds of Geographical Information System. WebGL is useful for confirming a relationship between geology and geography in 3D. In conclusion, the partial cutting tool developed in this study would contribute to create better conditions for promoting utilization of geological information. Future work is to increase the number of available WMTS layers and the types of output file format.

National Seabed Mapping Programmes Collaborate to Advance Marine Geomorphological Mapping in Adjoining European Seas

NASA Astrophysics Data System (ADS)

Monteys, X.; Guinan, J.; Green, S.; Gafeira, J.; Dove, D.; Baeten, N. J.; Thorsnes, T.

2017-12-01

Marine geomorphological mapping is an effective means of characterising and understanding the seabed and its features with direct relevance to; offshore infrastructure placement, benthic habitat mapping, conservation & policy, marine spatial planning, fisheries management and pure research. Advancements in acoustic survey techniques and data processing methods resulting in the availability of high-resolution marine datasets e.g. multibeam echosounder bathymetry and shallow seismic mean that geological interpretations can be greatly improved by combining with geomorphological maps. Since December 2015, representatives from the national seabed mapping programmes of Norway (MAREANO), Ireland (INFOMAR) and the United Kingdom (MAREMAP) have collaborated and established the MIM geomorphology working group) with the common aim of advancing best practice for geological mapping in their adjoining sea areas in north-west Europe. A recently developed two-part classification system for Seabed Geomorphology (`Morphology' and Geomorphology') has been established as a result of an initiative led by the British Geological Survey (BGS) with contributions from the MIM group (Dove et al. 2016). To support the scheme, existing BGS GIS tools (SIGMA) have been adapted to apply this two-part classification system and here we present on the tools effectiveness in mapping geomorphological features, along with progress in harmonising the classification and feature nomenclature. Recognising that manual mapping of seabed features can be time-consuming and subjective, semi-automated approaches for mapping seabed features and improving mapping efficiency is being developed using Arc-GIS based tools. These methods recognise, spatially delineate and morphologically describe seabed features such as pockmarks (Gafeira et al., 2012) and cold-water coral mounds. Such tools utilise multibeam echosounder data or any other bathymetric dataset (e.g. 3D seismic, Geldof et al., 2014) that can produce a

Comparing the performance of various digital soil mapping approaches to map physical soil properties

NASA Astrophysics Data System (ADS)

Laborczi, Annamária; Takács, Katalin; Pásztor, László

2015-04-01

Spatial information on physical soil properties is intensely expected, in order to support environmental related and land use management decisions. One of the most widely used properties to characterize soils physically is particle size distribution (PSD), which determines soil water management and cultivability. According to their size, different particles can be categorized as clay, silt, or sand. The size intervals are defined by national or international textural classification systems. The relative percentage of sand, silt, and clay in the soil constitutes textural classes, which are also specified miscellaneously in various national and/or specialty systems. The most commonly used is the classification system of the United States Department of Agriculture (USDA). Soil texture information is essential input data in meteorological, hydrological and agricultural prediction modelling. Although Hungary has a great deal of legacy soil maps and other relevant soil information, it often occurs, that maps do not exist on a certain characteristic with the required thematic and/or spatial representation. The recent developments in digital soil mapping (DSM), however, provide wide opportunities for the elaboration of object specific soil maps (OSSM) with predefined parameters (resolution, accuracy, reliability etc.). Due to the simultaneous richness of available Hungarian legacy soil data, spatial inference methods and auxiliary environmental information, there is a high versatility of possible approaches for the compilation of a given soil map. This suggests the opportunity of optimization. For the creation of an OSSM one might intend to identify the optimum set of soil data, method and auxiliary co-variables optimized for the resources (data costs, computation requirements etc.). We started comprehensive analysis of the effects of the various DSM components on the accuracy of the output maps on pilot areas. The aim of this study is to compare and evaluate different

Mind mapping in qualitative research.

