Shape accuracy optimization for cable-rib tension deployable antenna structure with tensioned cables

NASA Astrophysics Data System (ADS)

Liu, Ruiwei; Guo, Hongwei; Liu, Rongqiang; Wang, Hongxiang; Tang, Dewei; Song, Xiaoke

2017-11-01

Shape accuracy is of substantial importance in deployable structures as the demand for large-scale deployable structures in various fields, especially in aerospace engineering, increases. The main purpose of this paper is to present a shape accuracy optimization method to find the optimal pretensions for the desired shape of cable-rib tension deployable antenna structure with tensioned cables. First, an analysis model of the deployable structure is established by using finite element method. In this model, geometrical nonlinearity is considered for the cable element and beam element. Flexible deformations of the deployable structure under the action of cable network and tensioned cables are subsequently analyzed separately. Moreover, the influence of pretension of tensioned cables on natural frequencies is studied. Based on the results, a genetic algorithm is used to find a set of reasonable pretension and thus minimize structural deformation under the first natural frequency constraint. Finally, numerical simulations are presented to analyze the deployable structure under two kinds of constraints. Results show that the shape accuracy and natural frequencies of deployable structure can be effectively improved by pretension optimization.

Results from laboratory and field testing of nitrate measuring spectrophotometers

USGS Publications Warehouse

Snazelle, Teri T.

2015-01-01

In Phase II, the analyzers were deployed in field conditions at three diferent USGS sites. The measured nitrate concentrations were compared to discrete (reference) samples analyzed by the Direct UV method on a Shimadzu UV1800 bench top spectrophotometer, and by the National Environmental Methods Index (NEMI) method I-2548-11 at the USGS National Water Quality Laboratory. The first deployment at USGS site 0249620 on the East Pearl River in Hancock County, Mississippi, tested the ability of the TriOs ProPs (10-mm path length), Hach NITRATAX (5 mm), Satlantic SUNA (10 mm), and the S::CAN Spectro::lyser (5 mm) to accurately measure low-level (less than 2 mg-N/L) nitrate concentrations while observing the effect turbidity and colored dissolved organic matter (CDOM) would have on the analyzers' measurements. The second deployment at USGS site 01389005 Passaic River below Pompton River at Two Bridges, New Jersey, tested the analyzer's accuracy in mid-level (2-8 mg-N/L) nitrate concentrations. This site provided the means to test the analyzers' performance in two distinct matrices—the Passaic and the Pompton Rivers. In this deployment, three instruments tested in Phase I (TriOS, Hach, and SUNA) were deployed with the S::CAN Spectro::lyser (35 mm) already placed by the New Jersey Water Science Center (WSC). The third deployment at USGS site 05579610 Kickapoo Creek at 2100E Road near Bloomington, Illinois, tested the ability of the analyzers to measure high nitrate concentrations (greater than 8 mg-N/L) in turbid waters. For Kickapoo Creek, the HIF provided the TriOS (10 mm) and S::CAN (5 mm) from Phase I, and a SUNA V2 (5 mm) to be deployed adjacent to the Illinois WSC-owned Hach (2 mm). A total of 40 discrete samples were collected from the three deployment sites and analyzed. The nitrate concentration of the samples ranged from 0.3–22.2 mg-N/L. The average absolute difference between the TriOS measurements and discrete samples was 0.46 mg-N/L. For the combined data from the Hach 5-mm and 2-mm analyzers, the average absolute difference between the Hach samples and the discrete samples was 0.13 mg-N/L. For the SUNA and SUNA V2 combined data, the average absolute difference between the SUNA samples and the discrete samples was 0.66 mg-N/L. The average absolute difference between the S::CAN samples and the discrete samples was 0.63 mg-N/L.

Intelligent Transportation Systems (ITS) in Texas: Deployment Summary and Case Study of Deployment Methodologies

DOT National Transportation Integrated Search

2000-06-01

The state of the intelligent transportation systems (ITS) program in Texas is summarized and analyzed. The report first reviews the types of ITS deployments within each Texas Department of Transportation district. The methods used to plan, design, co...

Designing DNA nanodevices for compatibility with the immune system of higher organisms

NASA Astrophysics Data System (ADS)

Surana, Sunaina; Shenoy, Avinash R.; Krishnan, Yamuna

2015-09-01

DNA is proving to be a powerful scaffold to construct molecularly precise designer DNA devices. Recent trends reveal their ever-increasing deployment within living systems as delivery devices that not only probe but also program and re-program a cell, or even whole organisms. Given that DNA is highly immunogenic, we outline the molecular, cellular and organismal response pathways that designer nucleic acid nanodevices are likely to elicit in living systems. We address safety issues applicable when such designer DNA nanodevices interact with the immune system. In light of this, we discuss possible molecular programming strategies that could be integrated with such designer nucleic acid scaffolds to either evade or stimulate the host response with a view to optimizing and widening their applications in higher organisms.

Autonomous system for Web-based microarray image analysis.

PubMed

Bozinov, Daniel

2003-12-01

Software-based feature extraction from DNA microarray images still requires human intervention on various levels. Manual adjustment of grid and metagrid parameters, precise alignment of superimposed grid templates and gene spots, or simply identification of large-scale artifacts have to be performed beforehand to reliably analyze DNA signals and correctly quantify their expression values. Ideally, a Web-based system with input solely confined to a single microarray image and a data table as output containing measurements for all gene spots would directly transform raw image data into abstracted gene expression tables. Sophisticated algorithms with advanced procedures for iterative correction function can overcome imminent challenges in image processing. Herein is introduced an integrated software system with a Java-based interface on the client side that allows for decentralized access and furthermore enables the scientist to instantly employ the most updated software version at any given time. This software tool is extended from PixClust as used in Extractiff incorporated with Java Web Start deployment technology. Ultimately, this setup is destined for high-throughput pipelines in genome-wide medical diagnostics labs or microarray core facilities aimed at providing fully automated service to its users.

Longitudinal changes in glucocorticoid receptor exon 1F methylation and psychopathology after military deployment

PubMed Central

Schür, R R; Boks, M P; Rutten, B P F; Daskalakis, N P; de Nijs, L; van Zuiden, M; Kavelaars, A; Heijnen, C J; Joëls, M; Kahn, R S; Geuze, E; Vermetten, E; Vinkers, C H

2017-01-01

Several cross-sectional studies have demonstrated the relevance of DNA methylation of the glucocorticoid receptor exon 1F region (GR-1F) for trauma-related psychopathology. We conducted a longitudinal study to examine GR-1F methylation changes over time in relation to trauma exposure and the development of post-deployment psychopathology. GR-1F methylation (52 loci) was quantified using pyrosequencing in whole blood of 92 military men 1 month before and 6 months after a 4-month deployment period to Afghanistan. GR-1F methylation overall (mean methylation and the number of methylated loci) and functional methylation (methylation at loci associated with GR exon 1F expression) measures were examined. We first investigated the effect of exposure to potentially traumatic events during deployment on these measures. Subsequently, changes in GR-1F methylation were related to changes in mental health problems (total Symptom Checklist-90 score) and posttraumatic stress disorder (PTSD) symptoms (Self-Report Inventory for PTSD). Trauma exposure during deployment was associated with an increase in all methylation measures, but development of mental health problems 6 months after deployment was only significantly associated with an increased functional methylation. Emergence of post-deployment PTSD symptoms was not related to increased functional methylation over time. Pre-deployment methylation levels did not predict post-deployment psychopathology. To our knowledge, this is the first study to prospectively demonstrate trauma-related increases in GR-1F methylation, and it shows that only increases at specific functionally relevant sites predispose for post-deployment psychopathology. PMID:28742078

Heart rate variability: Pre-deployment predictor of post-deployment PTSD symptoms

PubMed Central

Pyne, Jeffrey M.; Constans, Joseph I.; Wiederhold, Mark D.; Gibson, Douglas P.; Kimbrell, Timothy; Kramer, Teresa L.; Pitcock, Jeffery A.; Han, Xiaotong; Williams, D. Keith; Chartrand, Don; Gevirtz, Richard N.; Spira, James; Wiederhold, Brenda K.; McCraty, Rollin; McCune, Thomas R.

2017-01-01

Heart rate variability is a physiological measure associated with autonomic nervous system activity. This study hypothesized that lower pre-deployment HRV would be associated with higher post-deployment post-traumatic stress disorder (PTSD) symptoms. Three-hundred-forty-three Army National Guard soldiers enrolled in the Warriors Achieving Resilience (WAR) study were analyzed. The primary outcome was PTSD symptom severity using the PTSD Checklist – Military version (PCL) measured at baseline, 3- and 12-month post-deployment. Heart rate variability predictor variables included: high frequency power (HF) and standard deviation of the normal cardiac inter-beat interval (SDNN). Generalized linear mixed models revealed that the pre-deployment PCL*ln(HF) interaction term was significant (p < 0.0001). Pre-deployment SDNN was not a significant predictor of post-deployment PCL. Covariates included age, pre-deployment PCL, race/ethnicity, marital status, tobacco use, childhood abuse, pre-deployment traumatic brain injury, and previous combat zone deployment. Pre-deployment heart rate variability predicts post-deployment PTSD symptoms in the context of higher pre-deployment PCL scores. PMID:27773678

Lab-on-a-Drone: Toward Pinpoint Deployment of Smartphone-Enabled Nucleic Acid-Based Diagnostics for Mobile Health Care

PubMed Central

2016-01-01

We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. Standard sample preparation is enabled by leveraging the drone’s motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging. PMID:26898247

Lab-on-a-Drone: Toward Pinpoint Deployment of Smartphone-Enabled Nucleic Acid-Based Diagnostics for Mobile Health Care.

PubMed

Priye, Aashish; Wong, Season; Bi, Yuanpeng; Carpio, Miguel; Chang, Jamison; Coen, Mauricio; Cope, Danielle; Harris, Jacob; Johnson, James; Keller, Alexandra; Lim, Richard; Lu, Stanley; Millard, Alex; Pangelinan, Adriano; Patel, Neal; Smith, Luke; Chan, Kamfai; Ugaz, Victor M

2016-05-03

We introduce a portable biochemical analysis platform for rapid field deployment of nucleic acid-based diagnostics using consumer-class quadcopter drones. This approach exploits the ability to isothermally perform the polymerase chain reaction (PCR) with a single heater, enabling the system to be operated using standard 5 V USB sources that power mobile devices (via battery, solar, or hand crank action). Time-resolved fluorescence detection and quantification is achieved using a smartphone camera and integrated image analysis app. Standard sample preparation is enabled by leveraging the drone's motors as centrifuges via 3D printed snap-on attachments. These advancements make it possible to build a complete DNA/RNA analysis system at a cost of ∼$50 ($US). Our instrument is rugged and versatile, enabling pinpoint deployment of sophisticated diagnostics to distributed field sites. This capability is demonstrated by successful in-flight replication of Staphylococcus aureus and λ-phage DNA targets in under 20 min. The ability to perform rapid in-flight assays with smartphone connectivity eliminates delays between sample collection and analysis so that test results can be delivered in minutes, suggesting new possibilities for drone-based systems to function in broader and more sophisticated roles beyond cargo transport and imaging.

Assessment of DoD’s Central Identification Lab and the Feasibility of Increasing Identification Rates

DTIC Science & Technology

2009-06-01

mtDNA exists in the ancient remains with which the CIL must work . Secondly, mtDNA is wholly maternally inherited as a single unit and allows for...they should be instructed to work for a certain number of days strictly on trying to find maternal -eligible donors. The most important objective of the...In addition to the impact frequent deployments have on the staff’s personal life , impacts on their work in the lab are also significant. First and

Analytical investigation of the dynamics of tethered constellations in Earth orbit (phase 2)

NASA Technical Reports Server (NTRS)

Lorenzini, E.; Arnold, D. A.; Grossi, M. D.; Gullahorn, G. E.

1985-01-01

The deployment maneuver of three axis vertical constellations with elastic tethers is analyzed. The deployment strategy devised previously was improved. Dampers were added to the system. Effective algorithms for damping out the fundamental vibrational modes of the system were implemented. Simulations of a complete deployment and a subsequent station keeping phase of a three mass constellation is shown.

Food and drinking water hygiene and intestinal protozoa in deployed German soldiers.

PubMed

Frickmann, Hagen; Schwarz, Norbert G; Wiemer, Dorothea F; Fischer, Marcellus; Tannich, Egbert; Scheid, Patrick L; Müller, Martin; Schotte, Ulrich; Bock, Wolfgang; Hagen, Ralf M

2013-03-01

This report analyzes the occurrence of Cryptosporidium spp., E. histolytica, and G. intestinalis in stool of returnees from military deployments and the impact of hygiene precautions. Between 2007 and 2010, stool samples of 830 returnees that were obtained 8-12 weeks after military deployments in Afghanistan, Uzbekistan, the Balkans, Democratic Republic of the Congo/Gabonese Republic, and Sudan and 292 control samples from non-deployed soldiers were analyzed by PCR for Cryptosporidium spp., E. histolytica, G. intestinalis, and the commensal indicator of fecal contamination E. dispar. Data on hygiene precautions were available. The soldiers were questioned regarding gastrointestinal and general symptoms. Among 1122 stool samples, 18 were positive for G. intestinalis, 10 for E. dispar, and no-one for Cryptosporidium spp. and E. histolytica. An increased risk of acquiring chronic parasitic infections in comparison with non-deployed controls was demonstrated only for G. intestinalis in Sudan, where standardized food and drinking water hygiene precautions could not be implemented. Standard food and drinking water hygiene precautions in the context of screened military field camps proved to be highly reliable in preventing food-borne and water-borne chronic infections and colonization by intestinal protozoa, leading to detection proportions similar to those in non-deployed controls.

Enhanced DNA Sensing via Catalytic Aggregation of Gold Nanoparticles

PubMed Central

Huttanus, Herbert M.; Graugnard, Elton; Yurke, Bernard; Knowlton, William B.; Kuang, Wan; Hughes, William L.; Lee, Jeunghoon

2014-01-01

A catalytic colorimetric detection scheme that incorporates a DNA-based hybridization chain reaction into gold nanoparticles was designed and tested. While direct aggregation forms an inter-particle linkage from only ones target DNA strand, the catalytic aggregation forms multiple linkages from a single target DNA strand. Gold nanoparticles were functionalized with thiol-modified DNA strands capable of undergoing hybridization chain reactions. The changes in their absorption spectra were measured at different times and target concentrations and compared against direct aggregation. Catalytic aggregation showed a multifold increase in sensitivity at low target concentrations when compared to direct aggregation. Gel electrophoresis was performed to compare DNA hybridization reactions in catalytic and direct aggregation schemes, and the product formation was confirmed in the catalytic aggregation scheme at low levels of target concentrations. The catalytic aggregation scheme also showed high target specificity. This application of a DNA reaction network to gold nanoparticle-based colorimetric detection enables highly-sensitive, field-deployable, colorimetric readout systems capable of detecting a variety of biomolecules. PMID:23891867

Detection of an enigmatic plethodontid Salamander using Environmental DNA

USGS Publications Warehouse

Pierson, Todd W.; Mckee, Anna; Spear, Stephen F.; Maerz, John C.; Camp, Carlos D.; Glenn, Travis C.

2016-01-01

The isolation and identification of environmental DNA (eDNA) offers a non-invasive and efficient method for the detection of rare and secretive aquatic wildlife, and it is being widely integrated into inventory and monitoring efforts. The Patch-Nosed Salamander (Urspelerpes brucei) is a tiny, recently discovered species of plethodontid salamander known only from headwater streams in a small region of Georgia and South Carolina. Here, we present results of a quantitative PCR-based eDNA assay capable of detecting Urspelerpes in more than 75% of 33 samples from five confirmed streams. We deployed the method at 31 additional streams and located three previously undocumented populations of Urspelerpes. We compare the results of our eDNA assay with our attempt to use aquatic leaf litterbags for the rapid detection of Urspelerpes and demonstrate the relative efficacy of the eDNA assay. We suggest that eDNA offers great potential for use in detecting other aquatic and semi-aquatic plethodontid salamanders.

Quantum dot-loaded monofunctionalized DNA icosahedra for single-particle tracking of endocytic pathways.

PubMed

Bhatia, Dhiraj; Arumugam, Senthil; Nasilowski, Michel; Joshi, Himanshu; Wunder, Christian; Chambon, Valérie; Prakash, Ved; Grazon, Chloé; Nadal, Brice; Maiti, Prabal K; Johannes, Ludger; Dubertret, Benoit; Krishnan, Yamuna

2016-12-01

Functionalization of quantum dots (QDs) with a single biomolecular tag using traditional approaches in bulk solution has met with limited success. DNA polyhedra consist of an internal void bounded by a well-defined three-dimensional structured surface. The void can house cargo and the surface can be functionalized with stoichiometric and spatial precision. Here, we show that monofunctionalized QDs can be realized by encapsulating QDs inside DNA icosahedra and functionalizing the DNA shell with an endocytic ligand. We deployed the DNA-encapsulated QDs for real-time imaging of three different endocytic ligands-folic acid, galectin-3 (Gal3) and the Shiga toxin B-subunit (STxB). Single-particle tracking of Gal3- or STxB-functionalized QD-loaded DNA icosahedra allows us to monitor compartmental dynamics along endocytic pathways. These DNA-encapsulated QDs, which bear a unique stoichiometry of endocytic ligands, represent a new class of molecular probes for quantitative imaging of endocytic receptor dynamics.

Genetic fallout in biocultural landscapes: molecular imperialism and the cultural politics of (not) seeing transgenes in Mexico.

PubMed

Christophe Bonneuil; Foyer, Jean; Wynne, Brian

2014-12-01

This article explores the trajectory of the global controversy over the introgression (or not) of transgenes from genetically modified maize into Mexican indigenous maize landraces. While a plurality of knowledge-making processes were deployed to render transgenes visible or invisible, we analyze how a particular in vitro based DNA-centered knowledge came to marginalize other forms of knowledge, thus obscuring other bio-cultural dimensions key to the understanding of gene flow and maize diversity. We show that dominant molecular norms of proof and standards of detection, which co-developed with the world of industrial monocropping and gene patenting, discarded and externalized non-compliant actors (i.e. complex maize genomes, human dimensions of gene flow). Operating in the name of high science, they hence obscured the complex biological and cultural processes that maintain crop diversity and enacted a cultural-political domination over the world of Mexican landraces and indigenous communities.

Airport Visibility Measuring Systems Elements of Deployment Cost Analysis

DOT National Transportation Integrated Search

1976-09-01

This report analyzes the deployment cost for different visibility measuring systems necessary to satisfy CAT I, II, and II operations. The analysis is based on airport operational requirements and data for commercially available visibility measuring ...

An analysis of the factors influencing ITS technology adoption and deployment.

DOT National Transportation Integrated Search

2011-11-11

This study analyzes the factors influencing the adoption of Intelligent Transportation Systems (ITS) technologies in the U.S. amongst state and local transportation agencies. Using data from the ITS Deployment Tracking survey, insight is provided on ...

A highly optimized grid deployment: the metagenomic analysis example.

PubMed

Aparicio, Gabriel; Blanquer, Ignacio; Hernández, Vicente

2008-01-01

Computational resources and computationally expensive processes are two topics that are not growing at the same ratio. The availability of large amounts of computing resources in Grid infrastructures does not mean that efficiency is not an important issue. It is necessary to analyze the whole process to improve partitioning and submission schemas, especially in the most critical experiments. This is the case of metagenomic analysis, and this text shows the work done in order to optimize a Grid deployment, which has led to a reduction of the response time and the failure rates. Metagenomic studies aim at processing samples of multiple specimens to extract the genes and proteins that belong to the different species. In many cases, the sequencing of the DNA of many microorganisms is hindered by the impossibility of growing significant samples of isolated specimens. Many bacteria cannot survive alone, and require the interaction with other organisms. In such cases, the information of the DNA available belongs to different kinds of organisms. One important stage in Metagenomic analysis consists on the extraction of fragments followed by the comparison and analysis of their function stage. By the comparison to existing chains, whose function is well known, fragments can be classified. This process is computationally intensive and requires of several iterations of alignment and phylogeny classification steps. Source samples reach several millions of sequences, which could reach up to thousands of nucleotides each. These sequences are compared to a selected part of the "Non-redundant" database which only implies the information from eukaryotic species. From this first analysis, a refining process is performed and alignment analysis is restarted from the results. This process implies several CPU years. The article describes and analyzes the difficulties to fragment, automate and check the above operations in current Grid production environments. This environment has been tuned-up from an experimental study which has tested the most efficient and reliable resources, the optimal job size, and the data transference and database reindexation overhead. The environment should re-submit faulty jobs, detect endless tasks and ensure that the results are correctly retrieved and workflow synchronised. The paper will give an outline on the structure of the system, and the preparation steps performed to deal with this experiment.

Preliminary Analysis of Delta-V Requirements for a Lunar CubeSat Impactor with Deployment Altitude Variations

NASA Astrophysics Data System (ADS)

Song, Young-Joo; Ho, Jin; Kim, Bang-Yeop

2015-09-01

Characteristics of delta-V requirements for deploying an impactor from a mother-ship at different orbital altitudes are analyzed in order to prepare for a future lunar CubeSat impactor mission. A mother-ship is assumed to be orbiting the moon with a circular orbit at a 90 deg inclination and having 50, 100, 150, 200 km altitudes. Critical design parameters that are directly related to the success of the impactor mission are also analyzed including deploy directions, CubeSat flight time, impact velocity, and associated impact angles. Based on derived delta-V requirements, required thruster burn time and fuel mass are analyzed by adapting four different miniaturized commercial onboard thrusters currently developed for CubeSat applications. As a result, CubeSat impact trajectories as well as thruster burn characteristics deployed at different orbital altitudes are found to satisfy the mission objectives. It is concluded that thrust burn time should considered as the more critical design parameter than the required fuel mass when deducing the onboard propulsion system requirements. Results provided through this work will be helpful in further detailed system definition and design activities for future lunar missions with a CubeSat-based payload.

DNA-programmable multiplexing for scalable, renewable redox protein bio-nanoelectronics.

PubMed

Withey, Gary D; Kim, Jin Ho; Xu, Jimmy

2008-11-01

A universal, site-addressable DNA linking strategy is deployed for the programmable assembly of multifunctional, long-lasting redox protein nanoelectronic devices. This addressable linker, the first incorporated into a redox enzyme-nanoelectronic system, promotes versatility and renewability by allowing the reconfiguration and replacement of enzymes at will. The linker is transferable to all redox proteins due to the simple conjugation chemistry involved. The efficacy of this linking strategy is assessed using two model enzymes, glucose oxidase (GOx) and alcohol dehydrogenase (ADH), self-assembled onto separate nanoelectrode regions comprised of a highly ordered carbon nanotube (CNT) array. The sequence-specificity of DNA hybridization provides the means of encoding spatial address to the self-assembling process that conjugates enzymes tagged with single-stranded DNA (ssDNA) to the tips of designated CNTs functionalized with the complementary strands. In this study, we demonstrate the feasibility of multiplexed, scalable, reconfigurable and renewable transduction of redox protein signals by virtue of DNA addressing.

An Aromatic Sensor with Aversion to Damaged Strands Confers Versatility to DNA Repair

PubMed Central

Maillard, Olivier; Solyom, Szilvia; Naegeli, Hanspeter

2007-01-01

It was not known how xeroderma pigmentosum group C (XPC) protein, the primary initiator of global nucleotide excision repair, achieves its outstanding substrate versatility. Here, we analyzed the molecular pathology of a unique Trp690Ser substitution, which is the only reported missense mutation in xeroderma patients mapping to the evolutionary conserved region of XPC protein. The function of this critical residue and neighboring conserved aromatics was tested by site-directed mutagenesis followed by screening for excision activity and DNA binding. This comparison demonstrated that Trp690 and Phe733 drive the preferential recruitment of XPC protein to repair substrates by mediating an exquisite affinity for single-stranded sites. Such a dual deployment of aromatic side chains is the distinctive feature of functional oligonucleotide/oligosaccharide-binding folds and, indeed, sequence homologies with replication protein A and breast cancer susceptibility 2 protein indicate that XPC displays a monomeric variant of this recurrent interaction motif. An aversion to associate with damaged oligonucleotides implies that XPC protein avoids direct contacts with base adducts. These results reveal for the first time, to our knowledge, an entirely inverted mechanism of substrate recognition that relies on the detection of single-stranded configurations in the undamaged complementary sequence of the double helix. PMID:17355181

Histological Diagnoses of Military Personnel Undergoing Lung Biopsy After Deployment to Southwest Asia.

PubMed

Madar, Cristian S; Lewin-Smith, Michael R; Franks, Teri J; Harley, Russell A; Klaric, John S; Morris, Michael J

2017-08-01

The current understanding of associations between lung disease and military deployment to Southwest Asia, including Iraq and Afghanistan, is both controversial and limited. We sought to clarify the relation between military deployment and biopsy-proven lung disease. Retrospective data were analyzed for military personnel with non-neoplastic lung biopsies evaluated at the Armed Forces Institute of Pathology or Joint Pathology Center (January 2005 to December 2012). Of 391 subjects, 137 (35.0%) had deployed to Southwest Asia prior to biopsy. Compared to non-deployed subjects, those deployed were younger (median age 37 vs. 51 years) with higher representation of African Americans (30.0 vs. 16.9%). Deployed patients were more likely diagnosed with non-necrotizing granulomas (OR 2.4). Non-deployed subjects had higher frequency of idiopathic interstitial pneumonias, particularly organizing pneumonia. Prevalence of small airways diseases including constrictive bronchiolitis was low. This study provides a broader understanding of diversity of biopsy-proven non-neoplastic lung disease as it relates to military deployment to Southwest Asia and importantly did not show an increased prevalence of small airway disease to include constrictive bronchiolitis.

Shuttle performance enhancements using an OMS payload bay kit

NASA Technical Reports Server (NTRS)

Templin, Kevin C.; Mallini, Charles J.

1991-01-01

The study focuses on the use of an orbital maneuvering system (OMS) payload bay kit (PBK) designed to utilize OMS tanks identical to those currently employed in the Orbiter OMS pods. Emphasis is placed on payload deployment capability and payload servicing/reboost capability augmentation from the point of view of payload mass, maximum deployment altitudes, and initial retrieval and final deployment altitudes. The deployment, servicing, and reboost requirements of the Hubble Space Telescope and Advanced X-ray and Astrophysics Facility are analyzed in order to show the benefits an OMS PBK can provide for these missions. It is shown that OMS PBKs can provide the required capability enhancement necessary to support deployment, reboost, and servicing of payloads requiring altitudes greater than 325 nautical miles.

Mendel Meets CSI: Forensic Genotyping as a Method to Teach Genetics & DNA Science

ERIC Educational Resources Information Center

Kurowski, Scotia; Reiss, Rebecca

2007-01-01

This article describes a forensic DNA science laboratory exercise for advanced high school and introductory college level biology courses. Students use a commercial genotyping kit and genetic analyzer or gene sequencer to analyze DNA recovered from a fictitious crime scene. DNA profiling and STR genotyping are outlined. DNA extraction, PCR, and…

Deployment and Adverse Pregnancy Outcomes: Primary Findings and Methodological Considerations.

