Analysis of Mycobacterium avium subspecies paratuberculosis mutant libraries reveals loci-dependent transposition biases and strategies to novel mutant discovery

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP), the etiologic agent of Johne’s disease, is one of the most important bacterial pathogens in ruminants. The lack of efficacious control measures demands a thorough understanding of MAP pathogenesis to develop new vaccines and diagnostic tests. The ge...

Genomic analysis reveals candidate genes for PPV resistance in apricot (Prunus armeniaca L.)

USDA-ARS?s Scientific Manuscript database

Sharka disease, caused by Plum pox virus (PPV), is the most important disease affecting Prunus species. A major PPV resistance locus (PPVres) was previously mapped to the upper part of apricot (Prunus armeniaca) linkage group 1. In this study, a physical map of the PPVres locus in the PPV resistan...

Geologic Mapping of Ascraeus Mons, Mars

NASA Technical Reports Server (NTRS)

Mohr, K. J.; Williams, D. A.; Garry, W. B.

2016-01-01

Ascraeus Mons (AM) is the northeastern most large shield volcano residing in the Tharsis province on Mars. We are funded by NASA's Mars Data Analysis Program to complete a digital geologic map based on the mapping style. Previous mapping of a limited area of these volcanoes using HRSC images (13-25 m/pixel) revealed a diverse distribution of volcanic landforms within the calderas, along the flanks, rift aprons, and surrounding plains. The general scientific objectives for which this mapping is based is to show the different lava flow morphologies across AM to better understand the evolution and geologic history.

Mapping Mathematics in Classroom Discourse

ERIC Educational Resources Information Center

Herbel-Eisenmann, Beth A.; Otten, Samuel

2011-01-01

This article offers a particular analytic method from systemic functional linguistics, "thematic analysis," which reveals the mathematical meaning potentials construed in discourse. Addressing concerns that discourse analysis is too often content-free, thematic analysis provides a way to represent semantic structures of mathematical content,…

Vegetative and geologic mapping of the western Seward Peninsula, Alaska, based on ERTS-1 imagery

NASA Technical Reports Server (NTRS)

Anderson, J. H.; Shapiro, L. H.; Belon, A. E.

1973-01-01

ERTS-1 scene 1009-22095 (Western Seward Peninsula, Alaska) has been studied, partly as a training exercise, to evaluate whether direct visual examination of individual and custom color-composite prints can provide new information on the vegetation and geology of this relatively well known area of Alaska. The vegetation analysis reveals seven major vegetation types, only four of which are described on existing vegetation maps. In addition, the ERTS analysis provides greater detail than the existing maps on the areal distribution of vegetation types. The geologic analysis demonstrates that most of the major rock units and geomorphic boundaries shown on the available geologic maps could also be identified on the ERTS data. Several major high-angle faults were observed, but the zones of thrust faults which are much less obvious.

Study of USGS/NASA land use classification system. [computer analysis from LANDSAT data

NASA Technical Reports Server (NTRS)

Spann, G. W.

1975-01-01

The results of a computer mapping project using LANDSAT data and the USGS/NASA land use classification system are summarized. During the computer mapping portion of the project, accuracies of 67 percent to 79 percent were achieved using Level II of the classification system and a 4,000 acre test site centered on Douglasville, Georgia. Analysis of response to a questionaire circulated to actual and potential LANDSAT data users reveals several important findings: (1) there is a substantial desire for additional information related to LANDSAT capabilities; (2) a majority of the respondents feel computer mapping from LANDSAT data could aid present or future projects; and (3) the costs of computer mapping are substantially less than those of other methods.

Analysis of the Immune Response to a Major Membrane Protein of Mycobacterium avium subsp. paratuberculosis in Experimentally and Naturally Infected Cattle

USDA-ARS?s Scientific Manuscript database

The 35 kDa major membrane protein (MMP) of Mycobacterium avium subsp. paratuberculosis (Map) is implicated in the pathogenesis of paratuberculosis (Ptb) in cattle. Understanding the immune response to MMP could reveal how Map evades immune elimination and provide information needed for developing a ...

Analysis of global oceanic rainfall from microwave data

NASA Technical Reports Server (NTRS)

Rao, M.

1978-01-01

A Global Rainfall Atlas was prepared from Nimbus 5 ESMR data. The Atlas includes global oceanic rainfall maps based on weekly, monthly and seasonal averages, complete through the end of 1975. Similar maps for 1973 and 1974 were studied. They reveal several previously unknown areas of enhanced rainfall and preliminary data on interannual variability of oceanic rainfall.

The Effect of Concept Mapping on Student Understanding and Correlation with Student Learning Styles

NASA Astrophysics Data System (ADS)

Mosley, William G.

This study investigated the use of concept mapping as a pedagogical strategy to promote change in the learning styles of pre-nursing students. Students' individual learning styles revealed two subsets of students; those who demonstrated a learning style that favors abstract conceptualization and those who demonstrated a learning style that favors concrete experience. Students in the experimental groups performed concept mapping activities designed to facilitate an integrative understanding of interactions between various organ systems of the body while the control group received a traditional didactic instruction without performing concept mapping activities. Both qualitative and quantitative data were collected in order to measure differences in student achievement. Analysis of the quantitative data revealed no significant change in the learning styles of students in either the control or experimental groups. Learning style groups were analyzed qualitatively for recurring or emergent themes that students identified as facilitating their learning. An analysis of qualitative data revealed that most students in the pre-nursing program were able to identify concepts within the class based upon visual cues, and a majority of these students exhibited the learning style of abstract conceptualization. As the laboratory experience for the course involves an examination of the anatomical structures of the human body, a visual identification of these structures seemed to be the most logical method to measure students' ability to identify anatomical structures.

Functional organization of glomerular maps in the mouse accessory olfactory bulb

PubMed Central

Hammen, Gary F.; Turaga, Diwakar; Holy, Timothy E.; Meeks, Julian P.

2014-01-01

Summary The mammalian accessory olfactory system (AOS) extracts information about species, sex, and individual identity from social odors, but its functional organization remains unclear. We imaged presynaptic Ca2+ signals in vomeronasal inputs to the accessory olfactory bulb (AOB) during peripheral stimulation using light sheet microscopy. Urine- and steroid-responsive glomeruli densely innervated the anterior AOB. Glomerular activity maps for sexually mature female mouse urine overlapped maps for juvenile and/or gonadectomized urine of both sexes, whereas maps for sexually mature male urine were highly distinct. Further spatial analysis revealed a complicated organization involving selective juxtaposition and dispersal of functionally-grouped glomerular classes. Glomeruli that were similarly tuned to urines were often closely associated, whereas more disparately tuned glomeruli were selectively dispersed. Maps to a panel of sulfated steroid odorants identified tightly-juxtaposed groups that were disparately tuned and dispersed groups that were similarly tuned. These results reveal a modular, non-chemotopic spatial organization in the AOB. PMID:24880215

Leveraging electronic health record documentation for Failure Mode and Effects Analysis team identification

PubMed Central

Carson, Matthew B; Lee, Young Ji; Benacka, Corrine; Mutharasan, R. Kannan; Ahmad, Faraz S; Kansal, Preeti; Yancy, Clyde W; Anderson, Allen S; Soulakis, Nicholas D

2017-01-01

Objective: Using Failure Mode and Effects Analysis (FMEA) as an example quality improvement approach, our objective was to evaluate whether secondary use of orders, forms, and notes recorded by the electronic health record (EHR) during daily practice can enhance the accuracy of process maps used to guide improvement. We examined discrepancies between expected and observed activities and individuals involved in a high-risk process and devised diagnostic measures for understanding discrepancies that may be used to inform quality improvement planning. Methods: Inpatient cardiology unit staff developed a process map of discharge from the unit. We matched activities and providers identified on the process map to EHR data. Using four diagnostic measures, we analyzed discrepancies between expectation and observation. Results: EHR data showed that 35% of activities were completed by unexpected providers, including providers from 12 categories not identified as part of the discharge workflow. The EHR also revealed sub-components of process activities not identified on the process map. Additional information from the EHR was used to revise the process map and show differences between expectation and observation. Conclusion: Findings suggest EHR data may reveal gaps in process maps used for quality improvement and identify characteristics about workflow activities that can identify perspectives for inclusion in an FMEA. Organizations with access to EHR data may be able to leverage clinical documentation to enhance process maps used for quality improvement. While focused on FMEA protocols, findings from this study may be applicable to other quality activities that require process maps. PMID:27589944

Quantitative workflow based on NN for weighting criteria in landfill suitability mapping

NASA Astrophysics Data System (ADS)

Abujayyab, Sohaib K. M.; Ahamad, Mohd Sanusi S.; Yahya, Ahmad Shukri; Ahmad, Siti Zubaidah; Alkhasawneh, Mutasem Sh.; Aziz, Hamidi Abdul

2017-10-01

Our study aims to introduce a new quantitative workflow that integrates neural networks (NNs) and multi criteria decision analysis (MCDA). Existing MCDA workflows reveal a number of drawbacks, because of the reliance on human knowledge in the weighting stage. Thus, new workflow presented to form suitability maps at the regional scale for solid waste planning based on NNs. A feed-forward neural network employed in the workflow. A total of 34 criteria were pre-processed to establish the input dataset for NN modelling. The final learned network used to acquire the weights of the criteria. Accuracies of 95.2% and 93.2% achieved for the training dataset and testing dataset, respectively. The workflow was found to be capable of reducing human interference to generate highly reliable maps. The proposed workflow reveals the applicability of NN in generating landfill suitability maps and the feasibility of integrating them with existing MCDA workflows.

QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance

PubMed Central

Ndeve, Arsenio Daniel; Huynh, Bao-Lam; Matthews, William Charles; Roberts, Philip Alan

2018-01-01

Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN). Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL) population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL) were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance. PMID:29300744

QTL mapping and transcriptome analysis of cowpea reveals candidate genes for root-knot nematode resistance.

PubMed

Santos, Jansen Rodrigo Pereira; Ndeve, Arsenio Daniel; Huynh, Bao-Lam; Matthews, William Charles; Roberts, Philip Alan

2018-01-01

Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. However, cowpea yield worldwide is markedly below the known potential due to abiotic and biotic stresses, including parasitism by root-knot nematodes (Meloidogyne spp., RKN). Two resistance genes with dominant effect, Rk and Rk2, have been reported to provide resistance against RKN in cowpea. Despite their description and use in breeding for resistance to RKN and particularly genetic mapping of the Rk locus, the exact genes conferring resistance to RKN remain unknown. In the present work, QTL mapping using recombinant inbred line (RIL) population 524B x IT84S-2049 segregating for a newly mapped locus and analysis of the transcriptome changes in two cowpea near-isogenic lines (NIL) were used to identify candidate genes for Rk and the newly mapped locus. A major QTL, designated QRk-vu9.1, associated with resistance to Meloidogyne javanica reproduction, was detected and mapped on linkage group LG9 at position 13.37 cM using egg production data. Transcriptome analysis on resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively, out of 19,922 unique genes mapped to the common bean reference genome. Among the differentially expressed genes, four and nine genes were found within the QRk-vu9.1 and QRk-vu11.1 QTL intervals, respectively. Six of these genes belong to the TIR-NBS-LRR family of resistance genes and three were upregulated at one or more time-points. Quantitative RT-PCR validated gene expression to be positively correlated with RNA-seq expression pattern for eight genes. Future functional analysis of these cowpea genes will enhance our understanding of Rk-mediated resistance and identify the specific gene responsible for the resistance.

Multivariate statistical analysis of stream-sediment geochemistry in the Grazer Paläozoikum, Austria

USGS Publications Warehouse

Weber, L.; Davis, J.C.

1990-01-01

The Austrian reconnaissance study of stream-sediment composition — more than 30000 clay-fraction samples collected over an area of 40000 km2 — is summarized in an atlas of regional maps that show the distributions of 35 elements. These maps, rich in information, reveal complicated patterns of element abundance that are difficult to compare on more than a small number of maps at one time. In such a study, multivariate procedures such as simultaneous R-Q mode components analysis may be helpful. They can compress a large number of variables into a much smaller number of independent linear combinations. These composite variables may be mapped and relationships sought between them and geological properties. As an example, R-Q mode components analysis is applied here to the Grazer Paläozoikum, a tectonic unit northeast of the city of Graz, which is composed of diverse lithologies and contains many mineral deposits.

Molecular and cellular organization of taste neurons in adult Drosophila pharynx

PubMed Central

Chen, Yu-Chieh (David); Dahanukar, Anupama

2017-01-01

SUMMARY The Drosophila pharyngeal taste organs are poorly characterized despite their location at important sites for monitoring food quality. Functional analysis of pharyngeal neurons has been hindered by the paucity of molecular tools to manipulate them, as well as their relative inaccessibility for neurophysiological investigations. Here, we generate receptor-to-neuron maps of all three pharyngeal taste organs by performing a comprehensive chemoreceptor-GAL4/LexA expression analysis. The organization of pharyngeal neurons reveals similarities and distinctions in receptor repertoires and neuronal groupings compared to external taste neurons. We validate the mapping results by pinpointing a single pharyngeal neuron required for feeding avoidance of L-canavanine. Inducible activation of pharyngeal taste neurons reveals functional differences between external and internal taste neurons and functional subdivision within pharyngeal sweet neurons. Our results provide road maps of pharyngeal taste organs in an insect model system for probing the role of these understudied neurons in controlling feeding behaviors. PMID:29212040

A comparative study of the effect of student and instructor cognitive mapping on student achievement and attitudes in introductory college biology for nonmajors

NASA Astrophysics Data System (ADS)

Dardis, Deborah J. Athas

Within a single research design, this investigation compared the effects of student and instructor cognitive mapping on student achievement and attitudes in introductory college biology for nonmajors. Subjects self-selected into either a Control Group that experienced no cognitive mapping, an Experimental Group 1 that experienced instructor cognitive mapping, or an Experimental Group 2 in which students constructed cognitive maps. Data were collected by a Students' Opinions of Teaching Poll and instructor prepared tests that included objective questions representing all levels of the cognitive domain. An ANCOVA revealed no significant differences in the academic achievement of students in the control and experimental groups. The academic performance of males and females was similar among all three groups of students and data confirmed a lack of interaction between gender and instructional strategy. This investigation confirmed that cognitive mapping will not disrupt a gender-neutral classroom environment. Students' opinions of teaching were overwhelmingly positive. A Kruskal Wallis analysis, followed by a nonparametric Tukey-type multiple comparison, revealed that students who experienced no mapping consistently rated the instructor with higher scores than did students who experienced instructor mapping. Students who cooperatively constructed cognitive maps reported the lowest scores on the opinion polls.

Mapping Landslides Susceptibility in a Traditional Northern Nigerian City

NASA Astrophysics Data System (ADS)

Oluwafemi, Olawale A.; Yakubu, Tahir A.; Muhammad, Mahmud U.; Shitta, Nyofo; Akinwumiju, Akinola S.

2018-05-01

As a result of dearth of relevant information about Landslides Susceptibility in Nigeria, the monitoring and assessment appears intractable. Hence, the study developed a Remote Sensing approach to mapping landslides susceptibility, landuse and landcover analysis in Jos South LGA, Plateau State, Nigeria. Field Observation, SPOT 5 2009 and 2012, ASTER DEM 2009, Geological Map 2006, Topographical Map 1966 were used to map Landslide Susceptibility and Landuse /Lancover Analysis in the study area. Geospatial Analytical Operations employed using ArcGIS 10.3 and Erdas Imagine 2014 include Spatial Modeling, Vectorization, Pre-lineament Extraction, Image Processing among others. Result showed that 72.38 % of the study area is underlain by granitic rocks. The landuse/cover types delineated for the study area include floodplain (29.27 %), farmland (23.96 %), sparsely vegetated land (15.43 %), built up area (13.65 %), vegetated outcrop (8.48 %), light vegetation (5.37 %), thick vegetation (2.39 %), water body (0.58 %), plantation (0.50 %) and mining pond (0.37 %). Landslide Susceptibility Analysis also revealed that 87 % of the study area is relatively at low to very low risk of landslide event. While only 13 % of the study area is at high to very high risk of landslide event. The study revealed that the susceptibility of landslide event is very low in the study area. However, possible landslide event in the hot spots could be pronounced and could destabilize the natural and man-made environmental systems of the study area.

CD4 T Cell Dependent Colitis Exacerbation Following Re-Exposure of Mycobacterium avium ssp. paratuberculosis.

PubMed

Suwandi, Abdulhadi; Bargen, Imke; Pils, Marina C; Krey, Martina; Zur Lage, Susanne; Singh, Anurag K; Basler, Tina; Falk, Christine S; Seidler, Ursula; Hornef, Mathias W; Goethe, Ralph; Weiss, Siegfried

2017-01-01

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of Johne's disease (JD), a chronic inflammatory bowel disease of cattle characterized by intermittent to chronic diarrhea. In addition, MAP has been isolated from Crohn's disease (CD) patients. The impact of MAP on severity of clinical symptoms in JD as well as its role in CD are yet unknown. We have previously shown that MAP is able to colonize inflamed enteric tissue and to exacerbate the inflammatory tissue response (Suwandi et al., 2014). In the present study, we analyzed how repeated MAP administration influences the course of dextran sulfate sodium (DSS)-induced colitis. In comparison to mice exposed to DSS or MAP only, repeated exposure of DSS-treated mice to MAP (DSS/MAP) revealed a significantly enhanced clinical score, reduction of colon length as well as severe CD4 + T cell infiltration into the colonic lamina propria . Functional analysis identified a critical role of CD4 + T cells in the MAP-induced disease exacerbation. Additionally, altered immune responses were observed when closely related mycobacteria species such as M. avium ssp. avium and M. avium ssp. hominissuis were administered. These data reveal the specific ability of MAP to aggravate intestinal inflammation and clinical symptoms. Overall, this phenotype is compatible with similar disease promoting capabilites of MAP in JD and CD.

CD4 T Cell Dependent Colitis Exacerbation Following Re-Exposure of Mycobacterium avium ssp. paratuberculosis

PubMed Central

Suwandi, Abdulhadi; Bargen, Imke; Pils, Marina C.; Krey, Martina; Zur Lage, Susanne; Singh, Anurag K.; Basler, Tina; Falk, Christine S.; Seidler, Ursula; Hornef, Mathias W.; Goethe, Ralph; Weiss, Siegfried

2017-01-01

Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of Johne's disease (JD), a chronic inflammatory bowel disease of cattle characterized by intermittent to chronic diarrhea. In addition, MAP has been isolated from Crohn's disease (CD) patients. The impact of MAP on severity of clinical symptoms in JD as well as its role in CD are yet unknown. We have previously shown that MAP is able to colonize inflamed enteric tissue and to exacerbate the inflammatory tissue response (Suwandi et al., 2014). In the present study, we analyzed how repeated MAP administration influences the course of dextran sulfate sodium (DSS)-induced colitis. In comparison to mice exposed to DSS or MAP only, repeated exposure of DSS-treated mice to MAP (DSS/MAP) revealed a significantly enhanced clinical score, reduction of colon length as well as severe CD4+ T cell infiltration into the colonic lamina propria. Functional analysis identified a critical role of CD4+ T cells in the MAP-induced disease exacerbation. Additionally, altered immune responses were observed when closely related mycobacteria species such as M. avium ssp. avium and M. avium ssp. hominissuis were administered. These data reveal the specific ability of MAP to aggravate intestinal inflammation and clinical symptoms. Overall, this phenotype is compatible with similar disease promoting capabilites of MAP in JD and CD. PMID:28361039

Textural and Mineralogical Analysis of Volcanic Rocks by µ-XRF Mapping.

PubMed

Germinario, Luigi; Cossio, Roberto; Maritan, Lara; Borghi, Alessandro; Mazzoli, Claudio

2016-06-01

In this study, µ-XRF was applied as a novel surface technique for quick acquisition of elemental X-ray maps of rocks, image analysis of which provides quantitative information on texture and rock-forming minerals. Bench-top µ-XRF is cost-effective, fast, and non-destructive, can be applied to both large (up to a few tens of cm) and fragile samples, and yields major and trace element analysis with good sensitivity. Here, X-ray mapping was performed with a resolution of 103.5 µm and spot size of 30 µm over sample areas of about 5×4 cm of Euganean trachyte, a volcanic porphyritic rock from the Euganean Hills (NE Italy) traditionally used in cultural heritage. The relative abundance of phenocrysts and groundmass, as well as the size and shape of the various mineral phases, were obtained from image analysis of the elemental maps. The quantified petrographic features allowed identification of various extraction sites, revealing an objective method for archaeometric provenance studies exploiting µ-XRF imaging.

A network approach of gene co-expression in the zea mays/Aspergillus flavus pathosystem to map host/pathogen interaction pathways

USDA-ARS?s Scientific Manuscript database

A gene co-expression network was generated using a dual RNA-seq study with the fungal pathogen A. flavus and its plant host Z. mays during the initial 3 days of infection. The analysis deciphered novel pathways and mapped genes of interest in both organisms during the infection. This network reveal...

Lake water quality mapping from LANDSAT

NASA Technical Reports Server (NTRS)

Scherz, J. P.

1977-01-01

The lakes in three LANDSAT scenes were mapped by the Bendix MDAS multispectral analysis system. Field checking the maps by three separate individuals revealed approximately 90-95% correct classification for the lake categories selected. Variations between observers was about 5%. From the MDAS color coded maps the lake with the worst algae problem was easily located. This lake was closely checked and a pollution source of 100 cows was found in the springs which fed this lake. The theory, lab work and field work which made it possible for this demonstration project to be a practical lake classification procedure are presented.

Reflectance measurements for the detection and mapping of soil limitations

NASA Technical Reports Server (NTRS)

Benson, L. A.; Frazee, C. J.

1973-01-01

During 1971 and 1972 research was conducted on two fallow fields in the proposed Oahe Irrigation Project to investigate the relationship between the tonal variations observed on aerial photographs and the principal soil limitations of the area. A grid sampling procedure was used to collected detailed field data during the 1972 growing season. The field data was compared to imagery collected on May 14, 1971 at 3050 meters altitude. The imagery and field data were initially evaluated by a visual analysis. Correlation and regression analysis revealed a highly significant correlation and regression analysis revealed a highly significant correlation between the digitized color infrared film data and soil properties such as organic matter content, color, depth to carbonates, bulk density and reflectivity. Computer classification of the multiemulsion film data resulted in maps delineating the areas containing claypan and erosion limitations. Reflectance data from the red spectral band provided the best results.

Time Series Analysis OF SAR Image Fractal Maps: The Somma-Vesuvio Volcanic Complex Case Study

NASA Astrophysics Data System (ADS)

Pepe, Antonio; De Luca, Claudio; Di Martino, Gerardo; Iodice, Antonio; Manzo, Mariarosaria; Pepe, Susi; Riccio, Daniele; Ruello, Giuseppe; Sansosti, Eugenio; Zinno, Ivana

2016-04-01

The fractal dimension is a significant geophysical parameter describing natural surfaces representing the distribution of the roughness over different spatial scale; in case of volcanic structures, it has been related to the specific nature of materials and to the effects of active geodynamic processes. In this work, we present the analysis of the temporal behavior of the fractal dimension estimates generated from multi-pass SAR images relevant to the Somma-Vesuvio volcanic complex (South Italy). To this aim, we consider a Cosmo-SkyMed data-set of 42 stripmap images acquired from ascending orbits between October 2009 and December 2012. Starting from these images, we generate a three-dimensional stack composed by the corresponding fractal maps (ordered according to the acquisition dates), after a proper co-registration. The time-series of the pixel-by-pixel estimated fractal dimension values show that, over invariant natural areas, the fractal dimension values do not reveal significant changes; on the contrary, over urban areas, it correctly assumes values outside the natural surfaces fractality range and show strong fluctuations. As a final result of our analysis, we generate a fractal map that includes only the areas where the fractal dimension is considered reliable and stable (i.e., whose standard deviation computed over the time series is reasonably small). The so-obtained fractal dimension map is then used to identify areas that are homogeneous from a fractal viewpoint. Indeed, the analysis of this map reveals the presence of two distinctive landscape units corresponding to the Mt. Vesuvio and Gran Cono. The comparison with the (simplified) geological map clearly shows the presence in these two areas of volcanic products of different age. The presented fractal dimension map analysis demonstrates the ability to get a figure about the evolution degree of the monitored volcanic edifice and can be profitably extended in the future to other volcanic systems with very distinctive characteristics, with the aim to perform land classification, such as the identification of areas characterized by similar soil use, slopes and exposures.

Assessing Local Knowledge Use in Agroforestry Management with Cognitive Maps

NASA Astrophysics Data System (ADS)

Isaac, Marney E.; Dawoe, Evans; Sieciechowicz, Krystyna

2009-06-01

Small-holder farmers often develop adaptable agroforestry management techniques to improve and diversify crop production. In the cocoa growing region of Ghana, local knowledge on such farm management holds a noteworthy role in the overall farm development. The documentation and analysis of such knowledge use in cocoa agroforests may afford an applicable framework to determine mechanisms driving farmer preference and indicators in farm management. This study employed 12 in-depth farmer interviews regarding variables in farm management as a unit of analysis and utilized cognitive mapping as a qualitative method of analysis. Our objectives were (1) to illustrate and describe agroforestry management variables and associated farm practices, (2) to determine the scope of decision making of individual farmers, and (3) to investigate the suitability of cognitive mapping as a tool for assessing local knowledge use. Results from the cognitive maps revealed an average of 16 ± 3 variables and 19 ± 3 links between management variables in the farmer cognitive maps. Farmer use of advantageous ecological processes was highly central to farm management (48% of all variables), particularly manipulation of organic matter, shade and food crop establishment, and maintenance of a tree stratum as the most common, highly linked variables. Over 85% of variables included bidirectional arrows, interpreted as farm management practices dominated by controllable factors, insofar as farmers indicated an ability to alter most farm characteristics. Local knowledge use on cocoa production revealed detailed indicators for site evaluation, thus affecting farm preparation and management. Our findings suggest that amid multisourced information under conditions of uncertainty, strategies for adaptable agroforestry management should integrate existing and localized management frameworks and that cognitive mapping provides a tool-based approach to advance such a management support system.

Assessing local knowledge use in agroforestry management with cognitive maps.

PubMed

Isaac, Marney E; Dawoe, Evans; Sieciechowicz, Krystyna

2009-06-01

Small-holder farmers often develop adaptable agroforestry management techniques to improve and diversify crop production. In the cocoa growing region of Ghana, local knowledge on such farm management holds a noteworthy role in the overall farm development. The documentation and analysis of such knowledge use in cocoa agroforests may afford an applicable framework to determine mechanisms driving farmer preference and indicators in farm management. This study employed 12 in-depth farmer interviews regarding variables in farm management as a unit of analysis and utilized cognitive mapping as a qualitative method of analysis. Our objectives were (1) to illustrate and describe agroforestry management variables and associated farm practices, (2) to determine the scope of decision making of individual farmers, and (3) to investigate the suitability of cognitive mapping as a tool for assessing local knowledge use. Results from the cognitive maps revealed an average of 16 +/- 3 variables and 19 +/- 3 links between management variables in the farmer cognitive maps. Farmer use of advantageous ecological processes was highly central to farm management (48% of all variables), particularly manipulation of organic matter, shade and food crop establishment, and maintenance of a tree stratum as the most common, highly linked variables. Over 85% of variables included bidirectional arrows, interpreted as farm management practices dominated by controllable factors, insofar as farmers indicated an ability to alter most farm characteristics. Local knowledge use on cocoa production revealed detailed indicators for site evaluation, thus affecting farm preparation and management. Our findings suggest that amid multisourced information under conditions of uncertainty, strategies for adaptable agroforestry management should integrate existing and localized management frameworks and that cognitive mapping provides a tool-based approach to advance such a management support system.

Mapping of the gene for the Mel{sub 1a}-melatonin receptor to human chromosome 4 (MTNR1A) and mouse chromosome 8 (Mtnr1a)

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

Slaugenhaupt, S.A.; Liebert, C.B.; Altherr, M.R.

The pineal hormone melatonin elicits potent circadian and reproductive effects in mammals. The authors report the chromosomal location of the gene for the Mel{sub 1a}-melatonin receptor that likely mediates these circadian and reproductive actions. PCR analysis of human-rodent somatic cell hybrids showed that the receptor gene (MTNR1A) maps to human chromosome 4q35.1. An interspecific backcross analysis revealed that the mouse gene (Mtnr1a) maps to the proximal portion of chromosome 8. These loci may be involved in genetically based circadian and neuroendocrine disorders. 14 refs., 1 fig.

Analysis of Fundus Shape in Highly Myopic Eyes by Using Curvature Maps Constructed from Optical Coherence Tomography

PubMed Central

Miyake, Masahiro; Yamashiro, Kenji; Akagi-Kurashige, Yumiko; Oishi, Akio; Tsujikawa, Akitaka; Hangai, Masanori; Yoshimura, Nagahisa

2014-01-01

Purpose To evaluate fundus shape in highly myopic eyes using color maps created through optical coherence tomography (OCT) image analysis. Methods We retrospectively evaluated 182 highly myopic eyes from 113 patients. After obtaining 12 lines of 9-mm radial OCT scans with the fovea at the center, the Bruch’s membrane line was plotted and its curvature was measured at 1-µm intervals in each image, which was reflected as a color topography map. For the quantitative analysis of the eye shape, mean absolute curvature and variance of curvature were calculated. Results The color maps allowed staphyloma visualization as a ring of green color at the edge and as that of orange-red color at the bottom. Analyses of mean and variance of curvature revealed that eyes with myopic choroidal neovascularization tended to have relatively flat posterior poles with smooth surfaces, while eyes with chorioretinal atrophy exhibited a steep, curved shape with an undulated surface (P<0.001). Furthermore, eyes with staphylomas and those without clearly differed in terms of mean curvature and the variance of curvature: 98.4% of eyes with staphylomas had mean curvature ≥7.8×10−5 [1/µm] and variance of curvature ≥0.26×10−8 [1/µm]. Conclusions We established a novel method to analyze posterior pole shape by using OCT images to construct curvature maps. Our quantitative analysis revealed that fundus shape is associated with myopic complications. These values were also effective in distinguishing eyes with staphylomas from those without. This tool for the quantitative evaluation of eye shape should facilitate future research of myopic complications. PMID:25259853

Dynamics of a distributed drill string system: Characteristic parameters and stability maps

NASA Astrophysics Data System (ADS)

Aarsnes, Ulf Jakob F.; van de Wouw, Nathan

2018-03-01

This paper involves the dynamic (stability) analysis of distributed drill-string systems. A minimal set of parameters characterizing the linearized, axial-torsional dynamics of a distributed drill string coupled through the bit-rock interaction is derived. This is found to correspond to five parameters for a simple drill string and eight parameters for a two-sectioned drill-string (e.g., corresponding to the pipe and collar sections of a drilling system). These dynamic characterizations are used to plot the inverse gain margin of the system, parametrized in the non-dimensional parameters, effectively creating a stability map covering the full range of realistic physical parameters. This analysis reveals a complex spectrum of dynamics not evident in stability analysis with lumped models, thus indicating the importance of analysis using distributed models. Moreover, it reveals trends concerning stability properties depending on key system parameters useful in the context of system and control design aiming at the mitigation of vibrations.

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

PubMed Central

2014-01-01

Background Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation. Results The linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes. Conclusion The obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a separate mapping population. We believe that haplotype information will become increasingly important in identifying marker-trait relationships and regions that are under selection pressure within breeding material. Our attempt at providing a biological basis for the discernment of sub-genomes warrants follow-up studies to streamline the naming of the sub-genomes among different octoploid strawberry maps. PMID:24581289

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map.

PubMed

van Dijk, Thijs; Pagliarani, Giulia; Pikunova, Anna; Noordijk, Yolanda; Yilmaz-Temel, Hulya; Meulenbroek, Bert; Visser, Richard G F; van de Weg, Eric

2014-03-01

Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phytophthora cactorum and Verticillium we built a genome-wide SSR linkage map for the cross Holiday x Korona. We used the previously published MADCE method to obtain full haplotype information for both of the parental cultivars, facilitating in-depth studies on their genomic organisation. The linkage map incorporates 508 segregating loci and represents each of the 28 chromosome pairs of octoploid strawberry, spanning an estimated length of 2050 cM. The sub-genomes are denoted according to their sequence divergence from F. vesca as revealed by marker performance. The map revealed high overall synteny between the sub-genomes, but also revealed two large inversions on LG2C and LG2D, of which the latter was confirmed using a separate mapping population. We discovered interesting breeding features within the parental cultivars by in-depth analysis of our haplotype data. The linkage map-derived homozygosity level of Holiday was similar to the pedigree-derived inbreeding level (33% and 29%, respectively). For Korona we found that the observed homozygosity level was over three times higher than expected from the pedigree (13% versus 3.6%). This could indicate selection pressure on genes that have favourable effects in homozygous states. The level of kinship between Holiday and Korona derived from our linkage map was 2.5 times higher than the pedigree-derived value. This large difference could be evidence of selection pressure enacted by strawberry breeders towards specific haplotypes. The obtained SSR linkage map provides a good base for QTL discovery. It also provides the first biologically relevant basis for the discernment and notation of sub-genomes. For the first time, we revealed genomic rearrangements that were verified in a separate mapping population. We believe that haplotype information will become increasingly important in identifying marker-trait relationships and regions that are under selection pressure within breeding material. Our attempt at providing a biological basis for the discernment of sub-genomes warrants follow-up studies to streamline the naming of the sub-genomes among different octoploid strawberry maps.

Cathepsin B is a novel gender-dependent determinant of cholesterol absorption from the intestine[S

PubMed Central

Wong, Winifred P. S.; Altemus, Jessica B.; Hester, James F.; Chan, Ernest R.; Côté, Jean-François; Serre, David; Sehayek, Ephraim

2013-01-01

We used a mouse C57BL/6J×CASA/Rk intercross to map a locus on chromosome 14 that displayed a gender-dependent effect on cholesterol absorption from the intestine. Studies in congenic animals revealed a complex locus with multiple operating genetic determinants resulting in alternating gender-dependent phenotypic effects. Fine-mapping narrowed the locus to a critical 6.3 Mb interval. Female subcongenics, but not males, of the critical interval displayed a decrease of 33% in cholesterol absorption. RNA-Seq analysis of female subcongenic jejunum revealed that cysteine protease cathepsin B (Ctsb) is a candidate to explain the interval effect. Consistent with the phenotype in critical interval subcongenics, female Ctsb knockout mice, but not males, displayed a decrease of 31% in cholesterol absorption. Although studies in Ctsb knockouts revealed a gender-dependent effect on cholesterol absorption, further fine-mapping dismissed a role for Ctsb in determining the effect of the critical 6.3 Mb interval on cholesterol absorption. PMID:23248330

Alteration mapping at Goldfield, Nevada, by cluster and discriminant analysis of Landsat digital data. [mapping of hydrothermally altered volcanic rocks

NASA Technical Reports Server (NTRS)

Ballew, G.

1977-01-01

The ability of Landsat multispectral digital data to differentiate among 62 combinations of rock and alteration types at the Goldfield mining district of Western Nevada was investigated by using statistical techniques of cluster and discriminant analysis. Multivariate discriminant analysis was not effective in classifying each of the 62 groups, with classification results essentially the same whether data of four channels alone or combined with six ratios of channels were used. Bivariate plots of group means revealed a cluster of three groups including mill tailings, basalt and all other rock and alteration types. Automatic hierarchical clustering based on the fourth dimensional Mahalanobis distance between group means of 30 groups having five or more samples was performed using Johnson's HICLUS program. The results of the cluster analysis revealed hierarchies of mill tailings vs. natural materials, basalt vs. non-basalt, highly reflectant rocks vs. other rocks and exclusively unaltered rocks vs. predominantly altered rocks. The hierarchies were used to determine the order in which sets of multiple discriminant analyses were to be performed and the resulting discriminant functions were used to produce a map of geology and alteration which has an overall accuracy of 70 percent for discriminating exclusively altered rocks from predominantly altered rocks.

Proteomic analysis to investigate color changes of chilled beef longissimus steaks held under carbon monoxide and high oxygen packaging.

PubMed

Yang, Xiaoyin; Wu, Shuang; Hopkins, David L; Liang, Rongrong; Zhu, Lixian; Zhang, Yimin; Luo, Xin

2018-08-01

This study investigated the proteome basis for color stability variations in beef steaks packaged under two modified atmosphere packaging (MAP) methods: HiOx-MAP (80% O 2 /20% CO 2 ) and CO-MAP (0.4% CO/30% CO 2 /69.6% N 2 ) during 15 days of storage. The color stability, pH, and sarcoplasmic proteome analysis of steaks were evaluated on days 0, 5, 10 and 15 of storage. Proteomic results revealed that the differential expression of the sarcoplasmic proteome during storage contributed to the variations in meat color stability between the two MAP methods. Compared with HiOx-MAP steaks, some glycolytic and energy metabolic enzymes important in NADH regeneration and antioxidant processes, antioxidant peroxiredoxins (thioredoxin-dependent peroxide reductase, peroxiredoxin-2, peroxiredoxin-6) and protein DJ-1 were more abundant in CO-MAP steaks. The over-expression of these proteins could induce CO-MAP steaks to maintain high levels of metmyoglobin reducing activity and oxygen consumption rate, resulting in CO-MAP steaks exhibiting better color stability than HiOx-MAP steaks during storage. Copyright © 2018 Elsevier Ltd. All rights reserved.

A 1463 Gene Cattle–Human Comparative Map With Anchor Points Defined by Human Genome Sequence Coordinates

PubMed Central

Everts-van der Wind, Annelie; Kata, Srinivas R.; Band, Mark R.; Rebeiz, Mark; Larkin, Denis M.; Everts, Robin E.; Green, Cheryl A.; Liu, Lei; Natarajan, Shreedhar; Goldammer, Tom; Lee, Jun Heon; McKay, Stephanie; Womack, James E.; Lewin, Harris A.

2004-01-01

A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle–human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH5000 panel to 1913. Of these, 1463 have significant BLASTN hits (E < e–5) against the human genome sequence. A cattle–human comparative map was created using human genome sequence coordinates of the paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle–human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes. PMID:15231756

Topological data analysis of contagion maps for examining spreading processes on networks.

PubMed

Taylor, Dane; Klimm, Florian; Harrington, Heather A; Kramár, Miroslav; Mischaikow, Konstantin; Porter, Mason A; Mucha, Peter J

2015-07-21

Social and biological contagions are influenced by the spatial embeddedness of networks. Historically, many epidemics spread as a wave across part of the Earth's surface; however, in modern contagions long-range edges-for example, due to airline transportation or communication media-allow clusters of a contagion to appear in distant locations. Here we study the spread of contagions on networks through a methodology grounded in topological data analysis and nonlinear dimension reduction. We construct 'contagion maps' that use multiple contagions on a network to map the nodes as a point cloud. By analysing the topology, geometry and dimensionality of manifold structure in such point clouds, we reveal insights to aid in the modelling, forecast and control of spreading processes. Our approach highlights contagion maps also as a viable tool for inferring low-dimensional structure in networks.

Topological data analysis of contagion maps for examining spreading processes on networks

NASA Astrophysics Data System (ADS)

Taylor, Dane; Klimm, Florian; Harrington, Heather A.; Kramár, Miroslav; Mischaikow, Konstantin; Porter, Mason A.; Mucha, Peter J.

2015-07-01

Social and biological contagions are influenced by the spatial embeddedness of networks. Historically, many epidemics spread as a wave across part of the Earth's surface; however, in modern contagions long-range edges--for example, due to airline transportation or communication media--allow clusters of a contagion to appear in distant locations. Here we study the spread of contagions on networks through a methodology grounded in topological data analysis and nonlinear dimension reduction. We construct `contagion maps' that use multiple contagions on a network to map the nodes as a point cloud. By analysing the topology, geometry and dimensionality of manifold structure in such point clouds, we reveal insights to aid in the modelling, forecast and control of spreading processes. Our approach highlights contagion maps also as a viable tool for inferring low-dimensional structure in networks.

Dissociable effects of reward and expectancy during evaluative feedback processing revealed by topographic ERP mapping analysis.

PubMed

Gheza, Davide; Paul, Katharina; Pourtois, Gilles

2017-11-24

Evaluative feedback provided during performance monitoring (PM) elicits either a positive or negative deflection ~250-300ms after its onset in the event-related potential (ERP) depending on whether the outcome is reward-related or not, as well as expected or not. However, it remains currently unclear whether these two deflections reflect a unitary process, or rather dissociable effects arising from non-overlapping brain networks. To address this question, we recorded 64-channel EEG in healthy adult participants performing a standard gambling task where valence and expectancy were manipulated in a factorial design. We analyzed the feedback-locked ERP data using a conventional ERP analysis, as well as an advanced topographic ERP mapping analysis supplemented with distributed source localization. Results reveal two main topographies showing opposing valence effects, and being differently modulated by expectancy. The first one was short-lived and sensitive to no-reward irrespective of expectancy. Source-estimation associated with this topographic map comprised mainly regions of the dorsal anterior cingulate cortex. The second one was primarily driven by reward, had a prolonged time-course and was monotonically influenced by expectancy. Moreover, this reward-related topographical map was best accounted for by intracranial generators estimated in the posterior cingulate cortex. These new findings suggest the existence of dissociable brain systems depending on feedback valence and expectancy. More generally, they inform about the added value of using topographic ERP mapping methods, besides conventional ERP measurements, to characterize qualitative changes occurring in the spatio-temporal dynamic of reward processing during PM. Copyright © 2017 Elsevier B.V. All rights reserved.

Synchrotron imaging reveals bone healing and remodelling strategies in extinct and extant vertebrates

PubMed Central

Anné, Jennifer; Edwards, Nicholas P.; Wogelius, Roy A.; Tumarkin-Deratzian, Allison R.; Sellers, William I.; van Veelen, Arjen; Bergmann, Uwe; Sokaras, Dimosthenis; Alonso-Mori, Roberto; Ignatyev, Konstantin; Egerton, Victoria M.; Manning, Phillip L.

2014-01-01

Current understanding of bone healing and remodelling strategies in vertebrates has traditionally relied on morphological observations through the histological analysis of thin sections. However, chemical analysis may also be used in such interpretations, as different elements are known to be absorbed and used by bone for different physiological purposes such as growth and healing. These chemical signatures are beyond the detection limit of most laboratory-based analytical techniques (e.g. scanning electron microscopy). However, synchrotron rapid scanning–X-ray fluorescence (SRS–XRF) is an elemental mapping technique that uniquely combines high sensitivity (ppm), excellent sample resolution (20–100 µm) and the ability to scan large specimens (decimetre scale) approximately 3000 times faster than other mapping techniques. Here, we use SRS–XRF combined with microfocus elemental mapping (2–20 µm) to determine the distribution and concentration of trace elements within pathological and normal bone of both extant and extinct archosaurs (Cathartes aura and Allosaurus fragilis). Results reveal discrete chemical inventories within different bone tissue types and preservation modes. Chemical inventories also revealed detail of histological features not observable in thin section, including fine structures within the interface between pathological and normal bone as well as woven texture within pathological tissue. PMID:24806709

Thermal Evolution of a Failed Flux Rope Eruption Revealed by Temperature Maps

NASA Astrophysics Data System (ADS)

Song, H.; Zhang, J.; CHEN, Y.

2013-12-01

Flux rope is generally considered to be the fundamental magnetic configuration of a coronal mass ejection (CME). Recent observations suggest that hot channel or blob structures during the eruptions be the direct observational manifestation of flux ropes. In this study, we report our analysis of thermal evolution of a failed solar eruption with an apparent flux rope embedded. The thermal structure of the eruption is revealed through differential emission measure (DEM) analysis technique, which shows detailed temperature maps in both high spatial resolution and high temperature resolution based on SDO/AIA observations. Our results show that the flux rope exists in the corona before the eruption, and its temperature can quickly rise to over 10 MK within one minute of the eruption. The correlation study between the flux rope temperature and the soft x-ray flux suggests that the flux rope should be heated through the direct thermal energy release of magnetic reconnection. Further, we study the kinematic evolution process of the flux rope, in an effort to find the physical mechanism that prevents the magnetic rope eruption to become a full coronal mass ejection. This kind of study using temperature maps might reveal where and when magnetic reconnection takes place during solar eruptions.

Minimal invasive epicardial lead implantation: optimizing cardiac resynchronization with a new mapping device for epicardial lead placement.

PubMed

Maessen, J G; Phelps, B; Dekker, A L A J; Dijkman, B

2004-05-01

To optimize resynchronization in biventricular pacing with epicardial leads, mapping to determine the best pacing site, is a prerequisite. A port access surgical mapping technique was developed that allowed multiple pace site selection and reproducible lead evaluation and implantation. Pressure-volume loops analysis was used for real time guidance in targeting epicardial lead placement. Even the smallest changes in lead position revealed significantly different functional results. Optimizing the pacing site with this technique allowed functional improvement up to 40% versus random pace site selection.

A Method to Reveal Fine-Grained and Diverse Conceptual Progressions during Learning

ERIC Educational Resources Information Center

Lombard, François; Merminod, Marie; Widmer, Vincent; Schneider, Daniel K.

2018-01-01

Empirical data on learners' conceptual progression is required to design curricula and guide students. In this paper, we present the Reference Map Change Coding (RMCC) method for revealing students' progression at a fine-grained level. The method has been developed and tested through the analysis of successive versions of the productions of eight…

Using Vegetation Maps to Provide Information on Soil Distribution

NASA Astrophysics Data System (ADS)

José Ibáñez, Juan; Pérez-Gómez, Rufino; Brevik, Eric C.; Cerdà, Artemi

2016-04-01

Many different types of maps (geology, hydrology, soil, vegetation, etc.) are created to inventory natural resources. Each of these resources is mapped using a unique set of criteria, including scales and taxonomies. Past research has indicated that comparing the results of different but related maps (e.g., soil and geology maps) may aid in identifying deficiencies in those maps. Therefore, this study was undertaken in the Almería Province (Andalusia, Spain) to (i) compare the underlying map structures of soil and vegetation maps and (ii) to investigate if a vegetation map can provide useful soil information that was not shown on a soil map. To accomplish this soil and vegetation maps were imported into ArcGIS 10.1 for spatial analysis. Results of the spatial analysis were exported to Microsoft Excel worksheets for statistical analyses to evaluate fits to linear and power law regression models. Vegetative units were grouped according to the driving forces that determined their presence or absence (P/A): (i) climatophilous (climate is the only determinant of P/A) (ii); lithologic-climate (climate and parent material determine PNV P/A); and (iii) edaphophylous (soil features determine PNV P/A). The rank abundance plots for both the soil and vegetation maps conformed to Willis or Hollow Curves, meaning the underlying structures of both maps were the same. Edaphophylous map units, which represent 58.5% of the vegetation units in the study area, did not show a good correlation with the soil map. Further investigation revealed that 87% of the edaphohygrophylous units (which demand more soil water than is supplied by other soil types in the surrounding landscape) were found in ramblas, ephemeral riverbeds that are not typically classified and mapped as soils in modern systems, even though they meet the definition of soil given by the most commonly used and most modern soil taxonomic systems. Furthermore, these edaphophylous map units tend to be islands of biodiversity that are threatened by anthropogenic activity in the region. Therefore, this study revealed areas in Almería Province that need to be revisited and studied pedologically. The vegetation mapped in these areas and the soils that support it are key components of the earth's critical zone that must be studied, understood, and preserved.

Fourier-Mellin moment-based intertwining map for image encryption

NASA Astrophysics Data System (ADS)

Kaur, Manjit; Kumar, Vijay

2018-03-01

In this paper, a robust image encryption technique that utilizes Fourier-Mellin moments and intertwining logistic map is proposed. Fourier-Mellin moment-based intertwining logistic map has been designed to overcome the issue of low sensitivity of an input image. Multi-objective Non-Dominated Sorting Genetic Algorithm (NSGA-II) based on Reinforcement Learning (MNSGA-RL) has been used to optimize the required parameters of intertwining logistic map. Fourier-Mellin moments are used to make the secret keys more secure. Thereafter, permutation and diffusion operations are carried out on input image using secret keys. The performance of proposed image encryption technique has been evaluated on five well-known benchmark images and also compared with seven well-known existing encryption techniques. The experimental results reveal that the proposed technique outperforms others in terms of entropy, correlation analysis, a unified average changing intensity and the number of changing pixel rate. The simulation results reveal that the proposed technique provides high level of security and robustness against various types of attacks.

Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile.

PubMed

Qi, Xiao-Hua; Xu, Xue-Wen; Lin, Xiao-Jian; Zhang, Wen-Jie; Chen, Xue-Hao

2012-03-01

High-throughput tag-sequencing (Tag-seq) analysis based on the Solexa Genome Analyzer platform was applied to analyze the gene expression profiling of cucumber plant at 5 time points over a 24h period of waterlogging treatment. Approximately 5.8 million total clean sequence tags per library were obtained with 143013 distinct clean tag sequences. Approximately 23.69%-29.61% of the distinct clean tags were mapped unambiguously to the unigene database, and 53.78%-60.66% of the distinct clean tags were mapped to the cucumber genome database. Analysis of the differentially expressed genes revealed that most of the genes were down-regulated in the waterlogging stages, and the differentially expressed genes mainly linked to carbon metabolism, photosynthesis, reactive oxygen species generation/scavenging, and hormone synthesis/signaling. Finally, quantitative real-time polymerase chain reaction using nine genes independently verified the tag-mapped results. This present study reveals the comprehensive mechanisms of waterlogging-responsive transcription in cucumber. Copyright © 2011 Elsevier Inc. All rights reserved.

AtomicJ: An open source software for analysis of force curves

NASA Astrophysics Data System (ADS)

Hermanowicz, Paweł; Sarna, Michał; Burda, Kvetoslava; Gabryś, Halina

2014-06-01

We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar.

PubMed

Croxford, Adam E; Rogers, Tom; Caligari, Peter D S; Wilkinson, Michael J

2008-01-01

* The provision of sequence-tagged site (STS) anchor points allows meaningful comparisons between mapping studies but can be a time-consuming process for nonmodel species or orphan crops. * Here, the first use of high-resolution melt analysis (HRM) to generate STS markers for use in linkage mapping is described. This strategy is rapid and low-cost, and circumvents the need for labelled primers or amplicon fractionation. * Using white lupin (Lupinus albus, x = 25) as a case study, HRM analysis was applied to identify 91 polymorphic markers from expressed sequence tag (EST)-derived and genomic libraries. Of these, 77 generated STS anchor points in the first fully resolved linkage map of the species. The map also included 230 amplified fragment length polymorphisms (AFLP) loci, spanned 1916 cM (84.2% coverage) and divided into the expected 25 linkage groups. * Quantitative trait loci (QTL) analyses performed on the population revealed genomic regions associated with several traits, including the agronomically important time to flowering (tf), alkaloid synthesis and stem height (Ph). Use of HRM-STS markers also allowed us to make direct comparisons between our map and that of the related crop, Lupinus angustifolius, based on the conversion of RFLP, microsatellite and single nucleotide polymorphism (SNP) markers into HRM markers.

Fine-mapping of qGW4.05, a major QTL for kernel weight and size in maize.

PubMed

Chen, Lin; Li, Yong-xiang; Li, Chunhui; Wu, Xun; Qin, Weiwei; Li, Xin; Jiao, Fuchao; Zhang, Xiaojing; Zhang, Dengfeng; Shi, Yunsu; Song, Yanchun; Li, Yu; Wang, Tianyu

2016-04-12

Kernel weight and size are important components of grain yield in cereals. Although some information is available concerning the map positions of quantitative trait loci (QTL) for kernel weight and size in maize, little is known about the molecular mechanisms of these QTLs. qGW4.05 is a major QTL that is associated with kernel weight and size in maize. We combined linkage analysis and association mapping to fine-map and identify candidate gene(s) at qGW4.05. QTL qGW4.05 was fine-mapped to a 279.6-kb interval in a segregating population derived from a cross of Huangzaosi with LV28. By combining the results of regional association mapping and linkage analysis, we identified GRMZM2G039934 as a candidate gene responsible for qGW4.05. Candidate gene-based association mapping was conducted using a panel of 184 inbred lines with variable kernel weights and kernel sizes. Six polymorphic sites in the gene GRMZM2G039934 were significantly associated with kernel weight and kernel size. The results of linkage analysis and association mapping revealed that GRMZM2G039934 is the most likely candidate gene for qGW4.05. These results will improve our understanding of the genetic architecture and molecular mechanisms underlying kernel development in maize.

A novel tandem repeat sequence located on human chromosome 4p: isolation and characterization.

PubMed

Kogi, M; Fukushige, S; Lefevre, C; Hadano, S; Ikeda, J E

1997-06-01

In an effort to analyze the genomic region of the distal half of human chromosome 4p, to where Huntington disease and other diseases have been mapped, we have isolated the cosmid clone (CRS447) that was likely to contain a region with specific repeat sequences. Clone CRS447 was subjected to detailed analysis, including chromosome mapping, restriction mapping, and DNA sequencing. Chromosome mapping by both a human-CHO hybrid cell panel and FISH revealed that CRS447 was predominantly located in the 4p15.1-15.3 region. CRS447 was shown to consist of tandem repeats of 4.7-kb units present on chromosome 4p. A single EcoRI unit was subcloned (pRS447), and the complete sequence was determined as 4752 nucleotides. When pRS447 was used as a probe, the number of copies of this repeat per haploid genome was estimated to be 50-70. Sequence analysis revealed that it contained two internal CA repeats and one putative ORF. Database search established that this sequence was unreported. However, two homologous STS markers were found in the database. We concluded that CRS447/pRS447 is a novel tandem repeat sequence that is mainly specific to human chromosome 4p.

Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity

PubMed Central

King, Andrew J; Montes, Luis R; Clarke, Jasper G; Affleck, Julie; Li, Yi; Witsenboer, Hanneke; van der Vossen, Edwin; van der Linde, Piet; Tripathi, Yogendra; Tavares, Evanilda; Shukla, Parul; Rajasekaran, Thirunavukkarasu; van Loo, Eibertus N; Graham, Ian A

2013-01-01

Current efforts to grow the tropical oilseed crop Jatropha curcas L. economically are hampered by the lack of cultivars and the presence of toxic phorbol esters (PE) within the seeds of most provenances. These PE restrict the conversion of seed cake into animal feed, although naturally occurring ‘nontoxic’ provenances exist which produce seed lacking PE. As an important step towards the development of genetically improved varieties of J. curcas, we constructed a linkage map from four F2 mapping populations. The consensus linkage map contains 502 codominant markers, distributed over 11 linkage groups, with a mean marker density of 1.8 cM per unique locus. Analysis of the inheritance of PE biosynthesis indicated that this is a maternally controlled dominant monogenic trait. This maternal control is due to biosynthesis of the PE occurring only within maternal tissues. The trait segregated 3 : 1 within seeds collected from F2 plants, and QTL analysis revealed that a locus on linkage group 8 was responsible for phorbol ester biosynthesis. By taking advantage of the draft genome assemblies of J. curcas and Ricinus communis (castor), a comparative mapping approach was used to develop additional markers to fine map this mutation within 2.3 cM. The linkage map provides a framework for the dissection of agronomic traits in J. curcas, and the development of improved varieties by marker-assisted breeding. The identification of the locus responsible for PE biosynthesis means that it is now possible to rapidly breed new nontoxic varieties. PMID:23898859

Linkage mapping in the oilseed crop Jatropha curcas L. reveals a locus controlling the biosynthesis of phorbol esters which cause seed toxicity.

PubMed

King, Andrew J; Montes, Luis R; Clarke, Jasper G; Affleck, Julie; Li, Yi; Witsenboer, Hanneke; van der Vossen, Edwin; van der Linde, Piet; Tripathi, Yogendra; Tavares, Evanilda; Shukla, Parul; Rajasekaran, Thirunavukkarasu; van Loo, Eibertus N; Graham, Ian A

2013-10-01

Current efforts to grow the tropical oilseed crop Jatropha curcas L. economically are hampered by the lack of cultivars and the presence of toxic phorbol esters (PE) within the seeds of most provenances. These PE restrict the conversion of seed cake into animal feed, although naturally occurring 'nontoxic' provenances exist which produce seed lacking PE. As an important step towards the development of genetically improved varieties of J. curcas, we constructed a linkage map from four F₂ mapping populations. The consensus linkage map contains 502 codominant markers, distributed over 11 linkage groups, with a mean marker density of 1.8 cM per unique locus. Analysis of the inheritance of PE biosynthesis indicated that this is a maternally controlled dominant monogenic trait. This maternal control is due to biosynthesis of the PE occurring only within maternal tissues. The trait segregated 3 : 1 within seeds collected from F₂ plants, and QTL analysis revealed that a locus on linkage group 8 was responsible for phorbol ester biosynthesis. By taking advantage of the draft genome assemblies of J. curcas and Ricinus communis (castor), a comparative mapping approach was used to develop additional markers to fine map this mutation within 2.3 cM. The linkage map provides a framework for the dissection of agronomic traits in J. curcas, and the development of improved varieties by marker-assisted breeding. The identification of the locus responsible for PE biosynthesis means that it is now possible to rapidly breed new nontoxic varieties. © 2013 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

An uncertainty and sensitivity analysis approach for GIS-based multicriteria landslide susceptibility mapping.

PubMed

Feizizadeh, Bakhtiar; Blaschke, Thomas

2014-03-04

GIS-based multicriteria decision analysis (MCDA) methods are increasingly being used in landslide susceptibility mapping. However, the uncertainties that are associated with MCDA techniques may significantly impact the results. This may sometimes lead to inaccurate outcomes and undesirable consequences. This article introduces a new GIS-based MCDA approach. We illustrate the consequences of applying different MCDA methods within a decision-making process through uncertainty analysis. Three GIS-MCDA methods in conjunction with Monte Carlo simulation (MCS) and Dempster-Shafer theory are analyzed for landslide susceptibility mapping (LSM) in the Urmia lake basin in Iran, which is highly susceptible to landslide hazards. The methodology comprises three stages. First, the LSM criteria are ranked and a sensitivity analysis is implemented to simulate error propagation based on the MCS. The resulting weights are expressed through probability density functions. Accordingly, within the second stage, three MCDA methods, namely analytical hierarchy process (AHP), weighted linear combination (WLC) and ordered weighted average (OWA), are used to produce the landslide susceptibility maps. In the third stage, accuracy assessments are carried out and the uncertainties of the different results are measured. We compare the accuracies of the three MCDA methods based on (1) the Dempster-Shafer theory and (2) a validation of the results using an inventory of known landslides and their respective coverage based on object-based image analysis of IRS-ID satellite images. The results of this study reveal that through the integration of GIS and MCDA models, it is possible to identify strategies for choosing an appropriate method for LSM. Furthermore, our findings indicate that the integration of MCDA and MCS can significantly improve the accuracy of the results. In LSM, the AHP method performed best, while the OWA reveals better performance in the reliability assessment. The WLC operation yielded poor results.

Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

PubMed Central

Shao, Changwei; Niu, Yongchao; Rastas, Pasi; Liu, Yang; Xie, Zhiyuan; Li, Hengde; Wang, Lei; Jiang, Yong; Tai, Shuaishuai; Tian, Yongsheng; Sakamoto, Takashi; Chen, Songlin

2015-01-01

High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1–8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species. PMID:25762582

Integration of Lupinus angustifolius L. (narrow-leafed lupin) genome maps and comparative mapping within legumes.

PubMed

Wyrwa, Katarzyna; Książkiewicz, Michał; Szczepaniak, Anna; Susek, Karolina; Podkowiński, Jan; Naganowska, Barbara

2016-09-01

Narrow-leafed lupin (Lupinus angustifolius L.) has recently been considered a reference genome for the Lupinus genus. In the present work, genetic and cytogenetic maps of L. angustifolius were supplemented with 30 new molecular markers representing lupin genome regions, harboring genes involved in nitrogen fixation during the symbiotic interaction of legumes and soil bacteria (Rhizobiaceae). Our studies resulted in the precise localization of bacterial artificial chromosomes (BACs) carrying sequence variants for early nodulin 40, nodulin 26, nodulin 45, aspartate aminotransferase P2, asparagine synthetase, cytosolic glutamine synthetase, and phosphoenolpyruvate carboxylase. Together with previously mapped chromosomes, the integrated L. angustifolius map encompasses 73 chromosome markers, including 5S ribosomal DNA (rDNA) and 45S rDNA, and anchors 20 L. angustifolius linkage groups to corresponding chromosomes. Chromosomal identification using BAC fluorescence in situ hybridization identified two BAC clones as narrow-leafed lupin centromere-specific markers, which served as templates for preliminary studies of centromere composition within the genus. Bioinformatic analysis of these two BACs revealed that centromeric/pericentromeric regions of narrow-leafed lupin chromosomes consisted of simple sequence repeats ordered into tandem repeats containing the trinucleotide and pentanucleotide simple sequence repeats AGG and GATAC, structured into long arrays. Moreover, cross-genus microsynteny analysis revealed syntenic patterns of 31 single-locus BAC clones among several legume species. The gene and chromosome level findings provide evidence of ancient duplication events that must have occurred very early in the divergence of papilionoid lineages. This work provides a strong foundation for future comparative mapping among legumes and may facilitate understanding of mechanisms involved in shaping legume chromosomes.

Stable Scalp EEG Spatiospectral Patterns Across Paradigms Estimated by Group ICA.

PubMed

Labounek, René; Bridwell, David A; Mareček, Radek; Lamoš, Martin; Mikl, Michal; Slavíček, Tomáš; Bednařík, Petr; Baštinec, Jaromír; Hluštík, Petr; Brázdil, Milan; Jan, Jiří

2018-01-01

Electroencephalography (EEG) oscillations reflect the superposition of different cortical sources with potentially different frequencies. Various blind source separation (BSS) approaches have been developed and implemented in order to decompose these oscillations, and a subset of approaches have been developed for decomposition of multi-subject data. Group independent component analysis (Group ICA) is one such approach, revealing spatiospectral maps at the group level with distinct frequency and spatial characteristics. The reproducibility of these distinct maps across subjects and paradigms is relatively unexplored domain, and the topic of the present study. To address this, we conducted separate group ICA decompositions of EEG spatiospectral patterns on data collected during three different paradigms or tasks (resting-state, semantic decision task and visual oddball task). K-means clustering analysis of back-reconstructed individual subject maps demonstrates that fourteen different independent spatiospectral maps are present across the different paradigms/tasks, i.e. they are generally stable.

Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

PubMed Central

Serin, Elise A. R.; Snoek, L. B.; Nijveen, Harm; Willems, Leo A. J.; Jiménez-Gómez, Jose M.; Hilhorst, Henk W. M.; Ligterink, Wilco

2017-01-01

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches. PMID:29259624

Interindividual registration and dose mapping for voxelwise population analysis of rectal toxicity in prostate cancer radiotherapy

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

Dréan, Gaël; Acosta, Oscar, E-mail: Oscar.Acosta@univ-rennes1.fr; Simon, Antoine

2016-06-15

Purpose: Recent studies revealed a trend toward voxelwise population analysis in order to understand the local dose/toxicity relationships in prostate cancer radiotherapy. Such approaches require, however, an accurate interindividual mapping of the anatomies and 3D dose distributions toward a common coordinate system. This step is challenging due to the high interindividual variability. In this paper, the authors propose a method designed for interindividual nonrigid registration of the rectum and dose mapping for population analysis. Methods: The method is based on the computation of a normalized structural description of the rectum using a Laplacian-based model. This description takes advantage of themore » tubular structure of the rectum and its centerline to be embedded in a nonrigid registration-based scheme. The performances of the method were evaluated on 30 individuals treated for prostate cancer in a leave-one-out cross validation. Results: Performance was measured using classical metrics (Dice score and Hausdorff distance), along with new metrics devised to better assess dose mapping in relation with structural deformation (dose-organ overlap). Considering these scores, the proposed method outperforms intensity-based and distance maps-based registration methods. Conclusions: The proposed method allows for accurately mapping interindividual 3D dose distributions toward a single anatomical template, opening the way for further voxelwise statistical analysis.« less

Expression quantitative trait loci and genetic regulatory network analysis reveals that Gabra2 is involved in stress responses in the mouse.

PubMed

Dai, Jiajuan; Wang, Xusheng; Chen, Ying; Wang, Xiaodong; Zhu, Jun; Lu, Lu

2009-11-01

Previous studies have revealed that the subunit alpha 2 (Gabra2) of the gamma-aminobutyric acid receptor plays a critical role in the stress response. However, little is known about the gentetic regulatory network for Gabra2 and the stress response. We combined gene expression microarray analysis and quantitative trait loci (QTL) mapping to characterize the genetic regulatory network for Gabra2 expression in the hippocampus of BXD recombinant inbred (RI) mice. Our analysis found that the expression level of Gabra2 exhibited much variation in the hippocampus across the BXD RI strains and between the parental strains, C57BL/6J, and DBA/2J. Expression QTL (eQTL) mapping showed three microarray probe sets of Gabra2 to have highly significant linkage likelihood ratio statistic (LRS) scores. Gene co-regulatory network analysis showed that 10 genes, including Gria3, Chka, Drd3, Homer1, Grik2, Odz4, Prkag2, Grm5, Gabrb1, and Nlgn1 are directly or indirectly associated with stress responses. Eleven genes were implicated as Gabra2 downstream genes through mapping joint modulation. The genetical genomics approach demonstrates the importance and the potential power of the eQTL studies in identifying genetic regulatory networks that contribute to complex traits, such as stress responses.

Islands of biogeodiversity in arid lands on a polygons map study: Detecting scale invariance patterns from natural resources maps.

PubMed

Ibáñez, J J; Pérez-Gómez, R; Brevik, Eric C; Cerdà, A

2016-12-15

Many maps (geology, hydrology, soil, vegetation, etc.) are created to inventory natural resources. Each of these resources is mapped using a unique set of criteria, including scales and taxonomies. Past research indicates that comparing results of related maps (e.g., soil and geology maps) may aid in identifying mapping deficiencies. Therefore, this study was undertaken in Almeria Province, Spain to (i) compare the underlying map structures of soil and vegetation maps and (ii) investigate if a vegetation map can provide useful soil information that was not shown on a soil map. Soil and vegetation maps were imported into ArcGIS 10.1 for spatial analysis, and results then exported to Microsoft Excel worksheets for statistical analyses to evaluate fits to linear and power law regression models. Vegetative units were grouped according to the driving forces that determined their presence or absence: (i) climatophilous (ii) lithologic-climate; and (iii) edaphophylous. The rank abundance plots for both the soil and vegetation maps conformed to Willis or Hollow Curves, meaning the underlying structures of both maps were the same. Edaphophylous map units, which represent 58.5% of the vegetation units in the study area, did not show a good correlation with the soil map. Further investigation revealed that 87% of the edaphohygrophilous units were found in ramblas, ephemeral riverbeds that are not typically classified and mapped as soils in modern systems, even though they meet the definition of soil given by the most commonly used and most modern soil taxonomic systems. Furthermore, these edaphophylous map units tend to be islands of biodiversity that are threatened by anthropogenic activity in the region. Therefore, this study revealed areas that need to be revisited and studied pedologically. The vegetation mapped in these areas and the soils that support it are key components of the earth's critical zone that must be studied, understood, and preserved. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamics of distribution and density of phreatophytes and other arid land plant communities

NASA Technical Reports Server (NTRS)

Turner, R. M. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Ground truth measurements of plant coverage on six satellite overflight dates reveal unique trends in coverage for the five desert or semi-desert communities selected. Densitometry and multispectral additive color viewing were used in a preliminary analysis of imagery using the electronic satellite image analyzer console at Stanford Research Institute. The densitometric analysis shows promise for mapping boundaries between plant communities. Color additive viewing of a chronologic sequence of the same scene shown in rapid order will provide a method for mapping phreatophyte communities.

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

NASA Astrophysics Data System (ADS)

Licatalosi, Donny D.; Mele, Aldo; Fak, John J.; Ule, Jernej; Kayikci, Melis; Chi, Sung Wook; Clark, Tyson A.; Schweitzer, Anthony C.; Blume, John E.; Wang, Xuning; Darnell, Jennifer C.; Darnell, Robert B.

2008-11-01

Protein-RNA interactions have critical roles in all aspects of gene expression. However, applying biochemical methods to understand such interactions in living tissues has been challenging. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova revealed extremely reproducible RNA-binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3' untranslated regions, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.

Asymptotically stable phase synchronization revealed by autoregressive circle maps

NASA Astrophysics Data System (ADS)

Drepper, F. R.

2000-11-01

A specially designed of nonlinear time series analysis is introduced based on phases, which are defined as polar angles in spaces spanned by a finite number of delayed coordinates. A canonical choice of the polar axis and a related implicit estimation scheme for the potentially underlying autoregressive circle map (next phase map) guarantee the invertibility of reconstructed phase space trajectories to the original coordinates. The resulting Fourier approximated, invertibility enforcing phase space map allows us to detect conditional asymptotic stability of coupled phases. This comparatively general synchronization criterion unites two existing generalizations of the old concept and can successfully be applied, e.g., to phases obtained from electrocardiogram and airflow recordings characterizing cardiorespiratory interaction.

The Views of the Teachers about the Mind Mapping Technique in the Elementary Life Science and Social Studies Lessons Based on the Constructivist Method

ERIC Educational Resources Information Center

Seyihoglu, Aysegul; Kartal, Ayca

2010-01-01

The purpose of this study is to reveal the opinions of teachers on using the mind mapping technique in Life Science and Social Studies lessons. The participants of the study are 20 primary education teachers. In this study, a semi-structured interview technique was used. For content analysis, the themes and codes were defined, based on the views…

Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.)

PubMed Central

Wei, Chunhua; Chen, Xiner; Wang, Zhongyuan; Liu, Qiyan; Li, Hao; Zhang, Yong; Ma, Jianxiang; Yang, Jianqiang

2017-01-01

The lobed leaf character is a unique morphologic trait in crops, featuring many potential advantages for agricultural productivity. Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies. PMID:28704497

Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.).

PubMed

Wei, Chunhua; Chen, Xiner; Wang, Zhongyuan; Liu, Qiyan; Li, Hao; Zhang, Yong; Ma, Jianxiang; Yang, Jianqiang; Zhang, Xian

2017-01-01

The lobed leaf character is a unique morphologic trait in crops, featuring many potential advantages for agricultural productivity. Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies.

Wildlife management by habitat units: A preliminary plan of action

NASA Technical Reports Server (NTRS)

Frentress, C. D.; Frye, R. G.

1975-01-01

Procedures for yielding vegetation type maps were developed using LANDSAT data and a computer assisted classification analysis (LARSYS) to assist in managing populations of wildlife species by defined area units. Ground cover in Travis County, Texas was classified on two occasions using a modified version of the unsupervised approach to classification. The first classification produced a total of 17 classes. Examination revealed that further grouping was justified. A second analysis produced 10 classes which were displayed on printouts which were later color-coded. The final classification was 82 percent accurate. While the classification map appeared to satisfactorily depict the existing vegetation, two classes were determined to contain significant error. The major sources of error could have been eliminated by stratifying cluster sites more closely among previously mapped soil associations that are identified with particular plant associations and by precisely defining class nomenclature using established criteria early in the analysis.

Visualizing disaster attitudes resulting from terrorist activities.

PubMed

Khalid, Halimahtun M; Helander, Martin G; Hood, Nilwan A

2013-09-01

The purpose of this study was to analyze people's attitudes to disasters by investigating how people feel, behave and think during disasters. We focused on disasters induced by humans, such as terrorist attacks. Two types of textual information were collected - from Internet blogs and from research papers. The analysis enabled forecasting of attitudes for the design of proactive disaster advisory scheme. Text was analyzed using a text mining tool, Leximancer. The outcome of this analysis revealed core themes and concepts in the text concerning people's attitudes. The themes and concepts were sorted into three broad categories: Affect, Behaviour, and Cognition (ABC), and the data was visualized in semantic maps. The maps reveal several knowledge pathways of ABC for developing attitudinal ontologies, which describe the relations between affect, behaviour and cognition, and the sequence in which they develop. Clearly, terrorist attacks induced trauma and people became highly vulnerable. Copyright © 2012 Elsevier Ltd and The Ergonomics Society. All rights reserved.

Porcine MAP3K5 analysis: molecular cloning, characterization, tissue expression pattern, and copy number variations associated with residual feed intake.

PubMed

Pu, L; Zhang, L C; Zhang, J S; Song, X; Wang, L G; Liang, J; Zhang, Y B; Liu, X; Yan, H; Zhang, T; Yue, J W; Li, N; Wu, Q Q; Wang, L X

2016-08-12

Mitogen-activated protein kinase kinase kinase 5 (MAP3K5) is essential for apoptosis, proliferation, differentiation, and immune responses, and is a candidate marker for residual feed intake (RFI) in pig. We cloned the full-length cDNA sequence of porcine MAP3K5 by rapid-amplification of cDNA ends. The 5451-bp gene contains a 5'-untranslated region (UTR) (718 bp), a coding region (3738 bp), and a 3'-UTR (995 bp), and encodes a peptide of 1245 amino acids, which shares 97, 99, 97, 93, 91, and 84% sequence identity with cattle, sheep, human, mouse, chicken, and zebrafish MAP3K5, respectively. The deduced MAP3K5 protein sequence contains two conserved domains: a DUF4071 domain and a protein kinase domain. Phylogenetic analysis showed that porcine MAP3K5 forms a separate branch to vicugna and camel MAP3K5. Tissue expression analysis using real-time quantitative polymerase chain reaction (qRT-PCR) revealed that MAP3K5 was expressed in the heart, liver, spleen, lung, kidney, muscle, fat, pancrea, ileum, and stomach tissues. Copy number variation was detected for porcine MAP3K5 and validated by qRT-PCR. Furthermore, a significant increase in average copy number was detected in the low RFI group when compared to the high RFI group in a Duroc pig population. These results provide useful information regarding the influence of MAP3K5 on RFI in pigs.

[ECOLOGICAL AND GEOGRAPHIC ANALYSIS OF THE SPREAD OF MITES OF THE FAMILY TROMBICULIDAE IN MONGOLIA].

PubMed

Karimova, T Yu; Kudryashova, N I; Lushchekina, A A; Neronov, V M

2016-01-01

The paper gives data on the fauna of chigger mites (Thrombiculinae), the ectoparasites of small mammals in Mongolia. The ecological and geographic analysis could reveal the major abiotic and biotic determinants of the spread of the chigger mites and make a map of their potential area.

A Genetic Linkage Map of the Hermaphrodite Teleost Fish Sparus aurata L.

PubMed Central

Franch, Rafaella; Louro, Bruno; Tsalavouta, Matina; Chatziplis, Dimitris; Tsigenopoulos, Costas S.; Sarropoulou, Elena; Antonello, Jenny; Magoulas, Andonis; Mylonas, Constantinos C.; Babbucci, Massimiliano; Patarnello, Tomaso; Power, Deborah M.; Kotoulas, Giorgos; Bargelloni, Luca

2006-01-01

The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60–90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal. PMID:16951080

A pigment analysis tool for hyperspectral images of cultural heritage artifacts

NASA Astrophysics Data System (ADS)

Bai, Di; Messinger, David W.; Howell, David

2017-05-01

The Gough Map, in the collection at the Bodleian Library, Oxford University, is one of the earliest surviving maps of Britain. Previous research deemed that it was likely created over the 15th century and afterwards it was extensively revised more than once. In 2015, the Gough Map was imaged using a hyperspectral imaging system at the Bodleian Library. The collection of the hyperspectral image (HSI) data was aimed at faded text enhancement for reading and pigment analysis for the material diversity of its composition and potentially the timeline of its creation. In this research, we introduce several methods to analyze the green pigments in the Gough Map, especially the number and spatial distribution of distinct green pigments. One approach, called the Gram Matrix, has been used to estimate the material diversity in a scene (i.e., endmember selection and dimensionality estimation). Here, we use the Gram Matrix technique to study the within-material differences of pigments in the Gough map with common visual color. We develop a pigment analysis tool that extracts visually common pixels, green pigments in this case, from the Gough Map and estimates its material diversity. It reveals that the Gough Map consists of at least six kinds of dominant green pigments. Both historical geographers and cartographic historians will benefit from this work to analyze the pigment diversity using HSI of cultural heritage artifacts.

Recent advances in the applications of vibrational spectroscopic imaging and mapping to pharmaceutical formulations

NASA Astrophysics Data System (ADS)

Ewing, Andrew V.; Kazarian, Sergei G.

2018-05-01

Vibrational spectroscopic imaging and mapping approaches have continued in their development and applications for the analysis of pharmaceutical formulations. Obtaining spatially resolved chemical information about the distribution of different components within pharmaceutical formulations is integral for improving the understanding and quality of final drug products. This review aims to summarise some key advances of these technologies over recent years, primarily since 2010. An overview of FTIR, NIR, terahertz spectroscopic imaging and Raman mapping will be presented to give a perspective of the current state-of-the-art of these techniques for studying pharmaceutical samples. This will include their application to reveal spatial information of components that reveals molecular insight of polymorphic or structural changes, behaviour of formulations during dissolution experiments, uniformity of materials and detection of counterfeit products. Furthermore, new advancements will be presented that demonstrate the continuing novel applications of spectroscopic imaging and mapping, namely in FTIR spectroscopy, for studies of microfluidic devices. Whilst much of the recently developed work has been reported by academic groups, examples of the potential impacts of utilising these imaging and mapping technologies to support industrial applications have also been reviewed.

Visualising inter-subject variability in fMRI using threshold-weighted overlap maps

NASA Astrophysics Data System (ADS)

Seghier, Mohamed L.; Price, Cathy J.

2016-02-01

Functional neuroimaging studies are revealing the neural systems sustaining many sensory, motor and cognitive abilities. A proper understanding of these systems requires an appreciation of the degree to which they vary across subjects. Some sources of inter-subject variability might be easy to measure (demographics, behavioural scores, or experimental factors), while others are more difficult (cognitive strategies, learning effects, and other hidden sources). Here, we introduce a simple way of visualising whole-brain consistency and variability in brain responses across subjects using threshold-weighted voxel-based overlap maps. The output quantifies the proportion of subjects activating a particular voxel or region over a wide range of statistical thresholds. The sensitivity of our approach was assessed in 30 healthy adults performing a matching task with their dominant hand. We show how overlap maps revealed many effects that were only present in a subsample of our group; we discuss how overlap maps can provide information that may be missed or misrepresented by standard group analysis, and how this information can help users to understand their data. In particular, we emphasize that functional overlap maps can be particularly useful when it comes to explaining typical (or atypical) compensatory mechanisms used by patients following brain damage.

Construction of a high-density genetic map for grape using next generation restriction-site associated DNA sequencing

PubMed Central

2012-01-01

Background Genetic mapping and QTL detection are powerful methodologies in plant improvement and breeding. Construction of a high-density and high-quality genetic map would be of great benefit in the production of superior grapes to meet human demand. High throughput and low cost of the recently developed next generation sequencing (NGS) technology have resulted in its wide application in genome research. Sequencing restriction-site associated DNA (RAD) might be an efficient strategy to simplify genotyping. Combining NGS with RAD has proven to be powerful for single nucleotide polymorphism (SNP) marker development. Results An F1 population of 100 individual plants was developed. In-silico digestion-site prediction was used to select an appropriate restriction enzyme for construction of a RAD sequencing library. Next generation RAD sequencing was applied to genotype the F1 population and its parents. Applying a cluster strategy for SNP modulation, a total of 1,814 high-quality SNP markers were developed: 1,121 of these were mapped to the female genetic map, 759 to the male map, and 1,646 to the integrated map. A comparison of the genetic maps to the published Vitis vinifera genome revealed both conservation and variations. Conclusions The applicability of next generation RAD sequencing for genotyping a grape F1 population was demonstrated, leading to the successful development of a genetic map with high density and quality using our designed SNP markers. Detailed analysis revealed that this newly developed genetic map can be used for a variety of genome investigations, such as QTL detection, sequence assembly and genome comparison. PMID:22908993

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.