PubMed

Tattersall, Christopher; Powell, Julia; Stroud, James; Pringle, Jan

We tested a theory that mind mapping could be used as a tool in qualitative research to transcribe and analyse an interview. We compared results derived from mind mapping with those from interpretive phenomenological analysis by examining patients' and carers' perceptions of a new nurse-led service. Mind mapping could be used to rapidly analyse simple qualitative audio-recorded interviews. More research is needed to establish the extent to which mind mapping can assist qualitative researchers.

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations

PubMed Central

Ates, Duygu; Aldemir, Secil; Alsaleh, Ahmad; Erdogmus, Semih; Nemli, Seda; Kahriman, Abdullah; Ozkan, Hakan; Vandenberg, Albert

2018-01-01

Background Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. Materials and methods A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including “CDC Redberry” x “ILL7502” (LR8), “ILL8006” x “CDC Milestone” (LR11) and “PI320937” x “Eston” (LR39). Results The lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps. Conclusion This high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data. PMID:29351563

Canonical Representations of the Simple Map

NASA Astrophysics Data System (ADS)

Kerwin, Olivia; Punjabi, Alkesh; Ali, Halima; Boozer, Allen

2007-11-01

The simple map is the simplest map that has the topology of a divertor tokamak. The simple map has three canonical representations: (i) toroidal flux and poloidal angle (ψ,θ) as canonical coordinates, (ii) the physical variables (R,Z) or (X,Y) as canonical coordinates, and (iii) the action-angle (J,ζ) or magnetic variables (ψ,θ) as canonical coordinates. We give the derivation of the simple map in the (X,Y) representation. The simple map in this representation has been studied extensively (Ref. 1 and references therein). We calculate the magnetic coordinates for the simple map, construct the simple map in magnetic coordinates, and calculate generic topological effects of magnetic perturbations in divertor tokamaks using the map. We also construct the simple map in (ψ,θ) representation. Preliminary results of these studies will be presented. This work is supported by US DOE OFES DE-FG02-01ER54624 and DE-FG02-04ER54793. [1] A. Punjabi, H. Ali, T. Evans, and A. Boozer, Phys Lett A 364 140--145 (2007).

Target-specific digital soil mapping supporting terroir mapping in Tokaj Wine Region, Hungary

NASA Astrophysics Data System (ADS)

Takács, Katalin; Szabó, József; Laborczi, Annamária; Szatmári, Gábor; László, Péter; Koós, Sándor; Bakacsi, Zsófia; Pásztor, László

2016-04-01

Tokaj Wine Region - located in Northeast-Hungary, at Hegyalja, in Tokaj Mountains - is a historical region for botrityzed dessert wine making. Very recently the sustainable quality wine production in the region was targeted, which requires detailed and "terroir-based approach" characterization of viticultural land and the survey of the state of vineyards. Terroir is a homogeneous area that relates to both environmental and cultural factors, that influence the grape and wine quality. Soil plays dominant role determining the viticultural potential and terroir delineation. According to viticultural experts the most relevant soil properties are drainage, water holding capacity, soil depth and pH. Not all of these soil characteristics can be directly measured, therefore the synthesis of observed soil properties is needed to satisfy the requirements of terroir mapping. The sampling strategy was designed to be representative to the combinations of basic environmental parameters (slope, aspect and geology) which determine the main soil properties of the vineyards. Field survey was carried out in two steps. At first soil samples were collected from 200 sites to obtain a general view about the pedology of the area. In the second stage further 650 samples were collected and the sampling strategy was designed based on spatial annealing technique taking into consideration the results of the preliminary survey and the local characteristics of vineyards. The data collection regarded soil type, soil depth, parent material, rate of erosion, organic matter content and further physical and chemical soil properties which support the inference of the proper soil parameters. In the framework of the recent project 33 primary and secondary soil property, soil class and soil function maps were compiled. A set of the resulting maps supports to meet the demands of the Hungarian standard viticultural potential assessment, while the majority of the maps is intended to be applied for terroir

Active Fire Mapping Program

MedlinePlus

Active Fire Mapping Program Current Large Incidents (Home) New Large Incidents Fire Detection Maps MODIS Satellite Imagery VIIRS Satellite Imagery Fire Detection GIS Data Fire Data in Google Earth ...