PubMed

Katon, Jodie; Cypel, Yasmin; Raza, Mubashra; Zephyrin, Laurie; Reiber, Gayle; Yano, Elizabeth M; Barth, Shannon; Schneiderman, Aaron

2017-02-01

Objective To characterize the pregnancy outcomes of women Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) Veterans including prevalence of preterm delivery, low birth weight, and macrosomia, and to highlight methodological limitations that can impact findings. Methods A retrospective cohort study was conducted starting in 2014 analyzing data from the 2009 to 2011 National Health Study for a New Generation of US Veterans, which sampled Veterans deployed and not deployed to OIF/OEF. All pregnancies resulting in a live birth were included, and categorized as occurring among non-deployers, before deployment, during deployment, or after deployment. Outcomes included preterm birth, low birth weight, and macrosomia. The association of deployment with selected outcomes was estimated using separate general estimating equations to account for lack of outcome independence among women contributing multiple pregnancies. Adjustment variables included maternal age at outcome, and race/ethnicity. Results There were 2276 live births (191 preterm births, 153 low birth weight infants, and 272 macrosomic infants). Compared with pregnancies before deployment, pregnancies among non-deployers and those after deployment appeared to have greater risk of preterm birth [non-deployers: odds ratio (OR) = 2.16, 95 % confidence interval (CI) 1.25, 3.72; after deployment: OR = 1.90, 95 % CI 0.90, 4.02]. A similar pattern was observed for low birth weight. No association of deployment with macrosomia was detected. Discussion Compared with non-deployers, those who eventually deploy appear to have better pregnancy outcomes prior to deployment, but this advantage is no longer apparent after deployment. Non-deployers may not be an appropriate reference group to study the putative health impacts of deployment on pregnancy outcomes.

Spatiotemporal variations in metal accumulation, RNA/DNA ratio and energy reserve in Perna viridis transplanted along a marine pollution gradient in Hong Kong.

PubMed

Yeung, Jamius W Y; Zhou, Guang-Jie; Leung, Kenneth M Y

2017-11-30

We examined spatiotemporal variations of metal levels and three growth related biomarkers, i.e., RNA/DNA ratio (RD), total energy reserve (Et) and condition index (CI), in green-lipped mussels Perna viridis transplanted into five locations along a pollution gradient in the marine environment of Hong Kong over 120days of deployment. There were significant differences in metal levels and biomarker responses among the five sites and six time points. Mussels in two clean sites displayed better CI and significantly lower levels of Ag, Cu, Pb and Zn in their tissues than the other sites. Temporal patterns of RD in P. viridis were found to be site-specific. Across all sites, Et decreased in P. viridis over the deployment period, though the rate of decrease varied significantly among the sites. Therefore, temporal variation of biomarkers should be taken to consideration in mussel-watch programs because such information can help discriminate pollution-induced change from natural variation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hinge specification for a square-faceted tetrahedral truss

NASA Technical Reports Server (NTRS)

Adams, L. R.

1984-01-01

A square-faceted tetrahedral truss is geometrically analyzed. Expressions are developed for single degree of freedom hinges which allow packaging of the structure into a configuration in which all members are parallel and closely packed in a square pattern. Deployment is sequential, thus providing control over the structure during deployment.

INVESTIGATION OF OPEN-PATH FTIR FOR FAST DEPLOYMENT EMERGENCY RESPONSE TO CHEMICAL THREATS AND ACCIDENTS.

EPA Science Inventory

We have performed a series of experiments to determine the tradeoff in detection sensitivity for implementing design features for an Open-Path Fourier Transform Infrared (OP-FTIR) chemical analyzer that would be quick to deploy under emergency response conditions. The fast-deplo...

Direct optical mapping of transcription factor binding sites on field-stretched λ-DNA in nanofluidic devices

PubMed Central

Sriram, K. K.; Yeh, Jia-Wei; Lin, Yii-Lih; Chang, Yi-Ren; Chou, Chia-Fu

2014-01-01

Mapping transcription factor (TF) binding sites along a DNA backbone is crucial in understanding the regulatory circuits that control cellular processes. Here, we deployed a method adopting bioconjugation, nanofluidic confinement and fluorescence single molecule imaging for direct mapping of TF (RNA polymerase) binding sites on field-stretched single DNA molecules. Using this method, we have mapped out five of the TF binding sites of E. coli RNA polymerase to bacteriophage λ-DNA, where two promoter sites and three pseudo-promoter sites are identified with the corresponding binding frequency of 45% and 30%, respectively. Our method is quick, robust and capable of resolving protein-binding locations with high accuracy (∼ 300 bp), making our system a complementary platform to the methods currently practiced. It is advantageous in parallel analysis and less prone to false positive results over other single molecule mapping techniques such as optical tweezers, atomic force microscopy and molecular combing, and could potentially be extended to general mapping of protein–DNA interaction sites. PMID:24753422

Six pitfalls in firewall deployment

NASA Astrophysics Data System (ADS)

Wilner, Bruce

1996-03-01

This note describes six key pitfalls in the deployment of popular commercial firewalls. The term `deployment' is intended to include the architecture of the firewall software itself, the integration of the firewall with the operating system platform, and the interconnection of the complete hardware/software combination within its target environment. After reviewing the evolution of Internet firewalls against the backdrop of classical trusted systems development, specific flaws and oversights in the familiar commercial deployments are analyzed in some detail. While significantly costlier solutions are available that address some of these problems, the analysis is applicable to the overwhelming majority of firewalls in use at both commercial and Government installations.

Clinical Utility of Epstein-Barr Virus DNA Testing in the Treatment of Nasopharyngeal Carcinoma Patients.

PubMed

Kim, Kelly Y; Le, Quynh-Thu; Yom, Sue S; Ng, Raymond H W; Chan, K C Allen; Bratman, Scott V; Welch, John J; Divi, Rao L; Petryshyn, Raymond A; Conley, Barbara A

2017-08-01

Epstein-Barr virus (EBV) DNA analysis has been shown to be useful for early detection, prognostication, and monitoring of treatment response of nasopharyngeal carcinoma (NPC), and the recent literature provides growing evidence of the clinical utility of EBV DNA testing, particularly to inform treatment decisions for NPC patients. Despite the fact that NPC is a rare disease, the NRG Oncology cooperative group has successfully activated a phase 2/3 randomized clinical trial for NPC with international partners and in that process has discovered that the development of a harmonized EBV DNA test is absolutely critical for integration into clinical trials and for future deployment in clinical and central laboratories. In November 2015, the National Cancer Institute (NCI) convened a workshop of international experts in the treatment of NPC and EBV testing to provide a forum for discussing the state of EBV DNA testing and its clinical utility, and to stimulate consideration of future studies and clinical practice guidelines for EBV DNA. This review provides a summary of that discussion. Published by Elsevier Inc.

Utility of a Fluorescence Microscopy Imaging System for Analyzing the DNA Ploidy of Pathological Megakaryocytes Including 5q- Syndrome.

PubMed

Nakahara, Takako; Suemori, Shinichiro; Tsujioka, Takayuki; Kataoka, Mikio; Kataoka, Hiromi; Shibakura, Misako; Tohyama, Kaoru

2018-06-01

To investigate megakaryocyte (MK) DNA ploidy in various hematological diseases, fluorescence microscopy imaging system (FMI) can be used to analyze DNA ploidy with cell morphology at the single-cell level by using specialized image-processing software. Here we compared DNA ploidy obtained by FMI measured with that obtained flow cytometry (FCM). With FMI, we could evaluate the DNA ploidy in long-term preserved bone marrow smear samples after staining. We next analyzed the MK DNA ploidy in 42 bone marrow smear samples including 26 myeloid neoplasm cases, and we compared the DNA ploidy and platelet counts in the patients' peripheral blood; the production of platelets was significantly high compared to DNA ploidy in the myeloproliferative neoplasms group. The FMI method revealed that the patients with 5q- syndrome exhibited relatively low DNA ploidy despite high platelet counts, and this result suggested that increased DNA ploidy is not indispensable to abundant platelet production. The FMI method for DNA ploidy will be a useful tool to clarify the relationship between DNA ploidy and platelet production by MKs.

The LC Domain of hnRNPA2 Adopts Similar Conformations in Hydrogel Polymers, Liquid-like Droplets and Nuclei

PubMed Central

Xiang, Siheng; Kato, Masato; Wu, Leeju; Lin, Yi; Ding, Ming; Zhang, Yajie; Yu, Yonghao; McKnight, Steven L.

2016-01-01

SUMMARY Many DNA and RNA regulatory proteins contain polypeptide domains that are unstructured when analyzed in cell lysates. These domains are typified by an over-representation of a limited number of amino acids and have been termed prion-like, intrinsically disordered or low complexity (LC) domains. When incubated at high concentration, certain of these LC domains polymerize into labile, amyloid-like fibers. Here we report methods allowing the generation of a molecular footprint of the polymeric state of the LC domain of hnRNPA2. By deploying this footprinting technique to probe the structure of the native hnRNPA2 protein present in isolated nuclei, we offer evidence that its LC domain exists in a similar conformation as that described for recombinant polymers of the protein. These observations favor biologic utility to the polymerization of LC domains in the pathway of information transfer from gene to message to protein. PMID:26544936

Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool.

PubMed

Hoenen, Thomas; Groseth, Allison; Rosenke, Kyle; Fischer, Robert J; Hoenen, Andreas; Judson, Seth D; Martellaro, Cynthia; Falzarano, Darryl; Marzi, Andrea; Squires, R Burke; Wollenberg, Kurt R; de Wit, Emmie; Prescott, Joseph; Safronetz, David; van Doremalen, Neeltje; Bushmaker, Trenton; Feldmann, Friederike; McNally, Kristin; Bolay, Fatorma K; Fields, Barry; Sealy, Tara; Rayfield, Mark; Nichol, Stuart T; Zoon, Kathryn C; Massaquoi, Moses; Munster, Vincent J; Feldmann, Heinz

2016-02-01

Rapid sequencing of RNA/DNA from pathogen samples obtained during disease outbreaks provides critical scientific and public health information. However, challenges exist for exporting samples to laboratories or establishing conventional sequencers in remote outbreak regions. We successfully used a novel, pocket-sized nanopore sequencer at a field diagnostic laboratory in Liberia during the current Ebola virus outbreak.

Teaching the Toolkit: A Laboratory Series to Demonstrate the Evolutionary Conservation of Metazoan Cell Signaling Pathways

ERIC Educational Resources Information Center

LeClair, Elizabeth E.

2008-01-01

A major finding of comparative genomics and developmental genetics is that metazoans share certain conserved, embryonically deployed signaling pathways that instruct cells as to their ultimate fate. Because the DNA encoding these pathways predates the evolutionary split of most animal groups, it should in principle be possible to clone…

Characterization of field isolates of Magnaporthe oryzae with mating type, DNA fingerprinting, and pathogenicity assays

USDA-ARS?s Scientific Manuscript database

Due to the harmful nature of the rice blast fungus, Magnaporthe oryzae, it is beneficial to characterize field isolates to help aid in the deployment of resistance (R) genes in rice. In the present study, 190 field isolates of M. oryzae, collected from rice fields of Yunnan province in China, were a...

Vibration characteristics of a deployable controllable-geometry truss boom

NASA Technical Reports Server (NTRS)

Dorsey, J. T.

1983-01-01

An analytical study was made to evaluate changes in the fundamental frequency of a two dimensional cantilevered truss boom at various stages of deployment. The truss could be axially deployed or retracted and undergo a variety of controlled geometry changes by shortening or lengthening the telescoping diagonal members in each bay. Both untapered and tapered versions of the truss boom were modeled and analyzed by using the finite element method. Large reductions in fundamental frequency occurred for both the untapered and tapered trusses when they were uniformly retracted or maneuvered laterally from their fully deployed position. These frequency reductions can be minimized, however, if truss geometries are selected which maintain cantilever root stiffness during truss maneuvers.

Internal validation of the RapidHIT® ID system.

PubMed

Wiley, Rachel; Sage, Kelly; LaRue, Bobby; Budowle, Bruce

2017-11-01

Traditionally, forensic DNA analysis has required highly skilled forensic geneticists in a dedicated laboratory to generate short tandem repeat (STR) profiles. STR profiles are routinely used either to associate or exclude potential donors of forensic biological evidence. The typing of forensic reference samples has become more demanding, especially with the requirement in some jurisdictions to DNA profile arrestees. The Rapid DNA (RDNA) platform, the RapidHIT ® ID (IntegenX ® , Pleasanton, CA), is a fully automated system capable of processing reference samples in approximately 90min with minimal human intervention. Thus, the RapidHIT ID instrument can be deployed to non-laboratory environments (e.g., booking stations) and run by trained atypical personnel such as law enforcement. In order to implement the RapidHIT ID platform, validation studies are needed to define the performance and limitations of the system. Internal validation studies were undertaken with four early-production RapidHIT ID units. Reliable and concordant STR profiles were obtained from reference buccal swabs. Throughout the study, no contamination was observed. The overall first-pass success rate with an "expert-like system" was 72%, which is comparable to another current RDNA platform commercially available. The system's second-pass success rate (involving manual interpretation on first-pass inconclusive results) increased to 90%. Inhibitors (i.e., coffee, smoking tobacco, and chewing tobacco) did not appear to affect typing by the instrument system; however, substrate (i.e., swab type) did impact typing success. Additionally, one desirable feature not available with other Rapid systems is that in the event of a system failed run, a swab can be recovered and subsequently re-analyzed in a new sample cartridge. Therefore, rarely should additional sampling or swab consumption be necessary. The RapidHIT ID system is a robust and reliable tool capable of generating complete STR profiles within the forensic DNA typing laboratory or with proper training in decentralized environments by non-laboratory personnel. Copyright © 2017 Elsevier B.V. All rights reserved.

Designing and Deploying Programming Courses: Strategies, Tools, Difficulties and Pedagogy

ERIC Educational Resources Information Center

Xinogalos, Stelios

2016-01-01

Designing and deploying programming courses is undoubtedly a challenging task. In this paper, an attempt to analyze important aspects of a sequence of two courses on imperative-procedural and object-oriented programming in a non-CS majors Department is made. This analysis is based on a questionnaire filled in by fifty students in a voluntary…

Joint Global War on Terror (GWOT) Vascular Injury Study 2

DTIC Science & Technology

2017-02-01

trauma, vascular injury management, survey , OIF, OEF, Iraq, Afghanistan, Iraq, deployment, training 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF...injury, extremity, vascular injury, vascular trauma, vascular injury management, survey , OIF, OEF, Iraq, Afghanistan, Iraq, deployment, training...Phase II will be analyzed to provide comprehensive descriptive information on the patient cohort pertaining to demographics, injury information and

MD PHEV/EV ARRA Project Data Collection and Reporting (Presentation)

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

Walkowicz, K.; Ramroth, L.; Duran, A.

2012-01-01

This presentation describes a National Renewable Energy Laboratory project to collect and analyze commercial fleet deployment data from medium-duty plug-in hybrid electric and all-electric vehicles that were deployed using funds from the American Recovery and Reinvestment Act. This work supports the Department of Energy's Vehicle Technologies Program and its Advanced Vehicle Testing Activity.

Coverage-guaranteed sensor node deployment strategies for wireless sensor networks.

PubMed

Fan, Gaojuan; Wang, Ruchuan; Huang, Haiping; Sun, Lijuan; Sha, Chao

2010-01-01

Deployment quality and cost are two conflicting aspects in wireless sensor networks. Random deployment, where the monitored field is covered by randomly and uniformly deployed sensor nodes, is an appropriate approach for large-scale network applications. However, their successful applications depend considerably on the deployment quality that uses the minimum number of sensors to achieve a desired coverage. Currently, the number of sensors required to meet the desired coverage is based on asymptotic analysis, which cannot meet deployment quality due to coverage overestimation in real applications. In this paper, we first investigate the coverage overestimation and address the challenge of designing coverage-guaranteed deployment strategies. To overcome this problem, we propose two deployment strategies, namely, the Expected-area Coverage Deployment (ECD) and BOundary Assistant Deployment (BOAD). The deployment quality of the two strategies is analyzed mathematically. Under the analysis, a lower bound on the number of deployed sensor nodes is given to satisfy the desired deployment quality. We justify the correctness of our analysis through rigorous proof, and validate the effectiveness of the two strategies through extensive simulation experiments. The simulation results show that both strategies alleviate the coverage overestimation significantly. In addition, we also evaluate two proposed strategies in the context of target detection application. The comparison results demonstrate that if the target appears at the boundary of monitored region in a given random deployment, the average intrusion distance of BOAD is considerably shorter than that of ECD with the same desired deployment quality. In contrast, ECD has better performance in terms of the average intrusion distance when the invasion of intruder is from the inside of monitored region.

The role of stress sensitization in progression of posttraumatic distress following deployment.

PubMed

Smid, Geert E; Kleber, Rolf J; Rademaker, Arthur R; van Zuiden, Mirjam; Vermetten, Eric

2013-11-01

Military personnel exposed to combat are at risk for experiencing post-traumatic distress that can progress over time following deployment. We hypothesized that progression of post-traumatic distress may be related to enhanced susceptibility to post-deployment stressors. This study aimed at examining the concept of stress sensitization prospectively in a sample of Dutch military personnel deployed in support of the conflicts in Afghanistan. In a cohort of soldiers (N = 814), symptoms of post-traumatic stress disorder (PTSD) were assessed before deployment as well as 2, 7, 14, and 26 months (N = 433; 53 %) after their return. Data were analyzed using latent growth modeling. Using multiple group analysis, we examined whether high combat stress exposure during deployment moderated the relation between post-deployment stressors and linear change in post-traumatic distress after deployment. A higher baseline level of post-traumatic distress was associated with more early life stressors (standardized regression coefficient = 0.30, p < 0.001). In addition, a stronger increase in posttraumatic distress during deployment was associated with more deployment stressors (standardized coefficient = 0.21, p < 0.001). A steeper linear increase in posttraumatic distress post-deployment (from 2 to 26 months) was predicted by more post-deployment stressors (standardized coefficient = 0.29, p < 0.001) in high combat stress exposed soldiers, but not in a less combat stress exposed group. The group difference in the predictive effect of post-deployment stressors on progression of post-traumatic distress was significant (χ²(1) = 7.85, p = 0.005). Progression of post-traumatic distress following combat exposure may be related to sensitization to the effects of post-deployment stressors during the first year following return from deployment.

Floating Offshore Wind in Hawaii: Potential for Jobs and Economic Impacts from Three Future Scenarios

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

Jimenez, Tony; Keyser, David; Tegen, Suzanne

Construction of the first offshore wind power plant in the United States began in 2015, off the coast of Rhode Island, using fixed platform structures that are appropriate for shallow seafloors, like those located off the East Coast and mid-Atlantic. However, floating platforms, which have yet to be deployed commercially, will likely need to be anchored to the deeper seafloor if deployed in Hawaiian waters. To analyze the employment and economic potential for floating offshore wind off Hawaii's coasts, the Bureau of Ocean Energy Management commissioned the National Renewable Energy Laboratory (NREL) to analyze two hypothetical deployment scenarios for Hawaii:more » 400 MW of offshore wind by 2050 and 800 MW of offshore wind by 2050. The results of this analysis can be used to better understand the general scale of economic opportunities that could result from offshore wind development.« less

Polycyclic Aromatic Hydrocarbons and Polychlorinated Dibenzo-p-Dioxins/Dibenzofurans in Microliter Samples of Human Serum as Exposure Indicators

PubMed Central

Xia, Xiaoyan; Carroll-Haddad, Alesia; Brown, Nicole; Utell, Mark J.; Mallon, Timothy; Hopke, Philip K.

2016-01-01

Objective The objectives were: 1) measure polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) in 100 μL of human serum and 2) assess PAH and PCDD/PCDF as markers of burn pit exposures during military deployments. Methods PAHs and PCDDs/PCDFs were analyzed in 100μL serum samples collected pre- and post-deployment from 200 persons deployed to Iraq or Afghanistan (CASE); 200 persons not deployed (CONTROL) with GC/MS. Results Naphthalene was found in ~83% of the samples and was statistically different between post-deployment CASE personnel and pre-deployment. 1,2,3,4,6,7,8-Heptachlorodibenzo-p-dioxin, Octachlorodibenzo-p-dioxin, 1,2,3,7,8,9-Hexachlorodibenzofuran, and 1,2,3,4,6,7,8-Heptachlorodibenzofuran were found in ~38% of samples. Concentrations were significantly different between CASE and CONTROL and between pre- and post-deployment samples. Conclusions PAH and PCDD/PCDF in serum can serve as exposure markers and measurements in small volumes is feasible for quantifying exposure to burn pits. PMID:27501107

Novel deployable morphing wing based on SMP composite

NASA Astrophysics Data System (ADS)

Yu, Kai; Sun, Shouhua; Liu, Liwu; Zhang, Zhen; Liu, Yanju; Leng, Jinsong

2009-07-01

In this paper, a novel kind of deployable morphing wing base on shape memory polymer (SMP) composite is designed and tested. While the deployment of the morphing wing still relies on the mechanisms to ensure the recovery force and the stability performance, the deploying process tends to be more steady and accurate by the application of SMP composite, which overcomes the inherent drawbacks of the traditional one, such as harmful impact to the flight balance, less accuracy during the deployment and complex mechanical masses. On the other hand, SMP composite is also designed as the wing's filler. During its shape recovery process, SMP composite stuffed in the wing helps to form an aerofoil for the wing and withstand the aerodynamic loads, leading to the compressed aerofoil recovering its original shape. To demonstrate the feasibility and the controllability of the designed deployable morphing wing, primary tests are also conducted, including the deploying speed of the morphing wing and SMP filler as the main testing aspects. Finally, Wing's deformation under the air loads is also analyzed by using the finite element method to validate the flight stability.

Child maltreatment among U.S. Air Force parents deployed in support of Operation Iraqi Freedom/Operation Enduring Freedom.

PubMed

Rabenhorst, Mandy M; McCarthy, Randy J; Thomsen, Cynthia J; Milner, Joel S; Travis, Wendy J; Colasanti, Marie P

2015-02-01

This study examined child maltreatment perpetration among 99,697 active-duty U.S. Air Force parents who completed a combat deployment. Using the deploying parent as the unit of analysis, we analyzed whether child maltreatment rates increased postdeployement relative to predeployment. These analyses extend previous research that used aggregate data and extend our previous work that used data from the same period but used the victim as the unit of analysis and included only deploying parents who engaged in child maltreatment. In this study, 2% (n = 1,746) of deploying parents perpetrated child maltreatment during the study period. Although no overall differences were found in child maltreatment rates postdeployment compared to predeployment, several maltreatment-related characteristics qualified this finding. Rates for emotional abuse and mild maltreatment were lower following deployment, whereas child maltreatment rates for severe maltreatment were higher following deployment. The finding that rates of severe child maltreatment, including incidents involving alcohol use, were higher postdeployment suggests a need for additional support services for parents following their return from combat deployment, with a focus on returning parents who have an alcohol use problem. © The Author(s) 2014.

Identifying DNA methylation in a nanochannel

NASA Astrophysics Data System (ADS)

Sun, Xiaoyin; Yasui, Takao; Yanagida, Takeshi; Kaji, Noritada; Rahong, Sakon; Kanai, Masaki; Nagashima, Kazuki; Kawai, Tomoji; Baba, Yoshinobu

2016-01-01

DNA methylation is a stable epigenetic modification, which is well known to be involved in gene expression regulation. In general, however, analyzing DNA methylation requires rather time consuming processes (24-96 h) via DNA replication and protein modification. Here we demonstrate a methodology to analyze DNA methylation at a single DNA molecule level without any protein modifications by measuring the contracted length and relaxation time of DNA within a nanochannel. Our methodology is based on the fact that methylation makes DNA molecules stiffer, resulting in a longer contracted length and a longer relaxation time (a slower contraction rate). The present methodology offers a promising way to identify DNA methylation without any protein modification at a single DNA molecule level within 2 h.

Mechanisms of Günther Tulip filter tilting during transfemoral placement.

PubMed

Matsui, Y; Horikawa, M; Ohta, K; Jahangiri Noudeh, Y; Kaufman, J A; Farsad, K

The purpose of this study was to characterize the mechanisms of Günther Tulip filter (GTF) tilting during transfemoral placement in an experimental model with further validation in a clinical series. In an experimental study, 120 GTF placements in an inferior vena cava (IVC) model were performed using 6 configurations of pre-deployment filter position. The angle between the pre-deployment filter axis and IVC axis, and the proximity of the constrained filter legs to IVC wall prior to deployment were evaluated. The association of those pre-deployment factors with post-deployment filter tilting was analyzed. The association noted in the experimental study was then evaluated in a retrospective clinical series of 21 patients. In the experimental study, there was a significant association between the pre-deployment angle and post-deployment filter tilting (P<0.0001). With a low pre-deployment angle (≤5°), a significant association was noted between filter tilting and the proximity of the constrained filter legs to the far IVC wall (P=0.001). In a retrospective clinical study, a significant association between the pre-deployment angle and post-deployment filter tilting was also noted with a linear regression model (P=0.026). Significant association of the pre-deployment angle with post-deployment GTF tilting was shown in both the experimental and clinical studies. The experimental study also showed that proximity of filter legs is relevant when pre-deployment angle is small. Addressing these factors may result in a lower incidence of filter tilting. Copyright © 2017 Editions françaises de radiologie. Published by Elsevier Masson SAS. All rights reserved.

Risk and protective factors for suicidal ideation and suicide attempts among deployed Danish soldiers from 1990 to 2009.

PubMed

Ejdesgaard, Bo Andersen; Zøllner, Lilian; Jensen, Børge Frank; Jørgensen, Hans-Ole; Kähler, Henrik

2015-01-01

The study was undertaken to identify risk and protective factors for suicidal ideation and suicide attempts among deployed Danish soldiers. Research on suicide among Danish veterans has only been conducted to a limited degree. The method applied was a questionnaire survey administered to a population of 1,264 Danish soldiers deployed from 1990 to 2009. The data were analyzed using backward logistic regression modeling in SAS 9.2. In the logistic regression analysis, the following were significant risk factors for suicidal ideation: drug abuse, a poor financial situation before deployment, a heavy workload and/or repatriation during deployment, and attending a poor athletic and recreation program after deployment. Significant protective factors against suicidal ideation were support from friends at home during deployment and appreciation by the general population after deployment. Significant risk factors for suicide attempts were an unhappy childhood and pointless tasks during deployment. No significant protective factors against suicide attempts were identified. On the basis of the results presented in this study, intervention against suicidal behavior would benefit from screening for certain childhood issues, drug abuse, and poor financial situation before deployment. During deployment, measures should be taken to minimize the amount of meaningless tasks and heavy workloads. At the same time, efficient ways of communicating with home should be ensured. After deployment, good athletic and recreation programs should be warranted for all military personnel-including repatriated soldiers. Finally, priority should be given to ensure public appreciation of what deployed soldiers accomplish. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

Swabbing firearms for handler's DNA.

PubMed

Richert, Nicholas J

2011-07-01

Obtaining quality DNA profiles from firearms can be instrumental in assisting criminal investigations. Typically, swabbings of firearms for handler's DNA are conducted on specific regions of the firearm prior to submission to the laboratory for analysis. This review examines and compares 32 cases whose gun swabbings were either analyzed individually according to the specific region which was swabbed, or analyzed collectively by combining the swabbings from all the individual areas. Those firearms whose swabs were analyzed separately exhibited lower DNA yields and consequently fewer loci exhibiting genotypes. Those cases whose swabs were analyzed collectively exhibited higher DNA yields and consequently greater numbers of loci exhibiting genotypes. These findings demonstrate that collective swabbings result in more complete profiles and lead to the recommendation that a firearm be swabbed in its entirety using no more than two swabs. © 2011 American Academy of Forensic Sciences.

