Comparison of SHOX and associated elements duplications distribution between patients (Lėri-Weill dyschondrosteosis/idiopathic short stature) and population sample.

PubMed

Hirschfeldova, Katerina; Solc, Roman

2017-09-05

The effect of heterozygous duplications of SHOX and associated elements on Lėri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS) development is less distinct when compared to reciprocal deletions. The aim of our study was to compare frequency and distribution of duplications within SHOX and associated elements between population sample and LWD (ISS) patients. A preliminary analysis conducted on Czech population sample of 250 individuals compared to our previously reported sample of 352 ISS/LWD Czech patients indicated that rather than the difference in frequency of duplications it is the difference in their distribution. Particularly, there was an increased frequency of duplications residing to the CNE-9 enhancer in our LWD/ISS sample. To see whether the obtained data are consistent across published studies we made a literature survey to get published cases with SHOX or associated elements duplication and formed the merged LWD, the merged ISS, and the merged population samples. Relative frequency of particular region duplication in each of those merged samples were calculated. There was a significant difference in the relative frequency of CNE-9 enhancer duplications (11 vs. 3) and complete SHOX (exon1-6b) duplications (4 vs. 24) (p-value 0.0139 and p-value 0.000014, respectively) between the merged LWD sample and the merged population sample. We thus propose that partial SHOX duplications and small duplications encompassing CNE-9 enhancer could be highly penetrant alleles associated with ISS and LWD development. Copyright © 2017 Elsevier B.V. All rights reserved.

Installation Restoration Program. Phase 2 - Confirmation/Quantification Stage 1. Dover Air Force Base, Dover, Delaware 19901. Volume 1 Technical Report

DTIC Science & Technology

1986-06-10

82174 m c r- %0~ tn r- cL LC 0 $44 bO CO 4 4- 4 -r- :x:c :41 La COOP w w-. u- r0.0)CO 0)~~~ 0) 0 0 O4- -4Ca co~i CO 0)00 0 >O- .H CO) 0O CO CO 0 o-4 Li...bChromatographs of samples MW 103 and field duplicate QA6b showed a peak matching the re- I tention time of vinyl chloride. The positive identity of...this peak was not confirmed by either second-column gas chromatographic analysis or by mass spectroscopy. Therefore, it cannot be definitely stated

Data Validation Package May 2016 Groundwater Sampling at the Lakeview, Oregon, Processing Site August 2016

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

Linard, Joshua; Hall, Steve

2016-08-01

This biennial event includes sampling five groundwater locations (four monitoring wells and one domestic well) at the Lakeview, Oregon, Processing Site. For this event, the domestic well (location 0543) could not be sampled because no one was in residence during the sampling event (Note: notification was provided to the resident prior to the event). Per Appendix A of the Groundwater Compliance Action Plan, sampling is conducted to monitor groundwater quality on a voluntary basis. Sampling and analyses were conducted as specified in the Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated).more » One duplicate sample was collected from location 0505. Water levels were measured at each sampled monitoring well. The constituents monitored at the Lakeview site are manganese and sulfate. Monitoring locations that exceeded the U.S. Environmental Protection Agency (EPA) Secondary Maximum Contaminant Levels for these constituents are listed in Table 1. Review of time-concentration graphs included in this report indicate that manganese and sulfate concentrations are consistent with historical measurements.« less

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

Johnson, Dick; Tsosie, Bernadette

Groundwater samples were collected from monitoring wells at the Bluewater, New Mexico, Disposal Site to monitor groundwater contaminants as specified in the 1997 Long-Term Surveillance Plan for the DOE Bluewater (UMTRCA Title II) Disposal Site Near Grants, New Mexico (LTSP). Sampling and analyses were conducted as specified in the Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). Duplicate samples were collected from locations 14(SG) and 21(M). Sampling originally scheduled for the week of May 11, 2015 was interrupted by heavy rainfall and later completed in June.

Data Validation Package - April and July 2015 Groundwater and Surface Water Sampling at the Gunnison, Colorado, Processing Site

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

Linard, Joshua; Campbell, Sam

This event included annual sampling of groundwater and surface water locations at the Gunnison, Colorado, Processing Site. Sampling and analyses were conducted as specified in Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites. Samples were collected from 28 monitoring wells, three domestic wells, and six surface locations in April at the processing site as specified in the 2010 Ground Water Compliance Action Plan for the Gunnison, Colorado, Processing Site. Domestic wells 0476 and 0477 were sampled in July because the homes were unoccupied in April, and the wells were not in use. Duplicate samplesmore » were collected from locations 0113, 0248, and 0477. One equipment blank was collected during this sampling event. Water levels were measured at all monitoring wells that were sampled. No issues were identified during the data validation process that requires additional action or follow-up.« less

Knowledge-based image processing for on-off type DNA microarray

NASA Astrophysics Data System (ADS)

Kim, Jong D.; Kim, Seo K.; Cho, Jeong S.; Kim, Jongwon

2002-06-01

This paper addresses the image processing technique for discriminating whether the probes are hybrized with target DNA in the Human Papilloma Virus (HPV) DNA Chip designed for genotyping HPV. In addition to the probes, the HPV DNA chip has markers that always react with the sample DNA. The positions of probe-dots in the final scanned image are fixed relative to the marker-dot locations with a small variation according to the accuracy of the dotter and the scanner. The probes are duplicated 4 times for the diagnostic stability. The prior knowledges such as the maker relative distance and the duplication information of probes is integrated into the template matching technique with the normalized correlation measure. Results show that the employment of both of the prior knowledges is to simply average the template matching measures over the positions of the markers and probes. The eventual proposed scheme yields stable marker locating and probe classification.

May 2013 Groundwater and Surface Water Sampling at the Rio Blanco, Colorado, Site (Data Validation Package)

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

Hutton, Rick

2013-10-01

Annual sampling was conducted at the Rio Blanco, Colorado, site for the Long-Term Hydrologic Monitoring Program May 14-16, 2013, to monitor groundwater and surface water for potential radionuclide contamination. Sampling and analyses were conducted as specified in Sampling and Analysis Plan for the U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). A duplicate sample was collected from location CER #1 Black Sulphur. Samples were analyzed for gamma-emitting radionuclides by high-resolution gamma spectrometry and for tritium using the conventional and enrichment methods.

NHEXAS PHASE I REGION 5 STUDY--QA ANALYTICAL RESULTS FOR METALS IN REPLICATES

EPA Science Inventory

This data set includes analytical results for measurements of metals in 490 duplicate (replicate) samples and for particles in 130 duplicate samples. Measurements were made for up to 11 metals in samples of air, dust, water, blood, and urine. Duplicate samples (samples collected ...

Planning for Continuity.

ERIC Educational Resources Information Center

DiMattia, Susan S.

2001-01-01

Describes procedures followed by librarians whose special libraries were destroyed or otherwise affected by the September 11 terrorist attacks. Discusses plans used from Y2K planning; the importance of having a disaster plan in place; moving locations; teamwork; and duplicating data in duplicate locations. Provides a list of pertinent resources.…

Phylogenetic investigation of human FGFR-bearing paralogons favors piecemeal duplication theory of vertebrate genome evolution.

PubMed

Ajmal, Wajya; Khan, Hiba; Abbasi, Amir Ali

2014-12-01

Understanding the genetic mechanisms underlying the organismal complexity and origin of novelties during vertebrate history is one of the central goals of evolutionary biology. Ohno (1970) was the first to postulate that whole genome duplications (WGD) have played a vital role in the evolution of new gene functions: permitting an increase in morphological, physiological and anatomical complexity during early vertebrate history. Here, we analyze the evolutionary history of human FGFR-bearing paralogon (human autosome 4/5/8/10) by the phylogenetic analysis of multigene families with triplicate and quadruplicate distribution on these chromosomes. Our results categorized the histories of 21 families into discrete co-duplicated groups. Genes of a particular co-duplicated group exhibit identical evolutionary history and have duplicated in concert with each other, whereas genes belonging to different groups have dissimilar histories and have not duplicated concurrently. Taken together with our previously published data, we submit that there is sufficient empirical evidence to disprove the 1R/2R hypothesis and to support the general prediction that vertebrate genome evolved by relatively small-scale, regional duplication events that spread across the history of life. Copyright © 2014 Elsevier Inc. All rights reserved.

NHEXAS PHASE I MARYLAND STUDY--STANDARD OPERATING PROCEDURE FOR DUPLICATE SAMPLING (F12)

EPA Science Inventory

This SOP is designed to provide both general and specific guidance for the collection of duplicate samples by Harvard School of Public Health/Emory University for the NHEXAS project. The purpose of the duplicate sampling was to ensure that the value obtained for a sample was ind...

Standardising analysis of carbon monoxide rebreathing for application in anti-doping.

PubMed

Alexander, Anthony C; Garvican, Laura A; Burge, Caroline M; Clark, Sally A; Plowman, James S; Gore, Christopher J

2011-03-01

Determination of total haemoglobin mass (Hbmass) via carbon monoxide (CO) depends critically on repeatable measurement of percent carboxyhaemoglobin (%HbCO) in blood with a hemoximeter. The main aim of this study was to determine, for an OSM3 hemoximeter, the number of replicate measures as well as the theoretical change in percent carboxyhaemoglobin required to yield a random error of analysis (Analyser Error) of ≤1%. Before and after inhalation of CO, nine participants provided a total of 576 blood samples that were each analysed five times for percent carboxyhaemoglobin on one of three OSM3 hemoximeters; with approximately one-third of blood samples analysed on each OSM3. The Analyser Error was calculated for the first two (duplicate), first three (triplicate) and first four (quadruplicate) measures on each OSM3, as well as for all five measures (quintuplicates). Two methods of CO-rebreathing, a 2-min and 10-min procedure, were evaluated for Analyser Error. For duplicate analyses of blood, the Analyser Error for the 2-min method was 3.7, 4.0 and 5.0% for the three OSM3s when the percent carboxyhaemoglobin increased by two above resting values. With quintuplicate analyses of blood, the corresponding errors reduced to .8, .9 and 1.0% for the 2-min method when the percent carboxyhaemoglobin increased by 5.5 above resting values. In summary, to minimise the Analyser Error to ∼≤1% on an OSM3 hemoximeter, researchers should make ≥5 replicates of percent carboxyhaemoglobin and the volume of CO administered should be sufficient increase percent carboxyhaemoglobin by ≥5.5 above baseline levels. Crown Copyright © 2010. Published by Elsevier Ltd. All rights reserved.

CFD modelling of sampling locations for early detection of spontaneous combustion in long-wall gob areas.

PubMed

Yuan, Liming; Smith, Alex C

In this study, computational fluid dynamics (CFD) modeling was conducted to optimize gas sampling locations for the early detection of spontaneous heating in longwall gob areas. Initial simulations were carried out to predict carbon monoxide (CO) concentrations at various regulators in the gob using a bleeder ventilation system. Measured CO concentration values at these regulators were then used to calibrate the CFD model. The calibrated CFD model was used to simulate CO concentrations at eight sampling locations in the gob using a bleederless ventilation system to determine the optimal sampling locations for early detection of spontaneous combustion.

Evolution of tuf genes: ancient duplication, differential loss and gene conversion.

PubMed

Lathe, W C; Bork, P

2001-08-03

The tuf gene of eubacteria, encoding the EF-tu elongation factor, was duplicated early in the evolution of the taxon. Phylogenetic and genomic location analysis of 20 complete eubacterial genomes suggests that this ancient duplication has been differentially lost and maintained in eubacteria.

Data Validation Package - June 2016 Groundwater and Surface Water Sampling at the Green River, Utah, Disposal Site

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

Linard, Joshua; Price, Jeffrey

This event included annual sampling of groundwater and surface water locations at the Green River, Utah, Disposal Site. Sampling and analyses were conducted as specified in Sampling and Analysis Plan for US. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated, http://energy.gov/lrnldownloads/sampling-and- analysis-plan-us-department-energy-office-legacy-management-sites). Samples were collected from 15 monitoring wells and two surface locations at the disposal site as specified in the draft 2011 Ground Water Compliance Action Plan for the Green River, Utah, Disposal Site. Planned monitoring locations are shown in Attachment 1, Sampling and Analysis Work Order. A duplicate sample was collected from location 0179. Onemore » equipment blank was collected during this sampling event. Water levels were measured at all monitoring wells that were sampled. See Attachment 2, Trip Reports for additional details. The analytical data and associated qualifiers can be viewed in environmental database reports and are also available for viewing with dynamic mapping via the GEMS (Geospatial Environmental Mapping System) website at http://gems.lm.doe.gov/#. No issues were identified during the data validation process that requires additional action or follow-up.« less

A computational method for estimating the PCR duplication rate in DNA and RNA-seq experiments.

PubMed

Bansal, Vikas

2017-03-14

PCR amplification is an important step in the preparation of DNA sequencing libraries prior to high-throughput sequencing. PCR amplification introduces redundant reads in the sequence data and estimating the PCR duplication rate is important to assess the frequency of such reads. Existing computational methods do not distinguish PCR duplicates from "natural" read duplicates that represent independent DNA fragments and therefore, over-estimate the PCR duplication rate for DNA-seq and RNA-seq experiments. In this paper, we present a computational method to estimate the average PCR duplication rate of high-throughput sequence datasets that accounts for natural read duplicates by leveraging heterozygous variants in an individual genome. Analysis of simulated data and exome sequence data from the 1000 Genomes project demonstrated that our method can accurately estimate the PCR duplication rate on paired-end as well as single-end read datasets which contain a high proportion of natural read duplicates. Further, analysis of exome datasets prepared using the Nextera library preparation method indicated that 45-50% of read duplicates correspond to natural read duplicates likely due to fragmentation bias. Finally, analysis of RNA-seq datasets from individuals in the 1000 Genomes project demonstrated that 70-95% of read duplicates observed in such datasets correspond to natural duplicates sampled from genes with high expression and identified outlier samples with a 2-fold greater PCR duplication rate than other samples. The method described here is a useful tool for estimating the PCR duplication rate of high-throughput sequence datasets and for assessing the fraction of read duplicates that correspond to natural read duplicates. An implementation of the method is available at https://github.com/vibansal/PCRduplicates .

Identification and characterization of large DNA deletions affecting oil quality traits in soybean seeds through transcriptome sequencing analysis.

PubMed

Goettel, Wolfgang; Ramirez, Martha; Upchurch, Robert G; An, Yong-Qiang Charles

2016-08-01

Identification and characterization of a 254-kb genomic deletion on a duplicated chromosome segment that resulted in a low level of palmitic acid in soybean seeds using transcriptome sequencing. A large number of soybean genotypes varying in seed oil composition and content have been identified. Understanding the molecular mechanisms underlying these variations is important for breeders to effectively utilize them as a genetic resource. Through design and application of a bioinformatics approach, we identified nine co-regulated gene clusters by comparing seed transcriptomes of nine soybean genotypes varying in oil composition and content. We demonstrated that four gene clusters in the genotypes M23, Jack and N0304-303-3 coincided with large-scale genome rearrangements. The co-regulated gene clusters in M23 and Jack mapped to a previously described 164-kb deletion and a copy number amplification of the Rhg1 locus, respectively. The coordinately down-regulated gene clusters in N0304-303-3 were caused by a 254-kb deletion containing 19 genes including a fatty acyl-ACP thioesterase B gene (FATB1a). This deletion was associated with reduced palmitic acid content in seeds and was the molecular cause of a previously reported nonfunctional FATB1a allele, fap nc . The M23 and N0304-304-3 deletions were located in duplicated genome segments retained from the Glycine-specific whole genome duplication that occurred 13 million years ago. The homoeologous genes in these duplicated regions shared a strong similarity in both their encoded protein sequences and transcript accumulation levels, suggesting that they may have conserved and important functions in seeds. The functional conservation of homoeologous genes may result in genetic redundancy and gene dosage effects for their associated seed traits, explaining why the large deletion did not cause lethal effects or completely eliminate palmitic acid in N0304-303-3.

Balloon-Borne Full-Column Greenhouse Gas Profiling Field Campaign Report

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

Fischer, Marc L

The vertical distributions of CO2, CH4, and other gases provide important constraints for the determination of terrestrial and ocean sources and sinks of carbon and other biogeochemical processes in the Earth system. The DOE Biological and Environmental Research Program (DOE-BER) and the NOAA Earth System Research Laboratory (NOAA-ESRL) collaborate to quantify the vertically resolved distribution of atmospheric carbon-cycle gases (CO2, and CH4) within approximately 99% of the atmospheric column at the DOE ARM Southern Great Plains Facility in Oklahoma. In 2015, flights were delayed while research at NOAA focused on evaluating sources of systematic errors in the gas collection andmore » analysis system and modifying the sampling system to provide duplicate air samples in a single flight package. In 2017, we look forward to proposing additional sampling and analysis at ARM-SGP (and other sites) that characterize the vertical distribution of CO2 and CH4 over time and space.« less

The Author’s Guide To Writing 412th Test Wing Technical Reports

DTIC Science & Technology

2014-12-01

control CAD computer aided design cc cubic centimeters C.O. carry-over c/o checkout USAF United States Air Force C1 rolling moment coefficient...cooling air. Mission Impact: Results in maintenance inability to reliably duplicate and isolate valid aircraft failures, and degrades reliability...air. Mission Impact: Results in maintenance inability to reliably duplicate and isolate valid aircraft failures, and degrades reliability of system

CoCoNUT: an efficient system for the comparison and analysis of genomes

PubMed Central

2008-01-01

Background Comparative genomics is the analysis and comparison of genomes from different species. This area of research is driven by the large number of sequenced genomes and heavily relies on efficient algorithms and software to perform pairwise and multiple genome comparisons. Results Most of the software tools available are tailored for one specific task. In contrast, we have developed a novel system CoCoNUT (Computational Comparative geNomics Utility Toolkit) that allows solving several different tasks in a unified framework: (1) finding regions of high similarity among multiple genomic sequences and aligning them, (2) comparing two draft or multi-chromosomal genomes, (3) locating large segmental duplications in large genomic sequences, and (4) mapping cDNA/EST to genomic sequences. Conclusion CoCoNUT is competitive with other software tools w.r.t. the quality of the results. The use of state of the art algorithms and data structures allows CoCoNUT to solve comparative genomics tasks more efficiently than previous tools. With the improved user interface (including an interactive visualization component), CoCoNUT provides a unified, versatile, and easy-to-use software tool for large scale studies in comparative genomics. PMID:19014477

Analyses of the NAC transcription factor gene family in Gossypium raimondii Ulbr.: chromosomal location, structure, phylogeny, and expression patterns.

PubMed

Shang, Haihong; Li, Wei; Zou, Changsong; Yuan, Youlu

2013-07-01

NAC domain proteins are plant-specific transcription factors known to play diverse roles in various plant developmental processes. In the present study, we performed the first comprehensive study of the NAC gene family in Gossypium raimondii Ulbr., incorporating phylogenetic, chromosomal location, gene structure, conserved motif, and expression profiling analyses. We identified 145 NAC transcription factor (NAC-TF) genes that were phylogenetically clustered into 18 distinct subfamilies. Of these, 127 NAC-TF genes were distributed across the 13 chromosomes, 80 (55%) were preferentially retained duplicates located in both duplicated regions and six were located in triplicated chromosomal regions. The majority of NAC-TF genes showed temporal-, spatial-, and tissue-specific expression patterns based on transcriptomic and qRT-PCR analyses. However, the expression patterns of several duplicate genes were partially redundant, suggesting the occurrence of sub-functionalization during their evolution. Based on their genomic organization, we concluded that genomic duplications contributed significantly to the expansion of the NAC-TF gene family in G. raimondii. Comprehensive analysis of their expression profiles could provide novel insights into the functional divergence among members of the NAC gene family in G. raimondii. © 2013 Institute of Botany, Chinese Academy of Sciences.

Data Validation Package April 2016 Groundwater and Surface Water Sampling at the Monticello, Utah, Disposal and Processing Sites August 2016

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

Nguyen, Jason; Smith, Fred

This semiannual event includes sampling groundwater and surface water at the Monticello Disposal and Processing Sites. Sampling and analyses were conducted as specified in the Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated) and Program Directive MNT-2016-01. Complete sample sets were collected from 42 of 48 planned locations (9 of 9 former mill site wells, 13 of 13 downgradient wells, 7 of 9 downgradient permeable reactive barrier wells, 4 of 7 seeps and wetlands, and 9 of 10 surface water locations). Planned monitoring locations are shown in Attachment 1, Sampling andmore » Analysis Work Order. Locations R6-M3, SW00-01, Seep 1, Seep 2, and Seep 5 were not sampled due to insufficient water availability. A partial sample was collected at location R4-M3 due to insufficient water. All samples from the permeable reactive barrier wells were filtered as specified in the program directive. Duplicate samples were collected from surface water location Sorenson and from monitoring wells 92-07 and RlO-Ml. Water levels were measured at all sampled wells and an additional set of wells. See Attachment2, Trip Report for additional details. The contaminants of concern (COCs) for the Monticello sites are arsenic, manganese, molybdenum, nitrate+ nitrite as nitrogen (nitrate+ nitrite as N), selenium, uranium, and vanadium. Locations with COCs that exceeded remediation goals are listed in Table 1 and Table 2. Time-concentration graphs of the COCs for all groundwater and surface water locations are included in Attachment 3, Data Presentation. An assessment of anomalous data is included in Attachment 4.« less

Data Validation Package June 2016 Groundwater and Surface Water Sampling at the Old and New Rifle, Colorado, Processing Sites September 2016

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

Bush, Richard; Lemke, Peter

Sampling Period: June 14–17 and July 7, 2016. Water samples were collected from 36 locations at New Rifle and Old Rifle, Colorado, Disposal/Processing Sites. Planned monitoring locations are shown in Attachment 1, Sampling and Analysis Work Order. Duplicate samples were collected from New Rifle locations 0216 and 0855, and Old Rifle location 0655. One equipment blank was collected after decontamination of non-dedicated equipment used to collect one surface water sample. See Attachment 2, Trip Report for additional details. Sampling and analyses were conducted as specified in the Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Managementmore » Sites (LMS/PRO/S04351, continually updated, http://energy.gov/lm/downloads/sampling-and- analysis-plan-us-department-energy-office-legacy-management-sites). New Rifle Site Samples were collected at the New Rifle site from 16 monitoring wells and 7 surface locations in compliance with the December 2008 Groundwater Compliance Action Plan [GCAP] for the New Rifle, Colorado, Processing Site (LMS/RFN/S01920). Monitoring well 0216 could not be sampled in June because it was surrounded by standing water due to the high river stage from spring runoff, it was later sampled in July. Monitoring well 0635 and surface location 0322 could not be sampled because access through the elk fence along Interstate 70 has not been completed at this time. Old Rifle Site Samples were collected at the Old Rifle site from eight monitoring wells and five surface locations in compliance with the December 2001 Ground Water Compliance Action Plan for the Old Rifle, Colorado, UMTRA Project Site (GJ0-2000-177-TAR).« less

Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens

PubMed Central

Chen, Jie; Moinard, Magalie; Xu, Jianping; Wang, Shouxian; Foulongne-Oriol, Marie; Zhao, Ruilin; Hyde, Kevin D.; Callac, Philippe

2016-01-01

The internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene cluster is widely used in fungal taxonomy and phylogeographic studies. The medicinal and edible mushroom Agaricus subrufescens has a worldwide distribution with a high level of polymorphism in the ITS region. A previous analysis suggested notable ITS sequence heterogeneity within the wild French isolate CA487. The objective of this study was to investigate the pattern and potential mechanism of ITS sequence heterogeneity within this strain. Using PCR, cloning, and sequencing, we identified three types of ITS sequences, A, B, and C with a balanced distribution, which differed from each other at 13 polymorphic positions. The phylogenetic comparisons with samples from different continents revealed that the type C sequence was similar to those found in Oceanian and Asian specimens of A. subrufescens while types A and B sequences were close to those found in the Americas or in Europe. We further investigated the inheritance of these three ITS sequence types by analyzing their distribution among single-spore isolates from CA487. In this analysis, three co-dominant markers were used firstly to distinguish the homokaryotic offspring from the heterokaryotic offspring. The homokaryotic offspring were then analyzed for their ITS types. Our genetic analyses revealed that types A and B were two alleles segregating at one locus ITSI, while type C was not allelic with types A and B but was located at another unlinked locus ITSII. Furthermore, type C was present in only one of the two constitutive haploid nuclei (n) of the heterokaryotic (n+n) parent CA487. These data suggest that there was a relatively recent introduction of the type C sequence and a duplication of the ITS locus in this strain. Whether other genes were also transferred and duplicated and their impacts on genome structure and stability remain to be investigated. PMID:27228131

Gene duplication and phylogeography of North American members of the Hart Park serogroup of avian rhabdoviruses.

PubMed

Allison, Andrew B; Mead, Daniel G; Palacios, Gustavo F; Tesh, Robert B; Holmes, Edward C

2014-01-05

Flanders virus (FLAV) and Hart Park virus (HPV) are rhabdoviruses that circulate in mosquito-bird cycles in the eastern and western United States, respectively, and constitute the only two North American representatives of the Hart Park serogroup. Previously, it was suggested that FLAV is unique among the rhabdoviruses in that it contains two pseudogenes located between the P and M genes, while the cognate sequence for HPV has been lacking. Herein, we demonstrate that FLAV and HPV do not contain pseudogenes in this region, but encode three small functional proteins designated as U1-U3 that apparently arose by gene duplication. To further investigate the U1-U3 region, we conducted the first large-scale evolutionary analysis of a member of the Hart Park serogroup by analyzing over 100 spatially and temporally distinct FLAV isolates. Our phylogeographic analysis demonstrates that although FLAV appears to be slowly evolving, phylogenetically divergent lineages co-circulate sympatrically. © 2013 Published by Elsevier Inc.

Cytomegaloviruses in a Community of Wild Nonhuman Primates in Taï National Park, Côte D’Ivoire

PubMed Central

Anoh, Augustin Etile; Murthy, Sripriya; Akoua-Koffi, Chantal; Couacy-Hymann, Emmanuel; Leendertz, Fabian Hubertus; Calvignac-Spencer, Sébastien; Ehlers, Bernhard

2017-01-01

Cytomegaloviruses (CMVs) are known to infect many mammals, including a number of nonhuman primates (NHPs). However, most data available arose from studies led on captive individuals and little is known about CMV diversity in wild NHPs. Here, we analyzed a community of wild nonhuman primates (seven species) in Taï National Park (TNP), Côte d’Ivoire, with two PCR systems targeting betaherpesviruses. CMV DNA was detected in 17/87 primates (4/7 species). Six novel CMVs were identified in sooty mangabeys, Campbell’s monkeys and Diana monkeys, respectively. In 3/17 positive individuals (from three NHP species), different CMVs were co-detected. A major part of the glycoprotein B coding sequences of the novel viruses was amplified and sequenced, and phylogenetic analyses were performed that included three previously discovered CMVs of western red colobus from TNP and published CMVs from other NHP species and geographic locations. We find that, despite this locally intensified sampling, NHP CMVs from TNP are completely host-specific, pinpointing the absence or rarity of cross-species transmission. We also show that on longer timescales the evolution of CMVs is characterized by frequent co-divergence with their hosts, although other processes, including lineage duplication and host switching, also have to be invoked to fully explain their evolutionary relationships. PMID:29286318

Data Validation Package October 2015 Groundwater and Surface Water Sampling at the Monticello, Utah, Processing Site January 2016

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

Nguyen, Jason; Smith, Fred

Sampling Period: October 12–14, 2015. This semiannual event includes sampling groundwater and surface water at the Monticello Mill Tailings Site. Sampling and analyses were conducted as specified in the 2004 Monticello Mill Tailings Site Operable Unit III Post-Record of Decision Monitoring Plan, Draft Final and Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). Samples were collected from 52 of 61 planned locations (15 of 17 former mill site wells, 17 of 18 downgradient wells, 9 of 9 downgradient permeable reactive barrier wells, 2 of 7 seeps and wetlands, and 9 ofmore » 10 surface water locations). Locations MW00-07, Seep 1, Seep 2, Seep 3, Seep 5, Seep 6, SW00-01, T01-13, and T01-19 were not sampled because of insufficient water availability. All samples were filtered as specified in the monitoring plan. Duplicate samples were collected from surface water location W3-04 and from monitoring wells 82-08, 92-09, and 92-10. Water levels were measured at all but one sampled well and an additional set of wells. The contaminants of concern (COCs) for the Monticello Mill Tailings Site are arsenic, manganese, molybdenum, nitrate + nitrite as nitrogen (nitrate + nitrite as N), selenium, uranium, and vanadium. Time-concentration graphs of the COCs for all groundwater and surface water locations are included in this report. Locations with COCs that exceeded remediation goals are listed.« less

Refining the regulatory region upstream of SOX9 associated with 46,XX testicular disorders of Sex Development (DSD).

PubMed

Hyon, Capucine; Chantot-Bastaraud, Sandra; Harbuz, Radu; Bhouri, Rakia; Perrot, Nicolas; Peycelon, Matthieu; Sibony, Mathilde; Rojo, Sandra; Piguel, Xavier; Bilan, Frederic; Gilbert-Dussardier, Brigitte; Kitzis, Alain; McElreavey, Ken; Siffroi, Jean-Pierre; Bashamboo, Anu

2015-08-01

Disorders of Sex Development (DSD) are a heterogeneous group of disorders affecting gonad and/or genito-urinary tract development and usually the endocrine-reproductive system. A genetic diagnosis is made in only around 20% of these cases. The genetic causes of 46,XX-SRY negative testicular DSD as well as ovotesticular DSD are poorly defined. Duplications involving a region located ∼600 kb upstream of SOX9, a key gene in testis development, were reported in several cases of 46,XX DSD. Recent studies have narrowed this region down to a 78 kb interval that is duplicated or deleted respectively in 46,XX or 46,XY DSD. We identified three phenotypically normal patients presenting with azoospermia and 46,XX testicular DSD. Two brothers carried a 83.8 kb duplication located ∼600 kb upstream of SOX9 that overlapped with the previously reported rearrangements. This duplication refines the minimal region associated with 46,XX-SRY negative DSD to a 40.7-41.9 kb element located ∼600 kb upstream of SOX9. Predicted enhancer elements and evolutionary-conserved binding sites for proteins known to be involved in testis determination are located within this region. © 2015 Wiley Periodicals, Inc.

Data Validation Package - July 2016 Groundwater Sampling at the Gunnison, Colorado, Disposal Site

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

Linard, Joshua; Campbell, Sam

Groundwater sampling at the Gunnison, Colorado, Disposal Site is conducted every 5 years to monitor disposal cell performance. During this event, samples were collected from eight monitoring wells as specified in the 1997 Long-Term Surveillance Plan for the Gunnison, Colorado, Disposal Site. Sampling and analyses were conducted as specified in the Sampling and Analysis Plan for US Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated, http://energy.gov/lm/downloads/sampling-and­ analysis-plan-us-department-energy-office-legacy-management-sites). Planned monitoring locations are shown in Attachment 1, Sampling and Analysis Work Order. A duplicate sample was collected from location 0723. Water levels were measured at all monitoring wells thatmore » were sampled and seven additional wells. The analytical data and associated qualifiers can be viewed in environmental database reports and are also available for viewing with dynamic mapping via the GEMS (Geospatial Environmental Mapping System) website at http://gems.lm.doe.gov/#. No issues were identified during the data validation process that require additional action or follow-up.« less

Segmental Duplications in Euchromatic Regions of Human Chromosome 5: A Source of Evolutionary Instability and Transcriptional Innovation

PubMed Central

Courseaux, Anouk; Richard, Florence; Grosgeorge, Josiane; Ortola, Christine; Viale, Agnes; Turc-Carel, Claude; Dutrillaux, Bernard; Gaudray, Patrick; Nahon, Jean-Louis

2003-01-01

Recent analyses of the structure of pericentromeric and subtelomeric regions have revealed that these particular regions of human chromosomes are often composed of blocks of duplicated genomic segments that have been associated with rapid evolutionary turnover among the genomes of closely related primates. In the present study, we show that euchromatic regions of human chromosome 5—5p14, 5p13, 5q13, 5q15–5q21—also display such an accumulation of segmental duplications. The structure, organization and evolution of those primate-specific sequences were studied in detail by combining in silico and comparative FISH analyses on human, chimpanzee, gorilla, orangutang, macaca, and capuchin chromosomes. Our results lend support to a two-step model of transposition duplication in the euchromatic regions, with a founder insertional event at the time of divergence between Platyrrhini and Catarrhini (25–35 million years ago) and an apparent burst of inter- and intrachromosomal duplications in the Hominidae lineage. Furthermore, phylogenetic analysis suggests that the chronology and, likely, molecular mechanisms, differ regarding the region of primary insertion—euchromatic versus pericentromeric regions. Lastly, we show that as their counterparts located near the heterochromatic region, the euchromatic segmental duplications have consistently reshaped their region of insertion during primate evolution, creating putative mosaic genes, and they are obvious candidates for causing ectopic rearrangements that have contributed to evolutionary/genomic instability. [Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: D. Le Paslier, A. McKenzie, J. Melki, C. Sargent, J. Scharf and S. Selig.] PMID:12618367

NHEXAS PHASE I ARIZONA STUDY--QA ANALYTICAL RESULTS FOR METALS IN REPLICATE SAMPLES

EPA Science Inventory

The Metals in Replicate Samples data set contains the analytical results of measurements of up to 27 metals in 133 replicate (duplicate) samples from 62 households. Measurements were made in samples of soil, blood, tap water, and drinking water. Duplicate samples for a small pe...

NHEXAS PHASE I REGION 5 STUDY--QA ANALYTICAL RESULTS FOR VOCS IN REPLICATES

EPA Science Inventory

This data set includes analytical results for measurements of VOCs in 204 duplicate (replicate) samples. Measurements were made for up to 23 VOCs in samples of air, water, and blood. Duplicate samples (samples collected along with or next to the original samples) were collected t...

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--QA ANALYTICAL RESULTS FOR METALS IN REPLICATE SAMPLES

EPA Science Inventory

The Metals in Replicate Samples data set contains the analytical results of measurements of up to 2 metals in 172 replicate (duplicate) samples from 86 households. Measurements were made in samples of blood. Duplicate samples for a small percentage of the total number of sample...

Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)

PubMed Central

Yang, Yaodong; Mason, Annaliese S.; Lei, Xintao; Ma, Zilong

2013-01-01

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events. PMID:23951162

Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).

PubMed

Xiao, Yong; Xia, Wei; Yang, Yaodong; Mason, Annaliese S; Lei, Xintao; Ma, Zilong

2013-01-01

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.

Genome Mutational and Transcriptional Hotspots Are Traps for Duplicated Genes and Sources of Adaptations.

PubMed

Fares, Mario A; Sabater-Muñoz, Beatriz; Toft, Christina

2017-05-01

Gene duplication generates new genetic material, which has been shown to lead to major innovations in unicellular and multicellular organisms. A whole-genome duplication occurred in the ancestor of Saccharomyces yeast species but 92% of duplicates returned to single-copy genes shortly after duplication. The persisting duplicated genes in Saccharomyces led to the origin of major metabolic innovations, which have been the source of the unique biotechnological capabilities in the Baker's yeast Saccharomyces cerevisiae. What factors have determined the fate of duplicated genes remains unknown. Here, we report the first demonstration that the local genome mutation and transcription rates determine the fate of duplicates. We show, for the first time, a preferential location of duplicated genes in the mutational and transcriptional hotspots of S. cerevisiae genome. The mechanism of duplication matters, with whole-genome duplicates exhibiting different preservation trends compared to small-scale duplicates. Genome mutational and transcriptional hotspots are rich in duplicates with large repetitive promoter elements. Saccharomyces cerevisiae shows more tolerance to deleterious mutations in duplicates with repetitive promoter elements, which in turn exhibit higher transcriptional plasticity against environmental perturbations. Our data demonstrate that the genome traps duplicates through the accelerated regulatory and functional divergence of their gene copies providing a source of novel adaptations in yeast. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling

PubMed Central

2010-01-01

Background Clock family genes encode transcription factors that regulate clock-controlled genes and thus regulate many physiological mechanisms/processes in a circadian fashion. Clock1 duplicates and copies of Clock3 and NPAS2-like genes were partially characterized (genomic sequencing) and mapped using family-based indels/SNPs in rainbow trout (RT)(Oncorhynchus mykiss), Arctic charr (AC)(Salvelinus alpinus), and Atlantic salmon (AS)(Salmo salar) mapping panels. Results Clock1 duplicates mapped to linkage groups RT-8/-24, AC-16/-13 and AS-2/-18. Clock3/NPAS2-like genes mapped to RT-9/-20, AC-20/-43, and AS-5. Most of these linkage group regions containing the Clock gene duplicates were derived from the most recent 4R whole genome duplication event specific to the salmonids. These linkage groups contain quantitative trait loci (QTL) for life history and growth traits (i.e., reproduction and cell cycling). Comparative synteny analyses with other model teleost species reveal a high degree of conservation for genes in these chromosomal regions suggesting that functionally related or co-regulated genes are clustered in syntenic blocks. For example, anti-müllerian hormone (amh), regulating sexual maturation, and ornithine decarboxylase antizymes (oaz1 and oaz2), regulating cell cycling, are contained within these syntenic blocks. Conclusions Synteny analyses indicate that regions homologous to major life-history QTL regions in salmonids contain many candidate genes that are likely to influence reproduction and cell cycling. The order of these genes is highly conserved across the vertebrate species examined, and as such, these genes may make up a functional cluster of genes that are likely co-regulated. CLOCK, as a transcription factor, is found within this block and therefore has the potential to cis-regulate the processes influenced by these genes. Additionally, clock-controlled genes (CCGs) are located in other life-history QTL regions within salmonids suggesting that at least in part, trans-regulation of these QTL regions may also occur via Clock expression. PMID:20670436

Simulating evolution of protein complexes through gene duplication and co-option.

PubMed

Haarsma, Loren; Nelesen, Serita; VanAndel, Ethan; Lamine, James; VandeHaar, Peter

2016-06-21

We present a model of the evolution of protein complexes with novel functions through gene duplication, mutation, and co-option. Under a wide variety of input parameters, digital organisms evolve complexes of 2-5 bound proteins which have novel functions but whose component proteins are not independently functional. Evolution of complexes with novel functions happens more quickly as gene duplication rates increase, point mutation rates increase, protein complex functional probability increases, protein complex functional strength increases, and protein family size decreases. Evolution of complexity is inhibited when the metabolic costs of making proteins exceeds the fitness gain of having functional proteins, or when point mutation rates get so large the functional proteins undergo deleterious mutations faster than new functional complexes can evolve. Copyright © 2016 Elsevier Ltd. All rights reserved.

NHEXAS PHASE I MARYLAND STUDY--QA ANALYTICAL RESULTS FOR PESTICIDES IN REPLICATE SAMPLES

EPA Science Inventory

The Pesticides in Replicates data set contains the analytical results of measurements of up to 10 pesticides in 68 replicate (duplicate) samples from 41 households. Measurements were made in samples of indoor air, dust, soil, drinking water, food, and beverages. Duplicate sampl...

Evidence of function for conserved noncoding sequences in Arabidopsis thaliana.

PubMed

Spangler, Jacob B; Subramaniam, Sabarinath; Freeling, Michael; Feltus, F Alex

2012-01-01

• Whole genome duplication events provide a lineage with a large reservoir of genes that can be molded by evolutionary forces into phenotypes that fit alternative environments. A well-studied whole genome duplication, the α-event, occurred in an ancestor of the model plant Arabidopsis thaliana. Retained segments of the α-event have been defined in recent years in the form of duplicate protein coding sequences (α-pairs) and associated conserved noncoding DNA sequences (CNSs). Our aim was to identify any association between CNSs and α-pair co-functionality at the gene expression level. • Here, we tested for correlation between CNS counts and α-pair co-expression and expression intensity across nine expression datasets: aerial tissue, flowers, leaves, roots, rosettes, seedlings, seeds, shoots and whole plants. • We provide evidence for a putative regulatory role of the CNSs. The association of CNSs with α-pair co-expression and expression intensity varied by gene function, subgene position and the presence of transcription factor binding motifs. A range of possible CNS regulatory mechanisms, including intron-mediated enhancement, messenger RNA fold stability and transcriptional regulation, are discussed. • This study provides a framework to understand how CNS motifs are involved in the maintenance of gene expression after a whole genome duplication event. © 2011 The Authors. New Phytologist © 2011 New Phytologist Trust.

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

PubMed Central

Yang, Ya; Moore, Michael J.; Brockington, Samuel F.; Soltis, Douglas E.; Wong, Gane Ka-Shu; Carpenter, Eric J.; Zhang, Yong; Chen, Li; Yan, Zhixiang; Xie, Yinlong; Sage, Rowan F.; Covshoff, Sarah; Hibberd, Julian M.; Nelson, Matthew N.; Smith, Stephen A.

2015-01-01

Many phylogenomic studies based on transcriptomes have been limited to “single-copy” genes due to methodological challenges in homology and orthology inferences. Only a relatively small number of studies have explored analyses beyond reconstructing species relationships. We sampled 69 transcriptomes in the hyperdiverse plant clade Caryophyllales and 27 outgroups from annotated genomes across eudicots. Using a combined similarity- and phylogenetic tree-based approach, we recovered 10,960 homolog groups, where each was represented by at least eight ingroup taxa. By decomposing these homolog trees, and taking gene duplications into account, we obtained 17,273 ortholog groups, where each was represented by at least ten ingroup taxa. We reconstructed the species phylogeny using a 1,122-gene data set with a gene occupancy of 92.1%. From the homolog trees, we found that both synonymous and nonsynonymous substitution rates in herbaceous lineages are up to three times as fast as in their woody relatives. This is the first time such a pattern has been shown across thousands of nuclear genes with dense taxon sampling. We also pinpointed regions of the Caryophyllales tree that were characterized by relatively high frequencies of gene duplication, including three previously unrecognized whole-genome duplications. By further combining information from homolog tree topology and synonymous distance between paralog pairs, phylogenetic locations for 13 putative genome duplication events were identified. Genes that experienced the greatest gene family expansion were concentrated among those involved in signal transduction and oxidoreduction, including a cytochrome P450 gene that encodes a key enzyme in the betalain synthesis pathway. Our approach demonstrates a new approach for functional phylogenomic analysis in nonmodel species that is based on homolog groups in addition to inferred ortholog groups. PMID:25837578

Health risk assessment of inorganic arsenic intake of Ronphibun residents via duplicate diet study.

PubMed

Saipan, Piyawat; Ruangwises, Suthep

2009-06-01

To assess health risk from exposure to inorganic arsenic via duplicate portion sampling method in Ronphibun residents. A hundred and forty samples (140 subject-days) were collected from participants in Ronphibun sub-district. Inorganic arsenic in duplicate diet sample was determined by acid digestion and hydride generation-atomic absorption spectrometry. Deterministic risk assessment is referenced throughout the present paper using United States Environmental Protection Agency (U.S. EPA) guidelines. The average daily dose and lifetime average daily dose of inorganic arsenic via duplicate diet were 0.0021 mg/kg/d and 0.00084 mg/kg/d, respectively. The risk estimates in terms of hazard quotient was 6.98 and cancer risk was 1.26 x 10(-3). The results of deterministic risk characterization both hazard quotient and cancer risk from exposure inorganic arsenic in duplicate diets were greater than safety risk levels of hazard quotient (1) and cancer risk (1 x 10(-4)).

NHEXAS PHASE I MARYLAND STUDY--QA ANALYTICAL RESULTS FOR METALS IN REPLICATE SAMPLES

EPA Science Inventory

The Metals in Replicates data set contains the analytical results of measurements of up to 11 metals in 88 replicate (duplicate) samples from 52 households. Measurements were made in samples of indoor and outdoor air, drinking water, food, and beverages. Duplicate samples for a...

Radon-222 content of natural gas samples from Upper and Middle Devonian sandstone and shale reservoirs in Pennsylvania—preliminary data

USGS Publications Warehouse

Rowan, E.L.; Kraemer, T.F.

2012-01-01

Samples of natural gas were collected as part of a study of formation water chemistry in oil and gas reservoirs in the Appalachian Basin. Nineteen samples (plus two duplicates) were collected from 11 wells producing gas from Upper Devonian sandstones and the Middle Devonian Marcellus Shale in Pennsylvania. The samples were collected from valves located between the wellhead and the gas-water separator. Analyses of the radon content of the gas indicated 222Rn (radon-222) activities ranging from 1 to 79 picocuries per liter (pCi/L) with an overall median of 37 pCi/L. The radon activities of the Upper Devonian sandstone samples overlap to a large degree with the activities of the Marcellus Shale samples.

May 2012 Groundwater and Surface Water Sampling at the Rio Blanco, Colorado, Site (Data Validation Package)

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

Hutton, Rick

2012-12-01

Annual sampling was conducted at the Rio Blanco, Colorado, site for the Long-Term Hydrologic Monitoring Program May 9-10, 2012, to monitor groundwater and surface water for potential radionuclide contamination. Sampling and analyses were conducted as specified in Sampling and Analysis Plan for the U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). A duplicate sample was collected from location Johnson Artesian WL. Samples were analyzed for gamma-emitting radionuclides by high-resolution gamma spectrometry and for tritium using the conventional and enrichment methods. Results of this monitoring at the Rio Blanco site demonstrate that groundwater and surface water outsidemore » the site boundaries have not been affected by project-related contaminants.« less

Mitochondrial DNA as a non-invasive biomarker: Accurate quantification using real time quantitative PCR without co-amplification of pseudogenes and dilution bias

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

Malik, Afshan N., E-mail: afshan.malik@kcl.ac.uk; Shahni, Rojeen; Rodriguez-de-Ledesma, Ana

2011-08-19

Highlights: {yields} Mitochondrial dysfunction is central to many diseases of oxidative stress. {yields} 95% of the mitochondrial genome is duplicated in the nuclear genome. {yields} Dilution of untreated genomic DNA leads to dilution bias. {yields} Unique primers and template pretreatment are needed to accurately measure mitochondrial DNA content. -- Abstract: Circulating mitochondrial DNA (MtDNA) is a potential non-invasive biomarker of cellular mitochondrial dysfunction, the latter known to be central to a wide range of human diseases. Changes in MtDNA are usually determined by quantification of MtDNA relative to nuclear DNA (Mt/N) using real time quantitative PCR. We propose that themore » methodology for measuring Mt/N needs to be improved and we have identified that current methods have at least one of the following three problems: (1) As much of the mitochondrial genome is duplicated in the nuclear genome, many commonly used MtDNA primers co-amplify homologous pseudogenes found in the nuclear genome; (2) use of regions from genes such as {beta}-actin and 18S rRNA which are repetitive and/or highly variable for qPCR of the nuclear genome leads to errors; and (3) the size difference of mitochondrial and nuclear genomes cause a 'dilution bias' when template DNA is diluted. We describe a PCR-based method using unique regions in the human mitochondrial genome not duplicated in the nuclear genome; unique single copy region in the nuclear genome and template treatment to remove dilution bias, to accurately quantify MtDNA from human samples.« less

Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses

PubMed Central

Schnable, James C.; Freeling, Michael; Lyons, Eric

2012-01-01

The grasses, Poaceae, are one of the largest and most successful angiosperm families. Like many radiations of flowering plants, the divergence of the major grass lineages was preceded by a whole-genome duplication (WGD), although these events are not rare for flowering plants. By combining identification of syntenic gene blocks with measures of gene pair divergence and different frequencies of ancient gene loss, we have separated the two subgenomes present in modern grasses. Reciprocal loss of duplicated genes or genomic regions has been hypothesized to reproductively isolate populations and, thus, speciation. However, in contrast to previous studies in yeast and teleost fishes, we found very little evidence of reciprocal loss of homeologous genes between the grasses, suggesting that post-WGD gene loss may not be the cause of the grass radiation. The sets of homeologous and orthologous genes and predicted locations of deleted genes identified in this study, as well as links to the CoGe comparative genomics web platform for analyzing pan-grass syntenic regions, are provided along with this paper as a resource for the grass genetics community. PMID:22275519

Mosaic: a position-effect variegation eye-color mutant in the mosquito Anopheles gambiae.

PubMed

Benedict, M Q; McNitt, L M; Cornel, A J; Collins, F H

2000-01-01

The Mosaic (Mos) mutation, isolated in the F1 of 60Co-irradiated mosquitoes, confers variegated eye color to third and fourth instar larvae, pupae, and adults of the mosquito Anopheles gambiae. Mos is recessive in wild pink eye (p+) individuals, but is dominant and confers areas of wild-type pigment in mutant pink eye backgrounds. Mos is located 14.4 cM from pink eye on the X chromosome and is associated with a duplication of division 2B euchromatin that has been inserted into division 6 heterochromatin. Various combinations of Mos, pink eye alleles, and the autosomal mutation red eye were produced. In all cases, the darker pigmented regions of the eye in Mos individuals show the phenotypic interactions expected if the phenotype of those regions is due to expression of a p+ allele. Expression of Mos is suppressed by rearing larvae at 32 degrees C relative to 22 degrees C. All of these characteristics are consistent with Mos being a duplicated wild copy of the pink eye gene undergoing position-effect variegation.

Stability of (13) C-Urea Breath Test Samples Over Time in the Diagnosis of Helicobacter pylori.

PubMed

Perets, Tsachi Tsadok; Shporn, Einav; Boltin, Doron; Dickman, Ram; Niv, Yaron

2016-05-01

The accuracy and repeatability of breath test in the diagnosis of Helicobacter pylori infection have not been adequately investigated. Although it has been shown that storage for long periods does not affect the analysis results, no data are available on the effect of repetitive testing. In this study, our aim was to evaluate the repeatability of the analyses of breath samples at room temperature. A total of 202 positive breath samples were collected in duplicates, before and after administration of 75 mg (13) C- urea dissolved in 100 ml of orange juice. Breath test results were expressed as delta (13) CO2 . The cut-off value was 3.5 parts per thousand. Each sample was analyzed in a mass spectrometer 7, 14, 21, and 28 days after collection. The accuracy calculation was based on the comparison of the delta (13) CO2 obtained in the three consecutive weeks following the first test run to the delta (13) CO2 obtained in the first test run. Two hundred (99%), 197 (97.52%), and 196 (97%) of the 202 samples tested positive in the second, third, and fourth test runs, respectively. The accuracy of the delta (13) CO2 was 98.6%, 99.2%, and 96.7% in the three consecutive runs, respectively. Short-term storage of 1 month does not affect sample stability or the results of (13) C-urea breath tests in up to three consecutive repeats. © 2015 Wiley Periodicals, Inc.

Molecular analyses of juvenile granulosa cell tumors bearing AKT1 mutations provide insights into tumor biology and therapeutic leads.

PubMed

Auguste, Aurélie; Bessière, Laurianne; Todeschini, Anne-Laure; Caburet, Sandrine; Sarnacki, Sabine; Prat, Jaime; D'angelo, Emanuela; De La Grange, Pierre; Ariste, Olivier; Lemoine, Fréderic; Legois, Bérangère; Sultan, Charles; Zider, Alain; Galmiche, Louise; Kalfa, Nicolas; Veitia, Reiner A

2015-12-01

Juvenile granulosa cell tumors (JGCTs) of the ovary are pediatric neoplasms representing 5% of all granulosa cell tumors (GCTs). Most GCTs are of adult type (AGCTs) and bear a mutation in the FOXL2 gene. The molecular basis of JGCTs is poorly understood, although mutations in the GNAS gene have been reported. We have detected in-frame duplications within the oncogene AKT1 in >60% of the JGCTs studied. Here, to evaluate the functional impact of these duplications and the existence of potential co-driver alterations, we have sequenced the transcriptome of four JGCTs and compared them with control transcriptomes. A search for gene variants detected only private alterations probably unrelated with tumorigenesis, suggesting that tandem duplications are the best candidates to underlie tumor formation in the absence of GNAS alterations. We previously showed that the duplications were specific to JGCTs. However, the screening of eight AGCTs samples without FOXL2 mutation showed the existence of an AKT1 duplication in one case, also having a stromal luteoma. The analysis of RNA-Seq data pinpointed a series of differentially expressed genes, involved in cytokine and hormone signaling and cell division-related processes. Further analyses pointed to the existence of a possible dedifferentiation process and suggested that most of the transcriptomic dysregulation might be mediated by a limited set of transcription factors perturbed by AKT1 activation. Finally, we show that commercially available AKT inhibitors can modulate the in vitro activity of various mutated forms. These results shed light on the pathogenesis of JGCTs and provide therapeutic leads for a targeted treatment. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Determination of Coenzyme Q10 Content in Raw Materials and Dietary Supplements by High-Performance Liquid Chromatography-UV: Collaborative Study

PubMed Central

Lunetta, Steven; Roman, Mark

2008-01-01

An international collaborative study was conducted of a high-performance liquid chromatographic (HPLC)-UV method for the determination of coenzyme Q10 (CoQ10, ubidecarenone) in raw materials and dietary supplements. Ten collaborating laboratories determined the total CoQ10 content in 8 blind duplicate samples. Sample materials included CoQ10 raw material and 4 finished product dietary supplements representing softgels, hardshell gelatin capsules, and chewable wafers. In addition, collaborating laboratories received a negative control and negative control spiked with CoQ10 at low and high levels to determine recovery. Materials were extracted with an acetonitrile–tetrahydrofuran–water mixture. Ferric chloride was added to the test solutions to ensure all CoQ10 was in the oxidized form. The HPLC analyses were performed on a C18 column using UV detection at 275 nm. Repeatability relative standard deviations (RSDr) ranged from 0.94 to 5.05%. Reproducibility relative standard deviations (RSDR) ranged from 3.08 to 17.1%, with HorRat values ranging from 1.26 to 5.17. Recoveries ranged from 74.0 to 115%. Based on these results, the method is recommended for Official First Action for determination of CoQ10 in raw materials and dietary supplement finished products containing CoQ10 at a concentration of >100 mg CoQ10/g test material. PMID:18727527

Determination of coenzyme Q10 content in raw materials and dietary supplements by high-performance liquid chromatography-UV: collaborative study.

PubMed

Lunetta, Steven; Roman, Mark

2008-01-01

An international collaborative study was conducted of a high-performance liquid chromatographic (HPLC)-UV method for the determination of coenzyme Q10 (CoQ10, ubidecarenone) in raw materials and dietary supplements. Ten collaborating laboratories determined the total CoQ10 content in 8 blind duplicate samples. Sample materials included CoQ10 raw material and 4 finished product dietary supplements representing softgels, hardshell gelatin capsules, and chewable wafers. In addition, collaborating laboratories received a negative control and negative control spiked with CoQ10 at low and high levels to determine recovery. Materials were extracted with an acetonitrile-tetrahydrofuran-water mixture. Ferric chloride was added to the test solutions to ensure all CoQ10 was in the oxidized form. The HPLC analyses were performed on a C18 column using UV detection at 275 nm. Repeatability relative standard deviations (RSDr) ranged from 0.94 to 5.05%. Reproducibility relative standard deviations (RSDR) ranged from 3.08 to 17.1%, with HorRat values ranging from 1.26 to 5.17. Recoveries ranged from 74.0 to 115%. Based on these results, the method is recommended for Official First Action for determination of CoQ10 in raw materials and dietary supplement finished products containing CoQ10 at a concentration of >100 mg CoQ10/g test material.

Evaluation of National Atmospheric Deposition Program measurements for co-located Sites CO89 and CO98 at Rocky Mountain National Park, 2012

USGS Publications Warehouse

,

2013-01-01

Median weekly absolute percent differences for selected parameters including: sample volume, 8.0 percent; ammonium concentration, 9.1 percent; nitrate concentration, 8.5 percent; sulfate concentration, 10.2 percent. Annual precipitation-weighted mean concentrations were higher for CO98 compared to CO89 for all analytes. The chemical concentration record for CO98 contains more valid samples than the CO89 record. Therefore, the CO98 record is more representative of 2012 total annual deposition at Loch Vale. Daily precipitation-depth records for the co-located precipitation gages were 100 percent complete, and the total annual precipitation depths between the sites differed by 0.1 percent for the year (91.5 and 91.4 cm).

Effects of Dehydroepiandrosterone Supplementation during Stressful Military Training: A Randomized, Controlled, Double-Blind Field Study

DTIC Science & Technology

2011-01-01

DHEAS. All samples were assayed for salivary DHEA in duplicate using a highly sensitive enzyme immunoassay (Salimetrics, LLC). The test used 50ml of...p , 0.0001, n ¼ 39). Similarly, samples were assayed for salivary DHEAS in duplicate using a highly sensitive enzyme immuno- assay (Salimetrics, LLC...assayed for salivary testosterone. This was performed in duplicate using a highly sensitive enzyme immunoassay (Salimetrics, LLC). The test used 25ml of

Dietary intakes of pesticides based on community duplicate diet samples

EPA Science Inventory

The calculation of dietary intake of selected pesticides was accomplished using food samples collected from individual representatives of a defined demographic community using a community duplicate diet approach. A community of nine participants was identified in Apopka, FL from...

Automated Data Base Implementation Requirements for the Avionics Planning Baseline - Army

DTIC Science & Technology

1983-07-01

PJRQT PJRSG .... PRJR owns PJRQTR Item EFT A32 A26 In record EFR Item ESFT A36 A40 In record ESFR Item EQPOC ALCPOC A20 In record EQR Iten EPHONE LPHONE...USING EF DUPLICATES ARE NOT ALLOWED WITHIN EQSEG. EF TYPE CHARACTER 4. EFT TYPE CHARACTER 32. EG TYPE CHARACTER 4. RECORD NAME IS ESFR LOCATION MODE... ESFR MANDATORY AUTOMATIC LINKED TO OWNER ASCENDING KEY IS ESF DUPLICATES NOT SET SELECTION THRU LOCATION MODE OF OWNER. SET NAME IS ESEQ MODE CHAIN

47 CFR 76.92 - Cable network non-duplication; extent of protection.

Code of Federal Regulations, 2013 CFR

2013-10-01

... within the geographic zone for a network program, the network non-duplication rights to which are held by... follows: (1) First, all television broadcast stations within whose specified zone the community of the... within whose secondary zone the community of the community unit is located, in whole or in part. (c) For...

47 CFR 76.92 - Cable network non-duplication; extent of protection.

Code of Federal Regulations, 2012 CFR

2012-10-01

... within the geographic zone for a network program, the network non-duplication rights to which are held by... follows: (1) First, all television broadcast stations within whose specified zone the community of the... within whose secondary zone the community of the community unit is located, in whole or in part. (c) For...

47 CFR 76.92 - Cable network non-duplication; extent of protection.

Code of Federal Regulations, 2014 CFR

2014-10-01

... within the geographic zone for a network program, the network non-duplication rights to which are held by... follows: (1) First, all television broadcast stations within whose specified zone the community of the... within whose secondary zone the community of the community unit is located, in whole or in part. (c) For...

WITHDRAWN: Reporting adverse events related to cosmetic products.

PubMed

Katz, Linda M

2017-02-01

The Publisher regrets that this article is an accidental duplication of an article that has already been published in Dermatitis, 27 (2016) 236-237, doi: 10.1097/DER.0000000000000195. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.

Atmospheric measurement of point source fossil fuel CO2 emissions

NASA Astrophysics Data System (ADS)

Turnbull, J. C.; Keller, E. D.; Baisden, W. T.; Brailsford, G.; Bromley, T.; Norris, M.; Zondervan, A.

2013-11-01

We use the Kapuni Gas Treatment Plant to examine methodologies for atmospheric monitoring of point source fossil fuel CO2 (CO2ff) emissions. The Kapuni plant, located in rural New Zealand, removes CO2 from locally extracted natural gas and vents that CO2 to the atmosphere, at a rate of ~0.1 Tg carbon per year. The plant is located in a rural dairy farming area, with no other significant CO2ff sources nearby, but large, diurnally varying, biospheric CO2 fluxes from the surrounding highly productive agricultural grassland. We made flask measurements of CO2 and 14CO2 (from which we derive the CO2ff component) and in situ measurements of CO2 downwind of the Kapuni plant, using a Helikite to sample transects across the emission plume from the surface up to 100 m a.g.l. We also determined the surface CO2ff content averaged over several weeks from the 14CO2 content of grass samples collected from the surrounding area. We use the WindTrax plume dispersion model to compare the atmospheric observations with the emissions reported by the Kapuni plant, and to determine how well atmospheric measurements can constrain the emissions. The model has difficulty accurately capturing the fluctuations and short-term variability in the Helikite samples, but does quite well in representing the observed CO2ff in 15 min averaged surface flask samples and in ~1 week integrated CO2ff averages from grass samples. In this pilot study, we found that using grass samples, the modeled and observed CO2ff emissions averaged over one week agreed to within 30%. The results imply that greater verification accuracy may be achieved by including more detailed meteorological observations and refining 14CO2 sampling strategies.

Distal 7q11.23 Duplication, an Emerging Microduplication Syndrome: A Case Report and Further Characterisation.

PubMed

Faundes, Víctor; Santa María, Lorena; Morales, Paulina; Curotto, Bianca; Parraguez, María M

2016-10-01

Chromosome 7q11.23 duplication syndrome is a well-recognised syndrome which involves the duplication of the same genes located in the Williams-Beuren critical region. However, in 2010, 4 patients were reported with a microduplication only in the HIP1 and YWHAG genes. We refer to this as a distal 7q11.23 duplication (dup7q11.23D). Here, we report the fifth de novo patient with dup7q11.23D, whose symptoms may be explained by YWHAG overexpression as was demonstrated recently in mice and obese patients. Finally, further studies will be necessary to delineate this emerging microduplication syndrome.

A deletion and a duplication in distal 22q11.2 deletion syndrome region. Clinical implications and review

PubMed Central

Fernández, Luis; Nevado, Julián; Santos, Fernando; Heine-Suñer, Damià; Martinez-Glez, Victor; García-Miñaur, Sixto; Palomo, Rebeca; Delicado, Alicia; Pajares, Isidora López; Palomares, María; García-Guereta, Luis; Valverde, Eva; Hawkins, Federico; Lapunzina, Pablo

2009-01-01

Background Individuals affected with DiGeorge and Velocardiofacial syndromes present with both phenotypic diversity and variable expressivity. The most frequent clinical features include conotruncal congenital heart defects, velopharyngeal insufficiency, hypocalcemia and a characteristic craniofacial dysmorphism. The etiology in most patients is a 3 Mb recurrent deletion in region 22q11.2. However, cases of infrequent deletions and duplications with different sizes and locations have also been reported, generally with a milder, slightly different phenotype for duplications but with no clear genotype-phenotype correlation to date. Methods We present a 7 month-old male patient with surgically corrected ASD and multiple VSDs, and dysmorphic facial features not clearly suggestive of 22q11.2 deletion syndrome, and a newborn male infant with cleft lip and palate and upslanting palpebral fissures. Karyotype, FISH, MLPA, microsatellite markers segregation studies and SNP genotyping by array-CGH were performed in both patients and parents. Results Karyotype and FISH with probe N25 were normal for both patients. MLPA analysis detected a partial de novo 1.1 Mb deletion in one patient and a novel partial familial 0.4 Mb duplication in the other. Both of these alterations were located at a distal position within the commonly deleted region in 22q11.2. These rearrangements were confirmed and accurately characterized by microsatellite marker segregation studies and SNP array genotyping. Conclusion The phenotypic diversity found for deletions and duplications supports a lack of genotype-phenotype correlation in the vicinity of the LCRC-LCRD interval of the 22q11.2 chromosomal region, whereas the high presence of duplications in normal individuals supports their role as polymorphisms. We suggest that any hypothetical correlation between the clinical phenotype and the size and location of these alterations may be masked by other genetic and/or epigenetic modifying factors. PMID:19490635

Testing of duplicate rinse aliquots for presence of Salmonella

USDA-ARS?s Scientific Manuscript database

Testing of chicken carcass rinses for Salmonella prevalence is often performed in duplicate because of the potential importance of the results, but anecdotal reports indicate that duplicate samples often disagree. This might be due to normal variation in microbiological methods or to the testing of...

Community duplicate diet methodology: A new tool for estimating dietary exposure to pesticides

EPA Science Inventory

An observational field study was conducted to assess the feasibility of a community duplicate diet collection method; a dietary monitoring procedure that is population-based. The purpose was to establish an alternative procedure to duplicate diet sampling that would be more effi...

Data for a regional approach to the development of an effects-based nutrient criterion for wadable streams

USGS Publications Warehouse

Crawford, J. Kent; Loper, Connie A.; Beaman, Joseph R.; Soehl, Anna G.; Brown, Will S.

2007-01-01

States are required by the U.S. Environmental Protection Agency to establish nutrient criteria (concentrations of nutrients above which water quality is deteriorated) as part of their water-quality regulations. A study of wadable streams in the Mid-Atlantic Region was undertaken by the U.S. Geological Survey, the U.S. Environmental Protection Agency, and the Maryland Department of the Environment, with assistance from the Pennsylvania Department of Environmental Protection, to help define current concentrations of nutrients in streams with the goal of associating different nutrient-concentration levels with their effects on water quality. During the summers of 2004 and 2005, diel concentrations of dissolved oxygen, nutrient concentrations, concentrations of chlorophyll a in attached algae, and algal-community structure were measured at 46 stream sites in Maryland, Pennsylvania, Virginia, and West Virginia. Data from this work can be used by individual state agencies to define nutrient criteria. Quality-control measures for the study included submitting blank samples, duplicate samples, and reference samples for analysis of nutrients, total organic carbon, chlorophyll a, and algal biomass. Duplicate and split samples were submitted for periphyton identifications. Three periphyton split samples were sent to an independent lab for a check on periphyton identifications. Neither total organic carbon nor nutrients were detected in blank samples. Concentrations of nutrients and total organic carbon were similar for most duplicate sample pairs, with the exception of a duplicate pair from Western Run. Concentrations of ammonia plus organic nitrogen for this duplicate pair differed by as much as 34 percent. Total organic carbon for the duplicate pair from Western Run differed by 102 percent. The U.S. Geological Survey National Water Quality Laboratory performance on the only valid reference sample submitted was excellent; the relative percent difference values were no larger than 5 percent for any constituent analyzed. For periphyton identifications, duplicate samples had Jaccard Coefficient of Community values slightly greater than 0.5. This indicates the periphyton sampling protocol used provided a sample that was only moderately reproducible. Jaccard Coefficients for three periphyton samples split between two independent labs were 0.2, 0.11, and 0.08. These very low values suggest a poor concurrence on species identifications performed by the two labs. As a result of these quality-control samples, the slides prepared for diatom identifications were sent to the Academy of Natural Sciences for re-identification. Caution is urged when interpreting periphyton-community information from this study. This report and the raw data from the study are available online at http://pubs.usgs.gov/ds257

Atmospheric measurement of point source fossil CO2 emissions

NASA Astrophysics Data System (ADS)

Turnbull, J. C.; Keller, E. D.; Baisden, T.; Brailsford, G.; Bromley, T.; Norris, M.; Zondervan, A.

2014-05-01

We use the Kapuni Gas Treatment Plant to examine methodologies for atmospheric monitoring of point source fossil fuel CO2 (CO2ff) emissions. The Kapuni plant, located in rural New Zealand, removes CO2 from locally extracted natural gas and vents that CO2 to the atmosphere, at a rate of ~0.1 Tg carbon per year. The plant is located in a rural dairy farming area, with no other significant CO2ff sources nearby, but large, diurnally varying, biospheric CO2 fluxes from the surrounding highly productive agricultural grassland. We made flask measurements of CO2 and 14CO2 (from which we derive the CO2ff component) and in situ measurements of CO2 downwind of the Kapuni plant, using a Helikite to sample transects across the emission plume from the surface up to 100 m above ground level. We also determined the surface CO2ff content averaged over several weeks from the 14C content of grass samples collected from the surrounding area. We use the WindTrax plume dispersion model to compare the atmospheric observations with the emissions reported by the Kapuni plant, and to determine how well atmospheric measurements can constrain the emissions. The model has difficulty accurately capturing the fluctuations and short-term variability in the Helikite samples, but does quite well in representing the observed CO2ff in 15 min averaged surface flask samples and in ~ one week integrated CO2ff averages from grass samples. In this pilot study, we found that using grass samples, the modeled and observed CO2ff emissions averaged over one week agreed to within 30%. The results imply that greater verification accuracy may be achieved by including more detailed meteorological observations and refining 14C sampling strategies.

Collaborative WorkBench (cwb): Enabling Experiment Execution, Analysis and Visualization with Increased Scientific Productivity

NASA Astrophysics Data System (ADS)

Maskey, Manil; Ramachandran, Rahul; Kuo, Kwo-Sen

2015-04-01

The Collaborative WorkBench (CWB) has been successfully developed to support collaborative science algorithm development. It incorporates many features that enable and enhance science collaboration, including the support for both asynchronous and synchronous modes of interactions in collaborations. With the former, members in a team can share a full range of research artifacts, e.g. data, code, visualizations, and even virtual machine images. With the latter, they can engage in dynamic interactions such as notification, instant messaging, file exchange, and, most notably, collaborative programming. CWB also implements behind-the-scene provenance capture as well as version control to relieve scientists of these chores. Furthermore, it has achieved a seamless integration between researchers' local compute environments and those of the Cloud. CWB has also been successfully extended to support instrument verification and validation. Adopted by almost every researcher, the current practice of downloading data to local compute resources for analysis results in much duplication and inefficiency. CWB leverages Cloud infrastructure to provide a central location for data used by an entire science team, thereby eliminating much of this duplication and waste. Furthermore, use of CWB in concert with this same Cloud infrastructure enables co-located analysis with data where opportunities of data-parallelism can be better exploited, thereby further improving efficiency. With its collaboration-enabling features apposite to steps throughout the scientific process, we expect CWB to fundamentally transform research collaboration and realize maximum science productivity.

Host specificity and genealogy of the louse Polyplax serrata on field mice, Apodemus species: a case of parasite duplication or colonisation?

PubMed

Stefka, Jan; Hypsa, Václav

2008-05-01

The genealogy, population structure and population dynamics of the sucking louse Polyplax serrata were analysed across four host species of the genus Apodemus. An analysis of 126 sequences of cytochrome c oxidase subunit I using phylogenetic approaches and haplotype networking revealed a clear structure of European samples, forming three distinct and genetically distant clades with different host specificities. Although a clear connection was detected between the host and parasite genealogies/phylogenies, a uniform pattern of co-speciation was not found. For example, a dramatic shift in the degree of host specificity was demonstrated for two related louse lineages living in sympatry and sharing one of their host species. While one of the louse lineages frequently parasitised two different host taxa (Apodemus sylvaticus and Apodemus flavicollis), the other louse lineage was strictly specific to A. flavicollis. The estimate of divergence time between the two louse lineages indicates that they may have arisen due to parasite duplication on A. flavicollis.

Data Validation Package, April and June 2016 Groundwater and Surface Water Sampling at the Gunnison, Colorado, Processing Site, October 2016

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

Linard, Joshua; Campbell, Sam

This event included annual sampling of groundwater and surface water locations at the Gunnison, Colorado, Processing Site. Sampling and analyses were conducted as specified in Sampling and Analysis Plan for US Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated, http://energy.gov/lm/downloads/sampling-and­ analysis-plan-us-department-energy-office-legacy-management-sites). Samples were collected from 28 monitoring wells, three domestic wells, and six surface locations in April at the processing site as specified in the draft 2010 Ground Water Compliance Action Plan for the Gunnison, Colorado, Processing Site. Planned monitoring locations are shown in Attachment 1, Sampling and Analysis Work Order. Domestic wells 0476 and 0477 weremore » sampled in June because the homes were unoccupied in April, and the wells were not in use. Duplicate samples were collected from locations 0126, 0477, and 0780. One equipment blank was collected during this sampling event. Water levels were measured at all monitoring wells that were sampled. See Attachment 2, Trip Reports for additional details. The analytical data and associated qualifiers can be viewed in environmental database reports and are also available for viewing with dynamic mapping via the GEMS (Geospatial Environmental Mapping System) website at http://gems.lm.doe.gov/#. No issues were identified during the data validation process that requires additional action or follow-up. An assessment of anomalous data is included in Attachment 3. Interpretation and presentation of results, including an assessment ofthe natural flushing compliance strategy, will be reported in the upcoming 2016 Verification Monitoring Report. U.S.« less

Genome-wide linkage and copy number variation analysis reveals 710 kb duplication on chromosome 1p31.3 responsible for autosomal dominant omphalocele

PubMed Central

Radhakrishna, Uppala; Nath, Swapan K; McElreavey, Ken; Ratnamala, Uppala; Sun, Celi; Maiti, Amit K; Gagnebin, Maryline; Béna, Frédérique; Newkirk, Heather L; Sharp, Andrew J; Everman, David B; Murray, Jeffrey C; Schwartz, Charles E; Antonarakis, Stylianos E; Butler, Merlin G

2017-01-01

Background Omphalocele is a congenital birth defect characterised by the presence of internal organs located outside of the ventral abdominal wall. The purpose of this study was to identify the underlying genetic mechanisms of a large autosomal dominant Caucasian family with omphalocele. Methods and findings A genetic linkage study was conducted in a large family with an autosomal dominant transmission of an omphalocele using a genome-wide single nucleotide polymorphism (SNP) array. The analysis revealed significant evidence of linkage (non-parametric NPL = 6.93, p=0.0001; parametric logarithm of odds (LOD) = 2.70 under a fully penetrant dominant model) at chromosome band 1p31.3. Haplotype analysis narrowed the locus to a 2.74 Mb region between markers rs2886770 (63014807 bp) and rs1343981 (65757349 bp). Molecular characterisation of this interval using array comparative genomic hybridisation followed by quantitative microsphere hybridisation analysis revealed a 710 kb duplication located at 63.5–64.2 Mb. All affected individuals who had an omphalocele and shared the haplotype were positive for this duplicated region, while the duplication was absent from all normal individuals of this family. Multipoint linkage analysis using the duplication as a marker yielded a maximum LOD score of 3.2 at 1p31.3 under a dominant model. The 710 kb duplication at 1p31.3 band contains seven known genes including FOXD3, ALG6, ITGB3BP, KIAA1799, DLEU2L, PGM1, and the proximal portion of ROR1. Importantly, this duplication is absent from the database of genomic variants. Conclusions The present study suggests that development of an omphalocele in this family is controlled by overexpression of one or more genes in the duplicated region. To the authors’ knowledge, this is the first reported association of an inherited omphalocele condition with a chromosomal rearrangement. PMID:22499347

Three neuropeptide Y receptor genes in the spiny dogfish, Squalus acanthias, support en bloc duplications in early vertebrate evolution.

PubMed

Salaneck, Erik; Ardell, David H; Larson, Earl T; Larhammar, Dan

2003-08-01

It has been debated whether the increase in gene number during early vertebrate evolution was due to multiple independent gene duplications or synchronous duplications of many genes. We describe here the cloning of three neuropeptide Y (NPY) receptor genes belonging to the Y1 subfamily in the spiny dogfish, Squalus acanthias, a cartilaginous fish. The three genes are orthologs of the mammalian subtypes Y1, Y4, and Y6, which are located in paralogous gene regions on different chromosomes in mammals. Thus, these genes arose by duplications of a chromosome region before the radiation of gnathostomes (jawed vertebrates). Estimates of duplication times from linearized trees together with evidence from other gene families supports two rounds of chromosome duplications or tetraploidizations early in vertebrate evolution. The anatomical distribution of mRNA was determined by reverse-transcriptase PCR and was found to differ from mammals, suggesting differential functional diversification of the new gene copies during the radiation of the vertebrate classes.

Is Location of Sex Associated with Sexual Risk Behaviour in Men Who Have Sex with Men? Systematic Review of Within-Subjects Studies.

PubMed

Melendez-Torres, G J; Nye, Elizabeth; Bonell, Chris

2016-06-01

To understand associations between location of sex and sexual risk, it is most helpful to compare sexual encounters within persons. We systematically reviewed within-subjects comparisons of sexual encounters reported by men who have sex with men (MSM) with respect to location of sex. Within-subjects comparisons of sexual risk and location of sex were eligible if they collected data post-1996 from samples of MSM. We independently screened results and full-text records in duplicate. Of 6,336 deduplicated records, we assessed 138 full-text studies and included six, most of which compared unprotected anal intercourse against other anal intercourse. This small, but high quality, body of evidence suggests that associations between attendance at sex-on-premises venues and person-level sexual risk may be due to overall propensity towards unprotected sex. However, there may be some location factors that promote or are associated with serononconcordant unprotected anal intercourse. Health promoters may wish to focus on person-level characteristics.

Two Cases of Type Va Extrahepatic Bile Duct Duplication With Distal Klatskin Tumor Surgically Treated with Whipple Procedure and Hepaticojejunostomy.

PubMed

Hammad, Tariq A; Alastal, Yaseen; Khan, Muhammad Ali; Hammad, Mohammad; Alaradi, Osama; Nigam, Ankesh; Sodeman, Thomas C; Nawras, Ali

2015-10-01

We describe the diagnostic and therapeutic challenges of a type Va extrahepatic bile duct duplication coexistent with distally located hilar cholangiocarcinoma (Klatskin tumor). We present 2 cases that were diagnosed preoperatively and treated with a modified surgical technique of a combined pylorus-preserving Whipple procedure and hepaticojejunostomy.

Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions

PubMed Central

Darai-Ramqvist, Eva; Sandlund, Agneta; Müller, Stefan; Klein, George; Imreh, Stefan; Kost-Alimova, Maria

2008-01-01

We have previously found that the borders of evolutionarily conserved chromosomal regions often coincide with tumor-associated deletion breakpoints within human 3p12-p22. Moreover, a detailed analysis of a frequently deleted region at 3p21.3 (CER1) showed associations between tumor breaks and gene duplications. We now report on the analysis of 54 chromosome 3 breaks by multipoint FISH (mpFISH) in 10 carcinoma-derived cell lines. The centromeric region was broken in five lines. In lines with highly complex karyotypes, breaks were clustered near known fragile sites, FRA3B, FRA3C, and FRA3D (three lines), and in two other regions: 3p12.3-p13 (∼75 Mb position) and 3q21.3-q22.1 (∼130 Mb position) (six lines). All locations are shown based on NCBI Build 36.1 human genome sequence. The last two regions participated in three of four chromosome 3 inversions during primate evolution. Regions at 75, 127, and 131 Mb positions carry a large (∼250 kb) segmental duplication (tumor break-prone segmental duplication [TBSD]). TBSD homologous sequences were found at 15 sites on different chromosomes. They were located within bands frequently involved in carcinoma-associated breaks. Thirteen of them have been involved in inversions during primate evolution; 10 were reused by breaks during mammalian evolution; 14 showed copy number polymorphism in man. TBSD sites showed an increase in satellite repeats, retrotransposed sequences, and other segmental duplications. We propose that the instability of these sites stems from specific organization of the chromosomal region, associated with location at a boundary between different CG-content isochores and with the presence of TBSDs and “instability elements,” including satellite repeats and retroviral sequences. PMID:18230801

Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions.