Analysis of ERTS imagery of Wyoming and its application to evaluation of Wyoming's natural resources

NASA Technical Reports Server (NTRS)

Houston, R. S. (Principal Investigator); Marrs, R. W.

1972-01-01

The author has identified the following significant results. The Wyoming ERTS investigation has been hindered only slightly by incomplete ERTS data sets and lack of coverage. Efforts to map cultural development, vegetation distributions, and various geomorphologic features are underway. Tectonic analysis of the Rock Springs area has isolated two linear features that may be very significant with regard to the regional structure of central Wyoming. Studies of the fracture systems of the Wind River Mountains are being completed. The fracture map, constructed from ERTS-1 interpretations, contains a great deal of structural information which was previously unavailable. Mapping of the Precambrian metasedimentary and metavolcanic terrain of the Granite Mountains is nearing completion, and interpretation of ERTS supporting aircraft data has revealed deposits of iron formation.

Hubble’s Global View of Jupiter During the Juno Mission

NASA Astrophysics Data System (ADS)

Simon, Amy A.; Wong, Michael H.; Orton, Glenn S.; Cosentino, Richard; Tollefson, Joshua; Johnson, Perianne

2017-10-01

With two observing programs designed for mapping clouds and hazes in Jupiter's atmosphere during the Juno mission, the Hubble Space Telescope is acquiring an unprecedented set of global maps for study. The Outer Planet Atmospheres Legacy program (OPAL, PI: Simon) and the Wide Field Coverage for Juno program (WFCJ, PI: Wong) are designed to enable frequent multi-wavelength global mapping of Jupiter, with many maps timed specifically for Juno’s perijove passes. Filters span wavelengths from 212 to 894 nm. Besides offering global views for Juno observation context, they also reveal a wealth of information about interesting atmospheric dynamical features. We will summarize the latest findings from these global mapping programs, including changes in the Great Red Spot, zonal wind profile analysis, and persistent cyclone-generated waves in the North Equatorial Belt.

Systems Biology Analysis of Gene Expression during In Vivo Mycobacterium avium paratuberculosis Enteric Colonization Reveals Role for Immune Tolerance

PubMed Central

Khare, Sangeeta; Lawhon, Sara D.; Drake, Kenneth L.; Nunes, Jairo E. S.; Figueiredo, Josely F.; Rossetti, Carlos A.; Gull, Tamara; Everts, Robin E.; Lewin, Harris A.; Galindo, Cristi L.; Garner, Harold R.; Adams, Leslie Garry

2012-01-01

Survival and persistence of Mycobacterium avium subsp. paratuberculosis (MAP) in the intestinal mucosa is associated with host immune tolerance. However, the initial events during MAP interaction with its host that lead to pathogen survival, granulomatous inflammation, and clinical disease progression are poorly defined. We hypothesize that immune tolerance is initiated upon initial contact of MAP with the intestinal Peyer's patch. To test our hypothesis, ligated ileal loops in neonatal calves were infected with MAP. Intestinal tissue RNAs were collected (0.5, 1, 2, 4, 8 and 12 hrs post-infection), processed, and hybridized to bovine gene expression microarrays. By comparing the gene transcription responses of calves infected with the MAP, informative complex patterns of expression were clearly visible. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis, and genes were grouped into the specific pathways and gene ontology categories to create a holistic model. This model revealed three different phases of responses: i) early (30 min and 1 hr post-infection), ii) intermediate (2, 4 and 8 hrs post-infection), and iii) late (12 hrs post-infection). We describe here the data that include expression profiles for perturbed pathways, as well as, mechanistic genes (genes predicted to have regulatory influence) that are associated with immune tolerance. In the Early Phase of MAP infection, multiple pathways were initiated in response to MAP invasion via receptor mediated endocytosis and changes in intestinal permeability. During the Intermediate Phase, perturbed pathways involved the inflammatory responses, cytokine-cytokine receptor interaction, and cell-cell signaling. During the Late Phase of infection, gene responses associated with immune tolerance were initiated at the level of T-cell signaling. Our study provides evidence that MAP infection resulted in differentially regulated genes, perturbed pathways and specifically modified mechanistic genes contributing to the colonization of Peyer's patch. PMID:22912686

Mystery Montage: A Holistic, Visual, and Kinesthetic Process for Expanding Horizons and Revealing the Core of a Teaching Philosophy

ERIC Educational Resources Information Center

Ennis, Kim; Priebe, Carly; Sharipova, Mayya; West, Kim

2012-01-01

Revealing the core of a teaching philosophy is the key to a concise and meaningful philosophy statement, but it can be an elusive goal. This paper offers a visual, kinesthetic, and holistic process for expanding the horizons of self-reflection, self-analysis, and self-knowledge. Mystery montage, a variation of visual mapping, storyboarding, and…

Dynamics of Hierarchical Urban Green Space Patches and Implications for Management Policy.

PubMed

Yu, Zhoulu; Wang, Yaohui; Deng, Jinsong; Shen, Zhangquan; Wang, Ke; Zhu, Jinxia; Gan, Muye

2017-06-06

Accurately quantifying the variation of urban green space is the prerequisite for fully understanding its ecosystem services. However, knowledge about the spatiotemporal dynamics of urban green space is still insufficient due to multiple challenges that remain in mapping green spaces within heterogeneous urban environments. This paper uses the city of Hangzhou to demonstrate an analysis methodology that integrates sub-pixel mapping technology and landscape analysis to fully investigate the spatiotemporal pattern and variation of hierarchical urban green space patches. Firstly, multiple endmember spectral mixture analysis was applied to time series Landsat data to derive green space coverage at the sub-pixel level. Landscape metric analysis was then employed to characterize the variation pattern of urban green space patches. Results indicate that Hangzhou has experienced a significant loss of urban greenness, producing a more fragmented and isolated vegetation landscape. Additionally, a remarkable amelioration of urban greenness occurred in the city core from 2002 to 2013, characterized by the significant increase of small-sized green space patches. The green space network has been formed as a consequence of new urban greening strategies in Hangzhou. These strategies have greatly fragmented the built-up areas and enriched the diversity of the urban landscape. Gradient analysis further revealed a distinct pattern of urban green space landscape variation in the process of urbanization. By integrating both sub-pixel mapping technology and landscape analysis, our approach revealed the subtle variation of urban green space patches which are otherwise easy to overlook. Findings from this study will help us to refine our understanding of the evolution of heterogeneous urban environments.

Dynamics of Hierarchical Urban Green Space Patches and Implications for Management Policy

PubMed Central

Yu, Zhoulu; Wang, Yaohui; Deng, Jinsong; Shen, Zhangquan; Wang, Ke; Zhu, Jinxia; Gan, Muye

2017-01-01

Accurately quantifying the variation of urban green space is the prerequisite for fully understanding its ecosystem services. However, knowledge about the spatiotemporal dynamics of urban green space is still insufficient due to multiple challenges that remain in mapping green spaces within heterogeneous urban environments. This paper uses the city of Hangzhou to demonstrate an analysis methodology that integrates sub-pixel mapping technology and landscape analysis to fully investigate the spatiotemporal pattern and variation of hierarchical urban green space patches. Firstly, multiple endmember spectral mixture analysis was applied to time series Landsat data to derive green space coverage at the sub-pixel level. Landscape metric analysis was then employed to characterize the variation pattern of urban green space patches. Results indicate that Hangzhou has experienced a significant loss of urban greenness, producing a more fragmented and isolated vegetation landscape. Additionally, a remarkable amelioration of urban greenness occurred in the city core from 2002 to 2013, characterized by the significant increase of small-sized green space patches. The green space network has been formed as a consequence of new urban greening strategies in Hangzhou. These strategies have greatly fragmented the built-up areas and enriched the diversity of the urban landscape. Gradient analysis further revealed a distinct pattern of urban green space landscape variation in the process of urbanization. By integrating both sub-pixel mapping technology and landscape analysis, our approach revealed the subtle variation of urban green space patches which are otherwise easy to overlook. Findings from this study will help us to refine our understanding of the evolution of heterogeneous urban environments. PMID:28587309

Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis

PubMed Central

Moore, Michael; Zhang, Chaolin; Gantman, Emily Conn; Mele, Aldo; Darnell, Jennifer C.; Darnell, Robert B.

2014-01-01

Summary Identifying sites where RNA binding proteins (RNABPs) interact with target RNAs opens the door to understanding the vast complexity of RNA regulation. UV-crosslinking and immunoprecipitation (CLIP) is a transformative technology in which RNAs purified from in vivo cross-linked RNA-protein complexes are sequenced to reveal footprints of RNABP:RNA contacts. CLIP combined with high throughput sequencing (HITS-CLIP) is a generalizable strategy to produce transcriptome-wide RNA binding maps with higher accuracy and resolution than standard RNA immunoprecipitation (RIP) profiling or purely computational approaches. Applying CLIP to Argonaute proteins has expanded the utility of this approach to mapping binding sites for microRNAs and other small regulatory RNAs. Finally, recent advances in data analysis take advantage of crosslinked-induced mutation sites (CIMS) to refine RNA-binding maps to single-nucleotide resolution. Once IP conditions are established, HITS-CLIP takes approximately eight days to prepare RNA for sequencing. Established pipelines for data analysis, including for CIMS, take 3-4 days. PMID:24407355

Functional mapping of language networks in the normal brain using a word-association task.

PubMed

Ghosh, Shantanu; Basu, Amrita; Kumaran, Senthil S; Khushu, Subash

2010-08-01

Language functions are known to be affected in diverse neurological conditions, including ischemic stroke, traumatic brain injury, and brain tumors. Because language networks are extensive, interpretation of functional data depends on the task completed during evaluation. The aim was to map the hemodynamic consequences of word association using functional magnetic resonance imaging (fMRI) in normal human subjects. Ten healthy subjects underwent fMRI scanning with a postlexical access semantic association task vs lexical processing task. The fMRI protocol involved a T2*-weighted gradient-echo echo-planar imaging (GE-EPI) sequence (TR 4523 ms, TE 64 ms, flip angle 90°) with alternate baseline and activation blocks. A total of 78 scans were taken (interscan interval = 3 s) with a total imaging time of 587 s. Functional data were processed in Statistical Parametric Mapping software (SPM2) with 8-mm Gaussian kernel by convolving the blood oxygenation level-dependent (BOLD) signal with an hemodynamic response function estimated by general linear method to generate SPM{t} and SPM{F} maps. Single subject analysis of the functional data (FWE-corrected, P≤0.001) revealed extensive activation in the frontal lobes, with overlaps among middle frontal gyrus (MFG), superior, and inferior frontal gyri. BOLD activity was also found in the medial frontal gyrus, middle occipital gyrus (MOG), anterior fusiform gyrus, superior and inferior parietal lobules, and to a smaller extent, the thalamus and right anterior cerebellum. Group analysis (FWE-corrected, P≤0.001) revealed neural recruitment of bilateral lingual gyri, left MFG, bilateral MOG, left superior occipital gyrus, left fusiform gyrus, bilateral thalami, and right cerebellar areas. Group data analysis revealed a cerebellar-occipital-fusiform-thalamic network centered around bilateral lingual gyri for word association, thereby indicating how these areas facilitate language comprehension by activating a semantic association network of words processed postlexical access. This finding is important when assessing the extent of cognitive damage and/or recovery and can be used for presurgical planning after optimization.

Evaluation of specimen preparation techniques for micro-PIXE localisation of elements in hyperaccumulating plants

NASA Astrophysics Data System (ADS)

Kachenko, Anthony G.; Siegele, Rainer; Bhatia, Naveen P.; Singh, Balwant; Ionescu, Mihail

2008-04-01

Hybanthus floribundus subsp. floribundus, a rare Australian Ni-hyperaccumulating shrub and Pityrogramma calomelanos var. austroamericana, an Australian naturalized As-hyperaccumulating fern are promising species for use in phytoremediation of contaminated sites. Micro-proton-induced X-ray emission (μ-PIXE) spectroscopy was used to map the elemental distribution of the accumulated metal(loid)s, Ca and K in leaf or pinnule tissues of the two plant species. Samples were prepared by two contrasting specimen preparation techniques: freeze-substitution in tetrahydrofuran (THF) and freeze-drying. The specimens were analysed to compare the suitability of each technique in preserving (i) the spatial elemental distribution and (ii) the tissue structure of the specimens. Further, the μ-PIXE results were compared with concentration of elements in the bulk tissue obtained by ICP-AES analysis. In H. floribundus subsp. floribundus, μ-PIXE analysis revealed Ni, Ca and K concentrations in freeze-dried leaf tissues were at par with bulk tissue concentrations. Elemental distribution maps illustrated that Ni was preferentially localised in the adaxial epidermal tissues (1% DW) and least concentration was found in spongy mesophyll tissues (0.53% DW). Conversely, elemental distribution maps of THF freeze-substituted tissues indicated significantly lower Ni, Ca and K concentrations than freeze-dried specimens and bulk tissue concentrations. Moreover, Ni concentrations were uniform across the whole specimen and no localisation was observed. In P. calomelanos var. austroamericana freeze-dried pinnule tissues, μ-PIXE revealed statistically similar As, Ca and K concentrations as compared to bulk tissue concentrations. Elemental distribution maps showed that As localisation was relatively uniform across the whole specimen. Once again, THF freeze-substituted tissues revealed a significant loss of As compared to freeze-dried specimens and the concentrations obtained by bulk tissue analysis. The results demonstrate that freeze-drying is a suitable sample preparation technique to study elemental distribution of ions in H. floribundus and P. calomelanos plant tissues using μ-PIXE spectroscopy. Furthermore, cellular structure was preserved in samples prepared using this technique.

A transcription map of the regions surrounding the CSF1R locus on human chromosome 5q31: Candidate genes for diastrophic dysplasia

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

Clines, G.; Lovett, M.

1994-09-01

Diastrophic dysplasia (DTD) is an autosomal recessive disorder of unknown pathogenesis that is characterized by abnormal skeletal and cartilage growth. Phenotypic characteristics of the disorder include short stature, scoliosis, and deformation of the first metacarpal. The diastrophic dysplasia gene has been localized to chromosome 5q31-33, within {approximately}60 kb of the colony stimulating factor 1 receptor gene (CSF1R). We have used direct cDNA selection to build a transcription map across {approximately}250 kb surrounding and including the CSF1R locus. cDNA pools from human placenta, activated T cells, cerebellum, Hela cells, fetal brain, chondrocytes, chondrosarcomas and osteosarcomas were multiplexed in these selections. Aftermore » two rounds of selection, an analysis revealed that {approximately}70% of the selected cDNAs were contained within the contig. DNA sequencing and cosmid mapping data from a collection of 310 clones revealed the presence of three new genes in this region that show no appreciable homologies on sequence database searches, as well as cDNA clones from the CSF1R and the PDGFRB loci (another of the known genes in the region). An additional cDNA was found with 100% homology to the gene encoding human ribosomal protein L7 (RPL7). This cDNA comprised {approximately}25% of all selected clones. However, further analysis of the genomic contig revealed the presence of an RPL7 processed pseudogene in very close proximity to the CSF1R and PDGFRB genes. The selection of processed pseudogenes is one previously anticipated artifact of selection metholodolgies, but has not been previously observed. Mutational analysis of the three new genes is underway in diastrophic dysplasia families, as is derivation of full length cDNA clones and the expansion of this detailed transcription map into a larger genomic contig.« less

Cloning, characterization, and physical mapping of the canine Prop-1 gene (PROP1): exclusion as a candidate for combined pituitary hormone deficiency in German shepherd dogs.

PubMed

Lantinga-van Leeuwen, I S; Kooistra, H S; Mol, J A; Renier, C; Breen, M; van Oost, B A

2000-01-01

Abnormalities in the genes encoding Pit-1 and Prop-1 have been reported to cause combined pituitary hormone deficiency (CPHD) in mice and humans. In dogs, a similar phenotype has been described in the German shepherd breed. We have previously reported that the Pit-1 gene (POU1F1) is not mutated in affected German shepherd dogs. In this study, we report the isolation and mapping of the canine Prop-1 gene (PROP1), and we assessed the involvement of PROP1 in German shepherd dog dwarfism. The canine PROP1 gene was found to contain three exons, encoding a 226 amino acid protein. The deduced amino acid sequence was 79% and 84% homologous with the mouse and human Prop-1 protein, respectively. Using fluorescence in situ hybridization, PROP1 was mapped to canine chromosome 11. Further mapping with a canine radiation hybrid panel showed co-localization with the polymorphic DNA marker AHT137. Sequence analysis of genomic DNA from dwarf German shepherd dogs revealed no alterations in the PROP1 gene. Moreover, linkage analysis of AHT137 revealed no co-segregation between the PROP1 locus and the CPHD phenotype, excluding this gene as candidate for canine CPHD and providing a new spontaneous model of hypopituitarism. Copyright 2000 S. Karger AG, Basel

Novel Sequence-Based Mapping of Recently Emerging H5NX Influenza Viruses Reveals Pandemic Vaccine Candidates

PubMed Central

Anderson, Christopher S.; DeDiego, Marta L.; Thakar, Juilee; Topham, David J.

2016-01-01

Recently, an avian influenza virus, H5NX subclade 2.3.4.4, emerged and spread to North America. This subclade has frequently reassorted, leading to multiple novel viruses capable of human infection. Four cases of human infections, three leading to death, have already occurred. Existing vaccine strains do not protect against these new viruses, raising a need to identify new vaccine candidate strains. We have developed a novel sequence-based mapping (SBM) tool capable of visualizing complex protein sequence data sets using a single intuitive map. We applied SBM on the complete set of avian H5 viruses in order to better understand hemagglutinin protein variance amongst H5 viruses and identify any patterns associated with this variation. The analysis successfully identified the original reassortments that lead to the emergence of this new subclade of H5 viruses, as well as their known unusual ability to re-assort among neuraminidase subtypes. In addition, our analysis revealed distinct clusters of 2.3.4.4 variants that would not be covered by existing strains in the H5 vaccine stockpile. The results suggest that our method may be useful for pandemic candidate vaccine virus selection. PMID:27494186

Differential detection of genetic Loci underlying stem and root lignin content in Populus.

PubMed

Yin, Tongming; Zhang, Xinye; Gunter, Lee; Priya, Ranjan; Sykes, Robert; Davis, Mark; Wullschleger, Stan D; Tuskan, Gerald A

2010-11-22

In this study, we established a comprehensive genetic map with a large number of progeny from a three-generation hybrid Populus intercross, and phenotyped the lignin content, S/G ratio and 28 cell wall subcomponents both in stems and roots for the mapping individuals. Phenotypic analysis revealed that lignin content and syringyl-to-guaiacyl (S/G) ratio using pyrolysis molecular beam mass spectroscopy (pyMBMS) varied among mapping individuals. Phenotypic analysis revealed that stem lignin content is significantly higher than that in root and the quantified traits can be classified into four distinct groups, with strong correlations observed among components within organs. Altogether, 179 coordinating QTLs were detected, and they were co-localized into 49 genetic loci, 27 of which appear to be pleiotropic. Many of the detected genetic loci were detected differentially in stem and root. This is the first report of separate genetic loci controlling cell wall phenotypes above and below ground. These results suggest that it may be possible to modify lignin content and composition via breed and/or engineer as a means of simultaneously improving Populus for cellulosic ethanol production and carbon sequestration.

Airborne laser-guided imaging spectroscopy to map forest trait diversity and guide conservation.

PubMed

Asner, G P; Martin, R E; Knapp, D E; Tupayachi, R; Anderson, C B; Sinca, F; Vaughn, N R; Llactayo, W

2017-01-27

Functional biogeography may bridge a gap between field-based biodiversity information and satellite-based Earth system studies, thereby supporting conservation plans to protect more species and their contributions to ecosystem functioning. We used airborne laser-guided imaging spectroscopy with environmental modeling to derive large-scale, multivariate forest canopy functional trait maps of the Peruvian Andes-to-Amazon biodiversity hotspot. Seven mapped canopy traits revealed functional variation in a geospatial pattern explained by geology, topography, hydrology, and climate. Clustering of canopy traits yielded a map of forest beta functional diversity for land-use analysis. Up to 53% of each mapped, functionally distinct forest presents an opportunity for new conservation action. Mapping functional diversity advances our understanding of the biosphere to conserve more biodiversity in the face of land use and climate change. Copyright © 2017, American Association for the Advancement of Science.

Micro-PIXE mapping of mineral distribution in mature grain of two pearl millet cultivars

NASA Astrophysics Data System (ADS)

Minnis-Ndimba, R.; Kruger, J.; Taylor, J. R. N.; Mtshali, C.; Pineda-Vargas, C. A.

2015-11-01

Micro-proton-induced X-ray emission (micro-PIXE) was used to map the distribution of several nutritionally important minerals found in the grain tissue of two cultivars of pearl millet (Pennisetum glaucum (L.) R. Br.). The distribution maps revealed that the predominant localisation of minerals was within the germ (consisting of the scutellum and embryo) and the outer grain layers (specifically the pericarp and aleurone); whilst the bulk of the endosperm tissue featured relatively low concentrations of the surveyed minerals. Within the germ, the scutellum was revealed as a major storage tissue for P and K, whilst Ca, Mn and Zn were more prominent within the embryo. Fe was revealed to have a distinctive distribution pattern, confined to the dorsal end of the scutellum; but was also highly concentrated in the outer grain layers. Interestingly, the hilar region was also revealed as a site of high accumulation of minerals, particularly for S, Ca, Mn, Fe and Zn, which may be part of a defensive strategy against infection or damage. Differences between the two cultivars, in terms of the bulk Fe and P content obtained via inductively coupled plasma optical emission spectrometry (ICP-OES), concurred with the average concentration data determined from the analysis of micro-PIXE spectra specifically extracted from the endosperm tissue.

Mathematics in the Making: Mapping Verbal Discourse in Polya's "Let Us Teach Guessing" Lesson

ERIC Educational Resources Information Center

Truxaw, Mary P.; DeFranco, Thomas C.

2007-01-01

This paper describes a detailed analysis of verbal discourse within an exemplary mathematics lesson--that is, George Polya teaching in the Mathematics Association of America [MAA] video classic, "Let Us Teach Guessing" (1966). The results of the analysis reveal an inductive model of teaching that represents recursive cycles rather than linear…

An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

PubMed Central

Peng, Wenzhu; Xu, Jian; Zhang, Yan; Feng, Jianxin; Dong, Chuanju; Jiang, Likun; Feng, Jingyan; Chen, Baohua; Gong, Yiwen; Chen, Lin; Xu, Peng

2016-01-01

High density genetic linkage maps are essential for QTL fine mapping, comparative genomics and high quality genome sequence assembly. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,194 SNP markers on 14,146 distinct loci for common carp based on high-throughput genotyping with the carp 250 K single nucleotide polymorphism (SNP) array in a mapping family. The genetic length of the consensus map was 10,595.94 cM with an average locus interval of 0.75 cM and an average marker interval of 0.38 cM. Comparative genomic analysis revealed high level of conserved syntenies between common carp and the closely related model species zebrafish and medaka. The genome scaffolds were anchored to the high-density linkage map, spanning 1,357 Mb of common carp reference genome. QTL mapping and association analysis identified 22 QTLs for growth-related traits and 7 QTLs for sex dimorphism. Candidate genes underlying growth-related traits were identified, including important regulators such as KISS2, IGF1, SMTLB, NPFFR1 and CPE. Candidate genes associated with sex dimorphism were also identified including 3KSR and DMRT2b. The high-density and high-resolution genetic linkage map provides an important tool for QTL fine mapping and positional cloning of economically important traits, and improving common carp genome assembly. PMID:27225429

Reconstruction of an SSR-based Magnaporthe oryzae physical map to locate avirulence gene AvrPi12.

PubMed

Li, Tonghui; Wen, Jianqiang; Zhang, Yaling; Correll, James; Wang, Ling; Pan, Qinghua

2018-05-31

Pathogen avirulence (Avr) genes can evolve rapidly when challenged by the widespread deployment of host genes for resistance. They can be effectively isolated by positional cloning provided a robust and well-populated genetic map is available. An updated, SSR-based physical map of the rice blast pathogen Magnaporthe oryzae (Mo) has been constructed based on 116 of the 120 SSRs used to assemble the last map, along with 18 newly developed ones. A comparison between the two versions of the map has revealed an altered marker content and order within most of the Mo chromosomes. The avirulence gene AvrPi12 was mapped in a population of 219 progeny derived from a cross between the two Mo isolates CHL42 and CHL357. A bulked segregant analysis indicated that the gene was located on chromosome 6, a conclusion borne out by an analysis of the pattern of segregation shown by individual isolates. Six additional PCR-based markers were developed to improve the map resolution in the key region. AvrPi12 was finally located within the sub-telomeric region of chromosome 6, distal to the SSR locus LSM6-5. The improved SSR-based linkage map should be useful as a platform for gene mapping and isolation in Mo. It was used to establish the location of AvrPi12, thereby providing a starting point for its positional cloning.

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

PubMed Central

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

2011-01-01

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

Serum Metabonomics of Mild Acute Pancreatitis.

PubMed

Xu, Hongmin; Zhang, Lei; Kang, Huan; Zhang, Jiandong; Liu, Jie; Liu, Shuye

2016-11-01

Mild acute pancreatitis (MAP) is a common acute abdominal disease, and exhibits rising incidence in recent decades. As an important component of systemic biology, metabonomics is a new discipline developed following genomics and proteomics. In this study, the objective was to analyze the serum metabonomics of patients with MAP, aiming to screen metabolic markers with potential diagnostic values. An analysis platform with ultra performance liquid chromatography-high-resolution mass spectrometry was used to screen the difference metabolites related to MAP diagnosis and disease course monitoring. A total of 432 endogenous metabolites were screened out from 122 serum samples, and 49 difference metabolites were verified, among which 12 difference metabolites were identified by nonparametric test. After material identification, eight metabolites exhibited reliable results, and their levels in MAP serum were higher than those in healthy serum. Four metabolites exhibited gradual downward trend with treatment process going on, and the differences were statistically significant (P < 0.05). Metabonomic analysis has revealed eight metabolites with potential diagnostic values toward MAP, among which four metabolites can be used to monitor the disease course. © 2016 Wiley Periodicals, Inc.

Trace elements in natural azurite pigments found in illuminated manuscript leaves investigated by synchrotron x-ray fluorescence and diffraction mapping

NASA Astrophysics Data System (ADS)

Smieska, Louisa M.; Mullett, Ruth; Ferri, Laurent; Woll, Arthur R.

2017-07-01

We present trace-element and composition analysis of azurite pigments in six illuminated manuscript leaves, dating from the thirteenth to sixteenth century, using synchrotron-based, large-area x-ray fluorescence (SR-XRF) and diffraction (SR-XRD) mapping. SR-XRF mapping reveals several trace elements correlated with azurite, including arsenic, zirconium, antimony, barium, and bismuth, that appear in multiple manuscripts but were not always detected by point XRF. Within some manuscript leaves, variations in the concentration of trace elements associated with azurite coincide with distinct regions of the illuminations, suggesting systematic differences in azurite preparation or purification. Variations of the trace element concentrations in azurite are greater among different manuscript leaves than the variations within each individual leaf, suggesting the possibility that such impurities reflect distinct mineralogical/geologic sources. SR-XRD maps collected simultaneously with the SR-XRF maps confirm the identification of azurite regions and are consistent with impurities found in natural mineral sources of azurite. In general, our results suggest the feasibility of using azurite trace element analysis for provenance studies of illuminated manuscript fragments, and demonstrate the value of XRF mapping in non-destructive determination of trace element concentrations within a single pigment.

Gridded uncertainty in fossil fuel carbon dioxide emission maps, a CDIAC example

DOE PAGES

Andres, Robert J.; Boden, Thomas A.; Higdon, David M.

2016-12-05

Due to a current lack of physical measurements at appropriate spatial and temporal scales, all current global maps and distributions of fossil fuel carbon dioxide (FFCO2) emissions use one or more proxies to distribute those emissions. These proxies and distribution schemes introduce additional uncertainty into these maps. This paper examines the uncertainty associated with the magnitude of gridded FFCO2 emissions. This uncertainty is gridded at the same spatial and temporal scales as the mass magnitude maps. This gridded uncertainty includes uncertainty contributions from the spatial, temporal, proxy, and magnitude components used to create the magnitude map of FFCO2 emissions. Throughoutmore » this process, when assumptions had to be made or expert judgment employed, the general tendency in most cases was toward overestimating or increasing the magnitude of uncertainty. The results of the uncertainty analysis reveal a range of 4–190 %, with an average of 120 % (2 σ) for populated and FFCO2-emitting grid spaces over annual timescales. This paper also describes a methodological change specific to the creation of the Carbon Dioxide Information Analysis Center (CDIAC) FFCO2 emission maps: the change from a temporally fixed population proxy to a temporally varying population proxy.« less

Gridded uncertainty in fossil fuel carbon dioxide emission maps, a CDIAC example

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

Andres, Robert J.; Boden, Thomas A.; Higdon, David M.

Due to a current lack of physical measurements at appropriate spatial and temporal scales, all current global maps and distributions of fossil fuel carbon dioxide (FFCO2) emissions use one or more proxies to distribute those emissions. These proxies and distribution schemes introduce additional uncertainty into these maps. This paper examines the uncertainty associated with the magnitude of gridded FFCO2 emissions. This uncertainty is gridded at the same spatial and temporal scales as the mass magnitude maps. This gridded uncertainty includes uncertainty contributions from the spatial, temporal, proxy, and magnitude components used to create the magnitude map of FFCO2 emissions. Throughoutmore » this process, when assumptions had to be made or expert judgment employed, the general tendency in most cases was toward overestimating or increasing the magnitude of uncertainty. The results of the uncertainty analysis reveal a range of 4–190 %, with an average of 120 % (2 σ) for populated and FFCO2-emitting grid spaces over annual timescales. This paper also describes a methodological change specific to the creation of the Carbon Dioxide Information Analysis Center (CDIAC) FFCO2 emission maps: the change from a temporally fixed population proxy to a temporally varying population proxy.« less

Gridded uncertainty in fossil fuel carbon dioxide emission maps, a CDIAC example

NASA Astrophysics Data System (ADS)

Andres, Robert J.; Boden, Thomas A.; Higdon, David M.

2016-12-01

Due to a current lack of physical measurements at appropriate spatial and temporal scales, all current global maps and distributions of fossil fuel carbon dioxide (FFCO2) emissions use one or more proxies to distribute those emissions. These proxies and distribution schemes introduce additional uncertainty into these maps. This paper examines the uncertainty associated with the magnitude of gridded FFCO2 emissions. This uncertainty is gridded at the same spatial and temporal scales as the mass magnitude maps. This gridded uncertainty includes uncertainty contributions from the spatial, temporal, proxy, and magnitude components used to create the magnitude map of FFCO2 emissions. Throughout this process, when assumptions had to be made or expert judgment employed, the general tendency in most cases was toward overestimating or increasing the magnitude of uncertainty. The results of the uncertainty analysis reveal a range of 4-190 %, with an average of 120 % (2σ) for populated and FFCO2-emitting grid spaces over annual timescales. This paper also describes a methodological change specific to the creation of the Carbon Dioxide Information Analysis Center (CDIAC) FFCO2 emission maps: the change from a temporally fixed population proxy to a temporally varying population proxy.

Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1

PubMed Central

Glubb, Dylan M.; Maranian, Mel J.; Michailidou, Kyriaki; Pooley, Karen A.; Meyer, Kerstin B.; Kar, Siddhartha; Carlebur, Saskia; O’Reilly, Martin; Betts, Joshua A.; Hillman, Kristine M.; Kaufmann, Susanne; Beesley, Jonathan; Canisius, Sander; Hopper, John L.; Southey, Melissa C.; Tsimiklis, Helen; Apicella, Carmel; Schmidt, Marjanka K.; Broeks, Annegien; Hogervorst, Frans B.; van der Schoot, C. Ellen; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Fasching, Peter A.; Ruebner, Matthias; Ekici, Arif B.; Beckmann, Matthias W.; Peto, Julian; dos-Santos-Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Pharoah, Paul D.P.; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Sawyer, Elinor J.; Tomlinson, Ian; Kerin, Michael J.; Miller, Nicola; Burwinkel, Barbara; Marme, Frederik; Yang, Rongxi; Surowy, Harald; Guénel, Pascal; Truong, Thérèse; Menegaux, Florence; Sanchez, Marie; Bojesen, Stig E.; Nordestgaard, Børge G.; Nielsen, Sune F.; Flyger, Henrik; González-Neira, Anna; Benitez, Javier; Zamora, M. Pilar; Arias Perez, Jose Ignacio; Anton-Culver, Hoda; Neuhausen, Susan L.; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Meindl, Alfons; Schmutzler, Rita K.; Brauch, Hiltrud; Ko, Yon-Dschun; Brüning, Thomas; Nevanlinna, Heli; Muranen, Taru A.; Aittomäki, Kristiina; Blomqvist, Carl; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Tanaka, Hideo; Dörk, Thilo; Bogdanova, Natalia V.; Helbig, Sonja; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M.; Wu, Anna H.; Tseng, Chiu-chen; Van Den Berg, David; Stram, Daniel O.; Lambrechts, Diether; Zhao, Hui; Weltens, Caroline; van Limbergen, Erik; Chang-Claude, Jenny; Flesch-Janys, Dieter; Rudolph, Anja; Seibold, Petra; Radice, Paolo; Peterlongo, Paolo; Barile, Monica; Capra, Fabio; Couch, Fergus J.; Olson, Janet E.; Hallberg, Emily; Vachon, Celine; Giles, Graham G.; Milne, Roger L.; McLean, Catriona; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick; Le Marchand, Loic; Simard, Jacques; Goldberg, Mark S.; Labrèche, France; Dumont, Martine; Teo, Soo Hwang; Yip, Cheng Har; See, Mee-Hoong; Cornes, Belinda; Cheng, Ching-Yu; Ikram, M. Kamran; Kristensen, Vessela; Zheng, Wei; Halverson, Sandra L.; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; Andrulis, Irene L.; Knight, Julia A.; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robert A.E.M.; Seynaeve, Caroline; Van Asperen, Christi J.; García-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J.; Lissowska, Jolanta; Czene, Kamila; Klevebring, Daniel; Darabi, Hatef; Eriksson, Mikael; Hooning, Maartje J.; Hollestelle, Antoinette; Martens, John W.M.; Collée, J. Margriet; Hall, Per; Li, Jingmei; Humphreys, Keith; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Cox, Angela; Cross, Simon S.; Reed, Malcolm W.R.; Blot, William; Signorello, Lisa B.; Cai, Qiuyin; Shah, Mitul; Ghoussaini, Maya; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K.; Noh, Dong-Young; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Tang, Anthony; Hamann, Ute; Torres, Diana; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; McKay, James; Olswold, Curtis; Slager, Susan; Toland, Amanda E.; Yannoukakos, Drakoulis; Shen, Chen-Yang; Wu, Pei-Ei; Yu, Jyh-Cherng; Hou, Ming-Feng; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Pita, Guillermo; Alonso, M. Rosario; Álvarez, Nuria; Herrero, Daniel; Tessier, Daniel C.; Vincent, Daniel; Bacot, Francois; Luccarini, Craig; Baynes, Caroline; Ahmed, Shahana; Healey, Catherine S.; Brown, Melissa A.; Ponder, Bruce A.J.; Chenevix-Trench, Georgia; Thompson, Deborah J.; Edwards, Stacey L.; Easton, Douglas F.; Dunning, Alison M.; French, Juliet D.

2015-01-01

Genome-wide association studies (GWASs) have revealed SNP rs889312 on 5q11.2 to be associated with breast cancer risk in women of European ancestry. In an attempt to identify the biologically relevant variants, we analyzed 909 genetic variants across 5q11.2 in 103,991 breast cancer individuals and control individuals from 52 studies in the Breast Cancer Association Consortium. Multiple logistic regression analyses identified three independent risk signals: the strongest associations were with 15 correlated variants (iCHAV1), where the minor allele of the best candidate, rs62355902, associated with significantly increased risks of both estrogen-receptor-positive (ER+: odds ratio [OR] = 1.24, 95% confidence interval [CI] = 1.21–1.27, ptrend = 5.7 × 10−44) and estrogen-receptor-negative (ER−: OR = 1.10, 95% CI = 1.05–1.15, ptrend = 3.0 × 10−4) tumors. After adjustment for rs62355902, we found evidence of association of a further 173 variants (iCHAV2) containing three subsets with a range of effects (the strongest was rs113317823 [pcond = 1.61 × 10−5]) and five variants composing iCHAV3 (lead rs11949391; ER+: OR = 0.90, 95% CI = 0.87–0.93, pcond = 1.4 × 10−4). Twenty-six percent of the prioritized candidate variants coincided with four putative regulatory elements that interact with the MAP3K1 promoter through chromatin looping and affect MAP3K1 promoter activity. Functional analysis indicated that the cancer risk alleles of four candidates (rs74345699 and rs62355900 [iCHAV1], rs16886397 [iCHAV2a], and rs17432750 [iCHAV3]) increased MAP3K1 transcriptional activity. Chromatin immunoprecipitation analysis revealed diminished GATA3 binding to the minor (cancer-protective) allele of rs17432750, indicating a mechanism for its action. We propose that the cancer risk alleles act to increase MAP3K1 expression in vivo and might promote breast cancer cell survival. PMID:25529635

Fine-scale mapping of the 5q11.2 breast cancer locus reveals at least three independent risk variants regulating MAP3K1.

PubMed

Glubb, Dylan M; Maranian, Mel J; Michailidou, Kyriaki; Pooley, Karen A; Meyer, Kerstin B; Kar, Siddhartha; Carlebur, Saskia; O'Reilly, Martin; Betts, Joshua A; Hillman, Kristine M; Kaufmann, Susanne; Beesley, Jonathan; Canisius, Sander; Hopper, John L; Southey, Melissa C; Tsimiklis, Helen; Apicella, Carmel; Schmidt, Marjanka K; Broeks, Annegien; Hogervorst, Frans B; van der Schoot, C Ellen; Muir, Kenneth; Lophatananon, Artitaya; Stewart-Brown, Sarah; Siriwanarangsan, Pornthep; Fasching, Peter A; Ruebner, Matthias; Ekici, Arif B; Beckmann, Matthias W; Peto, Julian; dos-Santos-Silva, Isabel; Fletcher, Olivia; Johnson, Nichola; Pharoah, Paul D P; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Sawyer, Elinor J; Tomlinson, Ian; Kerin, Michael J; Miller, Nicola; Burwinkel, Barbara; Marme, Frederik; Yang, Rongxi; Surowy, Harald; Guénel, Pascal; Truong, Thérèse; Menegaux, Florence; Sanchez, Marie; Bojesen, Stig E; Nordestgaard, Børge G; Nielsen, Sune F; Flyger, Henrik; González-Neira, Anna; Benitez, Javier; Zamora, M Pilar; Arias Perez, Jose Ignacio; Anton-Culver, Hoda; Neuhausen, Susan L; Brenner, Hermann; Dieffenbach, Aida Karina; Arndt, Volker; Stegmaier, Christa; Meindl, Alfons; Schmutzler, Rita K; Brauch, Hiltrud; Ko, Yon-Dschun; Brüning, Thomas; Nevanlinna, Heli; Muranen, Taru A; Aittomäki, Kristiina; Blomqvist, Carl; Matsuo, Keitaro; Ito, Hidemi; Iwata, Hiroji; Tanaka, Hideo; Dörk, Thilo; Bogdanova, Natalia V; Helbig, Sonja; Lindblom, Annika; Margolin, Sara; Mannermaa, Arto; Kataja, Vesa; Kosma, Veli-Matti; Hartikainen, Jaana M; Wu, Anna H; Tseng, Chiu-chen; Van Den Berg, David; Stram, Daniel O; Lambrechts, Diether; Zhao, Hui; Weltens, Caroline; van Limbergen, Erik; Chang-Claude, Jenny; Flesch-Janys, Dieter; Rudolph, Anja; Seibold, Petra; Radice, Paolo; Peterlongo, Paolo; Barile, Monica; Capra, Fabio; Couch, Fergus J; Olson, Janet E; Hallberg, Emily; Vachon, Celine; Giles, Graham G; Milne, Roger L; McLean, Catriona; Haiman, Christopher A; Henderson, Brian E; Schumacher, Fredrick; Le Marchand, Loic; Simard, Jacques; Goldberg, Mark S; Labrèche, France; Dumont, Martine; Teo, Soo Hwang; Yip, Cheng Har; See, Mee-Hoong; Cornes, Belinda; Cheng, Ching-Yu; Ikram, M Kamran; Kristensen, Vessela; Zheng, Wei; Halverson, Sandra L; Shrubsole, Martha; Long, Jirong; Winqvist, Robert; Pylkäs, Katri; Jukkola-Vuorinen, Arja; Kauppila, Saila; Andrulis, Irene L; Knight, Julia A; Glendon, Gord; Tchatchou, Sandrine; Devilee, Peter; Tollenaar, Robert A E M; Seynaeve, Caroline; Van Asperen, Christi J; García-Closas, Montserrat; Figueroa, Jonine; Chanock, Stephen J; Lissowska, Jolanta; Czene, Kamila; Klevebring, Daniel; Darabi, Hatef; Eriksson, Mikael; Hooning, Maartje J; Hollestelle, Antoinette; Martens, John W M; Collée, J Margriet; Hall, Per; Li, Jingmei; Humphreys, Keith; Shu, Xiao-Ou; Lu, Wei; Gao, Yu-Tang; Cai, Hui; Cox, Angela; Cross, Simon S; Reed, Malcolm W R; Blot, William; Signorello, Lisa B; Cai, Qiuyin; Shah, Mitul; Ghoussaini, Maya; Kang, Daehee; Choi, Ji-Yeob; Park, Sue K; Noh, Dong-Young; Hartman, Mikael; Miao, Hui; Lim, Wei Yen; Tang, Anthony; Hamann, Ute; Torres, Diana; Jakubowska, Anna; Lubinski, Jan; Jaworska, Katarzyna; Durda, Katarzyna; Sangrajrang, Suleeporn; Gaborieau, Valerie; Brennan, Paul; McKay, James; Olswold, Curtis; Slager, Susan; Toland, Amanda E; Yannoukakos, Drakoulis; Shen, Chen-Yang; Wu, Pei-Ei; Yu, Jyh-Cherng; Hou, Ming-Feng; Swerdlow, Anthony; Ashworth, Alan; Orr, Nick; Jones, Michael; Pita, Guillermo; Alonso, M Rosario; Álvarez, Nuria; Herrero, Daniel; Tessier, Daniel C; Vincent, Daniel; Bacot, Francois; Luccarini, Craig; Baynes, Caroline; Ahmed, Shahana; Healey, Catherine S; Brown, Melissa A; Ponder, Bruce A J; Chenevix-Trench, Georgia; Thompson, Deborah J; Edwards, Stacey L; Easton, Douglas F; Dunning, Alison M; French, Juliet D

2015-01-08

Genome-wide association studies (GWASs) have revealed SNP rs889312 on 5q11.2 to be associated with breast cancer risk in women of European ancestry. In an attempt to identify the biologically relevant variants, we analyzed 909 genetic variants across 5q11.2 in 103,991 breast cancer individuals and control individuals from 52 studies in the Breast Cancer Association Consortium. Multiple logistic regression analyses identified three independent risk signals: the strongest associations were with 15 correlated variants (iCHAV1), where the minor allele of the best candidate, rs62355902, associated with significantly increased risks of both estrogen-receptor-positive (ER(+): odds ratio [OR] = 1.24, 95% confidence interval [CI] = 1.21-1.27, ptrend = 5.7 × 10(-44)) and estrogen-receptor-negative (ER(-): OR = 1.10, 95% CI = 1.05-1.15, ptrend = 3.0 × 10(-4)) tumors. After adjustment for rs62355902, we found evidence of association of a further 173 variants (iCHAV2) containing three subsets with a range of effects (the strongest was rs113317823 [pcond = 1.61 × 10(-5)]) and five variants composing iCHAV3 (lead rs11949391; ER(+): OR = 0.90, 95% CI = 0.87-0.93, pcond = 1.4 × 10(-4)). Twenty-six percent of the prioritized candidate variants coincided with four putative regulatory elements that interact with the MAP3K1 promoter through chromatin looping and affect MAP3K1 promoter activity. Functional analysis indicated that the cancer risk alleles of four candidates (rs74345699 and rs62355900 [iCHAV1], rs16886397 [iCHAV2a], and rs17432750 [iCHAV3]) increased MAP3K1 transcriptional activity. Chromatin immunoprecipitation analysis revealed diminished GATA3 binding to the minor (cancer-protective) allele of rs17432750, indicating a mechanism for its action. We propose that the cancer risk alleles act to increase MAP3K1 expression in vivo and might promote breast cancer cell survival. Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

PXK locus in systemic lupus erythematosus: fine mapping and functional analysis reveals novel susceptibility gene ABHD6.

PubMed

Oparina, Nina Y; Delgado-Vega, Angelica M; Martinez-Bueno, Manuel; Magro-Checa, César; Fernández, Concepción; Castro, Rafaela Ortega; Pons-Estel, Bernardo A; D'Alfonso, Sandra; Sebastiani, Gian Domenico; Witte, Torsten; Lauwerys, Bernard R; Endreffy, Emoke; Kovács, László; Escudero, Alejandro; López-Pedrera, Chary; Vasconcelos, Carlos; da Silva, Berta Martins; Frostegård, Johan; Truedsson, Lennart; Martin, Javier; Raya, Enrique; Ortego-Centeno, Norberto; de Los Angeles Aguirre, Maria; de Ramón Garrido, Enrique; Palma, María-Jesús Castillo; Alarcon-Riquelme, Marta E; Kozyrev, Sergey V

2015-03-01

To perform fine mapping of the PXK locus associated with systemic lupus erythematosus (SLE) and study functional effects that lead to susceptibility to the disease. Linkage disequilibrium (LD) mapping was conducted by using 1251 SNPs (single nucleotide polymorphism) covering a 862 kb genomic region on 3p14.3 comprising the PXK locus in 1467 SLE patients and 2377 controls of European origin. Tag SNPs and genotypes imputed with IMPUTE2 were tested for association by using SNPTEST and PLINK. The expression QTLs data included three independent datasets for lymphoblastoid cells of European donors: HapMap3, MuTHER and the cross-platform eQTL catalogue. Correlation analysis of eQTLs was performed using Vassarstats. Alternative splicing for the PXK gene was analysed on mRNA from PBMCs. Fine mapping revealed long-range LD (>200 kb) extended over the ABHD6, RPP14, PXK, and PDHB genes on 3p14.3. The highly correlated variants tagged an SLE-associated haplotype that was less frequent in the patients compared with the controls (OR=0.89, p=0.00684). A robust correlation between the association with SLE and enhanced expression of ABHD6 gene was revealed, while neither expression, nor splicing alterations associated with SLE susceptibility were detected for PXK. The SNP allele frequencies as well as eQTL pattern analysed in the CEU and CHB HapMap3 populations indicate that the SLE association and the effect on ABHD6 expression are specific to Europeans. These results confirm the genetic association of the locus 3p14.3 with SLE in Europeans and point to the ABHD6 and not PXK, as the major susceptibility gene in the region. We suggest a pathogenic mechanism mediated by the upregulation of ABHD6 in individuals carrying the SLE-risk variants. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Multiomics in Grape Berry Skin Revealed Specific Induction of the Stilbene Synthetic Pathway by Ultraviolet-C Irradiation1

PubMed Central

Suzuki, Mami; Nakabayashi, Ryo; Ogata, Yoshiyuki; Sakurai, Nozomu; Tokimatsu, Toshiaki; Goto, Susumu; Suzuki, Makoto; Jasinski, Michal; Martinoia, Enrico; Otagaki, Shungo; Matsumoto, Shogo; Saito, Kazuki; Shiratake, Katsuhiro

2015-01-01

Grape (Vitis vinifera) accumulates various polyphenolic compounds, which protect against environmental stresses, including ultraviolet-C (UV-C) light and pathogens. In this study, we looked at the transcriptome and metabolome in grape berry skin after UV-C irradiation, which demonstrated the effectiveness of omics approaches to clarify important traits of grape. We performed transcriptome analysis using a genome-wide microarray, which revealed 238 genes up-regulated more than 5-fold by UV-C light. Enrichment analysis of Gene Ontology terms showed that genes encoding stilbene synthase, a key enzyme for resveratrol synthesis, were enriched in the up-regulated genes. We performed metabolome analysis using liquid chromatography-quadrupole time-of-flight mass spectrometry, and 2,012 metabolite peaks, including unidentified peaks, were detected. Principal component analysis using the peaks showed that only one metabolite peak, identified as resveratrol, was highly induced by UV-C light. We updated the metabolic pathway map of grape in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and in the KaPPA-View 4 KEGG system, then projected the transcriptome and metabolome data on a metabolic pathway map. The map showed specific induction of the resveratrol synthetic pathway by UV-C light. Our results showed that multiomics is a powerful tool to elucidate the accumulation mechanisms of secondary metabolites, and updated systems, such as KEGG and KaPPA-View 4 KEGG for grape, can support such studies. PMID:25761715

Multiomics in grape berry skin revealed specific induction of the stilbene synthetic pathway by ultraviolet-C irradiation.

PubMed

Suzuki, Mami; Nakabayashi, Ryo; Ogata, Yoshiyuki; Sakurai, Nozomu; Tokimatsu, Toshiaki; Goto, Susumu; Suzuki, Makoto; Jasinski, Michal; Martinoia, Enrico; Otagaki, Shungo; Matsumoto, Shogo; Saito, Kazuki; Shiratake, Katsuhiro

2015-05-01

Grape (Vitis vinifera) accumulates various polyphenolic compounds, which protect against environmental stresses, including ultraviolet-C (UV-C) light and pathogens. In this study, we looked at the transcriptome and metabolome in grape berry skin after UV-C irradiation, which demonstrated the effectiveness of omics approaches to clarify important traits of grape. We performed transcriptome analysis using a genome-wide microarray, which revealed 238 genes up-regulated more than 5-fold by UV-C light. Enrichment analysis of Gene Ontology terms showed that genes encoding stilbene synthase, a key enzyme for resveratrol synthesis, were enriched in the up-regulated genes. We performed metabolome analysis using liquid chromatography-quadrupole time-of-flight mass spectrometry, and 2,012 metabolite peaks, including unidentified peaks, were detected. Principal component analysis using the peaks showed that only one metabolite peak, identified as resveratrol, was highly induced by UV-C light. We updated the metabolic pathway map of grape in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and in the KaPPA-View 4 KEGG system, then projected the transcriptome and metabolome data on a metabolic pathway map. The map showed specific induction of the resveratrol synthetic pathway by UV-C light. Our results showed that multiomics is a powerful tool to elucidate the accumulation mechanisms of secondary metabolites, and updated systems, such as KEGG and KaPPA-View 4 KEGG for grape, can support such studies. © 2015 American Society of Plant Biologists. All Rights Reserved.

Short Communication: Genetic linkage map of Cucurbita maxima with molecular and morphological markers.

PubMed

Ge, Y; Li, X; Yang, X X; Cui, C S; Qu, S P

2015-05-22

Cucurbita maxima is one of the most widely cultivated vegetables in China and exhibits distinct morphological characteristics. In this study, genetic linkage analysis with 57 simple-sequence repeats, 21 amplified fragment length polymorphisms, 3 random-amplified polymorphic DNA, and one morphological marker revealed 20 genetic linkage groups of C. maxima covering a genetic distance of 991.5 cM with an average of 12.1 cM between adjacent markers. Genetic linkage analysis identified the simple-sequence repeat marker 'PU078072' 5.9 cM away from the locus 'Rc', which controls rind color. The genetic map in the present study will be useful for better mapping, tagging, and cloning of quantitative trait loci/gene(s) affecting economically important traits and for breeding new varieties of C. maxima through marker-assisted selection.

BARNARD 59: NO EVIDENCE FOR FURTHER FRAGMENTATION

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

Roman-Zuniga, C. G.; Frau, P.; Girart, J. M.

2012-03-10

The dense molecular clump at the center of the Barnard 59 (B59) complex is the only region in the Pipe Nebula that has formed a small, stellar cluster. The previous analysis of a high-resolution near-IR dust extinction map revealed that the nuclear region in B59 is a massive, mostly quiescent clump of 18.9 M{sub Sun }. The clump shows a monolithic profile, possibly indicating that the clump is on the way to collapse, with no evident fragmentation that could lead to another group of star systems. In this paper, we present new analysis that compares the dust extinction map withmore » a new dust emission radio-continuum map of higher spatial resolution. We confirm that the clump does not show any significant evidence for prestellar fragmentation at scales smaller than those probed previously.« less

Column ratio mapping: a processing technique for atomic resolution high-angle annular dark-field (HAADF) images.

PubMed

Robb, Paul D; Craven, Alan J

2008-12-01

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [110]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 angstroms-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome.

PubMed

Zhang, Zijun; Xing, Yi

2017-09-19

Crosslinking or RNA immunoprecipitation followed by sequencing (CLIP-seq or RIP-seq) allows transcriptome-wide discovery of RNA regulatory sites. As CLIP-seq/RIP-seq reads are short, existing computational tools focus on uniquely mapped reads, while reads mapped to multiple loci are discarded. We present CLAM (CLIP-seq Analysis of Multi-mapped reads). CLAM uses an expectation-maximization algorithm to assign multi-mapped reads and calls peaks combining uniquely and multi-mapped reads. To demonstrate the utility of CLAM, we applied it to a wide range of public CLIP-seq/RIP-seq datasets involving numerous splicing factors, microRNAs and m6A RNA methylation. CLAM recovered a large number of novel RNA regulatory sites inaccessible by uniquely mapped reads. The functional significance of these sites was demonstrated by consensus motif patterns and association with alternative splicing (splicing factors), transcript abundance (AGO2) and mRNA half-life (m6A). CLAM provides a useful tool to discover novel protein-RNA interactions and RNA modification sites from CLIP-seq and RIP-seq data, and reveals the significant contribution of repetitive elements to the RNA regulatory landscape of the human transcriptome. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis.

PubMed

Shao, Changwei; Niu, Yongchao; Rastas, Pasi; Liu, Yang; Xie, Zhiyuan; Li, Hengde; Wang, Lei; Jiang, Yong; Tai, Shuaishuai; Tian, Yongsheng; Sakamoto, Takashi; Chen, Songlin

2015-04-01

High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1-8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Visualizing human communication in business process simulations

NASA Astrophysics Data System (ADS)

Groehn, Matti; Jalkanen, Janne; Haho, Paeivi; Nieminen, Marko; Smeds, Riitta

1999-03-01

In this paper a description of business process simulation is given. Crucial part in the simulation of business processes is the analysis of social contacts between the participants. We will introduce a tool to collect log data and how this log data can be effectively analyzed using two different kind of methods: discussion flow charts and self-organizing maps. Discussion flow charts revealed the communication patterns and self-organizing maps are a very effective way of clustering the participants into development groups.

Semantic Mapping and Motion Planning with Turtlebot Roomba

NASA Astrophysics Data System (ADS)

Aslam Butt, Rizwan; Usman Ali, Syed M.

2013-12-01

In this paper, we have successfully demonstrated the semantic mapping and motion planning experiments on Turtlebot Robot using Microsoft Kinect in ROS environment. Moreover, we have also performed the comparative studies on various sampling based motion planning algorithms with Turtlebot in Open Motion Planning Library. Our comparative analysis revealed that Expansive Space Trees (EST) surmounted all other approaches with respect to memory occupation and processing time. We have also tried to summarize the related concepts of autonomous robotics which we hope would be helpful for beginners.

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

A cellular and regulatory map of the GABAergic nervous system of C. elegans

PubMed Central

Gendrel, Marie; Atlas, Emily G; Hobert, Oliver

2016-01-01

Neurotransmitter maps are important complements to anatomical maps and represent an invaluable resource to understand nervous system function and development. We report here a comprehensive map of neurons in the C. elegans nervous system that contain the neurotransmitter GABA, revealing twice as many GABA-positive neuron classes as previously reported. We define previously unknown glia-like cells that take up GABA, as well as 'GABA uptake neurons' which do not synthesize GABA but take it up from the extracellular environment, and we map the expression of previously uncharacterized ionotropic GABA receptors. We use the map of GABA-positive neurons for a comprehensive analysis of transcriptional regulators that define the GABA phenotype. We synthesize our findings of specification of GABAergic neurons with previous reports on the specification of glutamatergic and cholinergic neurons into a nervous system-wide regulatory map which defines neurotransmitter specification mechanisms for more than half of all neuron classes in C. elegans. DOI: http://dx.doi.org/10.7554/eLife.17686.001 PMID:27740909

The Synthesis Map Is a Multidimensional Educational Tool That Provides Insight into Students’ Mental Models and Promotes Students’ Synthetic Knowledge Generation

PubMed Central

Ortega, Ryan A.; Brame, Cynthia J.

2015-01-01

Concept mapping was developed as a method of displaying and organizing hierarchical knowledge structures. Using the new, multidimensional presentation software Prezi, we have developed a new teaching technique designed to engage higher-level skills in the cognitive domain. This tool, synthesis mapping, is a natural evolution of concept mapping, which utilizes embedding to layer information within concepts. Prezi’s zooming user interface lets the author of the presentation use both depth as well as distance to show connections between data, ideas, and concepts. Students in the class Biology of Cancer created synthesis maps to illustrate their knowledge of tumorigenesis. Students used multiple organizational schemes to build their maps. We present an analysis of student work, placing special emphasis on organization within student maps and how the organization of knowledge structures in student maps can reveal strengths and weaknesses in student understanding or instruction. We also provide a discussion of best practices for instructors who would like to implement synthesis mapping in their classrooms. PMID:25917385

Lack of species-specific difference in pulmonary function when using mouse versus human plasma in a mouse model of hemorrhagic shock.

PubMed

Peng, Zhanglong; Pati, Shibani; Fontaine, Magali J; Hall, Kelly; Herrera, Anthony V; Kozar, Rosemary A

2016-11-01

Clinical studies have demonstrated that the early and empiric use of plasma improves survival after hemorrhagic shock. We have demonstrated in rodent models of hemorrhagic shock that resuscitation with plasma is protective to the lungs compared with lactated Ringer's solution. As our long-term objective is to determine the molecular mechanisms that modulate plasma's protective effects in injured bleeding patients, we have used human plasma in a mouse model of hemorrhagic shock. The goal of the current experiments is to determine if there are significant adverse effects on lung injury when using human versus mouse plasma in an established murine model of hemorrhagic shock and laparotomy. Mice underwent laparotomy and 90 minutes of hemorrhagic shock to a mean arterial pressure (MAP) of 35 ± 5 mm Hg followed by resuscitation at 1× shed blood using either mouse fresh frozen plasma (FFP), human FFP, or human lyophilized plasma. Mean arterial pressure was recorded during shock and for the first 30 minutes of resuscitation. After 3 hours, animals were killed, and lungs collected for analysis. There was a significant increase in early MAP when mouse FFP was used to resuscitate animals compared with human FFP or human lyophilized plasma. However, despite these differences, analysis of the mouse lungs revealed no significant differences in pulmonary histopathology, lung permeability, or lung edema between all three plasma groups. Analysis of neutrophil infiltration in the lungs revealed that mouse FFP decreased neutrophil influx as measured by neutrophil staining; however, myeloperoxidase immunostaining revealed no significant differences in between groups. The study of human plasma in a mouse model of hemorrhagic shock is feasible but does reveal some differences compared with mouse plasma-based resuscitation in physiologic measures such as MAP postresuscitation. Measures of end organ function such as lung injury appear to be comparable in this acute model of hemorrhagic shock and resuscitation.

Genetic dissection and fine mapping of a novel dt gene associated with determinate growth habit in sesame.

PubMed

Zhang, Yanxin; Wang, Linhai; Gao, Yuan; Li, Donghua; Yu, Jingyin; Zhou, Rong; Zhang, Xiurong

2018-06-14

As an important oil crop, growth habit of sesame (Sesamum indicum L.) is naturally indeterminate, which brings about asynchronous maturity of capsules and causes loss of yield. The genetic basis of determinate growth habit in sesame was investigated by classical genetic analysis through multiple populations, results revealed that it was controlled by an unique recessive gene. The genotyping by sequencing (GBS) approach was employed for high-throughput SNP identification and genotyping in the F 2 population, then a high density bin map was constructed, the map was 1086.403 cM in length, which consisted of 1184 bins (13,679 SNPs), with an average of 0.918 cM between adjacent bins. Based on bin mapping in conjunction with SSR markers analysis in targeted region, the novel sesame determinacy gene was mapped on LG09 in a genome region of 41 kb. This study dissected genetic basis of determinate growth habit in sesame, constructed a new high-density bin map and mapped a novel determinacy gene. Results of this study demonstrate that we employed an optimized approach to get fine-accuracy, high-resolution and high-efficiency mapping result in sesame. The findings provided important foundation for sesame determinacy gene cloning and were expected to be applied in breeding for cultivars suited to mechanized production.

A climatology of total ozone mapping spectrometer data using rotated principal component analysis

NASA Astrophysics Data System (ADS)

Eder, Brian K.; Leduc, Sharon K.; Sickles, Joseph E.

1999-02-01

The spatial and temporal variability of total column ozone (Ω) obtained from the total ozone mapping spectrometer (TOMS version 7.0) during the period 1980-1992 was examined through the use of a multivariate statistical technique called rotated principal component analysis. Utilization of Kaiser's varimax orthogonal rotation led to the identification of 14, mostly contiguous subregions that together accounted for more than 70% of the total Ω variance. Each subregion displayed statistically unique Ω characteristics that were further examined through time series and spectral density analyses, revealing significant periodicities on semiannual, annual, quasi-biennial, and longer term time frames. This analysis facilitated identification of the probable mechanisms responsible for the variability of Ω within the 14 homogeneous subregions. The mechanisms were either dynamical in nature (i.e., advection associated with baroclinic waves, the quasi-biennial oscillation, or El Niño-Southern Oscillation) or photochemical in nature (i.e., production of odd oxygen (O or O3) associated with the annual progression of the Sun). The analysis has also revealed that the influence of a data retrieval artifact, found in equatorial latitudes of version 6.0 of the TOMS data, has been reduced in version 7.0.

Alteration mapping at Goldfield, Nevada, by cluster and discriminant analysis of LANDSAT digital data

NASA Technical Reports Server (NTRS)

Ballew, G.

1977-01-01

The ability of Landsat multispectral digital data to differentiate among 62 combinations of rock and alteration types at the Goldfield mining district of Western Nevada was investigated by using statistical techniques of cluster and discriminant analysis. Multivariate discriminant analysis was not effective in classifying each of the 62 groups, with classification results essentially the same whether data of four channels alone or combined with six ratios of channels were used. Bivariate plots of group means revealed a cluster of three groups including mill tailings, basalt and all other rock and alteration types. Automatic hierarchical clustering based on the fourth dimensional Mahalanobis distance between group means of 30 groups having five or more samples was performed. The results of the cluster analysis revealed hierarchies of mill tailings vs. natural materials, basalt vs. non-basalt, highly reflectant rocks vs. other rocks and exclusively unaltered rocks vs. predominantly altered rocks. The hierarchies were used to determine the order in which sets of multiple discriminant analyses were to be performed and the resulting discriminant functions were used to produce a map of geology and alteration which has an overall accuracy of 70 percent for discriminating exclusively altered rocks from predominantly altered rocks.

An uncertainty and sensitivity analysis approach for GIS-based multicriteria landslide susceptibility mapping

PubMed Central

Feizizadeh, Bakhtiar; Blaschke, Thomas

2014-01-01

GIS-based multicriteria decision analysis (MCDA) methods are increasingly being used in landslide susceptibility mapping. However, the uncertainties that are associated with MCDA techniques may significantly impact the results. This may sometimes lead to inaccurate outcomes and undesirable consequences. This article introduces a new GIS-based MCDA approach. We illustrate the consequences of applying different MCDA methods within a decision-making process through uncertainty analysis. Three GIS-MCDA methods in conjunction with Monte Carlo simulation (MCS) and Dempster–Shafer theory are analyzed for landslide susceptibility mapping (LSM) in the Urmia lake basin in Iran, which is highly susceptible to landslide hazards. The methodology comprises three stages. First, the LSM criteria are ranked and a sensitivity analysis is implemented to simulate error propagation based on the MCS. The resulting weights are expressed through probability density functions. Accordingly, within the second stage, three MCDA methods, namely analytical hierarchy process (AHP), weighted linear combination (WLC) and ordered weighted average (OWA), are used to produce the landslide susceptibility maps. In the third stage, accuracy assessments are carried out and the uncertainties of the different results are measured. We compare the accuracies of the three MCDA methods based on (1) the Dempster–Shafer theory and (2) a validation of the results using an inventory of known landslides and their respective coverage based on object-based image analysis of IRS-ID satellite images. The results of this study reveal that through the integration of GIS and MCDA models, it is possible to identify strategies for choosing an appropriate method for LSM. Furthermore, our findings indicate that the integration of MCDA and MCS can significantly improve the accuracy of the results. In LSM, the AHP method performed best, while the OWA reveals better performance in the reliability assessment. The WLC operation yielded poor results. PMID:27019609

Real-Time Mapping Spectroscopy on the Ground, in the Air, and in Space

NASA Astrophysics Data System (ADS)

Thompson, D. R.; Allwood, A.; Chien, S.; Green, R. O.; Wettergreen, D. S.

2016-12-01

Real-time data interpretation can benefit both remote in situ exploration and remote sensing. Basic analyses at the sensor can monitor instrument performance and reveal invisible science phenomena in real time. This promotes situational awareness for remote robotic explorers or campaign decision makers, enabling adaptive data collection, reduced downlink requirements, and coordinated multi-instrument observations. Fast analysis is ideal for mapping spectrometers providing unambiguous, quantitative geophysical measurements. This presentation surveys recent computational advances in real-time spectroscopic analysis for Earth science and planetary exploration. Spectral analysis at the sensor enables new operations concepts that significantly improve science yield. Applications include real-time detection of fugitive greenhouse emissions by airborne monitoring, real-time cloud screening and mineralogical mapping by orbital spectrometers, and adaptive measurement by the PIXL instrument on the Mars 2020 rover. Copyright 2016 California Institute of Technology. All Rights Reserved. We acknowledge support of the US Government, NASA, the Earth Science Division and Terrestrial Ecology program.

Utilizing ERTS-A imagery for tectonic analysis through study of the Bighorn Mountains Region

NASA Technical Reports Server (NTRS)

Hoppin, R. A. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Preliminary vegetation analysis has been undertaken on MSS scene 1085-17294, Oct. 16, 1973 in the Bighorn region. Forest Service maps showing detailed distribution of dominant forest types have been compared with MSS bands 5 and 7 positive transparencies, enlarged positive prints, and color imagery produced on an Addcol viewer. Patterns on the ERTS imagery match those on the Forest Service maps quite well. A tectonic map ovearlay of MSS band 7 of the Bighorn region reveals a strong concentration of linears in the uplift as compared to basins. Folds in the Bighorn Basin are visible where not covered by post-Paleocene deposits. In regions where far less is known of the geology than in this area, it might be possible to predict the subsurface occurrence of folds and lineaments on the basis of imagery analysis and more confidently explore covered areas for concealed oil structures and mineral deposits.

Population sequencing reveals breed and sub-species specific CNVs in cattle

USDA-ARS?s Scientific Manuscript database

Individualized copy number variation (CNV) maps have highlighted the need for population surveys of cattle to detect rare and common variants. While SNP and comparative genomic hybridization (CGH) arrays have provided preliminary data, next-generation sequence (NGS) data analysis offers an increased...

The Antarctic Ice.

ERIC Educational Resources Information Center

Radok, Uwe

1985-01-01

The International Antarctic Glaciological Project has collected information on the East Antarctic ice sheet since 1969. Analysis of ice cores revealed climatic history, and radar soundings helped map bedrock of the continent. Computer models of the ice sheet and its changes over time will aid in predicting the future. (DH)

The Molecular and Cellular Basis of Bitter Taste in Drosophila

PubMed Central

Weiss, Linnea A.; Dahanukar, Anupama; Kwon, Jae Young; Banerjee, Diya; Carlson, John R.

2011-01-01

Summary The extent of diversity among bitter-sensing neurons is a fundamental issue in the field of taste. Data are limited and conflicting as to whether bitter neurons are broadly tuned and uniform, resulting in indiscriminate avoidance of bitter stimuli, or diverse, allowing a more discerning evaluation of food sources. We provide a systematic analysis of how bitter taste is encoded by the major taste organ of the Drosophila head, the labellum. Each of 16 bitter compounds is tested physiologically against all 31 bitter neurons, revealing responses that are diverse in magnitude and dynamics. Four functional classes of bitter neurons are defined. Four corresponding classes are defined through expression analysis of all 68 Gr taste receptors. A receptor-to-neuron-to-tastant map is constructed. Misexpression of one receptor confers bitter responses as predicted by the map. These results reveal a degree of complexity that greatly expands the capacity of the system to encode bitter taste. PMID:21262465

Primary Student-Teachers' Conceptual Understanding of the Greenhouse Effect: A mixed method study

NASA Astrophysics Data System (ADS)

Ratinen, Ilkka Johannes

2013-04-01

The greenhouse effect is a reasonably complex scientific phenomenon which can be used as a model to examine students' conceptual understanding in science. Primary student-teachers' understanding of global environmental problems, such as climate change and ozone depletion, indicates that they have many misconceptions. The present mixed method study examines Finnish primary student-teachers' understanding of the greenhouse effect based on the results obtained via open-ended and closed-form questionnaires. The open-ended questionnaire considers primary student-teachers' spontaneous ideas about the greenhouse effect depicted by concept maps. The present study also uses statistical analysis to reveal respondents' conceptualization of the greenhouse effect. The concept maps and statistical analysis reveal that the primary student-teachers' factual knowledge and their conceptual understanding of the greenhouse effect are incomplete and even misleading. In the light of the results of the present study, proposals for modifying the instruction of climate change in science, especially in geography, are presented.

Task-evoked brain functional magnetic susceptibility mapping by independent component analysis (χICA).

PubMed

Chen, Zikuan; Calhoun, Vince D

2016-03-01

Conventionally, independent component analysis (ICA) is performed on an fMRI magnitude dataset to analyze brain functional mapping (AICA). By solving the inverse problem of fMRI, we can reconstruct the brain magnetic susceptibility (χ) functional states. Upon the reconstructed χ dataspace, we propose an ICA-based brain functional χ mapping method (χICA) to extract task-evoked brain functional map. A complex division algorithm is applied to a timeseries of fMRI phase images to extract temporal phase changes (relative to an OFF-state snapshot). A computed inverse MRI (CIMRI) model is used to reconstruct a 4D brain χ response dataset. χICA is implemented by applying a spatial InfoMax ICA algorithm to the reconstructed 4D χ dataspace. With finger-tapping experiments on a 7T system, the χICA-extracted χ-depicted functional map is similar to the SPM-inferred functional χ map by a spatial correlation of 0.67 ± 0.05. In comparison, the AICA-extracted magnitude-depicted map is correlated with the SPM magnitude map by 0.81 ± 0.05. The understanding of the inferiority of χICA to AICA for task-evoked functional map is an ongoing research topic. For task-evoked brain functional mapping, we compare the data-driven ICA method with the task-correlated SPM method. In particular, we compare χICA with AICA for extracting task-correlated timecourses and functional maps. χICA can extract a χ-depicted task-evoked brain functional map from a reconstructed χ dataspace without the knowledge about brain hemodynamic responses. The χICA-extracted brain functional χ map reveals a bidirectional BOLD response pattern that is unavailable (or different) from AICA. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.).

PubMed

Finkers-Tomczak, Anna; Bakker, Erin; de Boer, Jan; van der Vossen, Edwin; Achenbach, Ute; Golas, Tomasz; Suryaningrat, Suwardi; Smant, Geert; Bakker, Jaap; Goverse, Aska

2011-02-01

The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146-152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene.

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.

A comprehensive pathway map of epidermal growth factor receptor signaling

PubMed Central

Oda, Kanae; Matsuoka, Yukiko; Funahashi, Akira; Kitano, Hiroaki

2005-01-01

The epidermal growth factor receptor (EGFR) signaling pathway is one of the most important pathways that regulate growth, survival, proliferation, and differentiation in mammalian cells. Reflecting this importance, it is one of the best-investigated signaling systems, both experimentally and computationally, and several computational models have been developed for dynamic analysis. A map of molecular interactions of the EGFR signaling system is a valuable resource for research in this area. In this paper, we present a comprehensive pathway map of EGFR signaling and other related pathways. The map reveals that the overall architecture of the pathway is a bow-tie (or hourglass) structure with several feedback loops. The map is created using CellDesigner software that enables us to graphically represent interactions using a well-defined and consistent graphical notation, and to store it in Systems Biology Markup Language (SBML). PMID:16729045

Genetic mapping of QTL for the sizes of eight consecutive leaves below the tassel in maize (Zea mays L.).

PubMed

Yang, Cong; Tang, Dengguo; Qu, Jingtao; Zhang, Ling; Zhang, Lei; Chen, Zhengjie; Liu, Jian

2016-11-01

A set of RIL population was used to detect QTL associated with the sizes of eight consecutive leaves, across different environments, and ten QTL clusters were identified as main QTLs. One of the important parameters of the maize leaf architecture that affects light penetration into the canopy, leaf size, has long attracted breeders' attention for optimizing the plant type of maize and for maximizing the grain yield (GY). In this study, we used 253 RIL lines derived from a cross between B73 and SICAU1212 to investigate the leaf widths (LWs), leaf lengths (LLs), and leaf areas (LAs) of eight consecutive leaves of maize below the tassel and GY across different environments and to identify quantitative traits loci (QTLs) controlling the above-mentioned traits, using inclusive interval mapping for single-environment analysis plus a mixed-model-based composite interval mapping for joint analysis. A total of 171 and 159 putative QTLs were detected through these two mapping methods, respectively. Single-environment mapping revealed that 39 stable QTLs explained more than 10 % of the phenotypic variance, and 35 of the 39 QTLs were also detected by joint analysis. In addition, joint analysis showed that nine of the 159 QTLs exhibited significant QTL × environment interaction and 15 significant epistatic interactions were identified. Approximately 47.17 % of the QTLs for leaf architectural traits in joint analysis were concentrated in ten main chromosomal regions, namely, bins 1.07, 2.02, 3.06, 4.09, 5.01, 5.02, 5.03-5.04, 5.07, 6.07, and 8.05. This study should provide a basis for further fine-mapping of these main genetic regions and improvement of maize leaf architecture.

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat.

PubMed

Yan, Honghai; Bekele, Wubishet A; Wight, Charlene P; Peng, Yuanying; Langdon, Tim; Latta, Robert G; Fu, Yong-Bi; Diederichsen, Axel; Howarth, Catherine J; Jellen, Eric N; Boyle, Brian; Wei, Yuming; Tinker, Nicholas A

2016-11-01

Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.

Mapping the geogenic radon potential: methodology and spatial analysis for central Hungary.

PubMed

Szabó, Katalin Zsuzsanna; Jordan, Gyozo; Horváth, Ákos; Szabó, Csaba

2014-03-01

A detailed geogenic radon potential (GRP) mapping based on field soil gas radon and soil gas permeability measurements was carried out in this study. A conventional continuous variable approach was used in this study for GRP determination and to test its applicability to the selected area of Hungary. Spatial pattern of soil gas radon concentration, soil permeability and GRP and the relationship between geological formations and these parameters were studied by performing detailed spatial analysis. Exploratory data analysis revealed that higher soil gas radon activity concentration and GRP characterizes the mountains and hills than the plains. The highest values were found in the proluvial-deluvial sediments, rock debris on the downhill slopes eroded from hills. Among the Quaternary sediments, which characterize the study area, the fluvial sediment has the highest values, which are also located in the hilly areas. The lowest values were found in the plain areas covered by drift sand, fluvioeolic sand, fluvial sand and loess. As a conclusion, radon is related to the sediment cycle in the study area. A geogenic radon risk map was created, which assists human health risk assessment and risk reduction since it indicates the potential of the source of indoor radon. The map shows that low and medium geogenic radon potential characterizes the study area in central Hungary. High risk occurs only locally. The results reveal that Quaternary sediments are inhomogeneous from a radon point of view, fluvial sediment has medium GRP, whereas the other rock formations such as drift sand, fluioeolic sand, fluvial sand and loess, found in the study area, have low GRP. Copyright © 2013 Elsevier Ltd. All rights reserved.

Analysis of regolith electromagnetic scattering as constrained by high resolution Earth-based measurements of the lunar microwave emission

NASA Technical Reports Server (NTRS)

Keihm, S. J.

1983-01-01

When high resolution measurements of the phase variation of the lunar disk center brightness temperature revealed that in situ regolith electrical losses were larger than those measured on returned samples by a factor of 1.5 to 2.0 at centimeter wavelengths, the need for a refinement of the regolith model to include realistic treatment of scattering effects was identified. Two distinct scattering regimes are considered: vertial variations in dielectric constant and volume scattering due to subsurface rock fragments. Models of lunar regolith energy transport processes are now at the state for which a maximum scientific return could be realized from a lunar orbiter microwave mapping experiment. A detailed analysis, including the effects of scattering produced a set of nominal brightness temperature spectra for lunar equatorial regions, which can be used for mapping as a calibration reference for mapping variations in mineralogy and heat flow.

Chromosomal Mapping of Repetitive DNA Sequences in the Genus Bryconamericus (Characidae) and DNA Barcoding to Differentiate Populations.

PubMed

Santos, Angélica Rossotti Dos; Usso, Mariana Campaner; Gouveia, Juceli Gonzalez; Araya-Jaime, Cristian; Frantine-Silva, Wilson; Giuliano-Caetano, Lucia; Foresti, Fausto; Dias, Ana Lúcia

2017-06-01

The mapping of repetitive DNA sites by fluorescence in situ hybridization has been widely used for karyotype studies in different species of fish, especially when dealing with related species or even genera presenting high chromosome variability. This study analyzed three populations of Bryconamericus, with diploid number preserved, but with different karyotype formulae. Bryconamericus ecai, from the Forquetinha river/RS, presented three new cytotypes, increasing the number of karyotype forms to seven in this population. Other two populations of Bryconamericus sp. from the Vermelho stream/PR and Cambuta river/PR exhibited interpopulation variation. The chromosome mapping of rDNA sites revealed unique markings among the three populations, showing inter- and intrapopulation variability located in the terminal region. The molecular analysis using DNA barcoding complementing the cytogenetic analysis also showed differentiation among the three populations. The U2 small nuclear DNA repetitive sequence exhibited conserved features, being located in the interstitial region of a single chromosome pair. This is the first report on its occurrence in the genus Bryconamericus. Data obtained revealed a karyotype variability already assigned to the genus, along with polymorphism of ribosomal sites, demonstrating that this group of fish can be undergoing a divergent evolutionary process, constituting a substantive model for studies of chromosomal evolution.

Genetic and physical mapping of homologues of the virus resistance gene Rx1 and the cyst nematode resistance gene Gpa2 in potato.

PubMed

Bakker, E; Butterbach, P; Rouppe van der Voort, J; van der Vossen, E; van Vliet, J; Bakker, J; Goverse, A

2003-05-01

Nine resistance gene homologues (RGHs) were identified in two diploid potato clones (SH and RH), with a specific primer pair based on conserved motifs in the LRR domain of the potato cyst nematode resistance gene Gpa2 and the potato virus X resistance gene Rx1. A modified AFLP method was used to facilitate the genetic mapping of the RGHs in the four haplotypes under investigation. All nine RGHs appeared to be located in the Gpa2/ Rx1 cluster on chromosome XII. Construction of a physical map using bacterial artificial chromosome (BAC) clones for both the Solanum tuberosum ssp. tuberosum and the S. tuberosum ssp. andigena haplotype of SH showed that the RGHs are located within a stretch of less than 200 kb. Sequence analysis of the RGHs revealed that they are highly similar (93 to 95%) to Gpa2 and Rx1. The sequence identities among all RGHs range from 85 to 100%. Two pairs of RGHs are identical, or nearly so (100 and 99.9%), with each member located in a different genotype. Southern-blot analysis on genomic DNA revealed no evidence for additional homologues outside the Gpa2/ Rx1 cluster on chromosome XII.

