Serum protein concentrations from clinically healthy horses determined by agarose gel electrophoresis.

PubMed

Riond, Barbara; Wenger-Riggenbach, Bettina; Hofmann-Lehmann, Regina; Lutz, Hans

2009-03-01

Serum protein electrophoresis is a useful screening test in equine laboratory medicine. The method can provide valuable information about changes in the concentrations of albumin and alpha-, beta-, and gamma-globulins and thereby help characterize dysproteinemias in equine patients. Reference values for horses using agarose gel as a support medium have not been reported. The purpose of this study was to establish reference intervals for serum protein concentrations in adult horses using agarose gel electrophoresis and to assess differences between warm-blooded and heavy draught horses. In addition, the precision of electrophoresis for determining fraction percentages and the detection limit were determined. Blood samples were obtained from 126 clinically healthy horses, including 105 Thoroughbreds and 21 heavy draught horses of both sexes and ranging from 2 to 20 years of age. The total protein concentration was determined by an automated biuret method. Serum protein electrophoresis was performed using a semi-automated agarose gel electrophoresis system. Coefficients of variation (CVs) were calculated for within-run and within-assay precision. Data from warm-blooded and draught horses were compared using the Mann-Whitney U test. Within-run and within-assay CVs were <5% for all protein fractions. No significant difference was found between warm-blooded and heavy draught horses and so combined reference intervals (2.5-97.5%) were calculated for total protein (51.0-72.0 g/L), albumin (29.6-38.5 g/L), alpha(1)-globulin (1.9-3.1 g/L), alpha(2)-globulin (5.3-8.7 g/L), beta(1)-globulin (2.8-7.3g/L), beta(2)-globulin (2.2-6.0 g/L), and gamma-globulin (5.8-12.7 g/L) concentrations, and albumin/globulin ratio (0.93-1.65). Using agarose gel as the supporting matrix for serum protein electrophoresis in horses resulted in excellent resolution and accurate results that facilitated standardization into 6 protein fractions.

Behavior of variable V3 region from 16S rDNA of lactic acid bacteria in denaturing gradient gel electrophoresis.

PubMed

Ercolini, D; Moschetti, G; Blaiotta, G; Coppola, S

2001-03-01

Separation of amplified V3 region from 16S rDNA by denaturing gradient gel electrophoresis (DGGE) was tested as a tool for differentiation of lactic acid bacteria commonly isolated from food. Variable V3 regions of 21 reference strains and 34 wild strains referred to species belonging to the genera Pediococcus, Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, Weissella, and Streptococcus were analyzed. DGGE profiles obtained were species-specific for most of the cultures tested. Moreover, it was possible to group the remaining LAB reference strains according to the migration of their 16S V3 region in the denaturing gel. The results are discussed with reference to their potential in the analysis of LAB communities in food, besides shedding light on taxonomic aspects.

Envelope protein complexes of Mycobacterium avium subsp. paratuberculosis and their antigenicity

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease, a chronic enteric disease of ruminant animals. In the present study, blue native PAGE electrophoresis and 2D SDS-PAGE were used to separate MAP envelope protein complexes, followed by mass spectrometry (MS) ...

Evaluation of clinical pathology parameters in fecal PCR-positive or PCR-negative goats for Johne's disease.

PubMed

Bonelli, Francesca; Fratini, F; Turchi, B; Cantile, C; Ebani, V V; Colombani, G; Galiero, A; Sgorbini, M

2017-10-01

Johne's disease (JD) is an economically important infectious disease of ruminants caused by Mycobacterium avium subsp. paratuberculosis (MAP). This study evaluated the differences in various hematological and biochemical parameters between healthy goats and goats with JD. Forty goats were chosen randomly from a herd endemic for JD. A complete physical examination was performed. Blood and fresh fecal samples were collected from each goat. A complete blood cell (CBC) count and a protein electrophoresis were performed. Polymerase chain reaction (PCR) on fecal samples was performed in order to divide goats into two groups: group A "positive PCR on feces"; and group B "control (negative)." A Student's t test was performed for each parameter to verify differences between groups A vs B. Twenty goats were included in each group. Clinical signs likely related to JD were found in the history of 4/40 (10%) goats, while 36/40 (90%) goats were reported to be asymptomatic. CBC and electrophoresis values were within reference intervals in both groups. No differences were found for CBC parameters between the two groups. Values for alpha 1, beta, gamma globulins, and total protein (TP) were statistically higher in group A vs those in group B, while those for albumin and albumin/globulin (A/G) ratio were lower. An increase in TP, hypoalbuminemia, and hypergammaglobulinemia has been reported in group A, while no abnormalities were found concerning CBC. JD-positive goats seem to show earlier clinical pathological alternations than clinical signs. Protein electrophoresis may help the diagnosis of JD in asymptomatic goat herds, acting as an economical screening method.

Physical mapping withing the tuberous sclerosis linkage group in region 9q32-q34

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

Harris, R.M.; Carter, N.P.; Griffiths, B.

1993-02-01

Pulsed-field gel electrophoresis and flow dot-blot analysis have been used to construct a physical map of the q32-q34 region of chromosome 9, where one of the loci responsible for tuberous sclerosis (TSC1) has been mapped by genetic linkage. Five linked groups of markers have been defined by pulsed-field gel electrophoresis. The orientation of these groups and the order of markers within them were determined by hybridization to flow-sorted dot blots derived from a panel of cell lines of chromosome 9 translocations to place probes proximal or distal to each breakpoint. The local map order 9q32-q34 derived by application of thismore » combination of techniques is as follows: centromere - ALAD-1.3 Mb-ORM/20 kb/D9S16-GSN-250 kb-C5-HXB-1.9 Mb-D9S21-AK1-1.4 Mb-SPTAN1-ASS-800-kb-ABL-2 Mb-D0S10/350 Kb/DBH-telomere. 48 refs., 6 figs., 4 figs.« less

High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing

DTIC Science & Technology

2010-10-14

High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and Massively Parallel Sequencing...Venezuelan equine encephalitis virus (VEEV) genome. We initially used a capillary electrophoresis method to gain insight into the role of the VEEV...Smith JM, Schmaljohn CS (2010) High-Resolution Functional Mapping of the Venezuelan Equine Encephalitis Virus Genome by Insertional Mutagenesis and

Comparative secretome analyses of two Trichoderma reesei RUT-C30 and CL847 hypersecretory strains

PubMed Central

Herpoël-Gimbert, Isabelle; Margeot, Antoine; Dolla, Alain; Jan, Gwénaël; Mollé, Daniel; Lignon, Sabrina; Mathis, Hughes; Sigoillot, Jean-Claude; Monot, Frédéric; Asther, Marcel

2008-01-01

Background Due to its capacity to produce large amounts of cellulases, Trichoderma reesei is increasingly been researched in various fields of white biotechnology, especially in biofuel production from lignocellulosic biomass. The commercial enzyme mixtures produced at industrial scales are not well characterized, and their proteinaceous components are poorly identified and quantified. The development of proteomic methods has made it possible to comprehensively overview the enzymes involved in lignocellulosic biomass degradation which are secreted under various environmental conditions. Results The protein composition of the secretome produced by industrial T. reesei (strain CL847) grown on a medium promoting the production of both cellulases and hemicellulases was explored using two-dimensional electrophoresis and MALDI-TOF or LC-MS/MS protein identification. A total of 22 protein species were identified. As expected, most of them are potentially involved in biomass degradation. The 2D map obtained was then used to compare the secretomes produced by CL847 and another efficient cellulolytic T. reesei strain, Rut-C30, the reference cellulase-overproducing strain using lactose as carbon source and inducer of cellulases. Conclusion This study provides the most complete mapping of the proteins secreted by T. reesei to date. We report on the first use of proteomics to compare secretome composition between two cellulase-overproducing strains Rut-C30 and CL847 grown under similar conditions. Comparison of protein patterns in both strains highlighted many unexpected differences between cellulase cocktails. The results demonstrate that 2D electrophoresis is a promising tool for studying cellulase production profiles, whether for industrial characterization of an entire secretome or for a more fundamental study on cellulase expression at genome-wide scale. PMID:19105830

Capillary electrophoresis: principles and applications in illicit drug analysis.

PubMed

Tagliaro, F; Turrina, S; Smith, F P

1996-02-09

Capillary electrophoresis, which appeared in the early 1980s, is now rapidly expanding into many scientific disciplines, including analytical chemistry, biotechnology and biomedical and pharmaceutical sciences. In capillary electrophoresis,electrokinetic separations are carried out in tiny capillaries at high voltages (10-30 kV), thus obtaining high efficiencies (N > 10(5)) and excellent mass sensitivities (down to 10(-18)-10(-20) moles). The main features of capillary electrophoresis are: versatility of application (from inorganic ions to large DNA fragments), use of different separation modes with different selectivity, extremely low demands on sample volume, negligible running costs, possibility of interfacing with different detection systems, ruggedness and simplicity of instrumentation. Capillary electrophoresis applications in forensic sciences have appeared only recently, but are now rapidly growing, particularly in forensic toxicology. The present paper briefly describes the basic principles of capillary electrophoresis, from both the instrumental and analytical points of view. Furthermore, the main applications in the analysis of illicit/controlled drugs in both illicit preparations and biological samples are presented and discussed (43 references). It is concluded that the particular separation mechanism and the high complementarity of this technique to chromatography makes capillary electrophoresis a new powerful tool of investigation in the hands of forensic toxicologists.

An Investigation of Traveling-Wave Electrophoresis using a Trigonometric Potential

NASA Astrophysics Data System (ADS)

Vopal, James

Traveling-wave electrophoresis, a technique for microfluidic separations in lab-on-achip devices, is investigated using a trigonometric model that naturally incorporates the spatial periodicity of the device. Traveling-wave electrophoresis can be used to separate high-mobility ions from low-mobility ions in forensic and medical applications, with a separation threshold that can be tuned for specific applications by simply choosing the traveling wave frequency. Our simulations predict plateaus in the average ion velocity verses the mobility, plateaus that correspond to Farey fractions and yield Devil's staircases for non-zero discreteness values. The plateaus indicate that ions with different mobilities can travel with the same average velocity. To determine the conditions for chaos, Lyapunov exponents and contact maps are employed. Through the use of contact maps, the chaotic trajectories are determined to be either narrowband or broadband. Narrowband chaotic trajectories are exhibited in the plateaus of the average velocity, while broadband chaotic trajectories are exhibited where the average velocity varies nonmonotonically with the mobility. Narrowband chaos will be investigated in future work incorporating the role of diffusion. The results of this and future work can be used to develop new tools for electrophoretic separation.

A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome

PubMed Central

2011-01-01

Background Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH). Results First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map. Conclusions The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches. PMID:22142254

Bacterial community structure analysis of sediment in the Sagami River, Japan using a rapid approach based on two-dimensional DNA gel electrophoresis mapping with selective primer pairs.

PubMed

Liu, Guo-hua; Rajendran, Narasimmalu; Amemiya, Takashi; Itoh, Kiminori

2011-11-01

A rapid approach based on two-dimensional DNA gel electrophroesis (2-DGE) mapping with selective primer pairs was employed to analyze bacterial community structure in sediments from upstream, midstream and downstream of Sagami River in Japan. The 2-DGE maps indicated that Alpha- and Delta-proteobacteria were major bacterial populations in the upstream and midstream sediments. Further bacterial community structure analysis showed that richness proportion of Alpha- and Delta-proteobacterial groups reflected a trend toward decreasing from the upstream to downstream sediments. The biomass proportion of bacterial populations in the midstream sediment showed a significantly difference from that in the other sediments, suggesting that there may be an environmental pressure on the midstream bacterial community. Lorenz curves, together with Gini coefficients were successfully applied to the 2-DGE mapping data for resolving evenness of bacterial populations, and showed that the plotted curve from high-resolution 2-DGE mapping became less linear and more an exponential function than that of the 1-DGE methods such as chain length analysis and denaturing gradient gel electrophoresis, suggesting that the 2-DGE mapping may achieve a more detailed evaluation of bacterial community. In conclusion, the 2-DGE mapping combined with the selective primer pairs enables bacterial community structure analysis in river sediment and thus it can also monitor sediment pollution based on the change of bacterial community structure.

Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots

PubMed Central

Tian, Li; Peel, Gregory J; Lei, Zhentian; Aziz, Naveed; Dai, Xinbin; He, Ji; Watson, Bonnie; Zhao, Patrick X; Sumner, Lloyd W; Dixon, Richard A

2009-01-01

Background White lupin (Lupinus albus L.) roots efficiently take up and accumulate (heavy) metals, adapt to phosphate deficiency by forming cluster roots, and secrete antimicrobial prenylated isoflavones during development. Genomic and proteomic approaches were applied to identify candidate genes and proteins involved in antimicrobial defense and (heavy) metal uptake and translocation. Results A cDNA library was constructed from roots of white lupin seedlings. Eight thousand clones were randomly sequenced and assembled into 2,455 unigenes, which were annotated based on homologous matches in the NCBInr protein database. A reference map of developing white lupin root proteins was established through 2-D gel electrophoresis and peptide mass fingerprinting. High quality peptide mass spectra were obtained for 170 proteins. Microsomal membrane proteins were separated by 1-D gel electrophoresis and identified by LC-MS/MS. A total of 74 proteins were putatively identified by the peptide mass fingerprinting and the LC-MS/MS methods. Genomic and proteomic analyses identified candidate genes and proteins encoding metal binding and/or transport proteins, transcription factors, ABC transporters and phenylpropanoid biosynthetic enzymes. Conclusion The combined EST and protein datasets will facilitate the understanding of white lupin's response to biotic and abiotic stresses and its utility for phytoremediation. The root ESTs provided 82 perfect simple sequence repeat (SSR) markers with potential utility in breeding white lupin for enhanced agronomic traits. PMID:19123941

Comparison of methods used to diagnose generalized inflammatory disease in manatees (Trichechus manatus latirostris)

USGS Publications Warehouse

Harr, K.E.; Harvey, J.W.; Bonde, R.K.; Murphy, D.; Lowe, Mark; Menchaca, M.; Haubold, E.M.; Francis-Floyd, R.

2006-01-01

Manatees (Trichechus manatus latirostris) are afflicted with inflammatory and infectious disease secondary to human interaction, such as boat strike and entanglement, as well as “cold stress syndrome” and pneumonia. White-blood-cell count and fever, primary indicators of systemic inflammation in most species, are insensitive in diagnosing inflammatory disease in manatees. Acute phase-response proteins, such as haptoglobin and serum amyloid A, have proven to be sensitive measures of inflammation/infection in domestic large animal species. This study assessed diagnosis of generalized inflammatory disease by different methods including total white-blood-cell count, albumin: globulin ratio, gel electrophoresis analysis, C-reactive protein, alpha1 acid glycoprotein, haptoglobin, fibrinogen, and serum amyloid A. Samples were collected from 71 apparently healthy and 27 diseased animals during diagnostic medical examination. Serum amyloid A, measured by ELISA, followed by albumin:globulin ratio, measured by plasma gel electrophoresis, were most sensitive in diagnosing inflammatory disease, with diagnostic sensitivity and specificity of approximately 90%. The reference interval for serum amyloid A is <10–50 μg/ml with an equivocal interval of 51–70 μg/ml. The reference interval for albumin:globulin ratio by plasma gel electrophoresis is 0.7–1.1. Albumin: globulin ratio, calculated using biochemical techniques, was not accurate due to overestimation of albumin by bromcresol green dye-binding methodology. Albumin:globulin ratio, measured by serum gel electrophoresis, has a low sensitivity of 15% due to the lack of fibrinogen in the sample. Haptoglobin, measured by hemoglobin titration, had a reference interval of 0.4–2.4 mg/ml, a diagnostic sensitivity of 60%, and a diagnostic specificity of 93%. The haptoglobin assay is significantly affected by hemolysis. Fibrinogen, measured by heat precipitation, has a reference interval of 100–400 mg/dl, a diagnostic sensitivity of 40%, and a diagnostic specificity of 95%.

Comparison of methods used to diagnose generalized inflammatory disease in manatees (Trichechus manatus latirostris).

PubMed

Harr, Kendal; Harvey, John; Bonde, Robert; Murphy, David; Lowe, Mark; Menchaca, Maya; Haubold, Elsa; Francis-Floyd, Ruth

2006-06-01

Manatees (Trichechus manatus latirostris) are afflicted with inflammatory and infectious disease secondary to human interaction, such as boat strike and entanglement, as well as "cold stress syndrome" and pneumonia. White-blood-cell count and fever, primary indicators of systemic inflammation in most species, are insensitive in diagnosing inflammatory disease in manatees. Acute phase-response proteins, such as haptoglobin and serum amyloid A, have proven to be sensitive measures of inflammation/infection in domestic large animal species. This study assessed diagnosis of generalized inflammatory disease by different methods including total white-blood-cell count, albumin: globulin ratio, gel electrophoresis analysis, C-reactive protein, alpha, acid glycoprotein, haptoglobin, fibrinogen, and serum amyloid A. Samples were collected from 71 apparently healthy and 27 diseased animals during diagnostic medical examination. Serum amyloid A, measured by ELISA, followed by albumin:globulin ratio, measured by plasma gel electrophoresis, were most sensitive in diagnosing inflammatory disease, with diagnostic sensitivity and specificity of approximately 90%. The reference interval for serum amyloid A is <10-50 microg/ml with an equivocal interval of 51-70 microg/ml. The reference interval for albumin:globulin ratio by plasma gel electrophoresis is 0.7-1.1. Albumin: globulin ratio, calculated using biochemical techniques, was not accurate due to overestimation of albumin by bromcresol green dye-binding methodology. Albumin:globulin ratio, measured by serum gel electrophoresis, has a low sensitivity of 15% due to the lack of fibrinogen in the sample. Haptoglobin, measured by hemoglobin titration, had a reference interval of 0.4-2.4 mg/ml, a diagnostic sensitivity of 60%, and a diagnostic specificity of 93%. The haptoglobin assay is significantly affected by hemolysis. Fibrinogen, measured by heat precipitation, has a reference interval of 100-400 mg/dl, a diagnostic sensitivity of 40%, and a diagnostic specificity of 95%.

Analysis of Soluble Proteins in Natural Cordyceps sinensis from Different Producing Areas by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Two-dimensional Electrophoresis

PubMed Central

Li, Chun-Hong; Zuo, Hua-Li; Zhang, Qian; Wang, Feng-Qin; Hu, Yuan-Jia; Qian, Zheng-Ming; Li, Wen-Jia; Xia, Zhi-Ning; Yang, Feng-Qing

2017-01-01

Background: As one of the bioactive components in Cordyceps sinensis (CS), proteins were rarely used as index components to study the correlation between the protein components and producing areas of natural CS. Objective: Protein components of 26 natural CS samples produced in Qinghai, Tibet, and Sichuan provinces were analyzed and compared to investigate the relationship among 26 different producing areas. Materials and Methods: Proteins from 26 different producing areas were extracted by Tris-HCl buffer with Triton X-100, and separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2-DE). Results: The SDS-PAGE results indicated that the number of protein bands and optical density curves of proteins in 26 CS samples was a bit different. However, the 2-DE results showed that the numbers and abundance of protein spots in protein profiles of 26 samples were obviously different and showed certain association with producing areas. Conclusions: Based on the expression values of matched protein spots, 26 batches of CS samples can be divided into two main categories (Tibet and Qinghai) by hierarchical cluster analysis. SUMMARY The number of protein bands and optical density curves of proteins in 26 Cordyceps sinensis samples were a bit different on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein profilesNumbers and abundance of protein spots in protein profiles of 26 samples were obvious different on two-dimensional electrophoresis mapsTwenty-six different producing areas of natural Cordyceps sinensis samples were divided into two main categories (Tibet and Qinghai) by Hierarchical cluster analysis based on the values of matched protein spots. Abbreviations Used: SDS-PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis, 2-DE: Two-dimensional electrophoresis, Cordyceps sinensis: CS, TCMs: Traditional Chinese medicines PMID:28250651

Analysis of Soluble Proteins in Natural Cordyceps sinensis from Different Producing Areas by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Two-dimensional Electrophoresis.

PubMed

Li, Chun-Hong; Zuo, Hua-Li; Zhang, Qian; Wang, Feng-Qin; Hu, Yuan-Jia; Qian, Zheng-Ming; Li, Wen-Jia; Xia, Zhi-Ning; Yang, Feng-Qing

2017-01-01

As one of the bioactive components in Cordyceps sinensis (CS), proteins were rarely used as index components to study the correlation between the protein components and producing areas of natural CS. Protein components of 26 natural CS samples produced in Qinghai, Tibet, and Sichuan provinces were analyzed and compared to investigate the relationship among 26 different producing areas. Proteins from 26 different producing areas were extracted by Tris-HCl buffer with Triton X-100, and separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2-DE). The SDS-PAGE results indicated that the number of protein bands and optical density curves of proteins in 26 CS samples was a bit different. However, the 2-DE results showed that the numbers and abundance of protein spots in protein profiles of 26 samples were obviously different and showed certain association with producing areas. Based on the expression values of matched protein spots, 26 batches of CS samples can be divided into two main categories (Tibet and Qinghai) by hierarchical cluster analysis. The number of protein bands and optical density curves of proteins in 26 Cordyceps sinensis samples were a bit different on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein profilesNumbers and abundance of protein spots in protein profiles of 26 samples were obvious different on two-dimensional electrophoresis mapsTwenty-six different producing areas of natural Cordyceps sinensis samples were divided into two main categories (Tibet and Qinghai) by Hierarchical cluster analysis based on the values of matched protein spots. Abbreviations Used : SDS-PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis, 2-DE: Two-dimensional electrophoresis, Cordyceps sinensis : CS, TCMs: Traditional Chinese medicines.

Towards a physical map of the fertility genes on the heterochromatic Y chromosome of Drosophila hydei: families of repetitive sequences transcribed on the lampbrush loops Nooses and Threads are organized in extended clusters of several hundred kilobases.

PubMed

Trapitz, P; Glätzer, K H; Bünemann, H

1992-11-01

The understanding of structure and function of the so-called fertility genes of Drosophila is very limited due to their unusual size--several megabases--and their location on the heterochromatic Y chromosome. Since mapping of these genes has mainly been done by classical cytogenetic analyses using a small number of cytologically visible lampbrush loops as the sole markers for particular fertility genes, the resolution of the genetic map of the Y chromosome is restricted to 3-5 Mb. Here we demonstrate that a substantially finer subdivision of the megabase-sized fertility genes in the subtelomeric regions of the Y chromosome of Drosophila hydei can be achieved by a combination of digestion with restriction enzymes having 6 bp recognition sequences, and pulsed field gel electrophoresis. The physical subdivision is based upon large conserved fragments of repetitive DNA in the size range from 50 up to 1600 kb and refers to the long-range organization of several families of repetitive DNA involved in Y chromosomal transcription processes in primary spermatocytes. We conclude from our results that at least five different families of repetitive DNA specifically transcribed on the lampbrush loops nooses and threads are organized as extended clusters of several hundred kb, essentially free of interspersed non-repetitive sequences.

Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique.

PubMed

Intarapanich, Apichart; Kaewkamnerd, Saowaluck; Shaw, Philip J; Ukosakit, Kittipat; Tragoonrung, Somvong; Tongsima, Sissades

2015-01-01

DNA gel electrophoresis is a molecular biology technique for separating different sizes of DNA fragments. Applications of DNA gel electrophoresis include DNA fingerprinting (genetic diagnosis), size estimation of DNA, and DNA separation for Southern blotting. Accurate interpretation of DNA banding patterns from electrophoretic images can be laborious and error prone when a large number of bands are interrogated manually. Although many bio-imaging techniques have been proposed, none of them can fully automate the typing of DNA owing to the complexities of migration patterns typically obtained. We developed an image-processing tool that automatically calls genotypes from DNA gel electrophoresis images. The image processing workflow comprises three main steps: 1) lane segmentation, 2) extraction of DNA bands and 3) band genotyping classification. The tool was originally intended to facilitate large-scale genotyping analysis of sugarcane cultivars. We tested the proposed tool on 10 gel images (433 cultivars) obtained from polyacrylamide gel electrophoresis (PAGE) of PCR amplicons for detecting intron length polymorphisms (ILP) on one locus of the sugarcanes. These gel images demonstrated many challenges in automated lane/band segmentation in image processing including lane distortion, band deformity, high degree of noise in the background, and bands that are very close together (doublets). Using the proposed bio-imaging workflow, lanes and DNA bands contained within are properly segmented, even for adjacent bands with aberrant migration that cannot be separated by conventional techniques. The software, called GELect, automatically performs genotype calling on each lane by comparing with an all-banding reference, which was created by clustering the existing bands into the non-redundant set of reference bands. The automated genotype calling results were verified by independent manual typing by molecular biologists. This work presents an automated genotyping tool from DNA gel electrophoresis images, called GELect, which was written in Java and made available through the imageJ framework. With a novel automated image processing workflow, the tool can accurately segment lanes from a gel matrix, intelligently extract distorted and even doublet bands that are difficult to identify by existing image processing tools. Consequently, genotyping from DNA gel electrophoresis can be performed automatically allowing users to efficiently conduct large scale DNA fingerprinting via DNA gel electrophoresis. The software is freely available from http://www.biotec.or.th/gi/tools/gelect.

Characterization of carbohydrates using highly fluorescent 2-aminobenzoic acid tag following gel electrophoresis of glycoproteins.

PubMed

Anumula, K R; Du, P

1999-11-15

Application of the most sensitive fluorescent label 2-aminobenzoic acid (anthranilic acid, AA) for characterization of carbohydrates from the glycoproteins ( approximately 15 pmol) separated by polyacrylamide gel electrophoresis is described. AA label is used for the determination of both monosaccharide composition and oligosaccharide map. For the monosaccharide determination, bands containing the glycoprotein of interest are excised from the polyvinylidene fluoride (PVDF) membrane blots, hydrolyzed in 20% trifluoroacetic acid, derivatized, and analyzed by C-18 reversed-phase high-performance liquid chromatography. For the oligosaccharide mapping, bands were digested with peptide N-glycosidase F (PNGase F) in order to release the N-linked oligosaccharides, derivatized, and analyzed by normal-phase anion-exchange chromatography. For convenience, the PNGase F digestion was performed in 1:100 diluted ammonium hydroxide overnight. The oligosaccharide yield from ammonium hydroxide-PNGase F digestion was better or equal to all the other reported procedures, and the presumed "oligosaccharide-amine" product formed in the reaction mixture did not interfere with labeling of the oligosaccharides under the conditions used for derivatization. Sequencing of oligosaccharides can be performed using the same mapping method following treatment with an array of glycosidases. In addition, the mapping method is useful for determining the relative and simultaneous distribution of sialic acid and fucose. Copyright 1999 Academic Press.

Physical map of the Brucella melitensis 16 M chromosome.

PubMed Central

Allardet-Servent, A; Carles-Nurit, M J; Bourg, G; Michaux, S; Ramuz, M

1991-01-01

We present the first restriction map of the Brucella melitensis 16 M chromosome obtained by Southern blot hybridization of SpeI, XhoI, and XbaI fragments separated by pulsed-field gel electrophoresis. All restriction fragments (a total of 113) were mapped into an open circle. The main difficulty in mapping involved the exceedingly high number of restriction fragments, as was expected considering the 59% G + C content of the Brucella genome. Several cloned genes were placed on this map, especially rRNA operons which are repeated three times. The size of the B. melitensis chromosome, estimated as 2,600 kb long in a previous study, appeared longer (3,130 kb) by restriction mapping. This restriction map is an initial approach to achieve a genetic map of the Brucella chromosome. Images PMID:2007548

Further characterization of Chinese Leishmania isolates by isoenzyme electrophoresis.

PubMed

Xu, Z B; Liu, Z T; Long, J Y; Chai, J J; Chen, W K

1989-09-01

Ten Chinese Leishmania isolates from different endemic areas and hosts are characterized by isoenzyme electrophoresis for 9 enzymes. Seven were isolated from visceral leishmaniasis patients, one from an infected dog, one from a sandfly and one from a naturally infected racoon dog. Eight of the 10 isolates were indistinguishable in isoenzyme profile from the L infantum reference strain. The isoenzyme profiles of the remaining two isolates (from kala azar patients in Xinjiang) could not be characterized in this study and need further research.

PLASMA PROTEIN ELECTROPHORESIS AND SELECT ACUTE PHASE PROTEINS IN HEALTHY BONNETHEAD SHARKS (SPHYRNA TIBURO) UNDER MANAGED CARE.

PubMed

Hyatt, Michael W; Field, Cara L; Clauss, Tonya M; Arheart, Kristopher L; Cray, Carolyn

2016-12-01

Preventative health care of elasmobranchs is an important but understudied field of aquatic veterinary medicine. Evaluation of inflammation through the acute phase response is a valuable tool in health assessments. To better assess the health of bonnethead sharks ( Sphyrna tiburo ) under managed care, normal reference intervals of protein electrophoresis (EPH) and the acute phase proteins, C-reactive protein (CRP) and haptoglobin (HP), were established. Blood was collected from wild caught, captive raised bonnethead sharks housed at public aquaria. Lithium heparinized plasma was either submitted fresh or stored at -80°C prior to submission. Electrophoresis identified protein fractions with migration characteristics similar to other animals with albumin, α-1 globulin, α-2 globulin, β globulin, and γ globulin. These fractions were classified as fractions 1-5 as fractional contents are unknown in this species. Commercial reagents for CRP and HP were validated for use in bonnethead sharks. Reference intervals were established using the robust method recommended by the American Society for Veterinary Clinical Pathology for the calculation of 90% reference intervals. Once established, the diagnostic and clinical applicability of these reference intervals was used to assess blood from individuals with known infectious diseases that resulted in systemic inflammation and eventual death. Unhealthy bonnethead sharks had significantly decreased fraction 2, fraction 3, and fraction 3:4 ratio and significantly increased fraction 5, CRP, and HP. These findings advance our understanding of elasmobranch acute phase inflammatory response and health and aid clinicians in the diagnosis of inflammatory disease in bonnethead sharks.

Saccharomyces cerevisiae vaginitis: transmission from yeast used in baking.

PubMed

Nyirjesy, P; Vazquez, J A; Ufberg, D D; Sobel, J D; Boikov, D A; Buckley, H R

1995-09-01

To determine whether vaginitis due to Saccharomyces cerevisiae can be caused by exposure to exogenous sources of baker's yeast. Eight women with S cerevisiae vaginitis were identified from a cohort of women referred for the evaluation of chronic vaginal symptoms. In those with high-level exposure to exogenous sources of S cerevisiae, isolates from the vagina and those sources were sent in a blinded fashion for contour-clamped homogeneous electric-field electrophoresis. Four women from a cohort of approximately 750 referred patients had high-level exposures to S cerevisiae. In one of these patients, electrophoresis analysis revealed similarities between the strains isolated from her vagina, her husband's fingers, and the yeast he used in his pizza shop. Saccharomyces cerevisiae vaginitis can be the result of the inoculation of this yeast from exogenous sources.

Microchannel-electrode alignment and separation parameters comparison in microchip capillary electrophoresis by scanning electrochemical microscopy.

PubMed

Wang, Kang; Xia, Xing-Hua

2006-03-31

The end of separation channel in a microchip was electrochemically mapped using the feedback imaging mode of scanning electrochemical microscopy (SECM). This method provides a convenient way for microchannel-electrode alignment in microchip capillary electrophoresis. Influence of electrode-to-channel positions on separation parameters in this capillary electrophoresis-electrochemical detection (CE-ED) was then investigated. For the trapezoid shaped microchannel, detection in the central area resulted in the best apparent separation efficiency and peak shape. In the electrode-to-channel distance ranging from 65 to 15mum, the limiting peak currents of dopamine increased with the decrease of the detection distance due to the limited diffusion and convection of the sample band. Results showed that radial position and axial distance of the detection electrode to microchannel was important for the improvement of separation parameters in CE amperometric detection.

Inter- and Intra-subtype genotypic differences that differentiate Mycobacterium avium subspecies paratuberculosis strains

PubMed Central

2012-01-01

Background Mycobacterium avium subspecies paratuberculosis (Map) is the aetiological agent of Johne’s disease or paratuberculosis and is included within the Mycobacterium avium complex (MAC). Map strains are of two major types often referred to as ‘Sheep’ or ‘S-type’ and ‘Cattle’ or ‘C-type’. With the advent of more discriminatory typing techniques it has been possible to further classify the S-type strains into two groups referred to as Type I and Type III. This study was undertaken to genotype a large panel of S-type small ruminant isolates from different hosts and geographical origins and to compare them with a large panel of well documented C-type isolates to assess the genetic diversity of these strain types. Methods used included Mycobacterial Interspersed Repetitive Units - Variable-Number Tandem Repeat analysis (MIRU-VNTR), analysis of Large Sequence Polymorphisms by PCR (LSP analysis), Single Nucleotide Polymorphism (SNP) analysis of gyr genes, Pulsed-Field Gel Electrophoresis (PFGE) and Restriction Fragment Length Polymorphism analysis coupled with hybridization to IS900 (IS900-RFLP) analysis. Results The presence of LSPA4 and absence of LSPA20 was confirmed in all 24 Map S-type strains analysed. SNPs within the gyr genes divided the S-type strains into types I and III. Twenty four PFGE multiplex profiles and eleven different IS900-RFLP profiles were identified among the S-type isolates, some of them not previously published. Both PFGE and IS900-RFLP segregated the S-type strains into types I and III and the results concurred with those of the gyr SNP analysis. Nine MIRU-VNTR genotypes were identified in these isolates. MIRU-VNTR analysis differentiated Map strains from other members of Mycobacterium avium Complex, and Map S-type from C-type but not type I from III. Pigmented Map isolates were found of type I or III. Conclusion This is the largest panel of S-type strains investigated to date. The S-type strains could be further divided into two subtypes, I and III by some of the typing techniques (IS900-RFLP, PFGE and SNP analysis of the gyr genes). MIRU-VNTR did not divide the strains into the subtypes I and III but did detect genetic differences between isolates within each of the subtypes. Pigmentation is not exclusively associated with type I strains. PMID:23164429

Reference intervals for acute phase protein and serum protein electrophoresis values in captive Asian elephants (Elephas maximus).

PubMed

Isaza, Ramiro; Wiedner, Ellen; Hiser, Sarah; Cray, Carolyn

2014-09-01

Acute phase protein (APP) immunoassays and serum protein electrophoresis (SPEP) are assays for evaluating the inflammatory response and have use as diagnostic tools in a variety of species. Acute phase proteins are markers of inflammation that are highly conserved across different species while SPEP separates and quantifies serum protein fractions based on their physical properties. In the current study, serum samples from 35 clinically healthy Asian elephants (Elephas maximus) were analyzed using automated assays for C-reactive protein, serum amyloid A, and haptoglobin and SPEP. Robust methods were used to generate reference intervals for the APPs: C-reactive protein (1.3-12.8 mg/l), serum amyloid A (0-47.5 mg/l), and haptoglobin (0-1.10 mg/ml). In addition, SPEP was performed on these samples to establish reference intervals for each protein fraction. A combination of APPs and SPEP measurements are valuable adjunctive diagnostic tools in elephant health care. © 2014 The Author(s).

Capillary Electrophoresis - Optical Detection Systems

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

Sepaniak, M. J.

2001-08-06

Molecular recognition systems are developed via molecular modeling and synthesis to enhance separation performance in capillary electrophoresis and optical detection methods for capillary electrophoresis. The underpinning theme of our work is the rational design and development of molecular recognition systems in chemical separations and analysis. There have been, however, some subtle and exciting shifts in our research paradigm during this period. Specifically, we have moved from mostly separations research to a good balance between separations and spectroscopic detection for separations. This shift is based on our perception that the pressing research challenges and needs in capillary electrophoresis and electrokinetic chromatographymore » relate to the persistent detection and flow rate reproducibility limitations of these techniques (see page 1 of the accompanying Renewal Application for further discussion). In most of our work molecular recognition reagents are employed to provide selectivity and enhance performance. Also, an emerging trend is the use of these reagents with specially-prepared nano-scale materials. Although not part of our DOE BES-supported work, the modeling and synthesis of new receptors has indirectly supported the development of novel microcantilevers-based MEMS for the sensing of vapor and liquid phase analytes. This fortuitous overlap is briefly covered in this report. Several of the more significant publications that have resulted from our work are appended. To facilitate brevity we refer to these publications liberally in this progress report. Reference is also made to very recent work in the Background and Preliminary Studies Section of the Renewal Application.« less

Bioanalysis: its past, present, and some future.

PubMed

Righetti, Pier Giorgio

2004-07-01

An overview of about 100 years of bioanalysis is here disastrously attempted. The beginning of rigorous analytical systems can perhaps be traced back to the building and testing of the analytical ultracentrifuge by Svedberg and the apparatus for moving-boundary electrophoresis of Tiselius, both systems relying on expensive and hard to operate machines. In the sixties, Porath discovered porous beads for the determination of relative molecular mass (Mr) of proteins, based on the principle of molecular sieving. Concomitantly, Svensson and his pupil Vesterberg described a revolutionary principle for fractionating proteins in a nonisocratic environment, based on generation of stable pH gradients in an electric field, a technique that went down to history as isoelectric focusing (IEF). Polyacrylamide gel electrophoresis (PAGE), with the brilliant idea of discontinuous buffers, was brought to the limelight and in 1967, sodium dodecyl sulfate (SDS)-PAGE was described, permitting easy assessment of protein purity and reasonable measurements of Mr values of denatured polypeptide chains. By the mid seventies, another explosive concept was realized: orthogonal combination of two unrelated techniques, based on surface charge and mass fractionation, namely, two-dimensional (2-D) PAGE already in the very first papers by O'Farrell elaborated to its utmost sophistication. The eighties saw the systematic growth of 2-D PAGE, accompanied by systematic efforts to develop instrumentation for large-scale production of 2-D maps and computer evaluation for 2-D map analysis, based on the sophisticated algorithms adopted by astronomers for mapping stars in the sky. Another fundamental innovation in the field of IEF was the discovery of immobilized pH gradients (IPGs) that brought the much needed reproducibility in 2-D maps while allowing exquisite resolution in very narrow pH ranges. The nineties were definitely the decade of capillary zone electrophoresis, with the concomitant concept of automation and miniaturization in electrokinetic methodologies. Also 2-D map analysis witnessed a big revival, thanks to the adoption of IPGs for the first dimension. The enormous progress of mass spectrometry resulted in first reports on the analysis of macromolecules and the building of data bases on gene and protein banks. The third millennium is, perhaps, exasperating the concept of miniaturization at all costs, while not disdaining increasingly larger maps for 2-D analysis of complex protein mixtures.

Proteome profiling and functional classification of intracellular proteins from conidia of the human-pathogenic mold Aspergillus fumigatus.

PubMed

Teutschbein, Janka; Albrecht, Daniela; Pötsch, Maria; Guthke, Reinhard; Aimanianda, Vishukumar; Clavaud, Cécile; Latgé, Jean-Paul; Brakhage, Axel A; Kniemeyer, Olaf

2010-07-02

Aspergillus fumigatus is a ubiquitously distributed filamentous fungus that has emerged as one of the most serious life-threatening pathogens in immunocompromised patients. The mechanisms for its pathogenicity are poorly understood. Here, we analyzed the proteome of dormant A. fumigatus conidia as the fungal entity having the initial contact with the host. Applying two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), we established a 2-D reference map of conidial proteins. By MALDI-TOF mass spectrometry, we identified a total number of 449 different proteins. We show that 57 proteins of our map are over-represented in resting conidia compared to mycelium. Enzymes involved in reactive oxygen intermediates (ROI) detoxification, pigment biosynthesis, and conidial rodlet layer formation were highly abundant in A. fumigatus spores and most probably account for their enormous stress resistance. Interestingly, pyruvate decarboxylase and alcohol dehydrogenase were detectable in dormant conidia, suggesting that alcoholic fermentation plays a role during dormancy or early germination. Moreover, we show that enzymes for rapid reactivation of protein biosynthesis and metabolic processes are preserved in resting conidia, which therefore feature the potential to immediately respond to an environmental stimulus by germination. The generated data lay the foundations for further proteomic analyses and a better understanding of fungal pathogenesis.

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh].

PubMed

Dutta, Sutapa; Kumawat, Giriraj; Singh, Bikram P; Gupta, Deepak K; Singh, Sangeeta; Dogra, Vivek; Gaikwad, Kishor; Sharma, Tilak R; Raje, Ranjeet S; Bandhopadhya, Tapas K; Datta, Subhojit; Singh, Mahendra N; Bashasab, Fakrudin; Kulwal, Pawan; Wanjari, K B; K Varshney, Rajeev; Cook, Douglas R; Singh, Nagendra K

2011-01-20

Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥ 18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh

PubMed Central

2011-01-01

Background Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. Results In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. Conclusion We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea. PMID:21251263

Evaluation of in-channel amperometric detection using a dual-channel microchip electrophoresis device and a two-electrode potentiostat for reverse polarity separations

PubMed Central

Meneses, Diogenes; Gunasekara, Dulan B.; Pichetsurnthorn, Pann; da Silva, José A. F.; de Abreu, Fabiane C.; Lunte, Susan M.

2015-01-01

In-channel amperometric detection combined with dual-channel microchip electrophoresis is evaluated using a two-electrode isolated potentiostat for reverse polarity separations. The device consists of two separate channels with the working and reference electrodes placed at identical positions relative to the end of the channel, enabling noise subtraction. In previous reports of this configuration, normal polarity and a three-electrode detection system were used. In the two-electrode detection system described here, the electrode in the reference channel acts as both the counter and reference. The effect of electrode placement in the channels on noise and detector response was investigated using nitrite, tyrosine, and hydrogen peroxide as model compounds. The effects of electrode material and size and type of reference electrode on noise and the potential shift of hydrodynamic voltammograms for the model compounds were determined. In addition, the performance of two- and three-electrode configurations using Pt and Ag/AgCl reference electrodes was compared. Although the signal was attenuated with the Pt reference, the noise was also significantly reduced. It was found that lower LOD were obtained for all three compounds with the dual-channel configuration compared to single-channel, in-channel detection. The dual-channel method was then used for the detection of nitrite in a dermal microdialysis sample obtained from a sheep following nitroglycerin administration. PMID:25256669

Using Restriction Mapping to Teach Basic Skills in the Molecular Biology Lab

ERIC Educational Resources Information Center

Walsh, Lauren; Shaker, Elizabeth; De Stasio, Elizabeth A.

2007-01-01

Digestion of DNA with restriction enzymes, calculation of volumes and concentrations of reagents for reactions, and the separation of DNA fragments by agarose gel electrophoresis are common molecular biology techniques that are best taught through repetition. The following open-ended, investigative laboratory exercise in plasmid restriction…

UW Team Reaches Out to Grade- and High-School Students.

ERIC Educational Resources Information Center

Hood, Leroy

1994-01-01

Describes an outreach program designed to expose high school students to cutting-edge science. High school students are provided with hands-on experience in molecular biology (polymerase chain reaction, restriction mapping, chromatography, gel electrophoresis, human DNA sequencing, etc.) and may have an opportunity to participate in the Human…

Mathematical biodescriptors of proteomics maps: background and applications.

PubMed

Basak, Subhash C; Gute, Brian D

2008-05-01

This article reviews recent developments in the formulation and application of biodescriptors to characterize proteomics maps. Such biodescriptors can be derived by applying techniques from discrete mathematics (graph theory, linear algebra and information theory). This review focuses on the development of biodescriptors for proteomics maps derived from 2D gel electrophoresis. Preliminary results demonstrated that such descriptors have a reasonable ability to differentiate between proteomics patterns that result from exposure to closely related individual chemicals and complex mixtures, such as the jet fuel JP-8. Further research is required to evaluate the utility of these proteomics-based biodescriptors for drug discovery and predictive toxicology.

Imaging of Selenium by Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in 2-D Electrophoresis Gels and Biological Tissues.

PubMed

Cruz, Elisa Castañeda Santa; Susanne Becker, J; Sabine Becker, J; Sussulini, Alessandra

2018-01-01

Selenium and selenoproteins are important components of living organisms that play a role in different biological processes. Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) is a powerful analytical technique that has been employed to obtain distribution maps of selenium in biological tissues in a direct manner, as well as in selenoproteins, previously separated by their molecular masses and isoelectric points using two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). In this chapter, we present the protocols to perform LA-ICP-MS imaging experiments, allowing the distribution visualization and determination of selenium and/or selenoproteins in biological systems.

Analysis of bacterial populations in the environment using two-dimensional gel electrophoresis of genomic DNA and complementary DNA.

PubMed

Liu, Guo-Hua; Nakamura, Tatsuo; Amemiya, Takashi; Rajendran, Narasimmalu; Itoh, Kiminori

2011-01-01

Two-dimensional gel electrophoresis (2-DGE) mapping of genomic DNA and complementary DNA (cDNA) amplicons was attempted to analyze total and active bacterial populations within soil and activated sludge samples. Distinct differences in the number and species of bacterial populations and those that were metabolically active at the time of sampling were visually observed especially for the soil community. Statistical analyses and sequencing based on the 2-DGE data further revealed the relationships between total and active bacterial populations within each community. This high-resolution technique would be useful for obtaining a better understanding of bacterial population structures in the environment.

Changes induced by the Pepper mild mottle tobamovirus on the chloroplast proteome of Nicotiana benthamiana.

PubMed

Pineda, M; Sajnani, C; Barón, M

2010-01-01

We have analyzed the chloroplast proteome of Nicotiana benthamiana using two-dimensional gel electrophoresis and mass spectrometry followed by a database search. In order to improve the resolution of the two-dimensional electrophoresis gels, we have made separate maps for the low and the high pH range. At least 200 spots were detected. We identified 72 polypeptides, some being isoforms of different multiprotein families. In addition, changes in this chloroplast proteome induced by the infection with the Spanish strain of the Pepper mild mottle virus were investigated. Viral infection induced the down-regulation of several chloroplastidic proteins involved in both the photosynthetic electron-transport chain and the Benson-Calvin cycle.

Analytical characterization of recombinant hCG and comparative studies with reference product.

PubMed

Thennati, Rajamannar; Singh, Sanjay Kumar; Nage, Nitin; Patel, Yena; Bose, Sandip Kumar; Burade, Vinod; Ranbhor, Ranjit Sudhakar

2018-01-01

Regulatory agencies recommend a stepwise approach for demonstrating biosimilarity between a proposed biosimilar and reference biological product emphasizing for functional and structural characterization to trace if there is any difference which may impact safety and efficacy. We studied the comparative structural and biological attributes of recombinant human chorionic gonadotropin (rhCG), SB005, with reference product, Ovidrel ® and Ovitrelle ® . Recombiant hCG was approved in 2000 by the US Food and Drug Administration for the induction of final follicular maturation, early luteinization in infertile women as part of assisted reproductive technology program. It is also indicated for the induction of ovulation and pregnancy in ovulatory infertile patients whose cause of infertility is not due to ovarian failure. Primary structure was studied by intact mass analysis, peptide fingerprinting, peptide mass fingerprinting and sequence coverage analysis. Higher order structure was studied by circular dichroism, ultraviolet-visible spectroscopy, fluorescence spectroscopy, and disulfide bridge analysis. Different isoforms of reference product and SB005 were identified using capillary isoelectric focusing and capillary zone electrophoresis. Glycosylation was studied by N-glycan mapping using LC-ESI-MS, point of glycosylation, released glycan analysis using ultra performance liquid chromatography and sialic acid analysis. Product related impurities such as oligomer content analysis and oxidized impurities were studied using size exclusion chromatography and reverse phase high performance liquid chromatography, respectively. Biological activity in term of potency of reference product and SB005 was studied by in vivo analysis. In this study we have compared analytical similarity of recombinant rhCG (SB005) produced at Sun Pharmaceuticals with the reference product with respect to its primary, higher order structure, isoforms, charge variants, glycosylation, sialyation pattern, pharmacodynamic and in vivo efficacy. Our studies show that the in house produced rhCG has a high degree of structural and functional similarity with the reference product available in the market.

Analytical characterization of recombinant hCG and comparative studies with reference product

PubMed Central

Thennati, Rajamannar; Singh, Sanjay Kumar; Nage, Nitin; Patel, Yena; Bose, Sandip Kumar; Burade, Vinod

2018-01-01

Introduction Regulatory agencies recommend a stepwise approach for demonstrating biosimilarity between a proposed biosimilar and reference biological product emphasizing for functional and structural characterization to trace if there is any difference which may impact safety and efficacy. We studied the comparative structural and biological attributes of recombinant human chorionic gonadotropin (rhCG), SB005, with reference product, Ovidrel® and Ovitrelle®. Recombiant hCG was approved in 2000 by the US Food and Drug Administration for the induction of final follicular maturation, early luteinization in infertile women as part of assisted reproductive technology program. It is also indicated for the induction of ovulation and pregnancy in ovulatory infertile patients whose cause of infertility is not due to ovarian failure. Materials and methods Primary structure was studied by intact mass analysis, peptide fingerprinting, peptide mass fingerprinting and sequence coverage analysis. Higher order structure was studied by circular dichroism, ultraviolet-visible spectroscopy, fluorescence spectroscopy, and disulfide bridge analysis. Different isoforms of reference product and SB005 were identified using capillary isoelectric focusing and capillary zone electrophoresis. Glycosylation was studied by N-glycan mapping using LC-ESI-MS, point of glycosylation, released glycan analysis using ultra performance liquid chromatography and sialic acid analysis. Product related impurities such as oligomer content analysis and oxidized impurities were studied using size exclusion chromatography and reverse phase high performance liquid chromatography, respectively. Biological activity in term of potency of reference product and SB005 was studied by in vivo analysis. Results and Conclusion In this study we have compared analytical similarity of recombinant rhCG (SB005) produced at Sun Pharmaceuticals with the reference product with respect to its primary, higher order structure, isoforms, charge variants, glycosylation, sialyation pattern, pharmacodynamic and in vivo efficacy. Our studies show that the in house produced rhCG has a high degree of structural and functional similarity with the reference product available in the market. PMID:29430170

Electrophoretic Mobility Shift Assay (EMSA) for Detecting Protein-Nucleic Acid Interactions

PubMed Central

Hellman, Lance M.; Fried, Michael G.

2009-01-01

The gel electrophoresis mobility shift assay (EMSA) is used to detect protein complexes with nucleic acids. It is the core technology underlying a wide range of qualitative and quantitative analyses for the characterization of interacting systems. In the classical assay, solutions of protein and nucleic acid are combined and the resulting mixtures are subjected to electrophoresis under native conditions through polyacrylamide or agarose gel. After electrophoresis, the distribution of species containing nucleic acid is determined, usually by autoradiography of 32P-labeled nucleic acid. In general, protein-nucleic acid complexes migrate more slowly than the corresponding free nucleic acid. In this article, we identify the most important factors that determine the stabilities and electrophoretic mobilities of complexes under assay conditions. A representative protocol is provided and commonly used variants are discussed. Expected outcomes are briefly described. References to extensions of the method and a troubleshooting guide are provided. PMID:17703195

Markers and mapping revisited: finding your gene.

PubMed

Jones, Neil; Ougham, Helen; Thomas, Howard; Pasakinskiene, Izolda

2009-01-01

This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of this highly dynamic arena of plant science.

Adult amphibian epidermal proteins: biochemical characterization and developmental appearance.

PubMed

Reeves, O R

1975-08-01

The keratin-like proteins (KLPs) from the epidermis of adult frogs of the species Xenopus laevis have been isolated and biochemically characterized by means of polyacrylamide gel electrophoresis, amino acid analysis, tryptic peptide mapping, amino-terminal end-group analysis and isoelectric focusing. One particular protein fraction of rather unusual amino acid composition found only in epidermal tissue was isolated in quantity by preparative gel electrophoresis and monospecific antibodies prepared against it. Using this anti-KLP antibody preparation it was possible to show that at least one kine of keratin-like protein characteristic of the adult epidermis first appears within the larval epidermis during metamorphosis. This is the first reported biochemical characterization of a tissue-specific protien from adult amphibian skin.

Improvement of the solubilization of proteins in two-dimensional electrophoresis with immobilized pH gradients

PubMed Central

Rabilloud, Thierry; Adessi, C.; Giraudel, A.; Lunardi, J.

2007-01-01

Summary We have carried out the separation of sparingly-soluble (membrane and nuclear) proteins by high resolution two-dimensional electrophoresis. IEF with immobilized pH gradients leads to severe quantitative losses of proteins in the resulting 2-D map, although the resolution is usually kept high. We therefore tried to improve the solubility of proteins in this technique, by using denaturing cocktails containing various detergents and chaotropes. Best results were obtained by using a denaturing solution containing urea, thiourea, and detergents (both nonionic and zwitterionic). The usefulness of thiourea-containing denaturing mixtures are shown in this article on several models including microsomal and nuclear proteins and on tubulin, a protein highly prone to aggregation. PMID:9150907

Mono-PEGylation of Alpha-MMC and MAP30 from Momordica charantia L.: Production, Identification and Anti-Tumor Activity.

PubMed

Sun, Yun; Sun, Fenghui; Li, Jianlong; Wu, Minlu; Fan, Xiang; Meng, Yanfa; Meng, Yao

2016-10-31

PEGylation is a well-established and effective strategy to decrease immunogenicity, which can increase the stability and in vivo half-life time. However, the generation of multi-site modified products is inevitable due to the lysine chemistry, which will bring difficulties in subsequent research, such as purification and quantification. Site-specific modification by mPEG-succinimidyl carbonate (mPEG-SC) is a widely used method for N -terminal conjugation. In this study, we used it for site-directed modification on two ribosome-inactivating proteins (RIPs), alpha-momorcharin (α-MMC) and momordica anti-HIV protein (MAP30), from Momordica charantia L. According to the optimization of previous modification conditions, we compared Macro-Cap SP with SP-Sepharose FF chromatography for separating the final mPEGylated RIPs. Two kinds of methods both can obtain homogenous mPEGylated RIPs which were identified by sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE), isoelectric focusing electrophoresis (IEF), and matrix-assisted laser desorption ionization-time of flight/time of flight (MALDI-TOF/TOF) analysis. We also used iodine staining method to detect the amount of unmodified PEG. Furthermore, the inhibition activity of both mPEGylated and non-PEGylated RIPs against human lung adenocarcinoma epithelial A549 cells was detected. All of the results suggested that the mPEGylated α-MMC/MAP30 might be potentially developed as new anti-tumor drugs.

Development of SSR markers from Citrus clementina (Rutaceae) BAC end sequences and interspecific transferability in Citrus.

PubMed

Ollitrault, Frédérique; Terol, Javier; Pina, Jose Antonio; Navarro, Luis; Talon, Manuel; Ollitrault, Patrick

2010-11-01

Microsatellite primers were developed from bacterial artificial chromosome (BAC) end sequences of Citrus clementina and their transferability and polymorphism tested in the genus Citrus for future anchorage of physical and genetic maps and comparative interspecific genetic mapping. • Using PAGE and DNA silver staining, 79 primer pairs were selected for their transferability and polymorphism among 526 microsatellites mined in BES. A preliminary diversity study in Citrus was conducted with 18 of them, in C. reticulata, C. maxima, C. medica, C. sinensis, C. aurantium, C. paradisi, C. lemon, C. aurantifolia, and some papedas (wild citrus), using a capillary electrophoresis fragment analyzer. Intra- and interspecific polymorphism was observed, and heterozygous markers were identified for the different genotypes to be used for genetic mapping. • These results indicate the utility of the developed primers for comparative mapping studies and the integration of physical and genetic maps.

Systems and methods that generate height map models for efficient three dimensional reconstruction from depth information

DOEpatents

Frahm, Jan-Michael; Pollefeys, Marc Andre Leon; Gallup, David Robert

2015-12-08

Methods of generating a three dimensional representation of an object in a reference plane from a depth map including distances from a reference point to pixels in an image of the object taken from a reference point. Weights are assigned to respective voxels in a three dimensional grid along rays extending from the reference point through the pixels in the image based on the distances in the depth map from the reference point to the respective pixels, and a height map including an array of height values in the reference plane is formed based on the assigned weights. An n-layer height map may be constructed by generating a probabilistic occupancy grid for the voxels and forming an n-dimensional height map comprising an array of layer height values in the reference plane based on the probabilistic occupancy grid.

Harnessing Next-Generation Sequencing Capabilities for Microbial Forensics

DTIC Science & Technology

2014-07-15

content typing, rep-PCR, pulsed-field gel electrophoresis, optical mapping, and antimicrobial susceptibility testing (G. Gault et al., 2011; P...Tremlett, G, Pidd, 2011). This case demonstrates the vulnerability of our food supply and why unusual outbreaks involving endemic microbes must be taken as... food products to malevolent tampering, and the widespread international economic consequences that can occur even from limited product contamination

Erythrocyte membrane protein analysis by sodium dodecyl sulphate-capillary gel electrophoresis in the diagnosis of hereditary spherocytosis.

PubMed

Debaugnies, France; Cotton, Frédéric; Boutique, Charles; Gulbis, Béatrice

2011-03-01

Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) is currently the reference method for detecting protein deficiencies related to hereditary spherocytosis. The aim of the study was to evaluate an automated capillary gel electrophoresis system, the Experion instrument from BioRad, for its ability to separate and quantify the erythrocyte membrane proteins. The major erythrocyte membrane proteins (actin, protein 4.2, protein 4.1, band 3, ankyrin, α- and β-spectrin) were extracted and purified from membrane ghosts by centrifugation, immunoprecipitation and electroelution. Analyses were performed using SDS-PAGE and sodium dodecyl sulphate capillary gel electrophoresis (SDS-CGE) to establish a separation profile of the total ghosts. Then, the samples from patients received for investigations of erythrocyte membrane defects were analysed. Five of the seven expected erythrocyte membrane proteins were finally separated and identified. In the 20 studied cases, taking into account the screening test results and the clinical and family histories, the SDS-CGE method allowed us to achieve the same conclusion as with SDS-PAGE, except for the patient with elliptocytosis. The new SDS-CGE method presents interesting features that could make this instrument a powerful diagnostic tool for detection of erythrocyte membrane protein abnormalities, and can be proposed as an automated alternative method to the labour intensive SDS-PAGE analysis.

Attempt to run urinary protein electrophoresis using capillary technique.

PubMed

Falcone, Michele

2014-10-01

The study of urinary protein has a predominant place in the diagnosis of kidney disease. The most common technique is agarose gel electrophoresis (AGE). For several years, the technique of choice applied to the analysis of serum proteins has been CE, a system that uses capillary fused silica, subjected to high voltage to separate and measure serum proteins. The purpose of this paper was to perform capillary electrophoresis on urinary proteins which, at present, are not interpretable due to the many nonspecific peaks visible when using gel electrophoresis. In order to carry out our research, we used a capillary V8 analyzer together with an agarose gel system from the same company. AGE was taken as the reference method, for which urine was used without any pretreatment. For the V8 system, urine was subjected to purification on granular-activated carbon and then inserted into the V8 analyzer, selecting a program suitable for liquids with low protein content. We examined 19 urine samples collected over 24 hrs from both hospitalized and external patients with different types of proteinuria plus a serum diluted 1/61 considered as a control to recognize the bands. Both methods showed the same protein fractions and classified the proteinuria in a similar way. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomic analysis of amphiphilic proteins of hexaploid wheat kernels.

PubMed

Amiour, Nardjis; Merlino, Marielle; Leroy, Philippe; Branlard, Gérard

2002-06-01

Wheat proteins and specially gluten proteins have been well studied and are closely associated with baking products. Amphiphilic proteins (proteins that are soluble using nonionic detergent Triton X-114 ) also play an important role in wheat quality. Some of them, like puroindolines, are lipid binding proteins, and are strongly linked to dough foaming properties and to fine crumb texture. However many amphiphilic proteins are still unknown and both their physiological and technological functions remain to be analysed. In order to explore these proteins, proteomic analysis was carried out using 81 F9 lines, progeny obtained from an interspecific cross "W7984"x"Opata", and already used to built a map of more than 2000 molecular markers (International Triticeae Mapping Initiative, ITMImap). Two-dimensional electrophoresis (immobilized pH gradient (pH 6-11)x sodium dodecyl sulfate-polyacrylamide gel electrophoresis) was performed on amphiphilic proteins with three to five replicates for each line. Silver stained gels were analysed using Melanie 3 software. Genetic determinism was carried out on 170 spots segregating between the two parental hexaploïd wheats. Many of these spots were mapped on different chromosomes of the ITMImap. Spots of interest were identified using matrix-assisted laser desorption/ionization-time of flight and some of them were partly sequenced using electrospray ionization-tandem mass spectrometry. This proteomic approach provided some very useful information about some proteic components linked to bread wheat quality and particularly to kernel hardness.

Diagnostic reference range of κ/λ free light chain ratio to screen for Bence Jones proteinuria is not significantly influenced by GFR.

PubMed

Schmidt-Hieltjes, Yvonne; Elshof, Clemens; Roovers, Lian; Ruinemans-Koerts, Janneke

2016-05-01

The aim of our study was to analyse whether the κ/λ free light chain ratio reference range for screening for Bence Jones proteinuria should be dependent on the estimated glomerular filtration rate (eGFR). The serum κ/λ free light chain ratio, eGFR, serum M-protein and Bence Jones protein were measured in 544 patients for whom Bence Jones protein analysis was ordered. In the population of patients without Bence Jones proteinuria or a M-protein (n = 402), there is no gradual increase in κ/λ free light chain ratio with diminishing eGFR. The κ/λ free light chain ratio in this group was 0.56-1.86 (95% interval). With this diagnostic reference range of the κ/λ ratio, 105 of the 110 patients with Bence Jones protein could be identified correctly. Only five patients with Bence Jones proteinuria (<0.17 g/L) were missed, without diagnostic or therapeutic consequences. In 36 patients (6.6%), an abnormal κ/λ free light chain ratio was measured without the presence of Bence Jones proteinuria. A κ/λ free light chain ratio in serum can be used safely and efficiently to select urine samples which should be analysed for Bence Jones proteinuria with an electrophoresis/immunofixation technique. Using this diagnostic reference range, the number of urine samples which should be analysed by electrophoresis/immunofixation could be reduced by 74%. The diagnostic reference interval can be determined best in a group of patients for whom Bence Jones analysis is indicated. For calculation of this reference range, the eGFR value does not need to be taken into account. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Characterization of polysaccharides from Ganoderma spp. using saccharide mapping.

PubMed

Wu, Ding-Tao; Xie, Jing; Hu, De-Jun; Zhao, Jing; Li, Shao-Ping

2013-09-12

Polysaccharides from Ganoderma spp. and their adulterants were firstly investigated and compared using saccharide mapping, enzymatic (endo-1,3-β-D-glucanase and pectinase) digestion followed by polysaccharide analysis using carbohydrate gel electrophoresis analysis. The results showed that both 1,3-β-D-glucosidic and 1,4-α-D-galactosiduronic linkages were existed in Lingzhi (Ganoderma lucidum and Ganoderma sinense), and the similarity of polysaccharides from G. lucidum and G. sinense was high, which may contribute to rational use of Lingzhi. Different species of Ganoderma and their adulterants can be differentiated based on the saccharide mapping, which is helpful to well understand the structural characters of polysaccharides from different species of Ganoderma and to improve the quality control of polysaccharides in Lingzhi. Copyright © 2013 Elsevier Ltd. All rights reserved.

Global analysis of the Brucella melitensis proteome: Identification of proteins expressed in laboratory-grown culture.

PubMed

Wagner, Mary Ann; Eschenbrenner, Michel; Horn, Troy A; Kraycer, Jo Ann; Mujer, Cesar V; Hagius, Sue; Elzer, Philip; DelVecchio, Vito G

2002-08-01

Brucella melitensis is a facultative intracellular bacterial pathogen that causes brucellosis, a zoonotic disease primarily infecting sheep and goats, characterized by undulant fever, arthritic pain and other neurological disorders in humans. A comprehensive proteomic study of strain 16M was conducted to identify and characterize the proteins expressed in laboratory-grown culture. Using overlapping narrow range immobilized pH gradient strips for two-dimensional gel electrophoresis, 883 protein spots were detected between pH 3.5 and 11. The average isoelectric point and molecular weight values of the detected spots were 5.22 and 46.5 kDa, respectively. Of the 883 observed protein spots, 440 have been identified by matrix-assisted laser desorption/ionization-mass spectrometry. These proteins represent 187 discrete open reading frames (ORFs) or 6% of the predicted 3197 ORFs contained in the genome. The corresponding ORFs of the identified proteins are distributed evenly between each of the two circular B. melitensis chromosomes, indicating that both replicons are functionally active. The presented proteome map lists those protein spots identified to date in this study. This map may serve as a baseline reference for future proteomic studies aimed at the definition of biochemical pathways associated with stress responses, host specificity, pathogenicity and virulence. It will also assist in characterization of global proteomic effects in gene-knockout mutants. Ultimately, it may aid in our overall understanding of the cell biology of B. melitensis, an important bacterial pathogen.