Design and deploying study of a new petal-type deployable solid surface antenna

NASA Astrophysics Data System (ADS)

Huang, He; Guan, Fu-Ling; Pan, Liang-Lai; Xu, Yan

2018-07-01

Deployable solid surface reflector is still one of the most important ways to fulfill the ultra-high-accuracy and ultra-large-aperture reflector antennas. However the drawback of integrate stiffness is still a main problem for solid surface reflectors in the former research. To figure out this problem, a New Petal-type Deployable Solid Surface Antenna (NPDSSA) is developed in this study. A kind of drag springs are applied as linkages with adjacent petals to improve the integrate rigidity. The structural design is introduced and the geometric parameters are analyzed to find their effects on the rotation and package capacities. The software simulations and laboratory model tests are conducted to verify the deploying process of NPDSSA. Two models are employed to study the property of linkage butts and drag springs. It is indicated that model NPDSSA with the application of linkage butts and drag springs has better integrality and stability during the deploying. Finally it is concluded that NPDSSA is feasible for space applications.

Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool

PubMed Central

Groseth, Allison; Rosenke, Kyle; Fischer, Robert J.; Hoenen, Andreas; Judson, Seth D.; Martellaro, Cynthia; Falzarano, Darryl; Marzi, Andrea; Squires, R. Burke; Wollenberg, Kurt R.; de Wit, Emmie; Prescott, Joseph; Safronetz, David; van Doremalen, Neeltje; Bushmaker, Trenton; Feldmann, Friederike; McNally, Kristin; Bolay, Fatorma K.; Fields, Barry; Sealy, Tara; Rayfield, Mark; Nichol, Stuart T.; Zoon, Kathryn C.; Massaquoi, Moses; Munster, Vincent J.; Feldmann, Heinz

2016-01-01

Rapid sequencing of RNA/DNA from pathogen samples obtained during disease outbreaks provides critical scientific and public health information. However, challenges exist for exporting samples to laboratories or establishing conventional sequencers in remote outbreak regions. We successfully used a novel, pocket-sized nanopore sequencer at a field diagnostic laboratory in Liberia during the current Ebola virus outbreak. PMID:26812583

SKA2 Methylation is Involved in Cortisol Stress Reactivity and Predicts the Development of Post-Traumatic Stress Disorder (PTSD) After Military Deployment

PubMed Central

Boks, Marco P; Rutten, Bart P F; Geuze, Elbert; Houtepen, Lotte C; Vermetten, Eric; Kaminsky, Zachary; Vinkers, Christiaan H

2016-01-01

Genomic variation in the SKA2 gene has recently been identified as a promising suicide biomarker. In light of its role in glucocorticoid receptor transactivation, we investigated whether SKA2 DNA methylation influences cortisol stress reactivity and is involved in the development of post-traumatic stress disorder (PTSD). Increased SKA2 methylation was significantly associated with lower cortisol stress reactivity in 85 healthy individuals exposed to the Trier Social Stress Test (B=−173.40, t=−2.324, p-value=0.023). Next, we observed that longitudinal decreases in SKA2 methylation after deployment were associated with the emergence of post-deployment PTSD symptoms in a Dutch military cohort (N=93; B=−0.054, t=−3.706, p-value=3.66 × 10−4). In contrast, exposure to traumatic stress during deployment by itself resulted in longitudinal increases in SKA2 methylation (B=0.037, t=4.173, p-value=6.98 × 10−5). Using pre-deployment SKA2 methylation levels and childhood trauma exposure, we found that the previously published suicide prediction rule significantly predicted post-deployment PTSD symptoms (AUC=0.66, 95% CI: 0.53–0.79) with an optimal sensitivity of 0.81 and specificity of 0.91. Permutation analysis using random methylation loci supported these findings. Together, these data establish the importance of SKA2 for cortisol stress responsivity and the development of PTSD and provide further evidence that SKA2 is a promising biomarker for stress-related disorders including PTSD. PMID:26361058

SKA2 Methylation is Involved in Cortisol Stress Reactivity and Predicts the Development of Post-Traumatic Stress Disorder (PTSD) After Military Deployment.

PubMed

Boks, Marco P; Rutten, Bart P F; Geuze, Elbert; Houtepen, Lotte C; Vermetten, Eric; Kaminsky, Zachary; Vinkers, Christiaan H

2016-04-01

Genomic variation in the SKA2 gene has recently been identified as a promising suicide biomarker. In light of its role in glucocorticoid receptor transactivation, we investigated whether SKA2 DNA methylation influences cortisol stress reactivity and is involved in the development of post-traumatic stress disorder (PTSD). Increased SKA2 methylation was significantly associated with lower cortisol stress reactivity in 85 healthy individuals exposed to the Trier Social Stress Test (B=-173.40, t=-2.324, p-value=0.023). Next, we observed that longitudinal decreases in SKA2 methylation after deployment were associated with the emergence of post-deployment PTSD symptoms in a Dutch military cohort (N=93; B=-0.054, t=-3.706, p-value=3.66 × 10(-4)). In contrast, exposure to traumatic stress during deployment by itself resulted in longitudinal increases in SKA2 methylation (B=0.037, t=4.173, p-value=6.98 × 10(-5)). Using pre-deployment SKA2 methylation levels and childhood trauma exposure, we found that the previously published suicide prediction rule significantly predicted post-deployment PTSD symptoms (AUC=0.66, 95% CI: 0.53-0.79) with an optimal sensitivity of 0.81 and specificity of 0.91. Permutation analysis using random methylation loci supported these findings. Together, these data establish the importance of SKA2 for cortisol stress responsivity and the development of PTSD and provide further evidence that SKA2 is a promising biomarker for stress-related disorders including PTSD.

Floating Offshore Wind in Oregon: Potential for Jobs and Economic Impacts from Two Future Scenarios

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

Jimenez, Tony; Keyser, David; Tegen, Suzanne

Construction of the first offshore wind power plant in the United States began in 2015, off the coast of Rhode Island, using fixed platform structures that are appropriate for shallow seafloors, like those located off of the East Coast and mid-Atlantic. However, floating platforms, which have yet to be deployed commercially, will likely need to anchor to the deeper seafloor if deployed off of the West Coast. To analyze the employment and economic potential for floating offshore wind along the West Coast, the Bureau of Ocean Energy Management (BOEM) commissioned the National Renewable Energy Laboratory (NREL) to analyze two hypothetical,more » large-scale deployment scenarios for Oregon: 5,500 megawatts (MW) of offshore wind deployment in Oregon by 2050 (Scenario A), and 2,900 MW of offshore wind by 2050 (Scenario B). These levels of deployment could power approximately 1,600,000 homes (Scenario A) or 870,000 homes (Scenario B). Offshore wind would contribute to economic development in Oregon in the near future, and more substantially in the long term, especially if equipment and labor are sourced from within the state. According to the analysis, over the 2020-2050 period, Oregon floating offshore wind facilities could support 65,000-97,000 job-years and add $6.8 billion-$9.9 billion to the state GDP (Scenario A).« less

Deployer Performance Results for the TSS-1 Mission

NASA Technical Reports Server (NTRS)

Marshall, Leland S.; Geiger, Ronald V.

1995-01-01

Performance of the Tethered Satellite System (TSS) Deployer during the STS-46 mission (July and August 1992) is analyzed in terms of hardware operation at the component and system level. Although only a limited deployment of the satellite was achieved (256 meters vs 20 kilometers planned), the mission served to verify the basic capability of the Deployer to release, control and retrieve a tethered satellite. - Deployer operational flexibility that was demonstrated during the flight is also addressed. Martin Marietta was the prime contractor for the development of the Deployer, under management of the NASA George C. Marshall Space Flight Center (MSFC). The satellite was provided by Alenia, Torino, Italy under contract to the Agencia Spaziale Italiana (ASI). Proper operation of the avionics components and the majority of mechanisms was observed during the flight. System operations driven by control laws for the deployment and retrieval of the satellite were also successful for the limited deployment distance. Anomalies included separation problems for one of the two umbilical connectors between the Deployer and satellite, tether jamming (at initial Satellite fly-away and at a deployment distance of 224 meters), and a mechanical interference which prevented tether deployment beyond 256 meters. The Deployer was used in several off-nominal conditions to respond to these anomalies, which ultimately enabled a successful satellite retrieval and preservation of hardware integrity for a future re-flight. The paper begins with an introduction defining the significance of the TSS-1 mission. The body of the paper is divided into four major sections: (1) Description of Deployer System and Components, (2) Deployer Components/Systems Demonstrating Successful Operation, (3) Hardware Anomalies and Operational Responses, and (4) Design Modifications for the TSS-1R Re-flight Mission. Conclusions from the TSS-1 mission, including lessons learned are presented at the end of the manuscript.

Polyvalent Proteins, a Pervasive Theme in the Intergenomic Biological Conflicts of Bacteriophages and Conjugative Elements

PubMed Central

Iyer, Lakshminarayan M.; Burroughs, A. Maxwell; Anand, Swadha; de Souza, Robson F.

2017-01-01

ABSTRACT Intense biological conflicts between prokaryotic genomes and their genomic parasites have resulted in an arms race in terms of the molecular “weaponry” deployed on both sides. Using a recursive computational approach, we uncovered a remarkable class of multidomain proteins with 2 to 15 domains in the same polypeptide deployed by viruses and plasmids in such conflicts. Domain architectures and genomic contexts indicate that they are part of a widespread conflict strategy involving proteins injected into the host cell along with parasite DNA during the earliest phase of infection. Their unique feature is the combination of domains with highly disparate biochemical activities in the same polypeptide; accordingly, we term them polyvalent proteins. Of the 131 domains in polyvalent proteins, a large fraction are enzymatic domains predicted to modify proteins, target nucleic acids, alter nucleotide signaling/metabolism, and attack peptidoglycan or cytoskeletal components. They further contain nucleic acid-binding domains, virion structural domains, and 40 novel uncharacterized domains. Analysis of their architectural network reveals both pervasive common themes and specialized strategies for conjugative elements and plasmids or (pro)phages. The themes include likely processing of multidomain polypeptides by zincin-like metallopeptidases and mechanisms to counter restriction or CRISPR/Cas systems and jump-start transcription or replication. DNA-binding domains acquired by eukaryotes from such systems have been reused in XPC/RAD4-dependent DNA repair and mitochondrial genome replication in kinetoplastids. Characterization of the novel domains discovered here, such as RNases and peptidases, are likely to aid in the development of new reagents and elucidation of the spread of antibiotic resistance. IMPORTANCE This is the first report of the widespread presence of large proteins, termed polyvalent proteins, predicted to be transmitted by genomic parasites such as conjugative elements, plasmids, and phages during the initial phase of infection along with their DNA. They are typified by the presence of multiple domains with disparate activities combined in the same protein. While some of these domains are predicted to assist the invasive element in replication, transcription, or protection of their DNA, several are likely to target various host defense systems or modify the host to favor the parasite's life cycle. Notably, DNA-binding domains from these systems have been transferred to eukaryotes, where they have been incorporated into DNA repair and mitochondrial genome replication systems. PMID:28559295

A Portable, Field-Deployable Analyzer for Isotopic Water Measurements

NASA Astrophysics Data System (ADS)

Berman, E. S.; Gupta, M.; Huang, Y. W.; Lacelle, D.; McKay, C. P.; Fortson, S.

2015-12-01

Water stable isotopes have for many years been used to study the hydrological cycle, catchment hydrology, and polar climate among other applications. Typically, discrete water samples are collected and transported to a laboratory for isotope analysis. Due to the expense and labor associated with such sampling, isotope studies have generally been limited in scope and time-resolution. Field sampling of water isotopes has been shown in recent years to provide dense data sets with the increased time resolution illuminating substantially greater short term variability than is generally observed during discrete sampling. A truly portable instrument also opens the possibility to utilize the instrument as a tool for identifying which water samples would be particularly interesting for further laboratory investigation. To make possible such field measurements of liquid water isotopes, Los Gatos Research has developed a miniaturized, field-deployable liquid water isotope analyzer. The prototype miniature liquid water isotope analyzer (mini-LWIA) uses LGR's patented Off-Axis ICOS (Integrated Cavity Output Spectroscopy) technology in a rugged, Pelican case housing for easy transport and field operations. The analyzer simultaneously measures both δ2H and δ18O from liquid water, with both manual and automatic water introduction options. The laboratory precision for δ2H is 0.6 ‰, and for δ18O is 0.3 ‰. The mini-LWIA was deployed in the high Arctic during the summer of 2015 at Inuvik in the Canadian Northwest Territories. Samples were collected from Sachs Harbor, on the southwest coast of Banks Island, including buried basal ice from the Lurentide Ice Sheet, some ice wedges, and other types of ground ice. Methodology and water analysis results from this extreme field deployment will be presented.

Integrated Model to Assess Cloud Deployment Effectiveness When Developing an IT-strategy

NASA Astrophysics Data System (ADS)

Razumnikov, S.; Prankevich, D.

2016-04-01

Developing an IT-strategy of cloud deployment is a complex issue since even the stage of its formation necessitates revealing what applications will be the best possible to meet the requirements of a company business-strategy, evaluate reliability and safety of cloud providers and analyze staff satisfaction. A system of criteria, as well an integrated model to assess cloud deployment effectiveness is offered. The model makes it possible to identify what applications being at the disposal of a company, as well as new tools to be deployed are reliable and safe enough for implementation in the cloud environment. The data on practical use of the procedure to assess cloud deployment effectiveness by a provider of telecommunication services is presented. The model was used to calculate values of integral indexes of services to be assessed, then, ones, meeting the criteria and answering the business-strategy of a company, were selected.

Implications of Deployed and Nondeployed Fathers on Seventh Graders' California Achievement Test Scores during a Military Crisis.

ERIC Educational Resources Information Center

Pisano, Mark C.

The differences in California Achievement Test (CAT) scores from 1990 to 1991 in seventh graders, currently enrolled in Albritton Junior High School in the Fort Bragg Schools, of deployed and nondeployed fathers were analyzed. CAT percentile scores from 1990 and 1991 (1991 being the year of "Desert Storm") were obtained in reading, math…

Maximizing Societal Benefits Associated With Alternative Fuel Subsidies: The Case of Plug-in Hybrid Electric Vehicles

NASA Astrophysics Data System (ADS)

Nazir, Samir M.

Government seeks to improve the welfare of its citizenry and intervenes in marketplaces to maximize benefits when externalities are not captured. By analyzing how welfare changes from area to area across the country in response to the same intervention informs where government should act. This thesis analyzes the case of plug-in hybrid electric vehicles (PHEVs). PHEVs have many societal benefits, including improving national security, economic, environmental, and health advantages. The magnitude and distribution of these benefits depends on where PHEVs are deployed. This thesis develops and applies a methodology to determine if the benefits from PHEV deployment vary across the country and for ranking regions where positive PHEV consequences are likely to be maximized. The metrics in this method are proxies of key variables which predict the level of benefits in a county from the deployment of a PHEV there; they include population, health benefits from reduced ozone concentration, vehicle miles traveled per capita, existence of non-federal policies, and CO 2 intensity of electricity. By shedding light on how benefits from PHEV deployment vary across counties, this thesis seeks to better inform where to enact government interventions to maximize the benefits of this technology.

Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping

PubMed Central

Normanno, Davide; Vanzi, Francesco; Pavone, Francesco Saverio

2008-01-01

Gene expression regulation is a fundamental biological process which deploys specific sets of genomic information depending on physiological or environmental conditions. Several transcription factors (including lac repressor, LacI) are present in the cell at very low copy number and increase their local concentration by binding to multiple sites on DNA and looping the intervening sequence. In this work, we employ single-molecule manipulation to experimentally address the role of DNA supercoiling in the dynamics and stability of LacI-mediated DNA looping. We performed measurements over a range of degrees of supercoiling between −0.026 and +0.026, in the absence of axial stretching forces. A supercoiling-dependent modulation of the lifetimes of both the looped and unlooped states was observed. Our experiments also provide evidence for multiple structural conformations of the LacI–DNA complex, depending on torsional constraints. The supercoiling-dependent modulation demonstrated here adds an important element to the model of the lac operon. In fact, the complex network of proteins acting on the DNA in a living cell constantly modifies its topological and mechanical properties: our observations demonstrate the possibility of establishing a signaling pathway from factors affecting DNA supercoiling to transcription factors responsible for the regulation of specific sets of genes. PMID:18310101

Origin and composition of cell-free DNA in spent medium from human embryo culture during preimplantation development.

PubMed

Vera-Rodriguez, M; Diez-Juan, A; Jimenez-Almazan, J; Martinez, S; Navarro, R; Peinado, V; Mercader, A; Meseguer, M; Blesa, D; Moreno, I; Valbuena, D; Rubio, C; Simon, C

2018-04-01

What is the origin and composition of cell-free DNA in human embryo spent culture media? Cell-free DNA from human embryo spent culture media represents a mix of maternal and embryonic DNA, and the mixture can be more complex for mosaic embryos. In 2016, ~300 000 human embryos were chromosomally and/or genetically analyzed using preimplantation genetic testing for aneuploidies (PGT-A) or monogenic disorders (PGT-M) before transfer into the uterus. While progress in genetic techniques has enabled analysis of the full karyotype in a single cell with high sensitivity and specificity, these approaches still require an embryo biopsy. Thus, non-invasive techniques are sought as an alternative. This study was based on a total of 113 human embryos undergoing trophectoderm biopsy as part of PGT-A analysis. For each embryo, the spent culture media used between Day 3 and Day 5 of development were collected for cell-free DNA analysis. In addition to the 113 spent culture media samples, 28 media drops without embryo contact were cultured in parallel under the same conditions to use as controls. In total, 141 media samples were collected and divided into two groups: one for direct DNA quantification (53 spent culture media and 17 controls), the other for whole-genome amplification (60 spent culture media and 11 controls) and subsequent quantification. Some samples with amplified DNA (N = 56) were used for aneuploidy testing by next-generation sequencing; of those, 35 samples underwent single-nucleotide polymorphism (SNP) sequencing to detect maternal contamination. Finally, from the 35 spent culture media analyzed by SNP sequencing, 12 whole blastocysts were analyzed by fluorescence in situ hybridization (FISH) to determine the level of mosaicism in each embryo, as a possible origin for discordance between sample types. Trophectoderm biopsies and culture media samples (20 μl) underwent whole-genome amplification, then libraries were generated and sequenced for an aneuploidy study. For SNP sequencing, triads including trophectoderm DNA, cell-free DNA, and follicular fluid DNA were analyzed. In total, 124 SNPs were included with 90 SNPs distributed among all autosomes and 34 SNPs located on chromosome Y. Finally, 12 whole blastocysts were fixed and individual cells were analyzed by FISH using telomeric/centromeric probes for the affected chromosomes. We found a higher quantity of cell-free DNA in spent culture media co-cultured with embryos versus control media samples (P ≤ 0.001). The presence of cell-free DNA in the spent culture media enabled a chromosomal diagnosis, although results differed from those of trophectoderm biopsy analysis in most cases (67%). Discordant results were mainly attributable to a high percentage of maternal DNA in the spent culture media, with a median percentage of embryonic DNA estimated at 8%. Finally, from the discordant cases, 91.7% of whole blastocysts analyzed by FISH were mosaic and 75% of the analyzed chromosomes were concordant with the trophectoderm DNA diagnosis instead of the cell-free DNA result. This study was limited by the sample size and the number of cells analyzed by FISH. This is the first study to combine chromosomal analysis of cell-free DNA, SNP sequencing to identify maternal contamination, and whole-blastocyst analysis for detecting mosaicism. Our results provide a better understanding of the origin of cell-free DNA in spent culture media, offering an important step toward developing future non-invasive karyotyping that must rely on the specific identification of DNA released from human embryos. This work was funded by Igenomix S.L. There are no competing interests.

DNA-informed breeding of rosaceous crops: promises, progress and prospects

PubMed Central

Peace, Cameron P

2017-01-01

Crops of the Rosaceae family provide valuable contributions to rural economies and human health and enjoyment. Sustained solutions to production challenges and market demands can be met with genetically improved new cultivars. Traditional rosaceous crop breeding is expensive and time-consuming and would benefit from improvements in efficiency and accuracy. Use of DNA information is becoming conventional in rosaceous crop breeding, contributing to many decisions and operations, but only after past decades of solved challenges and generation of sufficient resources. Successes in deployment of DNA-based knowledge and tools have arisen when the ‘chasm’ between genomics discoveries and practical application is bridged systematically. Key steps are establishing breeder desire for use of DNA information, adapting tools to local breeding utility, identifying efficient application schemes, accessing effective services in DNA-based diagnostics and gaining experience in integrating DNA information into breeding operations and decisions. DNA-informed germplasm characterization for revealing identity and relatedness has benefitted many programs and provides a compelling entry point to reaping benefits of genomics research. DNA-informed germplasm evaluation for predicting trait performance has enabled effective reallocation of breeding resources when applied in pioneering programs. DNA-based diagnostics is now expanding from specific loci to genome-wide considerations. Realizing the full potential of this expansion will require improved accuracy of predictions, multi-trait DNA profiling capabilities, streamlined breeding information management systems, strategies that overcome plant-based features that limit breeding progress and widespread training of current and future breeding personnel and allied scientists. PMID:28326185

The deployment of routing protocols in distributed control plane of SDN.

PubMed

Jingjing, Zhou; Di, Cheng; Weiming, Wang; Rong, Jin; Xiaochun, Wu

2014-01-01

Software defined network (SDN) provides a programmable network through decoupling the data plane, control plane, and application plane from the original closed system, thus revolutionizing the existing network architecture to improve the performance and scalability. In this paper, we learned about the distributed characteristics of Kandoo architecture and, meanwhile, improved and optimized Kandoo's two levels of controllers based on ideological inspiration of RCP (routing control platform). Finally, we analyzed the deployment strategies of BGP and OSPF protocol in a distributed control plane of SDN. The simulation results show that our deployment strategies are superior to the traditional routing strategies.

A Novel Field Deployable Point-of-Care Diagnostic Test for Cutaneous Leishmaniasis

DTIC Science & Technology

2015-10-01

include localized cutaneous leishmaniasis (LCL), and destructive nasal and oropharyngeal lesions of mucosal leishmaniasis (ML). LCL in the New World...the high costs, personnel training and need of sophisticated equipment. Therefore, novel methods to detect leishmaniasis at the POC are urgently needed...To date, there is no field-standardized molecular method based on DNA amplification coupled with Lateral Flow reading to detect leishmaniasis

HLA Typing for Bone Marrow Transplantation

DTIC Science & Technology

2011-07-21

Confirmatory Testing DC Donor Center DIY Do it yourself DNA Deoxyribonucleic Acid DOD Department of Defense D/R Donor/Recipient EBMT European...testing information is complete, thus allowing for report card analysis earlier in the process. • Deployed functionality to allow cord banks the ability...inventory was labeled with a new Report Card Status: “PreOrder Condition”). • Developed features to support Local IDs and International Society Blood

Application of the microfluidic-assisted replication track analysis to measure DNA repair in human and mouse cells.

PubMed

Welcsh, Piri; Kehrli, Keffy; Lazarchuk, Pavlo; Ladiges, Warren; Sidorova, Julia

2016-10-01

Functional studies of the roles that DNA helicases play in human cells have benefited immensely from DNA fiber (or single molecule) technologies, which enable us to discern minute differences in behaviors of individual replication forks in genomic DNA in vivo. DNA fiber technologies are a group of methods that use different approaches to unravel and stretch genomic DNA to its contour length, and display it on a glass surface in order to immuno-stain nucleoside analog incorporation into DNA to reveal tracks (or tracts) of replication. We have previously adopted a microfluidic approach to DNA stretching and used it to analyze DNA replication. This method was introduced under the moniker maRTA or microfluidic-assisted Replication Track Analysis, and we have since used it to analyze roles of the RECQ helicases WRN and BLM, and other proteins in normal and perturbed replication. Here we describe a novel application of maRTA to detect and measure repair of DNA damage produced by three different agents relevant to etiology or therapy of cancer: methyl-methanesulfonate, UV irradiation, and mitomycin C. Moreover, we demonstrate the utility of this method by analyzing DNA repair in cells with reduced levels of WRN or of the base excision repair protein XRCC1. Copyright © 2016 Elsevier Inc. All rights reserved.

Ten Years of Analyzing the Duck Chart: How an NREL Discovery in 2008 Is

Science.gov Websites

examined how to plan for future large-scale integration of solar photovoltaic (PV) generation on the result, PV was deployed more widely, and system operators became increasingly concerned about how solar emerging energy and environmental policy initiatives pushing for higher levels of solar PV deployment. As a

Evaluation of Deployment Challenges of Wireless Sensor Networks at Signalized Intersections

PubMed Central

Azpilicueta, Leyre; López-Iturri, Peio; Aguirre, Erik; Martínez, Carlos; Astrain, José Javier; Villadangos, Jesús; Falcone, Francisco

2016-01-01

With the growing demand of Intelligent Transportation Systems (ITS) for safer and more efficient transportation, research on and development of such vehicular communication systems have increased considerably in the last years. The use of wireless networks in vehicular environments has grown exponentially. However, it is highly important to analyze radio propagation prior to the deployment of a wireless sensor network in such complex scenarios. In this work, the radio wave characterization for ISM 2.4 GHz and 5 GHz Wireless Sensor Networks (WSNs) deployed taking advantage of the existence of traffic light infrastructure has been assessed. By means of an in-house developed 3D ray launching algorithm, the impact of topology as well as urban morphology of the environment has been analyzed, emulating the realistic operation in the framework of the scenario. The complexity of the scenario, which is an intersection city area with traffic lights, vehicles, people, buildings, vegetation and urban environment, makes necessary the channel characterization with accurate models before the deployment of wireless networks. A measurement campaign has been conducted emulating the interaction of the system, in the vicinity of pedestrians as well as nearby vehicles. A real time interactive application has been developed and tested in order to visualize and monitor traffic as well as pedestrian user location and behavior. Results show that the use of deterministic tools in WSN deployment can aid in providing optimal layouts in terms of coverage, capacity and energy efficiency of the network. PMID:27455270

Evaluation of Deployment Challenges of Wireless Sensor Networks at Signalized Intersections.

PubMed

Azpilicueta, Leyre; López-Iturri, Peio; Aguirre, Erik; Martínez, Carlos; Astrain, José Javier; Villadangos, Jesús; Falcone, Francisco

2016-07-22

With the growing demand of Intelligent Transportation Systems (ITS) for safer and more efficient transportation, research on and development of such vehicular communication systems have increased considerably in the last years. The use of wireless networks in vehicular environments has grown exponentially. However, it is highly important to analyze radio propagation prior to the deployment of a wireless sensor network in such complex scenarios. In this work, the radio wave characterization for ISM 2.4 GHz and 5 GHz Wireless Sensor Networks (WSNs) deployed taking advantage of the existence of traffic light infrastructure has been assessed. By means of an in-house developed 3D ray launching algorithm, the impact of topology as well as urban morphology of the environment has been analyzed, emulating the realistic operation in the framework of the scenario. The complexity of the scenario, which is an intersection city area with traffic lights, vehicles, people, buildings, vegetation and urban environment, makes necessary the channel characterization with accurate models before the deployment of wireless networks. A measurement campaign has been conducted emulating the interaction of the system, in the vicinity of pedestrians as well as nearby vehicles. A real time interactive application has been developed and tested in order to visualize and monitor traffic as well as pedestrian user location and behavior. Results show that the use of deterministic tools in WSN deployment can aid in providing optimal layouts in terms of coverage, capacity and energy efficiency of the network.