Genetic Mapping and Phylogenetic Analysis Reveal Intraspecific Variation in Sex Chromosomes of the Virginian Strawberry.

PubMed

Wei, Na; Govindarajulu, Rajanikanth; Tennessen, Jacob A; Liston, Aaron; Ashman, Tia-Lynn

2017-10-30

With their extraordinary diversity in sexual systems, flowering plants offer unparalleled opportunities to understand sex determination and to reveal generalities in the evolution of sex chromosomes. Comparative genetic mapping of related taxa with good phylogenetic resolution can delineate the extent of sex chromosome diversity within plant groups, and lead the way to understanding the evolutionary drivers of such diversity. The North American octoploid wild strawberries provide such an opportunity. We performed linkage mapping using targeted sequence capture for the subdioecious western Fragaria virginiana ssp. platypetala and compared the location of its sex-determining region (SDR) to those of 2 other (sub)dioecious species, the eastern subspecies, F. virginiana ssp. virginiana (whose SDR is at 0-5.5 Mb on chromosome VI of the B2 subgenome), and the sister species F. chiloensis (whose SDR is at 37 Mb on chromosome VI of the Av subgenome). Male sterility was dominant in F. virginiana ssp. platypetala and mapped to a chromosome also in homeologous group VI. Likewise, one major quantitative trait locus (QTL) for female fertility overlapped the male sterility region. However, the SDR mapped to yet another subgenome (B1), and to a different location (13 Mb), but similar to the location inferred in one population of the naturally occurring hybrid between F. chiloensis and F. virginiana (F. ×ananassa ssp. cuneifolia). Phylogenetic analysis of chromosomes across the octoploid taxa showed consistent subgenomic composition reflecting shared evolutionary history but also reinforced within-species variation in the SDR-carrying chromosome, suggesting either repeated evolution, or recent turnovers in SDR. © The American Genetic Association 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Informative markers identification and multivariate analysis of selected DxP for the purpose of QTL mapping

NASA Astrophysics Data System (ADS)

Hazirah S., Z.; Maizura, I.; Rajinder, S.; Mohd Isa Z., A.; Ismanizan, I.

2014-09-01

A study was carried out to generate a linkage map of oil palm dura x pisifera (DXP) population. A subset of sample from a DXP mapping family was screened using 325 SSR primers, of which 221 were informative. To date, 150 SSRs have been genotyped across the entire DxP population via capillary sequencer, where 73 SSRs had 1:1 segregation ratio, 64 had 1:1:1:1, 3 had 3:1 and ten had 1:2:1 segregation ratios. Kolmogorov-Smirnov tests by SPSS revealed that most of the bunch quality components had normal distribution which fulfilled one of the pre-requisites to carry out phenotype-genotype correlation association.

Inventory and analysis of natural vegetation and related resources from space and high altitude photography

NASA Technical Reports Server (NTRS)

Poulton, C. E.; Faulkner, D. P.; Johnson, J. R.; Mouat, D. A.; Schrumpf, B. J.

1971-01-01

A high altitude photomosaic resource map of Site 29 was produced which provided an opportunity to test photo interpretation accuracy of natural vegetation resource features when mapped at a small (1:133,400) scale. Helicopter reconnaissance over 144 previously selected test points revealed a highly adequate level of photo interpretation accuracy. In general, the reasons for errors could be accounted for. The same photomosaic resource map enabled construction of interpretive land use overlays. Based on features of the landscape, including natural vegetation types, judgements for land use suitability were made and have been presented for two types of potential land use. These two, agriculture and urbanization, represent potential land use conflicts.

Transcriptional analysis of Penaeus stylirostris densovirus genes

USDA-ARS?s Scientific Manuscript database

Penaeus stylirostris densovirus (PstDNV) genome contains three open reading frames (ORFs), left, middle, and right, which encode a non-structural (NS) protein, an unknown protein, and a capsid protein (CP), respectively. Transcription mapping revealed that P2, P11 and P61 promoters transcribe the le...

Population sequencing reveals breed and sub-species specific CNVs in cattle

USDA-ARS?s Scientific Manuscript database

Individualized copy number variation (CNV) maps have highlighted the need for population surveys of cattle to detect the rare and common variants. While SNP and comparative genomic hybridization (CGH) arrays have provided preliminary data, next-generation sequence (NGS) data analysis offers an incre...

Evaluation of ERTS-1 imagery for mapping Quaternary deposits and landforms in the Great Plains and Midwest. [Illinois, Nebraska, Iowa, Missouri, and Kansas

NASA Technical Reports Server (NTRS)

Morrison, R. B. (Principal Investigator); Hallberg, G. R.

1973-01-01

The author has identified the following significant results. Maps at 1:1 million scale exemplifying the first phase of the investigation (which consists of the identification and mapping of landform and land use characteristics and surficial geologic materials directly from the ERTS-1 images without use of additional data) were prepared. For areas that have not been mapped at 1:500,000 or larger scales, maps will provide the first moderately detailed information on landform features and surficial materials. Much of the information mapped is significant for exploration and development of ground (and, locally, petroleum) and for applications in engineering and environmental geology, including land use planning. Analysis of drainage patterns, stream-divide relations and land use patterns has revealed several possible moraine-controlled divices of middle and early Pleistocene age. One is an extension of the Cedar Bluffs moraine of southeastern Nebraska. Another of these divides may correspond to the terminus of Nebraska drift in the Kansas City study area. The trends of parts of various ancient filled valleys also have been identified by analysis of charges in width of the present stream valleys. The alinements of certain segments of stream valleys in Kansas and Missouri appear to be controlled by regional faults or other structural features.

Ecoregions and ecodistricts: Ecological regionalizations for the Netherlands' environmental policy

NASA Astrophysics Data System (ADS)

Klijn, Frans; de Waal, Rein W.; Oude Voshaar, Jan H.

1995-11-01

For communicating data on the state of the environment to policy makers, various integrative frameworks are used, including regional integration. For this kind of integration we have developed two related ecological regionalizations, ecoregions and ecodistricts, which are two levels in a series of classifications for hierarchically nested ecosystems at different spatial scale levels. We explain the compilation of the maps from existing geographical data, demonstrating the relatively holistic, a priori integrated approach. The resulting maps are submitted to discriminant analysis to test the consistancy of the use of mapping characteristics, using data on individual abiotic ecosystem components from a national database on a 1-km2 grid. This reveals that the spatial patterns of soil, groundwater, and geomorphology correspond with the ecoregion and ecodistrict maps. Differences between the original maps and maps formed by automatically reclassifying 1-km2 cells with these discriminant components are found to be few. These differences are discussed against the background of the principal dilemma between deductive, a priori integrated, and inductive, a posteriori, classification.

Relative risk estimation of Chikungunya disease in Malaysia: An analysis based on Poisson-gamma model

NASA Astrophysics Data System (ADS)

Samat, N. A.; Ma'arof, S. H. Mohd Imam

2015-05-01

Disease mapping is a method to display the geographical distribution of disease occurrence, which generally involves the usage and interpretation of a map to show the incidence of certain diseases. Relative risk (RR) estimation is one of the most important issues in disease mapping. This paper begins by providing a brief overview of Chikungunya disease. This is followed by a review of the classical model used in disease mapping, based on the standardized morbidity ratio (SMR), which we then apply to our Chikungunya data. We then fit an extension of the classical model, which we refer to as a Poisson-Gamma model, when prior distributions for the relative risks are assumed known. Both results are displayed and compared using maps and we reveal a smoother map with fewer extremes values of estimated relative risk. The extensions of this paper will consider other methods that are relevant to overcome the drawbacks of the existing methods, in order to inform and direct government strategy for monitoring and controlling Chikungunya disease.

Network Analysis of Beliefs About the Scientific Enterprise: A comparison of scientists, middle school science teachers and eighth-grade science students

NASA Astrophysics Data System (ADS)

Peters-Burton, Erin; Baynard, Liz R.

2013-11-01

An understanding of the scientific enterprise is useful because citizens need to make systematic, rational decisions about projects involving scientific endeavors and technology, and a clearer understanding of scientific epistemology is beneficial because it could encourage more public engagement with science. The purpose of this study was to capture beliefs for three groups, scientists, secondary science teachers, and eighth-grade science students, about the ways scientific knowledge is generated and validated. Open-ended questions were framed by formal scientific epistemology and dimensions of epistemology recognized in the field of educational psychology. The resulting statements were placed in a card sort and mapped in a network analysis to communicate interconnections among ideas. Maps analyzed with multidimensional scaling revealed robust connections among students and scientists but not among teachers. Student and teacher maps illustrated the strongest connections among ideas about experiments while scientist maps present more descriptive and well-rounded ideas about the scientific enterprise. The students' map was robust in terms of numbers of ideas, but were lacking in a hierarchical organization of ideas. The teachers' map displayed an alignment with the learning standards of the state, but not a broader view of science. The scientists map displayed a hierarchy of ideas with elaboration of equally valued statements connected to several foundational statements. Network analysis can be helpful in forwarding the study of views of the nature of science because of the technique's ability to capture verbatim statements from participants and to display the strength of connections among the statements.

Surname distribution in France: a distance analysis by a distorted geographical map.

PubMed

Mourrieras, B; Darlu, P; Hochez, J; Hazout, S

1995-01-01

The distribution of surnames in 90 distinct regions in France during two successive periods, 1889-1915 and 1916-1940, is analysed from the civil birth registers of the 36,500 administrative units in France. A new approach, called 'Mobile Site Method' (MSM), is developed to allow representation of a surname distance matrix by a distorted geographical map. A surname distance matrix between the various regions in France is first calculated, then a distorted geographical map called the 'surname similarity map' is built up from the surname distances between regions. To interpret this map we draw (a) successive map contours obtained during the step-by-step distortion process, revealing zones of high surname dissimilarity, and (b) maps in grey levels representing the displacement magnitude, and allowing the segmentation of the geographical and surname maps into 'homogeneous surname zones'. By integrating geography and surname information in the same analysis, and by comparing results obtained for the two successive periods, the MSM approach produces convenient maps showing: (a) 'regionalism' of some peripheral populations such as Pays Basque, Alsace, Corsica and Brittany; (b) the presence of preferential axes of communications (Rhodanian corridor, Garonne valley); (c) barriers such as the Central Massif, Vosges; (d) the weak modifications of the distorted maps associated with the two periods studied suggest an extension (but limited) of the tendency of surname uniformity in France. These results are interpreted, in the nineteenth- and twentieth century context, as the consequences of a slow process of local migrations occurring over a long period of time.

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

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

PubMed Central

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

2011-01-01

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

Mass Spectrometry Analysis of Spatial Protein Networks by Colocalization Analysis (COLA).

PubMed

Mardakheh, Faraz K

2017-01-01

A major challenge in systems biology is comprehensive mapping of protein interaction networks. Crucially, such interactions are often dynamic in nature, necessitating methods that can rapidly mine the interactome across varied conditions and treatments to reveal change in the interaction networks. Recently, we described a fast mass spectrometry-based method to reveal functional interactions in mammalian cells on a global scale, by revealing spatial colocalizations between proteins (COLA) (Mardakheh et al., Mol Biosyst 13:92-105, 2017). As protein localization and function are inherently linked, significant colocalization between two proteins is a strong indication for their functional interaction. COLA uses rapid complete subcellular fractionation, coupled with quantitative proteomics to generate a subcellular localization profile for each protein quantified by the mass spectrometer. Robust clustering is then applied to reveal significant similarities in protein localization profiles, indicative of colocalization.

Fine mapping on chromosome 13q32-34 and brain expression analysis implicates MYO16 in schizophrenia.

PubMed

Rodriguez-Murillo, Laura; Xu, Bin; Roos, J Louw; Abecasis, Gonçalo R; Gogos, Joseph A; Karayiorgou, Maria

2014-03-01

We previously reported linkage of schizophrenia and schizoaffective disorder to 13q32-34 in the European descent Afrikaner population from South Africa. The nature of genetic variation underlying linkage peaks in psychiatric disorders remains largely unknown and both rare and common variants may be contributing. Here, we examine the contribution of common variants located under the 13q32-34 linkage region. We used densely spaced SNPs to fine map the linkage peak region using both a discovery sample of 415 families and a meta-analysis incorporating two additional replication family samples. In a second phase of the study, we use one family-based data set with 237 families and independent case-control data sets for fine mapping of the common variant association signal using HapMap SNPs. We report a significant association with a genetic variant (rs9583277) within the gene encoding for the myosin heavy-chain Myr 8 (MYO16), which has been implicated in neuronal phosphoinositide 3-kinase signaling. Follow-up analysis of HapMap variation within MYO16 in a second set of Afrikaner families and additional case-control data sets of European descent highlighted a region across introns 2-6 as the most likely region to harbor common MYO16 risk variants. Expression analysis revealed a significant increase in the level of MYO16 expression in the brains of schizophrenia patients. Our results suggest that common variation within MYO16 may contribute to the genetic liability to schizophrenia.

Comparative mapping of Raphanus sativus genome using Brassica markers and quantitative trait loci analysis for the Fusarium wilt resistance trait.

PubMed

Yu, Xiaona; Choi, Su Ryun; Ramchiary, Nirala; Miao, Xinyang; Lee, Su Hee; Sun, Hae Jeong; Kim, Sunggil; Ahn, Chun Hee; Lim, Yong Pyo

2013-10-01

Fusarium wilt (FW), caused by the soil-borne fungal pathogen Fusarium oxysporum is a serious disease in cruciferous plants, including the radish (Raphanus sativus). To identify quantitative trait loci (QTL) or gene(s) conferring resistance to FW, we constructed a genetic map of R. sativus using an F2 mapping population derived by crossing the inbred lines '835' (susceptible) and 'B2' (resistant). A total of 220 markers distributed in 9 linkage groups (LGs) were mapped in the Raphanus genome, covering a distance of 1,041.5 cM with an average distance between adjacent markers of 4.7 cM. Comparative analysis of the R. sativus genome with that of Arabidopsis thaliana and Brassica rapa revealed 21 and 22 conserved syntenic regions, respectively. QTL mapping detected a total of 8 loci conferring FW resistance that were distributed on 4 LGs, namely, 2, 3, 6, and 7 of the Raphanus genome. Of the detected QTL, 3 QTLs (2 on LG 3 and 1 on LG 7) were constitutively detected throughout the 2-year experiment. QTL analysis of LG 3, flanked by ACMP0609 and cnu_mBRPGM0085, showed a comparatively higher logarithm of the odds (LOD) value and percentage of phenotypic variation. Synteny analysis using the linked markers to this QTL showed homology to A. thaliana chromosome 3, which contains disease-resistance gene clusters, suggesting conservation of resistance genes between them.

Global mapping of Al, Cu, Fe, and Zn in-use stocks and in-ground resources

PubMed Central

Rauch, Jason N.

2009-01-01

Human activity has become a significant geomorphic force in modern times, resulting in unprecedented movements of material around Earth. An essential constituent of this material movement, the major industrial metals aluminium, copper, iron, and zinc in the human-built environment are mapped globally at 1-km nominal resolution for the year 2000 and compared with the locations of present-day in-ground resources. While the maps of in-ground resources generated essentially combine available databases, the mapping methodology of in-use stocks relies on the linear regression between gross domestic product and both in-use stock estimates and the Nighttime Lights of the World dataset. As the first global maps of in-use metal stocks, they reveal that a full 25% of the world's Fe, Al, Cu, and Zn in-use deposits are concentrated in three bands: (i) the Eastern seaboard from Washington, D.C. to Boston in the United States, (ii) England, Benelux into Germany and Northern Italy, and (iii) South Korea and Japan. This pattern is consistent across all metals investigated. In contrast, the global maps of primary metal resources reveal these deposits are more evenly distributed between the developed and developing worlds, with the distribution pattern differing depending on the metal. This analysis highlights the magnitude at which in-ground metal resources have been translocated to in-use stocks, largely from highly concentrated but globally dispersed in-ground deposits to more diffuse in-use stocks located primarily in developed urban regions. PMID:19858486

Activated actin-depolymerizing factor/cofilin sequesters phosphorylated microtubule-associated protein during the assembly of alzheimer-like neuritic cytoskeletal striations.

PubMed

Whiteman, Ineka T; Gervasio, Othon L; Cullen, Karen M; Guillemin, Gilles J; Jeong, Erica V; Witting, Paul K; Antao, Shane T; Minamide, Laurie S; Bamburg, James R; Goldsbury, Claire

2009-10-14

In Alzheimer's disease (AD), rod-like cofilin aggregates (cofilin-actin rods) and thread-like inclusions containing phosphorylated microtubule-associated protein (pMAP) tau form in the brain (neuropil threads), and the extent of their presence correlates with cognitive decline and disease progression. The assembly mechanism of these respective pathological lesions and the relationship between them is poorly understood, yet vital to understanding the causes of sporadic AD. We demonstrate that, during mitochondrial inhibition, activated actin-depolymerizing factor (ADF)/cofilin assemble into rods along processes of cultured primary neurons that recruit pMAP/tau and mimic neuropil threads. Fluorescence resonance energy transfer analysis revealed colocalization of cofilin-GFP (green fluorescent protein) and pMAP in rods, suggesting their close proximity within a cytoskeletal inclusion complex. The relationship between pMAP and cofilin-actin rods was further investigated using actin-modifying drugs and small interfering RNA knockdown of ADF/cofilin in primary neurons. The results suggest that activation of ADF/cofilin and generation of cofilin-actin rods is required for the subsequent recruitment of pMAP into the inclusions. Additionally, we were able to induce the formation of pMAP-positive ADF/cofilin rods by exposing cells to exogenous amyloid-beta (Abeta) peptides. These results reveal a common pathway for pMAP and cofilin accumulation in neuronal processes. The requirement of activated ADF/cofilin for the sequestration of pMAP suggests that neuropil thread structures in the AD brain may be initiated by elevated cofilin activation and F-actin bundling that can be caused by oxidative stress, mitochondrial dysfunction, or Abeta peptides, all suspected initiators of synaptic loss and neurodegeneration in AD.

Lessons from a phenotyping center revealed by the genome-guided mapping of powdery mildew resistance loci

USDA-ARS?s Scientific Manuscript database

The genomics era brought unprecedented tools for genetic analysis of host resistance, but careful attention is needed on obtaining accurate and reproducible phenotypes so that genomic results appropriately reflect biology. Phenotyping host resistance by natural infection in the field can produce var...

QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods.

PubMed

Win, Khin Thanda; Vegas, Juan; Zhang, Chunying; Song, Kihwan; Lee, Sanghyeob

2017-01-01

QTL mapping using NGS-assisted BSA was successfully applied to an F 2 population for downy mildew resistance in cucumber. QTLs detected by NGS-assisted BSA were confirmed by conventional QTL analysis. Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive foliar diseases in cucumber. QTL mapping is a fundamental approach for understanding the genetic inheritance of DM resistance in cucumber. Recently, many studies have reported that a combination of bulked segregant analysis (BSA) and next-generation sequencing (NGS) can be a rapid and cost-effective way of mapping QTLs. In this study, we applied NGS-assisted BSA to QTL mapping of DM resistance in cucumber and confirmed the results by conventional QTL analysis. By sequencing two DNA pools each consisting of ten individuals showing high resistance and susceptibility to DM from a F 2 population, we identified single nucleotide polymorphisms (SNPs) between the two pools. We employed a statistical method for QTL mapping based on these SNPs. Five QTLs, dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1, were detected and dm2.2 showed the largest effect on DM resistance. Conventional QTL analysis using the F 2 confirmed dm2.2 (R 2  = 10.8-24 %) and dm5.2 (R 2  = 14-27.2 %) as major QTLs and dm4.1 (R 2  = 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R 2  = 28.2 %) was detected by the conventional QTL method using an F 3 population. This study demonstrated the effectiveness of NGS-assisted BSA for mapping QTLs conferring DM resistance in cucumber and revealed the unique genetic inheritance of DM resistance in this population through two distinct major QTLs on chromosome 2 that mainly harbor DM resistance.

Parietal and superior frontal visuospatial maps activated by pointing and saccades

PubMed Central

Hagler, D.J.; Riecke, L.; Sereno, M.I.

2009-01-01

A recent study from our laboratory demonstrated that parietal cortex contains a map of visual space related to saccades and spatial attention and identified this area as the likely human homologue of the lateral intraparietal (LIP). A human homologue for the parietal reach region (PRR), thought to preferentially encode planned hand movements, has also been recently proposed. Both of these areas, originally identified in the macaque monkey, have been shown to encode space with eye-centered coordinates. Functional magnetic resonance imaging (fMRI) of humans was used to test the hypothesis that the putative human PRR contains a retinotopic map recruited by finger pointing but not saccades and to test more generally for differences in the visuospatial maps recruited by pointing and saccades. We identified multiple maps in both posterior parietal cortex and superior frontal cortex recruited for eye and hand movements, including maps not observed in previous mapping studies. Pointing and saccade maps were generally consistent within single subjects. We have developed new group analysis methods for phase-encoded data, which revealed subtle differences between pointing and saccades, including hemispheric asymmetries, but we did not find evidence of pointing-specific maps of visual space. PMID:17376706

Intrinsic Resting-State Functional Connectivity in the Human Spinal Cord at 3.0 T.

PubMed

San Emeterio Nateras, Oscar; Yu, Fang; Muir, Eric R; Bazan, Carlos; Franklin, Crystal G; Li, Wei; Li, Jinqi; Lancaster, Jack L; Duong, Timothy Q

2016-04-01

To apply resting-state functional magnetic resonance (MR) imaging to map functional connectivity of the human spinal cord. Studies were performed in nine self-declared healthy volunteers with informed consent and institutional review board approval. Resting-state functional MR imaging was performed to map functional connectivity of the human cervical spinal cord from C1 to C4 at 1 × 1 × 3-mm resolution with a 3.0-T clinical MR imaging unit. Independent component analysis (ICA) was performed to derive resting-state functional MR imaging z-score maps rendered on two-dimensional and three-dimensional images. Seed-based analysis was performed for cross validation with ICA networks by using Pearson correlation. Reproducibility analysis of resting-state functional MR imaging maps from four repeated trials in a single participant yielded a mean z score of 6 ± 1 (P < .0001). The centroid coordinates across the four trials deviated by 2 in-plane voxels ± 2 mm (standard deviation) and up to one adjacent image section ± 3 mm. ICA of group resting-state functional MR imaging data revealed prominent functional connectivity patterns within the spinal cord gray matter. There were statistically significant (z score > 3, P < .001) bilateral, unilateral, and intersegmental correlations in the ventral horns, dorsal horns, and central spinal cord gray matter. Three-dimensional surface rendering provided visualization of these components along the length of the spinal cord. Seed-based analysis showed that many ICA components exhibited strong and significant (P < .05) correlations, corroborating the ICA results. Resting-state functional MR imaging connectivity networks are qualitatively consistent with known neuroanatomic and functional structures in the spinal cord. Resting-state functional MR imaging of the human cervical spinal cord with a 3.0-T clinical MR imaging unit and standard MR imaging protocols and hardware reveals prominent functional connectivity patterns within the spinal cord gray matter, consistent with known functional and anatomic layouts of the spinal cord.

Multivariate analysis of historical data (2004-2013) in assessing the possible environmental impact of the Bellolampo landfill (Palermo).

PubMed

Indelicato, Serena; Bongiorno, David; Tuzzolino, Nicola; Mannino, Maria Rosaria; Muscarella, Rosalia; Fradella, Pasquale; Gargano, Maria Elena; Nicosia, Salvatore; Ceraulo, Leopoldo

2018-03-14

Multivariate analysis was performed on a large data set of groundwater and leachate samples collected during 9 years of operation of the Bellolampo municipal solid waste landfill (located above Palermo, Italy). The aim was to obtain the most likely correlations among the data. The analysis results are presented. Groundwater samples were collected in the period 2004-2013, whereas the leachate analysis refers to the period 2006-2013. For groundwater, statistical data evaluation revealed notable differences among the samples taken from the numerous wells located around the landfill. Characteristic parameters revealed by principal component analysis (PCA) were more deeply investigated, and corresponding thematic maps were drawn. The composition of the leachate was also thoroughly investigated. Several chemical macro-descriptors were calculated, and the results are presented. A comparison of PCA results for the leachate and groundwater data clearly reveals that the groundwater's main components substantially differ from those of the leachate. This outcome strongly suggests excluding leachate permeation through the multiple landfill lining.

Correlation of ERTS MSS data and earth coordinate systems

NASA Technical Reports Server (NTRS)

Malila, W. A. (Principal Investigator); Hieber, R. H.; Mccleer, A. P.

1973-01-01

The author has identified the following significant results. Experience has revealed a problem in the analysis and interpretation of ERTS-1 multispectral scanner (MSS) data. The problem is one of accurately correlating ERTS-1 MSS pixels with analysis areas specified on aerial photographs or topographic maps for training recognition computers and/or evaluating recognition results. It is difficult for an analyst to accurately identify which ERTS-1 pixels on a digital image display belong to specific areas and test plots, especially when they are small. A computer-aided procedure to correlate coordinates from topographic maps and/or aerial photographs with ERTS-1 data coordinates has been developed. In the procedure, a map transformation from earth coordinates to ERTS-1 scan line and point numbers is calculated using selected ground control points nad the method of least squares. The map transformation is then applied to the earth coordinates of selected areas to obtain the corresponding ERTS-1 point and line numbers. An optional provision allows moving the boundaries of the plots inward by variable distances so the selected pixels will not overlap adjacent features.

Development of a YAC contig covering the minimal region of a CSNB1 locus in Xp11

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

Boycott, K.M.; Gratton, K.J.; Moore, B.J.

1994-09-01

X-linked congenital stationary night blindness (CSNB1) is an eye disorder that includes impairment of night vision, reduced visual acuity and, in some cases, myopia and congenital nystagmus. Electroretinography reveals a marked reduction of the b-wave in affected individuals suggesting that X-linked CSNB is due to a molecular defect in the bipolar layer of the retina. Based on our studies of a large four generation family with X-linked CSNB, a CSNB1 locus was mapped to a 4-5 cM region at Xp11.23-Xp11.22 bounded telomerically by DXS426 and centromerically by DXS988. Using a panel of radiation and conventional somatic cell hybrids, a detailedmore » map of new and published STSs has been generated for the minimal region of CSNB1. PCR primer pairs for STSs has been generated for the minimal region of CSNB1. PCR primer pairs for twenty-five STSs, including eleven end-clones, were used to isolate YAC clones from CEPH, mega-CEPH, and X chromosome-specific YAC libraries. In total, fifty-two YACs were characterized for STS overlaps and assembled to provide a minimum of 3 Mb of physical coverage in the region between DXS426 and DXS988. Five gaps proximal to SYP are still to be closed. Our physical map suggests the following gene order: Xpter-OTAL1-GF1-DXS1011E-MG81-HUMCRAS2P-SYP-Xcen. STS analysis of the YACs revealed three subregions of the physical map which appear to be particularly susceptible to internal deletions and end-clone analysis demonstrated chimerism in six of seventeen YACs. A physical map of Xp11.23-Xp11.22 will provide a resource for the isolation of candidate genes for the X-linked CSNB gene which maps to this region.« less

Loss of Mitogen-Activated Protein Kinase Kinase Kinase 4 (MAP3K4) Reveals a Requirement for MAPK Signalling in Mouse Sex Determination

PubMed Central

Bogani, Debora; Siggers, Pam; Brixey, Rachel; Warr, Nick; Beddow, Sarah; Edwards, Jessica; Williams, Debbie; Wilhelm, Dagmar; Koopman, Peter; Flavell, Richard A.; Chi, Hongbo; Ostrer, Harry; Wells, Sara; Cheeseman, Michael; Greenfield, Andy

2009-01-01

Sex determination in mammals is controlled by the presence or absence of the Y-linked gene SRY. In the developing male (XY) gonad, sex-determining region of the Y (SRY) protein acts to up-regulate expression of the related gene, SOX9, a transcriptional regulator that in turn initiates a downstream pathway of testis development, whilst also suppressing ovary development. Despite the requirement for a number of transcription factors and secreted signalling molecules in sex determination, intracellular signalling components functioning in this process have not been defined. Here we report a role for the phylogenetically ancient mitogen-activated protein kinase (MAPK) signalling pathway in mouse sex determination. Using a forward genetic screen, we identified the recessive boygirl (byg) mutation. On the C57BL/6J background, embryos homozygous for byg exhibit consistent XY gonadal sex reversal. The byg mutation is an A to T transversion causing a premature stop codon in the gene encoding MAP3K4 (also known as MEKK4), a mitogen-activated protein kinase kinase kinase. Analysis of XY byg/byg gonads at 11.5 d post coitum reveals a growth deficit and a failure to support mesonephric cell migration, both early cellular processes normally associated with testis development. Expression analysis of mutant XY gonads at the same stage also reveals a dramatic reduction in Sox9 and, crucially, Sry at the transcript and protein levels. Moreover, we describe experiments showing the presence of activated MKK4, a direct target of MAP3K4, and activated p38 in the coelomic region of the XY gonad at 11.5 d post coitum, establishing a link between MAPK signalling in proliferating gonadal somatic cells and regulation of Sry expression. Finally, we provide evidence that haploinsufficiency for Map3k4 accounts for T-associated sex reversal (Tas). These data demonstrate that MAP3K4-dependent signalling events are required for normal expression of Sry during testis development, and create a novel entry point into the molecular and cellular mechanisms underlying sex determination in mice and disorders of sexual development in humans. PMID:19753101

Examining Science Teachers' Argumentation in a Teacher Workshop on Earthquake Engineering

NASA Astrophysics Data System (ADS)

Cavlazoglu, Baki; Stuessy, Carol

2018-02-01

The purpose of this study was to examine changes in the quality of science teachers' argumentation as a result of their engagement in a teacher workshop on earthquake engineering emphasizing distributed learning approaches, which included concept mapping, collaborative game playing, and group lesson planning. The participants were ten high school science teachers from US high schools who elected to attend the workshop. To begin and end the teacher workshop, teachers in small groups engaged in concept mapping exercises with other teachers. Researchers audio-recorded individual teachers' argumentative statements about the inclusion of earthquake engineering concepts in their concept maps, which were then analyzed to reveal the quality of teachers' argumentation. Toulmin's argumentation model formed the framework for designing a classification schema to analyze the quality of participants' argumentative statements. While the analysis of differences in pre- and post-workshop concept mapping exercises revealed that the number of argumentative statements did not change significantly, the quality of participants' argumentation did increase significantly. As these differences occurred concurrently with distributed learning approaches used throughout the workshop, these results provide evidence to support distributed learning approaches in professional development workshop activities to increase the quality of science teachers' argumentation. Additionally, these results support the use of concept mapping as a cognitive scaffold to organize participants' knowledge, facilitate the presentation of argumentation, and as a research tool for providing evidence of teachers' argumentation skills.

Quantitative proteomics revealed partial fungistatic mechanism of ammonia against conidial germination of nematode-trapping fungus Arthrobotrys oligospora ATCC24927.

PubMed

Liu, Tong; Tian, Dong-Wei; Zou, Li-Juan; Liu, Fang-Yu; Can, Qi-Yan; Yang, Jin-Kui; Xu, Jian-Ping; Huang, Xiao-Wei; Xi, Jia-Qin; Zhu, Ming-Liang; Mo, Ming-He; Zhang, Ke-Qin

2018-05-01

Ammonia is one of the fungistatic factors in soil that can suppress conidial germination, but the molecular mechanism underlying the suppression is unknown. In this study, the proteomes of fungistatic conidia, fresh conidia and germinated conidia of Arthrobotrys oligospora ATCC24927 were determined and quantified. The protein expression profile of fungistatic conidia was significantly different from those in the other two conditions. 281 proteins were down expressed in fungistatic conidia and characterized by GO annotation. Gene transcription analysis and inhibition of puromycin (a protein translation inhibitor) on conidial germination suggested that down expression of 33 protein translation related proteins might well result in repression of protein synthesis and inhibition of conidial germination. In addition, 16 down-expressed proteins were mapped to the Ras/mitogen-activated protein (Ras/MAP) regulatory networks which regulate conidial DNA synthesis. The conidial DNA synthesis was found to be definitely inhibited under by ammonia, and function studies of two Ras/MAP proteins by using knock-out strains provided partial evidence that Ras/MAP pathway regulate the conidial germination. These results suggested that down-expression of Ras/MAP related proteins might result in inhibition of DNA synthesis and finally result in inhibition conidial germination. This study revealed partial fungistatic mechanism of ammonia against conidial germination. Copyright © 2018 Elsevier Ltd. All rights reserved.

Impact of Plant Functional Types on Coherence Between Precipitation and Soil Moisture: A Wavelet Analysis

NASA Astrophysics Data System (ADS)

Liu, Qi; Hao, Yonghong; Stebler, Elaine; Tanaka, Nobuaki; Zou, Chris B.

2017-12-01

Mapping the spatiotemporal patterns of soil moisture within heterogeneous landscapes is important for resource management and for the understanding of hydrological processes. A critical challenge in this mapping is comparing remotely sensed or in situ observations from areas with different vegetation cover but subject to the same precipitation regime. We address this challenge by wavelet analysis of multiyear observations of soil moisture profiles from adjacent areas with contrasting plant functional types (grassland, woodland, and encroached) and precipitation. The analysis reveals the differing soil moisture patterns and dynamics between plant functional types. The coherence at high-frequency periodicities between precipitation and soil moisture generally decreases with depth but this is much more pronounced under woodland compared to grassland. Wavelet analysis provides new insights on soil moisture dynamics across plant functional types and is useful for assessing differences and similarities in landscapes with heterogeneous vegetation cover.

Homozygosity and linkage-disequilibrium mapping of the syndrome of congenital hypoparathyroidism, growth and mental retardation, and dysmorphism to a 1-cM interval on chromosome 1q42-43.

PubMed

Parvari, R; Hershkovitz, E; Kanis, A; Gorodischer, R; Shalitin, S; Sheffield, V C; Carmi, R

1998-07-01

The syndrome of hypoparathyroidism associated with growth retardation, developmental delay, and dysmorphism (HRD) is a newly described, autosomal recessive, congenital disorder with severe, often fatal consequences. Since the syndrome is very rare, with all parents of affected individuals being consanguineous, it is presumed to be caused by homozygous inheritance of a single recessive mutation from a common ancestor. To localize the HRD gene, we performed a genomewide screen using DNA pooling and homozygosity mapping for apparently unlinked kindreds. Analysis of a panel of 359 highly polymorphic markers revealed linkage to D1S235. The maximum LOD score obtained was 4.11 at a recombination fraction of 0. Analysis of three additional markers-GGAA6F06, D1S2678, and D1S179-in a 2-cM interval around D1S235 resulted in LOD scores >3. Analysis of additional chromosome 1 markers revealed evidence of genetic linkage disequilibrium and place the HRD locus within an approximately 1-cM interval defined by D1S1540 and D1S2678 on chromosome 1q42-43.

Homozygosity and linkage-disequilibrium mapping of the syndrome of congenital hypoparathyroidism, growth and mental retardation, and dysmorphism to a 1-cM interval on chromosome 1q42-43.

PubMed Central

Parvari, R; Hershkovitz, E; Kanis, A; Gorodischer, R; Shalitin, S; Sheffield, V C; Carmi, R

1998-01-01

The syndrome of hypoparathyroidism associated with growth retardation, developmental delay, and dysmorphism (HRD) is a newly described, autosomal recessive, congenital disorder with severe, often fatal consequences. Since the syndrome is very rare, with all parents of affected individuals being consanguineous, it is presumed to be caused by homozygous inheritance of a single recessive mutation from a common ancestor. To localize the HRD gene, we performed a genomewide screen using DNA pooling and homozygosity mapping for apparently unlinked kindreds. Analysis of a panel of 359 highly polymorphic markers revealed linkage to D1S235. The maximum LOD score obtained was 4.11 at a recombination fraction of 0. Analysis of three additional markers-GGAA6F06, D1S2678, and D1S179-in a 2-cM interval around D1S235 resulted in LOD scores >3. Analysis of additional chromosome 1 markers revealed evidence of genetic linkage disequilibrium and place the HRD locus within an approximately 1-cM interval defined by D1S1540 and D1S2678 on chromosome 1q42-43. PMID:9634513

Using rock art as an alternative science pedagogy

NASA Astrophysics Data System (ADS)

Allen, Casey D.

College-level and seventh-grade science students were studied to understand the power of a field index, the Rock Art Stability Index (RASI), for student learning about complex biophysical environmental processes. In order to determine if the studied population was representative, 584 college and seventh-grade students undertook a concept mapping exercise after they had learned basic weathering science via in-class lecture. Of this large group, a subset of 322 college students and 13 seventh-grade students also learned RASI through a field experience involving the analysis of rock weathering associated with petroglyphs. After learning weathering through RASI, students completed another concept map. This was a college population where roughly 46% had never taken a "lab science" course and nearly 22% were from minority (non-white) populations. Analysis of student learning through the lens of actor-network theory revealed that when landscape is viewed as process (i.e. many practices), science education embodies both an alternative science philosophy and an alternative materialistic worldview. When RASI components were analyzed after only lecture, student understanding of weathering displayed little connection between weathering form and weathering process. After using RASI in the field however, nearly all students made illustrative concept maps rich in connections between weathering form and weathering process for all subcomponents of RASI. When taken as an aggregate, and measured by an average concept map score, learning increased by almost 14%, Among college minority students, the average score increase approached 23%. Among female students, the average score increase was 16%. For seventh-grade students, scores increased by nearly 36%. After testing for normalcy with Kolmogorov-Smirnov, t-tests reveal that all of these increases were highly statistically significant at p<0.001. The growth in learning weathering science by minority students, as compared to non-minority students, was also statistically significant at p<0.01. These findings reveal the power of field work through RASI to strengthen cognitive linkages between complex biophysical processes and the corresponding rock weathering forms.

Application of Dempster-Shafer theory, spatial analysis and remote sensing for groundwater potentiality and nitrate pollution analysis in the semi-arid region of Khuzestan, Iran.

PubMed

Rahmati, Omid; Melesse, Assefa M

2016-10-15

Effective management and sustainable development of groundwater resources of arid and semi-arid environments require monitoring of groundwater quality and quantity. The aim of this paper is to develop a reasonable methodological framework for producing the suitability map for drinking water through the geographic information system, remote sensing and field surveys of the Andimeshk-Dezful, Khozestan province, Iran as a semi-arid region. This study investigated the delineation of groundwater potential zone based on Dempster-Shafer (DS) theory of evidence and evaluate its applicability for groundwater potentiality mapping. The study also analyzed the spatial distribution of groundwater nitrate concentration; and produced the suitability map for drinking water. The study has been carried out with the following steps: i) creation of maps of groundwater conditioning factors; ii) assessment of groundwater occurrence characteristics; iii) creation of groundwater potentiality map (GPM) and model validation; iv) collection and chemical analysis of water samples; v) assessment of groundwater nitrate pollution; and vi) creation of groundwater potentiality and quality map. The performance of the DS was also evaluated using the receiver operating characteristic (ROC) curve method and pumping test data to ensure its generalization ability, which eventually, the GPM showed 87.76% accuracy. The detailed analysis of groundwater potentiality and quality revealed that the 'non acceptable' areas covers an area of about 1479km(2) (60%). The study will provide significant information for groundwater management and exploitation in areas where groundwater is a major source of water and its exploration is critical to support drinking water need. Copyright © 2016 Elsevier B.V. All rights reserved.

A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions

PubMed Central

2013-01-01

Background Metabolomics has become increasingly popular in the study of disease phenotypes and molecular pathophysiology. One branch of metabolomics that encompasses the high-throughput screening of cellular metabolism is metabolic profiling. In the present study, the metabolic profiles of different tumour cells from colorectal carcinoma and breast adenocarcinoma were exposed to hypoxic and normoxic conditions and these have been compared to reveal the potential metabolic effects of hypoxia on the biochemistry of the tumour cells; this may contribute to their survival in oxygen compromised environments. In an attempt to analyse the complex interactions between metabolites beyond routine univariate and multivariate data analysis methods, correlation analysis has been integrated with a human metabolic reconstruction to reveal connections between pathways that are associated with normoxic or hypoxic oxygen environments. Results Correlation analysis has revealed statistically significant connections between metabolites, where differences in correlations between cells exposed to different oxygen levels have been highlighted as markers of hypoxic metabolism in cancer. Network mapping onto reconstructed human metabolic models is a novel addition to correlation analysis. Correlated metabolites have been mapped onto the Edinburgh human metabolic network (EHMN) with the aim of interlinking metabolites found to be regulated in a similar fashion in response to oxygen. This revealed novel pathways within the metabolic network that may be key to tumour cell survival at low oxygen. Results show that the metabolic responses to lowering oxygen availability can be conserved or specific to a particular cell line. Network-based correlation analysis identified conserved metabolites including malate, pyruvate, 2-oxoglutarate, glutamate and fructose-6-phosphate. In this way, this method has revealed metabolites not previously linked, or less well recognised, with respect to hypoxia before. Lactate fermentation is one of the key themes discussed in the field of hypoxia; however, malate, pyruvate, 2-oxoglutarate, glutamate and fructose-6-phosphate, which are connected by a single pathway, may provide a more significant marker of hypoxia in cancer. Conclusions Metabolic networks generated for each cell line were compared to identify conserved metabolite pathway responses to low oxygen environments. Furthermore, we believe this methodology will have general application within metabolomics. PMID:24153255

Image Analysis of DNA Fiber and Nucleus in Plants.

PubMed

Ohmido, Nobuko; Wako, Toshiyuki; Kato, Seiji; Fukui, Kiichi

2016-01-01

Advances in cytology have led to the application of a wide range of visualization methods in plant genome studies. Image analysis methods are indispensable tools where morphology, density, and color play important roles in the biological systems. Visualization and image analysis methods are useful techniques in the analyses of the detailed structure and function of extended DNA fibers (EDFs) and interphase nuclei. The EDF is the highest in the spatial resolving power to reveal genome structure and it can be used for physical mapping, especially for closely located genes and tandemly repeated sequences. One the other hand, analyzing nuclear DNA and proteins would reveal nuclear structure and functions. In this chapter, we describe the image analysis protocol for quantitatively analyzing different types of plant genome, EDFs and interphase nuclei.

Structural interpretations based on ERTS-1 imagery, Bighorn Region, Wyoming-Montana

NASA Technical Reports Server (NTRS)

Hoppin, R. A.

1973-01-01

Structural analysis is being carried out on bands MSS 5 and 7 of scene 1085-17294. Geologic strucutre is primarily revealed in the topographic relief and drainage. Topographic linears are particularly well developed in the bighorn uplift. Many of these occur along known faults and shear zones in the Precambrian core; several have not been previously mapped. These linears, however, do not continue into the younger rocks of the flanks or do so in a much less marked manner than in the core. Linears are far less abundant in the basin or are manifested only in very subtle tonal contrasts and somewhat straight drainage segments. Some of the linears are aligned along trends previously postulated on the basis of surface mapping to be lineaments. The imagery reveals little or no evidence of strike-slip displacements along these lineaments.

Awake craniotomy for excision of arteriovenous malformations? A qualitative comparison study with stereotactic radiosurgery.

PubMed

Chan, David Yuen Chung; Chan, Danny Tat Ming; Zhu, Cannon Xian Lun; Kan, Patricia Kwok Yee; Ng, Amelia Yikjin; Hsieh, Yi-Pin Sonia; Abrigo, Jill; Poon, Wai Sang; Wong, George Kwok Chu

2018-05-01

Treatment of arteriovenous malformations (AVM) located at the eloquent area has been a challenge. Awake brain mapping allows identification of a non-eloquent gyrus for intervention and can potentially facilitate resection with preservation of functions. An alternative treatment option is stereotactic radiosurgery (SRS). The objective of this study was to perform a qualitative comparison of the treatment outcome of awake AVM excision versus SRS. We conducted a 13-year retrospective review of AVM excision under awake craniotomy performed at Prince of Wales Hospital, Hong Kong, from 2003 to 2016. Patients' presentation, Spetzler-Martin (SM) grading, rate of obliteration and complication were reviewed and analyzed with the modified radiosurgery-based AVM score (RS score). Six patients had excision of AVM under awake mapping during this period of time. Two were SM Grade II and four were SM Grade III. Five located at the peri-rolandic region while one at the temporal language area. None had failed mapping. Five out of six achieved complete obliteration (83.3%). Qualitative comparative analysis had revealed better treatment outcome with awake AVM excision as compared to SRS with the obliteration rate of 100% versus 96% for RS score ≤1.00, 100% versus 78% for RS score 1.01-1.50, and 66% versus 50% for RS score >2.00 respectively. In conclusion, awake mapping and excision of AVMs at the eloquent area is feasible. Qualitative comparative analysis had revealed higher obliteration rate with awake AVM excision as compared to SRS. Copyright © 2018 Elsevier Ltd. All rights reserved.

In-vivo assessment of microvascular functional dynamics by combination of cmOCT and wavelet transform

NASA Astrophysics Data System (ADS)

Smirni, Salvatore; MacDonald, Michael P.; Robertson, Catherine P.; McNamara, Paul M.; O'Gorman, Sean; Leahy, Martin J.; Khan, Faisel

2018-02-01

The cutaneous microcirculation represents an index of the health status of the cardiovascular system. Conventional methods to evaluate skin microvascular function are based on measuring blood flow by laser Doppler in combination with reactive tests such as post-occlusive reactive hyperaemia (PORH). Moreover, the spectral analysis of blood flow signals by continuous wavelet transform (CWT) reveals nonlinear oscillations reflecting the functionality of microvascular biological factors, e.g. endothelial cells (ECs). Correlation mapping optical coherence tomography (cmOCT) has been previously described as an efficient methodology for the morphological visualisation of cutaneous micro-vessels. Here, we show that cmOCT flow maps can also provide information on the functional components of the microcirculation. A spectral domain optical coherence tomography (SD-OCT) imaging system was used to acquire 90 sequential 3D OCT volumes from the forearm of a volunteer, while challenging the micro-vessels with a PORH test. The volumes were sampled in a temporal window of 25 minutes, and were processed by cmOCT to obtain flow maps at different tissue depths. The images clearly show changes of flow in response to the applied stimulus. Furthermore, a blood flow signal was reconstructed from cmOCT maps intensities to investigate the microvascular nonlinear dynamics by CWT. The analysis revealed oscillations changing in response to PORH, associated with the activity of ECs and the sympathetic innervation. The results demonstrate that cmOCT may be potentially used as diagnostic tool for the assessment of microvascular function, with the advantage of also providing spatial resolution and structural information compared to the traditional laser Doppler techniques.

Mapping the determinants of health inequalities in social space: can Bourdieu help us?

PubMed

Gatrell, Anthony C; Popay, Jennie; Thomas, Carol

2004-09-01

Considerable research effort has been devoted to describing and explaining, at a variety of spatial scales, geographical inequalities in health outcomes within the developed world. Following Bourdieu, we argue that structures of the social world may be revealed in different kinds of 'social' space. We outline the relational thinking that underlies these ideas. We then 'map', using correspondence analysis (on which Bourdieu himself drew), the structure of social space according to the differential availability of some forms of capital, across four study areas in north-west England. We use logistic regression analysis to explain variation in psychological morbidity (GHQ-score) and then portray the significant predictors of morbidity using multiple correspondence analysis. The area of residence of the survey respondents is used to associate them with particular locations in these social spaces.

A Look Inside HIV Resistance through Retroviral Protease Interaction Maps

PubMed Central

Kontijevskis, Aleksejs; Prusis, Peteris; Petrovska, Ramona; Yahorava, Sviatlana; Mutulis, Felikss; Mutule, Ilze; Komorowski, Jan; Wikberg, Jarl E. S

2007-01-01

Retroviruses affect a large number of species, from fish and birds to mammals and humans, with global socioeconomic negative impacts. Here the authors report and experimentally validate a novel approach for the analysis of the molecular networks that are involved in the recognition of substrates by retroviral proteases. Using multivariate analysis of the sequence-based physiochemical descriptions of 61 retroviral proteases comprising wild-type proteases, natural mutants, and drug-resistant forms of proteases from nine different viral species in relation to their ability to cleave 299 substrates, the authors mapped the physicochemical properties and cross-dependencies of the amino acids of the proteases and their substrates, which revealed a complex molecular interaction network of substrate recognition and cleavage. The approach allowed a detailed analysis of the molecular–chemical mechanisms involved in substrate cleavage by retroviral proteases. PMID:17352531

A 1,681-locus consensus genetic map of cultivated cucumber including 67 NB-LRR resistance gene homolog and ten gene loci

PubMed Central

2013-01-01

Background Cucumber is an important vegetable crop that is susceptible to many pathogens, but no disease resistance (R) genes have been cloned. The availability of whole genome sequences provides an excellent opportunity for systematic identification and characterization of the nucleotide binding and leucine-rich repeat (NB-LRR) type R gene homolog (RGH) sequences in the genome. Cucumber has a very narrow genetic base making it difficult to construct high-density genetic maps. Development of a consensus map by synthesizing information from multiple segregating populations is a method of choice to increase marker density. As such, the objectives of the present study were to identify and characterize NB-LRR type RGHs, and to develop a high-density, integrated cucumber genetic-physical map anchored with RGH loci. Results From the Gy14 draft genome, 70 NB-containing RGHs were identified and characterized. Most RGHs were in clusters with uneven distribution across seven chromosomes. In silico analysis indicated that all 70 RGHs had EST support for gene expression. Phylogenetic analysis classified 58 RGHs into two clades: CNL and TNL. Comparative analysis revealed high-degree sequence homology and synteny in chromosomal locations of these RGH members between the cucumber and melon genomes. Fifty-four molecular markers were developed to delimit 67 of the 70 RGHs, which were integrated into a genetic map through linkage analysis. A 1,681-locus cucumber consensus map including 10 gene loci and spanning 730.0 cM in seven linkage groups was developed by integrating three component maps with a bin-mapping strategy. Physically, 308 scaffolds with 193.2 Mbp total DNA sequences were anchored onto this consensus map that covered 52.6% of the 367 Mbp cucumber genome. Conclusions Cucumber contains relatively few NB-LRR RGHs that are clustered and unevenly distributed in the genome. All RGHs seem to be transcribed and shared significant sequence homology and synteny with the melon genome suggesting conservation of these RGHs in the Cucumis lineage. The 1,681-locus consensus genetic-physical map developed and the RGHs identified and characterized herein are valuable genomics resources that may have many applications such as quantitative trait loci identification, map-based gene cloning, association mapping, marker-assisted selection, as well as assembly of a more complete cucumber genome. PMID:23531125

Topographic brain mapping of emotion-related hemisphere asymmetries.

PubMed

Roschmann, R; Wittling, W

1992-03-01

The study used topographic brain mapping of visual evoked potentials to investigate emotion-related hemisphere asymmetries. The stimulus material consisted of color photographs of human faces, grouped into two emotion-related categories: normal faces (neutral stimuli) and faces deformed by dermatological diseases (emotional stimuli). The pictures were presented tachistoscopically to 20 adult right-handed subjects. Brain activity was recorded by 30 EEG electrodes with linked ears as reference. The waveforms were averaged separately with respect to each of the two stimulus conditions. Statistical analysis by means of significance probability mapping revealed significant differences between stimulus conditions for two periods of time, indicating right hemisphere superiority in emotion-related processing. The results are discussed in terms of a 2-stage-model of emotional processing in the cerebral hemispheres.

Mapping analysis of scaffold/matrix attachment regions (s/MARs) from two different mammalian cell lines

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

Pilus, Nur Shazwani Mohd; Ahmad, Azrin; Yusof, Nurul Yuziana Mohd

Scaffold/matrix attachment regions (S/MARs) are potential element that can be integrated into expression vector to increase expression of recombinant protein. Many studies on S/MAR have been done but none has revealed the distribution of S/MAR in a genome. In this study, we have isolated S/MAR sequences from HEK293 and Chinese hamster ovary cell lines (CHO DG44) using two different methods utilizing 2 M NaCl and lithium-3,5-diiodosalicylate (LIS). The isolated S/MARs were sequenced using Next Generation Sequencing (NGS) platform. Based on reference mapping analysis against human genome database, a total of 8,994,856 and 8,412,672 contigs of S/MAR sequences were retrieved frommore » 2M NaCl and LIS extraction of HEK293 respectively. On the other hand, reference mapping analysis of S/MAR derived from CHO DG44 against our own CHO DG44 database have generated a total of 7,204,348 and 4,672,913 contigs from 2 M NaCl and LIS extraction method respectively.« less

Capability of applying morphometric parameters of relief in river basins for geomorphological zoning of a territory

NASA Astrophysics Data System (ADS)

Ivanov, M. A.; Yermolaev, O. P.

2018-01-01

Information about morphometric characteristics of relief is necessary for researches devoted to geographic characteristics of territory, its zoning, assessment of erosion processes, geoecological condition and others. For the Volga Federal District for the first time a spatial database of geomorphometric parameters 1: 200 000 scale was created, based on a river basin approach. Watersheds are used as a spatial units created by semi-automated method using the terrain and hydrological modeling techniques implemented in the TAS GIS and WhiteBox GIS. As input data DEMs SRTM and Aster GDEM and hydrographic network vectorized from topographic maps were used. Using DEM highlighted above for each river basin, basic morphometric relief characteristics such as mean height, slope steepness, slope length, height range, river network density and factor LS were calculated. Basins belonging to the geomorphological regions and landscape zones was determined, according to the map of geomorphological zoning and landscape map. Analysis of variance revealed a statistically significant relationship between these characteristics and geomorphological regions and landscape zones. Consequently, spatial trends of changes of analyzed morphometric characteristics were revealed.

GWA Mapping of Anthocyanin Accumulation Reveals Balancing Selection of MYB90 in Arabidopsis thaliana

PubMed Central

Bac-Molenaar, Johanna A.; Fradin, Emilie F.; Rienstra, Juriaan A.; Vreugdenhil, Dick; Keurentjes, Joost J. B.

2015-01-01

Induction of anthocyanin accumulation by osmotic stress was assessed in 360 accessions of Arabidopsis thaliana. A wide range of natural variation, with phenotypes ranging from green to completely red/purple rosettes, was observed. A genome wide association (GWA) mapping approach revealed that sequence diversity in a small 15 kb region on chromosome 1 explained 40% of the variation observed. Sequence and expression analyses of alleles of the candidate gene MYB90 identified a causal polymorphism at amino acid (AA) position 210 of this transcription factor of the anthocyanin biosynthesis pathway. This amino acid discriminates the two most frequent alleles of MYB90. Both alleles are present in a substantial part of the population, suggesting balancing selection between these two alleles. Analysis of the geographical origin of the studied accessions suggests that the macro climate is not the driving force behind positive or negative selection for anthocyanin accumulation. An important role for local climatic conditions is, therefore, suggested. This study emphasizes that GWA mapping is a powerful approach to identify alleles that are under balancing selection pressure in nature. PMID:26588092

Dynamic metabolome profiling reveals significant metabolic changes during grain development of bread wheat (Triticum aestivum L.).

PubMed

Zhen, Shoumin; Dong, Kun; Deng, Xiong; Zhou, Jiaxing; Xu, Xuexin; Han, Caixia; Zhang, Wenying; Xu, Yanhao; Wang, Zhimin; Yan, Yueming

2016-08-01

Metabolites in wheat grains greatly influence nutritional values. Wheat provides proteins, minerals, B-group vitamins and dietary fiber to humans. These metabolites are important to human health. However, the metabolome of the grain during the development of bread wheat has not been studied so far. In this work the first dynamic metabolome of the developing grain of the elite Chinese bread wheat cultivar Zhongmai 175 was analyzed, using non-targeted gas chromatography/mass spectrometry (GC/MS) for metabolite profiling. In total, 74 metabolites were identified over the grain developmental stages. Metabolite-metabolite correlation analysis revealed that the metabolism of amino acids, carbohydrates, organic acids, amines and lipids was interrelated. An integrated metabolic map revealed a distinct regulatory profile. The results provide information that can be used by metabolic engineers and molecular breeders to improve wheat grain quality. The present metabolome approach identified dynamic changes in metabolite levels, and correlations among such levels, in developing seeds. The comprehensive metabolic map may be useful when breeding programs seek to improve grain quality. The work highlights the utility of GC/MS-based metabolomics, in conjunction with univariate and multivariate data analysis, when it is sought to understand metabolic changes in developing seeds. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Comparison of manually produced and automated cross country movement maps using digital image processing techniques

NASA Technical Reports Server (NTRS)

Wynn, L. K.

1985-01-01

The Image-Based Information System (IBIS) was used to automate the cross country movement (CCM) mapping model developed by the Defense Mapping Agency (DMA). Existing terrain factor overlays and a CCM map, produced by DMA for the Fort Lewis, Washington area, were digitized and reformatted into geometrically registered images. Terrain factor data from Slope, Soils, and Vegetation overlays were entered into IBIS, and were then combined utilizing IBIS-programmed equations to implement the DMA CCM model. The resulting IBIS-generated CCM map was then compared with the digitized manually produced map to test similarity. The numbers of pixels comprising each CCM region were compared between the two map images, and percent agreement between each two regional counts was computed. The mean percent agreement equalled 86.21%, with an areally weighted standard deviation of 11.11%. Calculation of Pearson's correlation coefficient yielded +9.997. In some cases, the IBIS-calculated map code differed from the DMA codes: analysis revealed that IBIS had calculated the codes correctly. These highly positive results demonstrate the power and accuracy of IBIS in automating models which synthesize a variety of thematic geographic data.

Auditory Spatial Attention Representations in the Human Cerebral Cortex

PubMed Central

Kong, Lingqiang; Michalka, Samantha W.; Rosen, Maya L.; Sheremata, Summer L.; Swisher, Jascha D.; Shinn-Cunningham, Barbara G.; Somers, David C.

2014-01-01

Auditory spatial attention serves important functions in auditory source separation and selection. Although auditory spatial attention mechanisms have been generally investigated, the neural substrates encoding spatial information acted on by attention have not been identified in the human neocortex. We performed functional magnetic resonance imaging experiments to identify cortical regions that support auditory spatial attention and to test 2 hypotheses regarding the coding of auditory spatial attention: 1) auditory spatial attention might recruit the visuospatial maps of the intraparietal sulcus (IPS) to create multimodal spatial attention maps; 2) auditory spatial information might be encoded without explicit cortical maps. We mapped visuotopic IPS regions in individual subjects and measured auditory spatial attention effects within these regions of interest. Contrary to the multimodal map hypothesis, we observed that auditory spatial attentional modulations spared the visuotopic maps of IPS; the parietal regions activated by auditory attention lacked map structure. However, multivoxel pattern analysis revealed that the superior temporal gyrus and the supramarginal gyrus contained significant information about the direction of spatial attention. These findings support the hypothesis that auditory spatial information is coded without a cortical map representation. Our findings suggest that audiospatial and visuospatial attention utilize distinctly different spatial coding schemes. PMID:23180753

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

The Necessity for Routine Pre-operative Ultrasound Mapping Before Arteriovenous Fistula Creation: A Meta-analysis.

PubMed

Georgiadis, G S; Charalampidis, D G; Argyriou, C; Georgakarakos, E I; Lazarides, M K

2015-05-01

Existing guidelines suggest routine use of pre-operative color Doppler ultrasound (DUS) vessel mapping before the creation of arteriovenous fistulae (AVF); however, there is controversy about its benefit over traditional clinical examination or selective ultrasound use. This was a systematic review and meta-analysis of randomized controlled trials (RCTs) comparing routine DUS mapping before the creation of AVF with patients for whom the decision for AVF placement was based on clinical examination and selective ultrasound use. A search of MEDLINE/PubMed, SCOPUS, and the Cochrane Library was carried out in June 2014. The analyzed outcome measures were the immediate failure rate and the early/midterm adequacy of the fistula for hemodialysis. Additionally, assessment of the methodological quality of the included studies was carried out. Five studies (574 patients) were analyzed. A random effects model was used to pool the data. The pooled odds ratio (OR) for the immediate failure rate was 0.32 (95% confidence interval [CI] 0.17-0.60; p < .01), which was significantly in favor of the DUS mapping group. The pooled OR for the early/midterm adequacy for hemodialysis was 0.66 (95% CI 0.42-1.03; p = .06), with a trend in favor of the DUS mapping group; however, subgroup analysis revealed that routine DUS mapping was more beneficial than selective DUS (p < .05). The available evidence, based mainly on moderate quality RCTs, suggests that the pre-operative clinical examination should always be supplemented with routine DUS mapping before AVF creation. This policy avoids negative surgical explorations and significantly reduces the immediate AVF failure rate. Copyright © 2015 European Society for Vascular Surgery. Published by Elsevier Ltd. All rights reserved.

Coastal Mapping for Baseline Geoscience Knowledge to Support Community Hazard Assessment and Sustainable Development, Eastern Baffin Island, Nunavut

NASA Astrophysics Data System (ADS)

Forbes, D. L.; Bell, T.; Campbell, D. C.; Cowan, B.; Deering, R. L.; Hatcher, S. V.; Hughes Clarke, J. E.; Irvine, M.; Manson, G. K.; Smith, I. R.; Edinger, E.

2015-12-01

Since 2012 we have carried out extensive multibeam bathymetric and backscatter surveys in coastal waters of eastern Baffin Island, supplemented by sub-bottom imaging and coring. Shore-zone surveys have been undertaken in proximity to the communities of Iqaluit and Qikiqtarjuaq, following earlier work in Clyde River. These support benthic habitat mapping, geological exploration, analysis of past and present sea-level trends, and assessment of coastal hazards relating to climate change and seabed instability. Outputs include a seamless topographic-bathymetric digital elevation model (DEM) of extensive boulder-strewn tidal flats in the large tidal-range setting at Iqaluit, supporting analysis of coastal flooding, wave run-up, and sea-ice impacts on a rapidly developing urban waterfront in the context of climate change. Seabed mapping of inner Frobisher Bay seaward of Iqaluit reveals a potential local tsunami hazard in widespread submarine slope failures, the triggers, magnitudes, and ages of which are the subject of ongoing research. In fjords of the Cumberland Peninsula, this project has mapped numerous submerged delta terraces at 19 to 45 m present water depth. These attest to an early postglacial submerged shoreline, displaced by glacial-isostatic adjustment. It rises linearly over a distance of 100 km east to west, where a submerged boulder barricade on a -16 m shoreline was discovered at a proposed port site in Broughton Channel near Qikiqtarjuaq. Palaeotopographic mapping using the multibeam data revealed an enclosed estuarine environment quite different from the present-day open passage swept by tidal currents. At Clyde River, combined seabed and onshore DEMs with geohazard mapping provided foundation data for community assessment and planning under a local knowledge co-production initiative. The geohazard work identified portions of the town-site more vulnerable to both coastal flooding and potential thaw subsidence, while the shallow delta terrace suggested a reversal from falling to rising relative sea levels. Overall, the coastal mapping results constitute baseline geoscience knowledge infrastructure for navigation, fisheries, port engineering, municipal planning, and informing sustainability initiatives in the isolated coastal communities of this Arctic region.

Investigation of remote sensing to detect near-surface groundwater on irrigated lands

NASA Technical Reports Server (NTRS)

Ryland, D. W.; Schmer, F. A.; Moore, D. G.

1975-01-01

The application of remote sensing techniques was studied for detecting areas with high water tables in irrigated agricultural lands. Aerial data were collected by the LANDSAT-1 satellite and aircraft over the Kansas/Bostwick Irrigation District in Republic and Jewell Counties, Kansas. LANDSAT-1 data for May 12 and August 10, 1973, and aircraft flights (midday and predawn) on August 10 and 11, 1973, and June 25 and 26, 1974, were obtained. Surface and water table contour maps and active observation well hydrographs were obtained from the Bureau of Reclamation for use in the analysis. Results of the study reveal that LANDSAT-1 data (May MSS band 6 and August MSS band 7) correlate significantly (0.01 level) with water table depth for 144 active observation wells located throughout the Kansas/Bostwick Irrigation District. However, a map of water table depths of less than 1.83 meters prepared from the LANDSAT-1 data did not compare favorably with a map of seeped lands of less than 1.22 m (4 feet) to the water table. Field evaluation of the map is necessary for a complete analysis. Analysis of three fields on a within or single-field basis for the 1973 LANDSAT-1 data also showed significant correlation results.

Large-scale analysis of pedigree and sperm-typing data reveals PRDM9 allele-specific recombination maps in cattle

USDA-ARS?s Scientific Manuscript database

Meiotic recombination is a major driving force in promoting genetic and phenotypic variations in sexually reproducing organisms. Although PRDM9 is known to modulate the binding-specificity and location of recombination hotspots in humans and mice, its role, especially in domesticated animals like ca...

Multivariate analysis of the cotton seed ionome reveals integrated genetic signatures of abiotic stress-response

USDA-ARS?s Scientific Manuscript database

To mitigate the effects of heat and drought stress, an understanding of the genetic control of physiological responses to these environmental conditions is needed. To this end, we evaluated an upland cotton (Gossypium hirsutum L.) mapping population under water-limited and well-watered conditions in...

The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)

Treesearch

G.A. Tuskan; S. DiFazio; S. Jansson; J. Bohlmann; I. Grigoriev; U. Hellsten; N. Putnam; S. Ralph; S. Rombauts; A. Salamov; J. Schein; L. Sterck; A. Aerts; R.R. Bhalerao; R.P. Bhalerao; D. Blaudez; W. Boerjan; A. Brun; A. Brunner; V. Busov; M. Campbell; J. Carlson; M. Chalot; J. Chapman; G.-L. Chen; D. Cooper; P.M. Coutinho; J. Couturier; S. Covert; Q. Cronk; R. Cunningham; J. Davis; S. Degroeve; A. Dejardin; C. dePamphilis; J. Detter; B. Dirks; U. Dubchak; S. Duplessis; J. Ehlting; B. Ellis; K. Gendler; D. Goodstein; M. Gribskov; J. Grimwood; A. Groover; L. Gunter; B. Hamberger; B. Heinze; Y. Helariutta; B. Henrissat; D. Holligan; R. Holt; W. Huang; N. Islam-Faridi; S. Jones; M. Jones-Rhoades; R. Jorgensen; C. Joshi; J. Kangasjarvi; J. Karlsson; C. Kelleher; R. Kirkpatrick; M. Kirst; A. Kohler; U. Kalluri; F. Larimer; J. Leebens-Mack; J.-C. Leple; P. Locascio; Y. Lou; S. Lucas; F. Martin; B. Montanini; C. Napoli; D.R. Nelson; C. Nelson; K. Nieminen; O. Nilsson; V. Pereda; G. Peter; R. Philippe; G. Pilate; A. Poliakov; J. Razumovskaya; P. Richardson; C. Rinaldi; K. Ritland; P. Rouze; D. Ryaboy; J. Schumtz; J. Schrader; B. Segerman; H. Shin; A. Siddiqui; F. Sterky; A. Terry; C.-J. Tsai; E. Uberbacher; P. Unneberg; J. Vahala; K. Wall; S. Wessler; G. Yang; T. Yin; C. Douglas; M. Marra; G. Sandberg; Y. Van de Peer; D. Rokhsar

2006-01-01

We report the draft genome of the black cottonwood tree, Populus trichocarpa. Integration of shotgun sequence assembly with genetic mapping enabled chromosome-scale reconstruction of the genome. More than 45,000 putative protein-coding genes were identified. Analysis of the assembled genome revealed a whole-genome duplication event; about 8000 pairs...

An investigation of condition mapping and plot proportion calculation issues

Treesearch

Demetrios Gatziolis

2007-01-01

A systematic examination of Forest Inventory and Analysis condition data collected under the annual inventory protocol in the Pacific Northwest region between 2000 and 2004 revealed the presence of errors both in condition topology and plot proportion computations. When plots were compiled to generate population estimates, proportion errors were found to cause...

A large scale joint analysis of flowering time reveals independent temperate adaptations in maize

USDA-ARS?s Scientific Manuscript database

Modulating days to flowering is a key mechanism in plants for adapting to new environments, and variation in days to flowering drives population structure by limiting mating. To elucidate the genetic architecture of flowering across maize, a quantitative trait, we mapped flowering in five global pop...

Expression, purification, crystallization and preliminary crystallographic analysis of MxiH, a subunit of the Shigella flexneri type III secretion system needle

PubMed Central

Deane, Janet E.; Cordes, Frank S.; Roversi, Pietro; Johnson, Steven; Kenjale, Roma; Picking, William D.; Picking, Wendy L.; Lea, Susan M.; Blocker, Ariel

2006-01-01

A monodisperse truncation mutant of MxiH, the subunit of the needle from the Shigella flexneri type III secretion system (TTSS), has been overexpressed and purified. Crystals were grown of native and selenomethionine-labelled MxiHCΔ5 and diffraction data were collected to 1.9 Å resolution. The crystals belong to space group C2, with unit-cell parameters a = 183.4, b = 28.1, c = 27.8 Å, β = 96.5°. An anomalous difference Patterson map calculated with the data from the SeMet-labelled crystals revealed a single peak on the Harker section v = 0. Inspection of a uranyl derivative also revealed one peak in the isomorphous difference Patterson map on the Harker section v = 0. Analysis of the self-rotation function indicates the presence of a twofold non-crystallographic symmetry axis approximately along a. The calculated Matthews coefficient is 1.9 Å3 Da−1 for two molecules per asymmetric unit, corresponding to a solvent content of 33%. PMID:16511329

Expression, purification, crystallization and preliminary crystallographic analysis of MxiH, a subunit of the Shigella flexneri type III secretion system needle.

PubMed

Deane, Janet E; Cordes, Frank S; Roversi, Pietro; Johnson, Steven; Kenjale, Roma; Picking, William D; Picking, Wendy L; Lea, Susan M; Blocker, Ariel

2006-03-01

A monodisperse truncation mutant of MxiH, the subunit of the needle from the Shigella flexneri type III secretion system (TTSS), has been overexpressed and purified. Crystals were grown of native and selenomethionine-labelled MxiH(CDelta5) and diffraction data were collected to 1.9 A resolution. The crystals belong to space group C2, with unit-cell parameters a = 183.4, b = 28.1, c = 27.8 A, beta = 96.5 degrees. An anomalous difference Patterson map calculated with the data from the SeMet-labelled crystals revealed a single peak on the Harker section v = 0. Inspection of a uranyl derivative also revealed one peak in the isomorphous difference Patterson map on the Harker section v = 0. Analysis of the self-rotation function indicates the presence of a twofold non-crystallographic symmetry axis approximately along a. The calculated Matthews coefficient is 1.9 A3 Da(-1) for two molecules per asymmetric unit, corresponding to a solvent content of 33%.

Human retina-specific amine oxidase (RAO): cDNA cloning, tissue expression, and chromosomal mapping

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

Imamura, Yutaka; Kubota, Ryo; Wang, Yimin

In search of candidate genes for hereditary retinal disease, we have employed a subtractive and differential cDNA cloning strategy and isolated a novel retina-specific cDNA. Nucleotide sequence analysis revealed an open reading frame of 2187 bp, which encodes a 729-amino-acid protein with a calculated molecular mass of 80,644 Da. The putative protein contained a conserved domain of copper amine oxidase, which is found in various species from bacteria to mammals. It showed the highest homology to bovine serum amine oxidase, which is believed to control the level of serum biogenic amines. Northern blot analysis of human adult and fetal tissuesmore » revealed that the protein is expressed abundantly and specifically in retina as a 2.7-kb transcript. Thus, we considered this protein a human retina-specific amine oxidase (RAO). The RAO gene (AOC2) was mapped by fluorescence in situ hybridization to human chromosome 17q21. We propose that AOC2 may be a candidate gene for hereditary ocular diseases. 38 refs., 4 figs.« less

Mapping probabilities of extreme continental water storage changes from space gravimetry

NASA Astrophysics Data System (ADS)

Kusche, J.; Eicker, A.; Forootan, E.; Springer, A.; Longuevergne, L.

2016-12-01

Using data from the Gravity Recovery and Climate Experiment (GRACE) mission, we derive statistically robust 'hotspot' regions of high probability of peak anomalous - i.e. with respect to the seasonal cycle - water storage (of up to 0.7 m one-in-five-year return level) and flux (up to 0.14 m/mon). Analysis of, and comparison with, up to 32 years of ERA-Interim reanalysis fields reveals generally good agreement of these hotspot regions to GRACE results, and that most exceptions are located in the Tropics. However, a simulation experiment reveals that differences observed by GRACE are statistically significant, and further error analysis suggests that by around the year 2020 it will be possible to detect temporal changes in the frequency of extreme total fluxes (i.e. combined effects of mainly precipitation and floods) for at least 10-20% of the continental area, assuming that we have a continuation of GRACE by its follow-up GRACE-FO. J. Kusche et al. (2016): Mapping probabilities of extreme continental water storage changes from space gravimetry, Geophysical Research Letters, accepted online, doi:10.1002/2016GL069538

Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

PubMed Central

Nunes, José de Ribamar da Silva; Liu, Shikai; Pértille, Fábio; Perazza, Caio Augusto; Villela, Priscilla Marqui Schmidt; de Almeida-Val, Vera Maria Fonseca; Hilsdorf, Alexandre Wagner Silva; Liu, Zhanjiang; Coutinho, Luiz Lehmann

2017-01-01

Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs. PMID:28387238

Quantitative Trait Loci Mapping in Brassica rapa Revealed the Structural and Functional Conservation of Genetic Loci Governing Morphological and Yield Component Traits in the A, B, and C Subgenomes of Brassica Species

PubMed Central

Li, Xiaonan; Ramchiary, Nirala; Dhandapani, Vignesh; Choi, Su Ryun; Hur, Yoonkang; Nou, Ill-Sup; Yoon, Moo Kyoung; Lim, Yong Pyo

2013-01-01

Brassica rapa is an important crop species that produces vegetables, oilseed, and fodder. Although many studies reported quantitative trait loci (QTL) mapping, the genes governing most of its economically important traits are still unknown. In this study, we report QTL mapping for morphological and yield component traits in B. rapa and comparative map alignment between B. rapa, B. napus, B. juncea, and Arabidopsis thaliana to identify candidate genes and conserved QTL blocks between them. A total of 95 QTL were identified in different crucifer blocks of the B. rapa genome. Through synteny analysis with A. thaliana, B. rapa candidate genes and intronic and exonic single nucleotide polymorphisms in the parental lines were detected from whole genome resequenced data, a few of which were validated by mapping them to the QTL regions. Semi-quantitative reverse transcriptase PCR analysis showed differences in the expression levels of a few genes in parental lines. Comparative mapping identified five key major evolutionarily conserved crucifer blocks (R, J, F, E, and W) harbouring QTL for morphological and yield components traits between the A, B, and C subgenomes of B. rapa, B. juncea, and B. napus. The information of the identified candidate genes could be used for breeding B. rapa and other related Brassica species. PMID:23223793

Mitogen-Activated Protein Kinases Are Associated with the Regulation of Physiological Traits and Virulence in Fusarium oxysporum f. sp. cubense

PubMed Central

Ding, Zhaojian; Li, Minhui; Sun, Fei; Xi, Pinggen; Sun, Longhua; Zhang, Lianhui; Jiang, Zide

2015-01-01

Fusarium oxysporum f. sp. cubense (FOC) is an important soil-borne fungal pathogen causing devastating vascular wilt disease of banana plants and has become a great concern threatening banana production worldwide. However, little information is known about the molecular mechanisms that govern the expression of virulence determinants of this important fungal pathogen. In this study, we showed that null mutation of three mitogen-activated protein (MAP) kinase genes, designated as FoSlt2, FoMkk2 and FoBck1, respectively, led to substantial attenuation in fungal virulence on banana plants. Transcriptional analysis revealed that the MAP kinase signaling pathway plays a key role in regulation of the genes encoding production of chitin, peroxidase, beauvericin and fusaric acid. Biochemical analysis further confirmed the essential role of MAP kinases in modulating the production of fusaric acid, which was a crucial phytotoxin in accelerating development of Fusarium wilt symptoms in banana plants. Additionally, we found that the MAP kinase FoSlt2 was required for siderophore biosynthesis under iron-depletion conditions. Moreover, disruption of the MAP kinase genes resulted in abnormal hypha and increased sensitivity to Congo Red, Calcofluor White and H2O2. Taken together, these results depict the critical roles of MAP kinases in regulation of FOC physiology and virulence. PMID:25849862

Multivariate Analysis of the Cotton Seed Ionome Reveals a Shared Genetic Architecture

PubMed Central

Pauli, Duke; Ziegler, Greg; Ren, Min; Jenks, Matthew A.; Hunsaker, Douglas J.; Zhang, Min; Baxter, Ivan; Gore, Michael A.

2018-01-01

To mitigate the effects of heat and drought stress, a better understanding of the genetic control of physiological responses to these environmental conditions is needed. To this end, we evaluated an upland cotton (Gossypium hirsutum L.) mapping population under water-limited and well-watered conditions in a hot, arid environment. The elemental concentrations (ionome) of seed samples from the population were profiled in addition to those of soil samples taken from throughout the field site to better model environmental variation. The elements profiled in seeds exhibited moderate to high heritabilities, as well as strong phenotypic and genotypic correlations between elements that were not altered by the imposed irrigation regimes. Quantitative trait loci (QTL) mapping results from a Bayesian classification method identified multiple genomic regions where QTL for individual elements colocalized, suggesting that genetic control of the ionome is highly interrelated. To more fully explore this genetic architecture, multivariate QTL mapping was implemented among groups of biochemically related elements. This analysis revealed both additional and pleiotropic QTL responsible for coordinated control of phenotypic variation for elemental accumulation. Machine learning algorithms that utilized only ionomic data predicted the irrigation regime under which genotypes were evaluated with very high accuracy. Taken together, these results demonstrate the extent to which the seed ionome is genetically interrelated and predictive of plant physiological responses to adverse environmental conditions. PMID:29437829

Opportunities for Environmental Noise Mapping in Saudi Arabia: A Case of Traffic Noise Annoyance in an Urban Area in Jeddah City.

PubMed

Zytoon, Mohamed A

2016-05-13

As the traffic and other environmental noise generating activities are growing in The Kingdom of Saudi Arabia (KSA), adverse health and other impacts are expected to develop. The management of such problem involves many actions, of which noise mapping has been proven to be a helpful approach. The objective of the current study was to test the adequacy of the available data in KSA municipalities for generating urban noise maps and to verify the applicability of available environmental noise mapping and noise annoyance models for KSA. Therefore, noise maps were produced for Al-Fayha District in Jeddah City, KSA using commercially available noise mapping software and applying the French national computation method "NMPB" for traffic noise. Most of the data required for traffic noise prediction and annoyance analysis were available, either in the Municipality GIS department or in other governmental authorities. The predicted noise levels during the three time periods, i.e., daytime, evening, and nighttime, were found higher than the maximum recommended levels established in KSA environmental noise standards. Annoyance analysis revealed that high percentages of the District inhabitants were highly annoyed, depending on the type of planning zone and period of interest. These results reflect the urgent need to consider environmental noise reduction in KSA national plans. The accuracy of the predicted noise levels and the availability of most of the necessary data should encourage further studies on the use of noise mapping as part of noise reduction plans.

Combining Next Generation Sequencing with Bulked Segregant Analysis to Fine Map a Stem Moisture Locus in Sorghum (Sorghum bicolor L. Moench).