SfiI genomic cleavage map of Escherichia coli K-12 strain MG1655.

PubMed Central

Perkins, J D; Heath, J D; Sharma, B R; Weinstock, G M

1992-01-01

An SfiI restriction map of Escherichia coli K-12 strain MG1655 is presented. The map contains thirty-one cleavage sites separating fragments ranging in size from 407 kb to 3.7 kb. Several techniques were used in the construction of this map, including CHEF pulsed field gel electrophoresis; physical analysis of a set of twenty-six auxotrophic transposon insertions; correlation with the restriction map of Kohara and coworkers using the commercially available E. coli Gene Mapping Membranes; analysis of publicly available sequence information; and correlation of the above data with the combined genetic and physical map developed by Rudd, et al. The combination of these techniques has yielded a map in which all but one site can be localized within a range of +/- 2 kb, and over half the sites can be localized precisely by sequence data. Two sites present in the EcoSeq5 sequence database are not cleaved in MG1655 and four sites are noted to be sensitive to methylation by the dcm methylase. This map, combined with the NotI physical map of MG1655, can aid in the rapid, precise mapping of several different types of genetic alterations, including transposon mediated mutations and other insertions, inversions, deletions and duplications. Images PMID:1312707

Quantitate gossypol enantiomers in cotton flower petals and seed using capillary electrophoresis

USDA-ARS?s Scientific Manuscript database

Gossypol is a compound that occurs in the cotton plant and in leaves it protects the plant from insect herbivory. The compound also occurs in the seed. In this tissue it renders the seed toxic to non-ruminant animals. However, gossypol exists as a mixture of enantiomers referred to as (+)-gossypo...

Molecular characterization of the probiotic strain Bacillus cereus var. toyoi NCIMB 40112 and differentiation from food poisoning strains.

PubMed

Klein, Günter

2011-07-01

Bacillus cereus var. toyoi strain NCIMB 40112 (Toyocerin), a probiotic authorized in the European Union as feed additive for swine, bovines, poultry, and rabbits, was characterized by DNA fingerprinting applying pulsed-field gel electrophoresis and multilocus sequence typing and was compared with reference strains (of clinical and environmental origins). The probiotic strain was clearly characterized by pulsed-field gel electrophoresis using the restriction enzymes Apa I and Sma I resulting in unique DNA patterns. The comparison to the clinical reference strain B. cereus DSM 4312 was done with the same restriction enzymes, and again a clear differentiation of the two strains was possible by the resulting DNA patterns. The use of the restriction enzymes Apa I and Sma I is recommended for further studies. Furthermore, multilocus sequence typing analysis revealed a sequence type (ST 111) that was different from all known STs of B. cereus strains from food poisoning incidents. Thus, a strain characterization and differentiation from food poisoning strains for the probiotic strain was possible. Copyright ©, International Association for Food Protection

Low-level lasers and mRNA levels of reference genes used in Escherichia coli

NASA Astrophysics Data System (ADS)

Teixeira, A. F.; Machado, Y. L. R. C.; Fonseca, A. S.; Mencalha, A. L.

2016-11-01

Low-level lasers are widely used for the treatment of diseases and antimicrobial photodynamic therapy. Reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) is widely used to evaluate mRNA levels and output data from a target gene are commonly relative to a reference mRNA that cannot vary according to treatment. In this study, the level of reference genes from Escherichia coli exposed to red or infrared lasers at different fluences was evaluated. E. coli AB1157 cultures were exposed to red (660 nm) and infrared (808 nm) lasers, incubated (20 min, 37 °C), the total RNA was extracted, and cDNA synthesis was performed to evaluate mRNA levels from arcA, gyrA and rpoA genes by RT-qPCR. Melting curves and agarose gel electrophoresis were carried out to evaluate specific amplification. Data were analyzed by geNorm, NormFinder and BestKeeper. The melting curve and agarose gel electrophoresis showed specific amplification. Although mRNA levels from arcA, gyrA or rpoA genes presented no significant variations trough a traditional statistical analysis, Excel-based tools revealed that these reference genes are not suitable for E. coli cultures exposed to lasers. Our data showed that exposure to low-level red and infrared lasers at different fluences alter the mRNA levels from arcA, gyrA and rpoA in E. coli cells.

Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms.

PubMed

Schokraie, Elham; Hotz-Wagenblatt, Agnes; Warnken, Uwe; Mali, Brahim; Frohme, Marcus; Förster, Frank; Dandekar, Thomas; Hengherr, Steffen; Schill, Ralph O; Schnölzer, Martina

2010-03-03

Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. Here we present to the best of our knowledge the first comprehensive study of Milnesium tardigradum on the protein level. To establish a proteome reference map we developed optimized protocols for protein extraction from tardigrades in the active state and for separation of proteins by high resolution two-dimensional gel electrophoresis. Since only limited sequence information of M. tardigradum on the genome and gene expression level is available to date in public databases we initiated in parallel a tardigrade EST sequencing project to allow for protein identification by electrospray ionization tandem mass spectrometry. 271 out of 606 analyzed protein spots could be identified by searching against the publicly available NCBInr database as well as our newly established tardigrade protein database corresponding to 144 unique proteins. Another 150 spots could be identified in the tardigrade clustered EST database corresponding to 36 unique contigs and ESTs. Proteins with annotated function were further categorized in more detail by their molecular function, biological process and cellular component. For the proteins of unknown function more information could be obtained by performing a protein domain annotation analysis. Our results include proteins like protein member of different heat shock protein families and LEA group 3, which might play important roles in surviving extreme conditions. The proteome reference map of Milnesium tardigradum provides the basis for further studies in order to identify and characterize the biochemical mechanisms of tolerance to extreme desiccation. The optimized proteomics workflow will enable application of sensitive quantification techniques to detect differences in protein expression, which are characteristic of the active and anhydrobiotic states of tardigrades.

Proteomic Analysis of Tardigrades: Towards a Better Understanding of Molecular Mechanisms by Anhydrobiotic Organisms

PubMed Central

Schokraie, Elham; Hotz-Wagenblatt, Agnes; Warnken, Uwe; Mali, Brahim; Frohme, Marcus; Förster, Frank; Dandekar, Thomas; Hengherr, Steffen; Schill, Ralph O.; Schnölzer, Martina

2010-01-01

Background Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. Principal Findings Here we present to the best of our knowledge the first comprehensive study of Milnesium tardigradum on the protein level. To establish a proteome reference map we developed optimized protocols for protein extraction from tardigrades in the active state and for separation of proteins by high resolution two-dimensional gel electrophoresis. Since only limited sequence information of M. tardigradum on the genome and gene expression level is available to date in public databases we initiated in parallel a tardigrade EST sequencing project to allow for protein identification by electrospray ionization tandem mass spectrometry. 271 out of 606 analyzed protein spots could be identified by searching against the publicly available NCBInr database as well as our newly established tardigrade protein database corresponding to 144 unique proteins. Another 150 spots could be identified in the tardigrade clustered EST database corresponding to 36 unique contigs and ESTs. Proteins with annotated function were further categorized in more detail by their molecular function, biological process and cellular component. For the proteins of unknown function more information could be obtained by performing a protein domain annotation analysis. Our results include proteins like protein member of different heat shock protein families and LEA group 3, which might play important roles in surviving extreme conditions. Conclusions The proteome reference map of Milnesium tardigradum provides the basis for further studies in order to identify and characterize the biochemical mechanisms of tolerance to extreme desiccation. The optimized proteomics workflow will enable application of sensitive quantification techniques to detect differences in protein expression, which are characteristic of the active and anhydrobiotic states of tardigrades. PMID:20224743

Brassica napus seed endosperm - metabolism and signaling in a dead end tissue.

PubMed

Lorenz, Christin; Rolletschek, Hardy; Sunderhaus, Stephanie; Braun, Hans-Peter

2014-08-28

Oilseeds are an important element of human nutrition and of increasing significance for the production of industrial materials. The development of the seeds is based on a coordinated interplay of the embryo and its surrounding tissue, the endosperm. This study aims to give insights into the physiological role of endosperm for seed development in the oilseed crop Brassica napus. Using protein separation by two-dimensional (2D) isoelectric focusing (IEF)/SDS polyacrylamide gel electrophoresis (PAGE) and protein identification by mass spectrometry three proteome projects were carried out: (i) establishment of an endosperm proteome reference map, (ii) proteomic characterization of endosperm development and (iii) comparison of endosperm and embryo proteomes. The endosperm proteome reference map comprises 930 distinct proteins, including enzymes involved in genetic information processing, carbohydrate metabolism, environmental information processing, energy metabolism, cellular processes and amino acid metabolism. To investigate dynamic changes in protein abundance during seed development, total soluble proteins were extracted from embryo and endosperm fractions at defined time points. Proteins involved in sugar converting and recycling processes, ascorbate metabolism, amino acid biosynthesis and redox balancing were found to be of special importance for seed development in B. napus. Implications for the seed filling process and the function of the endosperm for seed development are discussed. The endosperm is of key importance for embryo development during seed formation in plants. We present a broad study for characterizing endosperm proteins in the oilseed plant B. napus. Furthermore, a project on the biochemical interplay between the embryo and the endosperm during seed development is presented. We provide evidence that the endosperm includes a complete set of enzymes necessary for plant primary metabolism. Combination of our results with metabolome data will further improve systems-level understanding of the seed filling process and provide rational strategies for plant bioengineering. Copyright © 2014 Elsevier B.V. All rights reserved.

Glycobiology of the cell surface: Its debt to cell electrophoresis 1940-65.

PubMed

Cook, Geoffrey M W

2016-06-01

This Review describes how in the period 1940-1959 cell electrophoresis (in the earlier literature often referred to as 'microelectrophoresis') was used to explore the surface chemistry of cells. Using the erythrocyte as a suitable model for the study of biological membranes, the early investigators were agreed on the presence of negatively charged groups at the surface of this cell. The contemporary dogma was that these were phosphate groups associated with phospholipids. Work in the 1960s, particularly on changes in the electrokinetic properties of erythrocytes following treatment with proteolytic enzymes, lead to the realization that the negatively charged groups at the red cell surface are predominantly due to sialic acids carried on glycoproteins. It quickly became apparent from cell electrophoresis that sialic acids have a ubiquitous presence on the surface of animal cells. This finding required that any complete model of the plasma membrane must include glycosylated molecules at the cell periphery, thus laying the foundations for the field termed 'Glycobiology of the Cell Surface'. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Research Area 7.4: Identifying a Path Towards Rapid Discrimination of Infection Disease Outbreaks

DTIC Science & Technology

2014-07-15

content typing, rep-PCR, pulsed-field gel electrophoresis, optical mapping, and antimicrobial susceptibility testing (G. Gault et al., 2011; P...Tremlett, G, Pidd, 2011). This case demonstrates the vulnerability of our food supply and why unusual outbreaks involving endemic microbes must be taken as... food products to malevolent tampering, and the widespread international economic consequences that can occur even from limited product contamination

2D-electrophoresis and the urine proteome map: where do we stand?

PubMed

Candiano, Giovanni; Santucci, Laura; Petretto, Andrea; Bruschi, Maurizio; Dimuccio, Veronica; Urbani, Andrea; Bagnasco, Serena; Ghiggeri, Gian Marco

2010-03-10

The discovery of urinary biomarkers is a main topic in clinical medicine. The development of proteomics has rapidly changed the knowledge on urine protein composition and probably will modify it again. Two-dimensional electrophoresis (2D-PAGE) coupled with mass spectrometry has represented for years the technique of choice for the analysis of urine proteins and it is time to draw some conclusions. This review will focus on major methodological aspects related to urine sample collection, storage and analysis by 2D-PAGE and attempt to define an advanced normal urine protein map. Overall, 1118 spots were reproducibly found in normal urine samples but only 275 were characterized as isoforms of 82 proteins. One-hundred height spots belonging to 30 proteins were also detected in plasma and corresponded to typical plasma components. The identity of most of the proteins found in normal urine by 2D-PAGE remains to be determined, the majority being low-molecular weight proteins (<30 kDa). Equalization procedures would also enhance sensitivity of the analysis and allow low abundance proteins to be characterized. Therefore, we are still on the way to define the normal urine composition. Technology advancements in concentrating procedure will improve sensitivity and give the possibility to purify proteins for mass spectrometry. Copyright (c) 2009 Elsevier B.V. All rights reserved.

Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow

PubMed Central

Morisawa, Hiraku; Hirota, Mikako; Toda, Tosifusa

2006-01-01

Background In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies. Results We developed an open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. It supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates. Conclusion Our new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved. PMID:17018156

A reference genetic map of C. clementina hort. ex Tan.; citrus evolution inferences from comparative mapping

PubMed Central

2012-01-01

Background Most modern citrus cultivars have an interspecific origin. As a foundational step towards deciphering the interspecific genome structures, a reference whole genome sequence was produced by the International Citrus Genome Consortium from a haploid derived from Clementine mandarin. The availability of a saturated genetic map of Clementine was identified as an essential prerequisite to assist the whole genome sequence assembly. Clementine is believed to be a ‘Mediterranean’ mandarin × sweet orange hybrid, and sweet orange likely arose from interspecific hybridizations between mandarin and pummelo gene pools. The primary goals of the present study were to establish a Clementine reference map using codominant markers, and to perform comparative mapping of pummelo, sweet orange, and Clementine. Results Five parental genetic maps were established from three segregating populations, which were genotyped with Single Nucleotide Polymorphism (SNP), Simple Sequence Repeats (SSR) and Insertion-Deletion (Indel) markers. An initial medium density reference map (961 markers for 1084.1 cM) of the Clementine was established by combining male and female Clementine segregation data. This Clementine map was compared with two pummelo maps and a sweet orange map. The linear order of markers was highly conserved in the different species. However, significant differences in map size were observed, which suggests a variation in the recombination rates. Skewed segregations were much higher in the male than female Clementine mapping data. The mapping data confirmed that Clementine arose from hybridization between ‘Mediterranean’ mandarin and sweet orange. The results identified nine recombination break points for the sweet orange gamete that contributed to the Clementine genome. Conclusions A reference genetic map of citrus, used to facilitate the chromosome assembly of the first citrus reference genome sequence, was established. The high conservation of marker order observed at the interspecific level should allow reasonable inferences of most citrus genome sequences by mapping next-generation sequencing (NGS) data in the reference genome sequence. The genome of the haploid Clementine used to establish the citrus reference genome sequence appears to have been inherited primarily from the ‘Mediterranean’ mandarin. The high frequency of skewed allelic segregations in the male Clementine data underline the probable extent of deviation from Mendelian segregation for characters controlled by heterozygous loci in male parents. PMID:23126659

Monitoring compliance to therapy during addiction treatments by means of hair analysis for drugs and drug metabolites using capillary zone electrophoresis coupled to time-of-flight mass spectrometry.

PubMed

Gottardo, Rossella; Fanigliulo, Ameriga; Sorio, Daniela; Liotta, Eloisa; Bortolotti, Federica; Tagliaro, Franco

2012-03-10

Capillary electrophoresis coupled to time-of-flight mass spectrometry was used in the present work for the determination of therapeutic and abused drugs and their metabolites in the hair of subjects undergoing addiction treatments, in order to monitor their compliance to therapy. For this purpose a rapid, qualitative drug screening method was adopted based on capillary electrophoresis hyphenated with time-of-flight mass spectrometry, which had earlier been developed and validated for the forensic-toxicological analysis of hair, limitedly to illicit/abused drugs [1]. Sampling of hair was carried out in order to refer to a time window of about two months from the date of sampling (i.e. 2cm ca. from cortex). A single extraction procedure was applied, allowing the determination in the hair matrix of "drugs of abuse" referred to the past abuses, and therapeutic drugs prescribed in the detoxification program as well as their metabolites. Analyte identification was based on accurate mass measurements and comparison of isotope patterns, providing the most likely matching between accurate mass value and elemental formula. Small molecules (<500Da) of forensic and toxicological interest could be identified unambiguously using mass spectrometric conditions tailored to meet a mass accuracy ≤5ppm. In the present study, the proposed approach proved suitable for the rapid broad spectrum screening of hair samples, although needing further confirmation of results by using fragmentation mass spectrometry. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

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…

Genetic diversity analysis of sugarcane germplasm based on fluorescence-labeled simple sequence repeat markers and a capillary electrophoresis-based genotyping platform

USDA-ARS?s Scientific Manuscript database

Genetic diversity analysis, which refers to the elaboration of total extent of genetic characteristics in the genetic makeup of a certain species, constitutes a classical strategy for the study of diversity, population genetic structure, and breeding practices. In this study, fluorescence-labeled se...

Global analysis of Brucella melitensis proteomes.

PubMed

Mujer, Cesar V; Wagner, Mary Ann; Eschenbrenner, Michel; Horn, Troy; Kraycer, Jo Ann; Redkar, Rajendra; Hagius, Sue; Elzer, Philip; Delvecchio, Vito G

2002-10-01

Brucella melitensis is a facultative, intracellular, gram-negative cocco-bacillus that causes Malta fever in humans and brucellosis in animals. There are at least six species in the genus, and the disease is classified as zoonotic because several species infect humans. Using 2-D gel electrophoresis and mass spectrometry, we have initiated (i) a comprehensive mapping and identification of all the expressed proteins of B. melitensis virulent strain 16M, and (ii) a comparative study of its proteome with the attentuated vaccinal strain Rev 1. Comprehensive proteome maps of all six Brucella species will be generated in order to obtain vital information for vaccine development, identification of pathogenicity islands, and establishment of host specificity and evolutionary relatedness.

A mapping closure for turbulent scalar mixing using a time-evolving reference field

NASA Technical Reports Server (NTRS)

Girimaji, Sharath S.

1992-01-01

A general mapping-closure approach for modeling scalar mixing in homogeneous turbulence is developed. This approach is different from the previous methods in that the reference field also evolves according to the same equations as the physical scalar field. The use of a time-evolving Gaussian reference field results in a model that is similar to the mapping closure model of Pope (1991), which is based on the methodology of Chen et al. (1989). Both models yield identical relationships between the scalar variance and higher-order moments, which are in good agreement with heat conduction simulation data and can be consistent with any type of epsilon(phi) evolution. The present methodology can be extended to any reference field whose behavior is known. The possibility of a beta-pdf reference field is explored. The shortcomings of the mapping closure methods are discussed, and the limit at which the mapping becomes invalid is identified.

The Importance of Measurement Errors for Deriving Accurate Reference Leaf Area Index Maps for Validation of Moderate-Resolution Satellite LAI Products

NASA Technical Reports Server (NTRS)

Huang, Dong; Yang, Wenze; Tan, Bin; Rautiainen, Miina; Zhang, Ping; Hu, Jiannan; Shabanov, Nikolay V.; Linder, Sune; Knyazikhin, Yuri; Myneni, Ranga B.

2006-01-01

The validation of moderate-resolution satellite leaf area index (LAI) products such as those operationally generated from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor data requires reference LAI maps developed from field LAI measurements and fine-resolution satellite data. Errors in field measurements and satellite data determine the accuracy of the reference LAI maps. This paper describes a method by which reference maps of known accuracy can be generated with knowledge of errors in fine-resolution satellite data. The method is demonstrated with data from an international field campaign in a boreal coniferous forest in northern Sweden, and Enhanced Thematic Mapper Plus images. The reference LAI map thus generated is used to assess modifications to the MODIS LAI/fPAR algorithm recently implemented to derive the next generation of the MODIS LAI/fPAR product for this important biome type.

Aeromonas isolates from human diarrheic stool and groundwater compared by pulsed-field gel electrophoresis.

PubMed

Borchardt, Mark A; Stemper, Mary E; Standridge, Jon H

2003-02-01

Gastrointestinal infections of Aeromonas species are generally considered waterborne; for this reason, Aeromonas hydrophila has been placed on the United States Environmental Protection Agency Contaminant Candidate List of emerging pathogens in drinking water. In this study, we compared pulsed-field gel electrophoresis patterns of Aeromonas isolates from stool specimens of patients with diarrhea with Aeromonas isolates from patients' drinking water. Among 2,565 diarrheic stool specimens submitted to a Wisconsin clinical reference laboratory, 17 (0.66%) tested positive for Aeromonas. Groundwater isolates of Aeromonas were obtained from private wells throughout Wisconsin and the drinking water of Aeromonas-positive patients. The analysis showed that the stool and drinking water isolates were genetically unrelated, suggesting that in this population Aeromonas gastrointestinal infections were not linked with groundwater exposures.

Aeromonas Isolates from Human Diarrheic Stool and Groundwater Compared by Pulsed-Field Gel Electrophoresis

PubMed Central

Stemper, Mary E.; Standridge, Jon H.

2003-01-01

Gastrointestinal infections of Aeromonas species are generally considered waterborne; for this reason, Aeromonas hydrophila has been placed on the United States Environmental Protection Agency Contaminant Candidate List of emerging pathogens in drinking water. In this study, we compared pulsed-field gel electrophoresis patterns of Aeromonas isolates from stool specimens of patients with diarrhea with Aeromonas isolates from patients’ drinking water. Among 2,565 diarrheic stool specimens submitted to a Wisconsin clinical reference laboratory, 17 (0.66%) tested positive for Aeromonas. Groundwater isolates of Aeromonas were obtained from private wells throughout Wisconsin and the drinking water of Aeromonas-positive patients. The analysis showed that the stool and drinking water isolates were genetically unrelated, suggesting that in this population Aeromonas gastrointestinal infections were not linked with groundwater exposures. PMID:12603994

Recent advances in nonpolar and polar organic monoliths for HPLC and CEC

PubMed Central

Jonnada, Murthy; Rathnasekara, Renuka; Rassi, Ziad El

2015-01-01

This article is aimed at providing a review of the progress made in the field over the period 2011 to present in order to expand in parts on two previous reviews (S. Karenga and Z. El Rassi, Electrophoresis, 2011, 32, 90-104; D. Gunasena and Z. El Rassi, Electrophoresis, 2012, 33, 251-261). In brief, this review article describes progress made in nonpolar and polar monoliths used in reversed phase HPLC and CEC (RPC/RP-CEC) and in hydrophilic interaction liquid chromatography/CEC (HILIC/HI-CEC), respectively. This article is by no means an exhaustive review of the literature; it is rather a survey of the recent progress made in the field with 69 references published on nonpolar and polar polymeric monoliths. PMID:25266173

Identifying a Path Towards Rapid Discrimination of Infection Disease Outbreaks: Harnessing Next-Generation Sequencing Capabilities for Microbial Forensics

DTIC Science & Technology

2014-07-15

content typing, rep-PCR, pulsed-field gel electrophoresis, optical mapping, and antimicrobial susceptibility testing (G. Gault et al., 2011; P...Tremlett, G, Pidd, 2011). This case demonstrates the vulnerability of our food supply and why unusual outbreaks involving endemic microbes must be taken as... food products to malevolent tampering, and the widespread international economic consequences that can occur even from limited product contamination

Use of diversity arrays technology markers for integration into a cotton reference map and anchoring to a recombinant inbred line map

USDA-ARS?s Scientific Manuscript database

A DArT marker platform is developed for the cotton genome to evaluate the use of DArT markers compared to AFLPs in mapping, and transferability across the mapping populations. We used a reference genetic map of tetraploid Gossypium that already contained ~5000 loci which coalesced into 26 chromosom...

Immunoturbidimetric quantification of serum immunoglobulin G concentration in foals.

PubMed

Bauer, J E; Brooks, T P

1990-08-01

Immunoturbidimetric determination of serum IgG concentration in foals was compared with the reference methods of single radial immunodiffusion and serum protein electrophoresis. High positive correlations were discovered when the technique was compared with either of these reference methods. The zinc sulfate turbidity test for serum IgG estimation was also evaluated. Although a positive correlation was discovered when the latter method was compared with reference methods, it was not as strong as the correlation between reference methods and the immunoturbidimetric method. The immunoturbidimetric method used in this study is specific and precise for equine serum IgG determination. It is rapid and, thus, is advantageous when timely evaluation of critically ill foals is necessary. The technique should be adaptable to various spectrophotometers and microcomputers for widespread application in veterinary medicine.

Error and Uncertainty in the Accuracy Assessment of Land Cover Maps

NASA Astrophysics Data System (ADS)

Sarmento, Pedro Alexandre Reis

Traditionally the accuracy assessment of land cover maps is performed through the comparison of these maps with a reference database, which is intended to represent the "real" land cover, being this comparison reported with the thematic accuracy measures through confusion matrixes. Although, these reference databases are also a representation of reality, containing errors due to the human uncertainty in the assignment of the land cover class that best characterizes a certain area, causing bias in the thematic accuracy measures that are reported to the end users of these maps. The main goal of this dissertation is to develop a methodology that allows the integration of human uncertainty present in reference databases in the accuracy assessment of land cover maps, and analyse the impacts that uncertainty may have in the thematic accuracy measures reported to the end users of land cover maps. The utility of the inclusion of human uncertainty in the accuracy assessment of land cover maps is investigated. Specifically we studied the utility of fuzzy sets theory, more precisely of fuzzy arithmetic, for a better understanding of human uncertainty associated to the elaboration of reference databases, and their impacts in the thematic accuracy measures that are derived from confusion matrixes. For this purpose linguistic values transformed in fuzzy intervals that address the uncertainty in the elaboration of reference databases were used to compute fuzzy confusion matrixes. The proposed methodology is illustrated using a case study in which the accuracy assessment of a land cover map for Continental Portugal derived from Medium Resolution Imaging Spectrometer (MERIS) is made. The obtained results demonstrate that the inclusion of human uncertainty in reference databases provides much more information about the quality of land cover maps, when compared with the traditional approach of accuracy assessment of land cover maps. None

An integrated pan-tropical biomass map using multiple reference datasets.

PubMed

Avitabile, Valerio; Herold, Martin; Heuvelink, Gerard B M; Lewis, Simon L; Phillips, Oliver L; Asner, Gregory P; Armston, John; Ashton, Peter S; Banin, Lindsay; Bayol, Nicolas; Berry, Nicholas J; Boeckx, Pascal; de Jong, Bernardus H J; DeVries, Ben; Girardin, Cecile A J; Kearsley, Elizabeth; Lindsell, Jeremy A; Lopez-Gonzalez, Gabriela; Lucas, Richard; Malhi, Yadvinder; Morel, Alexandra; Mitchard, Edward T A; Nagy, Laszlo; Qie, Lan; Quinones, Marcela J; Ryan, Casey M; Ferry, Slik J W; Sunderland, Terry; Laurin, Gaia Vaglio; Gatti, Roberto Cazzolla; Valentini, Riccardo; Verbeeck, Hans; Wijaya, Arief; Willcock, Simon

2016-04-01

We combined two existing datasets of vegetation aboveground biomass (AGB) (Proceedings of the National Academy of Sciences of the United States of America, 108, 2011, 9899; Nature Climate Change, 2, 2012, 182) into a pan-tropical AGB map at 1-km resolution using an independent reference dataset of field observations and locally calibrated high-resolution biomass maps, harmonized and upscaled to 14 477 1-km AGB estimates. Our data fusion approach uses bias removal and weighted linear averaging that incorporates and spatializes the biomass patterns indicated by the reference data. The method was applied independently in areas (strata) with homogeneous error patterns of the input (Saatchi and Baccini) maps, which were estimated from the reference data and additional covariates. Based on the fused map, we estimated AGB stock for the tropics (23.4 N-23.4 S) of 375 Pg dry mass, 9-18% lower than the Saatchi and Baccini estimates. The fused map also showed differing spatial patterns of AGB over large areas, with higher AGB density in the dense forest areas in the Congo basin, Eastern Amazon and South-East Asia, and lower values in Central America and in most dry vegetation areas of Africa than either of the input maps. The validation exercise, based on 2118 estimates from the reference dataset not used in the fusion process, showed that the fused map had a RMSE 15-21% lower than that of the input maps and, most importantly, nearly unbiased estimates (mean bias 5 Mg dry mass ha(-1) vs. 21 and 28 Mg ha(-1) for the input maps). The fusion method can be applied at any scale including the policy-relevant national level, where it can provide improved biomass estimates by integrating existing regional biomass maps as input maps and additional, country-specific reference datasets. © 2015 John Wiley & Sons Ltd.

Development of Ground Reference GIS for Assessing Land Cover Maps of Northeast Yellowstone National Park

NASA Technical Reports Server (NTRS)

Spruce, Joe; Warner, Amanda; Terrie, Greg; Davis, Bruce

2001-01-01

GIS technology and ground reference data often play vital roles in assessing land cover maps derived from remotely sensed data. This poster illustrates these roles, using results from a study done in Northeast Yellowstone National Park. This area holds many forest, range, and wetland cover types of interest to park managers. Several recent studies have focused on this locale, including the NASA Earth Observations Commercial Applications Program (EOCAP) hyperspectral project performed by Yellowstone Ecosystems Studies (YES) on riparian and in-stream habitat mapping. This poster regards a spin-off to the EOCAP project in which YES and NASA's Earth Science Applications Directorate explored the potential for synergistic use of hyperspecral, synthetic aperture radar, and multiband thermal imagery in mapping land cover types. The project included development of a ground reference GIS for site-specific data needed to evaluate maps from remotely sensed imagery. Field survey data included reflectance of plant communities, native and exotic plant species, and forest health conditions. Researchers also collected GPS points, annotated aerial photographs, and took hand held photographs of reference sites. The use of ESRI, ERDAS, and ENVI software enabled reference data entry into a GIS for comparision to georeferenced imagery and thematic maps. The GIS-based ground reference data layers supported development and assessment of multiple maps from remotely sensed data sets acquired over the study area.

Frames of reference for helicopter electronic maps - The relevance of spatial cognition and componential analysis

NASA Technical Reports Server (NTRS)

Harwood, Kelly; Wickens, Christopher D.

1991-01-01

Computer-generated map displays for NOE and low-level helicopter flight were formed according to prior research on maps, navigational problem solving, and spatial cognition in large-scale environments. The north-up map emphasized consistency of object location, wheareas, the track-up map emphasized map-terrain congruency. A component analysis indicates that different cognitive components, e.g., orienting and absolute object location, are supported to varying degrees by properties of different frames of reference.

Do Doppler color flow algorithms for mapping disturbed flow make sense?

PubMed

Gardin, J M; Lobodzinski, S M

1990-01-01

It has been suggested that a major advantage of Doppler color flow mapping is its ability to visualize areas of disturbed ("turbulent") flow, for example, in valvular stenosis or regurgitation and in shunts. To investigate how various color flow mapping instruments display disturbed flow information, color image processing was used to evaluate the most common velocity-variance color encoding algorithms of seven commercially available ultrasound machines. In six of seven machines, green was reportedly added by the variance display algorithms to map areas of disturbed flow. The amount of green intensity added to each pixel along the red and blue portions of the velocity reference color bar was calculated for each machine. In this study, velocities displayed on the reference color bar ranged from +/- 46 to +/- 64 cm/sec, depending on the Nyquist limit. Of note, changing the Nyquist limits depicted on the color reference bars did not change the distribution of the intensities of red, blue, or green within the contour of the reference map, but merely assigned different velocities to the pixels. Most color flow mapping algorithms in our study added increasing intensities of green to increasing positive (red) or negative (blue) velocities along their color reference bars. Most of these machines also added increasing green to red and blue color intensities horizontally across their reference bars as a marker of increased variance (spectral broadening). However, at any given velocity, marked variations were noted between different color flow mapping instruments in the amount of green added to their color velocity reference bars.(ABSTRACT TRUNCATED AT 250 WORDS)

Increasing the availability of national mapping products.

USGS Publications Warehouse

Roney, J.I.; Ogilvie, B.C.

1981-01-01

A discussion of the means employed by the US Geological Survey to facilitate map usage, covering aspects of project Map Accessibility Program including special rolled and folded map packaging, new market testing, parks and campgrounds program, expanded map dealer program, new booklet-type State sales index and catalog and new USGS map reference code. The USGS is seen as the producer of a tremendous nation-wide inventory of topographic and related map products available in unprecedented types, formats and scales, and as endeavouring to increase access to its products. The new USGS map reference code is appended. -J.C.Stone

Cell and Particle Interactions and Aggregation During Electrophoretic Motion

NASA Technical Reports Server (NTRS)

Davis, Robert H.

2000-01-01

The objectives of this research were (i) to perform experiments for observing and quantifying electrophoretic aggregation, (ii) to develop a theoretical description to appropriately analyze and compare with the experimental results, (iii) to study the combined effects of electrophoretic and gravitational aggregation of large particles, and the combined effects of electrophoretic and Brownian aggregation of small particles, and (iv) to perform a preliminary design of a potential future flight experiment involving electrophoretic aggregation. Electrophoresis refers to the motion of charged particles, droplets or molecules in response to an applied electric field. Electrophoresis is commonly used for analysis and separation of biological particles or molecules. When particles have different surface charge densities or potentials, they will migrate at different velocities in an electric field. This differential migration leads to the possibility that they will collide and aggregate, thereby preventing separation.

Construction and Annotation of a High Density SNP Linkage Map of the Atlantic Salmon (Salmo salar) Genome.

PubMed

Tsai, Hsin Y; Robledo, Diego; Lowe, Natalie R; Bekaert, Michael; Taggart, John B; Bron, James E; Houston, Ross D

2016-07-07

High density linkage maps are useful tools for fine-scale mapping of quantitative trait loci, and characterization of the recombination landscape of a species' genome. Genomic resources for Atlantic salmon (Salmo salar) include a well-assembled reference genome, and high density single nucleotide polymorphism (SNP) arrays. Our aim was to create a high density linkage map, and to align it with the reference genome assembly. Over 96,000 SNPs were mapped and ordered on the 29 salmon linkage groups using a pedigreed population comprising 622 fish from 60 nuclear families, all genotyped with the 'ssalar01' high density SNP array. The number of SNPs per group showed a high positive correlation with physical chromosome length (r = 0.95). While the order of markers on the genetic and physical maps was generally consistent, areas of discrepancy were identified. Approximately 6.5% of the previously unmapped reference genome sequence was assigned to chromosomes using the linkage map. Male recombination rate was lower than females across the vast majority of the genome, but with a notable peak in subtelomeric regions. Finally, using RNA-Seq data to annotate the reference genome, the mapped SNPs were categorized according to their predicted function, including annotation of ∼2500 putative nonsynonymous variants. The highest density SNP linkage map for any salmonid species has been created, annotated, and integrated with the Atlantic salmon reference genome assembly. This map highlights the marked heterochiasmy of salmon, and provides a useful resource for salmonid genetics and genomics research. Copyright © 2016 Tsai et al.

Combining high-throughput MALDI-TOF mass spectrometry and isoelectric focusing gel electrophoresis for virtual 2D gel-based proteomics.

PubMed

Lohnes, Karen; Quebbemann, Neil R; Liu, Kate; Kobzeff, Fred; Loo, Joseph A; Ogorzalek Loo, Rachel R

2016-07-15

The virtual two-dimensional gel electrophoresis/mass spectrometry (virtual 2D gel/MS) technology combines the premier, high-resolution capabilities of 2D gel electrophoresis with the sensitivity and high mass accuracy of mass spectrometry (MS). Intact proteins separated by isoelectric focusing (IEF) gel electrophoresis are imaged from immobilized pH gradient (IPG) polyacrylamide gels (the first dimension of classic 2D-PAGE) by matrix-assisted laser desorption/ionization (MALDI) MS. Obtaining accurate intact masses from sub-picomole-level proteins embedded in 2D-PAGE gels or in IPG strips is desirable to elucidate how the protein of one spot identified as protein 'A' on a 2D gel differs from the protein of another spot identified as the same protein, whenever tryptic peptide maps fail to resolve the issue. This task, however, has been extremely challenging. Virtual 2D gel/MS provides access to these intact masses. Modifications to our matrix deposition procedure improve the reliability with which IPG gels can be prepared; the new procedure is described. Development of this MALDI MS imaging (MSI) method for high-throughput MS with integrated 'top-down' MS to elucidate protein isoforms from complex biological samples is described and it is demonstrated that a 4-cm IPG gel segment can now be imaged in approximately 5min. Gel-wide chemical and enzymatic methods with further interrogation by MALDI MS/MS provide identifications, sequence-related information, and post-translational/transcriptional modification information. The MSI-based virtual 2D gel/MS platform may potentially link the benefits of 'top-down' and 'bottom-up' proteomics. Copyright © 2016 Elsevier Inc. All rights reserved.

Immunogenic membrane-associated proteins of Mycobacterium tuberculosis revealed by proteomics.

PubMed

Sinha, Sudhir; Kosalai, K; Arora, Shalini; Namane, Abdelkader; Sharma, Pawan; Gaikwad, Anil N; Brodin, Priscille; Cole, Stewart T

2005-07-01

Membrane-associated proteins of Mycobacterium tuberculosis offer a challenge, as well as an opportunity, in the quest for better therapeutic and prophylactic interventions against tuberculosis. The authors have previously reported that extraction with the detergent Triton X-114 (TX-114) is a useful step in proteomic analysis of mycobacterial cell membranes, and detergent-soluble membrane proteins of mycobacteria are potent stimulators of human T cells. In this study 1-D and 2-D gel electrophoresis-based protocols were used for the analysis of proteins in the TX-114 extract of M. tuberculosis membranes. Peptide mass mapping (using MALDI-TOF-MS, matrix assisted laser desorption/ionization time of flight mass spectrometry) of 116 samples led to the identification of 105 proteins, 9 of which were new to the M. tuberculosis proteome. Functional orthologues of 73 of these proteins were also present in Mycobacterium leprae, suggesting their relative importance. Bioinformatics predicted that as many as 73% of the proteins had a hydrophobic disposition. 1-D gel electrophoresis revealed more hydrophobic/transmembrane and basic proteins than 2-D gel electrophoresis. Identified proteins fell into the following major categories: protein synthesis, cell wall biogenesis/architecture and conserved hypotheticals/unknowns. To identify immunodominant proteins of the detergent phase (DP), 14 low-molecular-mass fractions prepared by continuous-elution gel electrophoresis were subjected to T cell activation assays using blood samples from BCG-vaccinated healthy donors from a tuberculosis endemic area. Analysis of the responses (cell proliferation and IFN-gamma production) showed that the immunodominance of certain DP fractions was most probably due to ribosomal proteins, which is consistent with both their specificity for mycobacteria and their abundance. Other membrane-associated proteins, including transmembrane proteins/lipoproteins and ESAT-6, did not appear to contribute significantly to the observed T cell responses.

Method and system for a network mapping service

DOEpatents

Bynum, Leo

2017-10-17

A method and system of publishing a map includes providing access to a plurality of map data files or mapping services between at least one publisher and at least one subscriber; defining a map in a map context comprising parameters and descriptors to substantially duplicate a map by reference to mutually accessible data or mapping services, publishing a map to a channel in a table file on server; accessing the channel by at least one subscriber, transmitting the mapping context from the server to the at least one subscriber, executing the map context by the at least one subscriber, and generating the map on a display software associated with the at least one subscriber by reconstituting the map from the references and other data in the mapping context.

Time-efficient high-resolution whole-brain three-dimensional macromolecular proton fraction mapping

PubMed Central

Yarnykh, Vasily L.

2015-01-01

Purpose Macromolecular proton fraction (MPF) mapping is a quantitative MRI method that reconstructs parametric maps of a relative amount of macromolecular protons causing the magnetization transfer (MT) effect and provides a biomarker of myelination in neural tissues. This study aimed to develop a high-resolution whole-brain MPF mapping technique utilizing a minimal possible number of source images for scan time reduction. Methods The described technique is based on replacement of an actually acquired reference image without MT saturation by a synthetic one reconstructed from R1 and proton density maps, thus requiring only three source images. This approach enabled whole-brain three-dimensional MPF mapping with isotropic 1.25×1.25×1.25 mm3 voxel size and scan time of 20 minutes. The synthetic reference method was validated against standard MPF mapping with acquired reference images based on data from 8 healthy subjects. Results Mean MPF values in segmented white and gray matter appeared in close agreement with no significant bias and small within-subject coefficients of variation (<2%). High-resolution MPF maps demonstrated sharp white-gray matter contrast and clear visualization of anatomical details including gray matter structures with high iron content. Conclusions Synthetic reference method improves resolution of MPF mapping and combines accurate MPF measurements with unique neuroanatomical contrast features. PMID:26102097

On-Chip Transport of Biological Fluids in MEMS Devices

DTIC Science & Technology

1999-02-01

this model has been extended for multi-dimensional geometries to simulate electroosmotic flow in microdevices. Electrophoresis model in CFD- ACE + will...integrated with CFD- ACE +. 7.0 REFERENCES 1. N. A. Patankar and H. H. Hu, "Numerical Simulation of Electroosmotic Flow," Analytical Chemistry, 70...Electroosmosis has been developed and successfully integrated with CFD- ACE + code. (ii) Extension of the above-mentioned model to simulate

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 progressing eucalypt research. PMID:22702473

An associative model of adaptive inference for learning word-referent mappings.

PubMed

Kachergis, George; Yu, Chen; Shiffrin, Richard M

2012-04-01

People can learn word-referent pairs over a short series of individually ambiguous situations containing multiple words and referents (Yu & Smith, 2007, Cognition 106: 1558-1568). Cross-situational statistical learning relies on the repeated co-occurrence of words with their intended referents, but simple co-occurrence counts cannot explain the findings. Mutual exclusivity (ME: an assumption of one-to-one mappings) can reduce ambiguity by leveraging prior experience to restrict the number of word-referent pairings considered but can also block learning of non-one-to-one mappings. The present study first trained learners on one-to-one mappings with varying numbers of repetitions. In late training, a new set of word-referent pairs were introduced alongside pretrained pairs; each pretrained pair consistently appeared with a new pair. Results indicate that (1) learners quickly infer new pairs in late training on the basis of their knowledge of pretrained pairs, exhibiting ME; and (2) learners also adaptively relax the ME bias and learn two-to-two mappings involving both pretrained and new words and objects. We present an associative model that accounts for both results using competing familiarity and uncertainty biases.

A Comprehensive Linkage Map of the Dog Genome

PubMed Central

Wong, Aaron K.; Ruhe, Alison L.; Dumont, Beth L.; Robertson, Kathryn R.; Guerrero, Giovanna; Shull, Sheila M.; Ziegle, Janet S.; Millon, Lee V.; Broman, Karl W.; Payseur, Bret A.; Neff, Mark W.

2010-01-01

We have leveraged the reference sequence of a boxer to construct the first complete linkage map for the domestic dog. The new map improves access to the dog's unique biology, from human disease counterparts to fascinating evolutionary adaptations. The map was constructed with ∼3000 microsatellite markers developed from the reference sequence. Familial resources afforded 450 mostly phase-known meioses for map assembly. The genotype data supported a framework map with ∼1500 loci. An additional ∼1500 markers served as map validators, contributing modestly to estimates of recombination rate but supporting the framework content. Data from ∼22,000 SNPs informing on a subset of meioses supported map integrity. The sex-averaged map extended 21 M and revealed marked region- and sex-specific differences in recombination rate. The map will enable empiric coverage estimates and multipoint linkage analysis. Knowledge of the variation in recombination rate will also inform on genomewide patterns of linkage disequilibrium (LD), and thus benefit association, selective sweep, and phylogenetic mapping approaches. The computational and wet-bench strategies can be applied to the reference genome of any nonmodel organism to assemble a de novo linkage map. PMID:19966068

Prostate Cancer in African-American Men: Serum Biomarkers for Early Detection Using Nanoparticles

DTIC Science & Technology

2009-11-01

NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8 . PERFORMING ORGANIZATION REPORT...b. ABSTRACT U c. THIS PAGE U UU 25 19b. TELEPHONE NUMBER (include area code) Standard Form 298 (Rev. 8 -98) Prescribed by ANSI Std. Z39.18 2...mapping; 8 . Gel electrophoresis; and 9. ‘Home-made’ QDs; We published a paper on the application of the b io-conjugated quantum dots (QDs) for

Counterion dye staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and tryptic gel digestion of stained protein for mass spectrometry.

PubMed

Cong, Wei-Tao; Wang, Xu; Hwang, Sun-Young; Jin, Li-Tai; Choi, Jung-Kap

2012-01-01

A fast and matrix-assisted laser desorption/ionization mass spectrometry compatible protein staining method in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis is described. It is based on the counterion dye staining method that employs oppositely charged two dyes, zincon and ethyl violet, to form an ion-pair complex. The protocol, including fixing, staining, and quick washing steps, can be completed in 1-1.5 h, depending upon gel thickness. It has the sensitivity comparable to the colloidal Coomassie Brilliant Blue G stain using phosphoric acid as a component of staining solution (4-8 ng). The counterion dye stain does not induce protein modifications that complicate interpretation of peptide mapping data from mass spectrometry. Considering the speed, sensitivity, and compatibility with mass spectrometry, the counterion dye stain may be more practical than any other dye-based protein stains for routine proteomic researches.

Selective determination of arginine-containing and tyrosine-containing peptides using capillary electrophoresis and laser-induced fluorescence detection.

PubMed

Cobb, K A; Novotny, M V

1992-01-01

The use of two different amino acid-selective fluorogenic reagents for the derivatization of peptides is investigated. One such scheme utilizes a selective reaction of benzoin with the guanidine moiety to derivatize arginine residues occurring in a peptide. The second scheme involves the formylation of tyrosine, followed by reaction with 4-methoxy-1,2-phenylenediamine. The use of capillary electrophoresis and laser-induced fluorescence detection allows enhanced efficiencies and sensitivities to be obtained for the separations of either arginine- or tyrosine-containing peptides. A helium-cadmium laser (325 nm) is ideally suited for the laser-based detection system due to a close match of the excitation maxima of derivatized peptides from both reactions. A detection limit of 270 amol is achieved for model arginine-containing peptides, while the detection limit for model tyrosine-containing peptides is measured at 390 amol. Both derivatization reactions are found to be useful for high-sensitivity peptide mapping applications in which only the peptides containing the derivatized amino acids are detected.

Multi-Site N-glycan mapping study 1: Capillary electrophoresis – laser induced fluorescence

PubMed Central

Szekrényes, Ákos; Park, SungAe Suhr; Santos, Marcia; Lew, Clarence; Jones, Aled; Haxo, Ted; Kimzey, Michael; Pourkaveh, Shiva; Szabó, Zoltán; Sosic, Zoran; Feng, Peng; Váradi, Csaba; de l'Escaille, François; Falmagne, Jean-Bernard; Sejwal, Preeti; Niedringhaus, Thomas; Michels, David; Freckleton, Gordon; Hamm, Melissa; Manuilov, Anastasiya; Schwartz, Melissa; Luo, Jiann-Kae; van Dyck, Jonathan; Leung, Pui-King; Olajos, Marcell; Gu, Yingmei; Gao, Kai; Wang, Wenbo; Wegstein, Jo; Tep, Samnang; Guttman, András

2016-01-01

An international team that included 20 independent laboratories from biopharmaceutical companies, universities, analytical contract laboratories and national authorities in the United States, Europe and Asia was formed to evaluate the reproducibility of sample preparation and analysis of N-glycans using capillary electrophoresis of 8-aminopyrene-1,3,6-trisulfonic acid (APTS)-labeled glycans with laser induced fluorescence (CE-LIF) detection (16 sites) and ultra high-performance liquid chromatography (UHPLC, 12 sites; results to be reported in a subsequent publication). All participants used the same lot of chemicals, samples, reagents, and columns/capillaries to run their assays. Migration time, peak area and peak area percent values were determined for all peaks with >0.1% peak area. Our results demonstrated low variability and high reproducibility, both, within any given site as well across all sites, which indicates that a standard N-glycan analysis platform appropriate for general use (clone selection, process development, lot release, etc.) within the industry can be established. PMID:26466659

[Analysis of total proteins in the seed of almond (Prunus dulcis) by two-dimensional electrophoresis].

PubMed

Li, Dong-dong; He, Shao-heng

2004-07-01

To analyse the total proteins in the seeds of almond (Prunus dulcis), one of the popular ingestent allergens in China, by two-dimensional electrophoresis. The total proteins of the seeds were extracted by trichloracetic acid (TCA) method, and then separated by isoelectric focusing as first dimension and SDS-PAGE as the second dimension. The spots of proteins were visualized by staining with Coomassie Brilliant Blue R-250. After analysis with software (ImageMaster 2D), 188 different proteins were detected. The isoelectric points (pI) for approximately 28% of total proteins were between 4.5-5.5, and the relative molecular mass (M(r)) of approximately 62% total proteins were between (20-25)x10(3). This was the first high-resolution, two-dimensional protein map of the seed of almond (Prunus dulcis) in China. Our finding has laid a solid foundation for further identification, characterization, gene cloning and standardization of allergenic proteins in the seed of almond (Prunus dulcis).

Effect of conductivity and concentration on the sample stream in the transverse axis of a continuous flow electrophoresis chamber

NASA Technical Reports Server (NTRS)

Miller, Teresa Y.; Williams, George O.; Snyder, Robert S.

1985-01-01

The resolution of continuous flow electrophoresis systems is generally measured by the spread of the sample bands in the direction of the electrophoretic migration. This paper evaluates the cross section of the sample bands in the plane perpendicular to the flow and shows that the spread in the direction perpendicular to the migration increased significantly with the applied electric field. Concentrated samples of monodisperse latex particles and vinyltoluene T-butylstyrene particles in sample buffers of different electrical conductivities were used to map the shape of the sample bands relative to the zero electric field case. As the electric field was applied, the sample band spread from an initial diameter of only one-third the chamber thickness until it approached the chamber walls where electroosmosis significantly reduced the resolution of separation. It can be shown, however, that it is possible to minimize these distortions by careful sample preparation and experiment design.

Gel electrophoresis of partially denatured DNA. Retardation effect: its analysis and application.

PubMed Central

Lyamichev, V I; Panyutin, I G; Lyubchenko YuL

1982-01-01

The hypothesis about the role of partial denaturation in DNA retardation during its electrophoresis in denaturing gel /1,2/ was tested. We used partially melted DNA molecules in which the size of the melted regions and their location were known. They were obtained through glyoxal treatment of the melted regions by a procedure allowing the denatured state to be fixed at any point within the melting range. The approach and the availability of the melting maps of DNAs made it possible to investigate DNA molecules differing in length and in the size of the melted regions. The presence of a denatured region at the end of the molecule or inside of it was shown to decrease its electrophoretic mobility, the effect depending on the size of the melted region and on the DNA length. On the basis of the experimental results an explanation is proposed for the cause of retardation in the case of partially denatured DNA. Images PMID:7133999

Isoforms of a cuticular protein from larvae of the meal beetle, Tenebrio molitor, studied by mass spectrometry in combination with Edman degradation and two-dimensional polyacrylamide gel electrophoresis.

PubMed Central

Haebel, S.; Jensen, C.; Andersen, S. O.; Roepstorff, P.

1995-01-01

Simultaneous sequencing, using a combination of mass spectrometry and Edman degradation, of three approximately 15-kDa variants of a cuticular protein extracted from the meal beetle Tenebrio molitor larva is demonstrated. The information obtained by matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) time-course monitoring of enzymatic digests was found essential to identify the differences among the three variants and for alignment of the peptides in the sequence. To determine whether each individual insect larva contains all three protein variants, proteins extracted from single animals were separated by two-dimensional gel electrophoresis, electroeluted from the gel spots, and analyzed by MALDI MS. Molecular weights of the proteins present in each sample could be obtained, and mass spectrometric mapping of the peptides after digestion with trypsin gave additional information. The protein isoforms were found to be allelic variants. PMID:7795523

Isoforms of a cuticular protein from larvae of the meal beetle, Tenebrio molitor, studied by mass spectrometry in combination with Edman degradation and two-dimensional polyacrylamide gel electrophoresis.

PubMed

Haebel, S; Jensen, C; Andersen, S O; Roepstorff, P

1995-03-01

Simultaneous sequencing, using a combination of mass spectrometry and Edman degradation, of three approximately 15-kDa variants of a cuticular protein extracted from the meal beetle Tenebrio molitor larva is demonstrated. The information obtained by matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) time-course monitoring of enzymatic digests was found essential to identify the differences among the three variants and for alignment of the peptides in the sequence. To determine whether each individual insect larva contains all three protein variants, proteins extracted from single animals were separated by two-dimensional gel electrophoresis, electroeluted from the gel spots, and analyzed by MALDI MS. Molecular weights of the proteins present in each sample could be obtained, and mass spectrometric mapping of the peptides after digestion with trypsin gave additional information. The protein isoforms were found to be allelic variants.

Recent progress in preparation and application of microfluidic chip electrophoresis

NASA Astrophysics Data System (ADS)

Cong, Hailin; Xu, Xiaodan; Yu, Bing; Yuan, Hua; Peng, Qiaohong; Tian, Chao

2015-05-01

Since its discovery in 1990, microfluidic chip electrophoresis (MCE) has allowed the development of applications with small size, fast analysis, low cost, high integration density and automatic level, which are easy to carry and have made commercialization efficient. MCE has been widely used in the areas of environmental protection, biochemistry, medicine and health, clinical testing, judicial expertise, food sanitation, pharmaceutical checking, drug testing, agrochemistry, biomedical engineering and life science. As one of the foremost fields in the research of capillary electrophoresis, MCE is the ultimate frontier to develop the miniaturized, integrated, automated all-in-one instruments needed in modern analytical chemistry. By adopting the advanced technologies of micro-machining, lasers and microelectronics, and the latest research achievements in analytical chemistry and biochemistry, the sampling, separation and detection systems of commonly used capillary electrophoresis are integrated with high densities onto glass, quartz, silicon or polymer wafers to form the MCE, which can finish the analysis of multi-step operations such as injection, enrichment, reaction, derivatization, separation, and collection of samples in a portable, efficient and super high speed manner. With reference to the different technological achievements in this area, the latest developments in MCE are reviewed in this article. The preparation mechanisms, surface modifications, and properties of different materials in MCE are compared, and the different sampling, separation and detection systems in MCE are summarized. The performance of MCE in analysis of fluorescent substance, metallic ion, sugar, medicine, nucleic acid, DNA, amino acid, polypeptide and protein is discussed, and the future direction of development is forecast.

Characterization of Proteinuria in Dogue de Bordeaux Dogs, a Breed Predisposed to a Familial Glomerulonephropathy: A Retrospective Study.

PubMed

Lavoué, Rachel; Trumel, Catherine; Smets, Pascale M Y; Braun, Jean-Pierre; Aresu, Luca; Daminet, Sylvie; Concordet, Didier; Palanché, Florence; Peeters, Dominique

2015-01-01

Dogue de Bordeaux dog has been reported to be predisposed to a familial glomerulonephropathy that displays some morphological modifications reported in focal and segmental glomerulosclerosis. Prevalence of quantitatively abnormal renal proteinuria was recently reported to be 33% in this breed. The nature of the proteinuria was assessed by sodium dodecyl sulfate-agarose gel electrophoresis and determinations of urinary markers (urinary retinol-binding protein, urinary N-acetyl-β-glucosaminidase, urinary albumin and urinary immunoglobulin G) on stored specimens. Diagnostic performances of sodium dodecyl sulfate-agarose gel electrophoresis to identify dogs with elevated urinary biomarkers were assessed. Samples from 102 adult Dogue de Bordeaux dogs (47 non-proteinuric [urine protein-to-creatinine ratio ≤ 0.2], 20 borderline-proteinuric [0.2< urine protein-to-creatinine ratio ≤ 0.5] and 35 proteinuric dogs [urine protein-to-creatinine ratio >0.5]) were used, of which 2 were suffering from familial glomerulonephropathy. The electrophoretic protein patterns, for all but one proteinuric dog, were indicative of a glomerular origin and, in all dogs, the urinary albumin concentration related to creatinine concentration and the urinary immunoglobulin G concentration related to creatinine concentration were above the upper limit of the reference interval established for the breed. Sensitivity and specificity of sodium dodecyl sulfate-agarose gel electrophoresis identifying dogs with elevated urinary albumin concentration were 94% and 92%, respectively, while diagnostic performance of sodium dodecyl sulfate-agarose gel electrophoresis in detecting dogs with elevated urinary immunoglobulin G concentration yielded sensitivity and specificity of 90% and 74%, respectively. These results suggest that all proteinuric and some borderline-proteinuric Dogue de Bordeaux dogs likely have underlying glomerular lesions and that sodium dodecyl sulfate-agarose gel electrophoresis and urinary markers might be useful to screen dogs with borderline-proteinuria. Additional investigations are warranted to assess if these findings are related to the familial glomerulonephropathy.

Ground mapping resolution accuracy of a scanning radiometer from a geostationary satellite.

PubMed

Stremler, F G; Khalil, M A; Parent, R J

1977-06-01

Measures of the spatial and spatial rate (frequency) mapping of scanned visual imagery from an earth reference system to a spin-scan geostationary satellite are examined. Mapping distortions and coordinate inversions to correct for these distortions are formulated in terms of geometric transformations between earth and satellite frames of reference. Probabilistic methods are used to develop relations for obtainable mapping resolution when coordinate inversions are employed.

An ethnically relevant consensus Korean reference genome is a step towards personal reference genomes

PubMed Central

Cho, Yun Sung; Kim, Hyunho; Kim, Hak-Min; Jho, Sungwoong; Jun, JeHoon; Lee, Yong Joo; Chae, Kyun Shik; Kim, Chang Geun; Kim, Sangsoo; Eriksson, Anders; Edwards, Jeremy S.; Lee, Semin; Kim, Byung Chul; Manica, Andrea; Oh, Tae-Kwang; Church, George M.; Bhak, Jong

2016-01-01

Human genomes are routinely compared against a universal reference. However, this strategy could miss population-specific and personal genomic variations, which may be detected more efficiently using an ethnically relevant or personal reference. Here we report a hybrid assembly of a Korean reference genome (KOREF) for constructing personal and ethnic references by combining sequencing and mapping methods. We also build its consensus variome reference, providing information on millions of variants from 40 additional ethnically homogeneous genomes from the Korean Personal Genome Project. We find that the ethnically relevant consensus reference can be beneficial for efficient variant detection. Systematic comparison of human assemblies shows the importance of assembly quality, suggesting the necessity of new technologies to comprehensively map ethnic and personal genomic structure variations. In the era of large-scale population genome projects, the leveraging of ethnicity-specific genome assemblies as well as the human reference genome will accelerate mapping all human genome diversity. PMID:27882922

A new method for mapping the three-dimensional atomic distribution within nanoparticles by atom probe tomography (APT).

PubMed

Kim, Se-Ho; Kang, Phil Woong; Park, O Ok; Seol, Jae-Bok; Ahn, Jae-Pyoung; Lee, Ji Yeong; Choi, Pyuck-Pa

2018-07-01

We present a new method of preparing needle-shaped specimens for atom probe tomography from freestanding Pd and C-supported Pt nanoparticles. The method consists of two steps, namely electrophoresis of nanoparticles on a flat Cu substrate followed by electrodeposition of a Ni film acting as an embedding matrix for the nanoparticles. Atom probe specimen preparation can be subsequently carried out by means of focused-ion-beam milling. Using this approach, we have been able to perform correlative atom probe tomography and transmission electron microscopy analyses on both nanoparticle systems. Reliable mass spectra and three-dimensional atom maps could be obtained for Pd nanoparticle specimens. In contrast, atom probe samples prepared from C-supported Pt nanoparticles showed uneven field evaporation and hence artifacts in the reconstructed atom maps. Our developed method is a viable means of mapping the three-dimensional atomic distribution within nanoparticles and is expected to contribute to an improved understanding of the structure-composition-property relationships of various nanoparticle systems. Copyright © 2018 Elsevier B.V. All rights reserved.

Superior Cognitive Mapping through Single Landmark-Related Learning than through Boundary-Related Learning

ERIC Educational Resources Information Center

Zhou, Ruojing; Mou, Weimin

2016-01-01

Cognitive mapping is assumed to be through hippocampus-dependent place learning rather than striatum-dependent response learning. However, we proposed that either type of spatial learning, as long as it involves encoding metric relations between locations and reference points, could lead to a cognitive map. Furthermore, the fewer reference points…

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.

[Inter-laboratory reproducibility of pulsed-field electrophoresis for the study of 12 types of Pseudomonas aeruginosa].

PubMed

Foissaud, V; Puyhardy, J M; Chapalain, J C; Salord, H; Depina, J J; Morillon, M; Nicolas, P; Perrier-Gros-Claude, J D

1999-12-01

The increasing hospital-to-hospital transmission of multiple drug-resistant bacteria is a major concern for bacteriology laboratories involved in nosocomial infection control. The interlaboratory reproducibility of pulsed-field gel electrophoresis (PFGE) for Pseudomonas aeruginosa typing was evaluated by asking four hospital laboratories (two in Lyon, one in Brest, and one in Marseille) to study 11 P. aeruginosa isolates, some of which were epidemiologically related, and the reference strain ATCC 27853. Two laboratories used the Genepath system, one the Chef DR II, system, and one the Chef Mapper system, Bio-Rad, restriction/Spe I. Profiles were read visually and by computerized comparison of restriction band molecular weights (Taxotron, software, PAD Grimont, Pasteur Institute, Paris, France). These two methods led to similar epidemiological conclusions. However, centralization of the data showed poor center-to-center reproducibility due to inadequate standardization of the procedure.

Occurrence of nonspecific reactions among stool specimens tested by the Abbott TestPack rotavirus enzyme immunoassay.

PubMed Central

Lipson, S M; Leonardi, G P; Salo, R J; Schutzbank, T E; Kaplan, M H

1990-01-01

Sixty-five stool specimens obtained from children suffering from gastroenteritis were tested for the presence of antigen to rotavirus by the Abbott TestPack Rotavirus (TestPack) enzyme immunoassay kit. The Kallestad Pathfinder enzyme immunoassay, polyacrylamide gel electrophoresis, immune electron microscopy, and virus isolation were utilized as reference assays. Fifty-four specimens were in accord by TestPack and Kallestad Pathfinder. Among 11 discordant specimens positive with TestPack but negative by Kallestad Pathfinder, rotavirus was not identified by polyacrylamide gel electrophoresis, immune electron microscopy, or isolation in primary African green monkey kidney cell cultures. TestPack displayed a performance specificity of 83%. The inordinately high number of stool specimens reported as false-positive by TestPack precludes the incorporation of this antigen detection kit into our routine regimen of diagnostic virologic testing. Images PMID:2166074

Immunoelectrophoresis - blood

MedlinePlus

IEP - serum; Immunoglobulin electrophoresis - blood; Gamma globulin electrophoresis; Serum immunoglobulin electrophoresis; Amyloidosis - electrophoresis serum; Multiple myeloma - serum electrophoresis; Waldenström - serum electrophoresis

Proteomic Analyses of the Unexplored Sea Anemone Bunodactis verrucosa

PubMed Central

Campos, Alexandre; Turkina, Maria V.; Ribeiro, Tiago; Osorio, Hugo; Vasconcelos, Vítor; Antunes, Agostinho

2018-01-01

Cnidarian toxic products, particularly peptide toxins, constitute a promising target for biomedicine research. Indeed, cnidarians are considered as the largest phylum of generally toxic animals. However, research on peptides and toxins of sea anemones is still limited. Moreover, most of the toxins from sea anemones have been discovered by classical purification approaches. Recently, high-throughput methodologies have been used for this purpose but in other Phyla. Hence, the present work was focused on the proteomic analyses of whole-body extract from the unexplored sea anemone Bunodactis verrucosa. The proteomic analyses applied were based on two methods: two-dimensional gel electrophoresis combined with MALDI-TOF/TOF and shotgun proteomic approach. In total, 413 proteins were identified, but only eight proteins were identified from gel-based analyses. Such proteins are mainly involved in basal metabolism and biosynthesis of antibiotics as the most relevant pathways. In addition, some putative toxins including metalloproteinases and neurotoxins were also identified. These findings reinforce the significance of the production of antimicrobial compounds and toxins by sea anemones, which play a significant role in defense and feeding. In general, the present study provides the first proteome map of the sea anemone B. verrucosa stablishing a reference for future studies in the discovery of new compounds. PMID:29364843

Multidimensional protein fractionation using ProteomeLab PF 2D™ for profiling amyotrophic lateral sclerosis immunity: A preliminary report

PubMed Central

Schlautman, Joshua D; Rozek, Wojciech; Stetler, Robert; Mosley, R Lee; Gendelman, Howard E; Ciborowski, Pawel

2008-01-01

Background The ProteomeLab™ PF 2D platform is a relatively new approach to global protein profiling. Herein, it was used for investigation of plasma proteome changes in amyotrophic lateral sclerosis (ALS) patients before and during immunization with glatiramer acetate (GA) in a clinical trial. Results The experimental design included immunoaffinity depletion of 12 most abundant proteins from plasma samples with the ProteomeLab™ IgY-12 LC10 column kit as first dimension separation, also referred to as immuno-partitioning. Second and third dimension separations of the enriched proteome were performed on the PF 2D platform utilizing 2D isoelectric focusing and RP-HPLC with the resulting fractions collected for analysis. 1D gel electrophoresis was added as a fourth dimension when sufficient protein was available. Protein identification from collected fractions was performed using nano-LC-MS/MS approach. Analysis of differences in the resulting two-dimensional maps of fractions obtained from the PF 2D and the ability to identify proteins from these fractions allowed sensitivity threshold measurements. Masked proteins in the PF 2D fractions are discussed. Conclusion We offer some insight into the strengths and limitations of this emerging proteomic platform. PMID:18789151

Two-dimensional proteome reference map of Prototheca zopfii revealed reduced metabolism and enhanced signal transduction as adaptation to an infectious life style.