PubMed

Darai-Ramqvist, Eva; Sandlund, Agneta; Müller, Stefan; Klein, George; Imreh, Stefan; Kost-Alimova, Maria

2008-03-01

We have previously found that the borders of evolutionarily conserved chromosomal regions often coincide with tumor-associated deletion breakpoints within human 3p12-p22. Moreover, a detailed analysis of a frequently deleted region at 3p21.3 (CER1) showed associations between tumor breaks and gene duplications. We now report on the analysis of 54 chromosome 3 breaks by multipoint FISH (mpFISH) in 10 carcinoma-derived cell lines. The centromeric region was broken in five lines. In lines with highly complex karyotypes, breaks were clustered near known fragile sites, FRA3B, FRA3C, and FRA3D (three lines), and in two other regions: 3p12.3-p13 ( approximately 75 Mb position) and 3q21.3-q22.1 ( approximately 130 Mb position) (six lines). All locations are shown based on NCBI Build 36.1 human genome sequence. The last two regions participated in three of four chromosome 3 inversions during primate evolution. Regions at 75, 127, and 131 Mb positions carry a large ( approximately 250 kb) segmental duplication (tumor break-prone segmental duplication [TBSD]). TBSD homologous sequences were found at 15 sites on different chromosomes. They were located within bands frequently involved in carcinoma-associated breaks. Thirteen of them have been involved in inversions during primate evolution; 10 were reused by breaks during mammalian evolution; 14 showed copy number polymorphism in man. TBSD sites showed an increase in satellite repeats, retrotransposed sequences, and other segmental duplications. We propose that the instability of these sites stems from specific organization of the chromosomal region, associated with location at a boundary between different CG-content isochores and with the presence of TBSDs and "instability elements," including satellite repeats and retroviral sequences.

An Oracle-based event index for ATLAS

NASA Astrophysics Data System (ADS)

Gallas, E. J.; Dimitrov, G.; Vasileva, P.; Baranowski, Z.; Canali, L.; Dumitru, A.; Formica, A.; ATLAS Collaboration

2017-10-01

The ATLAS Eventlndex System has amassed a set of key quantities for a large number of ATLAS events into a Hadoop based infrastructure for the purpose of providing the experiment with a number of event-wise services. Collecting this data in one place provides the opportunity to investigate various storage formats and technologies and assess which best serve the various use cases as well as consider what other benefits alternative storage systems provide. In this presentation we describe how the data are imported into an Oracle RDBMS (relational database management system), the services we have built based on this architecture, and our experience with it. We’ve indexed about 26 billion real data events thus far and have designed the system to accommodate future data which has expected rates of 5 and 20 billion events per year. We have found this system offers outstanding performance for some fundamental use cases. In addition, profiting from the co-location of this data with other complementary metadata in ATLAS, the system has been easily extended to perform essential assessments of data integrity and completeness and to identify event duplication, including at what step in processing the duplication occurred.

Copy number variation in the region harboring SOX9 gene in dogs with testicular/ovotesticular disorder of sex development (78,XX; SRY-negative).

PubMed

Marcinkowska-Swojak, Malgorzata; Szczerbal, Izabela; Pausch, Hubert; Nowacka-Woszuk, Joanna; Flisikowski, Krzysztof; Dzimira, Stanislaw; Nizanski, Wojciech; Payan-Carreira, Rita; Fries, Ruedi; Kozlowski, Piotr; Switonski, Marek

2015-10-01

Although the disorder of sex development in dogs with female karyotype (XX DSD) is quite common, its molecular basis is still unclear. Among mutations underlying XX DSD in mammals are duplication of a long sequence upstream of the SOX9 gene (RevSex) and duplication of the SOX9 gene (also observed in dogs). We performed a comparative analysis of 16 XX DSD and 30 control female dogs, using FISH and MLPA approaches. Our study was focused on a region harboring SOX9 and a region orthologous to the human RevSex (CanRevSex), which was located by in silico analysis downstream of SOX9. Two highly polymorphic copy number variable regions (CNVRs): CNVR1 upstream of SOX9 and CNVR2 encompassing CanRevSex were identified. Although none of the detected copy number variants were specific to either affected or control animals, we observed that the average number of copies in CNVR1 was higher in XX DSD. No copy variation of SOX9 was observed. Our extensive studies have excluded duplication of SOX9 as the common cause of XX DSD in analyzed samples. However, it remains possible that the causative mutation is hidden in highly polymorphic CNVR1.

Copy number variation in the region harboring SOX9 gene in dogs with testicular/ovotesticular disorder of sex development (78,XX; SRY-negative)

PubMed Central

Marcinkowska-Swojak, Malgorzata; Szczerbal, Izabela; Pausch, Hubert; Nowacka-Woszuk, Joanna; Flisikowski, Krzysztof; Dzimira, Stanislaw; Nizanski, Wojciech; Payan-Carreira, Rita; Fries, Ruedi; Kozlowski, Piotr; Switonski, Marek

2015-01-01

Although the disorder of sex development in dogs with female karyotype (XX DSD) is quite common, its molecular basis is still unclear. Among mutations underlying XX DSD in mammals are duplication of a long sequence upstream of the SOX9 gene (RevSex) and duplication of the SOX9 gene (also observed in dogs). We performed a comparative analysis of 16 XX DSD and 30 control female dogs, using FISH and MLPA approaches. Our study was focused on a region harboring SOX9 and a region orthologous to the human RevSex (CanRevSex), which was located by in silico analysis downstream of SOX9. Two highly polymorphic copy number variable regions (CNVRs): CNVR1 upstream of SOX9 and CNVR2 encompassing CanRevSex were identified. Although none of the detected copy number variants were specific to either affected or control animals, we observed that the average number of copies in CNVR1 was higher in XX DSD. No copy variation of SOX9 was observed. Our extensive studies have excluded duplication of SOX9 as the common cause of XX DSD in analyzed samples. However, it remains possible that the causative mutation is hidden in highly polymorphic CNVR1. PMID:26423656

NHEXAS PHASE I MARYLAND STUDY--PESTICIDES IN FOOD ANALYTICAL RESULTS

EPA Science Inventory

The Pesticides in Duplicate Diet Food data set contains analytical results for measurements of up to 10 pesticides in 682 food samples over 80 households. Each sample was collected as a duplicate of the food consumed by the primary respondent during a four-day period commencing ...

NHEXAS PHASE I MARYLAND STUDY--METALS IN FOOD ANALYTICAL RESULTS

EPA Science Inventory

The Metals in Duplicate Diet Food data set contains analytical results for measurements of up to 11 metals in 773 food samples over 80 households. Each sample was collected as a duplicate of the food consumed by the primary respondent during a four-day period commencing with the...

Adaptive Evolution and Divergence of SERPINB3: A Young Duplicate in Great Apes

PubMed Central

Gomes, Sílvia; Marques, Patrícia I.; Matthiesen, Rune; Seixas, Susana

2014-01-01

A series of duplication events led to an expansion of clade B Serine Protease Inhibitors (SERPIN), currently displaying a large repertoire of functions in vertebrates. Accordingly, the recent duplicates SERPINB3 and B4 located in human 18q21.3 SERPIN cluster control the activity of different cysteine and serine proteases, respectively. Here, we aim to assess SERPINB3 and B4 coevolution with their target proteases in order to understand the evolutionary forces shaping the accelerated divergence of these duplicates. Phylogenetic analysis of primate sequences placed the duplication event in a Hominoidae ancestor (∼30 Mya) and the emergence of SERPINB3 in Homininae (∼9 Mya). We detected evidence of strong positive selection throughout SERPINB4/B3 primate tree and target proteases, cathepsin L2 (CTSL2) and G (CTSG) and chymase (CMA1). Specifically, in the Homininae clade a perfect match was observed between the adaptive evolution of SERPINB3 and cathepsin S (CTSS) and most of sites under positive selection were located at the inhibitor/protease interface. Altogether our results seem to favour a coevolution hypothesis for SERPINB3, CTSS and CTSL2 and for SERPINB4 and CTSG and CMA1. A scenario of an accelerated evolution driven by host-pathogen interactions is also possible since SERPINB3/B4 are potent inhibitors of exogenous proteases, released by infectious agents. Finally, similar patterns of expression and the sharing of many regulatory motifs suggest neofunctionalization as the best fitted model of the functional divergence of SERPINB3 and B4 duplicates. PMID:25133778

Two sequence-ready contigs spanning the two copies of a 200-kb duplication on human 21q: partial sequence and polymorphisms.

PubMed

Potier, M; Dutriaux, A; Orti, R; Groet, J; Gibelin, N; Karadima, G; Lutfalla, G; Lynn, A; Van Broeckhoven, C; Chakravarti, A; Petersen, M; Nizetic, D; Delabar, J; Rossier, J

1998-08-01

Physical mapping across a duplication can be a tour de force if the region is larger than the size of a bacterial clone. This was the case of the 170- to 275-kb duplication present on the long arm of chromosome 21 in normal human at 21q11.1 (proximal region) and at 21q22.1 (distal region), which we described previously. We have constructed sequence-ready contigs of the two copies of the duplication of which all the clones are genuine representatives of one copy or the other. This required the identification of four duplicon polymorphisms that are copy-specific and nonallelic variations in the sequence of the STSs. Thirteen STSs were mapped inside the duplicated region and 5 outside but close to the boundaries. Among these STSs 10 were end clones from YACs, PACs, or cosmids, and the average interval between two markers in the duplicated region was 16 kb. Eight PACs and cosmids showing minimal overlaps were selected in both copies of the duplication. Comparative sequence analysis along the duplication showed three single-basepair changes between the two copies over 659 bp sequenced (4 STSs), suggesting that the duplication is recent (less than 4 mya). Two CpG islands were located in the duplication, but no genes were identified after a 36-kb cosmid from the proximal copy of the duplication was sequenced. The homology of this chromosome 21 duplicated region with the pericentromeric regions of chromosomes 13, 2, and 18 suggests that the mechanism involved is probably similar to pericentromeric-directed mechanisms described in interchromosomal duplications. Copyright 1998 Academic Press.

Intake of radioactive materials as assessed by the duplicate diet method in Fukushima.

PubMed

Sato, Osamu; Nonaka, Shunkichi; Tada, Jun Ichiro

2013-12-01

A large quantity of radioactive materials was released from Reactor-II of the Fukushima Daiichi Nuclear Power Plant (F-1 NPP). People living in the area affected by the release are concerned about internal exposures from the daily intakes of contaminated foodstuffs. In order to assess whether the people should be concerned, Co-op Fukushima (Consumer Co-operative in Fukushima Prefecture) conducted a broad survey of radiocaesium in daily meals for which local inhabitants voluntarily provided a set of duplicate meals. Analyses by the duplicate diet method were conducted from November 2011 to March 2012 and from June 2012 to September 2012, each covering 100 families throughout the prefecture. Among the 200 meals thus analysed, 12 were found to have (134)Cs and/or (137)Cs concentrations exceeding 1 Bq kg(-1). Even with the largest radiocaesium value in our survey, daily consumption of such meals throughout a year gave an annual committed effective dose that did not exceed 0.1 mSv.

Identification and genetic effect of a variable duplication in the promoter region of the cattle ADIPOQ gene

USDA-ARS?s Scientific Manuscript database

The ADIPOQ gene of cattle, is located in the vicinity of the quantitative trait locus (QTL) wich effects marbling, the rib eye muscle area and fat thickness on BTA1. In our study, a novel variable duplication (NW_003103812.1:g.9232067_9232133 dup) in the bovine ADIPOQ promoter region was identified ...

Length Variation in Mitochondrial DNA of the Minnow Cyprinella Spiloptera

PubMed Central

Broughton, R. E.; Dowling, T. E.

1994-01-01

Length differences in animal mitochondrial DNA (mtDNA) are common, frequently due to variation in copy number of direct tandem duplications. While such duplications appear to form without great difficulty in some taxonomic groups, they appear to be relatively short-lived, as typical duplication products are geographically restricted within species and infrequently shared among species. To better understand such length variation, we have studied a tandem and direct duplication of approximately 260 bp in the control region of the cyprinid fish, Cyprinella spiloptera. Restriction site analysis of 38 individuals was used to characterize population structure and the distribution of variation in repeat copy number. This revealed two length variants, including individuals with two or three copies of the repeat, and little geographic structure among populations. No standard length (single copy) genomes were found and heteroplasmy, a common feature of length variation in other taxa, was absent. Nucleotide sequence of tandem duplications and flanking regions localized duplication junctions in the phenylalanine tRNA and near the origin of replication. The locations of these junctions and the stability of folded repeat copies support the hypothesized importance of secondary structures in models of duplication formation. PMID:8001785

Correction to: The role of oral co-trimoxazole in treating Nocardia farcinica keratitis: a case report.

PubMed

Sharma, Neharika; O'Hagan, Stephen

2018-01-08

This article [1] was unintentionally published twice in this journal, by the same authors.The following [1] should be considered the version of record and used for citation purposes: "Neharika Sharma and Stephen O'Hagan, The role of oral co-trimoxazole in treating Nocardia farcinica keratitis: a case report. Journal of Ophthalmic Inflammation and Infection (2016) 6:21 DOI 10.1186/s12348-016-0087-y".The duplicate [2]: "Neharika Sharma and Stephen O'Hagan, The role of oral co-trimoxazole in treating Nocardia farcinica keratitis: a case report. Journal of Ophthalmic Inflammation and Infection (2016) 6:23 DOI 10.1186/s12348-016-0091-2" is to be ignored.BioMed Central apologizes to the readers of the journal for not detecting the duplication during the publication process.

Prevalence of exon 11 internal tandem duplications in the C-KIT proto-oncogene in Australian canine mast cell tumours.

PubMed

Tamlin, V S; Kessell, A E; Mccoy, R J; Dobson, E C; Smith, T S; Hebart, M; Brown, L; Mitrovic, D; Peaston, A E

2017-10-01

To measure the prevalence of internal tandem duplications (ITDs) in exon 11 of the proto-oncogene C-KIT in a sample of Australian cutaneous canine mast cell tumours (MCTs) drawn from general practice and to evaluate relationships between tumour mutation status and prognostic factors including signalment, tumour histological grade, tumour anatomical location and tumour size. C-KIT exon 11 ITDs were detected by PCR in DNA extracted from formalin-fixed, paraffin-embedded canine MCTs sourced from three veterinary diagnostic laboratories in Adelaide and Melbourne. Tumours were graded according to two different systems (Patnaik and Kiupel systems) by board-certified anatomical pathologists blinded to the PCR results. Relationships between tumour mutation status and prognostic factors were evaluated using a generalised binary logistic regression analysis. ITDs were identified in 13 of 74 cutaneous canine MCT samples, giving an overall prevalence of 17.6% (95% confidence interval: 8.9-26.2%). ITDs were detected in 10 of 18 Patnaik grade III MCTs (55.6%) and 11 of 22 Kiupel high-grade MCTs (50%). Wald chi-square analysis revealed that detection of tumour ITDs was significantly associated with both Patnaik's and Kiupel's histologic grading systems (each: P < 0.001). The presence of the ITDs in MCTs was not associated with signalment, tumour anatomical location or tumour size. The prevalence of C-KIT exon 11 ITDs in Australian canine MCTs is similar to the prevalence in overseas canine populations (overall prevalence in Australia approximately 18%). ITDs were more frequently identified in higher grade MCTs. © 2017 Australian Veterinary Association.

Digital gene expression analysis with sample multiplexing and PCR duplicate detection: A straightforward protocol.

PubMed

Rozenberg, Andrey; Leese, Florian; Weiss, Linda C; Tollrian, Ralph

2016-01-01

Tag-Seq is a high-throughput approach used for discovering SNPs and characterizing gene expression. In comparison to RNA-Seq, Tag-Seq eases data processing and allows detection of rare mRNA species using only one tag per transcript molecule. However, reduced library complexity raises the issue of PCR duplicates, which distort gene expression levels. Here we present a novel Tag-Seq protocol that uses the least biased methods for RNA library preparation combined with a novel approach for joint PCR template and sample labeling. In our protocol, input RNA is fragmented by hydrolysis, and poly(A)-bearing RNAs are selected and directly ligated to mixed DNA-RNA P5 adapters. The P5 adapters contain i5 barcodes composed of sample-specific (moderately) degenerate base regions (mDBRs), which later allow detection of PCR duplicates. The P7 adapter is attached via reverse transcription with individual i7 barcodes added during the amplification step. The resulting libraries can be sequenced on an Illumina sequencer. After sample demultiplexing and PCR duplicate removal with a free software tool we designed, the data are ready for downstream analysis. Our protocol was tested on RNA samples from predator-induced and control Daphnia microcrustaceans.

Measuring the ratio of CO2 efflux to O2 influx in tree stem respiration.

PubMed

Hilman, Boaz; Angert, Alon

2016-11-01

In recent studies, the ratio of tree stem CO 2 efflux to O 2 influx has been defined as the apparent respiratory quotient (ARQ). The metabolism of carbohydrates, the putative respiratory substrate in trees, is expected to yield an ARQ of 1.0. However, previous studies have reported ARQ values ranging between 0.23 and 0.90. These interesting results may indicate internal transport of respired CO 2 within stems; yet no simple field applicable methods for ARQ measurement have been available. Here, we report on the assembly of a closed circulating system called 'Hampadah', which uses CO 2 and O 2 analyzers to measure air samples from stem chambers. We tested the performance of the Hampadah with samples from 36 trees (Tetragastris panamensis (Engl.) Kuntze). Additionally, we showed the feasibility of measuring ARQ directly from stem chambers, using portable CO 2 and O 2 sensors, in both discrete and continuous modes of operation. The Hampadah measurement proved to be consistent with CO 2 gas standards (R 2 = 0.999) and with O 2 determined by O 2 /Ar measurements with a mass spectrometer (R 2 = 0.998). The Hampadah gave highly reproducible results for ARQ determination of field samples (±0.01 for duplicates). The portable sensors measurement showed good correlation with the Hampadah in measuring CO 2 , O 2 and ARQ (n = 5, R 2 = 0.97, 0.98 and 0.91, respectively). We have demonstrated here that the Hampadah and the sensors' methods enable accurate ARQ measurements for both laboratory and field research. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Incidense of spider mites in South Texas cotton fields

USDA-ARS?s Scientific Manuscript database

The incidence of spider mites was evaluated· in four locations of south Texas between Progreso (Hidalgo Co.) to Bishop (Nueces Co.). This is an area with a south to north transect of 125 miles from south Progreso to north Bishop (respectively).The other two intermediate sampled locations were Harlin...

Network-based analysis of oligodendrogliomas predicts novel cancer gene candidates within the region of the 1p/19q co-deletion.

PubMed

Gladitz, Josef; Klink, Barbara; Seifert, Michael

2018-06-11

Oligodendrogliomas are primary human brain tumors with a characteristic 1p/19q co-deletion of important prognostic relevance, but little is known about the pathology of this chromosomal mutation. We developed a network-based approach to identify novel cancer gene candidates in the region of the 1p/19q co-deletion. Gene regulatory networks were learned from gene expression and copy number data of 178 oligodendrogliomas and further used to quantify putative impacts of differentially expressed genes of the 1p/19q region on cancer-relevant pathways. We predicted 8 genes with strong impact on signaling pathways and 14 genes with strong impact on metabolic pathways widespread across the region of the 1p/19 co-deletion. Many of these candidates (e.g. ELTD1, SDHB, SEPW1, SLC17A7, SZRD1, THAP3, ZBTB17) are likely to push, whereas others (e.g. CAP1, HBXIP, KLK6, PARK7, PTAFR) might counteract oligodendroglioma development. For example, ELTD1, a functionally validated glioblastoma oncogene located on 1p, was overexpressed. Further, the known glioblastoma tumor suppressor SLC17A7 located on 19q was underexpressed. Moreover, known epigenetic alterations triggered by mutated SDHB in paragangliomas suggest that underexpressed SDHB in oligodendrogliomas may support and possibly enhance the epigenetic reprogramming induced by the IDH-mutation. We further analyzed rarely observed deletions and duplications of chromosomal arms within oligodendroglioma subcohorts identifying putative oncogenes and tumor suppressors that possibly influence the development of oligodendroglioma subgroups. Our in-depth computational study contributes to a better understanding of the pathology of the 1p/19q co-deletion and other chromosomal arm mutations. This might open opportunities for functional validations and new therapeutic strategies.

Germline or somatic GPR101 duplication leads to X-linked acrogigantism: a clinico-pathological and genetic study.

PubMed

Iacovazzo, Donato; Caswell, Richard; Bunce, Benjamin; Jose, Sian; Yuan, Bo; Hernández-Ramírez, Laura C; Kapur, Sonal; Caimari, Francisca; Evanson, Jane; Ferraù, Francesco; Dang, Mary N; Gabrovska, Plamena; Larkin, Sarah J; Ansorge, Olaf; Rodd, Celia; Vance, Mary L; Ramírez-Renteria, Claudia; Mercado, Moisés; Goldstone, Anthony P; Buchfelder, Michael; Burren, Christine P; Gurlek, Alper; Dutta, Pinaki; Choong, Catherine S; Cheetham, Timothy; Trivellin, Giampaolo; Stratakis, Constantine A; Lopes, Maria-Beatriz; Grossman, Ashley B; Trouillas, Jacqueline; Lupski, James R; Ellard, Sian; Sampson, Julian R; Roncaroli, Federico; Korbonits, Márta

2016-06-01

Non-syndromic pituitary gigantism can result from AIP mutations or the recently identified Xq26.3 microduplication causing X-linked acrogigantism (XLAG). Within Xq26.3, GPR101 is believed to be the causative gene, and the c.924G > C (p.E308D) variant in this orphan G protein-coupled receptor has been suggested to play a role in the pathogenesis of acromegaly.We studied 153 patients (58 females and 95 males) with pituitary gigantism. AIP mutation-negative cases were screened for GPR101 duplication through copy number variation droplet digital PCR and high-density aCGH. The genetic, clinical and histopathological features of XLAG patients were studied in detail. 395 peripheral blood and 193 pituitary tumor DNA samples from acromegaly patients were tested for GPR101 variants.We identified 12 patients (10 females and 2 males; 7.8 %) with XLAG. In one subject, the duplicated region only contained GPR101, but not the other three genes in found to be duplicated in the previously reported patients, defining a new smallest region of overlap of duplications. While females presented with germline mutations, the two male patients harbored the mutation in a mosaic state. Nine patients had pituitary adenomas, while three had hyperplasia. The comparison of the features of XLAG, AIP-positive and GPR101&AIP-negative patients revealed significant differences in sex distribution, age at onset, height, prolactin co-secretion and histological features. The pathological features of XLAG-related adenomas were remarkably similar. These tumors had a sinusoidal and lobular architecture. Sparsely and densely granulated somatotrophs were admixed with lactotrophs; follicle-like structures and calcifications were commonly observed. Patients with sporadic of familial acromegaly did not have an increased prevalence of the c.924G > C (p.E308D) GPR101 variant compared to public databases.In conclusion, XLAG can result from germline or somatic duplication of GPR101. Duplication of GPR101 alone is sufficient for the development of XLAG, implicating it as the causative gene within the Xq26.3 region. The pathological features of XLAG-associated pituitary adenomas are typical and, together with the clinical phenotype, should prompt genetic testing.

48. INTERIOR VIEW, FORMAL PARLOR LOCATED ON THE WEST SIDE ...

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

48. INTERIOR VIEW, FORMAL PARLOR LOCATED ON THE WEST SIDE OF THE CENTRAL PASSAGE, LOOKING SOUTH TO NORTH (DUPLICATE OF HABS No. AL-424-34) - Arlington Place, 331 Cotton Avenue, Southwest, Birmingham, Jefferson County, AL

Report for Batch Leach Analyses on Sediments at 100-HR-3 Operable Unit, Boreholes C7620, C7621, C7622, C7623, C7626, C7627, C7628, C7629, C7630, and C7866. Revision 1.

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

Lindberg, Michael J.

2012-04-25

This is a revision to a previously released report. This revision contains additional analytical results for the sample with HEIS number B2H4X7. Between November 4, 2010 and October 26, 2011 sediment samples were received from 100-HR-3 Operable Unit for geochemical studies. The analyses for this project were performed at the 331 building located in the 300 Area of the Hanford Site. The analyses were performed according to Pacific Northwest National Laboratory (PNNL) approved procedures and/or nationally recognized test procedures. The data sets include the sample identification numbers, analytical results, estimated quantification limits (EQL), and quality control data. The preparatory andmore » analytical quality control requirements, calibration requirements, acceptance criteria, and failure actions are defined in the on-line QA plan 'Conducting Analytical Work in Support of Regulatory Programs' (CAW). This QA plan implements the Hanford Analytical Services Quality Assurance Requirements Documents (HASQARD) for PNNL. Samples were received with a chain of custody (COC) and were analyzed according to the sample identification numbers supplied by the client. All Samples were refrigerated upon receipt until prepared for analysis. All samples were received with custody seals intact unless noted in the Case Narrative. Holding time is defined as the time from sample preparation to the time of analyses. The prescribed holding times were met for all analytes unless noted in the Case Narrative. All reported analytical results meet the requirements of the CAW or client specified SOW unless noted in the case narrative. Due to the requirements of the statement of work and sampling events in the field, the 28 day and the 48 hr requirements cannot be met. The statement of work requires samples to be selected at the completion of the borehole. It is not always possible to complete a borehole and have the samples shipped to the laboratory within the hold time requirements. Duplicate RPD for Uranium 238 (38.9%) was above the acceptance limit (35) in 1E05003-DUP1 for ICPMS-Tc-U-WE The sample result is less than 10 times the detection limits. Duplicate recoveries are not applicable to this analyte. Duplicate RPD for Silver 107 (68.2%) was above the acceptance limit (35) in 2C06004-DUP1 for ICPMS-RCRA-AE The sample result is less than 10 times the detection limits. Duplicate recoveries are not applicable to this analyte. Matrix Spike Recovery for Chromium, Hexavalent (48.8%) was outside acceptance limits (75-125) in 1E23001-MS1 for Hexavalent Chromium/Soil. Potential Matrix interference. Sample results associated with this batch are below the EQL. There should be no impact to the data as reported. Matrix Spike Recovery for Chromium, Hexavalent (50.2%) was outside acceptance limits (75-125) in 2B22010-MS1 for Hexavalent Chromium/Soil. Potential Matrix interference. Sample results associated with this batch are below the EQL. There should be no impact to the data as reported.« less

76 FR 77536 - Agency Information Collection Request. 60-Day Public Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-13

... required data elements from applicants. The SF-424 Project/Performance Site Location(s) form is a part of Grants.gov 's mission to reduce duplication of similar or identical forms and data sets, establish... Project/Performance Site Location(s) form and data set that will serve as a common form for various grant...

Conserved Non-Coding Regulatory Signatures in Arabidopsis Co-Expressed Gene Modules

PubMed Central

Spangler, Jacob B.; Ficklin, Stephen P.; Luo, Feng; Freeling, Michael; Feltus, F. Alex

2012-01-01

Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana co-expression networks were constructed after manually sorting 4,566 RNA profiling datasets into aerial, flower, leaf, root, rosette, seedling, seed, shoot, whole plant, and global (all samples combined) groups. Collectively, the ten networks contained 30% of the measurable genes of Arabidopsis and were circumscribed into 5,491 modules. Modules were scrutinized for cis regulatory mechanisms putatively encoded in conserved non-coding sequences (CNSs) previously identified as remnants of a whole genome duplication event. We determined the non-random association of 1,361 unique CNSs to 1,904 co-expression network gene modules. Furthermore, the CNS elements were placed in the context of known gene regulatory networks (GRNs) by connecting 250 CNS motifs with known GRN cis elements. Our results provide support for a regulatory role of some CNS elements and suggest the functional consequences of CNS activation of co-expression in specific gene sets dispersed throughout the genome. PMID:23024789

Conserved non-coding regulatory signatures in Arabidopsis co-expressed gene modules.

PubMed

Spangler, Jacob B; Ficklin, Stephen P; Luo, Feng; Freeling, Michael; Feltus, F Alex

2012-01-01

Complex traits and other polygenic processes require coordinated gene expression. Co-expression networks model mRNA co-expression: the product of gene regulatory networks. To identify regulatory mechanisms underlying coordinated gene expression in a tissue-enriched context, ten Arabidopsis thaliana co-expression networks were constructed after manually sorting 4,566 RNA profiling datasets into aerial, flower, leaf, root, rosette, seedling, seed, shoot, whole plant, and global (all samples combined) groups. Collectively, the ten networks contained 30% of the measurable genes of Arabidopsis and were circumscribed into 5,491 modules. Modules were scrutinized for cis regulatory mechanisms putatively encoded in conserved non-coding sequences (CNSs) previously identified as remnants of a whole genome duplication event. We determined the non-random association of 1,361 unique CNSs to 1,904 co-expression network gene modules. Furthermore, the CNS elements were placed in the context of known gene regulatory networks (GRNs) by connecting 250 CNS motifs with known GRN cis elements. Our results provide support for a regulatory role of some CNS elements and suggest the functional consequences of CNS activation of co-expression in specific gene sets dispersed throughout the genome.

Gene Duplication and Evolutionary Innovations in Hemoglobin-Oxygen Transport

PubMed Central

2016-01-01

During vertebrate evolution, duplicated hemoglobin (Hb) genes diverged with respect to functional properties as well as the developmental timing of expression. For example, the subfamilies of genes that encode the different subunit chains of Hb are ontogenetically regulated such that functionally distinct Hb isoforms are expressed during different developmental stages. In some vertebrate taxa, functional differentiation between co-expressed Hb isoforms may also contribute to physiologically important divisions of labor. PMID:27053736

Reducing representativeness and sampling errors in radio occultation-radiosonde comparisons

NASA Astrophysics Data System (ADS)

Gilpin, Shay; Rieckh, Therese; Anthes, Richard

2018-05-01

Radio occultation (RO) and radiosonde (RS) comparisons provide a means of analyzing errors associated with both observational systems. Since RO and RS observations are not taken at the exact same time or location, temporal and spatial sampling errors resulting from atmospheric variability can be significant and inhibit error analysis of the observational systems. In addition, the vertical resolutions of RO and RS profiles vary and vertical representativeness errors may also affect the comparison. In RO-RS comparisons, RO observations are co-located with RS profiles within a fixed time window and distance, i.e. within 3-6 h and circles of radii ranging between 100 and 500 km. In this study, we first show that vertical filtering of RO and RS profiles to a common vertical resolution reduces representativeness errors. We then test two methods of reducing horizontal sampling errors during RO-RS comparisons: restricting co-location pairs to within ellipses oriented along the direction of wind flow rather than circles and applying a spatial-temporal sampling correction based on model data. Using data from 2011 to 2014, we compare RO and RS differences at four GCOS Reference Upper-Air Network (GRUAN) RS stations in different climatic locations, in which co-location pairs were constrained to a large circle ( ˜ 666 km radius), small circle ( ˜ 300 km radius), and ellipse parallel to the wind direction ( ˜ 666 km semi-major axis, ˜ 133 km semi-minor axis). We also apply a spatial-temporal sampling correction using European Centre for Medium-Range Weather Forecasts Interim Reanalysis (ERA-Interim) gridded data. Restricting co-locations to within the ellipse reduces root mean square (RMS) refractivity, temperature, and water vapor pressure differences relative to RMS differences within the large circle and produces differences that are comparable to or less than the RMS differences within circles of similar area. Applying the sampling correction shows the most significant reduction in RMS differences, such that RMS differences are nearly identical to the sampling correction regardless of the geometric constraints. We conclude that implementing the spatial-temporal sampling correction using a reliable model will most effectively reduce sampling errors during RO-RS comparisons; however, if a reliable model is not available, restricting spatial comparisons to within an ellipse parallel to the wind flow will reduce sampling errors caused by horizontal atmospheric variability.

The Primary Results of Analyses on The Archaeal and Bacterial Diversity of Active Cave Environments Settled in Limestones at Southern Turkey

NASA Astrophysics Data System (ADS)

Tok, Ezgi; Kurt, Halil; Tunga Akarsubasi, A.

2016-04-01

The microbial diversity of cave sediments which are obtained from three different caves named Insuyu, Balatini and Altınbeşik located at Southern Turkey has been investigated using molecular methods for biomineralization . The total number of 22 samples were taken in duplicates from the critical zones of the caves at where the water activity is observed all year round. Microbial communities were monitored by 16S rRNA gene based PCR-DGGE (Polymerase Chain Reaction - Denaturating Gradient Gel Electrophoresis) methodology. DNA were extracted from the samples by The PowerSoil® DNA Isolation Kit (MO BIO Laboratories inc., CA) with the modifications on the producer's protocol. The synthetic DNA molecule poly-dIdC was used to increase the yield of PCR amplification via blocking the reaction between CaCO3 and DNA molecules. Thereafter samples were amplified by using both Archaeal and Bacterial universal primers (ref). Subsequently, archaeal and bacterial diversities in cave sediments, were investigated to be able to compare with respect to their similarities by using DGGE. DGGE patterns were analysed with BioNumerics software 5.1. Similarity matrix and dendograms of the DGGE profiles were generated based on the Dice correlation coefficient (band-based) and unweighted pair-group method with arithmetic mean (UPGMA). The structural diversity of the microbial community was examined by the Shannon index of general diversity (H). Similtaneously, geochemical analyses of the sediment samples were performed within the scope of this study. Total organic carbon (TOC), x-ray diffraction spectroscopy (XRD) and x-ray fluorescence spectroscopy (XRF) analysis of sediments were also implemented. The extensive results will be obtained at the next stages of the study currently carried on.

May 2011 Groundwater and Surface Water Sampling at the Rio Blanco, Colorado, Site (Data Validation Package)

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

Hutton, Rick

2011-12-01

Annual sampling was conducted at the Rio Blanco, Colorado, site for the Long-Term Hydrologic Monitoring Program May 16-17, 2011, to monitor groundwater and surface water for potential radionuclide contamination. Sampling and analyses were conducted as specified in Sampling and Analysis Plan for the U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). A duplicate sample was collected from location Johnson Artesian WL. Samples were analyzed by the U.S. Environmental Protection Agency (EPA) Radiation&Indoor Environments National Laboratory in Las Vegas, Nevada. Samples were analyzed for gamma-emitting radionuclides by high-resolution gamma spectrometry, and for tritium using the conventional method.more » Tritium was not measured using the enrichment method because the EPA laboratory no longer offers that service. Results of this monitoring at the Rio Blanco site demonstrate that groundwater and surface water outside the boundaries have not been affected by project-related contaminants.« less

Lead Determination and Heterogeneity Analysis in Soil from a Former Firing Range

NASA Astrophysics Data System (ADS)

Urrutia-Goyes, Ricardo; Argyraki, Ariadne; Ornelas-Soto, Nancy

2017-07-01

Public places can have an unknown past of pollutants deposition. The exposition to such contaminants can create environmental and health issues. The characterization of a former firing range in Athens, Greece will allow its monitoring and encourage its remediation. This study is focused on Pb contamination in the site due to its presence in ammunition. A dense sampling design with 91 location (10 m apart) was used to determine the spatial distribution of the element in the surface soil of the study area. Duplicates samples were also collected one meter apart from 8 random locations to estimate the heterogeneity of the site. Elemental concentrations were measured using a portable XRF device after simple sample homogenization in the field. Robust Analysis of Variance showed that the contributions to the total variance were 11% from sampling, 1% analytical, and 88% geochemical; reflecting the suitability of the technique. Moreover, the extended random uncertainty relative to the mean concentration was 91.5%; confirming the high heterogeneity of the site. Statistical analysis defined a very high contamination in the area yielding to suggest the need for more in-depth analysis of other contaminants and possible health risks.

Transmission dynamics of co-endemic Plasmodium vivax and P. falciparum in Ethiopia and prevalence of antimalarial resistant genotypes

PubMed Central

Yewhalaw, Delenasaw; Nguyen, Jennifer; Kebede, Estifanos; Zemene, Endalew; Getachew, Sisay; Tushune, Kora; Zhong, Daibin; Zhou, Guofa; Petros, Beyene; Yan, Guiyun

2017-01-01

Ethiopia is one of the few African countries where Plasmodium vivax is co-endemic with P. falciparum. Malaria transmission is seasonal and transmission intensity varies mainly by landscape and climate. Although the recent emergence of drug resistant parasites presents a major issue to malaria control in Ethiopia, little is known about the transmission pathways of parasite species and prevalence of resistant markers. This study used microsatellites to determine population diversity and gene flow patterns of P. falciparum (N = 226) and P. vivax (N = 205), as well as prevalence of drug resistant markers to infer the impact of gene flow and existing malaria treatment regimes. Plasmodium falciparum indicated a higher rate of polyclonal infections than P. vivax. Both species revealed moderate genetic diversity and similar population structure. Populations in the northern highlands were closely related to the eastern Rift Valley, but slightly distinct from the southern basin area. Gene flow via human migrations between the northern and eastern populations were frequent and mostly bidirectional. Landscape genetic analyses indicated that environmental heterogeneity and geographical distance did not constrain parasite gene flow. This may partly explain similar patterns of resistant marker prevalence. In P. falciparum, a high prevalence of mutant alleles was detected in codons related to chloroquine (pfcrt and pfmdr1) and sulfadoxine-pyrimethamine (pfdhps and pfdhfr) resistance. Over 60% of the samples showed pfmdr1 duplications. Nevertheless, no mutation was detected in pfK13 that relates to artemisinin resistance. In P. vivax, while sequences of pvcrt-o were highly conserved and less than 5% of the samples showed pvmdr duplications, over 50% of the samples had pvmdr1 976F mutation. It remains to be tested if this mutation relates to chloroquine resistance. Monitoring the extent of malaria spread and markers of drug resistance is imperative to inform policy for evidence-based antimalarial choice and interventions. To effectively reduce malaria burden in Ethiopia, control efforts should focus on seasonal migrant populations. PMID:28746333

Transmission dynamics of co-endemic Plasmodium vivax and P. falciparum in Ethiopia and prevalence of antimalarial resistant genotypes.

PubMed

Lo, Eugenia; Hemming-Schroeder, Elizabeth; Yewhalaw, Delenasaw; Nguyen, Jennifer; Kebede, Estifanos; Zemene, Endalew; Getachew, Sisay; Tushune, Kora; Zhong, Daibin; Zhou, Guofa; Petros, Beyene; Yan, Guiyun

2017-07-01

Ethiopia is one of the few African countries where Plasmodium vivax is co-endemic with P. falciparum. Malaria transmission is seasonal and transmission intensity varies mainly by landscape and climate. Although the recent emergence of drug resistant parasites presents a major issue to malaria control in Ethiopia, little is known about the transmission pathways of parasite species and prevalence of resistant markers. This study used microsatellites to determine population diversity and gene flow patterns of P. falciparum (N = 226) and P. vivax (N = 205), as well as prevalence of drug resistant markers to infer the impact of gene flow and existing malaria treatment regimes. Plasmodium falciparum indicated a higher rate of polyclonal infections than P. vivax. Both species revealed moderate genetic diversity and similar population structure. Populations in the northern highlands were closely related to the eastern Rift Valley, but slightly distinct from the southern basin area. Gene flow via human migrations between the northern and eastern populations were frequent and mostly bidirectional. Landscape genetic analyses indicated that environmental heterogeneity and geographical distance did not constrain parasite gene flow. This may partly explain similar patterns of resistant marker prevalence. In P. falciparum, a high prevalence of mutant alleles was detected in codons related to chloroquine (pfcrt and pfmdr1) and sulfadoxine-pyrimethamine (pfdhps and pfdhfr) resistance. Over 60% of the samples showed pfmdr1 duplications. Nevertheless, no mutation was detected in pfK13 that relates to artemisinin resistance. In P. vivax, while sequences of pvcrt-o were highly conserved and less than 5% of the samples showed pvmdr duplications, over 50% of the samples had pvmdr1 976F mutation. It remains to be tested if this mutation relates to chloroquine resistance. Monitoring the extent of malaria spread and markers of drug resistance is imperative to inform policy for evidence-based antimalarial choice and interventions. To effectively reduce malaria burden in Ethiopia, control efforts should focus on seasonal migrant populations.

Using atmospheric 14CO to constrain OH variability: concept and potential for future measurements

NASA Astrophysics Data System (ADS)

Petrenko, V. V.; Murray, L. T.; Smith, A. W.

2017-12-01

The primary source of 14C-containing carbon monoxide (14CO) in the atmosphere is via 14C production from 14N by secondary cosmic rays, and the primary sink is removal by OH. Variations in the global abundance of 14CO that are not explained by variations in 14C production are mainly driven by variations in the global abundance of OH. Monitoring OH variability via methyl chloroform is becoming increasingly difficult as methyl chloroform abundance is continuing to decline. Measurements of atmospheric 14CO have previously been successfully used to infer OH variability. However, these measurements are currently only continuing at one location (Baring Head, New Zealand), which is insufficient to infer global trends. We propose to restart global 14CO monitoring with the aim of providing another constraint on OH variability. A new analytical system for 14CO sampling and measurements is in development, which will allow to strongly reduce the required sample air volumes (previously ≥ 400 L) and simplify field logistics. A set of test measurements is planned, with sampling at the Mauna Loa Observatory. Preliminary work with a state-of-the-art chemical transport model is identifying the most promising locations for global 14CO sampling.

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR FIELD COLLECTION OF FOOD AND BEVERAGE SAMPLES (UA-F-15.1)

EPA Science Inventory

The purpose of this SOP is to provide a uniform procedure for the collection of a complete (all meals, snacks, and beverages), one-day (24 hour) duplicate diet sample from the primary respondent. Participants will keep a duplicate portion of all food consumed in a 24 hour period...

NHEXAS PHASE I ARIZONA STUDY--STANDARD OPERATING PROCEDURE FOR FIELD COLLECTION OF FOOD AND BEVERAGE SAMPLES (UA-F-15.1)

EPA Science Inventory

The purpose of this SOP is to provide a uniform procedure for the collection of a complete (all meals, snacks, and beverages), one-day (24 hour) duplicate diet sample from the primary respondent. Participants will keep a duplicate portion of all food consumed in a 24 hour period...

Error analysis of filtering operations in pixel-duplicated images of diabetic retinopathy

NASA Astrophysics Data System (ADS)

Mehrubeoglu, Mehrube; McLauchlan, Lifford

2010-08-01

In this paper, diabetic retinopathy is chosen for a sample target image to demonstrate the effectiveness of image enlargement through pixel duplication in identifying regions of interest. Pixel duplication is presented as a simpler alternative to data interpolation techniques for detecting small structures in the images. A comparative analysis is performed on different image processing schemes applied to both original and pixel-duplicated images. Structures of interest are detected and and classification parameters optimized for minimum false positive detection in the original and enlarged retinal pictures. The error analysis demonstrates the advantages as well as shortcomings of pixel duplication in image enhancement when spatial averaging operations (smoothing filters) are also applied.

CTEPP NC DATA QA/QC RESULTS

EPA Science Inventory

This data set contains the method performance results. This includes field blanks, method blanks, duplicate samples, analytical duplicates, matrix spikes, and surrogate recovery standards.

The Children’s Total Exposure to Persistent Pesticides and Other Persistent Pollutant (...

Comparative Evaluation of Three Homogenization Methods for Isolating Middle East Respiratory Syndrome Coronavirus Nucleic Acids From Sputum Samples for Real-Time Reverse Transcription PCR.

PubMed

Sung, Heungsup; Yong, Dongeun; Ki, Chang Seok; Kim, Jae Seok; Seong, Moon Woo; Lee, Hyukmin; Kim, Mi Na

2016-09-01

Real-time reverse transcription PCR (rRT-PCR) of sputum samples is commonly used to diagnose Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Owing to the difficulty of extracting RNA from sputum containing mucus, sputum homogenization is desirable prior to nucleic acid isolation. We determined optimal homogenization methods for isolating viral nucleic acids from sputum. We evaluated the following three sputum-homogenization methods: proteinase K and DNase I (PK-DNase) treatment, phosphate-buffered saline (PBS) treatment, and N-acetyl-L-cysteine and sodium citrate (NALC) treatment. Sputum samples were spiked with inactivated MERS-CoV culture isolates. RNA was extracted from pretreated, spiked samples using the easyMAG system (bioMérieux, France). Extracted RNAs were then subjected to rRT-PCR for MERS-CoV diagnosis (DiaPlex Q MERS-coronavirus, SolGent, Korea). While analyzing 15 spiked sputum samples prepared in technical duplicate, false-negative results were obtained with five (16.7%) and four samples (13.3%), respectively, by using the PBS and NALC methods. The range of threshold cycle (Ct) values observed when detecting upE in sputum samples was 31.1-35.4 with the PK-DNase method, 34.7-39.0 with the PBS method, and 33.9-38.6 with the NALC method. Compared with the control, which were prepared by adding a one-tenth volume of 1:1,000 diluted viral culture to PBS solution, the ranges of Ct values obtained by the PBS and NALC methods differed significantly from the mean control Ct of 33.2 (both P<0.0001). The PK-DNase method is suitable for homogenizing sputum samples prior to RNA extraction.

Comparative Evaluation of Three Homogenization Methods for Isolating Middle East Respiratory Syndrome Coronavirus Nucleic Acids From Sputum Samples for Real-Time Reverse Transcription PCR

PubMed Central

Yong, Dongeun; Ki, Chang-Seok; Kim, Jae-Seok; Seong, Moon-Woo; Lee, Hyukmin

2016-01-01

Background Real-time reverse transcription PCR (rRT-PCR) of sputum samples is commonly used to diagnose Middle East respiratory syndrome coronavirus (MERS-CoV) infection. Owing to the difficulty of extracting RNA from sputum containing mucus, sputum homogenization is desirable prior to nucleic acid isolation. We determined optimal homogenization methods for isolating viral nucleic acids from sputum. Methods We evaluated the following three sputum-homogenization methods: proteinase K and DNase I (PK-DNase) treatment, phosphate-buffered saline (PBS) treatment, and N-acetyl-L-cysteine and sodium citrate (NALC) treatment. Sputum samples were spiked with inactivated MERS-CoV culture isolates. RNA was extracted from pretreated, spiked samples using the easyMAG system (bioMérieux, France). Extracted RNAs were then subjected to rRT-PCR for MERS-CoV diagnosis (DiaPlex Q MERS-coronavirus, SolGent, Korea). Results While analyzing 15 spiked sputum samples prepared in technical duplicate, false-negative results were obtained with five (16.7%) and four samples (13.3%), respectively, by using the PBS and NALC methods. The range of threshold cycle (Ct) values observed when detecting upE in sputum samples was 31.1–35.4 with the PK-DNase method, 34.7–39.0 with the PBS method, and 33.9–38.6 with the NALC method. Compared with the control, which were prepared by adding a one-tenth volume of 1:1,000 diluted viral culture to PBS solution, the ranges of Ct values obtained by the PBS and NALC methods differed significantly from the mean control Ct of 33.2 (both P<0.0001). Conclusions The PK-DNase method is suitable for homogenizing sputum samples prior to RNA extraction. PMID:27374711

Evolution of herbivore-induced early defense signaling was shaped by genome-wide duplications in Nicotiana

PubMed Central

Zhou, Wenwu; Brockmöller, Thomas; Ling, Zhihao; Omdahl, Ashton; Baldwin, Ian T; Xu, Shuqing

2016-01-01

Herbivore-induced defenses are widespread, rapidly evolving and relevant for plant fitness. Such induced defenses are often mediated by early defense signaling (EDS) rapidly activated by the perception of herbivore associated elicitors (HAE) that includes transient accumulations of jasmonic acid (JA). Analyzing 60 HAE-induced leaf transcriptomes from closely-related Nicotiana species revealed a key gene co-expression network (M4 module) which is co-activated with the HAE-induced JA accumulations but is elicited independently of JA, as revealed in plants silenced in JA signaling. Functional annotations of the M4 module were consistent with roles in EDS and a newly identified hub gene of the M4 module (NaLRRK1) mediates a negative feedback loop with JA signaling. Phylogenomic analysis revealed preferential gene retention after genome-wide duplications shaped the evolution of HAE-induced EDS in Nicotiana. These results highlight the importance of genome-wide duplications in the evolution of adaptive traits in plants. DOI: http://dx.doi.org/10.7554/eLife.19531.001 PMID:27813478

Sampling for mercury at subnanogram per litre concentrations for load estimation in rivers

USGS Publications Warehouse

Colman, J.A.; Breault, R.F.

2000-01-01

Estimation of constituent loads in streams requires collection of stream samples that are representative of constituent concentrations, that is, composites of isokinetic multiple verticals collected along a stream transect. An all-Teflon isokinetic sampler (DH-81) cleaned in 75??C, 4 N HCl was tested using blank, split, and replicate samples to assess systematic and random sample contamination by mercury species. Mean mercury concentrations in field-equipment blanks were low: 0.135 ng??L-1 for total mercury (??Hg) and 0.0086 ng??L-1 for monomethyl mercury (MeHg). Mean square errors (MSE) for ??Hg and MeHg duplicate samples collected at eight sampling stations were not statistically different from MSE of samples split in the laboratory, which represent the analytical and splitting error. Low fieldblank concentrations and statistically equal duplicate- and split-sample MSE values indicate that no measurable contamination was occurring during sampling. Standard deviations associated with example mercury load estimations were four to five times larger, on a relative basis, than standard deviations calculated from duplicate samples, indicating that error of the load determination was primarily a function of the loading model used, not of sampling or analytical methods.

Salmonella spp. and Extended-Spectrum Cephalosporin-Resistant Escherichia coli Frequently Contaminate Broiler Chicken Transport Cages of an Organic Production Company.

PubMed

Mollenkopf, Dixie F; De Wolf, Brittany; Feicht, Sydnee M; Cenera, Johana K; King, Christy A; van Balen, Joany C; Wittum, Thomas E

2018-06-06

Antimicrobial resistant bacteria in retail meat pose a health hazard to the public, as does contamination of these products with Salmonella. Our aim was to determine the prevalence of Salmonella as well as Escherichia coli expressing AmpC and extended-spectrum beta-lactamase (ESBL) resistance phenotypes contaminating broiler transport cages and fresh, retail ground chicken meat. Sterile gauze sponges were used to collect duplicate cage floor samples from transport trailers that deliver market-ready birds to a single organic poultry-processing facility. With the exception of the first visit (n = 25), 50 duplicate cage floor samples were collected using moistened sterile gauze sponges on each of nine weekly visits during May, June, and July 2013. Additionally, fresh, retail ground chicken meat was sampled at each weekly visit from an on-site retail store located at the same processing facility. A total of 425 cage swabs and 72 ground chicken aliquots from 24 retail packages were collected and screened for the presence of Salmonella as well as E. coli expressing resistance to extended-spectrum cephalosporins using selective culture. We recovered Salmonella from 26.1% of cage swab samples and 2.8% of retail meat samples. E. coli expressing AmpC and ESBL resistance phenotypes were recovered from 84.9% and 22.6% of cage swabs and 77.8% and 11.1% of fresh, retail ground meat samples, respectively. Our results suggest that transport cages could potentially act as a source of broiler exposure to both Salmonella and enteric bacteria resistant to important antimicrobial drugs as they are transported for entry into the food supply as fresh, retail meat products.

The chimeric gene CHRFAM7A, a partial duplication of the CHRNA7 gene, is a dominant negative regulator of α7*nAChR function

PubMed Central

Araud, Tanguy; Graw, Sharon; Berger, Ralph; Lee, Michael; Neveu, Estelle; Bertrand, Daniel; Leonard, Sherry

2011-01-01

The human α7 neuronal nicotinic acetylcholine receptor gene (CHRNA7) is a candidate gene for schizophrenia and an important drug target for cognitive deficits in the disorder. Activation of the α7*nAChR, results in opening of the channel and entry of mono- and divalent cations, including Ca++, that presynaptically participates to neurotransmitter release and postsynaptically to down-stream changes in gene expression. Schizophrenic patients have low levels of α7*nAChR, as measured by binding of the ligand [125I]-α-bungarotoxin (I-BTX). The structure of the gene, CHRNA7, is complex. During evolution, CHRNA7 was partially duplicated as a chimeric gene (CHRFAM7A), which is expressed in the human brain and elsewhere in the body. The association between a 2bp deletion in CHRFAM7A and schizophrenia suggested that this duplicate gene might contribute to cognitive impairment. To examine the putative contribution of CHRFAM7A on receptor function, co-expression of α7 and the duplicate genes was carried out in cell lines and Xenopus oocytes. Expression of the duplicate alone yielded protein expression but no functional receptor and co-expression with α7 caused a significant reduction of the amplitude of the ACh-evoked currents. Reduced current amplitude was not correlated with a reduction of I-BTX binding, suggesting the presence of non-functional (ACh-silent) receptors. This hypothesis is supported by a larger increase of the ACh-evoked current by the allosteric modulator 1-(5-chloro-2,4-dimethoxy-phenyl)-3-(5-methyl-isoxazol-3-yl)-urea (PNU-120596) in cells expressing the duplicate than in the control. These results suggest that CHRFAM7A acts as a dominant negative modulator of CHRNA7 function and is critical for receptor regulation in humans. PMID:21718690

The chimeric gene CHRFAM7A, a partial duplication of the CHRNA7 gene, is a dominant negative regulator of α7*nAChR function.

PubMed

Araud, Tanguy; Graw, Sharon; Berger, Ralph; Lee, Michael; Neveu, Estele; Bertrand, Daniel; Leonard, Sherry

2011-10-15

The human α7 neuronal nicotinic acetylcholine receptor gene (CHRNA7) is a candidate gene for schizophrenia and an important drug target for cognitive deficits in the disorder. Activation of the α7*nAChR, results in opening of the channel and entry of mono- and divalent cations, including Ca(2+), that presynaptically participates to neurotransmitter release and postsynaptically to down-stream changes in gene expression. Schizophrenic patients have low levels of α7*nAChR, as measured by binding of the ligand [(125)I]-α-bungarotoxin (I-BTX). The structure of the gene, CHRNA7, is complex. During evolution, CHRNA7 was partially duplicated as a chimeric gene (CHRFAM7A), which is expressed in the human brain and elsewhere in the body. The association between a 2bp deletion in CHRFAM7A and schizophrenia suggested that this duplicate gene might contribute to cognitive impairment. To examine the putative contribution of CHRFAM7A on receptor function, co-expression of α7 and the duplicate genes was carried out in cell lines and Xenopus oocytes. Expression of the duplicate alone yielded protein expression but no functional receptor and co-expression with α7 caused a significant reduction of the amplitude of the ACh-evoked currents. Reduced current amplitude was not correlated with a reduction of I-BTX binding, suggesting the presence of non-functional (ACh-silent) receptors. This hypothesis is supported by a larger increase of the ACh-evoked current by the allosteric modulator 1-(5-chloro-2,4-dimethoxy-phenyl)-3-(5-methyl-isoxazol-3-yl)-urea (PNU-120596) in cells expressing the duplicate than in the control. These results suggest that CHRFAM7A acts as a dominant negative modulator of CHRNA7 function and is critical for receptor regulation in humans. Copyright © 2011 Elsevier Inc. All rights reserved.

Analysis of Duplicated Multiple-Samples Rank Data Using the Mack-Skillings Test.

PubMed

Carabante, Kennet Mariano; Alonso-Marenco, Jose Ramon; Chokumnoyporn, Napapan; Sriwattana, Sujinda; Prinyawiwatkul, Witoon

2016-07-01

Appropriate analysis for duplicated multiple-samples rank data is needed. This study compared analysis of duplicated rank preference data using the Friedman versus Mack-Skillings tests. Panelists (n = 125) ranked twice 2 orange juice sets: different-samples set (100%, 70%, vs. 40% juice) and similar-samples set (100%, 95%, vs. 90%). These 2 sample sets were designed to get contrasting differences in preference. For each sample set, rank sum data were obtained from (1) averaged rank data of each panelist from the 2 replications (n = 125), (2) rank data of all panelists from each of the 2 separate replications (n = 125 each), (3) jointed rank data of all panelists from the 2 replications (n = 125), and (4) rank data of all panelists pooled from the 2 replications (n = 250); rank data (1), (2), and (4) were separately analyzed by the Friedman test, although those from (3) by the Mack-Skillings test. The effect of sample sizes (n = 10 to 125) was evaluated. For the similar-samples set, higher variations in rank data from the 2 replications were observed; therefore, results of the main effects were more inconsistent among methods and sample sizes. Regardless of analysis methods, the larger the sample size, the higher the χ(2) value, the lower the P-value (testing H0 : all samples are not different). Analyzing rank data (2) separately by replication yielded inconsistent conclusions across sample sizes, hence this method is not recommended. The Mack-Skillings test was more sensitive than the Friedman test. Furthermore, it takes into account within-panelist variations and is more appropriate for analyzing duplicated rank data. © 2016 Institute of Food Technologists®

CTEPP-OH DATA QA/QC RESULTS

EPA Science Inventory

This data set contains the method performance results for CTEPP-OH. This includes field blanks, method blanks, duplicate samples, analytical duplicates, matrix spikes, and surrogate recovery standards.

The Children’s Total Exposure to Persistent Pesticides and Other Persisten...

A Preliminary Assessment of 3-Nitro-1,2,4-Triazol-5-One (NTO) as an Insensitive High Explosive

DTIC Science & Technology

1989-07-01

consisted of balled agglomerates of microfine NTO needles (Fig. 2b). Handling properties5 were poor. A final larger scale recrystallisation (20 g NTO...specification for the ERDE T of I test. Samples of 200 mg in glass test tubes were heated at 5"C/min till ignition occurred. Ignition was defined by...duplicate samples. Vacuum Thermal Stability 1251 The test procedure consisted of placing duplicate 5 g samples in glass sample tubes , attaching to a mercury

Volatile organic compounds at two oil and natural gas production well pads in Colorado and Texas using passive samplers.

PubMed

Eisele, Adam P; Mukerjee, Shaibal; Smith, Luther A; Thoma, Eben D; Whitaker, Donald A; Oliver, Karen D; Wu, Tai; Colon, Maribel; Alston, Lillian; Cousett, Tamira A; Miller, Michael C; Smith, Donald M; Stallings, Casson

2016-04-01

A pilot study was conducted in application of the U.S. Environmental Protection Agency (EPA) Methods 325A/B variant for monitoring volatile organic compounds (VOCs) near two oil and natural gas (ONG) production well pads in the Texas Barnett Shale formation and Colorado Denver-Julesburg Basin (DJB), along with a traffic-dominated site in downtown Denver, CO. As indicated in the EPA method, VOC concentrations were measured for 14-day sampling periods using passive-diffusive tube samplers with Carbopack X sorbent at fenceline perimeter and other locations. VOCs were significantly higher at the DJB well pad versus the Barnett well pad and were likely due to higher production levels at the DJB well pad during the study. Benzene and toluene were significantly higher at the DJB well pad versus downtown Denver. Except for perchloroethylene, VOCs measured at passive sampler locations (PSs) along the perimeter of the Barnett well pad were significantly higher than PSs farther away. At the DJB well pad, most VOC concentrations, except perchloroethylene, were significantly higher prior to operational changes than after these changes were made. Though limited, the results suggest passive samplers are precise (duplicate precision usually ≤10%) and that they can be useful to assess spatial gradients and operational conditions at well pad locations over time-integrated periods. Recently enacted EPA Methods 325A/B use passive-diffusive tube samplers to measure benzene at multiple fenceline locations at petrochemical refineries. This pilot study presents initial data demonstrating the utility of Methods 325A/B for monitoring at ONG facilities. Measurements revealed elevated concentrations reflective of production levels and spatial gradients of VOCs relative to source proximity at the Barnett well pad, as well as operational changes at the DJB well pad. Though limited, these findings indicate that Methods 325A/B can be useful in application to characterize VOCs at well pad boundaries.

Use of ATC to describe duplicate medications in primary care prescriptions.

PubMed

Lim, Chiao Mei; Aryani Md Yusof, Faridah; Selvarajah, Sharmini; Lim, Teck Onn

2011-10-01

We aimed to demonstrate the suitability of the Anatomical Therapeutic Chemical Classification (ATC) to describe duplicate drugs and duplicate drug classes in prescription data and describe the pattern of duplicates from public and private primary care clinics of Kuala Lumpur, Malaysia. We analyzed prescription data year 2005 from all 14 public clinics in Kuala Lumpur with 12,157 prescriptions, and a sample of 188 private clinics with 25,612 prescriptions. As ATC Level 5 code represents the molecule and Level 4 represents the pharmacological subgroup, we used repetitions of codes in the same prescription to describe duplicate drugs or duplicate drug classes and compared them between the public and private clinics. At Level 4 ATC, prescriptions with duplicates drug classes were 1.46% of all prescriptions in private and 0.04% in public clinics. At Level 5 ATC, prescriptions with duplicate drugs were 1.81% for private and 0.95% for public clinics. In private clinics at Level 5, 73.3% of prescriptions with duplicates involved systemic combination drugs; at Level 4, 40.3% involved systemic combination drugs. In the public sector at Level 5, 95.7% of prescriptions with duplicates involved topical products. Repetitions of the same ATC codes were mostly useful to describe duplicate medications; however, we recommend avoid using ATC codes for tropical products for this purpose due to ambiguity. Combination products were often involved in duplicate prescribing; redesign of these products might improve prescribing quality. Duplicates occurred more often in private clinics than public clinics in Malaysia.

Age distribution patterns of human gene families: divergent for Gene Ontology categories and concordant between different subcellular localizations.

PubMed

Liu, Gangbiao; Zou, Yangyun; Cheng, Qiqun; Zeng, Yanwu; Gu, Xun; Su, Zhixi

2014-04-01

The age distribution of gene duplication events within the human genome exhibits two waves of duplications along with an ancient component. However, because of functional constraint differences, genes in different functional categories might show dissimilar retention patterns after duplication. It is known that genes in some functional categories are highly duplicated in the early stage of vertebrate evolution. However, the correlations of the age distribution pattern of gene duplication between the different functional categories are still unknown. To investigate this issue, we developed a robust pipeline to date the gene duplication events in the human genome. We successfully estimated about three-quarters of the duplication events within the human genome, along with the age distribution pattern in each Gene Ontology (GO) slim category. We found that some GO slim categories show different distribution patterns when compared to the whole genome. Further hierarchical clustering of the GO slim functional categories enabled grouping into two main clusters. We found that human genes located in the duplicated copy number variant regions, whose duplicate genes have not been fixed in the human population, were mainly enriched in the groups with a high proportion of recently duplicated genes. Moreover, we used a phylogenetic tree-based method to date the age of duplications in three signaling-related gene superfamilies: transcription factors, protein kinases and G-protein coupled receptors. These superfamilies were expressed in different subcellular localizations. They showed a similar age distribution as the signaling-related GO slim categories. We also compared the differences between the age distributions of gene duplications in multiple subcellular localizations. We found that the distribution patterns of the major subcellular localizations were similar to that of the whole genome. This study revealed the whole picture of the evolution patterns of gene functional categories in the human genome.

Effects of long term space environment exposure on optical substrates and coatings (S0050-2)

NASA Technical Reports Server (NTRS)

Harvey, Keith; Mustico, Arthur; Vallimont, John

1993-01-01

Eastman Kodak Company included twelve substrate and coating samples on the Long Duration Exposure Facility (LDEF) structure. There were three Fused Silica and three Ultra Low Expansion (ULE) uncoated glass samples, two ULE samples with a high reflectance silver coating, two Fused Silica samples with an antireflectance coating, and two Fused silica samples with a solar rejection coating. A set of duplicate control samples was also manufactured and stored in a controlled environment for comparison purposes. Kodak's samples were included as a subset of the Georgia Institute of Technology tray, which was located on row 5-E, tray S0050-2. This placed the samples on the trailing edge of the structure, which protected them from the effects of atomic oxygen bombardment. An evaluation of the flight samples for effects from the 5 year mission showed that a contaminant was deposited on the samples, a micrometeoroid impact occurred on one of the samples, and the radiation darkening which was expected for the glass did not occur. The results are listed in more detail.

Characterization of de novo duplications in eight patients by using fluorescence in situ hybridization with chromosome-specific DNA libraries

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

Leana-Cox, J.; Wulfsberg, E.; Raffel, L.J.

Fluorescence in situ hybridization (FISH) with chromosome-specific DNA libraries was performed on samples from eight patients with de novo chromosomal duplications. In five cases, the clinical phenotype and/or cytogenetic evaluations suggested a likely origin of the duplicated material. In the remaining three cases, careful examination of the GTG-banding pattern indicated multiple possible origins; hybridization with more than one chromosome-specific library was performed on two of these cases. In all cases, FISH conclusively identified the chromosomal origin of the duplicated material. In addition, the hybridization pattern was useful in quantitatively delineating the duplication in two cases. 21 refs., 2 figs., 1more » tab.« less

Alimentary tract duplications in newborns and children: Diagnostic aspects and the role of laparoscopic treatment

PubMed Central

Patiño Mayer, Jan; Bettolli, Marcos

2014-01-01

Alimentary tract duplications are rare congenital lesions normally diagnosed in newborns and children that can occur anywhere from the mouth to the anus and have a reported incidence of approximately 1 in 4500 life births. Symptoms and clinical presentation vary greatly. The presentation varies according to age and location. The treatment finally is surgical; total resection when possible should be the aim of the intervention. In pediatric surgery minimally invasive surgical procedures became more and more important over the last decades. In consequence the operative procedure on alimentary tract duplications changed in this manner. We review on case reports and clinical reports on minimally invasive surgery in the treatment of alimentary tract duplications, determine the importance of minimally invasive techniques in the treatment of this rare entity and rule out that further studies in the field should be performed. PMID:25339813

Co-registration of In-Vivo Human MRI Brain Images to Postmortem Histological Microscopic Images

PubMed Central

Singh, M.; Rajagopalan, A.; Kim, T.-S.; Hwang, D.; Chui, H.; Zhang, X.-L.; Lee, A.-Y.; Zarow, C.

2009-01-01

Certain features such as small vascular lesions seen in human MRI are detected reliably only in postmortem histological samples by microscopic imaging. Co-registration of these microscopically detected features to their corresponding locations in the in-vivo images would be of great benefit to understanding the MRI signatures of specific diseases. Using non-linear Polynomial transformation, we report a method to co-register in-vivo MRIs to microscopic images of histological samples drawn off the postmortem brain. The approach utilizes digital photographs of postmortem slices as an intermediate reference to co-register the MRIs to microscopy. The overall procedure is challenging due to gross structural deformations in the postmortem brain during extraction and subsequent distortions in the histological preparations. Hemispheres of the brain were co-registered separately to mitigate these effects. Approaches relying on matching single-slices, multiple-slices and entire volumes in conjunction with different similarity measures suggested that using four slices at a time in combination with two sequential measures, Pearson correlation coefficient followed by mutual information, produced the best MRI-postmortem co-registration according to a voxel mismatch count. The accuracy of the overall registration was evaluated by measuring the 3D Euclidean distance between the locations of microscopically identified lesions on postmortem slices and their MRI-postmortem co-registered locations. The results show a mean 3D displacement of 5.1 ± 2.0 mm between the in-vivo MRI and microscopically determined locations for 21 vascular lesions in 11 subjects. PMID:19169415

46. INTERIOR VIEW, MUSIC ROOM LOCATED AT THE NORTHEAST CORNER ...

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

46. INTERIOR VIEW, MUSIC ROOM LOCATED AT THE NORTHEAST CORNER OF THE HOUSE ON THE FIRST FLOOR, LOOKING TO THE FIREPLACE IN THE EAST WALL (DUPLICATE OF HABS No. AL-424-32) - Arlington Place, 331 Cotton Avenue, Southwest, Birmingham, Jefferson County, AL

47. INTERIOR VIEW, DINING ROOM LOCATED AT THE SOUTHEAST CORNER ...

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

47. INTERIOR VIEW, DINING ROOM LOCATED AT THE SOUTHEAST CORNER OF THE HOUSE ON THE FIRST FLOOR, LOOKING TO THE FIREPLACE IN THE EAST WALL (DUPLICATE OF HABS No. AL-424-33) - Arlington Place, 331 Cotton Avenue, Southwest, Birmingham, Jefferson County, AL

Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L.

PubMed

David, Lior; Rosenberg, Noah A; Lavi, Uri; Feldman, Marcus W; Hillel, Jossi

2007-01-01

Genetic relationships among eight populations of domesticated carp (Cyprinus carpio L.), a species with a partially duplicated genome, were studied using 12 microsatellites and 505 AFLP bands. The populations included three aquacultured carp strains and five ornamental carp (koi) variants. Grass carp (Ctenopharyngodon idella) was used as an outgroup. AFLP-based gene diversity varied from 5% (grass carp) to 32% (koi) and reflected the reasonably well understood histories and breeding practices of the populations. A large fraction of the molecular variance was due to differences between aquacultured and ornamental carps. Further analyses based on microsatellite data, including cluster analysis and neighbor-joining trees, supported the genetic distinctiveness of aquacultured and ornamental carps, despite the recent divergence of the two groups. In contrast to what was observed for AFLP-based diversity, the frequency of heterozygotes based on microsatellites was comparable among all populations. This discrepancy can potentially be explained by duplication of some loci in Cyprinus carpio L., and a model that shows how duplication can increase heterozygosity estimates for microsatellites but not for AFLP loci is discussed. Our analyses in carp can help in understanding the consequences of genotyping duplicated loci and in interpreting discrepancies between dominant and co-dominant markers in species with recent genome duplication.

Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L.

PubMed Central

David, Lior; Rosenberg, Noah A; Lavi, Uri; Feldman, Marcus W; Hillel, Jossi

2007-01-01

Genetic relationships among eight populations of domesticated carp (Cyprinus carpio L.), a species with a partially duplicated genome, were studied using 12 microsatellites and 505 AFLP bands. The populations included three aquacultured carp strains and five ornamental carp (koi) variants. Grass carp (Ctenopharyngodon idella) was used as an outgroup. AFLP-based gene diversity varied from 5% (grass carp) to 32% (koi) and reflected the reasonably well understood histories and breeding practices of the populations. A large fraction of the molecular variance was due to differences between aquacultured and ornamental carps. Further analyses based on microsatellite data, including cluster analysis and neighbor-joining trees, supported the genetic distinctiveness of aquacultured and ornamental carps, despite the recent divergence of the two groups. In contrast to what was observed for AFLP-based diversity, the frequency of heterozygotes based on microsatellites was comparable among all populations. This discrepancy can potentially be explained by duplication of some loci in Cyprinus carpio L., and a model that shows how duplication can increase heterozygosity estimates for microsatellites but not for AFLP loci is discussed. Our analyses in carp can help in understanding the consequences of genotyping duplicated loci and in interpreting discrepancies between dominant and co-dominant markers in species with recent genome duplication. PMID:17433244

Multiplex ligation-dependent probe amplification for genetic screening in autism spectrum disorders: Efficient identification of known microduplications and identification of a novel microduplication in ASMT

PubMed Central

Cai, Guiqing; Edelmann, Lisa; Goldsmith, Juliet E; Cohen, Ninette; Nakamine, Alisa; Reichert, Jennifer G; Hoffman, Ellen J; Zurawiecki, Danielle M; Silverman, Jeremy M; Hollander, Eric; Soorya, Latha; Anagnostou, Evdokia; Betancur, Catalina; Buxbaum, Joseph D

2008-01-01

Background It has previously been shown that specific microdeletions and microduplications, many of which also associated with cognitive impairment (CI), can present with autism spectrum disorders (ASDs). Multiplex ligation-dependent probe amplification (MLPA) represents an efficient method to screen for such recurrent microdeletions and microduplications. Methods In the current study, a total of 279 unrelated subjects ascertained for ASDs were screened for genomic disorders associated with CI using MLPA. Fluorescence in situ hybridization (FISH), quantitative polymerase chain reaction (Q-PCR) and/or direct DNA sequencing were used to validate potential microdeletions and microduplications. Methylation-sensitive MLPA was used to characterize individuals with duplications in the Prader-Willi/Angelman (PWA) region. Results MLPA showed two subjects with typical ASD-associated interstitial duplications of the 15q11-q13 PWA region of maternal origin. Two additional subjects showed smaller, de novo duplications of the PWA region that had not been previously characterized. Genes in these two novel duplications include GABRB3 and ATP10A in one case, and MKRN3, MAGEL2 and NDN in the other. In addition, two subjects showed duplications of the 22q11/DiGeorge syndrome region. One individual was found to carry a 12 kb deletion in one copy of the ASPA gene on 17p13, which when mutated in both alleles leads to Canavan disease. Two subjects showed partial duplication of the TM4SF2 gene on Xp11.4, previously implicated in X-linked non-specific mental retardation, but in our subsequent analyses such variants were also found in controls. A partial duplication in the ASMT gene, located in the pseudoautosomal region 1 (PAR1) of the sex chromosomes and previously suggested to be involved in ASD susceptibility, was observed in 6–7% of the cases but in only 2% of controls (P = 0.003). Conclusion MLPA proves to be an efficient method to screen for chromosomal abnormalities. We identified duplications in 15q11-q13 and in 22q11, including new de novo small duplications, as likely contributing to ASD in the current sample by increasing liability and/or exacerbating symptoms. Our data indicate that duplications in TM4SF2 are not associated with the phenotype given their presence in controls. The results in PAR1/PAR2 are the first large-scale studies of gene dosage in these regions, and the findings at the ASMT locus indicate that further studies of the duplication of the ASMT gene are needed in order to gain insight into its potential involvement in ASD. Our studies also identify some limitations of MLPA, where single base changes in probe binding sequences alter results. In summary, our studies indicate that MLPA, with a focus on accepted medical genetic conditions, may be an inexpensive method for detection of microdeletions and microduplications in ASD patients for purposes of genetic counselling if MLPA-identified deletions are validated by additional methods. PMID:18925931

Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern

PubMed Central

2012-01-01

Background The photosynthetic oxygen-evolving photo system II (PS II) produces almost the entire oxygen in the atmosphere. This unique biochemical system comprises a functional core complex that is encoded by psbA and other genes. Unraveling the evolutionary dynamics of this gene is of particular interest owing to its direct role in oxygen production. psbA underwent gene duplication in leptosporangiates, in which both copies have been preserved since. Because gene duplication is often followed by the non-fictionalization of one of the copies and its subsequent erosion, preservation of both psbA copies pinpoint functional or regulatory specialization events. The aim of this study was to investigate the molecular evolution of psbA among fern lineages. Results We sequenced psbA , which encodes D1 protein in the core complex of PSII, in 20 species representing 8 orders of extant ferns; then we searched for selection and convolution signatures in psbA across the 11 fern orders. Collectively, our results indicate that: (1) selective constraints among D1 protein relaxed after the duplication in 4 leptosporangiate orders; (2) a handful positively selected codons were detected within species of single copy psbA, but none in duplicated ones; (3) a few sites among D1 protein were involved in co-evolution process which may intimate significant functional/structural communications between them. Conclusions The strong competition between ferns and angiosperms for light may have been the main cause for a continuous fixation of adaptive amino acid changes in psbA , in particular after its duplication. Alternatively, a single psbA copy may have undergone bursts of adaptive changes at the molecular level to overcome angiosperms competition. The strong signature of positive Darwinian selection in a major part of D1 protein is testament to this. At the same time, species own two psbA copies hardly have positive selection signals among the D1 protein coding sequences. In this study, eleven co-evolving sites have been detected via different molecules, which may be more important than others. PMID:22899792

Metallothionein Gene Duplications and Metal Tolerance in Natural Populations of Drosophila melanogaster

PubMed Central

Maroni, G.; Wise, J.; Young, J. E.; Otto, E.

1987-01-01

A search for duplications of the Drosophila melanogaster metallothionein gene (Mtn) yielded numerous examples of this type of chromosomal rearrangement. These duplications are distributed widely—we found them in samples from four continents, and they are functional—larvae carrying Mtn duplications produce more Mtn RNA and tolerate increased cadmium and copper concentrations. Six different duplication types were characterized by restriction-enzyme analyses using probes from the Mtn region. The restriction maps show that in four cases the sequences, ranging in size between 2.2 and 6.0 kb, are arranged as direct, tandem repeats; in two other cases, this basic pattern is modified by the insertion of a putative transposable element into one of the repeated units. Duplications of the D. melanogaster metallothionein gene such as those that we found in natural populations may represent early stages in the evolution of a gene family. PMID:2828157

Repeated measurements of transfer factor in rabbits: an animal model suitable for evaluation of short-term exposure.

PubMed

Dahlqvist, M; Lagerstrand, L; Nilsen, A

1994-01-01

Acute temporary changes in lung function may be of use as a biological exposure indicator. However, studies of humans occupationally exposed to complex airborne irritants are often expensive and time demanding. Therefore, an animal model could be a valuable complement. A rabbit model has been evaluated where transfer factor was measured twice during the same day, and with the rabbit awake and available for exposure, in between. Anaesthesia and intubation in 22 rabbits (2.6 [0.2] kg [Mean (SD)]) were immediately followed by two measurements of transfer factor and alveolar volume. Transfer factor was estimated by the single breath CO-technique used in humans. The samples were analysed for CO and He on a gas chromatograph. After one pair of measurements the rabbit was allowed to wake up and after 5 h the duplicate measurements were repeated. The mean values of transfer factor, alveolar volume and transfer constant were 0.50 (0.09) mmol min-1 kPa-1, 127 (8) ml and 3.9 (0.6) mmol min-1 kPa-1 l-1, respectively. The intraindividual coefficients of variation were 7.3%, 5.3% and 6.7%, respectively. Five hours later when the duplicate measurements were repeated, transfer factor, alveolar volume and transfer constant were unchanged still. The results suggest that relatively small changes in transfer factor may be detected without losing power, and thus that this model could be used as a biological exposure indicator.

Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms.

PubMed

Wang, Yupeng; Wang, Xiyin; Tang, Haibao; Tan, Xu; Ficklin, Stephen P; Feltus, F Alex; Paterson, Andrew H

2011-01-01

Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored. In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution. Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution.

Modes of Gene Duplication Contribute Differently to Genetic Novelty and Redundancy, but Show Parallels across Divergent Angiosperms

PubMed Central

Wang, Yupeng; Wang, Xiyin; Tang, Haibao; Tan, Xu; Ficklin, Stephen P.; Feltus, F. Alex; Paterson, Andrew H.