PubMed

Han, Yucui; Lv, Peng; Hou, Shenglin; Li, Suying; Ji, Guisu; Ma, Xue; Du, Ruiheng; Liu, Guoqing

2015-01-01

Sorghum is one of the most promising bioenergy crops. Stem juice yield, together with stem sugar concentration, determines sugar yield in sweet sorghum. Bulked segregant analysis (BSA) is a gene mapping technique for identifying genomic regions containing genetic loci affecting a trait of interest that when combined with deep sequencing could effectively accelerate the gene mapping process. In this study, a dry stem sorghum landrace was characterized and the stem water controlling locus, qSW6, was fine mapped using QTL analysis and the combined BSA and deep sequencing technologies. Results showed that: (i) In sorghum variety Jiliang 2, stem water content was around 80% before flowering stage. It dropped to 75% during grain filling with little difference between different internodes. In landrace G21, stem water content keeps dropping after the flag leaf stage. The drop from 71% at flowering time progressed to 60% at grain filling time. Large differences exist between different internodes with the lowest (51%) at the 7th and 8th internodes at dough stage. (ii) A quantitative trait locus (QTL) controlling stem water content mapped on chromosome 6 between SSR markers Ch6-2 and gpsb069 explained about 34.7-56.9% of the phenotypic variation for the 5th to 10th internodes, respectively. (iii) BSA and deep sequencing analysis narrowed the associated region to 339 kb containing 38 putative genes. The results could help reveal molecular mechanisms underlying juice yield of sorghum and thus to improve total sugar yield.

Fine Mapping on Chromosome 13q32–34 and Brain Expression Analysis Implicates MYO16 in Schizophrenia

PubMed Central

Rodriguez-Murillo, Laura; Xu, Bin; Roos, J Louw; Abecasis, Gonçalo R; Gogos, Joseph A; Karayiorgou, Maria

2014-01-01

We previously reported linkage of schizophrenia and schizoaffective disorder to 13q32–34 in the European descent Afrikaner population from South Africa. The nature of genetic variation underlying linkage peaks in psychiatric disorders remains largely unknown and both rare and common variants may be contributing. Here, we examine the contribution of common variants located under the 13q32–34 linkage region. We used densely spaced SNPs to fine map the linkage peak region using both a discovery sample of 415 families and a meta-analysis incorporating two additional replication family samples. In a second phase of the study, we use one family-based data set with 237 families and independent case–control data sets for fine mapping of the common variant association signal using HapMap SNPs. We report a significant association with a genetic variant (rs9583277) within the gene encoding for the myosin heavy-chain Myr 8 (MYO16), which has been implicated in neuronal phosphoinositide 3-kinase signaling. Follow-up analysis of HapMap variation within MYO16 in a second set of Afrikaner families and additional case–control data sets of European descent highlighted a region across introns 2–6 as the most likely region to harbor common MYO16 risk variants. Expression analysis revealed a significant increase in the level of MYO16 expression in the brains of schizophrenia patients. Our results suggest that common variation within MYO16 may contribute to the genetic liability to schizophrenia. PMID:24141571

A cellular and regulatory map of the cholinergic nervous system of C. elegans

PubMed Central

Pereira, Laura; Kratsios, Paschalis; Serrano-Saiz, Esther; Sheftel, Hila; Mayo, Avi E; Hall, David H; White, John G; LeBoeuf, Brigitte; Garcia, L Rene; Alon, Uri; Hobert, Oliver

2015-01-01

Nervous system maps are of critical importance for understanding how nervous systems develop and function. We systematically map here all cholinergic neuron types in the male and hermaphrodite C. elegans nervous system. We find that acetylcholine (ACh) is the most broadly used neurotransmitter and we analyze its usage relative to other neurotransmitters within the context of the entire connectome and within specific network motifs embedded in the connectome. We reveal several dynamic aspects of cholinergic neurotransmitter identity, including a sexually dimorphic glutamatergic to cholinergic neurotransmitter switch in a sex-shared interneuron. An expression pattern analysis of ACh-gated anion channels furthermore suggests that ACh may also operate very broadly as an inhibitory neurotransmitter. As a first application of this comprehensive neurotransmitter map, we identify transcriptional regulatory mechanisms that control cholinergic neurotransmitter identity and cholinergic circuit assembly. DOI: http://dx.doi.org/10.7554/eLife.12432.001 PMID:26705699

A second generation genetic linkage map of Japanese flounder (Paralichthys olivaceus)

PubMed Central

2010-01-01

Background Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine species in Northeast Asia. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. Commercial production of Japanese flounder could be increased by developing disease-resistant fish and improving commercially important traits. Previous maps have been constructed with AFLP markers and a limited number of microsatellite markers. In this study, improved genetic linkage maps are presented. In contrast with previous studies, these maps were built mainly with a large number of codominant markers so they can potentially be used to analyze different families and populations. Results Sex-specific genetic linkage maps were constructed for the Japanese flounder including a total of 1,375 markers [1,268 microsatellites, 105 single nucleotide polymorphisms (SNPs) and two genes]; 1,167 markers are linked to the male map and 1,067 markers are linked to the female map. The lengths of the male and female maps are 1,147.7 cM and 833.8 cM, respectively. Based on estimations of map lengths, the female and male maps covered 79 and 82% of the genome, respectively. Recombination ratio in the new maps revealed F:M of 1:0.7. All linkage groups in the maps presented large differences in the location of sex-specific recombination hot-spots. Conclusions The improved genetic linkage maps are very useful for QTL analyses and marker-assisted selection (MAS) breeding programs for economically important traits in Japanese flounder. In addition, SNP flanking sequences were blasted against Tetraodon nigroviridis (puffer fish) and Danio rerio (zebrafish), and synteny analysis has been carried out. The ability to detect synteny among species or genera based on homology analysis of SNP flanking sequences may provide opportunities to complement initial QTL experiments with candidate gene approaches from homologous chromosomal locations identified in related model organisms. PMID:20937088

Experimental mapping of DNA duplex shape enabled by global lineshape analyses of a nucleotide-independent nitroxide probe

PubMed Central

Ding, Yuan; Zhang, Xiaojun; Tham, Kenneth W.; Qin, Peter Z.

2014-01-01

Sequence-dependent variation in structure and dynamics of a DNA duplex, collectively referred to as ‘DNA shape’, critically impacts interactions between DNA and proteins. Here, a method based on the technique of site-directed spin labeling was developed to experimentally map shapes of two DNA duplexes that contain response elements of the p53 tumor suppressor. An R5a nitroxide spin label, which was covalently attached at a specific phosphate group, was scanned consecutively through the DNA duplex. X-band continuous-wave electron paramagnetic resonance spectroscopy was used to monitor rotational motions of R5a, which report on DNA structure and dynamics at the labeling site. An approach based on Pearson's coefficient analysis was developed to collectively examine the degree of similarity among the ensemble of R5a spectra. The resulting Pearson's coefficients were used to generate maps representing variation of R5a mobility along the DNA duplex. The R5a mobility maps were found to correlate with maps of certain DNA helical parameters, and were capable of revealing similarity and deviation in the shape of the two closely related DNA duplexes. Collectively, the R5a probe and the Pearson's coefficient-based lineshape analysis scheme yielded a generalizable method for examining sequence-dependent DNA shapes. PMID:25092920

Mapping the pericentric heterochromatin by comparative genomic hybridization analysis and chromosome deletions in Drosophila melanogaster

PubMed Central

He, Bing; Caudy, Amy; Parsons, Lance; Rosebrock, Adam; Pane, Attilio; Raj, Sandeep; Wieschaus, Eric

2012-01-01

Heterochromatin represents a significant portion of eukaryotic genomes and has essential structural and regulatory functions. Its molecular organization is largely unknown due to difficulties in sequencing through and assembling repetitive sequences enriched in the heterochromatin. Here we developed a novel strategy using chromosomal rearrangements and embryonic phenotypes to position unmapped Drosophila melanogaster heterochromatic sequence to specific chromosomal regions. By excluding sequences that can be mapped to the assembled euchromatic arms, we identified sequences that are specific to heterochromatin and used them to design heterochromatin specific probes (“H-probes”) for microarray. By comparative genomic hybridization (CGH) analyses of embryos deficient for each chromosome or chromosome arm, we were able to map most of our H-probes to specific chromosome arms. We also positioned sequences mapped to the second and X chromosomes to finer intervals by analyzing smaller deletions with breakpoints in heterochromatin. Using this approach, we were able to map >40% (13.9 Mb) of the previously unmapped heterochromatin sequences assembled by the whole-genome sequencing effort on arm U and arm Uextra to specific locations. We also identified and mapped 110 kb of novel heterochromatic sequences. Subsequent analyses revealed that sequences located within different heterochromatic regions have distinct properties, such as sequence composition, degree of repetitiveness, and level of underreplication in polytenized tissues. Surprisingly, although heterochromatin is generally considered to be transcriptionally silent, we detected region-specific temporal patterns of transcription in heterochromatin during oogenesis and early embryonic development. Our study provides a useful approach to elucidate the molecular organization and function of heterochromatin and reveals region-specific variation of heterochromatin. PMID:22745230

Family members' narratives of lifespace: Mapping changes before and after a brain injury causing driving disruption.

PubMed

Liang, Phyllis; Liddle, Jacki; Fleming, Jennifer; Gustafsson, Louise

2016-06-01

Family members of a person with an acquired brain injury often provide transport assistance during driving disruption with potential impacts on their own travel and participation within the community. The geographic area in which people travel and conduct their activities is known as lifespace. This study aimed to describe the quantitative changes in family members' lifespace after brain injury and understand their subjective experiences through interacting with maps during narratives. Mapping was embedded within in-depth semi-structured interviews with 15 family members. Two sets of maps were generated per participant showing the number of travel locations before and after brain injury. In the interviews, participants reflected on the perceived meaning of lifespace change. Qualitative data were analysed using a narrative approach. Quantitative data from the mapping revealed an increase in travel locations for nine participants, a decrease for five, and no change for one participant. Data analysis revealed four typologies which complemented and enriched the quantitative data: (i) I will do everything for him or her; (ii) Trying to fit all in; (iii) We spend all our time together now; (iv) I need to also care for myself. The findings describe the change in family members' lifespace after taking on the driver role following acquired brain injury. This study highlights the importance of understanding both quantitative and qualitative aspects of lifespace. The subjective experiences and consequences of lifespace changes are different from the impact on individuals with health conditions. Mapping in an interview as a tool has potential clinical utility. © 2016 Occupational Therapy Australia.

Multiscale correlations of iron phases and heavy metals in technogenic magnetic particles from contaminated soils.

PubMed

Yu, Xiuling; Lu, Shenggao

2016-12-01

Technogenic magnetic particles (TMPs) are carriers of heavy metals and organic contaminants, which derived from anthropogenic activities. However, little information on the relationship between heavy metals and TMP carrier phases at the micrometer scale is available. This study determined the distribution and association of heavy metals and magnetic phases in TMPs in three contaminated soils at the micrometer scale using micro-X-ray fluorescence (μ-XRF) and micro-X-ray absorption near-edge structure (μ-XANES) spectroscopy. Multiscale correlations of heavy metals in TMPs were elucidated using wavelet transform analysis. μ-XRF mapping showed that Fe was enriched and closely correlated with Co, Cr, and Pb in TMPs from steel industrial areas. Fluorescence mapping and wavelet analysis showed that ferroalloy was a major magnetic signature and heavy metal carrier in TMPs, because most heavy metals were highly associated with ferroalloy at all size scales. Multiscale analysis revealed that heavy metals in the TMPs were from multiple sources. Iron K-edge μ-XANES spectra revealed that metallic iron, ferroalloy, and magnetite were the main iron magnetic phases in the TMPs. The relative percentage of these magnetic phases depended on their emission sources. Heatmap analysis revealed that Co, Pb, Cu, Cr, and Ni were mainly derived from ferroalloy particles, while As was derived from both ferroalloy and metallic iron phases. Our results indicated the scale-dependent correlations of magnetic phases and heavy metals in TMPs. The combination of synchrotron based X-ray microprobe techniques and multiscale analysis provides a powerful tool for identifying the magnetic phases from different sources and quantifying the association of iron phases and heavy metals at micrometer scale. Copyright © 2016 Elsevier Ltd. All rights reserved.

Application of Remote Sensing in Geological Mapping, Case Study al Maghrabah Area - Hajjah Region, Yemen

NASA Astrophysics Data System (ADS)

Al-Nahmi, F.; Saddiqi, O.; Hilali, A.; Rhinane, H.; Baidder, L.; El arabi, H.; Khanbari, K.

2017-11-01

Remote sensing technology plays an important role today in the geological survey, mapping, analysis and interpretation, which provides a unique opportunity to investigate the geological characteristics of the remote areas of the earth's surface without the need to gain access to an area on the ground. The aim of this study is achievement a geological map of the study area. The data utilizes is Sentinel-2 imagery, the processes used in this study, the OIF Optimum Index Factor is a statistic value that can be used to select the optimum combination of three bands in a satellite image. It's based on the total variance within bands and correlation coefficient between bands, ICA Independent component analysis (3, 4, 6) is a statistical and computational technique for revealing hidden factors that underlie sets of random variables, measurements, or signals, MNF Minimum Noise Fraction (1, 2, 3) is used to determine the inherent dimensionality of image data to segregate noise in the data and to reduce the computational requirements for subsequent processing, Optimum Index Factor is a good method for choosing the best band for lithological mapping. ICA, MNF, also a practical way to extract the structural geology maps. The results in this paper indicate that, the studied area can be divided into four main geological units: Basement rocks (Meta volcanic, Meta sediments), Sedimentary rocks, Intrusive rocks, volcanic rocks. The method used in this study offers great potential for lithological mapping, by using Sentinel-2 imagery, the results were compared with existing geologic maps and were superior and could be used to update the existing maps.

Toward Integration of Comparative Genetic, Physical, Diversity, and Cytomolecular Maps for Grasses and Grains, Using the Sorghum Genome as a Foundation1

PubMed Central

Draye, Xavier; Lin, Yann-Rong; Qian, Xiao-yin; Bowers, John E.; Burow, Gloria B.; Morrell, Peter L.; Peterson, Daniel G.; Presting, Gernot G.; Ren, Shu-xin; Wing, Rod A.; Paterson, Andrew H.

2001-01-01

The small genome of sorghum (Sorghum bicolor L. Moench.) provides an important template for study of closely related large-genome crops such as maize (Zea mays) and sugarcane (Saccharum spp.), and is a logical complement to distantly related rice (Oryza sativa) as a “grass genome model.” Using a high-density RFLP map as a framework, a robust physical map of sorghum is being assembled by integrating hybridization and fingerprint data with comparative data from related taxa such as rice and using new methods to resolve genomic duplications into locus-specific groups. By taking advantage of allelic variation revealed by heterologous probes, the positions of corresponding loci on the wheat (Triticum aestivum), rice, maize, sugarcane, and Arabidopsis genomes are being interpolated on the sorghum physical map. Bacterial artificial chromosomes for the small genome of rice are shown to close several gaps in the sorghum contigs; the emerging rice physical map and assembled sequence will further accelerate progress. An important motivation for developing genomic tools is to relate molecular level variation to phenotypic diversity. “Diversity maps,” which depict the levels and patterns of variation in different gene pools, shed light on relationships of allelic diversity with chromosome organization, and suggest possible locations of genomic regions that are under selection due to major gene effects (some of which may be revealed by quantitative trait locus mapping). Both physical maps and diversity maps suggest interesting features that may be integrally related to the chromosomal context of DNA—progress in cytology promises to provide a means to elucidate such relationships. We seek to provide a detailed picture of the structure, function, and evolution of the genome of sorghum and its relatives, together with molecular tools such as locus-specific sequence-tagged site DNA markers and bacterial artificial chromosome contigs that will have enduring value for many aspects of genome analysis. PMID:11244113

Mapping of the bcl-2 oncogene on mouse chromosome 1.

PubMed

Mock, B A; Givol, D; D'Hoostelaere, L A; Huppi, K; Seldin, M F; Gurfinkel, N; Unger, T; Potter, M; Mushinski, J F

1988-01-01

Two bcl-2 alleles have been identified in inbred strains of mice by restriction fragment length polymorphism (RFLP). Analysis of a bcl-2 RFLP in a series of bilineal congenic strains (C.D2), developed as a tool for chromosomal mapping studies, revealed linkage of bcl-2 to the Idh-1/Pep-3 region of murine chromosome 1. The co-segregation of bcl-2 alleles with allelic forms of two other chromosome 1 loci, Ren-1,2 and Spna-1, in a set of back-cross progeny, positions bcl-2 7.8 cM centromeric from Ren-1,2.

Geologic Map of the Snegurochka Planitia Quadrangle (V-1): Implications for the Volcanic History of the North Polar Region of Venus

NASA Technical Reports Server (NTRS)

Hurwitz, D. M.; Head, J. W.

2010-01-01

Geologic mapping of Snegurochka Planitia (V-1) reveals a complex stratigraphy of tectonic and volcanic features that can provide insight into the geologic history of Venus and Archean Earth [1,2], including 1) episodes of both localized crustal uplift and mantle downwelling, 2) shifts from local to regional volcanic activity, and 3) a shift back to local volcanic activity. We present our interpretations of the volcanic history of the region surrounding the north pole of Venus and explore how analysis of new data support our interpretations

Global terrestrial Human Footprint maps for 1993 and 2009

PubMed Central

Venter, Oscar; Sanderson, Eric W.; Magrach, Ainhoa; Allan, James R.; Beher, Jutta; Jones, Kendall R.; Possingham, Hugh P.; Laurance, William F.; Wood, Peter; Fekete, Balázs M.; Levy, Marc A.; Watson, James E.M.

2016-01-01

Remotely-sensed and bottom-up survey information were compiled on eight variables measuring the direct and indirect human pressures on the environment globally in 1993 and 2009. This represents not only the most current information of its type, but also the first temporally-consistent set of Human Footprint maps. Data on human pressures were acquired or developed for: 1) built environments, 2) population density, 3) electric infrastructure, 4) crop lands, 5) pasture lands, 6) roads, 7) railways, and 8) navigable waterways. Pressures were then overlaid to create the standardized Human Footprint maps for all non-Antarctic land areas. A validation analysis using scored pressures from 3114×1 km2 random sample plots revealed strong agreement with the Human Footprint maps. We anticipate that the Human Footprint maps will find a range of uses as proxies for human disturbance of natural systems. The updated maps should provide an increased understanding of the human pressures that drive macro-ecological patterns, as well as for tracking environmental change and informing conservation science and application. PMID:27552448

Characterisation of volatile profile and sensory analysis of fresh-cut "Radicchio di Chioggia" stored in air or modified atmosphere.

PubMed

Cozzolino, Rosaria; Martignetti, Antonella; Pellicano, Mario Paolo; Stocchero, Matteo; Cefola, Maria; Pace, Bernardo; De Giulio, Beatrice

2016-02-01

The volatile profile of two hybrids of "Radicchio di Chioggia", Corelli and Botticelli, stored in air or passive modified atmosphere (MAP) during 12 days of cold storage, was monitored by solid phase micro-extraction (SPME) GC-MS. Botticelli samples were also subjected to sensory analysis. Totally, 61 volatile organic compounds (VOCs) were identified in the headspace of radicchio samples. Principal component analysis (PCA) showed that fresh product possessed a metabolic content similar to that of the MAP samples after 5 and 8 days of storage. Projection to latent structures by partial least squares (PLS) regression analysis showed the volatiles content of the samples varied depending only on the packaging conditions. Specifically, 12 metabolites describing the time evolution and explaining the effects of the different storage conditions were highlighted. Finally, a PCA analysis revealed that VOCs profile significantly correlated with sensory attributes. Copyright © 2015 Elsevier Ltd. All rights reserved.

STAYGREEN (CsSGR) is a candidate for the anthracnose (Colletotrichum orbiculare) resistance locus cla in Gy14 cucumber.

PubMed

Pan, Junsong; Tan, Junyi; Wang, Yuhui; Zheng, Xiangyang; Owens, Ken; Li, Dawei; Li, Yuhong; Weng, Yiqun

2018-04-21

Map-based cloning identified a candidate gene for resistance to the anthracnose fungal pathogen Colletotrichum orbiculare in cucumber, which reveals a novel function for the highly conserved STAYGREEN family genes for host disease resistance in plants. Colletotrichum orbiculare is a hemibiotrophic fungal pathogen that causes anthracnose disease in cucumber and other cucurbit crops. No host resistance genes against the anthracnose pathogens have been cloned in crop plants. Here, we reported fine mapping and cloning of a resistance gene to the race 1 anthracnose pathogen in cucumber inbred lines Gy14 and WI 2757. Phenotypic and QTL analysis in multiple populations revealed that a single recessive gene, cla, was underlying anthracnose resistance in both lines, but WI2757 carried an additional minor-effect QTL. Fine mapping using 150 Gy14 × 9930 recombinant inbred lines and 1043 F 2 individuals delimited the cla locus into a 32 kb region in cucumber Chromosome 5 with three predicted genes. Multiple lines of evidence suggested that the cucumber STAYGREEN (CsSGR) gene is a candidate for the anthracnose resistance locus. A single nucleotide mutation in the third exon of CsSGR resulted in the substitution of Glutamine in 9930 to Arginine in Gy14 in CsSGR protein which seems responsible for the differential anthracnose inoculation responses between Gy14 and 9930. Quantitative real-time PCR analysis indicated that CsSGR was significantly upregulated upon anthracnose pathogen inoculation in the susceptible 9930, while its expression was much lower in the resistant Gy14. Investigation of allelic diversities in natural cucumber populations revealed that the resistance allele in almost all improved cultivars or breeding lines of the U.S. origin was derived from PI 197087. This work reveals an unknown function for the highly conserved STAYGREEN (SGR) family genes for host disease resistance in plants.

Care maps for children with medical complexity.

PubMed

Adams, Sherri; Nicholas, David; Mahant, Sanjay; Weiser, Natalie; Kanani, Ronik; Boydell, Katherine; Cohen, Eyal

2017-12-01

Children with medical complexity require multiple providers and services to keep them well and at home. A care map is a patient/family-created diagram that pictorially maps out this complex web of services. This study explored what care maps mean for families and healthcare providers to inform potential for clinical use. Parents (n=15) created care maps (hand drawn n=10 and computer-generated n=5) and participated in semi-structured interviews about the process of developing care maps and their perceived impact. Healthcare providers (n=30) reviewed the parent-created care maps and participated in semi-structured interviews. Data were analysed for themes and emerging theory using a grounded theory analytical approach. Data analysis revealed 13 overarching themes that were further categorized into three domains: features (characteristics of care maps), functions (what care maps do), and emerging outcomes (benefits of care map use). These domains further informed a definition and a theoretical model of how care maps work. Our findings suggest that care maps may be a way of supporting patient- and family-centred care by graphically identifying and integrating experiences of the family as well as priorities for moving forward. Care maps were endorsed as a useful tool by families and providers. They help healthcare providers better understand parental priorities for care. Parents can create care maps to demonstrate the complex burden of care. They are a unique visual way to incorporate narrative medicine into practice. © 2017 Mac Keith Press.

Comparing orbiter and rover image-based mapping of an ancient sedimentary environment, Aeolis Palus, Gale crater, Mars

NASA Astrophysics Data System (ADS)

Stack, K. M.; Edwards, C. S.; Grotzinger, J. P.; Gupta, S.; Sumner, D. Y.; Calef, F. J.; Edgar, L. A.; Edgett, K. S.; Fraeman, A. A.; Jacob, S. R.; Le Deit, L.; Lewis, K. W.; Rice, M. S.; Rubin, D.; Williams, R. M. E.; Williford, K. H.

2016-12-01

This study provides the first systematic comparison of orbital facies maps with detailed ground-based geology observations from the Mars Science Laboratory (MSL) Curiosity rover to examine the validity of geologic interpretations derived from orbital image data. Orbital facies maps were constructed for the Darwin, Cooperstown, and Kimberley waypoints visited by the Curiosity rover using High Resolution Imaging Science Experiment (HiRISE) images. These maps, which represent the most detailed orbital analysis of these areas to date, were compared with rover image-based geologic maps and stratigraphic columns derived from Curiosity's Mast Camera (Mastcam) and Mars Hand Lens Imager (MAHLI). Results show that bedrock outcrops can generally be distinguished from unconsolidated surficial deposits in high-resolution orbital images and that orbital facies mapping can be used to recognize geologic contacts between well-exposed bedrock units. However, process-based interpretations derived from orbital image mapping are difficult to infer without known regional context or observable paleogeomorphic indicators, and layer-cake models of stratigraphy derived from orbital maps oversimplify depositional relationships as revealed from a rover perspective. This study also shows that fine-scale orbital image-based mapping of current and future Mars landing sites is essential for optimizing the efficiency and science return of rover surface operations.

Comparing orbiter and rover image-based mapping of an ancient sedimentary environment, Aeolis Palus, Gale crater, Mars

USGS Publications Warehouse

Stack, Kathryn M.; Edwards, Christopher; Grotzinger, J. P.; Gupta, S.; Sumner, D.; Edgar, Lauren; Fraeman, A.; Jacob, S.; LeDeit, L.; Lewis, K.W.; Rice, M.S.; Rubin, D.; Calef, F.; Edgett, K.; Williams, R.M.E.; Williford, K.H.

2016-01-01

This study provides the first systematic comparison of orbital facies maps with detailed ground-based geology observations from the Mars Science Laboratory (MSL) Curiosity rover to examine the validity of geologic interpretations derived from orbital image data. Orbital facies maps were constructed for the Darwin, Cooperstown, and Kimberley waypoints visited by the Curiosity rover using High Resolution Imaging Science Experiment (HiRISE) images. These maps, which represent the most detailed orbital analysis of these areas to date, were compared with rover image-based geologic maps and stratigraphic columns derived from Curiosity’s Mast Camera (Mastcam) and Mars Hand Lens Imager (MAHLI). Results show that bedrock outcrops can generally be distinguished from unconsolidated surficial deposits in high-resolution orbital images and that orbital facies mapping can be used to recognize geologic contacts between well-exposed bedrock units. However, process-based interpretations derived from orbital image mapping are difficult to infer without known regional context or observable paleogeomorphic indicators, and layer-cake models of stratigraphy derived from orbital maps oversimplify depositional relationships as revealed from a rover perspective. This study also shows that fine-scale orbital image-based mapping of current and future Mars landing sites is essential for optimizing the efficiency and science return of rover surface operations.

Generating high-accuracy urban distribution map for short-term change monitoring based on convolutional neural network by utilizing SAR imagery

NASA Astrophysics Data System (ADS)

Iino, Shota; Ito, Riho; Doi, Kento; Imaizumi, Tomoyuki; Hikosaka, Shuhei

2017-10-01

In the developing countries, urban areas are expanding rapidly. With the rapid developments, a short term monitoring of urban changes is important. A constant observation and creation of urban distribution map of high accuracy and without noise pollution are the key issues for the short term monitoring. SAR satellites are highly suitable for day or night and regardless of atmospheric weather condition observations for this type of study. The current study highlights the methodology of generating high-accuracy urban distribution maps derived from the SAR satellite imagery based on Convolutional Neural Network (CNN), which showed the outstanding results for image classification. Several improvements on SAR polarization combinations and dataset construction were performed for increasing the accuracy. As an additional data, Digital Surface Model (DSM), which are useful to classify land cover, were added to improve the accuracy. From the obtained result, high-accuracy urban distribution map satisfying the quality for short-term monitoring was generated. For the evaluation, urban changes were extracted by taking the difference of urban distribution maps. The change analysis with time series of imageries revealed the locations of urban change areas for short-term. Comparisons with optical satellites were performed for validating the results. Finally, analysis of the urban changes combining X-band, L-band and C-band SAR satellites was attempted to increase the opportunity of acquiring satellite imageries. Further analysis will be conducted as future work of the present study

Comparison of different digital elevation models and satellite imagery for lineament analysis: Implications for identification and spatial arrangement of fault zones in crystalline basement rocks of the southern Black Forest (Germany)

NASA Astrophysics Data System (ADS)

Meixner, J.; Grimmer, J. C.; Becker, A.; Schill, E.; Kohl, T.

2018-03-01

GIS-based remote sensing techniques and lineament mapping provide additional information on the spatial arrangement of faults and fractures in large areas with variable outcrop conditions. Due to inherent censoring and truncation bias mapping of lineaments is still a challenging task. In this study we show how statistical evaluations help to improve the reliability of lineament mappings by comparing two digital elevation models (ASTER, LIDAR) and satellite imagery data sets in the seismically active southern Black Forest. A statistical assessment of the orientation, average length, and the total length of mapped lineaments reveals an impact of the different resolutions of the data sets that allow to define maximum (censoring bias) and minimum (truncation bias) observable lineament length for each data set. The increase of the spatial resolution of the digital elevation model from 30 m × 30 m to 5 m × 5 m results in a decrease of total lineament length by about 40% whereby the average lineament lengths decrease by about 60%. Lineament length distributions of both data sets follow a power law distribution as documented elsewhere for fault and fracture systems. Predominant NE-, N-, NNW-, and NW-directions of the lineaments are observed in all data sets and correlate with well-known, mappable large-scale structures in the southern Black Forest. Therefore, mapped lineaments can be correlated with faults and hence display geological significance. Lineament density in the granite-dominated areas is apparently higher than in the gneiss-dominated areas. Application of a slip- and dilation tendency analysis on the fault pattern reveals largest reactivation potentials for WNW-ESE and N-S striking faults as strike-slip faults whereas normal faulting may occur along NW-striking faults within the ambient stress field. Remote sensing techniques in combination with highly resolved digital elevation models and a slip- and dilation tendency analysis thus can be used to quickly get first order results of the spatial arrangement of critically stressed faults in crystalline basement rocks.

Being First Matters: Topographical Representational Similarity Analysis of ERP Signals Reveals Separate Networks for Audiovisual Temporal Binding Depending on the Leading Sense.

PubMed

Cecere, Roberto; Gross, Joachim; Willis, Ashleigh; Thut, Gregor

2017-05-24

In multisensory integration, processing in one sensory modality is enhanced by complementary information from other modalities. Intersensory timing is crucial in this process because only inputs reaching the brain within a restricted temporal window are perceptually bound. Previous research in the audiovisual field has investigated various features of the temporal binding window, revealing asymmetries in its size and plasticity depending on the leading input: auditory-visual (AV) or visual-auditory (VA). Here, we tested whether separate neuronal mechanisms underlie this AV-VA dichotomy in humans. We recorded high-density EEG while participants performed an audiovisual simultaneity judgment task including various AV-VA asynchronies and unisensory control conditions (visual-only, auditory-only) and tested whether AV and VA processing generate different patterns of brain activity. After isolating the multisensory components of AV-VA event-related potentials (ERPs) from the sum of their unisensory constituents, we ran a time-resolved topographical representational similarity analysis (tRSA) comparing the AV and VA ERP maps. Spatial cross-correlation matrices were built from real data to index the similarity between the AV and VA maps at each time point (500 ms window after stimulus) and then correlated with two alternative similarity model matrices: AV maps = VA maps versus AV maps ≠ VA maps The tRSA results favored the AV maps ≠ VA maps model across all time points, suggesting that audiovisual temporal binding (indexed by synchrony perception) engages different neural pathways depending on the leading sense. The existence of such dual route supports recent theoretical accounts proposing that multiple binding mechanisms are implemented in the brain to accommodate different information parsing strategies in auditory and visual sensory systems. SIGNIFICANCE STATEMENT Intersensory timing is a crucial aspect of multisensory integration, determining whether and how inputs in one modality enhance stimulus processing in another modality. Our research demonstrates that evaluating synchrony of auditory-leading (AV) versus visual-leading (VA) audiovisual stimulus pairs is characterized by two distinct patterns of brain activity. This suggests that audiovisual integration is not a unitary process and that different binding mechanisms are recruited in the brain based on the leading sense. These mechanisms may be relevant for supporting different classes of multisensory operations, for example, auditory enhancement of visual attention (AV) and visual enhancement of auditory speech (VA). Copyright © 2017 Cecere et al.

Vegetational analysis with Skylab-3 imagery. [Perquimans County, North Carolina

NASA Technical Reports Server (NTRS)

Welby, C. W. (Principal Investigator); Holman, R. E.

1975-01-01

The author has identified the following significant results. Color infrared photography from Skylab 3 appeared to be superior to ERTS imagery in a vegetational study of northeastern North Carolina. An accuracy of 87% was achieved in delimiting species composition and zonation patterns of three coastal, vegetation classes. A vegetation map of Perquimans County, North Carolina, seemed to have a high degree of correlation with information provided by high altitude U-2 photography. Random verification sites revealed an overall interpretation accuracy above 84%. Comparison of maps drawn utilizing Skylab photography with North Carolina Dept. of Agriculture estimates of crop acreage revealed some marked discrepancies. The chief difference lies in the nonagricultural category in which there is a 30% discrepancy. This fact raised some questions as to the definition of nonagricultural land uses and methods used by the State Dept. of Agriculture to determine actual percentages of crops grown.

A Protein Interaction Map of the Kalimantacin Biosynthesis Assembly Line

PubMed Central

Uytterhoeven, Birgit; Lathouwers, Thomas; Voet, Marleen; Michiels, Chris W.; Lavigne, Rob

2016-01-01

The antimicrobial secondary metabolite kalimantacin (also called batumin) is produced by a hybrid polyketide/non-ribosomal peptide system in Pseudomonas fluorescens BCCM_ID9359. In this study, the kalimantacin biosynthesis gene cluster is analyzed by yeast two-hybrid analysis, creating a protein–protein interaction map of the entire assembly line. In total, 28 potential interactions were identified, of which 13 could be confirmed further. These interactions include the dimerization of ketosynthase domains, a link between assembly line modules 9 and 10, and a specific interaction between the trans-acting enoyl reductase BatK and the carrier proteins of modules 8 and 10. These interactions reveal fundamental insight into the biosynthesis of secondary metabolites. This study is the first to reveal interactions in a complete biosynthetic pathway. Similar future studies could build a strong basis for engineering strategies in such clusters. PMID:27853452

Bibliometric Analyses Reveal Patterns of Collaboration between ASMS Members

NASA Astrophysics Data System (ADS)

Palmblad, Magnus; van Eck, Nees Jan

2018-03-01

We have explored the collaborative network of the current American Society for Mass Spectrometry (ASMS) membership using bibliometric methods. The analysis shows that 4249 members are connected in a single, large, co-authorship graph, including the majority of the most published authors in the field of mass spectrometry. The map reveals topographical differences between university groups and national laboratories, and that the co-authors with the strongest links have long worked together at the same location. We have collected and summarized information on the geographical distribution of members, showing a high coverage of active researchers in North America and Western Europe. Looking at research fields, we could also identify a number of new or `hot' topics among ASMS members. Interactive versions of the maps are available on-line at https://goo.gl/UBNFMQ (collaborative network) and https://goo.gl/WV25vm (research topics). [Figure not available: see fulltext.

Matching biomedical ontologies based on formal concept analysis.

PubMed

Zhao, Mengyi; Zhang, Songmao; Li, Weizhuo; Chen, Guowei

2018-03-19

The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i.e., to empower FCA with as much as ontological knowledge as possible for identifying mappings across ontologies. We propose a method based on Formal Concept Analysis to identify and validate mappings across ontologies, including one-to-one mappings, complex mappings and correspondences between object properties. Our method, called FCA-Map, incrementally generates a total of five types of formal contexts and extracts mappings from the lattices derived. First, the token-based formal context describes how class names, labels and synonyms share lexical tokens, leading to lexical mappings (anchors) across ontologies. Second, the relation-based formal context describes how classes are in taxonomic, partonomic and disjoint relationships with the anchors, leading to positive and negative structural evidence for validating the lexical matching. Third, the positive relation-based context can be used to discover structural mappings. Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings. Last, the restriction-based formal context describes co-occurrence of classes across ontologies in anonymous ancestors of anchors, from which extended structural mappings and complex mappings can be identified. Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign demonstrates the effectiveness of FCA-Map and its competitiveness with the top-ranked systems. FCA-Map can achieve a better balance between precision and recall for large-scale domain ontologies through constructing multiple FCA structures, whereas it performs unsatisfactorily for smaller-sized ontologies with less lexical and semantic expressions. Compared with other FCA-based OM systems, the study in this paper is more comprehensive as an attempt to push the envelope of the Formal Concept Analysis formalism in ontology matching tasks. Five types of formal contexts are constructed incrementally, and their derived concept lattices are used to cluster the commonalities among classes at lexical and structural level, respectively. Experiments on large, real-world domain ontologies show promising results and reveal the power of FCA.

Studying Cosmic Evolution with 21 cm Intensity Mapping

NASA Astrophysics Data System (ADS)

Anderson, Christopher

This thesis describes early work in the developing field of 21-cm intensity mapping. The 21-cm line is a radio transition due to the hyperfine splitting of the ground state of neutral hydrogen (HI). Intensity mapping utilizes the aggregate redshifted 21-cm emission to map the three-dimensional distribution of HI on large scales. In principle, the 21-cm line can be utilized to map most of the volume of the observable Universe. But the signal is small, and dedicated instruments will be required to reach a high signal-to-noise ratio. Large spectrally smooth astrophysical foregrounds, which dwarf the 21-cm signal, present a significant challenge to the data analysis. I derive the fundamental physics of the 21-cm line and the size of the expected cosmological signal. I also provide an overview of the desired characteristics of a dedicated 21-cm instrument, and I list some instruments that are coming on-line in the next few years. I then describe the data analysis techniques and results for 21-cm intensity maps that were made with two existing radio telescopes, the Green Bank telescope (GBT) and the Parkes telescope. Both observations have detected the 21-cm HI signal by cross-correlating the 21-cm intensity maps with overlapping optical galaxy surveys. The GBT maps have been used to constrain the neutral hydrogen density at a mean redshift (z) of 0.8. The Parkes maps, at a mean redshift of 0.08, probe smaller scales. The Parkes 21-cm intensity maps reveal a lack of small-scale clustering when they are cross-correlated with 2dF optical galaxy maps. This lack of small-scale clustering is partially due to a scale-dependent and galaxy-color-dependent HI-galaxy cross- correlation coefficient. Lastly, I provide an overview of planned future analyses with the Parkes maps, with a proposed multi-beam receiver for the Green Bank telescope, and with simulations of systematic effects on foregrounds.

Joint explorative analysis of neuroreceptor subsystems in the human brain: application to receptor-transporter correlation using PET data.

PubMed

Cselényi, Zsolt; Lundberg, Johan; Halldin, Christer; Farde, Lars; Gulyás, Balázs

2004-10-01

Positron emission tomography (PET) has proved to be a highly successful technique in the qualitative and quantitative exploration of the human brain's neurotransmitter-receptor systems. In recent years, the number of PET radioligands, targeted to different neuroreceptor systems of the human brain, has increased considerably. This development paves the way for a simultaneous analysis of different receptor systems and subsystems in the same individual. The detailed exploration of the versatility of neuroreceptor systems requires novel technical approaches, capable of operating on huge parametric image datasets. An initial step of such explorative data processing and analysis should be the development of novel exploratory data-mining tools to gain insight into the "structure" of complex multi-individual, multi-receptor data sets. For practical reasons, a possible and feasible starting point of multi-receptor research can be the analysis of the pre- and post-synaptic binding sites of the same neurotransmitter. In the present study, we propose an unsupervised, unbiased data-mining tool for this task and demonstrate its usefulness by using quantitative receptor maps, obtained with positron emission tomography, from five healthy subjects on (pre-synaptic) serotonin transporters (5-HTT or SERT) and (post-synaptic) 5-HT(1A) receptors. Major components of the proposed technique include the projection of the input receptor maps to a feature space, the quasi-clustering and classification of projected data (neighbourhood formation), trans-individual analysis of neighbourhood properties (trajectory analysis), and the back-projection of the results of trajectory analysis to normal space (creation of multi-receptor maps). The resulting multi-receptor maps suggest that complex relationships and tendencies in the relationship between pre- and post-synaptic transporter-receptor systems can be revealed and classified by using this method. As an example, we demonstrate the regional correlation of the serotonin transporter-receptor systems. These parameter-specific multi-receptor maps can usefully guide the researchers in their endeavour to formulate models of multi-receptor interactions and changes in the human brain.

Atomic-scale luminescence measurement and theoretical analysis unveiling electron energy dissipation at a p-type GaAs(110) surface.

PubMed

Imada, Hiroshi; Miwa, Kuniyuki; Jung, Jaehoon; Shimizu, Tomoko K; Yamamoto, Naoki; Kim, Yousoo

2015-09-11

Luminescence of p-type GaAs was induced by electron injection from the tip of a scanning tunnelling microscope into a GaAs(110) surface. Atomically-resolved photon maps revealed a significant reduction in luminescence intensity at surface electronic states localized near Ga atoms. Theoretical analysis based on first principles calculations and a rate equation approach was performed to describe the perspective of electron energy dissipation at the surface. Our study reveals that non-radiative recombination through the surface states (SS) is a dominant process for the electron energy dissipation at the surface, which is suggestive of the fast scattering of injected electrons into the SS.

Relationship of geological and geothermal field properties: Midcontinent area, USA, an example

USGS Publications Warehouse

Forster, A.; Merriam, D.F.; Brower, J.C.

1993-01-01

Quantitative approaches to data analysis in the last decade have become important in basin modeling and mineral-resource estimation. The interrelation of geological, geophysical, geochemical, and geohydrological variables is important in adjusting a model to a real-world situation. Revealing the interdependences of variables can contribute in understanding the processes interacting in sedimentary basins. It is reasonably simple to compare spatial data of the same type but more difficult if different properties are involved. Statistical techniques, such as cluster analysis or principal components analysis, or some algebraic approaches can be used to ascertain the relations of standardized spatial data. In this example, structural configuration on five different stratigraphic horizons, one total sediment thickness map, and four maps of geothermal data were copared. As expected, the structural maps are highly related because all had undergone about the same deformation with differing degrees of intensity. The temperature gradients derived (1) from shallow borehole logging measurements under equilibrium conditions with the surrounding rock, and (2) from non-equilibrium bottom-hole temperatures (BHT) from deeper depths are mainly independent of each other. This was expected and confirmed also for the two temperature maps at 1000 ft which were constructed using both types of gradient values. Thus, it is evident that the use of a 2-point (BHT and surface temperature) straightline calculation of a mean temperature gradient gives different information about the geothermal regime than using gradients from temperatures logged under equilibrium conditions. Nevertheless, it is useful to determine to what a degree the larger dataset of nonequilibrium temperatures could reflect quantitative relationships to geologic conditions. Comparing all maps of geothermal information vs. the structural and the sediment thickness maps, it was determined that all correlations are moderately negative or slightly positive. These results are clearly shown by the cluster analysis and the principal components. Considering a close relationship between temperature and thermal conductivity of the sediments as observed for most of the Midcontinent area and relatively homogeneous heat-flow density conditions for the study area these results support the following assumptions: (1) undifferentiated geothermal gradients, computed from temperatures of different depth intervals and differing sediment properties, cannot contribute to an improved understanding of the temperature structure and its controls within the sedimentary cover, and (2) the quantitative approach of revealing such relations needs refined datasets of temperature information valid for the different depth levels or stratigraphic units. ?? 1993 International Association for Mathematical Geology.

Genotyping-by-sequencing enables linkage mapping in three octoploid cultivated strawberry families

PubMed Central

Salinas, Natalia; Tennessen, Jacob A.; Zurn, Jason D.; Sargent, Daniel James; Hancock, James; Bassil, Nahla V.

2017-01-01

Genotyping-by-sequencing (GBS) was used to survey genome-wide single-nucleotide polymorphisms (SNPs) in three biparental strawberry (Fragaria × ananassa) populations with the goal of evaluating this technique in a species with a complex octoploid genome. GBS sequence data were aligned to the F. vesca ‘Fvb’ reference genome in order to call SNPs. Numbers of polymorphic SNPs per population ranged from 1,163 to 3,190. Linkage maps consisting of 30–65 linkage groups were produced from the SNP sets derived from each parent. The linkage groups covered 99% of the Fvb reference genome, with three to seven linkage groups from a given parent aligned to any particular chromosome. A phylogenetic analysis performed using the POLiMAPS pipeline revealed linkage groups that were most similar to ancestral species F. vesca for each chromosome. Linkage groups that were most similar to a second ancestral species, F. iinumae, were only resolved for Fvb 4. The quantity of missing data and heterogeneity in genome coverage inherent in GBS complicated the analysis, but POLiMAPS resolved F. × ananassa chromosomal regions derived from diploid ancestor F. vesca. PMID:28875078

Recent Admixture in an Indian Population of African Ancestry

PubMed Central

Narang, Ankita; Jha, Pankaj; Rawat, Vimal; Mukhopadhayay, Arijit; Dash, Debasis; Basu, Analabha; Mukerji, Mitali

2011-01-01

Identification and study of genetic variation in recently admixed populations not only provides insight into historical population events but also is a powerful approach for mapping disease loci. We studied a population (OG-W-IP) that is of African-Indian origin and has resided in the western part of India for 500 years; members of this population are believed to be descendants of the Bantu-speaking population of Africa. We have carried out this study by using a set of 18,534 autosomal markers common between Indian, CEPH-HGDP, and HapMap populations. Principal-components analysis clearly revealed that the African-Indian population derives its ancestry from Bantu-speaking west-African as well as Indo-European-speaking north and northwest Indian population(s). STRUCTURE and ADMIXTURE analyses show that, overall, the OG-W-IPs derive 58.7% of their genomic ancestry from their African past and have very little inter-individual ancestry variation (8.4%). The extent of linkage disequilibrium also reveals that the admixture event has been recent. Functional annotation of genes encompassing the ancestry-informative markers that are closer in allele frequency to the Indian ancestral population revealed significant enrichment of biological processes, such as ion-channel activity, and cadherins. We briefly examine the implications of determining the genetic diversity of this population, which could provide opportunities for studies involving admixture mapping. PMID:21737057

Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity.

PubMed

Mao, Peng; Brown, Alexander J; Malc, Ewa P; Mieczkowski, Piotr A; Smerdon, Michael J; Roberts, Steven A; Wyrick, John J

2017-10-01

DNA base damage is an important contributor to genome instability, but how the formation and repair of these lesions is affected by the genomic landscape and contributes to mutagenesis is unknown. Here, we describe genome-wide maps of DNA base damage, repair, and mutagenesis at single nucleotide resolution in yeast treated with the alkylating agent methyl methanesulfonate (MMS). Analysis of these maps revealed that base excision repair (BER) of alkylation damage is significantly modulated by chromatin, with faster repair in nucleosome-depleted regions, and slower repair and higher mutation density within strongly positioned nucleosomes. Both the translational and rotational settings of lesions within nucleosomes significantly influence BER efficiency; moreover, this effect is asymmetric relative to the nucleosome dyad axis and is regulated by histone modifications. Our data also indicate that MMS-induced mutations at adenine nucleotides are significantly enriched on the nontranscribed strand (NTS) of yeast genes, particularly in BER-deficient strains, due to higher damage formation on the NTS and transcription-coupled repair of the transcribed strand (TS). These findings reveal the influence of chromatin on repair and mutagenesis of base lesions on a genome-wide scale and suggest a novel mechanism for transcription-associated mutation asymmetry, which is frequently observed in human cancers. © 2017 Mao et al.; Published by Cold Spring Harbor Laboratory Press.

Comparison of biochemical cartilage imaging techniques at 3 T MRI.

PubMed

Rehnitz, C; Kupfer, J; Streich, N A; Burkholder, I; Schmitt, B; Lauer, L; Kauczor, H-U; Weber, M-A

2014-10-01

To prospectively compare chemical-exchange saturation-transfer (CEST) with delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) and T2 mapping to assess the biochemical cartilage properties of the knee. Sixty-nine subjects were prospectively included (median age, 42 years; male/female = 32/37) in three cohorts: 10 healthy volunteers, 40 patients with clinically suspected cartilage lesions, and 19 patients about 1 year after microfracture therapy. T2 mapping, dGEMRIC, and CEST were performed at a 3 T MRI unit using a 15-channel knee coil. Parameter maps were evaluated using region-of-interest analysis of healthy cartilage, areas of chondromalacia and repair tissue. Differentiation of damaged from healthy cartilage was assessed using receiver-operating characteristic (ROC) analysis. Chondromalacia grade 2-3 had significantly higher CEST values (P = 0.001), lower dGEMRIC (T1-) values (P < 0.001) and higher T2 values (P < 0.001) when compared to the normal appearing cartilage. dGEMRIC and T2 mapping correlated moderately negative (Spearman coefficient r = -0.56, P = 0.0018) and T2 mapping and CEST moderately positive (r = 0.5, P = 0.007), while dGEMRIC and CEST did not significantly correlate (r = -0.311, P = 0.07). The repair tissue revealed lower dGEMRIC values (P < 0.001) and higher CEST values (P < 0.001) with a significant negative correlation (r = -0.589, P = 0.01), whereas T2 values were not different (P = 0.54). In healthy volunteers' cartilage, CEST and dGEMRIC showed moderate positive correlation (r = 0.56), however not reaching significance (P = 0.09). ROC-analysis demonstrated non-significant differences of T2 mapping vs CEST (P = 0.14), CEST vs dGEMRIC (P = 0.89), and T2 mapping vs dGEMRIC (P = 0.12). CEST is able to detect normal and damaged cartilage and is non-inferior in distinguishing both when compared to dGEMRIC and T2 mapping. Copyright © 2014 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Mapping urban tourist experience zones in downtown Raleigh, North Carolina

Treesearch

Holly Bosley Perry

2012-01-01

Aspatial analysis of tourism resources in a community can reveal relationships among places of interest that may otherwise be obscured by predetermined geographic boundaries. As part of a larger study on the spatial characteristics of an urban tourist destination, data were collected from tourism and urban planning professionals regarding their perceptions of the most-...

Analysis of Mycobacterium avium subsp. paratuberculosis mutant libraries reveals loci-dependent transcription biases and strategies to novel mutant discovery

USDA-ARS?s Scientific Manuscript database

Mycobacterium avium subsp. paratuberculosis (MAP) is the etiologic agent of Johne’s disease in ruminants and it has been implicated as a cause of Crohn’s disease in humans. The generation of comprehensive random mutant banks by transposon mutagenesis is a fundamental wide genomic technology utilized...

MAPPING TOXICANT-INDUCED NERVOUS SYSTEM DAMAGE WITH A CUPRIC SILVER STAIN: A QUANTITATIVE ANALYSIS OF NEURAL DEGENERATION INDUCED BY 3,4-METHYLENEDIOXYMETHAMPETHAMINE (MDMA)

EPA Science Inventory

The purpose of structural assessments in neurotoxicology is to provide a convincing picture of the location and extent of damage to the nervous system. ilver stains that selectively reveal neural degeneration hold particular promise in this regard. n this chapter we describe resu...

Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

USDA-ARS?s Scientific Manuscript database

Mutations often accompany DNA replication. Since there may be fewer cell cycles per year in the germlines of long-lived than short-lived angiosperms, the genomes of long-lived angiosperms may be diverging more slowly than those of short-lived angiosperms. Here we test this hypothesis. We first const...

Rooftop Solar Technical Potential for Low-to-Moderate Income Households in

Science.gov Websites

communities. A map of the United States, divided by county, is color-coded by the total solar technical of LMI households in the U.S. (approximately 43 percent), this analysis reveals two other important city governments, though to do so requires deployment on multi-family and renter-occupied buildings

Relationship of students' conceptual representations and problem-solving abilities in acid-base chemistry

NASA Astrophysics Data System (ADS)

Powers, Angela R.

2000-10-01

This study explored the relationship between secondary chemistry students' conceptual representations of acid-base chemistry, as shown in student-constructed concept maps, and their ability to solve acid-base problems, represented by their score on an 18-item paper and pencil test, the Acid-Base Concept Assessment (ABCA). The ABCA, consisting of both multiple-choice and short-answer items, was originally designed using a question-type by subtopic matrix, validated by a panel of experts, and refined through pilot studies and factor analysis to create the final instrument. The concept map task included a short introduction to concept mapping, a prototype concept map, a practice concept-mapping activity, and the instructions for the acid-base concept map task. The instruments were administered to chemistry students at two high schools; 108 subjects completed both instruments for this study. Factor analysis of ABCA results indicated that the test was unifactorial for these students, despite the intention to create an instrument with multiple "question-type" scales. Concept maps were scored both holistically and by counting valid concepts. The two approaches were highly correlated (r = 0.75). The correlation between ABCA score and concept-map score was 0.29 for holistically-scored concept maps and 0.33 for counted-concept maps. Although both correlations were significant, they accounted for only 8.8 and 10.2% of variance in ABCA scores, respectively. However, when the reliability of the instruments used is considered, more than 20% of the variance in ABCA scores may be explained by concept map scores. MANOVAs for ABCA and concept map scores by instructor, student gender, and year in school showed significant differences for both holistic and counted concept-map scores. Discriminant analysis revealed that the source of these differences was the instruction variable. Significant differences between classes receiving different instruction were found in the frequency of concepts listed by students for 9 of 10 concepts evaluated. Mean ABCA scores did not differ significantly between the two instruction groups. The results of this study failed to provide evidence of conceptual distinctions among different "types" of problem-solving items. The results suggested that several factors influence success in chemistry problem solving, including concept knowledge and organization. Further research into the nature of chemistry problems and problem solving is recommended.

Molecular Mapping of PMR1, a Novel Locus Conferring Resistance to Powdery Mildew in Pepper (Capsicum annuum).

PubMed

Jo, Jinkwan; Venkatesh, Jelli; Han, Koeun; Lee, Hea-Young; Choi, Gyung Ja; Lee, Hee Jae; Choi, Doil; Kang, Byoung-Cheorl

2017-01-01

Powdery mildew, caused by Leveillula taurica , is a major fungal disease affecting greenhouse-grown pepper ( Capsicum annuum ). Powdery mildew resistance has a complex mode of inheritance. In the present study, we investigated a novel powdery mildew resistance locus, PMR1 , using two mapping populations: 102 'VK515' F 2:3 families (derived from a cross between resistant parental line 'VK515R' and susceptible parental line 'VK515S') and 80 'PM Singang' F 2 plants (derived from the F 1 'PM Singang' commercial hybrid). Genetic analysis of the F 2:3 'VK515' and F 2 'PM Singang' populations revealed a single dominant locus for inheritance of the powdery mildew resistance trait. Genetic mapping showed that the PMR1 locus is located on syntenic regions of pepper chromosome 4 in a 4-Mb region between markers CZ2_11628 and HRM4.1.6 in 'VK515R'. Six molecular markers including one SCAR marker and five SNP markers were localized to a region 0 cM from the PMR1 locus. Two putative nucleotide-binding site leucine-rich repeat (NBS-LRR)-type disease resistance genes were identified in this PMR1 region. Genotyping-by-sequencing (GBS) and genetic mapping analysis revealed suppressed recombination in the PMR1 region, perhaps due to alien introgression. In addition, a comparison of species-specific InDel markers as well as GBS-derived SNP markers indicated that C. baccatum represents a possible source of such alien introgression of powdery mildew resistance into 'VK515R'. The molecular markers developed in this study will be especially helpful for marker-assisted selection in pepper breeding programs for powdery mildew resistance.

Microbiological changes, shelf life and identification of initial and spoilage microbiota of sea bream fillets stored under various conditions using 16S rRNA gene analysis.

PubMed

Parlapani, Foteini F; Kormas, Konstantinos Ar; Boziaris, Ioannis S

2015-09-01

Sea bream fillets are one of the most important value-added products of the seafood market. Fresh seafood spoils mainly owing to bacterial action. In this study an exploration of initial and spoilage microbiota of sea bream fillets stored under air and commercial modified atmosphere packaging (MAP) at 0 and 5 °C was conducted by 16S rRNA gene sequence analysis of isolates grown on plates. Sensory evaluation and enumeration of total viable counts and spoilage microorganisms were also conducted to determine shelf life and bacterial growth respectively. Different temperatures and atmospheres affected growth and synthesis of spoilage microbiota as well as shelf life. Shelf life under air at 0 and 5 °C was 14 and 5 days respectively, while under MAP it was 20 and 8 days respectively. Initial microbiota were dominated by Pseudomonas fluorescens, Psychrobacter and Macrococcus caseolyticus. Different temperatures and atmospheres affected the synthesis of spoilage microbiota. At the end of shelf life, different phylotypes of Pseudomonas closely related to Pseudomonas fragi were found to dominate in most cases, while Pseudomonas veronii dominated in fillets under MAP at 0 °C. Furthermore, in fillets under MAP at 5 °C, new dominant species such as Carnobacterium maltaromaticum, Carnobacterium divergens and Vagococcus fluvialis were revealed. Different temperature and atmospheric conditions affected bacterial growth, shelf life and the synthesis of spoilage microbiota. Molecular identification revealed species and strains of microorganisms that have not been reported before for sea bream fillets stored under various conditions, thus providing valuable information regarding microbiological spoilage. © 2014 Society of Chemical Industry.

Molecular Mapping of PMR1, a Novel Locus Conferring Resistance to Powdery Mildew in Pepper (Capsicum annuum)

PubMed Central

Jo, Jinkwan; Venkatesh, Jelli; Han, Koeun; Lee, Hea-Young; Choi, Gyung Ja; Lee, Hee Jae; Choi, Doil; Kang, Byoung-Cheorl

2017-01-01

Powdery mildew, caused by Leveillula taurica, is a major fungal disease affecting greenhouse-grown pepper (Capsicum annuum). Powdery mildew resistance has a complex mode of inheritance. In the present study, we investigated a novel powdery mildew resistance locus, PMR1, using two mapping populations: 102 ‘VK515' F2:3 families (derived from a cross between resistant parental line ‘VK515R' and susceptible parental line ‘VK515S') and 80 ‘PM Singang' F2 plants (derived from the F1 ‘PM Singang' commercial hybrid). Genetic analysis of the F2:3 ‘VK515' and F2 ‘PM Singang' populations revealed a single dominant locus for inheritance of the powdery mildew resistance trait. Genetic mapping showed that the PMR1 locus is located on syntenic regions of pepper chromosome 4 in a 4-Mb region between markers CZ2_11628 and HRM4.1.6 in ‘VK515R'. Six molecular markers including one SCAR marker and five SNP markers were localized to a region 0 cM from the PMR1 locus. Two putative nucleotide-binding site leucine-rich repeat (NBS-LRR)-type disease resistance genes were identified in this PMR1 region. Genotyping-by-sequencing (GBS) and genetic mapping analysis revealed suppressed recombination in the PMR1 region, perhaps due to alien introgression. In addition, a comparison of species-specific InDel markers as well as GBS-derived SNP markers indicated that C. baccatum represents a possible source of such alien introgression of powdery mildew resistance into ‘VK515R'. The molecular markers developed in this study will be especially helpful for marker-assisted selection in pepper breeding programs for powdery mildew resistance. PMID:29276524

Comparative sequence analysis of the potato cyst nematode resistance locus H1 reveals a major lack of co-linearity between three haplotypes in potato (Solanum tuberosum ssp.)

PubMed Central

Bakker, Erin; de Boer, Jan; van der Vossen, Edwin; Achenbach, Ute; Golas, Tomasz; Suryaningrat, Suwardi; Smant, Geert; Bakker, Jaap; Goverse, Aska

2010-01-01

The H1 locus confers resistance to the potato cyst nematode Globodera rostochiensis pathotypes 1 and 4. It is positioned at the distal end of chromosome V of the diploid Solanum tuberosum genotype SH83-92-488 (SH) on an introgression segment derived from S. tuberosum ssp. andigena. Markers from a high-resolution genetic map of the H1 locus (Bakker et al. in Theor Appl Genet 109:146–152, 2004) were used to screen a BAC library to construct a physical map covering a 341-kb region of the resistant haplotype coming from SH. For comparison, physical maps were also generated of the two haplotypes from the diploid susceptible genotype RH89-039-16 (S. tuberosum ssp. tuberosum/S. phureja), spanning syntenic regions of 700 and 319 kb. Gene predictions on the genomic segments resulted in the identification of a large cluster consisting of variable numbers of the CC-NB-LRR type of R genes for each haplotype. Furthermore, the regions were interspersed with numerous transposable elements and genes coding for an extensin-like protein and an amino acid transporter. Comparative analysis revealed a major lack of gene order conservation in the sequences of the three closely related haplotypes. Our data provide insight in the evolutionary mechanisms shaping the H1 locus and will facilitate the map-based cloning of the H1 resistance gene. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1472-9) contains supplementary material, which is available to authorized users. PMID:21049265

Structural and mechanical heterogeneity of the erythrocyte membrane reveals hallmarks of membrane stability.

PubMed

Picas, Laura; Rico, Félix; Deforet, Maxime; Scheuring, Simon

2013-02-26

The erythrocyte membrane, a metabolically regulated active structure that comprises lipid molecules, junctional complexes, and the spectrin network, enables the cell to undergo large passive deformations when passing through the microvascular system. Here we use atomic force microscopy (AFM) imaging and quantitative mechanical mapping at nanometer resolution to correlate structure and mechanics of key components of the erythrocyte membrane, crucial for cell integrity and function. Our data reveal structural and mechanical heterogeneity modulated by the metabolic state at unprecedented nanometer resolution. ATP-depletion, reducing skeletal junction phosphorylation in RBC cells, leads to membrane stiffening. Analysis of ghosts and shear-force opened erythrocytes show that, in the absence of cytosolic kinases, spectrin phosphorylation results in membrane stiffening at the extracellular face and a reduced junction remodeling in response to loading forces. Topography and mechanical mapping of single components at the cytoplasmic face reveal that, surprisingly, spectrin phosphorylation by ATP softens individual filaments. Our findings suggest that, besides the mechanical signature of each component, the RBC membrane mechanics is regulated by the metabolic state and the assembly of its structural elements.

Mapping the Risk of Soil-Transmitted Helminthic Infections in the Philippines

PubMed Central

Leonardo, Lydia; Gray, Darren J.; Carabin, Hélène; Halton, Kate; McManus, Donald P.; Williams, Gail M.; Rivera, Pilarita; Saniel, Ofelia; Hernandez, Leda; Yakob, Laith; McGarvey, Stephen T.; Clements, Archie C. A.

2015-01-01

Background In order to increase the efficient allocation of soil-transmitted helminth (STH) disease control resources in the Philippines, we aimed to describe for the first time the spatial variation in the prevalence of A. lumbricoides, T. trichiura and hookworm across the country, quantify the association between the physical environment and spatial variation of STH infection and develop predictive risk maps for each infection. Methodology/Principal Findings Data on STH infection from 35,573 individuals across the country were geolocated at the barangay level and included in the analysis. The analysis was stratified geographically in two major regions: 1) Luzon and the Visayas and 2) Mindanao. Bayesian geostatistical models of STH prevalence were developed, including age and sex of individuals and environmental variables (rainfall, land surface temperature and distance to inland water bodies) as predictors, and diagnostic uncertainty was incorporated. The role of environmental variables was different between regions of the Philippines. This analysis revealed that while A. lumbricoides and T. trichiura infections were widespread and highly endemic, hookworm infections were more circumscribed to smaller foci in the Visayas and Mindanao. Conclusions/Significance This analysis revealed significant spatial variation in STH infection prevalence within provinces of the Philippines. This suggests that a spatially targeted approach to STH interventions, including mass drug administration, is warranted. When financially possible, additional STH surveys should be prioritized to high-risk areas identified by our study in Luzon. PMID:26368819

Geological analysis of parts of the southern Arabian Shield based on Landsat imagery

NASA Astrophysics Data System (ADS)

Qari, Mohammed Yousef Hedaytullah T.

This thesis examines the capability and applicability of Landsat multispectral remote sensing data for geological analysis in the arid southern Arabian Shield, which is the eastern segment of the Nubian-Arabian Shield surrounding the Red Sea. The major lithologies in the study area are Proterozoic metavolcanics, metasediments, gneisses and granites. Three test-sites within the study area, located within two tectonic assemblages, the Asir Terrane and the Nabitah Mobile Belt, were selected for detailed comparison of remote sensing methods and ground geological studies. Selected digital image processing techniques were applied to full-resolution Landsat TM imagery and the results are interpreted and discussed. Methods included: image contrast improvement, edge enhancement for detecting lineaments and spectral enhancement for geological mapping. The last method was based on two principles, statistical analysis of the data and the use of arithmetical operators. New and detailed lithological and structural maps were constructed and compared with previous maps of these sites. Examples of geological relations identified using TM imagery include: recognition and mapping of migmatites for the first time in the Arabian Shield; location of the contact between the Asir Terrane and the Nabitah Mobile Belt; and mapping of lithologies, some of which were not identified on previous geological maps. These and other geological features were confirmed by field checking. Methods of lineament enhancement implemented in this study revealed structural lineaments, mostly mapped for the first time, which can be related to regional tectonics. Structural analysis showed that the southern Arabian Shield has been affected by at least three successive phases of deformation. The third phase is the most dominant and widespread. A crustal evolutionary model in the vicinity of the study area is presented showing four stages, these are: arc stage, accretion stage, collision stage and post-collision stage. The results of this study demonstrate that Landsat TM data can be used reliably for geological investigations in the Arabian Shield and comparable areas, particularly to generate detailed geological maps over large areas by using quantitative remote sensing methods, providing there is prior knowledge of part of the area.

[Genome-wide identification and expression analysis of the WRKY gene family in peach].

PubMed

Gu, Yan-bing; Ji, Zhi-rui; Chi, Fu-mei; Qiao, Zhuang; Xu, Cheng-nan; Zhang, Jun-xiang; Zhou, Zong-shan; Dong, Qing-long

2016-03-01

The WRKY transcription factors are one of the largest families of transcriptional regulators and play diverse regulatory roles in biotic and abiotic stresses, plant growth and development processes. In this study, the WRKY DNA-binding domain (Pfam Database number: PF03106) downloaded from Pfam protein families database was exploited to identify WRKY genes from the peach (Prunus persica 'Lovell') genome using HMMER 3.0. The obtained amino acid sequences were analyzed with DNAMAN 5.0, WebLogo 3, MEGA 5.1, MapInspect and MEME bioinformatics softwares. Totally 61 peach WRKY genes were found in the peach genome. Our phylogenetic analysis revealed that peach WRKY genes were classified into three Groups: Ⅰ, Ⅱ and Ⅲ. The WRKY N-terminal and C-terminal domains of Group Ⅰ (group I-N and group I-C) were monophyletic. The Group Ⅱ was sub-divided into five distinct clades (groupⅡ-a, Ⅱ-b, Ⅱ-c, Ⅱ-d and Ⅱ-e). Our domain analysis indicated that the WRKY regions contained a highly conserved heptapeptide stretch WRKYGQK at its N-terminus followed by a zinc-finger motif. The chromosome mapping analysis showed that peach WRKY genes were distributed with different densities over 8 chromosomes. The intron-exon structure analysis revealed that structures of the WRKY gene were highly conserved in the peach. The conserved motif analysis showed that the conserved motifs 1, 2 and 3, which specify the WRKY domain, were observed in all peach WRKY proteins, motif 5 as the unknown domain was observed in group Ⅱ-d, two WRKY domains were assigned to GroupⅠ. SqRT-PCR and qRT-PCR results indicated that 16 PpWRKY genes were expressed in roots, stems, leaves, flowers and fruits at various expression levels. Our analysis thus identified the PpWRKY gene families, and future functional studies are needed to reveal its specific roles.

Evaluation of ERTS-1 imagery for mapping Quaternary deposits and landforms in the Great Plains and Midwest

NASA Technical Reports Server (NTRS)

Morrison, R. B. (Principal Investigator); Hallberg, G. R.

1973-01-01

The author has identified the following significant results. The main landform associations and larger landforms are readily identifiable on the better images and commonly the gross associations of surficial Quaternary deposits also can be differentiated, primarily by information on landforms and soils. Maps showing the Quaternary geologic-terrain units that can be differentiated from the ERTS-1 images are being prepared for study areas in Illinois, Iowa, Missouri, Kansas, Nebraska, and South Dakota. Preliminary maps at 1:1 million scale are given of two of the study areas, the Peoria and Decatur, Illinois, 1 deg x 2 quadrangles. These maps exemplify the first phase of investigations, which consists of identifying and mapping landform and land use characteristics and geologic-surficial materials directly from ERTS-1 images alone, without input of additional data. These maps shown that commonly the boundaries of geologic-terrain units can be identified more accurately on ERTS-1 images than on topographic maps of 1:250,000 scale. From analysis of drainage patterns, stream-divide relations, and tone and textural variations on the ERTS-1 images, the trends of numerous moraines of Wisconsinan and possibly some of Illinoian age were mapped. In the Peoria study area the trend of a buried valley of the Mississippi River is revealed.

Dynamic Analysis of the Carotid-Kundalini Map

NASA Astrophysics Data System (ADS)

Wang, Xingyuan; Liang, Qingyong; Meng, Juan

The nature of the fixed points of the Carotid-Kundalini (C-K) map was studied and the boundary equation of the first bifurcation of the C-K map in the parameter plane is presented. Using the quantitative criterion and rule of chaotic system, the paper reveals the general features of the C-K Map transforming from regularity to chaos. The following conclusions are obtained: (i) chaotic patterns of the C-K map may emerge out of double-periodic bifurcation; (ii) the chaotic crisis phenomena are found. At the same time, the authors analyzed the orbit of critical point of the complex C-K Map and put forward the definition of Mandelbrot-Julia set of the complex C-K Map. The authors generalized the Welstead and Cromer's periodic scanning technique and using this technology constructed a series of the Mandelbrot-Julia sets of the complex C-K Map. Based on the experimental mathematics method of combining the theory of analytic function of one complex variable with computer aided drawing, we investigated the symmetry of the Mandelbrot-Julia set and studied the topological inflexibility of distribution of the periodic region in the Mandelbrot set, and found that the Mandelbrot set contains abundant information of the structure of Julia sets by finding the whole portray of Julia sets based on Mandelbrot set qualitatively.

Making clinical case-based learning in veterinary medicine visible: analysis of collaborative concept-mapping processes and reflections.

PubMed

Khosa, Deep K; Volet, Simone E; Bolton, John R

2014-01-01

The value of collaborative concept mapping in assisting students to develop an understanding of complex concepts across a broad range of basic and applied science subjects is well documented. Less is known about students' learning processes that occur during the construction of a concept map, especially in the context of clinical cases in veterinary medicine. This study investigated the unfolding collaborative learning processes that took place in real-time concept mapping of a clinical case by veterinary medical students and explored students' and their teacher's reflections on the value of this activity. This study had two parts. The first part investigated the cognitive and metacognitive learning processes of two groups of students who displayed divergent learning outcomes in a concept mapping task. Meaningful group differences were found in their level of learning engagement in terms of the extent to which they spent time understanding and co-constructing knowledge along with completing the task at hand. The second part explored students' and their teacher's views on the value of concept mapping as a learning and teaching tool. The students' and their teacher's perceptions revealed congruent and contrasting notions about the usefulness of concept mapping. The relevance of concept mapping to clinical case-based learning in veterinary medicine is discussed, along with directions for future research.

Operational monitoring of land-cover change using multitemporal remote sensing data

NASA Astrophysics Data System (ADS)

Rogan, John

2005-11-01

Land-cover change, manifested as either land-cover modification and/or conversion, can occur at all spatial scales, and changes at local scales can have profound, cumulative impacts at broader scales. The implication of operational land-cover monitoring is that researchers have access to a continuous stream of remote sensing data, with the long term goal of providing for consistent and repetitive mapping. Effective large area monitoring of land-cover (i.e., >1000 km2) can only be accomplished by using remotely sensed images as an indirect data source in land-cover change mapping and as a source for land-cover change model projections. Large area monitoring programs face several challenges: (1) choice of appropriate classification scheme/map legend over large, topographically and phenologically diverse areas; (2) issues concerning data consistency and map accuracy (i.e., calibration and validation); (3) very large data volumes; (4) time consuming data processing and interpretation. Therefore, this dissertation research broadly addresses these challenges in the context of examining state-of-the-art image pre-processing, spectral enhancement, classification, and accuracy assessment techniques to assist the California Land-cover Mapping and Monitoring Program (LCMMP). The results of this dissertation revealed that spatially varying haze can be effectively corrected from Landsat data for the purposes of change detection. The Multitemporal Spectral Mixture Analysis (MSMA) spectral enhancement technique produced more accurate land-cover maps than those derived from the Multitemporal Kauth Thomas (MKT) transformation in northern and southern California study areas. A comparison of machine learning classifiers showed that Fuzzy ARTMAP outperformed two classification tree algorithms, based on map accuracy and algorithm robustness. Variation in spatial data error (positional and thematic) was explored in relation to environmental variables using geostatistical interpolation techniques. Finally, the land-cover modification maps generated for three time intervals (1985--1990--1996--2000), with nine change-classes revealed important variations in land-cover gain and loss between northern and southern California study areas.

Comparative analysis of Airborne Visible/Infrared Imaging Spectrometer (AVIRIS), and Hyperspectral Thermal Emission Spectrometer (HyTES) longwave infrared (LWIR) hyperspectral data for geologic mapping

NASA Astrophysics Data System (ADS)

Kruse, Fred A.

2015-05-01

Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and spatially coincident Hyperspectral Thermal Emission Spectrometer (HyTES) data were used to map geology and alteration for a site in northern Death Valley, California and Nevada, USA. AVIRIS, with 224 bands at 10 nm spectral resolution over the range 0.4 - 2.5 μm at 3-meter spatial resolution were converted to reflectance using an atmospheric model. HyTES data with 256 bands at approximately 17 nm spectral resolution covering the 8 - 12 μm range at 4-meter spatial resolution were converted to emissivity using a longwave infrared (LWIR) radiative transfer atmospheric compensation model and a normalized temperature-emissivity separation approach. Key spectral endmembers were separately extracted for each wavelength region and identified, and the predominant material at each pixel was mapped for each range using Mixture-Tuned-Matched Filtering (MTMF), a partial unmixing approach. AVIRIS mapped iron oxides, clays, mica, and silicification (hydrothermal alteration); and the difference between calcite and dolomite. HyTES separated and mapped several igneous phases (not possible using AVIRIS), silicification, and validated separation of calcite from dolomite. Comparison of the material maps from the different modes, however, reveals complex overlap, indicating that multiple materials/processes exist in many areas. Combined and integrated analyses were performed to compare individual results and more completely characterize occurrences of multiple materials. Three approaches were used 1) integrated full-range analysis, 2) combined multimode classification, and 3) directed combined analysis in geologic context. Results illustrate that together, these two datasets provide an improved picture of the distribution of geologic units and subsequent alteration.

Identification of QTLs associated with oil content in a high-oil Brassica napus cultivar and construction of a high-density consensus map for QTLs comparison in B. napus.

PubMed

Wang, Xiaodong; Wang, Hao; Long, Yan; Li, Dianrong; Yin, Yongtai; Tian, Jianhua; Chen, Li; Liu, Liezhao; Zhao, Weiguo; Zhao, Yajun; Yu, Longjiang; Li, Maoteng

2013-01-01

Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between 'KenC-8' and 'N53-2', two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64-17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus.

High-Speed Real-Time Resting-State fMRI Using Multi-Slab Echo-Volumar Imaging

PubMed Central

Posse, Stefan; Ackley, Elena; Mutihac, Radu; Zhang, Tongsheng; Hummatov, Ruslan; Akhtari, Massoud; Chohan, Muhammad; Fisch, Bruce; Yonas, Howard

2013-01-01

We recently demonstrated that ultra-high-speed real-time fMRI using multi-slab echo-volumar imaging (MEVI) significantly increases sensitivity for mapping task-related activation and resting-state networks (RSNs) compared to echo-planar imaging (Posse et al., 2012). In the present study we characterize the sensitivity of MEVI for mapping RSN connectivity dynamics, comparing independent component analysis (ICA) and a novel seed-based connectivity analysis (SBCA) that combines sliding-window correlation analysis with meta-statistics. This SBCA approach is shown to minimize the effects of confounds, such as movement, and CSF and white matter signal changes, and enables real-time monitoring of RSN dynamics at time scales of tens of seconds. We demonstrate highly sensitive mapping of eloquent cortex in the vicinity of brain tumors and arterio-venous malformations, and detection of abnormal resting-state connectivity in epilepsy. In patients with motor impairment, resting-state fMRI provided focal localization of sensorimotor cortex compared with more diffuse activation in task-based fMRI. The fast acquisition speed of MEVI enabled segregation of cardiac-related signal pulsation using ICA, which revealed distinct regional differences in pulsation amplitude and waveform, elevated signal pulsation in patients with arterio-venous malformations and a trend toward reduced pulsatility in gray matter of patients compared with healthy controls. Mapping cardiac pulsation in cortical gray matter may carry important functional information that distinguishes healthy from diseased tissue vasculature. This novel fMRI methodology is particularly promising for mapping eloquent cortex in patients with neurological disease, having variable degree of cooperation in task-based fMRI. In conclusion, ultra-high-real-time speed fMRI enhances the sensitivity of mapping the dynamics of resting-state connectivity and cerebro-vascular pulsatility for clinical and neuroscience research applications. PMID:23986677

Identification of QTLs Associated with Oil Content in a High-Oil Brassica napus Cultivar and Construction of a High-Density Consensus Map for QTLs Comparison in B. napus

PubMed Central

Long, Yan; Li, Dianrong; Yin, Yongtai; Tian, Jianhua; Chen, Li; Liu, Liezhao; Zhao, Weiguo; Zhao, Yajun; Yu, Longjiang; Li, Maoteng

2013-01-01

Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between ‘KenC-8’ and ‘N53-2’, two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64–17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus. PMID:24312482

Mapping clinical outcomes expectations to treatment decisions: an application to vestibular schwannoma management.

PubMed

Cheung, Steven W; Aranda, Derick; Driscoll, Colin L W; Parsa, Andrew T

2010-02-01

Complex medical decision making obligates tradeoff assessments among treatment outcomes expectations, but an accessible tool to perform the necessary analysis is conspicuously absent. We aimed to demonstrate methodology and feasibility of adapting conjoint analysis for mapping clinical outcomes expectations to treatment decisions in vestibular schwannoma (VS) management. Prospective. Tertiary medical center and US-based otologists/neurotologists. Treatment preference profiles among VS stakeholders-61 younger and 74 older prospective patients, 61 observation patients, and 60 surgeons-were assessed for the synthetic VS case scenario of a 10-mm tumor in association with useful hearing and normal facial function. Treatment attribute utility. Conjoint analysis attribute levels were set in accordance to the results of a meta-analysis. Forty-five case series were disaggregated to formulate microsurgery facial nerve and hearing preservation outcomes expectations models. Attribute utilities were computed and mapped to the realistic treatment choices of translabyrinthine craniotomy, middle fossa craniotomy, and gamma knife radiosurgery. Among the treatment attributes of likelihoods of causing deafness, temporary facial weakness for 2 months, and incurable cancer within 20 years, and recovery time, permanent deafness was less important to tumor surgeons, and temporary facial weakness was more important to tumor surgeons and observation patients (Wilcoxon rank-sum, p < 0.001). Inverse mapping of preference profiles to realistic treatment choices showed all study cohorts were inclined to choose gamma knife radiosurgery. Mapping clinical outcomes expectations to treatment decisions for a synthetic clinical scenario revealed inhomogeneous drivers of choice selection among study cohorts. Medical decision engines that analyze personal preferences of outcomes expectations for VS and many other diseases may be developed to promote shared decision making among health care stakeholders and transparency in the informed consent process.

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.

Radarsat Antarctic Mapping Project: Antarctic Imaging Campaign 2

NASA Technical Reports Server (NTRS)

2001-01-01

The Radarsat Antarctic Mapping Project is a collaboration between NASA and the Canadian Space Agency to map Antarctica using synthetic aperture radar (SAR). The first Antarctic Mapping Mission (AMM-1) was successfully completed in October 1997. Data from the acquisition phase of the 1997 campaign have been used to achieve the primary goal of producing the first, high-resolution SAR image map of Antarctica. The limited amount of data suitable for interferometric analysis have also been used to produce remarkably detailed maps of surface velocity for a few selected regions. Most importantly, the results from AMM-1 are now available to the general science community in the form of various resolution, radiometrically calibrated and geometrically accurate image mosaics. The second Antarctic imaging campaign occurred during the fall of 2000. Modified from AMM-1, the satellite remained in north looking mode during AMM-2 restricting coverage to regions north of about -80 degrees latitude. But AMM-2 utilized for the first time RADARSAT-1 fine beams providing an unprecedented opportunity to image many of Antarctica's fast glaciers whose extent was revealed through AMM-1 data. AMM-2 also captured extensive data suitable for interferometric analysis of the surface velocity field. This report summarizes the science goals, mission objectives, and project status through the acquisition phase and the start of the processing phase. The reports describes the efforts of team members including Alaska SAR Facility, Jet Propulsion Laboratory, Vexcel Corporation, Goddard Space Flight Center, Wallops Flight Facility, Ohio State University, Environmental Research Institute of Michigan, White Sands Facility, Canadian Space Agency Mission Planning and Operations Groups, and the Antarctic Mapping Planning Group.