PubMed

Murugaiyan, Jayaseelan; Weise, Christoph; von Bergen, Martin; Roesler, Uwe

2013-09-01

Biochemical, serological, and genetic analyses have identified two genotypes of Prototheca zopfii, a unicellular microalga belonging to the family Chlorellaceae. The P. zopfii genotype 1, abundantly present in cow barns and environment, remains nonpathogenic, while P. zopfii genotype 2 has been isolated from cows with bovine mastitis. The present study was carried out to identify the protein expression level difference between the pathogenic and nonpathogenic strains of P. zopfii. A total of 782 protein spots were observed on the 2D fluorescence difference gel electrophoresis (2D DIGE) gels among which 63 and 44 proteins were identified to be overexpressed in genotypes 1 and 2, respectively. The limited number of protein entries specific for Prototheca in public repositories resulted mainly in the identification of proteins described in other algae, microorganisms, or plants. Gene ontology (GO) analysis indicated reduced carbohydrate metabolism in genotype 1, while genotype 2 displayed enhanced DNA binding, kinase activity, and signal transduction. These effects point to metabolic and signaling adaptations in the pathogenic strain and provide insights into the evolution of otherwise highly similar strains. All MS data have been deposited in the ProteomeXchange with identifier PXD000126. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proteomic Analyses of the Unexplored Sea Anemone Bunodactis verrucosa.

PubMed

Domínguez-Pérez, Dany; Campos, Alexandre; Alexei Rodríguez, Armando; Turkina, Maria V; Ribeiro, Tiago; Osorio, Hugo; Vasconcelos, Vítor; Antunes, Agostinho

2018-01-24

Cnidarian toxic products, particularly peptide toxins, constitute a promising target for biomedicine research. Indeed, cnidarians are considered as the largest phylum of generally toxic animals. However, research on peptides and toxins of sea anemones is still limited. Moreover, most of the toxins from sea anemones have been discovered by classical purification approaches. Recently, high-throughput methodologies have been used for this purpose but in other Phyla. Hence, the present work was focused on the proteomic analyses of whole-body extract from the unexplored sea anemone Bunodactis verrucosa . The proteomic analyses applied were based on two methods: two-dimensional gel electrophoresis combined with MALDI-TOF/TOF and shotgun proteomic approach. In total, 413 proteins were identified, but only eight proteins were identified from gel-based analyses. Such proteins are mainly involved in basal metabolism and biosynthesis of antibiotics as the most relevant pathways. In addition, some putative toxins including metalloproteinases and neurotoxins were also identified. These findings reinforce the significance of the production of antimicrobial compounds and toxins by sea anemones, which play a significant role in defense and feeding. In general, the present study provides the first proteome map of the sea anemone B. verrucosa stablishing a reference for future studies in the discovery of new compounds.

Comparative proteomics of human endothelial cell caveolae and rafts using two-dimensional gel electrophoresis and mass spectrometry.

PubMed

Sprenger, Richard R; Speijer, Dave; Back, Jaap Willem; De Koster, Chris G; Pannekoek, Hans; Horrevoets, Anton J G

2004-01-01

The human endothelial cell plasma membrane harbors two subdomains of similar lipid composition, caveolae and rafts, both crucially involved in various essential cellular processes like transcytosis, signal transduction and cholesterol homeostasis. Caveolin-enriched membranes, isolated by either cationic silica or buoyant density methods, were explored by comparing large series of two-dimensional (2-D) maps and subsequent identification of over 100 protein spots by matrix-assisted laser desorption/ionization (MALDI) peptide mass fingerprinting. Improved representation and identification of membrane proteins and valuable information on various post-translational modifications was achieved by the presented optimized procedures for solubilization, destaining and database searching/computing. Whereas the cationic silica purification yielded predominantly known endoplasmic reticulum residents, the cold-detergent method yielded a large number of known caveolae residents, including caveolin-1. Thus, a large part of this subproteome was established, including known (trans-)membrane, signal transduction and glycosyl phosphatidylinositol (GPI)-anchored proteins. Several predicted proteins from the human genome were isolated for the first time from biological samples, including SGRP58, SLP-2, C8ORF2, and XRP-2. These findings and various optimized procedures can serve as a reference to study the differential composition of endothelial cell caveolae and rafts, known to be involved in pathologies like cancer and cardiovascular disease.

Leveraging terminological resources for mapping between rare disease information sources.

PubMed

Rance, Bastien; Snyder, Michelle; Lewis, Janine; Bodenreider, Olivier

2013-01-01

Rare disease information sources are incompletely and inconsistently cross-referenced to one another, making it difficult for information seekers to navigate across them. The development of such cross-references established manually by experts is generally labor intensive and costly. To develop an automatic mapping between two of the major rare diseases information sources, GARD and Orphanet, by leveraging terminological resources, especially the UMLS. We map the rare disease terms from Orphanet and ORDR to the UMLS. We use the UMLS as a pivot to bridge between the rare disease terminologies. We compare our results to a mapping obtained through manually established cross-references to OMIM. Our mapping has a precision of 94%, a recall of 63% and an F1-score of 76%. Our automatic mapping should help facilitate the development of more complete and consistent cross-references between GARD and Orphanet, and is applicable to other rare disease information sources as well.

Quality evaluation of six bioactive constituents in goji berry based on capillary electrophoresis field amplified sample stacking.

PubMed

Wang, Wei-Feng; Yang, Jun-Li; Shi, Yan-Ping

2018-04-27

Goji berry, fruits of the plant Lycium barbarum L., has long been used as traditional medicine and functional food in China. In this work, a simple and easy-operation on-line concentration capillary electrophoresis (CE) for detection flavonoids in goji berry was developed by coupling of field amplified sample stacking (FASS) with an electroosmotic (EOF) pump driving water removal process. Due to the EOF pump and electrokinetic injection showing different influence on the concentration, the analytes injection condition should be systemically studied. Thereafter, the verification of the analytes injection conditions was achieved using response surface experimental design. Under the optimum conditions, 86-271 folds sensitivity enhancement upon normal capillary zone electrophoresis (CZE, 50 mbar × 5 s) were achieved for six flavonoids, and the detection limits ranged from 0.35 to 1.82 ng/mL; the LOQ ranged from 1.20 to 6.01 ng/mL. Eventually, the proposed method was applied to detect flavonoids in 30 goji berry samples from different habitats of China; and the results indicated that the flavonoids were rich in the eluent of 30-60% methanol, which provided a reference for extraction of goji berry flavonoids. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

hsp65 PCR-restriction analysis (PRA) with capillary electrophoresis in comparison to three other methods for identification of Mycobacterium species.

PubMed

Sajduda, Anna; Martin, Anandi; Portaels, Françoise; Palomino, Juan Carlos

2010-02-01

We developed a scheme for rapid identification of Mycobacterium species using an automated fluorescence capillary electrophoresis instrument. A 441-bp region of the hsp65 gene was examined using PCR-restriction analysis (PRA). The assay was initially evaluated on 38 reference strains. The observed sizes of restriction fragments were consistently smaller than the real sizes for each of the species as deduced from the sequence analysis (mean variance=7bp). Nevertheless, the obtained PRA patterns were highly reproducible and resulted in correct species identifications. A blind test was then successfully performed on 64 test isolates previously characterized by conventional biochemical methods, a commercial INNO-LiPA Mycobacteria assay and/or sequence determination of the 5' end of 16S rRNA gene. A total of 14 of 64 isolates were erroneously identified by conventional methods (78% accuracy). In contrast, PRA performed very well in comparison with the LiPA (89% concordance) and especially with DNA sequencing (93.3% of concordant results). Also, PRA identified seven isolates representing five previously unreported hsp65 alleles. We conclude that hsp65 PRA based on automated capillary electrophoresis is a rapid, simple and reliable method for identification of mycobacteria. Copyright 2010 Elsevier B.V. All rights reserved.

Gel Electrophoresis of Gold-DNA Nanoconjugates

DOE PAGES

Pellegrino, T.; Sperling, R. A.; Alivisatos, A. P.; ...

2007-01-01

Gold-DNA conjugates were investigated in detail by a comprehensive gel electrophoresis study based on 1200 gels. A controlled number of single-stranded DNA of different length was attached specifically via thiol-Au bonds to phosphine-stabilized colloidal gold nanoparticles. Alternatively, the surface of the gold particles was saturated with single stranded DNA of different length either specifically via thiol-Au bonds or by nonspecific adsorption. From the experimentally determined electrophoretic mobilities, estimates for the effective diameters of the gold-DNA conjugates were derived by applying two different data treatment approaches. The first method is based on making a calibration curve for the relation between effectivemore » diameters and mobilities with gold nanoparticles of known diameter. The second method is based on Ferguson analysis which uses gold nanoparticles of known diameter as reference database. Our study shows that effective diameters derived from gel electrophoresis measurements are affected with a high error bar as the determined values strongly depend on the method of evaluation, though relative changes in size upon binding of molecules can be detected with high precision. Furthermore, in this study, the specific attachment of DNA via gold-thiol bonds to Au nanoparticles is compared to nonspecific adsorption of DNA. Also, the maximum number of DNA molecules that can be bound per particle was determined.« less

Proteomics in the study of the molecular taxonomy and epidemiology of bacterial pathogens.

PubMed

Cash, Phillip

2009-06-01

The ability to discriminate bacterial isolates is important for a number of areas of research in Medical Microbiology, particularly in defining bacterial taxonomy and monitoring transmission in epidemiological investigations. Molecular techniques capable of typing bacteria at the level of the genome and proteome are now widely used for these investigations. This review considers two electrophoretic methods for typing bacteria on the basis of their proteomes, namely 1-D SDS-PAGE and 2-DE. The application of these two techniques for bacterial typing is described with reference to two publications that appeared in Electrophoresis [Costa, Electrophoresis 1990, 11, 382-391 and Cash et al., Electrophoresis 1997, 18, 1472-1482]. Even though these methods have been used for nearly 20 years to differentiate bacterial isolates they remain key technologies in proteome-based typing methods. The developments that have arisen from the two key papers are described in order to highlight the advantages and disadvantages in typing bacteria at the level of their proteomes. Some of the difficulties associated with electrophoretic typing methods can be overcome by using non-gel proteomic methods based on MS to provide improved sensitivity and specificity. The application of proteomic methods to investigate bacterial taxonomy, epidemiology and pathogenesis in general has significant potential in furthering our understanding of infectious diseases.

Assessing ecological departure from reference conditions with the Fire Regime Condition Class (FRCC) Mapping Tool

Treesearch

Stephen W. Barrett; Thomas DeMeo; Jeffrey L. Jones; J.D. Zeiler; Lee C. Hutter

2006-01-01

Knowledge of ecological departure from a range of reference conditions provides a critical context for managing sustainable ecosystems. Fire Regime Condition Class (FRCC) is a qualitative measure characterizing possible departure from historical fire regimes. The FRCC Mapping Tool was developed as an ArcMap extension utilizing the protocol identified by the Interagency...

Development and Characterization of Sodium Hyaluronate Microparticle-Based Sustained Release Formulation of Recombinant Human Growth Hormone Prepared by Spray-Drying.

PubMed

Kim, Sun J; Kim, Chan W

2016-02-01

The purpose of this study was to develop and characterize a sodium hyaluronate microparticle-based sustained release formulation of recombinant human growth hormone (SR-rhGH) prepared by spray-drying. Compared to freeze-drying, spray-dried SR-rhGH showed not only prolonged release profiles but also better particle property and injectability. The results of size-exclusion high-performance liquid chromatography showed that no aggregate was detected, and dimer was just about 2% and also did not increase with increase of inlet temperature up to 150 °C. Meanwhile, the results of reversed-phase high-performance liquid chromatography revealed that related proteins increased slightly from 4.6% at 100 °C to 6.3% at 150 °C. Thermal mapping test proved that product temperature did not become high to cause protein degradation during spray-drying because thermal energy was used for the evaporation of surface moisture of droplets. The structural characterization by peptide mapping, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and circular dichroism revealed that the primary, secondary, and tertiary structures of rhGH in SR-rhGH were highly comparable to those of reference somatropin materials. The biological characterization by rat weight gain and cell proliferation assays provided that bioactivity of SR-rhGH was equivalent to that of native hGH. These data establish that spray-dried SR-rhGH is highly stable by preserving intact rhGH and hyaluronate microparticle-based formulation by spray-drying can be an alternative delivery system for proteins. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Expression, Purification and Characterization of GMZ2'.10C, a Complex Disulphide-Bonded Fusion Protein Vaccine Candidate against the Asexual and Sexual Life-Stages of the Malaria-Causing Plasmodium falciparum Parasite.

PubMed

Mistarz, Ulrik H; Singh, Susheel K; Nguyen, Tam T T N; Roeffen, Will; Yang, Fen; Lissau, Casper; Madsen, Søren M; Vrang, Astrid; Tiendrebeogo, Régis W; Kana, Ikhlaq H; Sauerwein, Robert W; Theisen, Michael; Rand, Kasper D

2017-09-01

Production and characterization of a chimeric fusion protein (GMZ2'.10C) which combines epitopes of key malaria parasite antigens: glutamate-rich protein (GLURP), merozoite surface protein 3 (MSP3), and the highly disulphide bonded Pfs48/45 (10C). GMZ2'.10C is a potential candidate for a multi-stage malaria vaccine that targets both transmission and asexual life-cycle stages of the parasite. GMZ2'.10C was produced in Lactococcus lactis and purified using either an immunoaffinity purification (IP) or a conventional purification (CP) method. Protein purity and stability was analysed by RP-HPLC, SEC-HPLC, 2-site ELISA, gel-electrophoresis and Western blotting. Structural characterization (mass analysis, peptide mapping and cysteine connectivity mapping) was performed by LC-MS/MS. CP-GMZ2'.10C resulted in similar purity, yield, structure and stability as compared to IP-GMZ2'.10C. CP-GMZ2'.10C and IP-GMZ2'.10C both elicited a high titer of transmission blocking (TB) antibodies in rodents. The intricate disulphide-bond connectivity of C-terminus Pfs48/45 was analysed by tandem mass spectrometry and was established for GMZ2'.10C and two reference fusion proteins encompassing similar parts of Pfs48/45. GMZ2'.10C, combining GMZ2' and correctly-folded Pfs48/45 can be produced by the Lactoccus lactis P170 based expression system in purity and quality for pharmaceutical development and elicit high level of TB antibodies. The cysteine connectivity for the 10C region of Pfs48/45 was revealed experimentally, providing an important guideline for employing the Pfs48/45 antigen in vaccine design.

The Proteome of Shigella flexneri 2a 2457T Grown at 30 and 37 °C*

PubMed Central

Zhu, Li; Zhao, Ge; Stein, Robert; Zheng, Xuexue; Hu, Wei; Shang, Na; Bu, Xin; Liu, Xiankai; Wang, Jie; Feng, Erling; Wang, Bin; Zhang, Xuemin; Ye, Qinong; Huang, Peitang; Zeng, Ming; Wang, Hengliang

2010-01-01

To upgrade the proteome reference map of Shigella flexneri 2a 2457T, the protein expression profiles of log phase and stationary phase cells grown at 30 and 37 °C were thoroughly analyzed using multiple overlapping narrow pH range (between pH 4.0 and 11.0) two-dimensional gel electrophoresis. A total of 723 spots representing 574 protein entries were identified by MALDI-TOF/TOF MS, including the majority of known key virulence factors. 64 hypothetical proteins and six misannotated proteins were also experimentally identified. A comparison between the four proteome maps showed that most of the virulence-related proteins were up-regulated at 37 °C, and the differences were more notable in stationary phase cells, suggesting that the expressions of these virulence factors were not only controlled by temperature but also controlled by the nutrients available in the environment. The expression patterns of some virulence-related genes under the four different conditions suggested that they might also be regulated at the post-transcriptional level. A further significant finding was that the expression of the protein ArgT was dramatically up-regulated at 30 °C. The results of semiquantitative RT-PCR analysis showed that expression of argT was not regulated at the transcriptional level. Therefore, we carried out a series of experiments to uncover the mechanism regulating ArgT levels and found that the differential expression of ArgT was due to its degradation by a periplasmic protease, HtrA, whose activity, but not its synthesis, was affected by temperature. The cleavage site in ArgT was between position 160 (Val) and position 161 (Ala). These results may provide useful insights for understanding the physiology and pathogenesis of S. flexneri. PMID:20164057

The proteome of Shigella flexneri 2a 2457T grown at 30 and 37 degrees C.

PubMed

Zhu, Li; Zhao, Ge; Stein, Robert; Zheng, Xuexue; Hu, Wei; Shang, Na; Bu, Xin; Liu, Xiankai; Wang, Jie; Feng, Erling; Wang, Bin; Zhang, Xuemin; Ye, Qinong; Huang, Peitang; Zeng, Ming; Wang, Hengliang

2010-06-01

To upgrade the proteome reference map of Shigella flexneri 2a 2457T, the protein expression profiles of log phase and stationary phase cells grown at 30 and 37 degrees C were thoroughly analyzed using multiple overlapping narrow pH range (between pH 4.0 and 11.0) two-dimensional gel electrophoresis. A total of 723 spots representing 574 protein entries were identified by MALDI-TOF/TOF MS, including the majority of known key virulence factors. 64 hypothetical proteins and six misannotated proteins were also experimentally identified. A comparison between the four proteome maps showed that most of the virulence-related proteins were up-regulated at 37 degrees C, and the differences were more notable in stationary phase cells, suggesting that the expressions of these virulence factors were not only controlled by temperature but also controlled by the nutrients available in the environment. The expression patterns of some virulence-related genes under the four different conditions suggested that they might also be regulated at the post-transcriptional level. A further significant finding was that the expression of the protein ArgT was dramatically up-regulated at 30 degrees C. The results of semiquantitative RT-PCR analysis showed that expression of argT was not regulated at the transcriptional level. Therefore, we carried out a series of experiments to uncover the mechanism regulating ArgT levels and found that the differential expression of ArgT was due to its degradation by a periplasmic protease, HtrA, whose activity, but not its synthesis, was affected by temperature. The cleavage site in ArgT was between position 160 (Val) and position 161 (Ala). These results may provide useful insights for understanding the physiology and pathogenesis of S. flexneri.

Two-dimensional proteome reference maps for the human pathogenic filamentous fungus Aspergillus fumigatus.

PubMed

Vödisch, Martin; Albrecht, Daniela; Lessing, Franziska; Schmidt, André D; Winkler, Robert; Guthke, Reinhard; Brakhage, Axel A; Kniemeyer, Olaf

2009-03-01

The filamentous fungus Aspergillus fumigatus has become the most important airborne fungal pathogen causing life-threatening infections in immunosuppressed patients. We established a 2-D reference map for A. fumigatus. Using MALDI-TOF-MS/MS, we identified 381 spots representing 334 proteins. Proteins involved in cellular metabolism, protein synthesis, transport processes and cell cycle were most abundant. Furthermore, we established a protocol for the isolation of mitochondria of A. fumigatus and developed a mitochondrial proteome reference map. 147 proteins represented by 234 spots were identified.

Rapid Fast-Mapping Abilities in 2-Year-Olds

ERIC Educational Resources Information Center

Spiegel, Chad; Halberda, Justin

2011-01-01

Learning a new word consists of two primary tasks that have often been conflated into a single process: "referent selection", in which a child must determine the correct referent of a novel label, and "referent retention", which is the ability to store this newly formed label-object mapping in memory for later use. In addition, children must be…

Embodied Interaction Priority: Other's Body Part Affects Numeral-Space Mappings.

PubMed

You, Xuqun; Zhang, Yu; Zhu, Rongjuan; Guo, Yu

2018-01-01

Traditionally, the spatial-numerical association of response codes (SNARC) effect was presented in two-choice condition, in which only one individual reacted to both even (small) and odd (large) numbers. Few studies explored SNARC effect in a social situation. Moreover, there are many reference frames involved in SNARC effect, and it has not yet been investigated which reference frame is dominated when two participants perform the go-nogo task together. In the present study, we investigated which reference frame plays a primary role in SNARC effect when allocentric and egocentric reference frames were consistent or inconsistent in social settings. Furthermore, we explored how two actors corepresent number-space mapping interactively. Results of the two experiments demonstrated that egocentric reference frame was at work primarily when two reference frames were consistent and inconsistent. This shows that body-centered coordinate frames influence number-space mapping in social settings, and one actor may represent another actor's action and tasks.

Adaptive optimization of reference intensity for optical coherence imaging using galvanometric mirror tilting method

NASA Astrophysics Data System (ADS)

Kim, Ji-hyun; Han, Jae-Ho; Jeong, Jichai

2015-09-01

Integration time and reference intensity are important factors for achieving high signal-to-noise ratio (SNR) and sensitivity in optical coherence tomography (OCT). In this context, we present an adaptive optimization method of reference intensity for OCT setup. The reference intensity is automatically controlled by tilting a beam position using a Galvanometric scanning mirror system. Before sample scanning, the OCT system acquires two dimensional intensity map with normalized intensity and variables in color spaces using false-color mapping. Then, the system increases or decreases reference intensity following the map data for optimization with a given algorithm. In our experiments, the proposed method successfully corrected the reference intensity with maintaining spectral shape, enabled to change integration time without manual calibration of the reference intensity, and prevented image degradation due to over-saturation and insufficient reference intensity. Also, SNR and sensitivity could be improved by increasing integration time with automatic adjustment of the reference intensity. We believe that our findings can significantly aid in the optimization of SNR and sensitivity for optical coherence tomography systems.

Gold occurrences in the Greenville 1 degree by 2 degrees Quadrangle, South Carolina, Georgia, and North Carolina

USGS Publications Warehouse

D'Agostino, John P.; Mason, George T.; Zupan, Alan J.W.; Maybin, Arthur H.; German, Jerry M.; Abrams, Charlotte E.

1994-01-01

All of the gold mines, prospects, placers, and occurrences known in the Greenville 1° x 2° quadrangle are tabulated in this report. The table lists, in consecutive order by county (fig. 1), the map number of each feature, which is located either on the accompanying Greenville 1° x 2° quadrangle map or figure 2. The known name of the feature; the 7.5' topographic map on the which the gold site is located (if known, within 25 ft or 7.6 m), the Universal Transverse Mercator (UTM) northing and easting grid coordinates from the appropriate 7.5' topographic map; the commodity; remarks; and references are also listed. Some locations are known, but many sites are not verified and their locations are only approximate. References are listed in References Cited and referred to by number to save space.

Linkage maps of the Atlantic salmon (Salmo salar) genome derived from RAD sequencing

PubMed Central

2014-01-01

Background Genetic linkage maps are useful tools for mapping quantitative trait loci (QTL) influencing variation in traits of interest in a population. Genotyping-by-sequencing approaches such as Restriction-site Associated DNA sequencing (RAD-Seq) now enable the rapid discovery and genotyping of genome-wide SNP markers suitable for the development of dense SNP linkage maps, including in non-model organisms such as Atlantic salmon (Salmo salar). This paper describes the development and characterisation of a high density SNP linkage map based on SbfI RAD-Seq SNP markers from two Atlantic salmon reference families. Results Approximately 6,000 SNPs were assigned to 29 linkage groups, utilising markers from known genomic locations as anchors. Linkage maps were then constructed for the four mapping parents separately. Overall map lengths were comparable between male and female parents, but the distribution of the SNPs showed sex-specific patterns with a greater degree of clustering of sire-segregating SNPs to single chromosome regions. The maps were integrated with the Atlantic salmon draft reference genome contigs, allowing the unique assignment of ~4,000 contigs to a linkage group. 112 genome contigs mapped to two or more linkage groups, highlighting regions of putative homeology within the salmon genome. A comparative genomics analysis with the stickleback reference genome identified putative genes closely linked to approximately half of the ordered SNPs and demonstrated blocks of orthology between the Atlantic salmon and stickleback genomes. A subset of 47 RAD-Seq SNPs were successfully validated using a high-throughput genotyping assay, with a correspondence of 97% between the two assays. Conclusions This Atlantic salmon RAD-Seq linkage map is a resource for salmonid genomics research as genotyping-by-sequencing becomes increasingly common. This is aided by the integration of the SbfI RAD-Seq SNPs with existing reference maps and the draft reference genome, as well as the identification of putative genes proximal to the SNPs. Differences in the distribution of recombination events between the sexes is evident, and regions of homeology have been identified which are reflective of the recent salmonid whole genome duplication. PMID:24571138

URPD: a specific product primer design tool

PubMed Central

2012-01-01

Background Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users. Findings URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers. Conclusions URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/. PMID:22713312

URPD: a specific product primer design tool.

PubMed

Chuang, Li-Yeh; Cheng, Yu-Huei; Yang, Cheng-Hong

2012-06-19

Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users. URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers. URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/.

Leveraging Terminological Resources for Mapping between Rare Disease Information Sources

PubMed Central

Rance, Bastien; Snyder, Michelle; Lewis, Janine; Bodenreider, Olivier

2015-01-01

Background Rare disease information sources are incompletely and inconsistently cross-referenced to one another, making it difficult for information seekers to navigate across them. The development of such cross-references established manually by experts is generally labor intensive and costly. Objectives To develop an automatic mapping between two of the major rare diseases information sources, GARD and Orphanet, by leveraging terminological resources, especially the UMLS. Methods We map the rare disease terms from Orphanet and ORDR to the UMLS. We use the UMLS as a pivot to bridge between the rare disease terminologies. We compare our results to a mapping obtained through manually established cross-references to OMIM. Results Our mapping has a precision of 94%, a recall of 63% and an F1-score of 76%. Our automatic mapping should help facilitate the development of more complete and consistent cross-references between GARD and Orphanet, and is applicable to other rare disease information sources as well. PMID:23920611

Linking in situ LAI and fine resolution remote sensing data to map reference LAI over cropland and grassland using geostatistical regression method

NASA Astrophysics Data System (ADS)

He, Yaqian; Bo, Yanchen; Chai, Leilei; Liu, Xiaolong; Li, Aihua

2016-08-01

Leaf Area Index (LAI) is an important parameter of vegetation structure. A number of moderate resolution LAI products have been produced in urgent need of large scale vegetation monitoring. High resolution LAI reference maps are necessary to validate these LAI products. This study used a geostatistical regression (GR) method to estimate LAI reference maps by linking in situ LAI and Landsat TM/ETM+ and SPOT-HRV data over two cropland and two grassland sites. To explore the discrepancies of employing different vegetation indices (VIs) on estimating LAI reference maps, this study established the GR models for different VIs, including difference vegetation index (DVI), normalized difference vegetation index (NDVI), and ratio vegetation index (RVI). To further assess the performance of the GR model, the results from the GR and Reduced Major Axis (RMA) models were compared. The results show that the performance of the GR model varies between the cropland and grassland sites. At the cropland sites, the GR model based on DVI provides the best estimation, while at the grassland sites, the GR model based on DVI performs poorly. Compared to the RMA model, the GR model improves the accuracy of reference LAI maps in terms of root mean square errors (RMSE) and bias.

Application of whole genome sequence data in analyzing the molecular epidemiology of Shiga toxin-producing Escherichia coli O157:H7/H.

PubMed

Yokoyama, Eiji; Hirai, Shinichiro; Ishige, Taichiro; Murakami, Satoshi

2018-01-02

Seventeen clusters of Shiga toxin-producing Escherichia coli O157:H7/- (O157) strains, determined by cluster analysis of pulsed-field gel electrophoresis patterns, were analyzed using whole genome sequence (WGS) data to investigate this pathogen's molecular epidemiology. The 17 clusters included 136 strains containing strains from nine outbreaks, with each outbreak caused by a single source contaminated with the organism, as shown by epidemiological contact surveys. WGS data of these strains were used to identify single nucleotide polymorphisms (SNPs) by two methods: short read data were directly mapped to a reference genome (mapping derived SNPs) and common SNPs between the mapping derived SNPs and SNPs in assembled data of short read data (common SNPs). Among both SNPs, those that were detected in genes with a gap were excluded to remove ambiguous SNPs from further analysis. The effectiveness of both SNPs was investigated among all the concatenated SNPs that were detected (whole SNP set); SNPs were divided into three categories based on the genes in which they were located (i.e., backbone SNP set, O-island SNP set, and mobile element SNP set); and SNPs in non-coding regions (intergenic region SNP set). When SNPs from strains isolated from the nine single source derived outbreaks were analyzed using an unweighted pair group method with arithmetic mean tree (UPGMA) and a minimum spanning tree (MST), the maximum pair-wise distances of the backbone SNP set of the mapping derived SNPs were significantly smaller than those of the whole and intergenic region SNP set on both UPGMAs and MSTs. This significant difference was also observed when the backbone SNP set of the common SNPs were examined (Steel-Dwass test, P≤0.01). When the maximum pair-wise distances were compared between the mapping derived and common SNPs, significant differences were observed in those of the whole, mobile element, and intergenic region SNP set (Wilcoxon signed rank test, P≤0.01). When all the strains included in one complex on an MST or one cluster on a UPGMA were designated as the same genotype, the values of the Hunter-Gaston Discriminatory Power Index for the backbone SNP set of the mapping derived and common SNPs were higher than those of other SNP sets. In contrast, the mobile element SNP set could not robustly subdivide lineage I strains of tested O157 strains using both the mapping derived and common SNPs. These results suggested that the backbone SNP set were the most effective for analysis of WGS data for O157 in enabling an appropriation of its molecular epidemiology. Copyright © 2017 Elsevier B.V. All rights reserved.

Simultaneous comparison and assessment of eight remotely sensed maps of Philippine forests

NASA Astrophysics Data System (ADS)

Estoque, Ronald C.; Pontius, Robert G.; Murayama, Yuji; Hou, Hao; Thapa, Rajesh B.; Lasco, Rodel D.; Villar, Merlito A.

2018-05-01

This article compares and assesses eight remotely sensed maps of Philippine forest cover in the year 2010. We examined eight Forest versus Non-Forest maps reclassified from eight land cover products: the Philippine Land Cover, the Climate Change Initiative (CCI) Land Cover, the Landsat Vegetation Continuous Fields (VCF), the MODIS VCF, the MODIS Land Cover Type product (MCD12Q1), the Global Tree Canopy Cover, the ALOS-PALSAR Forest/Non-Forest Map, and the GlobeLand30. The reference data consisted of 9852 randomly distributed sample points interpreted from Google Earth. We created methods to assess the maps and their combinations. Results show that the percentage of the Philippines covered by forest ranges among the maps from a low of 23% for the Philippine Land Cover to a high of 67% for GlobeLand30. Landsat VCF estimates 36% forest cover, which is closest to the 37% estimate based on the reference data. The eight maps plus the reference data agree unanimously on 30% of the sample points, of which 11% are attributable to forest and 19% to non-forest. The overall disagreement between the reference data and Philippine Land Cover is 21%, which is the least among the eight Forest versus Non-Forest maps. About half of the 9852 points have a nested structure such that the forest in a given dataset is a subset of the forest in the datasets that have more forest than the given dataset. The variation among the maps regarding forest quantity and allocation relates to the combined effects of the various definitions of forest and classification errors. Scientists and policy makers must consider these insights when producing future forest cover maps and when establishing benchmarks for forest cover monitoring.

High resolution clear native electrophoresis for in-gel functional assays and fluorescence studies of membrane protein complexes.

PubMed

Wittig, Ilka; Karas, Michael; Schägger, Hermann

2007-07-01

Clear native electrophoresis and blue native electrophoresis are microscale techniques for the isolation of membrane protein complexes. The Coomassie Blue G-250 dye, used in blue native electrophoresis, interferes with in-gel fluorescence detection and in-gel catalytic activity assays. This problem can be overcome by omitting the dye in clear native electrophoresis. However, clear native electrophoresis suffers from enhanced protein aggregation and broadening of protein bands during electrophoresis and therefore has been used rarely. To preserve the advantages of both electrophoresis techniques we substituted Coomassie dye in the cathode buffer of blue native electrophoresis by non-colored mixtures of anionic and neutral detergents. Like Coomassie dye, these mixed micelles imposed a charge shift on the membrane proteins to enhance their anodic migration and improved membrane protein solubility during electrophoresis. This improved clear native electrophoresis offers a high resolution of membrane protein complexes comparable to that of blue native electrophoresis. We demonstrate the superiority of high resolution clear native electrophoresis for in-gel catalytic activity assays of mitochondrial complexes I-V. We present the first in-gel histochemical staining protocol for respiratory complex III. Moreover we demonstrate the special advantages of high resolution clear native electrophoresis for in-gel detection of fluorescent labeled proteins labeled by reactive fluorescent dyes and tagged by fluorescent proteins. The advantages of high resolution clear native electrophoresis make this technique superior for functional proteomics analyses.

A complete mass spectrometric map for the analysis of the yeast proteome and its application to quantitative trait analysis

PubMed Central

Picotti, Paola; Clement-Ziza, Mathieu; Lam, Henry; Campbell, David S.; Schmidt, Alexander; Deutsch, Eric W.; Röst, Hannes; Sun, Zhi; Rinner, Oliver; Reiter, Lukas; Shen, Qin; Michaelson, Jacob J.; Frei, Andreas; Alberti, Simon; Kusebauch, Ulrike; Wollscheid, Bernd; Moritz, Robert; Beyer, Andreas; Aebersold, Ruedi

2013-01-01

Complete reference maps or datasets, like the genomic map of an organism, are highly beneficial tools for biological and biomedical research. Attempts to generate such reference datasets for a proteome so far failed to reach complete proteome coverage, with saturation apparent at approximately two thirds of the proteomes tested, even for the most thoroughly characterized proteomes. Here, we used a strategy based on high-throughput peptide synthesis and mass spectrometry to generate a close to complete reference map (97% of the genome-predicted proteins) of the S. cerevisiae proteome. We generated two versions of this mass spectrometric map one supporting discovery- (shotgun) and the other hypothesis-driven (targeted) proteomic measurements. The two versions of the map, therefore, constitute a complete set of proteomic assays to support most studies performed with contemporary proteomic technologies. The reference libraries can be browsed via a web-based repository and associated navigation tools. To demonstrate the utility of the reference libraries we applied them to a protein quantitative trait locus (pQTL) analysis, which requires measurement of the same peptides over a large number of samples with high precision. Protein measurements over a set of 78 S. cerevisiae strains revealed a complex relationship between independent genetic loci, impacting on the levels of related proteins. Our results suggest that selective pressure favors the acquisition of sets of polymorphisms that maintain the stoichiometry of protein complexes and pathways. PMID:23334424

Digital files for northeast Asia geodynamics, mineral deposit location, and metallogenic belt maps, stratigraphic columns, descriptions of map units, and descriptions of metallogenic belts

USGS Publications Warehouse

Nokleberg, Warren J.; Badarch, Gombosuren; Berzin, Nikolai A.; Diggles, Michael F.; Hwang, Duk-Hwan; Khanchuk, Alexander I.; Miller, Robert J.; Naumova, Vera V.; Obolensky, Alexander A.; Ogasawara, Masatsugu; Parfenov, Leonid M.; Prokopiev, Andrei V.; Rodionov, Sergey M.; Yan, Hongquan

2004-01-01

This is the online version of a CD-ROM publication. It contains all of the data that are on the disc but extra files have been removed: index files, software installers, and Windows autolaunch files. This publication contains a a series of files for Northeast Asia geodynamics, mineral deposit location, and metallogenic belt maps descriptions of map units and metallogenic belts, and stratigraphic columns. This region includes Eastern Siberia, Russian Far East, Mongolia, Northeast China, South Korea, and Japan. The files include: (1) a geodynamics map at a scale of 1:5,000,000; (2) page-size stratigraphic columns for major terranes; (3) a generalized geodynamics map at a scale of 1:15,000,000; (4) a mineral deposit location map at a scale of 1:7,500,000; (5) metallogenic belt maps at a scale of 1:15,000,000; (6) detailed descriptions of geologic units with references; (7) detailed descriptions of metallogenic belts with references; and (8) summary mineral deposit and metallogenic belt tables. The purpose of this publication is to provide high-quality, digital graphic files for maps and figures, and Word files for explanations, descriptions, and references to customers and users.

Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium.

PubMed Central

Hackett, N R; Bobovnikova, Y; Heyrovska, N

1994-01-01

Phenotypic variants of Halobacterium salinarium NRC-1 arise at a frequency of 10(-2). These result from transpositions of halobacterial insertion sequences and rearrangements mediated by halobacterial insertion sequences. We have tested the hypothesis that such mutations are confined to only a portion of the genome by comparing the chromosomal restriction map of H. salinarium NRC-1 and that of the derivative S9, which was made in 1969. The two chromosomes were mapped by using two-dimensional pulsed-field gel electrophoresis and the restriction enzymes AflII, AseI, and DraI. A comparison of the two deduced maps showed a domain of about 210 kbp to be subject to many rearrangements, including an inversion in S9 relative to NRC-1. However, the rest of the chromosome was conserved among NRC-1, S9, and an independent Halobacterium isolate, GRB, previously mapped by St. Jean et al. (A. St. Jean, B. A. Trieselmann, and R. L. Charlebois, Nucleic Acids Res. 22:1476-1483, 1994). This concurs with data from eubacteria suggesting strong selective forces maintaining gene order even in the face of rearrangement events occurring at a high frequency. Images PMID:8002597

Conservation of chromosomal arrangement among three strains of the genetically unstable archaeon Halobacterium salinarium.

PubMed

Hackett, N R; Bobovnikova, Y; Heyrovska, N

1994-12-01

Phenotypic variants of Halobacterium salinarium NRC-1 arise at a frequency of 10(-2). These result from transpositions of halobacterial insertion sequences and rearrangements mediated by halobacterial insertion sequences. We have tested the hypothesis that such mutations are confined to only a portion of the genome by comparing the chromosomal restriction map of H. salinarium NRC-1 and that of the derivative S9, which was made in 1969. The two chromosomes were mapped by using two-dimensional pulsed-field gel electrophoresis and the restriction enzymes AflII, AseI, and DraI. A comparison of the two deduced maps showed a domain of about 210 kbp to be subject to many rearrangements, including an inversion in S9 relative to NRC-1. However, the rest of the chromosome was conserved among NRC-1, S9, and an independent Halobacterium isolate, GRB, previously mapped by St. Jean et al. (A. St. Jean, B. A. Trieselmann, and R. L. Charlebois, Nucleic Acids Res. 22:1476-1483, 1994). This concurs with data from eubacteria suggesting strong selective forces maintaining gene order even in the face of rearrangement events occurring at a high frequency.

Geologic map of Detrital, Hualapai, and Sacramento Valleys and surrounding areas, northwest Arizona

USGS Publications Warehouse

Beard, L. Sue; Kennedy, Jeffrey; Truini, Margot; Felger, Tracey

2011-01-01

A 1:250,000-scale geologic map and report covering the Detrital, Hualapai, and Sacramento valleys in northwest Arizona is presented for the purpose of improving understanding of the geology and geohydrology of the basins beneath those valleys. The map was compiled from existing geologic mapping, augmented by digital photogeologic reconnaissance mapping. The most recent geologic map for the area, and the only digital one, is the 1:1,000,000-scale Geologic Map of Arizona. The larger scale map presented here includes significantly more detailed geology than the Geologic Map of Arizona in terms of accuracy of geologic unit contacts, number of faults, fault type, fault location, and details of Neogene and Quaternary deposits. Many sources were used to compile the geology; the accompanying geodatabase includes a source field in the polygon feature class that lists source references for polygon features. The citations for the source field are included in the reference section.

Comparison of Serum Protein Electrophoresis Values in Wild and Captive Whooping Cranes ( Grus americana ).

PubMed

Hausmann, Jennifer C; Cray, Carolyn; Hartup, Barry K

2015-09-01

Protein electrophoresis of serum samples from endangered, wild whooping cranes ( Grus americana ) was performed to help assess the health of the only self-sustaining, migratory population in North America. Serum samples from wild adult cranes (n = 22) were taken at Aransas National Wildlife Refuge, Texas, USA during winter. Wild juvenile cranes (n = 26) were sampled at Wood Buffalo National Park, Northwest Territories, Canada, in midsummer. All captive crane samples were acquired from the International Crane Foundation, Baraboo, WI, USA. Captive adult cranes (n = 30) were sampled during annual examinations, and archived serum samples from captive juvenile cranes (n = 19) were selected to match the estimated age of wild juveniles. Wild juveniles had significantly lower concentrations of all protein fractions than wild adults, except for prealbumin and γ globulins. All protein fraction concentrations for wild juveniles were significantly lower compared with captive juveniles, except for prealbumin and γ globulins, which were higher. Wild adults had significantly greater γ globulin concentrations than captive adults. Captive juveniles had significantly lower prealbumin and albumin concentrations and albumin : globulin ratios than captive adults. The higher γ globulin concentrations in wild versus captive cranes are likely because of increased antigenic exposure and immune stimulation. Protein fraction concentrations vary significantly with age and natural history in this species. Reference intervals for serum protein electrophoresis results from captive adult whooping cranes are provided in this study.

Development of an On-animal Separation-based Sensor for Monitoring Drug Metabolism in Freely Roaming Sheep

PubMed Central

Scott, David E.; Willis, Sean D.; Gabbert, Seth; Johnson, Dave A.; Naylor, Erik; Janle, Elsa M.; Krichevsky, Janice E.; Lunte, Craig E.; Lunte, Susan M.

2015-01-01

The development of an on-animal separation-based sensor that can be employed for monitoring drug metabolism in a freely roaming sheep is described. The system consists of microdialysis sampling coupled directly to microchip electrophoresis with electrochemical detection (MD-ME-EC). Separations were accomplished using an all-glass chip with integrated platinum working and reference electrodes. Discrete samples from the microdialysis flow were introduced into the electrophoresis chip using a flow-gated injection approach. Electrochemical detection was accomplished in-channel using a two-electrode isolated potentiostat. Nitrite was separated by microchip electrophoresis using reverse polarity and a run buffer consisting of 50 mM phosphate at pH 7.4. The entire system was under telemetry control. The system was first tested with rats to monitor the production of nitrite following introduction of nitroglycerin into the subdermal tissue using a linear probe. The data acquired using the on-line MD-ME-EC system was compared to that obtained off-line analysis by liquid chromatography with electrochemical detection (LC-EC), using a second microdialysis probe implanted parallel to the first probe in the same animal. The MD-ME-EC device was then used on-animal to monitor the subdermal metabolism of nitroglycerin in sheep. The ultimate goal is to use this device to simultaneously monitor drug metabolism and behavior in a freely roaming animal. PMID:25697221

Research Spotlight: The next big thing is actually small.

PubMed

Garcia, Carlos D

2012-07-01

Recent developments in materials, surface modifications, separation schemes, detection systems and associated instrumentation have allowed significant advances in the performance of lab-on-a-chip devices. These devices, also referred to as micro total analysis systems (µTAS), offer great versatility, high throughput, short analysis time, low cost and, more importantly, performance that is comparable to standard bench-top instrumentation. To date, µTAS have demonstrated advantages in a significant number of fields including biochemical, pharmaceutical, military and environmental. Perhaps most importantly, µTAS represent excellent platforms to introduce students to microfabrication and nanotechnology, bridging chemistry with other fields, such as engineering and biology, enabling the integration of various skills and curricular concepts. Considering the advantages of the technology and the potential impact to society, our research program aims to address the need for simpler, more affordable, faster and portable devices to measure biologically active compounds. Specifically, the program is focused on the development and characterization of a series of novel strategies towards the realization of integrated microanalytical devices. One key aspect of our research projects is that the developed analytical strategies must be compatible with each other; therefore, enabling their use in integrated devices. The program combines spectroscopy, surface chemistry, capillary electrophoresis, electrochemical detection and nanomaterials. This article discusses some of the most recent results obtained in two main areas of emphasis: capillary electrophoresis, microchip-capillary electrophoresis, electrochemical detection and interaction of proteins with nanomaterials.

Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads

PubMed Central

Rebolledo-Mendez, Jovan; Hestand, Matthew S.; Coleman, Stephen J.; Zeng, Zheng; Orlando, Ludovic; MacLeod, James N.; Kalbfleisch, Ted

2015-01-01

The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight’s half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects’ and Twilight’s genome or due to errors in the reference. EquCab2 is regarded as “The Twilight Assembly.” The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo's BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies between new, high throughput genomic sequence data generated for Twilight and the EquCab2 reference assembly. Most of these represent errors in the assembly, while approximately 10,000 are demonstrated to be contributions from another horse. Other results are presented that include the binary alignment map file of the mapped Sanger reads, a list of variants identified as discrepancies between the source data and resulting reference, and a BED annotation file that lists the regions of the genome whose consensus was likely derived from low coverage alignments. PMID:26107638

Rapid fast-mapping abilities in 2-year-olds.

PubMed

Spiegel, Chad; Halberda, Justin

2011-05-01

Learning a new word consists of two primary tasks that have often been conflated into a single process: referent selection, in which a child must determine the correct referent of a novel label, and referent retention, which is the ability to store this newly formed label-object mapping in memory for later use. In addition, children must be capable of performing these tasks rapidly and repeatedly as they are frequently exposed to novel words during the course of natural conversation. Here we used a preferential pointing task to investigate 2-year-olds' (N=72) ability to infer the referent of a novel noun from a single ambiguous exposure and their ability to retain this mapping over time. Children were asked to identify the referent of a novel label on six critical trials distributed throughout the course of a 10-min study involving many familiar and novel objects. On these critical trials, images of a known object and a novel object (e.g., a ball and a nameless artifact constructed in the laboratory) appeared on two computer screens and a voice asked children to "point at the _____ [e.g., glark]." Following label onset, children were allowed only 3s during which to infer the correct referent, point at it, and potentially store this new word-object mapping. In a final posttest trial, all previously labeled novel objects appeared and children were asked to point to one of them (e.g., "Can you find the glark?"). To succeed, children needed to have initially mapped the novel labels correctly and retained these mappings over the course of the study. Despite the difficult demands of the current task, children successfully identified the target object on the retention trial. We conclude that 2-year-olds are able to fast map novel nouns during a brief single exposure under ambiguous labeling conditions. Copyright © 2010 Elsevier Inc. All rights reserved.

Distortions in memory for visual displays

NASA Technical Reports Server (NTRS)

Tversky, Barbara

1989-01-01

Systematic errors in perception and memory present a challenge to theories of perception and memory and to applied psychologists interested in overcoming them as well. A number of systematic errors in memory for maps and graphs are reviewed, and they are accounted for by an analysis of the perceptual processing presumed to occur in comprehension of maps and graphs. Visual stimuli, like verbal stimuli, are organized in comprehension and memory. For visual stimuli, the organization is a consequence of perceptual processing, which is bottom-up or data-driven in its earlier stages, but top-down and affected by conceptual knowledge later on. Segregation of figure from ground is an early process, and figure recognition later; for both, symmetry is a rapidly detected and ecologically valid cue. Once isolated, figures are organized relative to one another and relative to a frame of reference. Both perceptual (e.g., salience) and conceptual factors (e.g., significance) seem likely to affect selection of a reference frame. Consistent with the analysis, subjects perceived and remembered curves in graphs and rivers in maps as more symmetric than they actually were. Symmetry, useful for detecting and recognizing figures, distorts map and graph figures alike. Top-down processes also seem to operate in that calling attention to the symmetry vs. asymmetry of a slightly asymmetric curve yielded memory errors in the direction of the description. Conceptual frame of reference effects were demonstrated in memory for lines embedded in graphs. In earlier work, the orientation of map figures was distorted in memory toward horizontal or vertical. In recent work, graph lines, but not map lines, were remembered as closer to an imaginary 45 deg line than they had been. Reference frames are determined by both perceptual and conceptual factors, leading to selection of the canonical axes as a reference frame in maps, but selection of the imaginary 45 deg as a reference frame in graphs.

Serum chemistry of free-ranging white whales (Delphinapterus leucas) in Svalbard.

PubMed

Tryland, Morten; Thoresen, Stein Istre; Kovacs, Kit M; Lydersen, Christian

2006-06-01

Abnormal physiological conditions and diseases can change the concentrations of enzymes, metabolites, and minerals in the body. Serum chemistry information may thus be indicative of a specific disease; interpretation of such information requires knowledge of serum chemistry reference intervals from a seemingly healthy population of the species. The aim of this study was to obtain serum chemistry reference intervals for a population of white whales. Blood samples were collected from 21 free-ranging white whales (beluga; Delphinapterus leucas). The whales were live-captured in nets during 1996-2001 in Storfjorden, Van Mijenfjorden, and Van Keulenfjorden (Svalbard, Norway). While the whales were briefly physically restrained, blood was collected from the caudal vein into vacuum tubes without anticoagulant. The blood was left to clot for 4-6 hours before serum was obtained by centrifugation. The serum samples were then kept at -20 degrees C until analysis. Enzymes (aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase [ALP], creatine kinase, lactate dehydrogenase [LDH], amylase, lipase), metabolites (urea, creatinine, bilirubin, cholesterol, triglycerides, nonesterified fatty acids, glucose), and minerals (calcium, phosphate, magnesium, sodium, potassium, chloride) were analyzed in an Advia 1650 System (Bayer, Tarrytown, NY, USA). Cortisol was analyzed in an Immulite One system (Diagnostic Products Corporation, Los Angeles, CA, USA). The major blood proteins (albumin and globulins) were separated by gel electrophoresis in a Beckman Paragon electrophoresis system (Beckman Coulter, Inc., Fullerton, CA, USA). Serum values for all analytes were reported as median and range, and reference intervals were calculated as 10-90th percentiles. Activities of ALP and LDH and cortisol concentration were higher, and protein and bilirubin concentrations were lower compared with those previously reported for white whales from Canada; remaining results were strikingly similar in these 2 white whale populations. These data provide valuable serum chemistry reference intervals for future health assessments of white whales in Svalbard and other white whale populations, as well as captive individuals.

Mines, prospects, and occurrences of metallic (excluding gold), pegmatite, and rare-earth mineral commodities in the Greenville 1 degree by 2 degrees Quadrangle, South Carolina, Georgia, and North Carolina

USGS Publications Warehouse

D'Agostino, John P.; Zupan, Alan Jon; Maybin, Arthur H.; Abrams, Charlotte E.; German, Jerry M.

1994-01-01

All of the known mines, prospects, and occurrences of metallic (excluding gold, pegmatite, and rare-earth mineral commodities for the Greenville 1° x 2° quadrangle are tabulated in this report. The table lists, in consecutive order for each county (fig. 1), the map number of each item, which correlates and locates the item on the accompanying Greenville 1° x 2° quadrangle map. The known name of the feature; the 7.5' topographic map on the which the commodity site is located; the Universal Transverse Mercator (UTM) northing and easting grid coordinates from the appropriate 7.5' topographic map; the commodity; remarks; and references are also listed. Some locations are known, but many sites are not verified and their locations are only approximate. References are listed in References Cited and referred to by number to save space.

Fish species identification using PCR-RFLP analysis and lab-on-a-chip capillary electrophoresis: application to detect white fish species in food products and an interlaboratory study.

PubMed

Dooley, John J; Sage, Helen D; Clarke, Marie-Anne L; Brown, Helen M; Garrett, Stephen D

2005-05-04

Identification of 10 white fish species associated with U.K. food products was achieved using PCR-RFLP of the mitochondrial cytochrome b gene. Use of lab-on-a-chip capillary electrophoresis for end-point analysis enabled accurate sizing of DNA fragments and identification of fish species at a level of 5% (w/w) in a fish admixture. One restriction enzyme, DdeI, allowed discrimination of eight species. When combined with NlaIII and HaeIII, specific profiles for all 10 species were generated. The method was applied to a range of products and subjected to an interlaboratory study carried out by five U.K. food control laboratories. One hundred percent correct identification of single species samples and six of nine admixture samples was achieved by all laboratories. The results indicated that fish species identification could be carried out using a database of PCR-RFLP profiles without the need for reference materials.

Raw Cow Milk Bacterial Population Shifts Attributable to Refrigeration

PubMed Central

Lafarge, Véronique; Ogier, Jean-Claude; Girard, Victoria; Maladen, Véronique; Leveau, Jean-Yves; Gruss, Alexandra; Delacroix-Buchet, Agnès

2004-01-01

We monitored the dynamic changes in the bacterial population in milk associated with refrigeration. Direct analyses of DNA by using temporal temperature gel electrophoresis (TTGE) and denaturing gradient gel electrophoresis (DGGE) allowed us to make accurate species assignments for bacteria with low-GC-content (low-GC%) (<55%) and medium- or high-GC% (>55%) genomes, respectively. We examined raw milk samples before and after 24-h conservation at 4°C. Bacterial identification was facilitated by comparison with an extensive bacterial reference database (∼150 species) that we established with DNA fragments of pure bacterial strains. Cloning and sequencing of fragments missing from the database were used to achieve complete species identification. Considerable evolution of bacterial populations occurred during conservation at 4°C. TTGE and DGGE are shown to be a powerful tool for identifying the main bacterial species of the raw milk samples and for monitoring changes in bacterial populations during conservation at 4°C. The emergence of psychrotrophic bacteria such as Listeria spp. or Aeromonas hydrophila is demonstrated. PMID:15345453

Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study.

PubMed

de Vries, Paul S; Sabater-Lleal, Maria; Chasman, Daniel I; Trompet, Stella; Ahluwalia, Tarunveer S; Teumer, Alexander; Kleber, Marcus E; Chen, Ming-Huei; Wang, Jie Jin; Attia, John R; Marioni, Riccardo E; Steri, Maristella; Weng, Lu-Chen; Pool, Rene; Grossmann, Vera; Brody, Jennifer A; Venturini, Cristina; Tanaka, Toshiko; Rose, Lynda M; Oldmeadow, Christopher; Mazur, Johanna; Basu, Saonli; Frånberg, Mattias; Yang, Qiong; Ligthart, Symen; Hottenga, Jouke J; Rumley, Ann; Mulas, Antonella; de Craen, Anton J M; Grotevendt, Anne; Taylor, Kent D; Delgado, Graciela E; Kifley, Annette; Lopez, Lorna M; Berentzen, Tina L; Mangino, Massimo; Bandinelli, Stefania; Morrison, Alanna C; Hamsten, Anders; Tofler, Geoffrey; de Maat, Moniek P M; Draisma, Harmen H M; Lowe, Gordon D; Zoledziewska, Magdalena; Sattar, Naveed; Lackner, Karl J; Völker, Uwe; McKnight, Barbara; Huang, Jie; Holliday, Elizabeth G; McEvoy, Mark A; Starr, John M; Hysi, Pirro G; Hernandez, Dena G; Guan, Weihua; Rivadeneira, Fernando; McArdle, Wendy L; Slagboom, P Eline; Zeller, Tanja; Psaty, Bruce M; Uitterlinden, André G; de Geus, Eco J C; Stott, David J; Binder, Harald; Hofman, Albert; Franco, Oscar H; Rotter, Jerome I; Ferrucci, Luigi; Spector, Tim D; Deary, Ian J; März, Winfried; Greinacher, Andreas; Wild, Philipp S; Cucca, Francesco; Boomsma, Dorret I; Watkins, Hugh; Tang, Weihong; Ridker, Paul M; Jukema, Jan W; Scott, Rodney J; Mitchell, Paul; Hansen, Torben; O'Donnell, Christopher J; Smith, Nicholas L; Strachan, David P; Dehghan, Abbas

2017-01-01

An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10-8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10-8), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development.

Comparison of HapMap and 1000 Genomes Reference Panels in a Large-Scale Genome-Wide Association Study

PubMed Central

de Vries, Paul S.; Sabater-Lleal, Maria; Chasman, Daniel I.; Trompet, Stella; Kleber, Marcus E.; Chen, Ming-Huei; Wang, Jie Jin; Attia, John R.; Marioni, Riccardo E.; Weng, Lu-Chen; Grossmann, Vera; Brody, Jennifer A.; Venturini, Cristina; Tanaka, Toshiko; Rose, Lynda M.; Oldmeadow, Christopher; Mazur, Johanna; Basu, Saonli; Yang, Qiong; Ligthart, Symen; Hottenga, Jouke J.; Rumley, Ann; Mulas, Antonella; de Craen, Anton J. M.; Grotevendt, Anne; Taylor, Kent D.; Delgado, Graciela E.; Kifley, Annette; Lopez, Lorna M.; Berentzen, Tina L.; Mangino, Massimo; Bandinelli, Stefania; Morrison, Alanna C.; Hamsten, Anders; Tofler, Geoffrey; de Maat, Moniek P. M.; Draisma, Harmen H. M.; Lowe, Gordon D.; Zoledziewska, Magdalena; Sattar, Naveed; Lackner, Karl J.; Völker, Uwe; McKnight, Barbara; Huang, Jie; Holliday, Elizabeth G.; McEvoy, Mark A.; Starr, John M.; Hysi, Pirro G.; Hernandez, Dena G.; Guan, Weihua; Rivadeneira, Fernando; McArdle, Wendy L.; Slagboom, P. Eline; Zeller, Tanja; Psaty, Bruce M.; Uitterlinden, André G.; de Geus, Eco J. C.; Stott, David J.; Binder, Harald; Hofman, Albert; Franco, Oscar H.; Rotter, Jerome I.; Ferrucci, Luigi; Spector, Tim D.; Deary, Ian J.; März, Winfried; Greinacher, Andreas; Wild, Philipp S.; Cucca, Francesco; Boomsma, Dorret I.; Watkins, Hugh; Tang, Weihong; Ridker, Paul M.; Jukema, Jan W.; Scott, Rodney J.; Mitchell, Paul; Hansen, Torben; O'Donnell, Christopher J.; Smith, Nicholas L.; Strachan, David P.

2017-01-01

An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were associated using both HapMap and 1000G imputation. One locus identified using HapMap imputation was not significant using 1000G imputation. The genome-wide significance threshold of 5×10−8 is based on the number of independent statistical tests using HapMap imputation, and 1000G imputation may lead to further independent tests that should be corrected for. When using a stricter Bonferroni correction for the 1000G GWA study (P-value < 2.5×10−8), the number of loci significant only using HapMap imputation increased to 4 while the number of loci significant only using 1000G decreased to 5. In conclusion, 1000G imputation enabled the identification of 20% more loci than HapMap imputation, although the advantage of 1000G imputation became less clear when a stricter Bonferroni correction was used. More generally, our results provide insights that are applicable to the implementation of other dense reference panels that are under development. PMID:28107422

A reference consensus genetic map for molecular markers and economically important traits in faba bean (Vicia faba L.)

PubMed Central

2013-01-01

Background Faba bean (Vicia faba L.) is among the earliest domesticated crops from the Near East. Today this legume is a key protein feed and food worldwide and continues to serve an important role in culinary traditions throughout Middle East, Mediterranean region, China and Ethiopia. Adapted to a wide range of soil types, the main faba bean breeding objectives are to improve yield, resistance to biotic and abiotic stresses, seed quality and other agronomic traits. Genomic approaches aimed at enhancing faba bean breeding programs require high-quality genetic linkage maps to facilitate quantitative trait locus analysis and gene tagging for use in a marker-assisted selection. The objective of this study was to construct a reference consensus map in faba bean by joining the information from the most relevant maps reported so far in this crop. Results A combination of two approaches, increasing the number of anchor loci in diverse mapping populations and joining the corresponding genetic maps, was used to develop a reference consensus map in faba bean. The map was constructed from three main recombinant inbreed populations derived from four parental lines, incorporates 729 markers and is based on 69 common loci. It spans 4,602 cM with a range from 323 to 1041 loci in six main linkage groups or chromosomes, and an average marker density of one locus every 6 cM. Locus order is generally well maintained between the consensus map and the individual maps. Conclusion We have constructed a reliable and fairly dense consensus genetic linkage map that will serve as a basis for genomic approaches in faba bean research and breeding. The core map contains a larger number of markers than any previous individual map, covers existing gaps and achieves a wider coverage of the large faba bean genome as a whole. This tool can be used as a reference resource for studies in different genetic backgrounds, and provides a framework for transferring genetic information when using different marker technologies. Combined with syntenic approaches, the consensus map will increase marker density in selected genomic regions and will be useful for future faba bean molecular breeding applications. PMID:24377374

Design and tolerance analysis of a transmission sphere by interferometer model

NASA Astrophysics Data System (ADS)

Peng, Wei-Jei; Ho, Cheng-Fong; Lin, Wen-Lung; Yu, Zong-Ru; Huang, Chien-Yao; Hsu, Wei-Yao

2015-09-01

The design of a 6-in, f/2.2 transmission sphere for Fizeau interferometry is presented in this paper. To predict the actual performance during design phase, we build an interferometer model combined with tolerance analysis in Zemax. Evaluating focus imaging is not enough for a double pass optical system. Thus, we study the interferometer model that includes system error, wavefronts reflected from reference surface and tested surface. Firstly, we generate a deformation map of the tested surface. Because of multiple configurations in Zemax, we can get the test wavefront and the reference wavefront reflected from the tested surface and the reference surface of transmission sphere respectively. According to the theory of interferometry, we subtract both wavefronts to acquire the phase of tested surface. Zernike polynomial is applied to transfer the map from phase to sag and to remove piston, tilt and power. The restored map is the same as original map; because of no system error exists. Secondly, perturbed tolerances including fabrication of lenses and assembly are considered. The system error occurs because the test and reference beam are no longer common path perfectly. The restored map is inaccurate while the system error is added. Although the system error can be subtracted by calibration, it should be still controlled within a small range to avoid calibration error. Generally the reference wavefront error including the system error and the irregularity of the reference surface of 6-in transmission sphere is measured within peak-to-valley (PV) 0.1 λ (λ=0.6328 um), which is not easy to approach. Consequently, it is necessary to predict the value of system error before manufacture. Finally, a prototype is developed and tested by a reference surface with PV 0.1 λ irregularity.

Accuracy assessment of NOAA gridded daily reference evapotranspiration for the Texas High Plains

USGS Publications Warehouse

Moorhead, Jerry; Gowda, Prasanna H.; Hobbins, Michael; Senay, Gabriel; Paul, George; Marek, Thomas; Porter, Dana

2015-01-01

The National Oceanic and Atmospheric Administration (NOAA) provides daily reference evapotranspiration (ETref) maps for the contiguous United States using climatic data from North American Land Data Assimilation System (NLDAS). This data provides large-scale spatial representation of ETref, which is essential for regional scale water resources management. Data used in the development of NOAA daily ETref maps are derived from observations over surfaces that are different from short (grass — ETos) or tall (alfalfa — ETrs) reference crops, often in nonagricultural settings, which carries an unknown discrepancy between assumed and actual conditions. In this study, NOAA daily ETos and ETrs maps were evaluated for accuracy, using observed data from the Texas High Plains Evapotranspiration (TXHPET) network. Daily ETos, ETrs and the climatic data (air temperature, wind speed, and solar radiation) used for calculating ETref were extracted from the NOAA maps for TXHPET locations and compared against ground measurements on reference grass surfaces. NOAA ETrefmaps generally overestimated the TXHPET observations (1.4 and 2.2 mm/day ETos and ETrs, respectively), which may be attributed to errors in the NLDAS modeled air temperature and wind speed, to which reference ETref is most sensitive. Therefore, a bias correction to NLDAS modeled air temperature and wind speed data, or adjustment to the resulting NOAA ETref, may be needed to improve the accuracy of NOAA ETref maps.

Radiometric age map of Aleutian Islands

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of southcentral Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of southwest Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of southeast Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Radiometric age map of northern Alaska

USGS Publications Warehouse

Wilson, Frederic H.; Turner, D.L.

1975-01-01

This map includes published, thesis, and open-file radiometric data available to us as of June, 1975. Some dates are not plotted because of inadequate location data in the original references.The map is divided into five sections, based on 1:1,000,000 scale enlargements of the National Atlas maps of Alaska. Within each section (e.g., southeastern Alaska), radiometric dates are plotted and keyed to 1:250,000 scale quadrangles. Accompanying each map section is table 1, listing map numbers and the sample identification numbers used in DGGS Special Report 10: Radiometric Dates from Alaska-A 1975 Compilation”. The reader is referred to Special Report 10 for more complete information on location, rock type, dating method, and literature references for each age entry. A listing of dates in Special Report lo which require correction or deletion is included S table 2. Corrected and additional entries are listed in table 3. The listings in tables 2 and 3 follow the format of Special Report 10. Table 4 is a glossary of abbreviations used for quadrangle name, rock type, mineral dated, and type of dating method used.