2011-01-01

Background Both single gene and whole genome duplications (WGD) have recurred in angiosperm evolution. However, the evolutionary effects of different modes of gene duplication, especially regarding their contributions to genetic novelty or redundancy, have been inadequately explored. Results In Arabidopsis thaliana and Oryza sativa (rice), species that deeply sample botanical diversity and for which expression data are available from a wide range of tissues and physiological conditions, we have compared expression divergence between genes duplicated by six different mechanisms (WGD, tandem, proximal, DNA based transposed, retrotransposed and dispersed), and between positional orthologs. Both neo-functionalization and genetic redundancy appear to contribute to retention of duplicate genes. Genes resulting from WGD and tandem duplications diverge slowest in both coding sequences and gene expression, and contribute most to genetic redundancy, while other duplication modes contribute more to evolutionary novelty. WGD duplicates may more frequently be retained due to dosage amplification, while inferred transposon mediated gene duplications tend to reduce gene expression levels. The extent of expression divergence between duplicates is discernibly related to duplication modes, different WGD events, amino acid divergence, and putatively neutral divergence (time), but the contribution of each factor is heterogeneous among duplication modes. Gene loss may retard inter-species expression divergence. Members of different gene families may have non-random patterns of origin that are similar in Arabidopsis and rice, suggesting the action of pan-taxon principles of molecular evolution. Conclusion Gene duplication modes differ in contribution to genetic novelty and redundancy, but show some parallels in taxa separated by hundreds of millions of years of evolution. PMID:22164235

The Regional Geochemistry of Soils and Willow in a Metamorphic Bedrock Terrain, Seward Peninsula, Alaska, 2005, and Its Possible Relation to Moose

USGS Publications Warehouse

Gough, L.P.; Lamothe, P.J.; Sanzolone, R.F.; Drew, L.J.; Maier, J.A.K.

2009-01-01

In 2005 willow leaves (all variants of Salix pulchra) and A-, B-, and C-horizon soils were sampled at 10 sites along a transect near the Quarry prospect and 11 sites along a transect near the Big Hurrah mine for the purpose of defining the spatial variability of elements and the regional geochemistry of willow and soil over Paleozoic metamorphic rocks potentially high in cadmium (Cd). Willow, a favorite browse of moose (Alces alces), has been shown by various investigators to bioaccumulate Cd. Moose in this region show clinical signs of tooth wear and breakage and are declining in population for unknown reasons. A trace element imbalance in their diet has been proposed as a possible cause for these observations. Cadmium, in high enough concentrations, is one dietary trace element that potentially could produce such symptoms. We report both the summary statistics for elements in willow and soils and the results of an unbalanced, one-way, hierarchical analysis of variance (ANOVA) (general linear model, GLM), which was constructed to measure the geochemical variability in willow (and soil) at various distance scales across the Paleozoic geologic unit high in bioavailable Cd. All of the geochemical data are presented in the Appendices. The two locations are separated by approximately 80 kilometers (km); sites within a location are approximately 0.5 kilometers apart. Duplicate soil samples collected within a site were separated by 0.05 km or slightly less. Results of the GLM are element specific and range from having very little regional variability to having most of their variance at the top (greater than 80 km) level. For willow, a significant proportion of the total variance occurred at the 'between locations' level for ash yield, barium (Ba), Cd, calcium (Ca), cobalt (Co), nickel (Ni), and zinc (Zn). For soils, concentrations of elements in all three soil horizons were similar in that most of the variability in the geochemical data occurred at the 'between locations' and the 'among sites at a location' GLM levels. Most of the variation in concentrations of Cd in soils occurred among sites (separated by 0.5 km) at both locations across all soil horizons and not between the two locations. Cd distribution across the landscape may be due to variation in soil mineralogy, especially the amount of graphite in soil, which has been associated with Cd. Although samples were collected on the same geologic unit, the geochemistry of soils was demonstrated to be uniform with depth but highly variable between locations separated by 80 km. This exploratory study establishes the presence of elevated levels of Cd in willow growing over Paleozoic bedrock in the Seward Peninsula. Further work is needed to definitively link these high Cd levels in willow browse to the health of moose.

Calcium-activated potassium (BK) channels are encoded by duplicate slo1 genes in teleost fishes.

PubMed

Rohmann, Kevin N; Deitcher, David L; Bass, Andrew H

2009-07-01

Calcium-activated, large conductance potassium (BK) channels in tetrapods are encoded by a single slo1 gene, which undergoes extensive alternative splicing. Alternative splicing generates a high level of functional diversity in BK channels that contributes to the wide range of frequencies electrically tuned by the inner ear hair cells of many tetrapods. To date, the role of BK channels in hearing among teleost fishes has not been investigated at the molecular level, although teleosts account for approximately half of all extant vertebrate species. We identified slo1 genes in teleost and nonteleost fishes using polymerase chain reaction and genetic sequence databases. In contrast to tetrapods, all teleosts examined were found to express duplicate slo1 genes in the central nervous system, whereas nonteleosts that diverged prior to the teleost whole-genome duplication event express a single slo1 gene. Phylogenetic analyses further revealed that whereas other slo1 duplicates were the result of a single duplication event, an independent duplication occurred in a basal teleost (Anguilla rostrata) following the slo1 duplication in teleosts. A third, independent slo1 duplication (autotetraploidization) occurred in salmonids. Comparison of teleost slo1 genomic sequences to their tetrapod orthologue revealed a reduced number of alternative splice sites in both slo1 co-orthologues. For the teleost Porichthys notatus, a focal study species that vocalizes with maximal spectral energy in the range electrically tuned by BK channels in the inner ear, peripheral tissues show the expression of either one (e.g., vocal muscle) or both (e.g., inner ear) slo1 paralogues with important implications for both auditory and vocal physiology. Additional loss of expression of one slo1 paralogue in nonneural tissues in P. notatus suggests that slo1 duplicates were retained via subfunctionalization. Together, the results predict that teleost fish achieve a diversity of BK channel subfunction via gene duplication, rather than increased alternative splicing as witnessed for the tetrapod and invertebrate orthologue.

Calcium-Activated Potassium (BK) Channels Are Encoded by Duplicate slo1 Genes in Teleost Fishes

PubMed Central

Deitcher, David L.; Bass, Andrew H.

2009-01-01

Calcium-activated, large conductance potassium (BK) channels in tetrapods are encoded by a single slo1 gene, which undergoes extensive alternative splicing. Alternative splicing generates a high level of functional diversity in BK channels that contributes to the wide range of frequencies electrically tuned by the inner ear hair cells of many tetrapods. To date, the role of BK channels in hearing among teleost fishes has not been investigated at the molecular level, although teleosts account for approximately half of all extant vertebrate species. We identified slo1 genes in teleost and nonteleost fishes using polymerase chain reaction and genetic sequence databases. In contrast to tetrapods, all teleosts examined were found to express duplicate slo1 genes in the central nervous system, whereas nonteleosts that diverged prior to the teleost whole-genome duplication event express a single slo1 gene. Phylogenetic analyses further revealed that whereas other slo1 duplicates were the result of a single duplication event, an independent duplication occurred in a basal teleost (Anguilla rostrata) following the slo1 duplication in teleosts. A third, independent slo1 duplication (autotetraploidization) occurred in salmonids. Comparison of teleost slo1 genomic sequences to their tetrapod orthologue revealed a reduced number of alternative splice sites in both slo1 co-orthologues. For the teleost Porichthys notatus, a focal study species that vocalizes with maximal spectral energy in the range electrically tuned by BK channels in the inner ear, peripheral tissues show the expression of either one (e.g., vocal muscle) or both (e.g., inner ear) slo1 paralogues with important implications for both auditory and vocal physiology. Additional loss of expression of one slo1 paralogue in nonneural tissues in P. notatus suggests that slo1 duplicates were retained via subfunctionalization. Together, the results predict that teleost fish achieve a diversity of BK channel subfunction via gene duplication, rather than increased alternative splicing as witnessed for the tetrapod and invertebrate orthologue. PMID:19321796

DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads.

PubMed

Yavaş, Gökhan; Koyutürk, Mehmet; Gould, Meetha P; McMahon, Sarah; LaFramboise, Thomas

2014-03-05

With the advent of paired-end high throughput sequencing, it is now possible to identify various types of structural variation on a genome-wide scale. Although many methods have been proposed for structural variation detection, most do not provide precise boundaries for identified variants. In this paper, we propose a new method, Distribution Based detection of Duplication Boundaries (DB2), for accurate detection of tandem duplication breakpoints, an important class of structural variation, with high precision and recall. Our computational experiments on simulated data show that DB2 outperforms state-of-the-art methods in terms of finding breakpoints of tandem duplications, with a higher positive predictive value (precision) in calling the duplications' presence. In particular, DB2's prediction of tandem duplications is correct 99% of the time even for very noisy data, while narrowing down the space of possible breakpoints within a margin of 15 to 20 bps on the average. Most of the existing methods provide boundaries in ranges that extend to hundreds of bases with lower precision values. Our method is also highly robust to varying properties of the sequencing library and to the sizes of the tandem duplications, as shown by its stable precision, recall and mean boundary mismatch performance. We demonstrate our method's efficacy using both simulated paired-end reads, and those generated from a melanoma sample and two ovarian cancer samples. Newly discovered tandem duplications are validated using PCR and Sanger sequencing. Our method, DB2, uses discordantly aligned reads, taking into account the distribution of fragment length to predict tandem duplications along with their breakpoints on a donor genome. The proposed method fine tunes the breakpoint calls by applying a novel probabilistic framework that incorporates the empirical fragment length distribution to score each feasible breakpoint. DB2 is implemented in Java programming language and is freely available at http://mendel.gene.cwru.edu/laframboiselab/software.php.

Verification and characterization of chromosome duplication in haploid maize.

PubMed

de Oliveira Couto, E G; Resende Von Pinho, E V; Von Pinho, R G; Veiga, A D; de Carvalho, M R; de Oliveira Bustamante, F; Nascimento, M S

2015-06-26

Doubled haploid technology has been used by various private companies. However, information regarding chromosome duplication methodologies, particularly those concerning techniques used to identify duplication in cells, is limited. Thus, we analyzed and characterized artificially doubled haploids using microsatellites molecular markers, pollen viability, and flow cytometry techniques. Evaluated material was obtained using two different chromosome duplication protocols in maize seeds considered haploids, resulting from the cross between the haploid inducer line KEMS and 4 hybrids (GNS 3225, GNS 3032, GNS 3264, and DKB 393). Fourteen days after duplication, plant samples were collected and assessed by flow cytometry. Further, the plants were transplanted to a field, and samples were collected for DNA analyses using microsatellite markers. The tassels were collected during anthesis for pollen viability analyses. Haploid, diploid, and mixoploid individuals were detected using flow cytometry, demonstrating that this technique was efficient for identifying doubled haploids. The microsatellites markers were also efficient for confirming the ploidies preselected by flow cytometry and for identifying homozygous individuals. Pollen viability showed a significant difference between the evaluated ploidies when the Alexander and propionic-carmin stains were used. The viability rates between the plodies analyzed show potential for fertilization.

Significant expansion of exon-bordering protein domains during animal proteome evolution

PubMed Central

Liu, Mingyi; Walch, Heiko; Wu, Shaoping; Grigoriev, Andrei

2005-01-01

We present evidence of remarkable genome-wide mobility and evolutionary expansion for a class of protein domains whose borders locate close to the borders of their encoding exons. These exon-bordering domains are more numerous and widely distributed in the human genome than other domains. They also co-occur with more diverse domains to form a larger variety of domain architectures in human proteins. A systematic comparison of nine animal genomes from nematodes to mammals revealed that exon-bordering domains expanded faster than other protein domains in both abundance and distribution, as well as the diversity of co-occurring domains and the domain architectures of harboring proteins. Furthermore, exon-bordering domains exhibited a particularly strong preference for class 1-1 intron phase. Our findings suggest that exon-bordering domains were amplified and interchanged within a genome more often and/or more successfully than other domains during evolution, probably the result of extensive exon shuffling and gene duplication events. The diverse biological functions of these domains underscore the important role they play in the expansion and diversification of animal proteomes. PMID:15640447

Structure and transcriptional regulation of the major intrinsic protein gene family in grapevine.

PubMed

Wong, Darren Chern Jan; Zhang, Li; Merlin, Isabelle; Castellarin, Simone D; Gambetta, Gregory A

2018-04-11

The major intrinsic protein (MIP) family is a family of proteins, including aquaporins, which facilitate water and small molecule transport across plasma membranes. In plants, MIPs function in a huge variety of processes including water transport, growth, stress response, and fruit development. In this study, we characterize the structure and transcriptional regulation of the MIP family in grapevine, describing the putative genome duplication events leading to the family structure and characterizing the family's tissue and developmental specific expression patterns across numerous preexisting microarray and RNAseq datasets. Gene co-expression network (GCN) analyses were carried out across these datasets and the promoters of each family member were analyzed for cis-regulatory element structure in order to provide insight into their transcriptional regulation. A total of 29 Vitis vinifera MIP family members (excluding putative pseudogenes) were identified of which all but two were mapped onto Vitis vinifera chromosomes. In this study, segmental duplication events were identified for five plasma membrane intrinsic protein (PIP) and four tonoplast intrinsic protein (TIP) genes, contributing to the expansion of PIPs and TIPs in grapevine. Grapevine MIP family members have distinct tissue and developmental expression patterns and hierarchical clustering revealed two primary groups regardless of the datasets analyzed. Composite microarray and RNA-seq gene co-expression networks (GCNs) highlighted the relationships between MIP genes and functional categories involved in cell wall modification and transport, as well as with other MIPs revealing a strong co-regulation within the family itself. Some duplicated MIP family members have undergone sub-functionalization and exhibit distinct expression patterns and GCNs. Cis-regulatory element (CRE) analyses of the MIP promoters and their associated GCN members revealed enrichment for numerous CREs including AP2/ERFs and NACs. Combining phylogenetic analyses, gene expression profiling, gene co-expression network analyses, and cis-regulatory element enrichment, this study provides a comprehensive overview of the structure and transcriptional regulation of the grapevine MIP family. The study highlights the duplication and sub-functionalization of the family, its strong coordinated expression with genes involved in growth and transport, and the putative classes of TFs responsible for its regulation.

Presence of accessory penis, colonic duplication and several other congenital anomalies in a child: a very rare association.

PubMed

Chatterjee, Sayan; Mondal, Prabodh Chandra; Pandey, Shashi Bhushan; Achar, Arun

2014-10-01

An accessory penis is a very rare anomaly. Only five cases have been reported thus far to our knowledge. We present the case of a child aged 2 years and 10 months who had a penis-like structure (containing phallus and glans) attached to the right buttock. Associated anomalies were a non-communicating type of colonic duplication, a paramedian stenosed anal opening, a horse-shoe kidney, posterior urethral valves, scoliosis of the lumbo-sacral spine, polydactyly and equino-varus deformity of the right foot. As far as we can tell, this is the first report of an accessory penis associated with colonic duplication and other congenital anomalies. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

WITHDRAWN: Development of EMC-based empirical model for estimating spatial distribution of pollutant loads and its application in rural areas of Korea.

PubMed

Yi, Qitao; Li, Hui; Lee, Jin-Woo; Kim, Youngchul

2015-09-01

The Publisher regrets that this article is an accidental duplication of an article that has already been published in Desalination Water Treat., 27:1-3, 175-188, http://dx.doi.org/10.5004/dwt.2011.2736. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy. Copyright © 2015. Published by Elsevier B.V.

Estimating human exposure to perfluoroalkyl acids via solid food and drinks: Implementation and comparison of different dietary assessment methods.

PubMed

Papadopoulou, Eleni; Poothong, Somrutai; Koekkoek, Jacco; Lucattini, Luisa; Padilla-Sánchez, Juan Antonio; Haugen, Margaretha; Herzke, Dorte; Valdersnes, Stig; Maage, Amund; Cousins, Ian T; Leonards, Pim E G; Småstuen Haug, Line

2017-10-01

Diet is a major source of human exposure to hazardous environmental chemicals, including many perfluoroalkyl acids (PFAAs). Several assessment methods of dietary exposure to PFAAs have been used previously, but there is a lack of comparisons between methods. To assess human exposure to PFAAs through diet by different methods and compare the results. We studied the dietary exposure to PFAAs in 61 Norwegian adults (74% women, average age: 42 years) using three methods: i) by measuring daily PFAA intakes through a 1-day duplicate diet study (separately in solid and liquid foods), ii) by estimating intake after combining food contamination with food consumption data, as assessed by 2-day weighted food diaries and iii) by a Food Frequency Questionnaire (FFQ). We used existing food contamination data mainly from samples purchased in Norway and if not available, data from food purchased in other European countries were used. Duplicate diet samples (n=122) were analysed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to quantify 15 PFAAs (11 perfluoroalkyl carboxylates and 4 perfluoroalkyl sulfonates). Differences and correlations between measured and estimated intakes were assessed. The most abundant PFAAs in the duplicate diet samples were PFOA, PFOS and PFHxS and the median total intakes were 5.6ng/day, 11ng/day and 0.78ng/day, respectively. PFOS and PFOA concentrations were higher in solid than liquid samples. PFOS was the main contributor to the contamination in the solid samples (median concentration 14pg/g food), while it was PFOA in the liquid samples (median concentrations: 0.72pg/g food). High intakes of fats, oils, and eggs were statistically significantly related to high intakes of PFOS and PFOA from solid foods. High intake of milk and consumption of alcoholic beverages, as well as food in paper container were related to high PFOA intakes from liquid foods. PFOA intakes derived from food diary and FFQ were significantly higher than those derived from duplicate diet, but intakes of PFOS derived from food diary and FFQ were significantly lower than those derived from duplicate diet. We found a positive and statistically significant correlation between the PFOS intakes derived from duplicate diet with those using the food diary (rho=0.26, p-value=0.041), but not with the FFQ. Additionally, PFOA intakes derived by duplicate diet were significantly correlated with estimated intakes from liquid food derived from the food diary (rho=0.34, p=0.008) and estimated intakes from the FFQ (rho=0.25, p-value=0.055). We provide evidence that a food diary or a FFQ-based method can provide comparable intake estimates to PFOS and PFOA intakes derived from a duplicate diet study. These less burdensome methods are valuable and reliable tools to assess dietary exposure to PFASs in human studies. Copyright © 2017 Elsevier Inc. All rights reserved.

Delimitation of duplicated segments and identification of their parental origin in two partial chromosome 3p duplications.

PubMed

Antonini, Sylvie; Kim, Chong A; Sugayama, Sofia M; Vianna-Morgante, Angela M

2002-11-22

Two chromosome 3 short arm duplications identified through G-banding were further investigated using fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR) of microsatellite markers, aiming at mapping breakpoints and disclosing mechanisms of origin of these chromosome aberrations. Patient 1 was found to be a mosaic: a 3p12 --> 3p21 duplication was observed in most of his cells, and a normal cell line occurred with a frequency of about 3% in blood. In situ hybridization of chromosome 3 short- and long-arm libraries confirmed the short-arm duplication. Using FISH of short-arm sequences, the YAC 961_h_3 was shown to contain the proximal breakpoint (3p12.1 or 3p12.2), and the distal breakpoint was located between the YACs 729_c_3 and 806_h_2, which are adjacent in the WC 3.10 contig (3p21.1). In Patient 2, G-banding indicated a 3p21 --> 3p24 duplication, without mosaicism. In situ hybridization of chromosome 3 short- and long-arm libraries confirmed the duplication of short-arm sequences. FISH of chromosome 3 sequences showed that the YAC 749_a_7 spanned the proximal breakpoint (3p21.33). The distal breakpoint mapped to the interval between YACs 932_b_6 (3p24.3) and 909_b_6 (3p25). In both cases, microsatellite genotyping pointed to a rearrangement between paternal sister chromatids. Copyright 2002 Wiley-Liss, Inc.

Genome tailoring powered production of isobutanol in continuous CO2/H2 blend fermentation using engineered acetogen biocatalyst.

PubMed

Gak, Eugene; Tyurin, Michael; Kiriukhin, Michael

2014-05-01

The cell energy fraction that powered maintenance and expression of genes encoding pro-phage elements, pta-ack cluster, early sporulation, sugar ABC transporter periplasmic proteins, 6-phosphofructokinase, pyruvate kinase, and fructose-1,6-disphosphatase in acetogen Clostridium sp. MT871 was re-directed to power synthetic operon encoding isobutanol biosynthesis at the expense of these genes achieved via their elimination. Genome tailoring decreased cell duplication time by 7.0 ± 0.1 min (p < 0.05) compared to the parental strain, with intact genome and cell duplication time of 68 ± 1 min (p < 0.05). Clostridium sp. MT871 with tailored genome was UVC-mutated to withstand 6.1 % isobutanol in fermentation broth to prevent product inhibition in an engineered commercial biocatalyst producing 5 % (674.5 mM) isobutanol during two-step continuous fermentation of CO2/H2 gas blend. Biocatalyst Clostridium sp. MT871RG- 11IBR6 was engineered to express six copies of synthetic operon comprising optimized synthetic format dehydrogenase, pyruvate formate lyase, acetolactate synthase, acetohydroxyacid reductoisomerase, 2,3-dihydroxy-isovalerate dehydratase, branched-chain alpha-ketoacid decarboxylase gene, aldehyde dehydrogenase, and alcohol dehydrogenase, regaining cell duplication time of 68 ± 1 min (p < 0.05) for the parental strain. This is the first report on isobutanol production by an engineered acetogen biocatalyst suitable for commercial manufacturing of this chemical/fuel using continuous fermentation of CO2/H2 blend thus contributing to the reversal of global warming.

Using a colorimeter to develop an intrinsic silicone shade guide for facial prostheses.

PubMed

Over, L M; Andres, C J; Moore, B K; Goodacre, C J; Muñoz, C A

1998-12-01

To determine if using CIE L*a*b* color measurements of white facial skin could be correlated to those of silicone shade samples that visually matched the skin. Secondly, to see if a correlation in color measurements could be achieved between the silicone shade samples and duplicated silicone samples made using a shade-guide color formula. A color booth was designed according to ASTM specifications, and painted using a Munsell Value 8 gray. A Minolta colorimeter was used to make facial skin measurements on 15 white adults. The skin color was duplicated using custom-shaded silicone samples. A 7-step wedge silicone shade guide was then fabricated, representing the commonly encountered thicknesses when fabricating facial prostheses. The silicone samples were then measured with the Minolta colorimeter. The readings were compared with the previous L*a*b* readings from the corresponding patient's skin measurements, and the relative color difference was then calculated. Silicone samples were fabricated and analyzed for three of the patients to determine if duplication of the visually matched silicone specimen was possible using the silicone color formula, and if the duplicates were visually and colorimetrically equivalent to each other. The color difference Delta E and chromaticity was calculated, and the data were analyzed using a coefficient-of-variation formula expressed by percent. A Pearson Product Moment Correlation Coefficient was performed to determine if a correlation existed between the skin and the silicone samples at the p < or = .05 level. The highest correlation was found in the b* dimension for silicone thicknesses of 1 to 4 mm. For silicone thicknesses of 6 to 10 mm, the highest correlation was found in the L* dimension. All three dimensions had positive correlations (R2 > 0), but only the 1-mm and 4-mm b* readings were very strong. Patient and silicone L*a*b* measurement results showed very little change in the a* axis, while the L* and b* measurements showed more change in their numbers, with changes in depth for all patient silicone samples. Delta E numbers indicated the lowest Delta E at the 1-mm depth and the highest Delta E at the 10-mm depth. All duplicated samples matched their original silicone samples to a degree that visual evaluation could not distinguish any color differences. Using volumetric measurements, a shade guide was developed for all 15 patients. There was good correlation between the patient's colorimeter measurements and the silicone samples, with the b* color dimension the most reproducible, followed by the L* and the a*. Silicone samples at 6, 8, and 10 mm matched the patient the best, and this study showed that silicone samples can be duplicated successfully if a good patient-silicone match is obtained. Rayon flocking fibers and liquid makeup are effective at matching facial prostheses and can be used to develop a simple shade guide for patient application.

Identifying the European fossil fuel plumes in the atmosphere over the Northeast Atlantic Region through isotopic observations and numerical modelling.

PubMed

Geels, C; Christensen, J H; Hansen, A W; Heinemeier, J; Kiilsholm, S; Larsen, N W; Larsen, S E; Pedersen, T; Sørensen, L L; Brandt, J; Frohn, L M; Djurhuus, S

2006-06-01

As part of the Danish NEAREX project the origin and variability of anthropogenic atmospheric CO(2) over the Northeast Atlantic Region (NEAR) has been studied. The project consisted of a combination of experimental and modelling activities. Local volunteers operated CO(2) sampling stations, built at University of Copenhagen, for (14)C analysis at four locations (East Denmark, Shetland Isles, Faroe Isles and Iceland). The samples were only collected during winter periods of south-easterly winds in an attempt to trace air enriched in fossil-fuel derived CO(2) due to combustion of fossil fuels within European countries. In order to study the transport and concentration fields over the region in detail, a three-dimensional Eulerian hemispheric air pollution model has been extended to include the main anthropogenic sources for atmospheric CO(2). During the project period (1998-2001) only a few episodes of transport from Central Europe towards NEAR arose, which makes the data set for the evaluation of the method sparse. The analysed samples indicate that the signal for fossil CO(2), as expected, is largest (up to 3.7+/-0.4% fossil CO(2)) at the Danish location closest to the European emissions areas and much weaker (up to approximately 1.5+/-0.6% fossil CO(2)) at the most remote location. As the anthropogenic signal is weak in the clean atmosphere over NEAR these numbers will, however, be very sensitive to the assumed background (14)CO(2) activity and the precision of the measurements. The model simulations include the interplay between the driving processes from the emission into the boundary layer and the following horizontal/vertical mixing and atmospheric transport and are used to analyse the meteorological conditions leading to the observed events of high fossil CO(2) over NEAR. This information about the history of the air masses is essential if an observed signal is to be utilised for identifying and quantifying sources for fossil CO(2).

Directed evolution for thermostabilization of a hygromycin B phosphotransferase from Streptomyces hygroscopicus.

PubMed

Sugimoto, Naohisa; Takakura, Yasuaki; Shiraki, Kentaro; Honda, Shinya; Takaya, Naoki; Hoshino, Takayuki; Nakamura, Akira

2013-01-01

To obtain a selection marker gene functional in a thermophilic bacterium, Thermus thermophilus, an in vivo-directed evolutionary strategy was conducted on a hygromycin B phosphotransferase gene (hyg) from Streptomyces hygroscopicus. The expression of wild-type hyg in T. thermophilus provided hygromycin B (HygB) resistance up to 60 °C. Through selection of mutants showing HygB resistance at higher temperatures, eight amino acid substitutions and the duplication of three amino acids were identified. A variant containing seven substitutions and the duplication (HYG10) showed HygB resistance at a highest temperature of 74 °C. Biochemical and biophysical analyses of recombinant HYG and HYG10 revealed that HYG10 was in fact thermostabilized. Modeling of the three-dimensional structure of HYG10 suggests the possible roles of the various substitutions and the duplication on thermostabilization, of which three substitutions and the duplication located at the enzyme surface suggested that these mutations made the enzyme more hydrophilic and provided increased stability in aqueous solution.

A Duplicate Construction Experiment.

ERIC Educational Resources Information Center

Bridgeman, Brent

This experiment was designed to assess the ability of item writers to construct truly parallel tests based on a "duplicate-construction experiment" in which Cronbach argues that if the universe description and sampling are ideally refined, the two independently constructed tests will be entirely equivalent, and that within the limits of item…

DIETARY EXPOSURE FROM PESTICIDE APPLICATION ON FARMS IN THE AGRICULTURAL HEALTH PILOT STUDY

EPA Science Inventory

As part of total human exposure measurements performed on six farms in Iowa and North Carolina during the Agricultural Health Pilot Study, a household duplicate diet, several locally grown foods, an applicator meal, a child duplicate diet, and drinking water samples were collecte...

Measurement of vehicle contamination by exhaust gases

DOT National Transportation Integrated Search

1971-10-01

An investigation of the concentration of carbon : monoxide (CO) within the passenger compartment of motor : vehicles has been made. A sample handling system has been : developed to measure the concentrations of CO at as many as six locations inside a...

Characterization of luciferases and its paralogue in the Panamanian luminous click beetle Pyrophorus angustus: a click beetle luciferase lacks the fatty acyl-CoA synthetic activity.

PubMed

Oba, Yuichi; Kumazaki, Mizuho; Inouye, Satoshi

2010-02-15

Two luciferase genes (dPaLuc and vPaLuc) and one paralogue of luciferase (PaLL) were isolated from the Panamanian luminous click beetle, Pyrophorus angustus (Elateridae, Pyrophorinae). The transcripts of dPaLuc and vPaLuc were predominantly detected in the body parts with dorsal photophore and ventral photophore, respectively, and the transcript of PaLL was detected in both parts. The gene products of dPaLuc and vPaLuc possessed luminescence activity with firefly luciferin (lambda(max)=536 and 566 nm, respectively) but did not show significant activity of fatty acyl-CoA synthesis. On the other hand, the gene product of PaLL had fatty acyl-CoA synthetic activity with very weak luminescence activity. The catalytic properties of click beetle luciferase are different from our previous results that firefly luciferase has both luminescence activity and fatty acyl-CoA synthetic activity. These results suggested that the ancestral fatty acyl-CoA synthetase in the Pyrophorinae lineage has undergone gene duplication event, followed by specialization of one copy in luciferase. Subsequently, the luciferase was duplicated again and the two copies diverged in their luminescent color and expression pattern. Copyright 2009 Elsevier B.V. All rights reserved.

Elucidation of the Molecular Mechanism Driving Duplication of the HIV-1 PTAP Late Domain.

PubMed

Martins, Angelica N; Waheed, Abdul A; Ablan, Sherimay D; Huang, Wei; Newton, Alicia; Petropoulos, Christos J; Brindeiro, Rodrigo D M; Freed, Eric O

2016-01-15

HIV-1 uses cellular machinery to bud from infected cells. This cellular machinery is comprised of several multiprotein complexes known as endosomal sorting complexes required for transport (ESCRTs). A conserved late domain motif, Pro-Thr-Ala-Pro (PTAP), located in the p6 region of Gag (p6(Gag)), plays a central role in ESCRT recruitment to the site of virus budding. Previous studies have demonstrated that PTAP duplications are selected in HIV-1-infected patients during antiretroviral therapy; however, the consequences of these duplications for HIV-1 biology and drug resistance are unclear. To address these questions, we constructed viruses carrying a patient-derived PTAP duplication with and without drug resistance mutations in the viral protease. We evaluated the effect of the PTAP duplication on viral release efficiency, viral infectivity, replication capacity, drug susceptibility, and Gag processing. In the presence of protease inhibitors, we observed that the PTAP duplication in p6(Gag) significantly increased the infectivity and replication capacity of the virus compared to those of viruses bearing only resistance mutations in protease. Our biochemical analysis showed that the PTAP duplication, in combination with mutations in protease, enhances processing between the nucleocapsid and p6 domains of Gag, resulting in more complete Gag cleavage in the presence of protease inhibitors. These results demonstrate that duplication of the PTAP motif in p6(Gag) confers a selective advantage in viral replication by increasing Gag processing efficiency in the context of protease inhibitor treatment, thereby enhancing the drug resistance of the virus. These findings highlight the interconnected role of PTAP duplications and protease mutations in the development of resistance to antiretroviral therapy. Resistance to current drug therapy limits treatment options in many HIV-1-infected patients. Duplications in a Pro-Thr-Ala-Pro (PTAP) motif in the p6 domain of Gag are frequently observed in viruses derived from patients on protease inhibitor (PI) therapy. However, the reason that these duplications arise and their consequences for virus replication remain to be established. In this study, we examined the effect of PTAP duplication on PI resistance in the context of wild-type protease or protease bearing PI resistance mutations. We observe that PTAP duplication markedly enhances resistance to a panel of PIs. Biochemical analysis reveals that the PTAP duplication reverses a Gag processing defect imposed by the PI resistance mutations in the context of PI treatment. The results provide a long-sought explanation for why PTAP duplications arise in PI-treated patients. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Nondispersive infrared spectrometry for 13CO2/12CO2-measurements: a clinically feasible analyzer for stable isotope breath tests in gastroenterology.

PubMed

Braden, B; Caspary, W F; Lembcke, B

1999-06-01

13C-urea breath tests have become clinical routine for the diagnosis of Helicobacter pylori infection and other isotope breath tests have been invented e.g. for gastric emptying or quantitative liver function testing. Recently, isotope-selective nondispersive infrared spectrometers (NDIRS) have been developed for the analysis of the 13CO2/12CO2-enrichment in breath. In this study, we prospectively tested the validity of a newly developed NDIRS in comparison to isotope ratio mass spectrometry (IRMS). 142 patients with dyspeptic symptoms were tested for Helicobacter pylori infection using the 13C-urea breath test. The isotope ratio analysis of the breath samples was performed in duplicate both using IRMS and NDIRS. The results of the baseline-corrected 13CO2-exhalation values between IRMS and NDIRS were in excellent agreement. The mean difference between both methods was 0.28 +/- 1.93 delta/1000. Evaluating the qualitative urea breath test results in reference to IRMS as the reference the NDIRS had a sensitivity of 97.8% and a specificity of 98.9%. The isotope-selective nondispersive infrared spectroscopy is going to become a reliable, but low-cost and easy-to-operate alternative to expensive isotope ratio mass spectrometry in the analysis of 13C-breath tests.

Logistics and Maintenance Concepts for a Future Naval Force

DTIC Science & Technology

2001-12-01

Co - opetition . Currency-Doubleday. Retrieved December 10, 2001 from...Navigation CND Can Not Duplicate CO Commanding Officer COMNAVAIRLANT Commander Naval Forces Atlantic COSAL Consolidated Ship Allowance List CPO...ra ul ic s C or ro si on , O pe ra tio na l f lig ht co nt ro ls de gr ad at io n W id es pr ea d W ir e D am ag e X X X X X X X X

Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean.

PubMed

Innes, Roger W; Ameline-Torregrosa, Carine; Ashfield, Tom; Cannon, Ethalinda; Cannon, Steven B; Chacko, Ben; Chen, Nicolas W G; Couloux, Arnaud; Dalwani, Anita; Denny, Roxanne; Deshpande, Shweta; Egan, Ashley N; Glover, Natasha; Hans, Christian S; Howell, Stacy; Ilut, Dan; Jackson, Scott; Lai, Hongshing; Mammadov, Jafar; Del Campo, Sara Martin; Metcalf, Michelle; Nguyen, Ashley; O'Bleness, Majesta; Pfeil, Bernard E; Podicheti, Ram; Ratnaparkhe, Milind B; Samain, Sylvie; Sanders, Iryna; Ségurens, Béatrice; Sévignac, Mireille; Sherman-Broyles, Sue; Thareau, Vincent; Tucker, Dominic M; Walling, Jason; Wawrzynski, Adam; Yi, Jing; Doyle, Jeff J; Geffroy, Valérie; Roe, Bruce A; Maroof, M A Saghai; Young, Nevin D

2008-12-01

The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.

MLPA based detection of mutations in the dystrophin gene of 180 Polish families with Duchenne/Becker muscular dystrophy.

PubMed

Zimowski, Janusz G; Massalska, Diana; Holding, Mariola; Jadczak, Sylwia; Fidziańska, Elżbieta; Lusakowska, Anna; Kostera-Pruszczyk, Anna; Kamińska, Anna; Zaremba, Jacek

2014-01-01

Duchenne/Becker muscular dystrophy (DMD/BMD) is a recessive, X-linked disorder caused by a mutation in the dystrophin gene. Deletions account for approximately 60-65% of mutations, duplications for 5-10%. The remaining cases are mainly point mutations. According to Monaco theory clinical form of the disease depends on maintaining or disrupting the reading frame. The purpose of the study was to determine frequency and location of deletions and duplications in the dystrophin gene, to determine the compliance between maintaining/disrupting the reading frame and clinical form of the disease and to check the effectiveness of MLPA (multiplex ligation-dependent probe amplification) in the detection of these mutations in hemizygous patients and heterozygous female carriers. The material is composed of combined results of molecular diagnosis carried out in years 2009-2012 in 180 unrelated patients referred with the diagnosis of DMD/BMD tested by use of MLPA. We identified 110 deletions, 22 duplication (in one patient two different duplications were detected) and 2 point mutations. Deletions involved mainly exons 45-54 and 3-21, whereas most duplications involved exons 3-18. The compliance with Monaco theory was 95% for deletions and 76% for duplications. Most of mutations in the dystrophin gene were localized in the hot spots - different for deletions and duplications. MLPA enabled their quick identification, exact localization and determination whether or not they maintained or disrupted the reading frame. MLPA was also effective in detection of deletions and duplications in female carriers. Copyright © 2014 Polish Neurological Society. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

Medicago truncatula contains a second gene encoding a plastid located glutamine synthetase exclusively expressed in developing seeds.

PubMed

Seabra, Ana R; Vieira, Cristina P; Cullimore, Julie V; Carvalho, Helena G

2010-08-19

Nitrogen is a crucial nutrient that is both essential and rate limiting for plant growth and seed production. Glutamine synthetase (GS), occupies a central position in nitrogen assimilation and recycling, justifying the extensive number of studies that have been dedicated to this enzyme from several plant sources. All plants species studied to date have been reported as containing a single, nuclear gene encoding a plastid located GS isoenzyme per haploid genome. This study reports the existence of a second nuclear gene encoding a plastid located GS in Medicago truncatula. This study characterizes a new, second gene encoding a plastid located glutamine synthetase (GS2) in M. truncatula. The gene encodes a functional GS isoenzyme with unique kinetic properties, which is exclusively expressed in developing seeds. Based on molecular data and the assumption of a molecular clock, it is estimated that the gene arose from a duplication event that occurred about 10 My ago, after legume speciation and that duplicated sequences are also present in closely related species of the Vicioide subclade. Expression analysis by RT-PCR and western blot indicate that the gene is exclusively expressed in developing seeds and its expression is related to seed filling, suggesting a specific function of the enzyme associated to legume seed metabolism. Interestingly, the gene was found to be subjected to alternative splicing over the first intron, leading to the formation of two transcripts with similar open reading frames but varying 5' UTR lengths, due to retention of the first intron. To our knowledge, this is the first report of alternative splicing on a plant GS gene. This study shows that Medicago truncatula contains an additional GS gene encoding a plastid located isoenzyme, which is functional and exclusively expressed during seed development. Legumes produce protein-rich seeds requiring high amounts of nitrogen, we postulate that this gene duplication represents a functional innovation of plastid located GS related to storage protein accumulation exclusive to legume seed metabolism.

Analysis of EPA and DOE WIPP Air Sampling Data

EPA Pesticide Factsheets

During the April 2014 EPA visit to WIPP, EPA co-located four ambient air samplers with existing Department of Energy (DOE) ambient air samplers to independently corroborate DOE's reported air sampling results.

Ensuring the Safety and Security of Frozen Lung Cancer Tissue Collections through the Encapsulation of Dried DNA.

PubMed

Washetine, Kevin; Kara-Borni, Mehdi; Heeke, Simon; Bonnetaud, Christelle; Félix, Jean-Marc; Ribeyre, Lydia; Bence, Coraline; Ilié, Marius; Bordone, Olivier; Pedro, Marine; Maitre, Priscilla; Tanga, Virginie; Gormally, Emmanuelle; Mossuz, Pascal; Lorimier, Philippe; Marquette, Charles Hugo; Mouroux, Jérôme; Cohen, Charlotte; Lassalle, Sandra; Long-Mira, Elodie; Clément, Bruno; Dagher, Georges; Hofman, Véronique; Hofman, Paul

2018-06-11

Collected specimens for research purposes may or may not be made available depending on their scarcity and/or on the project needs. Their protection against degradation or in the event of an incident is pivotal. Duplication and storage on a different site is the best way to assure their sustainability. The conservation of samples at room temperature (RT) by duplication can facilitate their protection. We describe a security system for the collection of non-small cell lung cancers (NSCLC) stored in the biobank of the Nice Hospital Center, France, by duplication and conservation of lyophilized (dried), encapsulated DNA kept at RT. Therefore, three frozen tissue collections from non-smoking, early stage and sarcomatoid carcinoma NSCLC patients were selected for this study. DNA was extracted, lyophilized and encapsulated at RT under anoxic conditions using the DNAshell technology. In total, 1974 samples from 987 patients were encapsulated. Six and two capsules from each sample were stored in the biobanks of the Nice and Grenoble (France) Hospitals, respectively. In conclusion, DNA maintained at RT allows for the conservation, duplication and durability of collections of interest stored in biobanks. This is a low-cost and safe technology that requires a limited amount of space and has a low environmental impact.

An Assessment of Ares I-X Aeroacoustic Measurements with Comparisons to Pre-Flight Wind Tunnel Test Results

NASA Technical Reports Server (NTRS)

Nance, Donald K.; Reed, Darren K.

2011-01-01

During the recent successful launch of the Ares I-X Flight Test Vehicle, aeroacoustic data was gathered at fifty-seven locations along the vehicle as part of the Developmental Flight Instrumentation. Several of the Ares I-X aeroacoustic measurements were placed to duplicate measurement locations prescribed in pre-flight, sub-scale wind tunnel tests. For these duplicated measurement locations, comparisons have been made between aeroacoustic data gathered during the ascent phase of the Ares I-X flight test and wind tunnel test data. These comparisons have been made at closely matching flight conditions (Mach number and vehicle attitude) in order to preserve a one-to-one relationship between the flight and wind tunnel data. These comparisons and the current wind tunnel to flight scaling methodology are presented and discussed. The implications of using wind tunnel test data scaled under the current methodology to predict conceptual launch vehicle aeroacoustic environments are also discussed.

A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers

PubMed Central

2012-01-01

Background Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling. Results To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago. Conclusions Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants. PMID:23102090

A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers.

PubMed

Pavy, Nathalie; Pelgas, Betty; Laroche, Jérôme; Rigault, Philippe; Isabel, Nathalie; Bousquet, Jean

2012-10-26

Seed plants are composed of angiosperms and gymnosperms, which diverged from each other around 300 million years ago. While much light has been shed on the mechanisms and rate of genome evolution in flowering plants, such knowledge remains conspicuously meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the sheer size of their genomes represents a significant challenge for characterization, sequencing and assembling. To gain insight into the macro-organisation and long-term evolution of the conifer genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical approach based on kernel density estimation to analyse gene density and identified seven gene-rich isochors. Groups of co-localizing genes were also found that were transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses of 157 gene families for which at least two duplicates were mapped on the spruce genome indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much more translocated within and among spruce chromosomes than conifer-specific duplicates, which were mostly organised in tandem arrays. Both high synteny and collinearity were also observed between the genomes of spruce and pine, two conifers that diverged more than 100 million years ago. Taken together, these results indicate that much genomic evolution has occurred in the seed plant lineage before the split between gymnosperms and angiosperms, and that the pace of evolution of the genome macro-structure has been much slower in the gymnosperm lineage leading to extent conifers than that seen for the same period of time in flowering plants. This trend is largely congruent with the contrasted rates of diversification and morphological evolution observed between these two groups of seed plants.

21 CFR 177.1950 - Vinyl chloride-ethylene copolymers.

Code of Federal Regulations, 2014 CFR

2014-04-01

... in cyclohexanone at 30 °C is not less than 0.50 deciliter per gram as determined by ASTM method D1243... copol-ymer per 100 grams of sample tested as determined from the organic chlorine content. The organic... extractives. All determinations shall be done in duplicate using duplicate blanks. Approximately 400 grams of...

Emergence, development and diversification of the TGF-beta signalling pathway within the animal kingdom.

PubMed

Huminiecki, Lukasz; Goldovsky, Leon; Freilich, Shiri; Moustakas, Aristidis; Ouzounis, Christos; Heldin, Carl-Henrik

2009-02-03

The question of how genomic processes, such as gene duplication, give rise to co-ordinated organismal properties, such as emergence of new body plans, organs and lifestyles, is of importance in developmental and evolutionary biology. Herein, we focus on the diversification of the transforming growth factor-beta (TGF-beta) pathway -- one of the fundamental and versatile metazoan signal transduction engines. After an investigation of 33 genomes, we show that the emergence of the TGF-beta pathway coincided with appearance of the first known animal species. The primordial pathway repertoire consisted of four Smads and four receptors, similar to those observed in the extant genome of the early diverging tablet animal (Trichoplax adhaerens). We subsequently retrace duplications in ancestral genomes on the lineage leading to humans, as well as lineage-specific duplications, such as those which gave rise to novel Smads and receptors in teleost fishes. We conclude that the diversification of the TGF-beta pathway can be parsimoniously explained according to the 2R model, with additional rounds of duplications in teleost fishes. Finally, we investigate duplications followed by accelerated evolution which gave rise to an atypical TGF-beta pathway in free-living bacterial feeding nematodes of the genus Rhabditis. Our results challenge the view of well-conserved developmental pathways. The TGF-beta signal transduction engine has expanded through gene duplication, continually adopting new functions, as animals grew in anatomical complexity, colonized new environments, and developed an active immune system.

Assessing Children’s Dietary Pesticide Exposure: Direct Measurement of Pesticide Residues in 24-Hr Duplicate Food Samples

PubMed Central

Lu, Chensheng; Schenck, Frank J.; Pearson, Melanie A.; Wong, Jon W.

2010-01-01

Background The data presented here are a response to calls for more direct measurements of pesticide residues in foods consumed by children and provide an opportunity to compare direct measures of pesticide residues in foods representing actual consumption with those reported by the U.S. Department of Agriculture Pesticide Data Program. Objective We measured pesticide residues in 24-hr duplicate food samples collected from a group of 46 young children participating in the Children’s Pesticide Exposure Study (CPES). Methods Parents were instructed to collect 24-hr duplicate food samples of all conventional fruits, vegetables, and fruit juices equal to the quantity consumed by their children, similarly prewashed/prepared, and from the same source or batch. Individual or composite food items were analyzed for organophosphate (OP) and pyrethroid insecticide residues. Results We collected a total of 239 24-hr duplicate food samples collected from the 46 CPES children. We found 14% or 5% of those food samples contained at least one OP or pyrethroid insecticide, respectively. We measured a total of 11 OP insecticides, at levels ranging from 1 to 387 ng/g, and three pyrethroid insecticides, at levels ranging from 2 to 1,133 ng/g, in children’s food samples. We found that many of the food items consumed by the CPES children were also on the list of the most contaminated food commodities reported by the Environmental Working Group. Conclusions The frequent consumption of food commodities with episodic presence of pesticide residues that are suspected to cause developmental and neurological effects in young children supports the need for further mitigation. PMID:20639183

Therapeutic Duplicates in a Cohort of Hospitalized Elderly Patients: Results from the REPOSI Study.

PubMed

Pasina, Luca; Astuto, Sarah; Cortesi, Laura; Tettamanti, Mauro; Franchi, Carlotta; Marengoni, Alessandra; Mannucci, Pier Mannuccio; Nobili, Alessandro

2016-09-01

Explicit criteria for potentially inappropriate prescriptions in the elderly are recommended to avoid prescriptions of duplicate drug classes and to optimize monotherapy within a single drug class before a new agent is considered. Duplicate drug class prescription (or therapeutic duplicates) puts the patient at increased risk of adverse drug reactions with no additional therapeutic benefits. To our knowledge, the prevalence of elderly inpatients receiving therapeutic duplicates has never been studied. Our objective was to assess the prevalence of therapeutic duplicates at admission, discharge, and 3-month follow-up of hospitalized elderly patients. This cross-sectional prospective study was conducted in 97 Italian internal medicine and geriatric wards. Therapeutic duplicates were defined as at least two drugs of the same therapeutic class prescribed simultaneously to a patient. A patient's drug therapy at admission relates to prescriptions from general practitioners, whereas prescriptions at discharge are those from hospital internists or geriatricians. The study sample comprised 5821 admitted and 4983 discharged patients. In all, 143 therapeutic duplicates were found at admission and 170 at discharge. The prevalence of patients exposed to at least one therapeutic duplicate rose significantly from hospital admission (2.5 %) to discharge (3.4 %; p = 0.0032). Psychotropic drugs and drugs for peptic ulcer or gastroesophageal reflux disease were the most frequently involved. A total of 86.8 % of patients discharged with at least one therapeutic duplicate were still receiving them at 3-month follow-up. Hospitalization and drugs prescribed by internists and geriatricians are both factors associated with a small but definite increase in overall therapeutic duplicates in elderly patients admitted to internal medicine and geriatric wards. More attention should be paid to the indications for each drug prescribed, because therapeutic duplicates are not supported by evidence and increase both the risk of adverse drug reactions and costs. Identification of unnecessary therapeutic duplicates is essential for the optimization of polypharmacy.

Inherited partial direct duplication of 11q: First report and possible association with a midline developmental field defect

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

Witt, D.R.; Jenkins, L.; Pinheiro, S.

1994-09-01

A 36-year-old woman underwent amniocentesis for advanced maternal age. The fetal karyotype had an extra dark staining G band on the long arm of chromosome 11 with no other identifiable abnormalities. FISH studies using a chromosome 11 paint probe confirmed the origin of the extra band. The abnormality was identified as a partial duplication of 11q: 46,XX dir dup (11)(q13.5q21) or (q21q23.1). The specific duplicated band could not be identified with certainty. Detailed fetal sonograms were normal. Family studies revealed the identical duplication in the mother but normal karyotypes in both maternal grandparents. The mother had strabismus and a shortmore » tongue frenulum which required surgical correction. Menses occurred late in adolescence and complete development of secondary sexual characteristics was delayed until adulthood. An infertility evaluation revealed duplication of the uterus, cervix, and vagina. An evaluation for metorrhagia identified a pituitary adenoma which was resected. Her intelligence was normal. To our knowledge this is the first report of a heritable direct duplication of 11q. It is possible that one or more gene in the duplicated segment played a causal role in the pathophysiology of the patient`s anomalies through a disturbance of the so-called {open_quotes}midline developmental field{close_quotes}. Alternatively, the cytogenetic findings could be unrelated to the malformations. Rare instances of partial gain or loss of specific late-replicating heterochromatic regions without phenotypic effect have been reported. This region of 11q is also relatively late-replicating. This is consistent with previous reports suggesting a paucity of expressed genes in this 11q region. Molecular studies of the duplication are underway to determine the specific location and extent of duplication. Phenotypic evaluation of the patient`s baby will also be reported.« less

Fate of injected CO2 in the Wilcox Group, Louisiana, Gulf Coast Basin: Chemical and isotopic tracers of microbial–brine–rock–CO2 interactions

USGS Publications Warehouse

Shelton, Jenna L.; McIntosh, Jennifer C.; Warwick, Peter D.; Lee Zhi Yi, Amelia

2014-01-01

The “2800’ sandstone” of the Olla oil field is an oil and gas-producing reservoir in a coal-bearing interval of the Paleocene–Eocene Wilcox Group in north-central Louisiana, USA. In the 1980s, this producing unit was flooded with CO2 in an enhanced oil recovery (EOR) project, leaving ∼30% of the injected CO2 in the 2800’ sandstone post-injection. This study utilizes isotopic and geochemical tracers from co-produced natural gas, oil and brine to determine the fate of the injected CO2, including the possibility of enhanced microbial conversion of CO2 to CH4 via methanogenesis. Stable carbon isotopes of CO2, CH4 and DIC, together with mol% CO2 show that 4 out of 17 wells sampled in the 2800’ sandstone are still producing injected CO2. The dominant fate of the injected CO2appears to be dissolution in formation fluids and gas-phase trapping. There is some isotopic and geochemical evidence for enhanced microbial methanogenesis in 2 samples; however, the CO2 spread unevenly throughout the reservoir, and thus cannot explain the elevated indicators for methanogenesis observed across the entire field. Vertical migration out of the target 2800’ sandstone reservoir is also apparent in 3 samples located stratigraphically above the target sand. Reservoirs comparable to the 2800’ sandstone, located along a 90-km transect, were also sampled to investigate regional trends in gas composition, brine chemistry and microbial activity. Microbial methane, likely sourced from biodegradation of organic substrates within the formation, was found in all oil fields sampled, while indicators of methanogenesis (e.g. high alkalinity, δ13C-CO2 and δ13C-DIC values) and oxidation of propane were greatest in the Olla Field, likely due to its more ideal environmental conditions (i.e. suitable range of pH, temperature, salinity, sulfate and iron concentrations).

Mutation screening of patients with Alzheimer disease identifies APP locus duplication in a Swedish patient

PubMed Central

2011-01-01

Background Missense mutations in three different genes encoding amyloid-β precursor protein, presenilin 1 and presenilin 2 are recognized to cause familial early-onset Alzheimer disease. Also duplications of the amyloid precursor protein gene have been shown to cause the disease. At the Dept. of Geriatric Medicine, Karolinska University Hospital, Sweden, patients are referred for mutation screening for the identification of nucleotide variations and for determining copy-number of the APP locus. Methods We combined the method of microsatellite marker genotyping with a quantitative real-time PCR analysis to detect duplications in patients with Alzheimer disease. Results In 22 DNA samples from individuals diagnosed with clinical Alzheimer disease, we identified one patient carrying a duplication on chromosome 21 which included the APP locus. Further mapping of the chromosomal region by array-comparative genome hybridization showed that the duplication spanned a maximal region of 1.09 Mb. Conclusions This is the first report of an APP duplication in a Swedish Alzheimer patient and describes the use of quantitative real-time PCR as a tool for determining copy-number of the APP locus. PMID:22044463

Mutation screening of patients with Alzheimer disease identifies APP locus duplication in a Swedish patient.

PubMed

Thonberg, Håkan; Fallström, Marie; Björkström, Jenny; Schoumans, Jacqueline; Nennesmo, Inger; Graff, Caroline

2011-11-01

Missense mutations in three different genes encoding amyloid-β precursor protein, presenilin 1 and presenilin 2 are recognized to cause familial early-onset Alzheimer disease. Also duplications of the amyloid precursor protein gene have been shown to cause the disease. At the Dept. of Geriatric Medicine, Karolinska University Hospital, Sweden, patients are referred for mutation screening for the identification of nucleotide variations and for determining copy-number of the APP locus. We combined the method of microsatellite marker genotyping with a quantitative real-time PCR analysis to detect duplications in patients with Alzheimer disease. In 22 DNA samples from individuals diagnosed with clinical Alzheimer disease, we identified one patient carrying a duplication on chromosome 21 which included the APP locus. Further mapping of the chromosomal region by array-comparative genome hybridization showed that the duplication spanned a maximal region of 1.09 Mb. This is the first report of an APP duplication in a Swedish Alzheimer patient and describes the use of quantitative real-time PCR as a tool for determining copy-number of the APP locus.

114. VIEW, LOOKING NORTHEAST, OF CHEMISTRY LAB, LOCATED ON MEZZANINE ...

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

114. VIEW, LOOKING NORTHEAST, OF CHEMISTRY LAB, LOCATED ON MEZZANINE ABOVE AND EAST OF FLOTATION CELLS. MAIN USE WAS SAMPLE ANALYSIS TO DETERMINE OPTIMUM REAGENT MIXES AND QUANTITIES. - Shenandoah-Dives Mill, 135 County Road 2, Silverton, San Juan County, CO

Continuous multichannel monitoring of cave air carbon dioxide using a pumped non-dispersive infrared analyser

NASA Astrophysics Data System (ADS)

Mattey, D.

2012-04-01

The concentration of CO2 in cave air is one of the main controls on the rate of degassing of dripwater and on the kinetics of calcite precipitation forming speleothem deposits. Measurements of cave air CO2reveal great complexity in the spatial distribution among interconnected cave chambers and temporal changes on synoptic to seasonal time scales. The rock of Gibraltar hosts a large number of caves distributed over a 300 meter range in altitude and monthly sampling and analysis of air and water combined with continuous logging of temperature, humidity and drip discharge rates since 2004 reveals the importance of density-driven seasonal ventilation which drives large-scale advection of CO2-rich air though the cave systems. Since 2008 we have deployed automatic CO2 monitoring systems that regularly sample cave air from up to 8 locations distributed laterally and vertically in St Michaels Cave located near the top of the rock at 275m asl and Ragged Staff Cave located in the heart of the rock near sea level. The logging system is controlled by a Campbell Scientific CR1000 programmable datalogger which controls an 8 port manifold connected to sampling lines leading to different parts of the cave over a distance of up to 250 meters. The manifold is pumped at a rate of 5l per minute drawing air through 6mm or 8mm id polythene tubing via a 1m Nafion loop to reduce humidity to local ambient conditions. The outlet of the primary pump leads to an open split which is sampled by a second low flow pump which delivers air at 100ml/minute to a Licor 820 CO2 analyser. The software selects the port to be sampled, flushes the line for 2 minutes and CO2 analysed as a set of 5 measurements averaged over 10 second intervals. The system then switches to the next port and when complete shuts down to conserve power after using 20 watts over a 30 minute period of analysis. In the absence of local mains power (eg from the show cave lighting system) two 12v car batteries will power the system for analysis at 4h intervals for about 1 month. Two logging systems sampling cave air from 13 locations over a vertical range of 275m have run continuously for up to 5 years and return a very detailed picture of cave ventilation patterns and their responses to local weather and seasonal change.

Case Report: Whole exome sequencing helps in accurate molecular diagnosis in siblings with a rare co-occurrence of paternally inherited 22q12 duplication and autosomal recessive non-syndromic ichthyosis.

PubMed Central

Gupta, Aayush; Sharma, Yugal; Deo, Kirti; Vellarikkal, Shamsudheen; Jayarajan, Rijith; Dixit, Vishal; Verma, Ankit; Scaria, Vinod; Sivasubbu, Sridhar

2015-01-01

Lamellar ichthyosis (LI), considered an autosomal recessive monogenic genodermatosis, has an incidence of approximately 1 in 250,000. Usually associated with mutations in the transglutaminase gene ( TGM1), mutations in six other genes have, less frequently, been shown to be causative. Two siblings, born in a collodion membrane, presented with fish like scales all over the body. Karyotyping revealed duplication of the chromosome arm on 22q12+ in the father and two siblings. Whole exome sequencing revealed a homozygous p.Gly218Ser variation in TGM1; a variation reported earlier in an isolated Finnish population in association with autosomal recessive non-syndromic ichthyosis. This concurrence of a potentially benign 22q12+ duplication and LI, both rare individually, is reported here likely for the first time. PMID:26594337

Ascorbate peroxidase-related (APx-R) is not a duplicable gene.

PubMed

Dunand, Christophe; Mathé, Catherine; Lazzarotto, Fernanda; Margis, Rogério; Margis-Pinheiro, Marcia

2011-12-01

Phylogenetic, genomic and functional analyses have allowed the identification of a new class of putative heme peroxidases, so called APx-R (APx-Related). These new class, mainly present in the green lineage (including green algae and land plants), can also be detected in other unicellular chloroplastic organisms. Except for recent polyploid organisms, only single-copy of APx-R gene was detected in each genome, suggesting that the majority of the APx-R extra-copies were lost after chromosomal or segmental duplications. In a similar way, most APx-R co-expressed genes in Arabidopsis genome do not have conserved extra-copies after chromosomal duplications and are predicted to be localized in organelles, as are the APx-R. The member of this gene network can be considered as unique gene, well conserved through the evolution due to a strong negative selection pressure and a low evolution rate. © 2011 Landes Bioscience

Variable Penetrance of the 15q11.2 BP1-BP2 Microduplication in a Family with Cognitive and Language Impairment

PubMed Central

Benítez-Burraco, Antonio; Barcos-Martínez, Montserrat; Espejo-Portero, Isabel; Jiménez-Romero, Salud

2017-01-01

The 15q11.2 BP1-BP2 region is found duplicated or deleted in people with cognitive, language, and behavioral impairment. We report on a family (a father and 3 male twin siblings) that presents with a duplication of the 15q11.2 BP1-BP2 region and a variable phenotype: the father and the fraternal twin are normal carriers, whereas the monozygotic twins exhibit severe language and cognitive delay as well as behavioral disturbances. The genes located within the duplicated region are involved in brain development and function, and some of them are related to language processing. The probands' phenotype may result from changes in the expression level of some of these genes important for cognitive development. PMID:28588435

Posology and Field Efficacy Study with Novobiocin for Intramammary Infusion in Nonlactating Dairy Cows

PubMed Central

Swenson, G. H.

1979-01-01

Four dose levels of novobiocin (50, 200, 400, 600 mg) were compared with no drug for the intramammary treatment of Staphylococcus aureus, Streptococcus agalactiae and other streptococcal infections present in the udder of dairy cows at the initiation of the dry period. Treatment success was evaluated by comparing the microbiological status of duplicate pretreatment quarter milk samples collected at drying off with the microbiological status of duplicate quarter milk samples collected four to ten days postcalving. Infection status of 1318 cows in 75 herds in five geographic locations was determined. Treatment effects on infected cows were evaluated by least squares analysis of variance with treatment, herd, lactation number, days dry and milk production at drying off considered as variables. The dose of 400 mg novobiocin per quarter was demonstrated to be significantly more effective (P < 0.05) than no drug and significantly better than (P < 0.05) or equal to the other doses for curing infections caused by S. aureus, S. agalactiae and other streptococci. A significant reduction (P < 0.05) in the overall rate of new udder infections acquired during the dry period was observed in cows treated with ≥ 200 mg novobiocin at drying off. The data supported the conclusion that the cow rather than the quarter is the appropriate experimental unit in the evaluation of intramammary mastitis treatments. Herd and lactation number were the most significant variables affecting cures. PMID:548166

Can We Monitor Ecosystem Function Using Keeling Plot Analyses of Nocturnal Cold-Air Drainage?

NASA Astrophysics Data System (ADS)

Bond, B. J.; Ocheltree, T.; Pypker, T.; Unsworth, M. H.; Mix, A. C.; William, R.

2003-12-01

The carbon isotope signature of ecosystem respiration, δ 13CR, as measured by the Keeling Plot approach, has been related to short-term variations in weather and ecosystem function in several recent studies. In order to obtain an adequate range of [CO2] and to sample a consistent vegetation type, investigators typically select sampling locations in relatively flat terrain and uniform canopy cover, but these are unusual conditions for many forested ecosystems. In a pilot study, we are collecting samples for Keeling Plot analyses in cold-air drainage systems in small (60-100 ha), deeply-incised watersheds, one covered with old-growth (ca 450-years-old) Douglas-fir/hemlock forest and one covered with young (ca 45-years-old) Douglas-fir forest. We found that the nightly range of [CO2] was typically 380-460 ppm, sufficient to develop good estimates of δ 13CR. At any point in time there was little variation in [CO2] with height through the canopy (0.5-30m), so the required range was obtained by sampling over several hours. There was no indication that samples taken from different heights or at different times of night represented sources with different isotopic signatures. The isotopic signature of respired CO2 in the older watershed averaged about 1 per mil greater than that of the young watershed, and δ 13CR of both locations correlated with modeled stomatal conductance 6 days prior to flask sampling.

Dietary intakes of pesticides based on community duplicate diet samples.

PubMed

Melnyk, Lisa Jo; Xue, Jianping; Brown, G Gordon; McCombs, Michelle; Nishioka, Marcia; Michael, Larry C

2014-01-15

The calculation of dietary intake of selected pesticides was accomplished using food samples collected from individual representatives of a defined demographic community using a community duplicate diet approach. A community of nine participants was identified in Apopka, FL from which intake assessments of organophosphate (OP) and pyrethroid pesticides were made. From these nine participants, sixty-seven individual samples were collected and subsequently analyzed by gas chromatography/mass spectrometry. Measured concentrations were used to estimate dietary intakes for individuals and for the community. Individual intakes of total OP and pyrethroid pesticides ranged from 6.7 to 996 ng and 1.2 to 16,000 ng, respectively. The community intake was 256 ng for OPs and 3430 ng for pyrethroid pesticides. The most commonly detected pesticide was permethrin, but the highest overall intake was of bifenthrin followed by esfenvalerate. These data indicate that the community in Apopka, FL, as represented by the nine individuals, was potentially exposed to both OP and pyrethroid pesticides at levels consistent with a dietary model and other field studies in which standard duplicate diet samples were collected. Higher levels of pyrethroid pesticides were measured than OPs, which is consistent with decreased usage of OPs. The diversity of pyrethroid pesticides detected in food samples was greater than expected. Continually changing pesticide usage patterns need to be considered when determining analytes of interest for large scale epidemiology studies. The Community Duplicate Diet Methodology is a tool for researchers to meet emerging exposure measurement needs that will lead to more accurate assessments of intake which may enhance decisions for chemical regulation. Successfully determining the intake of pesticides through the dietary route will allow for accurate assessments of pesticide exposures to a community of individuals, thereby significantly enhancing the research benefit realized from epidemiological exposure studies. © 2013.

Determination of VOC emission rates and compositions for offset printing.

PubMed

Wadden, R A; Scheff, P A; Franke, J E; Conroy, L M; Keil, C B

1995-07-01

The release rates of volatile organic compounds (VOC) as fugitive emissions from offset printing are difficult to quantify, and the compositions are usually not known. Tests were conducted at three offset printing shops that varied in size and by process. In each case, the building shell served as the test "enclosure," and air flow and concentration measurements were made at each air entry and exit point. Emission rates and VOC composition were determined during production for (1) a small shop containing three sheetfed presses and two spirit duplicators (36,700 sheets, 47,240 envelopes and letterheads), (2) a medium-size industrial in-house shop with two webfed and three sheetfed presses, and one spirit duplicator (315,130 total sheets), and (3) one print room of a large commercial concern containing three webfed, heatset operations (1.16 x 10(6) ft) served by catalytic air pollution control devices. Each test consisted of 12 one-hour periods over two days. Air samples were collected simultaneously during each period at 7-14 specified locations within each space. The samples were analyzed by gas chromatography (GC) for total VOC and for 13-19 individual organics. Samples of solvents used at each shop were also analyzed by GC. Average VOC emission rates were 4.7-6.1 kg/day for the small sheetfed printing shop, 0.4-0.9 kg/day for the industrial shop, and 79-82 kg/day for the commercial print room. Emission compositions were similar and included benzene, toluene, xylenes, ethylbenzene, and hexane. Comparison of the emission rates with mass balance estimates based on solvent usage and composition were quite consistent.(ABSTRACT TRUNCATED AT 250 WORDS)

Is the co-location of GPs in primary care centres associated with a higher patient satisfaction? Evidence from a population survey in Italy.

PubMed

Bonciani, Manila; Barsanti, Sara; Murante, Anna Maria

2017-04-04

Several countries have co-located General Practitioners (GPs) in Primary Care Centres (PCCs) with other health and social care professionals in order to improve integrated care. It is not clear whether the co-location of a multidisciplinary team actually facilitates a positive patient experience concerning GP care. The aim of this study was to verify whether the co-location of GPs in PCCs is associated positively with patient satisfaction with their GP when patients have experience of a multidisciplinary team. We also investigated whether patients who frequently use health services, due to their complex needs, benefitted the most from the co-location of a multidisciplinary team. The study used data from a population survey carried out in Tuscany (central Italy) at the beginning of 2015 to evaluate the patients' experience and satisfaction with their GPs. Multilevel linear regression models were implemented to verify the relationship between patient satisfaction and co-location. This key explanatory variable was measured by considering both the list of GPs working in PCCs and the answers of surveyed patients who had experienced the co-location of their GP in a multidisciplinary team. We also explored the effect modification on patient satisfaction due to the use of hospitalisation, access to emergency departments and visits with specialists, by performing the multilevel modelling on two strata of patient data: frequent and non-frequent health service users. A sample of 2025 GP patients were included in the study, 757 of which were patients of GPs working in a PCC. Patient satisfaction with their GP was generally positive. Results showed that having a GP working within a PCC and the experience of the co-located multidisciplinary team were associated with a higher satisfaction (p < 0.01). For non-frequent users of health services on the other hand, the co-location of multidisciplinary team in PCCs was not significantly associated with patient satisfaction, whereas for frequent users, the strength of relationships identified in the overall model increased (p < 0.01). The co-location of GPs with other professionals and their joint working as experienced in PCCs seems to represent a greater benefit for patients, especially for those with complex needs who use primary care, hospitals, emergency care and specialized care frequently.

Appendix 5 Case Studies of Sampling and Monitoring

EPA Science Inventory

The North Fork of Clear Creek (NFCC), Colorado, is an acid-mine drainage impacted stream located approximately 48 km west of Denver, CO, is approximately 29 km long, and flows into the main stem of Clear Creek in Golden, CO. The entire Clear Creek watershed is a Superfund site, ...

Structural control of co-continuous poly(L-lactide)/poly(butylene succinate)/clay nanocomposites.

PubMed

Zhao, Li; Li, Yongjin; Shimizu, Hiroshi

2009-04-01

Poly(L-lactide) (PLLA)/poly(butylene succinate) (PBS) (55/45 w/w) blends with different amounts of nanoclay loadings were prepared using a specially designed high-shear extruder, HSE3000mini, which can reach a maximum shear rate of 4400 sec(-1). The resulted co-continuous structural morphologies were observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). SEM observation revealed that through the combination of various amounts of nanoclay loadings and processing under various shear conditions, the phase size of co-continuous structures of PLLA/PBS blends can be controlled over a wide range from several tens of micrometers to submicrometers. TEM observation shows that all the nanoclays are selectively dispersed in the PBS phase. We also found that clays in low-shear processed sample were mainly located at the interface of PBS phase, while in high-shear sample, the clays were mainly located inside of the PBS phase. It was considered that the dependence of nanoclay location in the PBS phase on the shear conditions, as well as the changing of the viscosity ratio of PBS and PLLA phase with different amounts of clay loading, play important roles in controlling the phase size of the co-continuous structures of PLLA/PBS blends.

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

PubMed Central

Anselmetti, Yoann; Patterson, Murray; Ponty, Yann; B�rard, S�verine; Chauve, Cedric; Scornavacca, Celine; Daubin, Vincent; Tannier, Eric

2017-01-01

DeCoSTAR is a software that aims at reconstructing the organization of ancestral genes or genomes in the form of sets of neighborhood relations (adjacencies) between pairs of ancestral genes or gene domains. It can also improve the assembly of fragmented genomes by proposing evolutionary-induced adjacencies between scaffolding fragments. Ancestral genes or domains are deduced from reconciled phylogenetic trees under an evolutionary model that considers gains, losses, speciations, duplications, and transfers as possible events for gene evolution. Reconciliations are either given as input or computed with the ecceTERA package, into which DeCoSTAR is integrated. DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered around parsimonious solutions, and statistical supports on ancestral and extant adjacencies are provided. DeCoSTAR supports the features of previously contributed tools that reconstruct ancestral adjacencies, namely DeCo, DeCoLT, ART-DeCo, and DeClone. In a few minutes, DeCoSTAR can reconstruct the evolutionary history of domains inside genes, of gene fusion and fission events, or of gene order along chromosomes, for large data sets including dozens of whole genomes from all kingdoms of life. We illustrate the potential of DeCoSTAR with several applications: ancestral reconstruction of gene orders for Anopheles mosquito genomes, multidomain proteins in Drosophila, and gene fusion and fission detection in Actinobacteria. Availability: http://pbil.univ-lyon1.fr/software/DeCoSTAR (Last accessed April 24, 2017). PMID:28402423

Natural History of Human Respiratory Syncytial Virus Inferred from Phylogenetic Analysis of the Attachment (G) Glycoprotein with a 60-Nucleotide Duplication

PubMed Central

Trento, Alfonsina; Viegas, Mariana; Galiano, Mónica; Videla, Cristina; Carballal, Guadalupe; Mistchenko, Alicia S.; Melero, José A.

2006-01-01

A total of 47 clinical samples were identified during an active surveillance program of respiratory infections in Buenos Aires (BA) (1999 to 2004) that contained sequences of human respiratory syncytial virus (HRSV) with a 60-nucleotide duplication in the attachment (G) protein gene. This duplication was analogous to that previously described for other three viruses also isolated in Buenos Aires in 1999 (A. Trento et al., J. Gen. Virol. 84:3115-3120, 2003). Phylogenetic analysis indicated that BA sequences with that duplication shared a common ancestor (dated about 1998) with other HRSV G sequences reported worldwide after 1999. The duplicated nucleotide sequence was an exact copy of the preceding 60 nucleotides in early viruses, but both copies of the duplicated segment accumulated nucleotide substitutions in more recent viruses at a rate apparently higher than in other regions of the G protein gene. The evolution of the viruses with the duplicated G segment apparently followed the overall evolutionary pattern previously described for HRSV, and this genotype has replaced other prevailing antigenic group B genotypes in Buenos Aires and other places. Thus, the duplicated segment represents a natural tag that can be used to track the dissemination and evolution of HRSV in an unprecedented setting. We have taken advantage of this situation to reexamine the molecular epidemiology of HRSV and to explore the natural history of this important human pathogen. PMID:16378999

Flask sample measurements for CO2, CH4 and CO using cavity ring-down spectrometry

NASA Astrophysics Data System (ADS)

Wang, J.-L.; Jacobson, G.; Rella, C. W.; Chang, C.-Y.; Liu, I.; Liu, W.-T.; Chew, C.; Ou-Yang, C.-F.; Liao, W.-C.; Chang, C.-C.

2013-08-01

In recent years, cavity ring-down spectrometry (CRDS) has been demonstrated to be a highly sensitive, stable and fast analytical technique for real-time in situ measurements of greenhouse gases. In this study, we propose the technique (which we call flask-CRDS) of analyzing whole air flask samples for CO2, CH4 and CO using a custom gas manifold designed to connect to a CRDS analyzer. Extremely stable measurements of these gases can be achieved over a large pressure range in the flask, from 175 to 760 Torr. The wide pressure range is conducive to flask sample measurement in three ways: (1) flask samples can be collected in low-pressure environments (e.g. high-altitude locations); (2) flask samples can be first analyzed for other trace gases with the remaining low-pressure sample for CRDS analysis of CO2, CH4 and CO; and (3) flask samples can be archived and re-analyzed for validation. The repeatability of this method (1σ of 0.07 ppm for CO2, 0.4 ppb for CH4, and 0.5 ppb for CO) was assessed by analyzing five canisters filled with the same air sample to a pressure of 200 Torr. An inter-comparison of the flask-CRDS data with in-situ CRDS measurements at a high-altitude mountain baseline station revealed excellent agreement, with differences of 0.10 ± 0.09 ppm (1σ) for CO2 and 0.9 ± 1.0 ppb for CH4. This study demonstrated that the flask-CRDS method was not only simple to build and operate but could also perform highly accurate and precise measurements of atmospheric CO2, CH4 and CO in flask samples.

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

Tsosie, Bernadette; Johnson, Richard

Groundwater samples were collected from monitoring wells at the Bluewater, New Mexico, Disposal Site to monitor groundwater contaminants as specified in the 1997 Long-Term Surveillance Plan for the DOE Bluewater (UMTRCA Title II) Disposal Site Near Grants, New Mexico (LTSP). Sampling and analyses were conducted as specified in the Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). A duplicate sample was collected from location HMC-951. Alluvium wells are completed in the alluvial sediments in the former channel of the Rio San Jose, which was covered by basalt lava flows known asmore » the El Malpais, and are identified by the suffix (M). Bedrock wells are completed in the San Andres Limestone/Glorieta Sandstone hydrologic unit (San Andres aquifer) and are identified by the suffix (SG). Wells HMC-951 and OBS-3 are also completed in the San Andres aquifer. The LTSP requires monitoring for molybdenum, selenium, uranium, and polychlorinated biphenyls (PCBs); PCB monitoring occurs only during November sampling events. This event included sampling for an expanded list of analytes to characterize the site aquifers and to support a regional groundwater investigation being conducted by the New Mexico Environment Department.« less

[Evaluation of the AOAC 985.29 enzimic gravimetric method for determination of dietary fiber in oat and corn grains].

PubMed

da Silva, Leila Picolli; Ciocca, Maria de Lourdes Santorio; Furlong, Eliana Badiale

2003-12-01

The precision attributes and use of the enzymatic-gravimetric method of Prosky et al. (1992) (AOAC 985.29) were evaluated using corn (BR 5202 Pampa) and oat (UFRGS 15) samples. The effect of laboratory batches carried out in different days were evaluated in six laboratory batches, using for each material one duplicate for total fiber (FT) determination, one duplicate for insoluble fiber (FI) determination and blank ones for FT and for FI (both in duplicate). In order to characterize repetitive aspects, five other FT and FI determinations added to each sample were evaluated, summing up 11 data. The low coefficients of variation in the first six batches were considered acceptable as an expression of expected total intralaboratory variation. The repetitive of the method was considered good for FT determinations (CVs < 10%). However, in the FI determination a high frequency of negative values of ash and blanks was found, impairing the repetitive aspects evaluation. The magnitude of the total gravimetric corrections varies with the kind of the sample and is especially influenced by the protein content.

76 FR 54768 - Notice of Suspension and Commencement of Proposed Debarment Proceedings; Schools and Libraries...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-02

... at http://www.fcc.gov . The text may also be purchased from the Commission's duplicating inspection... exchange, you and a co-conspirator paid the school official $79,382 in bribes and kickbacks for steering E...

Unequal crossing-over associated with asymmetrical synapsis between nomadic elements in the Drosophila melanogaster genome

PubMed Central

Goldberg, Michael L.; Sheen, Jenq-Yunn; Gehring, Walter J.; Green, M. M.

1983-01-01

The molecular structure of reciprocal duplications and deficiencies produced by unequal crossing-over at the white (w) locus of Drosophila melanogaster females heterozygous for the alleles wa and wa4 has been examined. A transposable, copia-like element is found at the rearrangement breakpoints. Further characterization indicates that asymmetrical pairing between two copies of this element, which are at least 60 kilobases apart in the parental chromosomes, followed by a crossover within the paired elements, is responsible for the duplication and deficiencies observed. The frequency of these events is high compared with normal homologous exchange, implying that synaptic pairing during meiosis must be sufficiently flexible as to allow efficient recognition of sequences located in nonidentical positions on homologous chromosomes. These results suggest a possible mechanism for the generation of tandem duplications in eukaryotic organisms. Images PMID:16593354

A Review of Double Common Bile Duct and Its Sequelae.