Opportunities for Environmental Noise Mapping in Saudi Arabia: A Case of Traffic Noise Annoyance in an Urban Area in Jeddah City

PubMed Central

Zytoon, Mohamed A.

2016-01-01

As the traffic and other environmental noise generating activities are growing in The Kingdom of Saudi Arabia (KSA), adverse health and other impacts are expected to develop. The management of such problem involves many actions, of which noise mapping has been proven to be a helpful approach. The objective of the current study was to test the adequacy of the available data in KSA municipalities for generating urban noise maps and to verify the applicability of available environmental noise mapping and noise annoyance models for KSA. Therefore, noise maps were produced for Al-Fayha District in Jeddah City, KSA using commercially available noise mapping software and applying the French national computation method “NMPB” for traffic noise. Most of the data required for traffic noise prediction and annoyance analysis were available, either in the Municipality GIS department or in other governmental authorities. The predicted noise levels during the three time periods, i.e., daytime, evening, and nighttime, were found higher than the maximum recommended levels established in KSA environmental noise standards. Annoyance analysis revealed that high percentages of the District inhabitants were highly annoyed, depending on the type of planning zone and period of interest. These results reflect the urgent need to consider environmental noise reduction in KSA national plans. The accuracy of the predicted noise levels and the availability of most of the necessary data should encourage further studies on the use of noise mapping as part of noise reduction plans. PMID:27187438

Microbial synthesis of Flower-shaped gold nanoparticles.

PubMed

Singh, Priyanka; Kim, Yeon Ju; Wang, Chao; Mathiyalagan, Ramya; Yang, Deok Chun

2016-09-01

The shape of nanoparticles has been recognized as an important attribute that determines their applicability in various fields. The flower shape (F-shape) has been considered and is being focused on, because of its enhanced properties when compared to the properties of the spherical shape. The present study proposed the microbial synthesis of F-shaped gold nanoparticles within 48 h using the Bhargavaea indica DC1 strain. The F-shaped gold nanoparticles were synthesized extracellularly by the reduction of auric acid in the culture supernatant of B. indica DC1. The shape, size, purity, and crystalline nature of F-shaped gold nanoparticles were revealed by various instrumental techniques including UV-Vis, FE-TEM, EDX, elemental mapping, XRD, and DLS. The UV-Vis absorbance showed a maximum peak at 536 nm. FE-TEM revealed the F-shaped structure of nanoparticles. The EDX peak obtained at 2.3 keV indicated the purity. The peaks obtained on XRD analysis corresponded to the crystalline nature of the gold nanoparticles. In addition, the results of elemental mapping indicated the maximum distribution of gold elements in the nanoproduct obtained. Particle size analysis revealed that the average diameter of the F-shaped gold nanoparticles was 106 nm, with a polydispersity index (PDI) of 0.178. Thus, the methodology developed for the synthesis of F-shaped gold nanoparticles is completely green and economical.

Resting-State Functional Magnetic Resonance Imaging for Language Preoperative Planning

PubMed Central

Branco, Paulo; Seixas, Daniela; Deprez, Sabine; Kovacs, Silvia; Peeters, Ronald; Castro, São L.; Sunaert, Stefan

2016-01-01

Functional magnetic resonance imaging (fMRI) is a well-known non-invasive technique for the study of brain function. One of its most common clinical applications is preoperative language mapping, essential for the preservation of function in neurosurgical patients. Typically, fMRI is used to track task-related activity, but poor task performance and movement artifacts can be critical limitations in clinical settings. Recent advances in resting-state protocols open new possibilities for pre-surgical mapping of language potentially overcoming these limitations. To test the feasibility of using resting-state fMRI instead of conventional active task-based protocols, we compared results from fifteen patients with brain lesions while performing a verb-to-noun generation task and while at rest. Task-activity was measured using a general linear model analysis and independent component analysis (ICA). Resting-state networks were extracted using ICA and further classified in two ways: manually by an expert and by using an automated template matching procedure. The results revealed that the automated classification procedure correctly identified language networks as compared to the expert manual classification. We found a good overlay between task-related activity and resting-state language maps, particularly within the language regions of interest. Furthermore, resting-state language maps were as sensitive as task-related maps, and had higher specificity. Our findings suggest that resting-state protocols may be suitable to map language networks in a quick and clinically efficient way. PMID:26869899

Mapping large extensions of flat dentin through digital microscopy: introduction to the method and possible applications.

PubMed

Reis, Claudia; De-Deus, Gustavo; Marins, Juliana; Fidel, Sandra; Fidel, Rivail; Paciornik, Sidnei

2012-08-01

To introduce a mapping method to characterize large dentin surfaces using digital microscopy and to discuss the advantages and possible applications of the method. Twenty unerupted third molars were sectioned transversally exposing coronal dentin surfaces. The microscopic mosaic method was used to generate a large field image with the resolution necessary to measure characteristics of dentin tubules. The AxioVision 4.7 software was used to control a motorized optical microscope and the process of acquiring approximately 400 small images to generate each dentin mosaic. An image analysis routine measured the number of tubules (NT) and the ratio between the total area of tubules and the area of the mosaic - the area fraction (AF) - of each mosaic. An automatic procedure transformed the mosaic image into a color map, providing a direct visual representation of tubule density through colors. The dentin maps were used for a comparative qualitative analysis of tubule density distribution of each sample. The results for NT (92450 to 196029 tubules/sample) and AF (4.12% to 11.10%) demonstrated a wide variation among dentin samples. The maps confirmed the microstructure variety, also revealing strong local variations in tubule density within each sample. The mapping method was able to perform dentin morphology characterization and is a valuable tool for producing a baseline for dentin adhesion studies. The method could be also useful in determining the real contribution of dentin structures to the final adhesion quality.

A Scoping Review and Prevalence Analysis of Soil-Transmitted Helminth Infections in Honduras

PubMed Central

Sanchez, Ana Lourdes; Gabrie, José Antonio; Rueda, María Mercedes; Mejia, Rosa Elena; Bottazzi, Maria Elena; Canales, Maritza

2014-01-01

Background Honduras is endemic for soil-transmitted helminth (STH) infections, but critical information gaps still remain on the prevalence and intensity of these infections as well as on their spatial distribution at subnational levels. Objectives Firstly, to review the research activity on STH infections in Honduras and secondly, to carry out a national prevalence analysis and map the geographical distribution of these infections in children. Methods A systematic search was conducted of the published and grey literature to identify scientific work on the impact and prevalence of STH infections done between May 1930 and June 30, 2012. International databases and Honduran journals were searched. Grey literature was gleaned from local libraries and key informants. Select studies conducted between 2001 and 2012 were used to produce prevalence maps and to investigate association between STH prevalence and socio-economic and environmental factors. Results Of 257 identified studies, 211 (21.4% peer-reviewed) were retained for analysis and categorized as clinical research (10.9%), treatment efficacy studies (8.1%) or epidemiological studies (81%). Prevalence analysis and geographical mapping included 36 epidemiological studies from Honduras's 18 departments and 23% of its municipalities. Overall STH prevalence was >50% in 40.6% of municipalities. Prevalences above 20% for each trichuriasis, ascariasis, and hookworm infection were found in 68%, 47.8%, and 7.2% of studied municipalities, respectively. Municipalities with lower human development index, less access to of potable water, and with higher annual precipitation showed higher STH prevalences. Conclusions This is the first study to provide a comprehensive historic review of STH research activity and prevalence in Honduras, revealing important knowledge gaps related to infection risk factors, disease burden, and anti-parasitic drug efficacy, among others. Our decade-long prevalence analysis reveals geographical differences in STH prevalence and these findings suggest that differential intervention strategies might be necessary in Honduras for the control of these infections. PMID:24466359

A scoping review and prevalence analysis of soil-transmitted helminth infections in Honduras.

PubMed

Sanchez, Ana Lourdes; Gabrie, José Antonio; Rueda, María Mercedes; Mejia, Rosa Elena; Bottazzi, Maria Elena; Canales, Maritza

2014-01-01

Honduras is endemic for soil-transmitted helminth (STH) infections, but critical information gaps still remain on the prevalence and intensity of these infections as well as on their spatial distribution at subnational levels. Firstly, to review the research activity on STH infections in Honduras and secondly, to carry out a national prevalence analysis and map the geographical distribution of these infections in children. A systematic search was conducted of the published and grey literature to identify scientific work on the impact and prevalence of STH infections done between May 1930 and June 30, 2012. International databases and Honduran journals were searched. Grey literature was gleaned from local libraries and key informants. Select studies conducted between 2001 and 2012 were used to produce prevalence maps and to investigate association between STH prevalence and socio-economic and environmental factors. Of 257 identified studies, 211 (21.4% peer-reviewed) were retained for analysis and categorized as clinical research (10.9%), treatment efficacy studies (8.1%) or epidemiological studies (81%). Prevalence analysis and geographical mapping included 36 epidemiological studies from Honduras's 18 departments and 23% of its municipalities. Overall STH prevalence was >50% in 40.6% of municipalities. Prevalences above 20% for each trichuriasis, ascariasis, and hookworm infection were found in 68%, 47.8%, and 7.2% of studied municipalities, respectively. Municipalities with lower human development index, less access to of potable water, and with higher annual precipitation showed higher STH prevalences. This is the first study to provide a comprehensive historic review of STH research activity and prevalence in Honduras, revealing important knowledge gaps related to infection risk factors, disease burden, and anti-parasitic drug efficacy, among others. Our decade-long prevalence analysis reveals geographical differences in STH prevalence and these findings suggest that differential intervention strategies might be necessary in Honduras for the control of these infections.

Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa).

PubMed

Nagano, Soichiro; Shirasawa, Kenta; Hirakawa, Hideki; Maeda, Fumi; Ishikawa, Masami; Isobe, Sachiko N

2017-05-12

The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its genetic and genomic analysis, and thus discrimination of subgenome-specific loci among the homoeologous chromosomes is needed. In the present study, we identified candidate subgenome-specific single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) loci, and constructed a linkage map using an S 1 mapping population of the cultivar 'Reikou' with an IStraw90 Axiom® SNP array and previously published SSR markers. The 'Reikou' linkage map consisted of 11,574 loci (11,002 SNPs and 572 SSR loci) spanning 2816.5 cM of 31 linkage groups. The 11,574 loci were located on 4738 unique positions (bin) on the linkage map. Of the mapped loci, 8999 (8588 SNPs and 411 SSR loci) showed a 1:2:1 segregation ratio of AA:AB:BB allele, which suggested the possibility of deriving loci from candidate subgenome-specific sequences. In addition, 2575 loci (2414 SNPs and 161 SSR loci) showed a 3:1 segregation of AB:BB allele, indicating they were derived from homoeologous genomic sequences. Comparative analysis of the homoeologous linkage groups revealed differences in genome structure among the subgenomes. Our results suggest that candidate subgenome-specific loci are randomly located across the genomes, and that there are small- to large-scale structural variations among the subgenomes. The mapped SNPs and SSR loci on the linkage map are expected to be seed points for the construction of pseudomolecules in the octoploid strawberry.

Applying time series Landsat data for vegetation change analysis in the Florida Everglades Water Conservation Area 2A during 1996-2016

NASA Astrophysics Data System (ADS)

Zhang, Caiyun; Smith, Molly; Lv, Jie; Fang, Chaoyang

2017-05-01

Mapping plant communities and documenting their changes is critical to the on-going Florida Everglades restoration project. In this study, a framework was designed to map dominant vegetation communities and inventory their changes in the Florida Everglades Water Conservation Area 2A (WCA-2A) using time series Landsat images spanning 1996-2016. The object-based change analysis technique was combined in the framework. A hybrid pixel/object-based change detection approach was developed to effectively collect training samples for historical images with sparse reference data. An object-based quantification approach was also developed to assess the expansion/reduction of a specific class such as cattail (an invasive species in the Everglades) from the object-based classifications of two dates of imagery. The study confirmed the results in the literature that cattail was largely expanded during 1996-2007. It also revealed that cattail expansion was constrained after 2007. Application of time series Landsat data is valuable to document vegetation changes for the WCA-2A impoundment. The digital techniques developed will benefit global wetland mapping and change analysis in general, and the Florida Everglades WCA-2A in particular.

Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA) Genes in Flax (Linum usitatissimum L.).

PubMed

Yurkevich, Olga Y; Kirov, Ilya V; Bolsheva, Nadezhda L; Rachinskaya, Olga A; Grushetskaya, Zoya E; Zoschuk, Svyatoslav A; Samatadze, Tatiana E; Bogdanova, Marina V; Lemesh, Valentina A; Amosova, Alexandra V; Muravenko, Olga V

2017-01-01

Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase ( CesA ) multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH)-based chromosomal localization of the CesA conserved fragment (KF011584.1), 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum . Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG) 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding.

Integration of Physical, Genetic, and Cytogenetic Mapping Data for Cellulose Synthase (CesA) Genes in Flax (Linum usitatissimum L.)

PubMed Central

Yurkevich, Olga Y.; Kirov, Ilya V.; Bolsheva, Nadezhda L.; Rachinskaya, Olga A.; Grushetskaya, Zoya E.; Zoschuk, Svyatoslav A.; Samatadze, Tatiana E.; Bogdanova, Marina V.; Lemesh, Valentina A.; Amosova, Alexandra V.; Muravenko, Olga V.

2017-01-01

Flax, Linum usitatissimum L., is a valuable multi-purpose plant, and currently, its genome is being extensively investigated. Nevertheless, mapping of genes in flax genome is still remaining a challenging task. The cellulose synthase (CesA) multigene family involving in the process of cellulose synthesis is especially important for metabolism of this fiber crop. For the first time, fluorescent in situ hybridization (FISH)-based chromosomal localization of the CesA conserved fragment (KF011584.1), 5S, and 26S rRNA genes was performed in landrace, oilseed, and fiber varieties of L. usitatissimum. Intraspecific polymorphism in chromosomal distribution of KF011584.1 and 5S DNA loci was revealed, and the generalized chromosome ideogram was constructed. Using BLAST analysis, available data on physical/genetic mapping and also whole-genome sequencing of flax, localization of KF011584.1, 45S, and 5S rRNA sequences on genomic scaffolds, and their anchoring to the genetic map were conducted. The alignment of the results of FISH and BLAST analyses indicated that KF011584.1 fragment revealed on chromosome 3 could be anchored to linkage group (LG) 11. The common LG for 45S and 5S rDNA was not found probably due to the polymorphic localization of 5S rDNA on chromosome 1. Our findings indicate the complexity of integration of physical, genetic, and cytogenetic mapping data for multicopy gene families in plants. Nevertheless, the obtained results can be useful for future progress in constructing of integrated physical/genetic/cytological maps in L. usitatissimum which are essential for flax breeding. PMID:28878799

The burden of neck pain: its meaning for persons with neck pain and healthcare providers, explored by concept mapping.

PubMed

van Randeraad-van der Zee, Carlijn H; Beurskens, Anna J H M; Swinkels, Raymond A H M; Pool, Jan J M; Batterham, Roy W; Osborne, Richard H; de Vet, Henrica C W

2016-05-01

To empirically define the concept of burden of neck pain. The lack of a clear understanding of this construct from the perspective of persons with neck pain and care providers hampers adequate measurement of this burden. An additional aim was to compare the conceptual model obtained with the frequently used Neck Disability Index (NDI). Concept mapping, combining qualitative (nominal group technique and group consensus) and quantitative research methods (cluster analysis and multidimensional scaling), was applied to groups of persons with neck pain (n = 3) and professionals treating persons with neck pain (n = 2). Group members generated statements, which were organized into concept maps. Group members achieved consensus about the number and description of domains and the researchers then generated an overall mind map covering the full breadth of the burden of neck pain. Concept mapping revealed 12 domains of burden of neck pain: impaired mobility neck, neck pain, fatigue/concentration, physical complaints, psychological aspects/consequences, activities of daily living, social participation, financial consequences, difficult to treat/difficult to diagnose, difference of opinion with care providers, incomprehension by social environment, and how person with neck pain deal with complaints. All ten items of the NDI could be linked to the mind map, but the NDI measures only part of the burden of neck pain. This study revealed the relevant domains for the burden of neck pain from the viewpoints of persons with neck pain and their care providers. These results can guide the identification of existing measurements instruments for each domain or the development of new ones to measure the burden of neck pain.

Candidate Loci for Yield-Related Traits in Maize Revealed by a Combination of MetaQTL Analysis and Regional Association Mapping

PubMed Central

Chen, Lin; An, Yixin; Li, Yong-xiang; Li, Chunhui; Shi, Yunsu; Song, Yanchun; Zhang, Dengfeng; Wang, Tianyu; Li, Yu

2017-01-01

Maize grain yield and related traits are complex and are controlled by a large number of genes of small effect or quantitative trait loci (QTL). Over the years, a large number of yield-related QTLs have been identified in maize and deposited in public databases. However, integrating and re-analyzing these data and mining candidate loci for yield-related traits has become a major issue in maize. In this study, we collected information on QTLs conferring maize yield-related traits from 33 published studies. Then, 999 of these QTLs were iteratively projected and subjected to meta-analysis to obtain metaQTLs (MQTLs). A total of 76 MQTLs were found across the maize genome. Based on a comparative genomics strategy, several maize orthologs of rice yield-related genes were identified in these MQTL regions. Furthermore, three potential candidate genes (Gene ID: GRMZM2G359974, GRMZM2G301884, and GRMZM2G083894) associated with kernel size and weight within three MQTL regions were identified using regional association mapping, based on the results of the meta-analysis. This strategy, combining MQTL analysis and regional association mapping, is helpful for functional marker development and rapid identification of candidate genes or loci. PMID:29312420

An overview of animal science research 1945-2011 through science mapping analysis.

PubMed

Rodriguez-Ledesma, A; Cobo, M J; Lopez-Pujalte, C; Herrera-Viedma, E

2015-12-01

The conceptual structure of the field of Animal Science (AS) research is examined by means of a longitudinal science mapping analysis. The whole of the AS research field is analysed, revealing its conceptual evolution. To this end, an automatic approach to detecting and visualizing hidden themes or topics and their evolution across a consecutive span of years was applied to AS publications of the JCR category 'Agriculture, Dairy & Animal Science' during the period 1945-2011. This automatic approach was based on a coword analysis and combines performance analysis and science mapping. To observe the conceptual evolution of AS, six consecutive periods were defined: 1945-1969, 1970-1979, 1980-1989, 1990-1999, 2000-2005 and 2006-2011. Research in AS was identified as having focused on ten main thematic areas: ANIMAL-FEEDING, SMALL-RUMINANTS, ANIMAL-REPRODUCTION, DAIRY-PRODUCTION, MEAT-QUALITY, SWINE-PRODUCTION, GENETICS-AND-ANIMAL-BREEDING, POULTRY, ANIMAL-WELFARE and GROWTH-FACTORS-AND-FATTY-ACIDS. The results show how genomic studies gain in weight and integrate with other thematic areas. The whole of AS research has become oriented towards an overall framework in which animal welfare, sustainable management and human health play a major role. All this would affect the future structure and management of livestock farming. © 2014 Blackwell Verlag GmbH.

New gravity anomaly map of Taiwan and its surrounding regions with some tectonic interpretations

NASA Astrophysics Data System (ADS)

Doo, Wen-Bin; Lo, Chung-Liang; Hsu, Shu-Kun; Tsai, Ching-Hui; Huang, Yin-Sheng; Wang, Hsueh-Fen; Chiu, Shye-Donq; Ma, Yu-Fang; Liang, Chin-Wei

2018-04-01

In this study, we compiled recently collected (from 2005 to 2015) and previously reported (published and open access) gravity data, including land, shipborne and satellite-derived data, for Taiwan and its surrounding regions. Based on the cross-over error analysis, all data were adjusted; and, new Free-air gravity anomalies were obtained, shedding light on the tectonics of the region. To obtain the Bouguer gravity anomalies, the densities of land terrain and marine sediments were assumed to be 2.53 and 1.80 g/cm3, respectively. The updated gravity dataset was gridded with a spacing of one arc-minute. Several previously unnoticed gravity features are revealed by the new maps and can be used in a broad range of applications: (1) An isolated gravity high is located between the Shoushan and the Kaoping Canyon off southwest Taiwan. (2) Along the Luzon Arc, both Free-air and Bouguer gravity anomaly maps reveal a significant gravity discontinuity feature at the latitude of 21°20‧N. (3) In the southwestern Okinawa Trough, the NE-SW trending cross-back-arc volcanic trail (CBVT) marks the low-high gravity anomaly (both Free-air and Bouguer) boundary.

Seasonal mapping of NICU temperature.

PubMed

Thomas, Karen A; Magbalot, Almita; Shinabarger, Kelley; Mokhnach, Larisa; Anderson, Marilyn; Diercks, Kristi; Millar, April; Thorngate, Lauren; Walker, Wendy; Dilback, Nancy; Berkan, Maureen

2010-04-01

To create a thermal map of ambient air, radiant, and evaporative temperatures and humidity throughout the NICU nursery by season across a calendar year. Each cubicle of the 32-bed NICU, distributed across 5 rooms, in a level III nursery was measured. Temperatures were recorded at a consistent time on one day during January, April, July, and October. An electronic monitor (QUESTemp degrees 34; Quest Technologies, Oconomowoc, Wisconsin) was used to measure dry bulb, wet bulb, and globe thermometer temperatures. Analysis of variance revealed statistically significant (P < .000) differences in season, room, and season by room interaction. Room ambient air temperatures differed by less than 2 degrees F across season. Radiant temperature paralleled air temperature. Humidity, the predominant difference across season, produced evaporative temperatures considerably lower than room air temperature, and the gradient between mean nursery dry bulb temperature and wet bulb temperature was 9.3 degrees F in summer and 16.8 degrees F in winter. The thermal map revealed seasonal thermal differences, particularly in humidity level and evaporative temperature. Room temperature alone does not reflect the total thermal environment. Recommendations include periodic assessment of nurseries along with air, evaporative, and radiant temperatures as well as humidity to fully appreciate the impact of the thermal environment on infants.

Seasonal mapping of NICU temperature.

PubMed

Thomas, Karen A; Magbalot, Almita; Shinabarger, Kelley; Mokhnach, Larisa; Anderson, Marilyn; Diercks, Kristi; Millar, April; Thorngate, Lauren; Walker, Wendy; Dilback, Nancy; Berkan, Maureen

2010-10-01

To create a thermal map of ambient air, radiant, and evaporative temperatures and humidity throughout the NICU nursery by season across a calendar year. Each cubicle of the 32-bed NICU, distributed across 5 rooms, in a level III nursery was measured. Temperatures were recorded at a consistent time on one day during January, April, July, and October. : An electronic monitor (QUESTemp ° 34; Quest Technologies, Oconomowoc, Wisconsin) was used to measure dry bulb, wet bulb, and globe thermometer temperatures. Analysis of variance revealed statistically significant (P ≤ .000) differences in season, room, and season by room interaction. Room ambient air temperatures differed by less than 2 ° F across season. Radiant temperature paralleled air temperature. Humidity, the predominant difference across season, produced evaporative temperatures considerably lower than room air temperature, and the gradient between mean nursery dry bulb temperature and wet bulb temperature was 9.3 ° F in summer and 16.8 ° F in winter. The thermal map revealed seasonal thermal differences, particularly in humidity level and evaporative temperature. Room temperature alone does not reflect the total thermal environment. Recommendations include periodic assessment of nurseries along with air, evaporative, and radiant temperatures as well as humidity to fully appreciate the impact of the thermal environment on infants.

Mapping of hemoglobin in erythrocytes and erythrocyte ghosts using two photon excitation fluorescence microscopy

NASA Astrophysics Data System (ADS)

Bukara, Katarina; Jovanić, Svetlana; Drvenica, Ivana T.; Stančić, Ana; Ilić, Vesna; Rabasović, Mihailo D.; Pantelić, Dejan; Jelenković, Branislav; Bugarski, Branko; Krmpot, Aleksandar J.

2017-02-01

The present study describes utilization of two photon excitation fluorescence (2PE) microscopy for visualization of the hemoglobin in human and porcine erythrocytes and their empty membranes (i.e., ghosts). High-quality, label- and fixation-free visualization of hemoglobin was achieved at excitation wavelength 730 nm by detecting visible autofluorescence. Localization in the suspension and spatial distribution (i.e., mapping) of residual hemoglobin in erythrocyte ghosts has been resolved by 2PE. Prior to the 2PE mapping, the presence of residual hemoglobin in the bulk suspension of erythrocyte ghosts was confirmed by cyanmethemoglobin assay. 2PE analysis revealed that the distribution of hemoglobin in intact erythrocytes follows the cells' shape. Two types of erythrocytes, human and porcine, characterized with discocyte and echinocyte morphology, respectively, showed significant differences in hemoglobin distribution. The 2PE images have revealed that despite an extensive washing out procedure after gradual hypotonic hemolysis, a certain amount of hemoglobin localized on the intracellular side always remains bound to the membrane and cannot be eliminated. The obtained results open the possibility to use 2PE microscopy to examine hemoglobin distribution in erythrocytes and estimate the purity level of erythrocyte ghosts in biotechnological processes.

Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization

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

Guan, Jian; Bywaters, Stephanie M.; Brendle, Sarah A.

2015-09-15

Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope.more » Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays. - Highlights: • We present HPV16-Fab complexes from neutralizing mAbs: H16.1A, H16.14J, and H263.A2. • The structure-function analysis revealed predominantly monovalent binding of each mAb. • Capsid–Fab interactions involved multiple loops from symmetry related L1 proteins. • Besides the known FG and HI loops, epitope mapping also identified DE, EF, and BC loops. • Neutralizing assays complement the structures to show multiple neutralization mechanisms.« less

Use of descriptive analysis and preference mapping for early-stage assessment of new and established apples.

PubMed

Cliff, Margaret A; Stanich, Kareen; Lu, Ran; Hampson, Cheryl R

2016-04-01

This research compared four new apple selections with 16 established apples using descriptive analysis (DA), instrumental analyses and preference mapping, in order to identify suitable selections for commercialization and further research. DA revealed that the new apple selections (PARC1, PARC2, PARC3, PARC4) were very similar in texture/mouthfeel (T) but differed in their flavor (F) and appearance (A) characteristics. Preference mapping revealed that consumers' T preferences were driven primarily by crispness, juiciness and lack of skin toughness, while F preferences were driven by sweetness, lack of tartness and presence of fruity flavor. Consumers' A preferences were driven by a high percentage of red color and degree of striping. The majority of consumers had similar T (82-85%) and F (88-92%) preferences for the early- and mid/late-harvest apples. In contrast, consumers' A preferences were differentiated into three subgroups (60%, 24%, 16%) for the early-harvest apples, but not for the mid/late-harvest apples. The new apple selections were among those most liked for T, F and A. This early-stage consumer research confirmed that the new apples were comparable, if not superior, to the established apples. As such, it provided the necessary feedback to industry to proceed with commercialization and optimization of cultural and storage practices. © 2015 Her Majesty the Queen in Right of Canada. Journal of the Science of Food and Agriculture © 2015 Society of Chemical Industry.

Identification and molecular characterization of MYB Transcription Factor Superfamily in C4 model plant foxtail millet (Setaria italica L.).

PubMed

Muthamilarasan, Mehanathan; Khandelwal, Rohit; Yadav, Chandra Bhan; Bonthala, Venkata Suresh; Khan, Yusuf; Prasad, Manoj

2014-01-01

MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I-X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli.

Transcriptome-wide N 6 -methyladenosine methylome profiling of porcine muscle and adipose tissues reveals a potential mechanism for transcriptional regulation and differential methylation pattern.

PubMed

Tao, Xuelian; Chen, Jianning; Jiang, Yanzhi; Wei, Yingying; Chen, Yan; Xu, Huaming; Zhu, Li; Tang, Guoqing; Li, Mingzhou; Jiang, Anan; Shuai, Surong; Bai, Lin; Liu, Haifeng; Ma, Jideng; Jin, Long; Wen, Anxiang; Wang, Qin; Zhu, Guangxiang; Xie, Meng; Wu, Jiayun; He, Tao; Huang, Chunyu; Gao, Xiang; Li, Xuewei

2017-04-28

N 6 -methyladenosine (m 6 A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and potential regulatory functions of reversible m 6 A methylation on mRNA have been revealed by mapping of m 6 A methylomes in several species. m 6 A modification in active gene regulation manifests itself as altered methylation profiles in a tissue-specific manner or in response to changing cellular or species living environment. However, up to date, there has no data on m 6 A porcine transcriptome-wide map and its potential biological roles in adipose deposition and muscle growth. In this work, we used methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq) technique to acquire the first ever m 6 A porcine transcriptome-wide map. Transcriptomes of muscle and adipose tissues from three different pig breeds, the wild boar, Landrace, and Rongchang pig, were used to generate these maps. Our findings show that there were 5,872 and 2,826 m 6 A peaks respectively, in the porcine muscle and adipose tissue transcriptomes. Stop codons, 3'-untranslated regions, and coding regions were found to be mainly enriched for m 6 A peaks. Gene ontology analysis revealed that common m 6 A peaks in nuclear genes are associated with transcriptional factors, suggestive of a relationship between m 6 A mRNA methylation and nuclear genome transcription. Some genes showed tissue- and breed-differential methylation, and have novel biological functions. We also found a relationship between the m 6 A methylation extent and the transcript level, suggesting a regulatory role for m 6 A in gene expression. This comprehensive map provides a solid basis for the determination of potential functional roles for RNA m 6 A modification in adipose deposition and muscle growth.

Global dynamics and diffusion in triaxial galactic models

NASA Astrophysics Data System (ADS)

Papaphilippou, Y.

We apply the Frequency Map Analysis method to the 3--dimensional logarithmic galactic potential in order to clarify the dynamical behaviour of triaxial power--law galactic models. All the fine dynamical details are displayed in the complete frequency map, a direct representation of the system's Arnol'd web. The influence of resonant lines and the extent of the chaotic zones are directly associated with the physical space of the system. Some new results related with the diffusion of galactic orbits are also discussed. This approach reveals many unknown dynamical features of triaxial galactic potentials and provides strong indications that chaos should be an innate characteristic of triaxial configurations.

The role of human and mouse Y chromosome genes in male infertility.

PubMed

Affara, N A; Mitchell, M J

2000-11-01

It was suggested by Ronald Fisher in 1931 that genes involved in benefit to the male (including spermatogenesis genes) would accumulate on the Y chromosome. The analysis of mouse Y chromosome deletions and the discovery of microdeletions of the human Y chromosome associated with diverse defective spermatogenic phenotypes has revealed the presence of intervals containing one or more genes controlling male germ cell differentiation. These intervals have been mapped, cloned and examined in detail for functional genes. This review discusses the genes mapping to critical spermatogenesis intervals and the evidence indicating which are the most likely candidates underlying Y-linked male infertility.

Groundwater assessment in Salboni Block, West Bengal (India) using remote sensing, geographical information system and multi-criteria decision analysis techniques

NASA Astrophysics Data System (ADS)

Jha, Madan K.; Chowdary, V. M.; Chowdhury, Alivia

2010-11-01

An approach is presented for the evaluation of groundwater potential using remote sensing, geographic information system, geoelectrical, and multi-criteria decision analysis techniques. The approach divides the available hydrologic and hydrogeologic data into two groups, exogenous (hydrologic) and endogenous (subsurface). A case study in Salboni Block, West Bengal (India), uses six thematic layers of exogenous parameters and four thematic layers of endogenous parameters. These thematic layers and their features were assigned suitable weights which were normalized by analytic hierarchy process and eigenvector techniques. The layers were then integrated using ArcGIS software to generate two groundwater potential maps. The hydrologic parameters-based groundwater potential zone map indicated that the `good' groundwater potential zone covers 27.14% of the area, the `moderate' zone 45.33%, and the `poor' zone 27.53%. A comparison of this map with the groundwater potential map based on subsurface parameters revealed that the hydrologic parameters-based map accurately delineates groundwater potential zones in about 59% of the area, and hence it is dependable to a certain extent. More than 80% of the study area has moderate-to-poor groundwater potential, which necessitates efficient groundwater management for long-term water security. Overall, the integrated technique is useful for the assessment of groundwater resources at a basin or sub-basin scale.

Assessing gains in teacher knowledge and confidence in a long-duration climate literacy initiative

NASA Astrophysics Data System (ADS)

Haine, D. B.; Kendall, L.; Yelton, S.

2013-12-01

Climate Literacy: Integrating Modeling & Technology Experiences (CLIMATE) in NC Classrooms, an interdisciplinary, global climate change program for NC high school science teachers is administered by UNC Chapel Hill's Institute for the Environment (IE) with funding from NASA's Innovations in Climate Education (NICE) Program. Currently in its third year, this year-long program serves 24 teaching fellows annually and combines hands-on climate science investigations with experiential learning in fragile ecosystem environments to achieve the following program goals: increased teacher knowledge of climate change science and predicted impacts; increased teacher knowledge of modeling and technology resources, with an emphasis on those provided by NASA; and increased teacher confidence in using technology to address climate change education. A mixed-methods evaluation approach that includes external evaluation is providing quantitative and qualitative data about the extent to which program goals are being achieved. With regard to increases in teacher knowledge, teachers often self-report an increase in knowledge as a result of a program activity; this session will describe our strategies for assessing actual gains in teacher knowledge which include pre- and post-collaborative concept mapping and pre- and post-open response questionnaires. For each evaluation approach utilized, the process of analyzing these qualitative data will be discussed and results shared. For example, a collaborative concept mapping activity for assessment of learning as a result of the summer institute was utilized to assess gains in content knowledge. Working in small groups, teachers were asked to identify key vocabulary terms and show their relationship to one another via a concept map to answer these questions: What is global climate change? What is/are the: evidence? mechanisms? causes? consequences? Concept maps were constructed at the beginning (pre) and again at the end (post) of the Summer Institute. Concept map analysis revealed that post-maps included more key terms/concepts on average than pre-concept maps and that 6-9 NEW terms were present on post-maps; these NEW terms were directly related to science content addressed during the summer institute. In an effort to assess knowledge gained as a result of participating in an experiential weekend retreat, a pre- and post-open response questionnaire focused on the spruce-fir forest, an ecosystem prominently featured during programming, was administered. Post-learning assessments revealed learning gains for 100% of participants, all of whom were able to provide responses that referenced specific content covered during the retreat. To demonstrate increased teacher confidence in using technology to support climate science instruction, teachers are asked to develop and pilot a lesson that integrates at least one NASA resource. In collaboration with an external evaluator, a rubric was developed to evaluate submitted lessons in an effort to assess progress at achieving this program goal. The process of developing this rubric as well as the results from this analysis will be shared along with the challenges and insights that have been revealed from analyzing submitted lessons.

Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei

PubMed Central

Yu, Yang; Zhang, Xiaojun; Yuan, Jianbo; Li, Fuhua; Chen, Xiaohan; Zhao, Yongzhen; Huang, Long; Zheng, Hongkun; Xiang, Jianhai

2015-01-01

The Pacific white shrimp Litopenaeus vannamei is the dominant crustacean species in global seafood mariculture. Understanding the genome and genetic architecture is useful for deciphering complex traits and accelerating the breeding program in shrimp. In this study, a genome survey was conducted and a high-density linkage map was constructed using a next-generation sequencing approach. The genome survey was used to identify preliminary genome characteristics and to generate a rough reference for linkage map construction. De novo SNP discovery resulted in 25,140 polymorphic markers. A total of 6,359 high-quality markers were selected for linkage map construction based on marker coverage among individuals and read depths. For the linkage map, a total of 6,146 markers spanning 4,271.43 cM were mapped to 44 sex-averaged linkage groups, with an average marker distance of 0.7 cM. An integration analysis linked 5,885 genome scaffolds and 1,504 BAC clones to the linkage map. Based on the high-density linkage map, several QTLs for body weight and body length were detected. This high-density genetic linkage map reveals basic genomic architecture and will be useful for comparative genomics research, genome assembly and genetic improvement of L. vannamei and other penaeid shrimp species. PMID:26503227

Age mapping and dating of monazite on the electron microprobe: Deconvoluting multistage tectonic histories

NASA Astrophysics Data System (ADS)

Williams, Michael L.; Jercinovic, Michael J.; Terry, Michael P.

1999-11-01

High-resolution X-ray mapping and dating of monazite on the electron microprobe are powerful geochronological tools for structural, metamorphic, and tectonic analysis. X-ray maps commonly show complex Th, U, and Pb zoning that reflects monazite growth and overgrowth events. Age maps constructed from the X-ray maps simplify the zoning and highlight age domains. Microprobe dating offers a rapid, in situ method for estimating ages of mapped domains. Application of these techniques has placed new constraints on the tectonic history of three areas. In western Canada, age mapping has revealed multiphase monazite, with older cores and younger rims, included in syntectonic garnet. Microprobe ages show that tectonism occurred ca. 1.9 Ga, 700 m.y. later than mylonitization in the adjacent Snowbird tectonic zone. In New Mexico, age mapping and dating show that the dominant fabric and triple-point metamorphism occurred during a 1.4 Ga reactivation, not during the 1.7 Ga Yavapai-Mazatzal orogeny. In Norway, monazite inclusions in garnet constrain high-pressure metamorphism to ca. 405 Ma, and older cores indicate a previously unrecognized component of ca. 1.0 Ga monazite. In all three areas, microprobe dating and age mapping have provided a critical textural context for geochronologic data and a better understanding of the complex age spectra of these multistage orogenic belts.

Value of Frequency Domain Resting-State Functional Magnetic Resonance Imaging Metrics Amplitude of Low-Frequency Fluctuation and Fractional Amplitude of Low-Frequency Fluctuation in the Assessment of Brain Tumor-Induced Neurovascular Uncoupling.

PubMed

Agarwal, Shruti; Lu, Hanzhang; Pillai, Jay J

2017-08-01

The aim of this study was to explore whether the phenomenon of brain tumor-related neurovascular uncoupling (NVU) in resting-state blood oxygen level-dependent functional magnetic resonance imaging (BOLD fMRI) (rsfMRI) may also affect the resting-state fMRI (rsfMRI) frequency domain metrics the amplitude of low-frequency fluctuation (ALFF) and fractional ALFF (fALFF). Twelve de novo brain tumor patients, who underwent clinical fMRI examinations, including task-based fMRI (tbfMRI) and rsfMRI, were included in this Institutional Review Board-approved study. Each patient displayed decreased/absent tbfMRI activation in the primary ipsilesional (IL) sensorimotor cortex in the absence of a corresponding motor deficit or suboptimal task performance, consistent with NVU. Z-score maps for the motor tasks were obtained from general linear model analysis (reflecting motor activation vs. rest). Seed-based correlation analysis (SCA) maps of sensorimotor network, ALFF, and fALFF were calculated from rsfMRI data. Precentral and postcentral gyri in contralesional (CL) and IL hemispheres were parcellated using an automated anatomical labeling template for each patient. Region of interest (ROI) analysis was performed on four maps: tbfMRI, SCA, ALFF, and fALFF. Voxel values in the CL and IL ROIs of each map were divided by the corresponding global mean of ALFF and fALFF in the cortical brain tissue. Group analysis revealed significantly decreased IL ALFF (p = 0.02) and fALFF (p = 0.03) metrics compared with CL ROIs, consistent with similar findings of significantly decreased IL BOLD signal for tbfMRI (p = 0.0005) and SCA maps (p = 0.0004). The frequency domain metrics ALFF and fALFF may be markers of lesion-induced NVU in rsfMRI similar to previously reported alterations in tbfMRI activation and SCA-derived resting-state functional connectivity maps.

Breed relationships facilitate fine-mapping studies: A 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds

PubMed Central

Parker, Heidi G.; Kukekova, Anna V.; Akey, Dayna T.; Goldstein, Orly; Kirkness, Ewen F.; Baysac, Kathleen C.; Mosher, Dana S.; Aguirre, Gustavo D.; Acland, Gregory M.; Ostrander, Elaine A.

2007-01-01

The features of modern dog breeds that increase the ease of mapping common diseases, such as reduced heterogeneity and extensive linkage disequilibrium, may also increase the difficulty associated with fine mapping and identifying causative mutations. One way to address this problem is by combining data from multiple breeds segregating the same trait after initial linkage has been determined. The multibreed approach increases the number of potentially informative recombination events and reduces the size of the critical haplotype by taking advantage of shortened linkage disequilibrium distances found across breeds. In order to identify breeds that likely share a trait inherited from the same ancestral source, we have used cluster analysis to divide 132 breeds of dog into five primary breed groups. We then use the multibreed approach to fine-map Collie eye anomaly (cea), a complex disorder of ocular development that was initially mapped to a 3.9-cM region on canine chromosome 37. Combined genotypes from affected individuals from four breeds of a single breed group significantly narrowed the candidate gene region to a 103-kb interval spanning only four genes. Sequence analysis revealed that all affected dogs share a homozygous deletion of 7.8 kb in the NHEJ1 gene. This intronic deletion spans a highly conserved binding domain to which several developmentally important proteins bind. This work both establishes that the primary cea mutation arose as a single disease allele in a common ancestor of herding breeds as well as highlights the value of comparative population analysis for refining regions of linkage. PMID:17916641

Multi-environment QTL analysis of grain morphology traits and fine mapping of a kernel-width QTL in Zheng58 × SK maize population.

PubMed

Raihan, Mohammad Sharif; Liu, Jie; Huang, Juan; Guo, Huan; Pan, Qingchun; Yan, Jianbing

2016-08-01

Sixteen major QTLs regulating maize kernel traits were mapped in multiple environments and one of them, qKW - 9.2 , was restricted to 630 Kb, harboring 28 putative gene models. To elucidate the genetic basis of kernel traits, a quantitative trait locus (QTL) analysis was conducted in a maize recombinant inbred line population derived from a cross between two diverse parents Zheng58 and SK, evaluated across eight environments. Construction of a high-density linkage map was based on 13,703 single-nucleotide polymorphism markers, covering 1860.9 cM of the whole genome. In total, 18, 26, 23, and 19 QTLs for kernel length, width, thickness, and 100-kernel weight, respectively, were detected on the basis of a single-environment analysis, and each QTL explained 3.2-23.7 % of the phenotypic variance. Sixteen major QTLs, which could explain greater than 10 % of the phenotypic variation, were mapped in multiple environments, implying that kernel traits might be controlled by many minor and multiple major QTLs. The major QTL qKW-9.2 with physical confidence interval of 1.68 Mbp, affecting kernel width, was then selected for fine mapping using heterogeneous inbred families. At final, the location of the underlying gene was narrowed down to 630 Kb, harboring 28 putative candidate-gene models. This information will enhance molecular breeding for kernel traits and simultaneously assist the gene cloning underlying this QTL, helping to reveal the genetic basis of kernel development in maize.

Establishment of a high-resolution 2-D reference map of human spermatozoal proteins from 12 fertile sperm-bank donors.

PubMed

Li, Ling-Wei; Fan, Li-Qing; Zhu, Wen-Bing; Nien, Hong-Chuan; Sun, Bo-Lan; Luo, Ke-Li; Liao, Ting-Ting; Tang, Le; Lu, Guang-Xiu

2007-05-01

To extend the analysis of the proteome of human spermatozoa and establish a 2-D gel electrophoresis (2-DE) reference map of human spermatozoal proteins in a pH range of 3.5-9.0. In order to reveal more protein spots, immobilized pH gradient strips (24 cm) of broad range of pH 3-10 and the narrower range of pH 6-9, as well as different overlapping narrow range pH immobilized pH gradient (IPG) strips, including 3.5-4.5, 4.0-5.0, 4.5-5.5, 5.0-6.0 and 5.5-6.7, were used. After 2-DE, several visually identical spots between the different pH range 2-D gel pairs were cut from the gels and confirmed by mass spectrometry and used as landmarks for computer analysis. The 2-D reference map with pH value from 3.5 to 9.0 was synthesized by using the ImageMaster analysis software. The overlapping spots were excluded, so that every spot was counted only once. A total of 3872 different protein spots were identified from the reference map, an approximately 3-fold increase compared to the broad range pH 3-10 IPG strip (1306 spots). The present 2-D pattern is a high resolution 2-D reference map for human fertile spermatozoal protein spots. A comprehensive knowledge of the protein composition of human spermatozoa is very meaningful in studying dysregulation of male fertility.

Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis.

PubMed

Nguyen, Phuong H

2006-12-01

Employing the recently developed hierarchical nonlinear principal component analysis (NLPCA) method of Saegusa et al. (Neurocomputing 2004;61:57-70 and IEICE Trans Inf Syst 2005;E88-D:2242-2248), the complexities of the free energy landscapes of several peptides, including triglycine, hexaalanine, and the C-terminal beta-hairpin of protein G, were studied. First, the performance of this NLPCA method was compared with the standard linear principal component analysis (PCA). In particular, we compared two methods according to (1) the ability of the dimensionality reduction and (2) the efficient representation of peptide conformations in low-dimensional spaces spanned by the first few principal components. The study revealed that NLPCA reduces the dimensionality of the considered systems much better, than did PCA. For example, in order to get the similar error, which is due to representation of the original data of beta-hairpin in low dimensional space, one needs 4 and 21 principal components of NLPCA and PCA, respectively. Second, by representing the free energy landscapes of the considered systems as a function of the first two principal components obtained from PCA, we obtained the relatively well-structured free energy landscapes. In contrast, the free energy landscapes of NLPCA are much more complicated, exhibiting many states which are hidden in the PCA maps, especially in the unfolded regions. Furthermore, the study also showed that many states in the PCA maps are mixed up by several peptide conformations, while those of the NLPCA maps are more pure. This finding suggests that the NLPCA should be used to capture the essential features of the systems. (c) 2006 Wiley-Liss, Inc.

Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.).

PubMed

Campbell, Raymond; Pont, Simon D A; Morris, Jenny A; McKenzie, Gaynor; Sharma, Sanjeev Kumar; Hedley, Pete E; Ramsay, Gavin; Bryan, Glenn J; Taylor, Mark A

2014-09-01

Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9. The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient 'genetical genomics' analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.

Fine Mapping and Candidate Gene Analysis of the Leaf-Color Gene ygl-1 in Maize

PubMed Central

Guan, Haiying; Xu, Xiangbo; He, Chunmei; Liu, Chunxiao; Liu, Qiang; Dong, Rui; Liu, Tieshan; Wang, Liming

2016-01-01

A novel yellow-green leaf mutant yellow-green leaf-1 (ygl-1) was isolated in self-pollinated progenies from the cross of maize inbred lines Ye478 and Yuanwu02. The mutant spontaneously showed yellow-green character throughout the lifespan. Meanwhile, the mutant reduced contents of chlorophyll and Car, arrested chloroplast development and lowered the capacity of photosynthesis compared with the wild-type Lx7226. Genetic analysis revealed that the mutant phenotype was controlled by a recessive nuclear gene. The ygl-1 locus was initially mapped to an interval of about 0.86 Mb in bin 1.01 on the short arm of chromosome 1 using 231 yellow-green leaf individuals of an F2 segregating population from ygl-1/Lx7226. Utilizing four new polymorphic SSR markers, the ygl-1 locus was narrowed down to a region of about 48 kb using 2930 and 2247 individuals of F2 and F3 mapping populations, respectively. Among the three predicted genes annotated within this 48 kb region, GRMZM2G007441, which was predicted to encode a cpSRP43 protein, had a 1-bp nucleotide deletion in the coding region of ygl-1 resulting in a frame shift mutation. Semi-quantitative RT-PCR analysis revealed that YGL-1 was constitutively expressed in all tested tissues and its expression level was not significantly affected in the ygl-1 mutant from early to mature stages, while light intensity regulated its expression both in the ygl-1 mutant and wild type seedlings. Furthermore, the mRNA levels of some genes involved in chloroplast development were affected in the six-week old ygl-1 plants. These findings suggested that YGL-1 plays an important role in chloroplast development of maize. PMID:27100184

Mechanisms for renal blood flow control early in diabetes as revealed by chronic flow measurement and transfer function analysis.

PubMed

Bell, Tracy D; DiBona, Gerald F; Wang, Ying; Brands, Michael W

2006-08-01

The purpose of this study was to establish the roles of the myogenic response and the TGF mechanism in renal blood flow (RBF) control at the very earliest stages of diabetes. Mean arterial pressure (MAP) and RBF were measured continuously, 18 h/d, in uninephrectomized control and diabetic rats, and transfer function analysis was used to determine the dynamic autoregulatory efficiency of the renal vasculature. During the control period, MAP averaged 91 +/- 0.5 and 89 +/- 0.4 mmHg, and RBF averaged 8.0 +/- 0.1 and 7.8 +/- 0.1 ml/min in the control and diabetic groups, respectively. Induction of diabetes with streptozotocin caused a marked and progressive increase in RBF in the diabetic rats, averaging 10 +/- 6% above control on day 1 of diabetes and 22 +/- 3 and 34 +/- 1% above control by the end of diabetes weeks 1 and 2. MAP increased approximately 9 mmHg during the 2 wk in the diabetic rats, and renal vascular resistance decreased. Transfer function analysis revealed significant increases in gain to positive values over the frequency ranges of both the TGF and myogenic mechanisms, beginning on day 1 of diabetes and continuing through day 14. These very rapid increases in RBF and transfer function gain suggest that autoregulation is impaired at the very onset of hyperglycemia in streptozotocin-induced type 1 diabetes and may play an important role in the increase in RBF and GFR in diabetes. Together with previous reports of decreases in chronically measured cardiac output and hindquarter blood flow, this suggests that there may be differential effects of diabetes on RBF versus nonrenal BF control.

Genome-wide association and prediction analysis in African cassava (Manihot esculenta) reveals the genetic architecture of resistance to cassava mosaic disease and prospects for rapid genetic improvement

USDA-ARS?s Scientific Manuscript database

Cassava (Manihot esculenta) is a crucial, under-researched crop feeding millions worldwide, especially in Africa. Cassava mosaic disease (CMD) has plagued production in Africa for over a century. Bi-parental mapping studies suggest primarily a single major gene mediates resistance. To be certain and...

Collagen organization in canine myxomatous mitral valve disease: an x-ray diffraction study.

PubMed

Hadian, Mojtaba; Corcoran, Brendan M; Han, Richard I; Grossmann, J Günter; Bradshaw, Jeremy P

2007-10-01

Collagen fibrils, a major component of mitral valve leaflets, play an important role in defining shape and providing mechanical strength and flexibility. Histopathological studies show that collagen fibrils undergo dramatic changes in the course of myxomatous mitral valve disease in both dogs and humans. However, little is known about the detailed organization of collagen in this disease. This study was designed to analyze and compare collagen fibril organization in healthy and lesional areas of myxomatous mitral valves of dogs, using synchrotron small-angle x-ray diffraction. The orientation, density, and alignment of collagen fibrils were mapped across six different valves. The findings reveal a preferred collagen alignment in the main body of the leaflets between two commissures. Qualitative and quantitative analysis of the data showed significant differences between affected and lesion-free areas in terms of collagen content, fibril alignment, and total tissue volume. Regression analysis of the amount of collagen compared to the total tissue content at each point revealed a significant relationship between these two parameters in lesion-free but not in affected areas. This is the first time this technique has been used to map collagen fibrils in cardiac tissue; the findings have important applications to human cardiology.

In Southern Africa, Brown Oculocutaneous Albinism (BOCA) Maps to the OCA2 Locus on Chromosome 15q: P-Gene Mutations Identified

PubMed Central

Manga, Prashiela; Kromberg, Jennifer G. R.; Turner, Angela; Jenkins, Trefor; Ramsay, Michele

2001-01-01

In southern Africa, brown oculocutaneous albinism (BOCA) is a distinct pigmentation phenotype. In at least two cases, it has occurred in the same families as tyrosinase-positive oculocutaneous albinism (OCA2), suggesting that it may be allelic, despite the fact that this phenotype was attributed to mutations in the TYRP1 gene in an American individual of mixed ancestry. Linkage analysis in five families mapped the BOCA locus to the same region as the OCA2 locus (maximum LOD 3.07; θ=0 using a six-marker haplotype). Mutation analysis of the human homologue of the mouse pink-eyed dilution gene (P), in 10 unrelated individuals with BOCA revealed that 9 had one copy of the 2.7-kb deletion. No other mutations were identified. Additional haplotype studies, based on closely linked markers (telomere to centromere: D15S1048, D15S1019, D15S1533, P-gene 2.7-kb deletion, D15S219, and D15S156) revealed several BOCA-associated P haplotypes. These could be divided into two core haplotypes, suggesting that a limited number of P-gene mutations give rise to this phenotype. PMID:11179026

Subtracting the sequence bias from partially digested MNase-seq data reveals a general contribution of TFIIS to nucleosome positioning.

PubMed

Gutiérrez, Gabriel; Millán-Zambrano, Gonzalo; Medina, Daniel A; Jordán-Pla, Antonio; Pérez-Ortín, José E; Peñate, Xenia; Chávez, Sebastián

2017-12-07

TFIIS stimulates RNA cleavage by RNA polymerase II and promotes the resolution of backtracking events. TFIIS acts in the chromatin context, but its contribution to the chromatin landscape has not yet been investigated. Co-transcriptional chromatin alterations include subtle changes in nucleosome positioning, like those expected to be elicited by TFIIS, which are elusive to detect. The most popular method to map nucleosomes involves intensive chromatin digestion by micrococcal nuclease (MNase). Maps based on these exhaustively digested samples miss any MNase-sensitive nucleosomes caused by transcription. In contrast, partial digestion approaches preserve such nucleosomes, but introduce noise due to MNase sequence preferences. A systematic way of correcting this bias for massively parallel sequencing experiments is still missing. To investigate the contribution of TFIIS to the chromatin landscape, we developed a refined nucleosome-mapping method in Saccharomyces cerevisiae. Based on partial MNase digestion and a sequence-bias correction derived from naked DNA cleavage, the refined method efficiently mapped nucleosomes in promoter regions rich in MNase-sensitive structures. The naked DNA correction was also important for mapping gene body nucleosomes, particularly in those genes whose core promoters contain a canonical TATA element. With this improved method, we analyzed the global nucleosomal changes caused by lack of TFIIS. We detected a general increase in nucleosomal fuzziness and more restricted changes in nucleosome occupancy, which concentrated in some gene categories. The TATA-containing genes were preferentially associated with decreased occupancy in gene bodies, whereas the TATA-like genes did so with increased fuzziness. The detected chromatin alterations correlated with functional defects in nascent transcription, as revealed by genomic run-on experiments. The combination of partial MNase digestion and naked DNA correction of the sequence bias is a precise nucleosomal mapping method that does not exclude MNase-sensitive nucleosomes. This method is useful for detecting subtle alterations in nucleosome positioning produced by lack of TFIIS. Their analysis revealed that TFIIS generally contributed to nucleosome positioning in both gene promoters and bodies. The independent effect of lack of TFIIS on nucleosome occupancy and fuzziness supports the existence of alternative chromatin dynamics during transcription elongation.

Physical and genetic map of Streptococcus thermophilus A054.

PubMed Central

Roussel, Y; Pebay, M; Guedon, G; Simonet, J M; Decaris, B

1994-01-01

The three restriction endonucleases SfiI, BssHII, and SmaI were found to generate fragments with suitable size distributions for mapping the genome of Streptococcus thermophilus A054. A total of 5, 8, and 24 fragments were produced with SfiI, BssHII, and SmaI, respectively. An average genome size of 1,824 kb was determined by summing the total fragment sizes obtained by digestions with these three enzymes. Partial and multiple digestions of genomic DNA in conjunction with Southern hybridization were used to map SfiI, BssHII, and SmaI fragments. All restriction fragments were arranged in a unique circular chromosome. Southern hybridization analysis with specific probes allowed 23 genetic markers to be located on the restriction map. Among them, six rrn loci were precisely located. The area of the chromosome containing the ribosomal operons was further detailed by mapping some of the ApaI and SgrAI sites. Comparison of macrorestriction patterns from three clones derived from strain A054 revealed two variable regions in the chromosome. One was associated with the tandem rrnD and rrnE loci, and the other was mapped in the region of the lactose operon. Images PMID:8002562

Fast approximate delivery of fluence maps for IMRT and VMAT

NASA Astrophysics Data System (ADS)

Balvert, Marleen; Craft, David

2017-02-01

In this article we provide a method to generate the trade-off between delivery time and fluence map matching quality for dynamically delivered fluence maps. At the heart of our method lies a mathematical programming model that, for a given duration of delivery, optimizes leaf trajectories and dose rates such that the desired fluence map is reproduced as well as possible. We begin with the single fluence map case and then generalize the model and the solution technique to the delivery of sequential fluence maps. The resulting large-scale, non-convex optimization problem was solved using a heuristic approach. We test our method using a prostate case and a head and neck case, and present the resulting trade-off curves. Analysis of the leaf trajectories reveals that short time plans have larger leaf openings in general than longer delivery time plans. Our method allows one to explore the continuum of possibilities between coarse, large segment plans characteristic of direct aperture approaches and narrow field plans produced by sliding window approaches. Exposing this trade-off will allow for an informed choice between plan quality and solution time. Further research is required to speed up the optimization process to make this method clinically implementable.

Genome-Based Metabolic Mapping and 13C Flux Analysis Reveal Systematic Properties of an Oleaginous Microalga Chlorella protothecoides

DOE PAGES

Wu, Chao; Xiong, Wei; Dai, Junbiao; ...

2014-12-15

We report that integrated and genome-based flux balance analysis, metabolomics, and 13C-label profiling of phototrophic and heterotrophic metabolism in Chlorella protothecoides, an oleaginous green alga for biofuel. The green alga Chlorella protothecoides, capable of autotrophic and heterotrophic growth with rapid lipid synthesis, is a promising candidate for biofuel production. Based on the newly available genome knowledge of the alga, we reconstructed the compartmentalized metabolic network consisting of 272 metabolic reactions, 270 enzymes, and 461 encoding genes and simulated the growth in different cultivation conditions with flux balance analysis. Phenotype-phase plane analysis shows conditions achieving theoretical maximum of the biomass andmore » corresponding fatty acid-producing rate for phototrophic cells (the ratio of photon uptake rate to CO 2 uptake rate equals 8.4) and heterotrophic ones (the glucose uptake rate to O 2 consumption rate reaches 2.4), respectively. Isotope-assisted liquid chromatography-mass spectrometry/mass spectrometry reveals higher metabolite concentrations in the glycolytic pathway and the tricarboxylic acid cycle in heterotrophic cells compared with autotrophic cells. We also observed enhanced levels of ATP, nicotinamide adenine dinucleotide (phosphate), reduced, acetyl-Coenzyme A, and malonyl-Coenzyme A in heterotrophic cells consistently, consistent with a strong activity of lipid synthesis. To profile the flux map in experimental conditions, we applied nonstationary 13C metabolic flux analysis as a complementing strategy to flux balance analysis. We found that the result reveals negligible photorespiratory fluxes and a metabolically low active tricarboxylic acid cycle in phototrophic C. protothecoides. In comparison, high throughput of amphibolic reactions and the tricarboxylic acid cycle with no glyoxylate shunt activities were measured for heterotrophic cells. Lastly, taken together, the metabolic network modeling assisted by experimental metabolomics and 13C labeling better our understanding on global metabolism of oleaginous alga, paving the way to the systematic engineering of the microalga for biofuel production.« less

Topographic Independent Component Analysis reveals random scrambling of orientation in visual space

PubMed Central

Martinez-Garcia, Marina; Martinez, Luis M.

2017-01-01

Neurons at primary visual cortex (V1) in humans and other species are edge filters organized in orientation maps. In these maps, neurons with similar orientation preference are clustered together in iso-orientation domains. These maps have two fundamental properties: (1) retinotopy, i.e. correspondence between displacements at the image space and displacements at the cortical surface, and (2) a trade-off between good coverage of the visual field with all orientations and continuity of iso-orientation domains in the cortical space. There is an active debate on the origin of these locally continuous maps. While most of the existing descriptions take purely geometric/mechanistic approaches which disregard the network function, a clear exception to this trend in the literature is the original approach of Hyvärinen and Hoyer based on infomax and Topographic Independent Component Analysis (TICA). Although TICA successfully addresses a number of other properties of V1 simple and complex cells, in this work we question the validity of the orientation maps obtained from TICA. We argue that the maps predicted by TICA can be analyzed in the retinal space, and when doing so, it is apparent that they lack the required continuity and retinotopy. Here we show that in the orientation maps reported in the TICA literature it is easy to find examples of violation of the continuity between similarly tuned mechanisms in the retinal space, which suggest a random scrambling incompatible with the maps in primates. The new experiments in the retinal space presented here confirm this guess: TICA basis vectors actually follow a random salt-and-pepper organization back in the image space. Therefore, the interesting clusters found in the TICA topology cannot be interpreted as the actual cortical orientation maps found in cats, primates or humans. In conclusion, Topographic ICA does not reproduce cortical orientation maps. PMID:28640816

Topographic Independent Component Analysis reveals random scrambling of orientation in visual space.

PubMed

Martinez-Garcia, Marina; Martinez, Luis M; Malo, Jesús

2017-01-01

Neurons at primary visual cortex (V1) in humans and other species are edge filters organized in orientation maps. In these maps, neurons with similar orientation preference are clustered together in iso-orientation domains. These maps have two fundamental properties: (1) retinotopy, i.e. correspondence between displacements at the image space and displacements at the cortical surface, and (2) a trade-off between good coverage of the visual field with all orientations and continuity of iso-orientation domains in the cortical space. There is an active debate on the origin of these locally continuous maps. While most of the existing descriptions take purely geometric/mechanistic approaches which disregard the network function, a clear exception to this trend in the literature is the original approach of Hyvärinen and Hoyer based on infomax and Topographic Independent Component Analysis (TICA). Although TICA successfully addresses a number of other properties of V1 simple and complex cells, in this work we question the validity of the orientation maps obtained from TICA. We argue that the maps predicted by TICA can be analyzed in the retinal space, and when doing so, it is apparent that they lack the required continuity and retinotopy. Here we show that in the orientation maps reported in the TICA literature it is easy to find examples of violation of the continuity between similarly tuned mechanisms in the retinal space, which suggest a random scrambling incompatible with the maps in primates. The new experiments in the retinal space presented here confirm this guess: TICA basis vectors actually follow a random salt-and-pepper organization back in the image space. Therefore, the interesting clusters found in the TICA topology cannot be interpreted as the actual cortical orientation maps found in cats, primates or humans. In conclusion, Topographic ICA does not reproduce cortical orientation maps.

Construction of the physical map of the gpa7 locus reveals that a large segment was deleted during rice domestication.

PubMed

Li, Xianran; Tian, Feng; Huang, Haiyan; Tan, Lubin; Zhu, Zuofeng; Hu, Songnian; Sun, Chuanqing

2008-06-01

To facilitate cloning gene(s) underlying gpa7, a deep-coverage BAC library was constructed for an isolate of common wild rice (Oryza rufipogon Griff.) collected from Dongxiang, Jiangxi Province, China (DXCWR). gpa7, a quantitative trait locus corresponding to grain number per panicle, is positioned in the short arm of chromosome 7. The BAC library containing 96,768 clones represents approximate 18 haploid genome equivalents. The contig spanning DXCWR gpa7 was constructed with a series of ordered markers. The putative physical map near the gpa7 locus of another accession of O. rufipogon (Accession: IRGC 105491) was also isolated in silico. Analysis of the physical maps of gpa7 indicated that a segment of about 150 kb was deleted during domestication of common wild rice.

Mixture Modeling for Background and Sources Separation in x-ray Astronomical Images

NASA Astrophysics Data System (ADS)

Guglielmetti, Fabrizia; Fischer, Rainer; Dose, Volker

2004-11-01

A probabilistic technique for the joint estimation of background and sources in high-energy astrophysics is described. Bayesian probability theory is applied to gain insight into the coexistence of background and sources through a probabilistic two-component mixture model, which provides consistent uncertainties of background and sources. The present analysis is applied to ROSAT PSPC data (0.1-2.4 keV) in Survey Mode. A background map is modelled using a Thin-Plate spline. Source probability maps are obtained for each pixel (45 arcsec) independently and for larger correlation lengths, revealing faint and extended sources. We will demonstrate that the described probabilistic method allows for detection improvement of faint extended celestial sources compared to the Standard Analysis Software System (SASS) used for the production of the ROSAT All-Sky Survey (RASS) catalogues.

A study of the utilization of ERTS-1 data from the Wabash River Basin

NASA Technical Reports Server (NTRS)

Landgrebe, D. A. (Principal Investigator)

1973-01-01

The author has identified the following significant results. Nine projects are defined, five ERTS data applications experiments and four supporting technology tasks. The most significant applications results were achieved in the soil association mapping, earth surface feature identification, and urban land use mapping efforts. Four soil association boundaries were accurately delineated from ERTS-1 imagery. A data bank has been developed to test surface feature classifications obtained from ERTS-1 data. Preliminary forest cover classifications indicated that the number of acres estimated tended to be greater than actually existed by 25%. Urban land use analysis of ERTS-1 data indicated highly accurate classification could be obtained for many urban catagories. The wooded residential category tended to be misclassified as woods or agricultural land. Further statistical analysis revealed that these classes could be separated using sample variance.

Broad Integration of Expression Maps and Co-Expression Networks Compassing Novel Gene Functions in the Brain

PubMed Central

Okamura-Oho, Yuko; Shimokawa, Kazuro; Nishimura, Masaomi; Takemoto, Satoko; Sato, Akira; Furuichi, Teiichi; Yokota, Hideo

2014-01-01

Using a recently invented technique for gene expression mapping in the whole-anatomy context, termed transcriptome tomography, we have generated a dataset of 36,000 maps of overall gene expression in the adult-mouse brain. Here, using an informatics approach, we identified a broad co-expression network that follows an inverse power law and is rich in functional interaction and gene-ontology terms. Our framework for the integrated analysis of expression maps and graphs of co-expression networks revealed that groups of combinatorially expressed genes, which regulate cell differentiation during development, were present in the adult brain and each of these groups was associated with a discrete cell types. These groups included non-coding genes of unknown function. We found that these genes specifically linked developmentally conserved groups in the network. A previously unrecognized robust expression pattern covering the whole brain was related to the molecular anatomy of key biological processes occurring in particular areas. PMID:25382412

Relative risk estimation for malaria disease mapping based on stochastic SIR-SI model in Malaysia

NASA Astrophysics Data System (ADS)

Samat, Nor Azah; Ma'arof, Syafiqah Husna Mohd Imam

2016-10-01

Disease mapping is a study on the geographical distribution of a disease to represent the epidemiology data spatially. The production of maps is important to identify areas that deserve closer scrutiny or more attention. In this study, a mosquito-borne disease called Malaria is the focus of our application. Malaria disease is caused by parasites of the genus Plasmodium and is transmitted to people through the bites of infected female Anopheles mosquitoes. Precautionary steps need to be considered in order to avoid the malaria virus from spreading around the world, especially in the tropical and subtropical countries, which would subsequently increase the number of Malaria cases. Thus, the purpose of this paper is to discuss a stochastic model employed to estimate the relative risk of malaria disease in Malaysia. The outcomes of the analysis include a Malaria risk map for all 16 states in Malaysia, revealing the high and low risk areas of Malaria occurrences.

Characterization of self assembly layers of octadecanephosphonic acid by polarisation modulation FT-IRRA spectroscopy mapping

NASA Astrophysics Data System (ADS)

Steiner, G.; Sablinskas, V.; Savchuk, O.; Bariseviciute, R.; Jähne, E.; Adler, H. J.; Salzer, R.

2003-12-01

Self assembly layers were studied by a polarization modulation FT-spectroscopy mapping technique. The optical lay out is based on polarization modulation FT infrared reflection absorption spectroscopy (PM-FT-IRRAS). Here we report for the first time on a PM-FT-IRRAS mapping instrument. Octadecanephosphonic acid adsorbed on a patterned aluminum/gold surface was investigated. The nature of chemical bonding at particular surface areas was evaluated by principal component analysis. The most prominent features of the PM-FT-IRRA spectra are the P-O and PO stretching vibrations. It is shown that octadecanephosphonic acid is adsorbed both on Al 2O 3 and on Au. Moreover, PM-FT-IRRAS maps reveal areas of non-equivalent structural features. Lateral dimensions of these areas are in the micrometer range. Such non-equivalencies may control the inhibition potential of SAMs on ignoble metals, hence become crucial to the quality of products as biosensors or microelectronic components.

Mapping the groundwater vulnerability for pollution at the pan African scale.

PubMed

Ouedraogo, Issoufou; Defourny, Pierre; Vanclooster, Marnik

2016-02-15

We estimated vulnerability and pollution risk of groundwater at the pan-African scale. We therefore compiled the most recent continental scale information on soil, land use, geology, hydrogeology and climate in a Geographical Information System (GIS) at a resolution of 15 km × 15 km and at the scale of 1:60,000,000. The groundwater vulnerability map was constructed by means of the DRASTIC method. The map reveals that groundwater is highly vulnerable in Central and West Africa, where the watertable is very low. In addition, very low vulnerability is found in the large sedimentary basins of the African deserts where groundwater is situated in very deep aquifers. The groundwater pollution risk map is obtained by overlaying the DRASTIC vulnerability map with land use. The northern, central and western part of the African continent is dominated by high pollution risk classes and this is very strongly related to shallow groundwater systems and the development of agricultural activities. Subsequently, we performed a sensitivity analysis to evaluate the relative importance of each parameter on groundwater vulnerability and pollution risk. The sensitivity analysis indicated that the removal of the impact of vadose zone, the depth of the groundwater, the hydraulic conductivity and the net recharge causes a large variation in the mapped vulnerability and pollution risk. The mapping model was validated using nitrate concentration data of groundwater as a proxy of pollution risk. Pan-African concentration data were inferred from a meta-analysis of literature data. Results shows a good match between nitrate concentration and the groundwater pollution risk classes. The pan African assessment of groundwater vulnerability and pollution risk is expected to be of particular value for water policy and for designing groundwater resources management programs. We expect, however, that this assessment can be strongly improved when better pan African monitoring data related to groundwater pollution will be integrated in the assessment methodology. Copyright © 2015 Elsevier B.V. All rights reserved.

Construction of a yeast artificial chromosome contig encompassing the chromosome 14 Alzheimer`s disease locus

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

Sharma, V.; Bonnycastle, L.; Poorkai, P.

1994-09-01

We have constructed a yeast artificial chromosome (YAC) contig of chromosome 14q24.3 which encompasses the chromosome 14 Alzheimer`s disease locus (AD3). Determined by linkage analysis of early-onset Alzheimer`s disease kindreds, this interval is bounded by the genetic markers D14S61-D14S63 and spans approximately 15 centimorgans. The contig consists of 29 markers and 74 YACs of which 57 are defined by one or more sequence tagged sites (STSs). The STS markers comprise 5 genes, 16 short tandem repeat polymorphisms and 8 cDNA clones. An additional number of genes, expressed sequence tags and cDNA fragments have been identified and localized to the contigmore » by hybridization and sequence analysis of anonymous clones isolated by cDNA direct selection techniques. A minimal contig of about 15 YACs averaging 0.5-1.5 megabase in length will span this interval and is, at first approximation, in rough agreement with the genetic map. For two regions of the contig, our coverage has relied on L1/THE fingerprint and Alu-PCR hybridization data of YACs provided by CEPH/Genethon. We are currently developing sequence tagged sites from these to confirm the overlaps revealed by the fingerprint data. Among the genes which map to the contig are transforming growth factor beta 3, c-fos, and heat shock protein 2A (HSPA2). C-fos is not a candidate gene for AD3 based on the sequence analysis of affected and unaffected individuals. HSPA2 maps to the proximal edge of the contig and Calmodulin 1, a candidate gene from 4q24.3, maps outside of the region. The YAC contig is a framework physical map from which cosmid or P1 clone contigs can be constructed. As more genes and cDNAs are mapped, a highly resolved transcription map will emerge, a necessary step towards positionally cloning the AD3 gene.« less

Prioritising coastal zone management issues through fuzzy cognitive mapping approach.

PubMed

Meliadou, Aleka; Santoro, Francesca; Nader, Manal R; Dagher, Manale Abou; Al Indary, Shadi; Salloum, Bachir Abi

2012-04-30

Effective public participation is an essential component of Integrated Coastal Zone Management implementation. To promote such participation, a shared understanding of stakeholders' objectives has to be built to ultimately result in common coastal management strategies. The application of quantitative and semi-quantitative methods involving tools such as Fuzzy Cognitive Mapping is presently proposed for reaching such understanding. In this paper we apply the Fuzzy Cognitive Mapping tool to elucidate the objectives and priorities of North Lebanon's coastal productive sectors, and to formalize their coastal zone perceptions and knowledge. Then, we investigate the potential of Fuzzy Cognitive Mapping as tool for support coastal zone management. Five round table discussions were organized; one for the municipalities of the area and one for each of the main coastal productive sectors (tourism, industry, fisheries, agriculture), where the participants drew cognitive maps depicting their views. The analysis of the cognitive maps showed a large number of factors perceived as affecting the current situation of the North Lebanon coastal zone that were classified into five major categories: governance, infrastructure, environment, intersectoral interactions and sectoral initiatives. Furthermore, common problems, expectations and management objectives for all sectors were exposed. Within this context, Fuzzy Cognitive Mapping proved to be an essential tool for revealing stakeholder knowledge and perception and understanding complex relationships. Copyright © 2011 Elsevier Ltd. All rights reserved.

Decoding the Formation of New Semantics: MVPA Investigation of Rapid Neocortical Plasticity during Associative Encoding through Fast Mapping.

PubMed

Atir-Sharon, Tali; Gilboa, Asaf; Hazan, Hananel; Koilis, Ester; Manevitz, Larry M

2015-01-01

Neocortical structures typically only support slow acquisition of declarative memory; however, learning through fast mapping may facilitate rapid learning-induced cortical plasticity and hippocampal-independent integration of novel associations into existing semantic networks. During fast mapping the meaning of new words and concepts is inferred, and durable novel associations are incidentally formed, a process thought to support early childhood's exuberant learning. The anterior temporal lobe, a cortical semantic memory hub, may critically support such learning. We investigated encoding of semantic associations through fast mapping using fMRI and multivoxel pattern analysis. Subsequent memory performance following fast mapping was more efficiently predicted using anterior temporal lobe than hippocampal voxels, while standard explicit encoding was best predicted by hippocampal activity. Searchlight algorithms revealed additional activity patterns that predicted successful fast mapping semantic learning located in lateral occipitotemporal and parietotemporal neocortex and ventrolateral prefrontal cortex. By contrast, successful explicit encoding could be classified by activity in medial and dorsolateral prefrontal and parahippocampal cortices. We propose that fast mapping promotes incidental rapid integration of new associations into existing neocortical semantic networks by activating related, nonoverlapping conceptual knowledge. In healthy adults, this is better captured by unique anterior and lateral temporal lobe activity patterns, while hippocampal involvement is less predictive of this kind of learning.

New insights into the geodiversity of the southeast Indian Ocean seafloor revealed by Malaysia Airlines flight MH370 search data

NASA Astrophysics Data System (ADS)

Picard, K.; Brooke, B. B.; Harris, P. T.; Siwabessy, J. P. W.; Coffin, M. F.; Tran, M.; Spinoccia, M.; Weales, J.; Macmillan-Lawler, M.; Sullivan, J.

2017-12-01

A large multibeam echo sounder (MBES) dataset (710, 000 km2, inclusive of transit data) was acquired in the SE Indian Ocean to assist the search for Malaysia Airlines Flight 370 (MH370). Here, we present the results of a geomorphic analysis of this new data and compare with the Global Seafloor Geomorphic Features Map (GSFM) that is based on coarser resolution satellite-derived bathymetry data. The analyses show that abyssal plains and basins are significantly more rugged than their representation in the GSFM, with a 20% increase in the extent of hills and mountains. The new model also reveals four times more seamounts than presented in the GSFM, suggesting a greater number of these features than previously estimated for the broader region and indeed globally. This is important considering the potential ecological significance of these high-relief structures. Analyses of the new data also enabled knolls, fans, valleys, canyons, troughs and holes to be identified, doubling the number of discrete features mapped and revealing the true geodiversity of the deep ocean in this area. This high-resolution mapping of the seafloor also provides new insights into the geological evolution of the region, both in terms of structural, tectonic, and sedimentary processes. For example, sub-parallel ridges extend over approximately 20% of the area mapped and their form and alignment provide valuable insight into Southeast Indian Ridge seafloor spreading processes. Rifting is recorded along the Broken Ridge - Diamantina Escarpment, with rift blocks and well-bedded sedimentary bedrock exposures discernible down to 2,400 m water depth. Ocean floor sedimentary processes are represented in sediment mass transport features, especially along and north of Broken Ridge, and pockmarks (the finest-scale features mapped) south of Diamantina Trench. The new MBES data highlight the complexity of the search area and serve to demonstrate how little we know about the 85-90% of the ocean floor that has not been mapped with this technology. The availability of high-resolution and accurate maps of the ocean floor can clearly provide new insights into the Earth's geological evolution, modern ocean floor processes, and the location of sites that are likely to have relatively high biodiversity.

Landsat Time-Series Analysis Opens New Approaches for Regional Glacier Mapping

NASA Astrophysics Data System (ADS)

Winsvold, S. H.; Kääb, A.; Nuth, C.; Altena, B.

2016-12-01

The archive of Landsat satellite scenes is important for mapping of glaciers, especially as it represents the longest running and continuous satellite record of sufficient resolution to track glacier changes over time. Contributing optical sensors newly launched (Landsat 8 and Sentinel-2A) or upcoming in the near future (Sentinel-2B), will promote very high temporal resolution of optical satellite images especially in high-latitude regions. Because of the potential that lies within such near-future dense time series, methods for mapping glaciers from space should be revisited. We present application scenarios that utilize and explore dense time series of optical data for automatic mapping of glacier outlines and glacier facies. Throughout the season, glaciers display a temporal sequence of properties in optical reflection as the seasonal snow melts away, and glacier ice appears in the ablation area and firn in the accumulation area. In one application scenario presented we simulated potential future seasonal resolution using several years of Landsat 5TM/7ETM+ data, and found a sinusoidal evolution of the spectral reflectance for on-glacier pixels throughout a year. We believe this is because of the short wave infrared band and its sensitivity to snow grain size. The parameters retrieved from the fitting sinus curve can be used for glacier mapping purposes, thus we also found similar results using e.g. the mean of summer band ratio images. In individual optical mapping scenes, conditions will vary (e.g., snow, ice, and clouds) and will not be equally optimal over the entire scene. Using robust statistics on stacked pixels reveals a potential for synthesizing optimal mapping scenes from a temporal stack, as we present in a further application scenario. The dense time series available from satellite imagery will also promote multi-temporal and multi-sensor based analyses. The seasonal pattern of snow and ice on a glacier seen in the optical time series can in the summer season also be observed using radar backscatter series. Optical sensors reveal the reflective properties at the surface, while radar sensors may penetrate the surface revealing properties from a certain volume.In an outlook to this contribution we have explored how we can combine information from SAR and optical sensor systems for different purposes.

Single cell versus large population analysis: cell variability in elemental intracellular concentration and distribution.