Broadband set-top box using MAP-CA processor

NASA Astrophysics Data System (ADS)

Bush, John E.; Lee, Woobin; Basoglu, Chris

2001-12-01

Advances in broadband access are expected to exert a profound impact in our everyday life. It will be the key to the digital convergence of communication, computer and consumer equipment. A common thread that facilitates this convergence comprises digital media and Internet. To address this market, Equator Technologies, Inc., is developing the Dolphin broadband set-top box reference platform using its MAP-CA Broadband Signal ProcessorT chip. The Dolphin reference platform is a universal media platform for display and presentation of digital contents on end-user entertainment systems. The objective of the Dolphin reference platform is to provide a complete set-top box system based on the MAP-CA processor. It includes all the necessary hardware and software components for the emerging broadcast and the broadband digital media market based on IP protocols. Such reference design requires a broadband Internet access and high-performance digital signal processing. By using the MAP-CA processor, the Dolphin reference platform is completely programmable, allowing various codecs to be implemented in software, such as MPEG-2, MPEG-4, H.263 and proprietary codecs. The software implementation also enables field upgrades to keep pace with evolving technology and industry demands.

Evaluation and Intercomparison of MODIS and GEOV1 Global Leaf Area Index Products over Four Sites in North China

PubMed Central

Li, Zhenwang; Tang, Huan; Zhang, Baohui; Yang, Guixia; Xin, Xiaoping

2015-01-01

This study investigated the performances of the Moderate Resolution Imaging Spectroradiometer (MODIS) and GEOLAND2 Version 1 (GEOV1) Leaf Area Index (LAI) products using ground measurements and LAI reference maps over four sites in North China for 2011–2013. The Terra + Aqua MODIS and Terra MODIS LAI retrieved by the main algorithm and GEOV1 LAI within the valid range were evaluated and intercompared using LAI reference maps to assess their uncertainty and seasonal variability The results showed that GEOV1 LAI is the most similar product with the LAI reference maps (R2 = 0.78 and RMSE = 0.59). The MODIS products performed well for biomes with low LAI values, but considerable uncertainty arose when the LAI was larger than 3. Terra + Aqua MODIS (R2 = 0.72 and RMSE = 0.68) was slightly more accurate than Terra MODIS (R2 = 0.57 and RMSE = 0.90) for producing slightly more successful observations. Both MODIS and GEOV1 products effectively followed the seasonal trajectory of the reference maps, and GEOV1 exhibited a smoother seasonal trajectory than MODIS. MODIS anomalies mainly occurred during summer and likely occurred because of surface reflectance uncertainty, shorter temporal resolutions and inconsistency between simulated and MODIS surface reflectances. This study suggests that further improvements of the MODIS LAI products should focus on finer algorithm inputs and improved seasonal variation modeling of MODIS observations. Future field work considering finer biome maps and better generation of LAI reference maps is still needed. PMID:25781509

APPLICATION OF A "VITURAL FIELD REFERENCE DATABASE" TO ASSESS LAND-COVER MAP ACCURACIES

EPA Science Inventory

An accuracy assessment was performed for the Neuse River Basin, NC land-cover/use
(LCLU) mapping results using a "Virtual Field Reference Database (VFRDB)". The VFRDB was developed using field measurement and digital imagery (camera) data collected at 1,409 sites over a perio...

Proteomic Analysis of Pigeonpea (Cajanus cajan) Seeds Reveals the Accumulation of Numerous Stress-Related Proteins.

PubMed

Krishnan, Hari B; Natarajan, Savithiry S; Oehrle, Nathan W; Garrett, Wesley M; Darwish, Omar

2017-06-14

Pigeonpea is one of the major sources of dietary protein for more than a billion people living in South Asia. This hardy legume is often grown in low-input and risk-prone marginal environments. Considerable research effort has been devoted by a global research consortium to develop genomic resources for the improvement of this legume crop. These efforts have resulted in the elucidation of the complete genome sequence of pigeonpea. Despite these developments, little is known about the seed proteome of this important crop. Here, we report the proteome of pigeonpea seed. To enable the isolation of maximum number of seed proteins, including those that are present in very low amounts, three different protein fractions were obtained by employing different extraction media. High-resolution two-dimensional (2-D) electrophoresis followed by MALDI-TOF-TOF-MS/MS analysis of these protein fractions resulted in the identification of 373 pigeonpea seed proteins. Consistent with the reported high degree of synteny between the pigeonpea and soybean genomes, a large number of pigeonpea seed proteins exhibited significant amino acid homology with soybean seed proteins. Our proteomic analysis identified a large number of stress-related proteins, presumably due to its adaptation to drought-prone environments. The availability of a pigeonpea seed proteome reference map should shed light on the roles of these identified proteins in various biological processes and facilitate the improvement of seed composition.

Geographic information systems (GIS) spatial data compilation of geodynamic, tectonic, metallogenic, mineral deposit, and geophysical maps and associated descriptive data for northeast Asia

USGS Publications Warehouse

Naumova, Vera V.; Patuk, Mikhail I.; Kapitanchuk, Marina Yu.; Nokleberg, Warren J.; Khanchuk, Alexander I.; Parfenov, Leonid M.; Rodionov, Sergey M.; Miller, Robert J.; Diggles, Michael F.

2006-01-01

This is the online version of a CD-ROM publication. It contains all of the data that are on the disc but extra files have been removed: index files, software installers, and Windows autolaunch files. The purpose of this publication is to provide a high-quality spatial data compilation (Geographical Information System or GIS) of geodynamic, mineral deposit, and metallogenic belt maps, and descriptive data for Northeast Asia for customers and users. This area consists of Eastern Siberia, Russian Far East, Mongolia, northern China, South Korea, and Japan. The GIS compilation contains integrated spatial data for: (1) a geodynamics map at a scale of 1:5,000,000; (2) a mineral deposit location map; (3) metallogenic belt maps; (4) detailed descriptions of geologic units, including tectonostratigraphic terranes, cratons, major melange zones, and overlap assemblages, with references; (5) detailed descriptions of metallogenic belts with references; (6) detailed mineral deposit descriptions with references; and (7) page-size stratigraphic columns for major terranes.

Methylxanthines: properties and determination in various objects

NASA Astrophysics Data System (ADS)

Andreeva, Elena Yu; Dmitrienko, Stanislava G.; Zolotov, Yurii A.

2012-05-01

Published data on the properties and determination of caffeine, theophylline, theobromine and some other methylxanthines in various objects are surveyed and described systematically. Different sample preparation procedures such as liquid extraction from solid matrices and liquid-liquid, supercritical fluid and solid-phase extraction are compared. The key methods of analysis including chromatography, electrophoresis, spectrometry and electrochemical methods are discussed. Examples of methylxanthine determination in plants, food products, energy beverages, pharmaceuticals, biological fluids and natural and waste waters are given. The bibliography includes 393 references.

High Throughput Screen to Identify Novel Drugs that Inhibit Prostate Cancer Metastasis

DTIC Science & Technology

2007-10-01

determined by electrophoresis on 8% denaturing polyacryl - amide gel containing 7 M urea. A 10-bp 32P-labeled ladder and sequencing reaction performed with...isolated from nuclear lysates from P69 and C4-2 cells. The bands shown as rectangles were excised after staining of the proteins in the gel and then...the same primer on a genomic clone was used as a reference. The gel was dried, and the radioactive signals were identified by phos- phorimaging (Storm

Characterization and discrimination of polysaccharides from different species of Cordyceps using saccharide mapping based on PACE and HPTLC.

PubMed

Wu, Ding-Tao; Cheong, Kit-Leong; Wang, Lan-Ying; Lv, Guang-Ping; Ju, Yao-Jun; Feng, Kun; Zhao, Jing; Li, Shao-Ping

2014-03-15

Polysaccharides from seven species of natural and cultured Cordyceps were firstly investigated and compared using saccharide mapping, partially acidic/enzymatic (α-amylase, β-glucanase and pectinase) digestion followed with polysaccharide analysis by using carbohydrate gel electrophoresis (PACE) and high performance thin layer chromatography (HPTLC) analysis, respectively, to obtain the comprehensive profiles of hydrolysates of the polysaccharides and their characters. The results showed that 1,4-α-D-glucosidic, 1,4-β-D-glucosidic and 1,4-α-D-galactosidic linkages were existed in natural and cultured Cordyceps sinensis, cultured Cordyceps militaris, natural Cordyceps gracilis and Cordyceps ciecadae. The similarity of polysaccharides from cultured C. militaris to natural C. sinensis was relatively high, which might contribute to the rational use of C. militaris. Moreover, different species of natural and cultured Cordyceps can be differentiated based on the saccharide mapping, which is helpful to well understand the structural characters of polysaccharides from different species of Cordyceps and to improve the quality control of polysaccharides in natural and cultured Cordyceps. Copyright © 2013 Elsevier Ltd. All rights reserved.

Automated Processing of 2-D Gel Electrophoretograms of Genomic DNA for Hunting Pathogenic DNA Molecular Changes.

PubMed

Takahashi; Nakazawa; Watanabe; Konagaya

1999-01-01

We have developed the automated processing algorithms for 2-dimensional (2-D) electrophoretograms of genomic DNA based on RLGS (Restriction Landmark Genomic Scanning) method, which scans the restriction enzyme recognition sites as the landmark and maps them onto a 2-D electrophoresis gel. Our powerful processing algorithms realize the automated spot recognition from RLGS electrophoretograms and the automated comparison of a huge number of such images. In the final stage of the automated processing, a master spot pattern, on which all the spots in the RLGS images are mapped at once, can be obtained. The spot pattern variations which seemed to be specific to the pathogenic DNA molecular changes can be easily detected by simply looking over the master spot pattern. When we applied our algorithms to the analysis of 33 RLGS images derived from human colon tissues, we successfully detected several colon tumor specific spot pattern changes.

Mapping replication origins in yeast chromosomes.

PubMed

Brewer, B J; Fangman, W L

1991-07-01

The replicon hypothesis, first proposed in 1963 by Jacob and Brenner, states that DNA replication is controlled at sites called origins. Replication origins have been well studied in prokaryotes. However, the study of eukaryotic chromosomal origins has lagged behind, because until recently there has been no method for reliably determining the identity and location of origins from eukaryotic chromosomes. Here, we review a technique we developed with the yeast Saccharomyces cerevisiae that allows both the mapping of replication origins and an assessment of their activity. Two-dimensional agarose gel electrophoresis and Southern hybridization with total genomic DNA are used to determine whether a particular restriction fragment acquires the branched structure diagnostic of replication initiation. The technique has been used to localize origins in yeast chromosomes and assess their initiation efficiency. In some cases, origin activation is dependent upon the surrounding context. The technique is also being applied to a variety of eukaryotic organisms.

Semantic Image Based Geolocation Given a Map (Author’s Initial Manuscript)

DTIC Science & Technology

2016-09-01

novel technique for detection and identification of building facades from geo-tagged reference view using the map and geometry of the building facades. We...2D map of the environment, and geometry of building facades. We evaluate our approach for building identification and geo-localization on a new...location recognition and building identification is done by matching the query view to a reference set, followed by estimation of 3D building facades

Continuous-flow electrophoresis: Membrane-associated deviations of buffer pH and conductivity

NASA Technical Reports Server (NTRS)

Smolka, A. J. K.; Mcguire, J. K.

1978-01-01

The deviations in buffer pH and conductivity which occur near the electrode membranes in continuous-flow electrophoresis were studied in the Beckman charged particle electrophoresis system and the Hanning FF-5 preparative electrophoresis instrument. The nature of the membranes separating the electrode compartments from the electrophoresis chamber, the electric field strength, and the flow rate of electrophoresis buffer were all found to influence the formation of the pH and conductivity gradients. Variations in electrode buffer flow rate and the time of electrophoresis were less important. The results obtained supported the hypothesis that a combination of Donnan membrane effects and the differing ionic mobilities in the electrophoresis buffer was responsible for the formation of the gradients. The significance of the results for the design and stable operation of continuous-flow electrophoresis apparatus was discussed.

Molecular characterization of Coxiella burnetii isolates.

PubMed Central

Jäger, C.; Willems, H.; Thiele, D.; Baljer, G.

1998-01-01

Restriction fragment length polymorphism (RFLP) was used for the differentiation of 80 Coxiella burnetii isolates derived from animals and humans in Europe, USA, Africa and Asia. After NotI restriction of total C. burnetii DNA and pulsed field gel electrophoresis (PFGE) 20 different restriction patterns were distinguished. The index of discrimination for this typing system was 0.86. Comparison and phylogenetic analysis of the different RFLP patterns revealed evolutionary relationships among groups that corresponded to the geographical origin of the isolates. This finding was confirmed by genetic mapping. No correlation between restriction group and virulence of isolates was detected. PMID:9593485

Limited tryptic proteolysis of the benzodiazepine binding proteins in different species reveals structural homologies.

PubMed

Friedl, W; Lentes, K U; Schmitz, E; Propping, P; Hebebrand, J

1988-12-01

Peptide mapping can be used to elucidate further the structural similarities of the benzodiazepine binding proteins in different vertebrate species. Crude synaptic membrane preparations were photoaffinity-labeled with [3H]flunitrazepam and subsequently degraded with various concentrations of trypsin. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by fluorography allowed a comparison of the molecular weights of photolabeled peptides in different species. Tryptic degradation led to a common peptide of 40K in all species investigated, a finding indicating that the benzodiazepine binding proteins are structurally homologous in higher bony fishes and tetrapods.

World Map Showing Surface and Subsurface Distribution, and Lithologic Character of Middle and Late Neoproterozoic Rocks

USGS Publications Warehouse

Stewart, John H.

2007-01-01

INTRODUCTION The map was prepared to outline the basic information on where Neoproterozoic rocks are present in the World, and of the lithologic character of these rocks. The information provides a better understanding of major Neoproterozoic tectonic subdivisions useful in paleogeographic and plate tectonic reconstructions. The time frame of the map is within the middle and late Neoproterozoic from approximately 870 to 540 Ma and is after widespread Mesoproterozoic Grenville-age collisional events that are considered to have formed the hypothetical supercontinent of Rodinia. Much of the time represented by the map is interpreted to be during the fragmentation of Rodinia. The recognition of Neoproterozoic rocks is commonly difficult because of limited isotopic or paloeontological dating. Thus, some rocks shown on the map could be older or younger than the age indicated. However, at the scale of the map the the problem may be minor. Enough information seems to be available to indicate the general age of the rocks. Many of the successions contain diamictite deposits considered to be glaciogenic and dated as middle or late Neoproterozoic. These deposits thus show a rough correlation of middle and late Neoproterozoic rocks of the world. The map is a Richardson map projection, except for Antarctica which is a polar projection. The map was prepared from about 650 references, shown in the text linked below under 'Sources of Information', used to outline distribution patterns, determine rock types, and provide information on the regional and local geologic framework of the rocks. The focus of the references is on the geologic information needed to prepare the map. Other information, such as plate tectonic reconstructions or paleomagnetic studies is generally not included. The 'Sources of Information' lists references alphabetically for each of 14 regions. In brackets is a code for each area. These codes provide help in locating the specific regions in the references.

Development in electrophoresis: instrumentation for two-dimensional gel electrophoresis of protein separation and application of capillary electrophoresis in micro-bioanalysis

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

Xu, Aoshuang

2008-01-01

This dissertation begins with a general introduction of topics related to this work. The following chapters contain three scientific manuscripts, each presented in a separate chapter with accompanying tables, figures, and literature citations. The final chapter summarizes the work and provides some prospective on this work. This introduction starts with a brief treatment of the basic principles of electrophoresis separation, followed by a discussion of gel electrophoresis and particularly polyacrylamide gel electrophoresis for protein separation, a summary of common capillary electrophoresis separation modes, and a brief treatment of micro-bioanalysis application of capillary electrophoresis, and ends with an overview of proteinmore » conformation and dynamics.« less

Reference frames in virtual spatial navigation are viewpoint dependent

PubMed Central

Török, Ágoston; Nguyen, T. Peter; Kolozsvári, Orsolya; Buchanan, Robert J.; Nadasdy, Zoltan

2014-01-01

Spatial navigation in the mammalian brain relies on a cognitive map of the environment. Such cognitive maps enable us, for example, to take the optimal route from a given location to a known target. The formation of these maps is naturally influenced by our perception of the environment, meaning it is dependent on factors such as our viewpoint and choice of reference frame. Yet, it is unknown how these factors influence the construction of cognitive maps. Here, we evaluated how various combinations of viewpoints and reference frames affect subjects' performance when they navigated in a bounded virtual environment without landmarks. We measured both their path length and time efficiency and found that (1) ground perspective was associated with egocentric frame of reference, (2) aerial perspective was associated with allocentric frame of reference, (3) there was no appreciable performance difference between first and third person egocentric viewing positions and (4) while none of these effects were dependent on gender, males tended to perform better in general. Our study provides evidence that there are inherent associations between visual perspectives and cognitive reference frames. This result has implications about the mechanisms of path integration in the human brain and may also inspire designs of virtual reality applications. Lastly, we demonstrated the effective use of a tablet PC and spatial navigation tasks for studying spatial and cognitive aspects of human memory. PMID:25249956

Reference frames in virtual spatial navigation are viewpoint dependent.

PubMed

Török, Agoston; Nguyen, T Peter; Kolozsvári, Orsolya; Buchanan, Robert J; Nadasdy, Zoltan

2014-01-01

Spatial navigation in the mammalian brain relies on a cognitive map of the environment. Such cognitive maps enable us, for example, to take the optimal route from a given location to a known target. The formation of these maps is naturally influenced by our perception of the environment, meaning it is dependent on factors such as our viewpoint and choice of reference frame. Yet, it is unknown how these factors influence the construction of cognitive maps. Here, we evaluated how various combinations of viewpoints and reference frames affect subjects' performance when they navigated in a bounded virtual environment without landmarks. We measured both their path length and time efficiency and found that (1) ground perspective was associated with egocentric frame of reference, (2) aerial perspective was associated with allocentric frame of reference, (3) there was no appreciable performance difference between first and third person egocentric viewing positions and (4) while none of these effects were dependent on gender, males tended to perform better in general. Our study provides evidence that there are inherent associations between visual perspectives and cognitive reference frames. This result has implications about the mechanisms of path integration in the human brain and may also inspire designs of virtual reality applications. Lastly, we demonstrated the effective use of a tablet PC and spatial navigation tasks for studying spatial and cognitive aspects of human memory.

Establishing a leaf proteome reference map for Ginkgo biloba provides insight into potential ethnobotanical uses

USDA-ARS?s Scientific Manuscript database

Although ginkgo (Maidenhair tree, Ginkgo biloba L.) is an ancient medicinal and ornamental tree, there has not previously been any systematic proteomic study of the leaves. Herein we describe results from the initial study identifying abundant ginkgo leaf proteins and present a gel reference map. Pr...

78 FR 19355 - Noise Exposure Map Notice: Receipt of Noise Compatibility Program and Request for Review

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-29

... of 49 U.S.C. 47501 et. seq (the Aviation Safety and Noise Abatement Act, hereinafter referred to as.... 47503 (the Aviation Safety and Noise Abatement Act, hereinafter referred to as ``the Act''), an airport... DEPARTMENT OF TRANSPORTATION Federal Aviation Administration Noise Exposure Map Notice: Receipt of...

Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine

PubMed Central

Wang, Minghui; Londo, Jason P.; Acharya, Charlotte B.; Mitchell, Sharon E.; Sun, Qi; Reisch, Bruce; Cadle-Davidson, Lance

2015-01-01

Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications. PMID:26244767

Not all memories are the same: Situational context influences spatial recall within one's city of residency.

PubMed

Meilinger, Tobias; Frankenstein, Julia; Simon, Nadine; Bülthoff, Heinrich H; Bresciani, Jean-Pierre

2016-02-01

Reference frames in spatial memory encoding have been examined intensively in recent years. However, their importance for recall has received considerably less attention. In the present study, passersby used tags to arrange a configuration map of prominent city center landmarks. It has been shown that such configurational knowledge is memorized within a north-up reference frame. However, participants adjusted their maps according to their body orientations. For example, when participants faced south, the maps were likely to face south-up. Participants also constructed maps along their location perspective-that is, the self-target direction. If, for instance, they were east of the represented area, their maps were oriented west-up. If the location perspective and body orientation were in opposite directions (i.e., if participants faced away from the city center), participants relied on location perspective. The results indicate that reference frames in spatial recall depend on the current situation rather than on the organization in long-term memory. These results cannot be explained by activation spread within a view graph, which had been used to explain similar results in the recall of city plazas. However, the results are consistent with forming and transforming a spatial image of nonvisible city locations from the current location. Furthermore, prior research has almost exclusively focused on body- and environment-based reference frames. The strong influence of location perspective in an everyday navigational context indicates that such a reference frame should be considered more often when examining human spatial cognition.

Comparison of Lipoprotein Electrophoresis and Apolipoprotein E Genotyping in Investigating Dysbetalipoproteinemia.

PubMed

Ahmed, Farhan; El-Kadiki, Alia; Gibbons, Stephen

2017-06-01

Dysbetalipoproteinemia is often associated with apolipoprotein E2E2 homozygosity; however, lipoprotein electrophoresis may also be used to assist in the diagnosis. The aim of this study was to compare apolipoprotein E (apo E) genotyping and lipoprotein electrophoresis in investigating dysbetalipoproteinemia. Data were collected over a three-year period from a lipid clinic in a tertiary referral centre and reviewed for apo E genotyping and lipoprotein electrophoresis. Sixty-two patients had both apo E genotyping and lipoprotein electrophoresis. Of these, 16 patients showed broad beta band on electrophoresis. However, only 3 of them had apo E2E2 homozygosity on genotyping. Lipoprotein electrophoresis and apo E genotyping results showed poor concordance. This was primarily due to visual interpretation error of lipoprotein electrophoresis which may over diagnose dysbetalipoproteinemia.

One Size Doesn't Fit All - RefEditor: Building Personalized Diploid Reference Genome to Improve Read Mapping and Genotype Calling in Next Generation Sequencing Studies

PubMed Central

Yuan, Shuai; Johnston, H. Richard; Zhang, Guosheng; Li, Yun; Hu, Yi-Juan; Qin, Zhaohui S.

2015-01-01

With rapid decline of the sequencing cost, researchers today rush to embrace whole genome sequencing (WGS), or whole exome sequencing (WES) approach as the next powerful tool for relating genetic variants to human diseases and phenotypes. A fundamental step in analyzing WGS and WES data is mapping short sequencing reads back to the reference genome. This is an important issue because incorrectly mapped reads affect the downstream variant discovery, genotype calling and association analysis. Although many read mapping algorithms have been developed, the majority of them uses the universal reference genome and do not take sequence variants into consideration. Given that genetic variants are ubiquitous, it is highly desirable if they can be factored into the read mapping procedure. In this work, we developed a novel strategy that utilizes genotypes obtained a priori to customize the universal haploid reference genome into a personalized diploid reference genome. The new strategy is implemented in a program named RefEditor. When applying RefEditor to real data, we achieved encouraging improvements in read mapping, variant discovery and genotype calling. Compared to standard approaches, RefEditor can significantly increase genotype calling consistency (from 43% to 61% at 4X coverage; from 82% to 92% at 20X coverage) and reduce Mendelian inconsistency across various sequencing depths. Because many WGS and WES studies are conducted on cohorts that have been genotyped using array-based genotyping platforms previously or concurrently, we believe the proposed strategy will be of high value in practice, which can also be applied to the scenario where multiple NGS experiments are conducted on the same cohort. The RefEditor sources are available at https://github.com/superyuan/refeditor. PMID:26267278

Mapping and proteomic analysis of albumin and globulin proteins in hexaploid wheat kernels (Triticum aestivum L.).

PubMed

Merlino, Marielle; Leroy, Philippe; Chambon, Christophe; Branlard, Gérard

2009-05-01

Albumins and globulins of wheat endosperm represent 20% of total kernel protein. They are soluble proteins, mainly enzymes and proteins involved in cell functions. Two-dimensional gel immobiline electrophoresis (2DE) (pH 4-7) x SDS-Page revealed around 2,250 spots. Ninety percent of the spots were common between the very distantly related cultivars 'Opata 85' and 'Synthetic W7984', the two parents of the International Triticeae Mapping Initiative (ITMI) progeny. 'Opata' had 130 specific spots while 'Synthetic' had 96. 2DE and image analysis of the soluble proteins present in 112 recombinant inbred lines of the F9-mapped ITMI progeny enabled 120 unbiased segregating spots to be mapped on 21 wheat (Triticum aestivum L. em. Thell) chromosomes. After trypsic digestion, mapped spots were subjected to MALDI-Tof or tandem mass spectrometry for protein identification by database mining. Among the 'Opata' and 'Synthetic' spots identified, many enzymes have already been mapped in the barley and rice genomes. Multigene families of Heat Shock Proteins, beta-amylases, UDP-glucose pyrophosphorylases, peroxydases and thioredoxins were successfully identified. Although other proteins remain to be identified, some differences were found in the number of segregating proteins involved in response to stress: 11 proteins found in the modern selected cultivar 'Opata 85' as compared to 4 in the new hexaploid ;Synthetic W7984'. In addition, 'Opata' and 'Synthetic' differed in the number of proteins involved in protein folding (2 and 10, respectively). The usefulness of the mapped enzymes for future research on seed composition and characteristics is discussed.

Lupus autoantibodies target ribosomal P proteins

PubMed Central

1985-01-01

All nine SLE (systemic lupus erythematosus) sera with antiribosomal antibody activity targeted the same three ribosomal protein antigens, of molecular masses 38 and 17/19 kD when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting. One serum reacted with an additional protein of approximately kD. Ribosomal subunit fractionation by composite gel electrophoresis and sucrose density ultracentrifugation showed that these proteins were part of the large subunit. Isoelectric focusing in agarose, and two-dimensional polyacrylamide gel electrophoresis revealed that the antigens had pI between 4.5 and 6.5, but that the 17/19 kD antigens were more acidic than the 38 kD antigen. Similarities in the molecular masses, charges, as well as the presence of highly conserved crossreactive epitopes, failure to bind to carboxymethylcellulose at pH 4.2, and extractability of the 17/19 kD proteins by 400 mM NH4Cl-ethanol at 0 degrees C indicated that these antigens were analogous to the proteins P0 (38 kD) and P1/P2 (17/19 kD) described previously (25, 36). Co-identity was confirmed using reference antibodies and antigen. Although antibodies to these proteins were only found in 5-10% of more than 50 sera screened by radioimmunoassay or Western blotting, the selective production of antibodies to epitopes on three (out of a total of more than 80) ribosomal proteins may provide further clues to autoantibody induction of SLE. PMID:2410526

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

Publications - Beikman, H.M., 1980 | Alaska Division of Geological &

Science.gov Websites

main content USGS Beikman, H.M., 1980 Publication Details Title: Geologic map of Alaska Authors Warehouse Bibliographic Reference Beikman, H.M., 1980, Geologic map of Alaska: U.S. Geological Survey, 1 USGS website Maps & Other Oversized Sheets Maps & Other Oversized Sheets Sheet 1 Geologic Map

A proteome-scale map of the human interactome network

PubMed Central

Rolland, Thomas; Taşan, Murat; Charloteaux, Benoit; Pevzner, Samuel J.; Zhong, Quan; Sahni, Nidhi; Yi, Song; Lemmens, Irma; Fontanillo, Celia; Mosca, Roberto; Kamburov, Atanas; Ghiassian, Susan D.; Yang, Xinping; Ghamsari, Lila; Balcha, Dawit; Begg, Bridget E.; Braun, Pascal; Brehme, Marc; Broly, Martin P.; Carvunis, Anne-Ruxandra; Convery-Zupan, Dan; Corominas, Roser; Coulombe-Huntington, Jasmin; Dann, Elizabeth; Dreze, Matija; Dricot, Amélie; Fan, Changyu; Franzosa, Eric; Gebreab, Fana; Gutierrez, Bryan J.; Hardy, Madeleine F.; Jin, Mike; Kang, Shuli; Kiros, Ruth; Lin, Guan Ning; Luck, Katja; MacWilliams, Andrew; Menche, Jörg; Murray, Ryan R.; Palagi, Alexandre; Poulin, Matthew M.; Rambout, Xavier; Rasla, John; Reichert, Patrick; Romero, Viviana; Ruyssinck, Elien; Sahalie, Julie M.; Scholz, Annemarie; Shah, Akash A.; Sharma, Amitabh; Shen, Yun; Spirohn, Kerstin; Tam, Stanley; Tejeda, Alexander O.; Trigg, Shelly A.; Twizere, Jean-Claude; Vega, Kerwin; Walsh, Jennifer; Cusick, Michael E.; Xia, Yu; Barabási, Albert-László; Iakoucheva, Lilia M.; Aloy, Patrick; De Las Rivas, Javier; Tavernier, Jan; Calderwood, Michael A.; Hill, David E.; Hao, Tong; Roth, Frederick P.; Vidal, Marc

2014-01-01

SUMMARY Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a systematic map of ~14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ~30% larger than what is available from small-scale studies published in the literature in the last few decades. While currently available information is highly biased and only covers a relatively small portion of the proteome, our systematic map appears strikingly more homogeneous, revealing a “broader” human interactome network than currently appreciated. The map also uncovers significant inter-connectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high quality interactome models will help “connect the dots” of the genomic revolution. PMID:25416956

Dual-reference digital holographic interferometry for analyzing high-density gradients in fluid mechanics.

PubMed

Desse, Jean-Michel; Olchewsky, François

2018-04-15

This Letter proposes a dual-reference digital holographic interferometer for analyzing the high refractive index encountered in transonic and supersonic flows. For that, a Wollaston prism is inserted in the reference arm in order to simultaneously generate two orthogonally polarized reference waves. As a consequence, recorded interferograms contain two crossed and perpendicular interference patterns that give two orders fully separated in the Fourier spectrum. It is then possible to analyze a transparent object regardless of the orientation of the refractive index gradient using the two phase maps reconstructed with each of the two first interference orders. Fusion of the phase maps yields a single phase map in which the phase singularities are removed. Experimental results demonstrate the suitability of the proposed approach for analyzing shock waves in the unsteady wake flow around a circular cylinder at Mach 0.75.

Characteristics of Marine Gravity Anomaly Reference Maps and Accuracy Analysis of Gravity Matching-Aided Navigation.

PubMed

Wang, Hubiao; Wu, Lin; Chai, Hua; Xiao, Yaofei; Hsu, Houtse; Wang, Yong

2017-08-10

The variation of a marine gravity anomaly reference map is one of the important factors that affect the location accuracy of INS/Gravity integrated navigation systems in underwater navigation. In this study, based on marine gravity anomaly reference maps, new characteristic parameters of the gravity anomaly were constructed. Those characteristic values were calculated for 13 zones (105°-145° E, 0°-40° N) in the Western Pacific area, and simulation experiments of gravity matching-aided navigation were run. The influence of gravity variations on the accuracy of gravity matching-aided navigation was analyzed, and location accuracy of gravity matching in different zones was determined. Studies indicate that the new parameters may better characterize the marine gravity anomaly. Given the precision of current gravimeters and the resolution and accuracy of reference maps, the location accuracy of gravity matching in China's Western Pacific area is ~1.0-4.0 nautical miles (n miles). In particular, accuracy in regions around the South China Sea and Sulu Sea was the highest, better than 1.5 n miles. The gravity characteristic parameters identified herein and characteristic values calculated in various zones provide a reference for the selection of navigation area and planning of sailing routes under conditions requiring certain navigational accuracy.

Characteristics of Marine Gravity Anomaly Reference Maps and Accuracy Analysis of Gravity Matching-Aided Navigation

PubMed Central

Wang, Hubiao; Chai, Hua; Xiao, Yaofei; Hsu, Houtse; Wang, Yong

2017-01-01

The variation of a marine gravity anomaly reference map is one of the important factors that affect the location accuracy of INS/Gravity integrated navigation systems in underwater navigation. In this study, based on marine gravity anomaly reference maps, new characteristic parameters of the gravity anomaly were constructed. Those characteristic values were calculated for 13 zones (105°–145° E, 0°–40° N) in the Western Pacific area, and simulation experiments of gravity matching-aided navigation were run. The influence of gravity variations on the accuracy of gravity matching-aided navigation was analyzed, and location accuracy of gravity matching in different zones was determined. Studies indicate that the new parameters may better characterize the marine gravity anomaly. Given the precision of current gravimeters and the resolution and accuracy of reference maps, the location accuracy of gravity matching in China’s Western Pacific area is ~1.0–4.0 nautical miles (n miles). In particular, accuracy in regions around the South China Sea and Sulu Sea was the highest, better than 1.5 n miles. The gravity characteristic parameters identified herein and characteristic values calculated in various zones provide a reference for the selection of navigation area and planning of sailing routes under conditions requiring certain navigational accuracy. PMID:28796158

[Assays of HbA1c and Amadori products in human biology].

PubMed

Gillery, P

2014-09-01

Different Amadori products, formed during the early steps of the non-enzymatic glycation of proteins, may be assayed in current practice in human biology. The most important marker is HbA1c, resulting from the binding of glucose to the N-terminal extremity of HbA beta chains. HbA1c may be evaluated by various techniques (ion exchange or affinity high performance liquid chromatography, capillary electrophoresis, immunoassay, enzymatic technique) and is considered the best marker of diabetic patient survey. Due to its irreversible and cumulative formation, it provides a retrospective information on the glycemic balance over the four to eight weeks preceding blood collection. It benefits from an international standardization, based on a reference method using liquid chromatography coupled to capillary electrophoresis or mass spectrometry, maintained by an international network of reference laboratories. When HbA1c assay cannot be used (anemia, hemolysis, hemoglobinopathy) or when a shorter period of glycemic equilibrium must be evaluated (child and adolescent, pregnancy, therapeutic changes), other Amadori products may be assayed, like plasma fructosamine (all plasma glycated proteins) or glycated albumin. Nevertheless, these assays are less used in practice, because their semiological value has been less evidenced. Besides, fructosamine assay lacks specificity, and glycated albumin assay has been described recently. An expanding use of HbA1c assay is expected, especially for the diagnosis of diabetes mellitus and the evaluation of other risks, especially cardiovascular ones. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Recent advances in preparative electrophoresis

NASA Technical Reports Server (NTRS)

Mosher, Richard A.; Thormann, Wolfgang; Egen, Ned B.; Couasnon, Pascal; Sammons, David W.

1987-01-01

Various approaches for preparative electrophoresis, and three new instruments for preparative electrophoresis are discussed. Consideration is given to isoelectric focusing, isotachophoresis, and zone electrophoresis, three gel-based electrophoresis methods. The design, functions, and performance of the Elphor VaP 21 device of Hannig (1982), the shear-stabilized BIOSTREAM separator of Thompson (1983), and the recycling isoelectric focusing device are described.

Department of Defense Strategy to Support Multi-Agency Bat Conservation Initiative within the State of Utah

DTIC Science & Technology

2008-02-28

Range, and Section are entered. Datum: Geometric reference surface. Original Site Location datum is defined by user’s map datum; e.g. NAD27...Section are entered. Datum: Geometric reference surface. Original Site Location datum is defined by user’s map datum; e.g. NAD27 Conus or NAD83...Calculated and recorded automatically if the fields UTM_N and UTM_E or Township, Range, and Section are entered. 41 Datum: Geometric reference surface

Multicolor in situ hybridization and linkage analysis order Charcot-Marie-Tooth type I (CMTIA) gene-region markers

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

Lebo, R.V.; Lynch, E.D.; Golbus, M.S.

1992-01-01

This study demonstrates a clear and current role for multicolor in situ hybridization in expediting positional cloning studies of unknown disease genes. Nine polymorphic DNA cosmids have been mapped to eight ordered locations spanning the Charcot-Marie-Tooth type 1 (CMT1A) disease gene region in distal band 17p11.2, by multicolor in situ hybridization. When used with linkage analysis, these methods have generated a fine physical map and have firmly assigned the CMT1A gene to distal band 17p11.2. Linkage analysis with four CMT1A pedigrees mapped the CMT1A gene with respect to two flanking markers. Additional loci were physically mapped and ordered by inmore » situ hybridization and analysis of phase-known recombinants in CMT1A pedigrees. These data demonstrate the ability of in situ hybridization to resolve loci within 0.5 Mb on early-metaphase chromosomes. Multicolor in situ hybridization also excluded the possibility of pericentric inversions in two unrelated patients with CMT1 and neurofibromatosis type 1. When used with pulsed-field gel electrophoresis, multicolor in situ hybridization can establish physical location, order, and distance in closely spaced chromosome loci.« less

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.

High-resolution gel electrophoresis and sodium dodecyl sulphate-agarose gel electrophoresis on urine samples for qualitative analysis of proteinuria in dogs.

PubMed

Giori, Luca; Tricomi, Flavia Marcella; Zatelli, Andrea; Roura, Xavier; Paltrinieri, Saverio

2011-07-01

The aims of the current study were to assess whether sodium dodecyl sulphate-agarose gel electrophoresis (SDS-AGE) and high-resolution electrophoresis (HRE) can identify dogs with a urinary protein-to-creatinine ratio (UPC ratio) >0.2 and whether HRE can provide preliminary information about the type of proteinuria, using SDS-AGE as a reference method. HRE and SDS-AGE were conducted on 87 urine samples classified according to the International Renal Interest Society as non-proteinuric (NP; UPC ratio: <0.20; 32/87), borderline proteinuric (BP; UPC ratio: 0.21-0.50; 15/87), or proteinuric (P; UPC ratio: >0.51; 40/87). SDS-AGE and HRE were positive in 14 out of 32 and 3 out of 32 NP samples and in 52 out of 55 and 40 out of 55 samples with a UPC ratio >0.20, respectively. The concordance between HRE or SDS and UPC ratio was comparable (κ = 0.59; κ = 0.55). However, specificity (90%) and positive likelihood ratio (7.76) were higher for HRE than for SDS-AGE (56% and 2.16) while sensitivity was lower (73% vs. 94%). The analysis of HRE results revealed that a percentage of albumin >41.4% and an albumin/α(1)-globulin ratio (alb/α(1) ratio) >1.46 can identify samples classified by SDS-AGE as affected by glomerular proteinuria while a percentage of α(1)-globulin >40.8% and an alb/α(1) ratio <0.84 can identify samples classified by SDS-AGE as affected by tubular proteinuria. In conclusion, both SDS-AGE and HRE could misclassify samples with a UPC ratio higher or lower than 0.20. Therefore, UPC ratio must always be determined before conducting these tests. The percentage of albumin and α(1)-globulin or the alb/α(1) ratio determined by HRE can provide preliminary information about the origin of proteinuria.

Time-resolved metabolomics reveals metabolic modulation in rice foliage

PubMed Central

Sato, Shigeru; Arita, Masanori; Soga, Tomoyoshi; Nishioka, Takaaki; Tomita, Masaru

2008-01-01

Background To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed. Results Using capillary electrophoresis mass spectrometry (CE-MS) and capillary electrophoresis diode-array detection (CE-DAD), we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (Oryza sativa L. ssp. japonica) at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM) allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N) metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks. Conclusion Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the underlying biochemical functions. The application of discrimination of unidentified metabolites and the identification of bottleneck enzymatic steps even to non-targeted comprehensive analysis promise to facilitate an understanding of large-scale interactions among components in biological systems. PMID:18564421

Analysis of proteomic differences between liquefied after-cataracts and normal lenses using two-dimensional gel electrophoresis and mass spectrometry

PubMed Central

Ge, Jia-Jia; Huang, Yu-Sen

2017-01-01

AIM To analyze and identify the proteomic differences between liquefied after-cataracts and normal lenses by means of liquefied chromatography-tandem mass spectrometry (LC-MS/MS). METHODS Three normal lenses and three liquefied after-cataracts were exposed to depolymerizing reagents to extract the total proteins. Protein concentrations were separated using two-dimensional gel electrophoresis (2-DE). The digitized images obtained with a GS-800 scanner were then analyzed with PDQuest7.0 software to detect the differentially-expressed protein spots. These protein spots were cut from the gel using a proteome work spot cutter and subjected to in-gel digestion with trypsin. The digested peptide separation was conducted by LC-MS/MS. RESULTS The 2-DE maps showed that lens proteins were in a pH range of 3-10 with a relative molecular weight of 21-70 kD. The relative molecular weight of the more abundant proteins was localized at 25-50 kD, and the isoelectric points were found to lie between PI 4-9. The maps also showed that the protein level within the liquefied after-cataracts was at 29 points and significantly lower than in normal lenses. The 29 points were identified by LC-MS/MS, and ten of these proteins were identified by mass spectrometry and database queries: beta-crystallin B1, glyceraldehyde-3-phosphate dehydrogenase, carbonyl reductase (NADPH) 1, cDNA FLJ55253, gamma-crystallin D, GAS2-like protein 3, sorbitol dehydrogenase, DNA FLJ60282, phosphoglycerate kinase, and filensin. CONCLUSION The level of the ten proteins may play an important role in the development of liquefied after-cataracts. PMID:28944190

Further characterization of the ABR gene in medulloblastoma

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

Wright-White, E.C.; Haken, M.S. von; McDonald J.D.

1994-09-01

Although brain tumors are the most common type of solid cancer in children, little is known about their etiology at the molecular genetic level. Using a panel of 20 chromosome 17p markers, we have previously determined that loss of distal chromosome 17p DNA sequences occurs in 14 of 35 specimens (40%) of medulloblastoma, one of the most common pediatric intracranial neoplasms. Analysis of these same tumors using a PCR-denaturing gradient gel electrophoresis technique has shown only two p53 gene mutations. These results suggest that a tumor suppressor gene in addition to p53 may be located on distal chromosome 17p. Consensusmore » deletion mapping of our specimens suggests that the smallest site of chromosomal loss in defined distally by marker 144-D6, the most telomeric probe as yet identified on chromosome 17p, and proximally by the ABR marker, a BCR homologous gene containing two highly polymorphic VNTR regions. We have used fluorescence in situ hybridization and pulsed-field gel electrophoresis to determine that the ABR gene lies transcriptionally oriented 5{prime} to 3{prime} at a distance of 240 kb from marker 144-D6. We have also constructed a cosmid contig map spanning 120 kb of this region. Using one of these cosmids as a probe, we have detected breakpoints in three of the tumor specimens that lie between the two VNTR regions within the ABR gene. We have subsequently designed PCR primers to cover the breakpoint region which include the ABR exons which have the strongest homology to the BCR gene (Mbcr region), and are screening our tumor specimens for mutations. These results suggest that loss of ABR gene sequences may be involved in the etiology of medulloblastoma.« less

Effects of Concreteness and Contiguity on Learning from Computer-Based Reference Maps

ERIC Educational Resources Information Center

Srinivasan, Sribhagyam; Lewis, Daphne D.; Crooks, Steven M.

2006-01-01

Today's technology has reached new heights that have not been fully implemented. One of the areas where technology has not yet reached its full potential is in education. This study examined the effects of concreteness of location names and contiguity of location names with textual information on learning from computer-based reference maps. The…

The role of reference in cross-situational word learning.

PubMed

Wang, Felix Hao; Mintz, Toben H

2018-01-01

Word learning involves massive ambiguity, since in a particular encounter with a novel word, there are an unlimited number of potential referents. One proposal for how learners surmount the problem of ambiguity is that learners use cross-situational statistics to constrain the ambiguity: When a word and its referent co-occur across multiple situations, learners will associate the word with the correct referent. Yu and Smith (2007) propose that these co-occurrence statistics are sufficient for word-to-referent mapping. Alternative accounts hold that co-occurrence statistics alone are insufficient to support learning, and that learners are further guided by knowledge that words are referential (e.g., Waxman & Gelman, 2009). However, no behavioral word learning studies we are aware of explicitly manipulate subjects' prior assumptions about the role of the words in the experiments in order to test the influence of these assumptions. In this study, we directly test whether, when faced with referential ambiguity, co-occurrence statistics are sufficient for word-to-referent mappings in adult word-learners. Across a series of cross-situational learning experiments, we varied the degree to which there was support for the notion that the words were referential. At the same time, the statistical information about the words' meanings was held constant. When we overrode support for the notion that words were referential, subjects failed to learn the word-to-referent mappings, but otherwise they succeeded. Thus, cross-situational statistics were useful only when learners had the goal of discovering mappings between words and referents. We discuss the implications of these results for theories of word learning in children's language acquisition. Copyright © 2017 Elsevier B.V. All rights reserved.

What is an evidence map? A systematic review of published evidence maps and their definitions, methods, and products.

PubMed

Miake-Lye, Isomi M; Hempel, Susanne; Shanman, Roberta; Shekelle, Paul G

2016-02-10

The need for systematic methods for reviewing evidence is continuously increasing. Evidence mapping is one emerging method. There are no authoritative recommendations for what constitutes an evidence map or what methods should be used, and anecdotal evidence suggests heterogeneity in both. Our objectives are to identify published evidence maps and to compare and contrast the presented definitions of evidence mapping, the domains used to classify data in evidence maps, and the form the evidence map takes. We conducted a systematic review of publications that presented results with a process termed "evidence mapping" or included a figure called an "evidence map." We identified publications from searches of ten databases through 8/21/2015, reference mining, and consulting topic experts. We abstracted the research question, the unit of analysis, the search methods and search period covered, and the country of origin. Data were narratively synthesized. Thirty-nine publications met inclusion criteria. Published evidence maps varied in their definition and the form of the evidence map. Of the 31 definitions provided, 67 % described the purpose as identification of gaps and 58 % referenced a stakeholder engagement process or user-friendly product. All evidence maps explicitly used a systematic approach to evidence synthesis. Twenty-six publications referred to a figure or table explicitly called an "evidence map," eight referred to an online database as the evidence map, and five stated they used a mapping methodology but did not present a visual depiction of the evidence. The principal conclusion of our evaluation of studies that call themselves "evidence maps" is that the implied definition of what constitutes an evidence map is a systematic search of a broad field to identify gaps in knowledge and/or future research needs that presents results in a user-friendly format, often a visual figure or graph, or a searchable database. Foundational work is needed to better standardize the methods and products of an evidence map so that researchers and policymakers will know what to expect of this new type of evidence review. Although an a priori protocol was developed, no registration was completed; this review did not fit the PROSPERO format.

Applications of space-electrophoresis in medicine. [for cellular separations in molecular biology

NASA Technical Reports Server (NTRS)

Bier, M.

1976-01-01

The nature of electrophoresis is reviewed and potential advances realizable in the field of biology and medicine from a space electrophoresis facility are examined. The ground-based applications of electrophoresis: (1) characterization of an ionized species; (2) determination of the quantitative composition of a complex mixture; and (3) isolation of the components of a mixture, separation achieved on the basis of the difference in transport rates is reviewed. The electrophoresis of living cells is considered, touching upon the following areas: the separation of T and B lymphocytes; the genetic influence on mouse lymphocyte mobilities; the abnormal production of specific and monoclonal immunoproteins; and the study of cancer. Schematic diagrams are presented of three types of electrophoresis apparatus: the column assembly for the static electrophoresis experiment on the Apollo-Soyuz mission, the continuous flow apparatus used in the same mission and a miniaturized electrophoresis apparatus.

Children's Understanding of Large-Scale Mapping Tasks: An Analysis of Talk, Drawings, and Gesture

ERIC Educational Resources Information Center

Kotsopoulos, Donna; Cordy, Michelle; Langemeyer, Melanie

2015-01-01

This research examined how children represent motion in large-scale mapping tasks that we referred to as "motion maps". The underlying mathematical content was transformational geometry. In total, 19 children, 8- to 10-year-old, created motion maps and captured their motion maps with accompanying verbal description digitally. Analysis of…

Mapping dominant runoff processes: an evaluation of different approaches using similarity measures and synthetic runoff simulations

NASA Astrophysics Data System (ADS)

Antonetti, Manuel; Buss, Rahel; Scherrer, Simon; Margreth, Michael; Zappa, Massimiliano

2016-07-01

The identification of landscapes with similar hydrological behaviour is useful for runoff and flood predictions in small ungauged catchments. An established method for landscape classification is based on the concept of dominant runoff process (DRP). The various DRP-mapping approaches differ with respect to the time and data required for mapping. Manual approaches based on expert knowledge are reliable but time-consuming, whereas automatic GIS-based approaches are easier to implement but rely on simplifications which restrict their application range. To what extent these simplifications are applicable in other catchments is unclear. More information is also needed on how the different complexities of automatic DRP-mapping approaches affect hydrological simulations. In this paper, three automatic approaches were used to map two catchments on the Swiss Plateau. The resulting maps were compared to reference maps obtained with manual mapping. Measures of agreement and association, a class comparison, and a deviation map were derived. The automatically derived DRP maps were used in synthetic runoff simulations with an adapted version of the PREVAH hydrological model, and simulation results compared with those from simulations using the reference maps. The DRP maps derived with the automatic approach with highest complexity and data requirement were the most similar to the reference maps, while those derived with simplified approaches without original soil information differed significantly in terms of both extent and distribution of the DRPs. The runoff simulations derived from the simpler DRP maps were more uncertain due to inaccuracies in the input data and their coarse resolution, but problems were also linked with the use of topography as a proxy for the storage capacity of soils. The perception of the intensity of the DRP classes also seems to vary among the different authors, and a standardised definition of DRPs is still lacking. Furthermore, we argue not to use expert knowledge for only model building and constraining, but also in the phase of landscape classification.

Using optical mapping data for the improvement of vertebrate genome assemblies.

PubMed

Howe, Kerstin; Wood, Jonathan M D

2015-01-01

Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. Because it is not subject to cloning, amplification, hybridisation or sequencing bias, it is ideally suited to the improvement of fragmented genome assemblies that can no longer be improved by classical methods. In addition, its low cost and rapid turnaround make it equally useful during the scaffolding process of de novo assembly from high throughput sequencing reads. We describe how optical mapping has been used in practice to produce high quality vertebrate genome assemblies. In particular, we detail the efforts undertaken by the Genome Reference Consortium (GRC), which maintains the reference genomes for human, mouse, zebrafish and chicken, and uses different optical mapping platforms for genome curation.

Map Classification: A Comparison of Schemes with Special Reference to the Continent of Africa. Occasional Papers, Number 154.

ERIC Educational Resources Information Center

Merrett, Christopher E.

This guide to the theory and practice of map classification begins with a discussion of the filing of maps and the function of map classification based on area and theme as illustrated by four maps of Africa. The description of the various classification systems which follows is divided into book schemes with provision for maps (including Dewey…

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

PubMed Central

Degner, Jacob F.; Marioni, John C.; Pai, Athma A.; Pickrell, Joseph K.; Nkadori, Everlyne; Gilad, Yoav; Pritchard, Jonathan K.

2009-01-01

Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE). Results: We generated 16 million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias toward higher mapping rates of the allele in the reference sequence, compared with the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, ∼5–10% of SNPs still have an inherent bias toward more effective mapping of one allele. Filtering out inherently biased SNPs removes 40% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data. Availability: Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome and analyzing the simulation output are available upon request from JFD. Raw short read data were deposited in GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE18156. Contact: jdegner@uchicago.edu; marioni@uchicago.edu; gilad@uchicago.edu; pritch@uchicago.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19808877

Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.

PubMed Central

Beier, Sebastian; Himmelbach, Axel; Colmsee, Christian; Zhang, Xiao-Qi; Barrero, Roberto A.; Zhang, Qisen; Li, Lin; Bayer, Micha; Bolser, Daniel; Taudien, Stefan; Groth, Marco; Felder, Marius; Hastie, Alex; Šimková, Hana; Staňková, Helena; Vrána, Jan; Chan, Saki; Muñoz-Amatriaín, María; Ounit, Rachid; Wanamaker, Steve; Schmutzer, Thomas; Aliyeva-Schnorr, Lala; Grasso, Stefano; Tanskanen, Jaakko; Sampath, Dharanya; Heavens, Darren; Cao, Sujie; Chapman, Brett; Dai, Fei; Han, Yong; Li, Hua; Li, Xuan; Lin, Chongyun; McCooke, John K.; Tan, Cong; Wang, Songbo; Yin, Shuya; Zhou, Gaofeng; Poland, Jesse A.; Bellgard, Matthew I.; Houben, Andreas; Doležel, Jaroslav; Ayling, Sarah; Lonardi, Stefano; Langridge, Peter; Muehlbauer, Gary J.; Kersey, Paul; Clark, Matthew D.; Caccamo, Mario; Schulman, Alan H.; Platzer, Matthias; Close, Timothy J.; Hansson, Mats; Zhang, Guoping; Braumann, Ilka; Li, Chengdao; Waugh, Robbie; Scholz, Uwe; Stein, Nils; Mascher, Martin

2017-01-01

Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX). PMID:28448065

Improving Signal-to-Noise Ratio in Scanning Transmission Electron Microscopy Energy-Dispersive X-Ray (STEM-EDX) Spectrum Images Using Single-Atomic-Column Cross-Correlation Averaging.

PubMed

Jeong, Jong Seok; Mkhoyan, K Andre

2016-06-01

Acquiring an atomic-resolution compositional map of crystalline specimens has become routine practice, thus opening possibilities for extracting subatomic information from such maps. A key challenge for achieving subatomic precision is the improvement of signal-to-noise ratio (SNR) of compositional maps. Here, we report a simple and reliable solution for achieving high-SNR energy-dispersive X-ray (EDX) spectroscopy spectrum images for individual atomic columns. The method is based on standard cross-correlation aided by averaging of single-column EDX maps with modifications in the reference image. It produces EDX maps with minimal specimen drift, beam drift, and scan distortions. Step-by-step procedures to determine a self-consistent reference map with a discussion on the reliability, stability, and limitations of the method are presented here.

78 FR 45941 - Changes in Flood Hazard Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-30

... (hereinafter referred to as flood hazard determinations) as shown on the indicated Letter of Map Revision (LOMR... Insurance Rate Maps (FIRMs), and in some cases the Flood Insurance Study (FIS) reports, currently in effect... respective Community Map Repository address listed in the table below and online through the FEMA Map Service...

High School Biology: A Group Approach to Concept Mapping.

ERIC Educational Resources Information Center

Brown, David S.

2003-01-01

Explains concept mapping as an instructional method in cooperative learning environments, and describes a study investigating the effectiveness of concept mapping on student learning during a photosynthesis and cellular respiration unit. Reports on the positive effects of concept mapping in the experimental group. (Contains 16 references.) (YDS)

Supramolecular gel electrophoresis of large DNA fragments.

PubMed

Tazawa, Shohei; Kobayashi, Kazuhiro; Oyoshi, Takanori; Yamanaka, Masamichi

2017-10-01

Pulsed-field gel electrophoresis is a frequent technique used to separate exceptionally large DNA fragments. In a typical continuous field electrophoresis, it is challenging to separate DNA fragments larger than 20 kbp because they migrate at a comparable rate. To overcome this challenge, it is necessary to develop a novel matrix for the electrophoresis. Here, we describe the electrophoresis of large DNA fragments up to 166 kbp using a supramolecular gel matrix and a typical continuous field electrophoresis system. C 3 -symmetric tris-urea self-assembled into a supramolecular hydrogel in tris-boric acid-EDTA buffer, a typical buffer for DNA electrophoresis, and the supramolecular hydrogel was used as a matrix for electrophoresis to separate large DNA fragments. Three types of DNA marker, the λ-Hind III digest (2 to 23 kbp), Lambda DNA-Mono Cut Mix (10 to 49 kbp), and Marker 7 GT (10 to 165 kbp), were analyzed in this study. Large DNA fragments of greater than 100 kbp showed distinct mobility using a typical continuous field electrophoresis system. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The limits of boundaries: unpacking localization and cognitive mapping relative to a boundary.

PubMed

Zhou, Ruojing; Mou, Weimin

2018-05-01

Previous research (Zhou, Mou, Journal of Experimental Psychology: Learning, Memory and Cognition 42(8):1316-1323, 2016) showed that learning individual locations relative to a single landmark, compared to learning relative to a boundary, led to more accurate inferences of inter-object spatial relations (cognitive mapping of multiple locations). Following our past findings, the current study investigated whether the larger number of reference points provided by a homogeneous circular boundary, as well as less accessible knowledge of direct spatial relations among the multiple reference points, would lead to less effective cognitive mapping relative to the boundary. Accordingly, we manipulated (a) the number of primary reference points (one segment drawn from a circular boundary, four such segments, vs. the complete boundary) available when participants were localizing four objects sequentially (Experiment 1) and (b) the extendedness of each of the four segments (Experiment 2). The results showed that cognitive mapping was the least accurate in the whole boundary condition. However, expanding each of the four segments did not affect the accuracy of cognitive mapping until the four were connected to form a continuous boundary. These findings indicate that when encoding locations relative to a homogeneous boundary, participants segmented the boundary into differentiated pieces and subsequently chose the most informative local part (i.e., the segment closest in distance to one location) as the primary reference point for a particular location. During this process, direct spatial relations among the reference points were likely not attended to. These findings suggest that people might encode and represent bounded space in a fragmented fashion when localizing within a homogeneous boundary.

The Release 6 reference sequence of the Drosophila melanogaster genome

DOE PAGES

Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.; ...

2015-01-14

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

The Release 6 reference sequence of the Drosophila melanogaster genome

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

Hoskins, Roger A.; Carlson, Joseph W.; Wan, Kenneth H.

Drosophila melanogaster plays an important role in molecular, genetic, and genomic studies of heredity, development, metabolism, behavior, and human disease. The initial reference genome sequence reported more than a decade ago had a profound impact on progress in Drosophila research, and improving the accuracy and completeness of this sequence continues to be important to further progress. We previously described improvement of the 117-Mb sequence in the euchromatic portion of the genome and 21 Mb in the heterochromatic portion, using a whole-genome shotgun assembly, BAC physical mapping, and clone-based finishing. Here, we report an improved reference sequence of the single-copy andmore » middle-repetitive regions of the genome, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping. These data substantially improve the accuracy and completeness of the reference sequence and the order and orientation of sequence scaffolds into chromosome arm assemblies. Representation of the Y chromosome and other heterochromatic regions is particularly improved. The new 143.9-Mb reference sequence, designated Release 6, effectively exhausts clone-based technologies for mapping and sequencing. Highly repeat-rich regions, including large satellite blocks and functional elements such as the ribosomal RNA genes and the centromeres, are largely inaccessible to current sequencing and assembly methods and remain poorly represented. In conclusion, further significant improvements will require sequencing technologies that do not depend on molecular cloning and that produce very long reads.« less

Capillary electrophoresis with electrochemiluminescent detection for highly sensitive assay of genetically modified organisms.

PubMed

Guo, Longhua; Yang, Huanghao; Qiu, Bin; Xiao, Xueyang; Xue, Linlin; Kim, Donghwan; Chen, Guonan

2009-12-01

A capillary electrophoresis coupled with electrochemiluminescent detection system (CE-ECL) was developed for the detection of polymerase chain reaction (PCR) amplicons. The ECL luminophore, tris(1,10-phenanthroline) ruthenium(II) (Ru(phen)(3)(2+)), was labeled to the PCR primers before amplification. Ru(phen)(3)(2+) was then introduced to PCR amplicons by PCR amplification. Eventually, the PCR amplicons were separated and detected by the homemade CE-ECL system. The detection of a typical genetically modified organism (GMO), Roundup Ready Soy (RRS), was shown as an example to demonstrate the reliability of the proposed approach. Four pairs of primers were amplified by multiple PCR (MPCR) simultaneously, three of which were targeted on the specific sequence of exogenous genes of RRS, and another was targeted on the endogenous reference gene of soybean. Both the conditions for PCR amplification and CE-ECL separation and detection were investigated in detail. Results showed that, under the optimal conditions, the proposed method can accurately identifying RRS. The corresponding limit of detection (LOD) was below 0.01% with 35 PCR cycles.

High-Performance Multiplex SNP Analysis of Three Hemochromatosis-Related Mutations With Capillary Array Electrophoresis Microplates

PubMed Central

Medintz, Igor; Wong, Wendy W.; Berti, Lorenzo; Shiow, Lawrence; Tom, Jennifer; Scherer, James; Sensabaugh, George; Mathies, Richard A.

2001-01-01

An assay is described for high-throughput single nucleotide polymorphism (SNP) genotyping on a microfabricated capillary array electrophoresis (CAE) microchip. The assay targets the three common variants at the HFE locus associated with the genetic disease hereditary hemochromatosis (HHC). The assay employs allele-specific PCR (ASPCR) for the C282Y (845g->a), H63D (187c->g), and S65C (193a->t) variants using fluorescently-labeled energy-transfer (ET) allele-specific primers. Using a 96-channel radial CAE microplate, the labeled ASPCR products generated from 96 samples in a reference Caucasian population are simultaneously separated with single-base-pair resolution and genotyped in under 10 min. Detection is accomplished with a laser-excited rotary four-color fluorescence scanner. The allele-specific amplicons are differentiated on the basis of both their size and the color of the label emission. This study is the first demonstration of the combined use of ASPCR with ET primers and microfabricated radial CAE microplates to perform multiplex SNP analyses in a clinically relevant population. PMID:11230165

Alterations in brain cerebral cortex proteome of rabies-infected cat.

PubMed

Kasempimolporn, Songsri; Lumlertdacha, Boonlert; Chulasugandha, Pannipa; Boonchang, Supatsorn; Sitprija, Visith

2014-07-01

Comparative proteome analysis using brain cerebral cortex tissues from cats and dogs infected with/without rabies virus were conducted using both two-dimensional gel-electrophoresis (2-DE) and 2-D fluorescence difference gel- electrophoresis (2D-DIGE) methods. The 2-DE gel images of all samples revealed >1,000 protein spots in each gel. Quantitative intensity analysis revealed the same overall protein pattern in certain regions of the gel, but the rabies-infected brains exhibited more protein spots than the non-infected controls. From approximately 880 protein spots detected by 2D-DIGE, 65 protein spots were increased and 46 were decreased. Eight of these protein spots were randomly selected and annotated by reference to previous known proteome data of rabid dog brains. They were similarly altered in both of the rabies-infected cats and dogs. A more detailed comparison of changes in proteomic profiles of brains between rabid cats and dogs should shed some light on the pathophysiological mechanism of rabies in domestic animals, as most rabies cases have been traceable to or believed to have originated from rabid dogs.

Unraveling the equine lymphocyte proteome: differential septin 7 expression associates with immune cells in equine recurrent uveitis.

PubMed

Degroote, Roxane L; Hauck, Stefanie M; Amann, Barbara; Hirmer, Sieglinde; Ueffing, Marius; Deeg, Cornelia A

2014-01-01

Equine recurrent uveitis is a spontaneous, lymphocyte-driven autoimmune disease. It affects horses worldwide and presents with painful remitting-relapsing inflammatory attacks of inner eye structures eventually leading to blindness. Since lymphocytes are the key players in equine recurrent uveitis, we were interested in potential changes of their protein repertoire which may be involved in disease pathogenesis. To create a reference for differential proteome analysis, we first unraveled the equine lymphocyte proteome by two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis and subsequently identified 352 protein spots. Next, we compared lymphocytes from ERU cases and healthy horses with a two-dimensional fluorescence difference in gel electrophoresis approach. With this technique, we identified seven differentially expressed proteins between conditions. One of the significantly lower expressed candidates, septin 7, plays a role in regulation of cell shape, motility and migration. Further analyses revealed T cells as the main cell type with decreased septin 7 abundance in equine recurrent uveitis. These findings point to a possible pathogenetic role of septin 7 in this sight-threatening disease.

Capillary electrophoresis of sialylated oligosaccharides in milk from different species.

PubMed

Monti, Lucia; Cattaneo, Tiziana Maria Piera; Orlandi, Mario; Curadi, Maria Claudia

2015-08-28

Oligosaccharides are relevant components of human milk, which have been quite well studied for their pre-biotic effect and their capacity in stimulating the immune system. Since oligosaccharides from milk of non-human mammals received so far less attention, the aim of this work was the application of capillary electrophoresis (CE) for the analysis of sialylated oligosaccharides in cow, goat and equine (mare and donkey) milk to possibly identify potential sources of oligosaccharides to use as health promoting ingredients in functional foods. Human milk was used as reference milk. A recent CE technique was applied to resolve and quantify 3-sialyllactose (3-SL), 6-sialyllactose (6-SL) and disialyl-lacto-N-tetraose (DSLNT). Analysis of non-human milk samples confirmed differences among species and individuals: DSLNT, which was the most abundant compound in human milk (455-805μg/mL) was missing in most of the samples. In most cases, 3-SL showed to be the most concentrated of the quantified analytes, with values ranging from 12 to 77μg/mL. Copyright © 2015 Elsevier B.V. All rights reserved.

Loop-mediated isothermal PCR (LAMP) for the diagnosis of falciparum malaria.