The fractal based analysis of human face and DNA variations during aging.

PubMed

Namazi, Hamidreza; Akrami, Amin; Hussaini, Jamal; Silva, Osmar N; Wong, Albert; Kulish, Vladimir V

2017-01-16

Human DNA is the main unit that shapes human characteristics and features such as behavior. Thus, it is expected that changes in DNA (DNA mutation) influence human characteristics and features. Face is one of the human features which is unique and also dependent on his gen. In this paper, for the first time we analyze the variations of human DNA and face simultaneously. We do this job by analyzing the fractal dimension of DNA walk and face during human aging. The results of this study show the human DNA and face get more complex by aging. These complexities are mapped on fractal exponents of DNA walk and human face. The method discussed in this paper can be further developed in order to investigate the direct influence of DNA mutation on the face variations during aging, and accordingly making a model between human face fractality and the complexity of DNA walk.

Analysis and Evaluation of Deployment Mechanism of a Tiny Rover in a Microgravity by Drop Tower Experiments

NASA Astrophysics Data System (ADS)

Nagaoka, Kenji; Yano, Hajime; Yoshimitsu, Tetsuo; Yoshida, Kazuya; Kubota, Takashi; Adachi, Tadashi; Kurisu, Masamitsu; Yatsunami, Hiroyuki; Kuroda, Yoji

This presentation introduces the analysis and evaluation of a deployment mechanism of a tiny rover by ZARM drop tower experiments. The mechanism is installed on the MINERVA-II2 system in the Hayabusa-2 project performed by JAXA. The MINERVA-II2 system includes a small exploration rover, and the rover will be released from the Hayabusa-2 spacecraft to the asteroid surface. After the rover lands on the surface, it will move over the surface and conduct scientific measurements. To achieve such a challenging mission, the deployment mechanism of the rover is one of the significant components. In particular, controlling the rover's landing velocity against the asteroid surface is required with high-reliability mechanism. In the MINERVA-II2 system, a reliable deployment mechanism using a metal spring is installed. By the simple mechanism, the rover's releasing velocity will be controlled within a required value. Although the performance evaluation and analysis are necessary before launch, it is difficult to experiment the deployment performance three-dimensionally on ground. In the MINERVA-II2 project, with the cooperation of ZARM, DLR and JAXA, we conducted microgravity experiments using a ZARM drop tower to examine the deployment performance in a three-dimensional microgravity. During the experiments, motion of the deployment mechanism and the rover were captured by an external camera mounted on the dropping chamber. After the drop, we analyzed the rover's releasing velocity based on image processing of the camera data. The experimental results confirmed that the deployment mechanism is feasible and reliable for controlling the rover's releasing velocity. In addition to the experiments, we analyzed a mechanical friction resistance of the mechanism from a theoretical viewpoint. These results contribute to design of spring stiffness and feedback to the development of the MINERVA-II2 flight model. Finally, the drop tower experiments were accomplished based on the agreement on the Hayabusa-2 project by DLR-JAXA. The chamber for the experiments was used, which was developed by the Hayabusa-2 project. In the experiments, we received technical and operations supports from ZARM. We sincerely express our acknowledgement to ZARM, DLR and JAXA.

NASA/American Cancer Society High-Resolution Flow Cytometry Project-I

NASA Technical Reports Server (NTRS)

Thomas, R. A.; Krishan, A.; Robinson, D. M.; Sams, C.; Costa, F.

2001-01-01

BACKGROUND: The NASA/American Cancer Society (ACS) flow cytometer can simultaneously analyze the electronic nuclear volume (ENV) and DNA content of cells. This study describes the schematics, resolution, reproducibility, and sensitivity of biological standards analyzed on this unit. METHODS: Calibrated beads and biological standards (lymphocytes, trout erythrocytes [TRBC], calf thymocytes, and tumor cells) were analyzed for ENV versus DNA content. Parallel data (forward scatter versus DNA) from a conventional flow cytometer were obtained. RESULTS: ENV linearity studies yielded an R value of 0.999. TRBC had a coefficient of variation (CV) of 1.18 +/- 0.13. DNA indexes as low as 1.02 were detectable. DNA content of lymphocytes from 42 females was 1.9% greater than that for 60 males, with a noninstrumental variability in total DNA content of 0.5%. The ENV/DNA ratio was constant in 15 normal human tissue samples, but differed in the four animal species tested. The ENV/DNA ratio for a hypodiploid breast carcinoma was 2.3 times greater than that for normal breast tissue. CONCLUSIONS: The high-resolution ENV versus DNA analyses are highly reliable, sensitive, and can be used for the detection of near-diploid tumor cells that are difficult to identify with conventional cytometers. ENV/DNA ratio may be a useful parameter for detection of aneuploid populations.

The Deployment of Routing Protocols in Distributed Control Plane of SDN

PubMed Central

Jingjing, Zhou; Di, Cheng; Weiming, Wang; Rong, Jin; Xiaochun, Wu

2014-01-01

Software defined network (SDN) provides a programmable network through decoupling the data plane, control plane, and application plane from the original closed system, thus revolutionizing the existing network architecture to improve the performance and scalability. In this paper, we learned about the distributed characteristics of Kandoo architecture and, meanwhile, improved and optimized Kandoo's two levels of controllers based on ideological inspiration of RCP (routing control platform). Finally, we analyzed the deployment strategies of BGP and OSPF protocol in a distributed control plane of SDN. The simulation results show that our deployment strategies are superior to the traditional routing strategies. PMID:25250395

Timing matters: error-prone gap filling and translesion synthesis in immunoglobulin gene hypermutation

PubMed Central

Sale, Julian E.; Batters, Christopher; Edmunds, Charlotte E.; Phillips, Lara G.; Simpson, Laura J.; Szüts, Dávid

2008-01-01

By temporarily deferring the repair of DNA lesions encountered during replication, the bypass of DNA damage is critical to the ability of cells to withstand genomic insults. Damage bypass can be achieved either by recombinational mechanisms that are generally accurate or by a process called translesion synthesis. Translesion synthesis involves replacing the stalled replicative polymerase with one of a number of specialized DNA polymerases whose active sites are able to tolerate a distorted or damaged DNA template. While this property allows the translesion polymerases to synthesize across damaged bases, it does so with the trade-off of an increased mutation rate. The deployment of these enzymes must therefore be carefully regulated. In addition to their important role in general DNA damage tolerance and mutagenesis, the translesion polymerases play a crucial role in converting the products of activation induced deaminase-catalysed cytidine deamination to mutations during immunoglobulin gene somatic hypermutation. In this paper, we specifically consider the control of translesion synthesis in the context of the timing of lesion bypass relative to replication fork progression and arrest at sites of DNA damage. We then examine how recent observations concerning the control of translesion synthesis might help refine our view of the mechanisms of immunoglobulin gene somatic hypermutation. PMID:19008194

DNA barcoding for biosecurity: case studies from the UK plant protection program.

PubMed

Hodgetts, Jennifer; Ostojá-Starzewski, Jozef C; Prior, Thomas; Lawson, Rebecca; Hall, Jayne; Boonham, Neil

2016-11-01

Since its conception, DNA barcoding has seen a rapid uptake within the research community. Nevertheless, as with many new scientific tools, progression towards the point of routine deployment within diagnostic laboratories has been slow. In this paper, we discuss the application of DNA barcoding in the Defra plant health diagnostic laboratories, where DNA barcoding is used primarily for the identification of invertebrate pests. We present a series of case studies that demonstrate the successful application of DNA barcoding but also reveal some potential limitations to expanded use. The regulated plant pest, Bursephalenchus xylophilus, and one of its vectors, Monochamus alternatus, were found in dining chairs. Some traded wood products are potentially high risk, allowing the movement of longhorn beetles; Trichoferus campestris, Leptura quadrifasciata, and Trichoferus holosericeus were found in a wooden cutlery tray, a railway sleeper, and a dining chair, respectively. An outbreak of Meloidogyne fallax was identified in Allium ampeloprasum and in three weed species. Reference sequences for UK native psyllids were generated to enable the development of rapid diagnostics to be used for monitoring following the release of Aphalara itadori as a biological control agent for Fallopia japonica.

Injury Patterns Sustained in Fatal Motor Vehicle Collisions with Driver's Third-Generation Airbag Deployment.

PubMed

Kuk, Mariya; Shkrum, Michael J

2018-05-01

The Office of the Chief Coroner for Ontario database for 2011-2012 was used to compare fatal injury patterns in drivers whose third-generation airbags deployed compared to first- and second-generation airbag deployments and airbag nondeployments with and without seatbelt use. There were 110 frontal and offset frontal crashes analyzed. The small sample size meant that the odds of craniocerebral, cervical spinal, thoracic, and abdominal injuries were not statistically different for airbag generation, deployment status, and seatbelt use; however, the risk of fatal thoracic injuries in third- and second-generation cases was increased. Seatbelt usage in third- and second-generation deployment cases reduced the risk of all injuries except abdominal trauma. High severity impacts and occupant compartment intrusion were frequently observed. The analyses in this retrospective study were challenged by data that were not collated in a standardized way and were limited in details about scene, vehicle, and driver variables. © 2017 American Academy of Forensic Sciences.

Optimization Techniques for 3D Graphics Deployment on Mobile Devices

NASA Astrophysics Data System (ADS)

Koskela, Timo; Vatjus-Anttila, Jarkko

2015-03-01

3D Internet technologies are becoming essential enablers in many application areas including games, education, collaboration, navigation and social networking. The use of 3D Internet applications with mobile devices provides location-independent access and richer use context, but also performance issues. Therefore, one of the important challenges facing 3D Internet applications is the deployment of 3D graphics on mobile devices. In this article, we present an extensive survey on optimization techniques for 3D graphics deployment on mobile devices and qualitatively analyze the applicability of each technique from the standpoints of visual quality, performance and energy consumption. The analysis focuses on optimization techniques related to data-driven 3D graphics deployment, because it supports off-line use, multi-user interaction, user-created 3D graphics and creation of arbitrary 3D graphics. The outcome of the analysis facilitates the development and deployment of 3D Internet applications on mobile devices and provides guidelines for future research.

A Novel Deployment Scheme Based on Three-Dimensional Coverage Model for Wireless Sensor Networks

PubMed Central

Xiao, Fu; Yang, Yang; Wang, Ruchuan; Sun, Lijuan

2014-01-01

Coverage pattern and deployment strategy are directly related to the optimum allocation of limited resources for wireless sensor networks, such as energy of nodes, communication bandwidth, and computing power, and quality improvement is largely determined by these for wireless sensor networks. A three-dimensional coverage pattern and deployment scheme are proposed in this paper. Firstly, by analyzing the regular polyhedron models in three-dimensional scene, a coverage pattern based on cuboids is proposed, and then relationship between coverage and sensor nodes' radius is deduced; also the minimum number of sensor nodes to maintain network area's full coverage is calculated. At last, sensor nodes are deployed according to the coverage pattern after the monitor area is subdivided into finite 3D grid. Experimental results show that, compared with traditional random method, sensor nodes number is reduced effectively while coverage rate of monitor area is ensured using our coverage pattern and deterministic deployment scheme. PMID:25045747

Cognitive person variables in the delay of gratification of older children at risk.

PubMed

Rodriguez, M L; Mischel, W; Shoda, Y

1989-08-01

The components of self-regulation were analyzed, extending the self-imposed delay of gratification paradigm to older children with social adjustment problems. Delay behavior was related to a network of conceptually relevant cognitive person variables, consisting of attention deployment strategies during delay, knowledge of delay rules, and intelligence. A positive relationship was demonstrated between concurrent indexes of intelligence, attention deployment, and actual delay time. Moreover, attention deployment, measured as an individual differences variable during the delay process, had a direct, positive effect on delay behavior. Specifically, as the duration of delay and the frustration of the situation increased, children who spent a higher proportion of the time distracting themselves from the tempting elements of the delay situation were able to delay longer. The effect of attention deployment on delay behavior was significant even when age, intelligence, and delay rule knowledge were controlled. Likewise, delay rule knowledge significantly predicted delay time, even when age, attention deployment, and intelligence were controlled.

DNA EMP Awareness Course Notes. Supplement to Third Edition.

DTIC Science & Technology

1978-07-31

UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE (When Data Entered) REPORT DOCUMENTATION PAGE READ INSTRUCTIONS BEFORE COMPLETING FORM I REPORT...the environment through system design and testing. FORM 143 E,,N F’NOV 65 IS OBSOLETE DD JAN73 1473 EDITION OF UNCLASSIFIED SECURITY CLASSIFICATION OF...fields generated tems mission and deployment factors by the prompt gammas. Other forms of EMP, where these environments should be con- such as

Genome-wide map of Apn1 binding sites under oxidative stress in Saccharomyces cerevisiae.

PubMed

Morris, Lydia P; Conley, Andrew B; Degtyareva, Natalya; Jordan, I King; Doetsch, Paul W

2017-11-01

The DNA is cells is continuously exposed to reactive oxygen species resulting in toxic and mutagenic DNA damage. Although the repair of oxidative DNA damage occurs primarily through the base excision repair (BER) pathway, the nucleotide excision repair (NER) pathway processes some of the same lesions. In addition, damage tolerance mechanisms, such as recombination and translesion synthesis, enable cells to tolerate oxidative DNA damage, especially when BER and NER capacities are exceeded. Thus, disruption of BER alone or disruption of BER and NER in Saccharomyces cerevisiae leads to increased mutations as well as large-scale genomic rearrangements. Previous studies demonstrated that a particular region of chromosome II is susceptible to chronic oxidative stress-induced chromosomal rearrangements, suggesting the existence of DNA damage and/or DNA repair hotspots. Here we investigated the relationship between oxidative damage and genomic instability utilizing chromatin immunoprecipitation combined with DNA microarray technology to profile DNA repair sites along yeast chromosomes under different oxidative stress conditions. We targeted the major yeast AP endonuclease Apn1 as a representative BER protein. Our results indicate that Apn1 target sequences are enriched for cytosine and guanine nucleotides. We predict that BER protects these sites in the genome because guanines and cytosines are thought to be especially susceptible to oxidative attack, thereby preventing large-scale genome destabilization from chronic accumulation of DNA damage. Information from our studies should provide insight into how regional deployment of oxidative DNA damage management systems along chromosomes protects against large-scale rearrangements. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Parallel gene analysis with allele-specific padlock probes and tag microarrays

PubMed Central

Banér, Johan; Isaksson, Anders; Waldenström, Erik; Jarvius, Jonas; Landegren, Ulf; Nilsson, Mats

2003-01-01

Parallel, highly specific analysis methods are required to take advantage of the extensive information about DNA sequence variation and of expressed sequences. We present a scalable laboratory technique suitable to analyze numerous target sequences in multiplexed assays. Sets of padlock probes were applied to analyze single nucleotide variation directly in total genomic DNA or cDNA for parallel genotyping or gene expression analysis. All reacted probes were then co-amplified and identified by hybridization to a standard tag oligonucleotide array. The technique was illustrated by analyzing normal and pathogenic variation within the Wilson disease-related ATP7B gene, both at the level of DNA and RNA, using allele-specific padlock probes. PMID:12930977

A field-deployable compound-specific isotope analyzer based on quantum cascade laser and hollow waveguide

NASA Astrophysics Data System (ADS)

Wu, Sheng; Deev, Andrei

2013-01-01

A field deployable Compound Specific Isotope Analyzer (CSIA) coupled with capillary chromatogrpahy based on Quantum Cascade (QC) lasers and Hollow Waveguide (HWG) with precision and chemical resolution matching mature Mass Spectroscopy has been achieved in our laboratory. The system could realize 0.3 per mil accuracy for 12C/13C for a Gas Chromatography (GC) peak lasting as short as 5 seconds with carbon molar concentration in the GC peak less than 0.5%. Spectroscopic advantages of HWG when working with QC lasers, i.e. single mode transmission, noiseless measurement and small sample volume, are compared with traditional free space and multipass spectroscopy methods.

Equine behavioral enrichment toys as tools for non-invasive recovery of viral and host DNA.

PubMed

Seeber, Peter A; Soilemetzidou, Sanatana E; East, Marion L; Walzer, Chris; Greenwood, Alex D

2017-09-01

Direct collection of samples from wildlife can be difficult and sometimes impossible. Non-invasive remote sampling for the purpose of DNA extraction is a potential tool for monitoring the presence of wildlife at the individual level, and for identifying the pathogens shed by wildlife. Equine herpesviruses (EHV) are common pathogens of equids that can be fatal if transmitted to other mammals. Transmission usually occurs by nasal aerosol discharge from virus-shedding individuals. The aim of this study was to validate a simple, non-invasive method to track EHV shedding in zebras and to establish an efficient protocol for genotyping individual zebras from environmental DNA (eDNA). A commercially available horse enrichment toy was deployed in captive Grévy's, mountain, and plains zebra enclosures and swabbed after 4-24 hr. Using eDNA extracted from these swabs four EHV strains (EHV-1, EHV-7, wild ass herpesvirus and zebra herpesvirus) were detected by PCR and confirmed by sequencing, and 12 of 16 zebras present in the enclosures were identified as having interacted with the enrichment toy by mitochondrial DNA amplification and sequencing. We conclude that, when direct sampling is difficult or prohibited, non-invasive sampling of eDNA can be a useful tool to determine the genetics of individuals or populations and for detecting pathogen shedding in captive wildlife. © 2017 Wiley Periodicals, Inc.

Small Hydropower Development in Rwanda: Trends, Opportunities and Challenges

NASA Astrophysics Data System (ADS)

Geoffrey, Gasore; Zimmerle, Daniel; Ntagwirumugara, Etienne

2018-04-01

The Rift Valley region of Sub-Saharan Africa represents a promising area for the development of small (<5MW) hydropower resources. This study compiles data from government and UN agency reports to analyze different development outlooks. The study found that there has been a rapid deployment of small hydropower in the last 10 years. From the current total deployed small hydro of 47.5 MW, 16.5MW (35%) were deployed from 1957 to 1984 while the remaining 31 MW (65%) were deployed from 2007 to 2017. While all systems constructed prior to 1985 are grid-connected, one third of the 24 facilities constructed after 2007 are connected to off-grid systems. The study provides an overview of the economic incentives for developing small hydropower systems in Rwanda and the potential contribution of that development to Rwanda’s electrification goals.

Fluorescence Microscopy of Nanochannel-Confined DNA.

PubMed

Westerlund, Fredrik; Persson, Fredrik; Fritzsche, Joachim; Beech, Jason P; Tegenfeldt, Jonas O

2018-01-01

Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level and both the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments and analyze the data.

Amplification of the major satellite DNA family (FA-SAT) in a cat fibrosarcoma might be related to chromosomal instability.

PubMed

Santos, Sara; Chaves, Raquel; Adega, Filomena; Bastos, Estela; Guedes-Pinto, Henrique

2006-01-01

Most mammalian chromosomes have satellite DNA sequences located at or near the centromeres, organized in arrays of variable size and higher order structure. The implications of these specific repetitive DNA sequences and their organization for centromere function are still quite cloudy. In contrast to most mammalian species, the domestic cat seems to have the major satellite DNA family (FA-SAT) localized primarily at the telomeres and secondarily at the centromeres of the chromosomes. In the present work, we analyzed chromosome preparations from a fibrosarcoma, in comparison with nontumor cells (epithelial tissue) from the same individual, by in situ hybridization of the FA-SAT cat satellite DNA family. This repetitive sequence was found to be amplified in the cat tumor chromosomes analyzed. The amplification of these satellite DNA sequences in the cat chromosomes with variable number and appearance (marker chromosomes) is discussed and might be related to mitotic instability, which could explain the exhibition of complex patterns of chromosome aberrations detected in the fibrosarcoma analyzed.

Versatile and Programmable DNA Logic Gates on Universal and Label-Free Homogeneous Electrochemical Platform.

PubMed

Ge, Lei; Wang, Wenxiao; Sun, Ximei; Hou, Ting; Li, Feng

2016-10-04

Herein, a novel universal and label-free homogeneous electrochemical platform is demonstrated, on which a complete set of DNA-based two-input Boolean logic gates (OR, NAND, AND, NOR, INHIBIT, IMPLICATION, XOR, and XNOR) is constructed by simply and rationally deploying the designed DNA polymerization/nicking machines without complicated sequence modulation. Single-stranded DNA is employed as the proof-of-concept target/input to initiate or prevent the DNA polymerization/nicking cyclic reactions on these DNA machines to synthesize numerous intact G-quadruplex sequences or binary G-quadruplex subunits as the output. The generated output strands then self-assemble into G-quadruplexes that render remarkable decrease to the diffusion current response of methylene blue and, thus, provide the amplified homogeneous electrochemical readout signal not only for the logic gate operations but also for the ultrasensitive detection of the target/input. This system represents the first example of homogeneous electrochemical logic operation. Importantly, the proposed homogeneous electrochemical logic gates possess the input/output homogeneity and share a constant output threshold value. Moreover, the modular design of DNA polymerization/nicking machines enables the adaptation of these homogeneous electrochemical logic gates to various input and output sequences. The results of this study demonstrate the versatility and universality of the label-free homogeneous electrochemical platform in the design of biomolecular logic gates and provide a potential platform for the further development of large-scale DNA-based biocomputing circuits and advanced biosensors for multiple molecular targets.

Centrifugal LabTube platform for fully automated DNA purification and LAMP amplification based on an integrated, low-cost heating system.

PubMed

Hoehl, Melanie M; Weißert, Michael; Dannenberg, Arne; Nesch, Thomas; Paust, Nils; von Stetten, Felix; Zengerle, Roland; Slocum, Alexander H; Steigert, Juergen

2014-06-01

This paper introduces a disposable battery-driven heating system for loop-mediated isothermal DNA amplification (LAMP) inside a centrifugally-driven DNA purification platform (LabTube). We demonstrate LabTube-based fully automated DNA purification of as low as 100 cell-equivalents of verotoxin-producing Escherichia coli (VTEC) in water, milk and apple juice in a laboratory centrifuge, followed by integrated and automated LAMP amplification with a reduction of hands-on time from 45 to 1 min. The heating system consists of two parallel SMD thick film resistors and a NTC as heating and temperature sensing elements. They are driven by a 3 V battery and controlled by a microcontroller. The LAMP reagents are stored in the elution chamber and the amplification starts immediately after the eluate is purged into the chamber. The LabTube, including a microcontroller-based heating system, demonstrates contamination-free and automated sample-to-answer nucleic acid testing within a laboratory centrifuge. The heating system can be easily parallelized within one LabTube and it is deployable for a variety of heating and electrical applications.

Imagining Sisyphus happy: DNA barcoding and the unnamed majority.

PubMed

Blaxter, Mark

2016-09-05

The vast majority of life on the Earth is physically small, and is classifiable as micro- or meiobiota. These organisms are numerically dominant and it is likely that they are also abundantly speciose. By contrast, the vast majority of taxonomic effort has been expended on 'charismatic megabionts': larger organisms where a wealth of morphology has facilitated Linnaean species definition. The hugely successful Linnaean project is unlikely to be extensible to the totality of approximately 10 million species in a reasonable time frame and thus alternative toolkits and methodologies need to be developed. One such toolkit is DNA barcoding, particularly in its metabarcoding or metagenetics mode, where organisms are identified purely by the presence of a diagnostic DNA sequence in samples that are not processed for morphological identification. Building on secure Linnaean foundations, classification of unknown (and unseen) organisms to molecular operational taxonomic units (MOTUs) and deployment of these MOTUs in biodiversity science promises a rewarding resolution to the Sisyphean task of naming all the world's species.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

Acoustic Metadata Management and Transparent Access to Networked Oceanographic Data Sets

DTIC Science & Technology

2015-09-30

the deployment that was analyzed. It contains a Start and End time that must lie within the timespan over which the instrument was deployed. A list...encounter – Detections record acoustic encounters. The start time denotes when the animals were first detected acoustically and the end time...systematically. Children of Detection include elements such as the Start and End times of the call, bin, or encounter, a species identifier from the

A new model for ancient DNA decay based on paleogenomic meta-analysis

PubMed Central

Ware, Roselyn; Smith, Oliver; Collins, Matthew

2017-01-01

Abstract The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics. PMID:28486705

A stowing and deployment strategy for large membrane space systems on the example of Gossamer-1

NASA Astrophysics Data System (ADS)

Seefeldt, Patric

2017-09-01

Deployment systems for innovative space applications such as solar sails require a technique for a controlled and autonomous deployment in space. The deployment process has a strong impact on the mechanism and structural design and sizing. On the example of the design implemented in the Gossamer-1 project of the German Aerospace Center (DLR), such a stowing and deployment process is analyzed. It is based on a combination of zig-zag folding and coiling of triangular sail segments spanned between crossed booms. The deployment geometry and forces introduced by the mechanism considered are explored in order to reveal how the loads are transferred through the membranes to structural components such as the booms. The folding geometry and force progressions are described by function compositions of an inverse trigonometric function with the considered trigonometric function itself. If these functions are evaluated over several periods of the trigonometric function, a non-smooth oscillating curve occurs. Depending on the trigonometric function, these are often vividly described as zig-zag or sawtooth functions. The developed functions are applied to the Gossamer-1 design. The deployment geometry reveals a tendency that the loads are transferred along the catheti of the sail segments and therefore mainly along the boom axes. The load introduced by the spool deployment mechanism is described. By combining the deployment geometry with that load, a prediction of the deployment load progression is achieved. The mathematical description of the stowing and deployment geometry, as well as the forces inflicted by the mechanism provides an understanding of how exactly the membrane deploys and through which edges the deployment forces are transferred. The mathematical analysis also gives an impression of sensitive parameters that could be influenced by manufacturing tolerances or unsymmetrical deployment of the sail segments. While the mathematical model was applied on the design of the Gossamer-1 hardware, it allows an analysis of other geometries. This is of particular interest as Gossamer-1 investigated deployment technology on a relatively small scale of 5m × 5m , while the currently considered solar sail missions require sails that are about one order of magnitude bigger.

Development and validation of a multiplex reaction analyzing eight miniSTRs of the X chromosome for identity and kinship testing with degraded DNA.

PubMed

Castañeda, María; Odriozola, Adrián; Gómez, Javier; Zarrabeitia, María T

2013-07-01

We report the development of an effective system for analyzing X chromosome-linked mini short tandem repeat loci with reduced-size amplicons (less than 220 bp), useful for analyzing highly degraded DNA samples. To generate smaller amplicons, we redesigned primers for eight X-linked microsatellites (DXS7132, DXS10079, DXS10074, DXS10075, DXS6801, DXS6809, DXS6789, and DXS6799) and established efficient conditions for a multiplex PCR system (miniX). The validation tests confirmed that it has good sensitivity, requiring as little as 20 pg of DNA, and performs well with DNA from paraffin-embedded tissues, thus showing potential for improved analysis and identification of highly degraded and/or very limited DNA samples. Consequently, this system may help to solve complex forensic cases, particularly when autosomal markers convey insufficient information.