PubMed

Kolli, Sindhura; Etienne, Denzil; Reddy, Madhavi; Shahzad, Ghulamullah

2018-02-01

A double or accessory common bile duct (ACBD) is a rare congenital anomaly. We report the case of a 60-year-old American Asian male, who was found to have a double or duplicated common bile duct after being admitted for evaluation of a pancreatic mass. A duplicated bile duct has the same mucosa histologically as a single bile duct. However, the opening of a duplicated bile duct lacks a sphincter allowing retrograde flow of gut contents which results in a higher probability of intraductal calculus formation. On rare occasions, it can predispose to liver abscesses, pancreatitis, pancreatic cancer, gallbladder cancer, gastric cancer, and ampullary cancer depending on the location of the opening of the ACBD. We present an integrative review of the limited cases of ACBD with correlation to the current case and discussion regarding the aspects of diagnosis and management.

Analysis of copy number variations in Holstein-Friesian cow genomes based on whole-genome sequence data.

PubMed

Mielczarek, M; Frąszczak, M; Giannico, R; Minozzi, G; Williams, John L; Wojdak-Maksymiec, K; Szyda, J

2017-07-01

Thirty-two whole genome DNA sequences of cows were analyzed to evaluate inter-individual variability in the distribution and length of copy number variations (CNV) and to functionally annotate CNV breakpoints. The total number of deletions per individual varied between 9,731 and 15,051, whereas the number of duplications was between 1,694 and 5,187. Most of the deletions (81%) and duplications (86%) were unique to a single cow. No relation between the pattern of variant sharing and a family relationship or disease status was found. The animal-averaged length of deletions was from 5,234 to 9,145 bp and the average length of duplications was between 7,254 and 8,843 bp. Highly significant inter-individual variation in length and number of CNV was detected for both deletions and duplications. The majority of deletion and duplication breakpoints were located in intergenic regions and introns, whereas fewer were identified in noncoding transcripts and splice regions. Only 1.35 and 0.79% of the deletion and duplication breakpoints were observed within coding regions. A gene with the highest number of deletion breakpoints codes for protein kinase cGMP-dependent type I, whereas the T-cell receptor α constant gene had the most duplication breakpoints. The functional annotation of genes with the largest incidence of deletion/duplication breakpoints identified 87/112 Kyoto Encyclopedia of Genes and Genomes pathways, but none of the pathways were significantly enriched or depleted with breakpoints. The analysis of Gene Ontology (GO) terms revealed that a cluster with the highest enrichment score among genes with many deletion breakpoints was represented by GO terms related to ion transport, whereas the GO term cluster mostly enriched among the genes with many duplication breakpoints was related to binding of macromolecules. Furthermore, when considering the number of deletion breakpoints per gene functional category, no significant differences were observed between the "housekeeping" and "strong selection" categories, but genes representing the "low selection pressure" group showed a significantly higher number of breakpoints. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

RETRACTED: Synthesis, characterization and catalytic activity of silver nanoparticles using Tribulus terrestris leaf extract

NASA Astrophysics Data System (ADS)

Ashokkumar, S.; Ravi, S.; Kathiravan, V.; Velmurugan, S.

2014-03-01

This article has been retracted: please see Elsevier Policy on Article Withdrawal. This article has been retracted at the request of the Editor. The article contains duplicate images (Fig. 5A and B as well as Fig. 5C and D) which differ only in magnification and orientation despite being described as different samples. Figure 3 displays duplicated data despite being described as different samples. The scientific community takes a very strong view on this scientific misbehavior and apologies are offered to readers of the journal that this was not detected during the submission process.

Data Validation Package: April 2016 Groundwater Sampling at the Falls City, Texas, Disposal Site

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

Jasso, Tashina; Widdop, Michael

Nine groundwater samples were collected at the Falls City, Texas, Disposal Site as specified in the March 2008 Long-Term Surveillance Plan for the US Department of Energy Falls City Uranium Mill Tailings Disposal Site, Falls City, Texas (DOE-LM/1602-2008). Sampling and analyses were conducted as specified in the Sampling and Analysis Plan for US Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). The wells sampled included the cell performance monitoring wells (0709, 0858, 0880, 0906, and 0921) and the groundwater monitoring wells (0862, 0886, 0891, 0924, and 0963). A duplicate sample was collected from location 0891. Water levelsmore » were measured at each sampled well. Historically, cell performance monitoring wells 0908 and 0916 have not produced water and were confirmed as dry during this sampling event. These wells are completed above the saturated interval in the formation. Notable observations for time-concentration graphs in this report include: (1) uranium concentrations in well 0891 continue to increase; (2) the uranium concentration in well 0880 is higher than the 2015 value and lower than the 2014 value, and it remains within the range of historical values; and (3) uranium concentrations in the other sampled wells are below 2 mg/L and consistent with previous results.« less

Mapping Air Quality Index of Carbon Monoxide (CO) in Medan City

NASA Astrophysics Data System (ADS)

Suryati, I.; Khair, H.

2017-03-01

This study aims to map and analyze air quality index of carbon monoxide (CO) in Medan City. This research used 12 (twelve) sampling points around in Medan with an hour duration each point. CO concentration was analyzed using the NDIR CO Analyzer sampling tool. The concentration CO was obtained between 1 ppm - 23 ppm, with an average concentration was 9.5 ppm. This condition is still below the national ambient air quality standard set by Government Regulation of Indonesian Republic Number 41-1999 amounted to 29 ppm. The result of CO concentration measurements was converted into air pollutant standard index, obtained the index value of 58 - 204. Surfer 10 was used to create map of air pollutant standard index for CO. The map illustrates very unhealthy area where located in the Medan Belawan district. The main factors affecting the concentration of CO are from transportation and meteorological factors.

Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies.

PubMed

Pohl, Nélida; Sison-Mangus, Marilou P; Yee, Emily N; Liswi, Saif W; Briscoe, Adriana D

2009-05-13

The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies. Sequences from ultraviolet-sensitive (UVRh), blue-sensitive (BRh), and long-wavelength sensitive (LWRh) opsins,EF-1 and COI were obtained from 27 taxa representing the five major butterfly families (5535 bp total). Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus (15.3-35.6 Mya) was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis (4.7-13.6 Mya), and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene (13.5-26.1 Mya). Our family-level results are congruent with recent estimates found in the literature and indicate an age of 84-113 million years for the divergence of all butterfly families. These results are consistent with diversification of the butterfly families following the radiation of angiosperms and suggest that some classes of opsin genes may be usefully employed for both phylogenetic reconstruction and divergence time estimation.

Orsomucoid: A new variant and additional duplicated ORM1 gene in Qatari population

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

Sebetan, I.M.; Alali, K.A.; Alzaman, A.

1994-09-01

A new genetically determined ORM2 variant and additional duplicated ORM1 gene were observed in Qatari population using isoelectric focusing in ultra thin layer polyacrylamide gels. The studied population samples indicate occurence of six ORM1 alleles and three ORM2 ones. A simple reliable method for separation of orsomucoid variations with comparison of different reported methods will be presented.

Congenital hyperinsulinism and Poland syndrome in association with 10p13-14 duplication.

PubMed

Giri, Dinesh; Patil, Prashant; Hart, Rachel; Didi, Mohammed; Senniappan, Senthil

2017-01-01

Poland syndrome (PS) is a rare congenital condition, affecting 1 in 30 000 live births worldwide, characterised by a unilateral absence of the sternal head of the pectoralis major and ipsilateral symbrachydactyly occasionally associated with abnormalities of musculoskeletal structures. A baby girl, born at 40 weeks' gestation with birth weight of 3.33 kg (-0.55 SDS) had typical phenotypical features of PS. She had recurrent hypoglycaemic episodes early in life requiring high concentration of glucose and glucagon infusion. The diagnosis of congenital hyperinsulinism (CHI) was biochemically confirmed by inappropriately high plasma concentrations of insulin and C-peptide and low plasma free fatty acids and β-hydroxyl butyrate concentrations during hypoglycaemia. Sequencing of ABCC8 , KCNJ11 and HNF4A did not show any pathogenic mutation. Microarray analysis revealed a novel duplication in the short arm of chromosome 10 at 10p13-14 region. This is the first reported case of CHI in association with PS and 10p duplication. We hypothesise that the HK1 located on the chromosome 10 encoding hexokinase-1 is possibly linked to the pathophysiology of CHI. Congenital hyperinsulinism (CHI) is known to be associated with various syndromes.This is the first reported association of CHI and Poland syndrome (PS) with duplication in 10p13-14.A potential underlying genetic link between 10p13-14 duplication, PS and CHI is a possibility.

The Pea light-independent photomorphogenesis1 Mutant Results from Partial Duplication of COP1 Generating an Internal Promoter and Producing Two Distinct Transcripts

PubMed Central

Sullivan, James A.; Gray, John C.

2000-01-01

The pea lip1 (light-independent photomorphogenesis1) mutant shows many of the characteristics of light-grown development when grown in continuous darkness. To investigate the identity of LIP1, cDNAs encoding the pea homolog of COP1, a repressor of photomorphogenesis identified in Arabidopsis, were isolated from wild-type and lip1 pea seedlings. lip1 seedlings contained a wild-type COP1 transcript as well as a larger COP1′ transcript that contained an internal in-frame duplication of 894 bp. The COP1′ transcript segregated with the lip1 phenotype in F2 seedlings and could be translated in vitro to produce a protein of ∼100 kD. The COP1 gene in lip1 peas contained a 7.5-kb duplication, consisting of exons 1 to 7 of the wild-type sequence, located 2.5 kb upstream of a region of genomic DNA identical to the wild-type COP1 DNA sequence. Transcription and splicing of the mutant COP1 gene was predicted to produce the COP1′ transcript, whereas transcription from an internal promoter in the 2.5-kb region of DNA located between the duplicated regions of COP1 would produce the wild-type COP1 transcript. The presence of small quantities of wild-type COP1 transcripts may reduce the severity of the phenotype produced by the mutated COP1′ protein. The genomic DNA sequences of the COP1 gene from wild-type and lip1 peas and the cDNA sequences of COP1 and COP1′ transcripts have been submitted to the EMBL database under the EMBL accession numbers AJ276591, AJ276592, AJ289773, and AJ289774, respectively. PMID:11041887

Report on Electrochemcial Corrosion Testing of 241-SY-102 Grab Samples from the 2012 Grab Sampling Campaign

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

Wyrwas, Richard B.; Lamothe, Margaret E.

2013-05-30

This report describes the results of the electrochemical testing performed on tank 241-SY-102 (SY-102) grab samples that were collected in support of corrosion mitigation. The objective of the work presented here was to determine corrosion resistance of tank SY-102 to the grab samples collected using electrochemical methods up to 50°C as well as to satisfy data quality objectives. Grab samples were collected at multiple elevations from Riser 003. The electrochemical corrosion testing was planned to consist of linear polarization resistance testing (LPR) and cyclic potentiodynamic polarization (CPP) testing at 50°C. The temperature would be lowered to 40 °C and themore » test repeated if the CPP curve indicated pitting corrosion at 50°C. Ifno pitting was indicated by the CPP curve, then a duplicate scan would be repeated at 50°C to confirm the first result. The testing would be complete if the duplicate CPP scan was consistent with the first. This report contains the CPP results of the testing of grab sample 2SY-12-03 and 2SY-12-03DUP composite sample tested under these conditions. There was no indication of pitting at 50°C, and the duplicate scan was in agreement with the first scan. Since no further testing was required, a third scan with a shorter rest time was performed and is present in this report.« less

Rice straw burning in Southeast Asia as a source of CO and COS to the atmosphere

NASA Astrophysics Data System (ADS)

Nguyen, Ba Cuong; Mihalopoulos, Nikolaos; Putaud, Jean-Philippe

1994-08-01

Atmospheric samples were collected during rice straw burning at four different locations in Viet Nam during the dry and wet seasons (March 1992, February 1993, and August 1992, respectively). The samples were analyzed for CO2, CO, and COS. The emission ratios relative to CO2 for rice straw burning during the dry season were comparable to those observed on samples collected during burning of savanna in Africa or forest in the United States. On the contrary, during the wet season the emission ratios for CO and COS relative to CO2 were 2 to 10 times higher. With these emission ratios and estimates of rice production from southeastern Asia, we estimated that burning of rice straw emits annually about 2.1 Tmol of CO (25 Tg C) and 0.6 Gmol of COS (0.02 Tg S) to the atmosphere. Taking into account these new results, CO and COS fluxes from biomass burning could be reevaluated by 5-21% and 10-67%, respectively, with regard to previous estimates of these gas emissions from all biomass burning activities.

Juvenile Atlantic cod behavior appears robust to near-future CO2 levels.

PubMed

Jutfelt, Fredrik; Hedgärde, Maria

2015-01-01

Ocean acidification caused by the anthropogenic release of CO2 is considered a major threat to marine ecosystems. One unexpected impact of elevated water CO2 levels is that behavioral alterations may occur in tropical reef fish and certain temperate fish species. These effects appear to alter many different types of sensory and cognitive functions; if widespread and persistent, they have the potential to cause ecosystem changes. We investigated whether economically and ecologically important Atlantic cod also display behavioral abnormalities by exposing 52 juvenile cod to control conditions (500 μatm, duplicate tanks) or an end-of-the-century ocean acidification scenario (1000 μatm, duplicate tanks) for one month, during which time the fish were examined for a range of behaviors that have been reported to be affected by elevated CO2 in other fish. The behaviors were swimming activity, as measured by number of lines crossed per minute, the emergence from shelter, determined by how long it took the fish to exit a shelter after a disturbance, relative lateralization (a measure of behavioral turning side preference), and absolute lateralization (the strength of behavioral symmetry). We found no effect of CO2 treatment on any of the four behaviors tested: activity (F = 1.61, p = 0.33), emergence from shelter (F = 0.13, p = 0.76), relative lateralization (F = 2.82, p = 0.50), and absolute lateralization (F = 0.80, p = 0.26). Our results indicate that the behavior of Atlantic cod could be resilient to the impacts of near-future levels of water CO2.

A Fleet of Low-Cost Sensor Based Air Quality Monitors Is Used to Measure Carbon Dioxide and Carbon Monoxide in Two Settings: In the Ambient Environment to Explore the Regional-Scale Spatial Variability of These Compounds Via a Distributed Network, and in Homes to Investigate How Heating during Winter Months can Impact Indoor Air Quality.

NASA Astrophysics Data System (ADS)

Casey, J. G.; Hannigan, M.; Collier, A. M.; Coffey, E.; Piedrahita, R.

2016-12-01

Affordable, small, portable, quiet tools to measure atmospheric trace gases and air quality enable novel experimental design and new findings. Members of the Hannigan Lab at the University of Colorado in Boulder have been working over the last few years to integrate emerging affordable gas sensors into such an air quality monitor. Presented here are carbon monoxide (CO) and carbon dioxide (CO2) measurements from two field experiments that utilized these tools. In the first experiment, ten air quality monitors were located northeast of Boulder throughout the Denver Julesburg oil and gas basin. The Colorado Department of Health and Environment has several air quality monitoring sites in this broader region, each in an Urban center. One goal of the experiment was to determine whether or not significant spatial variability of EPA criteria pollutants like CO, exists on a sub-regulatory monitoring grid scale. Another goal of the experiment was to compare rural sampling locations with urban sites. The monitors collected continuous data (sampling every 15 seconds) at each location over the course of several months. Our sensor calibration procedures are presented along with our observations and an analysis of the spatial and temporal variability in CO and CO2. In the second experiment, we used eight of our air quality monitors to better understand how home heating fuel type can impact indoor air quality in two communities on the Navajo Nation. We sought to compare air quality in homes using one of four different fuels for heat (wood, wood plus coal, pellet, and gas). There are many factors that contribute to indoor air quality and the impact of an emission source, like a woodstove, within a home. Having multiple, easily deployable, air quality monitors allowed us to account for many of these factors. We sampled four homes at a time, aiming for one home from each of our fuel groups in each sampling period. We sampled inside and outside of each home for a period of 3-4 days. In this way, we hoped to account for possible weather and outdoor air quality biases. CO and CO2 were measured and are put into context with acceptable levels. During periods when there were no emissions of CO and CO2, we used their rates of decay to calculate the home's air exchange rate via the tracer gas technique. The air exchange rate was then used to calculate emission rates for CO.

OCLC-MARC Tape Processing: A Functional Analysis.

ERIC Educational Resources Information Center

Miller, Bruce Cummings

1984-01-01

Analyzes structure of, and data in, the OCLC-MARC record in the form delivered via OCLC's Tape Subscription Service, and outlines important processing functions involved: "unreadable tapes," duplicate records and deduping, match processing, choice processing, locations processing, "automatic" and "input" stamps,…

A Y-Encoded Suppressor of Feminization Arose via Lineage-Specific Duplication of a Cytokinin Response Regulator in Kiwifruit[OPEN

PubMed Central

Ohtani, Haruka; Morimoto, Takuya; Beppu, Kenji; Kataoka, Ikuo

2018-01-01

Dioecy, the presence of male and female flowers on distinct individuals, has evolved independently in multiple plant lineages, and the genes involved in this differential development are just starting to be uncovered in a few species. Here, we used genomic approaches to investigate this pathway in kiwifruits (genus Actinidia). Genome-wide cataloging of male-specific subsequences, combined with transcriptome analysis, led to the identification of a type-C cytokinin response regulator as a potential sex determinant gene in this genus. Functional transgenic analyses in two model systems, Arabidopsis thaliana and Nicotiana tabacum, indicated that this gene acts as a dominant suppressor of carpel development, prompting us to name it Shy Girl (SyGI). Evolutionary analyses in a panel of Actinidia species revealed that SyGI is located in the Y-specific region of the genome and probably arose from a lineage-specific gene duplication. Comparisons with the duplicated autosomal counterpart, and with orthologs from other angiosperms, suggest that the SyGI-specific duplication and subsequent evolution of cis-elements may have played a key role in the acquisition of separate sexes in this species. PMID:29626069

Identification of 15 novel partial SHOX deletions and 13 partial duplications, and a review of the literature reveals intron 3 to be a hotspot region.

PubMed

Benito-Sanz, Sara; Belinchon-Martínez, Alberta; Aza-Carmona, Miriam; de la Torre, Carolina; Huber, Celine; González-Casado, Isabel; Ross, Judith L; Thomas, N Simon; Zinn, Andrew R; Cormier-Daire, Valerie; Heath, Karen E

2017-02-01

Short stature homeobox gene (SHOX) is located in the pseudoautosomal region 1 of the sex chromosomes. It encodes a transcription factor implicated in the skeletal growth. Point mutations, deletions or duplications of SHOX or its transcriptional regulatory elements are associated with two skeletal dysplasias, Léri-Weill dyschondrosteosis (LWD) and Langer mesomelic dysplasia (LMD), as well as in a small proportion of idiopathic short stature (ISS) individuals. We have identified a total of 15 partial SHOX deletions and 13 partial SHOX duplications in LWD, LMD and ISS patients referred for routine SHOX diagnostics during a 10 year period (2004-2014). Subsequently, we characterized these alterations using MLPA (multiplex ligation-dependent probe amplification assay), fine-tiling array CGH (comparative genomic hybridation) and breakpoint PCR. Nearly half of the alterations have a distal or proximal breakpoint in intron 3. Evaluation of our data and that in the literature reveals that although partial deletions and duplications only account for a small fraction of SHOX alterations, intron 3 appears to be a breakpoint hotspot, with alterations arising by non-allelic homologous recombination, non-homologous end joining or other complex mechanisms.

Aqueous geochemical data from the analysis of stream-water samples collected in June and July 2006-Taylor Mountains 1:250,00-scale quadrangle, Alaska

USGS Publications Warehouse

Wang, Bronwen; Mueller, Seth; Stetson, Sarah; Bailey, Elizabeth; Lee, Greg

2011-01-01

We report on the chemical analysis of water samples collected from the Taylor Mountains 1:250,000-scale quadrangle, Alaska. Parameters for which data are reported include pH, conductivity, water temperature, major cation and anion concentrations, trace-element concentrations, and dissolved organic-carbon concentrations. Samples were collected as part of a multiyear U.S. Geological Survey project entitled ?Geologic and Mineral Deposit Data for Alaskan Economic Development.? Data presented here are from samples collected in June and July 2006. The data are being released at this time with minimal interpretation. This is the third release of aqueous geochemical data from this project; aqueous geochemical data from samples collected in 2004 and 2005 were published previously. The data in this report augment but do not duplicate or supersede the previous data release. Site selection was based on a regional sampling strategy that focused on first- and second-order drainages. Water sample site selection was based on landscape parameters that included physiography, wetland extent, lithological changes, and a cursory field review of mineralogy from pan concentrates. Stream water in the Taylor Mountains quadrangle is dominated by bicarbonate (HCO3-), although in a few samples more than 50 percent of the anionic charge can be attributed to sulfate (SO42-). The major-cation chemistry ranges from Ca2+/Mg2+ dominated to a mix of Ca2+/Mg2+/Na++K+. Generally, good agreement was found between the major cations and anions in the duplicate samples. Many trace elements in these samples were at or near the analytical method detection limit, but good agreement was found between duplicate samples for elements with detectable concentrations. All field blank major-ion and trace-element concentrations were below detection.

A rare FANCA gene variation as a breast cancer susceptibility allele in an Iranian population

PubMed Central

Abbasi, Sakineh; Rasouli, Mina

2017-01-01

Fanconi Anemia (FA) is an autosomal recessive syndrome characterized by congenital abnormalities, progressive bone marrow failure and Fanconi anemia complementation group A (FANCA) is also a potential breast and ovarian cancer susceptibility gene. A novel allele with tandem duplication of 13 base pair sequence in promoter region was identified. To investigate whether the 13 base pair sequence of tandem duplication in promoter region of the FANCA gene is of high penetrance in patients with breast cancer and to determine if the presence of the duplicated allele was associated with an altered risk of breast cancer, the present study screened DNA in blood samples from 304 breast cancer patients and 295 normal individuals as controls. The duplication allele had a frequency of 35.4 and 21.2% in patients with breast cancer and normal controls, respectively. There was a significant increase in the frequency of the duplication allele in patients with familial breast cancer compared with controls (45.1%, P=0.001). Furthermore, the estimated risk of breast cancer in individuals with a homozygote [odds ratio (OR), 4.093; 95% confidence intervals (CI), 1.957–8.561] or heterozygote duplicated genotype (OR, 3.315; 95% CI, 1.996–5.506) was higher compared with the corresponding normal homozygote genotype. In conclusion, the present study indicated that the higher the frequency of the duplicated allele, the higher the risk of breast cancer. To the best of our knowledge, the present study is the first to report FANCA gene duplication in patients with breast cancer. PMID:28440412

A rare FANCA gene variation as a breast cancer susceptibility allele in an Iranian population.

PubMed

Abbasi, Sakineh; Rasouli, Mina

2017-06-01

Fanconi Anemia (FA) is an autosomal recessive syndrome characterized by congenital abnormalities, progressive bone marrow failure and Fanconi anemia complementation group A (FANCA) is also a potential breast and ovarian cancer susceptibility gene. A novel allele with tandem duplication of 13 base pair sequence in promoter region was identified. To investigate whether the 13 base pair sequence of tandem duplication in promoter region of the FANCA gene is of high penetrance in patients with breast cancer and to determine if the presence of the duplicated allele was associated with an altered risk of breast cancer, the present study screened DNA in blood samples from 304 breast cancer patients and 295 normal individuals as controls. The duplication allele had a frequency of 35.4 and 21.2% in patients with breast cancer and normal controls, respectively. There was a significant increase in the frequency of the duplication allele in patients with familial breast cancer compared with controls (45.1%, P=0.001). Furthermore, the estimated risk of breast cancer in individuals with a homozygote [odds ratio (OR), 4.093; 95% confidence intervals (CI), 1.957‑8.561] or heterozygote duplicated genotype (OR, 3.315; 95% CI, 1.996‑5.506) was higher compared with the corresponding normal homozygote genotype. In conclusion, the present study indicated that the higher the frequency of the duplicated allele, the higher the risk of breast cancer. To the best of our knowledge, the present study is the first to report FANCA gene duplication in patients with breast cancer.

Cecal duplication: A mimicker of intussusception: A case report and review.

PubMed

Radhakrishna, Veerabhadra; Rijhwani, Ashok; Jadhav, Bhushanrao

2018-07-01

Cecal duplication is a rare congenital anomaly and to the best of our knowledge, only 43 cases have been reported in the literature till date. Most of them present within the first year of life. They can mimic intussusception, and the delay in diagnosis can lead to high morbidity. A five-year boy presented with pain abdomen for a week. He was found to have ileocolic intussusception. The intussusception could only be partially reduced by the hydrostatic method. On laparotomy, a submucosal solid mass was found in the cecum with multiple enlarged lymph nodes. Mass was resected with clear margins and lymph nodes sampled. Histopathology was conclusive of cecal duplication. Post-operative course was uneventful, and the child is thriving well, last reviewed at three-year follow-up. Incomplete reduction of intussusception, intussusception with atypical presentation or intussusception in atypical age group should alert to the possibility of cecal duplication.

Quality control considerations for size exclusion chromatography with online ICP-MS: a powerful tool for evaluating the size dependence of metal-organic matter complexation.

PubMed

McKenzie, Erica R; Young, Thomas M

2013-01-01

Size exclusion chromatography (SEC), which separates molecules based on molecular volume, can be coupled with online inductively coupled plasma mass spectrometry (ICP-MS) to explore size-dependent metal-natural organic matter (NOM) complexation. To make effective use of this analytical dual detector system, the operator should be mindful of quality control measures. Al, Cr, Fe, Se, and Sn all exhibited columnless attenuation, which indicated unintended interactions with system components. Based on signal-to-noise ratio and peak reproducibility between duplicate analyses of environmental samples, consistent peak time and height were observed for Mg, Cl, Mn, Cu, Br, and Pb. Al, V, Fe, Co, Ni, Zn, Se, Cd, Sn, and Sb were less consistent overall, but produced consistent measurements in select samples. Ultrafiltering and centrifuging produced similar peak distributions, but glass fiber filtration produced more high molecular weight (MW) peaks. Storage in glass also produced more high MW peaks than did plastic bottles.

Methodology to determine the extent of anaerobic digestion, composting and CH4 oxidation in a landfill environment.

PubMed

Obersky, Lizanne; Rafiee, Reza; Cabral, Alexandre R; Golding, Suzanne D; Clarke, William P

2018-06-01

An examination of the processes contributing to the production of landfill greenhouse gas (GHG) emissions is required, as the actual level to which waste degrades anaerobically and aerobically beneath covers has not been differentiated. This paper presents a methodology to distinguish between the rate of anaerobic digestion (r AD ), composting (r COM ) and CH 4 oxidation (r OX ) in a landfill environment, by means of a system of mass balances developed for molecular species (CH 4 , CO 2 ) and stable carbon isotopes (δ 13 C-CO 2 and δ 13 C-CH 4 ). The technique was applied at two sampling locations on a sloped area of landfill. Four sampling rounds were performed over an 18 month period after a 1.0 m layer of fresh waste and 30-50 cm of silty clay loam had been placed over the area. Static chambers were used to measure the flux of the molecular and isotope species at the surface and soil gas probes were used to collect gas samples at depths of approximately 0.5, 1.0 and 1.5 m. Mass balances were based on the surface flux and the concentration of the molecular and isotopic species at the deepest sampling depth. The sensitivity of calculated rates was considered by randomly varying stoichiometric and isotopic parameters by ±5% to generate at least 500 calculations of r OX , r AD and r COM for each location in each sampling round. The resulting average value of r AD and r COM indicated anaerobic digestion and composting were equally dominant at both locations. Average values of r COM : ranged from 9.8 to 44.5 g CO 2 m -2  d -1 over the four sampling rounds, declining monotonically at one site and rising then falling at the other. Average values of r AD: ranged from 10.6 to 45.3 g CO 2 m -2  d -1 . Although the highest average r AD value occurred in the initial sampling round, all subsequent r AD values fell between 10 and 20 g CO 2 m -2  d -1 . r OX had the smallest activity contribution at both sites, with averages ranging from 1.6 to 8.6 g CO 2 m -2  d -1 . This study has demonstrated that for an interim cover, composting and anaerobic digestion of shallow landfill waste can occur simultaneously. Copyright © 2018 Elsevier Ltd. All rights reserved.

Comparison of variants of carbol-fuchsin solution in Ziehl-Neelsen for detection of acid-fast bacilli.

PubMed

Selvakumar, N; Sekar, M Gomathi; Rahman, F; Syamsunder, A; Duraipandian, M; Wares, F; Narayanan, P R

2005-02-01

To evaluate Ziehl-Neelsen (ZN) staining using variants of carbol-fuchsin solution, duplicate smears from 416 samples were stained with ZN, one set with 1% basic fuchsin and the other 0.3%. Another set of duplicate smears from 398 samples were stained with ZN, one with 1% basic fuchsin and the other 0.1%. The coded smears were read and discrepancies resolved. All samples underwent mycobacterial culture. The sensitivity of ZN using 0.3% (65%) and 1% basic fuchsin (62%) was comparable, while it was reduced using 0.1% (74%) compared to 1% basic fuchsin (83%). Reducing the concentration of basic fuchsin below 0.3% in ZN staining was found to significantly reduce its sensitivity.

IMPACT OF CRITICAL ANION SOIL SOLUTION CONCENTRATION ON ALUMINUM ACTIVITY IN ALPINE TUNDRA SOIL Andrew Evans, Jr.1 , Michael B. Jacobs2, and Jason R. Janke1, (1) Metropolitan State University of Denver, Dept. of Earth and Atmospheric Sciences, (2) Dept. of Chemistry, Denver, CO, United States.

NASA Astrophysics Data System (ADS)

Evans, A.

2015-12-01

Soil solution anionic composition can impact both plant and microbial activity in alpine tundra soils by altering biochemical cycling within the soil, either through base cation leaching, or shifts in aluminum controlling solid phases. Although anions play a critical role in the aqueous speciation of metals, relatively few high altitude field studies have examined their impact on aluminum controlling solid phases and aluminum speciation in soil water. For this study, thirty sampling sites were selected on Trail Ridge Road in Rocky Mountain National Park, Estes Park, CO, and sampled during July, the middle of the growing season. Sampling elevations ranged from approximately 3560 - 3710 m. Soil samples were collected to a depth of 15.24 cm, and the anions were extracted using a 2:1 D.I. water to soil ratio. Filtered extracts were analyzed using IC and ICP-MS. Soil solution NO3- concentrations were significantly higher for sampling locations east of Iceberg Pass (EIBP) (mean = 86.94 ± 119.8 mg/L) compared to locations west of Iceberg Pass (WIBP) (mean 1.481 ± 2.444 mg/L). Both F- and PO43- soil solution concentrations, 0.533 and 0.440 mg/L, respectively, were substantially lower, for sampling sites located EIBP, while locations WIBP averaged 0.773 and 0.829 mg/L respectively, for F- and PO43-. Sulfate concentration averaged 3.869 ± 3.059 mg/L for locations EIBP, and 3.891 ± 3.1970 for locations WIBP. Geochemical modeling of Al3+ in the soil solution indicated that a suite of aluminum hydroxyl sulfate minerals controlled Al3+ activity in the alpine tundra soil, with shifts between controlling solid phases occurring in the presence of elevated F- concentrations.

Particulate carbon and nitrogen and suspended particulate matter in the Sacramento River at Rio Vista, California, January 3 - May 26, 1983 and October 31, 1983 - November 29, 1984

USGS Publications Warehouse

Hager, Stephen W.

1994-01-01

Particulate matter was collected at Rio Vista, California, in two study periods; the first, from January 3 to May 26, 1983; the second from October 31, 1983 to November 29, 1984. Concentrations of suspended particulate matter were measured gravimetrically on silver membrane filters. The pooled standard deviation on replicated samples was 1.4 mg/L, giving a coefficient of variation of 5.7 percent. Concentrations of particulate carbon and nitrogen were measured during a Perkin-Elmer model 240C elemental analyzer to combust material collected on glass fiber filters. Refrigeration of samples prior to filtration was shown to be a likely influence on precision of duplicate analyses. Median deviations between duplicates for carbon were 5.4 percent during the first study period and 8.9 percent during the second. For nitrogen, median deviations were 4.9 percent and 7.2 percent, respectively. This report presents the data for concentrations of suspended particulate material, the duplicate analyses for particulate carbon and nitrogen, and the volumes of sample filtered for the particulate carbon and nitrogen analyses for both studies. Not all samples collected during the second study have been analyzed for particulate carbon and nitrogen.

Familial 4.3 Mb duplication of 21q22 sheds new light on the Down syndrome critical region

PubMed Central

Ronan, Anne; Fagan, Kerry; Christie, Louise; Conroy, Jeffrey; Nowak, Norma J; Turner, Gillian

2007-01-01

A 4.3 Mb duplication of chromosome 21 bands q22.13–q22.2 was diagnosed by interphase fluorescent in‐situ hybridisation (FISH) in a 31‐week gestational age baby with cystic hygroma and hydrops; the duplication was later found in the mother and in her 8‐year‐old daughter by the same method and confirmed by array comparative genomic hybridisation (aCGH). All had the facial gestalt of Down syndrome (DS). This is the smallest accurately defined duplication of chromosome 21 reported with a DS phenotype. The duplication encompasses the gene DYRK1 but not DSCR1 or DSCAM, all of which have previously been implicated in the causation of DS. Previous karyotype analysis and telomere screening of the mother, and karyotype analysis and metaphase FISH of a chorionic villus sample, had all failed to reveal the duplication. The findings in this family add to the identification and delineation of a “critical region” for the DS phenotype on chromosome 21. Cryptic chromosomal abnormalities can be missed on a routine karyotype for investigation of abnormal prenatal ultrasound findings, lending support to the use of aCGH analysis in this setting. PMID:17237124

Divergent evolution of part of the involucrin gene in the hominoids: Unique intragenic duplications in the gorilla and human

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

Teumer, J.; Green, H.

1989-02-01

The gene for involucrin, an epidermal protein, has been remodeled in the higher primates. Most of the coding region of the human gene consists of a modern segment of repeats derived from a 10-codon sequence present in the ancestral segment of the gene. The modern segment can be divided into early, middle, and late regions. The authors report here the nucleotide sequence of three alleles of the gorilla involucrin gene. Each possesses a modern segment homologous to that of the human and consisting of 10-codon repeats. The early and middle regions are similar to the corresponding regions of the humanmore » allele and are nearly identical among the different gorilla alleles. The late region consists of recent duplications whose pattern is unique in each of the gorilla alleles and in the human allele. The early region is located in what is now the 3{prime} third of the modern segment, and the late, polymorphic region is located in what is now the 5{prime} third. Therefore, as the modern segment expanded during evolution, its 3{prime} end became stabilized, and continuing duplications became confined to its 5{prime} end. The expansion of the involucrin coding region, which began long before the separation of the gorilla and human, has continued in both species after their separation.« less

Human exposure to polycyclic aromatic hydrocarbons (PAHs) using data from a duplicate diet study in Catalonia, Spain.

PubMed

Martorell, Isabel; Nieto, Antonio; Nadal, Martí; Perelló, Gemma; Marcé, Rosa M; Domingo, José L

2012-11-01

In this study, the dietary intake of 16 polycyclic aromatic hydrocarbons (PAHs) by the population of Tarragona County (Catalonia, Spain) was assessed using the duplicate diet approach. Duplicate diet samples, prepared as per consumption, were collected during September 2010 in various restaurants offering a variety of daily menus (breakfast, lunch, and dinner). For analysis of PAHs, a total of 90 composite samples were prepared. Analytical procedure of PAHs was performed by means of gas chromatography/mass spectrometry. Intake calculations were made for the standard male adult population. The highest intakes corresponded to acenaphthylene (12.7 μg/day), acenaphthene (12.4 μg/day), and fluorene (11.9 μg/day), while the lowest intake corresponded to dibenz[a,h]anthracene (0.12 μg/day), being also comparatively low those of pyrene, benzo[b]fluoranthene+benzo[j]fluoranthene, benzo[a]pyrene and benzo[ghi]perylene (0.13 μg/day in all cases). The results were compared with data from previous total diet studies (TDS) recently performed in the same geographical area. In the present study, the estimated mean dietary intake for a standard male adult living in Catalonia was 59.2 μg/day, a value notably higher than that found in our recent TDS (6.72 μg/day). However, it is essential to remark that important methodological differences exist between both surveys, reflecting that calculation methods should be similar when the purpose is to compare results from different surveys. In general terms, we conclude that for PAHs, duplicate diet studies may be a good alternative to total diet studies, especially when there are important economical limitations to perform a suitable TDS. The costs associated to the former may be notably lower, as they do not require such an extensive number of samples for chemical analysis. Moreover, a duplicate diet approach may even be more realistic, as cooked foodstuffs are used for dietary exposure assessment. Copyright © 2012 Elsevier Ltd. All rights reserved.

Analysis of dietary intake of selected metals in the NHEXAS-Maryland investigation.

PubMed Central

Ryan, P B; Scanlon, K A; MacIntosh, D L

2001-01-01

As part of a large pilot investigation of multimedia exposure to several classes of environmental contaminants, the National Human Exposure Assessment Survey (NHEXAS)-Maryland study, we collected 388 semiquantitative food checklists and duplicate diet solid food samples, analyzed for arsenic, cadmium, chromium, and lead concentrations, from 80 individuals in Maryland in 1995-1996 in a repeated measures design. Here we explore several methods to infer foods most strongly associated with concentrations of these metals observed in the duplicate diet in our data set. We employed two techniques in which logarithmically transformed metal concentrations in the duplicate diet were regressed on individual food item consumption using algorithms designed to identify the foods most associated with the observed duplicate diet concentrations. We also employed an alternative strategy in which foods to be used as independent variables in regression were selected using data collected in national food consumption and residue surveys, with regression procedures proceeding with the selected foods in a similar manner. The concordance of foods selected as major predictors among these three techniques is noteworthy and is discussed. Finally, the Dietary Exposure Potential Model (DEPM) was used with the Dietary Checklist data to predict duplicate diet concentrations within our sample. A comparison between the predicted values and those observed gave R(2) values of 0.180, 0.206, and 0.076 for As, Cd, and Pb, respectively (p < 0.0001 in all cases). We discuss the significance of these observations and the implications for dietary-exposure-based risk analysis and dietary intake epidemiology. PMID:11266320

[Analysis of genomic copy number variations in two unrelated neonates with 8p deletion and duplication associated with congenital heart disease].

PubMed

Mei, Mei; Yang, Lin; Zhan, Guodong; Wang, Huijun; Ma, Duan; Zhou, Wenhao; Huang, Guoying

2014-06-01

To screen for genomic copy number variations (CNVs) in two unrelated neonates with multiple congenital abnormalities using Affymetrix SNP chip and try to find the critical region associated with congenital heart disease. Two neonates were tested for genomic copy number variations by using Cytogenetic SNP chip.Rare CNVs with potential clinical significance were selected of which deletion segments' size was larger than 50 kb and duplication segments' size was larger than 150 kb based on the analysis of ChAs software, without false positive CNVs and segments of normal population. The identified CNVs were compared with those of the cases in DECIPHER and ISCA databases. Eleven rare CNVs with size from 546.6-27 892 kb were identified in the 2 neonates. The deletion region and size of case 1 were 8p23.3-p23.1 (387 912-11 506 771 bp) and 11.1 Mb respectively, the duplication region and size of case 1 were 8p23.1-p11.1 (11 508 387-43 321 279 bp) and 31.8 Mb respectively. The deletion region and size of case 2 were 8p23.3-p23.1 (46 385-7 809 878 bp) and 7.8 Mb respectively, the duplication region and size of case 2 were 8p23.1-p11.21 (12 260 914-40 917 092 bp) and 28.7 Mb respectively. The comparison with Decipher and ISCA databases supported previous viewpoint that 8p23.1 had been associated with congenital heart disease and the region between 7 809 878-11 506 771 bp may play a role in the severe cardiac defects associated with 8p23.1 deletions. Case 1 had serious cardiac abnormalities whose GATA4 was located in the duplication segment and the copy number increased while SOX7 was located in the deletion segment and the copy number decreased. The region between 7 809 878-11 506 771 bp in 8p23.1 is associated with heart defects and copy number variants of SOX7 and GATA4 may result in congenital heart disease.

Duplication and expression of CYC2-like genes in the origin and maintenance of corolla zygomorphy in Lamiales.

PubMed

Zhong, Jinshun; Kellogg, Elizabeth A

2015-01-01

Duplication, retention, and expression of CYCLOIDEA2 (CYC2)-like genes are thought to affect evolution of corolla symmetry. However, exactly what and how changes in CYC2-like genes correlate with the origin of corolla zygomorphy are poorly understood. We inferred and calibrated a densely sampled phylogeny of CYC2-like genes across the Lamiales and examined their expression in early diverging (EDL) and higher core clades (HCL). CYC2-like genes duplicated extensively in Lamiales, at least six times in core Lamiales (CL) around the Cretaceous-Paleogene (K-Pg) boundary, and seven more in EDL relatively more recently. Nested duplications and losses of CYC2-like paralogs are pervasive but may not correlate with transitions in corolla symmetry. We found evidence for dN/dS (ω) variation following gene duplications. CYC2-like paralogs in HCL show differential expression with higher expression in adaxial petals. Asymmetric expression but not recurrent duplication of CYC2-like genes correlates with the origin of corolla zygomorphy. Changes in both cis-regulatory and coding domains of CYC2-like genes are probably crucial for the evolution of corolla zygomorphy. Multiple selection regimes appear likely to play important roles in gene retention. The parallel duplications of CYC2-like genes are after the initial diversification of bumble bees and Euglossine bees. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

Estimation of Variance in the Case of Complex Samples.

ERIC Educational Resources Information Center

Groenewald, A. C.; Stoker, D. J.

In a complex sampling scheme it is desirable to select the primary sampling units (PSUs) without replacement to prevent duplications in the sample. Since the estimation of the sampling variances is more complicated when the PSUs are selected without replacement, L. Kish (1965) recommends that the variance be calculated using the formulas…

Regulatory divergence of homeologous Atlantic salmon elovl5 genes following the salmonid-specific whole-genome duplication.

PubMed

Carmona-Antoñanzas, Greta; Zheng, Xiaozhong; Tocher, Douglas R; Leaver, Michael J

2016-10-10

Fatty acyl elongase 5 (elovl5) is a critical enzyme in the vertebrate biosynthetic pathway which produces the physiologically essential long-chain polyunsaturated fatty acids (LC-PUFA), docosahexenoic acid (DHA), and eicosapentenoic acid (EPA) from 18 carbon fatty acids precursors. In contrast to most other vertebrates, Atlantic salmon possess two copies of elovl5 (elovl5a and elovl5b) as a result of a whole-genome duplication (WGD) which occurred at the base of the salmonid lineage. WGDs have had a major influence on vertebrate evolution, providing extra genetic material, enabling neofunctionalization to accelerate adaptation and speciation. However, little is known about the mechanisms by which such duplicated homeologous genes diverge. Here we show that homeologous Atlantic salmon elovl5a and elovl5b genes have been asymmetrically colonised by transposon-like elements. Identical locations and identities of insertions are also present in the rainbow trout duplicate elovl5 genes, but not in the nearest extant representative preduplicated teleost, the northern pike. Both elovl5 salmon duplicates possessed conserved regulatory elements that promoted Srebp1- and Srebp2-dependent transcription, and differences in the magnitude of Srebp response between promoters could be attributed to a tandem duplication of SRE and NF-Y cofactor binding sites in elovl5b. Furthermore, an insertion in the promoter region of elovl5a confers responsiveness to Lxr/Rxr transcriptional activation. Our results indicate that most, but not all, transposon mobilisation into elovl5 genes occurred after the split from the common ancestor of pike and salmon, but before more recent salmonid speciations, and that divergence of elovl5 regulatory regions have enabled neofuntionalization by promoting differential expression of these homeologous genes. Copyright © 2016 Elsevier B.V. All rights reserved.

Paracentric inversion of chromosome 2 associated with cryptic duplication of 2q14 and deletion of 2q37 in a patient with autism.

PubMed

Devillard, Françoise; Guinchat, Vincent; Moreno-De-Luca, Daniel; Tabet, Anne-Claude; Gruchy, Nicolas; Guillem, Pascale; Nguyen Morel, Marie-Ange; Leporrier, Nathalie; Leboyer, Marion; Jouk, Pierre-Simon; Lespinasse, James; Betancur, Catalina

2010-09-01

We describe a patient with autism and a paracentric inversion of chromosome 2q14.2q37.3, with a concurrent duplication of the proximal breakpoint at 2q14.1q14.2 and a deletion of the distal breakpoint at 2q37.3. The abnormality was derived from his mother with a balanced paracentric inversion. The inversion in the child appeared to be cytogenetically balanced but subtelomere FISH revealed a cryptic deletion at the 2q37.3 breakpoint. High-resolution single nucleotide polymorphism array confirmed the presence of a 3.5 Mb deletion that extended to the telomere, and showed a 4.2 Mb duplication at 2q14.1q14.2. FISH studies using a 2q14.2 probe showed that the duplicated segment was located at the telomeric end of chromosome 2q. This recombinant probably resulted from breakage of a dicentric chromosome. The child had autism, mental retardation, speech and language delay, hyperactivity, growth retardation with growth hormone deficiency, insulin-dependent diabetes, and mild facial dysmorphism. Most of these features have been previously described in individuals with simple terminal deletion of 2q37. Pure duplications of the proximal chromosome 2q are rare and no specific syndrome has been defined yet, so the contribution of the 2q14.1q14.2 duplication to the phenotype of the patient is unknown. These findings underscore the need to explore apparently balanced chromosomal rearrangements inherited from a phenotypically normal parent in subjects with autism and/or developmental delay. In addition, they provide further evidence indicating that chromosome 2q terminal deletions are among the most frequently reported cytogenetic abnormalities in individuals with autism.

Local geometric and electronic structures and origin of magnetism in Co-doped BaTiO3 multiferroics

NASA Astrophysics Data System (ADS)

Phan, The-Long; Thang, P. D.; Ho, T. A.; Manh, T. V.; Thanh, Tran Dang; Lam, V. D.; Dang, N. T.; Yu, S. C.

2015-05-01

We have prepared polycrystalline samples BaTi1-xCoxO3 (x = 0-0.1) by solid-state reaction. X-ray diffraction and Raman-scattering studies reveal the phase separation in crystal structure as changing Co-doping content (x). The samples with x = 0-0.01 are single phase in a tetragonal structure. At higher doping contents (x > 0.01), there is the formation and development of a secondary hexagonal phase. Magnetization measurements at room temperature indicate a coexistence of paramagnetic and weak-ferromagnetic behaviors in BaTi1-xCoxO3 samples with x > 0, while pure BaTiO3 is diamagnetic. Both these properties increase with increasing x. Analyses of X-ray absorption spectra recorded from BaTi1-xCoxO3 for the Co and Ti K-edges indicate the presence of Co2+ and Co3+ ions. They locate in the Ti4+ site of the tetragonal and hexagonal BaTiO3 structures. Particularly, there is a shift of oxidation state from Co2+ to Co3+ when Co-doping content increases. We believe that the paramagnetic nature in BaTi1-xCoxO3 samples is due to isolated Co2+ and Co3+ centers. The addition of Co3+ ions enhances the paramagnetic behavior. Meanwhile, the origin of ferromagnetism is due to lattice defects, which is less influenced by the changes caused by the variation in concentration of Co2+ and Co3+ ions.

Congenital hyperinsulinism and Poland syndrome in association with 10p13–14 duplication

PubMed Central

Giri, Dinesh; Patil, Prashant; Hart, Rachel; Didi, Mohammed

2017-01-01

Summary Poland syndrome (PS) is a rare congenital condition, affecting 1 in 30 000 live births worldwide, characterised by a unilateral absence of the sternal head of the pectoralis major and ipsilateral symbrachydactyly occasionally associated with abnormalities of musculoskeletal structures. A baby girl, born at 40 weeks’ gestation with birth weight of 3.33 kg (−0.55 SDS) had typical phenotypical features of PS. She had recurrent hypoglycaemic episodes early in life requiring high concentration of glucose and glucagon infusion. The diagnosis of congenital hyperinsulinism (CHI) was biochemically confirmed by inappropriately high plasma concentrations of insulin and C-peptide and low plasma free fatty acids and β-hydroxyl butyrate concentrations during hypoglycaemia. Sequencing of ABCC8, KCNJ11 and HNF4A did not show any pathogenic mutation. Microarray analysis revealed a novel duplication in the short arm of chromosome 10 at 10p13–14 region. This is the first reported case of CHI in association with PS and 10p duplication. We hypothesise that the HK1 located on the chromosome 10 encoding hexokinase-1 is possibly linked to the pathophysiology of CHI. Learning points: Congenital hyperinsulinism (CHI) is known to be associated with various syndromes. This is the first reported association of CHI and Poland syndrome (PS) with duplication in 10p13–14. A potential underlying genetic link between 10p13–14 duplication, PS and CHI is a possibility. PMID:28458900

Comprehensive review of the duplication 3q syndrome and report of a patient with Currarino syndrome and de novo duplication 3q26.32-q27.2.

PubMed

Dworschak, G C; Crétolle, C; Hilger, A; Engels, H; Korsch, E; Reutter, H; Ludwig, M

2017-05-01

Partial duplications of the long arm of chromosome 3, dup(3q), are a rare but well-described condition, sharing features of Cornelia de Lange syndrome. Around two thirds of cases are derived from unbalanced translocations, whereas pure dup(3q) have rarely been reported. Here, we provide an extensive review of the literature on dup(3q). This search revealed several patients with caudal malformations and anomalies, suggesting that caudal malformations or anomalies represent an inherent phenotypic feature of dup(3q). In this context, we report a patient with a pure de novo duplication 3q26.32-q27.2. The patient had the clinical diagnosis of Currarino syndrome (CS) (characterized by the triad of sacral anomalies, anorectal malformations and a presacral mass) and additional features, frequently detected in patients with a dup(3q). Mutations within the MNX1 gene were found to be causative in CS but no MNX1 mutation could be detected in our patient. Our comprehensive search for candidate genes located in the critical region of the duplication 3q syndrome, 3q26.3-q27, revealed a so far neglected phenotypic overlap of dup(3q) and the Pierpont syndrome, associated with a mutation of the TBL1XR1 gene on 3q26.32. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Substrate quality and nutrient availability influence CO2 production from tropical peat decomposition

NASA Astrophysics Data System (ADS)

Swails, E.; Jaye, D.; Verchot, L. V.; Hergoualc'h, K.; Wahyuni, N. S.; Borchard, N.; Lawrence, D.

2015-12-01

In Indonesia, peatlands are a major and growing source of greenhouse gas emissions due to increasing pressure from oil palm and pulp wood plantations. We are using a combination of field measures, laboratory experiments, and remote sensing to investigate relationships among land use, climatic factors and biogeochemical controls, and their influence on trace gas fluxes from tropical peat soils. Analysis of soils collected from peat sites on two major islands indicated substantial variation in peat substrate quality and nutrient content among land uses and geographic location. We conducted laboratory incubations to test the influence of substrate quality and nutrient availability on CO2 production from peat decomposition. Differences in peat characteristics attributable to land use change were tested by comparison of forest and oil palm peat samples collected from the same peat dome in Kalimantan. Regional differences in peat characteristics were tested by comparison of samples from Sumatra with samples from Kalimantan. We conducted additional experiments to test the influence of N and P availability and labile carbon on CO2 production. Under moisture conditions typical of oil palm plantations, CO2 production was higher from peat forest samples than from oil palm samples. CO2 production from Sumatra and Kalimantan oil palm samples was not different, despite apparent differences in nutrient content of these soils. N and P treatments representative of fertilizer application rates raised CO2 production from forest samples but not oil palm samples. Labile carbon treatments raised CO2 production in all samples. Our results suggest that decomposition of peat forest soils is nutrient limited, while substrate quality controls decomposition of oil palm soils post-conversion. Though fertilizer application could accelerate peat decomposition initially, fertilizer application may not influence long-term CO2 emissions from oil palm on peat.

Feasibility and Outcomes of Multiplex Ligation-Dependent Probe Amplification on Buccal Smears as a Screening Method for Microdeletions and Duplications among 300 Adults with an Intellectual Disability of Unknown Aetiology

ERIC Educational Resources Information Center

Peppink, D.; Douma-Kloppenburg, D. D.; de Rooij-Askes, E. S. P.; van Zoest, I. M.; Evenhuis, H. M.; Gille, J. J. P.; van Hagen, J. M.

2008-01-01

Background: Determining the aetiology of intellectual disability (ID) enables anticipation of specific comorbidity and can thus be beneficial. Blood sampling, however, is considered stressful for people with ID. Our aim was to evaluate the feasibility of a non-invasive screening technique of nine microdeletions/duplications among adults with ID of…

Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins

PubMed Central

2013-01-01

Background The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. Results By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all extant angiosperms. We predict single WGDs in the Manihot esculenta and Nicotiana benthamiana lineages, two WGDs for Linum usitatissimum and Phoenix dactylifera, and a triplication or two WGDs for Gossypium raimondii. Our data show another myosin duplication in the ancestor of the angiosperms that could be either the result of a single gene duplication or a remnant of a WGD. Conclusions We have shown that the myosin inventories in angiosperms retain evidence of numerous WGDs that happened throughout plant evolution. In contrast to other protein families, many myosins are still present in extant species. They are closely related and have similar domain architectures, and their phylogenetic grouping follows the genome duplications. Because of its broad taxonomic sampling the dataset provides the basis for reliable future identification of further whole genome duplications. PMID:24053117

Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins.

PubMed

Mühlhausen, Stefanie; Kollmar, Martin

2013-09-22

The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions. By analysing 67 completely sequenced plant genomes 775 myosins were identified and manually assembled. Phylogenetic trees of the myosin motor domains revealed orthologous and paralogous relationships and were consistent with recent species trees. Based on the myosin inventories and the phylogenetic trees, we have identified duplications of the entire myosin motor protein family at timings consistent with 23 WGDs, that had been reported before. We also predict 6 WGDs based on further protein family duplications. Notably, the myosin data support the two recently reported WGDs in the common ancestor of all extant angiosperms. We predict single WGDs in the Manihot esculenta and Nicotiana benthamiana lineages, two WGDs for Linum usitatissimum and Phoenix dactylifera, and a triplication or two WGDs for Gossypium raimondii. Our data show another myosin duplication in the ancestor of the angiosperms that could be either the result of a single gene duplication or a remnant of a WGD. We have shown that the myosin inventories in angiosperms retain evidence of numerous WGDs that happened throughout plant evolution. In contrast to other protein families, many myosins are still present in extant species. They are closely related and have similar domain architectures, and their phylogenetic grouping follows the genome duplications. Because of its broad taxonomic sampling the dataset provides the basis for reliable future identification of further whole genome duplications.

Results from twelve years of continuous monitoring of the soil CO2 flux at the Ketzin CO2 storage pilot site, Germany

NASA Astrophysics Data System (ADS)

Szizybalski, Alexandra; Zimmer, Martin; Pilz, Peter; Liebscher, Axel

2017-04-01

Under the coordination of the GFZ German Research Centre for Geosciences the complete life-cycle of a geological storage site for CO2 has been investigated and studied in detail over the past 12 years at Ketzin near Berlin, Germany. The test site is located at the southern flank of an anticlinal structure. Beginning with an exploration phase in 2004, drilling of the first three wells took place in 2007. From June 2008 to August 2013 about 67 kt of CO2 were injected into Upper Triassic sandstones at a depth of 630 to 650 m overlain by more than 165 m of shaley cap rocks. A comprehensive operational and scientific monitoring program forms the central part of the Ketzin project targeting at the reservoir itself, its overburden or above-zone and the surface. The surface monitoring is done by continuous soil CO2 flux measurements. These already started in 2005, more than three years prior to the injection phase using a survey chamber from LI-COR Inc. Twenty sampling locations were selected in the area of the anticline covering about 3 x 3 km. In order to obtain information on seasonal trends, measurements are performed at least once a month. The data set obtained prior to the injection serves as a basis for comparison with all further measurements during the injection and storage operations [Zimmer et al., 2010]. To refine the monitoring network, eight automatic, permanent soil CO2 flux stations were additionally installed in 2011 in the direct vicinity of the boreholes. Using this system, the CO2 soil flux is measured on an hourly basis. Over the whole monitoring time, soil temperature and moisture are recorded simultaneously and soil samples down to 70 cm depth were studied for their structure, carbon and nitrogen content. ver the whole monitoring time. Both, diurnal and seasonal flux variations can be detected and hence, provide a basis for interpretation of the measured data. Detailed analysis of the long-term monitoring at each station clearly reveals the influence of the soil composition. As most of the sampling positions are located next to agricultural roads and fields, the use of chemicals and harvesting may have an influence on the soil structure and the biology. Soil temperature, rain events and dry periods additionally affect the CO2 flux. Moreover, the microbial controlled increased CO2 production in early fall is also observed to depend on the actual location. Annual mean values of CO2 fluxes range from 10 to 82 t ha-1 a-1. As the CO2 flux measurements significantly reflect the specific site conditions, which can vary locally and over time, long-term trends must be carefully interpreted. Hence, complementary measurements of the soil gas composition were performed at selected locations. Zimmer, M., Pilz, P., Erzinger, J. (2011): Long-term surface carbon dioxide flux monitoring at the Ketzin carbon dioxide storage test site. Environmental Geosciences, 18, 119-130, doi:10.1306/eg.11181010017.

An Insertional Translocation in Neurospora That Generates Duplications Heterozygous for Mating Type

PubMed Central

Perkins, David D.

1972-01-01

In strain T(I→II)39311 a long interstitial segment is transposed from IL to IIR, where it is inserted in reversed order with respect to the centromere. In crosses of T x T essentially all asci have eight viable, black spores, and all progeny are phenotypically normal. When T(I→II)39311 is crossed by Normal sequence (N), the expected duplication class is viable while the corresponding deficiency is lethal; 44% of the asci have 8 Black (viable) spores and 0 White (inviable) spores, 41% have 4 Black: 4 White, and 10% have 6 Black: 2 White. These are the ascus types expected from normal centromere disjunction without crossing over (8B:0W and 4B:4W equally probable), and with crossing over between centromere and break point (6B:2W). On germination, 8B:0W asci give rise to only parental types—4 T and 4 N; 4B:4W asci usually give four duplication (Dup) progeny; and 6B:2W asci usually give 2 T, 2 N, 2 Dup. Thus one third of all viable, black ascospores contain duplications.—Recessive markers in the donor chromosome which contributes the translocated segment can be mapped by duplication coverage. Ratios of 2 Dominant: 1 Recessive vs. 1 Dominant: 2 Recessive distinguish location in or outside the transposed segment. Eleven loci including mating type have been shown to lie within the segment, and markers at four loci have been transferred into the segment by meiotic recombination. The frequency of marker transfer indicates that the inserted segment usually pairs with its homologue. Ascus types that would result from single exchanges within the insertion are infrequent, as expected if asci containing dicentric bridges usually do not survive.—Duplication ascospores germinate to produce distinctive inhibited colonies. Later these "escape" to grow like wild type, and genes that were initially heterozygous in the duplication segregate when escape occurs. As with duplications from pericentric inversion In(IL→IR)H4250 (Newmeyer and Taylor 1967), the initial inhibition is attributed to mating-type heterozygosity, and escape to a somatic event that makes mating type homoor hemizygous.—Twenty additional duplication-generating Neurospora rearrangements are listed and described briefly in an Appendix. PMID:17248574

Malate decarboxylases: evolution and roles of NAD(P)-ME isoforms in species performing C(4) and C(3) photosynthesis.

PubMed

Maier, Alexandra; Zell, Martina B; Maurino, Veronica G

2011-05-01

In the C(4) pathway of photosynthesis two types of malate decarboxylases release CO(2) in bundle sheath cells, NADP- and NAD-dependent malic enzyme (NADP-ME and NAD-ME), located in the chloroplasts and the mitochondria of these cells, respectively. The C(4) decarboxylases involved in C(4) photosynthesis did not evolve de novo; they were recruited from existing housekeeping isoforms. NADP-ME housekeeping isoforms would function in the control of malate levels during hypoxia, pathogen defence responses, and microspore separation, while NAD-ME participates in the respiration of malate in the tricarboxylic acid cycle. Recently, the existence of three enzymatic NAD-ME entities in Arabidopsis, occurring by alternative association of two subunits, was described as a novel mechanism to regulate NAD-ME activity under changing metabolic environments. The C(4) NADP-ME is thought to have evolved from a C(3) chloroplastic ancestor, which in turn would have evolved from an ancient cytosolic enzyme. In this way, the C(4) NADP-ME would have emerged through gene duplication, acquisition of a new promoter, and neo-functionalization. In contrast, there would exist a unique NAD-ME in C(4) plants, which would have been adapted to perform a dual function through changes in the kinetic and regulatory properties of the C(3) ancestors. In addition to this, for the evolution of C(4) NAD-ME, insertion of promoters or enhancers into the single-copy genes of the C(3) ancestors would have changed the expression without gene duplication.

Quantification of sequence exchange events between PMS2 and PMS2CL provides a basis for improved mutation scanning of Lynch syndrome patients.

PubMed

van der Klift, Heleen M; Tops, Carli M J; Bik, Elsa C; Boogaard, Merel W; Borgstein, Anne-Marijke; Hansson, Kerstin B M; Ausems, Margreet G E M; Gomez Garcia, Encarna; Green, Andrew; Hes, Frederik J; Izatt, Louise; van Hest, Liselotte P; Alonso, Angel M; Vriends, Annette H J T; Wagner, Anja; van Zelst-Stams, Wendy A G; Vasen, Hans F A; Morreau, Hans; Devilee, Peter; Wijnen, Juul T

2010-05-01

Heterozygous mutations in PMS2 are involved in Lynch syndrome, whereas biallelic mutations are found in Constitutional mismatch repair-deficiency syndrome patients. Mutation detection is complicated by the occurrence of sequence exchange events between the duplicated regions of PMS2 and PMS2CL. We investigated the frequency of such events with a nonspecific polymerase chain reaction (PCR) strategy, co-amplifying both PMS2 and PMS2CL sequences. This allowed us to score ratios between gene and pseudogene-specific nucleotides at 29 PSV sites from exon 11 to the end of the gene. We found sequence transfer at all investigated PSVs from intron 12 to the 3' end of the gene in 4 to 52% of DNA samples. Overall, sequence exchange between PMS2 and PMS2CL was observed in 69% (83/120) of individuals. We demonstrate that mutation scanning with PMS2-specific PCR primers and MLPA probes, designed on PSVs, in the 3' duplicated region is unreliable, and present an RNA-based mutation detection strategy to improve reliability. Using this strategy, we found 19 different putative pathogenic PMS2 mutations. Four of these (21%) are lying in the region with frequent sequence transfer and are missed or called incorrectly as homozygous with several PSV-based mutation detection methods. (c) 2010 Wiley-Liss, Inc.

Comprehensive analysis of TCP transcription factors and their expression during cotton (Gossypium arboreum) fiber early development

PubMed Central

Ma, Jun; Liu, Fang; Wang, Qinglian; Wang, Kunbo; Jones, Don C.; Zhang, Baohong

2016-01-01

TCP proteins are plant-specific transcription factors implicated to perform a variety of physiological functions during plant growth and development. In the current study, we performed for the first time the comprehensive analysis of TCP gene family in a diploid cotton species, Gossypium arboreum, including phylogenetic analysis, chromosome location, gene duplication status, gene structure and conserved motif analysis, as well as expression profiles in fiber at different developmental stages. Our results showed that G. arboreum contains 36 TCP genes, distributing across all of the thirteen chromosomes. GaTCPs within the same subclade of the phylogenetic tree shared similar exon/intron organization and motif composition. In addition, both segmental duplication and whole-genome duplication contributed significantly to the expansion of GaTCPs. Many these TCP transcription factor genes are specifically expressed in cotton fiber during different developmental stages, including cotton fiber initiation and early development. This suggests that TCP genes may play important roles in cotton fiber development. PMID:26857372

Region-Based Collision Avoidance Beaconless Geographic Routing Protocol in Wireless Sensor Networks.

PubMed

Lee, JeongCheol; Park, HoSung; Kang, SeokYoon; Kim, Ki-Il

2015-06-05

Due to the lack of dependency on beacon messages for location exchange, the beaconless geographic routing protocol has attracted considerable attention from the research community. However, existing beaconless geographic routing protocols are likely to generate duplicated data packets when multiple winners in the greedy area are selected. Furthermore, these protocols are designed for a uniform sensor field, so they cannot be directly applied to practical irregular sensor fields with partial voids. To prevent the failure of finding a forwarding node and to remove unnecessary duplication, in this paper, we propose a region-based collision avoidance beaconless geographic routing protocol to increase forwarding opportunities for randomly-deployed sensor networks. By employing different contention priorities into the mutually-communicable nodes and the rest of the nodes in the greedy area, every neighbor node in the greedy area can be used for data forwarding without any packet duplication. Moreover, simulation results are given to demonstrate the increased packet delivery ratio and shorten end-to-end delay, rather than well-referred comparative protocols.

Region-Based Collision Avoidance Beaconless Geographic Routing Protocol in Wireless Sensor Networks

PubMed Central

Lee, JeongCheol; Park, HoSung; Kang, SeokYoon; Kim, Ki-Il

2015-01-01

Due to the lack of dependency on beacon messages for location exchange, the beaconless geographic routing protocol has attracted considerable attention from the research community. However, existing beaconless geographic routing protocols are likely to generate duplicated data packets when multiple winners in the greedy area are selected. Furthermore, these protocols are designed for a uniform sensor field, so they cannot be directly applied to practical irregular sensor fields with partial voids. To prevent the failure of finding a forwarding node and to remove unnecessary duplication, in this paper, we propose a region-based collision avoidance beaconless geographic routing protocol to increase forwarding opportunities for randomly-deployed sensor networks. By employing different contention priorities into the mutually-communicable nodes and the rest of the nodes in the greedy area, every neighbor node in the greedy area can be used for data forwarding without any packet duplication. Moreover, simulation results are given to demonstrate the increased packet delivery ratio and shorten end-to-end delay, rather than well-referred comparative protocols. PMID:26057037

Comprehensive analysis of TCP transcription factors and their expression during cotton (Gossypium arboreum) fiber early development.

PubMed

Ma, Jun; Liu, Fang; Wang, Qinglian; Wang, Kunbo; Jones, Don C; Zhang, Baohong

2016-02-09

TCP proteins are plant-specific transcription factors implicated to perform a variety of physiological functions during plant growth and development. In the current study, we performed for the first time the comprehensive analysis of TCP gene family in a diploid cotton species, Gossypium arboreum, including phylogenetic analysis, chromosome location, gene duplication status, gene structure and conserved motif analysis, as well as expression profiles in fiber at different developmental stages. Our results showed that G. arboreum contains 36 TCP genes, distributing across all of the thirteen chromosomes. GaTCPs within the same subclade of the phylogenetic tree shared similar exon/intron organization and motif composition. In addition, both segmental duplication and whole-genome duplication contributed significantly to the expansion of GaTCPs. Many these TCP transcription factor genes are specifically expressed in cotton fiber during different developmental stages, including cotton fiber initiation and early development. This suggests that TCP genes may play important roles in cotton fiber development.

Determination of ash in coals unusually high in calcite and pyrite

USGS Publications Warehouse

Rees, O.W.; Selvig, W.A.

1942-01-01

The preliminary hearth heating method (A and E) gave results within the A. S. T. M. tolerances for all duplicates obtained in the same laboratory. Checks between different laboratories within A. S. T. M. tolerances were obtained for coals containing up to about 3.6 per cent mineral carbon dioxide, but these ashes contained larger amounts of retained sulfur. The determination of ash by the cold furnace method (B and F) gave duplicate results within A. S. T. M. tolerances for all samples in the U. S. Bureau of Mines laboratory and for samples up to about 1.6 per cent mineral carbon dioxide content in the Illinois Geological Survey laboratory. Checks between average values from the two laboratories were within A. S. T. M. tolerances for all samples.

Comparative genomics of ParaHox clusters of teleost fishes: gene cluster breakup and the retention of gene sets following whole genome duplications

PubMed Central

Siegel, Nicol; Hoegg, Simone; Salzburger, Walter; Braasch, Ingo; Meyer, Axel

2007-01-01

Background The evolutionary lineage leading to the teleost fish underwent a whole genome duplication termed FSGD or 3R in addition to two prior genome duplications that took place earlier during vertebrate evolution (termed 1R and 2R). Resulting from the FSGD, additional copies of genes are present in fish, compared to tetrapods whose lineage did not experience the 3R genome duplication. Interestingly, we find that ParaHox genes do not differ in number in extant teleost fishes despite their additional genome duplication from the genomic situation in mammals, but they are distributed over twice as many paralogous regions in fish genomes. Results We determined the DNA sequence of the entire ParaHox C1 paralogon in the East African cichlid fish Astatotilapia burtoni, and compared it to orthologous regions in other vertebrate genomes as well as to the paralogous vertebrate ParaHox D paralogons. Evolutionary relationships among genes from these four chromosomal regions were studied with several phylogenetic algorithms. We provide evidence that the genes of the ParaHox C paralogous cluster are duplicated in teleosts, just as it had been shown previously for the D paralogon genes. Overall, however, synteny and cluster integrity seems to be less conserved in ParaHox gene clusters than in Hox gene clusters. Comparative analyses of non-coding sequences uncovered conserved, possibly co-regulatory elements, which are likely to contain promoter motives of the genes belonging to the ParaHox paralogons. Conclusion There seems to be strong stabilizing selection for gene order as well as gene orientation in the ParaHox C paralogon, since with a few exceptions, only the lengths of the introns and intergenic regions differ between the distantly related species examined. The high degree of evolutionary conservation of this gene cluster's architecture in particular – but possibly clusters of genes more generally – might be linked to the presence of promoter, enhancer or inhibitor motifs that serve to regulate more than just one gene. Therefore, deletions, inversions or relocations of individual genes could destroy the regulation of the clustered genes in this region. The existence of such a regulation network might explain the evolutionary conservation of gene order and orientation over the course of hundreds of millions of years of vertebrate evolution. Another possible explanation for the highly conserved gene order might be the existence of a regulator not located immediately next to its corresponding gene but further away since a relocation or inversion would possibly interrupt this interaction. Different ParaHox clusters were found to have experienced differential gene loss in teleosts. Yet the complete set of these homeobox genes was maintained, albeit distributed over almost twice the number of chromosomes. Selection due to dosage effects and/or stoichiometric disturbance might act more strongly to maintain a modal number of homeobox genes (and possibly transcription factors more generally) per genome, yet permit the accumulation of other (non regulatory) genes associated with these homeobox gene clusters. PMID:17822543

Self-Irradiation Effects on 99Mo Reagents and Products

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

Carson, S.D.; Garcia, M.J.; McDonald, M.J.

1998-10-07

produced in 1996 and shipped to pharmaceutical houses for evaluation of compatibility with oxime solution used to precipitate `?vfo as the oxime complex is both air and light-sensitive, and containing a black precipitate that forms during shipment, presumably as a result of self- irradiation. Addition of sodium hypochlorite to the product solution prior to shipment prevents precipitate formation, indicating the precipitate is a reduced form of `%lo. to remove any precipitate. Duplicate aliquots of the filtered samples were titrated to a phenolphthalein irradiation and afler standing at room temperature for 86.4 hours. Precipitates were washed to a FTIR analysis ofmore » the white precipitate showed it to be alpha benzoin oxime. Since the basic After 86.4 hours, no precipitate had formed in bottles containing sodium hypochlorite. Black precipitate had formed in all bottles that did not contain sodium hypochlorite after 14.4 hours. The precipitate appeared to initially form on the surface of the HDPE sample bottles and Black precipitate was first noticed in sample set 1 after 28.8 hrs' irradiation. No visible sample containing precipitate was kept at room temperature in the original bottle. Precipitate in sample sets 2 and 3. Since no precipitate formed in these bottles, this was equivalent to duplicate samples. Once the precipitate in the 20-mL aliquots that had been set aside had returned to sample sets 1 through 3 and the samples with redissolved precipitate all experienced an average decrease in base strength of 0.013 meq mL-l. Sample 1-C had a decrease of 0.004 meq mL-l and sample 1-D had returned to the initial value of 0.198 meq mL-l. Raman spectra for the black precipitate from samples l-C, 1-D and supplemental sample set 1 Fig. 2. Raman spectra of the black precipitate formed in 9%40 product solutions after 28.8,43.2, 72 and 86.4 hours of `oCo irradiation in Sandia's Gamma Irradiation Facility. increase with time, as seen in the titration of 1-C and 1-D samples. The precipitate does not expect to see precipitate in the glass bottles. The fact that no precipitate is observed when the no precipitate is observed in a glass container is an indication that the rates of molybdenum that precipitate does not form when the solution is in a glass bottle. A hydrogen source other« less

The effect of ionic Co presence on the structural, optical and photocatalytic properties of modified cobalt-titanate nanotubes.

PubMed

Barrocas, B; Silvestre, A J; Rolo, A G; Monteiro, O C

2016-07-21

With the aim of producing materials with enhanced optical and photocatalytic properties, titanate nanotubes (TNTs) modified by cobalt doping (Co-TNT) and by Na(+)→ Co ion-exchange (TNT/Co) were successfully prepared by a hydrothermal method. The influence of the doping level and of the cobalt position in the TNT crystalline structure was studied. Although no perceptible influence of the cobalt ion position on the morphology of the prepared titanate nanotubes was observed, the optical behaviour of the cobalt modified samples is clearly dependent on the cobalt ions either substituting the Ti(4+) ions in the TiO6 octahedra building blocks of the TNT structure (doped samples) or replacing the Na(+) ions between the TiO6 interlayers (ion-exchange samples). The catalytic ability of these materials on pollutant photodegradation was investigated. First, the evaluation of hydroxyl radical formation using the terephthalic acid as a probe was performed. Afterwards, phenol, naphthol yellow S and brilliant green were used as model pollutants. Anticipating real world situations, photocatalytic experiments were performed using solutions combining these pollutants. The results show that the Co modified TNT materials (Co-TNT and TNT/Co) are good catalysts, the photocatalytic performance being dependent on the Co/Ti ratio and on the structural metal location. The Co(1%)-TNT doped sample was the best photocatalyst for all the degradation processes studied.

Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila melanogaster.

PubMed

Cridland, Julie M; Thornton, Kevin R

2010-01-13

Several recent studies have focused on the evolution of recently duplicated genes in Drosophila. Currently, however, little is known about the evolutionary forces acting upon duplications that are segregating in natural populations. We used a high-throughput, paired-end sequencing platform (Illumina) to identify structural variants in a population sample of African D. melanogaster. Polymerase chain reaction and sequencing confirmation of duplications detected by multiple, independent paired-ends showed that paired-end sequencing reliably uncovered the break points of structural rearrangements and allowed us to identify a number of tandem duplications segregating within a natural population. Our confirmation experiments show that rates of confirmation are very high, even at modest coverage. Our results also compare well with previous studies using microarrays (Emerson J, Cardoso-Moreira M, Borevitz JO, Long M. 2008. Natural selection shapes genome wide patterns of copy-number polymorphism in Drosophila melanogaster. Science. 320:1629-1631. and Dopman EB, Hartl DL. 2007. A portrait of copy-number polymorphism in Drosophila melanogaster. Proc Natl Acad Sci U S A. 104:19920-19925.), which both gives us confidence in the results of this study as well as confirms previous microarray results.We were also able to identify whole-gene duplications, such as a novel duplication of Or22a, an olfactory receptor, and identify copy-number differences in genes previously known to be under positive selection, like Cyp6g1, which confers resistance to dichlorodiphenyltrichloroethane. Several "hot spots" of duplications were detected in this study, which indicate that particular regions of the genome may be more prone to generating duplications. Finally, population frequency analysis of confirmed events also showed an excess of rare variants in our population, which indicates that duplications segregating in the population may be deleterious and ultimately destined to be lost from the population.

Fuel from wastewater : harnessing a potential energy source in Canada through the co-location of algae biofuel production to sources of effluent, heat and CO2.

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

Passell, Howard David; Whalen, Jake; Pienkos, Philip P.

2010-12-01

Sandia National Laboratories is collaborating with the National Research Council (NRC) Canada and the National Renewable Energy Laboratory (NREL) to develop a decision-support model that will evaluate the tradeoffs associated with high-latitude algae biofuel production co-located with wastewater, CO2, and waste heat. This project helps Canada meet its goal of diversifying fuel sources with algae-based biofuels. The biofuel production will provide a wide range of benefits including wastewater treatment, CO2 reuse and reduction of demand for fossil-based fuels. The higher energy density in algae-based fuels gives them an advantage over crop-based biofuels as the 'production' footprint required is much less,more » resulting in less water consumed and little, if any conversion of agricultural land from food to fuel production. Besides being a potential source for liquid fuel, algae have the potential to be used to generate electricity through the burning of dried biomass, or anaerobically digested to generate methane for electricity production. Co-locating algae production with waste streams may be crucial for making algae an economically valuable fuel source, and will certainly improve its overall ecological sustainability. The modeling process will address these questions, and others that are important to the use of water for energy production: What are the locations where all resources are co-located, and what volumes of algal biomass and oil can be produced there? In locations where co-location does not occur, what resources should be transported, and how far, while maintaining economic viability? This work is being funded through the U.S. Department of Energy (DOE) Biomass Program Office of Energy Efficiency and Renewable Energy, and is part of a larger collaborative effort that includes sampling, strain isolation, strain characterization and cultivation being performed by the NREL and Canada's NRC. Results from the NREL / NRC collaboration including specific productivities of selected algal strains will eventually be incorporated into this model.« less

A novel approach to quantifying the spatiotemporal behavior of instrumented grey seals used to sample the environment.

PubMed

Baker, Laurie L; Mills Flemming, Joanna E; Jonsen, Ian D; Lidgard, Damian C; Iverson, Sara J; Bowen, W Don

2015-01-01

Paired with satellite location telemetry, animal-borne instruments can collect spatiotemporal data describing the animal's movement and environment at a scale relevant to its behavior. Ecologists have developed methods for identifying the area(s) used by an animal (e.g., home range) and those used most intensely (utilization distribution) based on location data. However, few have extended these models beyond their traditional roles as descriptive 2D summaries of point data. Here we demonstrate how the home range method, T-LoCoH, can be expanded to quantify collective sampling coverage by multiple instrumented animals using grey seals (Halichoerus grypus) equipped with GPS tags and acoustic transceivers on the Scotian Shelf (Atlantic Canada) as a case study. At the individual level, we illustrate how time and space-use metrics quantifying individual sampling coverage may be used to determine the rate of acoustic transmissions received. Grey seals collectively sampled an area of 11,308 km (2) and intensely sampled an area of 31 km (2) from June-December. The largest area sampled was in July (2094.56 km (2)) and the smallest area sampled occurred in August (1259.80 km (2)), with changes in sampling coverage observed through time. T-LoCoH provides an effective means to quantify changes in collective sampling effort by multiple instrumented animals and to compare these changes across time. We also illustrate how time and space-use metrics of individual instrumented seal movement calculated using T-LoCoH can be used to account for differences in the amount of time a bioprobe (biological sampling platform) spends in an area.