PubMed

Paris, Daniel H; Imwong, Mallika; Faiz, Abul M; Hasan, Mahtabuddin; Yunus, Emran Bin; Silamut, Kamolrat; Lee, Sue J; Day, Nicholas P J; Dondorp, Arjen M

2007-11-01

A recently described loop-mediated isothermal polymerase chain reaction (LAMP) for molecular detection of Plasmodium falciparum was compared with microscopy, PfHRP2-based rapid diagnostic test (RDT), and nested polymerase chain reaction (PCR) as the "gold standard" in 115 Bangladeshi in-patients with fever. DNA extraction for LAMP was conducted by conventional methods or simple heating of the sample; test results were either assessed visually or by gel electrophoresis. Conventional DNA extraction followed by gel electrophoresis had the highest agreement with the reference method (81.7%, kappa = 0.64), with a sensitivity (95% CI) of 76.1% (68.3-83.9%), comparable to RDT and microscopy, but a specificity of 89.6% (84.0-95.2%) compared with 100% for RDT and microscopy. DNA extraction by heat treatment deteriorated specificity to unacceptable levels. LAMP enables molecular diagnosis of falciparum malaria in settings with limited technical resources but will need further optimization. The results are in contrast with a higher accuracy reported in an earlier study comparing LAMP with a non-validated PCR method.

Spatial cognition and navigation

NASA Technical Reports Server (NTRS)

Aretz, Anthony J.

1989-01-01

An experiment that provides data for the development of a cognitive model of pilot flight navigation is described. The experiment characterizes navigational awareness as the mental alignment of two frames of reference: (1) the ego centered reference frame that is established by the forward view out of the cockpit and (2) the world centered reference frame that is established by the aircraft's location on a map. The data support a model involving at least two components: (1) the perceptual encoding of the navigational landmarks and (2) the mental rotation of the map's world reference frame into alignment with the ego centered reference frame. The quantitative relationships of these two factors are provided as possible inputs for a computational model of spatial cognition during flight navigation.

Uncertainty Analysis in the Creation of a Fine-Resolution Leaf Area Index (LAI) Reference Map for Validation of Moderate Resolution LAI Products

EPA Science Inventory

The validation process for a moderate resolution leaf area index (LAI) product (i.e., MODIS) involves the creation of a high spatial resolution LAI reference map (Lai-RM), which when scaled to the moderate LAI resolution (i.e., >1 km) allows for comparison and analysis with this ...

Mashup Scheme Design of Map Tiles Using Lightweight Open Source Webgis Platform

NASA Astrophysics Data System (ADS)

Hu, T.; Fan, J.; He, H.; Qin, L.; Li, G.

2018-04-01

To address the difficulty involved when using existing commercial Geographic Information System platforms to integrate multi-source image data fusion, this research proposes the loading of multi-source local tile data based on CesiumJS and examines the tile data organization mechanisms and spatial reference differences of the CesiumJS platform, as well as various tile data sources, such as Google maps, Map World, and Bing maps. Two types of tile data loading schemes have been designed for the mashup of tiles, the single data source loading scheme and the multi-data source loading scheme. The multi-sources of digital map tiles used in this paper cover two different but mainstream spatial references, the WGS84 coordinate system and the Web Mercator coordinate system. According to the experimental results, the single data source loading scheme and the multi-data source loading scheme with the same spatial coordinate system showed favorable visualization effects; however, the multi-data source loading scheme was prone to lead to tile image deformation when loading multi-source tile data with different spatial references. The resulting method provides a low cost and highly flexible solution for small and medium-scale GIS programs and has a certain potential for practical application values. The problem of deformation during the transition of different spatial references is an important topic for further research.

Mines, prospects, and occurrences of nonmetallic mineral commodities in the Greenville 1 degree by 2 degrees Quadrangle, South Carolina, Georgia, and North Carolina

USGS Publications Warehouse

D'Agostino, John P.; O'Connor, Bruce J.; Zupan, Alan J.W.; Maybin, Arthur H.

1994-01-01

Mines, prospects, and occurrences of nonmetal mineral commodities in the Greenville 1° x 2° quadrangle are tabulated in this report. There are 488 symbols representing 579 mines, prospects, and occurrences located in the quadrangle. There are 379 symbols used for 466 features in Georgia, 106 symbols for 110 features in South Carolina, and 3 symbols for 3 features in North Carolina. The table lists, in consecutive orders for each county (fig. 1), the map number of each feature, which correlates and locates the item on the accompanying Greenville 1° x 2° quadrangle map. Also listed are the known name of the feature; the 7.5 topographic map on which the commodity site is located; the Transverse Mercator (UTM) northing and easting grid coordinates from the appropriate 7.5’ topographic map; the commodity; remarks; and references. Some locations are known, but many sites are not verified and their locations are only approximate. Reference are listed in References Cited and referred to by number to save space. The generalized tectonic framework for the quadrangle is shown in figure 2.

Two Electrophoresis Experiments for Freshmen in the Health Professions.

ERIC Educational Resources Information Center

Brabson, G. Dana; Waugh, David S.

1986-01-01

Describes procedures involved with paper electrophoresis separation of amino acids, gel electrophoresis separation of DNA, and design of an electrophoresis tank. Describes experiments using paper (amino acids) and gel (deoxyribonucleic acid fragments). Provides material lists, procedures, and discussion. (JM)

Kidney cell electrophoresis

NASA Technical Reports Server (NTRS)

Todd, P. W.

1985-01-01

Tasks were undertaken in support of two objectives. They are: (1) to carry out electrophoresis experiments on cells in microgravity; and (2) assess the feasibility of using purified kidney cells from embryonic kidney cultures as a source of important cell products. Investigations were carried out in the following areas: (1) ground based electrophoresis technology; (2) cell culture technology; (3) electrophoresis of cells; (4) urokinase assay research; (5) zero-g electrophoresis; and (6) flow cytometry.

Using genic sequence capture in combination with a syntenic pseudo genome to map a deletion mutant in a wheat species.

PubMed

Gardiner, Laura-Jayne; Gawroński, Piotr; Olohan, Lisa; Schnurbusch, Thorsten; Hall, Neil; Hall, Anthony

2014-12-01

Mapping-by-sequencing analyses have largely required a complete reference sequence and employed whole genome re-sequencing. In species such as wheat, no finished genome reference sequence is available. Additionally, because of its large genome size (17 Gb), re-sequencing at sufficient depth of coverage is not practical. Here, we extend the utility of mapping by sequencing, developing a bespoke pipeline and algorithm to map an early-flowering locus in einkorn wheat (Triticum monococcum L.) that is closely related to the bread wheat genome A progenitor. We have developed a genomic enrichment approach using the gene-rich regions of hexaploid bread wheat to design a 110-Mbp NimbleGen SeqCap EZ in solution capture probe set, representing the majority of genes in wheat. Here, we use the capture probe set to enrich and sequence an F2 mapping population of the mutant. The mutant locus was identified in T. monococcum, which lacks a complete genome reference sequence, by mapping the enriched data set onto pseudo-chromosomes derived from the capture probe target sequence, with a long-range order of genes based on synteny of wheat with Brachypodium distachyon. Using this approach we are able to map the region and identify a set of deleted genes within the interval. © 2014 The Authors.The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

Coastal flood inundation monitoring with Satellite C-band and L-band Synthetic Aperture Radar data

USGS Publications Warehouse

Ramsey, Elijah W.; Rangoonwala, Amina; Bannister, Terri

2013-01-01

Satellite Synthetic Aperture Radar (SAR) was evaluated as a method to operationally monitor the occurrence and distribution of storm- and tidal-related flooding of spatially extensive coastal marshes within the north-central Gulf of Mexico. Maps representing the occurrence of marsh surface inundation were created from available Advanced Land Observation Satellite (ALOS) Phased Array type L-Band SAR (PALSAR) (L-band) (21 scenes with HH polarizations in Wide Beam [100 m]) data and Environmental Satellite (ENVISAT) Advanced SAR (ASAR) (C-band) data (24 scenes with VV and HH polarizations in Wide Swath [150 m]) during 2006-2009 covering 500 km of the Louisiana coastal zone. Mapping was primarily based on a decrease in backscatter between reference and target scenes, and as an extension of previous studies, the flood inundation mapping performance was assessed by the degree of correspondence between inundation mapping and inland water levels. Both PALSAR- and ASAR-based mapping at times were based on suboptimal reference scenes; however, ASAR performance seemed more sensitive to reference-scene quality and other types of scene variability. Related to water depth, PALSAR and ASAR mapping accuracies tended to be lower when water depths were shallow and increased as water levels decreased below or increased above the ground surface, but this pattern was more pronounced with ASAR. Overall, PALSAR-based inundation accuracies averaged 84% (n = 160), while ASAR-based mapping accuracies averaged 62% (n = 245).

AXOPLASMIC PROTEINS OF THE SQUID GIANT NERVE FIBER WITH PARTICULAR REFERENCE TO THE FIBROUS PROTEIN

PubMed Central

Maxfield, Myles

1953-01-01

1. Axoplasm of squid giant nerve fibers is examined with the ultracentrifuge and electrophoresis apparatus and several distinct components demonstrated. 2. One of these components, a protein called axon filaments, is isolated by fractional extraction followed by differential ultracentrifugation and redissolving in glycine solution. Axon filaments are monodisperse by ultracentrifugation. Their physical chemical properties have been studied. 3. The existence of a reversible transformation of axon filaments into a particle of lower molecular weight and lower asymmetry has been demonstrated. PMID:13109156

Talbot-Lau x-ray deflectometry phase-retrieval methods for electron density diagnostics in high-energy density experiments.

PubMed

Valdivia, Maria Pia; Stutman, Dan; Stoeckl, Christian; Mileham, Chad; Begishev, Ildar A; Bromage, Jake; Regan, Sean P

2018-01-10

Talbot-Lau x-ray interferometry uses incoherent x-ray sources to measure refraction index changes in matter. These measurements can provide accurate electron density mapping through phase retrieval. An adaptation of the interferometer has been developed in order to meet the specific requirements of high-energy density experiments. This adaptation is known as a moiré deflectometer, which allows for single-shot capabilities in the form of interferometric fringe patterns. The moiré x-ray deflectometry technique requires a set of object and reference images in order to provide electron density maps, which can be costly in the high-energy density environment. In particular, synthetic reference phase images obtained ex situ through a phase-scan procedure, can provide a feasible solution. To test this procedure, an object phase map was retrieved from a single-shot moiré image obtained from a plasma-produced x-ray source. A reference phase map was then obtained from phase-stepping measurements using a continuous x-ray tube source in a small laboratory setting. The two phase maps were used to retrieve an electron density map. A comparison of the moiré and phase-stepping phase-retrieval methods was performed to evaluate single-exposure plasma electron density mapping for high-energy density and other transient plasma experiments. It was found that a combination of phase-retrieval methods can deliver accurate refraction angle mapping. Once x-ray backlighter quality is optimized, the ex situ method is expected to deliver electron density mapping with improved resolution. The steps necessary for improved diagnostic performance are discussed.

Centimeter-Level Robust Gnss-Aided Inertial Post-Processing for Mobile Mapping Without Local Reference Stations

NASA Astrophysics Data System (ADS)

Hutton, J. J.; Gopaul, N.; Zhang, X.; Wang, J.; Menon, V.; Rieck, D.; Kipka, A.; Pastor, F.

2016-06-01

For almost two decades mobile mapping systems have done their georeferencing using Global Navigation Satellite Systems (GNSS) to measure position and inertial sensors to measure orientation. In order to achieve cm level position accuracy, a technique referred to as post-processed carrier phase differential GNSS (DGNSS) is used. For this technique to be effective the maximum distance to a single Reference Station should be no more than 20 km, and when using a network of Reference Stations the distance to the nearest station should no more than about 70 km. This need to set up local Reference Stations limits productivity and increases costs, especially when mapping large areas or long linear features such as roads or pipelines. An alternative technique to DGNSS for high-accuracy positioning from GNSS is the so-called Precise Point Positioning or PPP method. In this case instead of differencing the rover observables with the Reference Station observables to cancel out common errors, an advanced model for every aspect of the GNSS error chain is developed and parameterized to within an accuracy of a few cm. The Trimble Centerpoint RTX positioning solution combines the methodology of PPP with advanced ambiguity resolution technology to produce cm level accuracies without the need for local reference stations. It achieves this through a global deployment of highly redundant monitoring stations that are connected through the internet and are used to determine the precise satellite data with maximum accuracy, robustness, continuity and reliability, along with advance algorithms and receiver and antenna calibrations. This paper presents a new post-processed realization of the Trimble Centerpoint RTX technology integrated into the Applanix POSPac MMS GNSS-Aided Inertial software for mobile mapping. Real-world results from over 100 airborne flights evaluated against a DGNSS network reference are presented which show that the post-processed Centerpoint RTX solution agrees with the DGNSS solution to better than 2.9 cm RMSE Horizontal and 5.5 cm RMSE Vertical. Such accuracies are sufficient to meet the requirements for a majority of airborne mapping applications.

A fruit quality gene map of Prunus

PubMed Central

2009-01-01

Background Prunus fruit development, growth, ripening, and senescence includes major biochemical and sensory changes in texture, color, and flavor. The genetic dissection of these complex processes has important applications in crop improvement, to facilitate maximizing and maintaining stone fruit quality from production and processing through to marketing and consumption. Here we present an integrated fruit quality gene map of Prunus containing 133 genes putatively involved in the determination of fruit texture, pigmentation, flavor, and chilling injury resistance. Results A genetic linkage map of 211 markers was constructed for an intraspecific peach (Prunus persica) progeny population, Pop-DG, derived from a canning peach cultivar 'Dr. Davis' and a fresh market cultivar 'Georgia Belle'. The Pop-DG map covered 818 cM of the peach genome and included three morphological markers, 11 ripening candidate genes, 13 cold-responsive genes, 21 novel EST-SSRs from the ChillPeach database, 58 previously reported SSRs, 40 RAFs, 23 SRAPs, 14 IMAs, and 28 accessory markers from candidate gene amplification. The Pop-DG map was co-linear with the Prunus reference T × E map, with 39 SSR markers in common to align the maps. A further 158 markers were bin-mapped to the reference map: 59 ripening candidate genes, 50 cold-responsive genes, and 50 novel EST-SSRs from ChillPeach, with deduced locations in Pop-DG via comparative mapping. Several candidate genes and EST-SSRs co-located with previously reported major trait loci and quantitative trait loci for chilling injury symptoms in Pop-DG. Conclusion The candidate gene approach combined with bin-mapping and availability of a community-recognized reference genetic map provides an efficient means of locating genes of interest in a target genome. We highlight the co-localization of fruit quality candidate genes with previously reported fruit quality QTLs. The fruit quality gene map developed here is a valuable tool for dissecting the genetic architecture of fruit quality traits in Prunus crops. PMID:19995417

The NASA atlas of the solar system

USGS Publications Warehouse

Greeley, Ronald; Batson, Raymond M.

1997-01-01

Describes every planet, moon, and body that has been the subject of a NASA mission, including images of 30 solar system objects and maps of 26 objects. The presentation includes geologic history, geologic and reference maps, and shaded relief maps.

Mobile Robot Self-Localization by Matching Range Maps Using a Hausdorff Measure

NASA Technical Reports Server (NTRS)

Olson, C. F.

1997-01-01

This paper examines techniques for a mobile robot to perform self-localization in natural terrain by comparing a dense range map computed from stereo imagery to a range map in a known frame of reference.

Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps

PubMed Central

Sharma, Sanjeev Kumar; Bolser, Daniel; de Boer, Jan; Sønderkær, Mads; Amoros, Walter; Carboni, Martin Federico; D’Ambrosio, Juan Martín; de la Cruz, German; Di Genova, Alex; Douches, David S.; Eguiluz, Maria; Guo, Xiao; Guzman, Frank; Hackett, Christine A.; Hamilton, John P.; Li, Guangcun; Li, Ying; Lozano, Roberto; Maass, Alejandro; Marshall, David; Martinez, Diana; McLean, Karen; Mejía, Nilo; Milne, Linda; Munive, Susan; Nagy, Istvan; Ponce, Olga; Ramirez, Manuel; Simon, Reinhard; Thomson, Susan J.; Torres, Yerisf; Waugh, Robbie; Zhang, Zhonghua; Huang, Sanwen; Visser, Richard G. F.; Bachem, Christian W. B.; Sagredo, Boris; Feingold, Sergio E.; Orjeda, Gisella; Veilleux, Richard E.; Bonierbale, Merideth; Jacobs, Jeanne M. E.; Milbourne, Dan; Martin, David Michael Alan; Bryan, Glenn J.

2013-01-01

The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker−based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal “pseudomolecules”. PMID:24062527

Length and area equivalents for interpreting wildland resource maps

Treesearch

Elliot L. Amidon; Marilyn S. Whitfield

1969-01-01

Map users must refer to an appropriate scale in interpreting wildland resource maps. Length and area equivalents for nine map scales commonly used have been computed. For each scale a 1-page table consists of map-to-ground equivalents, buffer strip or road widths, and cell dimensions required for a specified acreage. The conversion factors are stored in a Fortran...

Techniques For Focusing In Zone Electrophoresis

NASA Technical Reports Server (NTRS)

Sharnez, Rizwan; Twitty, Garland E.; Sammons, David W.

1994-01-01

In two techniques for focusing in zone electrophoresis, force of applied electrical field in each charged particle balanced by restoring force of electro-osmosis. Two techniques: velocity-gradient focusing (VGF), suitable for rectangular electrophoresis chambers; and field-gradient focusing (FGF), suitable for step-shaped electrophoresis chambers.

Wheat gliadin: digital imaging and database construction using a 4-band reference system of agarose isoelectric focusing patterns.

PubMed

Black, J A; Waggamon, K A

1992-01-01

An isoelectric focusing method using thin-layer agarose gel has been developed for wheat gliadin. Using flat-bed units with a third electrode, up to 72 samples per gel may be analyzed. Advantages over traditional acid polyacrylamide gel electrophoresis methodology include: faster run times, nontoxic media, and greater sample capacity. The method is suitable for fingerprinting or purity testing of wheat varieties. Using digital images captured by a flat-bed scanner, a 4-band reference system using isoelectric points was devised. Software enables separated bands to be assigned pI values based upon reference tracks. Precision of assigned isoelectric points is shown to be on the order of 0.02 pH units. Captured images may be stored in a computer database and compared to unknown patterns to enable an identification. Parameters for a match with a stored pattern may be adjusted for pI interval required for a match, and number of best matches.

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.

Mining e-Learning Domain Concept Map from Academic Articles

ERIC Educational Resources Information Center

Chen, Nian-Shing; Kinshuk; Wei, Chun-Wang; Chen, Hong-Jhe

2008-01-01

Recent researches have demonstrated the importance of concept map and its versatile applications especially in e-Learning. For example, while designing adaptive learning materials, designers need to refer to the concept map of a subject domain. Moreover, concept maps can show the whole picture and core knowledge about a subject domain. Research…

75 FR 61373 - Proposed Flood Elevation Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-05

... located at the community map repository (see below) for exact locations of all BFEs to be changed. Send... located at the community map repository (see below) for exact locations of all BFEs to be changed. Send.... Please refer to the revised Flood Insurance Rate Map located at the community map repository (see below...

Physical mapping of chromosome 17p13.3 in the region of a putative tumor suppressor gene important in medulloblastoma

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

McDonald, J.D.; Daneshvar, L.; Willert, J.R.

1994-09-01

Deletion mapping of a medulloblastoma tumor panel revealed loss of distal chromosome 17p13.3 sequences in tumors from 14 of 32 patients (44%). Of the 14 tumors showing loss of heterozygosity by restriction fragment length polymorphism analysis, 14 of 14 (100%) displayed loss of the telomeric marker p144-D6 (D17S34), while a probe for the ABR gene on 17p13.3 was lost in 7 of 8 (88%) informative cases. Using pulsed-field gel electrophoresis, we localized the polymorphic marker (VNTR-A) of the ABR gene locus to within 220 kb of the p144-D6 locus. A cosmid contig constructed in this region was used to demonstratemore » by fluorescence in situ hybridization that the ABR gene is oriented transcriptionally 5{prime} to 3{prime} toward the telomere. This report provides new physical mapping data for the ABR gene, which has not been previously shown to be deleted in medulloblastoma. These results provide further evidence for the existence of a second tumor suppressor gene distinct from p53 on distal chromosome 17p. 12 refs., 3 figs.« less

Culture phenotypes and molecular characterization of Mycobacterium avium subsp. paratuberculosis isolates from small ruminants.

PubMed

Dimareli-Malli, Z; Mazaraki, K; Stevenson, K; Tsakos, P; Zdragas, A; Giantzi, V; Petridou, E; Heron, I; Vafeas, G

2013-08-01

In this study the suitability of different solid media was investigated for the isolation of Mycobacterium avium subsp. paratuberculosis (Map) in order to identify the optimum single or combination of media to permit the isolation of all strain types from small ruminants. A subset of these Map strains was then further characterized by molecular typing methods to assess the genetic diversity of Map strains in the study area (Northern Greece). Map strains were isolated from tissues and faeces of infected goats (n=52) and sheep (n=8) and were analysed for polymorphisms in IS1311 to classify the strain type as Type C or S. The study found that M7H11 supplemented with mycobactin j, OADC and new born calf serum (M7H11+Mj) is the best single choice of medium for the primary isolation of Map of both Type C and S from small ruminants. The combination of M7H11+Mj and Herrolds egg yolk medium supplemented with mycobactin j and sodium pyruvate allowed the detection of all Map isolates in this study. Nineteen Map isolates were characterised by pulsed-field gel electrophoresis and the isolates demonstrated significant genetic diversity. Twelve different SnaBI and 16 distinct SpeI profiles were detected of which 25 have not been described previously and are new profiles. The combination of both enzyme profiles gave 13 different multiplex profiles. Ten different multiplex profiles were detected in goats and three in sheep. One ovine isolate gave the same multiplex profile as a caprine isolate and two different profiles were found within a single goat herd. Copyright © 2013 Elsevier Ltd. All rights reserved.

The Cutting Edge of Affinity Electrophoresis Technology

PubMed Central

Kinoshita, Eiji; Kinoshita-Kikuta, Emiko; Koike, Tohru

2015-01-01

Affinity electrophoresis is an important technique that is widely used to separate and analyze biomolecules in the fields of biology and medicine. Both quantitative and qualitative information can be gained through affinity electrophoresis. Affinity electrophoresis can be applied through a variety of strategies, such as mobility shift electrophoresis, charge shift electrophoresis or capillary affinity electrophoresis. These strategies are based on changes in the electrophoretic patterns of biological macromolecules that result from interactions or complex-formation processes that induce changes in the size or total charge of the molecules. Nucleic acid fragments can be characterized through their affinity to other molecules, for example transcriptional factor proteins. Hydrophobic membrane proteins can be identified by means of a shift in the mobility induced by a charged detergent. The various strategies have also been used in the estimation of association/disassociation constants. Some of these strategies have similarities to affinity chromatography, in that they use a probe or ligand immobilized on a supported matrix for electrophoresis. Such methods have recently contributed to profiling of major posttranslational modifications of proteins, such as glycosylation or phosphorylation. Here, we describe advances in analytical techniques involving affinity electrophoresis that have appeared during the last five years. PMID:28248262

21 CFR 862.2485 - Electrophoresis apparatus for clinical use.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Electrophoresis apparatus for clinical use. 862... Instruments § 862.2485 Electrophoresis apparatus for clinical use. (a) Identification. An electrophoresis apparatus for clinical use is a device intended to separate molecules or particles, including plasma...

21 CFR 862.2485 - Electrophoresis apparatus for clinical use.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Electrophoresis apparatus for clinical use. 862... Instruments § 862.2485 Electrophoresis apparatus for clinical use. (a) Identification. An electrophoresis apparatus for clinical use is a device intended to separate molecules or particles, including plasma...

Apparatus and method for mapping an area of interest

DOEpatents

Staab, Torsten A. Cohen, Daniel L.; Feller, Samuel [Fairfax, VA

2009-12-01

An apparatus and method are provided for mapping an area of interest using polar coordinates or Cartesian coordinates. The apparatus includes a range finder, an azimuth angle measuring device to provide a heading and an inclinometer to provide an angle of inclination of the range finder as it relates to primary reference points and points of interest. A computer is provided to receive signals from the range finder, inclinometer and azimuth angle measurer to record location data and calculate relative locations between one or more points of interest and one or more primary reference points. The method includes mapping of an area of interest to locate points of interest relative to one or more primary reference points and to store the information in the desired manner. The device may optionally also include an illuminator which can be utilized to paint the area of interest to indicate both points of interest and primary points of reference during and/or after data acquisition.

Intrusive Rock Database for the Digital Geologic Map of Utah

USGS Publications Warehouse

Nutt, C.J.; Ludington, Steve

2003-01-01

Digital geologic maps offer the promise of rapid and powerful answers to geologic questions using Geographic Information System software (GIS). Using modern GIS and database methods, a specialized derivative map can be easily prepared. An important limitation can be shortcomings in the information provided in the database associated with the digital map, a database which is often based on the legend of the original map. The purpose of this report is to show how the compilation of additional information can, when prepared as a database that can be used with the digital map, be used to create some types of derivative maps that are not possible with the original digital map and database. This Open-file Report consists of computer files with information about intrusive rocks in Utah that can be linked to the Digital Geologic Map of Utah (Hintze et al., 2000), an explanation of how to link the databases and map, and a list of references for the databases. The digital map, which represents the 1:500,000-scale Geologic Map of Utah (Hintze, 1980), can be obtained from the Utah Geological Survey (Map 179DM). Each polygon in the map has a unique identification number. We selected the polygons identified on the geologic map as intrusive rock, and constructed a database (UT_PLUT.xls) that classifies the polygons into plutonic map units (see tables). These plutonic map units are the key information that is used to relate the compiled information to the polygons on the map. The map includes a few polygons that were coded as intrusive on the state map but are largely volcanic rock; in these cases we note the volcanic rock names (rhyolite and latite) as used in the original sources Some polygons identified on the digital state map as intrusive rock were misidentified; these polygons are noted in a separate table of the database, along with some information about their true character. Fields may be empty because of lack of information from references used or difficulty in finding information. The information in the database is from a variety of sources, including geologic maps at scales ranging from 1:500,000 to 1:24,000, and thesis monographs. The references are shown twice: alphabetically and by region. The digital geologic map of Utah (Hintze and others, 2000) classifies intrusive rocks into only 3 categories, distinguished by age. They are: Ti, Tertiary intrusive rock; Ji, Upper to Middle Jurassic granite to quartz monzonite; and pCi, Early Proterozoic to Late Archean intrusive rock. Use of the tables provided in this report will permit selection and classification of those rocks by lithology and age. This database is a pilot study by the Survey and Analysis Project of the U.S. Geological Survey to characterize igneous rocks and link them to a digital map. The database, and others like it, will evolve as the project continues and other states are completed. We release this version now as an example, as a reference, and for those interested in Utah plutonic rocks.

[The sequential use of local vacuum magnetotherapy and papaverine electrophoresis with sinusoidal modulated currents in impotence].

PubMed

Karpukhin, I V; Bogomol'nyĭ, V A

1997-01-01

105 patients with chronic nonspecific prostatitis were examined and treated with papaverin electrophoresis using sinusoidal modulated currents (SMC) and local vacuum magnetotherapy (LVMT). Papaverin SMC electrophoresis and LVMT stimulated cavernous circulation. The highest stimulation was achieved at successive use of LVMT and the electrophoresis. LVMT followed by the electrophoresis maintained good cavernous circulation for 5-6 hours after the procedure in the course of which several spontaneous erections were observed.

Urtica dioica agglutinin: separation, identification, and quantitation of individual isolectins by capillary electrophoresis and capillary electrophoresis-mass spectrometry.

PubMed

Ganzera, Markus; Piereder, Daniela; Sturm, Sonja; Erdelmeier, Clemens; Stuppner, Hermann

2005-05-01

With benign prostatic hyperplasia (BPH) being a major health problem in ageing men, alternative therapeutic approaches (e.g., with phytopharmaceuticals) are of great interest. Based on pharmacological evidences, one of the most promising options in that respect are the lectins found in Urtica dioica (stinging nettle) roots. In this study the qualitative and quantitative analysis of individual isolectins in U. dioica extracts is described, which is the first report on using capillary electrophoresis (CE) for the analysis of lectins in plant material at all. By utilizing a 200 mM sodium acetate buffer (pH 3.75) a baseline separation and determination of four closely related isolectins was feasible within 20 min in the aqueous plant extracts. The individual compounds were identified based on reference compounds as well as data obtained from CE-mass spectrometry (MS) experiments. After modifying the optimized CE conditions to 100 mM ammonium formate buffer with pH 3.75 and a voltage of 15 kV, the isolectins were clearly assignable in positive electrospray ionization (ESI) mode. The quantitative results obtained by CE (the total lectin content varied from 0 to 0.42% in the samples) were accurate (recovery rates of spiked samples between 92.5 and 96.2%), precise (relative standard deviation < 5%) and in good agreement to those obtained by High-performance liquid chromatography (HPLC). As for peak resolution, assignable compounds and required separation time the newly developed CE method was clearly advantageous over the determination achieved by LC.

Model-based local density sharpening of cryo-EM maps

PubMed Central

Jakobi, Arjen J; Wilmanns, Matthias

2017-01-01

Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement. PMID:29058676

A natural-color mapping for single-band night-time image based on FPGA

NASA Astrophysics Data System (ADS)

Wang, Yilun; Qian, Yunsheng

2018-01-01

A natural-color mapping for single-band night-time image method based on FPGA can transmit the color of the reference image to single-band night-time image, which is consistent with human visual habits and can help observers identify the target. This paper introduces the processing of the natural-color mapping algorithm based on FPGA. Firstly, the image can be transformed based on histogram equalization, and the intensity features and standard deviation features of reference image are stored in SRAM. Then, the real-time digital images' intensity features and standard deviation features are calculated by FPGA. At last, FPGA completes the color mapping through matching pixels between images using the features in luminance channel.

Cell wall proteomics of the green alga Haematococcus pluvialis (Chlorophyceae).

PubMed

Wang, Sheng-Bing; Hu, Qiang; Sommerfeld, Milton; Chen, Feng

2004-03-01

The green microalga Haematococcus pluvialis can synthesize and accumulate large amounts of the ketocarotenoid astaxanthin, and undergo profound changes in cell wall composition and architecture during the cell cycle and in response to environmental stresses. In this study, cell wall proteins (CWPs) of H. pluvialis were systematically analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) coupled with peptide mass fingerprinting (PMF) and sequence-database analysis. In total, 163 protein bands were analyzed, which resulted in positive identification of 81 protein orthologues. The highly complex and dynamic composition of CWPs is manifested by the fact that the majority of identified CWPs are differentially expressed at specific stages of the cell cycle along with a number of common wall-associated 'housekeeping' proteins. The detection of cellulose synthase orthologue in the vegetative cells suggested that the biosynthesis of cellulose occurred during primary wall formation, in contrast to earlier observations that cellulose was exclusively present in the secondary wall of the organism. A transient accumulation of a putative cytokinin oxidase at the early stage of encystment pointed to a possible role in cytokinin degradation while facilitating secondary wall formation and/or assisting in cell expansion. This work represents the first attempt to use a proteomic approach to investigate CWPs of microalgae. The reference protein map constructed and the specific protein markers obtained from this study provide a framework for future characterization of the expression and physiological functions of the proteins involved in the biogenesis and modifications in the cell wall of Haematococcus and related organisms.

Automated matching of multiple terrestrial laser scans for stem mapping without the use of artificial references

NASA Astrophysics Data System (ADS)

Liu, Jingbin; Liang, Xinlian; Hyyppä, Juha; Yu, Xiaowei; Lehtomäki, Matti; Pyörälä, Jiri; Zhu, Lingli; Wang, Yunsheng; Chen, Ruizhi

2017-04-01

Terrestrial laser scanning has been widely used to analyze the 3D structure of a forest in detail and to generate data at the level of a reference plot for forest inventories without destructive measurements. Multi-scan terrestrial laser scanning is more commonly applied to collect plot-level data so that all of the stems can be detected and analyzed. However, it is necessary to match the point clouds of multiple scans to yield a point cloud with automated processing. Mismatches between datasets will lead to errors during the processing of multi-scan data. Classic registration methods based on flat surfaces cannot be directly applied in forest environments; therefore, artificial reference objects have conventionally been used to assist with scan matching. The use of artificial references requires additional labor and expertise, as well as greatly increasing the cost. In this study, we present an automated processing method for plot-level stem mapping that matches multiple scans without artificial references. In contrast to previous studies, the registration method developed in this study exploits the natural geometric characteristics among a set of tree stems in a plot and combines the point clouds of multiple scans into a unified coordinate system. Integrating multiple scans improves the overall performance of stem mapping in terms of the correctness of tree detection, as well as the bias and the root-mean-square errors of forest attributes such as diameter at breast height and tree height. In addition, the automated processing method makes stem mapping more reliable and consistent among plots, reduces the costs associated with plot-based stem mapping, and enhances the efficiency.

A Geophysical Atlas for Interpretation of Satellite-derived Data

NASA Technical Reports Server (NTRS)

Lowman, P. D., Jr. (Editor); Frey, H. V. (Editor); Davis, W. M.; Greenberg, A. P.; Hutchinson, M. K.; Langel, R. A.; Lowrey, B. E.; Marsh, J. G.; Mead, G. D.; Okeefe, J. A.

1979-01-01

A compilation of maps of global geophysical and geological data plotted on a common scale and projection is presented. The maps include satellite gravity, magnetic, seismic, volcanic, tectonic activity, and mantle velocity anomaly data. The Bibliographic references for all maps are included.

Capillary electrophoresis with indirect UV detection for the determination of stabilizers and citrates present in human albumin solutions.

PubMed

Jaworska, Małgorzata; Cygan, Paulina; Wilk, Małgorzata; Anuszewska, Elzbieta

2009-08-15

Sodium caprylate and N-acetyltryptophan are the most frequently used stabilizers that protect the albumin from aggregation or heat induced denaturation. In turn citrates - excipients remaining after fractionation process - can be treated as by-product favoring leaching aluminum out of glass containers whilst albumin solution is stored. With ionic nature these substances have all the markings of a subject for capillary electrophoresis analysis. Thus CE methods were proposed as new approach for quality control of human albumin solution in terms of determination of stabilizers and citrates residue. Human albumin solutions both 5% and 20% from various manufacturers were tested. Indirect detection mode was set to provide sufficient detectability of analytes lacking of chromophores. As being anions analytes were separated with reversed electroosmotic flow. As a result of method optimization two background electrolytes based on p-hydroxybenzoic acid and 2,6-pyridinedicarboxylic acid were selected for stabilizers and citrates separation, respectively. The optimized methods were successfully validated. For citrates that require quantification below 100microM the method demonstrated the precision less than 4% and the limit of detection at 4microM. In order to check the new methods accuracy and applicability the samples were additionally tested with selected reference methods. The proposed methods allow reliable quantification of stabilizers and citrates in human albumin solution that was confirmed by method validation as well as result comparison with reference methods. The CE methods are considered to be suitable for quality control yet simplifying and reducing cost of analysis.

Establishment of a Universal Size Standard Strain for Use with the PulseNet Standardized Pulsed-Field Gel Electrophoresis Protocols: Converting the National Databases to the New Size Standard

PubMed Central

Hunter, Susan B.; Vauterin, Paul; Lambert-Fair, Mary Ann; Van Duyne, M. Susan; Kubota, Kristy; Graves, Lewis; Wrigley, Donna; Barrett, Timothy; Ribot, Efrain

2005-01-01

The PulseNet National Database, established by the Centers for Disease Control and Prevention in 1996, consists of pulsed-field gel electrophoresis (PFGE) patterns obtained from isolates of food-borne pathogens (currently Escherichia coli O157:H7, Salmonella, Shigella, and Listeria) and textual information about the isolates. Electronic images and accompanying text are submitted from over 60 U.S. public health and food regulatory agency laboratories. The PFGE patterns are generated according to highly standardized PFGE protocols. Normalization and accurate comparison of gel images require the use of a well-characterized size standard in at least three lanes of each gel. Originally, a well-characterized strain of each organism was chosen as the reference standard for that particular database. The increasing number of databases, difficulty in identifying an organism-specific standard for each database, the increased range of band sizes generated by the use of additional restriction endonucleases, and the maintenance of many different organism-specific strains encouraged us to search for a more versatile and universal DNA size marker. A Salmonella serotype Braenderup strain (H9812) was chosen as the universal size standard. This strain was subjected to rigorous testing in our laboratories to ensure that it met the desired criteria, including coverage of a wide range of DNA fragment sizes, even distribution of bands, and stability of the PFGE pattern. The strategy used to convert and compare data generated by the new and old reference standards is described. PMID:15750058

Use of PCR and Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis Techniques for Differentiation of Prevotella intermedia Sensu Stricto and Prevotella nigrescens

PubMed Central

Premaraj, Thyagaseely; Kato, Naoki; Fukui, Katsuhito; Kato, Haru; Watanabe, Kunitomo

1999-01-01

Primers were designed from 16S rRNA sequences of Prevotella intermedia sensu stricto and Prevotella nigrescens and were used to discriminate these two species by PCR. The results were compared with those from the PCR technique using primers designed from arbitrarily primed PCR products by Guillot and Mouton (E. Guillot and C. Mouton, J. Clin. Microbiol. 35:1876–1882, 1997). The specificities of both assays were studied by using P. intermedia ATCC 25611, P. nigrescens ATCC 33563, 174 clinical isolates of P. intermedia sensu lato, and 59 reference strains and 58 clinical isolates of other Prevotella species and/or common oral flora. In addition, the usefulness and reliability of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in the differentiation of the two species were examined by comparing the results with those from PCR assays. The controversial lipase test for distinguishing these species was also carried out. Unambiguous differentiation was made by both PCR assays, and the results matched each other. The SDS-PAGE assay was found to misidentify a few strains tested, compared with the results of PCR assays. The lipase test was positive for both species, including the reference strains of P. intermedia and P. nigrescens. We conclude that both PCR assays are simple, rapid, reliable, and specific methods which could be used in clinical studies and that the lipase test is not valuable in the differentiation. The reliable discrimination of the two species by SDS-PAGE is questionable. PMID:10074526

Machine learning-based dual-energy CT parametric mapping

NASA Astrophysics Data System (ADS)

Su, Kuan-Hao; Kuo, Jung-Wen; Jordan, David W.; Van Hedent, Steven; Klahr, Paul; Wei, Zhouping; Helo, Rose Al; Liang, Fan; Qian, Pengjiang; Pereira, Gisele C.; Rassouli, Negin; Gilkeson, Robert C.; Traughber, Bryan J.; Cheng, Chee-Wai; Muzic, Raymond F., Jr.

2018-06-01

The aim is to develop and evaluate machine learning methods for generating quantitative parametric maps of effective atomic number (Zeff), relative electron density (ρ e), mean excitation energy (I x ), and relative stopping power (RSP) from clinical dual-energy CT data. The maps could be used for material identification and radiation dose calculation. Machine learning methods of historical centroid (HC), random forest (RF), and artificial neural networks (ANN) were used to learn the relationship between dual-energy CT input data and ideal output parametric maps calculated for phantoms from the known compositions of 13 tissue substitutes. After training and model selection steps, the machine learning predictors were used to generate parametric maps from independent phantom and patient input data. Precision and accuracy were evaluated using the ideal maps. This process was repeated for a range of exposure doses, and performance was compared to that of the clinically-used dual-energy, physics-based method which served as the reference. The machine learning methods generated more accurate and precise parametric maps than those obtained using the reference method. Their performance advantage was particularly evident when using data from the lowest exposure, one-fifth of a typical clinical abdomen CT acquisition. The RF method achieved the greatest accuracy. In comparison, the ANN method was only 1% less accurate but had much better computational efficiency than RF, being able to produce parametric maps in 15 s. Machine learning methods outperformed the reference method in terms of accuracy and noise tolerance when generating parametric maps, encouraging further exploration of the techniques. Among the methods we evaluated, ANN is the most suitable for clinical use due to its combination of accuracy, excellent low-noise performance, and computational efficiency.

Machine learning-based dual-energy CT parametric mapping.

PubMed

Su, Kuan-Hao; Kuo, Jung-Wen; Jordan, David W; Van Hedent, Steven; Klahr, Paul; Wei, Zhouping; Al Helo, Rose; Liang, Fan; Qian, Pengjiang; Pereira, Gisele C; Rassouli, Negin; Gilkeson, Robert C; Traughber, Bryan J; Cheng, Chee-Wai; Muzic, Raymond F

2018-06-08

The aim is to develop and evaluate machine learning methods for generating quantitative parametric maps of effective atomic number (Z eff ), relative electron density (ρ e ), mean excitation energy (I x ), and relative stopping power (RSP) from clinical dual-energy CT data. The maps could be used for material identification and radiation dose calculation. Machine learning methods of historical centroid (HC), random forest (RF), and artificial neural networks (ANN) were used to learn the relationship between dual-energy CT input data and ideal output parametric maps calculated for phantoms from the known compositions of 13 tissue substitutes. After training and model selection steps, the machine learning predictors were used to generate parametric maps from independent phantom and patient input data. Precision and accuracy were evaluated using the ideal maps. This process was repeated for a range of exposure doses, and performance was compared to that of the clinically-used dual-energy, physics-based method which served as the reference. The machine learning methods generated more accurate and precise parametric maps than those obtained using the reference method. Their performance advantage was particularly evident when using data from the lowest exposure, one-fifth of a typical clinical abdomen CT acquisition. The RF method achieved the greatest accuracy. In comparison, the ANN method was only 1% less accurate but had much better computational efficiency than RF, being able to produce parametric maps in 15 s. Machine learning methods outperformed the reference method in terms of accuracy and noise tolerance when generating parametric maps, encouraging further exploration of the techniques. Among the methods we evaluated, ANN is the most suitable for clinical use due to its combination of accuracy, excellent low-noise performance, and computational efficiency.

A study of cell electrophoresis as a means of purifying growth hormone secreting cells

NASA Technical Reports Server (NTRS)

Plank, Lindsay D.; Hymer, W. C.; Kunze, M. Elaine; Marks, Gary M.; Lanham, J. Wayne

1983-01-01

Growth hormone secreting cells of the rat anterior pituitary are heavily laden with granules of growth hormone and can be partialy purified on the basis of their resulting high density. Two methods of preparative cell electrophoresis were investigated as methods of enhancing the purification of growth hormone producing cells: density gradient electrophoresis and continuous flow electrophoresis. Both methods provided a two- to four-fold enrichment in growth hormone production per cell relative to that achieved by previous methods. Measurements of electrophoretic mobilities by two analytical methods, microscopic electrophoresis and laser-tracking electrophoresis, revealed very little distinction between unpurified anterior pituitary cell suspensions and somatotroph-enriched cell suspensions. Predictions calculated on the basis of analytical electrophoretic data are consistent with the hypothesis that sedimentation plays a significant role in both types of preparative electrophoresis and the electrophoretic mobility of the growth hormone secreting subpopulation of cells remains unknown.

Geometric registration of images by similarity transformation using two reference points

NASA Technical Reports Server (NTRS)

Kang, Yong Q. (Inventor); Jo, Young-Heon (Inventor); Yan, Xiao-Hai (Inventor)

2011-01-01

A method for registering a first image to a second image using a similarity transformation. The each image includes a plurality of pixels. The first image pixels are mapped to a set of first image coordinates and the second image pixels are mapped to a set of second image coordinates. The first image coordinates of two reference points in the first image are determined. The second image coordinates of these reference points in the second image are determined. A Cartesian translation of the set of second image coordinates is performed such that the second image coordinates of the first reference point match its first image coordinates. A similarity transformation of the translated set of second image coordinates is performed. This transformation scales and rotates the second image coordinates about the first reference point such that the second image coordinates of the second reference point match its first image coordinates.

Method and apparatus for displaying information

NASA Technical Reports Server (NTRS)

Huang, Sui (Inventor); Eichler, Gabriel (Inventor); Ingber, Donald E. (Inventor)

2010-01-01

A method for displaying large amounts of information. The method includes the steps of forming a spatial layout of tiles each corresponding to a representative reference element; mapping observed elements onto the spatial layout of tiles of representative reference elements; assigning a respective value to each respective tile of the spatial layout of the representative elements; and displaying an image of the spatial layout of tiles of representative elements. Each tile includes atomic attributes of representative elements. The invention also relates to an apparatus for displaying large amounts of information. The apparatus includes a tiler forming a spatial layout of tiles, each corresponding to a representative reference element; a comparator mapping observed elements onto said spatial layout of tiles of representative reference elements; an assigner assigning a respective value to each respective tile of said spatial layout of representative reference elements; and a display displaying an image of the spatial layout of tiles of representative reference elements.

Development of Public Immortal Mapping Populations, Molecular Markers and Linkage Maps for Rapid Cycling Brassica rapa and B. oleracea

USDA-ARS?s Scientific Manuscript database

In this study we describe public immortal mapping populations of self-compatible lines, molecular markers, and linkage maps for Brassica rapa and B. oleracea. We propose that these resources are valuable reference tools for the Brassica community. The B. rapa population consists of 150 recombinant...

Proteome Analysis of the Penicillin Producer Penicillium chrysogenum

PubMed Central

Jami, Mohammad-Saeid; Barreiro, Carlos; García-Estrada, Carlos; Martín, Juan-Francisco

2010-01-01

Proteomics is a powerful tool to understand the molecular mechanisms causing the production of high penicillin titers by industrial strains of the filamentous fungus Penicillium chrysogenum as the result of strain improvement programs. Penicillin biosynthesis is an excellent model system for many other bioactive microbial metabolites. The recent publication of the P. chrysogenum genome has established the basis to understand the molecular processes underlying penicillin overproduction. We report here the proteome reference map of P. chrysogenum Wisconsin 54-1255 (the genome project reference strain) together with an in-depth study of the changes produced in three different strains of this filamentous fungus during industrial strain improvement. Two-dimensional gel electrophoresis, peptide mass fingerprinting, and tandem mass spectrometry were used for protein identification. Around 1000 spots were visualized by “blue silver” colloidal Coomassie staining in a non-linear pI range from 3 to 10 with high resolution, which allowed the identification of 950 proteins (549 different proteins and isoforms). Comparison among the cytosolic proteomes of the wild-type NRRL 1951, Wisconsin 54-1255 (an improved, moderate penicillin producer), and AS-P-78 (a penicillin high producer) strains indicated that global metabolic reorganizations occurred during the strain improvement program. The main changes observed in the high producer strains were increases of cysteine biosynthesis (a penicillin precursor), enzymes of the pentose phosphate pathway, and stress response proteins together with a reduction in virulence and in the biosynthesis of other secondary metabolites different from penicillin (pigments and isoflavonoids). In the wild-type strain, we identified enzymes to utilize cellulose, sorbitol, and other carbon sources that have been lost in the high penicillin producer strains. Changes in the levels of a few specific proteins correlated well with the improved penicillin biosynthesis in the high producer strains. These results provide useful information to improve the production of many other bioactive secondary metabolites. PMID:20154335

QuickMap: a public tool for large-scale gene therapy vector insertion site mapping and analysis.

PubMed

Appelt, J-U; Giordano, F A; Ecker, M; Roeder, I; Grund, N; Hotz-Wagenblatt, A; Opelz, G; Zeller, W J; Allgayer, H; Fruehauf, S; Laufs, S

2009-07-01

Several events of insertional mutagenesis in pre-clinical and clinical gene therapy studies have created intense interest in assessing the genomic insertion profiles of gene therapy vectors. For the construction of such profiles, vector-flanking sequences detected by inverse PCR, linear amplification-mediated-PCR or ligation-mediated-PCR need to be mapped to the host cell's genome and compared to a reference set. Although remarkable progress has been achieved in mapping gene therapy vector insertion sites, public reference sets are lacking, as are the possibilities to quickly detect non-random patterns in experimental data. We developed a tool termed QuickMap, which uniformly maps and analyzes human and murine vector-flanking sequences within seconds (available at www.gtsg.org). Besides information about hits in chromosomes and fragile sites, QuickMap automatically determines insertion frequencies in +/- 250 kb adjacency to genes, cancer genes, pseudogenes, transcription factor and (post-transcriptional) miRNA binding sites, CpG islands and repetitive elements (short interspersed nuclear elements (SINE), long interspersed nuclear elements (LINE), Type II elements and LTR elements). Additionally, all experimental frequencies are compared with the data obtained from a reference set, containing 1 000 000 random integrations ('random set'). Thus, for the first time a tool allowing high-throughput profiling of gene therapy vector insertion sites is available. It provides a basis for large-scale insertion site analyses, which is now urgently needed to discover novel gene therapy vectors with 'safe' insertion profiles.

Random-breakage mapping method applied to human DNA sequences

NASA Technical Reports Server (NTRS)

Lobrich, M.; Rydberg, B.; Cooper, P. K.; Chatterjee, A. (Principal Investigator)

1996-01-01

The random-breakage mapping method [Game et al. (1990) Nucleic Acids Res., 18, 4453-4461] was applied to DNA sequences in human fibroblasts. The methodology involves NotI restriction endonuclease digestion of DNA from irradiated calls, followed by pulsed-field gel electrophoresis, Southern blotting and hybridization with DNA probes recognizing the single copy sequences of interest. The Southern blots show a band for the unbroken restriction fragments and a smear below this band due to radiation induced random breaks. This smear pattern contains two discontinuities in intensity at positions that correspond to the distance of the hybridization site to each end of the restriction fragment. By analyzing the positions of those discontinuities we confirmed the previously mapped position of the probe DXS1327 within a NotI fragment on the X chromosome, thus demonstrating the validity of the technique. We were also able to position the probes D21S1 and D21S15 with respect to the ends of their corresponding NotI fragments on chromosome 21. A third chromosome 21 probe, D21S11, has previously been reported to be close to D21S1, although an uncertainty about a second possible location existed. Since both probes D21S1 and D21S11 hybridized to a single NotI fragment and yielded a similar smear pattern, this uncertainty is removed by the random-breakage mapping method.

A novel method for simultaneous production of two ribosome-inactivating proteins, α-MMC and MAP30, from Momordica charantia L.

PubMed

Meng, Yao; Lin, Sen; Liu, Shuangfeng; Fan, Xiang; Li, Gangrui; Meng, Yanfa

2014-01-01

Alpha-momorcharin (α-MMC) and momordica anti-HIV protein (MAP30) from Momordica charantia L. have been confirmed to possess anti-tumor and anti-virus activities. Traditional purification methods of these two ribosome-inactivating proteins (RIPs) were separate which was time consuming and cost effective as well as low efficient. In order to obtain sufficient samples for researches, a strategy combining ion-exchange and gel filtration chromatography was developed and optimized in this study. Using this novel purification method, averagely 1162 mg of α-MMC and 535 mg of MAP30 were obtained from 400 g of Momordica charantia L seeds. The homogeneities of them were assessed by electrophoresis analysis. Determination of molecular weights of α-MMC and MAP30 were 28.585 kDa and 29.094 kDa by MALDI-TOF/TOF and pI were 9.02 and 9.12, respectively. The single glycoproteins were identified by Periodate-Schiff's base (PAS) and the saccharide content was tested to be 1.25% and 1.1% by anthrone-sulfuric acid method. Biological activities were evidenced by their ability to inhibit proliferation of lung adenocarcinoma A549 cell and to convert supercoiled plasmid pUC18 into relaxed forms. Finally, we also found that both two RIPs exhibited no superoxide dismutase (SOD) activity.

Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing

PubMed Central

Aokic, Jun-ya; Kawase, Junya; Hamada, Kazuhisa; Fujimoto, Hiroshi; Yamamoto, Ikki; Usuki, Hironori

2018-01-01

Greater amberjack (Seriola dumerili) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology. The assembled sequences were aligned onto a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map by sequence homology. A total of 215 of the longest amberjack sequences, with a total length of 622.8 Mbp (92% of the total length of the genome scaffolds), were lined up on the yellowtail RH map. We resequenced the whole genomes of 20 greater amberjacks and mapped the resulting sequences onto the reference genome sequence. About 186,000 nonredundant SNPs were successfully ordered on the reference genome. Further, we found differences in the genome structural variations between two greater amberjack populations using BreakDancer. We also analyzed the greater amberjack transcriptome and mapped the annotated sequences onto the reference genome sequence. PMID:29785397

How Geographic Maps Increase Recall of Instructional Text.

ERIC Educational Resources Information Center

Kulhavy, Raymond W.; And Others

1993-01-01

Reviews research on how geographic maps influence the recall of associated text and describes a theoretical model of map-text learning based on dual-coding theory and working memory operations. Instructional implications are explained, and recommendations for instructional applications are given. (Contains 84 references.) (LRW)

Direct dose mapping versus energy/mass transfer mapping for 4D dose accumulation: fundamental differences and dosimetric consequences.

PubMed

Li, Haisen S; Zhong, Hualiang; Kim, Jinkoo; Glide-Hurst, Carri; Gulam, Misbah; Nurushev, Teamour S; Chetty, Indrin J

2014-01-06

The direct dose mapping (DDM) and energy/mass transfer (EMT) mapping are two essential algorithms for accumulating the dose from different anatomic phases to the reference phase when there is organ motion or tumor/tissue deformation during the delivery of radiation therapy. DDM is based on interpolation of the dose values from one dose grid to another and thus lacks rigor in defining the dose when there are multiple dose values mapped to one dose voxel in the reference phase due to tissue/tumor deformation. On the other hand, EMT counts the total energy and mass transferred to each voxel in the reference phase and calculates the dose by dividing the energy by mass. Therefore it is based on fundamentally sound physics principles. In this study, we implemented the two algorithms and integrated them within the Eclipse treatment planning system. We then compared the clinical dosimetric difference between the two algorithms for ten lung cancer patients receiving stereotactic radiosurgery treatment, by accumulating the delivered dose to the end-of-exhale (EE) phase. Specifically, the respiratory period was divided into ten phases and the dose to each phase was calculated and mapped to the EE phase and then accumulated. The displacement vector field generated by Demons-based registration of the source and reference images was used to transfer the dose and energy. The DDM and EMT algorithms produced noticeably different cumulative dose in the regions with sharp mass density variations and/or high dose gradients. For the planning target volume (PTV) and internal target volume (ITV) minimum dose, the difference was up to 11% and 4% respectively. This suggests that DDM might not be adequate for obtaining an accurate dose distribution of the cumulative plan, instead, EMT should be considered.

Direct dose mapping versus energy/mass transfer mapping for 4D dose accumulation: fundamental differences and dosimetric consequences

NASA Astrophysics Data System (ADS)

Li, Haisen S.; Zhong, Hualiang; Kim, Jinkoo; Glide-Hurst, Carri; Gulam, Misbah; Nurushev, Teamour S.; Chetty, Indrin J.

2014-01-01

The direct dose mapping (DDM) and energy/mass transfer (EMT) mapping are two essential algorithms for accumulating the dose from different anatomic phases to the reference phase when there is organ motion or tumor/tissue deformation during the delivery of radiation therapy. DDM is based on interpolation of the dose values from one dose grid to another and thus lacks rigor in defining the dose when there are multiple dose values mapped to one dose voxel in the reference phase due to tissue/tumor deformation. On the other hand, EMT counts the total energy and mass transferred to each voxel in the reference phase and calculates the dose by dividing the energy by mass. Therefore it is based on fundamentally sound physics principles. In this study, we implemented the two algorithms and integrated them within the Eclipse treatment planning system. We then compared the clinical dosimetric difference between the two algorithms for ten lung cancer patients receiving stereotactic radiosurgery treatment, by accumulating the delivered dose to the end-of-exhale (EE) phase. Specifically, the respiratory period was divided into ten phases and the dose to each phase was calculated and mapped to the EE phase and then accumulated. The displacement vector field generated by Demons-based registration of the source and reference images was used to transfer the dose and energy. The DDM and EMT algorithms produced noticeably different cumulative dose in the regions with sharp mass density variations and/or high dose gradients. For the planning target volume (PTV) and internal target volume (ITV) minimum dose, the difference was up to 11% and 4% respectively. This suggests that DDM might not be adequate for obtaining an accurate dose distribution of the cumulative plan, instead, EMT should be considered.

A maize map standard with sequenced core markers, grass genome reference points and 932 expressed sequence tagged sites (ESTs) in a 1736-locus map.

PubMed Central

Davis, G L; McMullen, M D; Baysdorfer, C; Musket, T; Grant, D; Staebell, M; Xu, G; Polacco, M; Koster, L; Melia-Hancock, S; Houchins, K; Chao, S; Coe, E H

1999-01-01

We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available for gene discovery beyond the boundaries of maize mapping information into the expanse of map, sequence, and phenotype information from other grass species. This map provides a foundation for numerous basic and applied investigations including studies of gene organization, gene and genome evolution, targeted cloning, and dissection of complex traits. PMID:10388831

Chapter 4 - The LANDFIRE Prototype Project reference database

Treesearch

John F. Caratti

2006-01-01

This chapter describes the data compilation process for the Landscape Fire and Resource Management Planning Tools Prototype Project (LANDFIRE Prototype Project) reference database (LFRDB) and explains the reference data applications for LANDFIRE Prototype maps and models. The reference database formed the foundation for all LANDFIRE tasks. All products generated by the...

Geologic map of the Zarkashan-Anguri copper and gold deposits, Ghazni Province, Afghanistan, modified from the 1968 original map compilation of E.P. Meshcheryakov and V.P. Sayapin

USGS Publications Warehouse

Peters, Stephen G.; Stettner, Will R.; Masonic, Linda M.; Moran, Thomas W.

2011-01-01

This map is a modified version of Geological map of the area of Zarkashan-Anguri gold deposits, scale 1:50,000, which was compiled by E.P. Meshcheryakov and V.P. Sayapin in 1968. Scientists from the U.S. Geological Survey, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original document and related reports and also visited the field area in April 2010. This modified map, which includes a cross section, illustrates the geologic setting of the Zarkashan-Anguri copper and gold deposits. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross section and includes modifications based on our examination of that and other documents, and based on observations made and sampling undertaken during our field visit. (Refer to the Introduction and the References in the Map PDF for an explanation of our methodology and for complete citations of the original map and related reports.) Elevations on the cross section are derived from the original Soviet topography and may not match the newer topography used on the current map.

Estimating A Reference Standard Segmentation With Spatially Varying Performance Parameters: Local MAP STAPLE

PubMed Central

Commowick, Olivier; Akhondi-Asl, Alireza; Warfield, Simon K.

2012-01-01

We present a new algorithm, called local MAP STAPLE, to estimate from a set of multi-label segmentations both a reference standard segmentation and spatially varying performance parameters. It is based on a sliding window technique to estimate the segmentation and the segmentation performance parameters for each input segmentation. In order to allow for optimal fusion from the small amount of data in each local region, and to account for the possibility of labels not being observed in a local region of some (or all) input segmentations, we introduce prior probabilities for the local performance parameters through a new Maximum A Posteriori formulation of STAPLE. Further, we propose an expression to compute confidence intervals in the estimated local performance parameters. We carried out several experiments with local MAP STAPLE to characterize its performance and value for local segmentation evaluation. First, with simulated segmentations with known reference standard segmentation and spatially varying performance, we show that local MAP STAPLE performs better than both STAPLE and majority voting. Then we present evaluations with data sets from clinical applications. These experiments demonstrate that spatial adaptivity in segmentation performance is an important property to capture. We compared the local MAP STAPLE segmentations to STAPLE, and to previously published fusion techniques and demonstrate the superiority of local MAP STAPLE over other state-of-the- art algorithms. PMID:22562727

Capillary Zone Electrophoresis for the Analysis of Peptides: Fostering Students' Problem-Solving and Discovery Learning in an Undergraduate Laboratory Experiment

ERIC Educational Resources Information Center

Albright, Jessica C.; Beussman, Douglas J.

2017-01-01

Capillary electrophoresis is an important analytical separation method used to study a wide variety of samples, including those of biological origin. Capillary electrophoresis may be covered in the classroom, especially in advanced analytical courses, and while many students are exposed to gel electrophoresis in biology or biochemistry…

Affinity in electrophoresis.

PubMed

Heegaard, Niels H H

2009-06-01

The journal Electrophoresis has greatly influenced my approaches to biomolecular affinity studies. The methods that I have chosen as my main tools to study interacting biomolecules--native gel and later capillary zone electrophoresis--have been the topic of numerous articles in Electrophoresis. Below, the role of the journal in the development and dissemination of these techniques and applications reviewed. Many exhaustive reviews on affinity electrophoresis and affinity CE have been published in the last few years and are not in any way replaced by the present deliberations that are focused on papers published by the journal.

Method and apparatus for the simultaneous display and correlation of independently generated images

DOEpatents

Vaitekunas, Jeffrey J.; Roberts, Ronald A.

1991-01-01

An apparatus and method for location by location correlation of multiple images from Non-Destructive Evaluation (NDE) and other sources. Multiple images of a material specimen are displayed on one or more monitors of an interactive graphics system. Specimen landmarks are located in each image and mapping functions from a reference image to each other image are calcuated using the landmark locations. A location selected by positioning a cursor in the reference image is mapped to the other images and location identifiers are simultaneously displayed in those images. Movement of the cursor in the reference image causes simultaneous movement of the location identifiers in the other images to positions corresponding to the location of the reference image cursor.

Comparative Proteomic Analysis of Yak Follicular Fluid during Estrus

PubMed Central

Guo, Xian; Pei, Jie; Ding, Xuezhi; Chu, Min; Bao, Pengjia; Wu, Xiaoyun; Liang, Chunnian; Yan, Ping

2016-01-01

The breeding of yaks is highly seasonal, there are many crucial proteins involved in the reproduction control program, especially in follicular development. In order to isolate differential proteins between mature and immature follicular fluid (FF) of yak, the FF from yak follicles with different sizes were sampled respectively, and two-dimensional gel electrophoresis (2-DE) of the proteins was carried out. After silver staining, the Image Master 2D platinum software was used for protein analysis and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) was performed for differential protein identification. The expression level of transferrin and enolase superfamily member 1 (ENOSF1) was determined by Western blotting for verification analysis. The results showed that 2-DE obtained an electrophoresis map of proteins from mature and immature yak FF with high resolution and repeatability. A comparison of protein profiles identified 12 differently expressed proteins, out of which 10 of them were upregulated while 2 were downregulated. Western blotting showed that the expression of transferrin and ENOSF1 was enhanced with follicular development. Both the obtained protein profiles and the differently expressed proteins identified in this study provided experimental data related to follicular development during yak breeding seasons. This study also laid the foundation for understanding the microenvironment during oocyte development. PMID:26954118

In vivo conformation of mitochondrial DNA revealed by pulsed-field gel electrophoresis in the true slime mold, Physarum polycephalum.

PubMed

Sakurai, R; Sasaki, N; Takano, H; Abe, T; Kawano, S

2000-04-28

Pulsed-field gel electrophoresis (PFGE) was used to examine the in vivo and in vitro conformations of Physarum polycephalum mitochondrial DNA (mtDNA). We used plugs containing isolated mitochondria, isolated mitochondrial nucleoids (mt-nuclei), and isolated mtDNA, in addition to whole cells. The mtDNA contained in the myxamoebae, plasmodia, isolated mitochondria, and isolated mt-nuclei was circular, but most of the isolated mtDNA had been site-specifically fragmented and linearized during DNA preparation and storage under low ionic strength conditions. Restriction mapping of Physarum mtDNA by the direct digestion of the isolated mt-nuclei from two different strains, DP89 x AI16 and KM88 x AI16, resulted in the circular form. A linear mitochondrial plasmid, mF, is known to promote mitochondrial fusion and integration of itself into the mtDNA in Physarum. Linearization of mtDNA by the integration of the mF plasmid was demonstrated when we used PFGE to analyze isolated mitochondria from the plasmodial strain DP89 x NG7 carrying the mF plasmid (mF+). The PFGE system can be used not only to determine whether the form of mtDNA is linear or circular but also to analyze the dynamic conformational changes of mtDNA.

Mapping language to visual referents: Does the degree of image realism matter?

PubMed

Saryazdi, Raheleh; Chambers, Craig G

2018-01-01

Studies of real-time spoken language comprehension have shown that listeners rapidly map unfolding speech to available referents in the immediate visual environment. This has been explored using various kinds of 2-dimensional (2D) stimuli, with convenience or availability typically motivating the choice of a particular image type. However, work in other areas has suggested that certain cognitive processes are sensitive to the level of realism in 2D representations. The present study examined the process of mapping language to depictions of objects that are more or less realistic, namely photographs versus clipart images. A custom stimulus set was first created by generating clipart images directly from photographs of real objects. Two visual world experiments were then conducted, varying whether referent identification was driven by noun or verb information. A modest benefit for clipart stimuli was observed during real-time processing, but only for noun-driving mappings. The results are discussed in terms of their implications for studies of visually situated language processing. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

An ultra-dense SNP linkage map for the octoploid, cultivated strawberry and its application in genetic research

USDA-ARS?s Scientific Manuscript database

We will present an ultra-dense genetic linkage map for the octoploid, cultivated strawberry (Fragaria x ananassa) consisting of over 13K Axiom® based SNP markers and 150 previously mapped reference SSR loci. The high quality of the map is demonstrated by the short sizes of each of the 28 linkage gro...