Mapping the Stacks: Sustainability and User Experience of Animated Maps in Library Discovery Interfaces

ERIC Educational Resources Information Center

McMillin, Bill; Gibson, Sally; MacDonald, Jean

2016-01-01

Animated maps of the library stacks were integrated into the catalog interface at Pratt Institute and into the EBSCO Discovery Service interface at Illinois State University. The mapping feature was developed for optimal automation of the update process to enable a range of library personnel to update maps and call-number ranges. The development…

Inferring the most probable maps of underground utilities using Bayesian mapping model

NASA Astrophysics Data System (ADS)

Bilal, Muhammad; Khan, Wasiq; Muggleton, Jennifer; Rustighi, Emiliano; Jenks, Hugo; Pennock, Steve R.; Atkins, Phil R.; Cohn, Anthony

2018-03-01

Mapping the Underworld (MTU), a major initiative in the UK, is focused on addressing social, environmental and economic consequences raised from the inability to locate buried underground utilities (such as pipes and cables) by developing a multi-sensor mobile device. The aim of MTU device is to locate different types of buried assets in real time with the use of automated data processing techniques and statutory records. The statutory records, even though typically being inaccurate and incomplete, provide useful prior information on what is buried under the ground and where. However, the integration of information from multiple sensors (raw data) with these qualitative maps and their visualization is challenging and requires the implementation of robust machine learning/data fusion approaches. An approach for automated creation of revised maps was developed as a Bayesian Mapping model in this paper by integrating the knowledge extracted from sensors raw data and available statutory records. The combination of statutory records with the hypotheses from sensors was for initial estimation of what might be found underground and roughly where. The maps were (re)constructed using automated image segmentation techniques for hypotheses extraction and Bayesian classification techniques for segment-manhole connections. The model consisting of image segmentation algorithm and various Bayesian classification techniques (segment recognition and expectation maximization (EM) algorithm) provided robust performance on various simulated as well as real sites in terms of predicting linear/non-linear segments and constructing refined 2D/3D maps.

Mapping from Space - Ontology Based Map Production Using Satellite Imageries

NASA Astrophysics Data System (ADS)

Asefpour Vakilian, A.; Momeni, M.

2013-09-01

Determination of the maximum ability for feature extraction from satellite imageries based on ontology procedure using cartographic feature determination is the main objective of this research. Therefore, a special ontology has been developed to extract maximum volume of information available in different high resolution satellite imageries and compare them to the map information layers required in each specific scale due to unified specification for surveying and mapping. ontology seeks to provide an explicit and comprehensive classification of entities in all sphere of being. This study proposes a new method for automatic maximum map feature extraction and reconstruction of high resolution satellite images. For example, in order to extract building blocks to produce 1 : 5000 scale and smaller maps, the road networks located around the building blocks should be determined. Thus, a new building index has been developed based on concepts obtained from ontology. Building blocks have been extracted with completeness about 83%. Then, road networks have been extracted and reconstructed to create a uniform network with less discontinuity on it. In this case, building blocks have been extracted with proper performance and the false positive value from confusion matrix was reduced by about 7%. Results showed that vegetation cover and water features have been extracted completely (100%) and about 71% of limits have been extracted. Also, the proposed method in this article had the ability to produce a map with largest scale possible from any multi spectral high resolution satellite imagery equal to or smaller than 1 : 5000.

Mapping from Space - Ontology Based Map Production Using Satellite Imageries

NASA Astrophysics Data System (ADS)

Asefpour Vakilian, A.; Momeni, M.