Quality assured measurements of animal building emissions: gas concentrations.

PubMed

Heber, Albert J; Ni, Ji-Qin; Lim, Teng T; Tao, Pei-Chun; Schmidt, Amy M; Koziel, Jacek A; Beasley, David B; Hoff, Steven J; Nicolai, Richard E; Jacobson, Larry D; Zhang, Yuanhui

2006-10-01

Comprehensive field studies were initiated in 2002 to measure emissions of ammonia (NH3), hydrogen sulfide (H2S), carbon dioxide (CO2), methane (CH4), nonmethane hydrocarbons (NMHC), particulate matter <10 microm in diameter, and total suspended particulate from swine and poultry production buildings in the United States. This paper focuses on the quasicontinuous gas concentration measurement at multiple locations among paired barns in seven states. Documented principles, used in air pollution monitoring at industrial sources, were applied in developing quality assurance (QA) project plans for these studies. Air was sampled from multiple locations with each gas analyzed with one high quality commercial gas analyzer that was located in an environmentally controlled on-farm instrument shelter. A nominal 4 L/min gas sampling system was designed and constructed with Teflon wetted surfaces, bypass pumping, and sample line flow and pressure sensors. Three-way solenoids were used to automatically switch between multiple gas sampling lines with > or =10 min sampling intervals. Inside and outside gas sampling probes were between 10 and 115 m away from the analyzers. Analyzers used chemiluminescence, fluorescence, photoacoustic infrared, and photoionization detectors for NH3, H2S, CO2, CH4, and NMHC, respectively. Data were collected using personal computer-based data acquisition hardware and software. This paper discusses the methodology of gas concentration measurements and the unique challenges that livestock barns pose for achieving desired accuracy and precision, data representativeness, comparability and completeness, and instrument calibration and maintenance.

The Evolutionary Fates of a Large Segmental Duplication in Mouse

PubMed Central

Morgan, Andrew P.; Holt, J. Matthew; McMullan, Rachel C.; Bell, Timothy A.; Clayshulte, Amelia M.-F.; Didion, John P.; Yadgary, Liran; Thybert, David; Odom, Duncan T.; Flicek, Paul; McMillan, Leonard; de Villena, Fernando Pardo-Manuel

2016-01-01

Gene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127-kbp segmental duplication, R2d, in the house mouse (Mus musculus). R2d contains a single protein-coding gene, Cwc22. De novo assembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to nonallelic gene conversion events spanning tens of kilobases. R2d2 is also a hotspot for structural variation: its diploid copy number ranges from zero in the mouse reference genome to >80 in wild mice sampled from around the globe. Hemizygosity for high copy-number alleles of R2d2 is associated in cis with meiotic drive; suppression of meiotic crossovers; and copy-number instability, with a mutation rate in excess of 1 per 100 transmissions in some laboratory populations. Our results provide a striking example of allelic diversity generated by duplication and demonstrate the value of de novo assembly in a phylogenetic context for understanding the mutational processes affecting duplicate genes. PMID:27371833

Novel partial duplication of EYA1 causes branchiootic syndrome in a large Brazilian family.

PubMed

Dantas, Vitor G L; Freitas, Erika L; Della-Rosa, Valter A; Lezirovitz, Karina; de Moraes, Ana Maria S M; Ramos, Silvia B; Oiticica, Jeanne; Alves, Leandro U; Pearson, Peter L; Rosenberg, Carla; Mingroni-Netto, Regina C

2015-01-01

To identify novel genetic causes of syndromic hearing loss in Brazil. To map a candidate chromosomal region through linkage studies in an extensive Brazilian family and identify novel pathogenic variants using sequencing and array-CGH. Brazilian pedigree with individuals affected by BO syndrome characterized by deafness and malformations of outer, middle and inner ear, auricular and cervical fistulae, but no renal abnormalities. Whole genome microarray-SNP scanning on samples of 11 affected individuals detected a multipoint Lod score of 2.6 in the EYA1 gene region (chromosome 8). Sequencing of EYA1 in affected patients did not reveal pathogenic mutations. However, oligonucleotide-array-CGH detected a duplication of 71.8Kb involving exons 4 to 10 of EYA1 (heterozygous state). Real-time-PCR confirmed the duplication in fourteen of fifteen affected individuals and absence in 13 unaffected individuals. The exception involved a consanguineous parentage and was assumed to involve a different genetic mechanism. Our findings implicate this EYA1 partial duplication segregating with BO phenotype in a Brazilian pedigree and is the first description of a large duplication leading to the BOR/BO syndrome.

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers.

PubMed

Girardot, Charles; Scholtalbers, Jelle; Sauer, Sajoscha; Su, Shu-Yi; Furlong, Eileen E M

2016-10-08

The yield obtained from next generation sequencers has increased almost exponentially in recent years, making sample multiplexing common practice. While barcodes (known sequences of fixed length) primarily encode the sample identity of sequenced DNA fragments, barcodes made of random sequences (Unique Molecular Identifier or UMIs) are often used to distinguish between PCR duplicates and transcript abundance in, for example, single-cell RNA sequencing (scRNA-seq). In paired-end sequencing, different barcodes can be inserted at each fragment end to either increase the number of multiplexed samples in the library or to use one of the barcodes as UMI. Alternatively, UMIs can be combined with the sample barcodes into composite barcodes, or with standard Illumina® indexing. Subsequent analysis must take read duplicates and sample identity into account, by identifying UMIs. Existing tools do not support these complex barcoding configurations and custom code development is frequently required. Here, we present Je, a suite of tools that accommodates complex barcoding strategies, extracts UMIs and filters read duplicates taking UMIs into account. Using Je on publicly available scRNA-seq and iCLIP data containing UMIs, the number of unique reads increased by up to 36 %, compared to when UMIs are ignored. Je is implemented in JAVA and uses the Picard API. Code, executables and documentation are freely available at http://gbcs.embl.de/Je . Je can also be easily installed in Galaxy through the Galaxy toolshed.

The powdery mildew resistance gene REN1 co-segregates with an NBS-LRR gene cluster in two Central Asian grapevines

PubMed Central

2009-01-01

Background Grape powdery mildew is caused by the North American native pathogen Erysiphe necator. Eurasian Vitis vinifera varieties were all believed to be susceptible. REN1 is the first resistance gene naturally found in cultivated plants of Vitis vinifera. Results REN1 is present in 'Kishmish vatkana' and 'Dzhandzhal kara', two grapevines documented in Central Asia since the 1920's. These cultivars have a second-degree relationship (half sibs, grandparent-grandchild, or avuncular), and share by descent the chromosome on which the resistance allele REN1 is located. The REN1 interval was restricted to 1.4 cM using 38 SSR markers distributed across the locus and the segregation of the resistance phenotype in two progenies of collectively 461 offspring, derived from either resistant parent. The boundary markers delimit a 1.4-Mbp sequence in the PN40024 reference genome, which contains 27 genes with known functions, 2 full-length coiled-coil NBS-LRR genes, and 9 NBS-LRR pseudogenes. In the REN1 locus of PN40024, NBS genes have proliferated through a mixture of segmental duplications, tandem gene duplications, and intragenic recombination between paralogues, indicating that the REN1 locus has been inherently prone to producing genetic variation. Three SSR markers co-segregate with REN1, the outer ones confining the 908-kb array of NBS-LRR genes. Kinship and clustering analyses based on genetic distances with susceptible cultivars representative of Central Asian Vitis vinifera indicated that 'Kishmish vatkana' and 'Dzhandzhal kara' fit well into local germplasm. 'Kishmish vatkana' also has a parent-offspring relationship with the seedless table grape 'Sultanina'. In addition, the distant genetic relatedness to rootstocks, some of which are derived from North American species resistant to powdery mildew and have been used worldwide to guard against phylloxera since the late 1800's, argues against REN1 being infused into Vitis vinifera from a recent interspecific hybridisation. Conclusion The REN1 gene resides in an NBS-LRR gene cluster tightly delimited by two flanking SSR markers, which can assist in the selection of this DNA block in breeding between Vitis vinifera cultivars. The REN1 locus has multiple layers of structural complexity compared with its two closely related paralogous NBS clusters, which are located some 5 Mbp upstream and 4 Mbp downstream of the REN1 interval on the same chromosome. PMID:20042081

Duplication and concerted evolution in a master sex determiner under balancing selection.

PubMed

Privman, Eyal; Wurm, Yannick; Keller, Laurent

2013-05-07

The transformer (tra) gene is a key regulator in the signalling hierarchy controlling all aspects of somatic sexual differentiation in Drosophila and other insects. Here, we show that six of the seven sequenced ants have two copies of tra. Surprisingly, the two paralogues are always more similar within species than among species. Comparative sequence analyses indicate that this pattern is owing to the ongoing concerted evolution after an ancestral duplication rather than independent duplications in each of the six species. In particular, there was strong support for inter-locus recombination between the paralogues of the ant Atta cephalotes. In the five species where the location of paralogues is known, they are adjacent to each other in four cases and separated by only few genes in the fifth case. Because there have been extensive genomic rearrangements in these lineages, this suggests selection acting to conserve their synteny. In three species, we also find a signature of positive selection in one of the paralogues. In three bee species where information is available, the tra gene is also duplicated, the copies are adjacent and in at least one species there was recombination between paralogues. These results suggest that concerted evolution plays an adaptive role in the evolution of this gene family.

Genome wide in silico characterization of Dof gene families of pigeonpea (Cajanus cajan (L) Millsp.).

PubMed

Malviya, N; Gupta, S; Singh, V K; Yadav, M K; Bisht, N C; Sarangi, B K; Yadav, D

2015-02-01

The DNA binding with One Finger (Dof) protein is a plant specific transcription factor involved in the regulation of wide range of processes. The analysis of whole genome sequence of pigeonpea has identified 38 putative Dof genes (CcDof) distributed on 8 chromosomes. A total of 17 out of 38 CcDof genes were found to be intronless. A comprehensive in silico characterization of CcDof gene family including the gene structure, chromosome location, protein motif, phylogeny, gene duplication and functional divergence has been attempted. The phylogenetic analysis resulted in 3 major clusters with closely related members in phylogenetic tree revealed common motif distribution. The in silico cis-regulatory element analysis revealed functional diversity with predominance of light responsive and stress responsive elements indicating the possibility of these CcDof genes to be associated with photoperiodic control and biotic and abiotic stress. The duplication pattern showed that tandem duplication is predominant over segmental duplication events. The comparative phylogenetic analysis of these Dof proteins along with 78 soybean, 36 Arabidopsis and 30 rice Dof proteins revealed 7 major clusters. Several groups of orthologs and paralogs were identified based on phylogenetic tree constructed. Our study provides useful information for functional characterization of CcDof genes.

Genome-Wide Identification and Expression Analysis of NBS-Encoding Genes in Malus x domestica and Expansion of NBS Genes Family in Rosaceae

PubMed Central

Arya, Preeti; Kumar, Gulshan; Acharya, Vishal; Singh, Anil K.

2014-01-01

Nucleotide binding site leucine-rich repeats (NBS-LRR) disease resistance proteins play an important role in plant defense against pathogen attack. A number of recent studies have been carried out to identify and characterize NBS-LRR gene families in many important plant species. In this study, we identified NBS-LRR gene family comprising of 1015 NBS-LRRs using highly stringent computational methods. These NBS-LRRs were characterized on the basis of conserved protein motifs, gene duplication events, chromosomal locations, phylogenetic relationships and digital gene expression analysis. Surprisingly, equal distribution of Toll/interleukin-1 receptor (TIR) and coiled coil (CC) (1∶1) was detected in apple while the unequal distribution was reported in majority of all other known plant genome studies. Prediction of gene duplication events intriguingly revealed that not only tandem duplication but also segmental duplication may equally be responsible for the expansion of the apple NBS-LRR gene family. Gene expression profiling using expressed sequence tags database of apple and quantitative real-time PCR (qRT-PCR) revealed the expression of these genes in wide range of tissues and disease conditions, respectively. Taken together, this study will provide a blueprint for future efforts towards improvement of disease resistance in apple. PMID:25232838

Field Tests of Real-time In-situ Dissolved CO2 Monitoring for CO2 Leakage Detection in Groundwater

NASA Astrophysics Data System (ADS)

Yang, C.; Zou, Y.; Delgado, J.; Guzman, N.; Pinedo, J.

2016-12-01

Groundwater monitoring for detecting CO2 leakage relies on groundwater sampling from water wells drilled into aquifers. Usually groundwater samples are required be collected periodically in field and analyzed in the laboratory. Obviously groundwater sampling is labor and cost-intensive for long-term monitoring of large areas. Potential damage and contamination of water samples during the sampling process can degrade accuracy, and intermittent monitoring may miss changes in the geochemical parameters of groundwater, and therefore signs of CO2 leakage. Real-time in-situ monitoring of geochemical parameters with chemical sensors may play an important role for CO2 leakage detection in groundwater at a geological carbon sequestration site. This study presents field demonstration of a real-time in situ monitoring system capable of covering large areas for detection of low levels of dissolved CO2 in groundwater and reliably differentiating natural variations of dissolved CO2 concentration from small changes resulting from leakage. The sand-alone system includes fully distributed fiber optic sensors for carbon dioxide detection with a unique sensor technology developed by Intelligent Optical Systems. The systems were deployed to the two research sites: the Brackenridge Field Laboratory where the aquifer is shallow at depths of 10-20 ft below surface and the Devine site where the aquifer is much deeper at depths of 140 to 150 ft. Groundwater samples were periodically collected from the water wells which were installed with the chemical sensors and further compared to the measurements of the chemical sensors. Our study shows that geochemical monitoring of dissolved CO2 with fiber optic sensors could provide reliable CO2 leakage signal detection in groundwater as long as CO2 leakage signals are stronger than background noises at the monitoring locations.

Heavy metals in water of the San Pedro River in Chihuahua, Mexico and its potential health risk.

PubMed

Gutiérrez, Roberto L; Rubio-Arias, Hector; Quintana, Ray; Ortega, Juan Angel; Gutierrez, Melida

2008-06-01

The objective of this study was to determine the seasonal and downstream water quality variations of the San Pedro River in Chihuahua, Mexico. Water samples were collected monthly from October 2005 to August 2006 in triplicate, totaling 165 water samples. The five sampling locations were: below the Francisco I. Madero dam (LP); between Rosales and Delicias (RD); Meoqui (M); El Torreon (ET), and Julimes (LJ). The levels of As, Be, Ca, Cd, Co, Cu, Cr, Fe, Li, Mg, Mn, Mo, Ni, Pb, Sb, Se, Sr, Ti, Ta, V and Zn were measured using an Inductively Coupled Plasma- Optical Emission Spectrometry (ICP-OES) Perkin Elmer 2100. In addition, temperature, pH, electrical conductivity and total and fecal coliformes were determined. The statistical analysis considered a factorial treatment design; where factor A was the location point and factor B was sampling date. In addition, a multivariate technique looking for principal components was performed. The results indicated that some samples exceeded Mexican standards for As, Be, Ca, Cd, Co, Cr, Fe, Mn, Ni, Pb, Sb, Se, Sr and Zn. The As level must be considered for a red flag to the communities along the Rio San Pedro because both the monthly average level (0.10 mg L-1) and location (0.10 mg L-1) exceeded the Mexican and International norms. The multivariate analysis showed a predominant aggregation at the LP location, meaning that there was a predominance of As, Sr, Fe and Li. At the rest of the locations the elements did not present a tendency for aggregation. Statistics applied to sampling month showed that December, January, March and April were aggregated in a negative quadrant of component 1 indicating a predominance of V, Ni, Be, Fe and As. Overall, the results confirmed that this stretch of the San Pedro River is contaminated with heavy metals and other contaminants that might affect human health as well as the health of the ecosystem.

Heavy metals in water of the San Pedro River in Chihuahua, Mexico and its potential health risk

PubMed Central

Gutiérrez, Roberto L.; Rubio-Arias, Hector; Quintana, Ray; Ortega, Juan Angel; Gutierrez, Melida

2008-01-01

The objective of this study was to determine the seasonal and downstream water quality variations of the San Pedro River in Chihuahua, Mexico. Water samples were collected monthly from October 2005 to August 2006 in triplicate, totaling 165 water samples. The five sampling locations were: below the Francisco I. Madero dam (LP); between Rosales and Delicias (RD); Meoqui (M); El Torreon (ET), and Julimes (LJ). The levels of As, Be, Ca, Cd, Co, Cu, Cr, Fe, Li, Mg, Mn, Mo, Ni, Pb, Sb, Se, Sr, Ti, Ta, V and Zn were measured using an Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES) Perkin Elmer 2100. In addition, temperature, pH, electrical conductivity and total and fecal coliformes were determined. The statistical analysis considered a factorial treatment design; where factor A was the location point and factor B was sampling date. In addition, a multivariate technique looking for principal components was performed. The results indicated that some samples exceeded Mexican standards for As, Be, Ca, Cd, Co, Cr, Fe, Mn, Ni, Pb, Sb, Se, Sr and Zn. The As level must be considered for a red flag to the communities along the Rio San Pedro because both the monthly average level (0.10 mg L−1) and location (0.10 mg L−1) exceeded the Mexican and International norms. The multivariate analysis showed a predominant aggregation at the LP location, meaning that there was a predominance of As, Sr, Fe and Li. At the rest of the locations the elements did not present a tendency for aggregation. Statistics applied to sampling month showed that December, January, March and April were aggregated in a negative quadrant of component 1 indicating a predominance of V, Ni, Be, Fe and As. Overall, the results confirmed that this stretch of the San Pedro River is contaminated with heavy metals and other contaminants that might affect human health as well as the health of the ecosystem. PMID:18678922

South Philadelphia passive sampler and sensor study.

PubMed

Thoma, Eben D; Brantley, Halley L; Oliver, Karen D; Whitaker, Donald A; Mukerjee, Shaibal; Mitchell, Bill; Wu, Tai; Squier, Bill; Escobar, Elsy; Cousett, Tamira A; Gross-Davis, Carol Ann; Schmidt, Howard; Sosna, Dennis; Weiss, Hallie

2016-10-01

From June 2013 to March 2015, in total 41 passive sampler deployments of 2 wk duration each were conducted at 17 sites in South Philadelphia, PA, with results for benzene discussed here. Complementary time-resolved measurements with lower cost prototype fenceline sensors and an open-path ultraviolet differential optical absorption spectrometer were also conducted. Minimum passive sampler benzene concentrations for each sampling period ranged from 0.08 ppbv to 0.65 ppbv, with a mean of 0.25 ppbv, and were negatively correlated with ambient temperature (-0.01 ppbv/°C, R(2) = 0.68). Co-deployed duplicate passive sampler pairs (N = 609) demonstrated good precision with an average and maximum percent difference of 1.5% and 34%, respectively. A group of passive samplers located within 50 m of a refinery fenceline had a study mean benzene concentration of 1.22 ppbv, whereas a group of samplers located in communities >1 km distant from facilities had a mean of 0.29 ppbv. The difference in the means of these groups was statistically significant at the 95% confidence level (p < 0.001). A decreasing gradient in benzene concentrations moving away from the facilities was observed, as was a significant period-to-period variation. The highest recorded 2-wk average benzene concentration for the fenceline group was 3.11 ppbv. During this period, time-resolved data from the prototype sensors and the open-path spectrometer detected a benzene signal from the west on one day in particular, with the highest 5-min path-averaged benzene concentration measured at 24 ppbv. Using a variation of EPA's passive sampler refinery fenceline monitoring method, coupled with time-resolved measurements, a multiyear study in South Philadelphia informed benzene concentrations near facilities and in communities. The combination of measurement strategies can assist facilities in identification and mitigation of emissions from fugitive sources and improve information on air quality complex air sheds.

Recurrent duplications of the annexin A1 gene (ANXA1) in autism spectrum disorders.

PubMed

Correia, Catarina T; Conceição, Inês C; Oliveira, Bárbara; Coelho, Joana; Sousa, Inês; Sequeira, Ana F; Almeida, Joana; Café, Cátia; Duque, Frederico; Mouga, Susana; Roberts, Wendy; Gao, Kun; Lowe, Jennifer K; Thiruvahindrapuram, Bhooma; Walker, Susan; Marshall, Christian R; Pinto, Dalila; Nurnberger, John I; Scherer, Stephen W; Geschwind, Daniel H; Oliveira, Guiomar; Vicente, Astrid M

2014-04-10

Validating the potential pathogenicity of copy number variants (CNVs) identified in genome-wide studies of autism spectrum disorders (ASD) requires detailed assessment of case/control frequencies, inheritance patterns, clinical correlations, and functional impact. Here, we characterize a small recurrent duplication in the annexin A1 (ANXA1) gene, identified by the Autism Genome Project (AGP) study. From the AGP CNV genomic screen in 2,147 ASD individuals, we selected for characterization an ANXA1 gene duplication that was absent in 4,964 population-based controls. We further screened the duplication in a follow-up sample including 1,496 patients and 410 controls, and evaluated clinical correlations and family segregation. Sequencing of exonic/downstream ANXA1 regions was performed in 490 ASD patients for identification of additional variants. The ANXA1 duplication, overlapping the last four exons and 3'UTR region, had an overall prevalence of 11/3,643 (0.30%) in unrelated ASD patients but was not identified in 5,374 controls. Duplication carriers presented no distinctive clinical phenotype. Family analysis showed neuropsychiatric deficits and ASD traits in multiple relatives carrying the duplication, suggestive of a complex genetic inheritance. Sequencing of exonic regions and the 3'UTR identified 11 novel changes, but no obvious variants with clinical significance. We provide multilevel evidence for a role of ANXA1 in ASD etiology. Given its important role as mediator of glucocorticoid function in a wide variety of brain processes, including neuroprotection, apoptosis, and control of the neuroendocrine system, the results add ANXA1 to the growing list of rare candidate genetic etiological factors for ASD.

A method to estimate spatiotemporal air quality in an urban traffic corridor.

PubMed

Singh, Nongthombam Premananda; Gokhale, Sharad

2015-12-15

Air quality exposure assessment using personal exposure sampling or direct measurement of spatiotemporal air pollutant concentrations has difficulty and limitations. Most statistical methods used for estimating spatiotemporal air quality do not account for the source characteristics (e.g. emissions). In this study, a prediction method, based on the lognormal probability distribution of hourly-average-spatial concentrations of carbon monoxide (CO) obtained by a CALINE4 model, has been developed and validated in an urban traffic corridor. The data on CO concentrations were collected at three locations and traffic and meteorology within the urban traffic corridor.(1) The method has been developed with the data of one location and validated at other two locations. The method estimated the CO concentrations reasonably well (correlation coefficient, r≥0.96). Later, the method has been applied to estimate the probability of occurrence [P(C≥Cstd] of the spatial CO concentrations in the corridor. The results have been promising and, therefore, may be useful to quantifying spatiotemporal air quality within an urban area. Copyright © 2015 Elsevier B.V. All rights reserved.

Rainfall, discharge, and water-quality data during stormwater monitoring, H-1 storm drain, Oahu, Hawaii, July 1, 2009, to June 30, 2010

USGS Publications Warehouse

Presley, Todd K.; Jamison, Marcael T.J.

2010-01-01

Storm runoff water-quality samples were collected as part of the State of Hawaii Department of Transportation Stormwater Monitoring Program. The program is designed to assess the effects of highway runoff and urban runoff collected by the H-1 storm drain on the Manoa-Palolo Drainage Canal. This report summarizes rainfall, discharge, and water-quality data collected between July 1, 2009, and June 30, 2010. As part of this program, rainfall and continuous discharge data were collected at the H-1 storm drain. During the year, sampling strategy and sample processing methods were modified to improve the characterization of the effects of discharge from the storm drain on the Manoa-Palolo Drainage Canal. During July 1, 2009, to February 1, 2010, samples were collected from only the H-1 storm drain. Beginning February 2, 2010, samples were collected simultaneously from the H-1 storm drain and the Manoa-Palolo Drainage Canal at a location about 50 feet upstream of the discharge point of the H-1 storm drain. Three storms were sampled during July 1, 2009, to June 30, 2010. All samples were collected using automatic samplers. For the storm of August 12, 2009, grab samples (for oil and grease, and total petroleum hydrocarbons) and a composite sample were collected. The composite sample was analyzed for total suspended solids, nutrients, and selected dissolved and total (filtered and unfiltered) trace metals (cadmium, chromium, nickel, copper, lead, and zinc). Two storms were sampled in March 2010 at the H-1 storm drain and from the Manoa-Palolo Drainage Canal. Two samples were collected during the storm of March 4, 2010, and six samples were collected during the storm of March 8, 2010. These two storms were sampled using the modified strategy, in which discrete samples from the automatic sampler were processed and analyzed individually, rather than as a composite sample, using the simultaneously collected samples from the H-1 storm drain and from the Manoa-Palolo Drainage Canal. The discrete samples were analyzed for some or all of the following constituents: total suspended solids, nutrients, oil and grease, and selected dissolved (filtered) trace metals (cadmium, chromium, nickel, copper, lead, and zinc). Five quality-assurance/quality-control samples were analyzed during the year. These samples included one laboratory-duplicate, one field-duplicate, and one matrix-spike sample prepared and analyzed with the storm samples. In addition, two inorganic blank-water samples, one sample at the H-1 storm drain and one sample at the Manoa-Palolo Drainage Canal, were collected by running the blank water (water purified of all inorganic constituents) through the sampling and processing systems after cleaning automatic sampler lines to verify that the sampling lines were not contaminated.

Erratum: Retraction Note to: Experimental and Simulation Studies on Grain Growth in TiC- and WC-Based Cermets During Liquid Phase Sintering

NASA Astrophysics Data System (ADS)

Shin, Soon-Gi

2018-03-01

This article [1] has been retracted at the request of the Editor-in-Chief. Concerns were raised regarding substantial duplications with previous articles published in other journals in which S.-G. Shin is one of the co-authors.

Photonic Technology for Implementation of Generalizable Neural Networks: A Synthetic Approach

DTIC Science & Technology

1993-10-28

holographic medium, thus permitting duplication of a pretrainedI neural network in a manufacturing environment. Iamnfatrn I n • n wrnrm •mrmTv...usual heavy hole (hh) to first confined o. electron (le) excitonic transitions at - ljrm Co 05 wavelength, but even the light hole (1h) to leand

Origins of adaptive immunity.

PubMed

Liongue, Clifford; John, Liza B; Ward, Alister

2011-01-01

Adaptive immunity, involving distinctive antibody- and cell-mediated responses to specific antigens based on "memory" of previous exposure, is a hallmark of higher vertebrates. It has been argued that adaptive immunity arose rapidly, as articulated in the "big bang theory" surrounding its origins, which stresses the importance of coincident whole-genome duplications. Through a close examination of the key molecules and molecular processes underpinning adaptive immunity, this review suggests a less-extreme model, in which adaptive immunity emerged as part of longer evolutionary journey. Clearly, whole-genome duplications provided additional raw genetic materials that were vital to the emergence of adaptive immunity, but a variety of other genetic events were also required to generate some of the key molecules, whereas others were preexisting and simply co-opted into adaptive immunity.

Impact of duplicate gene copies on phylogenetic analysis and divergence time estimates in butterflies

PubMed Central

Pohl, Nélida; Sison-Mangus, Marilou P; Yee, Emily N; Liswi, Saif W; Briscoe, Adriana D

2009-01-01

Background The increase in availability of genomic sequences for a wide range of organisms has revealed gene duplication to be a relatively common event. Encounters with duplicate gene copies have consequently become almost inevitable in the context of collecting gene sequences for inferring species trees. Here we examine the effect of incorporating duplicate gene copies evolving at different rates on tree reconstruction and time estimation of recent and deep divergences in butterflies. Results Sequences from ultraviolet-sensitive (UVRh), blue-sensitive (BRh), and long-wavelength sensitive (LWRh) opsins,EF-1α and COI were obtained from 27 taxa representing the five major butterfly families (5535 bp total). Both BRh and LWRh are present in multiple copies in some butterfly lineages and the different copies evolve at different rates. Regardless of the phylogenetic reconstruction method used, we found that analyses of combined data sets using either slower or faster evolving copies of duplicate genes resulted in a single topology in agreement with our current understanding of butterfly family relationships based on morphology and molecules. Interestingly, individual analyses of BRh and LWRh sequences also recovered these family-level relationships. Two different relaxed clock methods resulted in similar divergence time estimates at the shallower nodes in the tree, regardless of whether faster or slower evolving copies were used, with larger discrepancies observed at deeper nodes in the phylogeny. The time of divergence between the monarch butterfly Danaus plexippus and the queen D. gilippus (15.3–35.6 Mya) was found to be much older than the time of divergence between monarch co-mimic Limenitis archippus and red-spotted purple L. arthemis (4.7–13.6 Mya), and overlapping with the time of divergence of the co-mimetic passionflower butterflies Heliconius erato and H. melpomene (13.5–26.1 Mya). Our family-level results are congruent with recent estimates found in the literature and indicate an age of 84–113 million years for the divergence of all butterfly families. Conclusion These results are consistent with diversification of the butterfly families following the radiation of angiosperms and suggest that some classes of opsin genes may be usefully employed for both phylogenetic reconstruction and divergence time estimation. PMID:19439087

Intra-urban spatial variability of PM2.5-bound carbonaceous components

NASA Astrophysics Data System (ADS)

Xie, Mingjie; Coons, Teresa L.; Dutton, Steven J.; Milford, Jana B.; Miller, Shelly L.; Peel, Jennifer L.; Vedal, Sverre; Hannigan, Michael P.

2012-12-01

The Denver Aerosol Sources and Health (DASH) study was designed to evaluate associations between PM2.5 species and sources and adverse human health effects. The DASH study generated a five-year (2003-2007) time series of daily speciated PM2.5 concentration measurements from a single, special-purpose monitoring site in Denver, CO. To evaluate the ability of this site to adequately represent the short term temporal variability of PM2.5 concentrations in the five county Denver metropolitan area, a one year supplemental set of PM2.5 samples was collected every sixth day at the original DASH monitoring site and concurrently at three additional sites. Two of the four sites, including the original DASH site, were located in residential areas at least 1.9 km from interstate highways. The other two sites were located within 0.3 km of interstate highways. Concentrations of elemental carbon (EC), organic carbon (OC), and 58 organic molecular markers were measured at each site. To assess spatial variability, site pairs were compared using the Pearson correlation coefficient (r) and coefficient of divergence (COD), a statistic that provides information on the degree of uniformity between monitoring sites. Bi-weekly co-located samples collected from July 2004 to September 2005 were also analyzed and used to estimate the uncertainty associated with sampling and analytical measurement for each species. In general, the two near-highway sites exhibited higher concentrations of EC, OC, polycyclic aromatic hydrocarbons (PAHs), and steranes than did the more residential sites. Lower spatial heterogeneity based on r and COD was inferred for all carbonaceous species after considering their divergence and lack of perfect correlations in co-located samples. Ratio-ratio plots combined with available gasoline- and diesel-powered motor vehicle emissions profiles for the region suggested a greater impact to high molecular weight (HMW) PAHs from diesel-powered vehicles at the near-highway sites and a more uniformly distributed impact to ambient hopanes from gasoline-powered motor vehicles at all four sites.

9 CFR 327.11 - Receipts to importers for import product samples.

Code of Federal Regulations, 2010 CFR

2010-01-01

... product samples. 327.11 Section 327.11 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE... laboratory examination are to be used exclusively for that purpose, official receipts shall be issued and... collected, date of collection, and that the sample was collected for laboratory examination. The duplicate...

Methods and apparatus for measuring small leaks from carbon dioxide sequestration facilities

DOEpatents

Nelson, Jr., David D.; Herndon, Scott C.

2018-01-02

In one embodiment, a CO.sub.2 leak detection instrument detects leaks from a site (e.g., a CO.sub.2 sequestration facility) using rapid concentration measurements of CO.sub.2, O.sub.2 and optionally water concentration that are achieved, for example, using laser spectroscopy (e.g. direct absorption laser spectroscopy). Water vapor in the sample gas may not be removed, or only partially removed. The sample gas may be collected using a multiplexed inlet assembly from a plurality of locations. CO.sub.2 and O.sub.2 concentrations may be corrected based on the water concentration. A resulting dataset of the CO.sub.2 and O.sub.2 concentrations is analyzed over time intervals to detect any changes in CO.sub.2 concentration that are not anti-correlated with O.sub.2 concentration, and to identify a potential CO.sub.2 leak in response thereto. The analysis may include determining eddy covariance flux measurements of sub-surface potential carbon.

47 CFR 76.111 - Cable sports blackout.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 4 2012-10-01 2012-10-01 false Cable sports blackout. 76.111 Section 76.111... CABLE TELEVISION SERVICE Network Non-duplication Protection, Syndicated Exclusivity and Sports Blackout § 76.111 Cable sports blackout. (a) No community unit located in whole or in part within the specified...

47 CFR 76.111 - Cable sports blackout.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 4 2013-10-01 2013-10-01 false Cable sports blackout. 76.111 Section 76.111... CABLE TELEVISION SERVICE Network Non-duplication Protection, Syndicated Exclusivity and Sports Blackout § 76.111 Cable sports blackout. (a) No community unit located in whole or in part within the specified...

47 CFR 76.111 - Cable sports blackout.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 4 2014-10-01 2014-10-01 false Cable sports blackout. 76.111 Section 76.111... CABLE TELEVISION SERVICE Network Non-duplication Protection, Syndicated Exclusivity and Sports Blackout § 76.111 Cable sports blackout. (a) No community unit located in whole or in part within the specified...

47 CFR 76.111 - Cable sports blackout.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 4 2010-10-01 2010-10-01 false Cable sports blackout. 76.111 Section 76.111... CABLE TELEVISION SERVICE Network Non-duplication Protection, Syndicated Exclusivity and Sports Blackout § 76.111 Cable sports blackout. (a) No community unit located in whole or in part within the specified...

47 CFR 76.111 - Cable sports blackout.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 4 2011-10-01 2011-10-01 false Cable sports blackout. 76.111 Section 76.111... CABLE TELEVISION SERVICE Network Non-duplication Protection, Syndicated Exclusivity and Sports Blackout § 76.111 Cable sports blackout. (a) No community unit located in whole or in part within the specified...

Environmental Technology Verification Report for Applikon MARGA Semi-Continuous Ambient Air Monitoring System

EPA Science Inventory

The verification test was conducted oer a period of 30 days (October 1 to October 31, 2008) and involved the continuous operation of duplicate semi-continuous monitoring technologies at the Burdens Creek Air Monitoring Site, an existing ambient-air monitoring station located near...

Control site location and transcriptional regulation in Escherichia coli.

PubMed Central

Collado-Vides, J; Magasanik, B; Gralla, J D

1991-01-01

The regulatory regions for 119 Escherichia coli promoters have been analyzed, and the locations of the regulatory sites have been cataloged. The following observations emerge. (i) More than 95% of promoters are coregulated with at least one other promoter. (ii) Virtually all sigma 70 promoters contain at least one regulatory site in a proximal position, touching at least position -65 with respect to the start point of transcription. There are not yet clear examples of upstream regulation in the absence of a proximal site. (iii) Operators within regulons appear in very variable proximal positions. By contrast, the proximal activation sites of regulons are much more fixed. (iv) There is a forbidden zone for activation elements downstream from approximately position -20 with respect to the start of transcription. By contrast, operators can occur throughout the proximal region. When activation elements appear in the forbidden zone, they repress. These latter examples usually involve autoregulation. (v) Approximately 40% of repressible promoters contain operator duplications. These occur either in certain regulons where duplication appears to be a requirement for repressor action or in promoters subject to complex regulation. (vi) Remote operator duplications occur in approximately 10% of repressible promoters. They generally appear when a multiple promoter region is coregulated by cyclic AMP receptor protein. (vii) Sigma 54 promoters do not require proximal or precisely positioned activator elements and are not generally subject to negative regulation. Rationales are presented for all of the above observations. PMID:1943993

Adrenal GIPR expression and chromosome 19q13 microduplications in GIP-dependent Cushing's syndrome.

PubMed

Lecoq, Anne-Lise; Stratakis, Constantine A; Viengchareun, Say; Chaligné, Ronan; Tosca, Lucie; Deméocq, Vianney; Hage, Mirella; Berthon, Annabel; Faucz, Fabio R; Hanna, Patrick; Boyer, Hadrien-Gaël; Servant, Nicolas; Salenave, Sylvie; Tachdjian, Gérard; Adam, Clovis; Benhamo, Vanessa; Clauser, Eric; Guiochon-Mantel, Anne; Young, Jacques; Lombès, Marc; Bourdeau, Isabelle; Maiter, Dominique; Tabarin, Antoine; Bertherat, Jérôme; Lefebvre, Hervé; de Herder, Wouter; Louiset, Estelle; Lacroix, André; Chanson, Philippe; Bouligand, Jérôme; Kamenický, Peter

2017-09-21

GIP-dependent Cushing's syndrome is caused by ectopic expression of glucose-dependent insulinotropic polypeptide receptor (GIPR) in cortisol-producing adrenal adenomas or in bilateral macronodular adrenal hyperplasias. Molecular mechanisms leading to ectopic GIPR expression in adrenal tissue are not known. Here we performed molecular analyses on adrenocortical adenomas and bilateral macronodular adrenal hyperplasias obtained from 14 patients with GIP-dependent adrenal Cushing's syndrome and one patient with GIP-dependent aldosteronism. GIPR expression in all adenoma and hyperplasia samples occurred through transcriptional activation of a single allele of the GIPR gene. While no abnormality was detected in proximal GIPR promoter methylation, we identified somatic duplications in chromosome region 19q13.32 containing the GIPR locus in the adrenocortical lesions derived from 3 patients. In 2 adenoma samples, the duplicated 19q13.32 region was rearranged with other chromosome regions, whereas a single tissue sample with hyperplasia had a 19q duplication only. We demonstrated that juxtaposition with cis-acting regulatory sequences such as glucocorticoid response elements in the newly identified genomic environment drives abnormal expression of the translocated GIPR allele in adenoma cells. Altogether, our results provide insight into the molecular pathogenesis of GIP-dependent Cushing's syndrome, occurring through monoallelic transcriptional activation of GIPR driven in some adrenal lesions by structural variations.

Analysis of LDLR mutations in familial hypercholesterolemia patients in Greece by use of the NanoChip microelectronic array technology.

PubMed

Laios, Eleftheria; Drogari, Euridiki

2006-12-01

Three mutations in the low density lipoprotein receptor (LDLR) gene account for 49% of familial hypercholesterolemia (FH) cases in Greece. We used the microelectronic array technology of the NanoChip Molecular Biology Workstation to develop a multiplex method to analyze these single-nucleotide polymorphisms (SNPs). Primer pairs amplified the region encompassing each SNP. The biotinylated PCR amplicon was electronically addressed to streptavidin-coated microarray sites. Allele-specific fluorescently labeled oligonucleotide reporters were designed and used for detection of wild-type and SNP sequences. Genotypes were compared to PCR-restriction fragment length polymorphism (PCR-RFLP). We developed three monoplex assays (1 SNP/site) and an optimized multiplex assay (3SNPs/site). We performed 92 Greece II, 100 Genoa, and 98 Afrikaner-2 NanoChip monoplex assays (addressed to duplicate sites and analyzed separately). Of the 580 monoplex genotypings (290 samples), 579 agreed with RFLP. Duplicate sites of one sample were not in agreement with each other. Of the 580 multiplex genotypings, 576 agreed with the monoplex results. Duplicate sites of three samples were not in agreement with each other, indicating requirement for repetition upon which discrepancies were resolved. The multiplex assay detects common LDLR mutations in Greek FH patients and can be extended to accommodate additional mutations.

Cellular Location and Expression of Na+, K+-ATPase α Subunits Affect the Anti-Proliferative Activity of Oleandrin

PubMed Central

Yang, Peiying; Cartwright, Carrie; Efuet, Ekem; Hamilton, Stanley R.; Wistuba, Ignacio Ivan; Menter, David; Addington, Crandell; Shureiqi, Imad; Newman, Robert A.

2015-01-01

The purpose of this study was to investigate whether intracellular distribution of Na+, K+-ATPase α3 subunit, a receptor for cardiac glycosides including oleandrin, is differentially altered in cancer versus normal cells and whether this altered distribution can be therapeutically targeted to inhibit cancer cell survival. The cellular distribution of Na+, K+-ATPase α3 isoform was investigated in paired normal and cancerous mucosa biopsy samples from patients with lung and colorectal cancers by immunohistochemical staining. The effects of oleandrin on α3 subunit intracellular distribution, cell death, proliferation, and EKR phosphorylation were examined in differentiated and undifferentiated human colon cancer CaCO-2 cells. While Na+, K+-ATPase α3 isoform was predominantly located near the cytoplasmic membrane in normal human colon and lung epithelia, the expression of this subunit in their paired cancer epithelia was shifted to a peri-nuclear position in both a qualitative and quantitative manner. Similarly, distribution of α3 isoform was also shifted from a cytoplasmic membrane location in differentiated human colon cancer CaCO-2 cells to a peri-nuclear position in undifferentiated CaCO-2 cells. Intriguingly, oleandrin exerted threefold stronger anti-proliferative activity in undifferentiated CaCO-2 cells (IC50, 8.25 nM) than in differentiated CaCO-2 cells (IC50, >25 nM). Oleandrin (10 to 20 nM) caused an autophagic cell death and altered ERK phosphorylation in undifferentiated but not in differentiated CaCO-2 cells. These data demonstrate that the intracellular location of Na+, K+-ATPase α3 isoform is altered in human cancer versus normal cells. These changes in α3 cellular location and abundance may indicate a potential target of opportunity for cancer therapy. PMID:23073998

Data Validation Package November 2015 Groundwater and Surface Water Sampling at the Old and New Rifle, Colorado, Processing Sites February 2016

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

Bush, Richard; Lemke, Peter

Water samples were collected from 36 locations at New Rifle and Old Rifle, Colorado, Processing Sites. Duplicate samples were collected from New Rifle locations 0659 and 0855, and Old Rifle location 0304. One equipment blank was collected after decontamination of non-dedicated equipment used to collect one surface water sample. Sampling and analyses were conducted as specified in the Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PRO/S04351, continually updated). New Rifle Site Samples were collected at the New Rifle site from 16 monitoring wells and 7 surface locations in compliance with the December 2008more » Groundwater Compliance Action Plan [GCAP] for the New Rifle, Colorado, Processing Site (LMS/RFN/S01920), with one exception: New Rifle location 0635 could not be sampled because it was inaccessible; a fence installed by the Colorado Department of Transportation prevents access to this location. DOE is currently negotiating access with the Colorado Department of Transportation. Analytes measured at the New Rifle site included contaminants of concern (COCs) (arsenic, molybdenum, nitrate + nitrite as nitrogen, selenium, uranium, and vanadium) ammonia as nitrogen, major cations, and major anions. Field measurements of total alkalinity, oxidation- reduction potential, pH, specific conductance, turbidity, and temperature were made at each location, and the water level was measured at each sampled well. A proposed alternate concentration limit (ACL) for vanadium of 50 milligrams per liter (mg/L), specific to the compliance (POC) wells (RFN-0217, -0659, -0664, and -0669) is included in the New Rifle GCAP. Vanadium concentrations in the POC wells were below the proposed ACL as shown in the time-concentration graphs in the Data Presentation section (Attachment 2). Time-concentration graphs from all other locations sampled are also included in Attachment 2. Sampling location RFN-0195 was misidentified for the June/August 2014 and November 2014 sampling events. (Well RFN-0609 was inadvertently sampled instead of RFN-0195 in 2014.) The results for RFN-0195 have been corrected, and are included in associated time-concentration graphs for this location. Recent results for RFN-0195 are consistent with established trends with the possible exception of vanadium. The most recent result for vanadium showed an increase over recent values. Vanadium concentrations at RFN-0195 and other locations will continue to be evaluated in the future to determine the potential for deviations from established trends. The surface water locations were sampled to monitor the impact of groundwater discharge. COC concentrations at Colorado River surface water locations RFN-0324 and RFN-0326, downgradient of the site, remained low and were consistent with historical results, as shown in the time-concentration graphs. COC concentrations did not indicate there are any impacts related to groundwater discharge to the river. In many cases, elevated COC concentrations at the New Rifle site pond locations were observed, as shown in the time-versus concentration graphs. As noted in the GCAP, this indicates impacts from groundwater discharge to the ponds. Old Rifle Site Samples were collected at the Old Rifle site from eight monitoring wells and five surface locations in compliance with the December 2001 Groundwater Compliance Action Plan for the Old Rifle, Colorado, UMTRA Project Site (GJ0-2000-177-TAR). Analytes measured at the Old Rifle site included COCs (selenium, uranium, and vanadium), major cations, and major anions. Field measurements of total alkalinity, oxidation-reduction potential, pH, specific conductance, turbidity, temperature, were made at each location, and the water level was measured at each sampled well. The monitoring strategy described in the GCAP is designed to determine progress of the natural flushing process in meeting compliance standards for site COCs. Standards for selenium and vanadium are the proposed ACLs of0.05 mg/L and 1.0 mg/L, respectively. For uranium the cleanup goal is the UMTRA standard of 0.044 mg/L or background, whichever is higher. As shown in the time concentration graphs, the uranium concentration exceeds the cleanup goal at groundwater monitoring locations RF0-0304, -0305, -0310, -0655, and -0656. The surface water locations were sampled to monitor the impact of groundwater discharge at Colorado River surface water locations adjacent to (RF0-0396) and downgradient of the site (RF0-0741). COC concentrations remain low and consistent with historical concentrations as shown in the time-concentration graphs (Attachment 2), which indicate no impacts from groundwater discharge to the river.« less

Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.).

PubMed

Vatansever, Recep; Koc, Ibrahim; Ozyigit, Ibrahim Ilker; Sen, Ugur; Uras, Mehmet Emin; Anjum, Naser A; Pereira, Eduarda; Filiz, Ertugrul

2016-12-01

Solanum tuberosum genome analysis revealed 12 StSULTR genes encoding 18 transcripts. Among genes annotated at group level ( StSULTR I-IV), group III members formed the largest SULTRs-cluster and were potentially involved in biotic/abiotic stress responses via various regulatory factors, and stress and signaling proteins. Employing bioinformatics tools, this study performed genome-wide identification and expression analysis of SULTR (StSULTR) genes in potato (Solanum tuberosum L.). Very strict homology search and subsequent domain verification with Hidden Markov Model revealed 12 StSULTR genes encoding 18 transcripts. StSULTR genes were mapped on seven S. tuberosum chromosomes. Annotation of StSULTR genes was also done as StSULTR I-IV at group level based mainly on the phylogenetic distribution with Arabidopsis SULTRs. Several tandem and segmental duplications were identified between StSULTR genes. Among these duplications, Ka/Ks ratios indicated neutral nature of mutations that might not be causing any selection. Two segmental and one-tandem duplications were calculated to occur around 147.69, 180.80 and 191.00 million years ago (MYA), approximately corresponding to the time of monocot/dicot divergence. Two other segmental duplications were found to occur around 61.23 and 67.83 MYA, which is very close to the origination of monocotyledons. Most cis-regulatory elements in StSULTRs were found associated with major hormones (such as abscisic acid and methyl jasmonate), and defense and stress responsiveness. The cis-element distribution in duplicated gene pairs indicated the contribution of duplication events in conferring the neofunctionalization/s in StSULTR genes. Notably, RNAseq data analyses unveiled expression profiles of StSULTR genes under different stress conditions. In particular, expression profiles of StSULTR III members suggested their involvement in plant stress responses. Additionally, gene co-expression networks of these group members included various regulatory factors, stress and signaling proteins, and housekeeping and some other proteins with unknown functions.

Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics.

PubMed

Guo, Yong; Qiu, Li-Juan

2013-01-01

The Dof domain protein family is a classic plant-specific zinc-finger transcription factor family involved in a variety of biological processes. There is great diversity in the number of Dof genes in different plants. However, there are only very limited reports on the characterization of Dof transcription factors in soybean (Glycine max). In the present study, 78 putative Dof genes were identified from the whole-genome sequence of soybean. The predicted GmDof genes were non-randomly distributed within and across 19 out of 20 chromosomes and 97.4% (38 pairs) were preferentially retained duplicate paralogous genes located in duplicated regions of the genome. Soybean-specific segmental duplications contributed significantly to the expansion of the soybean Dof gene family. These Dof proteins were phylogenetically clustered into nine distinct subgroups among which the gene structure and motif compositions were considerably conserved. Comparative phylogenetic analysis of these Dof proteins revealed four major groups, similar to those reported for Arabidopsis and rice. Most of the GmDofs showed specific expression patterns based on RNA-seq data analyses. The expression patterns of some duplicate genes were partially redundant while others showed functional diversity, suggesting the occurrence of sub-functionalization during subsequent evolution. Comprehensive expression profile analysis also provided insights into the soybean-specific functional divergence among members of the Dof gene family. Cis-regulatory element analysis of these GmDof genes suggested diverse functions associated with different processes. Taken together, our results provide useful information for the functional characterization of soybean Dof genes by combining phylogenetic analysis with global gene-expression profiling.

Diverse Cis-Regulatory Mechanisms Contribute to Expression Evolution of Tandem Gene Duplicates

PubMed Central

Baudouin-Gonzalez, Luís; Santos, Marília A; Tempesta, Camille; Sucena, Élio; Roch, Fernando; Tanaka, Kohtaro

2017-01-01

Abstract Pairs of duplicated genes generally display a combination of conserved expression patterns inherited from their unduplicated ancestor and newly acquired domains. However, how the cis-regulatory architecture of duplicated loci evolves to produce these expression patterns is poorly understood. We have directly examined the gene-regulatory evolution of two tandem duplicates, the Drosophila Ly6 genes CG9336 and CG9338, which arose at the base of the drosophilids between 40 and 60 Ma. Comparing the expression patterns of the two paralogs in four Drosophila species with that of the unduplicated ortholog in the tephritid Ceratitis capitata, we show that they diverged from each other as well as from the unduplicated ortholog. Moreover, the expression divergence appears to have occurred close to the duplication event and also more recently in a lineage-specific manner. The comparison of the tissue-specific cis-regulatory modules (CRMs) controlling the paralog expression in the four Drosophila species indicates that diverse cis-regulatory mechanisms, including the novel tissue-specific enhancers, differential inactivation, and enhancer sharing, contributed to the expression evolution. Our analysis also reveals a surprisingly variable cis-regulatory architecture, in which the CRMs driving conserved expression domains change in number, location, and specificity. Altogether, this study provides a detailed historical account that uncovers a highly dynamic picture of how the paralog expression patterns and their underlying cis-regulatory landscape evolve. We argue that our findings will encourage studying cis-regulatory evolution at the whole-locus level to understand how interactions between enhancers and other regulatory levels shape the evolution of gene expression. PMID:28961967

Virtual Microscope Views of the Apollo 11, 12, and 15 Lunar Samples

NASA Technical Reports Server (NTRS)

Gibson, E. K.; Tindle, A. G.; Kelley, S. P.; Pillinger, J. M.

2017-01-01

The Apollo virtual microscope is a means of viewing, over the Internet, polished thin sections of every rock in the Apollo lunar sample collections. It uses software that duplicates many of the functions of a petrological microscope.

Quantification of circulating mature endothelial cells using a whole blood four-color flow cytometric assay.

PubMed

Jacques, Nathalie; Vimond, Nadege; Conforti, Rosa; Griscelli, Franck; Lecluse, Yann; Laplanche, Agnes; Malka, David; Vielh, Philippe; Farace, Françoise

2008-09-15

Circulating endothelial cells (CEC) are currently proposed as a potential biomarker for measuring the impact of anti-angiogenic treatments in cancer. However, the lack of consensus on the appropriate method of CEC measurement has led to conflicting data in cancer patients. A validated assay adapted for evaluating the clinical utility of CEC in large cohorts of patients undergoing anti-angiogenic treatments is needed. We developed a four-color flow cytometric assay to measure CEC as CD31(+), CD146(+), CD45(-), 7-amino-actinomycin-D (7AAD)(-) events in whole blood. The distinctive features of the assay are: (1) staining of 1 ml whole blood, (2) use of a whole blood IgPE control to measure accurately background noise, (3) accumulation of a large number of events (almost 5 10(6)) to ensure statistical analysis, and (4) use of 10 microm fluorescent microbeads to evaluate the event size. Assay reproducibility was determined in duplicate aliquots of samples drawn from 20 metastatic cancer patients. Assay linearity was tested by spiking whole blood with low numbers of HUVEC. Five-color flow cytometric experiments with CD144 were performed to confirm the endothelial origin of the cells. CEC were measured in 20 healthy individuals and 125 patients with metastatic cancer. Reproducibility was good between duplicate aliquots (r(2)=0.948, mean difference between duplicates of 0.86 CEC/ml). Detected HUVEC correlated with spiked HUVEC (r(2)=0.916, mean recovery of 100.3%). Co-staining of CD31, CD146 and CD144 confirmed the endothelial nature of cells identified as CEC. Median CEC levels were 6.5/ml (range, 0-15) in healthy individuals and 15.0/ml (range, 0-179) in patients with metastatic carcinoma (p<0.001). The assay proposed here allows reproducible and sensitive measurement of CEC by flow cytometry and could help evaluate CEC as biomarkers of anti-angiogenic therapies in large cohorts of patients.

Abundance and diversity of CO2-fixing bacteria in grassland soils close to natural carbon dioxide springs.

PubMed

Videmsek, Urska; Hagn, Alexandra; Suhadolc, Marjetka; Radl, Viviane; Knicker, Heike; Schloter, Michael; Vodnik, Dominik

2009-07-01

Gaseous conditions at natural CO2 springs (mofettes) affect many processes in these unique ecosystems. While the response of plants to extreme and fluctuating CO2 concentrations ([CO2]) is relatively well documented, little is known on microbial life in mofette soil. Therefore, it was the aim of this study to investigate the abundance and diversity of CO2-fixing bacteria in grassland soils in different distances to a natural carbon dioxide spring. Samples of the same soil type were collected from the Stavesinci mofette, a natural CO2 spring which is known for very pure CO2 emissions, at different distances from the CO2 releasing vents, at locations that clearly differed in soil CO2 efflux (from 12.5 to over 200 micromol CO2 m(-2) s(-1) yearly average). Bulk and rhizospheric soil samples were included into analyses. The microbial response was followed by a molecular analysis of cbbL genes, encoding for the large subunit of RubisCO, a carboxylase which is of crucial importance for C assimilation in chemolitoautotrophic microbes. In all samples analyzed, the "red-like" type of cbbL genes could be detected. In contrast, the "green-like" type of cbbL could not be measured by the applied technique. Surprisingly, a reduction of "red-like" cbbL genes copies was observed in bulk soil and rhizosphere samples from the sites with the highest CO2 concentrations. Furthermore, the diversity pattern of "red-like" cbbL genes changed depending on the CO(2) regime. This indicates that only a part of the autotrophic CO2-fixing microbes could adapt to the very high CO2 concentrations and adverse life conditions that are governed by mofette gaseous regime.

Nitrogen isotopic analyses by isotope-ratio-monitoring gas chromatography/mass spectrometry

NASA Technical Reports Server (NTRS)

Merritt, D. A.; Hayes, J. M.

1994-01-01

Amino acids containing natural-abundance levels of 15N were derivatized and analyzed isotopically using a technique in which individual compounds are separated by gas chromatography, combusted on-line, and the product stream sent directly to an isotope-ratio mass spectrometer. For samples of N2 gas, standard deviations of ratio measurement were better than 0.1% (Units for delta are parts per thousand or per million (%).) for samples larger than 400 pmol and better than 0.5% for samples larger than 25 pmol (0.1% 15N is equivalent to 0.00004 atom % 15N). Results duplicated those of conventional, batchwise analyses to within 0.05%. For combustion of organic compounds yielding CO2/N2 ratios between 14 and 28, in particular for N-acetyl n-propyl derivatives of amino acids, delta values were within 0.25% of results obtained using conventional techniques and standard deviations were better than 0.35%. Pooled data for measurements of all amino acids produced an accuracy and precision of 0.04 and 0.23%, respectively, when 2 nmol of each amino acid was injected on column and 20% of the stream of combustion products was delivered to the mass spectrometer.

Dynamic Changes in Yeast Phosphatase Families Allow for Specialization in Phosphate and Thiamine Starvation.

PubMed

Nahas, John V; Iosue, Christine L; Shaik, Noor F; Selhorst, Kathleen; He, Bin Z; Wykoff, Dennis D

2018-05-10

Convergent evolution is often due to selective pressures generating a similar phenotype. We observe relatively recent duplications in a spectrum of Saccharomycetaceae yeast species resulting in multiple phosphatases that are regulated by different nutrient conditions - thiamine and phosphate starvation. This specialization is both transcriptional and at the level of phosphatase substrate specificity. In Candida glabrata , loss of the ancestral phosphatase family was compensated by the co-option of a different histidine phosphatase family with three paralogs. Using RNA-seq and functional assays, we identify one of these paralogs, CgPMU3 , as a thiamine phosphatase. We further determine that the 81% identical paralog CgPMU2 does not encode thiamine phosphatase activity; however, both are capable of cleaving the phosphatase substrate, 1-napthyl-phosphate. We functionally demonstrate that members of this family evolved novel enzymatic functions for phosphate and thiamine starvation, and are regulated transcriptionally by either nutrient condition, and observe similar trends in other yeast species. This independent, parallel evolution involving two different families of histidine phosphatases suggests that there were likely similar selective pressures on multiple yeast species to recycle thiamine and phosphate. In this work, we focused on duplication and specialization, but there is also repeated loss of phosphatases, indicating that the expansion and contraction of the phosphatase family is dynamic in many Ascomycetes. The dynamic evolution of the phosphatase gene families is perhaps just one example of how gene duplication, co-option, and transcriptional and functional specialization together allow species to adapt to their environment with existing genetic resources. Copyright © 2018, G3: Genes, Genomes, Genetics.

BcMF26a and BcMF26b Are Duplicated Polygalacturonase Genes with Divergent Expression Patterns and Functions in Pollen Development and Pollen Tube Formation in Brassica campestris

PubMed Central

Lyu, Meiling; Yu, Youjian; Jiang, Jingjing; Song, Limin; Liang, Ying; Ma, Zhiming; Xiong, Xingpeng; Cao, Jiashu

2015-01-01

Polygalacturonase (PG) is one of the cell wall hydrolytic enzymes involving in pectin degradation. A comparison of two highly conserved duplicated PG genes, namely, Brassica campestris Male Fertility 26a (BcMF26a) and BcMF26b, revealed the different features of their expression patterns and functions. We found that these two genes were orthologous genes of At4g33440, and they originated from a chromosomal segmental duplication. Although structurally similar, their regulatory and intron sequences largely diverged. QRT-PCR analysis showed that the expression level of BcMF26b was higher than that of BcMF26a in almost all the tested organs and tissues in Brassica campestris. Promoter activity analysis showed that, at reproductive development stages, BcMF26b promoter was active in tapetum, pollen grains, and pistils, whereas BcMF26a promoter was only active in pistils. In the subcellular localization experiment, BcMF26a and BcMF26b proteins could be localized to the cell wall. When the two genes were co-inhibited, pollen intine was formed abnormally and pollen tubes could not grow or stretch. Moreover, the knockout mutants of At4g33440 delayed the growth of pollen tubes. Therefore, BcMF26a/b can participate in the construction of pollen wall by modulating intine information and BcMF26b may play a major role in co-inhibiting transformed plants. PMID:26153985

Aqueous Geochemical Data From the Analysis of Stream-Water Samples Collected in June and July 2005--Taylor Mountains 1:250,000 Scale Quadrangle, Alaska

USGS Publications Warehouse

Wang, Bronwen; Mueller, Seth; Stetson, Sarah; Bailey, Elizabeth; Lee, Greg

2006-01-01

We report on the chemical analysis of water samples collected from the Taylor Mountains 1:250,000-scale quadrangle. Parameters for which data are reported include pH, conductivity, water temperature, major cation and anion concentrations, trace-element concentrations, and dissolved organic-carbon concentrations. Samples were collected as part of a multiyear U.S. Geological Survey project 'Geologic and Mineral Deposit Data for Alaskan Economic Development.' Data presented here are from samples collected in June and July of 2005. The data are being released at this time with minimal interpretation. This is the second release of aqueous geochemical data from this project; 2004 aqueous geochemical data were published previously (Wang and others, 2006). The data in this report augment but do not duplicate or supersede the previous data release. Site selection was based on a regional sampling strategy that focused on first- and second-order drainages. Water sample site selection was based on landscape parameters that included physiography, wetland extent, lithological changes, and a cursory field review of mineralogy from pan concentrates. Stream water in the Taylor Mountians quadrangle is dominated by bicarbonate (HCO3-), though in a few samples more than 50 percent of the anionic charge can be attributed to sulfate (SO42-). The major-cation chemistry ranges from Ca2+/Mg2+ dominated to a mix of Ca2+/Mg2+/Na++K+. In general, good agreement was found between the major cations and anions in the duplicate samples. Many trace elements in these samples were at or near the analytical method detection limit, but good agreement was found between duplicate samples for elements with detectable concentrations. With the exception of a total mercury concentration of 0.33 ng/L detected in a field blank, field blank major-ion and trace-elements concentrations were below detection.

Radiocarbon in Ecosystem Respiration and Soil Pore-Space CO2 with Surface Gas Flux, Air Temperature, and Soil Temperature and Moisture, Barrow, Alaska, 2012-2014

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

Lydia Vaughn; Margaret Torn; Rachel Porras

Dataset includes Delta14C measurements made from CO2 that was collected and purified in 2012-2014 from surface soil chambers, soil pore space, and background atmosphere. In addition to 14CO2 data, dataset includes co-located measurements of CO2 and CH4 flux, soil and air temperature, and soil moisture. Measurements and field samples were taken from intensive study site 1 areas A, B, and C, and the site 0 and AB transects, from specified positions in high-centered, flat-centered, and low centered polygons.

Assessing the potential ecological risk of Co, Cr, Cu, Fe and Zn in the sediments of Hooghly-Matla estuarine system, India.

PubMed

Ghosh, Somdeep; Bakshi, Madhurima; Kumar, Alok; Ramanathan, A L; Biswas, Jayanta Kumar; Bhattacharyya, Subarna; Chaudhuri, Punarbasu; Shaheen, Sabry M; Rinklebe, Jörg

2018-05-09

Hooghly-Matla estuarine system along with the Sundarbans mangroves forms one of the most diverse and vulnerable ecosystems in the world. We have investigated the distribution of Co, Cr, Cu, Fe and Zn along with sediment properties at six locations [Shamshernagar (S1), Kumirmari (S2 and S3), Petuaghat (S4), Tapoban (S5) and Chemaguri (S6)] in the Hooghly estuary and reclaimed islands of the Sundarbans for assessing the degree of contamination and potential ecological risks. Enrichment factor values (0.9-21.6) show enrichment of Co, Cu and Zn in the intertidal sediments considering all sampling locations and depth profiles. Geo-accumulation index values irrespective of sampling locations and depth revealed that Co and Cu are under class II and class III level indicating a moderate contamination of sediments. The pollution load index was higher than unity (1.6-2.1), and Co and Cu were the major contributors to the sediment pollution followed by Zn, Cr and Fe with the minimum values at S1 and the maximum values at S5. The sediments of the Hooghly-Matla estuarine region (S4, S5 and S6) showed considerable ecological risks, when compared with effect range low/effect range median and threshold effect level/probable effect level values. The variation in the distribution of the studied elements may be due to variation in discharge pattern and exposure to industrial effluent and domestic sewage, storm water and agricultural run-off and fluvial dynamics of the region. The study illuminates the necessity for the proper management of vulnerable coastal estuarine ecosystem by stringent pollution control measures along with regular monitoring and checking program.

Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis.

PubMed

Peeters, M; Huang, C L; Vonk, L A; Lu, Z F; Bank, R A; Helder, M N; Doulabi, B Zandieh

2016-11-01

Studies which consider the molecular mechanisms of degeneration and regeneration of cartilaginous tissues are seriously hampered by problematic ribonucleic acid (RNA) isolations due to low cell density and the dense, proteoglycan-rich extracellular matrix of cartilage. Proteoglycans tend to co-purify with RNA, they can absorb the full spectrum of UV light and they are potent inhibitors of polymerase chain reaction (PCR). Therefore, the objective of the present study is to compare and optimise different homogenisation methods and RNA isolation kits for an array of cartilaginous tissues. Tissue samples such as the nucleus pulposus (NP), annulus fibrosus (AF), articular cartilage (AC) and meniscus, were collected from goats and homogenised by either the MagNA Lyser or Freezer Mill. RNA of duplicate samples was subsequently isolated by either TRIzol (benchmark), or the RNeasy Lipid Tissue, RNeasy Fibrous Tissue, or Aurum Total RNA Fatty and Fibrous Tissue kits. RNA yield, purity, and integrity were determined and gene expression levels of type II collagen and aggrecan were measured by real-time PCR. No differences between the two homogenisation methods were found. RNA isolation using the RNeasy Fibrous and Lipid kits resulted in the purest RNA (A260/A280 ratio), whereas TRIzol isolations resulted in RNA that is not as pure, and show a larger difference in gene expression of duplicate samples compared with both RNeasy kits. The Aurum kit showed low reproducibility. For the extraction of high-quality RNA from cartilaginous structures, we suggest homogenisation of the samples by the MagNA Lyser. For AC, NP and AF we recommend the RNeasy Fibrous kit, whereas for the meniscus the RNeasy Lipid kit is advised.Cite this article: M. Peeters, C. L. Huang, L. A. Vonk, Z. F. Lu, R. A. Bank, M. N. Helder, B. Zandieh Doulabi. Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis. Bone Joint Res 2016;5:560-568. DOI: 10.1302/2046-3758.511.BJR-2016-0033.R3. © 2016 Peeters et al.

Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis

PubMed Central

Peeters, M.; Huang, C. L.; Vonk, L. A.; Lu, Z. F.; Bank, R. A.; Doulabi, B. Zandieh

2016-01-01

Objectives Studies which consider the molecular mechanisms of degeneration and regeneration of cartilaginous tissues are seriously hampered by problematic ribonucleic acid (RNA) isolations due to low cell density and the dense, proteoglycan-rich extracellular matrix of cartilage. Proteoglycans tend to co-purify with RNA, they can absorb the full spectrum of UV light and they are potent inhibitors of polymerase chain reaction (PCR). Therefore, the objective of the present study is to compare and optimise different homogenisation methods and RNA isolation kits for an array of cartilaginous tissues. Materials and Methods Tissue samples such as the nucleus pulposus (NP), annulus fibrosus (AF), articular cartilage (AC) and meniscus, were collected from goats and homogenised by either the MagNA Lyser or Freezer Mill. RNA of duplicate samples was subsequently isolated by either TRIzol (benchmark), or the RNeasy Lipid Tissue, RNeasy Fibrous Tissue, or Aurum Total RNA Fatty and Fibrous Tissue kits. RNA yield, purity, and integrity were determined and gene expression levels of type II collagen and aggrecan were measured by real-time PCR. Results No differences between the two homogenisation methods were found. RNA isolation using the RNeasy Fibrous and Lipid kits resulted in the purest RNA (A260/A280 ratio), whereas TRIzol isolations resulted in RNA that is not as pure, and show a larger difference in gene expression of duplicate samples compared with both RNeasy kits. The Aurum kit showed low reproducibility. Conclusion For the extraction of high-quality RNA from cartilaginous structures, we suggest homogenisation of the samples by the MagNA Lyser. For AC, NP and AF we recommend the RNeasy Fibrous kit, whereas for the meniscus the RNeasy Lipid kit is advised. Cite this article: M. Peeters, C. L. Huang, L. A. Vonk, Z. F. Lu, R. A. Bank, M. N. Helder, B. Zandieh Doulabi. Optimisation of high-quality total ribonucleic acid isolation from cartilaginous tissues for real-time polymerase chain reaction analysis. Bone Joint Res 2016;5:560–568. DOI: 10.1302/2046-3758.511.BJR-2016-0033.R3. PMID:27881439

Recurrent duplications of the annexin A1 gene (ANXA1) in autism spectrum disorders

PubMed Central

2014-01-01

Background Validating the potential pathogenicity of copy number variants (CNVs) identified in genome-wide studies of autism spectrum disorders (ASD) requires detailed assessment of case/control frequencies, inheritance patterns, clinical correlations, and functional impact. Here, we characterize a small recurrent duplication in the annexin A1 (ANXA1) gene, identified by the Autism Genome Project (AGP) study. Methods From the AGP CNV genomic screen in 2,147 ASD individuals, we selected for characterization an ANXA1 gene duplication that was absent in 4,964 population-based controls. We further screened the duplication in a follow-up sample including 1,496 patients and 410 controls, and evaluated clinical correlations and family segregation. Sequencing of exonic/downstream ANXA1 regions was performed in 490 ASD patients for identification of additional variants. Results The ANXA1 duplication, overlapping the last four exons and 3’UTR region, had an overall prevalence of 11/3,643 (0.30%) in unrelated ASD patients but was not identified in 5,374 controls. Duplication carriers presented no distinctive clinical phenotype. Family analysis showed neuropsychiatric deficits and ASD traits in multiple relatives carrying the duplication, suggestive of a complex genetic inheritance. Sequencing of exonic regions and the 3’UTR identified 11 novel changes, but no obvious variants with clinical significance. Conclusions We provide multilevel evidence for a role of ANXA1 in ASD etiology. Given its important role as mediator of glucocorticoid function in a wide variety of brain processes, including neuroprotection, apoptosis, and control of the neuroendocrine system, the results add ANXA1 to the growing list of rare candidate genetic etiological factors for ASD. PMID:24720851

CoNVaQ: a web tool for copy number variation-based association studies.

PubMed

Larsen, Simon Jonas; do Canto, Luisa Matos; Rogatto, Silvia Regina; Baumbach, Jan

2018-05-18

Copy number variations (CNVs) are large segments of the genome that are duplicated or deleted. Structural variations in the genome have been linked to many complex diseases. Similar to how genome-wide association studies (GWAS) have helped discover single-nucleotide polymorphisms linked to disease phenotypes, the extension of GWAS to CNVs has aided the discovery of structural variants associated with human traits and diseases. We present CoNVaQ, an easy-to-use web-based tool for CNV-based association studies. The web service allows users to upload two sets of CNV segments and search for genomic regions where the occurrence of CNVs is significantly associated with the phenotype. CoNVaQ provides two models: a simple statistical model using Fisher's exact test and a novel query-based model matching regions to user-defined queries. For each region, the method computes a global q-value statistic by repeated permutation of samples among the populations. We demonstrate our platform by using it to analyze a data set of HPV-positive and HPV-negative penile cancer patients. CoNVaQ provides a simple workflow for performing CNV-based association studies. It is made available as a web platform in order to provide a user-friendly workflow for biologists and clinicians to carry out CNV data analysis without installing any software. Through the web interface, users are also able to analyze their results to find overrepresented GO terms and pathways. In addition, our method is also available as a package for the R programming language. CoNVaQ is available at https://convaq.compbio.sdu.dk .

Analysis of hydroxamate siderophores in soil solution using liquid chromatography with mass spectrometry and tandem mass spectrometry with on-line sample preconcentration.

PubMed

Olofsson, Madelen A; Bylund, Dan

2015-10-01

A liquid chromatography with electrospray ionization mass spectrometry method was developed to quantitatively and qualitatively analyze 13 hydroxamate siderophores (ferrichrome, ferrirubin, ferrirhodin, ferrichrysin, ferricrocin, ferrioxamine B, D1 , E and G, neocoprogen I and II, coprogen and triacetylfusarinine C). Samples were preconcentrated on-line by a switch-valve setup prior to analyte separation on a Kinetex C18 column. Gradient elution was performed using a mixture of an ammonium formate buffer and acetonitrile. Total analysis time including column conditioning was 20.5 min. Analytes were fragmented by applying collision-induced dissociation, enabling structural identification by tandem mass spectrometry. Limit of detection values for the selected ion monitoring method ranged from 71 pM to 1.5 nM with corresponding values of two to nine times higher for the multiple reaction monitoring method. The liquid chromatography with mass spectrometry method resulted in a robust and sensitive quantification of hydroxamate siderophores as indicated by retention time stability, linearity, sensitivity, precision and recovery. The analytical error of the methods, assessed through random-order, duplicate analysis of soil samples extracted with a mixture of 10 mM phosphate buffer and methanol, appears negligible in relation to between-sample variations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Erratum: Retraction Note to: Self-Diagnosis of GFRP Composites Containing Carbon Powder and Fiber as Electrically Conductive Phases

NASA Astrophysics Data System (ADS)

Shin, Soon-Gi

2018-03-01

This article [1] has been retracted at the request of the Editor-in-Chief. Concerns were raised regarding substantial duplications with previous articles published in other journals in which S.-G. Shin is one of the co-authors. After a thorough analysis, we conclude that the concerns are valid.

10 CFR 431.76 - Uniform test method for the measurement of energy efficiency of commercial warm air furnaces.

Code of Federal Regulations, 2010 CFR

2010-01-01

... § 431.75) you must locate one or two sampling tubes within six inches downstream from the flue....75). If you use an open end tube, it must project into the flue one-third of the chimney connector diameter. If you use other methods of sampling CO2, you must place the sampling tube so as to obtain an...

Multistatic Array Sampling Scheme for Fast Near-Field Image Reconstruction

DTIC Science & Technology

2016-01-01

1 Multistatic Array Sampling Scheme for Fast Near-Field Image Reconstruction William F. Moulder, James D. Krieger, Denise T. Maurais-Galejs, Huy...described and validated experimentally with the formation of high quality microwave images. It is further shown that the scheme is more than two orders of... scheme (wherein transmitters and receivers are co-located) which require NTNR transmit-receive elements to achieve the same sampling. The second

Detection of pyrethroid pesticides and their environmental degradation products in duplicate diet samples

EPA Science Inventory

The abstract is for an oral presentation at the Asilomar Conference on Mass Spectrometry: Mass Spectrometry in Environmental Chemistry, Toxicology, and Health. It describes analytical method development and sample results for determination of pyrethroid pesticides and environme...

Transducin Duplicates in the Zebrafish Retina and Pineal Complex: Differential Specialisation after the Teleost Tetraploidisation

PubMed Central

Lagman, David; Callado-Pérez, Amalia; Franzén, Ilkin E.

2015-01-01

Gene duplications provide raw materials that can be selected for functional adaptations by evolutionary mechanisms. We describe here the results of 350 million years of evolution of three functionally related gene families: the alpha, beta and gamma subunits of transducins, the G protein involved in vision. Early vertebrate tetraploidisations resulted in separate transducin heterotrimers: gnat1/gnb1/gngt1 for rods, and gnat2/gnb3/gngt2 for cones. The teleost-specific tetraploidisation generated additional duplicates for gnb1, gnb3 and gngt2. We report here that the duplicates have undergone several types of subfunctionalisation or neofunctionalisation in the zebrafish. We have found that gnb1a and gnb1b are co-expressed at different levels in rods; gnb3a and gnb3b have undergone compartmentalisation restricting gnb3b to the dorsal and medial retina, however, gnb3a expression was detected only at very low levels in both larvae and adult retina; gngt2b expression is restricted to the dorsal and medial retina, whereas gngt2a is expressed ventrally. This dorsoventral distinction could be an adaptation to protect the lower part of the retina from intense light damage. The ontogenetic analysis shows earlier onset of expression in the pineal complex than in the retina, in accordance with its earlier maturation. Additionally, gnb1a but not gnb1b is expressed in the pineal complex, and gnb3b and gngt2b are transiently expressed in the pineal during ontogeny, thus showing partial temporal subfunctionalisation. These retina-pineal distinctions presumably reflect their distinct functional roles in vision and circadian rhythmicity. In summary, this study describes several functional differences between transducin gene duplicates resulting from the teleost-specific tetraploidisation. PMID:25806532

Lack of reliability of nanotechnology in the of free plasma DNA in samples of patients with prostate cancer

PubMed Central

2013-01-01

Background Several studies seek biological markers that give diagnostic and degree of tumor development. The aim of this study was to validate the determination of plasma DNA using nanotechnology (Nanovue™-NV) in samples of 80 patients with prostate cancer. Methods Blood samples of 80 patients of the Urology Ambulatory of Faculdade de Medicina do ABC with prostate cancer confirmed by anatomical-pathology criteria were analyzed. DNA extraction was performed using a GFX TM kit (Amersham Pharmacia Biotech, Inc, USA) following the adapted protocol. Plasma was subjected to centrifugation. Results There was a big difference between the first and the second value obtained by NanoVue Only two samples had no differences between duplicates. Maximum difference between duplicates was 38 μg/mL. Average variation between 51 samples was 10.29 μg/mL, although 21 samples had differences above this average. No correlation was observed between pDNA obtained by traditional spectrophotometry and by nanotechnology. Conclusion Determination of plasma DNA by nanotechnology was not reproducible. PMID:23311763

SPRUCE Peat Physical and Chemical Characteristics from Experimental Plot Cores, 2012

DOE Data Explorer

Iversen, C. M. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Hanson, P. J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Brice, D. J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Phillips, J. R. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; McFarlane, K. J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Hobbie, E. A. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.; Kolka, R. K. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A.

2012-01-01

This data set reports the results of physical and chemical analyses of peat core samples from the SPRUCE experimental study plots located in the S1-Bog. On August 13-15, 2012, a team of SPRUCE investigators and collaborators collected core samples of peat in the SPRUCE experimental plots. The goal was to characterize the biological, physical, and chemical characteristics of peat, and how those characteristics changed throughout the depth profile of the bog, prior to the initialization of the SPRUCE experimental warming and CO2 treatments. Cores were collected from 16 experimental plots; samples were collected from the hummock and hollow surfaces to depths of 200-300 cm in defined increments. Three replicate cores were collected from both hummock and hollow locations in each plot. The coring locations within each plot were mapped

UGT74S1 is the key player in controlling secoisolariciresinol diglucoside (SDG) formation in flax.