PubMed

Malucelli, Emil; Procopio, Alessandra; Fratini, Michela; Gianoncelli, Alessandra; Notargiacomo, Andrea; Merolle, Lucia; Sargenti, Azzurra; Castiglioni, Sara; Cappadone, Concettina; Farruggia, Giovanna; Lombardo, Marco; Lagomarsino, Stefano; Maier, Jeanette A; Iotti, Stefano

2018-01-01

The quantification of elemental concentration in cells is usually performed by analytical assays on large populations missing peculiar but important rare cells. The present article aims at comparing the elemental quantification in single cells and cell population in three different cell types using a new approach for single cells elemental analysis performed at sub-micrometer scale combining X-ray fluorescence microscopy and atomic force microscopy. The attention is focused on the light element Mg, exploiting the opportunity to compare the single cell quantification to the cell population analysis carried out by a highly Mg-selective fluorescent chemosensor. The results show that the single cell analysis reveals the same Mg differences found in large population of the different cell strains studied. However, in one of the cell strains, single cell analysis reveals two cells with an exceptionally high intracellular Mg content compared with the other cells of the same strain. The single cell analysis allows mapping Mg and other light elements in whole cells at sub-micrometer scale. A detailed intensity correlation analysis on the two cells with the highest Mg content reveals that Mg subcellular localization correlates with oxygen in a different fashion with respect the other sister cells of the same strain. Graphical abstract Single cells or large population analysis this is the question!

Effect of starter cultures and packaging methods on amino acid profile and eating quality characteristics of pork ham.

PubMed

Gogoi, Protiva; Borpuzari, R N; Borpuzari, T; Hazarika, R A; Bora, J R

2015-08-01

Wet cured pork hams were inoculated with a mixed starter cultures comprising of Lactobacillus acidophilus and Micrococcus varians M483 at the dose level of 106 cfu/g and the un inoculated hams served as controls. The amino acid profile of hams of the treated and the control groups stored at 4oC under MAP and VP and evaluated on 60th day of storage revealed that treated hams liberated higher concentration of free amino acids except for proline and methionine which were found in higher concentration (P < 0.01) in the MAP control samples. The MAP control samples liberated glutamic acid (85.65 ± 1.40 ppm), cystine (21.56 ± 1.14 ppm) and tyrosine (16.63 ± 1.94 ppm) whereas, the treated samples did not release these amino acids. The VP control samples too liberated cystine (6.98 ± 1.36 ppm) and arginine (42.70 ± 2.78 ppm) but the treated ham of the VP did not liberate these amino acids. The VP hams had higher concentration (P < 0.01) of free proline, glycine, alanine, valine, methionine, isoleucine, phenylalanine, lysine and histidine than the MAP samples. Colour analysis of ham using CIE Lab colour system revealed that the treated samples had significantly higher concentrations of L*, a* and b* components. The L* and a* values were higher in the MAP than under VP systems while the b* values were higher in the VP samples than the MAP samples. Neither the bacterial cultures nor the packaging system influenced the textural property of ham. Starter cultures inoculated hams were rated superior (P < 0.05) in terms of their sensory properties. Hams packaged under MAP were rated superior (P < 0.05) than those packaged under VP in terms of appearance, colour, taste, tenderness, flavour, juiciness and overall acceptability.

Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers.

PubMed

Berdugo-Cely, Jhon; Valbuena, Raúl Iván; Sánchez-Betancourt, Erika; Barrero, Luz Stella; Yockteng, Roxana

2017-01-01

The potato (Solanum tuberosum L.) is the fourth most important crop food in the world and Colombia has one of the most important collections of potato germplasm in the world (the Colombian Central Collection-CCC). Little is known about its potential as a source of genetic diversity for molecular breeding programs. In this study, we analyzed 809 Andigenum group accessions from the CCC using 5968 SNPs to determine: 1) the genetic diversity and population structure of the Andigenum germplasm and 2) the usefulness of this collection to map qualitative traits across the potato genome. The genetic structure analysis based on principal components, cluster analyses, and Bayesian inference revealed that the CCC can be subdivided into two main groups associated with their ploidy level: Phureja (diploid) and Andigena (tetraploid). The Andigena population was more genetically diverse but less genetically substructured than the Phureja population (three vs. five subpopulations, respectively). The association mapping analysis of qualitative morphological data using 4666 SNPs showed 23 markers significantly associated with nine morphological traits. The present study showed that the CCC is a highly diverse germplasm collection genetically and phenotypically, useful to implement association mapping in order to identify genes related to traits of interest and to assist future potato genetic breeding programs.

Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers

PubMed Central

Berdugo-Cely, Jhon; Valbuena, Raúl Iván; Sánchez-Betancourt, Erika; Barrero, Luz Stella

2017-01-01

The potato (Solanum tuberosum L.) is the fourth most important crop food in the world and Colombia has one of the most important collections of potato germplasm in the world (the Colombian Central Collection-CCC). Little is known about its potential as a source of genetic diversity for molecular breeding programs. In this study, we analyzed 809 Andigenum group accessions from the CCC using 5968 SNPs to determine: 1) the genetic diversity and population structure of the Andigenum germplasm and 2) the usefulness of this collection to map qualitative traits across the potato genome. The genetic structure analysis based on principal components, cluster analyses, and Bayesian inference revealed that the CCC can be subdivided into two main groups associated with their ploidy level: Phureja (diploid) and Andigena (tetraploid). The Andigena population was more genetically diverse but less genetically substructured than the Phureja population (three vs. five subpopulations, respectively). The association mapping analysis of qualitative morphological data using 4666 SNPs showed 23 markers significantly associated with nine morphological traits. The present study showed that the CCC is a highly diverse germplasm collection genetically and phenotypically, useful to implement association mapping in order to identify genes related to traits of interest and to assist future potato genetic breeding programs. PMID:28257509

A comprehensive whole-genome integrated cytogenetic map for the alpaca (Lama pacos).

PubMed

Avila, Felipe; Baily, Malorie P; Perelman, Polina; Das, Pranab J; Pontius, Joan; Chowdhary, Renuka; Owens, Elaine; Johnson, Warren E; Merriwether, David A; Raudsepp, Terje

2014-01-01

Genome analysis of the alpaca (Lama pacos, LPA) has progressed slowly compared to other domestic species. Here, we report the development of the first comprehensive whole-genome integrated cytogenetic map for the alpaca using fluorescence in situ hybridization (FISH) and CHORI-246 BAC library clones. The map is comprised of 230 linearly ordered markers distributed among all 36 alpaca autosomes and the sex chromosomes. For the first time, markers were assigned to LPA14, 21, 22, 28, and 36. Additionally, 86 genes from 15 alpaca chromosomes were mapped in the dromedary camel (Camelus dromedarius, CDR), demonstrating exceptional synteny and linkage conservation between the 2 camelid genomes. Cytogenetic mapping of 191 protein-coding genes improved and refined the known Zoo-FISH homologies between camelids and humans: we discovered new homologous synteny blocks (HSBs) corresponding to HSA1-LPA/CDR11, HSA4-LPA/CDR31 and HSA7-LPA/CDR36, and revised the location of breakpoints for others. Overall, gene mapping was in good agreement with the Zoo-FISH and revealed remarkable evolutionary conservation of gene order within many human-camelid HSBs. Most importantly, 91 FISH-mapped markers effectively integrated the alpaca whole-genome sequence and the radiation hybrid maps with physical chromosomes, thus facilitating the improvement of the sequence assembly and the discovery of genes of biological importance. © 2015 S. Karger AG, Basel.

Global Genomic Diversity of Oryza sativa Varieties Revealed by Comparative Physical Mapping

PubMed Central

Wang, Xiaoming; Kudrna, David A.; Pan, Yonglong; Wang, Hao; Liu, Lin; Lin, Haiyan; Zhang, Jianwei; Song, Xiang; Goicoechea, Jose Luis; Wing, Rod A.; Zhang, Qifa; Luo, Meizhong

2014-01-01

Bacterial artificial chromosome (BAC) physical maps embedding a large number of BAC end sequences (BESs) were generated for Oryza sativa ssp. indica varieties Minghui 63 (MH63) and Zhenshan 97 (ZS97) and were compared with the genome sequences of O. sativa spp. japonica cv. Nipponbare and O. sativa ssp. indica cv. 93-11. The comparisons exhibited substantial diversities in terms of large structural variations and small substitutions and indels. Genome-wide BAC-sized and contig-sized structural variations were detected, and the shared variations were analyzed. In the expansion regions of the Nipponbare reference sequence, in comparison to the MH63 and ZS97 physical maps, as well as to the previously constructed 93-11 physical map, the amounts and types of the repeat contents, and the outputs of gene ontology analysis, were significantly different from those of the whole genome. Using the physical maps of four wild Oryza species from OMAP (http://www.omap.org) as a control, we detected many conserved and divergent regions related to the evolution process of O. sativa. Between the BESs of MH63 and ZS97 and the two reference sequences, a total of 1532 polymorphic simple sequence repeats (SSRs), 71,383 SNPs, 1767 multiple nucleotide polymorphisms, 6340 insertions, and 9137 deletions were identified. This study provides independent whole-genome resources for intra- and intersubspecies comparisons and functional genomics studies in O. sativa. Both the comparative physical maps and the GBrowse, which integrated the QTL and molecular markers from GRAMENE (http://www.gramene.org) with our physical maps and analysis results, are open to the public through our Web site (http://gresource.hzau.edu.cn/resource/resource.html). PMID:24424778

The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis.

PubMed

Derakhshani, Hooman; De Buck, Jeroen; Mortier, Rienske; Barkema, Herman W; Krause, Denis O; Khafipour, Ehsan

2016-01-01

Current diagnostic tests for Johne's disease (JD), a chronic granulomatous inflammation of the gastrointestinal tract of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP), lack the sensitivity to identify infected animals at early (asymptomatic) stages of the disease. The objective was to determine the pattern of MAP-associated dysbiosis of intestinal microbiota as a potential biomarker for early detection of infected cattle. To that end, genomic DNA was extracted from ileal mucosa and fecal samples collected from 28 MAP-positive and five control calves. High-throughput Illumina sequencing of the V4 hypervariable region of the 16S rRNA gene was used for community profiling of ileal mucosa-associated (MAM) or fecal microbiota. The PERMANOVA analysis of unweighted UniFrac distances revealed distinct clustering of ileal MAM (P = 0.049) and fecal microbiota (P = 0.068) in MAP-infected vs. control cattle. Microbiota profile of MAP-infected animals was further investigated by linear discriminant analysis effective size (LEfSe); several bacterial taxa within the phylum Proteobacteria were overrepresented in ileal MAM of control calves. Moreover, based on reconstructed metagenomes (PICRUSt) of ileal MAM, functional pathways associated with MAP infection were inferred. Enrichment of lysine and histidine metabolism pathways, and underrepresentation of glutathione metabolism and leucine and isoleucine degradation pathways in MAP-infected calves suggested potential contributions of ileal MAM in development of intestinal inflammation. Finally, simultaneous overrepresentation of families Planococcaceae and Paraprevotellaceae, as well as underrepresentation of genera Faecalibacterium and Akkermansia in the fecal microbiota of infected cattle, served as potential biomarker for identifying infected cattle during subclinical stages of JD. Collectively, based on compositional and functional shifts in intestinal microbiota of infected cattle, we inferred that this dynamic network of microorganisms had an active role in intestinal homeostasis.

Locally advanced rectal cancer: post-chemoradiotherapy ADC histogram analysis for predicting a complete response.

PubMed

Cho, Seung Hyun; Kim, Gab Chul; Jang, Yun-Jin; Ryeom, Hunkyu; Kim, Hye Jung; Shin, Kyung-Min; Park, Jun Seok; Choi, Gyu-Seog; Kim, See Hyung

2015-09-01

The value of diffusion-weighted imaging (DWI) for reliable differentiation between pathologic complete response (pCR) and residual tumor is still unclear. Recently, a few studies reported that histogram analysis can be helpful to monitor the therapeutic response in various cancer research. To investigate whether post-chemoradiotherapy (CRT) apparent diffusion coefficient (ADC) histogram analysis can be helpful to predict a pCR in locally advanced rectal cancer (LARC). Fifty patients who underwent preoperative CRT followed by surgery were enrolled in this retrospective study, non-pCR (n = 41) and pCR (n = 9), respectively. ADC histogram analysis encompassing the whole tumor was performed on two post-CRT ADC600 and ADC1000 (b factors 0, 600 vs. 0, 1000 s/mm(2)) maps. Mean, minimum, maximum, SD, mode, 10th, 25th, 50th, 75th, 90th percentile ADCs, skewness, and kurtosis were derived. Diagnostic performance for predicting pCR was evaluated and compared. On both maps, 10th and 25th ADCs showed better diagnostic performance than that using mean ADC. Tenth percentile ADCs revealed the best diagnostic performance on both ADC600 (AZ 0.841, sensitivity 100%, specificity 70.7%) and ADC1000 (AZ 0.821, sensitivity 77.8%, specificity 87.8%) maps. In comparison between 10th percentile and mean ADC, the specificity was significantly improved on both ADC600 (70.7% vs. 53.7%; P = 0.031) and ADC1000 (87.8% vs. 73.2%; P = 0.039) maps. Post-CRT ADC histogram analysis is helpful for predicting pCR in LARC, especially, in improving the specificity, compared with mean ADC. © The Foundation Acta Radiologica 2014.

The use of error-category mapping in pharmacokinetic model analysis of dynamic contrast-enhanced MRI data.

PubMed

Gill, Andrew B; Anandappa, Gayathri; Patterson, Andrew J; Priest, Andrew N; Graves, Martin J; Janowitz, Tobias; Jodrell, Duncan I; Eisen, Tim; Lomas, David J

2015-02-01

This study introduces the use of 'error-category mapping' in the interpretation of pharmacokinetic (PK) model parameter results derived from dynamic contrast-enhanced (DCE-) MRI data. Eleven patients with metastatic renal cell carcinoma were enrolled in a multiparametric study of the treatment effects of bevacizumab. For the purposes of the present analysis, DCE-MRI data from two identical pre-treatment examinations were analysed by application of the extended Tofts model (eTM), using in turn a model arterial input function (AIF), an individually-measured AIF and a sample-average AIF. PK model parameter maps were calculated. Errors in the signal-to-gadolinium concentration ([Gd]) conversion process and the model-fitting process itself were assigned to category codes on a voxel-by-voxel basis, thereby forming a colour-coded 'error-category map' for each imaged slice. These maps were found to be repeatable between patient visits and showed that the eTM converged adequately in the majority of voxels in all the tumours studied. However, the maps also clearly indicated sub-regions of low Gd uptake and of non-convergence of the model in nearly all tumours. The non-physical condition ve ≥ 1 was the most frequently indicated error category and appeared sensitive to the form of AIF used. This simple method for visualisation of errors in DCE-MRI could be used as a routine quality-control technique and also has the potential to reveal otherwise hidden patterns of failure in PK model applications. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Mapping causal functional contributions derived from the clinical assessment of brain damage after stroke

PubMed Central

Zavaglia, Melissa; Forkert, Nils D.; Cheng, Bastian; Gerloff, Christian; Thomalla, Götz; Hilgetag, Claus C.

2015-01-01

Lesion analysis reveals causal contributions of brain regions to mental functions, aiding the understanding of normal brain function as well as rehabilitation of brain-damaged patients. We applied a novel lesion inference technique based on game theory, Multi-perturbation Shapley value Analysis (MSA), to a large clinical lesion dataset. We used MSA to analyze the lesion patterns of 148 acute stroke patients together with their neurological deficits, as assessed by the National Institutes of Health Stroke Scale (NIHSS). The results revealed regional functional contributions to essential behavioral and cognitive functions as reflected in the NIHSS, particularly by subcortical structures. There were also side specific differences of functional contributions between the right and left hemispheric brain regions which may reflect the dominance of the left hemispheric syndrome aphasia in the NIHSS. Comparison of MSA to established lesion inference methods demonstrated the feasibility of the approach for analyzing clinical data and indicated its capability for objectively inferring functional contributions from multiple injured, potentially interacting sites, at the cost of having to predict the outcome of unknown lesion configurations. The analysis of regional functional contributions to neurological symptoms measured by the NIHSS contributes to the interpretation of this widely used standardized stroke scale in clinical practice as well as clinical trials and provides a first approximation of a ‘map of stroke’. PMID:26448908

Mapping causal functional contributions derived from the clinical assessment of brain damage after stroke.

PubMed

Zavaglia, Melissa; Forkert, Nils D; Cheng, Bastian; Gerloff, Christian; Thomalla, Götz; Hilgetag, Claus C

2015-01-01

Lesion analysis reveals causal contributions of brain regions to mental functions, aiding the understanding of normal brain function as well as rehabilitation of brain-damaged patients. We applied a novel lesion inference technique based on game theory, Multi-perturbation Shapley value Analysis (MSA), to a large clinical lesion dataset. We used MSA to analyze the lesion patterns of 148 acute stroke patients together with their neurological deficits, as assessed by the National Institutes of Health Stroke Scale (NIHSS). The results revealed regional functional contributions to essential behavioral and cognitive functions as reflected in the NIHSS, particularly by subcortical structures. There were also side specific differences of functional contributions between the right and left hemispheric brain regions which may reflect the dominance of the left hemispheric syndrome aphasia in the NIHSS. Comparison of MSA to established lesion inference methods demonstrated the feasibility of the approach for analyzing clinical data and indicated its capability for objectively inferring functional contributions from multiple injured, potentially interacting sites, at the cost of having to predict the outcome of unknown lesion configurations. The analysis of regional functional contributions to neurological symptoms measured by the NIHSS contributes to the interpretation of this widely used standardized stroke scale in clinical practice as well as clinical trials and provides a first approximation of a 'map of stroke'.

Genetic mapping of variation in dauer larvae development in growing populations of Caenorhabditis elegans.

PubMed

Green, J W M; Snoek, L B; Kammenga, J E; Harvey, S C

2013-10-01

In the nematode Caenorhabditis elegans, the appropriate induction of dauer larvae development within growing populations is likely to be a primary determinant of genotypic fitness. The underlying genetic architecture of natural genetic variation in dauer formation has, however, not been thoroughly investigated. Here, we report extensive natural genetic variation in dauer larvae development within growing populations across multiple wild isolates. Moreover, bin mapping of introgression lines (ILs) derived from the genetically divergent isolates N2 and CB4856 reveals 10 quantitative trait loci (QTLs) affecting dauer formation. Comparison of individual ILs to N2 identifies an additional eight QTLs, and sequential IL analysis reveals six more QTLs. Our results also show that a behavioural, laboratory-derived, mutation controlled by the neuropeptide Y receptor homolog npr-1 can affect dauer larvae development in growing populations. These findings illustrate the complex genetic architecture of variation in dauer larvae formation in C. elegans and may help to understand how the control of variation in dauer larvae development has evolved.

The Arnol'd cat: Failure of the correspondence principle

NASA Astrophysics Data System (ADS)

Ford, Joseph; Mantica, Giorgio; Ristow, Gerald H.

1991-07-01

The classical Hamiltonian H = p2/2 m + ɛ( q2/2) Σδ[ s-( t/ T)] has an integrable mapping of the plane, [ qn+1 , pn+1 ]= [ qn+1 + pn, qn+2 pn], as its equations of motion. But then by introducing periodic boundary conditions via (mod 1) applied to both q and p variables, the equations of motion become the Arnol'd cat map, [ qn+1 , pn+1 ] = [ qn + pn, qn + 2 pn], (mod 1), revealing it to be one of the simplest fully chaotic systems which can be derived from a Hamiltonian and analyzed. Consequently, we here quantize the Arnol'd cat and examine its quantum motion for signs of chaos using algorithmic complexity as the litmus. Our analysis reveals that the quantum cat is not chaotic in the deep quantum domain nor does it become chaotic in the classical limit as required by the correspondence principle. We therefore conclude that the correspondence principle, as defined herein, fails for the quantum Arnol'd cat.

Revealing the velocity structure of the filamentary nebula in NGC 1275 in its entirety

NASA Astrophysics Data System (ADS)

Gendron-Marsolais, M.; Hlavacek-Larrondo, J.; Martin, T. B.; Drissen, L.; McDonald, M.; Fabian, A. C.; Edge, A. C.; Hamer, S. L.; McNamara, B.; Morrison, G.

2018-05-01

We have produced for the first time a detailed velocity map of the giant filamentary nebula surrounding NGC 1275, the Perseus cluster's brightest galaxy, and revealed a previously unknown rich velocity structure across the entire nebula. These new observations were obtained with the optical imaging Fourier transform spectrometer SITELLE at CFHT. With its wide field of view (˜11'×11'), SITELLE is the only integral field unit spectroscopy instrument able to cover the 80 kpc×55 kpc (3.8'×2.6') large nebula in NGC 1275. Our analysis of these observations shows a smooth radial gradient of the [N II]λ6583/Hα line ratio, suggesting a change in the ionization mechanism and source across the nebula. The velocity map shows no visible general trend or rotation, indicating that filaments are not falling uniformly onto the galaxy, nor being uniformly pulled out from it. Comparison between the physical properties of the filaments and Hitomi measurements of the X-ray gas dynamics in Perseus are also explored.

Exploiting Uniformly 13C-Labeled Carbohydrates for Probing Carbohydrate-Protein Interactions by NMR Spectroscopy.

PubMed

Nestor, Gustav; Anderson, Taigh; Oscarson, Stefan; Gronenborn, Angela M

2017-05-03

NMR of a uniformly 13 C-labeled carbohydrate was used to elucidate the atomic details of a sugar-protein complex. The structure of the 13 C-labeled Manα(1-2)Manα(1-2)ManαOMe trisaccharide ligand, when bound to cyanovirin-N (CV-N), was characterized and revealed that in the complex the glycosidic linkage torsion angles between the two reducing-end mannoses are different from the free trisaccharide. Distances within the carbohydrate were employed for conformational analysis, and NOE-based distance mapping between sugar and protein revealed that Manα(1-2)Manα(1-2)ManαOMe is bound more intimately with its two reducing-end mannoses into the domain A binding site of CV-N than with the nonreducing end unit. Taking advantage of the 13 C spectral dispersion of 13 C-labeled carbohydrates in isotope-filtered experiments is a versatile means for a simultaneous mapping of the binding interactions on both, the carbohydrate and the protein.

Seismic zonation of Port-Au-Prince using pixel- and object-based imaging analysis methods on ASTER GDEM

USGS Publications Warehouse

Yong, Alan; Hough, Susan E.; Cox, Brady R.; Rathje, Ellen M.; Bachhuber, Jeff; Dulberg, Ranon; Hulslander, David; Christiansen, Lisa; and Abrams, Michael J.

2011-01-01

We report about a preliminary study to evaluate the use of semi-automated imaging analysis of remotely-sensed DEM and field geophysical measurements to develop a seismic-zonation map of Port-au-Prince, Haiti. For in situ data, VS30 values are derived from the MASW technique deployed in and around the city. For satellite imagery, we use an ASTER GDEM of Hispaniola. We apply both pixel- and object-based imaging methods on the ASTER GDEM to explore local topography (absolute elevation values) and classify terrain types such as mountains, alluvial fans and basins/near-shore regions. We assign NEHRP seismic site class ranges based on available VS30 values. A comparison of results from imagery-based methods to results from traditional geologic-based approaches reveals good overall correspondence. We conclude that image analysis of RS data provides reliable first-order site characterization results in the absence of local data and can be useful to refine detailed site maps with sparse local data.

Mapping of the Gynoecy in Bitter Gourd (Momordica charantia) Using RAD-Seq Analysis

PubMed Central

Matsumura, Hideo; Miyagi, Norimichi; Taniai, Naoki; Fukushima, Mai; Tarora, Kazuhiko; Shudo, Ayano; Urasaki, Naoya

2014-01-01

Momordica charantia is a monoecious plant of the Cucurbitaceae family that has both male and female unisexual flowers. Its unique gynoecious line, OHB61-5, is essential as a maternal parent in the production of F1 cultivars. To identify the DNA markers for this gynoecy, a RAD-seq (restriction-associated DNA tag sequencing) analysis was employed to reveal genome-wide DNA polymorphisms and to genotype the F2 progeny from a cross between OHB61-5 and a monoecious line. Based on a RAD-seq analysis of F2 individuals, a linkage map was constructed using 552 co-dominant markers. In addition, after analyzing the pooled genomic DNA from monoecious or gynoecious F2 plants, several SNP loci that are genetically linked to gynoecy were identified. GTFL-1, the closest SNP locus to the putative gynoecious locus, was converted to a conventional DNA marker using invader assay technology, which is applicable to the marker-assisted selection of gynoecy in M. charantia breeding. PMID:24498029

Lead spatio-temporal pattern identification in urban microenvironments using moss bags and the Kohonen self-organizing maps

NASA Astrophysics Data System (ADS)

Deljanin, Isidora; Antanasijević, Davor; Vuković, Gordana; Urošević, Mira Aničić; Tomašević, Milica; Perić-Grujić, Aleksandra; Ristić, Mirjana

2015-09-01

The first investigation of the use of the Kohonen self-organizing map (SOM) which includes lead concentration and its isotopic composition in moss bags to assess the spatial and temporal patterns of lead in the urban microenvironments is presented in this paper. The moss bags experiment was carried out during 2011 in the city tunnel in Belgrade, as well as in street canyons at different heights (4, 8 and 16 m) and in public garages. The moss bags were exposed for 5 and 10 weeks. The results revealed that the 10 weeks period represents suitable exposure time in screening Pb isotopic composition in active biomonitoring analysis. The obtained results showed that the SOM analysis, by recognizing slight differences among moss samples regarding exposure time, horizontal and vertical spatial distribution, with both, contribution of stable lead isotopes and Pb concentration, could be recommended in biomonitoring analysis of lead distribution in urban microenvironments.

Mapping the Extracellular and Membrane Proteome Associated with the Vasculature and the Stroma in the Embryo*

PubMed Central

Soulet, Fabienne; Kilarski, Witold W.; Roux-Dalvai, Florence; Herbert, John M. J.; Sacewicz, Izabela; Mouton-Barbosa, Emmanuelle; Bicknell, Roy; Lalor, Patricia; Monsarrat, Bernard; Bikfalvi, Andreas

2013-01-01

In order to map the extracellular or membrane proteome associated with the vasculature and the stroma in an embryonic organism in vivo, we developed a biotinylation technique for chicken embryo and combined it with mass spectrometry and bioinformatic analysis. We also applied this procedure to implanted tumors growing on the chorioallantoic membrane or after the induction of granulation tissue. Membrane and extracellular matrix proteins were the most abundant components identified. Relative quantitative analysis revealed differential protein expression patterns in several tissues. Through a bioinformatic approach, we determined endothelial cell protein expression signatures, which allowed us to identify several proteins not yet reported to be associated with endothelial cells or the vasculature. This is the first study reported so far that applies in vivo biotinylation, in combination with robust label-free quantitative proteomics approaches and bioinformatic analysis, to an embryonic organism. It also provides the first description of the vascular and matrix proteome of the embryo that might constitute the starting point for further developments. PMID:23674615

Experimental and Automated Analysis Techniques for High-resolution Electrical Mapping of Small Intestine Slow Wave Activity

PubMed Central

Angeli, Timothy R; O'Grady, Gregory; Paskaranandavadivel, Niranchan; Erickson, Jonathan C; Du, Peng; Pullan, Andrew J; Bissett, Ian P

2013-01-01

Background/Aims Small intestine motility is governed by an electrical slow wave activity, and abnormal slow wave events have been associated with intestinal dysmotility. High-resolution (HR) techniques are necessary to analyze slow wave propagation, but progress has been limited by few available electrode options and laborious manual analysis. This study presents novel methods for in vivo HR mapping of small intestine slow wave activity. Methods Recordings were obtained from along the porcine small intestine using flexible printed circuit board arrays (256 electrodes; 4 mm spacing). Filtering options were compared, and analysis was automated through adaptations of the falling-edge variable-threshold (FEVT) algorithm and graphical visualization tools. Results A Savitzky-Golay filter was chosen with polynomial-order 9 and window size 1.7 seconds, which maintained 94% of slow wave amplitude, 57% of gradient and achieved a noise correction ratio of 0.083. Optimized FEVT parameters achieved 87% sensitivity and 90% positive-predictive value. Automated activation mapping and animation successfully revealed slow wave propagation patterns, and frequency, velocity, and amplitude were calculated and compared at 5 locations along the intestine (16.4 ± 0.3 cpm, 13.4 ± 1.7 mm/sec, and 43 ± 6 µV, respectively, in the proximal jejunum). Conclusions The methods developed and validated here will greatly assist small intestine HR mapping, and will enable experimental and translational work to evaluate small intestine motility in health and disease. PMID:23667749

A topographical map approach to representing treatment efficacy: a focus on positive psychology interventions.

PubMed

Gorlin, Eugenia I; Lee, Josephine; Otto, Michael W

2018-01-01

A recent meta-analysis by Bolier et al. indicated that positive psychology interventions have overall small to moderate effects on well-being, but results were quite heterogeneous across intervention trials. Such meta-analytic research helps condense information on the efficacy of a broad psychosocial intervention by averaging across many effects; however, such global averages may provide limited navigational guidance for selecting among specific interventions. Here, we introduce a novel method for displaying qualitative and quantitative information on the efficacy of interventions using a topographical map approach. As an initial prototype for demonstrating this method, we mapped 50 positive psychology interventions targeting well-being (as captured in the Bolier et al. [2013] meta-analysis, [Bolier, L., Haverman, M., Westerhof, G. J., Riper, H., Smit, F., & Bohlmeijer, E. (2013). Positive psychology interventions: A meta-analysis of randomized controlled studies. BMC Public Health, 13, 83]). Each intervention domain/subdomain was mapped according to its average effect size (indexed by vertical elevation), number of studies providing effect sizes (indexed by horizontal area), and therapist/client burden (indexed by shading). The geographical placement of intervention domains/subdomains was determined by their conceptual proximity, allowing viewers to gauge the general conceptual "direction" in which promising intervention effects can be found. The resulting graphical displays revealed several prominent features of the well-being intervention "landscape," such as more strongly and uniformly positive effects of future-focused interventions (including, goal-pursuit and optimism training) compared to past/present-focused ones.

Causality analysis of leading singular value decomposition modes identifies rotor as the dominant driving normal mode in fibrillation

NASA Astrophysics Data System (ADS)

Biton, Yaacov; Rabinovitch, Avinoam; Braunstein, Doron; Aviram, Ira; Campbell, Katherine; Mironov, Sergey; Herron, Todd; Jalife, José; Berenfeld, Omer

2018-01-01

Cardiac fibrillation is a major clinical and societal burden. Rotors may drive fibrillation in many cases, but their role and patterns are often masked by complex propagation. We used Singular Value Decomposition (SVD), which ranks patterns of activation hierarchically, together with Wiener-Granger causality analysis (WGCA), which analyses direction of information among observations, to investigate the role of rotors in cardiac fibrillation. We hypothesized that combining SVD analysis with WGCA should reveal whether rotor activity is the dominant driving force of fibrillation even in cases of high complexity. Optical mapping experiments were conducted in neonatal rat cardiomyocyte monolayers (diameter, 35 mm), which were genetically modified to overexpress the delayed rectifier K+ channel IKr only in one half of the monolayer. Such monolayers have been shown previously to sustain fast rotors confined to the IKr overexpressing half and driving fibrillatory-like activity in the other half. SVD analysis of the optical mapping movies revealed a hierarchical pattern in which the primary modes corresponded to rotor activity in the IKr overexpressing region and the secondary modes corresponded to fibrillatory activity elsewhere. We then applied WGCA to evaluate the directionality of influence between modes in the entire monolayer using clear and noisy movies of activity. We demonstrated that the rotor modes influence the secondary fibrillatory modes, but influence was detected also in the opposite direction. To more specifically delineate the role of the rotor in fibrillation, we decomposed separately the respective SVD modes of the rotor and fibrillatory domains. In this case, WGCA yielded more information from the rotor to the fibrillatory domains than in the opposite direction. In conclusion, SVD analysis reveals that rotors can be the dominant modes of an experimental model of fibrillation. Wiener-Granger causality on modes of the rotor domains confirms their preferential driving influence on fibrillatory modes.

A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

PubMed Central

2013-01-01

Background As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physical map of chromosome 3B. Here, we present improved strategies for the construction of highly integrated and ordered wheat physical maps, using chromosome 1BL as a template, and illustrate their potential for evolutionary studies and map-based cloning. Results Using a combination of novel high throughput marker assays and an assembly program, we developed a high quality physical map representing 93% of wheat chromosome 1BL, anchored and ordered with 5,489 markers including 1,161 genes. Analysis of the gene space organization and evolution revealed that gene distribution and conservation along the chromosome results from the superimposition of the ancestral grass and recent wheat evolutionary patterns, leading to a peak of synteny in the central part of the chromosome arm and an increased density of non-collinear genes towards the telomere. With a density of about 11 markers per Mb, the 1BL physical map provides 916 markers, including 193 genes, for fine mapping the 40 QTLs mapped on this chromosome. Conclusions Here, we demonstrate that high marker density physical maps can be developed in complex genomes such as wheat to accelerate map-based cloning, gain new insights into genome evolution, and provide a foundation for reference sequencing. PMID:23800011

GIS methodology for geothermal play fairway analysis: Example from the Snake River Plain volcanic province

USGS Publications Warehouse

DeAngelo, Jacob; Shervais, John W.; Glen, Jonathan; Nielson, Dennis L.; Garg, Sabodh; Dobson, Patrick; Gasperikova, Erika; Sonnenthal, Eric; Visser, Charles; Liberty, Lee M.; Siler, Drew; Evans, James P.; Santellanes, Sean

2016-01-01

Play fairway analysis in geothermal exploration derives from a systematic methodology originally developed within the petroleum industry and is based on a geologic and hydrologic framework of identified geothermal systems. We are tailoring this methodology to study the geothermal resource potential of the Snake River Plain and surrounding region. This project has contributed to the success of this approach by cataloging the critical elements controlling exploitable hydrothermal systems, establishing risk matrices that evaluate these elements in terms of both probability of success and level of knowledge, and building automated tools to process results. ArcGIS was used to compile a range of different data types, which we refer to as ‘elements’ (e.g., faults, vents, heatflow…), with distinct characteristics and confidence values. Raw data for each element were transformed into data layers with a common format. Because different data types have different uncertainties, each evidence layer had an accompanying confidence layer, which reflects spatial variations in these uncertainties. Risk maps represent the product of evidence and confidence layers, and are the basic building blocks used to construct Common Risk Segment (CRS) maps for heat, permeability, and seal. CRS maps quantify the variable risk associated with each of these critical components. In a final step, the three CRS maps were combined into a Composite Common Risk Segment (CCRS) map for analysis that reveals favorable areas for geothermal exploration. Python scripts were developed to automate data processing and to enhance the flexibility of the data analysis. Python scripting provided the structure that makes a custom workflow possible. Nearly every tool available in the ArcGIS ArcToolbox can be executed using commands in the Python programming language. This enabled the construction of a group of tools that could automate most of the processing for the project. Currently, our tools are repeatable, scalable, modifiable, and transferrable, allowing us to automate the task of data analysis and the production of CRS and CCRS maps. Our ultimate goal is to produce a toolkit that can be imported into ArcGIS and applied to any geothermal play type, with fully tunable parameters that will allow for the production of multiple versions of the CRS and CCRS maps in order to better test for sensitivity and to validate results.

Diagnostic classification of macular ganglion cell and retinal nerve fiber layer analysis: differentiation of false-positives from glaucoma.

PubMed

Kim, Ko Eun; Jeoung, Jin Wook; Park, Ki Ho; Kim, Dong Myung; Kim, Seok Hwan

2015-03-01

To investigate the rate and associated factors of false-positive diagnostic classification of ganglion cell analysis (GCA) and retinal nerve fiber layer (RNFL) maps, and characteristic false-positive patterns on optical coherence tomography (OCT) deviation maps. Prospective, cross-sectional study. A total of 104 healthy eyes of 104 normal participants. All participants underwent peripapillary and macular spectral-domain (Cirrus-HD, Carl Zeiss Meditec Inc, Dublin, CA) OCT scans. False-positive diagnostic classification was defined as yellow or red color-coded areas for GCA and RNFL maps. Univariate and multivariate logistic regression analyses were used to determine associated factors. Eyes with abnormal OCT deviation maps were categorized on the basis of the shape and location of abnormal color-coded area. Differences in clinical characteristics among the subgroups were compared. (1) The rate and associated factors of false-positive OCT maps; (2) patterns of false-positive, color-coded areas on the GCA deviation map and associated clinical characteristics. Of the 104 healthy eyes, 42 (40.4%) and 32 (30.8%) showed abnormal diagnostic classifications on any of the GCA and RNFL maps, respectively. Multivariate analysis revealed that false-positive GCA diagnostic classification was associated with longer axial length and larger fovea-disc angle, whereas longer axial length and smaller disc area were associated with abnormal RNFL maps. Eyes with abnormal GCA deviation map were categorized as group A (donut-shaped round area around the inner annulus), group B (island-like isolated area), and group C (diffuse, circular area with an irregular inner margin in either). The axial length showed a significant increasing trend from group A to C (P=0.001), and likewise, the refractive error was more myopic in group C than in groups A (P=0.015) and B (P=0.014). Group C had thinner average ganglion cell-inner plexiform layer thickness compared with other groups (group A=B>C, P=0.004). Abnormal OCT diagnostic classification should be interpreted with caution, especially in eyes with long axial lengths, large fovea-disc angles, and small optic discs. Our findings suggest that the characteristic patterns of OCT deviation map can provide useful clues to distinguish glaucomatous changes from false-positive findings. Copyright © 2015 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Submicron-Scale Heterogeneities in Nickel Sorption of Various Cell-Mineral Aggregates Formed by Fe(II)-Oxidizing Bacteria.

PubMed

Schmid, Gregor; Zeitvogel, Fabian; Hao, Likai; Ingino, Pablo; Adaktylou, Irini; Eickhoff, Merle; Obst, Martin

2016-01-05

Fe(II)-oxidizing bacteria form biogenic cell-mineral aggregates (CMAs) composed of microbial cells, extracellular organic compounds, and ferric iron minerals. CMAs are capable of immobilizing large quantities of heavy metals, such as nickel, via sorption processes. CMAs play an important role for the fate of heavy metals in the environment, particularly in systems characterized by elevated concentrations of dissolved metals, such as mine drainage or contaminated sediments. We applied scanning transmission (soft) X-ray microscopy (STXM) spectrotomography for detailed 3D chemical mapping of nickel sorbed to CMAs on the submicron scale. We analyzed different CMAs produced by phototrophic or nitrate-reducing microbial Fe(II) oxidation and, in addition, a twisted stalk structure obtained from an environmental biofilm. Nickel showed a heterogeneous distribution and was found to be preferentially sorbed to biogenically precipitated iron minerals such as Fe(III)-(oxyhydr)oxides and, to a minor extent, associated with organic compounds. Some distinct nickel accumulations were identified on the surfaces of CMAs. Additional information obtained from scatter plots and angular distance maps, showing variations in the nickel-iron and nickel-organic carbon ratios, also revealed a general correlation between nickel and iron. Although a high correlation between nickel and iron was observed in 2D maps, 3D maps revealed this to be partly due to projection artifacts. In summary, by combining different approaches for data analysis, we unambiguously showed the heterogeneous sorption behavior of nickel to CMAs.

Genetic linkage map and QTL identification for adventitious rooting traits in red gum eucalypts.

PubMed

Sumathi, Murugan; Bachpai, Vijaya Kumar Waman; Mayavel, A; Dasgupta, Modhumita Ghosh; Nagarajan, Binai; Rajasugunasekar, D; Sivakumar, Veerasamy; Yasodha, Ramasamy

2018-05-01

The eucalypt species, Eucalyptus tereticornis and Eucalyptus camaldulensis , show tolerance to drought and salinity conditions, respectively, and are widely cultivated in arid and semiarid regions of tropical countries. In this study, genetic linkage map was developed for interspecific cross E. tereticornis  ×  E. camaldulensis using pseudo-testcross strategy with simple sequence repeats (SSRs), intersimple sequence repeats (ISSRs), and sequence-related amplified polymorphism (SRAP) markers. The consensus genetic map comprised totally 283 markers with 84 SSRs, 94 ISSRs, and 105 SRAP markers on 11 linkage groups spanning 1163.4 cM genetic distance. Blasting the SSR sequences against E. grandis sequences allowed an alignment of 64% and the average ratio of genetic-to-physical distance was 1.7 Mbp/cM, which strengths the evidence that high amount of synteny and colinearity exists among eucalypts genome. Blast searches also revealed that 37% of SSRs had homologies with genes, which could potentially be used in the variety of downstream applications including candidate gene polymorphism. Quantitative trait loci (QTL) analysis for adventitious rooting traits revealed six QTL for rooting percent and root length on five chromosomes with interval and composite interval mapping. All the QTL explained 12.0-14.7% of the phenotypic variance, showing the involvement of major effect QTL on adventitious rooting traits. Increasing the density of markers would facilitate the detection of more number of small-effect QTL and also underpinning the genes involved in rooting process.

Multiscale phase mapping of LiFePO4-based electrodes by transmission electron microscopy and electron forward scattering diffraction.

PubMed

Robert, Donatien; Douillard, Thierry; Boulineau, Adrien; Brunetti, Guillaume; Nowakowski, Pawel; Venet, Denis; Bayle-Guillemaud, Pascale; Cayron, Cyril

2013-12-23

LiFePO4 and FePO4 phase distributions of entire cross-sectioned electrodes with various Li content are investigated from nanoscale to mesoscale, by transmission electron microscopy and by the new electron forward scattering diffraction technique. The distributions of the fully delithiated (FePO4) or lithiated particles (LiFePO4) are mapped on large fields of view (>100 × 100 μm(2)). Heterogeneities in thin and thick electrodes are highlighted at different scales. At the nanoscale, the statistical analysis of 64 000 particles unambiguously shows that the small particles delithiate first. At the mesoscale, the phase maps reveal a core-shell mechanism at the scale of the agglomerates with a preferential pathway along the electrode porosities. At larger scale, lithiation occurs in thick electrodes "stratum by stratum" from the surface in contact with electrolyte toward the current collector.

A GIS-BASED MULTI-CRITERIA EVALUATION SYSTEM FOR SELECTION OF LANDFILL SITES: a case study from Abu Dhabi, United Arab Emirates

NASA Astrophysics Data System (ADS)

Issa, S. M.; Shehhi, B. Al

2012-07-01

Landfill sites receive 92% of total annual solid waste produced by municipalities in the emirate of Abu Dhabi. In this study, candidate sites for an appropriate landfill location for the Abu Dhabi municipal area are determined by integrating geographic information systems (GIS) and multi-criteria evaluation (MCE) analysis. To identify appropriate landfill sites, eight input map layers including proximity to urban areas, proximity to wells and water table depth, geology and topography, proximity to touristic and archeological sites, distance from roads network, distance from drainage networks, and land slope are used in constraint mapping. A final map was generated which identified potential areas showing suitability for the location of the landfill site. Results revealed that 30% of the study area was identified as highly suitable, 25% as suitable, and 45% as unsuitable. The selection of the final landfill site, however, requires further field research.

Synchrotron X-ray reciprocal-space mapping, topography and diffraction resolution studies of macromolecular crystal quality.

PubMed

Boggon, T J; Helliwell, J R; Judge, R A; Olczak, A; Siddons, D P; Snell, E H; Stojanoff, V

2000-07-01

A comprehensive study of microgravity and ground-grown chicken egg-white lysozyme crystals is presented using synchrotron X-ray reciprocal-space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed reduced intrinsic mosaicities on average, but no differences in terms of strain over their ground-grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the ground-control case only a small volume of the crystal contributed to the intensity at the diffraction peak. The techniques prove to be highly complementary, with the reciprocal-space mapping providing a quantitative measure of the crystal mosaicity and strain (or variation in lattice spacing) and the topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out at the synchrotron.

Mapping organelle motion reveals a vesicular conveyor belt spatially replenishing secretory vesicles in stimulated chromaffin cells.

PubMed

Maucort, Guillaume; Kasula, Ravikiran; Papadopulos, Andreas; Nieminen, Timo A; Rubinsztein-Dunlop, Halina; Meunier, Frederic A

2014-01-01

How neurosecretory cells spatially adjust their secretory vesicle pools to replenish those that have fused and released their hormonal content is currently unknown. Here we designed a novel set of image analyses to map the probability of tracked organelles undergoing a specific type of movement (free, caged or directed). We then applied our analysis to time-lapse z-stack confocal imaging of secretory vesicles from bovine Chromaffin cells to map the global changes in vesicle motion and directionality occurring upon secretagogue stimulation. We report a defined region abutting the cortical actin network that actively transports secretory vesicles and is dissipated by actin and microtubule depolymerizing drugs. The directionality of this "conveyor belt" towards the cell surface is activated by stimulation. Actin and microtubule networks therefore cooperatively probe the microenvironment to transport secretory vesicles to the periphery, providing a mechanism whereby cells globally adjust their vesicle pools in response to secretagogue stimulation.

Synchrotron X-Ray Reciprocal Space Mapping, Topography and Diffraction Resolution Studies of Macromolecular Crystal Quality

NASA Technical Reports Server (NTRS)

Boggon, T. J.; Helliwell, J. R.; Judge, Russell A.; Siddons, D. P.; Snell, Edward H.; Stojanoff, V.

2000-01-01

A comprehensive study of microgravity and ground grown chicken egg white lysozyme crystals is presented using synchrotron X-ray reciprocal space mapping, topography techniques and diffraction resolution. Microgravity crystals displayed, on average, reduced intrinsic mosaicities but no differences in terms of stress over their earth grown counterparts. Topographic analysis revealed that in the microgravity case the majority of the crystal was contributing to the peak of the reflection at the appropriate Bragg angle. In the earth case at the diffraction peak only a small volume of the crystal contributed to the intensity. The techniques prove to be highly complementary with the reciprocal space mapping providing a quantitative measure of the crystal mosaicity and stress (or variation in lattice spacing) and topography providing a qualitative overall assessment of the crystal in terms of its X-ray diffraction properties. Structural data collection was also carried out both at the synchrotron and in the laboratory.

The synthesis map is a multidimensional educational tool that provides insight into students' mental models and promotes students' synthetic knowledge generation.

PubMed

Ortega, Ryan A; Brame, Cynthia J

2015-01-01

Concept mapping was developed as a method of displaying and organizing hierarchical knowledge structures. Using the new, multidimensional presentation software Prezi, we have developed a new teaching technique designed to engage higher-level skills in the cognitive domain. This tool, synthesis mapping, is a natural evolution of concept mapping, which utilizes embedding to layer information within concepts. Prezi's zooming user interface lets the author of the presentation use both depth as well as distance to show connections between data, ideas, and concepts. Students in the class Biology of Cancer created synthesis maps to illustrate their knowledge of tumorigenesis. Students used multiple organizational schemes to build their maps. We present an analysis of student work, placing special emphasis on organization within student maps and how the organization of knowledge structures in student maps can reveal strengths and weaknesses in student understanding or instruction. We also provide a discussion of best practices for instructors who would like to implement synthesis mapping in their classrooms. © 2015 R. A. Ortega and C. J. Brame et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Quantitative genetic-interaction mapping in mammalian cells

PubMed Central

Roguev, Assen; Talbot, Dale; Negri, Gian Luca; Shales, Michael; Cagney, Gerard; Bandyopadhyay, Sourav; Panning, Barbara; Krogan, Nevan J

2013-01-01

Mapping genetic interactions (GIs) by simultaneously perturbing pairs of genes is a powerful tool for understanding complex biological phenomena. Here we describe an experimental platform for generating quantitative GI maps in mammalian cells using a combinatorial RNA interference strategy. We performed ~11,000 pairwise knockdowns in mouse fibroblasts, focusing on 130 factors involved in chromatin regulation to create a GI map. Comparison of the GI and protein-protein interaction (PPI) data revealed that pairs of genes exhibiting positive GIs and/or similar genetic profiles were predictive of the corresponding proteins being physically associated. The mammalian GI map identified pathways and complexes but also resolved functionally distinct submodules within larger protein complexes. By integrating GI and PPI data, we created a functional map of chromatin complexes in mouse fibroblasts, revealing that the PAF complex is a central player in the mammalian chromatin landscape. PMID:23407553

Functional significance of co-occurring mutations in PIK3CA and MAP3K1 in breast cancer.

PubMed

Avivar-Valderas, Alvaro; McEwen, Robert; Taheri-Ghahfarokhi, Amir; Carnevalli, Larissa S; Hardaker, Elizabeth L; Maresca, Marcello; Hudson, Kevin; Harrington, Elizabeth A; Cruzalegui, Francisco

2018-04-20

The PI3Kα signaling pathway is frequently hyper-activated in breast cancer (BrCa), as a result of mutations/amplifications in oncogenes (e.g. HER2 ), decreased function in tumor suppressors (e.g. PTEN ) or activating mutations in key components of the pathway. In particular, activating mutations of PIK3CA (~45%) are frequently found in luminal A BrCa samples. Genomic studies have uncovered inactivating mutations in MAP3K1 (13-20%) and MAP2K4 (~8%), two upstream kinases of the JNK apoptotic pathway in luminal A BrCa samples. Further, simultaneous mutation of PIK3CA and MAP3K1 are found in ~11% of mutant PIK3CA tumors. How these two alterations may cooperate to elicit tumorigenesis and impact the sensitivity to PI3K and AKT inhibitors is currently unknown. Using CRISPR gene editing we have genetically disrupted MAP3K1 expression in mutant PIK3CA cell lines to specifically create in vitro models reflecting the mutational status of PIK3CA and MAP3K1 in BrCa patients. MAP3K1 deficient cell lines exhibited ~2.4-fold increased proliferation rate and decreased sensitivity to PI3Kα/δ(AZD8835) and AKT (AZD5363) inhibitors (~2.61 and ~5.23-fold IC 50 increases, respectively) compared with parental control cell lines. In addition, mechanistic analysis revealed that MAP3K1 disruption enhances AKT phosphorylation and downstream signaling and reduces sensitivity to AZD5363-mediated pathway inhibition. This appears to be a consequence of deficient MAP3K1-JNK signaling increasing IRS1 stability and therefore promoting IRS1 binding to p85, resulting in enhanced PI3Kα activity. Using 3D-MCF10A-PI3Kα H1047R models, we found that MAP3K1 depletion increased overall acinar volume and counteracted AZD5363-mediated reduction of acinar growth due to enhanced proliferation and reduced apoptosis. Furthermore, in vivo efficacy studies revealed that MAP3K1-deficient MCF7 tumors were less sensitive to AKT inhibitor treatment, compared with parental MCF7 tumors. Our study provides mechanistic and in vivo evidence indicating a role for MAP3K1 as a tumor suppressor gene at least in the context of PIK3CA -mutant backgrounds. Further, our work predicts that MAP3K1 mutational status may be considered as a predictive biomarker for efficacy in PI3K pathway inhibitor trials.

Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

PubMed

Horikoshi, Momoko; Mӓgi, Reedik; van de Bunt, Martijn; Surakka, Ida; Sarin, Antti-Pekka; Mahajan, Anubha; Marullo, Letizia; Thorleifsson, Gudmar; Hӓgg, Sara; Hottenga, Jouke-Jan; Ladenvall, Claes; Ried, Janina S; Winkler, Thomas W; Willems, Sara M; Pervjakova, Natalia; Esko, Tõnu; Beekman, Marian; Nelson, Christopher P; Willenborg, Christina; Wiltshire, Steven; Ferreira, Teresa; Fernandez, Juan; Gaulton, Kyle J; Steinthorsdottir, Valgerdur; Hamsten, Anders; Magnusson, Patrik K E; Willemsen, Gonneke; Milaneschi, Yuri; Robertson, Neil R; Groves, Christopher J; Bennett, Amanda J; Lehtimӓki, Terho; Viikari, Jorma S; Rung, Johan; Lyssenko, Valeriya; Perola, Markus; Heid, Iris M; Herder, Christian; Grallert, Harald; Müller-Nurasyid, Martina; Roden, Michael; Hypponen, Elina; Isaacs, Aaron; van Leeuwen, Elisabeth M; Karssen, Lennart C; Mihailov, Evelin; Houwing-Duistermaat, Jeanine J; de Craen, Anton J M; Deelen, Joris; Havulinna, Aki S; Blades, Matthew; Hengstenberg, Christian; Erdmann, Jeanette; Schunkert, Heribert; Kaprio, Jaakko; Tobin, Martin D; Samani, Nilesh J; Lind, Lars; Salomaa, Veikko; Lindgren, Cecilia M; Slagboom, P Eline; Metspalu, Andres; van Duijn, Cornelia M; Eriksson, Johan G; Peters, Annette; Gieger, Christian; Jula, Antti; Groop, Leif; Raitakari, Olli T; Power, Chris; Penninx, Brenda W J H; de Geus, Eco; Smit, Johannes H; Boomsma, Dorret I; Pedersen, Nancy L; Ingelsson, Erik; Thorsteinsdottir, Unnur; Stefansson, Kari; Ripatti, Samuli; Prokopenko, Inga; McCarthy, Mark I; Morris, Andrew P

2015-07-01

Reference panels from the 1000 Genomes (1000G) Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE) Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS), supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI) at genome-wide significance, and two for fasting glucose (FG), none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3) and FG (GCK and G6PC2). The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated.

Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation

PubMed Central

van de Bunt, Martijn; Surakka, Ida; Sarin, Antti-Pekka; Mahajan, Anubha; Marullo, Letizia; Thorleifsson, Gudmar; Hӓgg, Sara; Hottenga, Jouke-Jan; Ladenvall, Claes; Ried, Janina S.; Winkler, Thomas W.; Willems, Sara M.; Pervjakova, Natalia; Esko, Tõnu; Beekman, Marian; Nelson, Christopher P.; Willenborg, Christina; Ferreira, Teresa; Fernandez, Juan; Gaulton, Kyle J.; Steinthorsdottir, Valgerdur; Hamsten, Anders; Magnusson, Patrik K. E.; Willemsen, Gonneke; Milaneschi, Yuri; Robertson, Neil R.; Groves, Christopher J.; Bennett, Amanda J.; Lehtimӓki, Terho; Viikari, Jorma S.; Rung, Johan; Lyssenko, Valeriya; Perola, Markus; Heid, Iris M.; Herder, Christian; Grallert, Harald; Müller-Nurasyid, Martina; Roden, Michael; Hypponen, Elina; Isaacs, Aaron; van Leeuwen, Elisabeth M.; Karssen, Lennart C.; Mihailov, Evelin; Houwing-Duistermaat, Jeanine J.; de Craen, Anton J. M.; Deelen, Joris; Havulinna, Aki S.; Blades, Matthew; Hengstenberg, Christian; Erdmann, Jeanette; Schunkert, Heribert; Kaprio, Jaakko; Tobin, Martin D.; Samani, Nilesh J.; Lind, Lars; Salomaa, Veikko; Lindgren, Cecilia M.; Slagboom, P. Eline; Metspalu, Andres; van Duijn, Cornelia M.; Eriksson, Johan G.; Peters, Annette; Gieger, Christian; Jula, Antti; Groop, Leif; Raitakari, Olli T.; Power, Chris; Penninx, Brenda W. J. H.; de Geus, Eco; Smit, Johannes H.; Boomsma, Dorret I.; Pedersen, Nancy L.; Ingelsson, Erik; Thorsteinsdottir, Unnur; Stefansson, Kari; Ripatti, Samuli; Prokopenko, Inga; McCarthy, Mark I.; Morris, Andrew P.

2015-01-01

Reference panels from the 1000 Genomes (1000G) Project Consortium provide near complete coverage of common and low-frequency genetic variation with minor allele frequency ≥0.5% across European ancestry populations. Within the European Network for Genetic and Genomic Epidemiology (ENGAGE) Consortium, we have undertaken the first large-scale meta-analysis of genome-wide association studies (GWAS), supplemented by 1000G imputation, for four quantitative glycaemic and obesity-related traits, in up to 87,048 individuals of European ancestry. We identified two loci for body mass index (BMI) at genome-wide significance, and two for fasting glucose (FG), none of which has been previously reported in larger meta-analysis efforts to combine GWAS of European ancestry. Through conditional analysis, we also detected multiple distinct signals of association mapping to established loci for waist-hip ratio adjusted for BMI (RSPO3) and FG (GCK and G6PC2). The index variant for one association signal at the G6PC2 locus is a low-frequency coding allele, H177Y, which has recently been demonstrated to have a functional role in glucose regulation. Fine-mapping analyses revealed that the non-coding variants most likely to drive association signals at established and novel loci were enriched for overlap with enhancer elements, which for FG mapped to promoter and transcription factor binding sites in pancreatic islets, in particular. Our study demonstrates that 1000G imputation and genetic fine-mapping of common and low-frequency variant association signals at GWAS loci, integrated with genomic annotation in relevant tissues, can provide insight into the functional and regulatory mechanisms through which their effects on glycaemic and obesity-related traits are mediated. PMID:26132169

VNTR internal structure mapping at the {alpha}-globin 3{prime}HVR locus reveals a hierachy of related lineages in oceania

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

Martinson, J.J.; Clegg, J.B.; Boyce, A.J.

1994-09-01

Analysis of the {alpha}-globin gene complex in Oceania has revealed many different rearrangements which remove one of the adult globin genes. Frequencies of these deletion chromosomes are elevated by malarial resistance conferred by the resulting {alpha}-thalassaemia. One particular deletion chromosome, designated -{alpha}{sup 3.7}III, is found at high levels in Melanesia and Polynesia: RFLP haplotype analysis shows that this deletion is always found on chromosomes bearing the IIIa haplotype and is likely to be the product of one single rearrangement event. A subset of the -{alpha}{sup 3.7}III chromosomes carries a more recent mutation which generates the haemoglobin variant HbJ{sup Tongariki}. Wemore » have characterized the allelic variation at the 3{prime}HVR VNTR locus located 6 kb from the globin genes in each of these groups of chromosomes. We have determined the internal structure of these alleles by RFLP mapping of PCR-amplified DNA: within each group, the allelic diversity results from the insertion and/or deletion of small {open_quotes}motifs{close_quotes} of up to 6 adjacent repeats. Mapping of 3{prime}HVR alleles associated with other haplotypes reveals that these are composed of repeat arrays that are substantially different to those derived from IIIa chromosomes, indicating that interchromosomal recombination between heterologous haplotypes does not account for any of the diversity seen to date. We have recently shown that allelic size variation at the two VNTR loci flanking the {alpha}-globin complex is very closely linked to the haplotypes known to be present at this locus. Here we show that, within a haplotype, VNTR alleles are very closely related to each other on the basis of internal structure and demonstrate that intrachromosomal mutation processes involving small numbers of tandem repeats are the main cause of variation at this locus.« less

Genome sequence, comparative analysis and haplotype structure of the domestic dog.

PubMed

Lindblad-Toh, Kerstin; Wade, Claire M; Mikkelsen, Tarjei S; Karlsson, Elinor K; Jaffe, David B; Kamal, Michael; Clamp, Michele; Chang, Jean L; Kulbokas, Edward J; Zody, Michael C; Mauceli, Evan; Xie, Xiaohui; Breen, Matthew; Wayne, Robert K; Ostrander, Elaine A; Ponting, Chris P; Galibert, Francis; Smith, Douglas R; DeJong, Pieter J; Kirkness, Ewen; Alvarez, Pablo; Biagi, Tara; Brockman, William; Butler, Jonathan; Chin, Chee-Wye; Cook, April; Cuff, James; Daly, Mark J; DeCaprio, David; Gnerre, Sante; Grabherr, Manfred; Kellis, Manolis; Kleber, Michael; Bardeleben, Carolyne; Goodstadt, Leo; Heger, Andreas; Hitte, Christophe; Kim, Lisa; Koepfli, Klaus-Peter; Parker, Heidi G; Pollinger, John P; Searle, Stephen M J; Sutter, Nathan B; Thomas, Rachael; Webber, Caleb; Baldwin, Jennifer; Abebe, Adal; Abouelleil, Amr; Aftuck, Lynne; Ait-Zahra, Mostafa; Aldredge, Tyler; Allen, Nicole; An, Peter; Anderson, Scott; Antoine, Claudel; Arachchi, Harindra; Aslam, Ali; Ayotte, Laura; Bachantsang, Pasang; Barry, Andrew; Bayul, Tashi; Benamara, Mostafa; Berlin, Aaron; Bessette, Daniel; Blitshteyn, Berta; Bloom, Toby; Blye, Jason; Boguslavskiy, Leonid; Bonnet, Claude; Boukhgalter, Boris; Brown, Adam; Cahill, Patrick; Calixte, Nadia; Camarata, Jody; Cheshatsang, Yama; Chu, Jeffrey; Citroen, Mieke; Collymore, Alville; Cooke, Patrick; Dawoe, Tenzin; Daza, Riza; Decktor, Karin; DeGray, Stuart; Dhargay, Norbu; Dooley, Kimberly; Dooley, Kathleen; Dorje, Passang; Dorjee, Kunsang; Dorris, Lester; Duffey, Noah; Dupes, Alan; Egbiremolen, Osebhajajeme; Elong, Richard; Falk, Jill; Farina, Abderrahim; Faro, Susan; Ferguson, Diallo; Ferreira, Patricia; Fisher, Sheila; FitzGerald, Mike; Foley, Karen; Foley, Chelsea; Franke, Alicia; Friedrich, Dennis; Gage, Diane; Garber, Manuel; Gearin, Gary; Giannoukos, Georgia; Goode, Tina; Goyette, Audra; Graham, Joseph; Grandbois, Edward; Gyaltsen, Kunsang; Hafez, Nabil; Hagopian, Daniel; Hagos, Birhane; Hall, Jennifer; Healy, Claire; Hegarty, Ryan; Honan, Tracey; Horn, Andrea; Houde, Nathan; Hughes, Leanne; Hunnicutt, Leigh; Husby, M; Jester, Benjamin; Jones, Charlien; Kamat, Asha; Kanga, Ben; Kells, Cristyn; Khazanovich, Dmitry; Kieu, Alix Chinh; Kisner, Peter; Kumar, Mayank; Lance, Krista; Landers, Thomas; Lara, Marcia; Lee, William; Leger, Jean-Pierre; Lennon, Niall; Leuper, Lisa; LeVine, Sarah; Liu, Jinlei; Liu, Xiaohong; Lokyitsang, Yeshi; Lokyitsang, Tashi; Lui, Annie; Macdonald, Jan; Major, John; Marabella, Richard; Maru, Kebede; Matthews, Charles; McDonough, Susan; Mehta, Teena; Meldrim, James; Melnikov, Alexandre; Meneus, Louis; Mihalev, Atanas; Mihova, Tanya; Miller, Karen; Mittelman, Rachel; Mlenga, Valentine; Mulrain, Leonidas; Munson, Glen; Navidi, Adam; Naylor, Jerome; Nguyen, Tuyen; Nguyen, Nga; Nguyen, Cindy; Nguyen, Thu; Nicol, Robert; Norbu, Nyima; Norbu, Choe; Novod, Nathaniel; Nyima, Tenchoe; Olandt, Peter; O'Neill, Barry; O'Neill, Keith; Osman, Sahal; Oyono, Lucien; Patti, Christopher; Perrin, Danielle; Phunkhang, Pema; Pierre, Fritz; Priest, Margaret; Rachupka, Anthony; Raghuraman, Sujaa; Rameau, Rayale; Ray, Verneda; Raymond, Christina; Rege, Filip; Rise, Cecil; Rogers, Julie; Rogov, Peter; Sahalie, Julie; Settipalli, Sampath; Sharpe, Theodore; Shea, Terrance; Sheehan, Mechele; Sherpa, Ngawang; Shi, Jianying; Shih, Diana; Sloan, Jessie; Smith, Cherylyn; Sparrow, Todd; Stalker, John; Stange-Thomann, Nicole; Stavropoulos, Sharon; Stone, Catherine; Stone, Sabrina; Sykes, Sean; Tchuinga, Pierre; Tenzing, Pema; Tesfaye, Senait; Thoulutsang, Dawa; Thoulutsang, Yama; Topham, Kerri; Topping, Ira; Tsamla, Tsamla; Vassiliev, Helen; Venkataraman, Vijay; Vo, Andy; Wangchuk, Tsering; Wangdi, Tsering; Weiand, Michael; Wilkinson, Jane; Wilson, Adam; Yadav, Shailendra; Yang, Shuli; Yang, Xiaoping; Young, Geneva; Yu, Qing; Zainoun, Joanne; Zembek, Lisa; Zimmer, Andrew; Lander, Eric S

2005-12-08

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.

A cis-Regulatory Mutation of PDSS2 Causes Silky-Feather in Chickens

PubMed Central

Feng, Chungang; Gao, Yu; Dorshorst, Ben; Song, Chi; Gu, Xiaorong; Li, Qingyuan; Li, Jinxiu; Liu, Tongxin; Rubin, Carl-Johan; Zhao, Yiqiang; Wang, Yanqiang; Fei, Jing; Li, Huifang; Chen, Kuanwei; Qu, Hao; Shu, Dingming; Ashwell, Chris; Da, Yang; Andersson, Leif; Hu, Xiaoxiang; Li, Ning

2014-01-01

Silky-feather has been selected and fixed in some breeds due to its unique appearance. This phenotype is caused by a single recessive gene (hookless, h). Here we map the silky-feather locus to chromosome 3 by linkage analysis and subsequently fine-map it to an 18.9 kb interval using the identical by descent (IBD) method. Further analysis reveals that a C to G transversion located upstream of the prenyl (decaprenyl) diphosphate synthase, subunit 2 (PDSS2) gene is causing silky-feather. All silky-feather birds are homozygous for the G allele. The silky-feather mutation significantly decreases the expression of PDSS2 during feather development in vivo. Consistent with the regulatory effect, the C to G transversion is shown to remarkably reduce PDSS2 promoter activity in vitro. We report a new example of feather structure variation associated with a spontaneous mutation and provide new insight into the PDSS2 function. PMID:25166907

Descriptive Characteristics of Surface Water Quality in Hong Kong by a Self-Organising Map

PubMed Central

An, Yan; Zou, Zhihong; Li, Ranran

2016-01-01

In this study, principal component analysis (PCA) and a self-organising map (SOM) were used to analyse a complex dataset obtained from the river water monitoring stations in the Tolo Harbor and Channel Water Control Zone (Hong Kong), covering the period of 2009–2011. PCA was initially applied to identify the principal components (PCs) among the nonlinear and complex surface water quality parameters. SOM followed PCA, and was implemented to analyze the complex relationships and behaviors of the parameters. The results reveal that PCA reduced the multidimensional parameters to four significant PCs which are combinations of the original ones. The positive and inverse relationships of the parameters were shown explicitly by pattern analysis in the component planes. It was found that PCA and SOM are efficient tools to capture and analyze the behavior of multivariable, complex, and nonlinear related surface water quality data. PMID:26761018

Descriptive Characteristics of Surface Water Quality in Hong Kong by a Self-Organising Map.

PubMed

An, Yan; Zou, Zhihong; Li, Ranran

2016-01-08

In this study, principal component analysis (PCA) and a self-organising map (SOM) were used to analyse a complex dataset obtained from the river water monitoring stations in the Tolo Harbor and Channel Water Control Zone (Hong Kong), covering the period of 2009-2011. PCA was initially applied to identify the principal components (PCs) among the nonlinear and complex surface water quality parameters. SOM followed PCA, and was implemented to analyze the complex relationships and behaviors of the parameters. The results reveal that PCA reduced the multidimensional parameters to four significant PCs which are combinations of the original ones. The positive and inverse relationships of the parameters were shown explicitly by pattern analysis in the component planes. It was found that PCA and SOM are efficient tools to capture and analyze the behavior of multivariable, complex, and nonlinear related surface water quality data.

Morphologic dating of fault scarps using airborne laser swath mapping (ALSM) data

USGS Publications Warehouse

Hilley, G.E.; Delong, S.; Prentice, C.; Blisniuk, K.; Arrowsmith, J.R.

2010-01-01

Models of fault scarp morphology have been previously used to infer the relative age of different fault scarps in a fault zone using labor-intensive ground surveying. We present a method for automatically extracting scarp morphologic ages within high-resolution digital topography. Scarp degradation is modeled as a diffusive mass transport process in the across-scarp direction. The second derivative of the modeled degraded fault scarp was normalized to yield the best-fitting (in a least-squared sense) scarp height at each point, and the signal-to-noise ratio identified those areas containing scarp-like topography. We applied this method to three areas along the San Andreas Fault and found correspondence between the mapped geometry of the fault and that extracted by our analysis. This suggests that the spatial distribution of scarp ages may be revealed by such an analysis, allowing the recent temporal development of a fault zone to be imaged along its length.

Mapping pathological phenotypes in a mouse model of CDKL5 disorder.

PubMed

Amendola, Elena; Zhan, Yang; Mattucci, Camilla; Castroflorio, Enrico; Calcagno, Eleonora; Fuchs, Claudia; Lonetti, Giuseppina; Silingardi, Davide; Vyssotski, Alexei L; Farley, Dominika; Ciani, Elisabetta; Pizzorusso, Tommaso; Giustetto, Maurizio; Gross, Cornelius T

2014-01-01

Mutations in cyclin-dependent kinase-like 5 (CDKL5) cause early-onset epileptic encephalopathy, a neurodevelopmental disorder with similarities to Rett Syndrome. Here we describe the physiological, molecular, and behavioral phenotyping of a Cdkl5 conditional knockout mouse model of CDKL5 disorder. Behavioral analysis of constitutive Cdkl5 knockout mice revealed key features of the human disorder, including limb clasping, hypoactivity, and abnormal eye tracking. Anatomical, physiological, and molecular analysis of the knockout uncovered potential pathological substrates of the disorder, including reduced dendritic arborization of cortical neurons, abnormal electroencephalograph (EEG) responses to convulsant treatment, decreased visual evoked responses (VEPs), and alterations in the Akt/rpS6 signaling pathway. Selective knockout of Cdkl5 in excitatory and inhibitory forebrain neurons allowed us to map the behavioral features of the disorder to separable cell-types. These findings identify physiological and molecular deficits in specific forebrain neuron populations as possible pathological substrates in CDKL5 disorder.

Identification and Molecular Characterization of MYB Transcription Factor Superfamily in C4 Model Plant Foxtail Millet (Setaria italica L.)

PubMed Central

Muthamilarasan, Mehanathan; Khandelwal, Rohit; Yadav, Chandra Bhan; Bonthala, Venkata Suresh; Khan, Yusuf; Prasad, Manoj

2014-01-01

MYB proteins represent one of the largest transcription factor families in plants, playing important roles in diverse developmental and stress-responsive processes. Considering its significance, several genome-wide analyses have been conducted in almost all land plants except foxtail millet. Foxtail millet (Setaria italica L.) is a model crop for investigating systems biology of millets and bioenergy grasses. Further, the crop is also known for its potential abiotic stress-tolerance. In this context, a comprehensive genome-wide survey was conducted and 209 MYB protein-encoding genes were identified in foxtail millet. All 209 S. italica MYB (SiMYB) genes were physically mapped onto nine chromosomes of foxtail millet. Gene duplication study showed that segmental- and tandem-duplication have occurred in genome resulting in expansion of this gene family. The protein domain investigation classified SiMYB proteins into three classes according to number of MYB repeats present. The phylogenetic analysis categorized SiMYBs into ten groups (I - X). SiMYB-based comparative mapping revealed a maximum orthology between foxtail millet and sorghum, followed by maize, rice and Brachypodium. Heat map analysis showed tissue-specific expression pattern of predominant SiMYB genes. Expression profiling of candidate MYB genes against abiotic stresses and hormone treatments using qRT-PCR revealed specific and/or overlapping expression patterns of SiMYBs. Taken together, the present study provides a foundation for evolutionary and functional characterization of MYB TFs in foxtail millet to dissect their functions in response to environmental stimuli. PMID:25279462

A model to locate potential areas for lake sturgeon spawning habitat construction in the St. Clair–Detroit River System

USGS Publications Warehouse

Bennion, David; Manny, Bruce A.

2014-01-01

In response to a need for objective scientific information that could be used to help remediate loss of fish spawning habitat in the St. Clair River and Detroit River International Areas of Concern, this paper summarizes a large-scale geographic mapping investigation. Our study integrates data on two variables that many riverine fishes respond to in selecting where to spawn in these waters (water flow velocity and water depth) with available maps of the St. Clair–Detroit River System (SC–DRS). Our objectives were to locate and map these two physical components of fish habitat in the St. Clair and Detroit rivers and Lake St. Clair using a geographic information system (GIS) and to identify where, theoretically, fish spawning habitat could be remediated in these rivers. The target fish species to which this model applies is lake sturgeon (Acipenser fulvescens), but spawning reefs constructed for lake sturgeon in this system have been used for spawning by 17 species of fish. Our analysis revealed areas in each river that possessed suitable water velocity and depth for fish spawning and therefore could theoretically be remediated by the addition of rock-rubble substrate like that used at two previously remediated sites in the Detroit River at Belle Isle and Fighting Island. Results of our analysis revealed that only 3% of the total area of the SC–DRS possesses the necessary combination of water depth and high flow velocity to be indicated by the model as potential spawning habitat for lake sturgeon.

Genome-wide detection and characterization of positive selection in human populations.

PubMed

Sabeti, Pardis C; Varilly, Patrick; Fry, Ben; Lohmueller, Jason; Hostetter, Elizabeth; Cotsapas, Chris; Xie, Xiaohui; Byrne, Elizabeth H; McCarroll, Steven A; Gaudet, Rachelle; Schaffner, Stephen F; Lander, Eric S; Frazer, Kelly A; Ballinger, Dennis G; Cox, David R; Hinds, David A; Stuve, Laura L; Gibbs, Richard A; Belmont, John W; Boudreau, Andrew; Hardenbol, Paul; Leal, Suzanne M; Pasternak, Shiran; Wheeler, David A; Willis, Thomas D; Yu, Fuli; Yang, Huanming; Zeng, Changqing; Gao, Yang; Hu, Haoran; Hu, Weitao; Li, Chaohua; Lin, Wei; Liu, Siqi; Pan, Hao; Tang, Xiaoli; Wang, Jian; Wang, Wei; Yu, Jun; Zhang, Bo; Zhang, Qingrun; Zhao, Hongbin; Zhao, Hui; Zhou, Jun; Gabriel, Stacey B; Barry, Rachel; Blumenstiel, Brendan; Camargo, Amy; Defelice, Matthew; Faggart, Maura; Goyette, Mary; Gupta, Supriya; Moore, Jamie; Nguyen, Huy; Onofrio, Robert C; Parkin, Melissa; Roy, Jessica; Stahl, Erich; Winchester, Ellen; Ziaugra, Liuda; Altshuler, David; Shen, Yan; Yao, Zhijian; Huang, Wei; Chu, Xun; He, Yungang; Jin, Li; Liu, Yangfan; Shen, Yayun; Sun, Weiwei; Wang, Haifeng; Wang, Yi; Wang, Ying; Xiong, Xiaoyan; Xu, Liang; Waye, Mary M Y; Tsui, Stephen K W; Xue, Hong; Wong, J Tze-Fei; Galver, Luana M; Fan, Jian-Bing; Gunderson, Kevin; Murray, Sarah S; Oliphant, Arnold R; Chee, Mark S; Montpetit, Alexandre; Chagnon, Fanny; Ferretti, Vincent; Leboeuf, Martin; Olivier, Jean-François; Phillips, Michael S; Roumy, Stéphanie; Sallée, Clémentine; Verner, Andrei; Hudson, Thomas J; Kwok, Pui-Yan; Cai, Dongmei; Koboldt, Daniel C; Miller, Raymond D; Pawlikowska, Ludmila; Taillon-Miller, Patricia; Xiao, Ming; Tsui, Lap-Chee; Mak, William; Song, You Qiang; Tam, Paul K H; Nakamura, Yusuke; Kawaguchi, Takahisa; Kitamoto, Takuya; Morizono, Takashi; Nagashima, Atsushi; Ohnishi, Yozo; Sekine, Akihiro; Tanaka, Toshihiro; Tsunoda, Tatsuhiko; Deloukas, Panos; Bird, Christine P; Delgado, Marcos; Dermitzakis, Emmanouil T; Gwilliam, Rhian; Hunt, Sarah; Morrison, Jonathan; Powell, Don; Stranger, Barbara E; Whittaker, Pamela; Bentley, David R; Daly, Mark J; de Bakker, Paul I W; Barrett, Jeff; Chretien, Yves R; Maller, Julian; McCarroll, Steve; Patterson, Nick; Pe'er, Itsik; Price, Alkes; Purcell, Shaun; Richter, Daniel J; Sabeti, Pardis; Saxena, Richa; Schaffner, Stephen F; Sham, Pak C; Varilly, Patrick; Altshuler, David; Stein, Lincoln D; Krishnan, Lalitha; Smith, Albert Vernon; Tello-Ruiz, Marcela K; Thorisson, Gudmundur A; Chakravarti, Aravinda; Chen, Peter E; Cutler, David J; Kashuk, Carl S; Lin, Shin; Abecasis, Gonçalo R; Guan, Weihua; Li, Yun; Munro, Heather M; Qin, Zhaohui Steve; Thomas, Daryl J; McVean, Gilean; Auton, Adam; Bottolo, Leonardo; Cardin, Niall; Eyheramendy, Susana; Freeman, Colin; Marchini, Jonathan; Myers, Simon; Spencer, Chris; Stephens, Matthew; Donnelly, Peter; Cardon, Lon R; Clarke, Geraldine; Evans, David M; Morris, Andrew P; Weir, Bruce S; Tsunoda, Tatsuhiko; Johnson, Todd A; Mullikin, James C; Sherry, Stephen T; Feolo, Michael; Skol, Andrew; Zhang, Houcan; Zeng, Changqing; Zhao, Hui; Matsuda, Ichiro; Fukushima, Yoshimitsu; Macer, Darryl R; Suda, Eiko; Rotimi, Charles N; Adebamowo, Clement A; Ajayi, Ike; Aniagwu, Toyin; Marshall, Patricia A; Nkwodimmah, Chibuzor; Royal, Charmaine D M; Leppert, Mark F; Dixon, Missy; Peiffer, Andy; Qiu, Renzong; Kent, Alastair; Kato, Kazuto; Niikawa, Norio; Adewole, Isaac F; Knoppers, Bartha M; Foster, Morris W; Clayton, Ellen Wright; Watkin, Jessica; Gibbs, Richard A; Belmont, John W; Muzny, Donna; Nazareth, Lynne; Sodergren, Erica; Weinstock, George M; Wheeler, David A; Yakub, Imtaz; Gabriel, Stacey B; Onofrio, Robert C; Richter, Daniel J; Ziaugra, Liuda; Birren, Bruce W; Daly, Mark J; Altshuler, David; Wilson, Richard K; Fulton, Lucinda L; Rogers, Jane; Burton, John; Carter, Nigel P; Clee, Christopher M; Griffiths, Mark; Jones, Matthew C; McLay, Kirsten; Plumb, Robert W; Ross, Mark T; Sims, Sarah K; Willey, David L; Chen, Zhu; Han, Hua; Kang, Le; Godbout, Martin; Wallenburg, John C; L'Archevêque, Paul; Bellemare, Guy; Saeki, Koji; Wang, Hongguang; An, Daochang; Fu, Hongbo; Li, Qing; Wang, Zhen; Wang, Renwu; Holden, Arthur L; Brooks, Lisa D; McEwen, Jean E; Guyer, Mark S; Wang, Vivian Ota; Peterson, Jane L; Shi, Michael; Spiegel, Jack; Sung, Lawrence M; Zacharia, Lynn F; Collins, Francis S; Kennedy, Karen; Jamieson, Ruth; Stewart, John

2007-10-18

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.

Genetic analysis and fine mapping of LH1 and LH2, a set of complementary genes controlling late heading in rice (Oryza sativa L.)