2013-09-01

Determination of the maximum ability for feature extraction from satellite imageries based on ontology procedure using cartographic feature determination is the main objective of this research. Therefore, a special ontology has been developed to extract maximum volume of information available in different high resolution satellite imageries and compare them to the map information layers required in each specific scale due to unified specification for surveying and mapping. ontology seeks to provide an explicit and comprehensive classification of entities in all sphere of being. This study proposes a new method for automatic maximum map feature extraction and reconstruction of high resolution satellite images. For example, in order to extract building blocks to produce 1 : 5000 scale and smaller maps, the road networks located around the building blocks should be determined. Thus, a new building index has been developed based on concepts obtained from ontology. Building blocks have been extracted with completeness about 83 %. Then, road networks have been extracted and reconstructed to create a uniform network with less discontinuity on it. In this case, building blocks have been extracted with proper performance and the false positive value from confusion matrix was reduced by about 7 %. Results showed that vegetation cover and water features have been extracted completely (100 %) and about 71 % of limits have been extracted. Also, the proposed method in this article had the ability to produce a map with largest scale possible from any multi spectral high resolution satellite imagery equal to or smaller than 1 : 5000.

Global Geologic Map of Europa

NASA Technical Reports Server (NTRS)

Doggett, T.; Figueredo, P.; Greeley, R.; Hare, T.; Kolb, E.; Mullins, K.; Senske, D.; Tanaka, K.; Weiser, S.

2008-01-01

Europa, with its indications of a sub-ice ocean, is of keen interest to astrobiology and planetary geology. Knowledge of the global distribution and timing of Europan geologic units is a key step for the synthesis of data from the Galileo mission, and for the planning of future missions to the satellite. The first geologic map of Europa was produced at a hemisphere scale with low resolution Voyager data. Following the acquisition of higher resolution data by the Galileo mission, researchers have identified surface units and determined sequences of events in relatively small areas of Europa through geologic mapping using images at various resolutions acquired by Galileo's Solid State Imaging camera. These works provided a local to subregional perspective and employed different criteria for the determination and naming of units. Unified guidelines for the identification, mapping and naming of Europan geologic units were put forth by and employed in regional-to-hemispheric scale mapping which is now being expanded into a global geologic map. A global photomosaic of Galileo and Voyager data was used as a basemap for mapping in ArcGIS, following suggested methodology of all-stratigraphy for planetary mapping. The following units have been defined in global mapping and are listed in stratigraphic order from oldest to youngest: ridged plains material, Argadnel Regio unit, dark plains material, lineaments, disrupted plains material, lenticulated plains material and Chaos material.

Development and validation of a complementary map to enhance the existing 1998 to 2008 Abbreviated Injury Scale map

PubMed Central

2011-01-01

Introduction Many trauma registries have used the Abbreviated Injury Scale 1990 Revision Update 98 (AIS98) to classify injuries. In the current AIS version (Abbreviated Injury Scale 2005 Update 2008 - AIS08), injury classification and specificity differ substantially from AIS98, and the mapping tools provided in the AIS08 dictionary are incomplete. As a result, data from different AIS versions cannot currently be compared. The aim of this study was to develop an additional AIS98 to AIS08 mapping tool to complement the current AIS dictionary map, and then to evaluate the completed map (produced by combining these two maps) using double-coded data. The value of additional information provided by free text descriptions accompanying assigned codes was also assessed. Methods Using a modified Delphi process, a panel of expert AIS coders established plausible AIS08 equivalents for the 153 AIS98 codes which currently have no AIS08 map. A series of major trauma patients whose injuries had been double-coded in AIS98 and AIS08 was used to assess the maps; both of the AIS datasets had already been mapped to another AIS version using the AIS dictionary maps. Following application of the completed (enhanced) map with or without free text evaluation, up to six AIS codes were available for each injury. Datasets were assessed for agreement in injury severity measures, and the relative performances of the maps in accurately describing the trauma population were evaluated. Results The double-coded injuries sustained by 109 patients were used to assess the maps. For data conversion from AIS98, both the enhanced map and the enhanced map with free text description resulted in higher levels of accuracy and agreement with directly coded AIS08 data than the currently available dictionary map. Paired comparisons demonstrated significant differences between direct coding and the dictionary maps, but not with either of the enhanced maps. Conclusions The newly-developed AIS98 to AIS08

Development and validation of a complementary map to enhance the existing 1998 to 2008 Abbreviated Injury Scale map.