Distributed Interactive Simulation Protocol Extensions

DTIC Science & Technology

1993-05-28

company HQ. The OrgName and Type Code for a unit will be reported in the Notion or Perception I PDU( s ) for that unit. Any unit in a player’s Task Org...this order. The U.I. can have a mapping of that unique ID to some user entered ID if desired. Reference - No map reference is needed, the map( s ...Common (232):I Si. 0) 0xre~t 4 f ne0 W .bti ISM07 GUITI Unw.evwd (131 5u.on e4 ffifldedl) C L~cu S .an e p e a m (1 ) 1 A ~ w 2 O GS iI U~WW 2 - P S 54

Surface Charge Measurement of SonoVue, Definity and Optison: A Comparison of Laser Doppler Electrophoresis and Micro-Electrophoresis.

PubMed

Ja'afar, Fairuzeta; Leow, Chee Hau; Garbin, Valeria; Sennoga, Charles A; Tang, Meng-Xing; Seddon, John M

2015-11-01

Microbubble (MB) contrast-enhanced ultrasonography is a promising tool for targeted molecular imaging. It is important to determine the MB surface charge accurately as it affects the MB interactions with cell membranes. In this article, we report the surface charge measurement of SonoVue, Definity and Optison. We compare the performance of the widely used laser Doppler electrophoresis with an in-house micro-electrophoresis system. By optically tracking MB electrophoretic velocity in a microchannel, we determined the zeta potentials of MB samples. Using micro-electrophoresis, we obtained zeta potential values for SonoVue, Definity and Optison of -28.3, -4.2 and -9.5 mV, with relative standard deviations of 5%, 48% and 8%, respectively. In comparison, laser Doppler electrophoresis gave -8.7, +0.7 and +15.8 mV with relative standard deviations of 330%, 29,000% and 130%, respectively. We found that the reliability of laser Doppler electrophoresis is compromised by MB buoyancy. Micro-electrophoresis determined zeta potential values with a 10-fold improvement in relative standard deviation. Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Early comprehension of the Spanish plural*

PubMed Central

Arias-Trejo, Natalia; Cantrell, Lisa M.; Smith, Linda B.; Alva Canto, Elda A.

2015-01-01

Understanding how linguistic cues map to the environment is crucial for early language comprehension and may provide a way for bootstrapping and learning words. Research has suggested that learning how plural syntax maps to the perceptual environment may show a trajectory in which children first learn surrounding cues (verbs, modifiers) before a full mastery of the noun morpheme alone. The Spanish plural system of simple codas, dominated by one allomorph -s, and with redundant agreement markers, may facilitate early understanding of how plural linguistic cues map to novel referents. Two-year-old Mexican children correctly identified multiple novel object referents when multiple verbal cues in a phrase indicated plurality as well as in instances when the noun morphology in novel nouns was the ONLY indicator of plurality. These results demonstrate Spanish-speaking children’s ability to use plural noun inflectional morphology to infer novel word referents which may have implications for their word learning. PMID:24560441

Preparation of reference material for UGT1A1 (TA)n polymorphism genotyping.

PubMed

Mlakar, Vid; Mlakar, Simona Jurković; Marc, Janja; Ostanek, Barbara

2014-08-05

Gilbert's syndrome is one of the most common metabolic syndromes in the human population characterised by mild unconjugated hyperbilirubinemia resulting from reduced activity of the bilirubin conjugating enzyme UDP-glucuronosyltransferase (UGT1A1). Although Gilbert's syndrome is usually quite benign UGT1A1(TA)n genotyping is important in exclusion of more serious causes of hyperbilirubinemia and since it has significant implications for personalised medicine. The aim of our study was to develop plasmid based reference materials which could be used for UGT1A1(TA)n genotyping. Plasmids were generated using recombinant DNA technology and their number of repeats as well as the entire sequence verified by Sanger sequencing. Their suitability as reference materials was tested using sizing by capillary electrophoresis and denaturing high performance liquid chromatography. Plasmids containing all four different alleles (TA)5, (TA)6, (TA)7 and (TA)8 that are present in the human population as well as a plasmid with (TA)4 repeats were successfully generated. Prepared plasmid reference materials allow the creation of all possible UGT1A1(TA)n polymorphism genotypes and can serve as an efficient substitute for the human genomic DNA reference material in routine genotyping and in the development of new genotyping tests. Copyright © 2014 Elsevier B.V. All rights reserved.

Abnormal cerebrospinal fluid protein indices in schizophrenia.

PubMed

Kirch, D G; Kaufmann, C A; Papadopoulos, N M; Martin, B; Weinberger, D R

1985-10-01

Determinations of albumin and immunoglobulin G (IgG) were performed in paired cerebrospinal fluid (CSF) and serum samples from 24 subjects with schizophrenia. These determinations allowed calculation of two indices, one that is an indicator of integrity of the blood-brain barrier and the other a measure of selective IgG production within the central nervous system (CNS). In comparison with previously determined reference values, 7 of 24 (29%) subjects showed increased blood-brain barrier permeability, and 8 of 24 (33%) demonstrated elevated endogenous CNS IgG production. One of these eight also demonstrated oligoclonal banding on high-resolution protein electrophoresis of the CSF.

Hb taradale [beta82(EF6)Lys-->Arg]: a novel mutation at a 2,3-diphosphoglycerate binding site.

PubMed

Brennan, Stephen O; Sheen, Campbell; Chan, Tim; George, Peter M

2005-01-01

Hb Taradale [beta82(EF6)Lys-->Arg] was initially detected as a split Hb A0 peak on Hb A1c, monitoring. Red cell parameters, hemoglobin (Hb) electrophoresis and stability tests were normal. Mass spectrometry (ms) clearly identified a variant beta chain with a mass increase of 28 Da and peptide mapping located the mutation site to peptide betaT-9. DNA sequencing confirmed the presence of a novel beta82(EF6)Lys-->Arg mutation. This conservative substitution at a 2,3-diphosphoglycerate (2,3-DPG) binding site did not, however, appear to affect the P50 for oxygen binding.

Proteomic analysis of ethanol-induced embryotoxicity in cultured post-implantation rat embryos.

PubMed

Usami, Makoto; Mitsunaga, Katsuyoshi; Irie, Tomohiko; Miyajima, Atsuko; Doi, Osamu

2014-04-01

Protein expression changes were examined in day 10.5 rat embryos cultured for 24 hr in the presence of ethanol by using two-dimensional electrophoresis and mass spectrometry. Exposure to ethanol resulted in quantitative changes in many embryonic protein spots (16 decreased and 28 increased) at in vitro embryotoxic concentrations (130 and 195 mM); most changes occurred in a concentration-dependent manner. For these protein spots, 17 proteins were identified, including protein disulfide isomerase A3, alpha-fetoprotein, phosphorylated cofilin-1, and serum albumin. From the gene ontology classification and pathway mapping of the identified proteins, it was found that ethanol affected several biological processes involving oxidative stress and retinoid metabolism.

77 FR 55785 - Proposed Flood Elevation Determinations; Correction

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-11

... stream reach between the referenced locations above. Please refer to the revised Flood Insurance Rate Map located at the community map repository (see below) for exact locations of all BFEs to be changed. Send... Mechanicsville Maps are available for inspection at the Borough Hall, 1342 Pottsville Street, Mechanicsville, PA...

77 FR 46994 - Proposed Flood Elevation Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-07

... referenced locations above. Please refer to the revised Flood Insurance Rate Map located at the community map repository (see below) for exact locations of all BFEs to be changed. Send comments to Luis Rodriguez, Chief... Agency, 500 C Street SW., Washington, DC 20472. ADDRESSES City of Cleveland Maps are available for...

How To Put Your Maps on the Internet.

ERIC Educational Resources Information Center

Allen, David Yehling

Many libraries are creating raster images of paper maps and making them available over the Internet. This presentation provides an overview of imaging technology for map librarians and administrators considering such projects. References in footnotes and the bibliography enable those interested to explore technical questions in depth. There are…

75 FR 48235 - Rural Health Care Universal Service Support Mechanism

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-09

... references to recognized broadband mapping studies, such as NTIA's national broadband map, State or local... network area. In addition to referencing such NTIA or State broadband mapping studies, the applicant would... network design studies (but not in excess of the cap identified below); (2) engineering, materials and...

Comparative Maps of Human 19p13.3 and Mouse Chromosome 10 Allow Identification of Sequences at Evolutionary Breakpoints

PubMed Central

Puttagunta, Radhika; Gordon, Laurie A.; Meyer, Gary E.; Kapfhamer, David; Lamerdin, Jane E.; Kantheti, Prameela; Portman, Kathleen M.; Chung, Wendy K.; Jenne, Dieter E.; Olsen, Anne S.; Burmeister, Margit

2000-01-01

A cosmid/bacterial artificial chromosome (BAC) contiguous (contig) map of human chromosome (HSA) 19p13.3 has been constructed, and over 50 genes have been localized to the contig. Genes and anonymous ESTs from ≈4000 kb of human 19p13.3 were placed on the central mouse chromosome 10 map by genetic mapping and pulsed-field gel electrophoresis (PFGE) analysis. A region of ∼2500 kb of HSA 19p13.3 is collinear to mouse chromosome (MMU) 10. In contrast, the adjacent ≈1200 kb are inverted. Two genes are located in a 50-kb region after the inversion on MMU 10, followed by a region of homology to mouse chromosome 17. The synteny breakpoint and one of the inversion breakpoints has been localized to sequenced regions in human <5 kb in size. Both breakpoints are rich in simple tandem repeats, including (TCTG)n, (CT)n, and (GTCTCT)n, suggesting that simple repeat sequences may be involved in chromosome breaks during evolution. The overall size of the region in mouse is smaller, although no large regions are missing. Comparing the physical maps to the genetic maps showed that in contrast to the higher-than-average rate of genetic recombination in gene-rich telomeric region on HSA 19p13.3, the average rate of recombination is lower than expected in the homologous mouse region. This might indicate that a hot spot of recombination may have been lost in mouse or gained in human during evolution, or that the position of sequences along the chromosome (telomeric compared to the middle of a chromosome) is important for recombination rates. PMID:10984455

A physical map, including a BAC/PAC clone contig, of the Williams-Beuren syndrome--deletion region at 7q11.23.

PubMed

Peoples, R; Franke, Y; Wang, Y K; Pérez-Jurado, L; Paperna, T; Cisco, M; Francke, U

2000-01-01

Williams-Beuren syndrome (WBS) is a developmental disorder caused by haploinsufficiency for genes in a 2-cM region of chromosome band 7q11.23. With the exception of vascular stenoses due to deletion of the elastin gene, the various features of WBS have not yet been attributed to specific genes. Although >/=16 genes have been identified within the WBS deletion, completion of a physical map of the region has been difficult because of the large duplicated regions flanking the deletion. We present a physical map of the WBS deletion and flanking regions, based on assembly of a bacterial artificial chromosome/P1-derived artificial chromosome contig, analysis of high-throughput genome-sequence data, and long-range restriction mapping of genomic and cloned DNA by pulsed-field gel electrophoresis. Our map encompasses 3 Mb, including 1.6 Mb within the deletion. Two large duplicons, flanking the deletion, of >/=320 kb contain unique sequence elements from the internal border regions of the deletion, such as sequences from GTF2I (telomeric) and FKBP6 (centromeric). A third copy of this duplicon exists in inverted orientation distal to the telomeric flanking one. These duplicons show stronger sequence conservation with regard to each other than to the presumptive ancestral loci within the common deletion region. Sequence elements originating from beyond 7q11.23 are also present in these duplicons. Although the duplicons are not present in mice, the order of the single-copy genes in the conserved syntenic region of mouse chromosome 5 is inverted relative to the human map. A model is presented for a mechanism of WBS-deletion formation, based on the orientation of duplicons' components relative to each other and to the ancestral elements within the deletion region.

Immunoelectrophoresis - urine

MedlinePlus

Immunoglobulin electrophoresis - urine; Gamma globulin electrophoresis - urine; Urine immunoglobulin electrophoresis; IEP - urine ... A clean-catch urine sample is needed. The clean-catch method is used to prevent germs from the penis or vagina from getting ...

Publications - AR 2015 | Alaska Division of Geological & Geophysical

Science.gov Websites

Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic publication sales page for more information. Quadrangle(s): Alaska General Bibliographic Reference DGGS Staff

Publications - GMC 280 | Alaska Division of Geological & Geophysical

Science.gov Websites

Publications Search Statewide Maps New Releases Sales Interactive Maps Databases Sections Geologic please see our publication sales page for more information. Bibliographic Reference Piggott, Neil, and

Protein Electrophoresis/Immunofixation Electrophoresis

MedlinePlus

... underlying disease. Follow-up tests may include, for example, albumin , immunoelectrophoresis, serum free light chains , quantitative immunoglobuins , ... the disease and the effectiveness of treatment. Some examples of when an electrophoresis test may be ordered ...

Biophysical characterization and structure of the Fab fragment from the NIST reference antibody, RM 8671.

PubMed

Karageorgos, Ioannis; Gallagher, Elyssia S; Galvin, Connor; Gallagher, D Travis; Hudgens, Jeffrey W

2017-11-01

Monoclonal antibody pharmaceuticals are the fastest-growing class of therapeutics, with a wide range of clinical applications. To assure their safety, these protein drugs must demonstrate highly consistent purity and stability. Key to these objectives is higher order structure measurements validated by calibration to reference materials. We describe preparation, characterization, and crystal structure of the Fab fragment prepared from the NIST Reference Antibody RM 8671 (NISTmAb). NISTmAb is a humanized IgG1κ antibody, produced in murine cell culture and purified by standard biopharmaceutical production methods, developed at the National Institute of Standards and Technology (NIST) to serve as a reference material. The Fab fragment was derived from NISTmAb through papain cleavage followed by protein A based purification. The purified Fab fragment was characterized by SDS-PAGE, capillary gel electrophoresis, multi-angle light scattering, size exclusion chromatography, mass spectrometry, and x-ray crystallography. The crystal structure at 0.2 nm resolution includes four independent Fab molecules with complete light chains and heavy chains through Cys 223, enabling assessment of conformational variability and providing a well-characterized reference structure for research and engineering applications. This nonproprietary, publically available reference material of known higher-order structure can support metrology in biopharmaceutical applications, and it is a suitable platform for validation of molecular modeling studies. Published by Elsevier Ltd.

Combining Capillary Electrophoresis with Mass Spectrometry for Applications in Proteomics

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

Simpson, David C.; Smith, Richard D.

2005-04-01

Throughout the field of global proteomics, ranging from simple organism studies to human medical applications, the high sample complexity creates demands for improved separations and analysis techniques. Furthermore, with increased organism complexity, the correlation between proteome and genome becomes less certain due to extensive mRNA processing prior to translation. In this way, the same DNA sequence can potentially code for regions in a number of distinct proteins; quantitative differences in expression (or abundance) between these often-related species are of significant interest. Well-established proteomics techniques, which use genomic information to identify peptides that originate from protease digestion, often cannot easily distinguishmore » between such gene products; intact protein-level analyses are required to complete the picture, particularly for identifying post-translational modifications. While chromatographic techniques are currently better suited to peptide analysis, capillary electrophoresis (CE) in combination with mass spectrometry (MS) may become important for intact protein analysis. This review focuses on CE/MS instrumentation and techniques showing promise for such applications, highlighting those with greatest potential. Reference will also be made to developments relevant to peptide-level analyses for use in time- or sample-limited situations.« less

Development of micropump-actuated negative pressure pinched injection for parallel electrophoresis on array microfluidic chip.

PubMed

Li, Bowei; Jiang, Lei; Xie, Hua; Gao, Yan; Qin, Jianhua; Lin, Bingcheng

2009-09-01

A micropump-actuated negative pressure pinched injection method is developed for parallel electrophoresis on a multi-channel LIF detection system. The system has a home-made device that could individually control 16-port solenoid valves and a high-voltage power supply. The laser beam is excitated and distributes to the array separation channels for detection. The hybrid Glass-PDMS microfluidic chip comprises two common reservoirs, four separation channels coupled to their respective pneumatic micropumps and two reference channels. Due to use of pressure as a driving force, the proposed method has no sample bias effect for separation. There is only one high-voltage supply needed for separation without relying on the number of channels, which is significant for high-throughput analysis, and the time for sample loading is shortened to 1 s. In addition, the integrated micropumps can provide the versatile interface for coupling with other function units to satisfy the complicated demands. The performance is verified by separation of DNA marker and Hepatitis B virus DNA samples. And this method is also expected to show the potential throughput for the DNA analysis in the field of disease diagnosis.

Evaluation of the electroosmotic medium pump system for preparative disk gel electrophoresis.

PubMed

Hayakawa, M; Hosogi, Y; Takiguchi, H; Saito, S; Shiroza, T; Shibata, Y; Hiratsuka, K; Kiyama-Kishikawa, M; Abiko, Y

2001-01-15

This paper describes an improved electroosmotic elution system for preparative sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) based on the epochal idea of H. V. Tan et al. (Nucleic Acids Res. 1988, 16, 1921-1930). In this elution system, a semipermeable membrane, mounted under the gel terminal end, works as the elution pump as well as the partition of the elution chamber. We refer to this system as the "electroosmotic medium pump system." Operation of the constructed apparatus (3.6 cm i.d. disk gel column) and resolution of the protein bands were examined by separation of the model protein mixture (bovine serum albumin (BSA), ovalbumin, bovine carbonic anhydrase, soybean trypsin inhibitor) and purification of the membrane protein, dipeptidyl peptidase IV (DPP IV). The Spectra/Por 7 dialysis membrane provided a better flow profile for the elution buffer. The four model proteins of the protein mixture were able to be completely separated from each other and recovered without dilution. The maximum protein concentration of eluate achieved was 93 mg/ml, when applying a single component, BSA fraction V, as a sample. Furthermore, the multifunctional ectoenzyme, DPP IV, was purified in a single step. Copyright 2001 Academic Press.

A streamlined isolation method and the autoxidation profiles of tuna myoglobin.

PubMed

Nurilmala, Mala; Ushio, Hideki; Watabe, Shugo; Ochiai, Yoshihiro

2018-05-01

Determination of the redox state of myoglobin (Mb) gives useful information for evaluating the quality of tuna meat. To attain this purpose, a fast streamlined method has been established basically based on preparative native gel electrophoresis to isolate Mb from the dark muscle of Pacific bluefin tuna. Crude Mb fraction was prepared from dark muscle by ammonium sulfate saturation fractionation and subsequently Mb was purified by preparative native gel electrophoresis under the isoelectric pH of the Mb, resulting in absorption (or trapping) of all the contaminating proteins in the gel. Purified Mb was converted to oxy form with a trace amount of sodium hydrosulfite, and subsequently dialyzed against 50 mM sodium citrate (pH 5.6) or 50 mM sodium phosphate (pH 6.5). The purified tuna Mb was examined for the temperature and pH dependencies of autoxidation using horse Mb as a reference. Tuna Mb was oxidized 2.5-3 times faster than horse Mb irrespective of the pH conditions examined. The highest autoxidation rates both at 0 and 37 °C were observed at pH 5.6. These data were comparable to those obtained for Mbs isolated by conventional chromatographic methods.

On-line capillary electrophoresis-based enzymatic methodology for the study of polymer-drug conjugates.

PubMed

Coussot, G; Ladner, Y; Bayart, C; Faye, C; Vigier, V; Perrin, C

2015-01-09

This work aims at studying the potentialities of an on-line capillary electrophoresis (CE)-based digestion methodology for evaluating polymer-drug conjugates degradability in the presence of free trypsin (in-solution digestion). A sandwich plugs injection scheme with transverse diffusion of laminar profile (TDLFP) mode was used to achieve on-line digestions. Electrophoretic separation conditions were established using poly-l-Lysine (PLL) as reference substrate. Comparison with off-line digestion was carried out to demonstrate the feasibility of the proposed methodology. The applicability of the on-line CE-based digestion methodology was evaluated for two PLL-drug conjugates and for the four first generations of dendrigraft of lysine (DGL). Different electrophoretic profiles presenting the formation of di, tri, and tetralysine were observed for PLL-drug and DGL. These findings are in good agreement with the nature of the linker used to link the drug to PLL structure and the predicted degradability of DGL. The present on-line methodology applicability was also successfully proven for protein conjugates hydrolysis. In summary, the described methodology provides a powerful tool for the rapid study of biodegradable polymers. Copyright © 2014 Elsevier B.V. All rights reserved.

Establishment of the optimum two-dimensional electrophoresis system of ovine ovarian tissue.

PubMed

Jia, J L; Zhang, L P; Wu, J P; Wang, J; Ding, Q

2014-08-26

Lambing performance of sheep is the most important economic trait and is regarded as a critic factoring affecting the productivity in sheep industry. Ovary plays the most roles in lambing trait. To establish the optimum two-dimensional electrophoresis system (2-DE) of ovine ovarian tissue, the common protein extraction methods of animal tissue (trichloroacetic acid/acetone precipitation and direct schizolysis methods) were used to extract ovine ovarian protein, and 17-cm nonlinear immobilized PH 3-10 gradient strips were used for 2-DE. The sample handling, loading quantity of the protein sample, and isoelectric focusing (IEF) steps were manipulated and optimized in this study. The results indicate that the direct schizolysis III method, a 200-μg loading quantity of the protein sample, and IEF steps II (20°C active hydration, 14 h→500 V, 1 h→1000 V 1 h→1000-9000 V, 6 h→80,000 VH→500 V 24 h) are optimal for 2-DE analysis of ovine ovarian tissue. Therefore, ovine ovarian tissue proteomics 2-DE was preliminarily established by the optimized conditions in this study; meanwhile, the conditions identified herein could provide a reference for ovarian sample preparation and 2-DE using tissues from other animals.

[Effects of Aptamer-siRNA Nucleic Acid Compound on Growth and Apoptosis in Myeloid Leukemia Cell Line K562].

PubMed

Ping, Juan; Shen, Zhi-Hui; Wang, Bao-Quan; Zhao, Na; Li, Rui; Li, Mian; Pang, Xiao-Bin; Chen, Chuan-Bo

2015-04-01

To explore the effects of aptamer-siRNA nucleic acid compound on growth and apoptosis in myeloid leukemia cell line K562. the changes of cellular morphology and structure were observed by using fluorescence microscope, laser confocal microscope, JEM-4000EX transmission electron microscopy; MTT assay were performed to evaluate the sensibility of K562 cells to aptamer-siRNA compound, the apoptosis was detected by DNA gel electro-phoresis. The remarkably changes of morphology and structure of K562 cells treated with 200 µmol/L aptamer-siRNA were observed under fluorescence microscopy and electromicroscopy. As compared with control, the aptamer-siRNA compound showed more inhibitory effect on K562 cells and there was significant difference (P<0.05). The MTT assay showed that the IC50 value of aptamer-siRNA compound for K562 cells was 150 µmol/L. According to agarose gel electrophoresis observation, when the aptamer-siRNA compound showed effect on K562 cells, the typical DNA lader could be observed. The aptamer-siRNA compound can significantly induce K562 cell apoptosis, and provide reference for gene therapy of patients with chronic myelocytic lenkemia.

Grapevine tissues and phenology differentially affect soluble carbohydrates determination by capillary electrophoresis.

PubMed

Moreno, Daniela; Berli, Federico; Bottini, Rubén; Piccoli, Patricia N; Silva, María F

2017-09-01

Soluble carbohydrates distribution depends on plant physiology and, among other important factors, determines fruit yield and quality. In plant biology, the analysis of sugars is useful for many purposes, including metabolic studies. Capillary electrophoresis (CE) proved to be a powerful green separation technique with minimal sample preparation, even in complex plant tissues, that can provide high-resolution efficiency. Matrix effect refers to alterations in the analytical response caused by components of a sample other than the analyte of interest. Thus, the assessment and reduction of the matrix factor is fundamental for metabolic studies in different matrices. The present study evaluated the source and levels of matrix effects in the determination of most abundant sugars in grapevine tissues (mature and young leaves, berries and roots) at two phenological growth stages. Sucrose was the sugar that showed the least matrix effects, while fructose was the most affected analyte. Based on plant tissues, young leaves presented the smaller matrix effects, irrespectively of the phenology. These changes may be attributed to considerable differences at chemical composition of grapevine tissues with plant development. Therefore, matrix effect should be an important concern for plant metabolomics. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Separation of Native Allophycocyanin and R-Phycocyanin from Marine Red Macroalga Polysiphonia urceolata by the Polyacrylamide Gel Electrophoresis Performed in Novel Buffer Systems

PubMed Central

Wang, Yu; Gong, Xueqin; Wang, Shumei; Chen, Lixue; Sun, Li

2014-01-01

Three buffer systems of Imidazole−Acetic acid, HEPES−Imidazole/Bis-tris and Bis-tris−HEPES−MES were designed based on the principle of discontinuous polyacrylamide gel electrophoresis (PAGE) for the native PAGE which could be performed in pH 7.0 and 6.5 in order to analyze and prepare the minor components of allophycocyanin (AP) and R-phycocyanin (R-PC) from marine red macroalga Polysiphonia urceolata. These AP and R-PC phycobiliproteins are easily denatured in alkaline environments. The obtained results demonstrated that the PAGE modes performed in the buffer systems of HEPES−Imidazole/Bis-tris and Bis-tris−HEPES−MES gave the satisfactory resolution and separation of AP and R-PC proteins. The absorption and fluorescence spectra of the AP and R-PC proteins which were prepared by the established PAGE modes proved that they maintained natural spectroscopic characteristics. The established PAGE modes may also provide useful references and selections for some other proteins that are sensitive to alkaline environments or are not effectively separated by the classical PAGE modes performed normally in alkaline buffer systems. PMID:25166028

Affinity capillary electrophoresis and fluorescence spectroscopy for studying enantioselective interactions between omeprazole enantiomer and human serum albumin.

PubMed

Xu, Yujing; Hong, Tingting; Chen, Xueping; Ji, Yibing

2017-05-01

Baseline separation of omeprazole (OME) enantiomers was achieved by affinity capillary electrophoresis (ACE), using human serum albumin (HSA) as the chiral selector. The influence of several experimental variables such as HSA concentration, the type and content of organic modifiers, applied voltage and running buffer concentration on the separation was evaluated. The binding of esomeprazole (S-omeprazole, S-OME) and its R-enantiomer (R-omeprazole, R-OME) to HSA under simulated physiological conditions was studied by ACE and fluorescence spectroscopy which was considered as a reference method. ACE studies demonstrated that the binding constants of the two enantiomers and HSA were 3.18 × 10 3 M -1 and 5.36 × 10 3 M -1 , respectively. The binding properties including the fluorescence quenching mechanisms, binding constants, binding sites and the number of binding sites were obtained by fluorescence spectroscopy. Though the ACE method could not get enough data when compared with the fluorescence spectrum method, the separation and binding studies of chiral drugs could be achieved simultaneously via this method. This study is of great significance for the investigation and clinical application of chiral drugs. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optically Mapping Multiple Bacterial Genomes Simultaneously in a Single Run

DTIC Science & Technology

2011-11-21

sequence orientation. We have demonstrated mapping of Shigella dysenteriae and Escherichia coli simultaneously, despite their very close phylogenetic...relationship ( Shigella and Escherichia coli are generally considered to be within a single species, but are segregated at the genus level for historical...reasons [4]); two clones of Shigella would likely not map together successfully using the mixed DNA method. Similarly, based on reference maps being

Developing Land Use Land Cover Maps for the Lower Mekong Basin to Aid SWAT Hydrologic Modeling

NASA Astrophysics Data System (ADS)

Spruce, J.; Bolten, J. D.; Srinivasan, R.

2017-12-01

This presentation discusses research to develop Land Use Land Cover (LULC) maps for the Lower Mekong Basin (LMB). Funded by a NASA ROSES Disasters grant, the main objective was to produce updated LULC maps to aid the Mekong River Commission's (MRC's) Soil and Water Assessment Tool (SWAT) hydrologic model. In producing needed LULC maps, temporally processed MODIS monthly NDVI data for 2010 were used as the primary data source for classifying regionally prominent forest and agricultural types. The MODIS NDVI data was derived from processing MOD09 and MYD09 8-day reflectance data with the Time Series Product Tool, a custom software package. Circa 2010 Landsat multispectral data from the dry season were processed into top of atmosphere reflectance mosaics and then classified to derive certain locally common LULC types, such as urban areas and industrial forest plantations. Unsupervised ISODATA clustering was used to derive most LULC classifications. GIS techniques were used to merge MODIS and Landsat classifications into final LULC maps for Sub-Basins (SBs) 1-8 of the LMB. The final LULC maps were produced at 250-meter resolution and delivered to the MRC for use in SWAT modeling for the LMB. A map accuracy assessment was performed for the SB 7 LULC map with 14 classes. This assessment was performed by comparing random locations for sampled LULC types to geospatial reference data such as Landsat RGBs, MODIS NDVI phenologic profiles, high resolution satellite data from Google Map/Earth, and other reference data from the MRC (e.g., crop calendars). LULC accuracy assessment results for SB 7 indicated an overall agreement to reference data of 81% at full scheme specificity. However, by grouping 3 deciduous forest classes into 1 class, the overall agreement improved to 87%. The project enabled updated LULC maps, plus more specific rice types were classified compared to the previous LULC maps. The LULC maps from this project should improve the use of SWAT for modeling hydrology in the LMB, plus improve water and disaster management in a region vulnerable to flooding, droughts, and anthropogenic change (e.g., from dam building and other LULC change).

The automated reference toolset: A soil-geomorphic ecological potential matching algorithm

USGS Publications Warehouse

Nauman, Travis; Duniway, Michael C.

2016-01-01

Ecological inventory and monitoring data need referential context for interpretation. Identification of appropriate reference areas of similar ecological potential for site comparison is demonstrated using a newly developed automated reference toolset (ART). Foundational to identification of reference areas was a soil map of particle size in the control section (PSCS), a theme in US Soil Taxonomy. A 30-m resolution PSCS map of the Colorado Plateau (366,000 km2) was created by interpolating ∼5000 field soil observations using a random forest model and a suite of raster environmental spatial layers representing topography, climate, general ecological community, and satellite imagery ratios. The PSCS map had overall out of bag accuracy of 61.8% (Kappa of 0.54, p < 0.0001), and an independent validation accuracy of 93.2% at a set of 356 field plots along the southern edge of Canyonlands National Park, Utah. The ART process was also tested at these plots, and matched plots with the same ecological sites (ESs) 67% of the time where sites fell within 2-km buffers of each other. These results show that the PSCS and ART have strong application for ecological monitoring and sampling design, as well as assessing impacts of disturbance and land management action using an ecological potential framework. Results also demonstrate that PSCS could be a key mapping layer for the USDA-NRCS provisional ES development initiative.

Serum protein capillary electrophoresis and measurement of acute phase proteins in a captive cheetah (Acinonyx jubatus) population.

PubMed

Depauw, Sarah; Delanghe, Joris; Whitehouse-Tedd, Katherine; Kjelgaard-Hansen, Mads; Christensen, Michelle; Hesta, Myriam; Tugirimana, Pierrot; Budd, Jane; Dermauw, Veronique; Janssens, Geert P J

2014-09-01

Renal and gastrointestinal pathologies are widespread in the captive cheetah (Acinonyx jubatus) population but are often diagnosed at a late stage, because diagnostic tools are limited to the evaluation of clinical signs or general blood examination. Presently, no data are available on serum proteins and acute-phase proteins in cheetahs during health or disease, although they might be important to improve health monitoring. This study aimed to quantify serum proteins by capillary electrophoresis in 80 serum samples from captive cheetahs, categorized according to health status and disease type. Moreover, serum amyloid A concentrations were measured via a turbidimetric immunoassay validated in domestic cats, whereas haptoglobin and C-reactive protein were determined by non-species-specific functional tests. Cheetahs classified as healthy had serum protein and acute phase protein concentrations within reference ranges for healthy domestic cats. In contrast, unhealthy cheetahs had higher (P < 0.001) serum amyloid A, alpha2-globulin, and haptoglobin concentrations compared with the healthy subgroup. Moreover, serum amyloid A (P = 0.020), alpha2-globulin (P < 0.001) and haptoglobin (P = 0.001) concentrations in cheetahs suffering from chronic kidney disease were significantly greater compared to the reportedly healthy cheetahs. Our study indicates that serum proteins in the cheetah can be analyzed by routine capillary electrophoresis, whereas acute-phase proteins can be measured using available immunoassays or non-species-specific techniques, which are also likely to be applicable in other exotic felids. Moreover, results suggest that serum amyloid A and haptoglobin are important acute-phase proteins in the diseased cheetah and highlight the need to evaluate their role as early-onset markers for disease.

[Splenic infarction at high altitude, Huaraz-Peru (3,100 masl)].

PubMed

López de Guimaraes, Douglas; Menacho López, Julio; Villanueva Palacios, Jovita; Mosquera Vásquez, Vitaliano

2009-01-01

We report three cases of splenic infarction in healthy men for the first time that amounted to high altitudes, observed in the hospital "Victor Ramos Guardia" Huaraz (3100 m). Case 1 (1995) of 55 years, born in Cuba, from Lima, caucasian suddenly presented acute abdominal pain in epigastrium, distension, nausea and vomiting, was laparotomized for acute abdomen and surgical pathology revealed thrombosis with splenic infarction splenic artery and vein. During follow-up in Lima, hemoglobin electrophoresis showed that it was heterozygous carrier of the sickle trait (Hb A: 57% Hb S: 38.5%). Case 2 (1998) of 23 years, born in Cuba, from Lima, Black said acute abdominal pain in left hypochondrium, shortness of breath and chest pain, clinical examination and radiography of the abdomen showed the spleen volume increased. Case 3 (2006) of 17 years, natural and from Lima, mestizo, who came on tour promotion, acute abdominal pain referred onset in the epigastrium and left hypochondrium, headache, increase heat, nausea and vomiting, pharyngitis was found acute and painful, and spleen increased in size by clinical and x-ray of abdomen simple stand. None had no history of hemoglobinopathy and anemia. In general, medical management was supportive and cases 2 and 3 are recommended hemoglobin electrophoresis. We conclude that we must think of splenic infarction associated with height in any healthy person who is first at high altitude (> 3000m) and having a sudden acute abdominal pain in epigastrium and / or left hypochondrium, pain and palpable spleen and radiological study compatible with image. In this case is indicated by hemoglobin electrophoresis to determine whether there is an individual heterozygous carrier of the sickle trait. splenic infarction, high altitude, sickle trait, Huaraz.

β-Globin gene sequencing of hemoglobin Austin revises the historically reported electrophoretic migration pattern.

PubMed

Racsa, Lori D; Luu, Hung S; Park, Jason Y; Mitui, Midori; Timmons, Charles F

2014-06-01

Hemoglobin (Hb) Austin was defined in 1977, using amino acid sequencing of samples from 3 unrelated Mexican-Americans, as a substitution of serine for arginine at position 40 of the β-globin chain (Arg40Ser). Its electrophoretic migration on both cellulose acetate (pH 8.4) and citrate agar (pH 6.2) was reported between Hb F and Hb A, and this description persists in reference literature. OBJECTIVES.-To review the clinical features and redefine the diagnostic characteristics of Hb Austin. Eight samples from 6 unrelated individuals and 2 siblings, all with Hispanic surnames, were submitted for abnormal Hb identification between June 2010 and September 2011. High-performance liquid chromatography, isoelectric focusing (IEF), citrate agar electrophoresis, and bidirectional DNA sequencing of the entire β-globin gene were performed. DNA sequencing confirmed all 8 individuals to be heterozygous for Hb Austin (Arg40Ser). Retention time on high-performance liquid chromatography and migration on citrate agar electrophoresis were consistent with that identification. Migration on IEF, however, was not between Hb F and Hb A, as predicted from the report of cellulose acetate electrophoresis. By IEF, Hb Austin migrated anodal to ("faster than") Hb A. Hemoglobin Austin (Arg40Ser) appears on IEF as a "fast," anodally migrating, Hb variant, just as would be expected from its amino acid substitution. The cited historic report is, at best, not applicable to IEF and is probably erroneous. Our observation of 8 cases in 16 months suggests that this variant may be relatively common in some Hispanic populations, making its recognition important. Furthermore, gene sequencing is proving itself a powerful and reliable tool for definitive identification of Hb variants.

Genetics Home Reference: cri-du-chat syndrome

MedlinePlus

... Pinkel D. High-resolution mapping of genotype-phenotype relationships in cri du chat syndrome using array comparative ... for Links Data Files & API Site Map Subscribe Customer Support USA.gov Copyright Privacy Accessibility FOIA Viewers & ...

Efficient Decoding of Compressed Data.

ERIC Educational Resources Information Center

Bassiouni, Mostafa A.; Mukherjee, Amar

1995-01-01

Discusses the problem of enhancing the speed of Huffman decoding of compressed data. Topics addressed include the Huffman decoding tree; multibit decoding; binary string mapping problems; and algorithms for solving mapping problems. (22 references) (LRW)

Evaluation of automated global mapping of Reference Soil Groups of WRB2015

NASA Astrophysics Data System (ADS)

Mantel, Stephan; Caspari, Thomas; Kempen, Bas; Schad, Peter; Eberhardt, Einar; Ruiperez Gonzalez, Maria

2017-04-01

SoilGrids is an automated system that provides global predictions for standard numeric soil properties at seven standard depths down to 200 cm, currently at spatial resolutions of 1km and 250m. In addition, the system provides predictions of depth to bedrock and distribution of soil classes based on WRB and USDA Soil Taxonomy (ST). In SoilGrids250m(1), soil classes (WRB, version 2006) consist of the RSG and the first prefix qualifier, whereas in SoilGrids1km(2), the soil class was assessed at RSG level. Automated mapping of World Reference Base (WRB) Reference Soil Groups (RSGs) at a global level has great advantages. Maps can be updated in a short time span with relatively little effort when new data become available. To translate soil names of older versions of FAO/WRB and national classification systems of the source data into names according to WRB 2006, correlation tables are used in SoilGrids. Soil properties and classes are predicted independently from each other. This means that the combinations of soil properties for the same cells or soil property-soil class combinations do not necessarily yield logical combinations when the map layers are studied jointly. The model prediction procedure is robust and probably has a low source of error in the prediction of RSGs. It seems that the quality of the original soil classification in the data and the use of correlation tables are the largest sources of error in mapping the RSG distribution patterns. Predicted patterns of dominant RSGs were evaluated in selected areas and sources of error were identified. Suggestions are made for improvement of WRB2015 RSG distribution predictions in SoilGrids. Keywords: Automated global mapping; World Reference Base for Soil Resources; Data evaluation; Data quality assurance References 1 Hengl T, de Jesus JM, Heuvelink GBM, Ruiperez Gonzalez M, Kilibarda M, et al. (2016) SoilGrids250m: global gridded soil information based on Machine Learning. Earth System Science Data (ESSD), in review. 2 Hengl T, de Jesus JM, MacMillan RA, Batjes NH, Heuvelink GBM, et al. (2014) SoilGrids1km — Global Soil Information Based on Automated Mapping. PLoS ONE 9(8): e105992. doi:10.1371/journal.pone.0105992

Terrain Correction on the moving equal area cylindrical map projection of the surface of a reference ellipsoid

NASA Astrophysics Data System (ADS)

Ardalan, A.; Safari, A.; Grafarend, E.

2003-04-01

An operational algorithm for computing the ellipsoidal terrain correction based on application of closed form solution of the Newton integral in terms of Cartesian coordinates in the cylindrical equal area map projected surface of a reference ellipsoid has been developed. As the first step the mapping of the points on the surface of a reference ellipsoid onto the cylindrical equal area map projection of a cylinder tangent to a point on the surface of reference ellipsoid closely studied and the map projection formulas are computed. Ellipsoidal mass elements with various sizes on the surface of the reference ellipsoid is considered and the gravitational potential and the vector of gravitational intensity of these mass elements has been computed via the solution of Newton integral in terms of ellipsoidal coordinates. The geographical cross section areas of the selected ellipsoidal mass elements are transferred into cylindrical equal area map projection and based on the transformed area elements Cartesian mass elements with the same height as that of the ellipsoidal mass elements are constructed. Using the close form solution of the Newton integral in terms of Cartesian coordinates the potential of the Cartesian mass elements are computed and compared with the same results based on the application of the ellipsoidal Newton integral over the ellipsoidal mass elements. The results of the numerical computations show that difference between computed gravitational potential of the ellipsoidal mass elements and Cartesian mass element in the cylindrical equal area map projection is of the order of 1.6 × 10-8m^2/s^2 for a mass element with the cross section size of 10 km × 10 km and the height of 1000 m. For a 1 km × 1 km mass element with the same height, this difference is less than 1.5 × 10-4 m^2}/s^2. The results of the numerical computations indicate that a new method for computing the terrain correction based on the closed form solution of the Newton integral in terms of Cartesian coordinates and with accuracy of ellipsoidal terrain correction has been achieved! In this way one can enjoy the simplicity of the solution of the Newton integral in terms of Cartesian coordinates and at the same time the accuracy of the ellipsoidal terrain correction, which is needed for the modern theory of geoid computations.

Improving efficiency of a small forensic DNA laboratory: validation of robotic assays and evaluation of microcapillary array device.

PubMed

Crouse, Cecelia A; Yeung, Stephanie; Greenspoon, Susan; McGuckian, Amy; Sikorsky, Julie; Ban, Jeff; Mathies, Richard

2005-08-01

To present validation studies performed for the implementation of existing and new technologies to increase the efficiency in the forensic DNA Section of the Palm Beach County Sheriff's Office (PBSO) Crime Laboratory. Using federally funded grants, internal support, and an external Process Mapping Team, the PBSO collaborated with forensic vendors, universities, and other forensic laboratories to enhance DNA testing procedures, including validation of the DNA IQ magnetic bead extraction system, robotic DNA extraction using the BioMek2000, the ABI7000 Sequence Detection System, and is currently evaluating a micro Capillary Array Electrophoresis device. The PBSO successfully validated and implemented both manual and automated Promega DNA IQ magnetic bead extractions system, which have increased DNA profile results from samples with low DNA template concentrations. The Beckman BioMek2000 DNA robotic workstation has been validated for blood, tissue, bone, hair, epithelial cells (touch evidence), and mixed stains such as semen. There has been a dramatic increase in the number of samples tested per case since implementation of the robotic extraction protocols. The validation of the ABI7000 real-time quantitative polymerase chain reaction (qPCR) technology and the single multiplex short tandem repeat (STR) PowerPlex16 BIO amplification system has provided both a time and a financial benefit. In addition, the qPCR system allows more accurate DNA concentration data and the PowerPlex 16 BIO multiplex generates DNA profiles data in half the time when compared to PowerPlex1.1 and PowerPlex2.1 STR systems. The PBSO's future efficiency requirements are being addressed through collaboration with the University of California at Berkeley and the Virginia Division of Forensic Science to validate microcapillary array electrophoresis instrumentation. Initial data demonstrated the electrophoresis of 96 samples in less than twenty minutes. The PBSO demonstrated, through the validation of more efficient extraction and quantification technology, an increase in the number of evidence samples tested using robotic/DNA IQ magnetic bead DNA extraction, a decrease in the number of negative samples amplified due to qPCR and implementation of a single multiplex amplification system. In addition, initial studies show the microcapillary array electrophoresis device (microCAE) evaluation results provide greater sensitivity and faster STR analysis output than current platforms.

Kidney cell electrophoresis

NASA Technical Reports Server (NTRS)

Todd, P.

1980-01-01

The following aspects of kidney cell electrophoresis are discussed: (1) the development and testing of electrophoresis solutions; (2) optimization of freezing and thawing; (3) procedures for evaluation of separated kidney cells; and (4) electrophoretic mobility characterization of kidney cells.

Kidney cell electrophoresis

NASA Technical Reports Server (NTRS)

Todd, P.

1979-01-01

A kidney cell electrophoresis technique is described in four parts: (1) the development and testing of electrophoresis solutions; (2) optimization of freezing and thawing; (3) procedures for evaluation of separated kidney cells; and (4) electrophoretic mobility characteristics of kidney cells.

A genetic map and germplasm diversity estimation of Mangifera indica (mango) with SNPs

USDA-ARS?s Scientific Manuscript database

Mango (Mangifera indica) is often referred to as the “King of Fruits”. As the first steps in developing a mango genomics project, we genotyped 582 individuals comprising six mapping populations with 1054 SNP markers. The resulting consensus map had 20 linkage groups defined by 726 SNP markers with...

Mapping Success: Performance-Based Scholarships, Student Services, and Developmental Math at Hillsborough Community College

ERIC Educational Resources Information Center

Sommo, Colleen; Boynton, Melissa; Collado, Herbert; Diamond, John; Gardenhire, Alissa; Ratledge, Alyssa; Rudd, Timothy; Weiss, Michael J.

2014-01-01

In 2010, Hillsborough Community College (HCC), a large multicampus institution in Tampa, Florida, worked with MDRC to create the Mathematics Access Performance Scholarship (MAPS) program to help academically underprepared community college students succeed in developmental math. MAPS provides an incentive for low-income students referred to…

15-METER LANDSAT ANALYSES OF THE MISSISSIPPI RIVER - MAP SERIES FROM HEADWATERS IN THE GULF OF MEXICO

EPA Science Inventory

The purpose of the Mississippi River map series is to provide reference for ecological vulnerability throughout the entire Mississippi River Basin, which is a forthcoming product. This map series product consists of seven 32 inch x 40 inch posters, with a nominal scale of 1 inch ...

Map and Compass. Outdoor Living Skills Series. Instructor Manual.

ERIC Educational Resources Information Center

Ludwig, Gail S.

Designed for instructors with little or no map and compass experience, the self-contained manual contains background information, lesson plans, student handouts, and references for teaching the basic skills of map and compass use to junior high and senior high school students and youth groups. An introductory section briefly discusses the…

Estimating missing hourly climatic data using artificial neural network for energy balance based ET mapping applications

USDA-ARS?s Scientific Manuscript database

Remote sensing based evapotranspiration (ET) mapping has become an important tool for water resources management at a regional scale. Accurate hourly climatic data and reference ET are crucial input for successfully implementing remote sensing based ET models such as Mapping ET with internal calibra...

Gavagai Is as Gavagai Does: Learning Nouns and Verbs from Cross-Situational Statistics

ERIC Educational Resources Information Center

Monaghan, Padraic; Mattock, Karen; Davies, Robert A. I.; Smith, Alastair C.

2015-01-01

Learning to map words onto their referents is difficult, because there are multiple possibilities for forming these mappings. Cross-situational learning studies have shown that word-object mappings can be learned across multiple situations, as can verbs when presented in a syntactic context. However, these previous studies have presented either…

An automated approach to mapping corn from Landsat imagery

USGS Publications Warehouse

Maxwell, S.K.; Nuckols, J.R.; Ward, M.H.; Hoffer, R.M.

2004-01-01

Most land cover maps generated from Landsat imagery involve classification of a wide variety of land cover types, whereas some studies may only need spatial information on a single cover type. For example, we required a map of corn in order to estimate exposure to agricultural chemicals for an environmental epidemiology study. Traditional classification techniques, which require the collection and processing of costly ground reference data, were not feasible for our application because of the large number of images to be analyzed. We present a new method that has the potential to automate the classification of corn from Landsat satellite imagery, resulting in a more timely product for applications covering large geographical regions. Our approach uses readily available agricultural areal estimates to enable automation of the classification process resulting in a map identifying land cover as ‘highly likely corn,’ ‘likely corn’ or ‘unlikely corn.’ To demonstrate the feasibility of this approach, we produced a map consisting of the three corn likelihood classes using a Landsat image in south central Nebraska. Overall classification accuracy of the map was 92.2% when compared to ground reference data.

A Radio-Map Automatic Construction Algorithm Based on Crowdsourcing

PubMed Central

Yu, Ning; Xiao, Chenxian; Wu, Yinfeng; Feng, Renjian

2016-01-01

Traditional radio-map-based localization methods need to sample a large number of location fingerprints offline, which requires huge amount of human and material resources. To solve the high sampling cost problem, an automatic radio-map construction algorithm based on crowdsourcing is proposed. The algorithm employs the crowd-sourced information provided by a large number of users when they are walking in the buildings as the source of location fingerprint data. Through the variation characteristics of users’ smartphone sensors, the indoor anchors (doors) are identified and their locations are regarded as reference positions of the whole radio-map. The AP-Cluster method is used to cluster the crowdsourced fingerprints to acquire the representative fingerprints. According to the reference positions and the similarity between fingerprints, the representative fingerprints are linked to their corresponding physical locations and the radio-map is generated. Experimental results demonstrate that the proposed algorithm reduces the cost of fingerprint sampling and radio-map construction and guarantees the localization accuracy. The proposed method does not require users’ explicit participation, which effectively solves the resource-consumption problem when a location fingerprint database is established. PMID:27070623

A semester-long project for teaching basic techniques in molecular biology such as restriction fragment length polymorphism analysis to undergraduate and graduate students.

PubMed

DiBartolomeis, Susan M

2011-01-01

Several reports on science education suggest that students at all levels learn better if they are immersed in a project that is long term, yielding results that require analysis and interpretation. I describe a 12-wk laboratory project suitable for upper-level undergraduates and first-year graduate students, in which the students molecularly locate and map a gene from Drosophila melanogaster called dusky and one of dusky's mutant alleles. The mapping strategy uses restriction fragment length polymorphism analysis; hence, students perform most of the basic techniques of molecular biology (DNA isolation, restriction enzyme digestion and mapping, plasmid vector subcloning, agarose and polyacrylamide gel electrophoresis, DNA labeling, and Southern hybridization) toward the single goal of characterizing dusky and the mutant allele dusky(73). Students work as individuals, pairs, or in groups of up to four students. Some exercises require multitasking and collaboration between groups. Finally, results from everyone in the class are required for the final analysis. Results of pre- and postquizzes and surveys indicate that student knowledge of appropriate topics and skills increased significantly, students felt more confident in the laboratory, and students found the laboratory project interesting and challenging. Former students report that the lab was useful in their careers.

A Semester-Long Project for Teaching Basic Techniques in Molecular Biology Such as Restriction Fragment Length Polymorphism Analysis to Undergraduate and Graduate Students

PubMed Central

DiBartolomeis, Susan M.

2011-01-01

Several reports on science education suggest that students at all levels learn better if they are immersed in a project that is long term, yielding results that require analysis and interpretation. I describe a 12-wk laboratory project suitable for upper-level undergraduates and first-year graduate students, in which the students molecularly locate and map a gene from Drosophila melanogaster called dusky and one of dusky's mutant alleles. The mapping strategy uses restriction fragment length polymorphism analysis; hence, students perform most of the basic techniques of molecular biology (DNA isolation, restriction enzyme digestion and mapping, plasmid vector subcloning, agarose and polyacrylamide gel electrophoresis, DNA labeling, and Southern hybridization) toward the single goal of characterizing dusky and the mutant allele dusky73. Students work as individuals, pairs, or in groups of up to four students. Some exercises require multitasking and collaboration between groups. Finally, results from everyone in the class are required for the final analysis. Results of pre- and postquizzes and surveys indicate that student knowledge of appropriate topics and skills increased significantly, students felt more confident in the laboratory, and students found the laboratory project interesting and challenging. Former students report that the lab was useful in their careers. PMID:21364104

PoMaMo--a comprehensive database for potato genome data.

PubMed

Meyer, Svenja; Nagel, Axel; Gebhardt, Christiane

2005-01-01

A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes.

PoMaMo—a comprehensive database for potato genome data

PubMed Central

Meyer, Svenja; Nagel, Axel; Gebhardt, Christiane

2005-01-01

A database for potato genome data (PoMaMo, Potato Maps and More) was established. The database contains molecular maps of all twelve potato chromosomes with about 1000 mapped elements, sequence data, putative gene functions, results from BLAST analysis, SNP and InDel information from different diploid and tetraploid potato genotypes, publication references, links to other public databases like GenBank (http://www.ncbi.nlm.nih.gov/) or SGN (Solanaceae Genomics Network, http://www.sgn.cornell.edu/), etc. Flexible search and data visualization interfaces enable easy access to the data via internet (https://gabi.rzpd.de/PoMaMo.html). The Java servlet tool YAMB (Yet Another Map Browser) was designed to interactively display chromosomal maps. Maps can be zoomed in and out, and detailed information about mapped elements can be obtained by clicking on an element of interest. The GreenCards interface allows a text-based data search by marker-, sequence- or genotype name, by sequence accession number, gene function, BLAST Hit or publication reference. The PoMaMo database is a comprehensive database for different potato genome data, and to date the only database containing SNP and InDel data from diploid and tetraploid potato genotypes. PMID:15608284

The current state of the creation and modernization of national geodetic and cartographic resources in Poland

NASA Astrophysics Data System (ADS)

Doskocz, Adam

2016-01-01

All official data are currently integrated and harmonized in a spatial reference system. This paper outlines a national geodetic and cartographic resources in Poland. The national geodetic and cartographic resources are an important part of the spatial information infrastructure in the European Community. They also provide reference data for other resources of Spatial Data Infrastructure (SDI), including: main and detailed geodetic control networks, base maps, land and buildings registries, geodetic registries of utilities and topographic maps. This paper presents methods of producing digital map data and technical standards for field surveys, and in addition paper also presents some aspects of building Global and Regional SDI.

Integration of imagery and cartographic data through a common map base

NASA Technical Reports Server (NTRS)

Clark, J.

1983-01-01

Several disparate data types are integrated by using control points as the basis for spatially registering the data to a map base. The data are reprojected to match the coordinates of the reference UTM (Universal Transverse Mercator) map projection, as expressed in lines and samples. Control point selection is the most critical aspect of integrating the Thematic Mapper Simulator MSS imagery with the cartographic data. It is noted that control points chosen from the imagery are subject to error from mislocated points, either points that did not correlate well to the reference map or minor pixel offsets because of interactive cursorring errors. Errors are also introduced in map control points when points are improperly located and digitized, leading to inaccurate latitude and longitude coordinates. Nonsystematic aircraft platform variations, such as yawl, pitch, and roll, affect the spatial fidelity of the imagery in comparison with the quadrangles. Features in adjacent flight paths do not always correspond properly owing to the systematic panorama effect and alteration of flightline direction, as well as platform variations.

Individual Brain Charting, a high-resolution fMRI dataset for cognitive mapping.

PubMed

Pinho, Ana Luísa; Amadon, Alexis; Ruest, Torsten; Fabre, Murielle; Dohmatob, Elvis; Denghien, Isabelle; Ginisty, Chantal; Becuwe-Desmidt, Séverine; Roger, Séverine; Laurier, Laurence; Joly-Testault, Véronique; Médiouni-Cloarec, Gaëlle; Doublé, Christine; Martins, Bernadette; Pinel, Philippe; Eger, Evelyn; Varoquaux, Gaël; Pallier, Christophe; Dehaene, Stanislas; Hertz-Pannier, Lucie; Thirion, Bertrand

2018-06-12

Functional Magnetic Resonance Imaging (fMRI) has furthered brain mapping on perceptual, motor, as well as higher-level cognitive functions. However, to date, no data collection has systematically addressed the functional mapping of cognitive mechanisms at a fine spatial scale. The Individual Brain Charting (IBC) project stands for a high-resolution multi-task fMRI dataset that intends to provide the objective basis toward a comprehensive functional atlas of the human brain. The data refer to a cohort of 12 participants performing many different tasks. The large amount of task-fMRI data on the same subjects yields a precise mapping of the underlying functions, free from both inter-subject and inter-site variability. The present article gives a detailed description of the first release of the IBC dataset. It comprises a dozen of tasks, addressing both low- and high- level cognitive functions. This openly available dataset is thus intended to become a reference for cognitive brain mapping.

Superior cognitive mapping through single landmark-related learning than through boundary-related learning.

PubMed

Zhou, Ruojing; Mou, Weimin

2016-08-01

Cognitive mapping is assumed to be through hippocampus-dependent place learning rather than striatum-dependent response learning. However, we proposed that either type of spatial learning, as long as it involves encoding metric relations between locations and reference points, could lead to a cognitive map. Furthermore, the fewer reference points to specify individual locations, the more accurate a cognitive map of these locations will be. We demonstrated that participants have more accurate representations of vectors between 2 locations and of configurations among 3 locations when locations are individually encoded in terms of a single landmark than when locations are encoded in terms of a boundary. Previous findings have shown that learning locations relative to a boundary involve stronger place learning and higher hippocampal activation whereas learning relative to a single landmark involves stronger response learning and higher striatal activation. Recognizing this, we have provided evidence challenging the cognitive map theory but favoring our proposal. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Mapping mitochondrial heteroplasmy in a Leydig tumor by laser capture micro-dissection and cycling temperature capillary electrophoresis.

PubMed

Refinetti, Paulo; Arstad, Christian; Thilly, William G; Morgenthaler, Stephan; Ekstrøm, Per Olaf

2017-01-01

The growth of tumor cells is accompanied by mutations in nuclear and mitochondrial genomes creating marked genetic heterogeneity. Tumors also contain non-tumor cells of various origins. An observed somatic mitochondrial mutation would have occurred in a founding cell and spread through cell division. Micro-anatomical dissection of a tumor coupled with assays for mitochondrial point mutations permits new insights into this growth process. More generally, the ability to detect and trace, at a histological level, somatic mitochondrial mutations in human tissues and tumors, makes these mutations into markers for lineage tracing. A tumor was first sampled by a large punch biopsy and scanned for any significant degree of heteroplasmy in a set of sequences containing known mutational hotspots of the mitochondrial genome. A heteroplasmic tumor was sliced at a 12 μm thickness and placed on membranes. Laser capture micro-dissection was used to take 25000 μm 2 subsamples or spots. After DNA amplification, cycling temperature capillary electrophoresis (CTCE) was used on the laser captured samples to quantify mitochondrial mutant fractions. Of six testicular tumors studied, one, a Leydig tumor, was discovered to carry a detectable degree of heteroplasmy for two separate point mutations: a C → T mutation at bp 64 and a T → C mutation found at bp 152. From this tumor, 381 spots were sampled with laser capture micro-dissection. The ordered distribution of spots exhibited a wide range of fractions of the mutant sequences from 0 to 100% mutant copies. The two mutations co-distributed in the growing tumor indicating they were present on the same genome copies in the founding cell. Laser capture microdissection of sliced tumor samples coupled with CTCE-based point mutation assays provides an effective and practical means to obtain maps of mitochondrial mutational heteroplasmy within human tumors.

Development of Two Analytical Methods Based on Reverse Phase Chromatographic and SDS-PAGE Gel for Assessment of Deglycosylation Yield in N-Glycan Mapping.

PubMed

Eckard, Anahita D; Dupont, David R; Young, Johnie K

2018-01-01

N -lined glycosylation is one of the critical quality attributes (CQA) for biotherapeutics impacting the safety and activity of drug product. Changes in pattern and level of glycosylation can significantly alter the intrinsic properties of the product and, therefore, have to be monitored throughout its lifecycle. Therefore fast, precise, and unbiased N -glycan mapping assay is desired. To ensure these qualities, using analytical methods that evaluate completeness of deglycosylation is necessary. For quantification of deglycosylation yield, methods such as reduced liquid chromatography-mass spectrometry (LC-MS) and reduced capillary gel electrophoresis (CGE) have been commonly used. Here we present development of two additional methods to evaluate deglycosylation yield: one based on LC using reverse phase (RP) column and one based on reduced sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE gel) with offline software (GelAnalyzer). With the advent of rapid deglycosylation workflows in the market for N -glycan profiling replacing overnight incubation, we have aimed to quantify the level of deglycosylation in a selected rapid deglycosylation workflow. Our results have shown well resolved peaks of glycosylated and deglycosylated protein species with RP-LC method allowing simple quantification of deglycosylation yield of protein with high confidence. Additionally a good correlation, ≥0.94, was found between deglycosylation yields estimated by RP-LC method and that of reduced SDS-PAGE gel method with offline software. Evaluation of rapid deglycosylation protocol from GlycanAssure™ HyPerformance assay kit performed on fetuin and RNase B has shown complete deglycosylation within the recommended protocol time when evaluated with these techniques. Using this kit, N -glycans from NIST mAb were prepared in 1.4 hr and analyzed by hydrophilic interaction chromatography (HILIC) ultrahigh performance LC (UHPLC) equipped with a fluorescence detector (FLD). 37 peaks were resolved with good resolution. Excellent sample preparation repeatability was found with relative standard deviation (RSD) of <5% for peaks with >0.5% relative area.

Proteolytic fragmentation and peptide mapping of human carboxyamidomethylated tracheobronchial mucin.

PubMed

Rose, M C; Kaufman, B; Martin, B M

1989-05-15

Human tracheobronchial mucin was isolated from lung mucosal gel by chromatography on Sepharose 4B in the presence of dissociating and reducing agents, and its thiol residues were carboxyamidomethylated with iodo[1(-14)C]acetamide. The 14C-carboxyamido-methylated mucin was purified by chromatography on Sepharose 2B. No low molecular weight components were detected by molecular sieve chromatography or polyacrylamide gel electrophoresis in the presence of dissociating and reducing agents or by analytical density centrifugation in CsCl/guanidinium chloride. After digestion of the purified 14C-mucin with trypsin-L-1-tosylamido-2-phenylethyl chloromethyl ketone, three fractions (TR-1, TR-2, and TR-3) were observed by chromatography on Sepharose 4B. TR-1, a 260-kDa mucin glycopeptide fragment, contained all of the neutral hexose and blood group activity and 20% of the radioactivity in the undigested mucin. TR-1 was refractory to a second incubation with trypsin but could be digested by papain or Pronase to a smaller mucin glycopeptide fraction, as judged by the slight decrease in apparent molecular weight on Sepharose CL-4B. These mucin glycopeptides contained approximately 50% of the radioactivity in the TR-1 fraction, indicating that the glycosylated domains of carboxyamidomethylated tracheobronchial mucin contained thiol residues. The remainder of the radioactivity from papain or Pronase digests of TR-1 eluted, like the TR-3 fractions, in the salt fraction on Sepharose CL-4B. Peptide mapping of the nonglycosylated TR-3 fraction by TLC and high voltage electrophoresis yielded six principal and several less intensely stained ninhydrin reactive components, with the radiolabel concentrated in one of the latter peptides. Peptide purification of the TR-3 fraction by high pressure liquid chromatography on a C18 reverse phase column demonstrated the presence of four major peptides, with TR-3A being the dominant component. The TR-3D peptide contained S-carboxy-aminomethylcysteine and had 69% sequence similarity to the sgs-7 salivary glue protein of Drosophila.

Aligner optimization increases accuracy and decreases compute times in multi-species sequence data.

PubMed

Robinson, Kelly M; Hawkins, Aziah S; Santana-Cruz, Ivette; Adkins, Ricky S; Shetty, Amol C; Nagaraj, Sushma; Sadzewicz, Lisa; Tallon, Luke J; Rasko, David A; Fraser, Claire M; Mahurkar, Anup; Silva, Joana C; Dunning Hotopp, Julie C

2017-09-01

As sequencing technologies have evolved, the tools to analyze these sequences have made similar advances. However, for multi-species samples, we observed important and adverse differences in alignment specificity and computation time for bwa- mem (Burrows-Wheeler aligner-maximum exact matches) relative to bwa-aln. Therefore, we sought to optimize bwa-mem for alignment of data from multi-species samples in order to reduce alignment time and increase the specificity of alignments. In the multi-species cases examined, there was one majority member (i.e. Plasmodium falciparum or Brugia malayi ) and one minority member (i.e. human or the Wolbachia endosymbiont w Bm) of the sequence data. Increasing bwa-mem seed length from the default value reduced the number of read pairs from the majority sequence member that incorrectly aligned to the reference genome of the minority sequence member. Combining both source genomes into a single reference genome increased the specificity of mapping, while also reducing the central processing unit (CPU) time. In Plasmodium , at a seed length of 18 nt, 24.1 % of reads mapped to the human genome using 1.7±0.1 CPU hours, while 83.6 % of reads mapped to the Plasmodium genome using 0.2±0.0 CPU hours (total: 107.7 % reads mapping; in 1.9±0.1 CPU hours). In contrast, 97.1 % of the reads mapped to a combined Plasmodium- human reference in only 0.7±0.0 CPU hours. Overall, the results suggest that combining all references into a single reference database and using a 23 nt seed length reduces the computational time, while maximizing specificity. Similar results were found for simulated sequence reads from a mock metagenomic data set. We found similar improvements to computation time in a publicly available human-only data set.