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing

PubMed Central

Lutsik, Pavlo; Feuerbach, Lars; Arand, Julia; Lengauer, Thomas; Walter, Jörn; Bock, Christoph

2011-01-01

Bisulfite sequencing is a widely used method for measuring DNA methylation in eukaryotic genomes. The assay provides single-base pair resolution and, given sufficient sequencing depth, its quantitative accuracy is excellent. High-throughput sequencing of bisulfite-converted DNA can be applied either genome wide or targeted to a defined set of genomic loci (e.g. using locus-specific PCR primers or DNA capture probes). Here, we describe BiQ Analyzer HT (http://biq-analyzer-ht.bioinf.mpi-inf.mpg.de/), a user-friendly software tool that supports locus-specific analysis and visualization of high-throughput bisulfite sequencing data. The software facilitates the shift from time-consuming clonal bisulfite sequencing to the more quantitative and cost-efficient use of high-throughput sequencing for studying locus-specific DNA methylation patterns. In addition, it is useful for locus-specific visualization of genome-wide bisulfite sequencing data. PMID:21565797

General misincorporation frequency: Re-evaluation of the fidelity of DNA polymerases.

PubMed

Yang, Jie; Li, Bianbian; Liu, Xiaoying; Tang, Hong; Zhuang, Xiyao; Yang, Mingqi; Xu, Ying; Zhang, Huidong; Yang, Chun

2018-02-19

DNA replication in cells is performed in the presence of four dNTPs and four rNTPs. In this study, we re-evaluated the fidelity of DNA polymerases using the general misincorporation frequency consisting of three incorrect dNTPs and four rNTPs but not using the traditional special misincorporation frequency with only the three incorrect dNTPs. We analyzed both the general and special misincorporation frequencies of nucleotide incorporation opposite dG, rG, or 8-oxoG by Pseudomonas aeruginosa phage 1 (PaP1) DNA polymerase Gp90 or Sulfolobus solfataricus DNA polymerase Dpo4. Both misincorporation frequencies of other DNA polymerases published were also summarized and analyzed. The general misincorporation frequency is obviously higher than the special misincorporation frequency for many DNA polymerases, indicating the real fidelity of a DNA polymerase should be evaluated using the general misincorporation frequency. Copyright © 2018 Elsevier Inc. All rights reserved.

Medical Surveillance Monthly Report (MSMR). Volume 22, Number 6, June 2015

DTIC Science & Technology

2015-06-01

and then plateaued (with marked year-to-year variability) through 2010 (Figure 2). women and among those who were not deployed within the fi rst...acids were extracted with the QIAamp stool DNA kit (QIAGEN, USA). For the respiratory samples, detection and characterization of human infl uenza...research by the Walter Reed Army Institute of Research Division of Human Subjects Protection. Some of the authors are military service members. Th is

Investigating the Effects of Side Airbag Deployment in Real-World Crashes Using Crash Comparison Techniques

PubMed Central

Loftis, Kathryn L.; Weaver, Ashley A.; Stitzel, Joel D.

2011-01-01

The objective of this study was to investigate side airbag (SAB) deployment in near side crashes and compare injuries and contact points between occupants with and without SAB deployment. Using NASS 2000–2008 and selecting for near side cases, with PDOF ± 20 degrees from 90 or 270, for non-pregnant adult belted occupants, there were 20,253 (weighted) SAB deployments. NASS showed that SABs have been increasing within the fleet, comprising 2% of airbags in 2000 and increasing to 33% of airbags in 2008. To investigate deployed SABs, we developed a three-step methology to pair CIREN cases to study the effects of deployment on occupant outcome. The first step involved extracting near side impacts from CIREN with adult, non-pregnant occupants seated in row 1 (drivers or right front passengers). In the second step, each case was quantitatively compared to FMVSS 214 barrier test standards using a 6 point similarity scoring system. Cases scoring at least 3 points were then qualitatively analyzed and 33 pairs of cases of the same vehicle make/model but opposite SAB status were chosen. Occupants with deployed SAB had reduced occurrences and severity of head and face, neck and cervical spine, and thoracic injuries and fewer injurious contacts to side components including the door, a-pillar, and window sill. SAB deployment was statistically significant for reducing occupant MAIS and ISS and thorax airbags were statistically significant for reducing thoracic and neck/cervical spine injury severity. The average ISS with SAB deployment was 21, while the average ISS of those without was 33. This study establishes methods for performing comparisons between CIREN cases based on regulatory conditions and shows injury reduction in key body regions with SAB deployment. PMID:22105386

Hard is Normal: Military Families' Transitions Within the Process of Deployment.

PubMed

Yablonsky, Abigail M; Barbero, Edie Devers; Richardson, Jeanita W

2016-02-01

US military deployments have become more frequent and lengthier in duration since 2003. Over half of US military members are married, and many also have children. The authors sought to understand the process of deployment from the perspective of the military family. After a thorough search of the literature, 21 primary research reports of 19 studies with an aggregate sample of 874 were analyzed using qualitative metasynthesis. The deployment process was experienced in four temporal domains. The military family as a whole shared the pre-deployment transition: all family members felt uncertain about the future, needed to complete tasks to "get ready" for deployment, and experienced a sense of distancing in preparation for the upcoming separation. The AD member went through the deployment transition independently, needing to "stay engaged" with the military mission, building a surrogate family and simultaneously trying to maintain connection with the family at home. In parallel, the home front family was going through a transposement transition, moving forward as an altered family unit, taking on new roles and responsibilities, and trying to simultaneously connect with the deployed member and find support from other military families. In post-deployment, the family went through the "reintegration" transition together, managing expectations, and readjusting family roles, all needing understanding and appreciation for their sacrifices during the recent separation. Effective family communication was important for military family well-being after deployment but unexpectedly challenging for many. Clinical, research, and policy recommendations are discussed. © 2015 Wiley Periodicals, Inc. This article has been contributed to by a US Government employee and her work is in the public domain in the USA.

Concepts and analysis for precision segmented reflector and feed support structures

NASA Technical Reports Server (NTRS)

Miller, Richard K.; Thomson, Mark W.; Hedgepeth, John M.

1990-01-01

Several issues surrounding the design of a large (20-meter diameter) Precision Segmented Reflector are investigated. The concerns include development of a reflector support truss geometry that will permit deployment into the required doubly-curved shape without significant member strains. For deployable and erectable reflector support trusses, the reduction of structural redundancy was analyzed to achieve reduced weight and complexity for the designs. The stiffness and accuracy of such reduced member trusses, however, were found to be affected to a degree that is unexpected. The Precision Segmented Reflector designs were developed with performance requirements that represent the Reflector application. A novel deployable sunshade concept was developed, and a detailed parametric study of various feed support structural concepts was performed. The results of the detailed study reveal what may be the most desirable feed support structure geometry for Precision Segmented Reflector/Large Deployable Reflector applications.

Mental Well-being Considerations in Preparation for Disaster Health Care: Learning From Deployment.

PubMed

Mäkinen, Tytti H; Miettinen, Sari M; Kernohan, W George

2015-08-01

The mental well-being of internationally deployed disaster-relief workers has become an issue of concern. The psychological consequences for the relief worker being exposed to trauma and threats have been well documented; however, the role of pre-deployment preparation in supporting mental well-being has not received due attention, despite research indicating the need for it. This case series examines the experiences of deployed volunteers of one emergency-relief organization. The aim of this research was to identify the participants' interpretations of the appropriateness of the pre-deployment preparation they had received in light of supporting their mental well-being during and after deployment. The main research questions were: How appropriate was pre-deployment preparation in supporting mental well-being? What elements were lacking, and what else would be useful? Using a hermeneutic phenomenological approach, thematic, semi-structured interviews were conducted with six deployed volunteers of an international emergency-relief organization. Data were analyzed using content analysis. The participants in this study regarded the pre-deployment preparation they had received, on the whole, as appropriate in supporting their mental well-being. The seven main themes identified as important and supportive of mental well-being were: (1) realistic expectations, (2) team building and support, (3) self-awareness and self-care, (4) post-deployment support, (5) practical skills and creative solutions, (6) shared values and beliefs, and (7) safety and security. Specific areas identified as lacking within these themes included communication, self-care, post-deployment support, and safety and security. Themes identified as important for supporting mental well-being in this research largely were consistent with those in previous research. The generally positive experiences of the support received do not reflect results from existing research, where significant shortcomings in worker support have been expressed. However, important elements were also identified as lacking in this specific pre-deployment preparation.

Long-term greenhouse gas measurements from aircraft

NASA Astrophysics Data System (ADS)

Karion, A.; Sweeney, C.; Wolter, S.; Newberger, T.; Chen, H.; Andrews, A.; Kofler, J.; Neff, D.; Tans, P.

2012-10-01

In March 2009 the NOAA/ESRL/GMD Carbon Cycle and Greenhouse Gases Group collaborated with the US Coast Guard (USCG) to establish the Alaska Coast Guard (ACG) sampling site, a unique addition to NOAA's atmospheric monitoring network. This collaboration takes advantage of USCG bi-weekly Arctic Domain Awareness (ADA) flights, conducted with Hercules C-130 aircraft from March to November each year. NOAA has installed window-replacement inlet plates on two USCG C-130 aircraft and deploys a pallet with NOAA instrumentation on each ADA flight. Flights typically last 8 h and cover a very large area, traveling from Kodiak, AK in the south up to Barrow, AK in the north, and making altitude profiles near the coast as well as in the interior. NOAA instrumentation on each flight includes: a flask sampling system, a continuous CO2/CH4/CO/H2O analyzer, a continuous ozone analyzer, and an ambient temperature and humidity sensor. GPS time and location from the aircraft's navigation system are also collected. Air samples collected in flight are analyzed at NOAA/ESRL for the major greenhouse gases and a variety of halocarbons and hydrocarbons that influence climate, stratospheric ozone, and air quality. Instruments on this aircraft are designed and deployed to be able to collect air samples and data autonomously, so that NOAA personnel visit the site only for installation at the beginning of each season. We present an assessment of the cavity ring-down spectroscopy (CRDS) CO2/CH4/CO/H2O analyzer performance operating on an aircraft over a three-year period. We describe the overall system for making accurate greenhouse gas measurements using a CRDS analyzer on an aircraft with minimal operator interaction. Short and long-term stability of the CRDS analyzer over a seven-month deployment period is better than 0.15 ppm, 2 ppb, and 5 ppb for CO2, CH4, CO respectively, considering differences of on-board reference tank measurements from a laboratory calibration performed prior to deployment. This stability is not affected by variation in pressure or temperature during flight. Biases and standard deviations of comparisons with flask samples suggest that atmospheric variability, flask-to-flask variability, and possible flask sampling biases may be driving biases in the comparison between flasks and in-situ CRDS measurements.

Genes Are Us

ERIC Educational Resources Information Center

Keller, Alexandra; Smith, David; Harrop, Brenda; Lamit, Louis; Schroer, Melanie; Wymore, Adam; Ueckert, Catherine

2012-01-01

Almost all living organisms, including plants, fungi, insects, and humans, have DNA. Variation in DNA, or genetic variation, is responsible for most of the diversity one sees in nature. By analyzing DNA, it is possible to create a DNA fingerprint that is unique to an organism. DNA fingerprinting is used in several disciplines of science, including…

Outbreak of H3N2 influenza at a US military base in Djibouti during the H1N1 pandemic of 2009.

PubMed

Cosby, Michael T; Pimentel, Guillermo; Nevin, Remington L; Fouad Ahmed, Salwa; Klena, John D; Amir, Ehab; Younan, Mary; Browning, Robert; Sebeny, Peter J

2013-01-01

Influenza pandemics have significant operational impact on deployed military personnel working in areas throughout the world. The US Department of Defense global influenza-like illness (ILI) surveillance network serves an important role in establishing baseline trends and can be leveraged to respond to outbreaks of respiratory illness. We identified and characterized an operationally unique outbreak of H3N2 influenza at Camp Lemonnier, Djibouti occurring simultaneously with the H1N1 pandemic of 2009 [A(H1N1)pdm09]. Enhanced surveillance for ILI was conducted at Camp Lemonnier in response to local reports of a possible outbreak during the A(H1N1)pdm09 pandemic. Samples were collected from consenting patients presenting with ILI (utilizing a modified case definition) and who completed a case report form. Samples were cultured and analyzed using standard real-time reverse transcriptase PCR (rt-RT-PCR) methodology and sequenced genetic material was phylogenetically compared to other published strains. rt-RT-PCR and DNA sequencing revealed that 25 (78%) of the 32 clinical samples collected were seasonal H3N2 and only 2 (6%) were A(H1N1)pdm09 influenza. The highest incidence of H3N2 occurred during the month of May and 80% of these were active duty military personnel. Phylogenetic analysis revealed that sequenced H3N2 strains were genetically similar to 2009 strains from the United States of America, Australia, and South east Asia. This outbreak highlights challenges in the investigation of influenza among deployed military populations and corroborates the public health importance of maintaining surveillance systems for ILI that can be enhanced locally when needed.

Outbreak of H3N2 Influenza at a US Military Base in Djibouti during the H1N1 Pandemic of 2009

PubMed Central

Cosby, Michael T.; Pimentel, Guillermo; Nevin, Remington L.; Fouad Ahmed, Salwa; Klena, John D.; Amir, Ehab; Younan, Mary; Browning, Robert; Sebeny, Peter J.

2013-01-01

Background Influenza pandemics have significant operational impact on deployed military personnel working in areas throughout the world. The US Department of Defense global influenza-like illness (ILI) surveillance network serves an important role in establishing baseline trends and can be leveraged to respond to outbreaks of respiratory illness. Objective We identified and characterized an operationally unique outbreak of H3N2 influenza at Camp Lemonnier, Djibouti occurring simultaneously with the H1N1 pandemic of 2009 [A(H1N1)pdm09]. Methods Enhanced surveillance for ILI was conducted at Camp Lemonnier in response to local reports of a possible outbreak during the A(H1N1)pdm09 pandemic. Samples were collected from consenting patients presenting with ILI (utilizing a modified case definition) and who completed a case report form. Samples were cultured and analyzed using standard real-time reverse transcriptase PCR (rt-RT-PCR) methodology and sequenced genetic material was phylogenetically compared to other published strains. Results rt-RT-PCR and DNA sequencing revealed that 25 (78%) of the 32 clinical samples collected were seasonal H3N2 and only 2 (6%) were A(H1N1)pdm09 influenza. The highest incidence of H3N2 occurred during the month of May and 80% of these were active duty military personnel. Phylogenetic analysis revealed that sequenced H3N2 strains were genetically similar to 2009 strains from the United States of America, Australia, and South east Asia. Conclusions This outbreak highlights challenges in the investigation of influenza among deployed military populations and corroborates the public health importance of maintaining surveillance systems for ILI that can be enhanced locally when needed. PMID:24339995

Microsphere-Based Multiplex Analysis of DNA Methylation in Acute Myeloid Leukemia

PubMed Central

Wertheim, Gerald B.W.; Smith, Catherine; Figueroa, Maria E.; Kalos, Michael; Bagg, Adam; Carroll, Martin; Master, Stephen R.

2015-01-01

Aberrant regulation of DNA methylation is characteristic of cancer cells and clearly influences phenotypes of various malignancies. Despite clear correlations between DNA methylation and patient outcome, tests that directly measure multiple-locus DNA methylation are typically expensive and technically challenging. Previous studies have demonstrated that the prognosis of patients with acute myeloid leukemia can be predicted by the DNA methylation pattern of 18 loci. We have developed a novel strategy, termed microsphere HpaII tiny fragment enrichment by ligation-mediated PCR (MELP), to simultaneously analyze the DNA methylation pattern at these loci using methylation-specific DNA digestion, fluorescently labeled microspheres, and branched DNA hybridization. The method uses techniques that are inexpensive and easily performed in a molecular laboratory. MELP accurately reflects the methylation levels at each locus analyzed and segregates patients with acute myeloid leukemia into prognostic subgroups. Our results demonstrate the usefulness of MELP as a platform for simultaneous evaluation of DNA methylation of multiple loci. PMID:24373919

Ultrafast and Wide Range Analysis of DNA Molecules Using Rigid Network Structure of Solid Nanowires

PubMed Central

Rahong, Sakon; Yasui, Takao; Yanagida, Takeshi; Nagashima, Kazuki; Kanai, Masaki; Klamchuen, Annop; Meng, Gang; He, Yong; Zhuge, Fuwei; Kaji, Noritada; Kawai, Tomoji; Baba, Yoshinobu

2014-01-01

Analyzing sizes of DNA via electrophoresis using a gel has played an important role in the recent, rapid progress of biology and biotechnology. Although analyzing DNA over a wide range of sizes in a short time is desired, no existing electrophoresis methods have been able to fully satisfy these two requirements. Here we propose a novel method using a rigid 3D network structure composed of solid nanowires within a microchannel. This rigid network structure enables analysis of DNA under applied DC electric fields for a large DNA size range (100 bp–166 kbp) within 13 s, which are much wider and faster conditions than those of any existing methods. The network density is readily varied for the targeted DNA size range by tailoring the number of cycles of the nanowire growth only at the desired spatial position within the microchannel. The rigid dense 3D network structure with spatial density control plays an important role in determining the capability for analyzing DNA. Since the present method allows the spatial location and density of the nanostructure within the microchannels to be defined, this unique controllability offers a new strategy to develop an analytical method not only for DNA but also for other biological molecules. PMID:24918865

Ultrafast and Wide Range Analysis of DNA Molecules Using Rigid Network Structure of Solid Nanowires

NASA Astrophysics Data System (ADS)

Rahong, Sakon; Yasui, Takao; Yanagida, Takeshi; Nagashima, Kazuki; Kanai, Masaki; Klamchuen, Annop; Meng, Gang; He, Yong; Zhuge, Fuwei; Kaji, Noritada; Kawai, Tomoji; Baba, Yoshinobu

2014-06-01

Analyzing sizes of DNA via electrophoresis using a gel has played an important role in the recent, rapid progress of biology and biotechnology. Although analyzing DNA over a wide range of sizes in a short time is desired, no existing electrophoresis methods have been able to fully satisfy these two requirements. Here we propose a novel method using a rigid 3D network structure composed of solid nanowires within a microchannel. This rigid network structure enables analysis of DNA under applied DC electric fields for a large DNA size range (100 bp-166 kbp) within 13 s, which are much wider and faster conditions than those of any existing methods. The network density is readily varied for the targeted DNA size range by tailoring the number of cycles of the nanowire growth only at the desired spatial position within the microchannel. The rigid dense 3D network structure with spatial density control plays an important role in determining the capability for analyzing DNA. Since the present method allows the spatial location and density of the nanostructure within the microchannels to be defined, this unique controllability offers a new strategy to develop an analytical method not only for DNA but also for other biological molecules.

PHIT for Duty, a Personal Health Intervention Tool for Psychological Health and Traumatic Brain Injury

DTIC Science & Technology

2013-04-01

Findings Post deployment health problems. The top three post deployment health problems mentioned were depression, anxiety and sleep issues... anxiety ) are immediately available to the iVA, which is able to determine how to proceed with the user. The iVA may choose to schedule a screening... anxiety , sleep quality, depression, and alcohol use). For each domain, the screening data are analyzed by the iVA and a subsequent detailed assessment

Scalable Parallel Methods for Analyzing Metagenomics Data at Extreme Scale

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

Daily, Jeffrey A.

2015-05-01

The field of bioinformatics and computational biology is currently experiencing a data revolution. The exciting prospect of making fundamental biological discoveries is fueling the rapid development and deployment of numerous cost-effective, high-throughput next-generation sequencing technologies. The result is that the DNA and protein sequence repositories are being bombarded with new sequence information. Databases are continuing to report a Moore’s law-like growth trajectory in their database sizes, roughly doubling every 18 months. In what seems to be a paradigm-shift, individual projects are now capable of generating billions of raw sequence data that need to be analyzed in the presence of alreadymore » annotated sequence information. While it is clear that data-driven methods, such as sequencing homology detection, are becoming the mainstay in the field of computational life sciences, the algorithmic advancements essential for implementing complex data analytics at scale have mostly lagged behind. Sequence homology detection is central to a number of bioinformatics applications including genome sequencing and protein family characterization. Given millions of sequences, the goal is to identify all pairs of sequences that are highly similar (or “homologous”) on the basis of alignment criteria. While there are optimal alignment algorithms to compute pairwise homology, their deployment for large-scale is currently not feasible; instead, heuristic methods are used at the expense of quality. In this dissertation, we present the design and evaluation of a parallel implementation for conducting optimal homology detection on distributed memory supercomputers. Our approach uses a combination of techniques from asynchronous load balancing (viz. work stealing, dynamic task counters), data replication, and exact-matching filters to achieve homology detection at scale. Results for a collection of 2.56M sequences show parallel efficiencies of ~75-100% on up to 8K cores, representing a time-to-solution of 33 seconds. We extend this work with a detailed analysis of single-node sequence alignment performance using the latest CPU vector instruction set extensions. Preliminary results reveal that current sequence alignment algorithms are unable to fully utilize widening vector registers.« less

Validation of a rapid DNA process with the RapidHIT® ID system using GlobalFiler® Express chemistry, a platform optimized for decentralized testing environments.

PubMed

Salceda, Susana; Barican, Arnaldo; Buscaino, Jacklyn; Goldman, Bruce; Klevenberg, Jim; Kuhn, Melissa; Lehto, Dennis; Lin, Frank; Nguyen, Phong; Park, Charles; Pearson, Francesca; Pittaro, Rick; Salodkar, Sayali; Schueren, Robert; Smith, Corey; Troup, Charles; Tsou, Dean; Vangbo, Mattias; Wunderle, Justus; King, David

2017-05-01

The RapidHIT ® ID is a fully automated sample-to-answer system for short tandem repeat (STR)-based human identification. The RapidHIT ID has been optimized for use in decentralized environments and processes presumed single source DNA samples, generating Combined DNA Index System (CODIS)-compatible DNA profiles in less than 90min. The system is easy to use, requiring less than one minute of hands-on time. Profiles are reviewed using centralized linking software, RapidLINK™ (IntegenX, Pleasanton, CA), a software tool designed to collate DNA profiles from single or multiple RapidHIT ID systems at different geographic locations. The RapidHIT ID has been designed to employ GlobalFiler ® Express and AmpFLSTR ® NGMSElect™, Thermo Fisher Scientific (Waltham, MA) STR chemistries. The Developmental Validation studies were performed using GlobalFiler ® Express with single source reference samples according to Scientific Working Group for DNA Analysis Methods guidelines. These results show that multiple RapidHIT ID systems networked with RapidLINK software form a highly reliable system for wide-scale deployment in locations such as police booking stations and border crossings enabling real-time testing of arrestees, potential human trafficking victims, and other instances where rapid turnaround is essential. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Analysis of DNA Methylation Status in Bodily Fluids for Early Detection of Cancer

PubMed Central

Yokoi, Keigo; Yamashita, Keishi; Watanabe, Masahiko

2017-01-01

Epigenetic alterations by promoter DNA hypermethylation and gene silencing in cancer have been reported over the past few decades. DNA hypermethylation has great potential to serve as a screening marker, a prognostic marker, and a therapeutic surveillance marker in cancer clinics. Some bodily fluids, such as stool or urine, were obtainable without any invasion to the body. Thus, such bodily fluids were suitable samples for high throughput cancer surveillance. Analyzing the methylation status of bodily fluids around the cancer tissue may, additionally, lead to the early detection of cancer, because several genes in cancer tissues are reported to be cancer-specifically hypermethylated. Recently, several studies that analyzed the methylation status of DNA in bodily fluids were conducted, and some of the results have potential for future development and further clinical use. In fact, a stool DNA test was approved by the U.S. Food and Drug Administration (FDA) for the screening of colorectal cancer. Another promising methylation marker has been identified in various bodily fluids for several cancers. We reviewed studies that analyzed DNA methylation in bodily fluids as a less-invasive cancer screening. PMID:28358330

Ground Deployment Demonstration and Material Testing for Solar Sail

NASA Astrophysics Data System (ADS)

Huang, Xiaoqi; Cheng, Zhengai; Liu, Yufei; Wang, Li

2016-07-01

Solar Sail is a kind of spacecraft that can achieve extremely high velocity by light pressure instead of chemical fuel. The great accelerate rely on its high area-to-mass ratio. So solar sail is always designed in huge size and it use ultra thin and light weight materials. For 100-meter class solar sail, two key points must be considered in the design process. They are fold-deployment method, and material property change in space environment. To test and verify the fold-deployment technology, a 8*8m principle prototype was developed. Sail membrane folding in method of IKAROS, Nanosail-D , and new proposed L-shape folding pattern were tested on this prototype. Their deployment properties were investigated in detail, and comparisons were made between them. Also, the space environment suitability of ultra thin polyimide films as candidate solar sail material was analyzed. The preliminary test results showed that membrane by all the folding method could deploy well. Moreover, sail membrane folding by L-shape pattern deployed more rapidly and more organized among the three folding pattern tested. The mechanical properties of the polyimide had no significant change after electron irradiation. As the preliminary research on the key technology of solar sail spacecraft, in this paper, the results of the study would provide important basis on large-scale solar sail membrane select and fold-deploying method design.

An efficient genetic algorithm for maximum coverage deployment in wireless sensor networks.

PubMed

Yoon, Yourim; Kim, Yong-Hyuk

2013-10-01

Sensor networks have a lot of applications such as battlefield surveillance, environmental monitoring, and industrial diagnostics. Coverage is one of the most important performance metrics for sensor networks since it reflects how well a sensor field is monitored. In this paper, we introduce the maximum coverage deployment problem in wireless sensor networks and analyze the properties of the problem and its solution space. Random deployment is the simplest way to deploy sensor nodes but may cause unbalanced deployment and therefore, we need a more intelligent way for sensor deployment. We found that the phenotype space of the problem is a quotient space of the genotype space in a mathematical view. Based on this property, we propose an efficient genetic algorithm using a novel normalization method. A Monte Carlo method is adopted to design an efficient evaluation function, and its computation time is decreased without loss of solution quality using a method that starts from a small number of random samples and gradually increases the number for subsequent generations. The proposed genetic algorithms could be further improved by combining with a well-designed local search. The performance of the proposed genetic algorithm is shown by a comparative experimental study. When compared with random deployment and existing methods, our genetic algorithm was not only about twice faster, but also showed significant performance improvement in quality.

Functional consequences of inducible genetic elements from the p53 SOS response in a mammalian organ system.

PubMed

Guthrie, O'neil W

2017-10-01

In response to DNA damage from ultraviolet (UV) radiation, bacteria deploy the SOS response in order to limit cell death. This bacterial SOS response is characterized by an increase in the recA gene that transactivates expression of multiple DNA repair genes. The current series of experiments demonstrate that a mammalian organ system (the cochlea) that is not evolutionarily conditioned to UV radiation can elicit SOS responses that are reminiscent of that of bacteria. This mammalian SOS response is characterized by an increase in the p53 gene with activation of multiple DNA repair genes that harbor p53 response elements in their promoters. Furthermore, the experimental results provide support for the notion of a convergent trigger paradox, where independent SOS triggers facilitate disparate physiologic sequelae (loss vs. recovery of function). Therefore, it is proposed that the mammalian SOS response is multifunctional and manipulation of this endogenous response could be exploited in future biomedical interventions. Copyright © 2017 Elsevier Inc. All rights reserved.