PubMed

Fofana, Bourlaye; Ghose, Kaushik; McCallum, Jason; You, Frank M; Cloutier, Sylvie

2017-02-02

Flax lignan, commonly known as secoisolariciresinol (SECO) diglucoside (SDG), has recently been reported with health-promoting activities, including its positive impact in metabolic diseases. However, not much was reported on the biosynthesis of SDG and its monoglucoside (SMG) until lately. Flax UGT74S1 was recently reported to sequentially glucosylate SECO into SMG and SDG in vitro. However, whether this gene is the only UGT achieving SECO glucosylation in flax was not known. Flax genome-wide mining for UGTs was performed. Phylogenetic and gene duplication analyses, heterologous gene expression and enzyme assays were conducted to identify family members closely related to UGT74S1 and to establish their roles in SECO glucosylation. A total of 299 different UGTs were identified, of which 241 (81%) were duplicated. Flax UGTs diverged 2.4-153.6 MYA and 71% were found to be under purifying selection pressure. UGT74S1, a single copy gene located on chromosome 7, displayed no evidence of duplication and was deemed to be under positive selection pressure. The phylogenetic analysis identified four main clusters where cluster 4, which included UGT74S1, was the most diverse. The duplicated UGT74S4 and UGT74S3, located on chromosomes 8 and 14, respectively, were the most closely related to UGT74S1 and were differentially expressed in different tissues. Heterologous expression levels of UGT74S1, UGT74S4 and UGT74S3 proteins were similar but UGT74S4 and UGT74S3 glucosylation activity towards SECO was seven fold less than UGT74S1. In addition, they both failed to produce SDG, suggesting neofunctionalization following their divergence from UGT74S1. We showed that UGT74S1 is closely related to two duplicated genes, UGT74S4 and UGT74S3 which, unlike UGT74S1, failed to glucosylate SMG into SDG. The study suggests that UGT74S1 may be the key player in controlling SECO glucosylation into SDG in flax although its closely related genes may also contribute to a minor extent in supplying the SMG precursor to UGT74S1.

Genome-wide copy number variation analysis in extended families and unrelated individuals characterized for musical aptitude and creativity in music.

PubMed

Ukkola-Vuoti, Liisa; Kanduri, Chakravarthi; Oikkonen, Jaana; Buck, Gemma; Blancher, Christine; Raijas, Pirre; Karma, Kai; Lähdesmäki, Harri; Järvelä, Irma

2013-01-01

Music perception and practice represent complex cognitive functions of the human brain. Recently, evidence for the molecular genetic background of music related phenotypes has been obtained. In order to further elucidate the molecular background of musical phenotypes we analyzed genome wide copy number variations (CNVs) in five extended pedigrees and in 172 unrelated subjects characterized for musical aptitude and creative functions in music. Musical aptitude was defined by combination of the scores of three music tests (COMB scores): auditory structuring ability, Seashores test for pitch and for time. Data on creativity in music (herein composing, improvising and/or arranging music) was surveyed using a web-based questionnaire.Several CNVRs containing genes that affect neurodevelopment, learning and memory were detected. A deletion at 5q31.1 covering the protocadherin-α gene cluster (Pcdha 1-9) was found co-segregating with low music test scores (COMB) in both sample sets. Pcdha is involved in neural migration, differentiation and synaptogenesis. Creativity in music was found to co-segregate with a duplication covering glucose mutarotase gene (GALM) at 2p22. GALM has influence on serotonin release and membrane trafficking of the human serotonin transporter. Interestingly, genes related to serotonergic systems have been shown to associate not only with psychiatric disorders but also with creativity and music perception. Both, Pcdha and GALM, are related to the serotonergic systems influencing cognitive and motor functions, important for music perception and practice. Finally, a 1.3 Mb duplication was identified in a subject with low COMB scores in the region previously linked with absolute pitch (AP) at 8q24. No differences in the CNV burden was detected among the high/low music test scores or creative/non-creative groups. In summary, CNVs and genes found in this study are related to cognitive functions. Our result suggests new candidate genes for music perception related traits and supports the previous results from AP study.

Genome-Wide Copy Number Variation Analysis in Extended Families and Unrelated Individuals Characterized for Musical Aptitude and Creativity in Music

PubMed Central

Oikkonen, Jaana; Buck, Gemma; Blancher, Christine; Raijas, Pirre; Karma, Kai; Lähdesmäki, Harri; Järvelä, Irma

2013-01-01

Music perception and practice represent complex cognitive functions of the human brain. Recently, evidence for the molecular genetic background of music related phenotypes has been obtained. In order to further elucidate the molecular background of musical phenotypes we analyzed genome wide copy number variations (CNVs) in five extended pedigrees and in 172 unrelated subjects characterized for musical aptitude and creative functions in music. Musical aptitude was defined by combination of the scores of three music tests (COMB scores): auditory structuring ability, Seashores test for pitch and for time. Data on creativity in music (herein composing, improvising and/or arranging music) was surveyed using a web-based questionnaire. Several CNVRs containing genes that affect neurodevelopment, learning and memory were detected. A deletion at 5q31.1 covering the protocadherin-α gene cluster (Pcdha 1-9) was found co-segregating with low music test scores (COMB) in both sample sets. Pcdha is involved in neural migration, differentiation and synaptogenesis. Creativity in music was found to co-segregate with a duplication covering glucose mutarotase gene (GALM) at 2p22. GALM has influence on serotonin release and membrane trafficking of the human serotonin transporter. Interestingly, genes related to serotonergic systems have been shown to associate not only with psychiatric disorders but also with creativity and music perception. Both, Pcdha and GALM, are related to the serotonergic systems influencing cognitive and motor functions, important for music perception and practice. Finally, a 1.3 Mb duplication was identified in a subject with low COMB scores in the region previously linked with absolute pitch (AP) at 8q24. No differences in the CNV burden was detected among the high/low music test scores or creative/non-creative groups. In summary, CNVs and genes found in this study are related to cognitive functions. Our result suggests new candidate genes for music perception related traits and supports the previous results from AP study. PMID:23460800

Oculo-auriculo-vertebral spectrum, cat eye, and distal 22q11 microdeletion syndromes: a unique double rearrangement.

PubMed

Torti, Erin E; Braddock, Stephen R; Bernreuter, Kristen; Batanian, Jacqueline R

2013-08-01

An array-CGH on 19-year-old male showed a proximal 1.11 Mb duplication and a distal 1.7 Mb deletion of 22q11.2 regions flanking the Velocardiofacial/DiGeorge syndrome region that remained intact. FISH analyses revealed both abnormalities to be on the same homolog 22. This double rearrangement lead to the co-existence of two syndromes: Cat eye and distal 22q11.2 microdeletion syndromes with a rare associated phenotype of oculo-auriculo-vertebral spectrum (OAVS). A review of the literature indicates that this is the second report of a proximal duplication and the fifth report of a distal deletion and OAVS suggestive of a possible OAVS candidate gene in this region. Copyright © 2013 Wiley Periodicals, Inc.

CoLIde: a bioinformatics tool for CO-expression-based small RNA Loci Identification using high-throughput sequencing data.

PubMed

Mohorianu, Irina; Stocks, Matthew Benedict; Wood, John; Dalmay, Tamas; Moulton, Vincent

2013-07-01

Small RNAs (sRNAs) are 20-25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the genomic location of the constituent sRNAs, hindering existing approaches to identify sRNA loci. To infer the location of significant biological units, we propose an approach for sRNA loci detection called CoLIde (Co-expression based sRNA Loci Identification) that combines genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution. For CoLIde, we define a locus as a union of regions sharing the same pattern and located in close proximity on the genome. Biological relevance, detected through the analysis of size class distribution, is also calculated for each locus. CoLIde can be applied on ordered (e.g., time-dependent) or un-ordered (e.g., organ, mutant) series of samples both with or without biological/technical replicates. The method reliably identifies known types of loci and shows improved performance on sequencing data from both plants (e.g., A. thaliana, S. lycopersicum) and animals (e.g., D. melanogaster) when compared with existing locus detection techniques. CoLIde is available for use within the UEA Small RNA Workbench which can be downloaded from: http://srna-workbench.cmp.uea.ac.uk.

STRIDE: Species Tree Root Inference from Gene Duplication Events.

PubMed

Emms, David M; Kelly, Steven

2017-12-01

The correct interpretation of any phylogenetic tree is dependent on that tree being correctly rooted. We present STRIDE, a fast, effective, and outgroup-free method for identification of gene duplication events and species tree root inference in large-scale molecular phylogenetic analyses. STRIDE identifies sets of well-supported in-group gene duplication events from a set of unrooted gene trees, and analyses these events to infer a probability distribution over an unrooted species tree for the location of its root. We show that STRIDE correctly identifies the root of the species tree in multiple large-scale molecular phylogenetic data sets spanning a wide range of timescales and taxonomic groups. We demonstrate that the novel probability model implemented in STRIDE can accurately represent the ambiguity in species tree root assignment for data sets where information is limited. Furthermore, application of STRIDE to outgroup-free inference of the origin of the eukaryotic tree resulted in a root probability distribution that provides additional support for leading hypotheses for the origin of the eukaryotes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

LISTA, LISTA-HOP and LISTA-HON: a comprehensive compilation of protein encoding sequences and its associated homology databases from the yeast Saccharomyces.

PubMed Central

Dölz, R; Mossé, M O; Slonimski, P P; Bairoch, A; Linder, P

1994-01-01

We continued our effort to make a comprehensive database (LISTA) for the yeast Saccharomyces cerevisiae. In this database each sequence has been attributed a single genetic name. In the case of duplicated sequences a simple method has been applied to distinguish between sequences of one and the same gene from non-allelic sequences of duplicated genes. If necessary, synonyms are given in the case of allelic duplicated sequences. Thus sequences can be found either by the name or by synonyms given in LISTA. Each entry contains the genetic name, the mnemonic from the EMBL data bank, the codon bias, reference of the publication of the sequence, Chromosomal location as far as known, Swissprot and EMBL accession numbers. To obtain more information on the included sequences, each entry has been screened against non-redundant nucleotide and protein data bank collections resulting in LISTA-HON and LISTA-HOP. The LISTA data base can be linked to the associated data sets or to nucleotide and protein banks by the Sequence Retrieval System (SRS). PMID:7937046

75 FR 32866 - Special Local Regulations for Marine Events; Patuxent River, Solomons, MD

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-10

...-9329. To avoid duplication, please use only one of these four methods. See the ``Public Participation... four methods specified under ADDRESSES. Please explain why you believe a public meeting would be... Patuxent River, MD. The start and finish lines will be located near the Solomon's Pier. A large spectator...

32 CFR 286.28 - General provisions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... information pertaining to computer searches. (4) The term “duplication” refers to the process of making a copy...” refers to the process of examining documents located in response to a FOIA request to determine whether... of the expended amount of search time and duplication cost to date. (3) The elements to be considered...

Assessment the impact of samplers change on the uncertainty related to geothermalwater sampling

NASA Astrophysics Data System (ADS)

Wątor, Katarzyna; Mika, Anna; Sekuła, Klaudia; Kmiecik, Ewa

2018-02-01

The aim of this study is to assess the impact of samplers change on the uncertainty associated with the process of the geothermal water sampling. The study was carried out on geothermal water exploited in Podhale region, southern Poland (Małopolska province). To estimate the uncertainty associated with sampling the results of determinations of metasilicic acid (H2SiO3) in normal and duplicate samples collected in two series were used (in each series the samples were collected by qualified sampler). Chemical analyses were performed using ICP-OES method in the certified Hydrogeochemical Laboratory of the Hydrogeology and Engineering Geology Department at the AGH University of Science and Technology in Krakow (Certificate of Polish Centre for Accreditation No. AB 1050). To evaluate the uncertainty arising from sampling the empirical approach was implemented, based on double analysis of normal and duplicate samples taken from the same well in the series of testing. The analyses of the results were done using ROBAN software based on technique of robust statistics analysis of variance (rANOVA). Conducted research proved that in the case of qualified and experienced samplers uncertainty connected with the sampling can be reduced what results in small measurement uncertainty.

Basalt generation at the Apollo 12 site. Part 1: New data, classification, and re-evaluation

NASA Technical Reports Server (NTRS)

Neal, Clive R.; Hacker, Matthew D.; Snyder, Gregory A.; Taylor, Lawrence A.; Liu, Yun-Gang; Schmitt, Roman A.

1994-01-01

New data are reported from five previously unanalyzed Apollo 12 mare basalts that are incorporated into an evaluation of previous petrogenetic models and classification schemes for these basalts. This paper proposes a classification for Apollo 12 mare basalts on the basis of whole-rock Mg# (molar 100*(Mg/(Mg+Fe))) and Rb/Sr ratio (analyzed by isotope dilution), whereby the ilmenite, olivine, and pigeonite basalt groups are readily distinguished from each other. Scrutiny of the Apollo 12 feldspathic 'suite' demonstrates that two of the three basalts previously assigned to this group (12031, 12038, 12072) can be reclassified: 12031 is a plagioclase-rich pigeonite basalt; and 12072 is an olivine basalt. Only basalt 12038 stands out as a unique sample to the Apollo 12 site, but whether this represents a single sample from another flow at the Apollo 12 site or is exotic to this site is equivocal. The question of whether the olivine and pigeonite basalt suites are co-magmatic is addressed by incompatible trace-element chemistry: the trends defined by these two suites when Co/Sm and Sm/Eu ratios are plotted against Rb/Sr ratio demonstrate that these two basaltic types cannot be co-magmatic. Crystal fractionation/accumulation paths have been calculated and show that neither the pigeonite, olivine, or ilmenite basalts are related by this process. Each suite requires a distinct and separate source region. This study also examines sample heterogeneity and the degree to which whole-rock analyses are representative, which is critical when petrogenetic interpretation is undertaken. Sample heterogeneity has been investigated petrographically (inhomogeneous mineral distribution) with consideration of duplicate analyses, and whether a specific sample (using average data) plots consistently upon a fractionation trend when a number of different compostional parameters are considered. Using these criteria, four basalts have been identified where reported analyses are not representative of the whole-rock composition: 12005, an ilmenite basalt; 12006 and 12036, olivine basalts; and 12031 previously classified as a feldspathic basalt, but reclassified as part of the pigeonite suite.

Estimation of pyrethroid pesticide intake using regression modeling of food groups based on composite dietary samples

EPA Science Inventory

Population-based estimates of pesticide intake are needed to characterize exposure for particular demographic groups based on their dietary behaviors. Regression modeling performed on measurements of selected pesticides in composited duplicate diet samples allowed (1) estimation ...

Estimation of pyrethroid pesticide intake using regression modeling of food groups based on composite dietary samples..

EPA Science Inventory

Population-based estimates of pesticide intake are needed to characterize exposure for particular demographic groups based on their dietary behaviors. Regression modeling performed on measurements of selected pesticides in composited duplicate diet samples allowed (1) estimation ...

Estimation of pyrethroid pesticide intake using regression modeling of food groups based on composite dietary samples.

EPA Science Inventory

Population-based estimates of pesticide intake are needed to characterize exposure for particular demographic groups based on their dietary behaviors. Regression modeling performed on measurements of selected pesticides in composited duplicate diet samples allowed (1) estimation ...

Nicotine in environmental tobacco smoke (ETS): Comparison of mobile personal and stationary area sampling

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

Jenkins, R.A.; Moody, R.L.; Higgins, C.E.

1991-01-01

Previous investigations of personal vs. area sampling of ambient nicotine may not accurately reflect personal exposure to ETS nicotine in environments in which individuals are relatively mobile. The purpose of this study was to determine the extent to which a stationary area sampler could estimate actual personal exposure to ambient nicotine when the exposed individuals are moving in and through a field environment. For this study, personal samplers using Tenax, and area samplers using XAD-4, were employed. Evaluations of the two systems using controlled experimental atmospheres of ETS revealed no differences in the measured nicotine levels over a range ofmore » 1.0--150 {mu}g/m{sup 3}. Field studies were conductd at approximately 30 locations, including taverns, restaurants with salad bars, laundromats, gaming establishments, and transportation waiting areas. Ambient nicotine levels ranged from 0.0--90.6 {mu}g/m{sup 3}. There were considerable differences in individual nicotine levels over relatively short distances within a given environment, probably due to atmospheric inhomogeneities. The variability between duplicate samples of a particular type was such that no statistically significant difference between stationary area and mobile personal samplers could be discerned. 17 refs., 2 tabs.« less

Improved high-dimensional prediction with Random Forests by the use of co-data.

PubMed

Te Beest, Dennis E; Mes, Steven W; Wilting, Saskia M; Brakenhoff, Ruud H; van de Wiel, Mark A

2017-12-28

Prediction in high dimensional settings is difficult due to the large number of variables relative to the sample size. We demonstrate how auxiliary 'co-data' can be used to improve the performance of a Random Forest in such a setting. Co-data are incorporated in the Random Forest by replacing the uniform sampling probabilities that are used to draw candidate variables by co-data moderated sampling probabilities. Co-data here are defined as any type information that is available on the variables of the primary data, but does not use its response labels. These moderated sampling probabilities are, inspired by empirical Bayes, learned from the data at hand. We demonstrate the co-data moderated Random Forest (CoRF) with two examples. In the first example we aim to predict the presence of a lymph node metastasis with gene expression data. We demonstrate how a set of external p-values, a gene signature, and the correlation between gene expression and DNA copy number can improve the predictive performance. In the second example we demonstrate how the prediction of cervical (pre-)cancer with methylation data can be improved by including the location of the probe relative to the known CpG islands, the number of CpG sites targeted by a probe, and a set of p-values from a related study. The proposed method is able to utilize auxiliary co-data to improve the performance of a Random Forest.

Atmospheric CO2 Records from Sites Operated by the Fraunhofer Institute for Atmospheric Environment Research (1978 - 1992)

DOE Data Explorer

Sladkovic, R. [Fraunhofer Institute for Atmospheric Environmental Research (IFU), Garmisch-Partenkirchen, Germany; Scheel, H. E. [Fraunhofer Institute for Atmospheric Environmental Research (IFU), Garmisch-Partenkirchen, Germany; Seiler, W. [Fraunhofer Institute for Atmospheric Environmental Research (IFU), Garmisch-Partenkirchen, Germany

1997-01-01

The monitoring site at Garmisch-Partenkirchen is considered a grassland valley site. Because of strong local influence (vegetation and meteorology), the CO2 concentrations at Garmisch-Partenkirchen are higher and show greater seasonal amplitudes than the concentrations measured at Wank or Zugspitze. According to the filtered data, the annual atmospheric CO2 concentrations at Garmisch-Partenkirchen increased from 330.2 ppmv in 1978 to 345.1 ppmv in 1986 and from 347.6 ppmv in 1988 to 354.7 ppmv in 1992. The monitoring site at Wank Peak (WMO-BAPMoN station) is located on the grass-covered, rounded top of the mountain, just above the timberline. The mean annual CO2 concentrations at Wank Peak increased from 334.2 ppmv in 1980 to 348.6 ppmv in 1992. The station at Zugspitze is located near the summit of the highest mountain of the German Alps. In 1990, the site of CO2 sampling was changed from a location 250 m below the summit to a new monitoring station (2937 m above MSL) close to the mountain top. Compatibility of the results was seen from measurements conducted in parallel at the two sites for several months. Because of the high elevation of the mountain station, the CO2 measurements at Zugspitze can be considered free of regional contamination most of the time. The mean annual CO2 concentrations at Zugspitze increased from 333.7 ppmv in 1981 to 349.4 ppmv in 1992.

Eddy-Current Reference Standard

NASA Technical Reports Server (NTRS)

Ambrose, H. H., Jr.

1985-01-01

Magnetic properties of metallic reference standards duplicated and stabilized for eddy-current coil measurements over long times. Concept uses precisely machined notched samples of known annealed materials as reference standards.

Air quality monitoring of the post-operative recovery room and locations surrounding operating theaters in a medical center in Taiwan.

PubMed

Tang, Chin-Sheng; Wan, Gwo-Hwa

2013-01-01

To prevent surgical site infection (SSI), the airborne microbial concentration in operating theaters must be reduced. The air quality in operating theaters and nearby areas is also important to healthcare workers. Therefore, this study assessed air quality in the post-operative recovery room, locations surrounding the operating theater area, and operating theaters in a medical center. Temperature, relative humidity (RH), and carbon dioxide (CO2), suspended particulate matter (PM), and bacterial concentrations were monitored weekly over one year. Measurement results reveal clear differences in air quality in different operating theater areas. The post-operative recovery room had significantly higher CO2 and bacterial concentrations than other locations. Bacillus spp., Micrococcus spp., and Staphylococcus spp. bacteria often existed in the operating theater area. Furthermore, Acinetobacter spp. was the main pathogen in the post-operative recovery room (18%) and traumatic surgery room (8%). The mixed effect models reveal a strong correlation between number of people in a space and high CO2 concentration after adjusting for sampling locations. In conclusion, air quality in the post-operative recovery room and operating theaters warrants attention, and merits long-term surveillance to protect both surgical patients and healthcare workers.

Natural Genetic Transformation Generates a Population of Merodiploids in Streptococcus pneumoniae

PubMed Central

Zomer, Aldert; Bootsma, Hester J.; Prudhomme, Marc; Granadel, Chantal; Hermans, Peter W. M.; Polard, Patrice; Martin, Bernard; Claverys, Jean-Pierre

2013-01-01

Partial duplication of genetic material is prevalent in eukaryotes and provides potential for evolution of new traits. Prokaryotes, which are generally haploid in nature, can evolve new genes by partial chromosome duplication, known as merodiploidy. Little is known about merodiploid formation during genetic exchange processes, although merodiploids have been serendipitously observed in early studies of bacterial transformation. Natural bacterial transformation involves internalization of exogenous donor DNA and its subsequent integration into the recipient genome by homology. It contributes to the remarkable plasticity of the human pathogen Streptococcus pneumoniae through intra and interspecies genetic exchange. We report that lethal cassette transformation produced merodiploids possessing both intact and cassette-inactivated copies of the essential target gene, bordered by repeats (R) corresponding to incomplete copies of IS861. We show that merodiploidy is transiently stimulated by transformation, and only requires uptake of a ∼3-kb DNA fragment partly repeated in the chromosome. We propose and validate a model for merodiploid formation, providing evidence that tandem-duplication (TD) formation involves unequal crossing-over resulting from alternative pairing and interchromatid integration of R. This unequal crossing-over produces a chromosome dimer, resolution of which generates a chromosome with the TD and an abortive chromosome lacking the duplicated region. We document occurrence of TDs ranging from ∼100 to ∼900 kb in size at various chromosomal locations, including by self-transformation (transformation with recipient chromosomal DNA). We show that self-transformation produces a population containing many different merodiploid cells. Merodiploidy provides opportunities for evolution of new genetic traits via alteration of duplicated genes, unrestricted by functional selective pressure. Transient stimulation of a varied population of merodiploids by transformation, which can be triggered by stresses such as antibiotic treatment in S. pneumoniae, reinforces the plasticity potential of this bacterium and transformable species generally. PMID:24086154

Fatty acid-binding protein genes of the ancient, air-breathing, ray-finned fish, spotted gar (Lepisosteus oculatus).

PubMed

Venkatachalam, Ananda B; Fontenot, Quenton; Farrara, Allyse; Wright, Jonathan M

2018-03-01

With the advent of high-throughput DNA sequencing technology, the genomic sequence of many disparate species has led to the relatively new discipline of genomics, the study of genome structure, function and evolution. Much work has been focused on the role of whole genome duplications (WGD) in the architecture of extant vertebrate genomes, particularly those of teleost fishes which underwent a WGD early in the teleost radiation >230 million years ago (mya). Our past work has focused on the fate of duplicated copies of a multigene family coding for the intracellular lipid-binding protein (iLBP) genes in the teleost fishes. To define the evolutionary processes that determined the fate of duplicated genes and generated the structure of extant fish genomes, however, requires comparative genomic analysis with a fish lineage that diverged before the teleost WGD, such as the spotted gar (Lepisosteus oculatus), an ancient, air-breathing, ray-finned fish. Here, we describe the genomic organization, chromosomal location and tissue-specific expression of a subfamily of the iLBP genes that code for fatty acid-binding proteins (Fabps) in spotted gar. Based on this work, we have defined the minimum suite of fabp genes prior to their duplication in the teleost lineages ~230-400 mya. Spotted gar, therefore, serves as an appropriate outgroup, or ancestral/ancient fish, that did not undergo the teleost-specific WGD. As such, analyses of the spatio-temporal regulation of spotted gar genes provides a foundation to determine whether the duplicated fabp genes have been retained in teleost genomes owing to either sub- or neofunctionalization. Copyright © 2017 Elsevier Inc. All rights reserved.

Duplicated Enhancer Region Increases Expression of CTSB and Segregates with Keratolytic Winter Erythema in South African and Norwegian Families.

PubMed

Ngcungcu, Thandiswa; Oti, Martin; Sitek, Jan C; Haukanes, Bjørn I; Linghu, Bolan; Bruccoleri, Robert; Stokowy, Tomasz; Oakeley, Edward J; Yang, Fan; Zhu, Jiang; Sultan, Marc; Schalkwijk, Joost; van Vlijmen-Willems, Ivonne M J J; von der Lippe, Charlotte; Brunner, Han G; Ersland, Kari M; Grayson, Wayne; Buechmann-Moller, Stine; Sundnes, Olav; Nirmala, Nanguneri; Morgan, Thomas M; van Bokhoven, Hans; Steen, Vidar M; Hull, Peter R; Szustakowski, Joseph; Staedtler, Frank; Zhou, Huiqing; Fiskerstrand, Torunn; Ramsay, Michele

2017-05-04

Keratolytic winter erythema (KWE) is a rare autosomal-dominant skin disorder characterized by recurrent episodes of palmoplantar erythema and epidermal peeling. KWE was previously mapped to 8p23.1-p22 (KWE critical region) in South African families. Using targeted resequencing of the KWE critical region in five South African families and SNP array and whole-genome sequencing in two Norwegian families, we identified two overlapping tandem duplications of 7.67 kb (South Africans) and 15.93 kb (Norwegians). The duplications segregated with the disease and were located upstream of CTSB, a gene encoding cathepsin B, a cysteine protease involved in keratinocyte homeostasis. Included in the 2.62 kb overlapping region of these duplications is an enhancer element that is active in epidermal keratinocytes. The activity of this enhancer correlated with CTSB expression in normal differentiating keratinocytes and other cell lines, but not with FDFT1 or NEIL2 expression. Gene expression (qPCR) analysis and immunohistochemistry of the palmar epidermis demonstrated significantly increased expression of CTSB, as well as stronger staining of cathepsin B in the stratum granulosum of affected individuals than in that of control individuals. Analysis of higher-order chromatin structure data and RNA polymerase II ChIA-PET data from MCF-7 cells did not suggest remote effects of the enhancer. In conclusion, KWE in South African and Norwegian families is caused by tandem duplications in a non-coding genomic region containing an active enhancer element for CTSB, resulting in upregulation of this gene in affected individuals. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Natural genetic transformation generates a population of merodiploids in Streptococcus pneumoniae.

PubMed

Johnston, Calum; Caymaris, Stéphanie; Zomer, Aldert; Bootsma, Hester J; Prudhomme, Marc; Granadel, Chantal; Hermans, Peter W M; Polard, Patrice; Martin, Bernard; Claverys, Jean-Pierre

2013-01-01

Partial duplication of genetic material is prevalent in eukaryotes and provides potential for evolution of new traits. Prokaryotes, which are generally haploid in nature, can evolve new genes by partial chromosome duplication, known as merodiploidy. Little is known about merodiploid formation during genetic exchange processes, although merodiploids have been serendipitously observed in early studies of bacterial transformation. Natural bacterial transformation involves internalization of exogenous donor DNA and its subsequent integration into the recipient genome by homology. It contributes to the remarkable plasticity of the human pathogen Streptococcus pneumoniae through intra and interspecies genetic exchange. We report that lethal cassette transformation produced merodiploids possessing both intact and cassette-inactivated copies of the essential target gene, bordered by repeats (R) corresponding to incomplete copies of IS861. We show that merodiploidy is transiently stimulated by transformation, and only requires uptake of a ~3-kb DNA fragment partly repeated in the chromosome. We propose and validate a model for merodiploid formation, providing evidence that tandem-duplication (TD) formation involves unequal crossing-over resulting from alternative pairing and interchromatid integration of R. This unequal crossing-over produces a chromosome dimer, resolution of which generates a chromosome with the TD and an abortive chromosome lacking the duplicated region. We document occurrence of TDs ranging from ~100 to ~900 kb in size at various chromosomal locations, including by self-transformation (transformation with recipient chromosomal DNA). We show that self-transformation produces a population containing many different merodiploid cells. Merodiploidy provides opportunities for evolution of new genetic traits via alteration of duplicated genes, unrestricted by functional selective pressure. Transient stimulation of a varied population of merodiploids by transformation, which can be triggered by stresses such as antibiotic treatment in S. pneumoniae, reinforces the plasticity potential of this bacterium and transformable species generally.

Dried blood spot measurement: application in tacrolimus monitoring using limited sampling strategy and abbreviated AUC estimation.

PubMed

Cheung, Chi Yuen; van der Heijden, Jaques; Hoogtanders, Karin; Christiaans, Maarten; Liu, Yan Lun; Chan, Yiu Han; Choi, Koon Shing; van de Plas, Afke; Shek, Chi Chung; Chau, Ka Foon; Li, Chun Sang; van Hooff, Johannes; Stolk, Leo

2008-02-01

Dried blood spot (DBS) sampling and high-performance liquid chromatography tandem-mass spectrometry have been developed in monitoring tacrolimus levels. Our center favors the use of limited sampling strategy and abbreviated formula to estimate the area under concentration-time curve (AUC(0-12)). However, it is inconvenient for patients because they have to wait in the center for blood sampling. We investigated the application of DBS method in tacrolimus level monitoring using limited sampling strategy and abbreviated AUC estimation approach. Duplicate venous samples were obtained at each time point (C(0), C(2), and C(4)). To determine the stability of blood samples, one venous sample was sent to our laboratory immediately. The other duplicate venous samples, together with simultaneous fingerprick blood samples, were sent to the University of Maastricht in the Netherlands. Thirty six patients were recruited and 108 sets of blood samples were collected. There was a highly significant relationship between AUC(0-12), estimated from venous blood samples, and fingerprick blood samples (r(2) = 0.96, P < 0.0001). Moreover, there was an excellent correlation between whole blood venous tacrolimus levels in the two centers (r(2) = 0.97; P < 0.0001). The blood samples were stable after long-distance transport. DBS sampling can be used in centers using limited sampling and abbreviated AUC(0-12) strategy as drug monitoring.

Adrenal GIPR expression and chromosome 19q13 microduplications in GIP-dependent Cushing’s syndrome

PubMed Central

Lecoq, Anne-Lise; Stratakis, Constantine A.; Viengchareun, Say; Chaligné, Ronan; Tosca, Lucie; Hage, Mirella; Berthon, Annabel; Faucz, Fabio R.; Hanna, Patrick; Boyer, Hadrien-Gaël; Servant, Nicolas; Salenave, Sylvie; Tachdjian, Gérard; Adam, Clovis; Benhamo, Vanessa; Clauser, Eric; Guiochon-Mantel, Anne; Young, Jacques; Lombès, Marc; Bourdeau, Isabelle; Maiter, Dominique; Tabarin, Antoine; Bertherat, Jérôme; Lefebvre, Hervé; Louiset, Estelle; Lacroix, André; Bouligand, Jérôme; Kamenický, Peter

2017-01-01

GIP-dependent Cushing’s syndrome is caused by ectopic expression of glucose-dependent insulinotropic polypeptide receptor (GIPR) in cortisol-producing adrenal adenomas or in bilateral macronodular adrenal hyperplasias. Molecular mechanisms leading to ectopic GIPR expression in adrenal tissue are not known. Here we performed molecular analyses on adrenocortical adenomas and bilateral macronodular adrenal hyperplasias obtained from 14 patients with GIP-dependent adrenal Cushing’s syndrome and one patient with GIP-dependent aldosteronism. GIPR expression in all adenoma and hyperplasia samples occurred through transcriptional activation of a single allele of the GIPR gene. While no abnormality was detected in proximal GIPR promoter methylation, we identified somatic duplications in chromosome region 19q13.32 containing the GIPR locus in the adrenocortical lesions derived from 3 patients. In 2 adenoma samples, the duplicated 19q13.32 region was rearranged with other chromosome regions, whereas a single tissue sample with hyperplasia had a 19q duplication only. We demonstrated that juxtaposition with cis-acting regulatory sequences such as glucocorticoid response elements in the newly identified genomic environment drives abnormal expression of the translocated GIPR allele in adenoma cells. Altogether, our results provide insight into the molecular pathogenesis of GIP-dependent Cushing’s syndrome, occurring through monoallelic transcriptional activation of GIPR driven in some adrenal lesions by structural variations. PMID:28931750

Expansion of the receptor-like kinase/Pelle gene family and receptor-like proteins in Arabidopsis.

PubMed

Shiu, Shin Han; Bleecker, Anthony B

2003-06-01

Receptor-like kinases (RLKs) are a family of transmembrane proteins with versatile N-terminal extracellular domains and C-terminal intracellular kinases. They control a wide range of physiological responses in plants and belong to one of the largest gene families in the Arabidopsis genome with more than 600 members. Interestingly, this gene family constitutes 60% of all kinases in Arabidopsis and accounts for nearly all transmembrane kinases in Arabidopsis. Analysis of four fungal, six metazoan, and two Plasmodium sp. genomes indicates that the family was represented in all but fungal genomes, indicating an ancient origin for the family with a more recent expansion only in the plant lineages. The RLK/Pelle family can be divided into several subfamilies based on three independent criteria: the phylogeny based on kinase domain sequences, the extracellular domain identities, and intron locations and phases. A large number of receptor-like proteins (RLPs) resembling the extracellular domains of RLKs are also found in the Arabidopsis genome. However, not all RLK subfamilies have corresponding RLPs. Several RLK/Pelle subfamilies have undergone differential expansions. More than 33% of the RLK/Pelle members are found in tandem clusters, substantially higher than the genome average. In addition, 470 of the RLK/Pelle family members are located within the segmentally duplicated regions in the Arabidopsis genome and 268 of them have a close relative in the corresponding regions. Therefore, tandem duplications and segmental/whole-genome duplications represent two of the major mechanisms for the expansion of the RLK/Pelle family in Arabidopsis.

Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta)

PubMed Central

2010-01-01

Background Diatoms are one of the most species-rich groups of eukaryotic microbes known. Diatoms are also the only group of eukaryotic micro-algae with a diplontic life history, suggesting that the ancestral diatom switched to a life history dominated by a duplicated genome. A key mechanism of speciation among diatoms could be a propensity for additional stable genome duplications. Across eukaryotic taxa, genome size is directly correlated to cell size and inversely correlated to physiological rates. Differences in relative genome size, cell size, and acclimated growth rates were analyzed in isolates of the diatom Ditylum brightwellii. Ditylum brightwellii consists of two main populations with identical 18s rDNA sequences; one population is distributed globally at temperate latitudes and the second appears to be localized to the Pacific Northwest coast of the USA. These two populations co-occur within the Puget Sound estuary of WA, USA, although their peak abundances differ depending on local conditions. Results All isolates from the more regionally-localized population (population 2) possessed 1.94 ± 0.74 times the amount of DNA, grew more slowly, and were generally larger than isolates from the more globally distributed population (population 1). The ITS1 sequences, cell sizes, and genome sizes of isolates from New Zealand were the same as population 1 isolates from Puget Sound, but their growth rates were within the range of the slower-growing population 2 isolates. Importantly, the observed genome size difference between isolates from the two populations was stable regardless of time in culture or the changes in cell size that accompany the diatom life history. Conclusions The observed two-fold difference in genome size between the D. brightwellii populations suggests that whole genome duplication occurred within cells of population 1 ultimately giving rise to population 2 cells. The apparent regional localization of population 2 is consistent with a recent divergence between the populations, which are likely cryptic species. Genome size variation is known to occur in other diatom genera; we hypothesize that genome duplication may be an active and important mechanism of genetic and physiological diversification and speciation in diatoms. PMID:20044934

NDIA 2018 IM and EM Technology Symposium: Innovative Insensitive Munition Solutions for Enhanced Warfighter Effectiveness

DTIC Science & Technology

2018-04-26

decomposition of explosives, test materials and their mixtures. A DSC for each individual explosive, test material and mixture shall be run in duplicate... run in duplicate • Explosives and test materials are mixed in a 1:1 (w/w) ratio • Samples are heated at a rate of 5°C/min from room temperature to...warrants it. If a reaction occurs in ten trials, the load is reduced until there are no reactions observed in ten trials. The ESD test was run per a

Spatiotemporal variability of carbon dioxide and methane in a eutrophic lake

NASA Astrophysics Data System (ADS)

Loken, Luke; Crawford, John; Schramm, Paul; Stadler, Philipp; Stanley, Emily

2017-04-01

Lakes are important regulators of global carbon cycling and conduits of greenhouse gases to the atmosphere; however, most efflux estimates for individual lakes are based on extrapolations from a single location. Within-lake variability in carbon dioxide (CO2) and methane (CH4) arises from differences in water sources, physical mixing, and local transformations; all of which can be influenced by anthropogenic disturbances and vary at multiple temporal and spatial scales. During the 2016 open water season (March - December), we mapped surface water concentrations of CO2 and CH4 weekly in a eutrophic lake (Lake Mendota, WI, USA), which has a predominately agricultural and urban watershed. In total we produced 26 maps of each gas based on 10,000 point measurements distributed across the lake surface. Both gases displayed relatively consistent spatial patterns over the stratified period but exhibited remarkable heterogeneity on each sample date. CO2 was generally undersaturated (global mean: 0.84X atmospheric saturation) throughout the lake's pelagic zone and often differed near river inlets and shorelines. The lake was routinely extremely supersaturated with CH4 (global mean: 105X atmospheric saturation) with greater concentrations in littoral areas that contained organic-rich sediments. During fall mixis, both CO2 and CH4 increased substantially, and concentrations were not uniform across the lake surface. CO2 and CH4 were higher on the upwind side of the lake due to upwelling of enriched hypolimnetic water. While the lake acted as a modest sink for atmospheric CO2 during the stratified period, the lake released substantial amounts of CO2 during turnover and continually emitted CH4, offsetting any reduction in atmospheric warming potential from summertime CO2 uptake. These data-rich maps illustrate how lake-wide surface concentrations and lake-scale efflux estimates based on single point measurements diverge from spatially weighted calculations. Both gases are not well represented by a sample collected at lake's central buoy, and thus, extrapolations from a single sampling location may not be adequate to assess lake-wide CO2 and CH4 dynamics in human-dominated landscapes.

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

Gonzales-Vigil, Eliana; Bianchetti, Christopher M.; Phillips, Jr., George N.

Gene duplication is a major source of plant chemical diversity that mediates plant-herbivore interactions. There is little direct evidence, however, that novel chemical traits arising from gene duplication reduce herbivory. Higher plants use threonine deaminase (TD) to catalyze the dehydration of threonine (Thr) to {alpha}-ketobutyrate and ammonia as the committed step in the biosynthesis of isoleucine (Ile). Cultivated tomato and related Solanum species contain a duplicated TD paralog (TD2) that is coexpressed with a suite of genes involved in herbivore resistance. Analysis of TD2-deficient tomato lines showed that TD2 has a defensive function related to Thr catabolism in the gutmore » of lepidopteran herbivores. During herbivory, the regulatory domain of TD2 is removed by proteolysis to generate a truncated protein (pTD2) that efficiently degrades Thr without being inhibited by Ile. We show that this proteolytic activation step occurs in the gut of lepidopteran but not coleopteran herbivores, and is catalyzed by a chymotrypsin-like protease of insect origin. Analysis of purified recombinant enzymes showed that TD2 is remarkably more resistant to proteolysis and high temperature than the ancestral TD1 isoform. The crystal structure of pTD2 provided evidence that electrostatic interactions constitute a stabilizing feature associated with adaptation of TD2 to the extreme environment of the lepidopteran gut. These findings demonstrate a role for gene duplication in the evolution of a plant defense that targets and co-opts herbivore digestive physiology.« less

Functional characterization of duplicated Suppressor of Overexpression of Constans 1-like genes in petunia.

PubMed

Preston, Jill C; Jorgensen, Stacy A; Jha, Suryatapa G

2014-01-01

Flowering time is strictly controlled by a combination of internal and external signals that match seed set with favorable environmental conditions. In the model plant species Arabidopsis thaliana (Brassicaceae), many of the genes underlying development and evolution of flowering have been discovered. However, much remains unknown about how conserved the flowering gene networks are in plants with different growth habits, gene duplication histories, and distributions. Here we functionally characterize three homologs of the flowering gene Suppressor Of Overexpression of Constans 1 (SOC1) in the short-lived perennial Petunia hybrida (petunia, Solanaceae). Similar to A. thaliana soc1 mutants, co-silencing of duplicated petunia SOC1-like genes results in late flowering. This phenotype is most severe when all three SOC1-like genes are silenced. Furthermore, expression levels of the SOC1-like genes Unshaven (UNS) and Floral Binding Protein 21 (FBP21), but not FBP28, are positively correlated with developmental age. In contrast to A. thaliana, petunia SOC1-like gene expression did not increase with longer photoperiods, and FBP28 transcripts were actually more abundant under short days. Despite evidence of functional redundancy, differential spatio-temporal expression data suggest that SOC1-like genes might fine-tune petunia flowering in response to photoperiod and developmental stage. This likely resulted from modification of SOC1-like gene regulatory elements following recent duplication, and is a possible mechanism to ensure flowering under both inductive and non-inductive photoperiods.

Functional Characterization of Duplicated SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1-Like Genes in Petunia

PubMed Central

Preston, Jill C.; Jorgensen, Stacy A.; Jha, Suryatapa G.

2014-01-01

Flowering time is strictly controlled by a combination of internal and external signals that match seed set with favorable environmental conditions. In the model plant species Arabidopsis thaliana (Brassicaceae), many of the genes underlying development and evolution of flowering have been discovered. However, much remains unknown about how conserved the flowering gene networks are in plants with different growth habits, gene duplication histories, and distributions. Here we functionally characterize three homologs of the flowering gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) in the short-lived perennial Petunia hybrida (petunia, Solanaceae). Similar to A. thaliana soc1 mutants, co-silencing of duplicated petunia SOC1-like genes results in late flowering. This phenotype is most severe when all three SOC1-like genes are silenced. Furthermore, expression levels of the SOC1-like genes UNSHAVEN (UNS) and FLORAL BINDING PROTEIN 21 (FBP21), but not FBP28, are positively correlated with developmental age. In contrast to A. thaliana, petunia SOC1-like gene expression did not increase with longer photoperiods, and FBP28 transcripts were actually more abundant under short days. Despite evidence of functional redundancy, differential spatio-temporal expression data suggest that SOC1-like genes might fine-tune petunia flowering in response to photoperiod and developmental stage. This likely resulted from modification of SOC1-like gene regulatory elements following recent duplication, and is a possible mechanism to ensure flowering under both inductive and non-inductive photoperiods. PMID:24787903

An inexpensive light-scattering particle monitor: field validation

PubMed Central

Edwards, Rufus D.; Johnson, Michael; Shields, Kyra Naumoff; Allen, Tracy; Canuz, Eduardo; Smith, Kirk R.

2014-01-01

We have developed a small, light, passive, inexpensive, datalogging particle monitor called the “UCB” (University of California Berkeley particle monitor). Following previously published laboratory assessments, we present here results of tests of its performance in field settings at high particle concentrations. We demonstrate the mass sensitivity of the UCB in relation to gravimetric filter-based PM2.5 mass estimates as well as commercial light-scattering instruments co-located in field chamber tests and in kitchens of wood-burning households. The coefficient of variation of the unadjusted UCB mass response in relation to gravimetric estimates was 15%. Although requiring adjustment for differences in sensitivity, inter-monitor performance was consistently high (r2 > 0.99). Moreover, the UCB can consistently estimate PM2.5 mass concentrations in wood-burning kitchens (Pearson r2 = 0.89; N = 99), with good agreement between duplicate measures (Pearson r2 = 0.94; N = 88). In addition, with appropriate cleaning of the sensing chamber, UCB mass sensitivity does not decrease with time when used intensively in open woodfire kitchens, demonstrating the significant potential of this monitor. PMID:17909644

Biomass Burning Emissions of Black Carbon from African Sources

NASA Astrophysics Data System (ADS)

Aiken, A. C.; Leone, O.; Nitschke, K. L.; Dubey, M. K.; Carrico, C.; Springston, S. R.; Sedlacek, A. J., III; Watson, T. B.; Kuang, C.; Uin, J.; McMeeking, G. R.; DeMott, P. J.; Kreidenweis, S. M.; Robinson, A. L.; Yokelson, R. J.; Zuidema, P.

2016-12-01

Biomass burning (BB) emissions are a large source of carbon to the atmosphere via particles and gas phase species. Carbonaceous aerosols are emitted along with gas-phase carbon monoxide (CO) and carbon dioxide (CO2) that can be used to determine particulate emission ratios and modified combustion efficiencies. Black carbon (BC) aerosols are potentially underestimated in global models and are considered to be one of the most important global warming factors behind CO2. Half or more BC in the atmosphere is from BB, estimated at 6-9 Tg/yr (IPCC, 5AR) and contributing up to 0.6 W/m2 atmospheric warming (Bond et al., 2013). With a potential rise in drought and extreme events in the future due to climate change, these numbers are expected to increase. For this reason, we focus on BC and organic carbon aerosol species that are emitted from forest fires and compare their emission ratios, physical and optical properties to those from controlled laboratory studies of single-source BB fuels to understand BB carbonaceous aerosols in the atmosphere. We investigate BC in concentrated BB plumes as sampled from the new U.S. DOE ARM Program campaign, Layered Atlantic Smoke Interactions with Clouds (LASIC). The ARM Aerosol Mobile Facility 1 (AMF1) and Mobile Aerosol Observing System (MAOS) are currently located on Ascension Island in the South Atlantic Ocean, located midway between Angola and Brazil. The location was chosen for sampling maximum aerosol outflow from Africa. The far-field aged BC from LASIC is compared to BC from indoor generation from single-source fuels, e.g. African grass, sampled during Fire Lab At Missoula Experiments IV (FLAME-IV). BC is measured with a single-particle soot photometer (SP2) alongside numerous supporting instrumentation, e.g. particle counters, CO and CO2 detectors, aerosol scattering and absorption measurements, etc. FLAME-IV includes both direct emissions and well-mixed aerosol samples that have undergone dilution, cooling, and condensation. BC physical and optical properties change as particles are transported in the atmosphere due to oxidation, coagulation, and condensation which is observed in the laboratory BC data. Laboratory BC emissions and emission ratios are compared with those from LASIC to improve model treatment of BB BC emissions and aging in global climate models.

Relating Line Width and Optical Depth for CO Emission in the Large Mgellanic Cloud

NASA Astrophysics Data System (ADS)

Wojciechowski, Evan; Wong, Tony; Bandurski, Jeffrey; MC3 (Mapping CO in Molecular Clouds in the Magellanic Clouds) Team

2018-01-01

We investigate data produced from ALMA observations of giant molecular clouds (GMCs) located in the Large Magellanic Cloud (LMC), using 12CO(2–1) and 13CO(2–1) emission. The spectral line width is generally interpreted as tracing turbulent rather than thermal motions in the cloud, but could also be affected by optical depth, especially for the 12CO line (Hacar et al. 2016). We compare the spectral line widths of both lines with their optical depths, estimated from an LTE analysis, to evaluate the importance of optical depth effects. Our cloud sample includes two regions recently published by Wong et al. (2017, submitted): the Tarantula Nebula or 30 Dor, an HII region rife with turbulence, and the Planck cold cloud (PCC), located in a much calmer environment near the fringes of the LMC. We also include four additional LMC clouds, which span intermediate levels of star formation relative to these two clouds, and for which we have recently obtained ALMA data in Cycle 4.

Comparative toxicity of size-fractionated airborne particulate matter obtained from different cities in the United States

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

Gilmour, M.I.; McGee, J.; Duvall, R.M.

2007-07-01

Hundreds of epidemiological studies have shown that exposure to ambient particulate matter (PM) is associated with dose-dependent increases in morbidity and mortality. While early reports focused on PM less than 10 {mu}m (PM10), numerous studies have since shown that the effects can occur with PM stratified into ultrafine (UF), fine (FI), and coarse (CO) size modes despite the fact that these materials differ significantly in both evolution and chemistry. Furthermore the chemical makeup of these different size fractions can vary tremendously depending on location, meteorology, and source profile. For this reason, high-volume three-stage particle impactors with the capacity to collectmore » UF, FI, and CO particles were deployed to four different locations in the United States (Seattle, WA; Salt Lake City, UT; Sterling Forest and South Bronx, NY), and weekly samples were collected for 1 mo in each place. The particles were extracted, assayed for a standardized battery of chemical components, and instilled into mouse lungs (female BALB/c) at doses of 25 and 100 {mu}g. Eighteen hours later animals were euthanized and parameters of injury and inflammation were monitored in the bronchoalveolar lavage fluid and plasma. Of the four locations, the South Bronx coarse fraction was the most potent sample in both pulmonary and systemic biomarkers. Receptor source modeling on the PM2.5 samples showed that the South Bronx sample was heavily influenced by emissions from coal fired power plants (31%) and mobile sources (22%). Further studies will assess how source profiles correlate with the observed effects for all locations and size fractions.« less

[Estimation of dietary intake of radioactive materials by total diet methods].

PubMed

Uekusa, Yoshinori; Nabeshi, Hiromi; Tsutsumi, Tomoaki; Hachisuka, Akiko; Matsuda, Rieko; Teshima, Reiko

2014-01-01

Radioactive contamination in foods is a matter of great concern after the Tokyo Electric Power Company's Fukushima Daiichi nuclear power plant disaster caused by the Great East Japan Earthquake. In order to estimate human intake and annual committed effective dose of radioactive materials, market basket and duplicate diet samples from various areas in Japan were analyzed for cesium-134 ((134)Cs), -137 ((137)Cs), and natural radionuclide potassium-40 ((40)K) by γ-ray spectroscopy. Dietary intake of radioactive cesium around Fukushima area was somewhat higher than in other areas. However, maximum committed effective doses obtained by the market basket and duplicate diet samples were 0.0094 and 0.027 mSv/year, respectively, which are much lower than the maximum permissible dose (1 mSv/year) in foods in Japan.

A gene duplication/loss event in the ribulose-1,5-bisphosphate-carboxylase/oxygenase (rubisco) small subunit gene family among accessions of Arabidopsis thaliana.

PubMed

Schwarte, Sandra; Tiedemann, Ralph

2011-06-01

Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated.

Duplication and diversification of the LEAFY HULL STERILE1 and Oryza sativa MADS5 SEPALLATA lineages in graminoid Poales

PubMed Central

2012-01-01

Background Gene duplication and the subsequent divergence in function of the resulting paralogs via subfunctionalization and/or neofunctionalization is hypothesized to have played a major role in the evolution of plant form. The LEAFY HULL STERILE1 (LHS1) SEPALLATA (SEP) genes have been linked with the origin and diversification of the grass spikelet, but it is uncertain 1) when the duplication event that produced the LHS1 clade and its paralogous lineage Oryza sativa MADS5 (OSM5) occurred, and 2) how changes in gene structure and/or expression might have contributed to subfunctionalization and/or neofunctionalization in the two lineages. Methods Phylogenetic relationships among 84 SEP genes were estimated using Bayesian methods. RNA expression patterns were inferred using in situ hybridization. The patterns of protein sequence and RNA expression evolution were reconstructed using maximum parsimony (MP) and maximum likelihood (ML) methods, respectively. Results Phylogenetic analyses mapped the LHS1/OSM5 duplication event to the base of the grass family. MP character reconstructions estimated a change from cytosine to thymine in the first codon position of the first amino acid after the Zea mays MADS3 (ZMM3) domain converted a glutamine to a stop codon in the OSM5 ancestor following the LHS1/OSM5 duplication event. RNA expression analyses of OSM5 co-orthologs in Avena sativa, Chasmanthium latifolium, Hordeum vulgare, Pennisetum glaucum, and Sorghum bicolor followed by ML reconstructions of these data and previously published analyses estimated a complex pattern of gain and loss of LHS1 and OSM5 expression in different floral organs and different flowers within the spikelet or inflorescence. Conclusions Previous authors have reported that rice OSM5 and LHS1 proteins have different interaction partners indicating that the truncation of OSM5 following the LHS1/OSM5 duplication event has resulted in both partitioned and potentially novel gene functions. The complex pattern of OSM5 and LHS1 expression evolution is not consistent with a simple subfunctionalization model following the gene duplication event, but there is evidence of recent partitioning of OSM5 and LHS1 expression within different floral organs of A. sativa, C. latifolium, P. glaucum and S. bicolor, and between the upper and lower florets of the two-flowered maize spikelet. PMID:22340849

Influence of storage vial material on measurement of organophosphate flame retardant metabolites in urine.

PubMed

Carignan, Courtney C; Butt, Craig M; Stapleton, Heather M; Meeker, John D; Minguez-Alarcón, Lidia; Williams, Paige L; Hauser, Russ

2017-08-01

Use of organophosphate flame retardants (PFRs) has increased over the past decade with the phase out of polybrominated diphenyl ethers. Urinary metabolites of PFRs are used as biomarkers of exposure in epidemiologic research, which typically uses samples collected and stored in polypropylene plastic cryovials. However, a small study suggested that the storage vial material may influence reported concentrations. Therefore, we aimed to examine the influence of the storage vial material on analytical measurement of PFR urinary metabolites. Using urine samples collected from participants in the Environment and Reproductive Health (EARTH) Study, we analyzed the PFR metabolites in duplicate aliquots that were stored in glass and plastic vials (n = 31 pairs). Bis(1,3-dichloro-2-propyl) phosphate (BDCIPP), diphenyl phosphate (DPHP) and isopropyl-phenyl phenyl phosphate (ip-PPP) were detected in 98%, 97% and 87% of duplicates. We observed high correlations between glass-plastic duplicates for BDCIPP (r s  = 0.95), DPHP (r s  = 0.79) and ip-PPP (r s  = 0.82) (p < 0.0001). Urinary ip-PPP was an average of 0.04 ng/ml (p = 0.04) higher among samples stored in glass, with a mean relative difference of 14%. While this difference is statistically significant, it is small in magnitude. No differences were observed for BDCIPP or DPHP, however future research should seek to reduce the potential for type II error (false negatives). We conclude that storing urine samples in polypropylene plastic cryovials may result in slightly reduced concentrations of urinary ip-PPP relative to storage in glass vials and future research should seek to increase the sample size, reduce background variability and consider the material of the urine collection cup. Copyright © 2017 Elsevier Ltd. All rights reserved.

Levels of select PCB and PBDE congeners in human post-mortem brain reveal possible environmental involvement in 15q11-q13 duplication autism spectrum disorder

PubMed Central

Mitchell, Michelle M.; Woods, Rima; Chi, Lai-Har; Schmidt, Rebecca J.; Pessah, Isaac N.; Kostyniak, Paul J.; LaSalle, Janine M.

2013-01-01

Persistent organic pollutants (POPs), including polychlorinated biphenyls (PCBs) and polybrominated diphenylethers (PBDEs) that bioaccumulate in lipid-rich tissues are of concern as developmental neurotoxicants. Epigenetic mechanisms such as DNA methylation act at the interface of genetic and environmental factors implicated in autism-spectrum disorders. The relationship between POP levels and DNA methylation patterns in individuals with and without neurodevelopmental disorders has not been previously investigated. In this study, a total of 107 human frozen post-mortem brain samples were analyzed for 8 PCBs and 7 PBDEs by GC-micro electron capture detector and GC/MS using negative chemical ionization. Human brain samples were grouped as neurotypical controls (n=43), neurodevelopmental disorders with known genetic basis (n=32, including Down, Rett, Prader-Willi, Angelman, and 15q11-q13 duplication syndromes), and autism of unknown etiology (n=32). Unexpectedly, PCB 95 was significantly higher in the genetic neurodevelopmental group, but not idiopathic autism, as compared to neurotypical controls. Interestingly, samples with detectable PCB 95 levels were almost exclusively those with maternal 15q11-q13 duplication (Dup15q) or deletion in Prader-Willi syndrome. When sorted by birth year, Dup15q samples represented five out of six of genetic neurodevelopmental samples born after the 1976 PCB ban exhibiting detectable PCB 95 levels. Dup15q was the strongest predictor of PCB 95 exposure over age, gender, or year of birth. Dup15q brain showed lower levels of repetitive DNA methylation measured by LINE-1 pyrosequencing, but methylation levels were confounded by year of birth. These results demonstrate a novel paradigm by which specific POPs may predispose to genetic copy number variation of 15q11-q13. PMID:22930557

Evaluating greenhouse gas emissions from hydropower complexes on large rivers in Eastern Washington

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

Arntzen, Evan V.; Miller, Benjamin L.; O'Toole, Amanda C.

2013-03-15

Water bodies, such as freshwater lakes, are known to be net emitters of carbon dioxide (CO2), and methane (CH4). In recent years, significant greenhouse gas (GHG) emissions from tropical, boreal, and mid-latitude reservoirs have been reported. At a time when hydropower is increasing worldwide, better understanding of seasonal and regional variation in GHG emissions is needed in order to develop a predictive understanding of such fluxes within man-made impoundments. We examined power-producing dam complexes within xeric temperate locations in the northwestern United States. Sampling environments on the Snake (Lower Monumental Dam Complex) and Columbia Rivers (Priest Rapids Dam Complex) includedmore » tributary, mainstem, embayment, forebay, and tailrace areas during winter and summer 2012. At each sampling location, GHG measurement pathways included surface gas flux, degassing as water passed through dams during power generation, ebullition within littoral embayments, and direct sampling of hyporheic pore-water. Measurements were also carried out in a free-flowing reach of the Columbia River to estimate unaltered conditions. Surface flux resulted in very low emissions, with reservoirs acting as a sink for CO2 (up to –262 mg m-2 d-1, which is within the range previously reported for similarly located reservoirs). Surface flux of methane remained below 1 mg CH4 m-2d-1, a value well below fluxes reported previously for temperate reservoirs. Water passing through hydroelectric projects acted as a sink for CO2 during winter and a small source during summer, with mean degassing fluxes of –117 and 4.5 t CO2 d-1, respectively. Degassing of CH4 was minimal, with mean fluxes of 3.1 × 10-6 and –5.6 × 10-4 t CH4 d-1 during winter and summer, respectively. Gas flux due to ebullition was greater in coves located within reservoirs than in coves within the free flowing Hanford Reach–and CH4 flux exceeded that of CO2. Methane emissions varied widely across sampling locations, ranging from 10.5 to 1039 mg CH4 m-2 d-1, with mean fluxes of 324 mg CH4 m-2 d-1in Lower Monumental Dam reservoir and 482 mg CH4 m-2d-1 in the Priest Rapids Dam reservoir. The magnitude of methane flux due to ebullition was unexpectedly high, and falls within the range recently reported for other temperate reservoirs around the world, further suggesting that this methane source should be considered in estimates of global greenhouse gas emissions. Methane flux from sediment pore-water within littoral embayments averaged 4.2 mg m-2 d-1 during winter and 8.1 mg m-2 d-1 during summer, with a peak flux of 19.8 mg m-2d-1 (at the same location where CH4 ebullition was also the greatest). Carbon dioxide flux from sediment pore-water averaged approximately 80 mg m-2d-1 with little difference between winter and summer. Similar to emissions from ebullition, flux from sediment pore-water was higher in reservoirs than in the free flowing reach.« less

76 FR 35802 - Special Local Regulations for Marine Events; Patuxent River, Solomons, MD

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-20

... number is 202-366-9329. To avoid duplication, please use only one of these four methods. See the ``Public... four methods specified under ADDRESSES. Please explain why you believe a public meeting would be.... Naval Air Station Patuxent River, MD. The start and finish lines will be located near the Solomon's Pier...

Apportionment of carbon dioxide over central Europe: insights from combined measurements of atmospheric CO2 mixing ratios and carbon isotope composition

NASA Astrophysics Data System (ADS)

Zimnoch, M.; Jelen, D.; Galkowski, M.; Kuc, T.; Necki, J.; Chmura, L.; Gorczyca, Z.; Jasek, A.; Rozanski, K.

2012-04-01

The European continent, due to high population density and numerous sources of anthropogenic CO2 emissions, plays an important role in the global carbon budget. Nowadays, precise measurements of CO2 mixing ratios performed by both global and regional monitoring networks, combined with appropriate models of carbon cycle, allow quantification of the European input to the global atmospheric CO2 load. However, measurements of CO2 mixing ratios alone cannot provide the information necessary for the apportionment of fossil-fuel related and biogenic contributions to the total CO2 burden of the regional atmosphere. Additional information is required, for instance obtained through measurements of radiocarbon content in atmospheric carbon dioxide. Radiocarbon is a particularly useful tracer for detecting fossil carbon in the atmosphere on different spatial and temporal scales. Regular observations of atmospheric CO2mixing ratios and their isotope compositions have been performed during the period of 2005-2009 at two sites located in central Europe (southern Poland). The sites, only ca. 100 km apart, represent two extreme environments with respect to the extent of anthropogenic pressure: (i) the city of Krakow, representing typical urban environment with numerous sources of anthropogenic CO2, and (ii) remote mountain site Kasprowy Wierch, relatively free of local influences. Regular, quasi-continuous measurements of CO2 mixing ratios have been performed at both sites. In addition, cumulative samples of atmospheric CO2 have been collected (weekly sampling regime for Krakow and monthly for Kasprowy Wierch) to obtain mean carbon isotope signature (14C/12C and 13C/12C ratios) of atmospheric CO2 at both sampling locations. Partitioning of the local atmospheric CO2 load at both locations has been performed using isotope- and mass balance approach. In Krakow, the average fossil-fuel related contribution to the local atmospheric CO2 load was equal to approximately 3.4%. The biogenic component turned out to be of the same magnitude. Both components revealed a distinct seasonality, with the fossil-fuel related component reaching maximum values during winter months and the biogenic component shifted in phase by ca. 6 months. Seasonality of fossil-fuel related CO2 load in the local atmosphere is linked with seasonality of local CO2sources, mostly burning of fossil fuels for heating purposes. Positive values of biogenic component indicate prevalence of the local respiration and biomass burning processes over local photosynthesis. Summer maxima of biogenic CO2 component represent mostly local respiration activity. Direct measurements of soil CO2 fluxes in the Krakow region showed an approximately 10-fold increase of those fluxes during the summer months. Partitioning of the local CO2 budget for Kasprowy Wierch site revealed large differences in the derived components when compared to urban atmosphere of Krakow: the fossil-fuel related component was ca. 5 times lower whereas the biogenic component was negative in summer, pointing to the importance of photosynthetic sink associated with extensive forests in the neighborhood of the station. The isotope- and mass balance approach was also used to derive mean monthly 13C isotope signature of fossil-fuel related CO2 emissions in Krakow. Although the derived δ13CO2 values revealed large variability, they are confined in the range of 13C isotope composition being reported for various sources of CO2 emissions in the city (burning of coal and oil, burning of methane gas, traffic).

Levels of TBT and other selected organotin compounds in duplicate diet samples.

PubMed

Sousa, Ana C A; Coelho, Sónia D; Pastorinho, M Ramiro; Taborda-Barata, Luís; Nogueira, António J A; Isobe, Tomohiko; Kunisue, Tatsuya; Takahashi, Shin; Tanabe, Shinsuke

2017-01-01

Organotin compounds (OTs) are ubiquitous contaminants with a broad range of applications ranging from biocides and pesticides to catalysts for the production of polyurethane foams and silicones. The deleterious effects of some OTs (particularly tributyltin - TBT) upon wildlife and experimental animals are well documented and include endocrine disruption, immunotoxicity, neurotoxicity, genotoxicity and metabolic dysfunction in which obesity is included. However, virtually no data on the current human exposure levels is available. In order to bridge this gap, we quantified for the first time the levels of OTs in duplicate diet samples from members of the University of Aveiro in Portugal. OTs were detected in 32% of the 28 diet samples analyzed, at relatively low levels. TBT and monobutyltin were detected only in two samples and dibutyltin was detectable in three samples. Dioctyltin was quantified in four samples and monooctyltin in three samples. Phenyltins were below the detection limit in all the diet samples analyzed. Overall, for the vast majority of the samples (89%), the estimated daily intakes (EDI) of organotins through food were much lower than the established tolerable daily intakes (TDI). Hence, for the majority of the participants the risk associated with food ingestion is low. Copyright © 2016 Elsevier B.V. All rights reserved.

21 CFR 177.1950 - Vinyl chloride-ethylene copolymers.

Code of Federal Regulations, 2013 CFR

2013-04-01

... deciliter per gram as determined by ASTM method D1243-79, “Standard Test Method for Dilute Solution... vinyl chloride-ethylene copol-ymer per 100 grams of sample tested as determined from the organic... using duplicate blanks. Approximately 400 grams of sample (accurately weighed) shall be placed in a 2...

21 CFR 177.1950 - Vinyl chloride-ethylene copolymers.

Code of Federal Regulations, 2012 CFR

2012-04-01

... deciliter per gram as determined by ASTM method D1243-79, “Standard Test Method for Dilute Solution... vinyl chloride-ethylene copol-ymer per 100 grams of sample tested as determined from the organic... using duplicate blanks. Approximately 400 grams of sample (accurately weighed) shall be placed in a 2...

Multiple-Matrix Sampling: A Technique for Maximizing the Effectiveness of Lengthy Survey Instruments.

ERIC Educational Resources Information Center

Shemick, John M.

1983-01-01

In a project to identify and verify professional competencies for beginning industrial education teachers, researchers found a 173-item questionnaire unwieldy. Using multiple-matrix sampling, they distributed subsets of items to respondents, resulting in adequate returns as well as duplication, postage, and time savings. (SK)

The Fusarium Graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization

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

Cuomo, Christina A.; Guldener, Ulrich; Xu, Jin Rong

2007-09-07

We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher ratesmore » of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.« less

Dynamic Load Balancing Based on Constrained K-D Tree Decomposition for Parallel Particle Tracing

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

Zhang, Jiang; Guo, Hanqi; Yuan, Xiaoru

Particle tracing is a fundamental technique in flow field data visualization. In this work, we present a novel dynamic load balancing method for parallel particle tracing. Specifically, we employ a constrained k-d tree decomposition approach to dynamically redistribute tasks among processes. Each process is initially assigned a regularly partitioned block along with duplicated ghost layer under the memory limit. During particle tracing, the k-d tree decomposition is dynamically performed by constraining the cutting planes in the overlap range of duplicated data. This ensures that each process is reassigned particles as even as possible, and on the other hand the newmore » assigned particles for a process always locate in its block. Result shows good load balance and high efficiency of our method.« less

Investigating Associations Between Proliferation Indices, C-kit, and Lymph Node Stage in Canine Mast Cell Tumors.

PubMed

Krick, Erika Lauren; Kiupel, Matti; Durham, Amy C; Thaiwong, Tuddow; Brown, Dorothy C; Sorenmo, Karin U

Previous studies have evaluated cellular proliferation indices, KIT expression, and c-kit mutations to predict the clinical behavior of canine mast cell tumors (MCTs). The study purpose was to retrospectively compare mitotic index, argyrophilic nucleolar organizer regions (AgNORs)/nucleus, Ki-67 index, KIT labeling pattern, and internal tandem duplication mutations in c-KIT between stage I and stage II grade II MCTs. Medical records and tumor biopsy samples from dogs with Grade II MCTs with cytological or histopathological regional lymph node evaluation were included. Signalment, tumor location and stage, and presence of a recurrent versus de novo tumor were recorded. Mitotic index, AgNORs/nucleus, Ki-67, KIT staining pattern, and internal tandem duplication mutations in exon 11 of c-KIT were evaluated. Sixty-six tumors (51 stage I; 15 stage II) were included. Only AgNORs/nucleus and recurrent tumors were significantly associated with stage (odds ratio 2.8, 95% confidence interval [CI] 1.0-8.0, P = .049; odds ratio 8.8, 95% CI 1.1-69.5; P = .039). Receiver-operator characteristic analysis showed that the sensitivity and specificity of AgNORs/cell ≥ 1.87 were 93.3% and 27.4%, respectively, (area under the curve: 0.65) for predicting stage. Recurrent tumors and higher AgNORs/nucleus are associated with stage II grade II MCTs; however, an AgNOR cutoff value that reliably predicts lymph node metastasis was not determined.

COMPARATIVE ECLOGICAL CONDITION OF BAYOUS TEXAR, CHICO AND GRANDE

EPA Science Inventory

Water and sediment quality in three urban bayous or tidal estuaries located near Pensacola, Florida, were determined at 23 sampling stations over a three year period during which hurricane and dredging activity occurred. Our primary objective was to determine the environmental co...

The effects of evaporating essential oils on indoor air quality

NASA Astrophysics Data System (ADS)

Su, Huey-Jen; Chao, Chung-Jen; Chang, Ho-Yuan; Wu, Pei-Chih

Essential oils, predominantly comprised of a group of aromatic chemicals, have attracted increasing attention as they are introduced into indoor environments through various forms of consumer products via different venues. Our study aimed to characterize the profiles and concentrations of emitted volatile organic compounds (VOCs) when evaporating essential oils indoors. Three popular essential oils in the market, lavender, eucalyptus, and tea tree, based on a nation-wide questionnaire survey, were tested. Specific aromatic compounds of interest were sampled during evaporating the essential oils, and analyzed by GC-MS. Indoor carbon monoxide (CO), carbon dioxide (CO 2), total volatile organic compounds (TVOCs), and particulate matters (PM 10) were measured by real-time, continuous monitors, and duplicate samples for airborne fungi and bacteria were collected in different periods of the evaporation. Indoor CO (average concentration 1.48 vs. 0.47 ppm at test vs. background), CO 2 (543.21 vs. 435.47 ppm), and TVOCs (0.74 vs. 0.48 ppm) levels have increased significantly after evaporating essential oils, but not the PM 10 (2.45 vs. 2.42 ppm). The anti-microbial activity on airborne microbes, an effect claimed by the use of many essential oils, could only be found at the first 30-60 min after the evaporation began as the highest levels of volatile components in these essential oils appeared to emit into the air, especially in the case of tea tree oil. High emissions of linalool (0.092-0.787 mg m -3), eucalyptol (0.007-0.856 mg m -3), D-limonene (0.004-0.153 mg m -3), ρ-cymene (0.019-0.141 mg m -3), and terpinene-4-ol-1 (0.029-0.978 mg m -3), all from the family of terpenes, were observed, and warranted for further examination for their health implications, especially for their potential contribution to the increasing indoor levels of secondary pollutants such as formaldehyde and secondary organic aerosols (SOAs) in the presence of ozone.

Re-creation of single phase, and improvement of magnetic property of CoFe2O4 nanoparticles versus heat treatment

NASA Astrophysics Data System (ADS)

Tran, N.; Kim, D. H.; Phan, T. L.; Dang, N. T.; Bach, T. N.; Manh, D. H.; Lee, B. W.

2018-03-01

Our studies on the crystal characterization and magnetic property of CoFe2O4 nanoparticles (NPs) point out their instability in a specific temperature range. While as-prepared NPs exhibit single phase in a cubic spinel structure, annealing at temperatures T=673-1273 K leads to the development of an impurity phase of Fe2O3. Interestingly, annealing at higher temperatures re-creates the single phase of NPs. This strongly influences their magnetic property. The magnetic inhomogeneity and/or multiple phase exist in as-prepared NPs and in those annealed below 1273 K, better magnetic property is found in the samples with annealing temperature (Tan) higher than 1273 K. Ferromagnetic-paramagnetic phase transition temperatures of these samples are located around 815-850 K, and are less dependent on Tan. At room temperature, their saturation magnetization is located in the range of 41-55 emu/g, while the coercivity can be changed from 600 to 3200 Oe. These results are related to microstructures, structural phases, and exchange interactions between Fe and Co ions situated in the A and B sites of the spinel structure, which are modified by heat treatment.

CoLIde

PubMed Central

Mohorianu, Irina; Stocks, Matthew Benedict; Wood, John; Dalmay, Tamas; Moulton, Vincent

2013-01-01

Small RNAs (sRNAs) are 20–25 nt non-coding RNAs that act as guides for the highly sequence-specific regulatory mechanism known as RNA silencing. Due to the recent increase in sequencing depth, a highly complex and diverse population of sRNAs in both plants and animals has been revealed. However, the exponential increase in sequencing data has also made the identification of individual sRNA transcripts corresponding to biological units (sRNA loci) more challenging when based exclusively on the genomic location of the constituent sRNAs, hindering existing approaches to identify sRNA loci.   To infer the location of significant biological units, we propose an approach for sRNA loci detection called CoLIde (Co-expression based sRNA Loci Identification) that combines genomic location with the analysis of other information such as variation in expression levels (expression pattern) and size class distribution. For CoLIde, we define a locus as a union of regions sharing the same pattern and located in close proximity on the genome. Biological relevance, detected through the analysis of size class distribution, is also calculated for each locus. CoLIde can be applied on ordered (e.g., time-dependent) or un-ordered (e.g., organ, mutant) series of samples both with or without biological/technical replicates. The method reliably identifies known types of loci and shows improved performance on sequencing data from both plants (e.g., A. thaliana, S. lycopersicum) and animals (e.g., D. melanogaster) when compared with existing locus detection techniques. CoLIde is available for use within the UEA Small RNA Workbench which can be downloaded from: http://srna-workbench.cmp.uea.ac.uk. PMID:23851377

Percutaneous umbilical cord blood sampling - slideshow

MedlinePlus

... Duplication for commercial use must be authorized in writing by ADAM Health Solutions. About MedlinePlus Site Map FAQs Customer Support Get email updates Subscribe to RSS Follow us Disclaimers Copyright ...

Technical Update: Johnson Space Center system using a solid electrolytic cell in a remote location to measure oxygen fugacities in CO/CO2 controlled-atmosphere furnaces

NASA Technical Reports Server (NTRS)

Jurewicz, A. J. G.; Williams, R. J.; Le, L.; Wagstaff, J.; Lofgren, G.; Lanier, A.; Carter, W.; Roshko, A.

1993-01-01

Details are given for the design and application of a (one atmosphere) redox-control system. This system differs from that given in NASA Technical Memorandum 58234 in that it uses a single solid-electrolytic cell in a remote location to measure the oxygen fugacities of multiple CO/CO2 controlled-atmosphere furnaces. This remote measurement extends the range of sample-furnace conditions that can be measured using a solid-electrolytic cell, and cuts costs by extending the life of the sensors and by minimizing the number of sensors in use. The system consists of a reference furnace and an exhaust-gas manifold. The reference furnace is designed according to the redox control system of NASA Technical Memorandum 58234, and any number of CO/CO2 controlled-atmosphere furnaces can be attached to the exhaust-gas manifold. Using the manifold, the exhaust gas from individual CO/CO2 controlled atmosphere furnaces can be diverted through the reference furnace, where a solid-electrolyte cell is used to read the ambient oxygen fugacity. The oxygen fugacity measured in the reference furnace can then be used to calculate the oxygen fugacity in the individual CO/CO2 controlled-atmosphere furnace. A BASIC computer program was developed to expedite this calculation.

Solid-state nuclear magnetic resonance measurements of HIV fusion peptide 13CO to lipid 31P proximities support similar partially inserted membrane locations of the α helical and β sheet peptide structures.

PubMed

Gabrys, Charles M; Qiang, Wei; Sun, Yan; Xie, Li; Schmick, Scott D; Weliky, David P

2013-10-03

Fusion of the human immunodeficiency virus (HIV) membrane and the host cell membrane is an initial step of infection of the host cell. Fusion is catalyzed by gp41, which is an integral membrane protein of HIV. The fusion peptide (FP) is the ∼25 N-terminal residues of gp41 and is a domain of gp41 that plays a key role in fusion catalysis likely through interaction with the host cell membrane. Much of our understanding of the FP domain has been accomplished with studies of "HFP", i.e., a ∼25-residue peptide composed of the FP sequence but lacking the rest of gp41. HFP catalyzes fusion between membrane vesicles and serves as a model system to understand fusion catalysis. HFP binds to membranes and the membrane location of HFP is likely a significant determinant of fusion catalysis perhaps because the consequent membrane perturbation reduces the fusion activation energy. In the present study, many HFPs were synthesized and differed in the residue position that was (13)CO backbone labeled. Samples were then prepared that each contained a singly (13)CO labeled HFP incorporated into membranes that lacked cholesterol. HFP had distinct molecular populations with either α helical or oligomeric β sheet structure. Proximity between the HFP (13)CO nuclei and (31)P nuclei in the membrane headgroups was probed by solid-state NMR (SSNMR) rotational-echo double-resonance (REDOR) measurements. For many samples, there were distinct (13)CO shifts for the α helical and β sheet structures so that the proximities to (31)P nuclei could be determined for each structure. Data from several differently labeled HFPs were then incorporated into a membrane location model for the particular structure. In addition to the (13)CO labeled residue position, the HFPs also differed in sequence and/or chemical structure. "HFPmn" was a linear peptide that contained the 23 N-terminal residues of gp41. "HFPmn_V2E" contained the V2E mutation that for HIV leads to greatly reduced extent of fusion and infection. The present study shows that HFPmn_V2E induces much less vesicle fusion than HFPmn. "HFPtr" contained three strands with HFPmn sequence that were chemically cross-linked near their C-termini. HFPtr mimics the trimeric topology of gp41 and induces much more rapid and extensive vesicle fusion than HFPmn. For HFPmn and HFPtr, well-resolved α and β peaks were observed for A6-, L9-, and L12-labeled samples. For each of these samples, there were similar HFP (13)CO to lipid (31)P proximities in the α and β structures, which evidenced comparable membrane locations of the HFP in either structure including insertion into a single membrane leaflet. The data were also consistent with deeper insertion of HFPtr relative to HFPmn in both the α and β structures. The results supported a strong correlation between the membrane insertion depth of the HFP and its fusogenicity. More generally, the results supported membrane location of the HFP as an important determinant of its fusogenicity. The deep insertion of HFPtr in both the α and β structures provides the most relevant membrane location of the FP for HIV gp41-catalyzed membrane fusion because HIV gp41 is natively trimeric. Well-resolved α and β signals were observed in the HFPmn_V2E samples with L9- and L12- but not A6-labeling. The α signals were much more dominant for L9- and L12-labeled HFPmn_V2E than the corresponding HFPmn or HFPtr. The structural model for the less fusogenic HFPmn_V2E includes a shorter helix and less membrane insertion than either HFPmn or HFPtr. This greater helical population and different helical structure and membrane location could result in less membrane perturbation and lower fusogenicity of HFPmn_V2E and suggest that the β sheet fusion peptide is the most functionally relevant structure of HFPmn, HFPtr, and gp41.