Comparison of Two Capillary Gel Electrophoresis Systems for Clostridium difficile Ribotyping, Using a Panel of Ribotype 027 Isolates and Whole-Genome Sequences as a Reference Standard

PubMed Central

Xiao, Meng; Kong, Fanrong; Jin, Ping; Wang, Qinning; Xiao, Kelin; Jeoffreys, Neisha; James, Gregory

2012-01-01

PCR ribotyping is the most commonly used Clostridium difficile genotyping method, but its utility is limited by lack of standardization. In this study, we analyzed four published whole genomes and tested an international collection of 21 well-characterized C. difficile ribotype 027 isolates as the basis for comparison of two capillary gel electrophoresis (CGE)-based ribotyping methods. There were unexpected differences between the 16S-23S rRNA intergenic spacer region (ISR) allelic profiles of the four ribotype 027 genomes, but six bands were identified in all four and a seventh in three genomes. All seven bands and another, not identified in any of the whole genomes, were found in all 21 isolates. We compared sequencer-based CGE (SCGE) with three different primer pairs to the Qiagen QIAxcel CGE (QCGE) platform. Deviations from individual reference/consensus band sizes were smaller for SCGE (0 to 0.2 bp) than for QCGE (4.2 to 9.5 bp). Compared with QCGE, SCGE more readily distinguished bands of similar length (more discriminatory), detected bands of larger size and lower intensity (more sensitive), and assigned band sizes more accurately and reproducibly, making it more suitable for standardization. Specifically, QCGE failed to identify the largest ISR amplicon. Based on several criteria, we recommend the primer set 16S-USA/23S-USA for use in a proposed standard SCGE method. Similar differences between SCGE and QCGE were found on testing of 14 isolates of four other C. difficile ribotypes. Based on our results, ISR profiles based on accurate sequencer-based band lengths would be preferable to agarose gel-based banding patterns for the assignment of ribotypes. PMID:22692737

Automatic multiple applicator electrophoresis

NASA Technical Reports Server (NTRS)

Grunbaum, B. W.

1977-01-01

Easy-to-use, economical device permits electrophoresis on all known supporting media. System includes automatic multiple-sample applicator, sample holder, and electrophoresis apparatus. System has potential applicability to fields of taxonomy, immunology, and genetics. Apparatus is also used for electrofocusing.

Kidney Cell Electrophoresis

NASA Technical Reports Server (NTRS)

Todd, P.

1985-01-01

Materials and procedures for microgravity electrophoresis of living human embryonic kidney cells were evaluated, ground support in the form of analytical cell electrophoresis and flow cytometry was provided and cells returned from space flight were analyzed. Preflight culture media, electrophoresis buffer, fraction collection media, temperature profiles, and urokinase assay procedures were tested prior to flight. Electrophoretic mobility distributions of aliquots of the cell population to be fractionated in flight were obtained. The protocol established and utilized is given.

Geologic map of the Haji-Gak iron deposit, Bamyan Province, Afghanistan, modified from the 1965 original map compilation of M.S. Smirnov and I.K. Kusov

USGS Publications Warehouse

Renaud, Karine M.; Tucker, Robert D.; Peters, Stephen G.; Stettner, Will R.; Masonic, Linda M.; Moran, Thomas W.

2011-01-01

This map is a modified version of Geological-structural map of Hajigak iron-ore deposit, scale 1:10,000, which was compiled by M.S. Smirnov and I.K. Kusov in 1965. (Refer to the References Cited section in the Map PDF for complete citations of the original map and a related report.) USGS scientists, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original documents and also visited the field area in November 2009. This modified map illustrates the geological structure of the Haji-Gak iron deposit and includes cross sections of the same area. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross sections and includes modifications based on our examination of these documents. Elevations on the cross sections are derived from the original Soviet topography and may not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map. The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

Preliminary geologic map of the eastern Willapa Hills, Cowlitz, Lewis, and Wahkiakum Counties, Washington

USGS Publications Warehouse

Wells, Ray E.; Sawlan, Michael G.

2014-01-01

This digital map database and the PDF derived from the database were created from the analog geologic map: Wells, R.E. (1981), “Geologic map of the eastern Willapa Hills, Cowlitz, Lewis, and Wahkiakum Counties, Washington.” The geodatabase replicates the geologic mapping of the 1981 report with minor exceptions along water boundaries and also along the north and south map boundaries. Slight adjustments to contacts along water boundaries were made to correct differences between the topographic base map used in the 1981 compilation (analog USGS 15-minute series quadrangle maps at 1:62,500 scale) and the base map used for this digital compilation (scanned USGS 7.5-minute series quadrangle maps at 1:24,000 scale). These minor adjustments, however, did not materially alter the geologic map. No new field mapping was performed to create this digital map database, and no attempt was made to fit geologic contacts to the new 1:24,000 topographic base, except as noted above. We corrected typographical errors, formatting errors, and attribution errors (for example, the name change of Goble Volcanics to Grays River Volcanics following current State of Washington usage; Walsh and others, 1987). We also updated selected references, substituted published papers for abstracts, and cited published radiometric ages for the volcanic and plutonic rocks. The reader is referred to Magill and others (1982), Wells and Coe (1985), Walsh and others (1987), Moothart (1993), Payne (1998), Kleibacker (2001), McCutcheon (2003), Wells and others (2009), Chan and others (2012), and Wells and others (in press) for subsequent interpretations of the Willapa Hills geology.

Kidney cell electrophoresis, continuing task

NASA Technical Reports Server (NTRS)

Todd, P. W.

1985-01-01

Materials and procedures for microgravity electrophoresis of living human embryonic kidney cells were evaluated to provide ground support in the form of analytical cell electrophoresis and flow cytometry. Preflight culture media, electrophoresis buffer, fraction collection media, temperature profiles, and urokinase assay procedures were tested prior to flight. Electrophoretic mobility distributions of aliquots of the cell population to be fractionated in flight were obtained. Cells were prepared in suspension prior to flight in electrophoresis buffer and 10% calf serum. Electrophoretic separation proceeded in electrophoresis buffer without serum in the Continuous Flow Electrophoretic Separator, and fractions were collected into sample bags containing culture medium and concentrated serum. Fractions that yielded enough progeny cells were analyzed for morphology and electrophoretic mobility distributions. It is noted that the lowest mobility fraction studied produced higher mobility progeny while the other fractions produced progeny cells with mobilities related to the fractions from which they were collected.

Electrophoresis demonstration on Apollo 16

NASA Technical Reports Server (NTRS)

Snyder, R. S.

1972-01-01

Free fluid electrophoresis, a process used to separate particulate species according to surface charge, size, or shape was suggested as a promising technique to utilize the near zero gravity condition of space. Fluid electrophoresis on earth is disturbed by gravity-induced thermal convection and sedimentation. An apparatus was developed to demonstrate the principle and possible problems of electrophoresis on Apollo 14 and the separation boundary between red and blue dye was photographed in space. The basic operating elements of the Apollo 14 unit were used for a second flight demonstration on Apollo 16. Polystyrene latex particles of two different sizes were used to simulate the electrophoresis of large biological particles. The particle bands in space were extremely stable compared to ground operation because convection in the fluid was negligible. Electrophoresis of the polystyrene latex particle groups according to size was accomplished although electro-osmosis in the flight apparatus prevented the clear separation of two particle bands.

Publications - PIR 2002-3 | Alaska Division of Geological & Geophysical

Science.gov Websites

): Philip Smith Mountains Bibliographic Reference Stevens, D.S.P., 2014, Engineering-geologic map of the Digital Geospatial Data Philip Smith Mountains: Engineering-geologic map Data File Format File Size Info

Geologic map of the Khanneshin carbonatite complex, Helmand Province, Afghanistan, modified from the 1976 original map compilation of V.G. Cheremytsin

USGS Publications Warehouse

Tucker, Robert D.; Peters, Stephen G.; Schulz, Klaus J.; Renaud, Karine M.; Stettner, Will R.; Masonic, Linda M.; Packard, Patricia H.

2011-01-01

This map is a modified version of the Geological map of the Khanneshin carbonatite complex, scale 1:10,000, which was compiled by V.G. Cheremytsin in 1976. Scientists from the U.S. Geological Survey, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original map and also visited the field area in September 2009, August 2010, and February 2011. This modified map, which includes cross sections, illustrates the geologic structure of the Khanneshin carbonatite complex. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and cross sections and includes modifications based on our examination of that map and a related report, and based on observations made during our field visits. (Refer to the References section in the Map PDF for complete citations of the original map and related report.) Elevations on the cross section are derived from the original Soviet topography and may not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map. The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

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.

A general number-to-space mapping deficit in developmental dyscalculia.

PubMed

Huber, S; Sury, D; Moeller, K; Rubinsten, O; Nuerk, H-C

2015-01-01

Previous research on developmental dyscalculia (DD) suggested that deficits in the number line estimation task are related to a failure to represent number magnitude linearly. This conclusion was derived from the observation of logarithmically shaped estimation patterns. However, recent research questioned this idea of an isomorphic relationship between estimation patterns and number magnitude representation. In the present study, we evaluated an alternative hypothesis: impairments in the number line estimation task are due to a general deficit in mapping numbers onto space. Adults with DD and a matched control group had to learn linear and non-linear layouts of the number line via feedback. Afterwards, we assessed their performance how well they learnt the new number-space mappings. We found irrespective of the layouts worse performance of adults with DD. Additionally, in case of the linear layout, we observed that their performance did not differ from controls near reference points, but that differences between groups increased as the distance to reference point increased. We conclude that worse performance of adults with DD in the number line task might be due a deficit in mapping numbers onto space which can be partly overcome relying on reference points. Copyright © 2015 Elsevier Ltd. All rights reserved.

Precision Thickness Variation Mapping Via One-Transducer Ultrasonic High Resolution Profilometry for Sample With Irregular or Rough Surface

NASA Technical Reports Server (NTRS)

Roth, Don J. (Inventor)

1996-01-01

An apparatus and method for determination of sample thickness and surface depression utilizing ultrasonic pulses is discussed. The sample is held in a predetermined position by a support member having a reference surface. Ultrasonic pulses travel through a medium of known velocity propagation and reflect off the reference surface and a sample surface. Time of flight data of surface echoes are converted to distances between sample surfaces to obtain computer-generated thickness profiles and surface mappings.

A two-dimensional proteome reference map of Herbaspirillum seropedicae proteins.

PubMed

Chaves, Daniela Fojo Seixas; Ferrer, Pércio Pereira; de Souza, Emanuel Maltempi; Gruz, Leonardo Magalhães; Monteiro, Rose Adele; de Oliveira Pedrosa, Fábio

2007-10-01

Herbaspirillum seropedicae is an endophytic diazotroph associated with economically important crops such as rice, sugarcane, and wheat. Here, we present a 2-D reference map for H. seropedicae. Using MALDI-TOF-MS we identified 205 spots representing 173 different proteins with a calculated average of 1.18 proteins/gene. Seventeen hypothetical or conserved hypothetical ORFs were shown to code for true gene products. These data will support the genome annotation process and provide a basis on which to undertake comparative proteomic studies.

Using Gel Electrophoresis To Illustrate Protein Diversity and Isoelectric Point.

ERIC Educational Resources Information Center

Browning, Mark; Vanable, Joseph

2002-01-01

Demonstrates the differences in protein structures by focusing on isoelectric point with an experiment that is observable under certain pH levels in gel electrophoresis. Explains the electrophoresis procedure and reports results of the experiments. (YDS)

Physical mapping of the Gorlin syndrome region on 9q22 by pulsed field gel electrophoresis (PFGE) and FISH

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

Levanat, S.; Gailani, M.; Dean, M.

1994-09-01

Gorlin syndrome is an autosomal dominant disorder characterized by basal cell carcinomas, medulloblastomas, and ovarian fibromas, as well as widespread developmental defects. Linkage and tumor deletion studies localized the gene for this syndrome to the 3 cM region on chromosome 9q22 between D9S196 and D9S180. Several groups have constructed YAC contigs of this region, but many of the YACs are known to contain rearrangements. Mapping by PGE and FISH is useful in further characterization of the relationship between physical distance and genetic distance. We isolated seven cosmids mapping to this region (D9S180, D9S196, D9S287, Col 15A1, XPA and two newmore » anonymous cosmids). FISH gave a distance between D9S196 and D9S180 of at least 2 Mb and showed that Col15A1, previously considered as a candidate gene, mapped a few hundred kb distal to S180. For PFGE, DNA blocks from normal and 20 Gorlin syndrome patients were digested with 5 restriction enzymes and probed with single copy fragments of the seven cosmids. No aberrant bands have been identified in patients. Non-overlapping Not I fragments from these seven markers totalled 2.3 kb. Given an average gene density, a region of this size would contain 50-100 genes.« less

Quantitative evaluation of protein conformation in pharmaceuticals using cross-linking reactions coupled with LC-MS/MS analysis.

PubMed

Yamaguchi, Hideto; Hirakura, Yutaka; Shirai, Hiroki; Mimura, Hisashi; Toyo'oka, Toshimasa

2011-06-01

The need for a simple and high-throughput method for identifying the tertiary structure of protein pharmaceuticals has increased. In this study, a simple method for mapping the protein fold is proposed for use as a complementary quality test. This method is based on cross-linking a protein using a [bis(sulfosuccinimidyl)suberate (BS(3))], followed by peptide mapping by LC-MS. Consensus interferon (CIFN) was used as the model protein. The tryptic map obtained via liquid chromatography tandem mass spectroscopy (LC-MS/MS) and the mass mapping obtained via matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy were used to identify cross-linked peptides. While LC-MS/MS analyses found that BS(3) formed cross-links in the loop region of the protein, which was regarded as the biologically active site, sodium dodecyl-sulfate polyacrylamide gel electrophoresis demonstrated that cross-linking occurred within a protein molecule, but not between protein molecules. The occurrence of cross-links at the active site depends greatly on the conformation of the protein, which is determined by the denaturing conditions. Quantitative evaluation of the tertiary structure of CIFN was thus possible by monitoring the amounts of cross-linked peptides generated. Assuming that background information is available at the development stage, this method may be applicable to process development as a complementary test for quality control. Copyright © 2011 Elsevier B.V. All rights reserved.

[Relationship between reference values of fibrinogen and geographical factors based on neural network analysis].

PubMed

Li, Meng-Jiao; Ge, Miao; Wang, Cong-Xia; Cen, Min-Yi; Jiang, Ji-Lin; He, Jin-Wei; Lin, Qian-Yi; Liu, Xin

2016-08-20

To analyze the relationship between the reference values of fibrinogen (FIB) in healthy Chinese adults and geographical factors to provide scientific evidences for establishing the uniform standard. The reference values of FIB of 10701 Chinese healthy adults from 103 cities were collected to investigate their relationship with 18 geographical factors including spatial index, terrain index, climate index, and soil index. Geographical factors that significantly correlated with the reference values were selected for constructing the BP neural network model. The spatial distribution map of the reference value of FIB of healthy Chinese adults was fitted by disjunctive kriging interpolation. We used the 5-layer neural network and selected 2000 times of training covering 11 hidden layers to build the simulation rule for simulating the relationship between FIB and geographical environmental factors using the MATLAB software. s The reference value of FIB in healthy Chinese adults was significantly correlated with the latitude, sunshine duration, annual average temperature, annual average relative humidity, annual precipitation, annual range of air temperature, average annual soil gravel content, and soil cation exchange capacity (silt). The artificial neural networks were created to analyze the simulation of the selected indicators of geographical factors. The spatial distribution map of the reference values of FIB in healthy Chinese adults showed a distribution pattern that FIB levels were higher in the South and lower in the North, and higher in the East and lower in the West. When the geographical factors of a certain area are known, the reference values of FIB in healthy Chinese adults can be obtained by establishing the neural network mode or plotting the spatial distribution map.

Genotype Imputation for Latinos Using the HapMap and 1000 Genomes Project Reference Panels.

PubMed

Gao, Xiaoyi; Haritunians, Talin; Marjoram, Paul; McKean-Cowdin, Roberta; Torres, Mina; Taylor, Kent D; Rotter, Jerome I; Gauderman, William J; Varma, Rohit

2012-01-01

Genotype imputation is a vital tool in genome-wide association studies (GWAS) and meta-analyses of multiple GWAS results. Imputation enables researchers to increase genomic coverage and to pool data generated using different genotyping platforms. HapMap samples are often employed as the reference panel. More recently, the 1000 Genomes Project resource is becoming the primary source for reference panels. Multiple GWAS and meta-analyses are targeting Latinos, the most populous, and fastest growing minority group in the US. However, genotype imputation resources for Latinos are rather limited compared to individuals of European ancestry at present, largely because of the lack of good reference data. One choice of reference panel for Latinos is one derived from the population of Mexican individuals in Los Angeles contained in the HapMap Phase 3 project and the 1000 Genomes Project. However, a detailed evaluation of the quality of the imputed genotypes derived from the public reference panels has not yet been reported. Using simulation studies, the Illumina OmniExpress GWAS data from the Los Angles Latino Eye Study and the MACH software package, we evaluated the accuracy of genotype imputation in Latinos. Our results show that the 1000 Genomes Project AMR + CEU + YRI reference panel provides the highest imputation accuracy for Latinos, and that also including Asian samples in the panel can reduce imputation accuracy. We also provide the imputation accuracy for each autosomal chromosome using the 1000 Genomes Project panel for Latinos. Our results serve as a guide to future imputation based analysis in Latinos.

Regional Lung Ventilation Analysis Using Temporally Resolved Magnetic Resonance Imaging.

PubMed

Kolb, Christoph; Wetscherek, Andreas; Buzan, Maria Teodora; Werner, René; Rank, Christopher M; Kachelrie, Marc; Kreuter, Michael; Dinkel, Julien; Heuel, Claus Peter; Maier-Hein, Klaus

We propose a computer-aided method for regional ventilation analysis and observation of lung diseases in temporally resolved magnetic resonance imaging (4D MRI). A shape model-based segmentation and registration workflow was used to create an atlas-derived reference system in which regional tissue motion can be quantified and multimodal image data can be compared regionally. Model-based temporal registration of the lung surfaces in 4D MRI data was compared with the registration of 4D computed tomography (CT) images. A ventilation analysis was performed on 4D MR images of patients with lung fibrosis; 4D MR ventilation maps were compared with corresponding diagnostic 3D CT images of the patients and 4D CT maps of subjects without impaired lung function (serving as reference). Comparison between the computed patient-specific 4D MR regional ventilation maps and diagnostic CT images shows good correlation in conspicuous regions. Comparison to 4D CT-derived ventilation maps supports the plausibility of the 4D MR maps. Dynamic MRI-based flow-volume loops and spirograms further visualize the free-breathing behavior. The proposed methods allow for 4D MR-based regional analysis of tissue dynamics and ventilation in spontaneous breathing and comparison of patient data. The proposed atlas-based reference coordinate system provides an automated manner of annotating and comparing multimodal lung image data.

Accuracy assessment of NOAA's daily reference evapotranspiration maps for the Texas High Plains

USDA-ARS?s Scientific Manuscript database

The National Oceanic and Atmospheric Administration (NOAA) provides daily reference ET for the continental U.S. using climatic data from North American Land Data Assimilation System (NLDAS). This data provides large scale spatial representation for reference ET, which is essential for regional scal...

Getting the Most out of Electrophoresis Units

ERIC Educational Resources Information Center

Mulvihill, Charlotte

2007-01-01

At Oklahoma City Community College, they have developed gel electrophoresis activities that support active learning of many scientific concepts, including: pH, electrolysis, oxidation reduction, electrical currents, potentials, conductivity, molarity, gel electrophoresis, DNA and protein separation, and DNA fingerprinting. This article presents…

Electrophoresis of biological materials

NASA Technical Reports Server (NTRS)

1975-01-01

The selection of biological products was studied for electrophoresis in space. Free flow electrophoresis, isoelectric focusing, and isotachophoresis are described. The candidates discussed include: immunoglobulins and gamma globulins; isolated islet of langerhans from pancreas; bone marrow; tumor cells; kidney cells, cryoprecipitate; and column separated cultures.

Chapter 8 - Mapping existing vegetation composition and structure for the LANDFIRE Prototype Project

Treesearch

Zhiliang Zhu; James Vogelmann; Donald Ohlen; Jay Kost; Xuexia Chen; Brian Tolk

2006-01-01

The Landscape Fire and Resource Management Planning Tools Prototype Project, or LANDFIRE Prototype Project, required the mapping of existing vegetation composition (cover type) and structural stages at a 30-m spatial resolution to provide baseline vegetation data for the development of wildland fuel maps and for comparison to simulated historical vegetation reference...

43 CFR 3931.60 - Maps of underground and surface mine workings and in situ surface operations.

Code of Federal Regulations, 2011 CFR

2011-10-01

... workings and in situ surface operations. 3931.60 Section 3931.60 Public Lands: Interior Regulations....60 Maps of underground and surface mine workings and in situ surface operations. Maps of underground... reference to sea level. When required by the BLM, include vertical projections and cross sections in plan...

RF-Based Location Using Interpolation Functions to Reduce Fingerprint Mapping

PubMed Central

Ezpeleta, Santiago; Claver, José M.; Pérez-Solano, Juan J.; Martí, José V.

2015-01-01

Indoor RF-based localization using fingerprint mapping requires an initial training step, which represents a time consuming process. This location methodology needs a database conformed with RSSI (Radio Signal Strength Indicator) measures from the communication transceivers taken at specific locations within the localization area. But, the real world localization environment is dynamic and it is necessary to rebuild the fingerprint database when some environmental changes are made. This paper explores the use of different interpolation functions to complete the fingerprint mapping needed to achieve the sought accuracy, thereby reducing the effort in the training step. Also, different distributions of test maps and reference points have been evaluated, showing the validity of this proposal and necessary trade-offs. Results reported show that the same or similar localization accuracy can be achieved even when only 50% of the initial fingerprint reference points are taken. PMID:26516862

Cell wall proteome analysis of Mycobacterium smegmatis strain MC2 155

PubMed Central

2010-01-01

Background The usually non-pathogenic soil bacterium Mycobacterium smegmatis is commonly used as a model mycobacterial organism because it is fast growing and shares many features with pathogenic mycobacteria. Proteomic studies of M. smegmatis can shed light on mechanisms of mycobacterial growth, complex lipid metabolism, interactions with the bacterial environment and provide a tractable system for antimycobacterial drug development. The cell wall proteins are particularly interesting in this respect. The aim of this study was to construct a reference protein map for these proteins in M. smegmatis. Results A proteomic analysis approach, based on one dimensional polyacrylamide gel electrophoresis and LC-MS/MS, was used to identify and characterize the cell wall associated proteins of M. smegmatis. An enzymatic cell surface shaving method was used to determine the surface-exposed proteins. As a result, a total of 390 cell wall proteins and 63 surface-exposed proteins were identified. Further analysis of the 390 cell wall proteins provided the theoretical molecular mass and pI distributions and determined that 26 proteins are shared with the surface-exposed proteome. Detailed information about functional classification, signal peptides and number of transmembrane domains are given next to discussing the identified transcriptional regulators, transport proteins and the proteins involved in lipid metabolism and cell division. Conclusion In short, a comprehensive profile of the M. smegmatis cell wall subproteome is reported. The current research may help the identification of some valuable vaccine and drug target candidates and provide foundation for the future design of preventive, diagnostic, and therapeutic strategies against mycobacterial diseases. PMID:20412585

Proteomic analysis of chromoplasts from six crop species reveals insights into chromoplast function and development.

PubMed

Wang, Yong-Qiang; Yang, Yong; Fei, Zhangjun; Yuan, Hui; Fish, Tara; Thannhauser, Theodore W; Mazourek, Michael; Kochian, Leon V; Wang, Xiaowu; Li, Li

2013-02-01

Chromoplasts are unique plastids that accumulate massive amounts of carotenoids. To gain a general and comparative characterization of chromoplast proteins, this study performed proteomic analysis of chromoplasts from six carotenoid-rich crops: watermelon, tomato, carrot, orange cauliflower, red papaya, and red bell pepper. Stromal and membrane proteins of chromoplasts were separated by 1D gel electrophoresis and analysed using nLC-MS/MS. A total of 953-2262 proteins from chromoplasts of different crop species were identified. Approximately 60% of the identified proteins were predicted to be plastid localized. Functional classification using MapMan bins revealed large numbers of proteins involved in protein metabolism, transport, amino acid metabolism, lipid metabolism, and redox in chromoplasts from all six species. Seventeen core carotenoid metabolic enzymes were identified. Phytoene synthase, phytoene desaturase, ζ-carotene desaturase, 9-cis-epoxycarotenoid dioxygenase, and carotenoid cleavage dioxygenase 1 were found in almost all crops, suggesting relative abundance of them among the carotenoid pathway enzymes. Chromoplasts from different crops contained abundant amounts of ATP synthase and adenine nucleotide translocator, which indicates an important role of ATP production and transport in chromoplast development. Distinctive abundant proteins were observed in chromoplast from different crops, including capsanthin/capsorubin synthase and fibrillins in pepper, superoxide dismutase in watermelon, carrot, and cauliflower, and glutathione-S-transferease in papaya. The comparative analysis of chromoplast proteins among six crop species offers new insights into the general metabolism and function of chromoplasts as well as the uniqueness of chromoplasts in specific crop species. This work provides reference datasets for future experimental study of chromoplast biogenesis, development, and regulation in plants.

Near-infrared laser-induced fluorescence detection in capillary electrophoresis.

PubMed

McWhorter, S; Soper, S A

2000-04-01

As capillary electrophoresis continues to focus on miniaturization, either through reducing column dimensions or situating entire electrophoresis systems on planar chips, advances in detection become necessary to meet the challenges posed by these electrophoresis platforms. The challenges result from the fact that miniaturization requires smaller load volumes, demanding highly sensitive detection. In addition, many times multiple targets must be analyzed simultaneously (multiplexed applications), further complicating detection. Near-infrared (NIR) fluorescence offers an attractive alternative to visible fluorescence for critical applications in capillary electrophoresis due to the impressive limits of detection that can be generated, in part resulting from the low background levels that are observed in the NIR. Advances in instrumentation and fluorogenic labels appropriate for NIR monitoring have led to a growing number of examples of the use of NIR fluorescence in capillary electrophoresis. In this review, we will cover instrumental components used to construct ultrasensitive NIR fluorescence detectors, including light sources and photon transducers. In addition, we will discuss various types of labeling dyes appropriate for NIR fluorescence and finally, we will present several applications that have used NIR fluorescence in capillary electrophoresis, especially for DNA sequencing and fragment analysis.

HIA: a genome mapper using hybrid index-based sequence alignment.

PubMed

Choi, Jongpill; Park, Kiejung; Cho, Seong Beom; Chung, Myungguen

2015-01-01

A number of alignment tools have been developed to align sequencing reads to the human reference genome. The scale of information from next-generation sequencing (NGS) experiments, however, is increasing rapidly. Recent studies based on NGS technology have routinely produced exome or whole-genome sequences from several hundreds or thousands of samples. To accommodate the increasing need of analyzing very large NGS data sets, it is necessary to develop faster, more sensitive and accurate mapping tools. HIA uses two indices, a hash table index and a suffix array index. The hash table performs direct lookup of a q-gram, and the suffix array performs very fast lookup of variable-length strings by exploiting binary search. We observed that combining hash table and suffix array (hybrid index) is much faster than the suffix array method for finding a substring in the reference sequence. Here, we defined the matching region (MR) is a longest common substring between a reference and a read. And, we also defined the candidate alignment regions (CARs) as a list of MRs that is close to each other. The hybrid index is used to find candidate alignment regions (CARs) between a reference and a read. We found that aligning only the unmatched regions in the CAR is much faster than aligning the whole CAR. In benchmark analysis, HIA outperformed in mapping speed compared with the other aligners, without significant loss of mapping accuracy. Our experiments show that the hybrid of hash table and suffix array is useful in terms of speed for mapping NGS sequencing reads to the human reference genome sequence. In conclusion, our tool is appropriate for aligning massive data sets generated by NGS sequencing.

Fusion of Location Fingerprinting and Trilateration Based on the Example of Differential Wi-Fi Positioning

NASA Astrophysics Data System (ADS)

Retscher, G.

2017-09-01

Positioning of mobile users in indoor environments with Wireless Fidelity (Wi-Fi) has become very popular whereby location fingerprinting and trilateration are the most commonly employed methods. In both the received signal strength (RSS) of the surrounding access points (APs) are scanned and used to estimate the user's position. Within the scope of this study the advantageous qualities of both methods are identified and selected to benefit their combination. By a fusion of these technologies a higher performance for Wi-Fi positioning is achievable. For that purpose, a novel approach based on the well-known Differential GPS (DGPS) principle of operation is developed and applied. This approach for user localization and tracking is termed Differential Wi-Fi (DWi-Fi) by analogy with DGPS. From reference stations deployed in the area of interest differential measurement corrections are derived and applied at the mobile user side. Hence, range or coordinate corrections can be estimated from a network of reference station observations as it is done in common CORS GNSS networks. A low-cost realization with Raspberry Pi units is employed for these reference stations. These units serve at the same time as APs broadcasting Wi-Fi signals as well as reference stations scanning the receivable Wi-Fi signals of the surrounding APs. As the RSS measurements are carried out continuously at the reference stations dynamically changing maps of RSS distributions, so-called radio maps, are derived. Similar as in location fingerprinting this radio maps represent the RSS fingerprints at certain locations. From the areal modelling of the correction parameters in combination with the dynamically updated radio maps the location of the user can be estimated in real-time. The novel approach is presented and its performance demonstrated in this paper.

Construction of a general human chromosome jumping library, with application to cystic fibrosis

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

Collins, F.S.; Drumm, M.L.; Cole, J.L.

1987-02-27

In many genetic disorders, the responsible gene and its protein product are unknown. The technique known as reverse genetics, in which chromosomal map positions and genetically linked DNA markers are used to identify and clone such genes, is complicated by the fact that the molecular distances from the closest DNA markers to the gene itself are often too large to traverse by standard cloning techniques. To address this situation, a general human chromosome jumping library was constructed that allows the cloning of DNA sequences approximately 100 kilobases away from any starting point in genomic DNA. As an illustration of itsmore » usefulness, this library was searched for a jumping clone, starting at the met oncogene, which is a marker tightly linked to the cystic fibrosis gene that is located on human chromosome 7. Mapping of the new genomic fragment by pulsed field gel electrophoresis confirmed that it resides on chromosome 7 within 240 kilobases downstream of the met gene. The use of chromosome jumping should be applicable to any genetic locus for which a closely linked DNA marker is available.« less

Electrophoresis for genotyping: microtiter array diagonal gel electrophoresis on horizontal polyacrylamide gels, hydrolink, or agarose.

PubMed

Day, I N; Humphries, S E

1994-11-01

Electrophoresis of DNA has been performed traditionally in either an agarose or acrylamide gel matrix. Considerable effort has been directed to improved quality agaroses capable of high resolution, but for small fragments, such as those from polymerase chain reaction (PCR) and post-PCR digests, acrylamide still offers the highest resolution. Although agarose gels can easily be prepared in an open-faced format to gain the conveniences of horizontal electrophoresis, acrylamide does not polymerize in the presence of air and the usual configurations for gel preparation lead to electrophoresis in the vertical dimension. We describe here a very simple device and method to prepare and manipulate horizontal polyacrylamide gels (H-PAGE). In addition, the open-faced horizontal arrangement enables loading of arrays of wells. Since many procedures are undertaken in standard 96-well microtiter plates, we have also designed a device which preserves the exact configuration of the 8 x 12 array and enables electrophoresis in tracks following a 71.6 degrees diagonal between wells (MADGE, microtiter array diagonal gel electrophoresis), using either acrylamide or agarose. This eliminates almost all of the staff time taken in setup, loading, and recordkeeping and offers high resolution for genotyping pattern recognition. The nature and size of the gels allow direct stacking of gels in one tank, so that a tank used typically to analyze 30-60 samples can readily be used to analyze 1000-2000 samples. The gels would also enable robotic loading. Electrophoresis allows analysis of size and charge, parameters inaccessible to liquid-phase methods: thus, genotyping size patterns, variable length repeats, and haplotypes is possible, as well as adaptability to typing of point variations using protocols which create a difference detectable by electrophoresis.

Changes in muscle protein composition induced by disuse atrophy - Analysis by two-dimensional electrophoresis

NASA Technical Reports Server (NTRS)

Ellis, S.; Giometti, C. S.; Riley, D. A.

1985-01-01

Using 320 g rats, a two-dimensional electrophoretic analysis of muscle proteins in the soleus and EDL muscles from hindlimbs maintained load-free for 10 days is performed. Statistical analysis of the two-dimensional patterns of control and suspended groups reveals more protein alteration in the soleus muscle, with 25 protein differences, than the EDL muscle, with 9 protein differences, as a result of atrophy. Most of the soleus differences reside in minor components. It is suggested that the EDL may also show alteration in its two-dimensional protein map, even though no significant atrophy occurred in muscle wet weight. It is cautioned that strict interpretation of data must take into account possible endocrine perturbations.

Replicative Intermediates of Human Papillomavirus Type 11 in Laryngeal Papillomas: Site of Replication Initiation and Direction of Replication

NASA Astrophysics Data System (ADS)

Auborn, K. J.; Little, R. D.; Platt, T. H. K.; Vaccariello, M. A.; Schildkraut, C. L.

1994-07-01

We have examined the structures of replication intermediates from the human papillomavirus type 11 genome in DNA extracted from papilloma lesions (laryngeal papillomas). The sites of replication initiation and termination utilized in vivo were mapped by using neutral/neutral and neutral/alkaline two-dimensional agarose gel electrophoresis methods. Initiation of replication was detected in or very close to the upstream regulatory region (URR; the noncoding, regulatory sequences upstream of the open reading frames in the papillomavirus genome). We also show that replication forks proceed bidirectionally from the origin and converge 180circ opposite the URR. These results demonstrate the feasibility of analysis of replication of viral genomes directly from infected tissue.

Ink-native electrophoresis: an alternative to blue-native electrophoresis more suitable for in-gel detection of enzymatic activity.

PubMed

Kaneko, Keisuke; Sueyoshi, Noriyuki; Kameshita, Isamu; Ishida, Atsuhiko

2013-09-15

Blue-native electrophoresis (BNE) is a useful technique for analyzing protein complexes, but the Coomassie brilliant blue (CBB) dye used in BNE often hampers in-gel detection of enzymatic activity. Here we report an improved method, termed ink-native electrophoresis (INE), in which Pelikan 4001 fountain pen ink is used as a charge-shifting agent instead of CBB. INE is more suitable than BNE for in-gel detection of protein kinase activity after polyacrylamide gel electrophoresis (PAGE), and its performance in protein complex separation is comparable to that of conventional BNE. INE may provide a powerful tool to isolate and analyze various protein complexes. Copyright © 2013 Elsevier Inc. All rights reserved.

Development of bufferless gel electrophoresis chip for easy preparation and rapid DNA separation.

PubMed

Oleksandrov, Sergiy; Aman, Abdurazak; Lim, Wanyoung; Kim, Younghee; Bae, Nam Ho; Lee, Kyoung G; Lee, Seok Jae; Park, Sungsu

2018-02-01

This work presents a handy, fast, and compact bufferless gel electrophoresis chip (BGEC), which consists of precast agarose gel confined in a disposable plastic body with electrodes. It does not require large volumes of buffer to fill reservoirs, or the process of immersing the gel in the buffer. It withstands voltages up to 28.4 V/cm, thereby allowing DNA separation within 10 min with a similar separation capability to the standard gel electrophoresis. The results suggest that our BGEC is highly suitable for in situ gel electrophoresis in forensic, epidemiological settings and crime scenes where standard gel electrophoresis equipment cannot be brought in while quick results are needed. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Differential identification of Candida species and other yeasts by analysis of (/sup 35/S)methionine-labeled polypeptide profiles

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

Shen, H.D.; Choo, K.B.; Tsai, W.C.

1988-12-01

This paper describes a scheme for differential identification of Candida species and other yeasts based on autoradiographic analysis of protein profiles of (/sup 35/S)methionine-labeled cellular proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Using ATCC strains as references, protein profile analysis showed that different Candida and other yeast species produced distinctively different patterns. Good agreement in results obtained with this approach and with other conventional systems was observed. Being accurate and reproducible, this approach provides a basis for the development of an alternative method for the identification of yeasts isolated from clinical specimens.

Publications - GMC 262 | Alaska Division of Geological & Geophysical

Science.gov Websites

DGGS GMC 262 Publication Details Title: Map location and geological logs of core for 7 1991 diamond Reference Cominco American Inc., 1996, Map location and geological logs of core for 7 1991 diamond drill

Selecting PPE for the Workplace (Personal Protective Equipment for the Eyes and Face)

MedlinePlus

... Additional References Site Map Credits Selecting Personal Protective Equipment (PPE) for the Workplace Impact Heat Chemicals Dust Optical Radiation OSHA Requirements Home | Selecting Personal Protective Equipment (PPE) for the Workplace | OSHA Requirements Site Map | ...

Monitoring refolding of tailspike endorhamnosidase using capillary electrophoresis-laser induced tryptophan fluorescence

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

Jensen, P.K.; Lee, Cheng S.; King, J.A.

1997-12-31

The use of capillary electrophoresis equipped with laser-induced tryptophan fluorescence detection is presented for monitoring the refolding pathway of phage P22 tailspike endorhamnosidase. Upon initiation of refolding, tailspike polypeptides rapidly fold into structured monomeric intermediates with a high content of secondary structure. These monomeric species associate to form the triple-chain defined folding intermediates, the protrimers. Conversion of the protrimer into the native, sodium dodecyl sulfate (SDS) resistant tailspike protein is the rate-limiting step in the refolding pathway. Refolding kinetics and yield measured by capillary electrophoresis are in good agreement with those obtained via native gel electrophoresis, SDS polyacrylamide gel electrophoresismore » (SDS-PAGE) and fluorescence spectrophotometry. To enhance separation resolution between protrimer and native protein in capillary electrophoresis, the use of poly(ethylene oxide) is investigated for the introduction of a sieving separation mechanism. The increased viscosity of the electrophoresis buffer may also play a role in resolution enhancement.« less

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

PubMed

Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

2010-09-01

The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.

Geologic map of the western Haji-Gak iron deposit, Bamyan Province, Afghanistan, modified from the 1965 original map compilation of V.V. Reshetniak and I.K. Kusov

USGS Publications Warehouse

Renaud, Karine M.; Tucker, Robert D.; Peters, Stephen G.; Stettner, Will R.; Masonic, Linda M.; Moran, Thomas W.

2011-01-01

This map is a modified version of Geologic-prospecting plan of western area of Hajigak iron-ore deposit, scale 1:2,000, which was compiled by V.V. Reshetniak and I.K. Kusov in 1965. (Refer to the References Cited section in the Map PDF for complete citations of the original map and related reports.) USGS scientists, in cooperation with the Afghan Geological Survey and the Task Force for Business and Stability Operations of the U.S. Department of Defense, studied the original documents and also visited the field area in November 2009. This modified map illustrates the geological structure of the western Haji-Gak iron deposit and includes cross sections of the same area. The map reproduces the topology (contacts, faults, and so forth) of the original Soviet map and includes modifications based on our examination of that document. We constructed the cross sections from data derived from the original map. Elevations on the cross sections are derived from the original Soviet topography and may not match the newer topography used on the current map. We have attempted to translate the original Russian terminology and rock classification into modern English geologic usage as literally as possible without changing any genetic or process-oriented implications in the original descriptions. We also use the age designations from the original map. The unit colors on the map and cross sections differ from the colors shown on the original version. The units are colored according to the color and pattern scheme of the Commission for the Geological Map of the World (CGMW) (http://www.ccgm.org).

Electric field-mediated transport of plasmid DNA in tumor interstitium in vivo.

PubMed

Henshaw, Joshua W; Zaharoff, David A; Mossop, Brian J; Yuan, Fan

2007-11-01

Local pulsed electric field application is a method for improving non-viral gene delivery. Mechanisms of the improvement include electroporation and electrophoresis. To understand how electrophoresis affects pDNA delivery in vivo, we quantified the magnitude of electric field-induced interstitial transport of pDNA in 4T1 and B16.F10 tumors implanted in mouse dorsal skin-fold chambers. Four different electric pulse sequences were used in this study, each consisted of 10 identical pulses that were 100 or 400 V/cm in strength and 20 or 50 ms in duration. The interval between consecutive pulses was 1 s. The largest distance of transport was obtained with the 400 V/cm and 50 ms pulse, and was 0.23 and 0.22 microm/pulse in 4T1 and B16.F10 tumors, respectively. There were no significant differences in transport distances between 4T1 and B16.F10 tumors. Results from in vivo mapping and numerical simulations revealed an approximately uniform intratumoral electric field that was predominantly in the direction of the applied field. The data in the study suggested that interstitial transport of pDNA induced by a sequence of ten electric pulses was ineffective for macroscopic delivery of genes in tumors. However, the induced transport was more efficient than passive diffusion.

Growth hormone-releasing hormone stimulates and somatostatin inhibits the release of a novel protein by cultured rat pituitary cells.

PubMed

Tachibana, K; Marquardt, H; Yokoya, S; Friesen, H G

1988-10-01

We have reported that the secretion of at least 17 distinct peptides [including rat (rGH)] GH by cultured rat pituitary cells was stimulated by GH-releasing hormone and inhibited by somatostatin, when analyzed by two-dimensional polyacrylamide gel electrophoresis. Three of these peptides (no. 23, 24, and 25) were not rGH immunoreactive. In order to determine whether these three peptides are fragments, degradation products or posttranscriptionally modified forms of rGH, rGH and peptide no. 23 were characterized structurally. From partial peptide maps of rGH and peptide no. 23 by V8 protease or chymotrypsin, it appeared that these peptides were not related to each other. By N-terminal microsequencing of two-dimensional polyacrylamide gel electrophoresis purified peptide, we have obtained the sequence of 24 N-terminal amino acid residues of peptide no. 23. This sequence has no significant homology with rGH or any other reported protein sequence. Antiserum was generated against a synthetic oligopeptide corresponding to amino acid residues 3-24 of peptide no. 23. The antiserum cross-reacted with peptides no. 23, 24, and 25 upon Western blot analysis. These results indicate that peptide no. 23 has a novel structure unrelated to other pituitary hormones. Since its secretion is influenced by GH-releasing hormone and somatostatin, peptide no. 23 may represent a previously unrecognized structurally unique growth factor.

Protein expression profiles of human lymph and plasma mapped by 2D-DIGE and 1D SDS–PAGE coupled with nanoLC–ESI–MS/MS bottom-up proteomics

PubMed Central

Clement, Cristina C.; Aphkhazava, David; Nieves, Edward; Callaway, Myrasol; Olszewski, Waldemar; Rotzschke, Olaf; Santambrogio, Laura

2013-01-01

In this study a proteomic approach was used to define the protein content of matched samples of afferent prenodal lymph and plasma derived from healthy volunteers. The analysis was performed using two analytical methodologies coupled with nanoliquid chromatography-tandem mass spectrometry: one-dimensional gel electrophoresis (1DEF nanoLC Orbitrap–ESI–MS/MS), and two-dimensional fluorescence difference-in-gel electrophoresis (2D-DIGE nanoLC–ESI–MS/MS). The 253 significantly identified proteins (p<0.05), obtained from the tandem mass spectrometry data, were further analyzed with pathway analysis (IPA) to define the functional signature of prenodal lymph and matched plasma. The 1DEF coupled with nanoLC–MS–MS revealed that the common proteome between the two biological fluids (144 out of 253 proteins) was dominated by complement activation and blood coagulation components, transporters and protease inhibitors. The enriched proteome of human lymph (72 proteins) consisted of products derived from the extracellular matrix, apoptosis and cellular catabolism. In contrast, the enriched proteome of human plasma (37 proteins) consisted of soluble molecules of the coagulation system and cell–cell signaling factors. The functional networks associated with both common and source-distinctive proteomes highlight the principal biological activity of these immunologically relevant body fluids. PMID:23202415

Measurement of myocardial native T1 in cardiovascular diseases and norm in 1291 subjects.

PubMed

Liu, Joanna M; Liu, Alexander; Leal, Joana; McMillan, Fiona; Francis, Jane; Greiser, Andreas; Rider, Oliver J; Myerson, Saul; Neubauer, Stefan; Ferreira, Vanessa M; Piechnik, Stefan K

2017-09-28

Native T1-mapping provides quantitative myocardial tissue characterization for cardiovascular diseases (CVD), without the need for gadolinium. However, its translation into clinical practice is hindered by differences between techniques and the lack of established reference values. We provide typical myocardial T1-ranges for 18 commonly encountered CVDs using a single T1-mapping technique - Shortened Look-Locker Inversion Recovery (ShMOLLI), also used in the large UK Biobank and Hypertrophic Cardiomyopathy Registry study. We analyzed 1291 subjects who underwent CMR (1.5-Tesla, MAGNETOM-Avanto, Siemens Healthcare, Erlangen, Germany) between 2009 and 2016, who had a single CVD diagnosis, with mid-ventricular T1-map assessment. A region of interest (ROI) was placed on native T1-maps in the "most-affected myocardium", characterized by the presence of late gadolinium enhancement (LGE), or regional wall motion abnormalities (RWMA) on cines. Another ROI was placed in the "reference myocardium" as far as possible from LGE/RWMA, and in the septum if no focal abnormality was present. To further define normality, we included native T1 of healthy subjects from an existing dataset after sub-endocardial pixel-erosions. Native T1 of patients with normal CMR (938 ± 21 ms) was similar compared to healthy subjects (941 ± 23 ms). Across all patient groups (57 ± 19 yrs., 65% males), focally affected myocardium had significantly different T1 value compared to reference myocardium (all p < 0.001). In the affected myocardium, cardiac amyloidosis (1119 ± 61 ms) had the highest native T1 compared to normal and all other CVDs, while iron-overload (795 ± 58 ms) and Anderson-Fabry disease (863 ± 23 ms) had the lowest native reference T1 (all p < 0.001). Future studies designed to detect the large T1 differences between affected and reference myocardium are estimated to require small sample-sizes (n < 50). However, studies designed to detect the small T1 differences between reference myocardium in CVDs and healthy controls can require several thousand of subjects. We provide typical T1-ranges for common clinical cardiac conditions in the largest cohort to-date, using ShMOLLI T1-mapping at 1.5 T. Sample-size calculations from this study may be useful for the design of future studies and trials that use T1-mapping as an endpoint.

Loess in Europe—its spatial distribution based on a European Loess Map, scale 1:2,500,000

NASA Astrophysics Data System (ADS)

Haase, D.; Fink, J.; Haase, G.; Ruske, R.; Pécsi, M.; Richter, H.; Altermann, M.; Jäger, K.-D.

2007-05-01

The paper focuses on the concept, mapping and discussion of loess distribution in Western, Central and Eastern Europe at a scale of 1:2,500,000. The research work is based on studies and data compilation primarily carried out in the 1970s and 1980s [Fink, J., Haase, G., Ruske, R., 1977. Bemerkungen zur Lößkarte von Europe 1:2,5 Mio. Petermanns Geographische Mitteilungen 2(77), 81-94; Fink, J., 1969 Les progres de l' etude de loess en Europe. Bulletin de l' Association française pour l' etude du Quarternaire 3-12. Haase, G., Ruske, R., Fink, J., 1983. Conception, preparation and some results of the Loess Map of Europe on a scale 1:2,5 Million. INQUA Newsletter 1983(1), 7-10] and completed recently by additional material and literature references. Reference is also made to recent GIS-based data processing and visualisation techniques that were utilised for the final version of the European Loess Map. The paper provides an overview of the history of the conceptualisation of the map as well as on the loess study in Europe, and than considers the cartographic data on loess sediment formation and distribution in Europe. The classification of loess and loess-like sediments and their distribution throughout Europe as reproduced in the map are discussed [Haase, G., Lieberoth, I., Ruske, R., 1970. Sedimente und Paläoböden im Lössgürtel. In: Richter, H., Haase, G., Lieberoth, I., Ruske, R. (Eds.), Periglazial-Löß-Paläolithikum om JUngpleistozän der Deutschen Demokratischen Republik; Petermanns Geographische Mitteilungen 274, 99-212]. The paper illustrates the final state of the loess distribution map of Europe at a scale of 1:2,500,000 and the digital data references on which it is based. Some applications of the map are suggested.

Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY

PubMed Central

2012-01-01

Background Chemical shift mapping is an important technique in NMR-based drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule's introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically, which is not efficient for high-throughput drug screening. Results We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C-labeling, to resolve the ambiguities for a one-to-one mapping. On the three proteins, it achieves an average accuracy of 94% or better. Conclusions Our mathematical programming approach for modeling chemical shift mapping as a graph problem, while modeling the errors directly, is potentially a time- and cost-effective first step for high-throughput drug screening based on limited NMR data and homologous 3D structures. PMID:22536902

A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases.

PubMed

Jain, Chirag; Dilthey, Alexander; Koren, Sergey; Aluru, Srinivas; Phillippy, Adam M

2018-04-30

Emerging single-molecule sequencing technologies from Pacific Biosciences and Oxford Nanopore have revived interest in long-read mapping algorithms. Alignment-based seed-and-extend methods demonstrate good accuracy, but face limited scalability, while faster alignment-free methods typically trade decreased precision for efficiency. In this article, we combine a fast approximate read mapping algorithm based on minimizers with a novel MinHash identity estimation technique to achieve both scalability and precision. In contrast to prior methods, we develop a mathematical framework that defines the types of mapping targets we uncover, establish probabilistic estimates of p-value and sensitivity, and demonstrate tolerance for alignment error rates up to 20%. With this framework, our algorithm automatically adapts to different minimum length and identity requirements and provides both positional and identity estimates for each mapping reported. For mapping human PacBio reads to the hg38 reference, our method is 290 × faster than Burrows-Wheeler Aligner-MEM with a lower memory footprint and recall rate of 96%. We further demonstrate the scalability of our method by mapping noisy PacBio reads (each ≥5 kbp in length) to the complete NCBI RefSeq database containing 838 Gbp of sequence and >60,000 genomes.

Monoclonal protein reference change value as determined by gel-based serum protein electrophoresis.

PubMed

Salamatmanesh, Mina; McCudden, Christopher R; McCurdy, Arleigh; Booth, Ronald A

2018-01-01

The International Myeloma Working Group recommendations for monitoring disease progression or response include quantitation of the involved monoclonal immunoglobulin. They have defined the minimum change criteria of ≧25% with an absolute change of no <5g/L for either minimal response or progression. Limited evidence is available to accurately determine the magnitude of change in a monoclonal protein to reflect a true change in clinical status. Here we determined the analytical and biological variability of monoclonal proteins in stable monoclonal gammopathy of undetermined significance (MGUS) patients. Analytical variability (CVa) of normal protein fractions and monoclonal proteins were assessed agarose gel-based serum protein electrophoresis. Sixteen clinically stable MGUS patients were identified from our clinical hematology database. Individual biological variability (CVi) was determined and used to calculate a monoclonal protein reference change value (RCV). Analytical variability of the normal protein fractions (albumin, alpha-1, alpha-2, beta, total gamma) ranged from 1.3% for albumin to 5.8% for the alpha-1 globulins. CVa of low (5.6g/L) and high (32.2g/L) concentration monoclonal proteins were 3.1% and 22.2%, respectively. Individual CVi of stable patients ranged from 3.5% to 24.5% with a CVi of 12.9%. The reference change value (RCV) at a 95% probability was determined to be 36.7% (low) 39.6% (high) using our CVa and CVi. Serial monitoring of monoclonal protein concentration is important for MGUS and multiple myeloma patients. Accurate criteria for interpreting a change in monoclonal protein concentration are required for appropriate decision making. We used QC results and real-world conditions to assess imprecision of serum protein fractions including low and high monoclonal protein fractions and clinically stable MGUS patients to determine CVi and RCV. The calculated RCVs of 36.7% (low) and 39.6% (high) in this study were greater that reported previously and greater than the established criteria for relapse. Response criteria may be reassessed to increase sensitivity and specificity for detection of response. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

The Role of Competition in Word Learning via Referent Selection

ERIC Educational Resources Information Center

Horst, Jessica S.; Scott, Emilly J.; Pollard, Jessica A.

2010-01-01

Previous research suggests that competition among the objects present during referent selection influences young children's ability to learn words in fast mapping tasks. The present study systematically explored this issue with 30-month-old children. Children first received referent selection trials with a target object and either two, three or…

Publications - SR 32 | Alaska Division of Geological & Geophysical Surveys

Science.gov Websites

DGGS SR 32 Publication Details Title: Oil and gas basins map of Alaska Authors: Ehm, Arlen Publication ): Alaska Statewide Bibliographic Reference Ehm, Arlen, 1983, Oil and gas basins map of Alaska: Alaska Sheets Sheet 1 Oil and gas basins map of Alaska, scale 1:2,500,000 (21.0 M) Keywords Alaska Statewide

A self-reference PRF-shift MR thermometry method utilizing the phase gradient

NASA Astrophysics Data System (ADS)

Langley, Jason; Potter, William; Phipps, Corey; Huang, Feng; Zhao, Qun

2011-12-01

In magnetic resonance (MR) imaging, the most widely used and accurate method for measuring temperature is based on the shift in proton resonance frequency (PRF). However, inter-scan motion and bulk magnetic field shifts can lead to inaccurate temperature measurements in the PRF-shift MR thermometry method. The self-reference PRF-shift MR thermometry method was introduced to overcome such problems by deriving a reference image from the heated or treated image, and approximates the reference phase map with low-order polynomial functions. In this note, a new approach is presented to calculate the baseline phase map in self-reference PRF-shift MR thermometry. The proposed method utilizes the phase gradient to remove the phase unwrapping step inherent to other self-reference PRF-shift MR thermometry methods. The performance of the proposed method was evaluated using numerical simulations with temperature distributions following a two-dimensional Gaussian function as well as phantom and in vivo experimental data sets. The results from both the numerical simulations and experimental data show that the proposed method is a promising technique for measuring temperature.

Compensating for Electro-Osmosis in Electrophoresis

NASA Technical Reports Server (NTRS)

Rhodes, Percy H.; Snyder, Robert S.

1987-01-01

Simple mechanical adjustment eliminates transverse velocity component. New apparatus for moving-wall electrophoresis increases degree of collimation of chemical species in sample stream. Electrophoresis chamber set at slight angle in horizontal plane to adjust angle between solution flow and wall motion. Component of velocity created cancels electro-osmotic effect.

Improved Electrophoresis Cell

NASA Technical Reports Server (NTRS)

Rhodes, P. H.; Snyder, R. S.

1982-01-01

Several proposed modifications are expected to improve performance of a continous-flow electrophoresis cell. Changes would allow better control of buffer flow and would increase resolution by suppressing thermal gradients. Improved electrophoresis device would have high resolution and be easy to operate. Improvements would allow better flow control and heat dissipation.

Scientists Develop Precision Maps for Other Planets

NASA Astrophysics Data System (ADS)

Kumar, Mohi

2013-03-01

Earth and planetary scientists are united by their need for accurate maps. Without them, features studied have no reference point, attempts to understand how our and other planets evolved have no context, and missions flown to other planets lack purpose. "Making maps out of data is critical to further progress in our fields," explained Randolph Kirk of the U.S. Geological Survey's (USGS) Astrogeology Science Center, based in Flagstaff, Ariz. "Building maps helps other people find what's out there."

An Example of Unsupervised Networks Kohonen's Self-Organizing Feature Map

NASA Technical Reports Server (NTRS)

Niebur, Dagmar

1995-01-01

Kohonen's self-organizing feature map belongs to a class of unsupervised artificial neural network commonly referred to as topographic maps. It serves two purposes, the quantization and dimensionality reduction of date. A short description of its history and its biological context is given. We show that the inherent classification properties of the feature map make it a suitable candidate for solving the classification task in power system areas like load forecasting, fault diagnosis and security assessment.

Database for the geologic map of upper Eocene to Holocene volcanic and related rocks in the Cascade Range, Washington

USGS Publications Warehouse

Barron, Andrew D.; Ramsey, David W.; Smith, James G.

2014-01-01

This digital database contains information used to produce the geologic map published as Sheet 1 in U.S. Geological Survey Miscellaneous Investigations Series Map I-2005. (Sheet 2 of Map I-2005 shows sources of geologic data used in the compilation and is available separately). Sheet 1 of Map I-2005 shows the distribution and relations of volcanic and related rock units in the Cascade Range of Washington at a scale of 1:500,000. This digital release is produced from stable materials originally compiled at 1:250,000 scale that were used to publish Sheet 1. The database therefore contains more detailed geologic information than is portrayed on Sheet 1. This is most noticeable in the database as expanded polygons of surficial units and the presence of additional strands of concealed faults. No stable compilation materials exist for Sheet 1 at 1:500,000 scale. The main component of this digital release is a spatial database prepared using geographic information systems (GIS) applications. This release also contains links to files to view or print the map sheet, main report text, and accompanying mapping reference sheet from Map I-2005. For more information on volcanoes in the Cascade Range in Washington, Oregon, or California, please refer to the U.S. Geological Survey Volcano Hazards Program website.

Map showing general availability of ground water in the Alton-Kolob coal-fields area, Utah

USGS Publications Warehouse

Price, Don

1982-01-01

This is one of a series of maps that describes the geology and related natural resources of the Alton-Kolob coal-fields area, Utah. Shown on this map is the general availability of ground water as indicated by potential yields of individual wells and expected depth to water in wells. Most data used to compile this map were collected by the U.S. Geological Survey in cooperation with the Utah Department of Natural Resources Division of Water Rights. Other sources of data included the U.S. Geological Survey 7½- and 15-minute topographic quadrangle maps, unpublished reports of field evaluations of potential shock-watering sites by U.S. Geological Survey personnel, and the geologic map of Utah (Stokes, 1964).This map is very generalized and is intended chiefly for planning purposes. It should be used with discretion. For more detailed information about the availability of ground water in various parts of the map area the reader is referred to the following reports: Thomas and Taylor (1946); Marine (1963); Sandberg (1963, 1966); Carpenter, Robinson, and Bjorklund (1964, 1967); Feltis (1966); Goode (1964, 1966); Cordova, Sandberg, and McConkie (1972); Cordova (1978, 1981); and Bjorklund, Sumison, and Sandberg (1977, 1978). For a general description of the chemical quality of ground water in the Alton-Kolob coal-fields area the reader is referred to Price (1981).

Large-Scale Development of Cost-Effective Single-Nucleotide Polymorphism Marker Assays for Genetic Mapping in Pigeonpea and Comparative Mapping in Legumes

PubMed Central

Saxena, Rachit K.; Varma Penmetsa, R.; Upadhyaya, Hari D.; Kumar, Ashish; Carrasquilla-Garcia, Noelia; Schlueter, Jessica A.; Farmer, Andrew; Whaley, Adam M.; Sarma, Birinchi K.; May, Gregory D.; Cook, Douglas R.; Varshney, Rajeev K.

2012-01-01

Single-nucleotide polymorphisms (SNPs, >2000) were discovered by using RNA-seq and allele-specific sequencing approaches in pigeonpea (Cajanus cajan). For making the SNP genotyping cost-effective, successful competitive allele-specific polymerase chain reaction (KASPar) assays were developed for 1616 SNPs and referred to as PKAMs (pigeonpea KASPar assay markers). Screening of PKAMs on 24 genotypes [23 from cultivated species and 1 wild species (Cajanus scarabaeoides)] defined a set of 1154 polymorphic markers (77.4%) with a polymorphism information content (PIC) value from 0.04 to 0.38. One thousand and ninety-four PKAMs showed polymorphisms between parental lines of the reference mapping population (C. cajan ICP 28 × C. scarabaeoides ICPW 94). By using high-quality marker genotyping data on 167 F2 lines from the population, a comprehensive genetic map comprising 875 PKAMs with an average inter-marker distance of 1.11 cM was developed. Previously mapped 35 simple sequence repeat markers were integrated into the PKAM map and an integrated genetic map of 996.21 cM was constructed. Mapped PKAMs showed a higher degree of synteny with the genome of Glycine max followed by Medicago truncatula and Lotus japonicus and least with Vigna unguiculata. These PKAMs will be useful for genetics research and breeding applications in pigeonpea and for utilizing genome information from other legume species. PMID:23103470

Extended length microchannels for high density high throughput electrophoresis systems

DOEpatents

Davidson, James C.; Balch, Joseph W.

2000-01-01

High throughput electrophoresis systems which provide extended well-to-read distances on smaller substrates, thus compacting the overall systems. The electrophoresis systems utilize a high density array of microchannels for electrophoresis analysis with extended read lengths. The microchannel geometry can be used individually or in conjunction to increase the effective length of a separation channel while minimally impacting the packing density of channels. One embodiment uses sinusoidal microchannels, while another embodiment uses plural microchannels interconnected by a via. The extended channel systems can be applied to virtually any type of channel confined chromatography.

BAIT: Organizing genomes and mapping rearrangements in single cells.

PubMed

Hills, Mark; O'Neill, Kieran; Falconer, Ester; Brinkman, Ryan; Lansdorp, Peter M

2013-01-01

Strand-seq is a single-cell sequencing technique to finely map sister chromatid exchanges (SCEs) and other rearrangements. To analyze these data, we introduce BAIT, software which assigns templates and identifies and localizes SCEs. We demonstrate BAIT can refine completed reference assemblies, identifying approximately 21 Mb of incorrectly oriented fragments and placing over half (2.6 Mb) of the orphan fragments in mm10/GRCm38. BAIT also stratifies scaffold-stage assemblies, potentially accelerating the assembling and finishing of reference genomes. BAIT is available at http://sourceforge.net/projects/bait/.

Capillary electrophoresis electrospray ionization mass spectrometry interface

DOEpatents

Smith, Richard D.; Severs, Joanne C.

1999-01-01

The present invention is an interface between a capillary electrophoresis separation capillary end and an electrospray ionization mass spectrometry emitter capillary end, for transporting an anolyte sample from a capillary electrophoresis separation capillary to a electrospray ionization mass spectrometry emitter capillary. The interface of the present invention has: (a) a charge transfer fitting enclosing both of the capillary electrophoresis capillary end and the electrospray ionization mass spectrometry emitter capillary end; (b) a reservoir containing an electrolyte surrounding the charge transfer fitting; and (c) an electrode immersed into the electrolyte, the electrode closing a capillary electrophoresis circuit and providing charge transfer across the charge transfer fitting while avoiding substantial bulk fluid transfer across the charge transfer fitting. Advantages of the present invention have been demonstrated as effective in providing high sensitivity and efficient analyses.

Copolymers For Capillary Gel Electrophoresis

DOEpatents

Liu, Changsheng; Li, Qingbo

2005-08-09

This invention relates to an electrophoresis separation medium having a gel matrix of at least one random, linear copolymer comprising a primary comonomer and at least one secondary comonomer, wherein the comonomers are randomly distributed along the copolymer chain. The primary comonomer is an acrylamide or an acrylamide derivative that provides the primary physical, chemical, and sieving properties of the gel matrix. The at least one secondary comonomer imparts an inherent physical, chemical, or sieving property to the copolymer chain. The primary and secondary comonomers are present in a ratio sufficient to induce desired properties that optimize electrophoresis performance. The invention also relates to a method of separating a mixture of biological molecules using this gel matrix, a method of preparing the novel electrophoresis separation medium, and a capillary tube filled with the electrophoresis separation medium.

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome.

PubMed

Ribeiro, Antonio; Golicz, Agnieszka; Hackett, Christine Anne; Milne, Iain; Stephen, Gordon; Marshall, David; Flavell, Andrew J; Bayer, Micha

2015-11-11

Single Nucleotide Polymorphisms (SNPs) are widely used molecular markers, and their use has increased massively since the inception of Next Generation Sequencing (NGS) technologies, which allow detection of large numbers of SNPs at low cost. However, both NGS data and their analysis are error-prone, which can lead to the generation of false positive (FP) SNPs. We explored the relationship between FP SNPs and seven factors involved in mapping-based variant calling - quality of the reference sequence, read length, choice of mapper and variant caller, mapping stringency and filtering of SNPs by read mapping quality and read depth. This resulted in 576 possible factor level combinations. We used error- and variant-free simulated reads to ensure that every SNP found was indeed a false positive. The variation in the number of FP SNPs generated ranged from 0 to 36,621 for the 120 million base pairs (Mbp) genome. All of the experimental factors tested had statistically significant effects on the number of FP SNPs generated and there was a considerable amount of interaction between the different factors. Using a fragmented reference sequence led to a dramatic increase in the number of FP SNPs generated, as did relaxed read mapping and a lack of SNP filtering. The choice of reference assembler, mapper and variant caller also significantly affected the outcome. The effect of read length was more complex and suggests a possible interaction between mapping specificity and the potential for contributing more false positives as read length increases. The choice of tools and parameters involved in variant calling can have a dramatic effect on the number of FP SNPs produced, with particularly poor combinations of software and/or parameter settings yielding tens of thousands in this experiment. Between-factor interactions make simple recommendations difficult for a SNP discovery pipeline but the quality of the reference sequence is clearly of paramount importance. Our findings are also a stark reminder that it can be unwise to use the relaxed mismatch settings provided as defaults by some read mappers when reads are being mapped to a relatively unfinished reference sequence from e.g. a non-model organism in its early stages of genomic exploration.