PubMed

Palmer, Cameron S; Franklyn, Melanie; Read-Allsopp, Christine; McLellan, Susan; Niggemeyer, Louise E

2011-05-08

Many trauma registries have used the Abbreviated Injury Scale 1990 Revision Update 98 (AIS98) to classify injuries. In the current AIS version (Abbreviated Injury Scale 2005 Update 2008 - AIS08), injury classification and specificity differ substantially from AIS98, and the mapping tools provided in the AIS08 dictionary are incomplete. As a result, data from different AIS versions cannot currently be compared. The aim of this study was to develop an additional AIS98 to AIS08 mapping tool to complement the current AIS dictionary map, and then to evaluate the completed map (produced by combining these two maps) using double-coded data. The value of additional information provided by free text descriptions accompanying assigned codes was also assessed. Using a modified Delphi process, a panel of expert AIS coders established plausible AIS08 equivalents for the 153 AIS98 codes which currently have no AIS08 map. A series of major trauma patients whose injuries had been double-coded in AIS98 and AIS08 was used to assess the maps; both of the AIS datasets had already been mapped to another AIS version using the AIS dictionary maps. Following application of the completed (enhanced) map with or without free text evaluation, up to six AIS codes were available for each injury. Datasets were assessed for agreement in injury severity measures, and the relative performances of the maps in accurately describing the trauma population were evaluated. The double-coded injuries sustained by 109 patients were used to assess the maps. For data conversion from AIS98, both the enhanced map and the enhanced map with free text description resulted in higher levels of accuracy and agreement with directly coded AIS08 data than the currently available dictionary map. Paired comparisons demonstrated significant differences between direct coding and the dictionary maps, but not with either of the enhanced maps. The newly-developed AIS98 to AIS08 complementary map enabled transformation of the

Computer-assisted map projection research

USGS Publications Warehouse

Snyder, John Parr

1985-01-01

Computers have opened up areas of map projection research which were previously too complicated to utilize, for example, using a least-squares fit to a very large number of points. One application has been in the efficient transfer of data between maps on different projections. While the transfer of moderate amounts of data is satisfactorily accomplished using the analytical map projection formulas, polynomials are more efficient for massive transfers. Suitable coefficients for the polynomials may be determined more easily for general cases using least squares instead of Taylor series. A second area of research is in the determination of a map projection fitting an unlabeled map, so that accurate data transfer can take place. The computer can test one projection after another, and include iteration where required. A third area is in the use of least squares to fit a map projection with optimum parameters to the region being mapped, so that distortion is minimized. This can be accomplished for standard conformal, equalarea, or other types of projections. Even less distortion can result if complex transformations of conformal projections are utilized. This bulletin describes several recent applications of these principles, as well as historical usage and background.

High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

PubMed Central

2012-01-01

Background Cucurbita pepo is a member of the Cucurbitaceae family, the second- most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species. The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). Results We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations. Conclusion Our results show that massive sequencing in different genotypes is an excellent tool for SNP discovery, and that the Illumina GoldenGate platform can be successfully applied to constructing genetic maps and performing QTL analysis in Cucurbita. This is the first SNP-based genetic map in the Cucurbita genus and is an invaluable new tool for biological research, especially considering that most

Integrable mappings with transcendental invariants

NASA Astrophysics Data System (ADS)

Grammaticos, B.; Ramani, A.

2007-06-01

We examine a family of integrable mappings which possess rational invariants involving polynomials of arbitrarily high degree. Next we extend these mappings to the case where their parameters are functions of the independent variable. The resulting mappings do not preserve any invariant but are solvable by linearisation. Using this result we then proceed to construct the solution of the initial autonomous mappings and use it to explicitly construct the invariant, which turns out to be transcendental in the generic case.