SPRUCE Pretreatment Plant Tissue Analyses, 2009 through 2013

DOE Data Explorer

Phillips, J. R. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Brice, D. J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Hanson, P. J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Childs, J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Iversen, C. M. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Norby, R. J. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A; Warren, J. M. [Oak Ridge National Laboratory, U.S. Department of Energy, Oak Ridge, Tennessee, U.S.A

2009-12-01

This data set reports the results of elemental analyses of foliar and stem/woody twig plant tissues collected at the SPRUCE site in 2009, 2012, and 2013. Samples were obtained at various locations around the S1 Bog and from within the developing experimental treatment plots. These are pretreatment vegetation samples, collected prior to initiation of the SPRUCE experiment heating and elevated CO2 treatments.

Discrepancies in reporting the CAG repeat lengths for Huntington's disease

PubMed Central

Quarrell, Oliver W; Handley, Olivia; O'Donovan, Kirsty; Dumoulin, Christine; Ramos-Arroyo, Maria; Biunno, Ida; Bauer, Peter; Kline, Margaret; Landwehrmeyer, G Bernhard

2012-01-01

Huntington's disease results from a CAG repeat expansion within the Huntingtin gene; this is measured routinely in diagnostic laboratories. The European Huntington's Disease Network REGISTRY project centrally measures CAG repeat lengths on fresh samples; these were compared with the original results from 121 laboratories across 15 countries. We report on 1326 duplicate results; a discrepancy in reporting the upper allele occurred in 51% of cases, this reduced to 13.3% and 9.7% when we applied acceptable measurement errors proposed by the American College of Medical Genetics and the Draft European Best Practice Guidelines, respectively. Duplicate results were available for 1250 lower alleles; discrepancies occurred in 40% of cases. Clinically significant discrepancies occurred in 4.0% of cases with a potential unexplained misdiagnosis rate of 0.3%. There was considerable variation in the discrepancy rate among 10 of the countries participating in this study. Out of 1326 samples, 348 were re-analysed by an accredited diagnostic laboratory, based in Germany, with concordance rates of 93% and 94% for the upper and lower alleles, respectively. This became 100% if the acceptable measurement errors were applied. The central laboratory correctly reported allele sizes for six standard reference samples, blind to the known result. Our study differs from external quality assessment (EQA) schemes in that these are duplicate results obtained from a large sample of patients across the whole diagnostic range. We strongly recommend that laboratories state an error rate for their measurement on the report, participate in EQA schemes and use reference materials regularly to adjust their own internal standards. PMID:21811303

Determination of 137Cs and 60Co pollution in the area of the Laguna Verde Nuclear Power Plant, Mexico.

PubMed

Salas Mar, Bernardo

2015-11-01

The project 'Radiological Analysis of Environmental Samples in the Gulf of Mexico and the coast of Quintana Roo', had the aim of identifying and quantifying anthropogenic radionuclides in environmental samples consisting of silt, sand and sea water. This paper presents the results of the radiological analysis of these samples, which was made in the multichannel system for gamma spectrometry with hyperpure germanium detector in the Laboratory of Radiological Analysis of Environmental Samples, located at the Physics Department, Faculty of Sciences, of the Autonomous National University of Mexico (UNAM). The sampled points are along the coast of the contiguous states of Tamaulipas, Veracruz, Tabasco, Campeche, Yucatan and Quintana Roo. This paper presents the qualitative and quantitative concentrations of the main identified anthropogenic radionuclides (60)Co and (137)Cs. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

DMD mutation spectrum analysis in 613 Chinese patients with dystrophinopathy.

PubMed

Guo, Ruolan; Zhu, Guosheng; Zhu, Huimin; Ma, Ruiyu; Peng, Ying; Liang, Desheng; Wu, Lingqian

2015-08-01

Dystrophinopathy is a group of inherited diseases caused by mutations in the DMD gene. Within the dystrophinopathy spectrum, Duchenne and Becker muscular dystrophies are common X-linked recessive disorders that mainly feature striated muscle necrosis. We combined multiplex ligation-dependent probe amplification with Sanger sequencing to detect large deletions/duplications and point mutations in the DMD gene in 613 Chinese patients. A total of 571 (93.1%) patients were diagnosed, including 428 (69.8%) with large deletions/duplications and 143 (23.3%) with point mutations. Deletion/duplication breakpoints gathered mostly in introns 44-55. Reading frame rules could explain 88.6% of deletion mutations. We identified seventy novel point mutations that had not been previously reported. Spectrum expansion and genotype-phenotype analysis of DMD mutations on such a large sample size in Han Chinese population would provide new insights into the pathogenic mechanism underlying dystrophinopathies.

Studies on the structural changes during curing of epoxy and its blend with CTBN

NASA Astrophysics Data System (ADS)

Srivastava, Kavita; Rathore, Ashwani Kumar; Srivastava, Deepak

2018-01-01

Cashew nut shell liquid (CNSL), an agricultural renewable resource material, produces natural phenolic distillates such as cardanol. Cardanol condenses with formaldehyde at the ortho- and para-position of the phenolic ring under acidic or alkaline condition to yield a series of polymers of novolac- or resol-type phenolic resins. These phenolic resins may further be modified by epoxidation with epichlorohydrin to duplicate the performance of such phenolic-type novolacs (CFN). The structural changes during curing of blend samples of epoxy and carboxyl terminated poly (butadiene-co-acrylonitrile) (CTBN) were studies by Fourier-transform infrared (FTIR) spectrophotometer. The epoxy samples were synthesized by biomass material, cardanol. Blend sample was prepared by physical mixing of CTBN ranging between 0 and 20 weight percent CTBN liquid rubber into cardanol-based epoxidized novolac (CEN) resin. The FTIR spectrum of uncured blend sample clearly indicated that there appeared a band in the region of 3200-3500 cm- 1 which might be due to the presence of phenolic hydroxyl group and sbnd OH group of the opened epoxide. Pure epoxy resin showed peaks near 856 cm- 1 which might be due to oxirane functionality of the epoxidized novolac resin. Both epoxy and its blend sample was cured with polyamine. The cure temperature of CEN resin was found to be decreased by the incorporation of CTBN. The decomposition behavior was also studied by thermogravimetric analyzer (TGA). Two-step decomposition behavior was observed in both epoxy and its blend samples.

Studies on the structural changes during curing of epoxy and its blend with CTBN.

PubMed

Srivastava, Kavita; Rathore, Ashwani Kumar; Srivastava, Deepak

2018-01-05

Cashew nut shell liquid (CNSL), an agricultural renewable resource material, produces natural phenolic distillates such as cardanol. Cardanol condenses with formaldehyde at the ortho- and para-position of the phenolic ring under acidic or alkaline condition to yield a series of polymers of novolac- or resol-type phenolic resins. These phenolic resins may further be modified by epoxidation with epichlorohydrin to duplicate the performance of such phenolic-type novolacs (CFN). The structural changes during curing of blend samples of epoxy and carboxyl terminated poly (butadiene-co-acrylonitrile) (CTBN) were studies by Fourier-transform infrared (FTIR) spectrophotometer. The epoxy samples were synthesized by biomass material, cardanol. Blend sample was prepared by physical mixing of CTBN ranging between 0 and 20weightpercent CTBN liquid rubber into cardanol-based epoxidized novolac (CEN) resin. The FTIR spectrum of uncured blend sample clearly indicated that there appeared a band in the region of 3200-3500cm -1 which might be due to the presence of phenolic hydroxyl group and OH group of the opened epoxide. Pure epoxy resin showed peaks near 856cm -1 which might be due to oxirane functionality of the epoxidized novolac resin. Both epoxy and its blend sample was cured with polyamine. The cure temperature of CEN resin was found to be decreased by the incorporation of CTBN. The decomposition behavior was also studied by thermogravimetric analyzer (TGA). Two-step decomposition behavior was observed in both epoxy and its blend samples. Copyright © 2017 Elsevier B.V. All rights reserved.

A consolidated environmental monitoring plan for Aberdeen Proving Ground, Maryland

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

Ebinger, M.H.; Hansen, W.R.

1997-04-01

The US Army operates facilities in Edgewood and Aberdeen under several licenses from the Nuclear Regulatory Commission (NRC). Compliance with each license is time consuming and could potentially result in duplicated efforts to demonstrate compliance with existing environmental regulations. The goal of the ERM plan is to provide the sampling necessary to ensure that operations at Edgewood and Aberdeen are within applicable regulatory guidelines and to provide a means of ensuring that adverse effects to the environment are minimized. Existing sampling plans and environmental data generated from those plans are briefly reviewed as part of the development of the presentmore » ERM plan. The new ERM plan was designed to provide data that can be used for assessing risks to the environment and to humans using Aberdeen and Edgewood areas. Existing sampling is modified and new sampling is proposed based on the results of the long-term DU fate study. In that study, different environmental pathways were identified that would show transport of DU at Aberdeen. Those pathways would also be impacted by other radioactive constituents from Aberdeen and Edgewood areas. The ERM plan presented in this document includes sampling from Edgewood and Aberdeen facilities. The main radioactive constituents of concern at Edgewood are C, P, N, S, H, I, Co, Cs, Ca, Sr and U that are used in radiolabeling different compounds and tracers for different reactions and syntheses. Air and water sampling are the thrust of efforts at the Edgewood area.« less

Measuring the degree of integrated tuberculosis and HIV service delivery in Cape Town, South Africa.

PubMed

Uyei, Jennifer; Coetzee, David; Macinko, James; Weinberg, Sharon L; Guttmacher, Sally

2014-01-01

To address the considerable tuberculosis (TB)/HIV co-infected population in Cape Town, a number of clinics have made an effort of varying degrees to integrate TB and HIV services. This article describes the development of a theory-based survey instrument designed to quantify the extent to which services were integrated in 33 clinics and presents the results of the survey. Using principal factor analysis, eight factors were extracted and used to make comparisons across three types of clinics: co-located TB and antiretroviral therapy (ART) services, clinics with TB services only and clinics with ART only. Clinics with co-located services scored highest on measures related to integrated TB/ART service delivery compared to clinics with single services, but within group variability was high indicating that co-location of TB and ART services is a necessary but insufficient condition for integrated service delivery. In addition, we found almost all clinics with only TB services in our sample had highly integrated pre-ART services, suggesting that integration of these services across a large number of clinics is feasible and acceptable to clinic staff. TB clinics with highly integrated pre-ART services appear to be efficient sites for introducing ART given that co-infected patients are already engaged in care, and may potentially facilitate earlier access to treatment and minimize loss to follow-up.

Microbial Communities in Terrestrial CO2 Springs: Insights into the Long-Term Effects of Carbon Sequestration on Subsurface Microorganisms

NASA Astrophysics Data System (ADS)

Santillan, E. F. U.; Major, J. R.; Bennett, P.

2014-12-01

Over long timescales, microbial populations and communities living in environments where CO2 has been sequestered will adapt to this environmental stress. Their presence and activities can have implications for fluid flow, geochemistry, and the fate of the stored CO2. Because of the interplay between microorganisms and environment, many environmental factors beyond CO2 will also contribute to community structure, including groundwater composition and mineralogy. To determine the long-term effect of CO2 on microbial communities, we analyzed terrestrial CO2 springs as analogues to CO2 sequestration in 3 locations in the United States: the Little Grand Wash Fault (LGW), UT; Bravo Dome (BD), NM; and Klickitat Mineral Spring (KMS), WA. These sites differed in multiple aspects such as depth, salinity, Fe content, and mineralogy. LGW and BD were located in the Colorado Plateau in sedimentary locations while KMS was located within the Columbia River Basalt Group. Sites were compared to non-CO2 springs in similar sedimentary formations for comparison. Microbial communities from sedimentary formations were characterized by low diversity and the dominance of the phylotypes Acinetobacter or Burkholderia compared to non-CO2 springs, suggesting community stress and the selection of specific organisms most resilient to CO2. Communities in the basalt formation were more diverse, though diversity is lower than a non-CO2 community sampled from the same formation (Lavalleur and Colwell 2013). Organisms present at the basalt site contained novel lineages, such as the OP candidate phyla. KMS was also the only site containing Archaea, such as Methanoplanus, suggesting CH4 production at depth. Statistical analyses indicate other factors such as depth and nutrient availability may be other factors that can affect diversity in addition to CO2. Growth of a CO2-tolerant organism from LGW also shows organisms in these environments are viable. Results confirm the presence of microbial communities at high PCO2 and suggest that while CO2 is one environmental stress that can lower diversity, many other environmental factors can also influence survival. Lavalleur, H.J., Colwell, F.S., 2013. Microbial characterization of basalt formation waters targeted for geological carbon sequestration. FEMS Microbiology Ecology 85, 62-73.

Population Level Purifying Selection and Gene Expression Shape Subgenome Evolution in Maize.

PubMed

Pophaly, Saurabh D; Tellier, Aurélien

2015-12-01

The maize ancestor experienced a recent whole-genome duplication (WGD) followed by gene erosion which generated two subgenomes, the dominant subgenome (maize1) experiencing fewer deletions than maize2. We take advantage of available extensive polymorphism and gene expression data in maize to study purifying selection and gene expression divergence between WGD retained paralog pairs. We first report a strong correlation in nucleotide diversity between duplicate pairs, except for upstream regions. We then show that maize1 genes are under stronger purifying selection than maize2. WGD retained genes have higher gene dosage and biased Gene Ontologies consistent with previous studies. The relative gene expression of paralogs across tissues demonstrates that 98% of duplicate pairs have either subfunctionalized in a tissuewise manner or have diverged consistently in their expression thereby preventing functional complementation. Tissuewise subfunctionalization seems to be a hallmark of transcription factors, whereas consistent repression occurs for macromolecular complexes. We show that dominant gene expression is a strong determinant of the strength of purifying selection, explaining the inferred stronger negative selection on maize1 genes. We propose a novel expression-based classification of duplicates which is more robust to explain observed polymorphism patterns than the subgenome location. Finally, upstream regions of repressed genes exhibit an enrichment in transposable elements which indicates a possible mechanism for expression divergence. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microduplication of 7q36.3 encompassing the SHH long-range regulator (ZRS) in a patient with triphalangeal thumb-polysyndactyly syndrome and congenital heart disease

PubMed Central

Liu, Zhenghua; Yin, Ni; Gong, Lianghui; Tan, Zhiping; Yin, Bangliang; Yang, Yifeng; Luo, Cheng

2017-01-01

Triphalangeal thumb-polysyndactyly syndrome (TPT-PS) is an autosomal dominant disorder with complete penetrance and a variable expression consisting of opposable triphalangeal thumbs, duplication of the distal thumb phalanx, pre-axial polydactyly and duplication of the big toes (hallux). The causative gene of TPT-PS has been mapped to 7q36.3. Sonic hedgehog (SHH) expressed in the zone of polarizing activity (ZPA) has an important role in defining the anterior-posterior axis and numbers of digits in limb bud development. Point mutation or duplication in the ZPA regulatory sequence (ZRS), a cis-regulator of SHH, will lead to TPT-PS. The present study describes a 1-year-old female congenital heart disease (CHD) patient with TPT-PS phenotype. In this Han Chinese family with TPT-PS, high resolution single nucleotide polymorphism array technology identified a novel 0.29 Mb duplication comprising ZRS at 7q36.3 where LMBR1 is located. Additionally, a novel deletion of 22q11.21 was detected in the proband with Tetralogy of Fallot. However, the parents and other relatives of the patient did not harbor this genomic lesion nor CHD. The findings supported the hypothesis that an increased copy number variation of ZRS is the genetic mechanism underlying the phenotype of TPT-PS, and corroborated that 22q11.21 deletion is a genetic cause of CHD. PMID:28035386

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

none,

Oak Ridge Associated Universities (ORAU), under the Oak Ridge Institute for Science and Education (ORISE) contract, collected split surface water samples with Nuclear Fuel Services (NFS) representatives on June 12, 2013. Representatives from the U.S. Nuclear Regulatory Commission (NRC) and the Tennessee Department of Environment and Conservation were also in attendance. Samples were collected at four surface water stations, as required in the approved Request for Technical Assistance number 11-018. These stations included Nolichucky River upstream (NRU), Nolichucky River downstream (NRD), Martin Creek upstream (MCU), and Martin Creek downstream (MCD). Both ORAU and NFS performed gross alpha and gross betamore » analyses, and Table 1 presents the comparison of results using the duplicate error ratio (DER), also known as the normalized absolute difference. A DER ≤ 3 indicates at a 99% confidence interval that split sample results do not differ significantly when compared to their respective one standard deviation (sigma) uncertainty (ANSI N42.22). The NFS split sample report specifies 95% confidence level of reported uncertainties (NFS 2013). Therefore, standard two sigma reporting values were divided by 1.96. In conclusion, most DER values were less than 3 and results are consistent with low (e.g., background) concentrations. The gross beta result for sample 5198W0014 was the exception. The ORAU gross beta result of 6.30 ± 0.65 pCi/L from location NRD is well above NFS's non-detected result of 1.56 ± 0.59 pCi/L. NFS's data package includes no detected result for any radionuclide at location NRD. At NRC's request, ORAU performed gamma spectroscopic analysis of sample 5198W0014 to identify analytes contributing to the relatively elevated gross beta results. This analysis identified detected amounts of naturally-occurring constituents, most notably Ac-228 from the thorium decay series, and does not suggest the presence of site-related contamination.« less

Assessing duplication and loss of APETALA1/FRUITFULL homologs in Ranunculales

PubMed Central

Pabón-Mora, Natalia; Hidalgo, Oriane; Gleissberg, Stefan; Litt, Amy

2013-01-01

Gene duplication and loss provide raw material for evolutionary change within organismal lineages as functional diversification of gene copies provide a mechanism for phenotypic variation. Here we focus on the APETALA1/FRUITFULL MADS-box gene lineage evolution. AP1/FUL genes are angiosperm-specific and have undergone several duplications. By far the most significant one is the core-eudicot duplication resulting in the euAP1 and euFUL clades. Functional characterization of several euAP1 and euFUL genes has shown that both function in proper floral meristem identity, and axillary meristem repression. Independently, euAP1 genes function in floral meristem and sepal identity, whereas euFUL genes control phase transition, cauline leaf growth, compound leaf morphogenesis and fruit development. Significant functional variation has been detected in the function of pre-duplication basal-eudicot FUL-like genes, but the underlying mechanisms for change have not been identified. FUL-like genes in the Papaveraceae encode all functions reported for euAP1 and euFUL genes, whereas FUL-like genes in Aquilegia (Ranunculaceae) function in inflorescence development and leaf complexity, but not in flower or fruit development. Here we isolated FUL-like genes across the Ranunculales and used phylogenetic approaches to analyze their evolutionary history. We identified an early duplication resulting in the RanFL1 and RanFL2 clades. RanFL1 genes were present in all the families sampled and are mostly under strong negative selection in the MADS, I and K domains. RanFL2 genes were only identified from Eupteleaceae, Papaveraceae s.l., Menispermaceae and Ranunculaceae and show relaxed purifying selection at the I and K domains. We discuss how asymmetric sequence diversification, new motifs, differences in codon substitutions and likely protein-protein interactions resulting from this Ranunculiid-specific duplication can help explain the functional differences among basal-eudicot FUL-like genes. PMID:24062757

Lineage-specific co-evolution of the Egf receptor/ligand signaling system.

PubMed

Laisney, Juliette A G C; Braasch, Ingo; Walter, Ronald B; Meierjohann, Svenja; Schartl, Manfred

2010-01-27

The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed with different subsets of Egfr ligands. This fish-specific occurrence of Egf receptor specialization offers unique opportunities to study the functions of different Egf receptor-ligand combinations and their biological outputs in vertebrates. Furthermore, our results strongly support the use of homologous ligands in future studies, as sufficient cross-specificity is very unlikely for this ligand/receptor system.

Lineage-specific co-evolution of the Egf receptor/ligand signaling system

PubMed Central

2010-01-01

Background The epidermal growth factor receptor (Egfr) with its numerous ligands has fundamental roles in development, cell differentiation and physiology. Dysfunction of the receptor-ligand system contributes to many human malignancies. Consistent with such various tasks, the Egfr gene family has expanded during vertebrate evolution as a consequence of several rounds of whole genome duplication. Of particular interest is the effect of the fish-specific whole genome duplication (FSGD) on the ligand-receptor system, as it has supplied this largest group of vertebrates with additional opportunities for sub- and/or neofunctionalization in this signaling system. Results We identified the predicted components of the Egf receptor-ligand signaling system in teleost fishes (medaka, platyfish, stickleback, pufferfishes and zebrafish). We found two duplicated egfr genes, egfra and egfrb, in all available teleost genomes. Surprisingly only one copy for each of the seven Egfr ligands could be identified in most fishes, with zebrafish hbegf being the only exception. Special focus was put on medaka, for which we more closely investigated all Egf receptors and Egfr ligands. The different expression patterns of egfra, egfrb and their ligands in medaka tissues and embryo stages suggest differences in role and function. Preferential co-expression of different subsets of Egfr ligands corroborates the possible subfunctionalization and specialization of the two receptors in adult tissues. Bioinformatic analyses of the ligand-receptor interface between Egfr and its ligands show a very weak evolutionary conservation within this region. Using in vitro analyses of medaka Egfra, we could show that this receptor is only activated by medaka ligands, but not by human EGF. Altogether, our data suggest a lineage-specific Egfr/Egfr ligand co-evolution. Conclusions Our data indicate that medaka Egfr signaling occurs via its two copies, Egfra and Egfrb, each of them being preferentially coexpressed with different subsets of Egfr ligands. This fish-specific occurrence of Egf receptor specialization offers unique opportunities to study the functions of different Egf receptor-ligand combinations and their biological outputs in vertebrates. Furthermore, our results strongly support the use of homologous ligands in future studies, as sufficient cross-specificity is very unlikely for this ligand/receptor system. PMID:20105326

Determination of perfluoroalkyl carboxylic, sulfonic, and phosphonic acids in food.

PubMed

Ullah, Shahid; Alsberg, Tomas; Vestergren, Robin; Berger, Urs

2012-11-01

A sensitive and accurate method was developed and validated for simultaneous analysis of perfluoroalkyl carboxylic acids, sulfonic acids, and phosphonic acids (PFPAs) at low picograms per gram concentrations in a variety of food matrices. The method employed extraction with acetonitrile/water and cleanup on a mixed-mode co-polymeric sorbent (C8 + quaternary amine) using solid-phase extraction. High-performance liquid chromatographic separation was achieved on a C18 column using a mobile phase gradient containing 5 mM 1-methyl piperidine for optimal chromatographic resolution of PFPAs. A quadrupole time-of-flight high-resolution mass spectrometer operating in negative ion mode was used as detector. Method detection limits were in the range of 0.002 to 0.02 ng g(-1) for all analytes. Sample preparation (extraction and cleanup) recoveries at a spiking level of 0.1 ng g(-1) to a baby food composite were in the range of 59 to 98 %. A strong matrix effect was observed in the analysis of PFPAs in food extracts, which was tentatively assigned to sorption of PFPAs to the injection vial in the solvent-based calibration standard. The method was successfully applied to a range of different food matrices including duplicate diet samples, vegetables, meat, and fish samples.

Measurement of delta13C and delta18O Isotopic Ratios of CaCO3 by a Thermoquest Finnigan GasBench II Delta Plus XL Continous Flow Isotope Ratio Mass Spectrometer with Application to Devils Hole Core DH-11 Calcite

USGS Publications Warehouse

Revesz, Kinga M.; Landwehr, Jurate Maciunas; Keybl, Jaroslav Edward

2001-01-01

A new method was developed to analyze the stable carbon and oxygen isotope ratios of small samples (400?20 ?g) of calcium carbonate. This new method streamlines the classical phosphoric acid - calcium carbonate (H3PO4 - CaCO3) reaction method by making use of a Thermoquest-Finnigan GasBench II preparation device and a Delta Plus XL continuous flow isotope ratio mass spectrometer. To obtain reproducible and accurate results, optimal conditions for the H3PO4 - CaCO3 reaction had to be determined. At the acid-carbonate reaction temperature suggested by the equipment manufacturer, the oxygen isotope ratio results were unsatisfactory (standard deviation () greater than 1.5 per mill), probably because of a secondary reaction. When the acid-carbonate reaction temperature was lowered to 26?C and the reaction time was increased to 24 hours, the precision of the carbon and oxygen isotope ratios for duplicate analyses improved to 0.1 and 0.2 per mill, respectively. The method was tested by analyzing calcite from Devils Hole, Nevada, which was formed by precipitation from ground water onto the walls of a sub-aqueous cavern during the last 500,000 years. Isotope-ratio values previously had been obtained by the classical method for Devils Hole core DH-11. The DH-11 core had been recently re-sampled, and isotope-ratio values were obtained using this new method. The results were comparable to those obtained by the classical method. The consistency of the isotopic results is such that an alignment offset could be identified in the re-sampled core material, a cutting error that was then independently confirmed. The reproducibility of the isotopic values is demonstrated by a correlation of approximately 0.96 for both isotopes, after correcting for an alignment offset. This result indicates that the new method is a viable alternative to the classical method. In particular, the new method requires less sample material permitting finer resolution and allows automation of some processes resulting in considerable timesavings.

Abrasion-Erosion Evaluation of Concrete Mixtures for Stilling Basin Repairs, Kinzua Dam, Pennsylvania.

DTIC Science & Technology

1983-09-01

principal investigator. Mr. Steven A. Ragan prepared the concrete . mixtures; Mr. Dale Glass , Mr. Frank W. Dorsey, and Mr. Roger Buttner con- Vducted the...from the Buffalo Slag Co., Franklinville, New York. This fine aggregate is classified as a glacial sand and is composed primarily of limestone and...LAS SYMBOL NO.. PITT-8 S-1 TYPE OF MATERIAL Fine Aggregate LOCATION; Franklin, NY PRODUCER: Buffalo Slag Co. SAMPLED BY: Pittsburgh District Personnel

Fuel from Wastewater - Harnessing a Potential Energy Source in Canada through the Co-location of Algae Biofuel Production to Sources of Effluent, Heat and CO2

NASA Astrophysics Data System (ADS)

Klise, G. T.; Roach, J. D.; Passell, H. D.; Moreland, B. D.; O'Leary, S. J.; Pienkos, P. T.; Whalen, J.

2010-12-01

Sandia National Laboratories is collaborating with the National Research Council (NRC) Canada and the National Renewable Energy Laboratory (NREL) to develop a decision-support model that will evaluate the tradeoffs associated with high-latitude algae biofuel production co-located with wastewater, CO2, and waste heat. This project helps Canada meet its goal of diversifying fuel sources with algae-based biofuels. The biofuel production will provide a wide range of benefits including wastewater treatment, CO2 reuse and reduction of demand for fossil-based fuels. The higher energy density in algae-based fuels gives them an advantage over crop-based biofuels as the “production” footprint required is much less, resulting in less water consumed and little, if any conversion of agricultural land from food to fuel production. Besides being a potential source for liquid fuel, algae have the potential to be used to generate electricity through the burning of dried biomass, or anaerobically digested to generate methane for electricity production. Co-locating algae production with waste streams may be crucial for making algae an economically valuable fuel source, and will certainly improve its overall ecological sustainability. The modeling process will address these questions, and others that are important to the use of water for energy production: What are the locations where all resources are co-located, and what volumes of algal biomass and oil can be produced there? In locations where co-location does not occur, what resources should be transported, and how far, while maintaining economic viability? This work is being funded through the U.S. Department of Energy (DOE) Biomass Program Office of Energy Efficiency and Renewable Energy, and is part of a larger collaborative effort that includes sampling, strain isolation, strain characterization and cultivation being performed by the NREL and Canada’s NRC. Results from the NREL / NRC collaboration including specific productivities of selected algal strains will eventually be incorporated into this model. Joint activities in algal biofuel research involving Sandia National Labs, NREL, and Canada’s NRC are supported by the U.S. - Canada Clean Energy Dialogue Secretariat. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-AC04-94AL85000.

Integrated Ultra-Wideband Tracking and Carbon Dioxide Sensing System Design for International Space Station Applications

NASA Technical Reports Server (NTRS)

Ni, Jianjun (David); Hafermalz, David; Dusl, John; Barton, Rick; Wagner, Ray; Ngo, Phong

2015-01-01

A three-dimensional (3D) Ultra-Wideband (UWB) Time-of-Arrival (TOA) tracking system has been studied at NASA Johnson Space Center (JSC) to provide the tracking capability inside the International Space Station (ISS) modules for various applications. One of applications is to locate and report the location where crew experienced possible high level of carbon-dioxide (CO2) and felt upset. Recent findings indicate that frequent, short-term crew exposure to elevated CO2 levels combined with other physiological impacts of microgravity may lead to a number of detrimental effects, including loss of vision. To evaluate the risks associated with transient elevated CO2 levels and design effective countermeasures, doctors must have access to frequent CO2 measurements in the immediate vicinity of individual crew members along with simultaneous measurements of their location in the space environment. To achieve this goal, a small, low-power, wearable system that integrates an accurate CO2 sensor with an ultra-wideband (UWB) radio capable of real-time location estimation and data communication is proposed. This system would be worn by crew members or mounted on a free-flyer and would automatically gather and transmit sampled sensor data tagged with real-time, high-resolution location information. Under the current proposed effort, a breadboard prototype of such a system has been developed. Although the initial effort is targeted to CO2 monitoring, the concept is applicable to other types of sensors. For the initial effort, a micro-controller is leveraged to integrate a low-power CO2 sensor with a commercially available UWB radio system with ranging capability. In order to accurately locate those places in a multipath intensive environment like ISS modules, it requires a robust real-time location system (RTLS) which can provide the required accuracy and update rate. A 3D UWB TOA tracking system with two-way ranging has been proposed and studied. The designed system will be tested in the Wireless Habitat Testbed which simulates the ISS module environment. This report describes the research and development effort for this prototype integrated UWB tracking and CO2 sensing system. The remainder of the report is organized as follows. In Section II, the TOA tracking methodology is introduced and the 3D tracking algorithm is derived. The simulation results are discussed in Section III. In Section VI, prototype system design and field tests are discussed. Some concluding remarks and future works are presented in Section V.

Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone.

PubMed

Trappe, Kathrin; Emde, Anne-Katrin; Ehrlich, Hans-Christian; Reinert, Knut

2014-12-15

The landscape of structural variation (SV) including complex duplication and translocation patterns is far from resolved. SV detection tools usually exhibit low agreement, are often geared toward certain types or size ranges of variation and struggle to correctly classify the type and exact size of SVs. We present Gustaf (Generic mUlti-SpliT Alignment Finder), a sound generic multi-split SV detection tool that detects and classifies deletions, inversions, dispersed duplications and translocations of ≥ 30 bp. Our approach is based on a generic multi-split alignment strategy that can identify SV breakpoints with base pair resolution. We show that Gustaf correctly identifies SVs, especially in the range from 30 to 100 bp, which we call the next-generation sequencing (NGS) twilight zone of SVs, as well as larger SVs >500 bp. Gustaf performs better than similar tools in our benchmark and is furthermore able to correctly identify size and location of dispersed duplications and translocations, which otherwise might be wrongly classified, for example, as large deletions. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Mining Co-Location Patterns with Clustering Items from Spatial Data Sets

NASA Astrophysics Data System (ADS)

Zhou, G.; Li, Q.; Deng, G.; Yue, T.; Zhou, X.

2018-05-01

The explosive growth of spatial data and widespread use of spatial databases emphasize the need for the spatial data mining. Co-location patterns discovery is an important branch in spatial data mining. Spatial co-locations represent the subsets of features which are frequently located together in geographic space. However, the appearance of a spatial feature C is often not determined by a single spatial feature A or B but by the two spatial features A and B, that is to say where A and B appear together, C often appears. We note that this co-location pattern is different from the traditional co-location pattern. Thus, this paper presents a new concept called clustering terms, and this co-location pattern is called co-location patterns with clustering items. And the traditional algorithm cannot mine this co-location pattern, so we introduce the related concept in detail and propose a novel algorithm. This algorithm is extended by join-based approach proposed by Huang. Finally, we evaluate the performance of this algorithm.

Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms.

PubMed

Chen, Bin; Zhong, Daibin; Monteiro, Antónia

2006-06-17

HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in GenBank, and address the diversity, evolution, gene structure, conservation and nomenclature of the HSP90 family of genes across all organisms. Twelve new genes and a new type HSP90C2 were identified. The chromosomal location, exon splicing, and prediction of whether they are functional copies were documented, as well as the amino acid length and molecular mass of their polypeptides. The conserved regions across all protein sequences, and signature sequences in each subfamily were determined, and a standardized nomenclature system for this gene family is presented. The proeukaryote HSP90 homologue, HTPG, exists in most Bacteria species but not in Archaea, and it evolved into three lineages (Groups A, B and C) via two gene duplication events. None of the organellar-localized HSP90s were derived from endosymbionts of early eukaryotes. Mitochondrial TRAP and endoplasmic reticulum HSP90B separately originated from the ancestors of HTPG Group A in Firmicutes-like organisms very early in the formation of the eukaryotic cell. TRAP is monophyletic and present in all Animalia and some Protista species, while HSP90B is paraphyletic and present in all eukaryotes with the exception of some Fungi species, which appear to have lost it. Both HSP90C (chloroplast HSP90C1 and location-undetermined SP90C2) and cytosolic HSP90A are monophyletic, and originated from HSP90B by independent gene duplications. HSP90C exists only in Plantae, and was duplicated into HSP90C1 and HSP90C2 isoforms in higher plants. HSP90A occurs across all eukaryotes, and duplicated into HSP90AA and HSP90AB in vertebrates. Diplomonadida was identified as the most basal organism in the eukaryote lineage. The present study presents the first comparative genomic study and evolutionary analysis of the HSP90 family of genes across all kingdoms of organisms. HSP90 family members underwent multiple duplications and also subsequent losses during their evolution. This study established an overall framework of information for the family of genes, which may facilitate and stimulate the study of this gene family across all organisms.

Nonhomologous recombination between defective poliovirus and coxsackievirus genomes suggests a new model of genetic plasticity for picornaviruses.

PubMed

Holmblat, Barbara; Jégouic, Sophie; Muslin, Claire; Blondel, Bruno; Joffret, Marie-Line; Delpeyroux, Francis

2014-08-05

Most of the circulating vaccine-derived polioviruses (cVDPVs) implicated in poliomyelitis outbreaks in Madagascar have been shown to be recombinants between the type 2 poliovirus (PV) strain of the oral polio vaccine (Sabin 2) and another species C human enterovirus (HEV-C), such as type 17 coxsackie A virus (CA17) in particular. We studied intertypic genetic exchanges between PV and non-PV HEV-C by developing a recombination model, making it possible to rescue defective type 2 PV RNA genomes with a short deletion at the 3' end by the cotransfection of cells with defective or infectious CA17 RNAs. We isolated over 200 different PV/CA17 recombinants, using murine cells expressing the human PV receptor (PVR) and selecting viruses with PV capsids. We found some homologous (H) recombinants and, mostly, nonhomologous (NH) recombinants presenting duplications of parental sequences preferentially located in the regions encoding proteins 2A, 2B, and 3A. Short duplications appeared to be stable, whereas longer duplications were excised during passaging in cultured cells or after multiplication in PVR-transgenic mice, generating H recombinants with diverse sites of recombination. This suggests that NH recombination events may be a transient, intermediate step in the generation and selection of the fittest H recombinants. In addition to the classical copy-choice mechanism of recombination thought to generate mostly H recombinants, there may also be a modular mechanism of recombination, involving NH recombinant precursors, shaping the genomes of recombinant enteroviruses and other picornaviruses. Importance: The multiplication of circulating vaccine-derived polioviruses (cVDPVs) in poorly immunized human populations can render these viruses pathogenic, causing poliomyelitis outbreaks. Most cVDPVs are intertypic recombinants between a poliovirus (PV) strain and another human enterovirus, such as type 17 coxsackie A viruses (CA17). For further studies of the genetic exchanges between PV and CA17, we have developed a model of recombination, making it possible to rescue defective PV RNA genomes with a short deletion by cotransfecting cells with the defective PV genome and CA17 genomic RNA. Numerous recombinants were found, including homologous PV/CA17 recombinants, but mostly nonhomologous recombinants presenting duplications of parental sequences preferentially located in particular regions. Long duplications were excised by passages in cultured cells or in mice, generating diverse homologous recombinants. Recombination leading to nonhomologous recombinants, which evolve into homologous recombinants, may therefore be seen as a model of genetic plasticity in enteroviruses and, possibly, in other RNA viruses. Copyright © 2014 Holmblat et al.

Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms

PubMed Central

Chen, Bin; Zhong, Daibin; Monteiro, Antónia

2006-01-01

Background HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in GenBank, and address the diversity, evolution, gene structure, conservation and nomenclature of the HSP90 family of genes across all organisms. Results Twelve new genes and a new type HSP90C2 were identified. The chromosomal location, exon splicing, and prediction of whether they are functional copies were documented, as well as the amino acid length and molecular mass of their polypeptides. The conserved regions across all protein sequences, and signature sequences in each subfamily were determined, and a standardized nomenclature system for this gene family is presented. The proeukaryote HSP90 homologue, HTPG, exists in most Bacteria species but not in Archaea, and it evolved into three lineages (Groups A, B and C) via two gene duplication events. None of the organellar-localized HSP90s were derived from endosymbionts of early eukaryotes. Mitochondrial TRAP and endoplasmic reticulum HSP90B separately originated from the ancestors of HTPG Group A in Firmicutes-like organisms very early in the formation of the eukaryotic cell. TRAP is monophyletic and present in all Animalia and some Protista species, while HSP90B is paraphyletic and present in all eukaryotes with the exception of some Fungi species, which appear to have lost it. Both HSP90C (chloroplast HSP90C1 and location-undetermined SP90C2) and cytosolic HSP90A are monophyletic, and originated from HSP90B by independent gene duplications. HSP90C exists only in Plantae, and was duplicated into HSP90C1 and HSP90C2 isoforms in higher plants. HSP90A occurs across all eukaryotes, and duplicated into HSP90AA and HSP90AB in vertebrates. Diplomonadida was identified as the most basal organism in the eukaryote lineage. Conclusion The present study presents the first comparative genomic study and evolutionary analysis of the HSP90 family of genes across all kingdoms of organisms. HSP90 family members underwent multiple duplications and also subsequent losses during their evolution. This study established an overall framework of information for the family of genes, which may facilitate and stimulate the study of this gene family across all organisms. PMID:16780600

Mapping Potential Amplification and Transmission Hotspots for MERS-CoV, Kenya.

PubMed

Gikonyo, Stephen; Kimani, Tabitha; Matere, Joseph; Kimutai, Joshua; Kiambi, Stella G; Bitek, Austine O; Juma Ngeiywa, K J Z; Makonnen, Yilma J; Tripodi, Astrid; Morzaria, Subhash; Lubroth, Juan; Rugalema, Gabriel; Fasina, Folorunso Oludayo

2018-03-16

Dromedary camels have been implicated consistently as the source of Middle East respiratory syndrome coronavirus (MERS-CoV) human infections and attention to prevent and control it has focused on camels. To understanding the epidemiological role of camels in the transmission of MERS-CoV, we utilized an iterative empirical process in Geographic Information System (GIS) to identify and qualify potential hotspots for maintenance and circulation of MERS-CoV, and produced risk-based surveillance sites in Kenya. Data on camel population and distribution were used to develop camel density map, while camel farming system was defined using multi-factorial criteria including the agro-ecological zones (AEZs), production and marketing practices. Primary and secondary MERS-CoV seroprevalence data from specific sites were analyzed, and location-based prevalence matching with camel densities was conducted. High-risk convergence points (migration zones, trade routes, camel markets, slaughter slabs) were profiled and frequent cross-border camel movement mapped. Results showed that high camel-dense areas and interaction (markets and migration zones) were potential hotspot for transmission and spread. Cross-border contacts occurred with in-migrated herds at hotspot locations. AEZ differential did not influence risk distribution and plausible risk factors for spatial MERS-CoV hotspots were camel densities, previous cases of MERS-CoV, high seroprevalence and points of camel convergences. Although Kenyan camels are predisposed to MERS-CoV, no shedding is documented to date. These potential hotspots, determined using anthropogenic, system and trade characterizations should guide selection of sampling/surveillance sites, high-risk locations, critical areas for interventions and policy development in Kenya, as well as instigate further virological examination of camels.

Characterization of Spatial Impact of Particles Emitted from a Cement Material Production Facility on Outdoor Particle Deposition in the Surrounding Community.

PubMed

Yu, Chang Ho; Fan, Zhihua Tina; McCandlish, Elizabeth; Stern, Alan H; Lioy, Paul J

2011-10-01

The objective of this study was to estimate the contribution of a facility that processes steel production slag into raw material for cement production to local outdoor particle deposition in Camden, NJ. A dry deposition sampler that can house four 37-mm quartz fiber filters was developed and used for the collection of atmospheric particle deposits. Two rounds of particle collection (3-4 weeks each) were conducted in 8-11 locations 200-800 m downwind of the facility. Background samples were concurrently collected in a remote area located ∼2 km upwind from the facility. In addition, duplicate surface wipe samples were collected side-by-side from each of the 13 locations within the same sampling area during the first deposition sampling period. One composite source material sample was also collected from a pile stored in the facility. Both the bulk of the source material and the <38 μm fraction subsample were analyzed to obtain the elemental source profile. The particle deposition flux in the study area was higher (24-83 mg/m 2 ·day) than at the background sites (13-17 mg/m 2 ·day). The concentration of Ca, a major element in the cement source production material, was found to exponentially decrease with increasing downwind distance from the facility (P < 0.05). The ratio of Ca/Al, an indicator of Ca enrichment due to anthropogenic sources in a given sample, showed a similar trend. These observations suggest a significant contribution of the facility to the local particle deposition. The contribution of the facility to outdoor deposited particle mass was further estimated by three independent models using the measurements obtained from this study. The estimated contributions to particle deposition in the study area were 1.8-7.4% from the regression analysis of the Ca concentration in particle deposition samples against the distance from the facility, 0-11% from the U.S. Environmental Protection Agency (EPA) Chemical Mass Balance (CMB) source-receptor model, and 7.6-13% from the EPA Industrial Source Complex Short Term (ISCST3) dispersion model using the particle-size-adjusted permit-based emissions estimates. [Box: see text].

Carbon and oxygen isotopic composition of coal and carbon dioxide derived from laboratory coal combustion: A preliminary study

USGS Publications Warehouse

Warwick, Peter D.; Ruppert, Leslie F.

2016-01-01

The concentration of carbon dioxide (CO2) in the atmosphere has dramatically increased from the start of the industrial revolution in the mid-1700s to present levels exceeding 400 ppm. Carbon dioxide derived from fossil fuel combustion is a greenhouse gas and a major contributor to on-going climate change. Carbon and oxygen stable isotope geochemistry is a useful tool to help model and predict the contributions of anthropogenic sources of CO2 in the global carbon cycle. Surprisingly few studies have addressed the carbon and oxygen isotopic composition of CO2 derived from coal combustion. The goal of this study is to document the relationships between the carbon and oxygen isotope signatures of coal and signatures of the CO2 produced from laboratory coal combustion in atmospheric conditions.Six coal samples were selected that represent various geologic ages (Carboniferous to Tertiary) and coal ranks (lignite to bituminous). Duplicate splits of the six coal samples were ignited and partially combusted in the laboratory at atmospheric conditions. The resulting coal-combustion gases were collected and the molecular composition of the collected gases and isotopic analyses of δ13C of CO2, δ13C of CH4, and δ18O of CO2 were analysed by a commercial laboratory. Splits (~ 1 g) of the un-combusted dried ground coal samples were analyzed for δ13C and δ18O by the U.S. Geological Survey Reston Stable Isotope Laboratory.The major findings of this preliminary work indicate that the isotopic signatures of δ13C (relative to the Vienna Pee Dee Belemnite scale, VPDB) of CO2 resulting from coal combustion are similar to the δ13CVPDB signature of the bulk coal (− 28.46 to − 23.86 ‰) and are not similar to atmospheric δ13CVPDB of CO2 (~ − 8 ‰, see http://www.esrl.noaa.gov/gmd/outreach/isotopes/c13tellsus.html). The δ18O values of bulk coal are strongly correlated to the coal dry ash yields and appear to have little or no influence on the δ18O values of CO2 resulting from coal combustion in open atmospheric conditions. There is a wide range of δ13C values of coal reported in the literature and the δ13C values from this study generally follow reported ranges for higher plants over geologic time. The values of δ18O (relative to Vienna Standard Mean Ocean Water) of CO2 derived from atmospheric combustion of coal and other high-carbon fuels (peat and coal) range from + 19.03 to + 27.03‰ and are similar to atmospheric oxygen δ18OVSMOW values which average + 23.8‰. Further work is needed on a broader set of samples to better define the relationships between coal composition and combustion-derived gases.

Lead in duplicate diet samples from an academic community.

PubMed

Coelho, Sónia D; Pastorinho, M Ramiro; Itai, Takaaki; Isobe, Tomohiko; Kunisue, Tatsuya; Nogueira, António J A; Tanabe, Shinsuke; Sousa, Ana C A

2016-12-15

Lead is a naturally occurring element that with the advent of the industrial era became a serious environmental and public health issue. Leaded gasoline, lead based paints, use of lead in plumbing and water pipes, ceramics with lead-containing glazes and tobacco smoke are potential sources of lead exposure for humans. Despite these multiple sources, food is still considered the most important one for the general non-smoking population. Hence, in the present study, the dietary intake of lead was determined in duplicate diet samples provided by 30 participants working or studying at University of Aveiro, Portugal. Pb was detected in all the analysed samples with values ranging between 0.009 and 0.10mgkg -1 ww which correspond to estimated daily intakes between 0.22 and 3.5μgkg-bw -1 day -1 . Risk estimations disclose that at least 3.3% and 26.7% of the participants might suffer cardiovascular and nephrotoxic effects, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

Air Quality Monitoring of the Post-Operative Recovery Room and Locations Surrounding Operating Theaters in a Medical Center in Taiwan

PubMed Central

Tang, Chin-Sheng; Wan, Gwo-Hwa

2013-01-01

To prevent surgical site infection (SSI), the airborne microbial concentration in operating theaters must be reduced. The air quality in operating theaters and nearby areas is also important to healthcare workers. Therefore, this study assessed air quality in the post-operative recovery room, locations surrounding the operating theater area, and operating theaters in a medical center. Temperature, relative humidity (RH), and carbon dioxide (CO2), suspended particulate matter (PM), and bacterial concentrations were monitored weekly over one year. Measurement results reveal clear differences in air quality in different operating theater areas. The post-operative recovery room had significantly higher CO2 and bacterial concentrations than other locations. Bacillus spp., Micrococcus spp., and Staphylococcus spp. bacteria often existed in the operating theater area. Furthermore, Acinetobacter spp. was the main pathogen in the post-operative recovery room (18%) and traumatic surgery room (8%). The mixed effect models reveal a strong correlation between number of people in a space and high CO2 concentration after adjusting for sampling locations. In conclusion, air quality in the post-operative recovery room and operating theaters warrants attention, and merits long-term surveillance to protect both surgical patients and healthcare workers. PMID:23573296

January 2012 Groundwater Sampling at the Gnome-Coach, New Mexico, Site (Data Validation Package)

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

Findlay, Richard C.

2012-12-01

Annual sampling was conducted January 18, 2012, to monitor groundwater for potential radionuclide contamination at the Gnome-Coach site in New Mexico. The sampling was performed as specified in the Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PLN/S04351, continually updated). Well LRL-7 was not sampled per instruction from the lead. A duplicate sample was collected from well USGS-1 and water levels were measured in the monitoring wells onsite.

January 2011 Groundwater Sampling at the Gnome-Coach, New Mexico, Site (Data Validation Package)

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

Findlay, Richard C.

2011-11-01

Annual sampling was conducted January 19, 2011, to monitor groundwater for potential radionuclide contamination at the Gnome-Coach site in New Mexico. The sampling was performed as specified in the Sampling and Analysis Plan for U.S. Department of Energy Office of Legacy Management Sites (LMS/PLN/S04351, continually updated). Well LRL-7 was not sampled per instruction from the lead. A duplicate sample was collected from well USGS-1.Water levels were measured in the monitoring wells onsite.

Detecting Kerogen as a Biosignature Using Co-located UV Time-Gated Raman and Fuorescence Spectroscopy

NASA Astrophysics Data System (ADS)

Shkolyar, S.; Eshelman, E.; Farmer, J. D.; Hamilton, D.; Daly, M. G.; Youngbull, C.

2017-12-01

The Mars 2020 mission will analyze samples in situ and identify any that could have preserved biosignatures in ancient habitable environments for later return to Earth. Highest-priority targeted samples include aqueously formed sedimentary lithologies containing fossil biosignatures as aromatic carbon (kerogen). In this study, we analyze non-extracted, naturally preserved kerogen in a diverse suite of realistic Mars analogs using combined UV excitation time-gated (UV-TG) Raman and laser-induced fluorescence spectroscopy. We interrogated kerogen and its host matrix in samples to: (1) explore the capabilities of UV-TG Raman and fluorescence spectroscopy for detecting kerogen in high-priority targets in the search for a Martian fossil record; (2) assess the effectiveness of time-gating and UV laser wavelength in reducing fluorescence; and (3) identify sample-specific issues which could challenge rover-based identifications of kerogen using UV-TG Raman spectroscopy. We found that ungated UV Raman is suited to identify diagnostic kerogen Raman bands without interfering fluorescence and that fluorescence features indicating kerogen are detectable. These data highlight the value of using both co-located Raman and fluorescence data sets together to strengthen the confidence of kerogen detection as a potential biosignature and are obtainable by SHERLOC onboard Mars 2020.

Could the IMS Infrasound Stations Support a Global Network of Small Aperture Seismic Arrays?

NASA Astrophysics Data System (ADS)

J, Gibbons, Steven; Kværna, Tormod; Mykkeltveit, Svein

2015-04-01

The infrasound stations of the International Monitoring System are arrays consisting of up to 15 sites and with apertures of up to 3 km. The arrays are distributed remarkably uniformly over the globe and provide excellent coverage of South America, Africa, and Antarctica. This is to say that there are many infrasound arrays in regions many thousands of kilometers from the closest seismic array. Several infrasound arrays are in the immediate vicinity of existing 3-component seismic stations and these provide us with examples of how typical seismic signals look at these locations. We can make idealized estimates of the predicted performance of seismic arrays, consisting of seismometers at each site of the infrasound arrays, by duplicating the signals from the 3-C stations at all sites of the array. However, the true performance of seismic arrays at these sites will depend both upon Signal-to-Noise Ratios of seismic signals and the coherence of both signal and noise between sensors. These properties can only be determined experimentally. Recording seismic data of sufficient quality at many of these arrays may require borehole deployments since the microbarometers in the infrasound arrays are often situated in vaults placed in soft sediments. The geometries of all the current IMS infrasound arrays are examined and compared and we demonstrate that, from a purely geometrical perspective, essentially all the array configurations would provide seismic arrays with acceptable slowness resolution for both regional and teleseismic phase arrivals. Seismic arrays co-located with the infrasound arrays in many regions would likely enhance significantly the seismic monitoring capability in parts of the world where only 3-component stations are currently available. Co-locating seismic and infrasound sensors would facilitate the development of seismic arrays that share the infrastructure of the infrasound arrays, reducing the development and operational costs. Hosting countries might find such added capabilities valuable from a national perspective. In addition, the seismic recordings may also help to identify the sources of infrasound signals with consequences for improved event screening and evaluating models of infrasound propagation and atmospheric properties.

Cyclic carbonation calcination studies of limestone and dolomite for CO{sub 2} separation from combustion flue gases - article no. 011801

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

Senthoorselvan, S.; Gleis, S.; Hartmut, S.

2009-01-15

Naturally occurring limestone and dolomite samples, originating from different geographical locations, were tested as potential sorbents for carbonation/calcination based CO{sub 2} capture from combustion flue gases. Samples have been studied in a thermogravimetric analyzer under simulated flue gas conditions at three calcination temperatures, viz., 750{sup o}C, 875{sup o}C, and 930{sup o}C for four carbonation calcination reaction (CCR) cycles. The dolomite sample exhibited the highest rate of carbonation than the tested limestones. At the third cycle, its CO{sub 2} capture capacity per kilogram of the sample was nearly equal to that of Gotland, the highest reacting limestone tested. At the fourthmore » cycle it surpassed Gotland, despite the fact that the CaCO{sub 3} content of the Sibbo dolomite was only 2/3 of that of the Gotland. Decay coefficients were calculated by a curve fitting exercise and its value is lowest for the Sibbo dolomite. That means, most probably its capture capacity per kilogram of the sample would remain higher well beyond the fourth cycle. There was a strong correlation between the calcination temperature, the specific surface area of the calcined samples, and the degree of carbonation. It was observed that the higher the calcination temperature, the lower the sorbent reactivity. For a given limestone/dolomite sample, sorbents CO{sub 2} capture capacity depended on the number of CCR cycles and the calcination temperature. According to the equilibrium thermodynamics, the CO{sub 2} partial pressure in the calciner should be lowered to lower the calcination temperature. This can be achieved by additional steam supply into the calciner. Steam could then be condensed in an external condenser to single out the CO{sub 2} stream from the exit gas mixture of the calciner. A calciner design based on this concept is illustrated.« less

Optimized spectroscopic scheme for enhanced precision CO measurements with applications to urban source attribution

NASA Astrophysics Data System (ADS)

Nottrott, A.; Hoffnagle, J.; Farinas, A.; Rella, C.

2014-12-01

Carbon monoxide (CO) is an urban pollutant generated by internal combustion engines which contributes to the formation of ground level ozone (smog). CO is also an excellent tracer for emissions from mobile combustion sources. In this work we present an optimized spectroscopic sampling scheme that enables enhanced precision CO measurements. The scheme was implemented on the Picarro G2401 Cavity Ring-Down Spectroscopy (CRDS) analyzer which measures CO2, CO, CH4 and H2O at 0.2 Hz. The optimized scheme improved the raw precision of CO measurements by 40% from 5 ppb to 3 ppb. Correlations of measured CO2, CO, CH4 and H2O from an urban tower were partitioned by wind direction and combined with a concentration footprint model for source attribution. The application of a concentration footprint for source attribution has several advantages. The upwind extent of the concentration footprint for a given sensor is much larger than the flux footprint. Measurements of mean concentration at the sensor location can be used to estimate source strength from a concentration footprint, while measurements of the vertical concentration flux are necessary to determine source strength from the flux footprint. Direct measurement of vertical concentration flux requires high frequency temporal sampling and increases the cost and complexity of the measurement system.

Exploring the 13CO/C18O abundance ratio towards Galactic young stellar objects and HII regions

NASA Astrophysics Data System (ADS)

Areal, M. B.; Paron, S.; Celis Peña, M.; Ortega, M. E.

2018-05-01

Aims: Determining molecular abundance ratios is important not only for the study of Galactic chemistry, but also because they are useful to estimate physical parameters in a large variety of interstellar medium environments. One of the most important molecules for tracing the molecular gas in the interstellar medium is CO, and the 13CO/C18O abundance ratio is usually used to estimate molecular masses and densities of regions with moderate to high densities. Nowadays isotope ratios are in general indirectly derived from elemental abundances ratios. We present the first 13CO/C18O abundance ratio study performed from CO isotope observations towards a large sample of Galactic sources of different natures at different locations. Methods: To study the 13CO/C18O abundance ratio, we used 12CO J = 3 - 2 data obtained from the CO High-Resolution Survey, 13CO and C18O J = 3 - 2 data from the 13CO/C18O (J = 3 - 2) Heterodyne Inner Milky Way Plane Survey, and some complementary data extracted from the James Clerk Maxwell Telescope database. We analyzed a sample of 198 sources composed of young stellar objects (YSOs), and HII and diffuse HII regions as catalogued in the Red MSX Source Survey in 27.°5 ≤ l ≤ 46.°5 and |b|0.°5. Results: Most of the analyzed sources are located in the galactocentric distance range 4.0-6.5 kpc. We found that YSOs have, on average, lower 13CO/C18O abundance ratios than HII and diffuse HII regions. Taking into account that the gas associated with YSOs should be less affected by the radiation than in the case of the others sources, selective far-UV photodissociation of C18O is confirmed. The 13CO/C18O abundance ratios obtained in this work are systematically lower than those predicted from the known elemental abundance relations. These results will be useful in future studies of molecular gas related to YSOs and HII regions based on the observation of these isotopes.

Temporal and spatial variation of trace elements in atmospheric deposition around the industrial area of Puchuncaví-Ventanas (Chile) and its influence on exceedances of lead and cadmium critical loads in soils.

PubMed

Rueda-Holgado, F; Calvo-Blázquez, L; Cereceda-Balic, F; Pinilla-Gil, E

2016-02-01

Fractionation of elemental contents in atmospheric samples is useful to evaluate pollution levels for risk assessment and pollution sources assignment. We present here the main results of long-term characterization of atmospheric deposition by using a recently developed atmospheric elemental fractionation sampler (AEFS) for major and trace elements monitoring around an important industrial complex located in Puchuncaví region (Chile). Atmospheric deposition samples were collected during two sampling campaigns (2010 and 2011) at four sampling locations: La Greda (LG), Los Maitenes (LM), Puchuncaví (PU) and Valle Alegre (VA). Sample digestion and ICP-MS gave elements deposition values (Al, As, Ba, Cd, Co, Cu, Fe, K, Mn, Pb, Sb, Ti, V and Zn) in the insoluble fraction of the total atmospheric deposition. Results showed that LG location, the closest location to the industrial complex, was the more polluted sampling site having the highest values for the analyzed elements. PU and LM were the next more polluted and, finally, the lowest elements concentrations were registered at VA. The application of Principal Component Analysis and Cluster Analysis identified industrial, traffic and mineral-crustal factors. We found critical loads exceedances for Pb at all sampling locations in the area affected by the industrial emissions, more significant in LG close to the industrial complex, with a trend to decrease in 2011, whereas no exceedances due to atmospheric deposition were detected for Cd. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

PubMed Central

Liu, Shengyi; Liu, Yumei; Yang, Xinhua; Tong, Chaobo; Edwards, David; Parkin, Isobel A. P.; Zhao, Meixia; Ma, Jianxin; Yu, Jingyin; Huang, Shunmou; Wang, Xiyin; Wang, Junyi; Lu, Kun; Fang, Zhiyuan; Bancroft, Ian; Yang, Tae-Jin; Hu, Qiong; Wang, Xinfa; Yue, Zhen; Li, Haojie; Yang, Linfeng; Wu, Jian; Zhou, Qing; Wang, Wanxin; King, Graham J; Pires, J. Chris; Lu, Changxin; Wu, Zhangyan; Sampath, Perumal; Wang, Zhuo; Guo, Hui; Pan, Shengkai; Yang, Limei; Min, Jiumeng; Zhang, Dong; Jin, Dianchuan; Li, Wanshun; Belcram, Harry; Tu, Jinxing; Guan, Mei; Qi, Cunkou; Du, Dezhi; Li, Jiana; Jiang, Liangcai; Batley, Jacqueline; Sharpe, Andrew G; Park, Beom-Seok; Ruperao, Pradeep; Cheng, Feng; Waminal, Nomar Espinosa; Huang, Yin; Dong, Caihua; Wang, Li; Li, Jingping; Hu, Zhiyong; Zhuang, Mu; Huang, Yi; Huang, Junyan; Shi, Jiaqin; Mei, Desheng; Liu, Jing; Lee, Tae-Ho; Wang, Jinpeng; Jin, Huizhe; Li, Zaiyun; Li, Xun; Zhang, Jiefu; Xiao, Lu; Zhou, Yongming; Liu, Zhongsong; Liu, Xuequn; Qin, Rui; Tang, Xu; Liu, Wenbin; Wang, Yupeng; Zhang, Yangyong; Lee, Jonghoon; Kim, Hyun Hee; Denoeud, France; Xu, Xun; Liang, Xinming; Hua, Wei; Wang, Xiaowu; Wang, Jun; Chalhoub, Boulos; Paterson, Andrew H

2014-01-01

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. PMID:24852848

sup 60 Co. gamma. -rays induce predominantly C/G to G/C transversions in double-stranded M13 DNA

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

Hoebee, B.; Loman, H.; Brouwer, J.

Upon irradiation with gamma rays of an oxygenated aqueous solution of double-stranded M13 DNA, a very specific mutation spectrum was found with respect to both the type and the positions in the DNA sequence. Of the 23 mutations, which were sequenced, 16 represent a C/G to G/C transversion. A C/G to T/A transition was found once and a G/C to T/A transversion twice. The remaining 4 mutations are frameshifts, 2 are identical and formed by the insertion of a G/C basepair; the other 2 mutations are due to a duplication of 10 basepairs situated at different positions but with amore » remarkable homology in base sequence. Fourteen mutations, including the 2 duplications are found in the neighborhood of a TGCT/ACGA sequence.« less

Spatial and Temporal Distribution of Polycyclic Aromatic Hydrocarbons and Elemental Carbon in Bakersfield, California

PubMed Central

Noth, Elizabeth M.; Lurmann, Fred; Northcross, Amanda; Perrino, Charles; Vaughn, David; Hammond, S. Katharine

2016-01-01

Despite increasing evidence that airborne polycyclic aromatic hydrocarbon (PAH) exposures contribute to adverse health outcomes for sensitive populations, limited data are available on short-term intraurban spatial distributions for use in epidemiologic research. Exposure assessments for airborne PAHs are uncommon because air sampling for PAHs is a labor-, equipment-, and time-intensive task. To address this gap we measured wintertime PAH concentrations during 2010-2011 in Bakersfield, California, USA, a major city in the Southern San Joaquin Valley. Specifically, 58 96-hour integrated PAH samples were collected during 4 time periods at 14 locations from November 2010 to January 2011; duplicates were collected at two sites. We also collected elemental carbon (EC) at the same 14 sites and analyzed the two time periods with the highest ambient PAH pollution. We used linear regression models to quantify the relationship between potential spatial and temporal predictors of PAH concentrations. We found that wintertime PAH concentrations in Bakersfield, CA, are best predicted by meteorological variables and traffic proximity. Our model explains a moderate amount of the variability in the data (R2=0.58), likely reflecting the major sources of PAHs in Bakersfield. We also observed that PAH concentrations were more spatially variable than EC concentrations. Comparing our data to historical monitoring data at one location in Bakersfield showed that the relatively low PAH concentrations during the 2010-2011 winter in Bakersfield is part of a long-term trend in decreasing PAH concentrations. PMID:28083077

Spatial contrasts of seasonal and intraflock broiler litter trace gas emissions, physical and chemical properties.

PubMed

Miles, D M; Brooks, J P; Sistani, K

2011-01-01

Comprehensive mitigation strategies for gaseous emissions from broiler operations requires knowledge of the litters' physical and chemical properties, gas evolution, bird effects, as well as broiler house management and structure. This research estimated broiler litter surface fluxes for ammonia (NH3), nitrous oxide (N2O), and carbon dioxide (CO2). Ancillary measurements of litter temperature, litter total N, ammonium (NH4+), total C content, moisture, and pH were also made. Grid sampling was imposed over the floor area of two commercial broiler houses at the beginning (Day 1), middle (Day 23), and end (Day 43) of a winter and subsequent summer flock housed on reused pine shavings litter. The grid was composed of 36 points, three locations across the width, and 12 locations down the length of the houses. To observe feeder and waterer (F/W) influences on the parameters, eight additional sample locations were added in a crisscross pattern among these automated supply lines. Color variograms illustrate the nature of parameter changes within each flock and between seasons. Overall trends for the NH3, N2O, and CO2 gas fluxes indicate an increase in magnitude with bird age during a flock for both summer and winter, but flux estimates were reduced in areas where compacted litter (i.e., caked litter or cake) formed at the end of the flocks (at F/W locations and in the fan area). End of flock gas fluxes were estimated at 1040 mg NH3 m(-2) h(-1), 20 mg N2O m(-2) h(-1), and 24,200 mg CO2 m(-2) h(-1) in winter; and 843 mg NH3 m(-2) h(-1), 18 mg N2O m(-2) h(-1)), and 27,200 mg CO2 m(-2) h(-1) in summer. The results of intensive sample efforts during winter and summer flocks, reported visually using contour plots, offer a resource to the poultry industry and researchers for creating new management strategies for improving production and controlling gas evolution. Particularly, efforts could focus on designing housing systems that minimize extremes in litter compaction. The extremes are undesirable with more friable litter prone to greater gas evolution and more compacted litter providing a slippery, disease-sustaining surface.

On the Structure-Property Relationships of Cation-Exchanged ZK-5 Zeolites for CO 2 Adsorption

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

Pham, Trong D.; Hudson, Matthew R.; Brown, Craig M.

2017-02-16

The CO 2 adsorption properties of cation-exchanged Li-, Na-, K-, and Mg-ZK-5 zeolites were correlated to the molecular structures determined by Rietveld refinements of synchrotron powder X-ray diffraction patterns. Li-, K-, and Na-ZK-5 all exhibited high isosteric heats of adsorption (Qst) at low CO 2 coverage, with Na-ZK-5 having the highest Qst (ca. 49 kJ mol -1). Mg2+ was located at the center of the zeolite hexagonal prism with the cation inaccessible to CO 2, leading to a much lower Qst (ca. 30 kJ mol-1) and lower overall uptake capacity. Multiple CO 2 adsorption sites were identified at a givenmore » CO 2 loading amount for all four cation-exchanged ZK-5 adsorbents. Site A at the flat eight-membered ring windows and site B/B* in the γ-cages were the primary adsorption sites in Li - and Na-ZK-5 zeolites. Relatively strong dual-cation adsorption sites contributed significantly to an enhanced electrostatic interaction for CO 2 in all ZK-5 samples. This interaction gives rise to a migration of Li + and Mg 2+ cations from their original locations at the center of the hexagonal prisms toward the α-cages, in which they interact more strongly with the adsorbed CO 2.« less

Autopolyploidy genome duplication preserves other ancient genome duplications in Atlantic salmon (Salmo salar).

PubMed

Christensen, Kris A; Davidson, William S

2017-01-01

Salmonids (e.g. Atlantic salmon, Pacific salmon, and trouts) have a long legacy of genome duplication. In addition to three ancient genome duplications that all teleosts are thought to share, salmonids have had one additional genome duplication. We explored a methodology for untangling these duplications from each other to better understand them in Atlantic salmon. In this methodology, homeologous regions (paralogous/duplicated genomic regions originating from a whole genome duplication) from the most recent genome duplication were assumed to have duplicated genes at greater density and have greater sequence similarity. This assumption was used to differentiate duplicated gene pairs in Atlantic salmon that are either from the most recent genome duplication or from earlier duplications. From a comparison with multiple vertebrate species, it is clear that Atlantic salmon have retained more duplicated genes from ancient genome duplications than other vertebrates--often at higher density in the genome and containing fewer synonymous mutations. It may be that polysomic inheritance is the mechanism responsible for maintaining ancient gene duplicates in salmonids. Polysomic inheritance (when multiple chromosomes pair during meiosis) is thought to be relatively common in salmonids compared to other vertebrate species. These findings illuminate how genome duplications may not only increase the number of duplicated genes, but may also be involved in the maintenance of them from previous genome duplications as well.

Dual-laser-beam-induced breakdown spectroscopy of copper using simultaneous continuous wave CO(2) and Q-switched Nd:YAG lasers.

PubMed

Shoursheini, S Z; Parvin, P; Sajad, B; Bassam, M A

2009-04-01

In this work, we investigate the enhancement of Cu emission lines of a micro-plasma induced by a Nd:YAG laser due to the thermal effect of simultaneous irradiation by a continuous wave (CW) CO(2) laser. The enhancement of the emission lines was achieved at a higher temperature with minimal distortion of the target when the focal point of the Nd:YAG laser was located approximately 1 mm away from the sample surface.

Element concentrations in soils and other surficial materials of Alaska

USGS Publications Warehouse

Gough, L.P.; Severson, R.C.; Shacklette, H.T.

1988-01-01

Mean concentrations of 35 elements, ash yields, and pH have been estimated for samples of sils and other unconsolidated surficial materials from 266 collection locations throughout Alaska. These background values can be applied to studies of environmental geochemistry and health, wildlife management, and soil-forming processes in cold climates and to computation of element abundances on a regional or worldwide scale. Limited data for an additoinal eight elements are also presented. Materials were collected using a one-way, three-level, analysis-of-variance samplling design in which collecting procedures were simplified for the convenience of the many volunteer field workers. The sample collectors were asked to avoid locations of known mineral deposits and obvious contamination, to take samples at a depth of about 20 cm where possible, and to take a replicate sample about 100 m distant from the first sample collected. With more than 60 percent of the samples replicated and 14 percent of the samples split for duplicate laboratory analyses, reliable estimates were made of the variability in element concentrations at two geographic scales and of the error associated with sample handling and laboratory procedures. Mean concentrations of most elements in surficial materials from the state of alaska correspond well with those reported in similar materials from the conterminous United STatess. Most element concentrations and ranges in samples of stream and lake sediments from Alaska, however, as reported in the literature, do not correspond well with those found in surficial materials of this study. This lack of correspondence is attributed to (1) a merger of two kinds ofsediments (stream and lake) for calculating means; (2) elimination from the sediment mean calculations of values below the limit of quantitative determination; (3) analytical methods different from those of the surficial materials study; and (4) most importantly, the inherent differences in chemistry of the materials. The distribution of variability in element concentrations o Alaskan surficial-material samples was, for most elements, largely among sampling locations, with only a samll part of the variability occurring between replicate samples at a location. The geochemical uniformity within sampling locations in Alaska is an expression of uniform geochemical cycling processes within small geographic areas. The concentration values for 35 elements in 266 samples were plotted on maps by symbols representing classes of concentration frequency distributions. These plotted symbols form patterns that may or may not be possible to interpret but nevertheless show differences that are observable at several geographical scales. The largest pattern is one generally low concentrations of many elements in materials from arctic and oceanic tundra regions, as contrasted to their often high concentrations in samples from interior and southeastern Alaska. The patttern for sodium isespecially pronounced. Intermediate-sized patterns are shown, for example, by the generally high values for magnesium and low values for silicon in the coastal forest region of southeastern Alaska. Many elements occur at low concentratoins in samples from the Alaskan peninsula and the Aleutian Islands. The degree of confidence in patterns of element abundance is expected to be in direct proportion to the number of samples included in the area. As the patterns become smaller, the probability increases that the patterns are not reproducible.

Airsheds, Isotopes and Ecosystem Metabolism in Mountainous Terrain

NASA Astrophysics Data System (ADS)

Sulzman, E.; Barnard, H.; Bond, B. J.; Czarnomski, N. M.; Hauck, M.; Kayler, Z.; Mix, A. C.; Pypker, T.; Rugh, W.; Unsworth, M.

2005-12-01

At least 20% of the terrestrial surface of the earth is covered by mountains, which contain many of the world's most productive ecosystems. Interactions between vegetation and the physical environment are often very different in mountains than on flat land. However, few studies have addressed these unique interactions, and many of the tools used to measure and monitor ecosystem metabolism are difficult or impossible to use in complex, mountainous terrain. In a project we call the "Andrews Airshed study" located in western Oregon Cascades, we aim to identify and explore sources of variation in the isotopic composition of ecosystem respiration (δ13CR-eco) and airflow patterns in cold-air drainage, with the eventual aim of "inverting" this understanding so that we can use δ13CR-eco to monitor intra- and inter-annual variations in ecosystem metabolism on a basin scale. We are measuring patterns of airflow, quantifying the CO2 concentration in the flow, and measuring the carbon isotope composition of ecosystem-respired CO2 as well as soil-respired CO2 (δ13CR-soil), which accounts for more than half of δ13CR-eco. We have designed an automated air sampling device that we programmed to sample air at 10 ppm intervals from 30 m above the stream in our 100 ha, deeply-incised watershed. Samples are collected via Valco valves into stainless steel tubing that can be connected directly to an isotope ratio mass spectrometer. We also designed and installed soil gas sampling probes, which are located in five 10 m2 sampling plots from ridge top to valley floor to the opposite ridge top. Weekly samples (May-Sept, 2005) of air from soil and the nocturnal air flow show seasonal variation in δ13CR-eco over a 2 per mil range, with more enriched values corresponding to lower soil moisture. Soil-respired CO2 also reveal seasonality and are isotopically enriched compared with above-ground air. δ13CR-soil values from north- and south-facing slopes of the watershed differ by 1 per mil, with south-facing values consistently enriched relative to those of the north-facing slope. We are concurrently conducting studies to determine the appropriate footprint of respired CO2 in the nocturnal airstream, which will allow us to overlay the data properly.

Co-victims of Homicide: A Systematic Review of the Literature.

PubMed

Connolly, Jennifer; Gordon, Ronit

2015-10-01

This systematic literature review examines the effects of homicide on surviving family members, the "co-victims" or "survivors" of homicide. A content analysis was conducted on 40 articles identified through a search of the literature. The research samples were predominately located in the United States, but included two U.K. samples, one Jamaican sample, and one sample from Israel. All articles were written in English. Three themes were identified. Nineteen articles explored the psychological, academic, social, occupational, and familial effects of homicide. Thirteen articles considered survivors' grieving process and how it was altered by experiences with the criminal justice system as well as coping strategies used by survivors to deal with their grief. Eight articles explored treatment interventions available to help surviving family members deal with their grief. Key findings from the articles, limitations of the current research, and implications for future research, policy, and practice are included. © The Author(s) 2014.

Pathways of human exposure to cobalt in Katanga, a mining area of the D.R. Congo.

PubMed

Cheyns, Karlien; Banza Lubaba Nkulu, Célestin; Ngombe, Léon Kabamba; Asosa, Jimmy Ngoy; Haufroid, Vincent; De Putter, Thierry; Nawrot, Tim; Kimpanga, Célestin Muleka; Numbi, Oscar Luboya; Ilunga, Benjamin Kabyla; Nemery, Benoit; Smolders, Erik

2014-08-15

Human exposure biomonitoring in the African Copperbelt (Katanga, southern D.R. Congo) revealed elevated cobalt (Co) exposure in the general population. This study was designed to identify the Co exposure routes for the non-occupationally exposed population in that area. The concentration of Co was measured in environmental and urine samples collected in urban and rural communities close to metal mining and/or refining plants, villages near a lake receiving effluents from metal refining plants, and control rural areas without industrial pollution. Drinking water, uncooked food items (maize flour, washed vegetables, fish and meat), indoor and outdoor dust samples were collected at each location. A food questionnaire was used to estimate dietary Co intake for adults and children. Geometric mean urine-Co (U-Co) concentrations were 4.5-fold (adults) and 6.6-fold (children) higher in the polluted than in the control area, with U-Co values being intermediate in the lakeside area. Average Co concentrations in environmental samples differed 6-40-fold between these areas. U-Co was positively correlated with most environmental Co concentrations, the highest correlations being found with Co in drinking water, vegetables and fruit. Estimated average total Co intake for adults was 63 (±42) μg/day in the control area, 94 (±55) μg/day in the lakeside villages and 570 (±100) μg Co/day in the polluted areas. U-Co was significantly related to modelled Co intake (R(2)=0.48, adults and R(2)=0.47, children; log-log relationship). Consumption of legumes, i.e. sweet potato leaves (polluted) and cereals+fish (lakeside) was the largest contributor to Co intake in adults, whereas dust ingestion appeared to contribute substantially in children in the polluted area. In conclusion, dietary Co is the main source of Co exposure in the polluted area and Co is efficiently transferred from soil and water in the human food chain. Copyright © 2014 Elsevier B.V. All rights reserved.

A Compendium of Scale Surface Microstructures: Ni(pt)al Coatings Oxidized at 1150 C for 2000 1-h Cycles

NASA Technical Reports Server (NTRS)

Smialek, James L.; Garg, Anita

2010-01-01

The surface structure of scales formed on Ni(Pt)Al coatings was characterized by SEM/EDS/BSE in plan view. Two nominally identical {100} samples of aluminide coated CMSX4 single crystal were oxidized at 1150 C for 2000 1-h cycles and were found to produce somewhat disparate behavior. One sample, with less propensity for coating grain boundary ridge deformation, presented primarily alpha-Al2O3 scale structures, with minimal weight loss and spallation. The original scale structure, still retained over most of the sample, consisted of the classic theta-alpha transformation-induced ridge network structure, with approx. 25 nm crystallographic steps and terraces indicative of surface rearrangement to low energy alumina planes. The scale grain boundary ridges were often decorated with a fine, uniform distribution of (Hf,Ti)O2 particles. Another sample, producing steady state weight losses, exhibited much interfacial spallation and a complex assortment of different structures. Broad areas of interfacial spalling, crystallographically-faceted (Ni,Co)(Al,Cr)2O4 spinel, with an alpha-Al2O3 base scale, were the dominant features. Other regions exhibited nodular spinel grains, with fine or (Ta,Ti)-rich (rutile) particles decorating or interspersed with the spinel. While these features were consistent with a coating that presented more deformation at extruded grain boundaries, the root cause of the different behavior between the duplicate samples could not be conclusively identified.

Information Design for Synchronization and Co-ordination of Modern, Complex, Multi-National Operations

DTIC Science & Technology

2011-06-01

are collection biases in operation, either independently of or driven specifically by the original hypothesis). Information incest • . Stripping...out data duplicates does not necessarily mean that information incest has been prevented, if insufficient context comes back to strip out the real... incest and procedural gaps) will require the mechanisms to be found in the ‘quasi-complex’. The Liaison Officer in a conventional military

A Survey of Insider Attack Detection Research

DTIC Science & Technology

2008-08-25

modeling of statistical features , such as the frequency of events, the duration of events, the co-occurrence of multiple events combined through...forms of attack that have been reported [Error! Reference source not found.]. For example: • Unauthorized extraction , duplication, or exfiltration...network level. Schultz pointed out that not one approach will work but solutions need to be based on multiple sensors to be able to find any combination

Modern pollen data from North America and Greenland for multi-scale paleoenvironmental applications

USGS Publications Warehouse

Whitmore, J.; Gajewski, K.; Sawada, M.; Williams, J.W.; Shuman, B.; Bartlein, P.J.; Minckley, T.; Viau, A.E.; Webb, T.; Shafer, S.; Anderson, P.; Brubaker, L.