Mapping From an Instrumented Glove to a Robot Hand

NASA Technical Reports Server (NTRS)

Goza, Michael

2005-01-01

An algorithm has been developed to solve the problem of mapping from (1) a glove instrumented with joint-angle sensors to (2) an anthropomorphic robot hand. Such a mapping is needed to generate control signals to make the robot hand mimic the configuration of the hand of a human attempting to control the robot. The mapping problem is complicated by uncertainties in sensor locations caused by variations in sizes and shapes of hands and variations in the fit of the glove. The present mapping algorithm is robust in the face of these uncertainties, largely because it includes a calibration sub-algorithm that inherently adapts the mapping to the specific hand and glove, without need for measuring the hand and without regard for goodness of fit. The algorithm utilizes a forward-kinematics model of the glove derived from documentation provided by the manufacturer of the glove. In this case, forward-kinematics model signifies a mathematical model of the glove fingertip positions as functions of the sensor readings. More specifically, given the sensor readings, the forward-kinematics model calculates the glove fingertip positions in a Cartesian reference frame nominally attached to the palm. The algorithm also utilizes an inverse-kinematics model of the robot hand. In this case, inverse-kinematics model signifies a mathematical model of the robot finger-joint angles as functions of the robot fingertip positions. Again, more specifically, the inverse-kinematics model calculates the finger-joint commands needed to place the fingertips at specified positions in a Cartesian reference frame that is attached to the palm of the robot hand and that nominally corresponds to the Cartesian reference frame attached to the palm of the glove. Initially, because of the aforementioned uncertainties, the glove fingertip positions calculated by the forwardkinematics model in the glove Cartesian reference frame cannot be expected to match the robot fingertip positions in the robot-hand Cartesian reference frame. A calibration must be performed to make the glove and robot-hand fingertip positions correspond more precisely. The calibration procedure involves a few simple hand poses designed to provide well-defined fingertip positions. One of the poses is a fist. In each of the other poses, a finger touches the thumb. The calibration subalgorithm uses the sensor readings from these poses to modify the kinematical models to make the two sets of fingertip positions agree more closely.

HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads

PubMed Central

Li, Pinghao; Jiang, Xiaoqian; Wang, Shuang; Kim, Jihoon; Xiong, Hongkai; Ohno-Machado, Lucila

2014-01-01

Background and objective Short-read sequencing is becoming the standard of practice for the study of structural variants associated with disease. However, with the growth of sequence data largely surpassing reasonable storage capability, the biomedical community is challenged with the management, transfer, archiving, and storage of sequence data. Methods We developed Hierarchical mUlti-reference Genome cOmpression (HUGO), a novel compression algorithm for aligned reads in the sorted Sequence Alignment/Map (SAM) format. We first aligned short reads against a reference genome and stored exactly mapped reads for compression. For the inexact mapped or unmapped reads, we realigned them against different reference genomes using an adaptive scheme by gradually shortening the read length. Regarding the base quality value, we offer lossy and lossless compression mechanisms. The lossy compression mechanism for the base quality values uses k-means clustering, where a user can adjust the balance between decompression quality and compression rate. The lossless compression can be produced by setting k (the number of clusters) to the number of different quality values. Results The proposed method produced a compression ratio in the range 0.5–0.65, which corresponds to 35–50% storage savings based on experimental datasets. The proposed approach achieved 15% more storage savings over CRAM and comparable compression ratio with Samcomp (CRAM and Samcomp are two of the state-of-the-art genome compression algorithms). The software is freely available at https://sourceforge.net/projects/hierachicaldnac/with a General Public License (GPL) license. Limitation Our method requires having different reference genomes and prolongs the execution time for additional alignments. Conclusions The proposed multi-reference-based compression algorithm for aligned reads outperforms existing single-reference based algorithms. PMID:24368726

BatMis: a fast algorithm for k-mismatch mapping.

PubMed

Tennakoon, Chandana; Purbojati, Rikky W; Sung, Wing-Kin

2012-08-15

Second-generation sequencing (SGS) generates millions of reads that need to be aligned to a reference genome allowing errors. Although current aligners can efficiently map reads allowing a small number of mismatches, they are not well suited for handling a large number of mismatches. The efficiency of aligners can be improved using various heuristics, but the sensitivity and accuracy of the alignments are sacrificed. In this article, we introduce Basic Alignment tool for Mismatches (BatMis)--an efficient method to align short reads to a reference allowing k mismatches. BatMis is a Burrows-Wheeler transformation based aligner that uses a seed and extend approach, and it is an exact method. Benchmark tests show that BatMis performs better than competing aligners in solving the k-mismatch problem. Furthermore, it can compete favorably even when compared with the heuristic modes of the other aligners. BatMis is a useful alternative for applications where fast k-mismatch mappings, unique mappings or multiple mappings of SGS data are required. BatMis is written in C/C++ and is freely available from http://code.google.com/p/batmis/

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

Simkin, T.; Tilling, R.I.; Taggart, J.N.

The Earth's physiographic features overlain by its volcanoes, earthquake epicenters, and the movement of its major tectonic plates are shown in this map. This computer-generated map of the world provides a base that shows the topography of the land surface and the sea floor; the additions of color and shaded relief help to distinguish significant features. From the Volcano Reference file of the Smithsonian Institution, nearly 1,450 volcanoes active during the past 10,000 yr are plotted on the map in four categories. From the files of the National Earthquake Information Center (US Geological Survey), epicenters selected from 1,300 large eventsmore » (magnitude {>=} 7.0) from 1987 onward and from 140,000 instrumentally recorded earthquakes (magnitude {>=} 4.0) from 1960 to the present are plotted on this map according to two magnitude categories and two depth categories. This special map is intended as a teaching aid for classroom use and as a general reference for research. It is designed to show prominent global features when viewed from a distance; more detailed features are visible on closer inspection.« less

Unified View of Backward Backtracking in Short Read Mapping

NASA Astrophysics Data System (ADS)

Mäkinen, Veli; Välimäki, Niko; Laaksonen, Antti; Katainen, Riku

Mapping short DNA reads to the reference genome is the core task in the recent high-throughput technologies to study e.g. protein-DNA interactions (ChIP-seq) and alternative splicing (RNA-seq). Several tools for the task (bowtie, bwa, SOAP2, TopHat) have been developed that exploit Burrows-Wheeler transform and the backward backtracking technique on it, to map the reads to their best approximate occurrences in the genome. These tools use different tailored mechanisms for small error-levels to prune the search phase significantly. We propose a new pruning mechanism that can be seen a generalization of the tailored mechanisms used so far. It uses a novel idea of storing all cyclic rotations of fixed length substrings of the reference sequence with a compressed index that is able to exploit the repetitions created to level out the growth of the input set. For RNA-seq we propose a new method that combines dynamic programming with backtracking to map efficiently and correctly all reads that span two exons. Same mechanism can also be used for mapping mate-pair reads.

Resolution Measurement from a Single Reconstructed Cryo-EM Density Map with Multiscale Spectral Analysis.

PubMed

Yang, Yu-Jiao; Wang, Shuai; Zhang, Biao; Shen, Hong-Bin

2018-06-25

As a relatively new technology to solve the three-dimensional (3D) structure of a protein or protein complex, single-particle reconstruction (SPR) of cryogenic electron microscopy (cryo-EM) images shows much superiority and is in a rapidly developing stage. Resolution measurement in SPR, which evaluates the quality of a reconstructed 3D density map, plays a critical role in promoting methodology development of SPR and structural biology. Because there is no benchmark map in the generation of a new structure, how to realize the resolution estimation of a new map is still an open problem. Existing approaches try to generate a hypothetical benchmark map by reconstructing two 3D models from two halves of the original 2D images for cross-reference, which may result in a premature estimation with a half-data model. In this paper, we report a new self-reference-based resolution estimation protocol, called SRes, that requires only a single reconstructed 3D map. The core idea of SRes is to perform a multiscale spectral analysis (MSSA) on the map through multiple size-variable masks segmenting the map. The MSSA-derived multiscale spectral signal-to-noise ratios (mSSNRs) reveal that their corresponding estimated resolutions will show a cliff jump phenomenon, indicating a significant change in the SSNR properties. The critical point on the cliff borderline is demonstrated to be the right estimator for the resolution of the map.

Mapping language to the world: the role of iconicity in the sign language input.

PubMed

Perniss, Pamela; Lu, Jenny C; Morgan, Gary; Vigliocco, Gabriella

2018-03-01

Most research on the mechanisms underlying referential mapping has assumed that learning occurs in ostensive contexts, where label and referent co-occur, and that form and meaning are linked by arbitrary convention alone. In the present study, we focus on iconicity in language, that is, resemblance relationships between form and meaning, and on non-ostensive contexts, where label and referent do not co-occur. We approach the question of language learning from the perspective of the language input. Specifically, we look at child-directed language (CDL) in British Sign Language (BSL), a language rich in iconicity due to the affordances of the visual modality. We ask whether child-directed signing exploits iconicity in the language by highlighting the similarity mapping between form and referent. We find that CDL modifications occur more often with iconic signs than with non-iconic signs. Crucially, for iconic signs, modifications are more frequent in non-ostensive contexts than in ostensive contexts. Furthermore, we find that pointing dominates in ostensive contexts, and suggest that caregivers adjust the semiotic resources recruited in CDL to context. These findings offer first evidence for a role of iconicity in the language input and suggest that iconicity may be involved in referential mapping and language learning, particularly in non-ostensive contexts. © 2017 John Wiley & Sons Ltd.

Population genetic analysis of oral treponemes by multilocus enzyme electrophoresis.

PubMed

Dahle, U R; Olsen, I; Tronstad, L; Caugant, D A

1995-10-01

Seventeen treponemes recently isolated from necrotic pulps, periodontal and periapical infections and 17 previously well characterized oral treponemal strains were analyzed by multilocus enzyme electrophoresis. Ten genetic loci were characterized on the basis of the electrophoretic mobilities of their enzymatic products. All loci were polymorphic. The average number of alleles per locus was 7.8. The genetic diversity among the electrophoretic types at each locus ranged from 0.624 to 0.836 with a mean genetic diversity per locus of 0.751. The 34 strains represented 34 electrophoretic types, constituting 6 main divisions (I-VI) separated at genetic distances greater than 0.75. Several of the previously characterized treponemes revealed multiple bands of enzyme activity at several loci, indicating that they were not pure. The characterized strains usually clustered within established species, whereas fresh clinical isolates overlapped species borders. There was a large genetic difference between some reference and clinical strains, indicating that the latter may contain undescribed species. Treponema socranskii and Treponema denticola strains clustered in distinct divisions (IV and V, respectively), with the exception of T. denticola strain FDC 51B2 and T. socranskii subsp. paredis strain VPI D46CPE1, both previously well described. This indicated that the taxonomic assignment of these 2 strains should be reconsidered.

Detection and Quantification of Inorganic and Organic Anions in Natural, Potable, and Wastewaters in Northern New York Using Capillary Zone Electrophoresis and Indirect UV Detection

PubMed Central

Varden, Lara; Smith, Britannia; Bou-Abdallah, Fadi

2017-01-01

Capillary zone electrophoresis (CZE) is a sensitive and rapid technique used for determining traces of inorganic and organic anions in potable, natural, and wastewaters. Here, CZE with indirect UV-diode array detection (CZE-DAD) was employed with a background electrolyte system comprising of an Agilent Technologies proprietary basic anion buffer at pH 12.0 and a forensic anion detection method. The limits of detection (LOD) for this method ranged between 3 and 5 ppm and involved hydrodynamic injection of 50 mbar for 6 s with a negative polarity separation voltage of −30 kV at 30°C, a detection wavelength of 350 nm and indirect reference of 275 nm. Fourteen different anions were checked for in the water samples that were examined and included bromide, chloride, thiosulfate, nitrate, nitrite, sulfate, azide, carbonate, fluoride, arsenate, phosphate, acetate, lactate, and silicate. The water samples were collected from Northern New York towns and the Raquette River water system, the third longest river in New York State and the largest watershed of the central and western Adirondacks. The concentrations detected for these anions ranged from <5.0 ppm to 260 ppm. PMID:29057145

Biodiversity of Bacterial Ecosystems in Traditional Egyptian Domiati Cheese▿

PubMed Central

El-Baradei, Gaber; Delacroix-Buchet, Agnès; Ogier, Jean-Claude

2007-01-01

Bacterial biodiversity occurring in traditional Egyptian soft Domiati cheese was studied by PCR-temporal temperature gel electrophoresis (TTGE) and PCR-denaturing gradient gel electrophoresis (DGGE). Bands were identified using a reference species database (J.-C. Ogier et al., Appl. Environ. Microbiol. 70:5628-5643, 2004); de novo bands having nonidentified migration patterns were identified by DNA sequencing. Results reveal a novel bacterial profile and extensive bacterial biodiversity in Domiati cheeses, as reflected by the numerous bands present in TTGE and DGGE patterns. The dominant lactic acid bacteria (LAB) identified were as follows: Leuconostoc mesenteroides, Lactococcus garvieae, Aerococcus viridans, Lactobacillus versmoldensis, Pediococcus inopinatus, and Lactococcus lactis. Frequent non-LAB species included numerous coagulase-negative staphylococci, Vibrio spp., Kocuria rhizophila, Kocuria kristinae, Kocuria halotolerans, Arthrobacter spp./Brachybacterium tyrofermentans. This is the first time that the majority of these species has been identified in Domiati cheese. Nearly all the dominant and frequent bacterial species are salt tolerant, and several correspond to known marine bacteria. As Domiati cheese contains 5.4 to 9.5% NaCl, we suggest that these bacteria are likely to have an important role in the ripening process. This first systematic study of the microbial composition of Domiati cheeses reveals great biodiversity and evokes a role for marine bacteria in determining cheese type. PMID:17189434

Biodiversity of bacterial ecosystems in traditional Egyptian Domiati cheese.

PubMed

El-Baradei, Gaber; Delacroix-Buchet, Agnès; Ogier, Jean-Claude

2007-02-01

Bacterial biodiversity occurring in traditional Egyptian soft Domiati cheese was studied by PCR-temporal temperature gel electrophoresis (TTGE) and PCR-denaturing gradient gel electrophoresis (DGGE). Bands were identified using a reference species database (J.-C. Ogier et al., Appl. Environ. Microbiol. 70:5628-5643, 2004); de novo bands having nonidentified migration patterns were identified by DNA sequencing. Results reveal a novel bacterial profile and extensive bacterial biodiversity in Domiati cheeses, as reflected by the numerous bands present in TTGE and DGGE patterns. The dominant lactic acid bacteria (LAB) identified were as follows: Leuconostoc mesenteroides, Lactococcus garvieae, Aerococcus viridans, Lactobacillus versmoldensis, Pediococcus inopinatus, and Lactococcus lactis. Frequent non-LAB species included numerous coagulase-negative staphylococci, Vibrio spp., Kocuria rhizophila, Kocuria kristinae, Kocuria halotolerans, Arthrobacter spp./Brachybacterium tyrofermentans. This is the first time that the majority of these species has been identified in Domiati cheese. Nearly all the dominant and frequent bacterial species are salt tolerant, and several correspond to known marine bacteria. As Domiati cheese contains 5.4 to 9.5% NaCl, we suggest that these bacteria are likely to have an important role in the ripening process. This first systematic study of the microbial composition of Domiati cheeses reveals great biodiversity and evokes a role for marine bacteria in determining cheese type.

Determination of multidrug resistance mechanisms in Clostridium perfringens type A isolates using RNA sequencing and 2D-electrophoresis.

PubMed

Ma, Yu-Hua; Ye, Gui-Sheng

2018-06-11

In this study, we screened differentially expressed genes in a multidrug-resistant isolate strain of Clostridium perfringens by RNA sequencing. We also separated and identified differentially expressed proteins (DEPs) in the isolate strain by two-dimensional electrophoresis (2-DE) and mass spectrometry (MS). The RNA sequencing results showed that, compared with the control strain, 1128 genes were differentially expressed in the isolate strain, and these included 227 up-regulated genes and 901 down-regulated genes. Bioinformatics analysis identified the following genes and gene categories that are potentially involved in multidrug resistance (MDR) in the isolate strain: drug transport, drug response, hydrolase activity, transmembrane transporter, transferase activity, amidase transmembrane transporter, efflux transmembrane transporter, bacterial chemotaxis, ABC transporter, and others. The results of the 2-DE showed that 70 proteins were differentially expressed in the isolate strain, 45 of which were up-regulated and 25 down-regulated. Twenty-seven DEPs were identified by MS and these included the following protein categories: ribosome, antimicrobial peptide resistance, and ABC transporter, all of which may be involved in MDR in the isolate strain of C. perfringens. The results provide reference data for further investigations on the drug resistant molecular mechanisms of C. perfringens.

Computer Vision Evidence Supporting Craniometric Alignment of Rat Brain Atlases to Streamline Expert-Guided, First-Order Migration of Hypothalamic Spatial Datasets Related to Behavioral Control

PubMed Central

Khan, Arshad M.; Perez, Jose G.; Wells, Claire E.; Fuentes, Olac

2018-01-01

The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982) or Swanson (S, first published in 1992) as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. Such data migration would allow scientists to accurately contextualize neuroanatomical data mapped exclusively in only one atlas with data mapped in the other. Here, we provide a tool that allows levels from any of the seven published editions of atlases comprising three distinct PW reference spaces to be aligned to atlas levels from any of the four published editions representing S reference space. This alignment is based on registration of the anteroposterior stereotaxic coordinate (z) measured from the skull landmark, Bregma (β). Atlas level alignments performed along the z axis using one-dimensional Cleveland dot plots were in general agreement with alignments obtained independently using a custom-made computer vision application that utilized the scale-invariant feature transform (SIFT) and Random Sample Consensus (RANSAC) operation to compare regions of interest in photomicrographs of Nissl-stained tissue sections from the PW and S reference spaces. We show that z-aligned point source data (unpublished hypothalamic microinjection sites) can be migrated from PW to S space to a first-order approximation in the mediolateral and dorsoventral dimensions using anisotropic scaling of the vector-formatted atlas templates, together with expert-guided relocation of obvious outliers in the migrated datasets. The migrated data can be contextualized with other datasets mapped in S space, including neuronal cell bodies, axons, and chemoarchitecture; to generate data-constrained hypotheses difficult to formulate otherwise. The alignment strategies provided in this study constitute a basic starting point for first-order, user-guided data migration between PW and S reference spaces along three dimensions that is potentially extensible to other spatial reference systems for the rat brain. PMID:29765309

A National Trial on Differences in Cerebral Perfusion Pressure Values by Measurement Location.

PubMed

McNett, Molly M; Bader, Mary Kay; Livesay, Sarah; Yeager, Susan; Moran, Cristina; Barnes, Arianna; Harrison, Kimberly R; Olson, DaiWai M

2018-04-01

Cerebral perfusion pressure (CPP) is a key parameter in management of brain injury with suspected impaired cerebral autoregulation. CPP is calculated by subtracting intracranial pressure (ICP) from mean arterial pressure (MAP). Despite consensus on importance of CPP monitoring, substantial variations exist on anatomical reference points used to measure arterial MAP when calculating CPP. This study aimed to identify differences in CPP values based on measurement location when using phlebostatic axis (PA) or tragus (Tg) as anatomical reference points. The secondary study aim was to determine impact of differences on patient outcomes at discharge. This was a prospective, repeated measures, multi-site national trial. Adult ICU patients with neurological injury necessitating ICP and CPP monitoring were consecutively enrolled from seven sites. Daily MAP/ICP/CPP values were gathered with the arterial transducer at the PA, followed by the Tg as anatomical reference points. A total of 136 subjects were enrolled, resulting in 324 paired observations. There were significant differences for CPP when comparing values obtained at PA and Tg reference points (p < 0.000). Differences remained significant in repeated measures model when controlling for clinical factors (mean CPP-PA = 80.77, mean CPP-Tg = 70.61, p < 0.000). When categorizing CPP as binary endpoint, 18.8% of values were identified as adequate with PA values, yet inadequate with CPP values measured at the Tg. Findings identify numerical differences for CPP based on anatomical reference location and highlight importance of a standard reference point for both clinical practice and future trials to limit practice variations and heterogeneity of findings.

A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs.

PubMed

Muchero, Wellington; Diop, Ndeye N; Bhat, Prasanna R; Fenton, Raymond D; Wanamaker, Steve; Pottorff, Marti; Hearne, Sarah; Cisse, Ndiaga; Fatokun, Christian; Ehlers, Jeffrey D; Roberts, Philip A; Close, Timothy J

2009-10-27

Consensus genetic linkage maps provide a genomic framework for quantitative trait loci identification, map-based cloning, assessment of genetic diversity, association mapping, and applied breeding in marker-assisted selection schemes. Among "orphan crops" with limited genomic resources such as cowpea [Vigna unguiculata (L.) Walp.] (2n = 2x = 22), the use of transcript-derived SNPs in genetic maps provides opportunities for automated genotyping and estimation of genome structure based on synteny analysis. Here, we report the development and validation of a high-throughput EST-derived SNP assay for cowpea, its application in consensus map building, and determination of synteny to reference genomes. SNP mining from 183,118 ESTs sequenced from 17 cDNA libraries yielded approximately 10,000 high-confidence SNPs from which an Illumina 1,536-SNP GoldenGate genotyping array was developed and applied to 741 recombinant inbred lines from six mapping populations. Approximately 90% of the SNPs were technically successful, providing 1,375 dependable markers. Of these, 928 were incorporated into a consensus genetic map spanning 680 cM with 11 linkage groups and an average marker distance of 0.73 cM. Comparison of this cowpea genetic map to reference legumes, soybean (Glycine max) and Medicago truncatula, revealed extensive macrosynteny encompassing 85 and 82%, respectively, of the cowpea map. Regions of soybean genome duplication were evident relative to the simpler diploid cowpea. Comparison with Arabidopsis revealed extensive genomic rearrangement with some conserved microsynteny. These results support evolutionary closeness between cowpea and soybean and identify regions for synteny-based functional genomics studies in legumes.

Effect of Spatial Locality Prefetching on Structural Locality

DTIC Science & Technology

1991-12-01

Pollution module calculates the SLC and CAM cache pollution percentages. And finally, the Generate Reference Frequency List module produces the output...3.2.5 Generate Reference Frequency List 3.2.6 Each program module in the structure chart is mapped into an Ada package. By performing this encapsulation...call routine to generate reference -- frequency list -- end if -- end loop -- close input, output, and reference files end Cache Simulator Figure 3.5

Music-therapy analyzed through conceptual mapping

NASA Astrophysics Data System (ADS)

Martinez, Rodolfo; de la Fuente, Rebeca

2002-11-01

Conceptual maps have been employed lately as a learning tool, as a modern study technique, and as a new way to understand intelligence, which allows for the development of a strong theoretical reference, in order to prove the research hypothesis. This paper presents a music-therapy analysis based on this tool to produce a conceptual mapping network, which ranges from magic through the rigor of the hard sciences.

Principles of Geological Mapping of Marine Sediments (with Special Reference to the African Continental Margin). Unesco Reports in Marine Science No. 37.

ERIC Educational Resources Information Center

Lisitzin, Alexandre P.

Designed to serve as a complement to the Unesco Technical Papers in Marine Science, this report concentrates on theoretical and practical problems of geological mapping of the sea floor. An introduction is given to geological mapping procedures at continental margins as well as some practical recommendations taking as an example the African region…

Subjectivity in Design Education: The Perception of the City through Personal Maps

ERIC Educational Resources Information Center

Yilmaz, Ebru

2016-01-01

Our mental maps related to the cities are limited by our personal perception and fragmented in the process. There are many inner and outer effects that shape our mental maps, and as a result the fragmented whole refers to the total city image in our minds. To represent this image, an experimental study has been conducted with a group of students.…

Simulation of Two Dimensional Electrophoresis and Tandem Mass Spectrometry for Teaching Proteomics

ERIC Educational Resources Information Center

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations--2D electrophoresis and tandem mass spectrometry.…

Gel Electrophoresis on a Budget to Dye for

ERIC Educational Resources Information Center

Yu, Julie H.

2010-01-01

Gel electrophoresis is one of the most important tools used in molecular biology and has facilitated the entire field of genetic engineering by enabling the separation of nucleic acids and proteins. However, commercial electrophoresis kits can cost up to $800 for each setup, which is cost prohibitive for most classroom budgets. This article…

Electrophoresis for biological production

NASA Technical Reports Server (NTRS)

Mccreight, L. R.

1977-01-01

Preparative electrophoresis may provide a unique method for meeting ever more stringent purity requirements. Prolonged near zero gravity in space may permit the operation of preparative electrophoresis equipment with 100 times greater throughput than is currently available. Some experiments with influenza Virus Antigen, Erythropoietin and Antihemophaliac Factor, along with process and economic projections, are briefly reviewed.

Inexpensive and Safe DNA Gel Electrophoresis Using Household Materials

ERIC Educational Resources Information Center

Ens, S.; Olson, A. B.; Dudley, C.; Ross, N. D., III; Siddiqi, A. A.; Umoh, K. M.; Schneegurt, M. A.

2012-01-01

Gel electrophoresis is the single most important molecular biology technique and it is central to life sciences research, but it is often too expensive for the secondary science classroom or homeschoolers. A simple safe low-cost procedure is described here that uses household materials to construct and run DNA gel electrophoresis. Plastic…

Design, development, test, and evaluation of an automated analytical electrophoresis apparatus

NASA Technical Reports Server (NTRS)

Bartels, P. A.; Bier, M.

1977-01-01

An Automated Analytical Electrophoresis Apparatus (AAEA) was designed, developed, assembled, and preliminarily tested. The AAEA was demonstrated to be a feasible apparatus for automatically acquiring, displaying, and storing (and eventually analyzing) electrophoresis mobility data from living blood cells. The apparatus and the operation of its major assemblies are described in detail.

The Optimization of Electrophoresis on a Glass Microfluidic Chip and its Application in Forensic Science.

PubMed

Han, Jun P; Sun, Jing; Wang, Le; Liu, Peng; Zhuang, Bin; Zhao, Lei; Liu, Yao; Li, Cai X

2017-11-01

Microfluidic chips offer significant speed, cost, and sensitivity advantages, but numerous parameters must be optimized to provide microchip electrophoresis detection. Experiments were conducted to study the factors, including sieving matrices (the concentration and type), surface modification, analysis temperature, and electric field strengths, which all impact the effectiveness of microchip electrophoresis detection of DNA samples. Our results showed that the best resolution for ssDNA was observed using 4.5% w/v (7 M urea) lab-fabricated LPA gel, dynamic wall coating of the microchannel, electrophoresis temperatures between 55 and 60°C, and electrical fields between 350 and 450 V/cm on the microchip-based capillary electrophoresis (μCE) system. One base-pair resolution could be achieved in the 19-cm-length microchannel. Furthermore, both 9947A standard genomic DNA and DNA extracted from blood spots were demonstrated to be successfully separated with well-resolved DNA peaks in 8 min. Therefore, the microchip electrophoresis system demonstrated good potential for rapid forensic DNA analysis. © 2017 American Academy of Forensic Sciences.

On-line DNA analysis system with rapid thermal cycling

DOEpatents

Swerdlow, Harold P.; Wittwer, Carl T.

1999-01-01

An apparatus particularly suited for subjecting biological samples to any necessary sample preparation tasks, subjecting the sample to rapid thermal cycling, and then subjecting the sample to subsequent on-line analysis using one or more of a number of analytical techniques. The apparatus includes a chromatography device including an injection means, a chromatography pump, and a chromatography column. In addition, the apparatus also contains a capillary electrophoresis device consisting of a capillary electrophoresis column with an inlet and outlet end, a means of injection, and means of applying a high voltage to cause the differential migration of species of interest through the capillary column. Effluent from the liquid chromatography column passes over the inlet end of the capillary electrophoresis column through a tee structure and when the loading of the capillary electrophoresis column is desired, a voltage supply is activated at a precise voltage and polarity over a specific duration to cause sample species to be diverted from the flowing stream to the capillary electrophoresis column. A laser induced fluorescence detector preferably is used to analyze the products separated while in the electrophoresis column.

On-line DNA analysis system with rapid thermal cycling

DOEpatents

Swerdlow, H.P.; Wittwer, C.T.

1999-08-10

This application describes an apparatus particularly suited for subjecting biological samples to any necessary sample preparation tasks, subjecting the sample to rapid thermal cycling, and then subjecting the sample to subsequent on-line analysis using one or more of a number of analytical techniques. The apparatus includes a chromatography device including an injection means, a chromatography pump, and a chromatography column. In addition, the apparatus also contains a capillary electrophoresis device consisting of a capillary electrophoresis column with an inlet and outlet end, a means of injection, and means of applying a high voltage to cause the differential migration of species of interest through the capillary column. Effluent from the liquid chromatography column passes over the inlet end of the capillary electrophoresis column through a tee structure and when the loading of the capillary electrophoresis column is desired, a voltage supply is activated at a precise voltage and polarity over a specific duration to cause sample species to be diverted from the flowing stream to the capillary electrophoresis column. A laser induced fluorescence detector preferably is used to analyze the products separated while in the electrophoresis column. 6 figs.

Dynamic computer simulations of electrophoresis: three decades of active research.

PubMed

Thormann, Wolfgang; Caslavska, Jitka; Breadmore, Michael C; Mosher, Richard A

2009-06-01

Dynamic models for electrophoresis are based upon model equations derived from the transport concepts in solution together with user-inputted conditions. They are able to predict theoretically the movement of ions and are as such the most versatile tool to explore the fundamentals of electrokinetic separations. Since its inception three decades ago, the state of dynamic computer simulation software and its use has progressed significantly and Electrophoresis played a pivotal role in that endeavor as a large proportion of the fundamental and application papers were published in this periodical. Software is available that simulates all basic electrophoretic systems, including moving boundary electrophoresis, zone electrophoresis, ITP, IEF and EKC, and their combinations under almost exactly the same conditions used in the laboratory. This has been employed to show the detailed mechanisms of many of the fundamental phenomena that occur in electrophoretic separations. Dynamic electrophoretic simulations are relevant for separations on any scale and instrumental format, including free-fluid preparative, gel, capillary and chip electrophoresis. This review includes a historical overview, a survey of current simulators, simulation examples and a discussion of the applications and achievements of dynamic simulation.

Telomere Organization in the Ligninolytic Basidiomycete Pleurotus ostreatus▿ †

PubMed Central

Pérez, Gúmer; Pangilinan, Jasmyn; Pisabarro, Antonio G.; Ramírez, Lucía

2009-01-01

Telomeres are structural and functional chromosome regions that are essential for the cell cycle to proceed normally. They are, however, difficult to map genetically and to identify in genome-wide sequence programs because of their structure and repetitive nature. We studied the telomeric and subtelomeric organization in the basidiomycete Pleurotus ostreatus using a combination of molecular and bioinformatics tools that permitted us to determine 19 out of the 22 telomeres expected in this fungus. The telomeric repeating unit in P. ostreatus is TTAGGG, and the numbers of repetitions of this unit range between 25 and 150. The mapping of the telomere restriction fragments to linkage groups 6 and 7 revealed polymorphisms compatible with those observed by pulsed field gel electrophoresis separation of the corresponding chromosomes. The subtelomeric regions in Pleurotus contain genes similar to those described in other eukaryotic systems. The presence of a cluster of laccase genes in chromosome 6 and a bipartite structure containing a Het-related protein and an alcohol dehydrogenase are especially relevant; this bipartite structure is characteristic of the Pezizomycotina fungi Neurospora crassa and Aspergillus terreus. As far as we know, this is the first report describing the presence of such structures in basidiomycetes and the location of a laccase gene cluster in the subtelomeric region, where, among others, species-specific genes allowing the organism to adapt rapidly to the environment usually map. PMID:19114509

Occurrence of Double Monoclonal Bands on Protein Electrophoresis: An Unusual Finding.

PubMed

Srinivasan, Vishrut K; Bhagat, Priyanka; Bansal, Frainey; Chhabra, Seema

2016-06-01

Various techniques of protein electrophoresis are used for detection of monoclonal proteins/paraproteins in serum and/or urine of patients with monoclonal gammopathies. These are detected as the so-called 'M' bands (monoclonal bands) on serum protein electrophoresis and/or immunofixation electrophoresis. In most cases, a single M-band is detected. However, more than one M-band can be detected in the samples of a minor proportion of patients. This condition is termed as 'double gammopathy' or 'biclonal gammopathy'. A knowledge of such an unusual occurrence is essential for recognition and appropriate interpretation of this entity.

Binary Oscillatory Crossflow Electrophoresis

NASA Technical Reports Server (NTRS)

Molloy, Richard F.; Gallagher, Christopher T.; Leighton, David T., Jr.

1996-01-01

We present preliminary results of our implementation of a novel electrophoresis separation technique: Binary Oscillatory Cross flow Electrophoresis (BOCE). The technique utilizes the interaction of two driving forces, an oscillatory electric field and an oscillatory shear flow, to create an active binary filter for the separation of charged species. Analytical and numerical studies have indicated that this technique is capable of separating proteins with electrophoretic mobilities differing by less than 10%. With an experimental device containing a separation chamber 20 cm long, 5 cm wide, and 1 mm thick, an order of magnitude increase in throughput over commercially available electrophoresis devices is theoretically possible.

77 FR 18766 - Proposed Flood Elevation Determinations

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-28

... DEPARTMENT OF HOMELAND SECURITY Federal Emergency Management Agency 44 CFR Part 67 [Docket ID FEMA-2010-0003; Internal Agency Docket No. FEMA-B-1114] Proposed Flood Elevation Determinations Correction... locations above. Please refer to the revised Flood Insurance Rate Map located at the community map...

50 CFR 17.94 - Critical habitats.

Code of Federal Regulations, 2010 CFR

2010-10-01

... the listed species within these defined Critical Habitats. (See part 402 for rules concerning this prohibition; see also part 424 for rules concerning the determination of Critical Habitat). (b) The map... of a Critical Habitat. Such maps are provided for reference purposes to guide Federal agencies and...

A high resolution radiation hybrid map of wheat chromosome 4A

USDA-ARS?s Scientific Manuscript database

Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequenc...

Images Are Not the (Only) Truth: Brain Mapping, Visual Knowledge, and Iconoclasm.

ERIC Educational Resources Information Center

Beaulieu, Anne

2002-01-01

Debates the paradoxical nature of claims about the emerging contributions of functional brain mapping. Examines the various ways that images are deployed and rejected and highlights an approach that provides insight into the current demarcation of imaging. (Contains 68 references.) (DDR)

Spatial Patterns of NLCD Land Cover Change Thematic Accuracy (2001 - 2011)

EPA Science Inventory

Research on spatial non-stationarity of land cover classification accuracy has been ongoing for over two decades. We extend the understanding of thematic map accuracy spatial patterns by: 1) quantifying spatial patterns of map-reference agreement for class-specific land cover c...

Thematic accuracy of the 1992 National Land-Cover Data for the western United States

USGS Publications Warehouse

Wickham, J.D.; Stehman, S.V.; Smith, J.H.; Yang, L.

2004-01-01

The MultiResolution Land Characteristics (MRLC) consortium sponsored production of the National Land Cover Data (NLCD) for the conterminous United States, using Landsat imagery collected on a target year of 1992 (1992 NLCD). Here we report the thematic accuracy of the 1992 NLCD for the six western mapping regions. Reference data were collected in each region for a probability sample of pixels stratified by map land-cover class. Results are reported for each of the six mapping regions with agreement defined as a match between the primary or alternate reference land-cover label and a mode class of the mapped 3×3 block of pixels centered on the sample pixel. Overall accuracy at Anderson Level II was low and variable across the regions, ranging from 38% for the Midwest to 70% for the Southwest. Overall accuracy at Anderson Level I was higher and more consistent across the regions, ranging from 82% to 85% for five of the six regions, but only 74% for the South-central region.

Comprehensive geo-spatial data creation for Najran region in the KSA

NASA Astrophysics Data System (ADS)

Alrajhi, M.; Hawarey, M.

2009-04-01

The General Directorate for Surveying and Mapping (GDSM) of the Deputy Ministry for Land and Surveying (DMLS) of the Ministry of Municipal and Rural Affairs (MOMRA) in the Kingdom of Saudi Arabia (KSA) has the exclusive mandate to carry out aerial photography and produce large-scale detailed maps for about 220 cities and villages in the KSA. This presentation is about the comprehensive geo-spatial data creation for the Najran region, South KSA, that was founded on country-wide horizontal geodetic ground control using Global Navigation Satellite Systems (GNSS) within the MOMRA's Terrestrial Reference Frame 2000 (MTRF2000) that is tied to International Terrestrial Reference Frame 2000 (ITRF2000) Epoch 2004.0, and vertical geodetic ground control using precise digital leveling in reference to Jeddah 1969 mean sea level, and included aerial photography of area 917 km2 at 1:5,500 scale and 14,304 km2 at 1:45,000 scale, full aerial triangulation, and production of orthophoto maps at scale of 1:10,000 (298 sheets) for 14,304 km2, with aerial photography lasting from May 2006 until July 2006.

Comprehensive geo-spatial data creation for Ar-Riyadh region in the KSA

NASA Astrophysics Data System (ADS)

Alrajhi, M.; Hawarey, M.

2009-04-01

The General Directorate for Surveying and Mapping (GDSM) of the Deputy Ministry for Land and Surveying (DMLS) of the Ministry of Municipal and Rural Affairs (MOMRA) in the Kingdom of Saudi Arabia (KSA) has the exclusive mandate to carry out aerial photography and produce large-scale detailed maps for about 220 cities and villages in the KSA. This presentation is about the comprehensive geo-spatial data creation for the Ar-Riyadh region, Central KSA, that was founded on country-wide horizontal geodetic ground control using Global Navigation Satellite Systems (GNSS) within the MOMRA's Terrestrial Reference Frame 2000 (MTRF2000) that is tied to International Terrestrial Reference Frame 2000 (ITRF2000) Epoch 2004.0, and vertical geodetic ground control using precise digital leveling in reference to Jeddah 1969 mean sea level, and included aerial photography of area 3,000 km2 at 1:5,500 scale and 10,000 km2 at 1:45,000 scale, full aerial triangulation, and production of orthophoto maps at scale of 1:10,000 (480 sheets) for 10,000 km2, with aerial photography lasting from July 2007 thru August 2007.

Comprehensive geo-spatial data creation for Asir region in the KSA

NASA Astrophysics Data System (ADS)

Alrajhi, M.; Hawarey, M.

2009-04-01

The General Directorate for Surveying and Mapping (GDSM) of the Deputy Ministry for Land and Surveying (DMLS) of the Ministry of Municipal and Rural Affairs (MOMRA) in the Kingdom of Saudi Arabia (KSA) has the exclusive mandate to carry out aerial photography and produce large-scale detailed maps for about 220 cities and villages in the KSA. This presentation is about the comprehensive geo-spatial data creation for the Asir region, South West KSA, that was founded on country-wide horizontal geodetic ground control using Global Navigation Satellite Systems (GNSS) within the MOMRA's Terrestrial Reference Frame 2000 (MTRF2000) that is tied to International Terrestrial Reference Frame 2000 (ITRF2000) Epoch 2004.0, and vertical geodetic ground control using precise digital leveling in reference to Jeddah 1969 mean sea level, and included aerial photography of area 2,188 km2 at 1:5,500 scale and 32,640 km2 at 1:45,000 scale, full aerial triangulation, and production of orthophoto maps at scale of 1:10,000 (680 sheets) for 32,640 km2, with aerial photography lasting from July 2007 thru October 2007.

Construction of the physical map for three loci in chromosome band 13q14: comparison to the genetic map.

PubMed Central

Higgins, M J; Turmel, C; Noolandi, J; Neumann, P E; Lalande, M

1990-01-01

Pulsed-field gel electrophoresis (PFGE) and deletion mapping are being used to construct a physical map of the long arm of human chromosome 13. The present study reports a 2700-kilobase (kb) Not I long-range restriction map encompassing the 13q14-specific loci D13S10, D13S21, and D13S22, which are detected by the cloned DNA markers p7D2, pG24E2.4, and pG14E1.9, respectively. Analysis of a panel of seven cell lines that showed differential methylation at a Not I site between D13S10 and D13S21 proved physical linkage of the two loci to the same 875-kb Not I fragment. D13S22 mapped to a different Not I fragment, precluding the possibility that D13S22 is located between D13S10 and D13S21. PFGE analysis of Not I partial digests placed the 1850-kb Not I fragment containing D13S22 immediately adjacent to the 875-kb fragment containing the other two loci. The proximal rearrangement breakpoint in a cell line carrying a del13(q14.1q21.2) was detected by D13S21 but not by D13S10, demonstrating that D13S21 lies proximal to D13S10. Quantitative analysis of hybridization signals of the three DNA probes to DNA from the same cell line indicated that only D13S10 was deleted, establishing the order of these loci to be cen-D13S22-D13S21-D13S10-tel. Surprisingly, this order was estimated to be 35,000 times less likely than that favored by genetic linkage analysis. Images PMID:1970636

A Physical Map, Including a BAC/PAC Clone Contig, of the Williams-Beuren Syndrome–Deletion Region at 7q11.23

PubMed Central

Peoples, Risa; Franke, Yvonne; Wang, Yu-Ker; Pérez-Jurado, Luis; Paperna, Tamar; Cisco, Michael; Francke, Uta

2000-01-01

Summary Williams-Beuren syndrome (WBS) is a developmental disorder caused by haploinsufficiency for genes in a 2-cM region of chromosome band 7q11.23. With the exception of vascular stenoses due to deletion of the elastin gene, the various features of WBS have not yet been attributed to specific genes. Although ⩾16 genes have been identified within the WBS deletion, completion of a physical map of the region has been difficult because of the large duplicated regions flanking the deletion. We present a physical map of the WBS deletion and flanking regions, based on assembly of a bacterial artificial chromosome/P1-derived artificial chromosome contig, analysis of high-throughput genome-sequence data, and long-range restriction mapping of genomic and cloned DNA by pulsed-field gel electrophoresis. Our map encompasses 3 Mb, including 1.6 Mb within the deletion. Two large duplicons, flanking the deletion, of ⩾320 kb contain unique sequence elements from the internal border regions of the deletion, such as sequences from GTF2I (telomeric) and FKBP6 (centromeric). A third copy of this duplicon exists in inverted orientation distal to the telomeric flanking one. These duplicons show stronger sequence conservation with regard to each other than to the presumptive ancestral loci within the common deletion region. Sequence elements originating from beyond 7q11.23 are also present in these duplicons. Although the duplicons are not present in mice, the order of the single-copy genes in the conserved syntenic region of mouse chromosome 5 is inverted relative to the human map. A model is presented for a mechanism of WBS-deletion formation, based on the orientation of duplicons' components relative to each other and to the ancestral elements within the deletion region. PMID:10631136

Applied cartographic communication: map symbolization for atlases.

USGS Publications Warehouse

Morrison, J.L.

1984-01-01

A detailed investigation of the symbolization used on general-purpose atlas reference maps. It indicates how theories of cartographic communication can be put into practice. Two major points emerge. First, that a logical scheme can be constructed from existing cartographic research and applied to an analysis of the choice of symbolization on a map. Second, the same structure appears to allow the cartographer to specify symbolization as a part of map design. An introductory review of cartographic communication is followed by an analysis of selected maps' usage of point, area and line symbols, boundaries, text and colour usage.-after Author

Geomorphology and depositional subenvironments of Gulf Islands National Seashore, Perdido Key and Santa Rosa Island, Florida

USGS Publications Warehouse

Morton, Robert A.; Montgomery, Marilyn C.

2010-01-01

The primary mapping procedures were supervised functions within a Geographic Information System (GIS) that were applied to delineate and classify depositional subenvironments and features, collectively referred to as map units. The delineated boundaries of the map units were exported to create one shapefile, and are differentiated by the field "Type" in the associated attribute table. Map units were delineated and classified based on differences in tonal patterns of features in contrast to adjacent features observed on orthophotography. Land elevations from recent lidar surveys served as supplementary data to assist in delineating the map unit boundaries.

Using a detailed uncertainty analysis to adjust mapped rates of forest disturbance derived from Landsat time series data (Invited)

NASA Astrophysics Data System (ADS)

Cohen, W. B.; Yang, Z.; Stehman, S.; Huang, C.; Healey, S. P.

2013-12-01

Forest ecosystem process models require spatially and temporally detailed disturbance data to accurately predict fluxes of carbon or changes in biodiversity over time. A variety of new mapping algorithms using dense Landsat time series show great promise for providing disturbance characterizations at an annual time step. These algorithms provide unprecedented detail with respect to timing, magnitude, and duration of individual disturbance events, and causal agent. But all maps have error and disturbance maps in particular can have significant omission error because many disturbances are relatively subtle. Because disturbance, although ubiquitous, can be a relatively rare event spatially in any given year, omission errors can have a great impact on mapped rates. Using a high quality reference disturbance dataset, it is possible to not only characterize map errors but also to adjust mapped disturbance rates to provide unbiased rate estimates with confidence intervals. We present results from a national-level disturbance mapping project (the North American Forest Dynamics project) based on the Vegetation Change Tracker (VCT) with annual Landsat time series and uncertainty analyses that consist of three basic components: response design, statistical design, and analyses. The response design describes the reference data collection, in terms of the tool used (TimeSync), a formal description of interpretations, and the approach for data collection. The statistical design defines the selection of plot samples to be interpreted, whether stratification is used, and the sample size. Analyses involve derivation of standard agreement matrices between the map and the reference data, and use of inclusion probabilities and post-stratification to adjust mapped disturbance rates. Because for NAFD we use annual time series, both mapped and adjusted rates are provided at an annual time step from ~1985-present. Preliminary evaluations indicate that VCT captures most of the higher intensity disturbances, but that many of the lower intensity disturbances (thinnings, stress related to insects and disease, etc.) are missed. Because lower intensity disturbances are a large proportion of the total set of disturbances, adjusting mapped disturbance rates to include these can be important for inclusion in ecosystem process models. The described statistical disturbance rate adjustments are aspatial in nature, such that the basic underlying map is unchanged. For spatially explicit ecosystem modeling, such adjustments, although important, can be difficult to directly incorporate. One approach for improving the basic underlying map is an ensemble modeling approach that uses several different complementary maps, each derived from a different algorithm and having their own strengths and weaknesses relative to disturbance magnitude and causal agent of disturbance. We will present results from a pilot study associated with the Landscape Change Monitoring System (LCMS), an emerging national-level program that builds upon NAFD and the well-established Monitoring Trends in Burn Severity (MTBS) program.

Description of polymerase chain reaction and sequencing DNA Mycobacterium tuberculosis from specimen sputum of tuberculosis patients in Medan

NASA Astrophysics Data System (ADS)

Lily; Siregar, Y.; Ilyas, S.

2018-03-01

This study purposed to describe the product Polymerase Chain Reaction (PCR) and sequencing of DNA Mycobacterium (M.) tuberculosis from sputum of tuberculosis (TB) patients in Medan. Sputum was collected from patients that diagnosed with pulmonary TB by a physician. Specimen processed by PCR method of Li et al. and sequencing at Macrogen Laboratory. All of 12 product PCR were showed brightness bands at 126 base pair (bp). These results indicated similarity to the study of Li et al. Sequencing analysis showed the presence of a mutation and non-mutation groups of M. tuberculosis. The reference and outcome berange of the mutation and non-mutation of M. tuberculosis were 56-107, 59-85, 60-120 and 63-94, respectively. The percentage bp difference between the outcome and references for mutation and non-mutation were 3.448-6.569and 3.278-7.428%, respectively. In conclusion, the successful amplification of PCR products in a 1.5% agarose gel electrophoresis where all 12 sputa contained rpoB-positive M. tuberculosis and 0.644% difference was found between the outcome with reference bp of the mutation and non-mutation M. tuberculosis groups.

Anatomy of a hash-based long read sequence mapping algorithm for next generation DNA sequencing.

PubMed

Misra, Sanchit; Agrawal, Ankit; Liao, Wei-keng; Choudhary, Alok

2011-01-15

Recently, a number of programs have been proposed for mapping short reads to a reference genome. Many of them are heavily optimized for short-read mapping and hence are very efficient for shorter queries, but that makes them inefficient or not applicable for reads longer than 200 bp. However, many sequencers are already generating longer reads and more are expected to follow. For long read sequence mapping, there are limited options; BLAT, SSAHA2, FANGS and BWA-SW are among the popular ones. However, resequencing and personalized medicine need much faster software to map these long sequencing reads to a reference genome to identify SNPs or rare transcripts. We present AGILE (AliGnIng Long rEads), a hash table based high-throughput sequence mapping algorithm for longer 454 reads that uses diagonal multiple seed-match criteria, customized q-gram filtering and a dynamic incremental search approach among other heuristics to optimize every step of the mapping process. In our experiments, we observe that AGILE is more accurate than BLAT, and comparable to BWA-SW and SSAHA2. For practical error rates (< 5%) and read lengths (200-1000 bp), AGILE is significantly faster than BLAT, SSAHA2 and BWA-SW. Even for the other cases, AGILE is comparable to BWA-SW and several times faster than BLAT and SSAHA2. http://www.ece.northwestern.edu/~smi539/agile.html.

Quantitative susceptibility mapping: Report from the 2016 reconstruction challenge.

PubMed

Langkammer, Christian; Schweser, Ferdinand; Shmueli, Karin; Kames, Christian; Li, Xu; Guo, Li; Milovic, Carlos; Kim, Jinsuh; Wei, Hongjiang; Bredies, Kristian; Buch, Sagar; Guo, Yihao; Liu, Zhe; Meineke, Jakob; Rauscher, Alexander; Marques, José P; Bilgic, Berkin

2018-03-01

The aim of the 2016 quantitative susceptibility mapping (QSM) reconstruction challenge was to test the ability of various QSM algorithms to recover the underlying susceptibility from phase data faithfully. Gradient-echo images of a healthy volunteer acquired at 3T in a single orientation with 1.06 mm isotropic resolution. A reference susceptibility map was provided, which was computed using the susceptibility tensor imaging algorithm on data acquired at 12 head orientations. Susceptibility maps calculated from the single orientation data were compared against the reference susceptibility map. Deviations were quantified using the following metrics: root mean squared error (RMSE), structure similarity index (SSIM), high-frequency error norm (HFEN), and the error in selected white and gray matter regions. Twenty-seven submissions were evaluated. Most of the best scoring approaches estimated the spatial frequency content in the ill-conditioned domain of the dipole kernel using compressed sensing strategies. The top 10 maps in each category had similar error metrics but substantially different visual appearance. Because QSM algorithms were optimized to minimize error metrics, the resulting susceptibility maps suffered from over-smoothing and conspicuity loss in fine features such as vessels. As such, the challenge highlighted the need for better numerical image quality criteria. Magn Reson Med 79:1661-1673, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

Comparison of (GTG)5-oligonucleotide and ribosomal intergenic transcribed spacer (ITS)-PCR for molecular typing of Klebsiella isolates.

PubMed

Ryberg, Anna; Olsson, Crister; Ahrné, Siv; Monstein, Hans-Jürg

2011-02-01

Molecular typing of Klebsiella species has become important for monitoring dissemination of β-lactamase-producers in hospital environments. The present study was designed to evaluate poly-trinucleotide (GTG)(5)- and rDNA intergenic transcribed spacer (ITS)-PCR fingerprint analysis for typing of Klebsiella pneumoniae and Klebsiella oxytoca isolates. Multiple displacement amplified DNA derived from 19 K. pneumoniae (some with an ESBL-phenotype), 35 K. oxytoca isolates, five K. pneumoniae, two K. oxytoca, three Raoultella, and one Enterobacter aerogenes type and reference strains underwent (GTG)(5) and ITS-PCR analysis. Dendrograms were constructed using cosine coefficient and the Neighbour joining method. (GTG)(5) and ITS-PCR analysis revealed that K. pneumoniae and K. oxytoca isolates, reference and type strains formed distinct cluster groups, and tentative subclusters could be established. We conclude that (GTG)(5) and ITS-PCR analysis combined with automated capillary electrophoresis provides promising tools for molecular typing of Klebsiella isolates. Copyright © 2010 Elsevier B.V. All rights reserved.

NIST Efforts to Quality-Assure Gunpowder Measurements

NASA Technical Reports Server (NTRS)

MacCrehan, William A.; Reardon, Michelle R.

2000-01-01

In the past few years, the National Institute for Standards and Technology (NIST) has been promoting the idea of quantitatively determining the additives in smokeless gunpowder using micellar capillary electrophoresis as a means of investigating the criminal use of hand guns and pipe bombs. As a part of this effort, we have evaluated both supercritical fluid and ultrasonic solvent extractions for the quantitative recovery of nitroglycerin (NG), diphenylamine (DPA), N-nitrosodiphenylamine (NnDPA), and ethyl centralite (EC) from gunpowder. Recoveries were evaluated by repeat extraction and matrix spiking experiments. The final extraction protocol provides greater than 95 percent recoveries. To help other researches validate their own analytical method for additive determinations, NIST is exploring the development of a standard reference material, Additives in Smokeless Gunpowder. The evaluated method is being applied to two double-base (NG-containing) powders, one stabilized with diphenylamine and the other with ethyl centralite. As part of this reference material development effort, we are conducting an interlaboratory comparison exercise among the forensic and military gunpowder measurement community.

Characterization of Escherichia coli O157:H7 in New Zealand using multiple-locus variable-number tandem-repeat analysis.

PubMed

Dyet, K H; Robertson, I; Turbitt, E; Carter, P E

2011-03-01

Recently, multiple-locus variable-number tandem-repeat analysis (MLVA) has been proposed as an alternative to pulsed-field gel electrophoresis (PFGE) for characterization of Escherichia coli O157:H7. In this study we characterized 118 E. coli O157:H7 isolates from cases of gastrointestinal disease in New Zealand using XbaI PFGE profiles and a MLVA scheme that assessed variability in eight polymorphic loci. The 118 isolates characterized included all 80 E. coli O157:H7 referred to New Zealand's Enteric Reference Laboratory in 2006 and 29 phage-type 2 isolates from 2005. When applied to these isolates the discriminatory power of PFGE and MLVA was not significantly different. However, MLVA data may be more epidemiologically relevant as isolates from family clusters of disease had identical MLVA profiles, even when the XbaI PFGE profiles differed slightly. Furthermore, most isolates with indistinguishable XbaI PFGE profiles that did not appear to be epidemiologically related had distinct MLVA profiles.

Middle Atmosphere Program. Handbook for MAP. Volume 16: Atmospheric Structure and Its Variation in the Region 20 to 120 Km. Draft of a New Reference Middle Atmosphere

NASA Technical Reports Server (NTRS)

Labitzke, K. (Editor); Barnett, J. J. (Editor); Edwards, B. (Editor)

1985-01-01

A draft of a new reference atmosphere for the region between 20 and 80 km which depends largely on recent satellite experiments covering the globe from 80 deg S to 80 deg N is given. A separate international tropical reference atmosphere is given, as well as reference ozone models for the middle atmosphere.

Permeability of soils in Mississippi

USGS Publications Warehouse

O'Hara, Charles G.

1994-01-01

The permeability of soils in Mississippi was determined and mapped using a geographic information system (GIS). Soil permeabilities in Mississippi were determined to range in value from nearly 0.0 to values exceeding 5.0 inches per hour. The U.S. Soil Conservation Service's State Soil Geographic Data Base (STATSGO) was used as the primary source of data for the determination of area-weighted soil permeability. STATSGO provides soil layer properties that are spatially referenced to mapped areas. These mapped areas are referred to as polygons in the GIS. The polygons arc boundaries of soils mapped as a group and are given unique Map Unit Identifiers (MUIDs). The data describing the physical characteristics of the soils within each polygon are stored in a tabular data base format and are referred to as attributes. The U.S. Soil Conservation Service developed STATSGO to be primarily used as a guide for regional resource planning, management, and monitoring. STATSGO was designed so that soil information could be extracted from properties tables at the layer level, combined by component, and statistically expanded to cover the entire map unit. The results of this study provide a mapped value for permeability which is representative of the vertical permeability of soils in that area. The resultant permeability map provides a representative vertical soil permeability for a given area sufficient for county, multi- county, and area planning, and will be used as the soil permeability data component in the evaluation of the susceptibility of major aquifers to contami- nation in Mississippi.

Electrophoresis tests on STS-3 and ground control experiments - A basis for future biological sample selections

NASA Technical Reports Server (NTRS)

Morrison, D. R.; Lewis, M. L.

1982-01-01

Static zone electrophoresis is an electrokinetic method of separating macromolecules and small particles. However, its application for the isolation of biological cells and concentrated protein solutions is limited by sedimentation and convection. Microgravity eliminates or reduces sedimentation, floatation, and density-driven convection arising from either Joule heating or concentration differences. The advantages of such an environment were first demonstrated in space during the Apollo 14 and 16 missions. In 1975 the Electrophoresis Technology Experiment (MA-011) was conducted during the Apollo-Soyuz Test Project flight. In 1979 a project was initiated to repeat the separations of human kidney cells. One of the major objectives of the Electrophoresis Equipment Verification Tests (EEVT) on STS-3 was to repeat and thereby validate the first successful electrophoretic separation of human kidney cells. Attention is given to the EEVT apparatus, the preflight electrophoresis, and inflight operational results.

A physical map of the human regulator of complement activation gene cluster linking the complement genes CR1, CR2, DAF, and C4BP

PubMed Central

1988-01-01

We report the organization of the human genes encoding the complement components C4-binding protein (C4BP), C3b/C4b receptor (CR1), decay accelerating factor (DAF), and C3dg receptor (CR2) within the regulator of complement activation (RCA) gene cluster. Using pulsed field gel electrophoresis analysis these genes have been physically linked and aligned as CR1-CR2-DAF-C4BP in an 800-kb DNA segment. The very tight linkage between the CR1 and the C4BP loci, contrasted with the relative long DNA distance between these genes, suggests the existence of mechanisms interfering with recombination within the RCA gene cluster. PMID:2450163

A clone-free, single molecule map of the domestic cow (Bos taurus) genome.

PubMed

Zhou, Shiguo; Goldstein, Steve; Place, Michael; Bechner, Michael; Patino, Diego; Potamousis, Konstantinos; Ravindran, Prabu; Pape, Louise; Rincon, Gonzalo; Hernandez-Ortiz, Juan; Medrano, Juan F; Schwartz, David C

2015-08-28

The cattle (Bos taurus) genome was originally selected for sequencing due to its economic importance and unique biology as a model organism for understanding other ruminants, or mammals. Currently, there are two cattle genome sequence assemblies (UMD3.1 and Btau4.6) from groups using dissimilar assembly algorithms, which were complemented by genetic and physical map resources. However, past comparisons between these assemblies revealed substantial differences. Consequently, such discordances have engendered ambiguities when using reference sequence data, impacting genomic studies in cattle and motivating construction of a new optical map resource--BtOM1.0--to guide comparisons and improvements to the current sequence builds. Accordingly, our comprehensive comparisons of BtOM1.0 against the UMD3.1 and Btau4.6 sequence builds tabulate large-to-immediate scale discordances requiring mediation. The optical map, BtOM1.0, spanning the B. taurus genome (Hereford breed, L1 Dominette 01449) was assembled from an optical map dataset consisting of 2,973,315 (439 X; raw dataset size before assembly) single molecule optical maps (Rmaps; 1 Rmap = 1 restriction mapped DNA molecule) generated by the Optical Mapping System. The BamHI map spans 2,575.30 Mb and comprises 78 optical contigs assembled by a combination of iterative (using the reference sequence: UMD3.1) and de novo assembly techniques. BtOM1.0 is a high-resolution physical map featuring an average restriction fragment size of 8.91 Kb. Comparisons of BtOM1.0 vs. UMD3.1, or Btau4.6, revealed that Btau4.6 presented far more discordances (7,463) vs. UMD3.1 (4,754). Overall, we found that Btau4.6 presented almost double the number of discordances than UMD3.1 across most of the 6 categories of sequence vs. map discrepancies, which are: COMPLEX (misassembly), DELs (extraneous sequences), INSs (missing sequences), ITs (Inverted/Translocated sequences), ECs (extra restriction cuts) and MCs (missing restriction cuts). Alignments of UMD3.1 and Btau4.6 to BtOM1.0 reveal discordances commensurate with previous reports, and affirm the NCBI's current designation of UMD3.1 sequence assembly as the "reference assembly" and the Btau4.6 as the "alternate assembly." The cattle genome optical map, BtOM1.0, when used as a comprehensive and largely independent guide, will greatly assist improvements to existing sequence builds, and later serve as an accurate physical scaffold for studies concerning the comparative genomics of cattle breeds.

Techniques for investigation of an apparent outbreak of infections with Candida glabrata.

PubMed Central

Arif, S; Barkham, T; Power, E G; Howell, S A

1996-01-01

A cluster of Candida glabrata isolates recovered from seven patients in an intensive care unit over a 10-week period were compared with a collection of isolates from six epidemiologically distinct outpatients and a reference strain by several DNA typing methods. Restriction enzyme analysis with HinII distinguished 13 strains from the 14 sources and was the method of choice. Pulsed-field gel electrophoresis and random amplification of polymorphic DNA both detected nine types from the 14 sources; however, the results of these two methods did not always correlate. These methods demonstrated that five of the seven patients had distinguishable strains and that cross-infection was unlikely. PMID:8862586

Improved maize reference genome with single-molecule technologies.

PubMed

Jiao, Yinping; Peluso, Paul; Shi, Jinghua; Liang, Tiffany; Stitzer, Michelle C; Wang, Bo; Campbell, Michael S; Stein, Joshua C; Wei, Xuehong; Chin, Chen-Shan; Guill, Katherine; Regulski, Michael; Kumari, Sunita; Olson, Andrew; Gent, Jonathan; Schneider, Kevin L; Wolfgruber, Thomas K; May, Michael R; Springer, Nathan M; Antoniou, Eric; McCombie, W Richard; Presting, Gernot G; McMullen, Michael; Ross-Ibarra, Jeffrey; Dawe, R Kelly; Hastie, Alex; Rank, David R; Ware, Doreen

2017-06-22

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.

Networked differential GPS system

NASA Technical Reports Server (NTRS)

Sheynblat, Leonid (Inventor); Kalafus, Rudolph M. (Inventor); Loomis, Peter V. W. (Inventor); Mueller, K. Tysen (Inventor)

1994-01-01

An embodiment of the present invention relates to a worldwide network of differential GPS reference stations (NDGPS) that continually track the entire GPS satellite constellation and provide interpolations of reference station corrections tailored for particular user locations between the reference stations Each reference station takes real-time ionospheric measurements with codeless cross-correlating dual-frequency carrier GPS receivers and computes real-time orbit ephemerides independently. An absolute pseudorange correction (PRC) is defined for each satellite as a function of a particular user's location. A map of the function is constructed, with iso-PRC contours. The network measures the PRCs at a few points, so-called reference stations and constructs an iso-PRC map for each satellite. Corrections are interpolated for each user's site on a subscription basis. The data bandwidths are kept to a minimum by transmitting information that cannot be obtained directly by the user and by updating information by classes and according to how quickly each class of data goes stale given the realities of the GPS system. Sub-decimeter-level kinematic accuracy over a given area is accomplished by establishing a mini-fiducial network.

Geologic map of Yosemite National Park and vicinity, California

USGS Publications Warehouse

Huber, N.K.; Bateman, P.C.; Wahrhaftig, Clyde

1989-01-01

This digital map database represents the general distribution of bedrock and surficial deposits of the Yosemite National Park vicinity. It was produced directly from the file used to create the print version in 1989. The Yosemite National Park region is comprised of portions of 15 7.5 minute quadrangles. The original publication of the map in 1989 included the map, described map units and provided correlations, as well as a geologic summary and references, all on the same sheet. 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 1:125,000 or smaller.

Geologic maps of the eastern Alaska Range, Alaska (1:63,360 scale)

USGS Publications Warehouse

Nokleberg, Warren J.; Aleinikoff, John N.; Bond, Gerard C.; Ferrians, Oscar J.; Herzon, Paige L.; Lange, Ian M.; Miyaoka, Ronny T.; Richter, Donald H.; Schwab, Carl E.; Silva, Steven R.; Smith, Thomas E.; Zehner, Richard E.

2015-01-01

This report provides a description of map units for a suite of 44 inch-to-mile (1:63,360-scale) geologic quadrangle maps of the eastern Alaska Range. This report also contains a geologic and tectonic summary and a comprehensive list of references pertaining to geologic mapping and specialized studies of the region. In addition to the geologic maps of the eastern Alaska Range, this package includes a list of map units and an explanation of map symbols and abbreviations. The geologic maps display detailed surficial and bedrock geology, structural and stratigraphic data, portrayal of the active Denali fault that bisects the core of the east–west-trending range, and portrayal of other young faults along the north and south flanks of the range.