PubMed Central

Liu, Shuang; Wang, Feng; Gao, Li Jun; Li, Jin Hua; Li, Rong Bai; Gao, Han Liang; Deng, Guo Fu; Yang, Jin Shui; Luo, Xiao Jin

2012-01-01

Heading date in rice (Oryza sativa L.) is a critical agronomic trait with a complex inheritance. To investigate the genetic basis and mechanism of gene interaction in heading date, we conducted genetic analysis on segregation populations derived from crosses among the indica cultivars Bo B, Yuefeng B and Baoxuan 2. A set of dominant complementary genes controlling late heading, designated LH1 and LH2, were detected by molecular marker mapping. Genetic analysis revealed that Baoxuan 2 contains both dominant genes, while Bo B and Yuefeng B each possess either LH1 or LH2. Using larger populations with segregant ratios of 3 : 1, we fine-mapped LH1 to a 63-kb region near the centromere of chromosome 7 flanked by markers RM5436 and RM8034, and LH2 to a 177-kb region on the short arm of chromosome 8 between flanking markers Indel22468-3 and RM25. Some candidate genes were identified through sequencing of Bo B and Yuefeng B in these target regions. Our work provides a solid foundation for further study on gene interaction in heading date and has application in marker-assisted breeding of photosensitive hybrid rice in China. PMID:23341744

Genetic analysis and fine mapping of LH1 and LH2, a set of complementary genes controlling late heading in rice (Oryza sativa L.).

PubMed

Liu, Shuang; Wang, Feng; Gao, Li Jun; Li, Jin Hua; Li, Rong Bai; Gao, Han Liang; Deng, Guo Fu; Yang, Jin Shui; Luo, Xiao Jin

2012-12-01

Heading date in rice (Oryza sativa L.) is a critical agronomic trait with a complex inheritance. To investigate the genetic basis and mechanism of gene interaction in heading date, we conducted genetic analysis on segregation populations derived from crosses among the indica cultivars Bo B, Yuefeng B and Baoxuan 2. A set of dominant complementary genes controlling late heading, designated LH1 and LH2, were detected by molecular marker mapping. Genetic analysis revealed that Baoxuan 2 contains both dominant genes, while Bo B and Yuefeng B each possess either LH1 or LH2. Using larger populations with segregant ratios of 3 : 1, we fine-mapped LH1 to a 63-kb region near the centromere of chromosome 7 flanked by markers RM5436 and RM8034, and LH2 to a 177-kb region on the short arm of chromosome 8 between flanking markers Indel22468-3 and RM25. Some candidate genes were identified through sequencing of Bo B and Yuefeng B in these target regions. Our work provides a solid foundation for further study on gene interaction in heading date and has application in marker-assisted breeding of photosensitive hybrid rice in China.

Integrated change detection and temporal trajectory analysis of coastal wetlands using high spatial resolution Korean Multi-Purpose Satellite series imagery

NASA Astrophysics Data System (ADS)

Nguyen, Hoang Hai; Tran, Hien; Sunwoo, Wooyeon; Yi, Jong-hyuk; Kim, Dongkyun; Choi, Minha

2017-04-01

A series of multispectral high-resolution Korean Multi-Purpose Satellite (KOMPSAT) images was used to detect the geographical changes in four different tidal flats between the Yellow Sea and the west coast of South Korea. The method of unsupervised classification was used to generate a series of land use/land cover (LULC) maps from satellite images, which were then used as input for temporal trajectory analysis to detect the temporal change of coastal wetlands and its association with natural and anthropogenic activities. The accurately classified LULC maps of KOMPSAT images, with overall accuracy ranging from 83.34% to 95.43%, indicate that these multispectral high-resolution satellite data are highly applicable to the generation of high-quality thematic maps for extracting wetlands. The result of the trajectory analysis showed that, while the variation of the tidal flats in the Gyeonggi and Jeollabuk provinces was well correlated with the regular tidal regimes, the reductive trajectory of the wetland areas belonging to the Saemangeum province was caused by a high degree of human-induced activities including large reclamation and urbanization. The conservation of the Jeungdo Wetland Protected Area in the Jeollanam province revealed that effective social and environmental policies could help in protecting coastal wetlands from degradation.

Visualization maps for the evolution of research hotspots in the field of regional health information networks.

PubMed

Wang, Yanjun; Zheng, Jianzhong; Zhang, Ailian; Zhou, Wei; Dong, Haiyuan

2018-03-01

The aim of this study was to reveal research hotspots in the field of regional health information networks (RHINs) and use visualization techniques to explore their evolution over time and differences between countries. We conducted a literature review for a 50-year period and compared the prevalence of certain index terms during the periods 1963-1993 and 1994-2014 and in six countries. We applied keyword frequency analysis, keyword co-occurrence analysis, multidimensional scaling analysis, and network visualization technology. The total number of keywords was found to increase with time. From 1994 to 2014, the research priorities shifted from hospital planning to community health planning. The number of keywords reflecting information-based research increased. The density of the knowledge network increased significantly, and partial keywords condensed into knowledge groups. All six countries focus on keywords including Information Systems; Telemedicine; Information Service; Medical Records Systems, Computerized; Internet; etc.; however, the level of development and some research priorities are different. RHIN research has generally increased in popularity over the past 50 years. The research hotspots are evolving and are at different levels of development in different countries. Knowledge network mapping and perceptual maps provide useful information for scholars, managers, and policy-makers.

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation.

PubMed

Preissl, Sebastian; Fang, Rongxin; Huang, Hui; Zhao, Yuan; Raviram, Ramya; Gorkin, David U; Zhang, Yanxiao; Sos, Brandon C; Afzal, Veena; Dickel, Diane E; Kuan, Samantha; Visel, Axel; Pennacchio, Len A; Zhang, Kun; Ren, Bing

2018-03-01

Analysis of chromatin accessibility can reveal transcriptional regulatory sequences, but heterogeneity of primary tissues poses a significant challenge in mapping the precise chromatin landscape in specific cell types. Here we report single-nucleus ATAC-seq, a combinatorial barcoding-assisted single-cell assay for transposase-accessible chromatin that is optimized for use on flash-frozen primary tissue samples. We apply this technique to the mouse forebrain through eight developmental stages. Through analysis of more than 15,000 nuclei, we identify 20 distinct cell populations corresponding to major neuronal and non-neuronal cell types. We further define cell-type-specific transcriptional regulatory sequences, infer potential master transcriptional regulators and delineate developmental changes in forebrain cellular composition. Our results provide insight into the molecular and cellular dynamics that underlie forebrain development in the mouse and establish technical and analytical frameworks that are broadly applicable to other heterogeneous tissues.

Mapping reversible photoswitching of molecular-resistance fluctuations during the conformational transformation of azobenzene-terminated molecular switches.

PubMed

Cho, Duckhyung; Yang, Myungjae; Shin, Narae; Hong, Seunghun

2018-06-07

We report a direct mapping and analysis of electrical noise in azobenzene-terminated molecular monolayers, revealing reversible photoswitching of the molecular-resistance fluctuations in the layers. In this work, a conducting atomic force microscope combined with a homemade spectrum analyzer was used to image electrical current and noise at patterned self-assembled monolayers (SAMs) of azobenzene-terminated molecular wires on a gold substrate. We analyzed the current and noise imaging data to obtain maps of molecular resistances and amount of mean-square fluctuations in the resistances of the regions of trans-azobenzene and a cis/trans-azobenzene mixture. We revealed that the fluctuations in the molecular resistances in the SAMs were enhanced after the trans-to-cis isomerization, while the resistances were reduced. This result could be attributed to enhanced disorders in the molecular arrangements in the cis-SAMs. Furthermore, we observed that the changes in the resistance fluctuations were reversible with respect to repeated trans-to-cis and cis-to-trans isomerizations, indicating that the effects originated from reversible photoswitching of the molecular structures rather than irreversible damages of the molecules. These findings provide valuable insights into the electrical fluctuations in photoswitchable molecules, which could be utilized in further studies on molecular switches and molecular electronics in general. © 2018 IOP Publishing Ltd.

Quantitative Mapping of Pore Fraction Variations in Silicon Nitride Using an Ultrasonic Contact Scan Technique

NASA Technical Reports Server (NTRS)

Roth, Don J.; Kiser, James D.; Swickard, Suzanne M.; Szatmary, Steven A.; Kerwin, David P.

1993-01-01

An ultrasonic scan procedure using the pulse-echo contact configuration was employed to obtain maps of pore fraction variations in sintered silicon nitride samples in terms of ultrasonic material properties. Ultrasonic velocity, attenuation coefficient, and reflection coefficient images were obtained simultaneously over a broad band of frequencies (e.g., 30 to 110 MHz) by using spectroscopic analysis. Liquid and membrane (dry) coupling techniques and longitudinal and shear-wave energies were used. The major results include the following: Ultrasonic velocity (longitudinal and shear wave) images revealed and correlated with the extent of average through-thickness pore fraction variations in the silicon nitride disks. Attenuation coefficient images revealed pore fraction nonuniformity due to the scattering that occurred at boundaries between regions of high and low pore fraction. Velocity and attenuation coefficient images were each nearly identical for machined and polished disks, making the method readily applicable to machined materials. Velocity images were similar for wet and membrane coupling. Maps of apparent Poisson's ratio constructed from longitudinal and shear-wave velocities quantified Poisson's ratio variations across a silicon nitride disk. Thermal wave images of a disk indicated transient thermal behavior variations that correlated with observed variations in pore fraction and velocity and attenuation coefficients.

Frequency maps as a probe of secular evolution in the Milky Way

NASA Astrophysics Data System (ADS)

Valluri, Monica

2015-03-01

The frequency analysis of the orbits of halo stars and dark matter particles from a cosmological hydrodynamical simulation of a disk galaxy from the MUGS collaboration (Stinson et al. 2010) shows that even if the shape of the dark matter halo is nearly oblate, only about 50% of its orbits are on short-axis tubes, confirming a previous result: under baryonic condensation all orbit families can deform their shapes without changing orbital type (Valluri et al. 2010). Orbits of dark matter particles and halo stars are very similar reflecting their common accretion origin and the influence of baryons. Frequency maps provide a compact representation of the 6-D phase space distribution that also reveals the history of the halo (Valluri et al. 2012). The 6-D phase space coordinates for a large population of halo stars in the Milky Way that will be obtained from future surveys can be used to reconstruct the phase-space distribution function of the stellar halo. The similarity between the frequency maps of halo stars and dark matter particles (Fig. 1) implies that reconstruction of the stellar halo distribution function can reveal the phase space distribution of the unseen dark matter particles and provide evidence for secular evolution. MV is supported by NSF grant AST-0908346 and the Elizabeth Crosby grant.

Adverse effects of metallic artifacts on voxel-wise analysis and tract-based spatial statistics in diffusion tensor imaging.

PubMed

Goto, Masami; Abe, Osamu; Hata, Junichi; Fukunaga, Issei; Shimoji, Keigo; Kunimatsu, Akira; Gomi, Tsutomu

2017-02-01

Background Diffusion tensor imaging (DTI) is a magnetic resonance imaging (MRI) technique that reflects the Brownian motion of water molecules constrained within brain tissue. Fractional anisotropy (FA) is one of the most commonly measured DTI parameters, and can be applied to quantitative analysis of white matter as tract-based spatial statistics (TBSS) and voxel-wise analysis. Purpose To show an association between metallic implants and the results of statistical analysis (voxel-wise group comparison and TBSS) for fractional anisotropy (FA) mapping, in DTI of healthy adults. Material and Methods Sixteen healthy volunteers were scanned with 3-Tesla MRI. A magnetic keeper type of dental implant was used as the metallic implant. DTI was acquired three times in each participant: (i) without a magnetic keeper (FAnon1); (ii) with a magnetic keeper (FAimp); and (iii) without a magnetic keeper (FAnon2) as reproducibility of FAnon1. Group comparisons with paired t-test were performed as FAnon1 vs. FAnon2, and as FAnon1 vs. FAimp. Results Regions of significantly reduced and increased local FA values were revealed by voxel-wise group comparison analysis (a P value of less than 0.05, corrected with family-wise error), but not by TBSS. Conclusion Metallic implants existing outside the field of view produce artifacts that affect the statistical analysis (voxel-wise group comparisons) for FA mapping. When statistical analysis for FA mapping is conducted by researchers, it is important to pay attention to any dental implants present in the mouths of the participants.

MiRNAs with Apoptosis Regulating Potential Are Differentially Expressed in Chronic Exercise-Induced Physiologically Hypertrophied Hearts

PubMed Central

Ramprasath, Tharmarajan; Kalpana, Krishnan

2015-01-01

Physiological cardiac hypertrophy is an adaptive mechanism, induced during chronic exercise. As it is reversible and not associated with cardiomyocyte death, it is considered as a natural tactic to prevent cardiac dysfunction and failure. Though, different studies revealed the importance of microRNAs (miRNAs) in pathological hypertrophy, their role during physiological hypertrophy is largely unexplored. Hence, this study is aimed at revealing the global expression profile of miRNAs during physiological cardiac hypertrophy. Chronic swimming protocol continuously for eight weeks resulted in induction of physiological hypertrophy in rats and histopathology revealed the absence of tissue damage, apoptosis or fibrosis. Subsequently, the total RNA was isolated and small RNA sequencing was executed. Analysis of small RNA reads revealed the differential expression of a large set of miRNAs during physiological hypertrophy. The expression profile of the significantly differentially expressed miRNAs was validated by qPCR. In silico prediction of target genes by miRanda, miRdB and TargetScan and subsequent qPCR analysis unraveled that miRNAs including miR-99b, miR-100, miR-19b, miR-10, miR-208a, miR-133, miR-191a, miR-22, miR-30e and miR-181a are targeting the genes that primarily regulate cell proliferation and cell death. Gene ontology and pathway mapping showed that the differentially expressed miRNAs and their target genes were mapped to apoptosis and cell death pathways principally via PI3K/Akt/mTOR and MAPK signaling. In summary, our data indicates that regulation of these miRNAs with apoptosis regulating potential can be one of the major key factors in determining pathological or physiological hypertrophy by controlling fibrosis, apoptosis and cell death mechanisms. PMID:25793527

Bacterial Community and Spoilage Profiles Shift in Response to Packaging in Yellow-Feather Broiler, a Highly Popular Meat in Asia

PubMed Central

Wang, Huhu; Zhang, Xinxiao; Wang, Guangyu; Jia, Kun; Xu, Xinglian; Zhou, Guanghong

2017-01-01

The consumption of yellow-feathered broiler has been advocated for purchasing with chilled meat rather than live broilers in Asia due to the outbreaks of animal influenza. Here, the microbial community of chilled yellow-feathered broiler response to modified-air packaging (MAP, 80% CO2/20% N2) and penetrated-air packaging (PAP, air-filling) during storage was revealed by a combination of whole-metagenome shotgun sequencing and traditional isolation methods, and the volatile organic compounds and proteolytic activity of representative dominant isolates were also accessed. The results revealed that MAP prolonged shelf life from 4 to 8 days compared to PAP, when the numbers of total viable counts and lactic acid bacteria reached more than 7 log CFU/g. Aeromonas, Acinetobacter, Escherichia, and Streptococcus occupied the bacteria communities in initial broiler carcasses. MAP dramatically increased the bacteria diversity during storage compared to PAP. Clear shifts of the dominant bacteria species were obviously observed, with the top genera of Aeromonas, Lactococcus, Serratia, and Shewanella in MAP, whereas the microbial communities in PAP were largely dominated by Pseudomonas. The isolates of Pseudomonas from PAP carcasses and Aeromonas from MAP carcasses displayed strong proteolytic activities. Meanwhile, the principal component analysis based on the volatile organic compounds indicated that the metabolic profiles greatly varied between each treatment, and no link between the natural odor of spoilage meat in situ and the volatile odor of the dominant isolates incubated in standard culture was found. These data could lead to new insights into the bacteria communities of yellow-feathered broiler meat during storage and would benefit the development of novel preservative approaches. PMID:29312261

High-resolution mapping of a fruit firmness-related quantitative trait locus in tomato reveals epistatic interactions associated with a complex combinatorial locus.

PubMed

Chapman, Natalie H; Bonnet, Julien; Grivet, Laurent; Lynn, James; Graham, Neil; Smith, Rebecca; Sun, Guiping; Walley, Peter G; Poole, Mervin; Causse, Mathilde; King, Graham J; Baxter, Charles; Seymour, Graham B

2012-08-01

Fruit firmness in tomato (Solanum lycopersicum) is determined by a number of factors including cell wall structure, turgor, and cuticle properties. Firmness is a complex polygenic trait involving the coregulation of many genes and has proved especially challenging to unravel. In this study, a quantitative trait locus (QTL) for fruit firmness was mapped to tomato chromosome 2 using the Zamir Solanum pennellii interspecific introgression lines (ILs) and fine-mapped in a population consisting of 7,500 F2 and F3 lines from IL 2-3 and IL 2-4. This firmness QTL contained five distinct subpeaks, Fir(s.p.)QTL2.1 to Fir(s.p.)QTL2.5, and an effect on a distal region of IL 2-4 that was nonoverlapping with IL 2-3. All these effects were located within an 8.6-Mb region. Using genetic markers, each subpeak within this combinatorial locus was mapped to a physical location within the genome, and an ethylene response factor (ERF) underlying Fir(s.p.)QTL2.2 and a region containing three pectin methylesterase (PME) genes underlying Fir(s.p.)QTL2.5 were nominated as QTL candidate genes. Statistical models used to explain the observed variability between lines indicated that these candidates and the nonoverlapping portion of IL 2-4 were sufficient to account for the majority of the fruit firmness effects. Quantitative reverse transcription-polymerase chain reaction was used to quantify the expression of each candidate gene. ERF showed increased expression associated with soft fruit texture in the mapping population. In contrast, PME expression was tightly linked with firm fruit texture. Analysis of a range of recombinant lines revealed evidence for an epistatic interaction that was associated with this combinatorial locus.

Use of a bacterial expression vector to map the varicella-zoster virus major glycoprotein gene, gC.

PubMed Central

Ellis, R W; Keller, P M; Lowe, R S; Zivin, R A

1985-01-01

The genome of varicella-zoster virus (VZV) encodes at least three major glycoprotein genes. Among viral gene products, the gC gene products are the most abundant glycoproteins and induce a substantial humoral immune response (Keller et al., J. Virol. 52:293-297, 1984). We utilized two independent approaches to map the gC gene. Small fragments of randomly digested VZV DNA were inserted into a bacterial expression vector. Bacterial colonies transformed by this vector library were screened serologically for antigen expression with monoclonal antibodies to gC. Hybridization of the plasmid DNA from a gC antigen-positive clone revealed homology to the 3' end of the VZV Us segment. In addition, mRNA from VZV-infected cells was hybrid selected by a set of VZV DNA recombinant plasmids and translated in vitro, and polypeptide products were immunoprecipitated by convalescent zoster serum or by monoclonal antibodies to gC. This analysis revealed that the mRNA encoding a 70,000-dalton polypeptide precipitable by anti-gC antibodies mapped to the HindIII C fragment, which circumscribes the entire Us region. We conclude that the VZV gC glycoprotein gene maps to the 3' end of the Us region and is expressed as a 70,000-dalton primary translational product. These results are consistent with the recently reported DNA sequence of Us (A.J. Davison, EMBO J. 2:2203-2209, 1983). Furthermore, glycosylation appears not to be required for a predominant portion of the antigenicity of gC glycoproteins. We also report the tentative map assignments for eight other VZV primary translational products. Images PMID:2981365

New whole-body sensory-motor gradients revealed using phase-locked analysis and verified using multivoxel pattern analysis and functional connectivity.

PubMed

Zeharia, Noa; Hertz, Uri; Flash, Tamar; Amedi, Amir

2015-02-18

Topographic organization is one of the main principles of organization in the human brain. Specifically, whole-brain topographic mapping using spectral analysis is responsible for one of the greatest advances in vision research. Thus, it is intriguing that although topography is a key feature also in the motor system, whole-body somatosensory-motor mapping using spectral analysis has not been conducted in humans outside M1/SMA. Here, using this method, we were able to map a homunculus in the globus pallidus, a key target area for deep brain stimulation, which has not been mapped noninvasively or in healthy subjects. The analysis clarifies contradictory and partial results regarding somatotopy in the caudal-cingulate zone and rostral-cingulate zone in the medial wall and in the putamen. Most of the results were confirmed at the single-subject level and were found to be compatible with results from animal studies. Using multivoxel pattern analysis, we could predict movements of individual body parts in these homunculi, thus confirming that they contain somatotopic information. Using functional connectivity, we demonstrate interhemispheric functional somatotopic connectivity of these homunculi, such that the somatotopy in one hemisphere could have been found given the connectivity pattern of the corresponding regions of interest in the other hemisphere. When inspecting the somatotopic and nonsomatotopic connectivity patterns, a similarity index indicated that the pattern of connected and nonconnected regions of interest across different homunculi is similar for different body parts and hemispheres. The results show that topographical gradients are even more widespread than previously assumed in the somatosensory-motor system. Spectral analysis can thus potentially serve as a gold standard for defining somatosensory-motor system areas for basic research and clinical applications. Copyright © 2015 the authors 0270-6474/15/352845-15$15.00/0.

Nd Isotope and U-Th-Pb Age Mapping of Single Monazite Grains by Laser Ablation Split Stream Analysis

NASA Astrophysics Data System (ADS)

Fisher, C. M.; Hanchar, J. M.; Miller, C. F.; Phillips, S.; Vervoort, J. D.; Martin, W.

2015-12-01

Monazite is a common accessory mineral that occurs in medium to high grade metamorphic and Ca-poor felsic igneous rocks, and often controls the LREE budget (including Sm and Nd) of the host rock in which it crystallizes. Moreover, it contains appreciable U and Th, making it an ideal mineral for determining U-Th-Pb ages and Sm-Nd isotopic compositions, both of which are readily determined using in situ techniques with very high spatial resolution like LA-MC-ICPMS. Here, we present the results of laser ablation split stream analyses (LASS), which allows for simultaneous determination of the age and initial Nd isotopic composition in a single analysis. Analyses were done using a 20mm laser spot that allowed for detailed Nd isotope mapping of monazite grains (~30 analyses per ~250mm sized grain). Combined with LREE ratios (e.g., Sm/Nd, Ce/Gd, and Eu anomalies) these results yield important petrogenetic constraints on the evolution of peraluminous granites from the Old Woman-Piute batholith in southeastern California. Our findings also allow an improved understanding of the causes of isotope heterogeneity in granitic rocks. U-Th-Pb age mapping across the crystals reveals a single Cretaceous age for all grains with precision and accuracy typical of laser ablation analyses (~2%). In contrast, the concurrent Nd isotope mapping yields homogeneous initial Nd isotope compositions for some grains and large initial intra-grain variations of up to 8 epsilon units in others. The grains that yield homogeneous Nd isotope compositions have REE ratios suggesting that they crystallized in a fractionally crystallizing magma. Conversely, other grains, which also record fractional crystallization of both feldspar and LREE rich minerals, demonstrate a change in the Nd isotope composition of the magma during crystallization of monazite. Comparison of inter- and intra-grain Nd isotope compositions reveals further details on the potential mechanisms responsible for isotope heterogeneity present in single rock samples. This method highlights the potential of single grain isotope mapping of LREE phases such as monazite, allanite, and titanite for understanding both igneous and metamorphic petrogenesis.

Transcriptome Analysis of Nine Tissues to Discover Genes Involved in the Biosynthesis of Active Ingredients in Sophora flavescens.

PubMed

Han, Rongchun; Takahashi, Hiroki; Nakamura, Michimi; Bunsupa, Somnuk; Yoshimoto, Naoko; Yamamoto, Hirobumi; Suzuki, Hideyuki; Shibata, Daisuke; Yamazaki, Mami; Saito, Kazuki

2015-01-01

Sophora flavescens AITON (kurara) has long been used to treat various diseases. Although several research findings revealed the biosynthetic pathways of its characteristic chemical components as represented by matrine, insufficient analysis of transcriptome data hampered in-depth analysis of the underlying putative genes responsible for the biosynthesis of pharmaceutical chemical components. In this study, more than 200 million fastq format reads were generated by Illumina's next-generation sequencing approach using nine types of tissue from S. flavescens, followed by CLC de novo assembly, ultimately yielding 83,325 contigs in total. By mapping the reads back to the contigs, reads per kilobase of the transcript per million mapped reads values were calculated to demonstrate gene expression levels, and overrepresented gene ontology terms were evaluated using Fisher's exact test. In search of the putative genes relevant to essential metabolic pathways, all 1350 unique enzyme commission numbers were used to map pathways against the Kyoto Encyclopedia of Genes and Genomes. By analyzing expression patterns, we proposed some candidate genes involved in the biosynthesis of isoflavonoids and quinolizidine alkaloids. Adopting RNA-Seq analysis, we obtained substantially credible contigs for downstream work. The preferential expression of the gene for putative lysine/ornithine decarboxylase committed in the initial step of matrine biosynthesis in leaves and stems was confirmed in semi-quantitative polymerase chain reaction (PCR) analysis. The findings in this report may serve as a stepping-stone for further research into this promising medicinal plant.

Connecting long distance: semantic distance in analogical reasoning modulates frontopolar cortex activity.

PubMed

Green, Adam E; Kraemer, David J M; Fugelsang, Jonathan A; Gray, Jeremy R; Dunbar, Kevin N

2010-01-01

Solving problems often requires seeing new connections between concepts or events that seemed unrelated at first. Innovative solutions of this kind depend on analogical reasoning, a relational reasoning process that involves mapping similarities between concepts. Brain-based evidence has implicated the frontal pole of the brain as important for analogical mapping. Separately, cognitive research has identified semantic distance as a key characteristic of the kind of analogical mapping that can support innovation (i.e., identifying similarities across greater semantic distance reveals connections that support more innovative solutions and models). However, the neural substrates of semantically distant analogical mapping are not well understood. Here, we used functional magnetic resonance imaging (fMRI) to measure brain activity during an analogical reasoning task, in which we parametrically varied the semantic distance between the items in the analogies. Semantic distance was derived quantitatively from latent semantic analysis. Across 23 participants, activity in an a priori region of interest (ROI) in left frontopolar cortex covaried parametrically with increasing semantic distance, even after removing effects of task difficulty. This ROI was centered on a functional peak that we previously associated with analogical mapping. To our knowledge, these data represent a first empirical characterization of how the brain mediates semantically distant analogical mapping.

SNP Marker Integration and QTL Analysis of 12 Agronomic and Morphological Traits in F8 RILs of Pepper (Capsicum annuum L.)

PubMed Central

Lu, Fu-Hao; Kwon, Soon-Wook; Yoon, Min-Young; Kim, Ki-Taek; Cho, Myeong-Cheoul; Yoon, Moo-Kyung; Park, Yong-Jin

2012-01-01

Red pepper, Capsicum annuum L., has been attracting geneticists’ and breeders’ attention as one of the important agronomic crops. This study was to integrate 41 SNP markers newly developed from comparative transcriptomes into a previous linkage map, and map 12 agronomic and morphological traits into the integrated map. A total of 39 markers found precise position and were assigned to 13 linkage groups (LGs) as well as the unassigned LGe, leading to total 458 molecular markers present in this genetic map. Linkage mapping was supported by the physical mapping to tomato and potato genomes using BLAST retrieving, revealing at least two-thirds of the markers mapped to the corresponding LGs. A sum of 23 quantitative trait loci from 11 traits was detected using the composite interval mapping algorithm. A consistent interval between a035_1 and a170_1 on LG5 was detected as a main-effect locus among the resistance QTLs to Phytophthora capsici at high-, intermediate- and low-level tests, and interactions between the QTLs for high-level resistance test were found. Considering the epistatic effect, those QTLs could explain up to 98.25% of the phenotype variations of resistance. Moreover, 17 QTLs for another eight traits were found to locate on LG3, 4, and 12 mostly with varying phenotypic contribution. Furthermore, the locus for corolla color was mapped to LG10 as a marker. The integrated map and the QTLs identified would be helpful for current genetics research and crop breeding, especially in the Solanaceae family. PMID:22684870

Discovery and characterization of antibody variants using mass spectrometry-based comparative analysis for biosimilar candidates of monoclonal antibody drugs.

PubMed

Li, Wenhua; Yang, Bin; Zhou, Dongmei; Xu, Jun; Ke, Zhi; Suen, Wen-Chen

2016-07-01

Liquid chromatography mass spectrometry (LC-MS) is the most commonly used technique for the characterization of antibody variants. MAb-X and mAb-Y are two approved IgG1 subtype monoclonal antibody drugs recombinantly produced in Chinese hamster ovary (CHO) cells. We report here that two unexpected and rare antibody variants have been discovered during cell culture process development of biosimilars for these two approved drugs through intact mass analysis. We then used comprehensive mass spectrometry-based comparative analysis including reduced light, heavy chains, and domain-specific mass as well as peptide mapping analysis to fully characterize the observed antibody variants. The "middle-up" mass comparative analysis demonstrated that the antibody variant from mAb-X biosimilar candidate was caused by mass variation of antibody crystalline fragment (Fc), whereas a different variant with mass variation in antibody antigen-binding fragment (Fab) from mAb-Y biosimilar candidate was identified. Endoproteinase Lys-C digested peptide mapping and tandem mass spectrometry analysis further revealed that a leucine to glutamine change in N-terminal 402 site of heavy chain was responsible for the generation of mAb-X antibody variant. Lys-C and trypsin coupled non-reduced and reduced peptide mapping comparative analysis showed that the formation of the light-heavy interchain trisulfide bond resulted in the mAb-Y antibody variant. These two cases confirmed that mass spectrometry-based comparative analysis plays a critical role for the characterization of monoclonal antibody variants, and biosimilar developers should start with a comprehensive structural assessment and comparative analysis to decrease the risk of the process development for biosimilars. Copyright © 2016 Elsevier B.V. All rights reserved.

Using Concept Maps to Reveal Conceptual Typologies

ERIC Educational Resources Information Center

Hay, David B.; Kinchin, Ian M.

2006-01-01

Purpose: The purpose of this paper is to explain and develop a classification of cognitive structures (or typologies of thought), previously designated as spoke, chain and network thinking by Kinchin "et al." Design/methodology/approach: The paper shows how concept mapping can be used to reveal these conceptual typologies and endeavours to place…

From blood oxygenation level dependent (BOLD) signals to brain temperature maps.

PubMed

Sotero, Roberto C; Iturria-Medina, Yasser

2011-11-01

A theoretical framework is presented for converting Blood Oxygenation Level Dependent (BOLD) images to brain temperature maps, based on the idea that disproportional local changes in cerebral blood flow (CBF) as compared with cerebral metabolic rate of oxygen consumption (CMRO₂) during functional brain activity, lead to both brain temperature changes and the BOLD effect. Using an oxygen limitation model and a BOLD signal model, we obtain a transcendental equation relating CBF and CMRO₂ changes with the corresponding BOLD signal, which is solved in terms of the Lambert W function. Inserting this result in the dynamic bioheat equation describing the rate of temperature changes in the brain, we obtain a nonautonomous ordinary differential equation that depends on the BOLD response, which is solved numerically for each brain voxel. Temperature maps obtained from a real BOLD dataset registered in an attention to visual motion experiment were calculated, obtaining temperature variations in the range: (-0.15, 0.1) which is consistent with experimental results. The statistical analysis revealed that significant temperature activations have a similar distribution pattern than BOLD activations. An interesting difference was the activation of the precuneus in temperature maps, a region involved in visuospatial processing, an effect that was not observed on BOLD maps. Furthermore, temperature maps were more localized to gray matter regions than the original BOLD maps, showing less activated voxels in white matter and cerebrospinal fluid.

How visual attention is modified by disparities and textures changes?

NASA Astrophysics Data System (ADS)

Khaustova, Dar'ya; Fournier, Jérome; Wyckens, Emmanuel; Le Meur, Olivier

2013-03-01

The 3D image/video quality of experience is a multidimensional concept that depends on 2D image quality, depth quantity and visual comfort. The relationship between these parameters is not yet clearly defined. From this perspective, we aim to understand how texture complexity, depth quantity and visual comfort influence the way people observe 3D content in comparison with 2D. Six scenes with different structural parameters were generated using Blender software. For these six scenes, the following parameters were modified: texture complexity and the amount of depth changing the camera baseline and the convergence distance at the shooting side. Our study was conducted using an eye-tracker and a 3DTV display. During the eye-tracking experiment, each observer freely examined images with different depth levels and texture complexities. To avoid memory bias, we ensured that each observer had only seen scene content once. Collected fixation data were used to build saliency maps and to analyze differences between 2D and 3D conditions. Our results show that the introduction of disparity shortened saccade length; however fixation durations remained unaffected. An analysis of the saliency maps did not reveal any differences between 2D and 3D conditions for the viewing duration of 20 s. When the whole period was divided into smaller intervals, we found that for the first 4 s the introduced disparity was conducive to the section of saliency regions. However, this contribution is quite minimal if the correlation between saliency maps is analyzed. Nevertheless, we did not find that discomfort (comfort) had any influence on visual attention. We believe that existing metrics and methods are depth insensitive and do not reveal such differences. Based on the analysis of heat maps and paired t-tests of inter-observer visual congruency values we deduced that the selected areas of interest depend on texture complexities.

OMEGA: Observatoire pour la Minéralogie, l'Eau, les Glaces et l'Activité

NASA Astrophysics Data System (ADS)

Bibring, J.-P.; Soufflot, A.; Berthé, M.; Langevin, Y.; Gondet, B.; Drossart, P.; Bouyé, M.; Combes, M.; Puget, P.; Semery, A.; Bellucci, G.; Formisano, V.; Moroz, V.; Kottsov, V.; Bonello, G.; Erard, S.; Forni, O.; Gendrin, A.; Manaud, N.; Poulet, F.; Poulleau, G.; Encrenaz, T.; Fouchet, T.; Melchiori, R.; Altieri, F.; Ignatiev, N.; Titov, D.; Zasova, L.; Coradini, A.; Capacionni, F.; Cerroni, P.; Fonti, S.; Mangold, N.; Pinet, P.; Schmitt, B.; Sotin, C.; Hauber, E.; Hoffmann, H.; Jaumann, R.; Keller, U.; Arvidson, R.; Mustard, J.; Forget, F.

2004-08-01

The OMEGA visible and near-IR mapping spectrometer will reveal the mineralogical and molecular composition of the surface and atmosphere of Mars through the spectral analysis of the diffused solar light and surface thermal emission. It will provide global coverage at medium resolution (2-5 km) for altitudes from 1500 km to 4000 km, and high-resolution (<350 m) spectral images of selected areas.

Genetic Mapping of a Mutant Defective in d, l-Alanine Racemase in Bacillus subtilis 168

PubMed Central

Dul, Michael J.; Young, Frank E.

1973-01-01

Genetic analysis of a d-alanine requiring mutant (dal) of Bacillus subtilis reveals that the gene that codes for d,l-alanine racemase is linked to purB. The order of genes in this region of the chromosome is purB, pig, tsi, dal. Thus there are at least two clusters of genes that regulate cell wall biosynthesis in B. subtilis. PMID:4199510

Comparative proteomic analysis of lung tissue from guinea pigs with Leptospiral Pulmonary Haemorrhage Syndrome (LPHS) reveals a decrease in abundance of host proteins involved in cytoskeletal and cellular organization

USDA-ARS?s Scientific Manuscript database

The recent completion of the complete genome sequence of the guinea pig (Cavia porcellus) provides innovative opportunities to apply proteomic technologies to an important animal model of disease. In this study, a 2-D guinea pig proteome lung map was used to investigate the pathogenic mechanisms of ...

A GENOME-WIDE LINKAGE AND ASSOCIATION SCAN REVEALS NOVEL LOCI FOR AUTISM

PubMed Central

Weiss, Lauren A.; Arking, Dan E.

2009-01-01

Summary Although autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success 1. Genome-wide association studies (GWAS) using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits (http://www.genome.gov/26525384). Consequently, we initiated a linkage and association mapping study using half a million genome-wide SNPs in a common set of 1,031 multiplex autism families (1,553 affected offspring). We identified regions of suggestive and significant linkage on chromosomes 6q27 and 20p13, respectively. Initial analysis did not yield genome-wide significant associations; however, genotyping of top hits in additional families revealed a SNP on chromosome 5p15 (between SEMA5A and TAS2R1) that was significantly associated with autism (P = 2 × 10−7). We also demonstrated that expression of SEMA5A is reduced in brains from autistic patients, further implicating SEMA5A as an autism susceptibility gene. The linkage regions reported here provide targets for rare variation screening while the discovery of a single novel association demonstrates the action of common variants. PMID:19812673

Silicone intraocular lens surface calcification in a patient with asteroid hyalosis.

PubMed

Matsumura, Kazuhiro; Takano, Masahiko; Shimizu, Kimiya; Nemoto, Noriko

2012-07-01

To confirm a substance presence on the posterior intraocular lens (IOL) surface in a patient with asteroid hyalosis. An 80-year-old man had IOLs for approximately 12 years. Opacities and neodymium-doped yttrium aluminum garnet pits were observed on the posterior surface of the right IOL. Asteroid hyalosis and an epiretinal membrane were observed OD. An IOL exchange was performed on 24 March 2008, and the explanted IOL was analyzed using a light microscope and a transmission electron microscope with a scanning electron micrograph and an energy-dispersive X-ray spectrometer for elemental analysis. To confirm asteroid hyalosis, asteroid bodies were examined with the ionic liquid (EtMeIm+ BF4-) method using a field emission scanning electron microscope (FE-SEM) with digital beam control RGB mapping. X-ray spectrometry of the deposits revealed high calcium and phosphorus peaks. Spectrometry revealed that the posterior IOL surface opacity was due to a calcium-phosphorus compound. Examination of the asteroid bodies using FE-SEM with digital beam control RGB mapping confirmed calcium and phosphorus as the main components. Calcium hydrogen phosphate dihydrate deposits were probably responsible for the posterior IOL surface opacity. Furthermore, analysis of the asteroid bodies demonstrated that calcium and phosphorus were its main components.

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

PubMed Central

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

2014-01-01

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

KSC-01pp0887

NASA Image and Video Library

2001-04-20

KENNEDY SPACE CENTER, FLA. -- Inside the Spacecraft Assembly and Encapsulation Facility 2, a covered Microwave Anisotropy Probe (MAP) satellite is revealed after removal of the container (far right). MAP will undergo testing in the SAEF-2 before its scheduled launch June 30 from Cape Canaveral Air Force Station on a Delta II rocket into a lunar-assisted trajectory to the Sun-Earth for a 27-month mission (3 months transit, 24 months observing). The MAP instrument consists of a set of passively cooled microwave radiometers with 1.4x 1.6-meter diameter primary reflectors to provide the desired angular resolution. MAP measures small fluctuations in the temperature of the cosmic microwave background radiation to an accuracy of one millionth of a degree. These measurements should reveal the size, matter content, age, geometry and fate of the universe. They will also reveal the primordial structure that grew to form galaxies and will test ideas about the origins of these primordial structures. The MAP instrument will be continuously shaded from the Sun, Earth, and Moon by the spacecraft. It is a product of Goddard Space Flight Center in partnership with Princeton University

An ontology-based exploration of the concepts and relationships in the activities and participation component of the international classification of functioning, disability and health.

PubMed

Della Mea, Vincenzo; Simoncello, Andrea

2012-02-28

The International Classification of Functioning, Disability and Health (ICF) is a classification of health and health-related issues, aimed at describing and measuring health and disability at both individual and population levels. Here we discuss a preliminary qualitative and quantitative analysis of the relationships used in the Activities and Participation component of ICF, and a preliminary mapping to SUMO (Suggested Upper Merged Ontology) concepts. The aim of the analysis is to identify potential logical problems within this component of ICF, and to understand whether activities and participation might be defined more formally than in the current version of ICF. In the relationship analysis, we used four predicates among those available in SUMO for processes (Patient, Instrument, Agent, and subProcess). While at the top level subsumption was used in most cases (90%), at the lower levels the percentage of other relationships rose to 41%. Chapters were heterogeneous in the relationships used and some of the leaves of the tree seemed to represent properties or parts of the parent concept rather than subclasses. Mapping of ICF to SUMO proved partially feasible, with the activity concepts being mapped mostly (but not totally) under the IntentionalProcess concept in SUMO. On the other hand, the participation concept has not been mapped to any upper level concept. Our analysis of the relationships within ICF revealed issues related to confusion between classes and their properties, incorrect classifications, and overemphasis on subsumption, confirming what already observed by other researchers. However, it also suggested some properties for Activities that could be included in a more formal model: number of agents involved, the instrument used to carry out the activity, the object of the activity, complexity of the task, and an enumeration of relevant subtasks.

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis

PubMed Central

Mason, Annaliese S.; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E.; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A. P.; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N.

2016-01-01

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. PMID:26614742

Centromere Locations in Brassica A and C Genomes Revealed Through Half-Tetrad Analysis.

PubMed

Mason, Annaliese S; Rousseau-Gueutin, Mathieu; Morice, Jérôme; Bayer, Philipp E; Besharat, Naghmeh; Cousin, Anouska; Pradhan, Aneeta; Parkin, Isobel A P; Chèvre, Anne-Marie; Batley, Jacqueline; Nelson, Matthew N

2016-02-01

Locating centromeres on genome sequences can be challenging. The high density of repetitive elements in these regions makes sequence assembly problematic, especially when using short-read sequencing technologies. It can also be difficult to distinguish between active and recently extinct centromeres through sequence analysis. An effective solution is to identify genetically active centromeres (functional in meiosis) by half-tetrad analysis. This genetic approach involves detecting heterozygosity along chromosomes in segregating populations derived from gametes (half-tetrads). Unreduced gametes produced by first division restitution mechanisms comprise complete sets of nonsister chromatids. Along these chromatids, heterozygosity is maximal at the centromeres, and homologous recombination events result in homozygosity toward the telomeres. We genotyped populations of half-tetrad-derived individuals (from Brassica interspecific hybrids) using a high-density array of physically anchored SNP markers (Illumina Brassica 60K Infinium array). Mapping the distribution of heterozygosity in these half-tetrad individuals allowed the genetic mapping of all 19 centromeres of the Brassica A and C genomes to the reference Brassica napus genome. Gene and transposable element density across the B. napus genome were also assessed and corresponded well to previously reported genetic map positions. Known centromere-specific sequences were located in the reference genome, but mostly matched unanchored sequences, suggesting that the core centromeric regions may not yet be assembled into the pseudochromosomes of the reference genome. The increasing availability of genetic markers physically anchored to reference genomes greatly simplifies the genetic and physical mapping of centromeres using half-tetrad analysis. We discuss possible applications of this approach, including in species where half-tetrads are currently difficult to isolate. Copyright © 2016 by the Genetics Society of America.

Systems Analysis of Early Host Gene Expression Provides Clues for Transient Mycobacterium avium ssp avium vs. Persistent Mycobacterium avium ssp paratuberculosis Intestinal Infections

PubMed Central

Khare, Sangeeta; Drake, Kenneth L.; Lawhon, Sara D.; Nunes, Jairo E. S.; Figueiredo, Josely F.; Rossetti, Carlos A.; Gull, Tamara; Everts, Robin E.; Lewin, Harris. A.; Adams, Leslie Garry

2016-01-01

It has long been a quest in ruminants to understand how two very similar mycobacterial species, Mycobacterium avium ssp. paratuberculosis (MAP) and Mycobacterium avium ssp. avium (MAA) lead to either a chronic persistent infection or a rapid-transient infection, respectively. Here, we hypothesized that when the host immune response is activated by MAP or MAA, the outcome of the infection depends on the early activation of signaling molecules and host temporal gene expression. To test our hypothesis, ligated jejuno-ileal loops including Peyer’s patches in neonatal calves were inoculated with PBS, MAP, or MAA. A temporal analysis of the host transcriptome profile was conducted at several times post-infection (0.5, 1, 2, 4, 8 and 12 hours). When comparing the transcriptional responses of calves infected with the MAA versus MAP, discordant patterns of mucosal expression were clearly evident, and the numbers of unique transcripts altered were moderately less for MAA-infected tissue than were mucosal tissues infected with the MAP. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis. Bayesian network modeling identified mechanistic genes, gene-to-gene relationships, pathways and Gene Ontologies (GO) biological processes that are involved in specific cell activation during infection. MAP and MAA had significant different pathway perturbation at 0.5 and 12 hours post inoculation. Inverse processes were observed between MAP and MAA response for epithelial cell proliferation, negative regulation of chemotaxis, cell-cell adhesion mediated by integrin and regulation of cytokine-mediated signaling. MAP inoculated tissue had significantly lower expression of phagocytosis receptors such as mannose receptor and complement receptors. This study reveals that perturbation of genes and cellular pathways during MAP infection resulted in host evasion by mucosal membrane barrier weakening to access entry in the ileum, inhibition of Ca signaling associated with decreased phagosome-lysosome fusion as well as phagocytosis inhibition, bias toward Th2 cell immune response accompanied by cell recruitment, cell proliferation and cell differentiation; leading to persistent infection. Contrarily, MAA infection was related to cellular responses associated with activation of molecular pathways that release chemicals and cytokines involved with containment of infection and a strong bias toward Th1 immune response, resulting in a transient infection. PMID:27653506

Systems Analysis of Early Host Gene Expression Provides Clues for Transient Mycobacterium avium ssp avium vs. Persistent Mycobacterium avium ssp paratuberculosis Intestinal Infections.

PubMed

Khare, Sangeeta; Drake, Kenneth L; Lawhon, Sara D; Nunes, Jairo E S; Figueiredo, Josely F; Rossetti, Carlos A; Gull, Tamara; Everts, Robin E; Lewin, Harris A; Adams, Leslie Garry

It has long been a quest in ruminants to understand how two very similar mycobacterial species, Mycobacterium avium ssp. paratuberculosis (MAP) and Mycobacterium avium ssp. avium (MAA) lead to either a chronic persistent infection or a rapid-transient infection, respectively. Here, we hypothesized that when the host immune response is activated by MAP or MAA, the outcome of the infection depends on the early activation of signaling molecules and host temporal gene expression. To test our hypothesis, ligated jejuno-ileal loops including Peyer's patches in neonatal calves were inoculated with PBS, MAP, or MAA. A temporal analysis of the host transcriptome profile was conducted at several times post-infection (0.5, 1, 2, 4, 8 and 12 hours). When comparing the transcriptional responses of calves infected with the MAA versus MAP, discordant patterns of mucosal expression were clearly evident, and the numbers of unique transcripts altered were moderately less for MAA-infected tissue than were mucosal tissues infected with the MAP. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis. Bayesian network modeling identified mechanistic genes, gene-to-gene relationships, pathways and Gene Ontologies (GO) biological processes that are involved in specific cell activation during infection. MAP and MAA had significant different pathway perturbation at 0.5 and 12 hours post inoculation. Inverse processes were observed between MAP and MAA response for epithelial cell proliferation, negative regulation of chemotaxis, cell-cell adhesion mediated by integrin and regulation of cytokine-mediated signaling. MAP inoculated tissue had significantly lower expression of phagocytosis receptors such as mannose receptor and complement receptors. This study reveals that perturbation of genes and cellular pathways during MAP infection resulted in host evasion by mucosal membrane barrier weakening to access entry in the ileum, inhibition of Ca signaling associated with decreased phagosome-lysosome fusion as well as phagocytosis inhibition, bias toward Th2 cell immune response accompanied by cell recruitment, cell proliferation and cell differentiation; leading to persistent infection. Contrarily, MAA infection was related to cellular responses associated with activation of molecular pathways that release chemicals and cytokines involved with containment of infection and a strong bias toward Th1 immune response, resulting in a transient infection.

Architecture of cognitive flexibility revealed by lesion mapping

PubMed Central

Barbey, Aron K.; Colom, Roberto; Grafman, Jordan

2013-01-01

Neuroscience has made remarkable progress in understanding the architecture of human intelligence, identifying a distributed network of brain structures that support goal-directed, intelligent behavior. However, the neural foundations of cognitive flexibility and adaptive aspects of intellectual function remain to be well characterized. Here, we report a human lesion study (n = 149) that investigates the neural bases of key competencies of cognitive flexibility (i.e., mental flexibility and the fluent generation of new ideas) and systematically examine their contributions to a broad spectrum of cognitive and social processes, including psychometric intelligence (Wechsler Adult Intelligence Scale), emotional intelligence (Mayer, Salovey, Caruso Emotional Intelligence Test), and personality (Neuroticism–Extraversion–Openness Personality Inventory). Latent variable modeling was applied to obtain error-free indices of each factor, followed by voxel-based lesion-symptom mapping to elucidate their neural substrates. Regression analyses revealed that latent scores for psychometric intelligence reliably predict latent scores for cognitive flexibility (adjusted R2 = 0.94). Lesion mapping results further indicated that these convergent processes depend on a shared network of frontal, temporal, and parietal regions, including white matter association tracts, which bind these areas into an integrated system. A targeted analysis of the unique variance explained by cognitive flexibility further revealed selective damage within the right superior temporal gyrus, a region known to support insight and the recognition of novel semantic relations. The observed findings motivate an integrative framework for understanding the neural foundations of adaptive behavior, suggesting that core elements of cognitive flexibility emerge from a distributed network of brain regions that support specific competencies for human intelligence. PMID:23721727

Reconstructions of human history by mapping dental markers in living Eurasian populations

NASA Astrophysics Data System (ADS)

Kashibadze, Vera F.; Nasonova, Olga G.; Nasonov, Dmitry S.

2013-01-01

Using advances in gene geography and anthropophenetics, the phenogeographical method for anthropological research was initiated and developed using dental data. Statistical and cartographical analyses are provided for 498 living Eurasian populations. Mapping principal components supplied evidence for the phene pool structure in Eurasian populations, and for reconstructions of Homo sapiens history on the continent. Longitudinal variability seems to be the most important regularity revealed by principal components analysis (PCA) and mapping, indicating the division of the whole area into western and eastern main provinces. So, the most ancient scenario in the history of Eurasian populations developed from two perspective different groups: a western group related to ancient populations of West Asia and an eastern one rooted in ancestry in South and/or East Asia. In spite of the enormous territory and the revealed divergence, the populations of the continent have undergone wide scale and intensive timeespace interaction. Many details in the revealed landscapes are background to different historical events. Migrations and assimilation are two essential phenomena in Eurasian history: the widespread of the western combination through the whole continent to the Pacific coastline and the movement of the paradoxical combinations of eastern and western markers from South or Central Asia to the east and west. Taking into account that no additional eastern combinations in the total variation in Asian groups have been found, but that mixed or western markers' sets and that eastern dental characteristics are traced in Asia since Homo erectus, the assumption is made in favour of the hetero-level assimilation in the eastern province and of net-like evolution of H. sapiens.

SSR-enriched genetic linkage maps of bermudagrass (Cynodon dactylon × transvaalensis), and their comparison with allied plant genomes.

PubMed

Khanal, Sameer; Kim, Changsoo; Auckland, Susan A; Rainville, Lisa K; Adhikari, Jeevan; Schwartz, Brian M; Paterson, Andrew H

2017-04-01

We report SSR-enriched genetic maps of bermudagrass that: (1) reveal partial residual polysomic inheritance in the tetraploid species, and (2) provide insights into the evolution of chloridoid genomes. This study describes genetic linkage maps of two bermudagrass species, Cynodon dactylon (T89) and Cynodon transvaalensis (T574), that integrate heterologous microsatellite markers from sugarcane into frameworks built with single-dose restriction fragments (SDRFs). A maximum likelihood approach was used to construct two separate parental maps from a population of 110 F 1 progeny of a cross between the two parents. The T89 map is based on 291 loci on 34 cosegregating groups (CGs), with an average marker spacing of 12.5 cM. The T574 map is based on 125 loci on 14 CGs, with an average marker spacing of 10.7 cM. Six T89 and one T574 CG(s) deviated from disomic inheritance. Furthermore, marker segregation data and linkage phase analysis revealed partial residual polysomic inheritance in T89, suggesting that common bermudagrass is undergoing diploidization following whole genome duplication (WGD). Twenty-six T89 CGs were coalesced into 9 homo(eo)logous linkage groups (LGs), while 12 T574 CGs were assembled into 9 LGs, both putatively representing the basic chromosome complement (x = 9) of the species. Eight T89 and two T574 CGs remain unassigned. The marker composition of bermudagrass ancestral chromosomes was inferred by aligning T89 and T574 homologs, and used in comparisons to sorghum and rice genome sequences based on 108 and 91 significant blast hits, respectively. Two nested chromosome fusions (NCFs) shared by two other chloridoids (i.e., zoysiagrass and finger millet) and at least three independent translocation events were evident during chromosome number reduction from 14 in the polyploid common ancestor of Poaceae to 9 in Cynodon.

Gender differences of the morphology of the distal femur and proximal tibia in a Korean population.

PubMed

Lim, Hong-Chul; Bae, Ji-Hoon; Yoon, Ji-Yeol; Kim, Seung-Ju; Kim, Jae-Gyoon; Lee, Jae-Moon

2013-01-01

We conducted this study to determine whether the sizes of distal femurs and proximal tibiae in Korean men and women are different, and to assess suitability of the sizes of prostheses currently used in Korea. We performed morphological analysis of proximal tibia and distal femur on 115 patients (56 male, 59 female) using MRI to investigate a gender difference. Tibial mediolateral dimension (tMAP), tibial medial anteroposterior dimension (tMAP), tibial lateral anteroposterior dimension (tLAP) femoral mediolateral dimension (fML), femoral medial anteroposterior dimension (fMAP), and femoral lateral anteroposterior dimension (fLAP) were measured. The ratio of tMAP and tLAP to tML (plateau aspect ratio, tAP/tML×100%), and that of fMAP and fLAP to fML (condylar aspect ratio, fAP/fML×100%) were calculated. The measurements were compared with the similar dimensions of four total knee implants currently used. The tML and tAP lengths showed a significant gender difference (P<0.05). The plateau aspect ratio (tMAP/tML) revealed a significant difference between male (0.74±0.05) and female (0.68±0.04, P<0.05). For morphotype of distal femur, males were found to have significantly large values (P<0.05) in the parameters, except for fLAP. With regards to the ratio of the ML width to the AP length, the women showed a narrower ML width than the men. Both genders were distributed within the range of the dimensions of the prostheses currently used prostheses. Korean population revealed that women have smaller dimensions than male counterparts. In both genders, a relatively small size of prostheses matches distal femur and proximal tibia better among the implants currently used in Korea. Copyright © 2012 Elsevier B.V. All rights reserved.

Can Satellite Remote Sensing be Applied in Geological Mapping in Tropics?

NASA Astrophysics Data System (ADS)

Magiera, Janusz

2018-03-01

Remote sensing (RS) techniques are based on spectral data registered by RS scanners as energy reflected from the Earth's surface or emitted by it. In "geological" RS the reflectance (or emittence) should come from rock or sediment. The problem in tropical and subtropical areas is a dense vegetation. Spectral response from the rocks and sediments is gathered only from the gaps among the trees and shrubs. Images of high resolution are appreciated here, therefore. New generation of satellites and scanners (Digital Globe WV2, WV3 and WV4) yield imagery of spatial resolution of 2 m and up to 16 spectral bands (WV3). Images acquired by Landsat (TM, ETM+, OLI) and Sentinel 2 have good spectral resolution too (6-12 bands in visible and infrared) and, despite lower spatial resolution (10-60 m of pixel size) are useful in extracting lithological information too. Lithological RS map may reveal good precision (down to a single rock or outcrop of a meter size). Supplemented with the analysis of Digital Elevation Model and high resolution ortophotomaps (Google Maps, Bing etc.) allows for quick and cheap mapping of unsurveyed areas.

The acute transcriptional response of the coral Acropora millepora to immune challenge: expression of GiMAP/IAN genes links the innate immune responses of corals with those of mammals and plants.

PubMed

Weiss, Yvonne; Forêt, Sylvain; Hayward, David C; Ainsworth, Tracy; King, Rob; Ball, Eldon E; Miller, David J

2013-06-14

As a step towards understanding coral immunity we present the first whole transcriptome analysis of the acute responses of Acropora millepora to challenge with the bacterial cell wall derivative MDP and the viral mimic poly I:C, defined immunogens provoking distinct but well characterised responses in higher animals. These experiments reveal similarities with the responses both of arthropods and mammals, as well as coral-specific effects. The most surprising finding was that MDP specifically induced three members of the GiMAP gene family, which has been implicated in immunity in mammals but is absent from Drosophila and Caenorhabditis. Like their mammalian homologs, GiMAP genes are arranged in a tandem cluster in the coral genome. A phylogenomic survey of this gene family implies ancient origins, multiple independent losses and lineage-specific expansions during animal evolution. Whilst functional convergence cannot be ruled out, GiMAP expression in corals may reflect an ancestral role in immunity, perhaps in phagolysosomal processing.

Genome-wide maps of nuclear lamina interactions in single human cells.

PubMed

Kind, Jop; Pagie, Ludo; de Vries, Sandra S; Nahidiazar, Leila; Dey, Siddharth S; Bienko, Magda; Zhan, Ye; Lajoie, Bryan; de Graaf, Carolyn A; Amendola, Mario; Fudenberg, Geoffrey; Imakaev, Maxim; Mirny, Leonid A; Jalink, Kees; Dekker, Job; van Oudenaarden, Alexander; van Steensel, Bas

2015-09-24

Mammalian interphase chromosomes interact with the nuclear lamina (NL) through hundreds of large lamina-associated domains (LADs). We report a method to map NL contacts genome-wide in single human cells. Analysis of nearly 400 maps reveals a core architecture consisting of gene-poor LADs that contact the NL with high cell-to-cell consistency, interspersed by LADs with more variable NL interactions. The variable contacts tend to be cell-type specific and are more sensitive to changes in genome ploidy than the consistent contacts. Single-cell maps indicate that NL contacts involve multivalent interactions over hundreds of kilobases. Moreover, we observe extensive intra-chromosomal coordination of NL contacts, even over tens of megabases. Such coordinated loci exhibit preferential interactions as detected by Hi-C. Finally, the consistency of NL contacts is inversely linked to gene activity in single cells and correlates positively with the heterochromatic histone modification H3K9me3. These results highlight fundamental principles of single-cell chromatin organization. VIDEO ABSTRACT. Copyright © 2015 Elsevier Inc. All rights reserved.

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia.

PubMed

Amir, El-ad David; Davis, Kara L; Tadmor, Michelle D; Simonds, Erin F; Levine, Jacob H; Bendall, Sean C; Shenfeld, Daniel K; Krishnaswamy, Smita; Nolan, Garry P; Pe'er, Dana

2013-06-01

New high-dimensional, single-cell technologies offer unprecedented resolution in the analysis of heterogeneous tissues. However, because these technologies can measure dozens of parameters simultaneously in individual cells, data interpretation can be challenging. Here we present viSNE, a tool that allows one to map high-dimensional cytometry data onto two dimensions, yet conserve the high-dimensional structure of the data. viSNE plots individual cells in a visual similar to a scatter plot, while using all pairwise distances in high dimension to determine each cell's location in the plot. We integrated mass cytometry with viSNE to map healthy and cancerous bone marrow samples. Healthy bone marrow automatically maps into a consistent shape, whereas leukemia samples map into malformed shapes that are distinct from healthy bone marrow and from each other. We also use viSNE and mass cytometry to compare leukemia diagnosis and relapse samples, and to identify a rare leukemia population reminiscent of minimal residual disease. viSNE can be applied to any multi-dimensional single-cell technology.

Estimating landscape carrying capacity through maximum clique analysis

USGS Publications Warehouse

Donovan, Therese; Warrington, Greg; Schwenk, W. Scott; Dinitz, Jeffrey H.

2012-01-01

Habitat suitability (HS) maps are widely used tools in wildlife science and establish a link between wildlife populations and landscape pattern. Although HS maps spatially depict the distribution of optimal resources for a species, they do not reveal the population size a landscape is capable of supporting--information that is often crucial for decision makers and managers. We used a new approach, "maximum clique analysis," to demonstrate how HS maps for territorial species can be used to estimate the carrying capacity, N(k), of a given landscape. We estimated the N(k) of Ovenbirds (Seiurus aurocapillus) and bobcats (Lynx rufus) in an 1153-km2 study area in Vermont, USA. These two species were selected to highlight different approaches in building an HS map as well as computational challenges that can arise in a maximum clique analysis. We derived 30-m2 HS maps for each species via occupancy modeling (Ovenbird) and by resource utilization modeling (bobcats). For each species, we then identified all pixel locations on the map (points) that had sufficient resources in the surrounding area to maintain a home range (termed a "pseudo-home range"). These locations were converted to a mathematical graph, where any two points were linked if two pseudo-home ranges could exist on the landscape without violating territory boundaries. We used the program Cliquer to find the maximum clique of each graph. The resulting estimates of N(k) = 236 Ovenbirds and N(k) = 42 female bobcats were sensitive to different assumptions and model inputs. Estimates of N(k) via alternative, ad hoc methods were 1.4 to > 30 times greater than the maximum clique estimate, suggesting that the alternative results may be upwardly biased. The maximum clique analysis was computationally intensive but could handle problems with < 1500 total pseudo-home ranges (points). Given present computational constraints, it is best suited for species that occur in clustered distributions (where the problem can be broken into several, smaller problems), or for species with large home ranges relative to grid scale where resampling the points to a coarser resolution can reduce the problem to manageable proportions.

Analysis of protein glycation products by MALDI-TOF/MS.

PubMed

Kislinger, Thomas; Humeny, Andreas; Peich, Carlo C; Becker, Cord-Michael; Pischetsrieder, Monika

2005-06-01

Matrix-assisted laser desorption ionization-mass spectrometry with time-of-flight detection (MALDI-TOF/MS) is a promising tool to analyze advanced glycation end product (AGE)-modified proteins. The combination of soft ionization (MALDI) with time-of-flight mass detection allows analysis of peptides and proteins of a molecular mass up to 300 kDa with minimal sample workup. Because the direct structural analysis of intact AGE proteins is not possible due to the formation of broad and poorly resolved peaks, peptide mapping was introduced into the analysis of AGE proteins by MALDI-TOF/MS, allowing site-specific analysis of defined AGEs. When methylglyoxal-modified lysozyme was subjected to MALDI-TOF/MS peptide mapping, methylimidazolone and argpyrimidine attached to the arginine residue and carboxyethyl (CEL) bound to the lysine were detected on peptide(aa1-7) (KVFGRCE). In contrast, only one methylimidazolone was found on peptide(aa8-35) (LAAAMKRHGLDNYRGYSLGNWVCAAKFE) and peptide(aa120-129) (VQAWIRGCRL), respectively. The analysis of AGE protein, which had been incubated with glucose, revealed the presence of an Amadori product and a carboxymethyl residue (CML) on peptide(aa1-7) and peptide(aa8-35), as well as an imidazolone A on peptide(aa120-129). Furthermore, the early Maillard reaction of lysozyme, which had been glycated by seven different sugars, was monitored by MALDI-TOF/MS peptide mapping. Finally, this approach was successfully applied for site- and product-specific relative quantification of AGEs. For example, kinetics of CML and Amadori product formation on peptide(aa1-7), as well as imidazolone A formation on peptide(aa120-129), were determined.

Mapping of non-numerical domains on space: a systematic review and meta-analysis.

PubMed

Macnamara, Anne; Keage, Hannah A D; Loetscher, Tobias

2018-02-01

The spatial numerical association of response code (SNARC) effect is characterized by low numbers mapped to the left side of space and high numbers mapped to the right side of space. In addition to numbers, SNARC-like effects have been found in non-numerical magnitude domains such as time, size, letters, luminance, and more, whereby the smaller/earlier and larger/later magnitudes are typically mapped to the left and right of space, respectively. The purpose of this systematic and meta-analytic review was to identify and summarise all empirical papers that have investigated horizontal (left-right) SNARC-like mappings using non-numerical stimuli. A systematic search was conducted using EMBASE, Medline, and PsycINFO, where 2216 publications were identified, with 57 papers meeting the inclusion criteria (representing 112 experiments). Ninety-five of these experiments were included in a meta-analysis, resulting in an overall effect size of d = .488 for a SNARC-like effect. Additional analyses revealed a significant effect size advantage for explicit instruction tasks compared with implicit instructions, yet yielded no difference for the role of expertise on SNARC-like effects. There was clear evidence for a publication bias in the field, but the impact of this bias is likely to be modest, and it is unlikely that the SNARC-like effect is a pure artefact of this bias. The similarities in the response properties for the spatial mappings of numerical and non-numerical domains support the concept of a general higher order magnitude system. Yet, further research will need to be conducted to identify all the factors modulating the strength of the spatial associations.

Allelic Analysis of Sheath Blight Resistance with Association Mapping in Rice

PubMed Central

Jia, Limeng; Yan, Wengui; Zhu, Chengsong; Agrama, Hesham A.; Jackson, Aaron; Yeater, Kathleen; Li, Xiaobai; Huang, Bihu; Hu, Biaolin; McClung, Anna; Wu, Dianxing

2012-01-01

Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r = −0.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice. PMID:22427867

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.

PubMed

Staňková, Helena; Hastie, Alex R; Chan, Saki; Vrána, Jan; Tulpová, Zuzana; Kubaláková, Marie; Visendi, Paul; Hayashi, Satomi; Luo, Mingcheng; Batley, Jacqueline; Edwards, David; Doležel, Jaroslav; Šimková, Hana

2016-07-01

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

PodNet, a protein-protein interaction network of the podocyte.

PubMed

Warsow, Gregor; Endlich, Nicole; Schordan, Eric; Schordan, Sandra; Chilukoti, Ravi K; Homuth, Georg; Moeller, Marcus J; Fuellen, Georg; Endlich, Karlhans

2013-07-01

Interactions between proteins crucially determine cellular structure and function. Differential analysis of the interactome may help elucidate molecular mechanisms during disease development; however, this analysis necessitates mapping of expression data on protein-protein interaction networks. These networks do not exist for the podocyte; therefore, we built PodNet, a literature-based mouse podocyte network in Cytoscape format. Using database protein-protein interactions, we expanded PodNet to XPodNet with enhanced connectivity. In order to test the performance of XPodNet in differential interactome analysis, we examined podocyte developmental differentiation and the effect of cell culture. Transcriptomes of podocytes in 10 different states were mapped on XPodNet and analyzed with the Cytoscape plugin ExprEssence, based on the law of mass action. Interactions between slit diaphragm proteins are most significantly upregulated during podocyte development and most significantly downregulated in culture. On the other hand, our analysis revealed that interactions lost during podocyte differentiation are not regained in culture, suggesting a loss rather than a reversal of differentiation for podocytes in culture. Thus, we have developed PodNet as a valuable tool for differential interactome analysis in podocytes, and we have identified established and unexplored regulated interactions in developing and cultured podocytes.

Identifying changes in the support networks of end-of-life carers using social network analysis

PubMed Central

Leonard, Rosemary; Horsfall, Debbie; Noonan, Kerrie

2015-01-01

End-of-life caring is often associated with reduced social networks for both the dying person and for the carer. However, those adopting a community participation and development approach, see the potential for the expansion and strengthening of networks. This paper uses Knox, Savage and Harvey's definitions of three generations social network analysis to analyse the caring networks of people with a terminal illness who are being cared for at home and identifies changes in these caring networks that occurred over the period of caring. Participatory network mapping of initial and current networks was used in nine focus groups. The analysis used key concepts from social network analysis (size, density, transitivity, betweenness and local clustering) together with qualitative analyses of the group's reflections on the maps. The results showed an increase in the size of the networks and that ties between the original members of the network strengthened. The qualitative data revealed the importance between core and peripheral network members and the diverse contributions of the network members. The research supports the value of third generation social network analysis and the potential for end-of-life caring to build social capital. PMID:24644162

Whole-exome analysis of foetal autopsy tissue reveals a frameshift mutation in OBSL1, consistent with a diagnosis of 3-M Syndrome.

PubMed

Marshall, Christian R; Farrell, Sandra A; Cushing, Donna; Paton, Tara; Stockley, Tracy L; Stavropoulos, Dimitri J; Ray, Peter N; Szego, Michael; Lau, Lynette; Pereira, Sergio L; Cohn, Ronald D; Wintle, Richard F; Abuzenadah, Adel M; Abu-Elmagd, Muhammad; Scherer, Stephen W

2015-01-01

We report a consanguineous couple that has experienced three consecutive pregnancy losses following the foetal ultrasound finding of short limbs. Post-termination examination revealed no skeletal dysplasia, but some subtle proximal limb shortening in two foetuses, and a spectrum of mildly dysmorphic features. Karyotype was normal in all three foetuses (46, XX) and comparative genomic hybridization microarray analysis detected no pathogenic copy number variants. Whole-exome sequencing and genome-wide homozygosity mapping revealed a previously reported frameshift mutation in the OBSL1 gene (c.1273insA p.T425nfsX40), consistent with a diagnosis of 3-M Syndrome 2 (OMIM #612921), which had not been anticipated from the clinical findings. Our study provides novel insight into the early clinical manifestations of this form of 3-M syndrome, and demonstrates the utility of whole exome sequencing as a tool for prenatal diagnosis in particular when there is a family history suggestive of a recurrent set of clinical symptoms.

From kissing to belly stridulation: comparative analysis reveals surprising diversity, rapid evolution, and much homoplasy in the mating behaviour of 27 species of sepsid flies (Diptera: Sepsidae).

PubMed

Puniamoorthy, N; Ismail, M R B; Tan, D S H; Meier, R

2009-11-01

Our understanding of how fast mating behaviour evolves in insects is rather poor due to a lack of comparative studies among insect groups for which phylogenetic relationships are known. Here, we present a detailed study of the mating behaviour of 27 species of Sepsidae (Diptera) for which a well-resolved and supported phylogeny is available. We demonstrate that mating behaviour is extremely diverse in sepsids with each species having its own mating profile. We define 32 behavioural characters and document them with video clips. Based on sister species comparisons, we provide several examples where mating behaviour evolves faster than all sexually dimorphic morphological traits. Mapping the behaviours onto the molecular tree reveals much homoplasy, comparable to that observed for third positions of mitochondrial protein-encoding genes. A partitioned Bremer support (PBS) analysis reveals conflict between the molecular and behavioural data, but behavioural characters have higher PBS values per parsimony-informative character than DNA sequence characters.

Modeling Chinese ionospheric layer parameters based on EOF analysis

NASA Astrophysics Data System (ADS)

Yu, You; Wan, Weixing; Xiong, Bo; Ren, Zhipeng; Zhao, Biqiang; Zhang, Yun; Ning, Baiqi; Liu, Libo

2015-05-01

Using 24-ionosonde observations in and around China during the 20th solar cycle, an assimilative model is constructed to map the ionospheric layer parameters (foF2, hmF2, M(3000)F2, and foE) over China based on empirical orthogonal function (EOF) analysis. First, we decompose the background maps from the International Reference Ionosphere model 2007 (IRI-07) into different EOF modes. The obtained EOF modes consist of two factors: the EOF patterns and the corresponding EOF amplitudes. These two factors individually reflect the spatial distributions (e.g., the latitudinal dependence such as the equatorial ionization anomaly structure and the longitude structure with east-west difference) and temporal variations on different time scales (e.g., solar cycle, annual, semiannual, and diurnal variations) of the layer parameters. Then, the EOF patterns and long-term observations of ionosondes are assimilated to get the observed EOF amplitudes, which are further used to construct the Chinese Ionospheric Maps (CIMs) of the layer parameters. In contrast with the IRI-07 model, the mapped CIMs successfully capture the inherent temporal and spatial variations of the ionospheric layer parameters. Finally, comparison of the modeled (EOF and IRI-07 model) and observed values reveals that the EOF model reproduces the observation with smaller root-mean-square errors and higher linear correlation coefficients. In addition, IRI discrepancy at the low latitude especially for foF2 is effectively removed by EOF model.

Modeling Chinese ionospheric layer parameters based on EOF analysis

NASA Astrophysics Data System (ADS)

Yu, You; Wan, Weixing

2016-04-01

Using 24-ionosonde observations in and around China during the 20th solar cycle, an assimilative model is constructed to map the ionospheric layer parameters (foF2, hmF2, M(3000)F2, and foE) over China based on empirical orthogonal function (EOF) analysis. First, we decompose the background maps from the International Reference Ionosphere model 2007 (IRI-07) into different EOF modes. The obtained EOF modes consist of two factors: the EOF patterns and the corresponding EOF amplitudes. These two factors individually reflect the spatial distributions (e.g., the latitudinal dependence such as the equatorial ionization anomaly structure and the longitude structure with east-west difference) and temporal variations on different time scales (e.g., solar cycle, annual, semiannual, and diurnal variations) of the layer parameters. Then, the EOF patterns and long-term observations of ionosondes are assimilated to get the observed EOF amplitudes, which are further used to construct the Chinese Ionospheric Maps (CIMs) of the layer parameters. In contrast with the IRI-07 model, the mapped CIMs successfully capture the inherent temporal and spatial variations of the ionospheric layer parameters. Finally, comparison of the modeled (EOF and IRI-07 model) and observed values reveals that the EOF model reproduces the observation with smaller root-mean-square errors and higher linear correlation co- efficients. In addition, IRI discrepancy at the low latitude especially for foF2 is effectively removed by EOF model.

Meta-analysis of Polyploid Cotton QTL Shows Unequal Contributions of Subgenomes to a Complex Network of Genes and Gene Clusters Implicated in Lint Fiber Development

PubMed Central

Rong, Junkang; Feltus, F. Alex; Waghmare, Vijay N.; Pierce, Gary J.; Chee, Peng W.; Draye, Xavier; Saranga, Yehoshua; Wright, Robert J.; Wilkins, Thea A.; May, O. Lloyd; Smith, C. Wayne; Gannaway, John R.; Wendel, Jonathan F.; Paterson, Andrew H.

2007-01-01

QTL mapping experiments yield heterogeneous results due to the use of different genotypes, environments, and sampling variation. Compilation of QTL mapping results yields a more complete picture of the genetic control of a trait and reveals patterns in organization of trait variation. A total of 432 QTL mapped in one diploid and 10 tetraploid interspecific cotton populations were aligned using a reference map and depicted in a CMap resource. Early demonstrations that genes from the non-fiber-producing diploid ancestor contribute to tetraploid lint fiber genetics gain further support from multiple populations and environments and advanced-generation studies detecting QTL of small phenotypic effect. Both tetraploid subgenomes contribute QTL at largely non-homeologous locations, suggesting divergent selection acting on many corresponding genes before and/or after polyploid formation. QTL correspondence across studies was only modest, suggesting that additional QTL for the target traits remain to be discovered. Crosses between closely-related genotypes differing by single-gene mutants yield profoundly different QTL landscapes, suggesting that fiber variation involves a complex network of interacting genes. Members of the lint fiber development network appear clustered, with cluster members showing heterogeneous phenotypic effects. Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks. PMID:17565937

Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development.

PubMed

Rong, Junkang; Feltus, F Alex; Waghmare, Vijay N; Pierce, Gary J; Chee, Peng W; Draye, Xavier; Saranga, Yehoshua; Wright, Robert J; Wilkins, Thea A; May, O Lloyd; Smith, C Wayne; Gannaway, John R; Wendel, Jonathan F; Paterson, Andrew H

2007-08-01

QTL mapping experiments yield heterogeneous results due to the use of different genotypes, environments, and sampling variation. Compilation of QTL mapping results yields a more complete picture of the genetic control of a trait and reveals patterns in organization of trait variation. A total of 432 QTL mapped in one diploid and 10 tetraploid interspecific cotton populations were aligned using a reference map and depicted in a CMap resource. Early demonstrations that genes from the non-fiber-producing diploid ancestor contribute to tetraploid lint fiber genetics gain further support from multiple populations and environments and advanced-generation studies detecting QTL of small phenotypic effect. Both tetraploid subgenomes contribute QTL at largely non-homeologous locations, suggesting divergent selection acting on many corresponding genes before and/or after polyploid formation. QTL correspondence across studies was only modest, suggesting that additional QTL for the target traits remain to be discovered. Crosses between closely-related genotypes differing by single-gene mutants yield profoundly different QTL landscapes, suggesting that fiber variation involves a complex network of interacting genes. Members of the lint fiber development network appear clustered, with cluster members showing heterogeneous phenotypic effects. Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks.

Carotenoids co-localize with hydroxyapatite, cholesterol, and other lipids in calcified stenotic aortic valves. Ex vivo Raman maps compared to histological patterns.

PubMed

Bonetti, A; Bonifacio, A; Della Mora, A; Livi, U; Marchini, M; Ortolani, F

2015-04-20

Unlike its application for atherosclerotic plaque analysis, Raman microspectroscopy was sporadically used to check the sole nature of bioapatite deposits in stenotic aortic valves, neglecting the involvement of accumulated lipids/lipoproteins in the calcific process. Here, Raman microspectroscopy was employed for examination of stenotic aortic valve leaflets to add information on nature and distribution of accumulated lipids and their correlation with mineralization in the light of its potential precocious diagnostic use. Cryosections from surgically explanted stenotic aortic valves (n=4) were studied matching Raman maps against specific histological patterns. Raman maps revealed the presence of phospholipids/triglycerides and cholesterol, which showed spatial overlapping with one another and Raman-identified hydroxyapatite. Moreover, the Raman patterns correlated with those displayed by both von-Kossa-calcium- and Nile-blue-stained serial cryosections. Raman analysis also provided the first identification of carotenoids, which co-localized with the identified lipid moieties. Additional fit concerned the distribution of collagen and elastin. The good correlation of Raman maps with high-affinity staining patterns proved that Raman microspectroscopy is a reliable tool in evaluating calcification degree, alteration/displacement of extracellular matrix components, and accumulation rate of different lipid forms in calcified heart valves. In addition, the novel identification of carotenoids supports the concept that valve stenosis is an atherosclerosis-like valve lesion, consistently with their previous Raman microspectroscopical identification inside atherosclerotic plaques.

EEG microstates during resting represent personality differences.

PubMed

Schlegel, Felix; Lehmann, Dietrich; Faber, Pascal L; Milz, Patricia; Gianotti, Lorena R R

2012-01-01

We investigated the spontaneous brain electric activity of 13 skeptics and 16 believers in paranormal phenomena; they were university students assessed with a self-report scale about paranormal beliefs. 33-channel EEG recordings during no-task resting were processed as sequences of momentary potential distribution maps. Based on the maps at peak times of Global Field Power, the sequences were parsed into segments of quasi-stable potential distribution, the 'microstates'. The microstates were clustered into four classes of map topographies (A-D). Analysis of the microstate parameters time coverage, occurrence frequency and duration as well as the temporal sequence (syntax) of the microstate classes revealed significant differences: Believers had a higher coverage and occurrence of class B, tended to decreased coverage and occurrence of class C, and showed a predominant sequence of microstate concatenations from A to C to B to A that was reversed in skeptics (A to B to C to A). Microstates of different topographies, putative "atoms of thought", are hypothesized to represent different types of information processing.The study demonstrates that personality differences can be detected in resting EEG microstate parameters and microstate syntax. Microstate analysis yielded no conclusive evidence for the hypothesized relation between paranormal belief and schizophrenia.

Transcriptional atlas of cardiogenesis maps congenital heart disease interactome.

PubMed

Li, Xing; Martinez-Fernandez, Almudena; Hartjes, Katherine A; Kocher, Jean-Pierre A; Olson, Timothy M; Terzic, Andre; Nelson, Timothy J

2014-07-01

Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, knowledge of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Mapping the dynamic transcriptional landscape of cardiogenesis from a genomic perspective is essential to integrate the knowledge of heart development into translational applications that accelerate disease discovery efforts toward mechanistic-based treatment strategies. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide dynamic expression landscape of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, revealed stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling known genetic underpinnings of CHD, we deconstructed a disease-centric dynamic interactome encoded within this cardiogenic atlas to identify stage-specific developmental disturbances clustered on regulation of epithelial-to-mesenchymal transition (EMT), BMP signaling, NF-AT signaling, TGFb-dependent EMT, and Notch signaling. Collectively, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease. Copyright © 2014 the American Physiological Society.