Pluto Color Map

NASA Image and Video Library

2017-01-20

This new, detailed global mosaic color map of Pluto is based on a series of three color filter images obtained by the Ralph/Multispectral Visual Imaging Camera aboard New Horizons during the NASA spacecraft's close flyby of Pluto in July 2015. The mosaic shows how Pluto's large-scale color patterns extend beyond the hemisphere facing New Horizons at closest approach- which were imaged at the highest resolution. North is up; Pluto's equator roughly bisects the band of dark red terrains running across the lower third of the map. Pluto's giant, informally named Sputnik Planitia glacier - the left half of Pluto's signature "heart" feature -- is at the center of this map. http://photojournal.jpl.nasa.gov/catalog/PIA11707

Iterative framework radiation hybrid mapping

USDA-ARS?s Scientific Manuscript database

Building comprehensive radiation hybrid maps for large sets of markers is a computationally expensive process, since the basic mapping problem is equivalent to the traveling salesman problem. The mapping problem is also susceptible to noise, and as a result, it is often beneficial to remove markers ...

The Map Corner.

ERIC Educational Resources Information Center

Cheyney, Arnold B.; Capone, Donald L.

This teaching resource is aimed at helping students develop the skills necessary to locate places on the earth. Designed as a collection of map skill exercises rather than a sequential program of study, this program expects that students have access to and some knowledge of how to use globes, maps, atlases, and encyclopedias. The volume contains 6…

A sugar pine consensus map: Comparative mapping between the Pinus subgenus Pinus and the subgenus Strobus

Treesearch

Kathleen D. Jermstad; Andrew J. Eckert; Bohun B. Kinloch; Dean A. Davis; Deems C. Burton; Annette D. Mix; Jill L. Wegrzyn; David B. Neale

2011-01-01

We have constructed a consensus genetic linkage map for sugar pine using three mapping populations that segregate for resistance to white pine blister rust, a disease caused by the fungal pathogen Cronartium ribicola. The major gene of resistance, Cr1, was mapped in two of the populations and included in the consensus map, which contains 400 markers organized into 19...

Mars Global Geologic Mapping: Amazonian Results

NASA Technical Reports Server (NTRS)

Tanaka, K. L.; Dohm, J. M.; Irwin, R.; Kolb, E. J.; Skinner, J. A., Jr.; Hare, T. M.

2008-01-01

We are in the second year of a five-year effort to map the geology of Mars using mainly Mars Global Surveyor, Mars Express, and Mars Odyssey imaging and altimetry datasets. Previously, we have reported on details of project management, mapping datasets (local and regional), initial and anticipated mapping approaches, and tactics of map unit delineation and description [1-2]. For example, we have seen how the multiple types and huge quantity of image data as well as more accurate and detailed altimetry data now available allow for broader and deeper geologic perspectives, based largely on improved landform perception, characterization, and analysis. Here, we describe early mapping results, which include updating of previous northern plains mapping [3], including delineation of mainly Amazonian units and regional fault mapping, as well as other advances.

US Topo—Topographic maps for the Nation

USGS Publications Warehouse

Fishburn, Kristin A.; Carswell, William J.

2017-06-23

Building on the success of 125 years of mapping, the U.S. Geological Survey created US Topo, a georeferenced digital map produced from The National Map data. US Topo maps are designed to be used like the traditional 7.5-minute quadrangle paper topographic maps for which the U.S. Geological Survey is so well known. However, in contrast to paper-based maps, US Topo maps provide modern technological advantages that support faster, wider public distribution and basic, onscreen geospatial analysis, including the georeferencing capability to display the ground coordinate location as the user moves the cursor around the map.

Venus Quadrangle Geological Mapping: Use of Geoscience Data Visualization Systems in Mapping and Training