2005-01-01

The modern pollen network in North America and Greenland is presented as a database for use in quantitative calibration studies and paleoenvironmental reconstructions. The georeferenced database includes 4634 samples from all regions of the continent and 134 pollen taxa that range from ubiquitous to regionally diagnostic taxa. Climate data and vegetation characteristics were assigned to every site. Automated and manual procedures were used to verify the accuracy of geographic coordinates and identify duplicate records among datasets, incomplete pollen sums, and other potential errors. Data are currently available for almost all of North America, with variable density. Pollen taxonomic diversity, as measured by the Shannon-Weiner coefficient, varies as a function of location, as some vegetation regions are dominated by one or two major pollen producers, while other regions have a more even composition of pollen taxa. Squared-chord distances computed between samples show that most modern pollen samples find analogues within their own vegetation zone. Both temperature and precipitation inferred from best analogues are highly correlated with observed values but temperature exhibits the strongest relation. Maps of the contemporary distribution of several pollen types in relation to the range of the plant taxon illustrate the correspondence between plant and pollen ranges. ?? 2005 Elsevier Ltd. All rights reserved.

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

PubMed

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

2005-02-01

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

Arterial blood gas reference values for sea level and an altitude of 1,400 meters.

PubMed

Crapo, R O; Jensen, R L; Hegewald, M; Tashkin, D P

1999-11-01

Blood gas measurements were collected on healthy lifetime nonsmokers at sea level (n = 96) and at an altitude of 1,400 meters (n = 243) to establish reference equations. At each study site, arterial blood samples were analyzed in duplicate on two separate blood gas analyzers and CO-oximeters. Arterial blood gas variables included Pa(O(2)), Pa(CO(2)), pH, and calculated alveolar-arterial PO(2) difference (AaPO(2)). CO-oximeter variables were Hb, COHb, MetHb, and Sa(O(2)). Subjects were 18 to 81 yr of age with 166 male and 173 female. Outlier data were excluded from multiple regression analysis, and reference equations were fitted to the data in two ways: (1) best fit using linear, squared, and cross-product terms; (2) simple equations, including only the variables that explained at least 3% of the variance. Two sets of equations were created: (1) using only the sea level data and (2) using the combined data with barometric pressure as an independent variable. Comparisons with earlier studies revealed small but significant differences; the decline in Pa(O(2)) with age at each altitude was consistent with most previous studies. At sea level, the equation that included barometric pressure predicted Pa(O(2)) slightly better than the sea level specific equation. The inclusion of barometric pressure in the equations allows better prediction of blood gas reference values at sea level and at altitudes as high as 1,400 meters.

Dependency of Ecosystem Respiration in a Cool Temperate Bog on Peat Temperature and Water Table

NASA Astrophysics Data System (ADS)

Moore, T.; Lafleur, P.; Roulet, N.; Frolking, S.

2003-12-01

We measured ecosystem respiration (ER) from nighttime net ecosystem exchange of carbon dioxide determined from an eddy covariance tower located in a large ombrotrophic bog near Ottawa, Canada. Measurements were made from May to October over 5 years, 1998 to 2002. Ecosystem respiration ranged from <0.05 mg CO2/m2/s in spring (May) and late fall (late October) to 0.10-0.15 mg CO2/m2/s during the summer (July-August). As anticipated, there was a strong relationship between ER and peat temperatures, such as at a depth of 5 cm (r2 = 0.63). Q10 over 5° to 15° C varied from 2.2 to 4.2 depending upon the choice of temperature level and location within a hummock or hollow. Unexpected for a wetland ecosystem, there was only a weak relationship between ER and water table position (r2 = 0.11). Comparison of ER in early and late summer, 2002 with similar surface temperature revealed no significant difference in ER. A laboratory incubation of peat cores at different moisture contents showed that CO2 production was reduced by drying in the surface samples, but there was little decrease in samples from below a depth of 30 cm. We believe that the lack of correlation between ER and water table position in this ecosystem results from an increase in CO2 production at depth compensating a decrease in production of CO2 by heterotrophic respiration in the near surface layers and autotrophic respiration in the moss community.

Validating predictions of evolving porosity and permeability in carbonate reservoir rocks exposed to CO2-brine

NASA Astrophysics Data System (ADS)

Smith, M. M.; Hao, Y.; Carroll, S.

2017-12-01

Improving our ability to better forecast the extent and impact of changes in porosity and permeability due to CO2-brine-carbonate reservoir interactions should lower uncertainty in long-term geologic CO2 storage capacity estimates. We have developed a continuum-scale reactive transport model that simulates spatial and temporal changes to porosity, permeability, mineralogy, and fluid composition within carbonate rocks exposed to CO2 and brine at storage reservoir conditions. The model relies on two primary parameters to simulate brine-CO2-carbonate mineral reaction: kinetic rate constant(s), kmineral, for carbonate dissolution; and an exponential parameter, n, relating porosity change to resulting permeability. Experimental data collected from fifteen core-flooding experiments conducted on samples from the Weyburn (Saskatchewan, Canada) and Arbuckle (Kansas, USA) carbonate reservoirs were used to calibrate the reactive-transport model and constrain the useful range of k and n values. Here we present the results of our current efforts to validate this model and the use of these parameter values, by comparing predictions of extent and location of dissolution and the evolution of fluid permeability against our results from new core-flood experiments conducted on samples from the Duperow Formation (Montana, USA). Agreement between model predictions and experimental data increase our confidence that these parameter ranges need not be considered site-specific but may be applied (within reason) at various locations and reservoirs. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

An assessment of indoor air quality in recent Mexican immigrant housing in Commerce City, Colorado

NASA Astrophysics Data System (ADS)

Miller, Shelly L.; Scaramella, Peter; Campe, Joseph; Goss, Cynthia W.; Diaz-Castillo, Sandra; Hendrikson, Ed; DiGuiseppi, Carolyn; Litt, Jill

An indoor air quality assessment was conducted on 100 homes of recent Mexican immigrants in Commerce City, Colorado, an urban industrial community north of Denver. Head of households were administered a family health survey, filled out an activity diary, and participated in a home inspection. Carbon monoxide (CO) and carbon dioxide (CO 2) were measured for 24 h inside the main living area and outside of the homes. Harvard Impactors were used to collect 24-h samples of PM 2.5 at the same locations for gravimetric analysis. Dust samples were collected by vacuuming carpeting and flooring at four locations within the home and analyzed by ELISA for seven allergens. Mean indoor and outdoor PM 2.5 levels were 27.2 and 8.5 μg m -3, respectively. Indoor PM 2.5 and CO 2 were elevated in homes for which the number of hours with door/window open was zero compared to homes in which the number of hours was high (>15 h). Indoor PM 2.5 levels did not correlate with outdoor levels and tended to increase with number of inhabitants, and results indicate that the source of indoor particles were occupants and their activities, excluding smoking and cooking. Mean indoor CO 2 and CO levels were 1170 and 2.4 ppm, respectively. Carbon monoxide was higher than the 24-h National Ambient Air Quality Standard in 3 of the homes. The predominant allergens were cat ( Fel d 1) and mouse ( Mus m 1) allergens, found in 20 and 34 homes, respectively.

Construction and application of an intelligent air quality monitoring system for healthcare environment.

PubMed

Yang, Chao-Tung; Liao, Chi-Jui; Liu, Jung-Chun; Den, Walter; Chou, Ying-Chyi; Tsai, Jaw-Ji

2014-02-01

Indoor air quality monitoring in healthcare environment has become a critical part of hospital management and policy. Manual air sampling and analysis are cost-inhibitive and do not provide real-time air quality data and response measures. In this month-long study over 14 sampling locations in a public hospital in Taiwan, we observed a positive correlation between CO(2) concentration and population, total bacteria, and particulate matter concentrations, thus monitoring CO(2) concentration as a general indicator for air quality could be a viable option. Consequently, an intelligent environmental monitoring system consisting of a CO(2)/temperature/humidity sensor, a digital plug, and a ZigBee Router and Coordinator was developed and tested. The system also included a backend server that received and analyzed data, as well as activating ventilation and air purifiers when CO(2) concentration exceeded a pre-set value. Alert messages can also be delivered to offsite users through mobile devices.

Profiling of gene duplication patterns of sequenced teleost genomes: evidence for rapid lineage-specific genome expansion mediated by recent tandem duplications.

PubMed

Lu, Jianguo; Peatman, Eric; Tang, Haibao; Lewis, Joshua; Liu, Zhanjiang

2012-06-15

Gene duplication has had a major impact on genome evolution. Localized (or tandem) duplication resulting from unequal crossing over and whole genome duplication are believed to be the two dominant mechanisms contributing to vertebrate genome evolution. While much scrutiny has been directed toward discerning patterns indicative of whole-genome duplication events in teleost species, less attention has been paid to the continuous nature of gene duplications and their impact on the size, gene content, functional diversity, and overall architecture of teleost genomes. Here, using a Markov clustering algorithm directed approach we catalogue and analyze patterns of gene duplication in the four model teleost species with chromosomal coordinates: zebrafish, medaka, stickleback, and Tetraodon. Our analyses based on set size, duplication type, synonymous substitution rate (Ks), and gene ontology emphasize shared and lineage-specific patterns of genome evolution via gene duplication. Most strikingly, our analyses highlight the extraordinary duplication and retention rate of recent duplicates in zebrafish and their likely role in the structural and functional expansion of the zebrafish genome. We find that the zebrafish genome is remarkable in its large number of duplicated genes, small duplicate set size, biased Ks distribution toward minimal mutational divergence, and proportion of tandem and intra-chromosomal duplicates when compared with the other teleost model genomes. The observed gene duplication patterns have played significant roles in shaping the architecture of teleost genomes and appear to have contributed to the recent functional diversification and divergence of important physiological processes in zebrafish. We have analyzed gene duplication patterns and duplication types among the available teleost genomes and found that a large number of genes were tandemly and intrachromosomally duplicated, suggesting their origin of independent and continuous duplication. This is particularly true for the zebrafish genome. Further analysis of the duplicated gene sets indicated that a significant portion of duplicated genes in the zebrafish genome were of recent, lineage-specific duplication events. Most strikingly, a subset of duplicated genes is enriched among the recently duplicated genes involved in immune or sensory response pathways. Such findings demonstrated the significance of continuous gene duplication as well as that of whole genome duplication in the course of genome evolution.

Evaluation of nonpoint-source contamination, Wisconsin: Selected data for 1992 water year

USGS Publications Warehouse

Graczyk, D.J.; Walker, J.F.; Greb, S.R.; Corsi, Steven R.; Owens, D.W.

1993-01-01

This report presents the annual results of the U.S. Geological Survey's (USGS) watershed-management evaluation monitoring program in Wisconsin. The overall objective of each individual project in the program is to determine if the water chemistry in the receiving stream has changed as a result of the implementation of land-management practices in the watershed. This is accomplished through monitoring of water chemistry and ancillary variables before best-management practices (BMP's) are installed ('pre-BMP'), during installation ('transitional'), and after ('post-BMP') watershed- management plans have been completely implemented. Fecal-coliform (FC) counts ranged between 10 and 310,00/100 mL. A large range of values occurred within duplicate and triplicate samples as well as over time. The median percentage difference between duplicate and triplicate samples was 17 percent although 4 out of the total 60 duplicate and triplicate samples had differences greater than 100 percent. A decrease in FC counts generally occurred over the duration of the 4-day analyses. Linear regression models of the log-concentration values (dependent variable) with respect to time (independent variable) were calculated for all samples. Negative slopes were found for 14 of the 15 samples. Slopes varied from +0.5 to -38.4 percent gain/loss/day, with a median slope of -8.5 percent/day. A t-test was applied to the data to examine whether or not significant differences in FC counts exist with respect to holding times. Because the T-test only compares two treatments, the test was conducted 3 times (0 versus 24-hr holding time, 0 versus 48-hr holding time, and 0 versus 72-hr holding time). Setting the level of significance at p less than 0.05 and assuming equal variances, 27 percent (all from Bower and Otter Creeks) of the samples demonstrated a significant difference in colony count over the first 24 hr, 40 percent over 48 hr, and 47 percent over 72 hr. All samples that exhibited a significant change in colony count were because of a decrease in colony count of the sample.

A Tool for Comparative Collection Analysis: Conducting a Shelflist Sample to Construct a Collection Profile.

ERIC Educational Resources Information Center

Paskoff, Beth M.; Perrault, Anna H.

1990-01-01

Describes a project that examined a random sample of 5 percent of a shelflist to provide detailed information about the distribution of imprints according to age and language, percentage of duplication, and distribution of serial and monographic formats. It is concluded that the resulting collection profile provides a multidimensional, quantified…

Population Education in Mathematics: Some Sample Lessons for the Secondary Level.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and the Pacific.

This booklet consists of five sample lessons integrating population education into mathematics instruction. It is one of four in a series. Materials differ from those in an earlier series (1980) in that lessons are presented at the secondary level only; there is no duplication of lessons from the earlier series in content and teaching strategies.…

Bioavailable Ferric Iron (BAFelll) Assay

DTIC Science & Technology

2007-02-01

citrate dithionite bicarbonate CDBFe citrate dithionite bicarbonate extractable iron cDCE cis-Dichloroethene CDM Camp Dresser & McKee Inc...Defense (DoD) installations. Camp Dresser & McKee Inc. (CDM), in cooperation with the Naval Facilities Engineering Services Center (NFESC), was the...several upgradient and/or cross - gradient background soil samples. Duplicate analysis of samples is recommended. While these recommendations are not

Population Education in Science: Some Sample Lessons for the Secondary Level.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and the Pacific.

This booklet consists of six sample lessons integrating population education into science instruction. It is one of four in a series. Materials differ from those in an earlier series (1980) in that lessons are presented at the secondary level only; there is no duplication of lessons from the earlier series in terms of content and teaching…

The American Teacher, 1984-1995, Metropolitan Life Survey. Old Problems, New Challenges.

ERIC Educational Resources Information Center

Harris (Louis) and Associates, Inc., New York, NY.

During the past decade there have been considerable efforts to reform the American public school system. This survey, based on 15-minute telephone interviews with a nationally representative sample of 1,011 public school teachers in the United States, duplicates the sampling and interviewing process used in a similar study in 1984 and 1985. In…

A discovery of novel microRNAs in the silkworm (Bombyx mori) genome.

PubMed

Yu, Xiaomin; Zhou, Qing; Cai, Yimei; Luo, Qibin; Lin, Hongbin; Hu, Songnian; Yu, Jun

2009-12-01

MicroRNAs (miRNAs) are pivotal regulators involved in various physiological and pathological processes via their post-transcriptional regulation of gene expressions. We sequenced 14 libraries of small RNAs constructed from samples spanning the life cycle of silkworms, and discovered 50 novel miRNAs previously not known in animals and verified 43 of them using stem-loop RT-PCR. Our genome-wide analyses of 27 species-specific miRNAs suggest they arise from transposable elements, protein-coding genes duplication/transposition and random foldback sequences; which is consistent with the idea that novel animal miRNAs may evolve from incomplete self-complementary transcripts and become fixed in the process of co-adaptation with their targets. Computational prediction suggests that the silkworm-specific miRNAs may have a preference of regulating genes that are related to life-cycle-associated traits, and these genes can serve as potential targets for subsequent studies of the modulating networks in the development of Bombyx mori.

Deuterium retention and release behaviours of tungsten and deuterium co-deposited layers

NASA Astrophysics Data System (ADS)

Qiao, L.; Zhang, H. W.; Xu, J.; Chai, L. Q.; Hu, M.; Wang, P.

2018-04-01

Tungsten (W) layer deposited in argon and deuterium atmosphere by magnetron sputtering was used as a model system to study the deuterium (D) retention and release behavior in co-deposited W layer. After deposition several selected samples were exposed in deuterium plasma at 370 K with a flux of 4.0 × 1021 D/(m2 s) up to a fluence of 1.1 × 1025 D/m2. Structures of co-deposited W layers are investigated by field-emission scanning electron microscopy (FESEM) and X-ray diffraction (XRD), and the corresponding D retention and release behaviors are studied as functions of deposition and exposure parameters using thermal desorption spectroscopy (TDS). Two main D release peaks were detected from TDS spectra located near 600 and 800 K in these W and D co-deposited layers, and total deuterium retention increased linearly as a function of W layer's thickness. After deuterium plasma exposure, the total D retention amount in W layer increases significantly and D release peak shifts to lower temperature. Clearly, despite the high density of defects expected in co-deposited W layers, the initial deuterium retention before exposure to the deuterium plasma is low even for the samples with a W&D layer. But due to the high densities of defects, during the deuterium plasma exposure the deuterium retention increases faster for co-deposited layer than for the bulk W sample.

Microsurgical anatomy of the extracerebral segment of recurrent artery of Heubner in the Mexican population.

PubMed

Gasca-González, Oscar Octavio; Delgado-Reyes, Luis; Pérez-Cruz, Julio César

2011-01-01

The recurrent artery of Heubner (RAH) is originated commonly from the anterior cerebral artery. Its extracerebral segment is directed toward the anterior perforate substance where it penetrates the cortex. The RAH was dissected from 15 human brains from Mexican population, and the presence, length, branches, course and either RHAs or anterior communicating artery complex variants were reported. The RAH was found in 93% of the hemispheres and duplicated in 39% of the hemispheres. The RAH was duplicated in at least a hemisphere in 46.6% of the brains; 40% of the brains had a RAH in every hemisphere. It was duplicated in every hemisphere in 20%. A single artery at a hemisphere was found in 26.6% and double at the other hemisphere. With a length between 13.6 and 36.7 mm (mean: 24.2 mm) and giving rise to 1-9 branches (mean: 3.9 branches), the RAH originated from the juxtacommunicating segment in 44% of the cases, from A2 in 41%, from A1 in 5% and as a branch of the frontopolar artery in 10%. It had an oblique course in 38%, an L in 31%, sinuous in 18% and an inverted L in 13%. In 53.3% of the brains, some variant of the anterior communicating artery complex was found. Because of the common anatomy of the RAH and its variants, we must consider the probability of finding it duplicated; therefore, it is necessary to make minute dissections of the region to locate or to secure the absence of the RAH.

Evaluation of point mutations in dystrophin gene in Iranian Duchenne and Becker muscular dystrophy patients: introducing three novel variants.

PubMed

Haghshenas, Maryam; Akbari, Mohammad Taghi; Karizi, Shohreh Zare; Deilamani, Faravareh Khordadpoor; Nafissi, Shahriar; Salehi, Zivar

2016-06-01

Duchenne and Becker muscular dystrophies (DMD and BMD) are X-linked neuromuscular diseases characterized by progressive muscular weakness and degeneration of skeletal muscles. Approximately two-thirds of the patients have large deletions or duplications in the dystrophin gene and the remaining one-third have point mutations. This study was performed to evaluate point mutations in Iranian DMD/BMD male patients. A total of 29 DNA samples from patients who did not show any large deletion/duplication mutations following multiplex polymerase chain reaction (PCR) and multiplex ligation-dependent probe amplification (MLPA) screening were sequenced for detection of point mutations in exons 50-79. Also exon 44 was sequenced in one sample in which a false positive deletion was detected by MLPA method. Cycle sequencing revealed four nonsense, one frameshift and two splice site mutations as well as two missense variants.

Boron in Pariette Wetland Sediments, Aquatic Vegetation & Benthic Organisms

NASA Astrophysics Data System (ADS)

Vasudeva, P.; Jones, C. P.; Powelson, D.; Jacobson, A. R.

2015-12-01

The Pariette Wetlands are comprised of 20 ponds located in Utah's Uintah Basin. Boron concentration in the Pariette Wetlands have been observed to exceed the total maximum daily limit of 750 µg L-1. Considering water flow in and out of the wetlands, boron is accumulating within the wetlands where it is sorbed to sediments and bioconcentrated by wetland plant and macro invertebrates. Since boron is an avian teratogen, an estimate of boron ingestion exposure is warranted. Samples from 3 of the 23 Pariette Wetland ponds with one pond near the inlet, one near the outlet, and one in the middle were collected. Five sampling points were designated along a 100 m transect of each pond. At each sampling point duplicate (or triplicate) samples of water, sediments, benthic organisms and wetland vegetation were collected. The sediments were collected with a KB-corer and divided at depths of 0-2 cm, 2-7 cm, and 7+ cm from the sediment surface. Sample splits were sent to the USU Bug lab for identification of invertebrate species. Whenever this transect was not intercepting vegetation, 2-3 additional sample sites were identified at the pond within stands of representative vegetation where bird nests are located. The plant parts used for boron analyses will include seeds, shoot and roots of vascular plants, as well as algae or duckweeds skimmed from the surface. Samples were processed within 2 days of collection. Water samples filtered through a 0.45 μ membrane filter were analyzed for DOC, pH and ECe. The dried and washed vegetation samples were ground and stored. The benthic organisms and macro invertebrates were netted at the water surface. The dried samples were weighed, ground and stored. Samples were weighed, oven dried and reweighed. For plant and macro-invertebrate samples, a nitric and hydrogen peroxide digestion procedure is used to dissolve environmentally available elements. The Hot Water extraction and DTPA-Sorbitol extraction were compared to estimate wetland plant available boron in the sediments. Boron in water, soil/sediment extracts and digested plant materials was analyzed by Azomethine-H colorimetric method. Additional Sample Characterization Analyses were conducted to interpret results and explain differences in the fate of boron among the sample sites.

Exploring the Definitions and Discourse of Co-Location

ERIC Educational Resources Information Center

Griffiths, Eve

2015-01-01

The phenomenon of co-location is not new, but there is very little research that focuses specifically on co-located schools and the teaching and learning that takes place therein. This article focuses on the term "co-location" and considers the sometimes vague discourse and definitions surrounding the term. The article recommends that…

Testing Binary Mixing Models for Lavas Erupted Along the Reykjanes Ridge: Insights From C-He Relationships

NASA Astrophysics Data System (ADS)

de Leeuw, G. A.; Hilton, D. R.; Shaw, A. M.; Murton, B. J.; Taylor, R. N.

2002-12-01

We report new CO2 abundance and isotope data for 36 basalt glasses erupted along the Reykjanes Ridge between latitudes 57.5 and 63°N. Lavas can be divided into (a) water-rich samples (~0.4 wt.%), erupted at depths < 775m north of 61.5°N, and (b) samples with water ~ 0.2 wt.%, erupted at depths of 620 - 2060 m and located between 57.5 and 61.5°N. Based upon He-Pb isotope systematics (Hilton et al., EPSL, 2000), deeper samples (category b) lie along binary mixing trajectories between plume-like (3He/4He ~ 30RA; 206Pb/204Pb ~ 18.7) and MORB-like endmembers (3He/4He ~ 8RA; 206Pb/204Pb ~ 18.0). Shallow samples (category a) do not fall on mixing trajectories: consistent with volatile loss followed by addition of a crustal contaminant, resulting in lower 3He/4He ratios. The aim of this study is to test whether binary mixing trends are observed using C-He relationships. All samples were analyzed using incremental heating techniques which allows for resolution of vesicle-sited CO2 from CO2 dissolved within the glass matrix. Results show that samples north of 61.5 °N (category a) have low CO2 contents in both the vesicle (2-37 ppm) and dissolved (15-61 ppm) phases. The isotopic composition of the CO2 varies between -8 and -34‰ (vesicle) and -6 and -10‰ (glass). The combined effect of low CO2 concentrations and low δ13C values are consistent with extensive gas loss +/- contamination of volatile-poor magmas with an isotopically-light C component. In contrast, samples in category b have significantly higher CO2 abundances (vesicles: 7-318 ppm; glass: 9-200 ppm) and higher and less variable δ13C values (vesicles: -5 to -26‰ ; glass: -4 to -11‰ ). This suggests that category b samples have not been subjected to the same degree of degassing and/or contamination as samples in category a. By combining the vesicle-sited CO2 abundances with He-contents determined by crushing (Hilton, op. cit), CO2/3He ratios for the vesicle phase can be derived. We observe high ratios (3x109 to 2x1010) in the more degassed category a samples. Category b CO2/3He ratios show a trend from low CO2/3He values (3x108) and MORB-like 206Pb/204Pb to high CO2/3He values (up to 2x1010) and more radiogenic 206Pb/204Pb. There are two possible explanations for the observed trends: 1) degassing followed by contamination with a high CO2/3He crustal component. This process controls C-He relationships in low concentration (highly degassed) samples close to Iceland. 2) mixing between a MORB-like source (CO2/3He ~ 2x109) and an enriched source with a higher initial CO2/3He value. This process controls samples in category b.

Comparison of Pore-Network and Lattice Boltzmann Models for Pore-Scale Modeling of Geological Storage of CO2 in Natural Reservoir Rocks

NASA Astrophysics Data System (ADS)

Kohanpur, A. H.; Chen, Y.; Valocchi, A. J.; Tudek, J.; Crandall, D.

2016-12-01

CO2-brine flow in deep natural rocks is the focus of attention in geological storage of CO2. Understanding rock/flow properties at pore-scale is a vital component in field-scale modeling and prediction of fate of injected CO2. There are many challenges in working at the pore scale, such as size and selection of representative elementary volume (REV), particularly for material with complex geometry and heterogeneity, and the high computational costs. These issues factor into trade-offs that need to be made in choosing and applying pore-scale models. On one hand, pore-network modeling (PNM) simplifies the geometry and flow equations but can provide characteristic curves on fairly large samples. On the other hand, the lattice Boltzmann method (LBM) solves Navier-Stokes equations on the real geometry but is limited to small samples due to its high computational costs. Thus, both methods have some advantages but also face some challenges, which warrants a more detailed comparison and evaluation. In this study, we used industrial and micro-CT scans of actual reservoir rock samples to characterize pore structure at different resolutions. We ran LBM models directly on the characterized geometry and PNM on the equivalent 3D extracted network to determine single/two-phase flow properties during drainage and imbibition processes. Specifically, connectivity, absolute permeability, relative permeability curve, capillary pressure curve, and interface location are compared between models. We also did simulations on several subsamples from different locations including different domain sizes and orientations to encompass analysis of heterogeneity and isotropy. This work is primarily supported as part of the Center for Geologic Storage of CO2, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science and partially supported by the International Institute for Carbon-Neutral Energy Research (WPI-I2CNER) based at Kyushu University, Japan.

Evolutionary history of the enolase gene family.

PubMed

Tracy, M R; Hedges, S B

2000-12-23

The enzyme enolase [EC 4.2.1.11] is found in all organisms, with vertebrates exhibiting tissue-specific isozymes encoded by three genes: alpha (alpha), beta (beta), and gamma (gamma) enolase. Limited taxonomic sampling of enolase has obscured the timing of gene duplication events. To help clarify the evolutionary history of the gene family, cDNAs were sequenced from six taxa representing major lineages of vertebrates: Chiloscyllium punctatum (shark), Amia calva (bowfin), Salmo trutta (trout), Latimeria chalumnae (coelacanth), Lepidosiren paradoxa (South American lungfish), and Neoceratodus forsteri (Australian lungfish). Phylogenetic analysis of all enolase and related gene sequences revealed an early gene duplication event prior to the last common ancestor of living organisms. Several distantly related archaebacterial sequences were designated as 'enolase-2', whereas all other enolase sequences were designated 'enolase-1'. Two of the three isozymes of enolase-1, alpha- and beta-enolase, were discovered in actinopterygian, sarcopterygian, and chondrichthian fishes. Phylogenetic analysis of vertebrate enolases revealed that the two gene duplications leading to the three isozymes of enolase-1 occurred subsequent to the divergence of living agnathans, near the Proterozoic/Phanerozoic boundary (approximately 550Mya). Two copies of enolase, designated alpha(1) and alpha(2), were found in the trout and are presumed to be the result of a genome duplication event.

Duplicate Abalone Egg Coat Proteins Bind Sperm Lysin Similarly, but Evolve Oppositely, Consistent with Molecular Mimicry at Fertilization

PubMed Central

Aagaard, Jan E.; Springer, Stevan A.; Soelberg, Scott D.; Swanson, Willie J.

2013-01-01

Sperm and egg proteins constitute a remarkable paradigm in evolutionary biology: despite their fundamental role in mediating fertilization (suggesting stasis), some of these molecules are among the most rapidly evolving ones known, and their divergence can lead to reproductive isolation. Because of strong selection to maintain function among interbreeding individuals, interacting fertilization proteins should also exhibit a strong signal of correlated divergence among closely related species. We use evidence of such molecular co-evolution to target biochemical studies of fertilization in North Pacific abalone (Haliotis spp.), a model system of reproductive protein evolution. We test the evolutionary rates (d N/d S) of abalone sperm lysin and two duplicated egg coat proteins (VERL and VEZP14), and find a signal of co-evolution specific to ZP-N, a putative sperm binding motif previously identified by homology modeling. Positively selected residues in VERL and VEZP14 occur on the same face of the structural model, suggesting a common mode of interaction with sperm lysin. We test this computational prediction biochemically, confirming that the ZP-N motif is sufficient to bind lysin and that the affinities of VERL and VEZP14 are comparable. However, we also find that on phylogenetic lineages where lysin and VERL evolve rapidly, VEZP14 evolves slowly, and vice versa. We describe a model of sexual conflict that can recreate this pattern of anti-correlated evolution by assuming that VEZP14 acts as a VERL mimic, reducing the intensity of sexual conflict and slowing the co-evolution of lysin and VERL. PMID:23408913

Evolution of Gene Duplication in Plants1[OPEN

PubMed Central

2016-01-01

Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication. PMID:27288366

Evolution of Gene Duplication in Plants.

PubMed

Panchy, Nicholas; Lehti-Shiu, Melissa; Shiu, Shin-Han

2016-08-01

Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication. © 2016 American Society of Plant Biologists. All Rights Reserved.

Analysis of copy number variation in Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals.

PubMed

Swaminathan, Shanker; Huentelman, Matthew J; Corneveaux, Jason J; Myers, Amanda J; Faber, Kelley M; Foroud, Tatiana; Mayeux, Richard; Shen, Li; Kim, Sungeun; Turk, Mari; Hardy, John; Reiman, Eric M; Saykin, Andrew J

2012-01-01

Copy number variations (CNVs) are genomic regions that have added (duplications) or deleted (deletions) genetic material. They may overlap genes affecting their function and have been shown to be associated with disease. We previously investigated the role of CNVs in late-onset Alzheimer's disease (AD) and mild cognitive impairment using Alzheimer's Disease Neuroimaging Initiative (ADNI) and National Institute of Aging-Late Onset AD/National Cell Repository for AD (NIA-LOAD/NCRAD) Family Study participants, and identified a number of genes overlapped by CNV calls. To confirm the findings and identify other potential candidate regions, we analyzed array data from a unique cohort of 1617 Caucasian participants (1022 AD cases and 595 controls) who were clinically characterized and whose diagnosis was neuropathologically verified. All DNA samples were extracted from brain tissue. CNV calls were generated and subjected to quality control (QC). 728 cases and 438 controls who passed all QC measures were included in case/control association analyses including candidate gene and genome-wide approaches. Rates of deletions and duplications did not significantly differ between cases and controls. Case-control association identified a number of previously reported regions (CHRFAM7A, RELN and DOPEY2) as well as a new gene (HLA-DRA). Meta-analysis of CHRFAM7A indicated a significant association of the gene with AD and/or MCI risk (P = 0.006, odds ratio = 3.986 (95% confidence interval 1.490-10.667)). A novel APP gene duplication was observed in one case sample. Further investigation of the identified genes in independent and larger samples is warranted.

[Compliance with the treatment by patients with the co-infection HIV/tuberculosis: integrative literature review].

PubMed

Neves, Lis Aparecida de Souza; Reis, Renata Karina; Gir, Elucir

2010-12-01

This is an integrative review whose objective was to evaluate the evidences available in the literature about the factors associated to the compliance with the treatment by patients with the co-infection HIV/TB. Articles published in the period from 2002 to 2008, in the databases LILACS and MEDLINE were analyzed. The material was categorized according to the year of publication, periodical, study location and factors related to the compliance. The final sample included eight articles. The factors found, associated to the compliance with the treatment of the co-infection HIV/TB, related to: the individual and his lifestyle (previous TB treatment, fear of stigma and discrimination, use of chemical substances, depression, social support); the disease and the medication (type of medication regime, use of other medication, adverse effects, difficulty to diagnose TB in these patients); and the health services (operational problems to follow up the treatment, training of the professionals, supervision, different locations to treat TB and HIV).

[Genome-wide identification and analysis of WRKY transcription factors in Medicago truncatula].

PubMed

Song, Hui; Nan, Zhibiao

2014-02-01

WRKY gene family plays important roles in plant by involving in transcriptional regulations during various physiologically processes such as development, metabolism and responses to biotic and abiotic stresses. WRKY genes have been identified in various plants. However, only few WRKY genes in Medicago truncatula have been identified with systematic analysis and comparison. In this study, we identified 93 WRKY genes through analyses of M. truncatula genome. These genes include 19 type-I genes, 49 type II genes and 13 type-III genes, and 12 non-regular type genes. All of these genes were characterized through analyses of gene duplication, chromosomal locations, structural diversity, conserved protein motifs and phylogenetic relations. The results showed that 11 times of gene duplication event occurred in WRKY gene family involving 24 genes. WRKY genes, containing 6 gene clusters, are unevenly distributed into chromosome 1 to 6, and there is the purifying selection pressure in WRKY group III genes.

A case report: Becker muscular dystrophy presenting with epilepsy and dysgnosia induced by duplication mutation of Dystrophin gene.

PubMed

Miao, Jing; Feng, Jia-Chun; Zhu, Dan; Yu, Xue-Fan

2016-12-12

Becker muscular dystrophy (BMD), a genetic disorder of X-linked recessive inheritance, typically presents with gradually progressive muscle weakness. The condition is caused by mutations of Dystrophin gene located at Xp21.2. Epilepsy is an infrequent manifestation of BMD, while cases of BMD with dysgnosia are extremely rare. We describe a 9-year-old boy with BMD, who presented with epilepsy and dysgnosia. Serum creatine kinase level was markedly elevated (3665 U/L). Wechsler intelligence tests showed a low intelligence quotient (IQ = 65). Electromyogram showed slight myogenic changes and skeletal muscle biopsy revealed muscular dystrophy. Immunohistochemical staining showed partial positivity of sarcolemma for dystrophin-N. Multiplex ligation-dependent probe amplification revealed a duplication mutation in exons 37-44 in the Dystrophin gene. The present case report helps to better understand the clinical and genetic features of BMD.

Human ETS2 gene on chromosome 21 is not rearranged in Alzheimer disease

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

Sacchi, N.; Nalbantoglu, J.; Sergovich, F.R.

1988-10-01

The human ETS2 gene, a member of the ETS gene family, with sequence homology with the retroviral ets sequence of the avian erythroblastosis retrovirus E26 is located on chromosome 21. Molecular genetic analysis of Down syndrome (DS) patients with partial trisomy 21 allowed us to reinforce the supposition that ETS2 may be a gene of the minimal DS genetic region. It was originally proposed that a duplication of a portion of the DS region represents the genetic basis of Alzheimer disease, a condition associated also with DS. No evidence of either rearrangements or duplications of ETS2 could be detected inmore » DNA from fibroblasts and brain tissue of Alzheimer disease patients with either the sporadic or the familiar form of the disease. Thus, an altered ETS2 gene dosage does not seem to be a genetic cause or component of Alzheimer disease.« less

CNS sites cooperate to detect duplicate subjects with a clinical trial subject registry.

PubMed

Shiovitz, Thomas M; Wilcox, Charles S; Gevorgyan, Lilit; Shawkat, Adnan

2013-02-01

To report the results of the first 1,132 subjects in a pilot project where local central nervous system trial sites collaborated in the use of a subject database to identify potential duplicate subjects. Central nervous system sites in Los Angeles and Orange County, California, were contacted by the lead author to seek participation in the project. CTSdatabase, a central nervous system-focused trial subject registry, was utilized to track potential subjects at pre-screen. Subjects signed an institutional review board-approved authorization prior to participation, and site staff entered their identifiers by accessing a website. Sites were prompted to communicate with each other or with the database administrator when a match occurred between a newly entered subject and a subject already in the database. Between October 30, 2011, and August 31, 2012, 1,132 subjects were entered at nine central nervous system sites. Subjects continue to be entered, and more sites are anticipated to begin participation by the time of publication. Initially, there were concerns at a few sites over patient acceptance, financial implications, and/or legal and privacy issues, but these were eventually overcome. Patient acceptance was estimated to be above 95 percent. Duplicate Subjects (those that matched several key identifiers with subjects at different sites) made up 7.78 percent of the sample and Certain Duplicates (matching identifiers with a greater than 1 in 10 million likelihood of occurring by chance in the general population) accounted for 3.45 percent of pre-screens entered into the database. Many of these certain duplicates were not consented for studies because of the information provided by the registry. The use of a clinical trial subject registry and cooperation between central nervous system trial sites can reduce the number of duplicate and professional subjects entering clinical trials. To be fully effective, a trial subject database could be integrated into protocols across pharmaceutical companies, thereby mandating site participation and increasing the likelihood that duplicate subjects will be removed before they enter (and negatively affect) clinical trials.

RETRACTED: The revised stratigraphy of the hominin-bearing site of Kromdraai (Gauteng, South Africa) and associated perspectives.

PubMed

Bruxelles, Laurent; Maire, Richard; Beaudet, Amélie; Couzens, Raymond; Duranthon, Francis; Fourvel, Jean-Baptiste; Stratford, Dominic; Thackeray, Francis; Braga, José

2018-01-01

This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the co-Editors-in-Chief and the authors. The Results and Discussion of this article duplicate significant parts of book chapter "A revised stratigraphy of Kromdraai", published by L.B., R.M., R.C., F.T. and J.B. in Braga, J. and Thackeray, J.F. (Eds.), "Kromdraai. A Birthplace of Paranthropus in the Cradle of Humankind" (2016, SUN MeDIA MeTRO, pp. 31-47), https://doi.org/10.18820/9781928355076. One of the conditions of submission of a paper to Journal of Human Evolution is that authors declare explicitly that that their work is original and has not been published previously. Reuse of any data should be appropriately cited. As such this article represents an abuse of the scientific publishing system. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process. Copyright © 2017 Elsevier Ltd. All rights reserved.

Heterogeneous conservation of Dlx paralog co-expression in jawed vertebrates.

PubMed

Debiais-Thibaud, Mélanie; Metcalfe, Cushla J; Pollack, Jacob; Germon, Isabelle; Ekker, Marc; Depew, Michael; Laurenti, Patrick; Borday-Birraux, Véronique; Casane, Didier

2013-01-01

The Dlx gene family encodes transcription factors involved in the development of a wide variety of morphological innovations that first evolved at the origins of vertebrates or of the jawed vertebrates. This gene family expanded with the two rounds of genome duplications that occurred before jawed vertebrates diversified. It includes at least three bigene pairs sharing conserved regulatory sequences in tetrapods and teleost fish, but has been only partially characterized in chondrichthyans, the third major group of jawed vertebrates. Here we take advantage of developmental and molecular tools applied to the shark Scyliorhinus canicula to fill in the gap and provide an overview of the evolution of the Dlx family in the jawed vertebrates. These results are analyzed in the theoretical framework of the DDC (Duplication-Degeneration-Complementation) model. The genomic organisation of the catshark Dlx genes is similar to that previously described for tetrapods. Conserved non-coding elements identified in bony fish were also identified in catshark Dlx clusters and showed regulatory activity in transgenic zebrafish. Gene expression patterns in the catshark showed that there are some expression sites with high conservation of the expressed paralog(s) and other expression sites with events of paralog sub-functionalization during jawed vertebrate diversification, resulting in a wide variety of evolutionary scenarios within this gene family. Dlx gene expression patterns in the catshark show that there has been little neo-functionalization in Dlx genes over gnathostome evolution. In most cases, one tandem duplication and two rounds of vertebrate genome duplication have led to at least six Dlx coding sequences with redundant expression patterns followed by some instances of paralog sub-functionalization. Regulatory constraints such as shared enhancers, and functional constraints including gene pleiotropy, may have contributed to the evolutionary inertia leading to high redundancy between gene expression patterns.

Population Education in Health and Home Economics: Some Sample Lessons for the Secondary Level.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and the Pacific.

This booklet contains five sample lessons integrating population education into health and home economics instruction. It is one of four in a series. Materials differ from those in an earlier series (1980) in that lessons are presented at the secondary level only; there is no duplication of lessons from the earlier series in content and teaching…

Population Education in Social Studies: Some Sample Lessons for the Secondary Level.

ERIC Educational Resources Information Center

United Nations Educational, Scientific, and Cultural Organization, Bangkok (Thailand). Regional Office for Education in Asia and the Pacific.

This booklet consists of 10 sample lessons integrating population education into the social studies. It is one of four in a series. Materials differ from those in an earlier series (1980) in that lessons are presented at the secondary level only; there is no duplication of lessons from the earlier series in terms of content and teaching…

Edge-SIFT: discriminative binary descriptor for scalable partial-duplicate mobile search.

PubMed

Zhang, Shiliang; Tian, Qi; Lu, Ke; Huang, Qingming; Gao, Wen

2013-07-01

As the basis of large-scale partial duplicate visual search on mobile devices, image local descriptor is expected to be discriminative, efficient, and compact. Our study shows that the popularly used histogram-based descriptors, such as scale invariant feature transform (SIFT) are not optimal for this task. This is mainly because histogram representation is relatively expensive to compute on mobile platforms and loses significant spatial clues, which are important for improving discriminative power and matching near-duplicate image patches. To address these issues, we propose to extract a novel binary local descriptor named Edge-SIFT from the binary edge maps of scale- and orientation-normalized image patches. By preserving both locations and orientations of edges and compressing the sparse binary edge maps with a boosting strategy, the final Edge-SIFT shows strong discriminative power with compact representation. Furthermore, we propose a fast similarity measurement and an indexing framework with flexible online verification. Hence, the Edge-SIFT allows an accurate and efficient image search and is ideal for computation sensitive scenarios such as a mobile image search. Experiments on a large-scale dataset manifest that the Edge-SIFT shows superior retrieval accuracy to Oriented BRIEF (ORB) and is superior to SIFT in the aspects of retrieval precision, efficiency, compactness, and transmission cost.

High prevalence of chitotriosidase deficiency in Peruvian Amerindians exposed to chitin-bearing food and enteroparasites.

PubMed

Manno, N; Sherratt, S; Boaretto, F; Coico, F Mejìa; Camus, C Espinoza; Campos, C Jara; Musumeci, S; Battisti, A; Quinnell, R J; León, J Mostacero; Vazza, G; Mostacciuolo, M L; Paoletti, M G; Falcone, F H

2014-11-26

The human genome encodes a gene for an enzymatically active chitinase (CHIT1) located in a single copy on Chromosome 1, which is highly expressed by activated macrophages and in other cells of the innate immune response. Several dysfunctional mutations are known in CHIT1, including a 24-bp duplication in Exon 10 causing catalytic deficiency. This duplication is a common variant conserved in many human populations, except in West and South Africans. Thus it has been proposed that human migration out of Africa and the consequent reduction of exposure to chitin from environmental factors may have enabled the conservation of dysfunctional mutations in human chitinases. Our data obtained from 85 indigenous Amerindians from Peru, representative of populations characterized by high prevalence of chitin-bearing enteroparasites and intense entomophagy, reveal a very high frequency of the 24-bp duplication (47.06%), and of other single nucleotide polymorphisms which are known to partially affect enzymatic activity (G102S: 42.7% and A442G/V: 25.5%). Our finding is in line with a founder effect, but appears to confute our previous hypothesis of a protective role against parasite infection and sustains the discussion on the redundancy of chitinolytic function. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Duplication of the External Auditory Canal: Two Cases and a Review of the Literature

PubMed Central

Goudakos, John K.; Blioskas, Sarantis; Psillas, George; Vital, Victor; Markou, Konstantinos

2012-01-01

The objective of the present paper is to describe the clinical presentation, diagnostic process, surgical treatment, and outcome of 2 patients with first branchial cleft anomaly. The first case was an 8-year-old girl presented with an elastic lesion located in the left infra-auricular area, in close relation with the lobule, duplicating the external auditory canal. The magnetic resonance imaging revealed a lesion, appearing as a rather well-circumscribed mass within the left parotid gland and duplicating the ear canal. A superficial parotidectomy was subsequently performed, with total excision of the cyst. The second patient was a 15-year-old girl presented with a congenital fistula of the right lateral neck. At superficial parotidectomy, a total excision of the fistula was performed. During the operation the tract was recorded to lay between the branches of the facial nerve, extending with a blind ending canal parallel to the external acoustic meatus. Conclusively, first branchial cleft anomalies are rare malformations with cervical, parotid, or auricular clinical manifestations. Diagnosis of first branchial cleft lesions is achieved mainly through careful physical examination. Complete surgical excision with wide exposure of the lesion is essential in order to achieve permanent cure and avoid recurrence. PMID:23213587

An Ancient Duplication of Apple MYB Transcription Factors Is Responsible for Novel Red Fruit-Flesh Phenotypes1[C][W

PubMed Central

Chagné, David; Lin-Wang, Kui; Espley, Richard V.; Volz, Richard K.; How, Natalie M.; Rouse, Simon; Brendolise, Cyril; Carlisle, Charmaine M.; Kumar, Satish; De Silva, Nihal; Micheletti, Diego; McGhie, Tony; Crowhurst, Ross N.; Storey, Roy D.; Velasco, Riccardo; Hellens, Roger P.; Gardiner, Susan E.; Allan, Andrew C.

2013-01-01

Anthocyanin accumulation is coordinated in plants by a number of conserved transcription factors. In apple (Malus × domestica), an R2R3 MYB transcription factor has been shown to control fruit flesh and foliage anthocyanin pigmentation (MYB10) and fruit skin color (MYB1). However, the pattern of expression and allelic variation at these loci does not explain all anthocyanin-related apple phenotypes. One such example is an open-pollinated seedling of cv Sangrado that has green foliage and develops red flesh in the fruit cortex late in maturity. We used methods that combine plant breeding, molecular biology, and genomics to identify duplicated MYB transcription factors that could control this phenotype. We then demonstrated that the red-flesh cortex phenotype is associated with enhanced expression of MYB110a, a paralog of MYB10. Functional characterization of MYB110a showed that it was able to up-regulate anthocyanin biosynthesis in tobacco (Nicotiana tabacum). The chromosomal location of MYB110a is consistent with a whole-genome duplication event that occurred during the evolution of apple within the Maloideae family. Both MYB10 and MYB110a have conserved function in some cultivars, but they differ in their expression pattern and response to fruit maturity. PMID:23096157

Genome-wide characterization of GRAS family genes in Medicago truncatula reveals their evolutionary dynamics and functional diversification

PubMed Central

Zhang, Hailing; Cao, Yingping; Shang, Chen; Li, Jikai; Wang, Jianli; Wu, Zhenying; Ma, Lichao; Qi, Tianxiong; Fu, Chunxiang; Hu, Baozhong

2017-01-01

The GRAS gene family is a large plant-specific family of transcription factors that are involved in diverse processes during plant development. Medicago truncatula is an ideal model plant for genetic research in legumes, and specifically for studying nodulation, which is crucial for nitrogen fixation. In this study, 59 MtGRAS genes were identified and classified into eight distinct subgroups based on phylogenetic relationships. Motifs located in the C-termini were conserved across the subgroups, while motifs in the N-termini were subfamily specific. Gene duplication was the main evolutionary force for MtGRAS expansion, especially proliferation of the LISCL subgroup. Seventeen duplicated genes showed strong effects of purifying selection and diverse expression patterns, highlighting their functional importance and diversification after duplication. Thirty MtGRAS genes, including NSP1 and NSP2, were preferentially expressed in nodules, indicating possible roles in the process of nodulation. A transcriptome study, combined with gene expression analysis under different stress conditions, suggested potential functions of MtGRAS genes in various biological pathways and stress responses. Taken together, these comprehensive analyses provide basic information for understanding the potential functions of GRAS genes, and will facilitate further discovery of MtGRAS gene functions. PMID:28945786

Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots.

PubMed

Wang, Yupeng; Ficklin, Stephen P; Wang, Xiyin; Feltus, F Alex; Paterson, Andrew H

2016-01-01

Different modes of gene duplication including whole-genome duplication (WGD), and tandem, proximal and dispersed duplications are widespread in angiosperm genomes. Small-scale, stochastic gene relocations and transposed gene duplications are widely accepted to be the primary mechanisms for the creation of dispersed duplicates. However, here we show that most surviving ancient dispersed duplicates in core eudicots originated from large-scale gene relocations within a narrow window of time following a genome triplication (γ) event that occurred in the stem lineage of core eudicots. We name these surviving ancient dispersed duplicates as relocated γ duplicates. In Arabidopsis thaliana, relocated γ, WGD and single-gene duplicates have distinct features with regard to gene functions, essentiality, and protein interactions. Relative to γ duplicates, relocated γ duplicates have higher non-synonymous substitution rates, but comparable levels of expression and regulation divergence. Thus, relocated γ duplicates should be distinguished from WGD and single-gene duplicates for evolutionary investigations. Our results suggest large-scale gene relocations following the γ event were associated with the diversification of core eudicots.

Large-Scale Gene Relocations following an Ancient Genome Triplication Associated with the Diversification of Core Eudicots

PubMed Central

Wang, Yupeng; Ficklin, Stephen P.; Wang, Xiyin; Feltus, F. Alex; Paterson, Andrew H.

2016-01-01

Different modes of gene duplication including whole-genome duplication (WGD), and tandem, proximal and dispersed duplications are widespread in angiosperm genomes. Small-scale, stochastic gene relocations and transposed gene duplications are widely accepted to be the primary mechanisms for the creation of dispersed duplicates. However, here we show that most surviving ancient dispersed duplicates in core eudicots originated from large-scale gene relocations within a narrow window of time following a genome triplication (γ) event that occurred in the stem lineage of core eudicots. We name these surviving ancient dispersed duplicates as relocated γ duplicates. In Arabidopsis thaliana, relocated γ, WGD and single-gene duplicates have distinct features with regard to gene functions, essentiality, and protein interactions. Relative to γ duplicates, relocated γ duplicates have higher non-synonymous substitution rates, but comparable levels of expression and regulation divergence. Thus, relocated γ duplicates should be distinguished from WGD and single-gene duplicates for evolutionary investigations. Our results suggest large-scale gene relocations following the γ event were associated with the diversification of core eudicots. PMID:27195960

High-throughput sequencing analysis of the bacteria in the dust storm which passed over Canberra, Australia on 22-23 September 2009

NASA Astrophysics Data System (ADS)

Munday, Chris; De Deckker, Patrick; Tapper, Nigel; Allison, Gwen

2014-05-01

Following a prolonged drought in Australia in the first decade of the 21st century, several dust storms affected the heavily populated East coast of Australia. The largest such storm occurred on 22-23 September 2009 and had a front of an estimated 3000km. A 24hr average PM10 concentration of over 2,000μg/m3 was recorded in several locations and an hourly peak of over 15,000μg/m3 was recorded (Leys et al. 2011). Over two time periods duplicate aerosol samples were collected on 47mm diameter cellulose nitrate membranes at a location removed from anthropogenic influences. One set of samples was collected in the afternoon the dust event started and another was collected overnight. Additionally, overnight rainfall was collected in a sterile bottle.DNA was directly extracted one membrane from each time point for molecular cloning and high throughput sequencing, while the other was cultivated on Tryptic Soy Agar (TSA). High throughput sequencing was performed using the 454 Titanium platform. From the three samples, 19,945 curated sequences were obtained representing 942 OTUS, with the three samples approximately equal in number. Unclassified Rhizobiales and Stenotrophomonas were the most abundant groups which could be attributed names. A total of 942 OTUs were identified (cutoff = 0.03), and despite the temporal relation of the samples, only eleven were found in all three samples, indicating that the dust storm evolved in composition as it passed over the region. Approximately 800 and 500 CFU/m3 were found in the two cultivated samples, tenfold more than was collected from previous dust events (Lim et al, 2011). Identification of cultivars revealed a dominance of the gram positive Firmicutes phylum, while the clone library showed a more even distribution of taxa, with Actinobacteria the most common and Firmicutes comprising less than 10% of sequences. Collectively, the analyses indicate that the concentration of cultivable organisms during the dust storm dramatically relative to calm conditions. A diverse and variable population of microorganisms were present reflecting the vast source and dynamic nature of the storm.

Productive Homologous and Non-homologous Recombination of Hepatitis C Virus in Cell Culture

PubMed Central

Li, Yi-Ping; Mikkelsen, Lotte S.; Gottwein, Judith M.; Bukh, Jens

2013-01-01

Genetic recombination is an important mechanism for increasing diversity of RNA viruses, and constitutes a viral escape mechanism to host immune responses and to treatment with antiviral compounds. Although rare, epidemiologically important hepatitis C virus (HCV) recombinants have been reported. In addition, recombination is an important regulatory mechanism of cytopathogenicity for the related pestiviruses. Here we describe recombination of HCV RNA in cell culture leading to production of infectious virus. Initially, hepatoma cells were co-transfected with a replicating JFH1ΔE1E2 genome (genotype 2a) lacking functional envelope genes and strain J6 (2a), which has functional envelope genes but does not replicate in culture. After an initial decrease in the number of HCV positive cells, infection spread after 13–36 days. Sequencing of recovered viruses revealed non-homologous recombinants with J6 sequence from the 5′ end to the NS2–NS3 region followed by JFH1 sequence from Core to the 3′ end. These recombinants carried duplicated sequence of up to 2400 nucleotides. HCV replication was not required for recombination, as recombinants were observed in most experiments even when two replication incompetent genomes were co-transfected. Reverse genetic studies verified the viability of representative recombinants. After serial passage, subsequent recombination events reducing or eliminating the duplicated region were observed for some but not all recombinants. Furthermore, we found that inter-genotypic recombination could occur, but at a lower frequency than intra-genotypic recombination. Productive recombination of attenuated HCV genomes depended on expression of all HCV proteins and tolerated duplicated sequence. In general, no strong site specificity was observed. Non-homologous recombination was observed in most cases, while few homologous events were identified. A better understanding of HCV recombination could help identification of natural recombinants and thereby lead to improved therapy. Our findings suggest mechanisms for occurrence of recombinants observed in patients. PMID:23555245

Exploring the effects of data quality, data worth, and redundancy of CO2 gas pressure and saturation data on reservoir characterization through PEST Inversion

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

Fang, Zhufeng; Hou, Zhangshuan; Lin, Guang

2014-04-01

This study examined the impacts of reservoir properties on CO2 migration after subsurface injection and evaluated the possibility of characterizing reservoir properties using CO2 monitoring data such as saturation distribution. The injection reservoir was assumed to be located 1400-1500 m below the ground surface such that CO2 remained in the supercritical state. The reservoir was assumed to contain layers with alternating conductive and resistive properties, which is analogous to actual geological formations such as the Mount Simon Sandstone unit. The CO2 injection simulation used a cylindrical grid setting in which the injection well was situated at the center of themore » domain, which extended up to 8000 m from the injection well. The CO2 migration was simulated using the PNNL-developed simulator STOMP-CO2e (the water-salt-CO2 module). We adopted a nonlinear parameter estimation and optimization modeling software package, PEST, for automated reservoir parameter estimation. We explored the effects of data quality, data worth, and data redundancy on the detectability of reservoir parameters using CO2 saturation monitoring data, by comparing PEST inversion results using data with different levels of noises, various numbers of monitoring wells and locations, and different data collection spacing and temporal sampling intervals. This study yielded insight into the use of CO2 saturation monitoring data for reservoir characterization and how to design the monitoring system to optimize data worth and reduce data redundancy.« less

Stomatal response of swordfern to volcanogenic CO2 and SO2 from Kilauea volcano

NASA Astrophysics Data System (ADS)

Tanner, Lawrence H.; Smith, David L.; Allan, Amanda

2007-08-01

The experimentally determined relationship between atmospheric pCO2 and plant stomata has been used to interpret large but transient changes in atmospheric composition, such as may have resulted from the eruptions of flood basalt. However, this relationship has not been tested in the field, i.e. in the vicinity of active volcanoes, to examine the specific effects of volcanogenic emissions. Moreover, the interpretation of paleoatmospheric pCO2 from fossil stomatal data assumes that the stomatal response resulted solely from variation in pCO2 and ignores the potential effect of outgassed SO2. We hypothesize that volcanogenic SO2 also has a significant effect on leaf stomata and test this hypothesis by measuring the stomatal index of the common swordfern (Nephrolepis exaltata) in the plumes of the actively outgassing vents of Kilauea volcano. We find that, compared to control locations, stomatal index is lowest at sample sites in the plume of Halema'uma'u Crater, where concentrations of both CO2 and SO2 are much higher than background. However, sites located directly in the plume of Pu'u O'o, where SO2 levels are high, but CO2 levels are not, also yield low values of stomatal index. We propose that shifts in the stomatal index of fossil leaves may record transient atmospheric increases in both SO2 and CO2, such as may be caused by eruptions of flood basalts. Calculations of pCO2 based on stomatal frequency are likely to be exaggerated.

Critical region within 22q11.2 linked to higher rate of autism spectrum disorder.

PubMed

Clements, Caitlin C; Wenger, Tara L; Zoltowski, Alisa R; Bertollo, Jennifer R; Miller, Judith S; de Marchena, Ashley B; Mitteer, Lauren M; Carey, John C; Yerys, Benjamin E; Zackai, Elaine H; Emanuel, Beverly S; McDonald-McGinn, Donna M; Schultz, Robert T

2017-01-01

Previous studies have reported no clear critical region for medical comorbidities in children with deletions or duplications of 22q11.2. The purpose of this study was to evaluate whether individuals with small nested deletions or duplications of the LCR-A to B region of 22q11.2 show an elevated rate of autism spectrum disorder (ASD) compared to individuals with deletions or duplications that do not include this region. We recruited 46 patients with nested deletions ( n  = 33) or duplications ( n  = 13) of 22q11.2, including LCR-A to B ( n del  = 11), LCR-A to C ( n del  = 4), LCR-B to D ( n del  = 14; n dup  = 8), LCR-C to D ( n del  = 4; n dup  = 2), and smaller nested regions ( n  = 3). Parent questionnaire, record review, and, for a subset, in-person evaluation were used for ASD diagnostic classification. Rates of ASD in individuals with involvement of LCR-B to LCR-D were compared with Fisher's exact test to LCR-A to LCR-B for deletions, and to a previously published sample of LCR-A to LCR-D for duplications. The rates of medical comorbidities and psychiatric diagnoses were determined from questionnaires and chart review. We also report group mean differences on psychiatric questionnaires. Individuals with deletions involving LCR-A to B showed a 39-44% rate of ASD compared to 0% in individuals whose deletions did not involve LCR-A to B. We observed similar rates of medical comorbidities in individuals with involvement of LCR-A to B and LCR-B to D for both duplications and deletions, consistent with prior studies. Children with nested deletions of 22q11.2 may be at greater risk for autism spectrum disorder if the region includes LCR-A to LCR-B. Replication is needed.

The impact of a medication record sharing program among diabetes patients under a single-payer system: The role of inquiry rate.

PubMed

Lin, Jin-Hung; Cheng, Shou-Hsia

2018-08-01

Taiwan's single health insurer introduced a medication record exchange platform, the PharmaCloud program, in 2013. This study aimed to evaluate the effects of the medication record inquiry rate on medication duplication among patients with diabetes. A retrospective pre-post design with a comparison group was conducted using nationwide health insurance claim data of diabetic patients from 2013 to 2014. Patients whose medication record inquiry rate fell within the upper 25th percentile were classified as the high-inquiry group, and the others as the low-inquiry group. The dependent variables were the likelihood of receiving duplicated medication and the overlapped medication days of the study subjects. Generalized estimation equations with difference-in-difference analysis were calculated to examine the net effect of the PharmaCloud inquiry rate for a matched sub-sample. In total, 106,508 patients with diabetes were randomly selected. From 2013 to 2014, the medication duplication rate was reduced 7.76 percentile (54.12%-46.36%) for the high-inquiry group and 9.58 percentile (63.72%-54.14%) for the low-inquiry group; the average medication overlap periods were shortened 4.36 days (8.49-4.13) and 6.29 days (11.28-4.99), respectively. The regression models showed patients in the high-inquiry group were more likely to receive duplicated medication (OR = 1.11, 95% C.I. = 1.07-1.16) and with longer overlapped days (7.53%, P = 0.0081) after the program. The medication record sharing program has reduced medication duplication among diabetes patients. However, higher inquiry rate did not lead to greater reduction in medication duplication; the overall effect might be due to enhanced internal control via prescription alert system in hospitals rather physician's review of the records. Copyright © 2018 Elsevier B.V. All rights reserved.

A false single nucleotide polymorphism generated by gene duplication compromises meat traceability.

PubMed

Sanz, Arianne; Ordovás, Laura; Zaragoza, Pilar; Sanz, Albina; de Blas, Ignacio; Rodellar, Clementina

2012-07-01

Controlling meat traceability using SNPs is an effective method of ensuring food safety. We have analyzed several SNPs to create a panel for bovine genetic identification and traceability studies. One of these was the transversion g.329C>T (Genbank accession no. AJ496781) on the cytochrome P450 17A1 gene, which has been included in previously published panels. Using minisequencing reactions, we have tested 701 samples belonging to eight Spanish cattle breeds. Surprisingly, an excess of heterozygotes was detected, implying an extreme departure from Hardy-Weinberg equilibrium (P<0.001). By alignment analysis and sequencing, we detected that the g.329C>T SNP is a false positive polymorphism, which allows us to explain the inflated heterozygotic value. We recommend that this ambiguous SNP, as well as other polymorphisms located in this region, should not be used in identification, traceability or disease association studies. Annotation of these false SNPs should improve association studies and avoid misinterpretations. Copyright © 2012 Elsevier Ltd. All rights reserved.

Geothermal He and CO2 variations at Changbaishan intra-plate volcano (NE China) and the nature of the sub-continental lithospheric mantle

NASA Astrophysics Data System (ADS)

Hahm, D.; Hilton, D. R.; Cho, M.; Wei, H.; Kim, K.-R.

2008-11-01

We report new He and CO2 data for geothermal fluids from Changbaishan Volcano located on the border of China and North Korea. Helium isotope ratios reach a maximum of 5.4 RA (where RA = 3He/4He in air) whereas carbon isotope values (δ 13C) fall between -2 and -7 ‰ (vs. PDB). The ratio of CO2/3He varies between 0.5-7.1 (×109) for gas samples but is considerably higher (~1012) in waters. The combined He-CO2 systematics reveal the clear imprint of a dominant subducted slab contribution to the total CO2 inventory. We conclude that these geothermal volatiles originate from the sub-continental lithospheric mantle (SCLM) in NE China and represent ancient fluids captured by prior metasomatic events.

Ambient endotoxin in PM10 and association with inflammatory activity, air pollutants, and meteorology, in Chitwan, Nepal.

PubMed

Mahapatra, Parth Sarathi; Jain, Sumeet; Shrestha, Sujan; Senapati, Shantibhusan; Puppala, Siva Praveen

2018-03-15

Endotoxin associated with ambient PM (particulate matter) has been linked to adverse respiratory symptoms, but there have been few studies of ambient endotoxin and its association with co-pollutants and inflammation. Our aim was to measure endotoxin associated with ambient PM 10 (particulate matter with aerodynamic diameter<10μm) in summer 2016 at four locations in Chitwan, Nepal, and investigate its association with meteorology, co-pollutants, and inflammatory activity. PM 10 concentrations were recorded and filter paper samples were collected using E-samplers; PM 1, PM 2.5 , black carbon (BC), methane (CH 4 ), and carbon monoxide (CO) were also measured. The Limulus amebocyte lysate (LAL) assay was used for endotoxin quantification and the nuclear factor kappa B (NFκB) activation assay to assess inflammatory activity. The mean concentration of PM 10 at the different locations ranged from 136 to 189μg/m 3 , and of endotoxin from 0.29 to 0.53EU/m 3 . Pollutant presence was positively correlated with endotoxin. Apart from relative humidity, meteorological variations had no significant impact on endotoxin concentration. NF-κB activity was negatively correlated with endotoxin concentration. To the best of our knowledge, this study provides the first measurements of ambient endotoxin associated with PM 10 in Nepal. Endotoxin and co-pollutants were positively associated indicating a similar source. Endotoxin was negatively correlated with inflammatory activity as a result of a time-limited forest fire event during the sampling period. Studies of co-pollutants suggested that the higher levels of endotoxin related to biomass burning were accompanied by increased levels of anti-inflammatory agents, which suppressed the endotoxin inflammatory effect. Copyright © 2017. Published by Elsevier B.V.

Genomic organization and evolution of the Atlantic salmon hemoglobin repertoire

PubMed Central

2010-01-01

Background The genomes of salmonids are considered pseudo-tetraploid undergoing reversion to a stable diploid state. Given the genome duplication and extensive biological data available for salmonids, they are excellent model organisms for studying comparative genomics, evolutionary processes, fates of duplicated genes and the genetic and physiological processes associated with complex behavioral phenotypes. The evolution of the tetrapod hemoglobin genes is well studied; however, little is known about the genomic organization and evolution of teleost hemoglobin genes, particularly those of salmonids. The Atlantic salmon serves as a representative salmonid species for genomics studies. Given the well documented role of hemoglobin in adaptation to varied environmental conditions as well as its use as a model protein for evolutionary analyses, an understanding of the genomic structure and organization of the Atlantic salmon α and β hemoglobin genes is of great interest. Results We identified four bacterial artificial chromosomes (BACs) comprising two hemoglobin gene clusters spanning the entire α and β hemoglobin gene repertoire of the Atlantic salmon genome. Their chromosomal locations were established using fluorescence in situ hybridization (FISH) analysis and linkage mapping, demonstrating that the two clusters are located on separate chromosomes. The BACs were sequenced and assembled into scaffolds, which were annotated for putatively functional and pseudogenized hemoglobin-like genes. This revealed that the tail-to-tail organization and alternating pattern of the α and β hemoglobin genes are well conserved in both clusters, as well as that the Atlantic salmon genome houses substantially more hemoglobin genes, including non-Bohr β globin genes, than the genomes of other teleosts that have been sequenced. Conclusions We suggest that the most parsimonious evolutionary path leading to the present organization of the Atlantic salmon hemoglobin genes involves the loss of a single hemoglobin gene cluster after the whole genome duplication (WGD) at the base of the teleost radiation but prior to the salmonid-specific WGD, which then produced the duplicated copies seen today. We also propose that the relatively high number of hemoglobin genes as well as the presence of non-Bohr β hemoglobin genes may be due to the dynamic life history of salmon and the diverse environmental conditions that the species encounters. Data deposition: BACs S0155C07 and S0079J05 (fps135): GenBank GQ898924; BACs S0055H05 and S0014B03 (fps1046): GenBank GQ898925 PMID:20923558

Alphacoronaviruses in new World bats: Prevalence, persistence, phylogeny, and potential for interaction with humans

USGS Publications Warehouse

Osborne, C.; Cryan, P.M.; O'Shea, T.J.; Oko, L.M.; Ndaluka, C.; Calisher, C.H.; Berglund, A.D.; Klavetter, M.L.; Bowen, R.A.; Holmes, K.V.; Dominguez, S.R.

2011-01-01

Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.

Alphacoronaviruses in New World Bats: Prevalence, Persistence, Phylogeny, and Potential for Interaction with Humans

USGS Publications Warehouse

Osborne, Christina; Cryan, Paul M.; O'Shea, Thomas J.; Oko, Lauren M.; Ndaluka, Christina; Calisher, Charles H.; Berglund, Andrew D.; Klavetter, Mead L.; Holmes, Kathryn V.; Dominguez, Samuel R.; Montgomery, Joel Mark

2011-01-01

Bats are reservoirs for many different coronaviruses (CoVs) as well as many other important zoonotic viruses. We sampled feces and/or anal swabs of 1,044 insectivorous bats of 2 families and 17 species from 21 different locations within Colorado from 2007 to 2009. We detected alphacoronavirus RNA in bats of 4 species: big brown bats (Eptesicus fuscus), 10% prevalence; long-legged bats (Myotis volans), 8% prevalence; little brown bats (Myotis lucifugus), 3% prevalence; and western long-eared bats (Myotis evotis), 2% prevalence. Overall, juvenile bats were twice as likely to be positive for CoV RNA as adult bats. At two of the rural sampling sites, CoV RNAs were detected in big brown and long-legged bats during the three sequential summers of this study. CoV RNA was detected in big brown bats in all five of the urban maternity roosts sampled throughout each of the periods tested. Individually tagged big brown bats that were positive for CoV RNA and later sampled again all became CoV RNA negative. Nucleotide sequences in the RdRp gene fell into 3 main clusters, all distinct from those of Old World bats. Similar nucleotide sequences were found in amplicons from gene 1b and the spike gene in both a big-brown and a long-legged bat, indicating that a CoV may be capable of infecting bats of different genera. These data suggest that ongoing evolution of CoVs in bats creates the possibility of a continued threat for emergence into hosts of other species. Alphacoronavirus RNA was detected at a high prevalence in big brown bats in roosts in close proximity to human habitations (10%) and known to have direct contact with people (19%), suggesting that significant potential opportunities exist for cross-species transmission of these viruses. Further CoV surveillance studies in bats throughout the Americas are warranted.

Large Direct Repeats Flank Genomic Rearrangements between a New Clinical Isolate of Francisella tularensis subsp. tularensis A1 and Schu S4

DTIC Science & Technology

2010-02-03

occur at locations 1,374,336–1,408,246 ( DRI ) and 1,767,671– 1,801,581 (DRII) in Schu S4. In addition, a 5358 bp segment of Table 2. VNTR markers and...iglABCD operon were found in NE061598. The location of DRI and DRII in both Schu S4 and NE061598 are shown in figures 2A and 2B. In addition, DRIII (III...loss of the first 207 bp in DRI of NE061598 (Figure 2). Similar chromosomal changes mediated by these duplicated regions were also observed between Schu

Coexistence of Two blaNDM-5 Genes on an IncF Plasmid as Revealed by Nanopore Sequencing.

PubMed

Feng, Yu; Liu, Lu; McNally, Alan; Zong, Zhiyong

2018-05-01

In a carbapenem-resistant Escherichia coli clinical isolate of sequence type 167, two copies of bla NDM-5 were found on a 144,225-bp IncF self-transmissible plasmid of the F36:A4:B - type. Both bla NDM-5 genes were located in 11,065-bp regions flanked by two copies of IS 26 The two regions were identical in sequence but were present at different locations on the plasmid, suggesting a duplication of the same region. This study highlights the complex genetic contexts of bla NDM-5 . Copyright © 2018 American Society for Microbiology.

Shaping Si, NiCo, and glass substrates via stresses in the coatings

NASA Astrophysics Data System (ADS)

Wang, Xiaoli; Yao, Youwei; Ye, Shi; Liu, Tianchen; Assoufid, Lahsen; Cao, Jian; Ulmer, M. P.

2016-09-01

Here we report progress toward the fabrication of adaptive or active Si X-ray mirrors via a two step process. The first step is to curve a Si flat and then coat it with Terfenol-D that will allow the shape control via the application of a magnetic field. The goal is to create a mirror whose local (a few mm-length scale) slope can be changed and left for several hours or more. The current work described here was done in on Si to demonstrate the ability to produce the initial curvature, and in parallel, work to on magnetically hard NiCo 5 cm x 5 cm square plus on a glass sample. The glass sample was used a proto-type to model making changes in two different locations on a mirror. The NiCo sample was used to show that a magnetic field can be retained in a magnetically hard substrate such that the magnetically induced stress in the Terfenol-D was able to maintain a deformation for as long as time permitted to make the measurement which was 71 hours.

The early stages of duplicate gene evolution

PubMed Central

Moore, Richard C.; Purugganan, Michael D.

2003-01-01

Gene duplications are one of the primary driving forces in the evolution of genomes and genetic systems. Gene duplicates account for 8–20% of the genes in eukaryotic genomes, and the rates of gene duplication are estimated at between 0.2% and 2% per gene per million years. Duplicate genes are believed to be a major mechanism for the establishment of new gene functions and the generation of evolutionary novelty, yet very little is known about the early stages of the evolution of duplicated gene pairs. It is unclear, for example, to what extent selection, rather than neutral genetic drift, drives the fixation and early evolution of duplicate loci. Analysis of recently duplicated genes in the Arabidopsis thaliana genome reveals significantly reduced species-wide levels of nucleotide polymorphisms in the progenitor and/or duplicate gene copies, suggesting that selective sweeps accompany the initial stages of the evolution of these duplicated gene pairs. Our results support recent theoretical work that indicates that fates of duplicate gene pairs may be determined in the initial phases of duplicate gene evolution and that positive selection plays a prominent role in the evolutionary dynamics of the very early histories of duplicate nuclear genes. PMID:14671323

The benefits of co-location in primary care practices: the perspectives of general practitioners and patients in 34 countries.

PubMed

Bonciani, M; Schäfer, W; Barsanti, S; Heinemann, S; Groenewegen, P P

2018-02-21

There is no clear evidence as to whether the co-location of primary care professionals in the same facility positively influences their way of working and the quality of healthcare as perceived by patients. The aim of this study was to identify the relationships between general practitioner (GP) co-location with other GPs and/or other professionals and the GP outcomes and patients' experiences. We wanted to test whether GP co-location is related to a broader range of services provided, the use of clinical governance tools and inter-professional collaboration, and whether the patients of co-located GPs perceive a better quality of care in terms of accessibility, comprehensiveness and continuity of care with their GPs. The source of data was the QUALICOPC study (Quality and Costs of Primary Care in Europe), which involved surveys of GPs and their patients in 34 countries, mostly in Europe. In order to study the relationships between GP co-location and both GPs' outcomes and patients' experience, multilevel linear regression analysis was carried out. The GP questionnaire was filled in by 7183 GPs and the patient experience questionnaire by 61,931 patients. Being co-located with at least one other professional is the most common situation of the GPs involved in the study. Compared with single-handed GP practices, GP co-location are positively associated with the GP outcomes. Considering the patients' perspective, comprehensiveness of care has the strongest negative relationship of GP co-location of all the dimensions of patient experiences analysed. The paper highlights that GP mono- and multi-disciplinary co-location is related to positive outcomes at a GP level, such as a broader provision of technical procedures, increased collaboration among different providers and wider coordination with secondary care. However, GP co-location, particularly in a multidisciplinary setting, is related to less positive patient experiences, especially in countries with health systems characterised by a weak primary care structure.

Activity-Dependent Dysfunction in Visual and Olfactory Sensory Systems in Mouse Models of Down Syndrome

PubMed Central

Saqran, Lubna; Herrick, Scott P.; Frosch, Matthew P.; Hyman, Bradley T.

2017-01-01

Activity-dependent synaptic plasticity plays a critical role in the refinement of circuitry during postnatal development and may be disrupted in conditions that cause intellectual disability, such as Down syndrome (DS). To test this hypothesis, visual cortical plasticity was assessed in Ts65Dn mice that harbor a chromosomal duplication syntenic to human chromosome 21q. We find that Ts65Dn mice demonstrate a defect in ocular dominance plasticity (ODP) following monocular deprivation. This phenotype is similar to that of transgenic mice that express amyloid precursor protein (APP), which is duplicated in DS and in Ts65DN mice; however, normalizing APP gene copy number in Ts65Dn mice fails to rescue plasticity. Ts1Rhr mice harbor a duplication of the telomeric third of the Ts65Dn-duplicated sequence and demonstrate the same ODP defect, suggesting a gene or genes sufficient to drive the phenotype are located in that smaller duplication. In addition, we find that Ts65Dn mice demonstrate an abnormality in olfactory system connectivity, a defect in the refinement of connections to second-order neurons in the olfactory bulb. Ts1Rhr mice do not demonstrate a defect in glomerular refinement, suggesting that distinct genes or sets of genes underlie visual and olfactory system phenotypes. Importantly, these data suggest that developmental plasticity and connectivity are impaired in sensory systems in DS model mice, that such defects may contribute to functional impairment in DS, and that these phenotypes, present in male and female mice, provide novel means for examining the genetic and molecular bases for neurodevelopmental impairment in model mice in vivo. SIGNIFICANCE STATEMENT Our understanding of the basis for intellectual impairment in Down syndrome is hindered by the large number of genes duplicated in Trisomy 21 and a lack of understanding of the effect of disease pathology on the function of neural circuits in vivo. This work describes early postnatal developmental abnormalities in visual and olfactory sensory systems in Down syndrome model mice, which provide insight into defects in the function of neural circuits in vivo and provide an approach for exploring the genetic and molecular basis for impairment in the disease. In addition, these findings raise the possibility that basic dysfunction in primary sensory circuitry may illustrate mechanisms important for global learning and cognitive impairment in Down syndrome patients. PMID:28899917

Small Aperture Telescope Observations of Co-located Geostationary Satellites

NASA Astrophysics Data System (ADS)

Scott, R.; Wallace, B.

As geostationary orbit (GEO) continues to be populated, satellite operators are increasing usage of co-location techniques to maximize usage of fewer GEO longitude slots. Co-location is an orbital formation strategy where two or more geostationary satellites reside within one GEO stationkeeping box. The separation strategy used to prevent collision between the co-located satellites generally uses eccentricity (radial separation) and inclination (latitude separation) vector offsets. This causes the satellites to move in relative motion ellipses about each other as the relative longitude drift between the satellites is near zero. Typical separations between the satellites varies from 1 to 100 kilometers. When co-located satellites are observed by optical ground based space surveillance sensors the participants appear to be separated by a few minutes of arc or less in angular extent. Under certain viewing geometries, these satellites appear to visually conjunct even though the satellites are, in fact, well separated spatially. In situations where one of the co-located satellites is more optically reflective than the other, the reflected sunglint from the more reflective satellite can overwhelm the other. This less frequently encountered issue causes the less reflective satellite to be glint masked in the glare of the other. This paper focuses on space surveillance observations on co-located Canadian satellites using a small optical telescope operated by Defence R&D Canada - Ottawa. The two above mentioned problems (cross tagging and glint masking) are investigated and we quantify the results for Canadian operated geostationary satellites. The performance of two line element sets when making in-frame CCD image correlation between the co-located satellites is also examined. Relative visual magnitudes between the co-located members are also inspected and quantified to determine the susceptibility of automated telescopes to glint masking of co-located satellite members.

Pyloric duplications: review and case study.

PubMed

Cooper, S; Abrams, R S; Carbaugh, R A

1995-12-01

Gastric duplications are unusual congenital anomalies that often require surgical treatment. Pyloric duplications are particularly rare; few are reported in the English literature. This article reviews the literature on pyloric duplications and describes a pyloric duplication associated with hypertrophic pyloric stenosis in a 5-week-old child and a duplication that recurred 7 years later.