A mapping and monitoring assessment of the Philippines' mangrove forests from 1990 to 2010

USGS Publications Warehouse

Long, Jordan; Napton, Darrell; Giri, Chandra; Graesser, Jordan

2014-01-01

Information on the present condition and spatiotemporal dynamics of mangrove forests is needed for land-change studies and integrated natural resources planning and management. Although several national mangrove estimates for the Philippines exist, information is unavailable at sufficient spatial and thematic detail for change analysis. Historical and contemporary mangrove distribution maps of the Philippines for 1990 and 2010 were prepared at nominal 30-m spatial resolution using Landsat satellite data. Image classification was performed using a supervised decision tree classification approach. Additionally, decadal land-cover change maps from 1990 to 2010 were prepared to depict changes in mangrove area. Total mangrove area decreased 10.5% from 1990 to 2010. Comparison of estimates produced from this study with selected historical mangrove area estimates revealed that total mangrove area decreased by approximately half (51.8%) from 1918 to 2010. This study provides the most current and reliable data regarding the Philippines mangrove area and spatial distribution and delineates where and when mangrove change has occurred in recent decades. The results from this study are useful for developing conservation strategies, biodiversity loss mitigation efforts, and future monitoring and analysis.

[Medical and ecological assessment of climate effects on urolithiasis morbidity in population of Primorsky territory].

PubMed

Koval'chuk, V K

2004-01-01

The article presents medicoecological estimation of quantitative relations between monsoon climate and urolithiasis primary morbidity in the Primorsky Territory. Quantitative estimation of the climate was performed by V. I. Rusanov (1973) who calculated daily meteorological data for 1 p.m. throughout 1991-1999. Primary urolithiasis morbidity for this period of time was provided by regional health department. The data were processed by methods of medical mapping and paired correlation analysis. In the Territory, mapping revealed the same location of the zones with high frequency of discomfortable weather of class V and VI causing chilblain in positive air temperatures and zones with elevated primary urolithiasis morbidity in children and adults. Correlation analysis confirmed mapping results and determined significant negative correlations between frequency of relatively comfortable moment weather classes II-IV and morbidity of children and adults, positive correlation between frequency of discomfortable class VI and adult morbidity. Thus, high frequency of days per year with discomfortable classes of moment weather in low positive air temperatures may be one of the factors of urolithiasis risk in population of the Primorsky Territory. Climatic factors should be taken into consideration in planning primary prophylaxis of this disease in the Primorsky Territory.

Comparing Tactile Maps and Haptic Digital Representations of a Maritime Environment

ERIC Educational Resources Information Center

Simonnet, Mathieu; Vieilledent, Steephane; Jacobson, R. Daniel; Tisseau, Jacques

2011-01-01

A map exploration and representation exercise was conducted with participants who were totally blind. Representations of maritime environments were presented either with a tactile map or with a digital haptic virtual map. We assessed the knowledge of spatial configurations using a triangulation technique. The results revealed that both types of…

Genome Comparisons Reveal a Dominant Mechanism of Chromosome Number Reduction in Grasses and Accelerated Genome Evolution in Triticeae

USDA-ARS?s Scientific Manuscript database

Single nucleotide polymorphism was employed in the construction of a high-resolution, expressed sequence tag (EST) map of Aegilops tauschii, the diploid source of the wheat D genome. Comparison of the map with the rice and sorghum genome sequences revealed 50 inversions and translocations; 2, 8, and...

Coarse analysis of collective behaviors: Bifurcation analysis of the optimal velocity model for traffic jam formation

NASA Astrophysics Data System (ADS)

Miura, Yasunari; Sugiyama, Yuki

2017-12-01

We present a general method for analyzing macroscopic collective phenomena observed in many-body systems. For this purpose, we employ diffusion maps, which are one of the dimensionality-reduction techniques, and systematically define a few relevant coarse-grained variables for describing macroscopic phenomena. The time evolution of macroscopic behavior is described as a trajectory in the low-dimensional space constructed by these coarse variables. We apply this method to the analysis of the traffic model, called the optimal velocity model, and reveal a bifurcation structure, which features a transition to the emergence of a moving cluster as a traffic jam.

Online testable concept maps: benefits for learning about the pathogenesis of disease.

PubMed

Ho, Veronica; Kumar, Rakesh K; Velan, Gary

2014-07-01

Concept maps have been used to promote meaningful learning and critical thinking. Although these are crucially important in all disciplines, evidence for the benefits of concept mapping for learning in medicine is limited. We performed a randomised crossover study to assess the benefits of online testable concept maps for learning in pathology by volunteer junior medical students. Participants (n = 65) were randomly allocated to either of two groups with equivalent mean prior academic performance, in which they were given access to either online maps or existing online resources for a 2-week block on renal disease. Groups then crossed over for a 2-week block on hepatic disease. Outcomes were assessed using timed online quizzes, which included questions unrelated to topics in the pathogenesis maps as an internal control. Questionnaires were administered to evaluate students' acceptance of the maps. In both blocks, the group with access to pathogenesis maps achieved significantly higher average scores than the control group on quiz questions related to topics covered by the maps (Block 1: p < 0.001, Cohen's d = 0.9; Block 2: p = 0.008, Cohen's d = 0.7). However, mean scores on unrelated questions did not differ significantly between the groups. In a third block on pancreatic disease, both groups received pathogenesis maps and collectively performed significantly better on quiz topics related to the maps than on unrelated topics (p < 0.01, Cohen's d = 0.5). Regression analysis revealed that access to pathogenesis maps was the dominant contributor to variance in performance on map-related quiz questions. Responses to questionnaire items on pathogenesis maps were overwhelmingly positive in both groups. These results indicate that online testable pathogenesis maps are well accepted and can improve learning of concepts in pathology by medical students. © 2014 John Wiley & Sons Ltd.

Lymphatic mapping for gastric adenocarcinoma.

PubMed

Hundley, Jon C; Shen, Perry; Shiver, Stephen A; Geisinger, Kim R; Levine, Edward A

2002-11-01

The role of lymphadenectomy for gastric carcinoma has been debated for decades. Lymphatic mapping has revolutionized the treatment of melanoma and breast cancer. However, its potential utility in guiding lymphadenectomy for gastric carcinoma is unknown. Therefore we initiated a trial to investigate lymphatic mapping for gastric carcinoma at Wake Forest University Baptist Medical Center. Lymphatic mapping for gastric carcinoma was attempted in 14 cases of gastric carcinoma. Mapping was performed by perilesional injection of isosulfan blue and the first node in the draining basin was harvested and sent fresh to pathology. Sentinel lymph nodes (SLNs) were evaluated by hematoxylin and eosin (H&E) staining. Immunohistochemical analysis was performed on all SLNs that were found to be negative on initial histologic studies. Radical gastrectomy with celiac node dissection was performed in all cases. SLNs were identified in 14 cases. In one case the technique was abandoned because of bulk nodal disease. The average number of SLNs found in each case was 2.8 with a range of one to five. Eight of 14 patients were found to have SLNs positive for metastatic carcinoma. In seven of these patients pathologic analysis of the final resection specimen confirmed the presence of nodal disease. In one case carcinoma was found in a SLN on touch preparation and no nodal disease was noted in the resection specimen. Immunohistochemical studies performed on SLNs found to be negative on initial H&E histologic analysis failed to reveal the presence of carcinoma. The overall sensitivity and specificity were found to be 72.7 and 75 per cent, respectively. Lymphatic mapping is technically possible in the setting of gastric carcinoma and SLNs can be successfully identified in the majority of cases. Upstaging occurred in one case which may have ramifications for adjuvant therapy. SLN positivity accurately predicts the presence of additional nodal disease beyond the SLN in the final resection specimen (positive predictive value 89%). However, SLN negativity does not definitively prove that the remaining nodal basin is free of disease (negative predictive value 50%). Lymphatic mapping for gastric carcinoma is a promising technique worthy of further investigation.

A Chromosome-Scale Assembly of the Bactrocera cucurbitae Genome Provides Insight to the Genetic Basis of white pupae

PubMed Central

Sim, Sheina B.; Geib, Scott M.

2017-01-01

Genetic sexing strains (GSS) used in sterile insect technique (SIT) programs are textbook examples of how classical Mendelian genetics can be directly implemented in the management of agricultural insect pests. Although the foundation of traditionally developed GSS are single locus, autosomal recessive traits, their genetic basis are largely unknown. With the advent of modern genomic techniques, the genetic basis of sexing traits in GSS can now be further investigated. This study is the first of its kind to integrate traditional genetic techniques with emerging genomics to characterize a GSS using the tephritid fruit fly pest Bactrocera cucurbitae as a model. These techniques include whole-genome sequencing, the development of a mapping population and linkage map, and quantitative trait analysis. The experiment designed to map the genetic sexing trait in B. cucurbitae, white pupae (wp), also enabled the generation of a chromosome-scale genome assembly by integrating the linkage map with the assembly. Quantitative trait loci analysis revealed SNP loci near position 42 MB on chromosome 3 to be tightly linked to wp. Gene annotation and synteny analysis show a near perfect relationship between chromosomes in B. cucurbitae and Muller elements A–E in Drosophila melanogaster. This chromosome-scale genome assembly is complete, has high contiguity, was generated using a minimal input DNA, and will be used to further characterize the genetic mechanisms underlying wp. Knowledge of the genetic basis of genetic sexing traits can be used to improve SIT in this species and expand it to other economically important Diptera. PMID:28450369

Titanic exploration with GIS

USGS Publications Warehouse

Kerski, J.J.

2004-01-01

To help teachers and students investigate one of the world's most famous historical events using the geographic perspective and GIS tools and methods, the U.S. Geological Survey (USGS) created a set of educational lessons based on the RMS Titanic's April 1912 sailing. With these lessons, student researchers can learn about latitude and longitude, map projections, ocean currents, databases, maps, and images through the analysis of the route, warnings, sinking, rescue, and eventual discovery of the submerged ocean liner in 1985. They can also consider the human and physical aspects of the maiden voyage in the North Atlantic Ocean at a variety of scales, from global to regional to local. Likewise, their investigations can reveal how the sinking of the Titanic affected future shipping routes.

Mapping protease substrates using a biotinylated phage substrate library.

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

Scholle, M. D.; Kriplani, U.; Pabon, A.

We describe a bacteriophage M13 substrate library encoding the AviTag (BirA substrate) and combinatorial heptamer peptides displayed at the N terminus of the mature form of capsid protein III. Phages are biotinylated efficiently (> or = 50%) when grown in E. coli cells coexpressing BirA, and such viral particles can be immobilized on a streptavidin-coated support and released by protease cleavage within the combinatorial peptide. We have used this library to map the specificity of human Factor Xa and a neuropeptidase, neurolysin (EC3.4.24.16). Validation by analysis of isolated peptide substrates has revealed that neurolysin recognizes the motif hydrophobic-X-Pro-Arg-hydrophobic, where Arg-hydrophobicmore » is the scissile bond.« less

Team talk and team activity in simulated medical emergencies: a discourse analytical approach.

PubMed

Gundrosen, Stine; Andenæs, Ellen; Aadahl, Petter; Thomassen, Gøril

2016-11-14

Communication errors can reduce patient safety, especially in emergency situations that require rapid responses by experts in a number of medical specialties. Talking to each other is crucial for utilizing the collective expertise of the team. Here we explored the functions of "team talk" (talking between team members) with an emphasis on the talk-work relationship in interdisciplinary emergency teams. Five interdisciplinary medical emergency teams were observed and videotaped during in situ simulations at an emergency department at a university hospital in Norway. Team talk and simultaneous actions were transcribed and analysed. We used qualitative discourse analysis to perform structural mapping of the team talk and to analyse the function of online commentaries (real-time observations and assessments of observations based on relevant cues in the clinical situation). Structural mapping revealed recurring and diverse patterns. Team expansion stood out as a critical phase in the teamwork. Online commentaries that occurred during the critical phase served several functions and demonstrated the inextricable interconnections between team talk and actions. Discourse analysis allowed us to capture the dynamics and complexity of team talk during a simulated emergency situation. Even though the team talk did not follow a predefined structure, the team members managed to manoeuvre safely within the complex situation. Our results support that online commentaries contributes to shared team situation awareness. Discourse analysis reveals naturally occurring communication strategies that trigger actions relevant for safe practice and thus provides supplemental insights into what comprises "good" team communication in medical emergencies.

Identification and nucleotide sequence analysis of the repetitive DNA element in the genome of fish lymphocystis disease virus.

PubMed

Schnitzler, P; Delius, H; Scholz, J; Touray, M; Orth, E; Darai, G

1987-12-01

The genome of the fish lymphocystis disease virus (FLDV) was screened for the existence of repetitive DNA sequences using a defined and complete gene library of the viral genome (98 kbp) by DNA-DNA hybridization, heteroduplex analysis, and restriction fine mapping. A repetitive DNA sequence was detected at the coordinates 0.034 to 0.057 and 0.718 to 0.736 map units (m.u.) of the FLDV genome. The first region (0.034 to 0.057 m.u.) corresponds to the 5' terminus of the EcoRI FLDV DNA fragment B (0.034 to 0.165 m.u.) and the second region (0.718 to 0.736 m.u.) is identical to the EcoRI DNA fragment M of the viral genome. The DNA nucleotide sequence of the EcoRI FLDV DNA fragment M was determined. This analysis revealed the presence of many short direct and inverted repetitions, e.g., a 18-mer direct repetition (TTTAAAATTTAATTAA) that started at nucleotide positions 812 and 942 and a 14-mer inverted repeat (TTAAATTTAAATTT) at nucleotide positions 820 and 959. Only short open reading frames were detected within this region. The DNA repetitions are discussed as sequences that play a possible regulatory role for virus replication. Furthermore, hybridization experiments revealed that the repetitive DNA sequences are conserved in the genome of different strains of fish lymphocystis disease virus isolated from two species of Pleuronectidae (flounder and dab).

Identification and fine mapping of a stay-green gene (Brnye1) in pakchoi (Brassica campestris L. ssp. chinensis).

PubMed

Wang, Nan; Liu, Zhiyong; Zhang, Yun; Li, Chengyu; Feng, Hui

2018-03-01

Using bulked segregant analysis combined with next-generation sequencing, we delimited the Brnye1 gene responsible for the stay-green trait of nye in pakchoi. Sequence analysis identified Bra019346 as the candidate gene. "Stay-green" refers to a plant trait whereby leaves remain green during senescence. This trait is useful in the cultivation of pakchoi (Brassica campestris L. ssp. chinensis), which is marketed as a green leaf product. This study aimed to identify the gene responsible for the stay-green trait in pakchoi. We identified a stay-green mutant in pakchoi, which we termed "nye". Genetic analysis revealed that the stay-green trait is controlled by a single recessive gene, Brnye1. Using the BSA-seq method, a 3.0-Mb candidate region was mapped on chromosome A03, which helped us localize Brnye1 to an 81.01-kb interval between SSR markers SSRWN27 and SSRWN30 via linkage analysis in an F 2 population. We identified 12 genes in this region, 11 of which were annotated based on the Brassica rapa annotation database, and one was a functionally unknown gene. An orthologous gene of the Arabidopsis gene AtNYE1, Bra019346, was identified as the potential candidate for Brnye1. Sequence analysis revealed a 40-bp insertion in the second exon of Bra019346 in nye, which generated the TAA stop codon. A candidate gene-specific Indel marker in 1561 F 2 individuals showed perfect cosegregation with Brnye1 in the nye mutant. These results provide a foundation for uncovering the molecular mechanism of the stay-green trait in pakchoi.

A Hurricane Hits Home: An Interactive Science Museum Exhibit on Ocean Mapping and Marine Debris

NASA Astrophysics Data System (ADS)

Butkiewicz, T.; Vasta, D. J.; Gager, N. C.; Fruth, B. W.; LeClair, J.

2016-12-01

As part of the outreach component for a project involving the detection and analysis of marine debris generated by Super Storm Sandy, The Center for Coastal and Ocean Mapping / Joint Hydrographic Center partnered with The Seacoast Science Center to develop an interactive museum exhibit that engages the public with a touchscreen based game revolving around the detection and identification of marine debris. "A Hurricane Hits Home" is a multi-station touchscreen exhibit geared towards children, and integrates a portion of a historical wooden shipwreck into its physical design. The game invites museum guests to examine a number of coastal regions and harbors in Sandy affected areas. It teaches visitors about modern mapping technology by having them control boats with multibeam sonars and airplanes with lidar sensors. They drag these vehicles around maps to reveal the underlying bathymetry below the satellite photos. They learn the applications and limitations of sonar and lidar by where the vehicles can and cannot collect survey data (e.g. lidar doesn't work in deep water, and the boat can't go in shallow areas). As users collect bathymetry data, they occasionally reveal marine debris objects on the seafloor. Once all the debris objects in a level have been located, the game challenges them to identify them based on their appearance in the bathymetry data. They must compare the simulated bathymetry images of the debris targets to photos of possible objects, and choose the correct matches to achieve a high score. The exhibit opened January 2016 at the Seacoast Science Center in Rye, NH.

Neural substrates of lower extremity motor, balance, and gait function after supratentorial stroke using voxel-based lesion symptom mapping.

PubMed

Moon, Hyun Im; Pyun, Sung-Bom; Tae, Woo-Suk; Kwon, Hee Kyu

2016-07-01

Stroke impairs motor, balance, and gait function and influences activities of daily living. Understanding the relationship between brain lesions and deficits can help clinicians set goals during rehabilitation. We sought to elucidate the neural substrates of lower extremity motor, balance, and ambulation function using voxel-based lesion symptom mapping (VLSM) in supratentorial stroke patients. We retrospectively screened patients who met the following criteria: first-ever stroke, supratentorial lesion, and available brain magnetic resonance imaging (MRI) data. MRIs of 133 stroke patients were selected for VLSM analysis. We generated statistical maps of lesions related to lower extremity motor (lower extremity Fugl-Meyer assessment, LEFM), balance (Berg Balance Scale, BBS), and gait (Functional Ambulation Category, FAC) using VLSM. VLSM revealed that lower LEFM scores were associated with damage to the bilateral basal ganglia, insula, internal capsule, and subgyral white matter adjacent to the corona radiata. The lesions were more widely distributed in the left than in the right hemisphere, representing motor and praxis function necessary for performing tasks. However, no associations between lesion maps and balance and gait function were established. Motor impairment of the lower extremities was associated with lesions in the basal ganglia, insula, internal capsule, and white matter adjacent to the corona radiata. However, VLSM revealed no specific lesion locations with regard to balance and gait function. This might be because balance and gait are complex skills that require spatial and temporal integration of sensory input and execution of movement patterns. For more accurate prediction, factors other than lesion location need to be investigated.

NanoSIMS Reveals New Structural and Elemental Signatures of Early Life

NASA Technical Reports Server (NTRS)

Oehler, Dorothy Z.; Mostefaoui, Smail; Meibom, Anders; Selo, Madeleine; Robert, Francois; McKay, David S.

2006-01-01

The young technology of NanoSIMS is unlocking new information from organic matter in ancient sediments. We have used this technique to characterize sub-micron scale element composition of Proterozoic organics that are clearly biogenic as a guide for interpreting problematic structures in terrestrial or extraterrestrial samples. We used the NanoSIMS 50 of the National Museum of Natural History in Paris to map carbon, nitrogen (as CN), and sulfur in organic structures from the approximately 0.8 Ga Bitter Springs Formation. We analyzed spheroidal and filamentous microfossils as well as organic laminae that appeared amorphous by optical and scanning electron microscopy. In clear-cut microfossils, a coincidence between optical images and NanoSIMS element maps suggests a biological origin for the mapped carbon, sulfur, and nitrogen; this conclusion is supported by high resolution NanoSIMS maps showing identical spatial distributions of C, CN and S. High resolution images also demonstrate distinctive nano structure of the filaments and spheroids. In the amorphous laminae, NanoSIMS reveals morphologies reminiscent of compressed microfossils. Distinct CN/C ratios of the spheroids, filaments, and laminae may reflect their biological precursors (cell walls, cyanobacterial sheaths, and microbial communities/biofilms, respectively). Similar amorphous laminae comprise a preponderance of the organic matter in many Precambrian deposits. Thus it is possible that NanoSIMS will provide fresh insight into a large body of previously uninterpretable material. Additionally, NanoSIMS analysis may establish new biosignatures that will be helpful for assessing the origin and biogenicity of controversial Archean structures and any organic materials that may occur in Martian or other extraterrestrial samples.

Production and actions of the anandamide metabolite prostamide E2 in the renal medulla.

PubMed

Ritter, Joseph K; Li, Cao; Xia, Min; Poklis, Justin L; Lichtman, Aron H; Abdullah, Rehab A; Dewey, William L; Li, Pin-Lan

2012-09-01

Medullipin has been proposed to be an antihypertensive lipid hormone released from the renal medulla in response to increased arterial pressure and renal medullary blood flow. Because anandamide (AEA) possesses characteristics of this purported hormone, the present study tested the hypothesis that AEA or one of its metabolites represents medullipin. AEA was demonstrated to be enriched in the kidney medulla compared with cortex. Western blotting and enzymatic analyses of renal cortical and medullary microsomes revealed opposite patterns of enrichment of two AEA-metabolizing enzymes, with fatty acid amide hydrolase higher in the renal cortex and cyclooxygenase-2 (COX-2) higher in the renal medulla. In COX-2 reactions with renal medullary microsomes, prostamide E2, the ethanolamide of prostaglandin E₂, was the major product detected. Intramedullarily infused AEA dose-dependently increased urine volume and sodium and potassium excretion (15-60 nmol/kg/min) but had little effect on mean arterial pressure (MAP). The renal excretory effects of AEA were blocked by intravenous infusion of celecoxib (0.1 μg/kg/min), a selective COX-2 inhibitor, suggesting the involvement of a prostamide intermediate. Plasma kinetic analysis revealed longer elimination half-lives for AEA and prostamide E2 compared with prostaglandin E₂. Intravenous prostamide E2 reduced MAP and increased renal blood flow (RBF), actions opposite to those of angiotensin II. Coinfusion of prostamide E2 inhibited angiotensin II effects on MAP and RBF. These results suggest that AEA and/or its prostamide metabolites in the renal medulla may represent medullipin and function as a regulator of body fluid and MAP.

Genetic diversity and investigation of polledness in divergent goat populations using 52 088 SNPs.

PubMed

Kijas, James W; Ortiz, Judit S; McCulloch, Russell; James, Andrew; Brice, Blair; Swain, Ben; Tosser-Klopp, Gwenola

2013-06-01

The recent availability of a genome-wide SNP array for the goat genome dramatically increases the power to investigate aspects of genetic diversity and to conduct genome-wide association studies in this important domestic species. We collected and analysed genotypes from 52 088 SNPs in Boer, Cashmere and Rangeland goats that had both polled and horned individuals. Principal components analysis revealed a clear genetic division between animals for each population, and model-based clustering successfully detected evidence of admixture that matched aspects of their recorded history. For example, shared co-ancestry was detected, suggesting Boer goats have been introgressed into the Rangeland population. Further, allele frequency data successfully tracked the altered genetic profile that has taken place after 40 years of breeding Australian Cashmere goats using the Rangeland animals as the founding population. Genome-wide association mapping of the POLL locus revealed a strong signal on goat chromosome 1. The 769-kb critical interval contained the polled intersex syndrome locus, confirming the genetic basis in non-European animals is the same as identified previously in Saanen goats. Interestingly, analysis of the haplotypes carried by a small set of sex-reversed animals, known to be associated with polledness, revealed some animals carried the wild-type chromosome associated with the presence of horns. This suggests a more complex basis for the relationship between polledness and the intersex condition than initially thought while validating the application of the goat SNP50 BeadChip for fine-mapping traits in goat. © The Author(s) and Commonwealth of Australia. Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

Isotropy analyses of the Planck convergence map

NASA Astrophysics Data System (ADS)

Marques, G. A.; Novaes, C. P.; Bernui, A.; Ferreira, I. S.

2018-01-01

The presence of matter in the path of relic photons causes distortions in the angular pattern of the cosmic microwave background (CMB) temperature fluctuations, modifying their properties in a slight but measurable way. Recently, the Planck Collaboration released the estimated convergence map, an integrated measure of the large-scale matter distribution that produced the weak gravitational lensing (WL) phenomenon observed in Planck CMB data. We perform exhaustive analyses of this convergence map calculating the variance in small and large regions of the sky, but excluding the area masked due to Galactic contaminations, and compare them with the features expected in the set of simulated convergence maps, also released by the Planck Collaboration. Our goal is to search for sky directions or regions where the WL imprints anomalous signatures to the variance estimator revealed through a χ2 analyses at a statistically significant level. In the local analysis of the Planck convergence map, we identified eight patches of the sky in disagreement, in more than 2σ, with what is observed in the average of the simulations. In contrast, in the large regions analysis we found no statistically significant discrepancies, but, interestingly, the regions with the highest χ2 values are surrounding the ecliptic poles. Thus, our results show a good agreement with the features expected by the Λ cold dark matter concordance model, as given by the simulations. Yet, the outliers regions found here could suggest that the data still contain residual contamination, like noise, due to over- or underestimation of systematic effects in the simulation data set.

Terrain analysis of the racetrack basin and the sliding rocks of Death Valley

USGS Publications Warehouse

Messina, P.; Stoffer, P.

2000-01-01

The Racetrack Playa's unusual surface features known as sliding rocks have been the subject of an ongoing debate and several mapping projects for half a century, although the causative mechanism remains unresolved. Clasts ranging in volume from large pebbles to medium boulders have, unwitnessed, maneuvered around the nearly flat dry lake over considerable distances. The controversy has persisted partly because eyewitness accounts of the phenomenon continue to be lacking, and the earlier mapping missions were limited in method and geographic range. In July 1996, we generated the first complete map of all observed sliding rock trails by submeter differential Global Positioning System (DGPS) mapping technology. The resulting map shows 162 sliding rocks and associated trails to an accuracy of approximately 30 cm. Although anemometer data are not available in the Racetrack wilderness, wind is clearly a catalyst for sliding rock activity; an inferred wind rose was constructed from DGPS trail segment data. When the entire trail network is examined in plan, some patterns emerge, although other (perhaps expected relations) remain elusive: terrain analysis of the surrounding topography demonstrates that the length and morphology of trails are more closely related to where rocks rested at the onset of motion than to any physical attribute of the rocks themselves. Follow-up surveys in May 1998, May 1999, August 1999, and November 1999 revealed little modification of the July, 1996 sliding rock configuration. Only four rocks were repositioned during the El Nino winter of 1997-1998, suggesting that activity may not be restricted to winter storms. (C) 2000 Elsevier Science B.V. All rights reserved.

Atom probe tomographic mapping directly reveals the atomic distribution of phosphorus in resin embedded ferritin

DOE PAGES

Perea, Daniel E.; Liu, Jia; Bartrand, Jonah A. G.; ...

2016-02-29

In this study, we report the atomic-scale analysis of biological interfaces using atom probe tomography. Embedding the protein ferritin in an organic polymer resin lacking nitrogen provided chemical contrast to visualize atomic distributions and distinguish organic-organic and organic-inorganic interfaces. The sample preparation method can be directly extended to further enhance the study of biological, organic and inorganic nanomaterials relevant to health, energy or the environment.

Structure of the c-Ki-ras gene in a rat fibrosarcoma induced by 1,8-dinitropyrene.

PubMed Central

Tahira, T; Hayashi, K; Ochiai, M; Tsuchida, N; Nagao, M; Sugimura, T

1986-01-01

Restriction enzyme maps were made of the region around exons 1 and 2 of activated c-Ki-ras of a fibrosarcoma (1,8-DNP2) induced in a rat by 1,8-dinitropyrene. Nucleotide sequence analysis revealed that activated c-Ki-ras shows a G----T transversion in codon 12 and consequently encodes cysteine instead of glycine in normal rat c-Ki-ras. PMID:3023884

Simulated mossy fiber associated feedforward circuit functioning as a highpass filter.

PubMed

Zalay, Osbert C; Bardakjian, Berj L

2006-01-01

Learning and memory rely on the strict regulation of communication between neurons in the hippocampus. The mossy fiber (MF) pathway connects the dentate gyrus to the auto-associative CA3 network, and the information it carries is controlled by a feedforward circuit combining disynaptic inhibition with monosynaptic excitation. Analysis of the MF associated circuit using a mapped clock oscillator (MCO) model reveals the circuit to be a highpass filter.

Atmospheric waves and dynamics beneath Jupiter's clouds from radio wavelength observations

NASA Astrophysics Data System (ADS)

Cosentino, Richard G.; Butler, Bryan; Sault, Bob; Morales-Juberías, Raúl; Simon, Amy; de Pater, Imke

2017-08-01

We observed Jupiter at wavelengths near 2 cm with the Karl G. Jansky Very Large Array (VLA) in February 2015. These frequencies are mostly sensitive to variations in ammonia abundance and probe between ∼ 0.5 - 2.0 bars of pressure in Jupiter's atmosphere; within and below the visible cloud deck which has its base near 0.7 bars. The resultant observed data were projected into a cylindrical map of the planet with spatial resolution of ∼1500 km at the equator. We have examined the data for atmospheric waves and observed a prominent bright belt of radio hotspot features near 10°N, likely connected to the same equatorial wave associated with the 5-μm hotspots. We conducted a passive tracer power spectral wave analysis for the entire map and latitude regions corresponding to eastward and westward jets and compare our results to previous studies. The power spectra analysis revealed that the atmosphere sampled in our observation (excluding the NEB region) is in a 2-D turbulent regime and its dynamics are predominately governed by the shallow water equations. The Great Red Spot (GRS) is also very prominent and has a noticeable meridional asymmetry and we compare it, and nearby storms, with optical images. We find that the meridional radio profile has a global north-south hemisphere distinction and find correlations of it to optical intensity banding and to shear zones of the zonal wind profile over select regions of latitude. Amateur optical images taken before and after our observation complemented the radio wavelength map to investigate dynamics of the equatorial region in Jupiter's atmosphere. We find that two radio hotspots at 2 cm are well correlated with optical plumes in the NEB, additionally revealing they are not the same 5 μm hotspot features correlated with optical dark patches between adjacent plumes. This analysis exploits the VLA's upgraded sensitivity and explores the opportunities now possible when studying gas giants, especially atmospheric dynamics of layers beneath upper level clouds.

3D-QSAR and Molecular Docking Studies on Derivatives of MK-0457, GSK1070916 and SNS-314 as Inhibitors against Aurora B Kinase

PubMed Central

Zhang, Baidong; Li, Yan; Zhang, Huixiao; Ai, Chunzhi

2010-01-01

Development of anticancer drugs targeting Aurora B, an important member of the serine/threonine kinases family, has been extensively focused on in recent years. In this work, by applying an integrated computational method, including comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), homology modeling and molecular docking, we investigated the structural determinants of Aurora B inhibitors based on three different series of derivatives of 108 molecules. The resultant optimum 3D-QSAR models exhibited (q2 = 0.605, r2pred = 0.826), (q2 = 0.52, r2pred = 0.798) and (q2 = 0.582, r2pred = 0.971) for MK-0457, GSK1070916 and SNS-314 classes, respectively, and the 3D contour maps generated from these models were analyzed individually. The contour map analysis for the MK-0457 model revealed the relative importance of steric and electrostatic effects for Aurora B inhibition, whereas, the electronegative groups with hydrogen bond donating capacity showed a great impact on the inhibitory activity for the derivatives of GSK1070916. Additionally, the predictive model of the SNS-314 class revealed the great importance of hydrophobic favorable contour, since hydrophobic favorable substituents added to this region bind to a deep and narrow hydrophobic pocket composed of residues that are hydrophobic in nature and thus enhanced the inhibitory activity. Moreover, based on the docking study, a further comparison of the binding modes was accomplished to identify a set of critical residues that play a key role in stabilizing the drug-target interactions. Overall, the high level of consistency between the 3D contour maps and the topographical features of binding sites led to our identification of several key structural requirements for more potency inhibitors. Taken together, the results will serve as a basis for future drug development of inhibitors against Aurora B kinase for various tumors. PMID:21151441

3D-QSAR and molecular docking studies on derivatives of MK-0457, GSK1070916 and SNS-314 as inhibitors against Aurora B kinase.

PubMed

Zhang, Baidong; Li, Yan; Zhang, Huixiao; Ai, Chunzhi

2010-11-02

Development of anticancer drugs targeting Aurora B, an important member of the serine/threonine kinases family, has been extensively focused on in recent years. In this work, by applying an integrated computational method, including comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), homology modeling and molecular docking, we investigated the structural determinants of Aurora B inhibitors based on three different series of derivatives of 108 molecules. The resultant optimum 3D-QSAR models exhibited (q(2) = 0.605, r(2) (pred) = 0.826), (q(2) = 0.52, r(2) (pred) = 0.798) and (q(2) = 0.582, r(2) (pred) = 0.971) for MK-0457, GSK1070916 and SNS-314 classes, respectively, and the 3D contour maps generated from these models were analyzed individually. The contour map analysis for the MK-0457 model revealed the relative importance of steric and electrostatic effects for Aurora B inhibition, whereas, the electronegative groups with hydrogen bond donating capacity showed a great impact on the inhibitory activity for the derivatives of GSK1070916. Additionally, the predictive model of the SNS-314 class revealed the great importance of hydrophobic favorable contour, since hydrophobic favorable substituents added to this region bind to a deep and narrow hydrophobic pocket composed of residues that are hydrophobic in nature and thus enhanced the inhibitory activity. Moreover, based on the docking study, a further comparison of the binding modes was accomplished to identify a set of critical residues that play a key role in stabilizing the drug-target interactions. Overall, the high level of consistency between the 3D contour maps and the topographical features of binding sites led to our identification of several key structural requirements for more potency inhibitors. Taken together, the results will serve as a basis for future drug development of inhibitors against Aurora B kinase for various tumors.

Atmospheric Waves and Dynamics Beneath Jupiters Clouds from Radio Wavelength Observations

NASA Technical Reports Server (NTRS)

Cosentino, Richard G.; Butler, Bryan; Sault, Bob; Morales-Juberias, Raul; Simon, Amy; De Pater, Imke

2017-01-01

We observed Jupiter at wavelengths near 2 cm with the Karl G. Jansky Very Large Array (VLA) in February 2015. These frequencies are mostly sensitive to variations in ammonia abundance and probe between approx. 0.5- 2.0 bars of pressure in Jupiters atmosphere; within and below the visible cloud deck which has its base near 0.7 bars. The resultant observed data were projected into a cylindrical map of the planet with spatial resolution of approx. 1500 km at the equator. We have examined the data for atmospheric waves and observed a prominent bright belt of radio hotspot features near 10 N, likely connected to the same equatorial wave associated with the 5-m hotspots. We conducted a passive tracer power spectral wave analysis for the entire map and latitude regions corresponding to eastward and westward jets and compare our results to previous studies. The power spectra analysis revealed that the atmosphere sampled in our observation (excluding the NEB region) is in a 2-D turbulent regime and its dynamics are predominately governed by the shallow water equations. The Great Red Spot (GRS) is also very prominent and has a noticeable meridional asymmetry and we compare it, and nearby storms, with optical images. We find that the meridional radio profile has a global north-south hemisphere distinction and find correlations of it to optical intensity banding and to shear zones of the zonal wind profile over select regions of latitude. Amateur optical images taken before and after our observation complemented the radio wave- length map to investigate dynamics of the equatorial region in Jupiters atmosphere. We find that two radio hotspots at 2 cm are well correlated with optical plumes in the NEB, additionally revealing they are not the same 5 m hotspot features correlated with optical dark patches between adjacent plumes. This analysis exploits the VLAs upgraded sensitivity and explores the opportunities now possible when studying gas giants, especially atmospheric dynamics of layers beneath upper level clouds.

Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes.

PubMed

Marone, Daniela; Russo, Maria A; Laidò, Giovanni; De Vita, Pasquale; Papa, Roberto; Blanco, Antonio; Gadaleta, Agata; Rubiales, Diego; Mastrangelo, Anna M

2013-08-19

Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat. The objective of this study was to identify the wheat genomic regions that are involved in the control of powdery mildew resistance through a quantitative trait loci (QTL) meta-analysis approach. This meta-analysis allows the use of collected QTL data from different published studies to obtain consensus QTL across different genetic backgrounds, thus providing a better definition of the regions responsible for the trait, and the possibility to obtain molecular markers that will be suitable for marker-assisted selection. Five QTL for resistance to powdery mildew were identified under field conditions in the durum-wheat segregating population Creso × Pedroso. An integrated map was developed for the projection of resistance genes/ alleles and the QTL from the present study and the literature, and to investigate their distribution in the wheat genome. Molecular markers that correspond to candidate genes for plant responses to pathogens were also projected onto the map, particularly considering NBS-LRR and receptor-like protein kinases. More than 80 independent QTL and 51 resistance genes from 62 different mapping populations were projected onto the consensus map using the Biomercator statistical software. Twenty-four MQTL that comprised 2-6 initial QTL that had widely varying confidence intervals were found on 15 chromosomes. The co-location of the resistance QTL and genes was investigated. Moreover, from analysis of the sequences of DArT markers, 28 DArT clones mapped on wheat chromosomes have been shown to be associated with the NBS-LRR genes and positioned in the same regions as the MQTL for powdery mildew resistance. The results from the present study provide a detailed analysis of the genetic basis of resistance to powdery mildew in wheat. The study of the Creso × Pedroso durum-wheat population has revealed some QTL that had not been previously identified. Furthermore, the analysis of the co-localization of resistance loci and functional markers provides a large list of candidate genes and opens up a new perspective for the fine mapping and isolation of resistance genes, and for the marker-assisted improvement of resistance in wheat.

Genetic basis of qualitative and quantitative resistance to powdery mildew in wheat: from consensus regions to candidate genes

PubMed Central

2013-01-01

Background Powdery mildew (Blumeria graminis f. sp. tritici) is one of the most damaging diseases of wheat. The objective of this study was to identify the wheat genomic regions that are involved in the control of powdery mildew resistance through a quantitative trait loci (QTL) meta-analysis approach. This meta-analysis allows the use of collected QTL data from different published studies to obtain consensus QTL across different genetic backgrounds, thus providing a better definition of the regions responsible for the trait, and the possibility to obtain molecular markers that will be suitable for marker-assisted selection. Results Five QTL for resistance to powdery mildew were identified under field conditions in the durum-wheat segregating population Creso × Pedroso. An integrated map was developed for the projection of resistance genes/ alleles and the QTL from the present study and the literature, and to investigate their distribution in the wheat genome. Molecular markers that correspond to candidate genes for plant responses to pathogens were also projected onto the map, particularly considering NBS-LRR and receptor-like protein kinases. More than 80 independent QTL and 51 resistance genes from 62 different mapping populations were projected onto the consensus map using the Biomercator statistical software. Twenty-four MQTL that comprised 2–6 initial QTL that had widely varying confidence intervals were found on 15 chromosomes. The co-location of the resistance QTL and genes was investigated. Moreover, from analysis of the sequences of DArT markers, 28 DArT clones mapped on wheat chromosomes have been shown to be associated with the NBS-LRR genes and positioned in the same regions as the MQTL for powdery mildew resistance. Conclusions The results from the present study provide a detailed analysis of the genetic basis of resistance to powdery mildew in wheat. The study of the Creso × Pedroso durum-wheat population has revealed some QTL that had not been previously identified. Furthermore, the analysis of the co-localization of resistance loci and functional markers provides a large list of candidate genes and opens up a new perspective for the fine mapping and isolation of resistance genes, and for the marker-assisted improvement of resistance in wheat. PMID:23957646

Self-Portrait with Mortar Board: A Study of Academic Identity Using the Map, the Novel and the Grid

ERIC Educational Resources Information Center

King, Virginia

2013-01-01

This paper introduces the "map", the "novel" and the "grid", three strategies inspired by the creative arts that potentially enrich higher education research by revealing layers of truth otherwise difficult to discern. The "map" was inspired by the "Map of an Englishman," an etching by Grayson…

Surface Chemistry Maps

NASA Image and Video Library

2015-03-13

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

Truncation- and motif-based pan-cancer analysis reveals tumor-suppressing kinases.

PubMed

Hudson, Andrew M; Stephenson, Natalie L; Li, Cynthia; Trotter, Eleanor; Fletcher, Adam J; Katona, Gitta; Bieniasz-Krzywiec, Patrycja; Howell, Matthew; Wirth, Chris; Furney, Simon; Miller, Crispin J; Brognard, John

2018-04-17

A major challenge in cancer genomics is identifying "driver" mutations from the many neutral "passenger" mutations within a given tumor. To identify driver mutations that would otherwise be lost within mutational noise, we filtered genomic data by motifs that are critical for kinase activity. In the first step of our screen, we used data from the Cancer Cell Line Encyclopedia and The Cancer Genome Atlas to identify kinases with truncation mutations occurring within or before the kinase domain. The top 30 tumor-suppressing kinases were aligned, and hotspots for loss-of-function (LOF) mutations were identified on the basis of amino acid conservation and mutational frequency. The functional consequences of new LOF mutations were biochemically validated, and the top 15 hotspot LOF residues were used in a pan-cancer analysis to define the tumor-suppressing kinome. A ranked list revealed MAP2K7, an essential mediator of the c-Jun N-terminal kinase (JNK) pathway, as a candidate tumor suppressor in gastric cancer, despite its mutational frequency falling within the mutational noise for this cancer type. The majority of mutations in MAP2K7 abolished its catalytic activity, and reactivation of the JNK pathway in gastric cancer cells harboring LOF mutations in MAP2K7 or the downstream kinase JNK suppressed clonogenicity and growth in soft agar, demonstrating the functional relevance of inactivating the JNK pathway in gastric cancer. Together, our data highlight a broadly applicable strategy to identify functional cancer driver mutations and define the JNK pathway as tumor-suppressive in gastric cancer. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis

PubMed Central

Ramakrishnan, M.; Ceasar, S. Antony; Vinod, K. K.; Duraipandiyan, V.; Ajeesh Krishna, T. P.; Upadhyaya, Hari D.; Al-Dhabi, N. A.

2017-01-01

A germplasm assembly of 128 finger millet genotypes from 18 countries was evaluated for seedling-stage phosphorus (P) responses by growing them in P sufficient (Psuf) and P deficient (Pdef) treatments. Majority of the genotypes showed adaptive responses to low P condition. Based on phenotype behaviour using the best linear unbiased predictors for each trait, genotypes were classified into, P responsive, low P tolerant and P non-responsive types. Based on the overall phenotype performance under Pdef, 10 genotypes were identified as low P tolerants. The low P tolerant genotypes were characterised by increased shoot and root length and increased root hair induction with longer root hairs under Pdef, than under Psuf. Association mapping of P response traits using mixed linear models revealed four quantitative trait loci (QTLs). Two QTLs (qLRDW.1 and qLRDW.2) for low P response affecting root dry weight explained over 10% phenotypic variation. In silico synteny analysis across grass genomes for these QTLs identified putative candidate genes such as Ser-Thr kinase and transcription factors such as WRKY and basic helix-loop-helix (bHLH). The QTLs for response under Psuf were mapped for traits such as shoot dry weight (qHSDW.1) and root length (qHRL.1). Putative associations of these QTLs over the syntenous regions on the grass genomes revealed proximity to cytochrome P450, phosphate transporter and pectin methylesterase inhibitor (PMEI) genes. This is the first report of the extent of phenotypic variability for P response in finger millet genotypes during seedling-stage, along with the QTLs and putative candidate genes associated with P starvation tolerance. PMID:28820887

Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis.

PubMed

Ramakrishnan, M; Ceasar, S Antony; Vinod, K K; Duraipandiyan, V; Ajeesh Krishna, T P; Upadhyaya, Hari D; Al-Dhabi, N A; Ignacimuthu, S

2017-01-01

A germplasm assembly of 128 finger millet genotypes from 18 countries was evaluated for seedling-stage phosphorus (P) responses by growing them in P sufficient (Psuf) and P deficient (Pdef) treatments. Majority of the genotypes showed adaptive responses to low P condition. Based on phenotype behaviour using the best linear unbiased predictors for each trait, genotypes were classified into, P responsive, low P tolerant and P non-responsive types. Based on the overall phenotype performance under Pdef, 10 genotypes were identified as low P tolerants. The low P tolerant genotypes were characterised by increased shoot and root length and increased root hair induction with longer root hairs under Pdef, than under Psuf. Association mapping of P response traits using mixed linear models revealed four quantitative trait loci (QTLs). Two QTLs (qLRDW.1 and qLRDW.2) for low P response affecting root dry weight explained over 10% phenotypic variation. In silico synteny analysis across grass genomes for these QTLs identified putative candidate genes such as Ser-Thr kinase and transcription factors such as WRKY and basic helix-loop-helix (bHLH). The QTLs for response under Psuf were mapped for traits such as shoot dry weight (qHSDW.1) and root length (qHRL.1). Putative associations of these QTLs over the syntenous regions on the grass genomes revealed proximity to cytochrome P450, phosphate transporter and pectin methylesterase inhibitor (PMEI) genes. This is the first report of the extent of phenotypic variability for P response in finger millet genotypes during seedling-stage, along with the QTLs and putative candidate genes associated with P starvation tolerance.

Gene mapping and functional analysis of the novel leaf color gene SiYGL1 in foxtail millet [Setaria italica (L.) P. Beauv].

PubMed

Li, Wen; Tang, Sha; Zhang, Shuo; Shan, Jianguo; Tang, Chanjuan; Chen, Qiannan; Jia, Guanqing; Han, Yuanhuai; Zhi, Hui; Diao, Xianmin

2016-05-01

Setaria italica and its wild ancestor Setaria viridis are emerging as model systems for genetics and functional genomics research. However, few systematic gene mapping or functional analyses have been reported in these promising C4 models. We herein isolated the yellow-green leaf mutant (siygl1) in S. italica using forward genetics approaches. Map-based cloning revealed that SiYGL1, which is a recessive nuclear gene encoding a magnesium-chelatase D subunit (CHLD), is responsible for the mutant phenotype. A single Phe to Leu amino acid change occurring near the ATPase-conserved domain resulted in decreased chlorophyll (Chl) accumulation and modified chloroplast ultrastructure. However, the mutation enhanced the light-use efficiency of the siygl1 mutant, suggesting that the mutated CHLD protein does not completely lose its original activity, but instead, gains novel features. A transcriptional analysis of Chl a oxygenase revealed that there is a strong negative feedback control of Chl b biosynthesis in S. italica. The SiYGL1 mRNA was expressed in all examined tissues, with higher expression observed in the leaves. Comparison of gene expression profiles in wild-type and siygl1 mutant plants indicated that SiYGL1 regulates a subset of genes involved in photosynthesis (rbcL and LHCB1), thylakoid development (DEG2) and chloroplast signaling (SRP54CP). These results provide information regarding the mutant phenotype at the transcriptional level. This study demonstrated that the genetic material of a Setaria species could be ideal for gene discovery investigations using forward genetics approaches and may help to explain the molecular mechanisms associated with leaf color variation. © 2015 Scandinavian Plant Physiology Society.

Patterns in response to chronic terrorism threats: A construct of emotional, cognitive, and behavioral responses among Israeli citizens.

PubMed

Cohen-Louck, Keren; Saka, Yael

2017-10-01

Israeli citizens are exposed to unpredictable and chronic terrorism threats that significantly jeopardize their personal sense of safety. The purpose of the present study is to present how Israeli discourse is structured with regard to emotional, cognitive, and behavioral responses to chronic terrorism threats and to understand the range of responses as well as map the risk and protective factors of this existential threat. Semistructured in-depth interviews were conducted with 40 Israeli adults (22 women and 18 men). Qualitative analysis revealed three patterns of responses to ongoing terrorism: emotional, cognitive, and behavioral. Emotional responses include fear, worry, sense of empathy, and detachment. Cognitive responses include situational assessment and pursuit of solutions, the use of traumatic imagining, beliefs in fate and luck, and optimism. Behavioral responses include looking for information, alertness, and habituation. The findings also revealed another response, which combines cognitive and behavioral responses. Some of the responses are innovative and unique to the threat of terrorism. Mapping the responses revealed mental health risk factors, as well as protective factors that can help structure personal and national resilience. These findings have implications on the treatment and prevention of personal and social pathologies, and how to effectively cope with terrorism threats. Copyright © 2016 John Wiley & Sons, Ltd.

Genetically based location from triploid populations and gene ontology of a 3.3-mb genome region linked to Alternaria brown spot resistance in citrus reveal clusters of resistance genes.

PubMed

Cuenca, José; Aleza, Pablo; Vicent, Antonio; Brunel, Dominique; Ollitrault, Patrick; Navarro, Luis

2013-01-01

Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids.

The gene for autosomal dominant cerebellar ataxia type II is located in a 5-cM region in 3p12-p13: genetic and physical mapping of the SCA7 locus.

PubMed

David, G; Giunti, P; Abbas, N; Coullin, P; Stevanin, G; Horta, W; Gemmill, R; Weissenbach, J; Wood, N; Cunha, S; Drabkin, H; Harding, A E; Agid, Y; Brice, A

1996-12-01

Two families with autosomal dominant cerebellar ataxia with pigmentary macular dystrophy (ADCA type II) were investigated. Analysis of 23 parent-child couples demonstrated the existence of marked anticipation, greater in paternal than in maternal transmissions, with earlier age at onset and a more rapid clinical course in successive generations. Clinical analysis revealed the presence of a great variability in age at onset, initial symptom, and associated signs, confirming the characteristic clinical heterogeneity of ADCA type II. The gene for ADCA type II previously was mapped to the spinocerebellar ataxia 7 (SCA7) locus on chromosome 3p12-p21.1. Linkage analysis of the two new families of different geographic origin confirmed the characteristic genetic homogeneity of ADCA type II, distinguishing it from ADCA type I. Haplotype analysis permitted refinement of the SCA7 region to the 5-cM interval between markers D3S1312 and D3S1600 on chromosome 3p12-p13. Eighteen sequence-tagged sites were used for the construction of an integrated map of the candidate region, based on a YACs contig. The entire candidate region is contained in a single nonchimeric YAC of 660 kb. The probable involvement of a CAG trinucleotide expansion, suggested by previous studies, should greatly facilitate the identification of the gene for ADCA type II.

The gene for autosomal dominant cerebellar ataxia type II is located in a 5-cM region in 3p12-p13: genetic and physical mapping of the SCA7 locus.

PubMed Central

David, G.; Giunti, P.; Abbas, N.; Coullin, P.; Stevanin, G.; Horta, W.; Gemmill, R.; Weissenbach, J.; Wood, N.; Cunha, S.; Drabkin, H.; Harding, A. E.; Agid, Y.; Brice, A.

1996-01-01

Two families with autosomal dominant cerebellar ataxia with pigmentary macular dystrophy (ADCA type II) were investigated. Analysis of 23 parent-child couples demonstrated the existence of marked anticipation, greater in paternal than in maternal transmissions, with earlier age at onset and a more rapid clinical course in successive generations. Clinical analysis revealed the presence of a great variability in age at onset, initial symptom, and associated signs, confirming the characteristic clinical heterogeneity of ADCA type II. The gene for ADCA type II previously was mapped to the spinocerebellar ataxia 7 (SCA7) locus on chromosome 3p12-p21.1. Linkage analysis of the two new families of different geographic origin confirmed the characteristic genetic homogeneity of ADCA type II, distinguishing it from ADCA type I. Haplotype analysis permitted refinement of the SCA7 region to the 5-cM interval between markers D3S1312 and D3S1600 on chromosome 3p12-p13. Eighteen sequence-tagged sites were used for the construction of an integrated map of the candidate region, based on a YACs contig. The entire candidate region is contained in a single nonchimeric YAC of 660 kb. The probable involvement of a CAG trinucleotide expansion, suggested by previous studies, should greatly facilitate the identification of the gene for ADCA type II. PMID:8940279

Genetically Based Location from Triploid Populations and Gene Ontology of a 3.3-Mb Genome Region Linked to Alternaria Brown Spot Resistance in Citrus Reveal Clusters of Resistance Genes

PubMed Central

Cuenca, José; Aleza, Pablo; Vicent, Antonio; Brunel, Dominique; Ollitrault, Patrick; Navarro, Luis

2013-01-01

Genetic analysis of phenotypical traits and marker-trait association in polyploid species is generally considered as a challenge. In the present work, different approaches were combined taking advantage of the particular genetic structures of 2n gametes resulting from second division restitution (SDR) to map a genome region linked to Alternaria brown spot (ABS) resistance in triploid citrus progeny. ABS in citrus is a serious disease caused by the tangerine pathotype of the fungus Alternaria alternata. This pathogen produces ACT-toxin, which induces necrotic lesions on fruit and young leaves, defoliation and fruit drop in susceptible genotypes. It is a strong concern for triploid breeding programs aiming to produce seedless mandarin cultivars. The monolocus dominant inheritance of susceptibility, proposed on the basis of diploid population studies, was corroborated in triploid progeny. Bulk segregant analysis coupled with genome scan using a large set of genetically mapped SNP markers and targeted genetic mapping by half tetrad analysis, using SSR and SNP markers, allowed locating a 3.3 Mb genomic region linked to ABS resistance near the centromere of chromosome III. Clusters of resistance genes were identified by gene ontology analysis of this genomic region. Some of these genes are good candidates to control the dominant susceptibility to the ACT-toxin. SSR and SNP markers were developed for efficient early marker-assisted selection of ABS resistant hybrids. PMID:24116149

Lidar-enhanced geologic mapping, examples from the Medford and Hood River areas, Oregon

NASA Astrophysics Data System (ADS)

Wiley, T. J.; McClaughry, J. D.

2012-12-01

Lidar-based 3-foot digital elevation models (DEMs) and derivatives (slopeshade, hillshade, contours) were used to help map geology across 1700 km2 (650 mi2) near Hood River and Medford, Oregon. Techniques classically applied to interpret coarse DEMs and small-scale topographic maps were adapted to take advantage of lidar's high resolution. Penetration and discrimination of plant cover by the laser system allowed recognition of fine patterns and textures related to underlying geologic units and associated soils. Surficial geologic maps were improved by the ability to examine tiny variations in elevation and slope. Recognition of low-relief features of all sizes was enhanced where pixel elevation ranges of centimeters to meters, established by knowledge of the site or by trial, were displayed using thousands of sequential colors. Features can also be depicted relative to stream level by preparing a DEM that compensates for gradient. Near Medford, lidar-derived contour maps with 1- to 3-foot intervals revealed incised bajada with young, distal lobes defined by concentric contour lines. Bedrock geologic maps were improved by recognizing geologic features associated with surface textures and patterns or topographic anomalies. In sedimentary and volcanic terrain, structure was revealed by outcrops or horizons lying at one stratigraphic level. Creating a triangulated irregular network (TIN) facet from positions of three or more such points gives strike and dip. Each map area benefited from hundreds of these measurements. A more extensive DEM in the plane of the TIN facet can be subtracted from surface elevation (lidar DEM) to make a DEM with elevation zero where the stratigraphic horizon lies at the surface. The distribution of higher and lower stratigraphic horizons can be shown by highlighting areas similarly higher or lower on the same DEM. Poor fit of contacts or faults projected between field traverses suggest the nature and amount of intervening geologic structure. Intrusive bodies were locally delimited by linear mounds where contact metamorphism hardened soft, fractured country rock. Bedrock faults were revealed where fault traces formed topographic anomalies or where topography associated with stratigraphic horizons or bedding-parallel textural fabrics was offset. This was important for identification of young faults and associated earthquake hazards. Previously unknown Holocene faults southwest of Hood River appear as subtle lineaments redirecting modern drainages or offsetting glacial moraines or glaciated bedrock. West of Medford, the presence young faulting was confirmed by elevation data that showed bedrock in the channel of the Rogue River at higher elevations below Gold Ray dam than in boreholes upstream. Such obscure structural features would have gone unrecognized using traditional topographic analysis or field reconnaissance. Fieldwork verified that lidar techniques improved our early geologic models, resolution of geologic features, and mapping of surficial and bedrock geology between traverses.

Concept Mapping

ERIC Educational Resources Information Center

Technology & Learning, 2005

2005-01-01

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

With or without spikes: localization of focal epileptic activity by simultaneous electroencephalography and functional magnetic resonance imaging

PubMed Central

Grouiller, Frédéric; Thornton, Rachel C.; Groening, Kristina; Spinelli, Laurent; Duncan, John S.; Schaller, Karl; Siniatchkin, Michael; Lemieux, Louis; Seeck, Margitta; Michel, Christoph M.

2011-01-01

In patients with medically refractory focal epilepsy who are candidates for epilepsy surgery, concordant non-invasive neuroimaging data are useful to guide invasive electroencephalographic recordings or surgical resection. Simultaneous electroencephalography and functional magnetic resonance imaging recordings can reveal regions of haemodynamic fluctuations related to epileptic activity and help localize its generators. However, many of these studies (40–70%) remain inconclusive, principally due to the absence of interictal epileptiform discharges during simultaneous recordings, or lack of haemodynamic changes correlated to interictal epileptiform discharges. We investigated whether the presence of epilepsy-specific voltage maps on scalp electroencephalography correlated with haemodynamic changes and could help localize the epileptic focus. In 23 patients with focal epilepsy, we built epilepsy-specific electroencephalographic voltage maps using averaged interictal epileptiform discharges recorded during long-term clinical monitoring outside the scanner and computed the correlation of this map with the electroencephalographic recordings in the scanner for each time frame. The time course of this correlation coefficient was used as a regressor for functional magnetic resonance imaging analysis to map haemodynamic changes related to these epilepsy-specific maps (topography-related haemodynamic changes). The method was first validated in five patients with significant haemodynamic changes correlated to interictal epileptiform discharges on conventional analysis. We then applied the method to 18 patients who had inconclusive simultaneous electroencephalography and functional magnetic resonance imaging studies due to the absence of interictal epileptiform discharges or absence of significant correlated haemodynamic changes. The concordance of the results with subsequent intracranial electroencephalography and/or resection area in patients who were seizure free after surgery was assessed. In the validation group, haemodynamic changes correlated to voltage maps were similar to those obtained with conventional analysis in 5/5 patients. In 14/18 patients (78%) with previously inconclusive studies, scalp maps related to epileptic activity had haemodynamic correlates even when no interictal epileptiform discharges were detected during simultaneous recordings. Haemodynamic changes correlated to voltage maps were spatially concordant with intracranial electroencephalography or with the resection area. We found better concordance in patients with lateral temporal and extratemporal neocortical epilepsy compared to medial/polar temporal lobe epilepsy, probably due to the fact that electroencephalographic voltage maps specific to lateral temporal and extratemporal epileptic activity are more dissimilar to maps of physiological activity. Our approach significantly increases the yield of simultaneous electroencephalography and functional magnetic resonance imaging to localize the epileptic focus non-invasively, allowing better targeting for surgical resection or implantation of intracranial electrode arrays. PMID:21752790

Revealing the Relationship between Reading Interest and Critical Thinking Skills through Remap GI and Remap Jigsaw

ERIC Educational Resources Information Center

Zubaidah, Siti; Corebima, Aloysius Duran; Mahanal, Susriyati; Mistianah

2018-01-01

The aim of this research was to reveal the relationship between student's reading interest and critical thinking skills through Reading Concept Map Group Investigation (Remap GI) and Reading Concept Map Jigsaw (Remap Jigsaw) learning models. To do so, two science classes from first grade of two Senior High Schools in Malang, Indonesia were…

Physical mapping of chromosome 12q breakpoints in lipoma, pleomorphic salivary gland adenoma, uterine leiomyoma, and myxoid liposarcoma

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

Schoenmakers, E.F.P.M.; Kools, P.F.J.; Mols, R.

1994-03-15

The authors report here the physical mapping of recurrent chromosome 12q13-q15 breakpoints in cell lines derived from primary myxoid liposarcoma, lipoma, uterine leiomyoma, and pleomorphic adenoma of the salivary glands. In fluorescence in situ hybridization (FISH) experiments, they first mapped the position of the chromosome 12 translocation breakpoint in uterine leiomyoma cell line LM-30.1/SV40 relative to loci COL2A1, D12S4, D12S17, D12S6, D12S19, D12S8, and D12S7. It mapped between linkage probes CRI-C86 (D12S19) and p7G11 (D12S8). They then isolated YAC clones using CRI-C86- and p7G11-derived sequence-tagged sites, constructed corresponding YAC contigs of 310 and 800 kb, respectively, and a mixture ofmore » them was used to routinely study the various tumor cell lines by FISH analysis. The chromosome 12 breakpoints of all tumor cell lines tested mapped between cosmids LLNL12NCO1-98C10 and LLNL12NCO1-113D12. None of the breakpoints appeared to map within any of the isolated YAC clones. Furthermore, FISH analysis using cosmid LLNL12-NCO1-144G3, which maps at the CHOP locus, revealed that the chromosome 12 breakpoints in all cell lines of the three benign solid tumors that were tested were located distal to the chromosome 12 translocation breakpoint with the CHOP gene in myxoid liposarcoma cells with t(12;16). In conclusion, the studies seem to indicate that the chromosome 12 breakpoints of myxoid liposarcoma, lipoma, uterine leiomyoma, and pleomorphic adenoma of the salivary glands are all clustered within the 7-cM interval between D12S19 and D12S8, with those of the benign solid tumors distal to CHOP. Finally, the MYF5 gene mapped telomeric to LLNL12NCO1-113D12, and the MIP gene mapped centromeric to the chromosome 12 translocation breakpoint in myxoid liposarcoma cells. 56 refs., 5 figs., 3 tabs.« less

Analysis of storage possibility of raw and smoked breast meat of oat-fattened White Kołuda® goose based on their quality characteristics.

PubMed

Damaziak, K; Stelmasiak, A; Michalczuk, M; Wyrwisz, J; Moczkowska, M; Marcinkowska-Lesiak, M M; Niemiec, J; Wierzbicka, A

2016-09-01

Raw and smoked (spickgans) fillets of oat-fattened White Kołuda® goose were packed in: PET - ethylene terephthalate bags; VSP - 99% vacuum; MAP1 - 80% O2, 20% CO2; MAP2 - 70% N2, 30% O2; MAP3 - 30% O2, 40% N2, 30% CO2, and stored at a temperature of 2°C. On the day of packaging (0 d) and during storage of raw (5, 7, 10 d) and smoked fillets (5, 10, 15 d), the samples were analyzed for weight losses, physicochemical traits, and chemical composition. The study demonstrated the effect of storage time and packaging method on storage yield of raw and smoked fillets. In VSP, the raw fillets were characterized by the lowest amount of leakage, whereas spickgans were characterized by the highest storage yield and weight loss. The analysis of the effect of the modified atmosphere demonstrated the lowest weight loss of raw fillets at, simultaneously, the smallest amount of leakage in MAP1. The spickgans stored in MAP2 showed higher weight, higher yield after storage, and lower storage loss in all terms of analyses compared to MAP1 and MAP3. The greatest cooking loss at simultaneously the lowest pH values was determined for the samples stored in VSP. The WBSF values of raw fillets were decreasing along with storage time, in contrast to WBSF values of spickgans, in which case the value of this parameter increased compared to 0 d. Raw fillets stored in MAP1 and MAP3 were characterized by the most significant increase in the value of L*, by a decrease in the value of a* and an increase in that of b* parameter. Visual assessment of spickgans on 15 d of storage revealed the presence of white sediment on the surface of products, except for the samples stored in VSP. The study demonstrated the effect of storage time on the contents of protein and fat in raw fillets and on the contents of salt and fat in spickgans. © 2016 Poultry Science Association Inc.

Seismic-zonation of Port-au-Prince using pixel- and object-based imaging analysis methods on ASTER GDEM

USGS Publications Warehouse

Yong, A.; Hough, S.E.; Cox, B.R.; Rathje, E.M.; Bachhuber, J.; Dulberg, R.; Hulslander, D.; Christiansen, L.; Abrams, M.J.

2011-01-01

We report about a preliminary study to evaluate the use of semi-automated imaging analysis of remotely-sensed DEM and field geophysical measurements to develop a seismic-zonation map of Port-au-Prince, Haiti. For in situ data, Vs30 values are derived from the MASW technique deployed in and around the city. For satellite imagery, we use an ASTER GDEM of Hispaniola. We apply both pixel- and object-based imaging methods on the ASTER GDEM to explore local topography (absolute elevation values) and classify terrain types such as mountains, alluvial fans and basins/near-shore regions. We assign NEHRP seismic site class ranges based on available Vs30 values. A comparison of results from imagery-based methods to results from traditional geologic-based approaches reveals good overall correspondence. We conclude that image analysis of RS data provides reliable first-order site characterization results in the absence of local data and can be useful to refine detailed site maps with sparse local data. ?? 2011 American Society for Photogrammetry and Remote Sensing.

A Rapid Method of Genomic Array Analysis of Scaffold/Matrix Attachment Regions (S/MARs) Identifies a 2.5-Mb Region of Enhanced Scaffold/Matrix Attachment at a Human Neocentromere

PubMed Central

Sumer, Huseyin; Craig, Jeffrey M.; Sibson, Mandy; Choo, K.H. Andy

2003-01-01

Human neocentromeres are fully functional centromeres that arise at previously noncentromeric regions of the genome. We have tested a rapid procedure of genomic array analysis of chromosome scaffold/matrix attachment regions (S/MARs), involving the isolation of S/MAR DNA and hybridization of this DNA to a genomic BAC/PAC array. Using this procedure, we have defined a 2.5-Mb domain of S/MAR-enriched chromatin that fully encompasses a previously mapped centromere protein-A (CENP-A)-associated domain at a human neocentromere. We have independently verified this procedure using a previously established fluorescence in situ hybridization method on salt-treated metaphase chromosomes. In silico sequence analysis of the S/MAR-enriched and surrounding regions has revealed no outstanding sequence-related predisposition. This study defines the S/MAR-enriched domain of a higher eukaryotic centromere and provides a method that has broad application for the mapping of S/MAR attachment sites over large genomic regions or throughout a genome. PMID:12840048

Analysis of Colonial Currency

NASA Astrophysics Data System (ADS)

Kurkowski, Michael; Cangany, Catherine; Jordan, Louis; Manukyan, Khachatur; Schultz, Zachary; Wiescher, Michael

2017-09-01

This project entailed studying the cellulose in paper, the ink, colorants, and other materials used to produce American colonial currency. The technique primarily used in this project was X-Ray Fluorescence Spectroscopy (XRF). XRF mapping was used to provide both elemental analysis of large-scale objects as well as microscopic examination of individual pigment particles in ink, in addition to the inorganic additives used to prepare paper. The combination of elemental mapping with Fourier Transform Infrared (FTIR) and Raman Spectroscopies permits an efficient analysis of the currency. These spectroscopic methods help identify the molecular composition of the pigments. This combination of atomic and molecular analytical techniques provided an in-depth characterization of the paper currency on the macro, micro, and molecular levels. We have identified several of pigments that were used in the preparation of inks and colorants. Also, different inorganic crystals, such as alumina-silicates, have been detected in different papers. The FTIR spectroscopy allowed us to determine the type of cellulose fiber used in the production of paper currency. Our future research will be directed toward revealing important historical relationships between currencies printed throughout the colonies. ISLA Da Vinci Grant.

Properties of anodic oxides grown on a hafnium–tantalum–titanium thin film library

PubMed Central

Mardare, Andrei Ionut; Ludwig, Alfred; Savan, Alan; Hassel, Achim Walter

2014-01-01

A ternary thin film combinatorial materials library of the valve metal system Hf–Ta–Ti obtained by co-sputtering was studied. The microstructural and crystallographic analysis of the obtained compositions revealed a crystalline and textured surface, with the exception of compositions with Ta concentration above 48 at.% which are amorphous and show a flat surface. Electrochemical anodization of the composition spread thin films was used for analysing the growth of the mixed surface oxides. Oxide formation factors, obtained from the potentiodynamic anodization curves, as well as the dielectric constants and electrical resistances, obtained from electrochemical impedance spectroscopy, were mapped along two dimensions of the library using a scanning droplet cell microscope. The semiconducting properties of the anodic oxides were mapped using Mott–Schottky analysis. The degree of oxide mixing was analysed qualitatively using x-ray photoelectron spectroscopy depth profiling. A quantitative analysis of the surface oxides was performed and correlated to the as-deposited metal thin film compositions. In the concurrent transport of the three metal cations during oxide growth a clear speed order of Ti > Hf > Ta was proven. PMID:27877648

Shape analysis of corpus callosum in autism subtype using planar conformal mapping

NASA Astrophysics Data System (ADS)

He, Qing; Duan, Ye; Yin, Xiaotian; Gu, Xianfeng; Karsch, Kevin; Miles, Judith

2009-02-01

A number of studies have documented that autism has a neurobiological basis, but the anatomical extent of these neurobiological abnormalities is largely unknown. In this study, we aimed at analyzing highly localized shape abnormalities of the corpus callosum in a homogeneous group of autism children. Thirty patients with essential autism and twenty-four controls participated in this study. 2D contours of the corpus callosum were extracted from MR images by a semiautomatic segmentation method, and the 3D model was constructed by stacking the contours. The resulting 3D model had two openings at the ends, thus a new conformal parameterization for high genus surfaces was applied in our shape analysis work, which mapped each surface onto a planar domain. Surface matching among different individual meshes was achieved by re-triangulating each mesh according to a template surface. Statistical shape analysis was used to compare the 3D shapes point by point between patients with autism and their controls. The results revealed significant abnormalities in the anterior most and anterior body in essential autism group.

Variability of Changjiang Diluted Water revealed by a 45-year long-term ocean hindcast and Self-Organizing Maps analysis

NASA Astrophysics Data System (ADS)

Zeng, Xiangming; He, Ruoying; Zong, Haibo

2017-08-01

Based on long-term realistic ocean circulation hindcast for in the Bohai, Yellow, and East China Seas, 45 years (1961-2005) of sea surface salinity data were analyzed using Self-Organizing Maps (SOM) to have a better understanding of the Changjiang Diluted Water (CDW) variation. Three spatial patterns were revealed by the SOM: normal, transition, and extension. The normal pattern mainly occurs from December to May while the CDW hugs China's east coast closely and flows southward. The extension pattern is dominant from June to October when the CDW extends northwestward toward Jeju Island in an omega shape. The transition pattern prevails for the rest of the year. Pattern-averaged temperature, circulation, and chlorophyll-a concentration show significant differences. CDW area and its eastern most extension were explored as a function of the Changjiang runoff and regional upwelling index. We found that Changjiang runoff and upwelling index can be reasonable predictors for the overall CDW area, while ambient circulation determines the distribution and structure of the CDW, and thus the CDW eastern most extension.

Inflammation-related alterations of lipids after spinal cord injury revealed by Raman spectroscopy

NASA Astrophysics Data System (ADS)

Tamosaityte, Sandra; Galli, Roberta; Uckermann, Ortrud; Sitoci-Ficici, Kerim H.; Koch, Maria; Later, Robert; Schackert, Gabriele; Koch, Edmund; Steiner, Gerald; Kirsch, Matthias

2016-06-01

Spinal cord injury (SCI) triggers several lipid alterations in nervous tissue. It is characterized by extensive demyelination and the inflammatory response leads to accumulation of activated microglia/macrophages, which often transform into foam cells by accumulation of lipid droplets after engulfment of the damaged myelin sheaths. Using an experimental rat model, Raman microspectroscopy was applied to retrieve the modifications of the lipid distribution following SCI. Coherent anti-Stokes Raman scattering (CARS) and endogenous two-photon fluorescence (TPEF) microscopies were used for the detection of lipid-laden inflammatory cells. The Raman mapping of CH2 deformation mode intensity at 1440 cm-1 retrieved the lipid-depleted injury core. Preserved white matter and inflammatory regions with myelin fragmentation and foam cells were localized by specifically addressing the distribution of esterified lipids, i.e., by mapping the intensity of the carbonyl Raman band at 1743 cm-1, and were in agreement with CARS/TPEF microscopy. Principal component analysis revealed that the inflammatory regions are notably rich in saturated fatty acids. Therefore, Raman spectroscopy enabled to specifically detect inflammation after SCI and myelin degradation products.

Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3' Ends.

PubMed

Holmqvist, Erik; Li, Lei; Bischler, Thorsten; Barquist, Lars; Vogel, Jörg

2018-05-15

The conserved RNA-binding protein ProQ has emerged as the centerpiece of a previously unknown third large network of post-transcriptional control in enterobacteria. Here, we have used in vivo UV crosslinking and RNA sequencing (CLIP-seq) to map hundreds of ProQ binding sites in Salmonella enterica and Escherichia coli. Our analysis of these binding sites, many of which are conserved, suggests that ProQ recognizes its cellular targets through RNA structural motifs found in small RNAs (sRNAs) and at the 3' end of mRNAs. Using the cspE mRNA as a model for 3' end targeting, we reveal a function for ProQ in protecting mRNA against exoribonucleolytic activity. Taken together, our results underpin the notion that ProQ governs a post-transcriptional network distinct from those of the well-characterized sRNA-binding proteins, CsrA and Hfq, and suggest a previously unrecognized, sRNA-independent role of ProQ in stabilizing mRNAs. Copyright © 2018 Elsevier Inc. All rights reserved.

Comparative transcriptomics with self-organizing map reveals cryptic photosynthetic differences between two accessions of North American Lake cress.

PubMed

Nakayama, Hokuto; Sakamoto, Tomoaki; Okegawa, Yuki; Kaminoyama, Kaori; Fujie, Manabu; Ichihashi, Yasunori; Kurata, Tetsuya; Motohashi, Ken; Al-Shehbaz, Ihsan; Sinha, Neelima; Kimura, Seisuke

2018-02-19

Because natural variation in wild species is likely the result of local adaptation, it provides a valuable resource for understanding plant-environmental interactions. Rorippa aquatica (Brassicaceae) is a semi-aquatic North American plant with morphological differences between several accessions, but little information available on any physiological differences. Here, we surveyed the transcriptomes of two R. aquatica accessions and identified cryptic physiological differences between them. We first reconstructed a Rorippa phylogeny to confirm relationships between the accessions. We performed large-scale RNA-seq and de novo assembly; the resulting 87,754 unigenes were then annotated via comparisons to different databases. Between-accession physiological variation was identified with transcriptomes from both accessions. Transcriptome data were analyzed with principal component analysis and self-organizing map. Results of analyses suggested that photosynthetic capability differs between the accessions. Indeed, physiological experiments revealed between-accession variation in electron transport rate and the redox state of the plastoquinone pool. These results indicated that one accession may have adapted to differences in temperature or length of the growing season.

Auditing Knowledge toward Leveraging Organizational IQ in Healthcare Organizations.

PubMed

Shahmoradi, Leila; Karami, Mahtab; Farzaneh Nejad, Ahmadreza

2016-04-01

In this study, a knowledge audit was conducted based on organizational intelligence quotient (OIQ) principles of Iran's Ministry of Health and Medical Education (MOHME) to determine levers that can enhance OIQ in healthcare. The mixed method study was conducted within the MOHME. The study population consisted of 15 senior managers and policymakers. A tool based on literature review and panel expert opinions was developed to perform a knowledge audit. The significant results of this auditing revealed the following: lack of defined standard processes for organizing knowledge management (KM), lack of a knowledge map, absence of a trustee to implement KM, absence of specialists to produce a knowledge map, individuals' unwillingness to share knowledge, implicitness of knowledge format, occasional nature of knowledge documentation for repeated use, lack of a mechanism to determine repetitive tasks, lack of a reward system for the formation of communities, groups and networks, non-updatedness of the available knowledge, and absence of commercial knowledge. The analysis of the audit findings revealed that three levers for enhancing OIQ, including structure and process, organizational culture, and information technology must be created or modified.

Auditing Knowledge toward Leveraging Organizational IQ in Healthcare Organizations

PubMed Central

Shahmoradi, Leila; Farzaneh Nejad, Ahmadreza

2016-01-01

Objectives In this study, a knowledge audit was conducted based on organizational intelligence quotient (OIQ) principles of Iran's Ministry of Health and Medical Education (MOHME) to determine levers that can enhance OIQ in healthcare. Methods The mixed method study was conducted within the MOHME. The study population consisted of 15 senior managers and policymakers. A tool based on literature review and panel expert opinions was developed to perform a knowledge audit. Results The significant results of this auditing revealed the following: lack of defined standard processes for organizing knowledge management (KM), lack of a knowledge map, absence of a trustee to implement KM, absence of specialists to produce a knowledge map, individuals' unwillingness to share knowledge, implicitness of knowledge format, occasional nature of knowledge documentation for repeated use, lack of a mechanism to determine repetitive tasks, lack of a reward system for the formation of communities, groups and networks, non-updatedness of the available knowledge, and absence of commercial knowledge. Conclusions The analysis of the audit findings revealed that three levers for enhancing OIQ, including structure and process, organizational culture, and information technology must be created or modified. PMID:27200221

Mapping the literature of nurse-midwifery

PubMed Central

Seaton, Helen J.

2006-01-01

Objective: This article is part of a project for mapping the literature of nursing. The purpose is to identify the core journals in nurse-midwifery and to determine the extent to which these titles are covered by standard indexing sources. Methods: Cited references from two source journals were analyzed to discover the most frequently cited publications, including their format, age, and amount of dispersion, as well as the indexes that offer the most complete coverage. Results: A study of the literature of nurse-midwifery reveals that the field is diverse, including such topics as women's health, obstetrics, gynecology, and parent-child relations, in addition to the practice of nurse-midwifery itself. Journals were the most heavily cited format, and analysis revealed that ten journals provided one-third of all the references in the study. Conclusions: A combination of Science Citation Index and Social Sciences Citation Index or PubMed/MEDLINE provided the best overall coverage because of the field's reliance on medical journals. CINAHL had the most complete coverage for the nurse-midwifery journals as well as nursing journals in general. PMID:16710467

Unbiased Protein Association Study on the Public Human Proteome Reveals Biological Connections between Co-Occurring Protein Pairs

PubMed Central

2017-01-01

Mass-spectrometry-based, high-throughput proteomics experiments produce large amounts of data. While typically acquired to answer specific biological questions, these data can also be reused in orthogonal ways to reveal new biological knowledge. We here present a novel method for such orthogonal data reuse of public proteomics data. Our method elucidates biological relationships between proteins based on the co-occurrence of these proteins across human experiments in the PRIDE database. The majority of the significantly co-occurring protein pairs that were detected by our method have been successfully mapped to existing biological knowledge. The validity of our novel method is substantiated by the extremely few pairs that can be mapped to existing knowledge based on random associations between the same set of proteins. Moreover, using literature searches and the STRING database, we were able to derive meaningful biological associations for unannotated protein pairs that were detected using our method, further illustrating that as-yet unknown associations present highly interesting targets for follow-up analysis. PMID:28480704

Texture analysis of apparent diffusion coefficient maps for treatment response assessment in prostate cancer bone metastases-A pilot study.

PubMed

Reischauer, Carolin; Patzwahl, René; Koh, Dow-Mu; Froehlich, Johannes M; Gutzeit, Andreas

2018-04-01

To evaluate whole-lesion volumetric texture analysis of apparent diffusion coefficient (ADC) maps for assessing treatment response in prostate cancer bone metastases. Texture analysis is performed in 12 treatment-naïve patients with 34 metastases before treatment and at one, two, and three months after the initiation of androgen deprivation therapy. Four first-order and 19 second-order statistical texture features are computed on the ADC maps in each lesion at every time point. Repeatability, inter-patient variability, and changes in the feature values under therapy are investigated. Spearman rank's correlation coefficients are calculated across time to demonstrate the relationship between the texture features and the serum prostate specific antigen (PSA) levels. With few exceptions, the texture features exhibited moderate to high precision. At the same time, Friedman's tests revealed that all first-order and second-order statistical texture features changed significantly in response to therapy. Thereby, the majority of texture features showed significant changes in their values at all post-treatment time points relative to baseline. Bivariate analysis detected significant correlations between the great majority of texture features and the serum PSA levels. Thereby, three first-order and six second-order statistical features showed strong correlations with the serum PSA levels across time. The findings in the present work indicate that whole-tumor volumetric texture analysis may be utilized for response assessment in prostate cancer bone metastases. The approach may be used as a complementary measure for treatment monitoring in conjunction with averaged ADC values. Copyright © 2018 Elsevier B.V. All rights reserved.