A new model for ancient DNA decay based on paleogenomic meta-analysis.

PubMed

Kistler, Logan; Ware, Roselyn; Smith, Oliver; Collins, Matthew; Allaby, Robin G

2017-06-20

The persistence of DNA over archaeological and paleontological timescales in diverse environments has led to a revolutionary body of paleogenomic research, yet the dynamics of DNA degradation are still poorly understood. We analyzed 185 paleogenomic datasets and compared DNA survival with environmental variables and sample ages. We find cytosine deamination follows a conventional thermal age model, but we find no correlation between DNA fragmentation and sample age over the timespans analyzed, even when controlling for environmental variables. We propose a model for ancient DNA decay wherein fragmentation rapidly reaches a threshold, then subsequently slows. The observed loss of DNA over time may be due to a bulk diffusion process in many cases, highlighting the importance of tissues and environments creating effectively closed systems for DNA preservation. This model of DNA degradation is largely based on mammal bone samples due to published genomic dataset availability. Continued refinement to the model to reflect diverse biological systems and tissue types will further improve our understanding of ancient DNA breakdown dynamics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Formation of template-switching artifacts by linear amplification.

PubMed

Chakravarti, Dhrubajyoti; Mailander, Paula C

2008-07-01

Linear amplification is a method of synthesizing single-stranded DNA from either a single-stranded DNA or one strand of a double-stranded DNA. In this protocol, molecules of a single primer DNA are extended by multiple rounds of DNA synthesis at high temperature using thermostable DNA polymerases. Although linear amplification generates the intended full-length single-stranded product, it is more efficient over single-stranded templates than double-stranded templates. We analyzed linear amplification over single- or double-stranded mouse H-ras DNA (exon 1-2 region). The single-stranded H-ras template yielded only the intended product. However, when the double-stranded template was used, additional artifact products were observed. Increasing the concentration of the double-stranded template produced relatively higher amounts of these artifact products. One of the artifact DNA bands could be mapped and analyzed by sequencing. It contained three template-switching products. These DNAs were formed by incomplete DNA strand extension over the template strand, followed by switching to the complementary strand at a specific Ade nucleotide within a putative hairpin sequence, from which DNA synthesis continued over the complementary strand.

High-Resolution Melting (HRM) of Hypervariable Mitochondrial DNA Regions for Forensic Science.

PubMed

Dos Santos Rocha, Alípio; de Amorim, Isis Salviano Soares; Simão, Tatiana de Almeida; da Fonseca, Adenilson de Souza; Garrido, Rodrigo Grazinoli; Mencalha, Andre Luiz

2018-03-01

Forensic strategies commonly are proceeding by analysis of short tandem repeats (STRs); however, new additional strategies have been proposed for forensic science. Thus, this article standardized the high-resolution melting (HRM) of DNA for forensic analyzes. For HRM, mitochondrial DNA (mtDNA) from eight individuals were extracted from mucosa swabs by DNAzol reagent, samples were amplified by PCR and submitted to HRM analysis to identify differences in hypervariable (HV) regions I and II. To confirm HRM, all PCR products were DNA sequencing. The data suggest that is possible discriminate DNA from different samples by HRM curves. Also, uncommon dual-dissociation was identified in a single PCR product, increasing HRM analyzes by evaluation of melting peaks. Thus, HRM is accurate and useful to screening small differences in HVI and HVII regions from mtDNA and increase the efficiency of laboratory routines based on forensic genetics. © 2017 American Academy of Forensic Sciences.

Office of Naval Research Graduate Traineeship Award in Ocean Acoustics for Ankita Deepak Jain

DTIC Science & Technology

2012-09-30

Ziegesar, O., “Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific,” Molecular Ecology 7(6): 695-707 (1998) ...ocean, and correlating measured noise with local wind speed. Mexican waters of the North Pacific Ocean are known to be wintering grounds for humpback ... whales [10]. During this experiment, many marine mammal vocalizations were recorded by the deployed hydrophones. We are in the process of

ChIP-seq.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

Owing to its digital nature, ChIP-seq has become the standard method for genome-wide ChIP analysis. Using next-generation sequencing platforms (notably the Illumina Genome Analyzer), millions of short sequence reads can be obtained. The densities of recovered ChIP sequence reads along the genome are used to determine the binding sites of the protein. Although a relatively small amount of ChIP DNA is required for ChIP-seq, the current sequencing platforms still require amplification of the ChIP DNA by ligation-mediated PCR (LM-PCR). This protocol, which involves linker ligation followed by size selection, is the standard ChIP-seq protocol using an Illumina Genome Analyzer. The size-selected ChIP DNA is amplified by LM-PCR and size-selected for the second time. The purified ChIP DNA is then loaded into the Genome Analyzer. The ChIP DNA can also be processed in parallel for ChIP-chip results. © 2018 Cold Spring Harbor Laboratory Press.

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline.

PubMed

Reid, Jeffrey G; Carroll, Andrew; Veeraraghavan, Narayanan; Dahdouli, Mahmoud; Sundquist, Andreas; English, Adam; Bainbridge, Matthew; White, Simon; Salerno, William; Buhay, Christian; Yu, Fuli; Muzny, Donna; Daly, Richard; Duyk, Geoff; Gibbs, Richard A; Boerwinkle, Eric

2014-01-29

Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clinical practice. This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, and sharing validated tools and results. To address these challenges, we have developed the Mercury analysis pipeline and deployed it in local hardware and the Amazon Web Services cloud via the DNAnexus platform. Mercury is an automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. By taking advantage of cloud computing and with Mercury implemented on the DNAnexus platform, we have demonstrated a powerful combination of a robust and fully validated software pipeline and a scalable computational resource that, to date, we have applied to more than 10,000 whole genome and whole exome samples.

Demand Response and Energy Storage Integration Study

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

Ma, Ookie; Cheung, Kerry; Olsen, Daniel J.

2016-03-01

Demand response and energy storage resources present potentially important sources of bulk power system services that can aid in integrating variable renewable generation. While renewable integration studies have evaluated many of the challenges associated with deploying large amounts of variable wind and solar generation technologies, integration analyses have not yet fully incorporated demand response and energy storage resources. This report represents an initial effort in analyzing the potential integration value of demand response and energy storage, focusing on the western United States. It evaluates two major aspects of increased deployment of demand response and energy storage: (1) Their operational valuemore » in providing bulk power system services and (2) Market and regulatory issues, including potential barriers to deployment.« less

Space Station tethered refueling facility operations

NASA Technical Reports Server (NTRS)

Kiefel, E. R.; Rudolph, L. K.; Fester, D. A.

1986-01-01

The space-based orbital transfer vehicle will require a large cryogenic fuel storage facility at the Space Station. An alternative to fuel storage onboard the Space Station, is on a tethered orbital refueling facility (TORF) which is separated from the Space Station by a sufficient distance to induce a gravity gradient to settle the propellants. Facility operations are a major concern associated with a tethered LO2/LH2 storage depot. A study was carried out to analyze these operations so as to identify the preferred TORF deployment direction (up or down) and whether the TORF should be permanently or intermittently deployed. The analyses considered safety, contamination, rendezvous, servicing, transportation rate, communication, and viewing. An upwardly, intermittently deployed facility is the preferred configuration for a tethered cryogenic fuel storage.

Demand Response and Energy Storage Integration Study

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

Ma, Ookie; Cheung, Kerry

Demand response and energy storage resources present potentially important sources of bulk power system services that can aid in integrating variable renewable generation. While renewable integration studies have evaluated many of the challenges associated with deploying large amounts of variable wind and solar generation technologies, integration analyses have not yet fully incorporated demand response and energy storage resources. This report represents an initial effort in analyzing the potential integration value of demand response and energy storage, focusing on the western United States. It evaluates two major aspects of increased deployment of demand response and energy storage: (1) Their operational valuemore » in providing bulk power system services and (2) Market and regulatory issues, including potential barriers to deployment.« less

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

Short, J.W.; Harris, P.M.

Mussels (Mytilus trossulus) were deployed at 22 locations inside Prince William Sound and 16 locations outside the Sound at depths of 1, 5 and 25 m for 2 to 8 weeks to determine the biological availability and persistence of petroleum-derived hydrocarbons from the Exxon Valdez Oil (EVO) spill. Four successive deployments were made in 1989, and two each in 1990 and 1991. Mussels were analyzed for 27 alkane and 43 polynuclear aromatic hydrocarbon (PAH) analytes. PAH concentrations derived from EVO in mussels decreased with depth, time, and distance from heavily oiled beaches. Hydrocarbon accumulation derived from EVO by deployed musselsmore » indicates petroleum hydrocarbons were available to subsurface marine fauna the summer following the spill, which may be a route of oil ingestion exposure by fauna at high trophic levels.« less

Analyzing the Impacts of a Biogas-to-Electricity Purchase Incentive on Electric Vehicle Deployment with the MA 3T Vehicle Choice Model

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

Podkaminer, Kara; Xie, Fei; Lin, Zhenhong

In 2014, the EPA approved a biogas-to-electricity pathway under the Renewable Fuel Standard (RFS). However, no specific applications for this pathway have been approved to date. This analysis helps understand the impact of the pathway by representing the biogas-to-electricity pathway as a point of purchase incentive and tests the impact of this incentive on EV deployment using a vehicle consumer choice model.

Medical-encounter mental health diagnoses, non-fatal injury and polypharmacy indicators of risk for accident death in the US Army enlisted soldiers, 2004-2009.

PubMed

Lewandowski-Romps, Lisa; Schroeder, Heather M; Berglund, Patricia A; Colpe, Lisa J; Cox, Kenneth; Hauret, Keith; Hay, Jeffrey D; Jones, Bruce; Little, Roderick J A; Mitchell, Colter; Schoenbaum, Michael; Schulz, Paul; Stein, Murray B; Ursano, Robert J; Heeringa, Steven G

2018-06-01

Accidents are a leading cause of deaths in U.S. active duty personnel. Understanding accident deaths during wartime could facilitate future operational planning and inform risk prevention efforts. This study expands prior research, identifying health risk factors associated with U.S. Army accident deaths during the Afghanistan and Iraq war. Military records for 2004-2009 enlisted, active duty, Regular Army soldiers were analyzed using logistic regression modeling to identify mental health, injury, and polypharmacy (multiple narcotic and/or psychotropic medications) predictors of accident deaths for current, previously, and never deployed groups. Deployed soldiers with anxiety diagnoses showed higher risk for accident deaths. Over half had anxiety diagnoses prior to being deployed, suggesting anticipatory anxiety or symptom recurrence may contribute to high risk. For previously deployed soldiers, traumatic brain injury (TBI) indicated higher risk. Two-thirds of these soldiers had first TBI medical-encounter while non-deployed, but mild, combat-related TBIs may have been undetected during deployments. Post-Traumatic Stress Disorder (PTSD) predicted higher risk for never deployed soldiers, as did polypharmacy which may relate to reasons for deployment ineligibility. Health risk predictors for Army accident deaths are identified and potential practice and policy implications discussed. Further research could test for replicability and expand models to include unobserved factors or modifiable mechanisms related to high risk. PTSD predicted high risk among those never deployed, suggesting importance of identification, treatment, and prevention of non-combat traumatic events. Finally, risk predictors overlapped with those identified for suicides, suggesting effective intervention might reduce both types of deaths. Copyright © 2017 Elsevier Inc. All rights reserved.

Systematic random sampling of the comet assay.

PubMed

McArt, Darragh G; Wasson, Gillian R; McKerr, George; Saetzler, Kurt; Reed, Matt; Howard, C Vyvyan

2009-07-01

The comet assay is a technique used to quantify DNA damage and repair at a cellular level. In the assay, cells are embedded in agarose and the cellular content is stripped away leaving only the DNA trapped in an agarose cavity which can then be electrophoresed. The damaged DNA can enter the agarose and migrate while the undamaged DNA cannot and is retained. DNA damage is measured as the proportion of the migratory 'tail' DNA compared to the total DNA in the cell. The fundamental basis of these arbitrary values is obtained in the comet acquisition phase using fluorescence microscopy with a stoichiometric stain in tandem with image analysis software. Current methods deployed in such an acquisition are expected to be both objectively and randomly obtained. In this paper we examine the 'randomness' of the acquisition phase and suggest an alternative method that offers both objective and unbiased comet selection. In order to achieve this, we have adopted a survey sampling approach widely used in stereology, which offers a method of systematic random sampling (SRS). This is desirable as it offers an impartial and reproducible method of comet analysis that can be used both manually or automated. By making use of an unbiased sampling frame and using microscope verniers, we are able to increase the precision of estimates of DNA damage. Results obtained from a multiple-user pooled variation experiment showed that the SRS technique attained a lower variability than that of the traditional approach. The analysis of a single user with repetition experiment showed greater individual variances while not being detrimental to overall averages. This would suggest that the SRS method offers a better reflection of DNA damage for a given slide and also offers better user reproducibility.

Comparative analysis of protocols for DNA extraction from soybean caterpillars.

PubMed

Palma, J; Valmorbida, I; da Costa, I F D; Guedes, J V C

2016-04-07

Genomic DNA extraction is crucial for molecular research, including diagnostic and genome characterization of different organisms. The aim of this study was to comparatively analyze protocols of DNA extraction based on cell lysis by sarcosyl, cetyltrimethylammonium bromide, and sodium dodecyl sulfate, and to determine the most efficient method applicable to soybean caterpillars. DNA was extracted from specimens of Chrysodeixis includens and Spodoptera eridania using the aforementioned three methods. DNA quantification was performed using spectrophotometry and high molecular weight DNA ladders. The purity of the extracted DNA was determined by calculating the A260/A280 ratio. Cost and time for each DNA extraction method were estimated and analyzed statistically. The amount of DNA extracted by these three methods was sufficient for PCR amplification. The sarcosyl method yielded DNA of higher purity, because it generated a clearer pellet without viscosity, and yielded high quality amplification products of the COI gene I. The sarcosyl method showed lower cost per extraction and did not differ from the other methods with respect to preparation times. Cell lysis by sarcosyl represents the best method for DNA extraction in terms of yield, quality, and cost effectiveness.

Effect of dactyloscopic powders on DNA profiling from enhanced fingerprints: results from an experimental study.

PubMed

Tozzo, Pamela; Giuliodori, Alice; Rodriguez, Daniele; Caenazzo, Luciana

2014-03-01

We conducted a study on the effect of fingerprint enhancement methods on subsequent short tandem repeat profiling. First, we performed a study typing blood traces deposited on 5 different surfaces, treated with 8 types of dactyloscopic powders. Three different DNA extraction methods were used. Subsequently, we analyzed latent fingerprints on the same 5 surfaces enhanced with the 8 different powders used in the first part of the study. This study has demonstrated that DNA profiling can be performed on fingerprints left on different substrates, and the substrate will affect the amount of DNA that can be recovered for DNA typing. In the first phase of the study, a profile was obtained in 92% of the 120 samples analyzed; in the second part, in 55% of the 80 samples analyzed, we obtained a profile complete in 32.5% of the cases. From the results obtained, it seems that the powders used in latent fingerprints enhancement, rather than having a direct inhibitory effect on extraction and amplification of DNA, may cause partial degradation of DNA, reducing the efficiency of amplification reaction. It should not be forgotten that these results were obtained under laboratory conditions, and in real caseworks, there may still be different problems involved.

DNA content of hepatocyte and erythrocyte nuclei of the spined loach (Cobitis taenia L.) and its polyploid forms.

PubMed

Juchno, Dorota; Lackowska, Bozena; Boron, Alicja; Kilarski, Wincenty

2010-09-01

We analyzed the DNA content of hepatocyte and erythrocyte nuclei of the spined loach Cobitis taenia (diploid) and its allopolyploid forms. Twenty triploid females and one tetraploid were used. At least 20,000 hepatocyte and erythrocyte nuclei were acquired and analyzed by flow cytometry. C. taenia erythrocyte nuclei contain 3.15 +/- 0.21 pg of DNA and the hepatocyte nuclei 4.45 +/- 0.46 pg of DNA. Triploid Cobitis have 5.08 +/- 0.41 pg of DNA in erythrocyte nuclei and 6.11 +/- 0.40 pg of DNA in hepatocyte nuclei, whereas the tetraploid erythrocyte and hepatocyte nuclei contained 6.60 and 7.40 pg of DNA, respectively. In general, the DNA contents correlate positively with the ploidy level of the fish investigated. The DNA content variation in the hepatocyte and erythrocyte nuclei may be due to differences in extent of chromatin condensation, which is more pronounced in the erythrocyte than hepatocyte nuclei, or to the several orders of ploidy that occur in the parenchymal liver cells.

Histological analysis and ancient DNA amplification of human bone remains found in caius iulius polybius house in pompeii.

PubMed

Cipollaro, M; Di Bernado, G; Forte, A; Galano, G; De Masi, L; Galderisi, U; Guarino, F M; Angelini, F; Cascino, A

1999-09-01

Thirteen skeletons found in the Caius Iulius Polybius house, which has been the object of intensive study since its discovery in Pompeii 250 years ago, have provided an opportunity to study either bone diagenesis by histological investigation or ancient DNA by polymerase chain reaction analysis. DNA analysis was done by amplifying both X- and Y-chromosomes amelogenin loci and Y-specific alphoid repeat locus. The von Willebrand factor (vWF) microsatellite locus on chromosome 12 was also analyzed for personal identification in two individuals showing alleles with 10/11 and 12/12 TCTA repeats, respectively. Technical problems were the scarcity of DNA content from osteocytes, DNA molecule fragmentation, microbial contamination which change bone structure, contaminating human DNA which results from mishandling, and frequent presence of Taq DNA polymerase inhibiting molecules like polyphenols and heavy metals. The results suggest that the remains contain endogenous human DNA that can be amplified and analyzed. The amplifiability of DNA corresponds to the bone preservation and dynamics of the burial conditions subsequent to the 79 A.D. eruption.

Determinants of affinity and mode of DNA binding at the carboxy terminus of the bacteriophage SPO1-encoded type II DNA-binding protein, TF1.

PubMed

Andera, L; Geiduschek, E P

1994-03-01

The role of the carboxy-terminal amino acids of the bacteriophage SPO1-encoded type II DNA-binding protein, TF1, in DNA binding was analyzed. Chain-terminating mutations truncating the normally 99-amino-acid TF1 at amino acids 96, 97, and 98 were constructed, as were missense mutations substituting cysteine, arginine, and serine for phenylalanine at amino acid 97 and tryptophan for lysine at amino acid 99. The binding of the resulting proteins to a synthetic 44-bp binding site in 5-(hydroxymethyl)uracil DNA, to binding sites in larger SPO1 [5-(hydroxymethyl)uracil-containing] DNA fragments, and to thymine-containing homologous DNA was analyzed by gel retardation and also by DNase I and hydroxy radical footprinting. We conclude that the C tail up to and including phenylalanine at amino acid 97 is essential for DNA binding and that the two C-terminal amino acids, 98 and 99, are involved in protein-protein interactions between TF1 dimers bound to DNA.

Cell-free DNA characteristics and chimerism analysis in patients after allogeneic cell transplantation.

PubMed

Duque-Afonso, Jesus; Waterhouse, Miguel; Pfeifer, Dietmar; Follo, Marie; Duyster, Justus; Bertz, Hartmut; Finke, Jürgen

2018-02-01

Cell-free DNA (cfDNA) isolated from plasma or serum has received increasing interest for diagnostic applications in pregnancy, solid tumors and solid organ transplantation. The reported clinical usefulness of cfDNA obtained from plasma or serum in patients undergoing allogeneic cell transplantation (alloHSCT) is scarce. To analyze the potential clinical utility of cfDNA chimerism analysis after alloHSCT. A total of 196 samples obtained from 110 patients were investigated for their chimeric status both in peripheral blood and plasma using standard PCR for microsatellite amplification. Plasma DNA size distribution was analyzed using capillary electrophoresis. The mean cfDNA concentration in the transplanted patients was 469ng/ml (range: 50-10,700ng/ml). The size range of almost 80% of the analyzed fragments was between 80 and 200bp. In 41 out of the 110 patients included in the study a mixture of donor and recipient plasma cfDNA was detected. There was a statistically significant difference in the percentage of plasma mixed chimerism between the patients without transplant related complications and the patients with either GvHD (p<0.05) or relapse (p<0.01). In those patients who showed improvement of GvHD also displayed a decrease in the observable percentage of recipient cfDNA during GvHD treatment. In patients without improvement or even with worsening of acute GvHD, stable or increasing levels of recipient cfDNA were detected. cfDNA in combination with peripheral blood and bone marrow cell chimerism analysis might improve its utility in the clinic in particular in those patients with clinical complications after alloHSCT. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Risk Factors, Methods, and Timing of Suicide Attempts Among US Army Soldiers

PubMed Central

Ursano, Robert J.; Kessler, Ronald C.; Stein, Murray B.; Naifeh, James A.; Aliaga, Pablo A.; Fullerton, Carol S.; Wynn, Gary H.; Vegella, Patti L.; Ng, Tsz Hin Hinz; Zhang, Bailey G.; Wryter, Christina L.; Sampson, Nancy A.; Kao, Tzu-Cheg; Colpe, Lisa J.; Schoenbaum, Michael; McCarroll, James E.; Cox, Kenneth L.; Heeringa, Steven G.

2016-01-01

IMPORTANCE Suicide attempts in the US Army have risen in the past decade. Understanding the association between suicide attempts and deployment, as well as method and timing of suicide attempts, can assist in developing interventions. OBJECTIVE To examine suicide attempt risk factors, methods, and timing among soldiers currently deployed, previously deployed, and never deployed at the time this study was conducted. DESIGN, SETTING, AND PARTICIPANTS This longitudinal, retrospective cohort study of Regular Army–enlisted soldiers on active duty from 2004 through 2009 used individual-level person-month records to examine risk factors (sociodemographic, service related, and mental health), method, and time of suicide attempt by deployment status (never, currently, and previously deployed). Administrative data for the month before each of 9650 incident suicide attempts and an equal-probability sample of 153 528 control person-months for other soldiers were analyzed using a discrete-time survival framework. MAIN OUTCOMES AND MEASURES Suicide attempts and career, mental health, and demographic predictors were obtained from administrative and medical records. RESULTS Of the 9650 enlisted soldiers who attempted suicide, 86.3% were male, 68.4% were younger than 30 years, 59.8% were non-Hispanic white, 76.5%were high school educated, and 54.7% were currently married. The 40.4% of enlisted soldiers who had never been deployed (n = 12 421 294 person-months) accounted for 61.1% of enlisted soldiers who attempted suicide (n = 5894 cases). Risk among those never deployed was highest in the second month of service (103 per 100 000 person-months). Risk among soldiers on their first deployment was highest in the sixth month of deployment (25 per 100 000 person-months). For those previously deployed, risk was highest at 5 months after return (40 per 100 000 person-months). Currently and previously deployed soldiers were more likely to attempt suicide with a firearm than those never deployed (currently deployed: OR, 4.0; 95% CI, 2.9–5.6; previously deployed: OR, 2.7; 95% CI, 1.8–3.9). Across deployment status, suicide attempts were more likely among soldiers who were women (currently deployed: OR, 3.4; 95% CI, 3.0–4.0; previously deployed: OR, 1.5; 95% CI, 1.4–1.7; and never deployed: OR, 2.4; 95% CI, 2.3–2.6), in their first 2 years of service (currently deployed: OR, 1.9; 95% CI, 1.5–2.3; previously deployed: OR, 2.2; 95% CI, 1.9–2.7; and never deployed: OR, 3.1; 95% CI, 2.7–3.6), and had a recently received a mental health diagnosis in the previous month (currently deployed: OR, 29.8; 95% CI, 25.0–35.5; previously deployed: OR, 22.2; 95% CI, 20.1–24.4; and never deployed: OR, 15.0; 95% CI, 14.2–16.0). Among soldiers with 1 previous deployment, odds of a suicide attempt were higher for those who screened positive for depression or posttraumatic stress disorder after return from deployment and particularly at follow-up screening, about 4 to 6 months after deployment (depression: OR, 1.4; 95% CI, 1.1–1.9; posttraumatic stress disorder: OR, 2.4; 95% CI, 2.1–2.8). CONCLUSIONS AND RELEVANCE Identifying the timing and risk factors for suicide attempt in soldiers requires consideration of environmental context, individual characteristics, and mental health. These factors can inform prevention efforts. PMID:27224848

Risk Factors, Methods, and Timing of Suicide Attempts Among US Army Soldiers.

PubMed

Ursano, Robert J; Kessler, Ronald C; Stein, Murray B; Naifeh, James A; Aliaga, Pablo A; Fullerton, Carol S; Wynn, Gary H; Vegella, Patti L; Ng, Tsz Hin Hinz; Zhang, Bailey G; Wryter, Christina L; Sampson, Nancy A; Kao, Tzu-Cheg; Colpe, Lisa J; Schoenbaum, Michael; McCarroll, James E; Cox, Kenneth L; Heeringa, Steven G

2016-07-01

Suicide attempts in the US Army have risen in the past decade. Understanding the association between suicide attempts and deployment, as well as method and timing of suicide attempts, can assist in developing interventions. To examine suicide attempt risk factors, methods, and timing among soldiers currently deployed, previously deployed, and never deployed at the time this study was conducted. This longitudinal, retrospective cohort study of Regular Army-enlisted soldiers on active duty from 2004 through 2009 used individual-level person-month records to examine risk factors (sociodemographic, service related, and mental health), method, and time of suicide attempt by deployment status (never, currently, and previously deployed). Administrative data for the month before each of 9650 incident suicide attempts and an equal-probability sample of 153 528 control person-months for other soldiers were analyzed using a discrete-time survival framework. Suicide attempts and career, mental health, and demographic predictors were obtained from administrative and medical records. Of the 9650 enlisted soldiers who attempted suicide, 86.3% were male, 68.4% were younger than 30 years, 59.8% were non-Hispanic white, 76.5% were high school educated, and 54.7% were currently married. The 40.4% of enlisted soldiers who had never been deployed (n = 12 421 294 person-months) accounted for 61.1% of enlisted soldiers who attempted suicide (n = 5894 cases). Risk among those never deployed was highest in the second month of service (103 per 100 000 person-months). Risk among soldiers on their first deployment was highest in the sixth month of deployment (25 per 100 000 person-months). For those previously deployed, risk was highest at 5 months after return (40 per 100 000 person-months). Currently and previously deployed soldiers were more likely to attempt suicide with a firearm than those never deployed (currently deployed: OR, 4.0; 95% CI, 2.9-5.6; previously deployed: OR, 2.7; 95% CI, 1.8-3.9). Across deployment status, suicide attempts were more likely among soldiers who were women (currently deployed: OR, 3.4; 95% CI, 3.0-4.0; previously deployed: OR, 1.5; 95% CI, 1.4-1.7; and never deployed: OR, 2.4; 95% CI, 2.3-2.6), in their first 2 years of service (currently deployed: OR, 1.9; 95% CI, 1.5-2.3; previously deployed: OR, 2.2; 95% CI, 1.9-2.7; and never deployed: OR, 3.1; 95% CI, 2.7-3.6), and had a recently received a mental health diagnosis in the previous month (currently deployed: OR, 29.8; 95% CI, 25.0-35.5; previously deployed: OR, 22.2; 95% CI, 20.1-24.4; and never deployed: OR, 15.0; 95% CI, 14.2-16.0). Among soldiers with 1 previous deployment, odds of a suicide attempt were higher for those who screened positive for depression or posttraumatic stress disorder after return from deployment and particularly at follow-up screening, about 4 to 6 months after deployment (depression: OR, 1.4; 95% CI, 1.1-1.9; posttraumatic stress disorder: OR, 2.4; 95% CI, 2.1-2.8). Identifying the timing and risk factors for suicide attempt in soldiers requires consideration of environmental context, individual characteristics, and mental health. These factors can inform prevention efforts.

Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA

NASA Astrophysics Data System (ADS)

Fye, Richard M.; Benham, Craig J.

1999-03-01

Local denaturation, the separation at specific sites of the two strands comprising the DNA double helix, is one of the most fundamental processes in biology, required to allow the base sequence to be read both in DNA transcription and in replication. In living organisms this process can be mediated by enzymes which regulate the amount of superhelical stress imposed on the DNA. We present a numerically exact technique for analyzing a model of denaturation in superhelically stressed DNA. This approach is capable of predicting the locations and extents of transition in circular superhelical DNA molecules of kilobase lengths and specified base pair sequences. It can also be used for closed loops of DNA which are typically found in vivo to be kilobases long. The analytic method consists of an integration over the DNA twist degrees of freedom followed by the introduction of auxiliary variables to decouple the remaining degrees of freedom, which allows the use of the transfer matrix method. The algorithm implementing our technique requires O(N2) operations and O(N) memory to analyze a DNA domain containing N base pairs. However, to analyze kilobase length DNA molecules it must be implemented in high precision floating point arithmetic. An accelerated algorithm is constructed by imposing an upper bound M on the number of base pairs that can simultaneously denature in a state. This accelerated algorithm requires O(MN) operations, and has an analytically bounded error. Sample calculations show that it achieves high accuracy (greater than 15 decimal digits) with relatively small values of M (M<0.05N) for kilobase length molecules under physiologically relevant conditions. Calculations are performed on the superhelical pBR322 DNA sequence to test the accuracy of the method. With no free parameters in the model, the locations and extents of local denaturation predicted by this analysis are in quantitatively precise agreement with in vitro experimental measurements. Calculations performed on the fructose-1,6-bisphosphatase gene sequence from yeast show that this approach can also accurately treat in vivo denaturation.

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

PubMed

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

2000-04-28

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

Protection of cadmium chloride induced DNA damage by Lamiaceae plants

PubMed Central

Thirugnanasampandan, Ramaraj; Jayakumar, Rajarajeswaran

2011-01-01

Objective To analyze the total phenolic content, DNA protecting and radical scavenging activity of ethanolic leaf extracts of three Lamiaceae plants, i.e. Anisomelos malabarica (A. malabarica), Leucas aspera (L. aspera) and Ocimum basilicum (O. basilicum). Methods The total polyphenols and flavonoids were analyzed in the ethanolic leaf extracts of the lamiaceae plants. To determine the DNA protecting activity, various concentrations of the plant extracts were prepared and treated on cultured HepG2 human lung cancer cells. The pretreated cells were exposed to H2O2 to induce DNA damage through oxidative stress. Comet assay was done and the tail length of individual comets was measured. Nitric oxide and superoxide anion scavenging activities of lamiaceae plants were analyzed. Results Among the three plant extracts, the highest amount of total phenolic content was found in O. basilicum (189.33 mg/g), whereas A. malabarica showed high levels of flavonoids (10.66 mg/g). O. basilicum also showed high levels of DNA protecting (85%) and radical scavenging activity. Conclusions The results of this study shows that bioactive phenols present in lamiaceae plants may prevent carcinogenesis through scavenging free radicals and inhibiting DNA damage. PMID:23569799

Hemodynamic Changes Caused by Flow Diverters in Rabbit Aneurysm Models: Comparison of Virtual and Realistic FD Deployments Based on Micro-CT Reconstruction

PubMed Central

Fang, Yibin; Yu, Ying; Cheng, Jiyong; Wang, Shengzhang; Wang, Kuizhong; Liu, Jian-Min; Huang, Qinghai

2013-01-01

Adjusting hemodynamics via flow diverter (FD) implantation is emerging as a novel method of treating cerebral aneurysms. However, most previous FD-related hemodynamic studies were based on virtual FD deployment, which may produce different hemodynamic outcomes than realistic (in vivo) FD deployment. We compared hemodynamics between virtual FD and realistic FD deployments in rabbit aneurysm models using computational fluid dynamics (CFD) simulations. FDs were implanted for aneurysms in 14 rabbits. Vascular models based on rabbit-specific angiograms were reconstructed for CFD studies. Real FD configurations were reconstructed based on micro-CT scans after sacrifice, while virtual FD configurations were constructed with SolidWorks software. Hemodynamic parameters before and after FD deployment were analyzed. According to the metal coverage (MC) of implanted FDs calculated based on micro-CT reconstruction, 14 rabbits were divided into two groups (A, MC >35%; B, MC <35%). Normalized mean wall shear stress (WSS), relative residence time (RRT), inflow velocity, and inflow volume in Group A were significantly different (P<0.05) from virtual FD deployment, but pressure was not (P>0.05). The normalized mean WSS in Group A after realistic FD implantation was significantly lower than that of Group B. All parameters in Group B exhibited no significant difference between realistic and virtual FDs. This study confirmed MC-correlated differences in hemodynamic parameters between realistic and virtual FD deployment. PMID:23823503

New Trends of Digital Data Storage in DNA

PubMed Central

2016-01-01

With the exponential growth in the capacity of information generated and the emerging need for data to be stored for prolonged period of time, there emerges a need for a storage medium with high capacity, high storage density, and possibility to withstand extreme environmental conditions. DNA emerges as the prospective medium for data storage with its striking features. Diverse encoding models for reading and writing data onto DNA, codes for encrypting data which addresses issues of error generation, and approaches for developing codons and storage styles have been developed over the recent past. DNA has been identified as a potential medium for secret writing, which achieves the way towards DNA cryptography and stenography. DNA utilized as an organic memory device along with big data storage and analytics in DNA has paved the way towards DNA computing for solving computational problems. This paper critically analyzes the various methods used for encoding and encrypting data onto DNA while identifying the advantages and capability of every scheme to overcome the drawbacks identified priorly. Cryptography and stenography techniques have been analyzed in a critical approach while identifying the limitations of each method. This paper also identifies the advantages and limitations of DNA as a memory device and memory applications. PMID:27689089

New Trends of Digital Data Storage in DNA.

PubMed

De Silva, Pavani Yashodha; Ganegoda, Gamage Upeksha

With the exponential growth in the capacity of information generated and the emerging need for data to be stored for prolonged period of time, there emerges a need for a storage medium with high capacity, high storage density, and possibility to withstand extreme environmental conditions. DNA emerges as the prospective medium for data storage with its striking features. Diverse encoding models for reading and writing data onto DNA, codes for encrypting data which addresses issues of error generation, and approaches for developing codons and storage styles have been developed over the recent past. DNA has been identified as a potential medium for secret writing, which achieves the way towards DNA cryptography and stenography. DNA utilized as an organic memory device along with big data storage and analytics in DNA has paved the way towards DNA computing for solving computational problems. This paper critically analyzes the various methods used for encoding and encrypting data onto DNA while identifying the advantages and capability of every scheme to overcome the drawbacks identified priorly. Cryptography and stenography techniques have been analyzed in a critical approach while identifying the limitations of each method. This paper also identifies the advantages and limitations of DNA as a memory device and memory applications.

Posttraumatic Stress and Physical Health Functioning: Moderating Effects of Deployment and Postdeployment Social Support in OEF/OIF/OND Veterans

PubMed Central

Luciano, Matthew T.; McDevitt-Murphy, Meghan E.

2016-01-01

Research indicates that posttraumatic stress disorder (PTSD) is strongly associated with physical health difficulties, and that social support may be protective for both problems. Social support, however, is often broadly conceptualized. The present analysis explores how Veteran-specific social support (during military deployment and postdeployment) may moderate the relationship between PTSD and physical health functioning. Participants were recruited from a VA Medical Center. Self-report data was analyzed from 63 Veterans (17.46% female; 42.86% White) who had been deployed in support of Operation Enduring Freedom, Operation Iraqi Freedom, and Operation New Dawn (OEF/OIF/OND). Data indicate that military deployment social support moderated the relationship between PTSD and pain (β = .02, p = .02) while postdeployment social support moderated the relationship between PTSD and general health perceptions (β = .03, p = .01). These findings may be used to better understand the role of support in influencing psychological and physiological processes. PMID:27660993

Gender differences in substance use treatment utilization in the year prior to deployment in Army service members☆

PubMed Central

Wooten, Nikki R.; Mohr, Beth A.; Lundgren, Lena M.; Adams, Rachel Sayko; Merrick, Elizabeth L.; Williams, Thomas V.; Larson, Mary Jo

2013-01-01

Although military men have heavier drinking patterns, military women experience equal or higher rates of dependence symptoms and similar rates of alcohol-related problems as men at lower levels of consumption. Thus, gender may be important for understanding substance use treatment (SUT) utilization before deployment. Military health system data were analyzed to examine gender differences in both substance use diagnosis (SUDX) and SUT in 152,447 Army service members returning from deployments in FY2010. Propensity score analysis of probability of SUDX indicated that women had lower odds (AOR: 0.91, 95% CI: 0.86–0.96) of military lifetime SUDX. After adjusting for lifetime SUDX using propensity score analysis, multivariate regression found women had substantially lower odds (AOR: 0.61; 95% CI: 0.54–0.70) of using SUT the year prior to deployment. Findings suggest gender disparities in military-provided SUT and a need to consider whether military substance use assessment protocols are sensitive to gender differences. PMID:23726826

Using Docker Compose for the Simple Deployment of an Integrated Drug Target Screening Platform.

PubMed

List, Markus

2017-06-10

Docker virtualization allows for software tools to be executed in an isolated and controlled environment referred to as a container. In Docker containers, dependencies are provided exactly as intended by the developer and, consequently, they simplify the distribution of scientific software and foster reproducible research. The Docker paradigm is that each container encapsulates one particular software tool. However, to analyze complex biomedical data sets, it is often necessary to combine several software tools into elaborate workflows. To address this challenge, several Docker containers need to be instantiated and properly integrated, which complicates the software deployment process unnecessarily. Here, we demonstrate how an extension to Docker, Docker compose, can be used to mitigate these problems by providing a unified setup routine that deploys several tools in an integrated fashion. We demonstrate the power of this approach by example of a Docker compose setup for a drug target screening platform consisting of five integrated web applications and shared infrastructure, deployable in just two lines of codes.

Medical and physical readiness of the U.S. Army Reserve for Noble Eagle/Enduring Freedom/Iraqi Freedom: recommendations for future mobilizations.

PubMed

Ruble, Paul; Silverman, Michael; Harrell, Janie; Ringenberg, Lynnette; Fruendt, Jonathan; Walters, Terry; Christiansen, Loren; Llorente, Maria; Barnett, Scott D; Scherb, Barbara; Lumpkin, Eddie; Mitchell, Deborah

2005-06-01

The U.S. Army Reserve plays an important role in the war-fighting capabilities of the U.S. military. There have been concerns, however, regarding the health and physical readiness of this force. Recently Army Reservists were mobilized for Operation Noble Eagle/Iraqi Freedom. We report on both the medical waivers requested and issues related to soldiers found medically nonavailable for deployment on data collected and analyzed from several mobilization sites. Four hundred thirty-one medical waivers were requested. Of 60,000 mobilized, approximately 2.7% were found to be medically nonavailable for deployment, predominately enlisted and male. The most common problems identified were orthopedic, psychiatric, diabetes, asthma, obstetrical-gynecological, and cardiac. The overall prevalence of medically nonavailable for deployment of Army Reservists was low. Most of the conditions leading to nondeployable troops were attributable to chronic disease. Interventions to decrease the level of medically nonavailable for deployment and to lessen mobilization site operations are being implemented.

Military Sexual Trauma Among US Servicewomen During Deployment: A Qualitative Study

PubMed Central

Grindlay, Kate; Holt, Kelsey; Manski, Ruth; Grossman, Daniel

2014-01-01

Objectives. We explored qualitatively US servicewomen’s experiences with and perceptions of military sexual trauma (MST), reporting, and related services. Methods. From May 2011 to January 2012, we conducted 22 telephone interviews with US servicewomen deployed overseas between 2002 and 2011. We analyzed data thematically with modified grounded theory methods. Results. Factors identified as contributing to MST included deployment dynamics, military culture, and lack of consequences for perpetrators. Participants attributed low MST reporting to negative reactions and blame from peers and supervisors, concerns about confidentiality, and stigma. Unit cohesion was cited as both a facilitator and a barrier to reporting. Availability and awareness of MST services during deployment varied. Barriers to care seeking were similar to reporting barriers and included confidentiality concerns and stigma. We identified several avenues to address MST, including strengthening consequences for perpetrators. Conclusions. We identified barriers to MST reporting and services. Better understanding of these issues will allow policymakers to improve MST prevention and services. PMID:24328617

Utilizing Building Usage Assessment: Determining Deployment of Student Workers in an Academic Library

ERIC Educational Resources Information Center

Buller, Ryan F.

2014-01-01

Generating, collecting, and analyzing building usage statistics can greatly increase the ability of an access services unit to meet the changing dynamic of patron needs in an academic library. By analyzing three different data points, the Access Services Unit in Malpass Library at Western Illinois University was able to determine the most…

DNA Sequencing Technologies within the Chemical and Biological Defense Enterprise: How to Position the Department of Defense to Maximize the Use of These Emerging Technologies - JUPITR

DTIC Science & Technology

2015-07-01

sharing, the Pathosphere.org open-system architecture is now deployed and available on the Amazon cloud . The site has over 100 users from...SUPPLEMENTARY NOTES 14. ABSTRACT: To generate accurate and actionable disease data that can be integrated into the broader Department of Defense...PREFACE The work described in this report was authorized under the Joint United States Forces Korea Portal and Integrated Threat Recognition

Floating Offshore Wind in California: Gross Potential for Jobs and Economic Impacts from Two Future Scenarios

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

Speer, Bethany; Keyser, David; Tegen, Suzanne

Construction of the first offshore wind farm in the United States began in 2015, using fixed platform structures that are appropriate for shallow seafloors, like those located off of the East Coast and mid-Atlantic. However, floating platforms, which have yet to be deployed commercially, will likely need to anchor to the deeper seafloor if deployed off of the West Coast. To analyze the employment and economic potential for floating offshore wind along the West Coast, the Bureau of Ocean Energy Management (BOEM) has commissioned the National Renewable Energy Laboratory (NREL) to analyze two hypothetical, large-scale deployment scenarios for California: 16more » GW of offshore wind by 2050 (Scenario A) and 10 GW of offshore wind by 2050 (Scenario B). The results of this analysis can be used to better understand the general scales of economic opportunities that could result from offshore wind development. Results show total state gross domestic product (GDP) impacts of $16.2 billion in Scenario B or $39.7 billion in Scenario A for construction; and $3.5 billion in Scenario B or $7.9 billion in Scenario A for the operations phases.« less

Resource Evaluation and Energy Production Estimate for a Tidal Energy Conversion Installation using Acoustic Flow Measurements

NASA Astrophysics Data System (ADS)

Gagnon, Ian; Baldwin, Ken; Wosnik, Martin

2015-11-01

The ``Living Bridge'' project plans to install a tidal turbine at Memorial Bridge in the Piscataqua River at Portsmouth, NH. A spatio-temporal tidal energy resource assessment was performed using long term bottom-deployed Acoustic Doppler Current Profilers ADCP. Two locations were evaluated: at the planned deployment location and mid-channel. The goal was to determine the amount of available kinetic energy that can be converted into usable electrical energy on the bridge. Changes in available kinetic energy with ebb/flood and spring/neap tidal cycles and electrical energy demand were analyzed. A system model is used to calculate the net energy savings using various tidal generator and battery bank configurations. Differences in the tidal characteristics between the two measurement locations are highlighted. Different resource evaluation methodologies were also analyzed, e.g., using a representative ADCP ``bin'' vs. a more refined, turbine-geometry-specific methodology, and using static bin height vs. bin height that move w.r.t. the free surface throughout a tidal cycle (representative of a bottom-fixed or floating turbine deployment, respectively). ADCP operating frequencies and bin sizes affect the standard deviation of measurements, and measurement uncertainties are evaluated. Supported by NSF-IIP grant 1430260.

Deployment-based lifetime optimization model for homogeneous Wireless Sensor Network under retransmission.

PubMed

Li, Ruiying; Liu, Xiaoxi; Xie, Wei; Huang, Ning

2014-12-10

Sensor-deployment-based lifetime optimization is one of the most effective methods used to prolong the lifetime of Wireless Sensor Network (WSN) by reducing the distance-sensitive energy consumption. In this paper, data retransmission, a major consumption factor that is usually neglected in the previous work, is considered. For a homogeneous WSN, monitoring a circular target area with a centered base station, a sensor deployment model based on regular hexagonal grids is analyzed. To maximize the WSN lifetime, optimization models for both uniform and non-uniform deployment schemes are proposed by constraining on coverage, connectivity and success transmission rate. Based on the data transmission analysis in a data gathering cycle, the WSN lifetime in the model can be obtained through quantifying the energy consumption at each sensor location. The results of case studies show that it is meaningful to consider data retransmission in the lifetime optimization. In particular, our investigations indicate that, with the same lifetime requirement, the number of sensors needed in a non-uniform topology is much less than that in a uniform one. Finally, compared with a random scheme, simulation results further verify the advantage of our deployment model.

Energy Balanced Strategies for Maximizing the Lifetime of Sparsely Deployed Underwater Acoustic Sensor Networks

PubMed Central

Luo, Hanjiang; Guo, Zhongwen; Wu, Kaishun; Hong, Feng; Feng, Yuan

2009-01-01

Underwater acoustic sensor networks (UWA-SNs) are envisioned to perform monitoring tasks over the large portion of the world covered by oceans. Due to economics and the large area of the ocean, UWA-SNs are mainly sparsely deployed networks nowadays. The limited battery resources is a big challenge for the deployment of such long-term sensor networks. Unbalanced battery energy consumption will lead to early energy depletion of nodes, which partitions the whole networks and impairs the integrity of the monitoring datasets or even results in the collapse of the entire networks. On the contrary, balanced energy dissipation of nodes can prolong the lifetime of such networks. In this paper, we focus on the energy balance dissipation problem of two types of sparsely deployed UWA-SNs: underwater moored monitoring systems and sparsely deployed two-dimensional UWA-SNs. We first analyze the reasons of unbalanced energy consumption in such networks, then we propose two energy balanced strategies to maximize the lifetime of networks both in shallow and deep water. Finally, we evaluate our methods by simulations and the results show that the two strategies can achieve balanced energy consumption per node while at the same time prolong the networks lifetime. PMID:22399970

Promoter-enhancer interactions identified from Hi-C data using probabilistic models and hierarchical topological domains.

PubMed

Ron, Gil; Globerson, Yuval; Moran, Dror; Kaplan, Tommy

2017-12-21

Proximity-ligation methods such as Hi-C allow us to map physical DNA-DNA interactions along the genome, and reveal its organization into topologically associating domains (TADs). As the Hi-C data accumulate, computational methods were developed for identifying domain borders in multiple cell types and organisms. Here, we present PSYCHIC, a computational approach for analyzing Hi-C data and identifying promoter-enhancer interactions. We use a unified probabilistic model to segment the genome into domains, which we then merge hierarchically and fit using a local background model, allowing us to identify over-represented DNA-DNA interactions across the genome. By analyzing the published Hi-C data sets in human and mouse, we identify hundreds of thousands of putative enhancers and their target genes, and compile an extensive genome-wide catalog of gene regulation in human and mouse. As we show, our predictions are highly enriched for ChIP-seq and DNA accessibility data, evolutionary conservation, eQTLs and other DNA-DNA interaction data.

The value of cell-free DNA for molecular pathology.

PubMed

Stewart, Caitlin M; Kothari, Prachi D; Mouliere, Florent; Mair, Richard; Somnay, Saira; Benayed, Ryma; Zehir, Ahmet; Weigelt, Britta; Dawson, Sarah-Jane; Arcila, Maria E; Berger, Michael F; Tsui, Dana Wy

2018-04-01

Over the past decade, advances in molecular biology and genomics techniques have revolutionized the diagnosis and treatment of cancer. The technological advances in tissue profiling have also been applied to the study of cell-free nucleic acids, an area of increasing interest for molecular pathology. Cell-free nucleic acids are released from tumour cells into the surrounding body fluids and can be assayed non-invasively. The repertoire of genomic alterations in circulating tumour DNA (ctDNA) is reflective of both primary tumours and distant metastatic sites, and ctDNA can be sampled multiple times, thereby overcoming the limitations of the analysis of single biopsies. Furthermore, ctDNA can be sampled regularly to monitor response to treatment, to define the evolution of the tumour genome, and to assess the acquisition of resistance and minimal residual disease. Recently, clinical ctDNA assays have been approved for guidance of therapy, which is an exciting first step in translating cell-free nucleic acid research tests into clinical use for oncology. In this review, we discuss the advantages of cell-free nucleic acids as analytes in different body fluids, including blood plasma, urine, and cerebrospinal fluid, and their clinical applications in solid tumours and haematological malignancies. We will also discuss practical considerations for clinical deployment, such as preanalytical factors and regulatory requirements. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

A Social Potential Fields Approach for Self-Deployment and Self-Healing in Hierarchical Mobile Wireless Sensor Networks

PubMed Central

González-Parada, Eva; Cano-García, Jose; Aguilera, Francisco; Sandoval, Francisco; Urdiales, Cristina

2017-01-01

Autonomous mobile nodes in mobile wireless sensor networks (MWSN) allow self-deployment and self-healing. In both cases, the goals are: (i) to achieve adequate coverage; and (ii) to extend network life. In dynamic environments, nodes may use reactive algorithms so that each node locally decides when and where to move. This paper presents a behavior-based deployment and self-healing algorithm based on the social potential fields algorithm. In the proposed algorithm, nodes are attached to low cost robots to autonomously navigate in the coverage area. The proposed algorithm has been tested in environments with and without obstacles. Our study also analyzes the differences between non-hierarchical and hierarchical routing configurations in terms of network life and coverage. PMID:28075364

A Social Potential Fields Approach for Self-Deployment and Self-Healing in Hierarchical Mobile Wireless Sensor Networks.

PubMed

González-Parada, Eva; Cano-García, Jose; Aguilera, Francisco; Sandoval, Francisco; Urdiales, Cristina

2017-01-09

Autonomous mobile nodes in mobile wireless sensor networks (MWSN) allow self-deployment and self-healing. In both cases, the goals are: (i) to achieve adequate coverage; and (ii) to extend network life. In dynamic environments, nodes may use reactive algorithms so that each node locally decides when and where to move. This paper presents a behavior-based deployment and self-healing algorithm based on the social potential fields algorithm. In the proposed algorithm, nodes are attached to low cost robots to autonomously navigate in the coverage area. The proposed algorithm has been tested in environments with and without obstacles. Our study also analyzes the differences between non-hierarchical and hierarchical routing configurations in terms of network life and coverage.

High-Efficiency Ligation and Recombination of DNA Fragments by Vertebrate Cells

NASA Astrophysics Data System (ADS)

Miller, Cynthia K.; Temin, Howard M.

1983-05-01

DNA-mediated gene transfer (transfection) is used to introduce specific genes into vertebrate cells. Events soon after transfection were quantitatively analyzed by determining the infectivity of the DNA from an avian retrovirus and of mixtures of subgenomic fragments of this DNA. The limiting step of transfection with two DNA molecules is the uptake by a single cell of both DNA's in a biologically active state. Transfected cells mediate ligation and recombination of physically unlinked DNA's at nearly 100 percent efficiency.

Biomarkers of oxidative stress and DNA damage in agricultural workers: A pilot study

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

Muniz, Juan F.; McCauley, Linda; Scherer, J.

Oxidative stress and DNA damage have been proposed as mechanisms linking pesticide exposure to health effects such as cancer and neurological diseases. A study of pesticide applicators and farmworkers was conducted to examine the relationship between organophosphate pesticide exposure and biomarkers of oxidative stress and DNA damage. Urine samples were analyzed for OP metabolites and 8-hydroxy-2'-deoxyguanosine (8-OH-dG). Lymphocytes were analyzed for oxidative DNA repair activity and DNA damage (Comet assay), and serum was analyzed for lipid peroxides (i.e., malondialdehyde, MDA). Cellular damage in agricultural workers was validated using lymphocyte cell cultures. Urinary OP metabolites were significantly higher in farmworkers andmore » applicators (p < 0.001) when compared to controls. 8-OH-dG levels were 8.5 times and 2.3 times higher in farmworkers or applicators (respectively) than in controls. Serum MDA levels were 4.9 times and 24 times higher in farmworkers or applicators (respectively) than in controls. DNA damage (Comet assay) and oxidative DNA repair were significantly greater in lymphocytes from applicators and farmworkers when compared with controls. Markers of oxidative stress (i.e., increased reactive oxygen species and reduced glutathione levels) and DNA damage were also observed in lymphocyte cell cultures treated with an OP. The findings from these in vivo and in vitro studies indicate that organophosphate pesticides induce oxidative stress and DNA damage in agricultural workers. These biomarkers may be useful for increasing our understanding of the link between pesticides and a number of health effects.« less

Detection of Cytosine methylation in ancient DNA from five native american populations using bisulfite sequencing.

PubMed

Smith, Rick W A; Monroe, Cara; Bolnick, Deborah A

2015-01-01

While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/μL generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches.

Green synthesis, characterization and anticancer potential of platinum nanoparticles Bioplatin.

PubMed

Bendale, Yogesh; Bendale, Vineeta; Paul, Saili; Bhattacharyya, Soumya Sundar

2012-06-01

In the present study, the anticancer potential of platinum nanoparticles Bioplatin is explored and the mode of interactions of Bioplatin with calf thymus DNA and honey was analyzed. Bioplatin was synthesized with the help of green nanotechnology and characterized by particle size, zeta potential and surface morphology. The interaction of Bioplatin with DNA and honey was also checked with the help of circular dichroism spectroscopy and Fourier-transform infrared spectroscopy, respectively. The anticancer potential of Bioplatin was evaluated on peripheral blood mononuclear cells and A375 cells in vitro by analyzing results of MTT (3-(4,5)-dimethyl-thiahiazo-(-z-y1)-3,5-di-phenytetrazoliumromide), fluorescence microscopic studies and DNA fragmentation assay. Bioplatin exhibited a small particle size of 137.5 nm and a surface charge of -35.8 mV. Bioplatin interacted with DNA and brought in effective changes in structure and conformation of DNA, and formed a new complex that increased its stability of DNA intercalated with the base pair of DNA. In vitro studies demonstrated that Bioplatin arrested cell proliferation, and induced chromatin condensation and internucleosomal DNA fragmentation. Bioplatin induces apoptosis in cancer cells and may have some beneficial effect against human carcinoma. It interacts with DNA, brings stabilization to DNA, and thus prevents the replication of DNA.

Raman-based system for DNA sequencing-mapping and other separations

DOEpatents

Vo-Dinh, Tuan

1994-01-01

DNA sequencing and mapping are performed by using a Raman spectrometer with a surface enhanced Raman scattering (SERS) substrate to enhance the Raman signal. A SERS label is attached to a DNA fragment and then analyzed with the Raman spectrometer to identify the DNA fragment according to characteristics of the Raman spectrum generated.

DNA in the Criminal Justice System: The DNA Success Story in Perspective.

PubMed

Mapes, Anna A; Kloosterman, Ate D; de Poot, Christianne J

2015-07-01

Current figures on the efficiency of DNA as an investigative tool in criminal investigations only tell part of the story. To get the DNA success story in the right perspective, we examined all forensic reports from serious (N = 116) and high-volume crime cases (N = 2791) over the year 2011 from one police region in the Netherlands. These data show that 38% of analyzed serious crime traces (N = 384) and 17% of analyzed high-volume crime traces (N = 386) did not result in a DNA profile. Turnaround times (from crime scene to DNA report) were 66 days for traces from serious crimes and 44 days for traces from high-volume crimes. Suspects were truly identified through a match with the Offender DNA database of the Netherlands in 3% of the serious crime cases and in 1% of the high-volume crime cases. These data are important for both the forensic laboratory and the professionals in the criminal justice system to further optimize forensic DNA testing as an investigative tool. © 2015 American Academy of Forensic Sciences.

Forensics and mitochondrial DNA: applications, debates, and foundations.

PubMed

Budowle, Bruce; Allard, Marc W; Wilson, Mark R; Chakraborty, Ranajit

2003-01-01

Debate on the validity and reliability of scientific methods often arises in the courtroom. When the government (i.e., the prosecution) is the proponent of evidence, the defense is obliged to challenge its admissibility. Regardless, those who seek to use DNA typing methodologies to analyze forensic biological evidence have a responsibility to understand the technology and its applications so a proper foundation(s) for its use can be laid. Mitochondrial DNA (mtDNA), an extranuclear genome, has certain features that make it desirable for forensics, namely, high copy number, lack of recombination, and matrilineal inheritance. mtDNA typing has become routine in forensic biology and is used to analyze old bones, teeth, hair shafts, and other biological samples where nuclear DNA content is low. To evaluate results obtained by sequencing the two hypervariable regions of the control region of the human mtDNA genome, one must consider the genetically related issues of nomenclature, reference population databases, heteroplasmy, paternal leakage, recombination, and, of course, interpretation of results. We describe the approaches, the impact some issues may have on interpretation of mtDNA analyses, and some issues raised in the courtroom.

Novel Tools in Determining the Physiological Demands and Nutritional Practices of Ontario FireRangers during Fire Deployments

PubMed Central

Robertson, A. H.; Larivière, C.; Leduc, C. R.; McGillis, Z.; Eger, T.; Godwin, A.; Larivière, M.; Dorman, S. C.

2017-01-01

Introduction The seasonal profession of wildland fire fighting in Canada requires individuals to work in harsh environmental conditions that are physically demanding. The purpose of this study was to use novel technologies to evaluate the physiological demands and nutritional practices of Canadian FireRangers during fire deployments. Methods Participants (n = 21) from a northern Ontario Fire Base volunteered for this study and data collection occurred during the 2014 fire season and included Initial Attack (IA), Project Fire (P), and Fire Base (B) deployments. Deployment-specific energy demands and physiological responses were measured using heart-rate variability (HRV) monitoring devices (Zephyr BioHarness3 units). Food consumption behaviour and nutrient quantity and quality were captured using audio-video food logs on iPod Touches and analyzed by NutriBase Pro 11 software. Results Insufficient kilocalories were consumed relative to expenditure for all deployment types. Average daily kilocalories consumed: IA: 3758 (80% consumption rate); P: 2945±888.8; B: 2433±570.8. Average daily kilocalorie expenditure: IA: 4538±106.3; P: 4012±1164.8; B: 2842±649.9. The Average Macronutrient Distribution Range (AMDR) for protein was acceptable: 22–25% (across deployment types). Whereas the AMDR for fat and carbohydrates were high: 40–50%; and low: 27–37% respectively, across deployment types. Conclusions This study is the first to use the described methodology to simultaneously evaluate energy expenditures and nutritional practices in an occupational setting. The results support the use of HRV monitoring and video-food capture, in occupational field settings, to assess job demands. FireRangers expended the most energy during IA, and the least during B deployments. These results indicate the need to develop strategies centered on maintaining physical fitness and improving food practices. PMID:28107380

Self Reported Incidence and Morbidity of Acute Respiratory Illness among Deployed U.S. Military in Iraq and Afghanistan

PubMed Central

Soltis, Bryony W.; Sanders, John W.; Putnam, Shannon D.; Tribble, David R.; Riddle, Mark S.

2009-01-01

Background Historically, respiratory infections have had a significant impact on U.S. military missions. Deployed troops are particularly at high risk due to close living conditions, stressful work environments and increased exposure to pathogens. To date, there are limited data available on acute respiratory illness (ARI) among troops deployed in support of ongoing military operations, specifically Operation Enduring Freedom (OEF) and Operation Iraqi Freedom (OIF). Methods Using self-report data from two sources collected from troops deployed to Iraq, Afghanistan and the surrounding region, we analyzed incidence and risk factors for ARI. Military personnel on mid-deployment Rest & Recuperation (R&R) or during redeployment were eligible to participate in the voluntary self-report survey. Results Overall, 39.5% reported having at least one ARI. Of these, 18.5% sought medical care and 33.8% reported having decreased job performance. The rate of self-reported ARI was 15 episodes per 100 person-months among those taking the voluntary survey, and 24.7 episodes per 100 person-months among those taking the clinic health questionnaire. Negative binomial regression analysis found female sex, Navy branch of service and lack of flush toilets to be independently associated with increased rates of ARI. Deployment to OIF, increasing age and higher rank were also positively associated with ARI risk. Conclusions The overall percentage of deployed military personnel reporting at least one acute respiratory illness decreased since earlier parts of OIF/OEF. However, the reported effect on job performance increased tremendously. The most important factors associated with increased respiratory infection are female sex, Navy branch of service, lack of improved latrine facilities, deployment to OIF, increasing age and higher rank. PMID:19584919

Novel Tools in Determining the Physiological Demands and Nutritional Practices of Ontario FireRangers during Fire Deployments.

PubMed

Robertson, A H; Larivière, C; Leduc, C R; McGillis, Z; Eger, T; Godwin, A; Larivière, M; Dorman, S C

2017-01-01

The seasonal profession of wildland fire fighting in Canada requires individuals to work in harsh environmental conditions that are physically demanding. The purpose of this study was to use novel technologies to evaluate the physiological demands and nutritional practices of Canadian FireRangers during fire deployments. Participants (n = 21) from a northern Ontario Fire Base volunteered for this study and data collection occurred during the 2014 fire season and included Initial Attack (IA), Project Fire (P), and Fire Base (B) deployments. Deployment-specific energy demands and physiological responses were measured using heart-rate variability (HRV) monitoring devices (Zephyr BioHarness3 units). Food consumption behaviour and nutrient quantity and quality were captured using audio-video food logs on iPod Touches and analyzed by NutriBase Pro 11 software. Insufficient kilocalories were consumed relative to expenditure for all deployment types. Average daily kilocalories consumed: IA: 3758 (80% consumption rate); P: 2945±888.8; B: 2433±570.8. Average daily kilocalorie expenditure: IA: 4538±106.3; P: 4012±1164.8; B: 2842±649.9. The Average Macronutrient Distribution Range (AMDR) for protein was acceptable: 22-25% (across deployment types). Whereas the AMDR for fat and carbohydrates were high: 40-50%; and low: 27-37% respectively, across deployment types. This study is the first to use the described methodology to simultaneously evaluate energy expenditures and nutritional practices in an occupational setting. The results support the use of HRV monitoring and video-food capture, in occupational field settings, to assess job demands. FireRangers expended the most energy during IA, and the least during B deployments. These results indicate the need to develop strategies centered on maintaining physical fitness and improving food practices.

Envisioning a Low-Cost Solar Future: Exploring the Potential Impact of Achieving the SunShot 2030 Targets for Photovoltaics

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

Cole, Wesley J; Frew, Bethany A; Gagnon, Pieter J

In the context of recent dramatic solar energy cost reductions, the U.S. Department of Energy set new levelized cost of energy goals for photovoltaics (PV) to achieve by 2030 to enable significantly greater PV adoption: $0.03/kWh for utility-scale, $0.04/kWh for commercial, and $0.05/kWh for residential PV systems. We analyze the potential impacts of achieving these 'SunShot 2030' cost targets for the contiguous United States using the Regional Energy Deployment System (ReEDS) and Distributed Generation (dGen) capacity expansion models. We consider the impacts under a wide range of future conditions. We find that PV could provide 13%-18% of U.S. electricity demandmore » in 2030 and 28%-64% of demand if the SunShot 2030 goals are achieved, with PV deployment increasing in every state. The availability of low-cost storage has the largest impact on projected deployment, followed by natural gas prices and electricity demand. For comparison, PV deployed under a business-as-usual scenario could provide only 5% of generation in 2030 and 17% in 2050. We find that the high levels of PV deployment explored here lead to lower electricity prices and system costs, lower carbon dioxide emissions, lower water consumption, increased renewable energy curtailment, and increased storage deployment compared with the business-as-usual scenario.« less

Preparedness Evaluation of French Military Orthopedic Surgeons Before Deployment.

PubMed

Choufani, Camille; Barbier, Olivier; Mayet, Aurélie; Rigal, Sylvain; Mathieu, Laurent

2018-06-13

A deployed military orthopedic surgeon is a trauma surgeon working in austere conditions. The first aim of this study was to analyze the current activity of French military orthopedic surgeons in the field and to identify the differences of the combat zone with their daily practice. The second aim was to assess the adequacy of the preparedness they received before their deployment and to identify additional needs that could be addressed in future training. An evaluation survey was sent to all French military orthopedic surgeons deployed in theaters of operations between 2004 and 2014. An analogic visual scale of 10 was used to evaluate their surgical activity abroad and prior training. A total of 55 surgeons, with a median deployment number of 7, were included in this study after they answered the survey. Debridement and external fixation were the most common orthopedic procedures. The practice of general surgery was mostly concerned with vascular and abdominal injuries as part of damage control procedures. Median scores were ranked at seven for surgical preparedness, five for physical readiness, and three for mental preparedness. There was a significant inverse relationship between the number of missions performed and the evaluation of surgical preparedness. The higher they perceived their mental preparedness, the better they estimated their surgical preparedness. In the French Army, deployed orthopedic surgeons perform general surgical activity. Their initial training must be adapted to this constraint and enhanced by continuing medical education.

Continuous, high-resolution spatial mapping of water isotopes in oceanic environment using a CRDS analyzer combined with a continuous water sampler.

NASA Astrophysics Data System (ADS)

Kim-Hak, David; Huang, Kuan; Winkler, Renato

2016-04-01

The recent advancements of the laser-based technology -in particular Cavity Ring Down Spectroscopy, CRDS- gave birth to a new generation of water stable isotope analyzers that are user-friendly, compact and field deployable providing in-situ measurements. Furthermore, with last year's launch of the Continuous Water Sampler front-end, CWS, the analyzer system added two additional dimensions to liquid water measurements: real-time and continuous. These features enable the user to construct high resolution water isotope data sets through time and space. Campaigns on the Sacramento-San Joaquin River Delta with the US Geological Survey where the CWS-CRDS system was deployed onto a boat to spatially map sections of the delta, validated the CWS performance and demonstrated its durability on brackish water. The next step for the CWS is to explore oceanic applications with seawater. Early in-house laboratory experiments showed stable performance with brine waters (3% concentration). For the field experiment, we have collaborated with the China State Oceanic Administration to deploy the CWS-CRDS in oceanic environments on cruises along the costal China and Antarctic. Here, we present the results of the analysis collected onboard and compared them with discrete sampling measurements. The long-term test has also allowed us to assess the durability and expected lifetime of the CWS membrane and to recommend the proper maintenance procedure for optimum performance under oceanic conditions.

Continuous, high-resolution spatial mapping of water isotopes in oceanic environment using a CRDS analyzer combined with a continuous water sampler.

NASA Astrophysics Data System (ADS)

Kim-Hak, D.; Huang, K.

2016-02-01

The recent advancements of the laser-based technology -in particular Cavity Ring Down Spectroscopy, CRDS- gave birth to a new generation of water stable isotope analyzers that are user-friendly, compact and field deployable providing in-situ measurements. Furthermore, with last year's launch of the Continuous Water Sampler front-end, CWS, the analyzer system added two additional dimensions to liquid water measurements: real-time and continuous. These features enable the user to construct high resolution water isotope data sets through time and space. Campaigns on the Sacramento-San Joaquin River Delta with the US Geological Survey where the CWS-CRDS system was deployed onto a boat to spatially map sections of the delta, validated the CWS performance and demonstrated its durability on brackish water. The next step for the CWS is to explore oceanic applications with seawater. Early in-house laboratory experiments showed stable performance with brine waters (3% concentration). For the field experiment, we have collaborated with the China State Oceanic Administration to deploy the CWS-CRDS in oceanic environments on cruises along the costal China and Antarctic. Here, we present the results of the analysis collected onboard and compared them with discrete sampling measurements. The long-term test has also allowed us to assess the durability and expected lifetime of the CWS membrane and to recommend the proper maintenance procedure for optimum performance under oceanic conditions.

Borrow the Buoys: DOE’s Lidar Buoy Loan Program

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

None

2017-02-27

After a 19-month deployment off the coast of Virginia, one of PNNL’s research buoys has returned to shore where researchers can analyze the data recorded by the buoy. The data revealed a few major takeaways that will inform future buoy deployments, including the times and conditions when data measurement is most accurate. Through the Department of Energy's Wind Energy Technologies Office's Lidar Buoy Loan Program, managed by PNNL, interested parties can borrow the buoys for year and contribute invaluable data to the wind energy community.

Part I: Minicircle vector technology limits DNA size restrictions on ex vivo gene delivery using nanoparticle vectors: Overcoming a translational barrier in neural stem cell therapy.

PubMed

Fernandes, Alinda R; Chari, Divya M

2016-09-28

Genetically engineered neural stem cell (NSC) transplant populations offer key benefits in regenerative neurology, for release of therapeutic biomolecules in ex vivo gene therapy. NSCs are 'hard-to-transfect' but amenable to 'magnetofection'. Despite the high clinical potential of this approach, the low and transient transfection associated with the large size of therapeutic DNA constructs is a critical barrier to translation. We demonstrate for the first time that DNA minicircles (small DNA vectors encoding essential gene expression components but devoid of a bacterial backbone, thereby reducing construct size versus conventional plasmids) deployed with magnetofection achieve the highest, safe non-viral DNA transfection levels (up to 54%) reported so far for primary NSCs. Minicircle-functionalized magnetic nanoparticle (MNP)-mediated gene delivery also resulted in sustained gene expression for up to four weeks. All daughter cell types of engineered NSCs (neurons, astrocytes and oligodendrocytes) were transfected (in contrast to conventional plasmids which usually yield transfected astrocytes only), offering advantages for targeted cell engineering. In addition to enhancing MNP functionality as gene delivery vectors, minicircle technology provides key benefits from safety/scale up perspectives. Therefore, we consider the proof-of-concept of fusion of technologies used here offers high potential as a clinically translatable genetic modification strategy for cell therapy. Copyright © 2016 Elsevier B.V. All rights reserved.

Deployment of a multi-link flexible structure

NASA Astrophysics Data System (ADS)

Na, Kyung-Su; Kim, Ji-Hwan

2006-06-01

Deployment of a multi-link beam structure undergoing locking is analyzed in the Timoshenko beam theory. In the modeling of the system, dynamic forces are assumed to be torques and restoring forces due to the torsion spring at each joint. Hamilton's principle is used to determine the equations of motion and the finite element method is adopted to analyze the system. Newmark time integration and Newton-Raphson iteration methods are used to solve for the non-linear equations of motion at each time step. The locking at the joints of the multi-link flexible structure is analyzed by the momentum balance method. Numerical results are compared with the previous experimental data. The angles and angular velocities of each joint, tip displacement, and velocity of each link are investigated to study the motions of the links at each time step. To analyze the effect of thickness on the motion of the link, the angle and the tip displacement of each link are compared according to the various slenderness ratios. Additionally, in order to investigate the effect of shear, the tip displacements of a Timoshenko beam are compared with those of an Euler-Bernoulli beam.

Raman-based system for DNA sequencing-mapping and other separations

DOEpatents

Vo-Dinh, T.

1994-04-26

DNA sequencing and mapping are performed by using a Raman spectrometer with a surface enhanced Raman scattering (SERS) substrate to enhance the Raman signal. A SERS label is attached to a DNA fragment and then analyzed with the Raman spectrometer to identify the DNA fragment according to characteristics of the Raman spectrum generated. 11 figures.

Human beta-globin gene polymorphisms characterized in DNA extracted from ancient bones 12,000 years old.

PubMed

Béraud-Colomb, E; Roubin, R; Martin, J; Maroc, N; Gardeisen, A; Trabuchet, G; Goosséns, M

1995-12-01

Analyzing the nuclear DNA from ancient human bones is an essential step to the understanding of genetic diversity in current populations, provided that such systematic studies are experimentally feasible. This article reports the successful extraction and amplification of nuclear DNA from the beta-globin region from 5 of 10 bone specimens up to 12,000 years old. These have been typed for beta-globin frameworks by sequencing through two variable positions and for a polymorphic (AT) chi (T) gamma microsatellite 500 bp upstream of the beta-globin gene. These specimens of human remains are somewhat older than those analyzed in previous nuclear gene sequencing reports and considerably older than those used to study high-copy-number human mtDNA. These results show that the systematic study of nuclear DNA polymorphisms of ancient populations is feasible.

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments.

PubMed

Youngblut, Nicholas D; Barnett, Samuel E; Buckley, Daniel H

2018-01-01

DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) that simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments.

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

PubMed Central

Youngblut, Nicholas D.; Barnett, Samuel E.; Buckley, Daniel H.

2018-01-01

DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) that simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments. PMID:29643843

Measurements of soil, surface water, and groundwater CO2 concentration variability within Earth's critical zone: low-cost, long-term, high-temporal resolution monitoring

NASA Astrophysics Data System (ADS)

Blackstock, J. M.; Covington, M. D.; Williams, S. G. W.; Myre, J. M.; Rodriguez, J.

2017-12-01

Variability in CO2 fluxes within Earth's Critical zone occurs over a wide range of timescales. Resolving this and its drivers requires high-temporal resolution monitoring of CO2 both in the soil and aquatic environments. High-cost (> 1,000 USD) gas analyzers and data loggers present cost-barriers for investigations with limited budgets, particularly if high spatial resolution is desired. To overcome high-costs, we developed an Arduino based CO2 measuring platform (i.e. gas analyzer and data logger). The platform was deployed at multiple sites within the Critical Zone overlying the Springfield Plateau aquifer in Northwest Arkansas, USA. The CO2 gas analyzer used in this study was a relatively low-cost SenseAir K30. The analyzer's optical housing was covered by a PTFE semi-permeable membrane allowing for gas exchange between the analyzer and environment. Total approximate cost of the monitoring platform was 200 USD (2% detection limit) to 300 USD (10% detection limit) depending on the K30 model used. For testing purposes, we deployed the Arduino based platform alongside a commercial monitoring platform. CO2 concentration time series were nearly identical. Notably, CO2 cycles at the surface water site, which operated from January to April 2017, displayed a systematic increase in daily CO2 amplitude. Preliminary interpretation suggests key observation of seasonally increasing stream metabolic function. Other interpretations of observed cyclical and event-based behavior are out of the scope of the study; however, the presented method describes an accurate near-hourly characterization of CO2 variability. The new platform has been shown to be operational for several months, and we infer reliable operation for much longer deployments (> 1 year) given adequate environmental protection and power supply. Considering cost-savings, this platform is an attractive option for continuous, accurate, low-power, and low-cost CO2 monitoring for remote locations, globally.

Enviro-Net: From Networks of Ground-Based Sensor Systems to a Web Platform for Sensor Data Management

PubMed Central

Pastorello, Gilberto Z.; Sanchez-Azofeifa, G. Arturo; Nascimento, Mario A.

2011-01-01

Ecosystems monitoring is essential to properly understand their development and the effects of events, both climatological and anthropological in nature. The amount of data used in these assessments is increasing at very high rates. This is due to increasing availability of sensing systems and the development of new techniques to analyze sensor data. The Enviro-Net Project encompasses several of such sensor system deployments across five countries in the Americas. These deployments use a few different ground-based sensor systems, installed at different heights monitoring the conditions in tropical dry forests over long periods of time. This paper presents our experience in deploying and maintaining these systems, retrieving and pre-processing the data, and describes the Web portal developed to help with data management, visualization and analysis. PMID:22163965

Comparative thermal analysis of the Space Station Freedom photovoltaic deployable boom structure using TRASYS, NEVADA, and SINDA programs

NASA Technical Reports Server (NTRS)

Baumeister, Joseph F.; Beach, Duane E.; Armand, Sasan C.

1989-01-01

The proposed Space Station Photovoltaic Deployable Boom was analyzed for operating temperatures. The boom glass/epoxy structure design needs protective shielding from environmental degradation. The protective shielding optical properties (solar absorptivity and emissivity) dictate the operating temperatures of the boom components. The Space Station Boom protective shielding must also withstand the effects of the extendible/retractable coiling acting within the mast canister. A thermal analysis method was developed for the Space Station Deployable Boom to predict transient temperatures for a variety of surface properties. The modeling procedures used to evaluate temperatures within the boom structure incorporated the TRASYS, NEVADA, and SINDA thermal analysis programs. Use of these programs led to a comparison between TRASYS and NEVADA analysis methods. Comparing TRASYS and NEVADA results exposed differences in the environmental solar flux predictions.

Comparative thermal analysis of the space station Freedom photovoltaic deployable boom structure using TRASYS, NEVADA, and SINDA programs

NASA Technical Reports Server (NTRS)

Baumeister, Joseph F.; Beach, Duane E.; Armand, Sasan C.

1989-01-01

The proposed Space Station Photovoltaic Deployable Boom was analyzed for operating temperatures. The boom glass/epoxy structure design needs protective shielding from environmental degradation. The protective shielding optical properties (solar absorptivity and emissivity) dictate the operating temperatures of the boom components. The Space Station Boom protective shielding must also withstand the effects of the extendible/retractable coiling action within the mast canister. A thermal analysis method was developed for the Space Station Deployable Boom to predict transient temperatures for a variety of surface properties. The modeling procedures used to evaluate temperatures within the boom structure incorporated the TRASYS, NEVADA, and SINDA thermal analysis programs. Use of these programs led to a comparison between TRASYS and NEVADA analysis methods. Comparing TRASYS and NEVADA results exposed differences in the environmental solar flux predictions.

Radar cross-section measurements and simulation of a tethered satellite. The small expendable deployer system end-mass payload

NASA Technical Reports Server (NTRS)

Cravey, Robin L.; Fralick, Dion T.; Vedeler, Erik

1995-01-01

The first Small Expendable Deployer System (SEDS-1), a tethered satellite system, was developed by NASA and launched March 29, 1993 as a secondary payload on a United State Air Force (USAF) Delta-2 launch vehicle. The SEDS-1 successfully deployed an instrumented end-mass payload (EMP) on a 20-km nonconducting tether from the second stage of the Delta 2. This paper describes the effort of NASA Langley Research Center's Antenna and Microwave Research Branch to provide assistance to the SEDS Investigators Working Group (IWG) in determining EMP dynamics by analyzing the mission radar skin track data. The radar cross section measurements taken and simulations done for this study are described and comparisons of the measured data with the simulated data for the EMP at 6 GHz are presented.

Altered LINE-1 Methylation in Mothers of Children with Down Syndrome

PubMed Central

Babić Božović, Ivana; Stanković, Aleksandra; Živković, Maja; Vraneković, Jadranka; Kapović, Miljenko; Brajenović-Milić, Bojana

2015-01-01

Down syndrome (DS, also known as trisomy 21) most often results from chromosomal nondisjunction during oogenesis. Numerous studies sustain a causal link between global DNA hypomethylation and genetic instability. It has been suggested that DNA hypomethylation might affect the structure and dynamics of chromatin regions that are critical for chromosome stability and segregation, thus favouring chromosomal nondisjunction during meiosis. Maternal global DNA hypomethylation has not yet been analyzed as a potential risk factor for chromosome 21 nondisjunction. This study aimed to asses the risk for DS in association with maternal global DNA methylation and the impact of endogenous and exogenous factors that reportedly influence DNA methylation status. Global DNA methylation was analyzed in peripheral blood lymphocytes by quantifying LINE-1 methylation using the MethyLight method. Levels of global DNA methylation were significantly lower among mothers of children with maternally derived trisomy 21 than among control mothers (P = 0.000). The combination of MTHFR C677T genotype and diet significantly influenced global DNA methylation (R2 = 4.5%, P = 0.046). The lowest values of global DNA methylation were observed in mothers with MTHFR 677 CT+TT genotype and low dietary folate. Although our findings revealed an association between maternal global DNA hypomethylation and trisomy 21 of maternal origin, further progress and final conclusions regarding the role of global DNA methylation and the occurrence of trisomy 21 are facing major challenges. PMID:26017139

DNAVaxDB: the first web-based DNA vaccine database and its data analysis

PubMed Central

2014-01-01

Since the first DNA vaccine studies were done in the 1990s, thousands more studies have followed. Here we report the development and analysis of DNAVaxDB (http://www.violinet.org/dnavaxdb), the first publically available web-based DNA vaccine database that curates, stores, and analyzes experimentally verified DNA vaccines, DNA vaccine plasmid vectors, and protective antigens used in DNA vaccines. All data in DNAVaxDB are annotated from reliable resources, particularly peer-reviewed articles. Among over 140 DNA vaccine plasmids, some plasmids were more frequently used in one type of pathogen than others; for example, pCMVi-UB for G- bacterial DNA vaccines, and pCAGGS for viral DNA vaccines. Presently, over 400 DNA vaccines containing over 370 protective antigens from over 90 infectious and non-infectious diseases have been curated in DNAVaxDB. While extracellular and bacterial cell surface proteins and adhesin proteins were frequently used for DNA vaccine development, the majority of protective antigens used in Chlamydophila DNA vaccines are localized to the inner portion of the cell. The DNA vaccine priming, other vaccine boosting vaccination regimen has been widely used to induce protection against infection of different pathogens such as HIV. Parasitic and cancer DNA vaccines were also systematically analyzed. User-friendly web query and visualization interfaces are available in DNAVaxDB for interactive data search. To support data exchange, the information of DNA vaccines, plasmids, and protective antigens is stored in the Vaccine Ontology (VO). DNAVaxDB is targeted to become a timely and vital source of DNA vaccines and related data and facilitate advanced DNA vaccine research and development. PMID:25104313

SweeD: likelihood-based detection of selective sweeps in thousands of genomes.

PubMed

Pavlidis, Pavlos; Živkovic, Daniel; Stamatakis, Alexandros; Alachiotis, Nikolaos

2013-09-01

The advent of modern DNA sequencing technology is the driving force in obtaining complete intra-specific genomes that can be used to detect loci that have been subject to positive selection in the recent past. Based on selective sweep theory, beneficial loci can be detected by examining the single nucleotide polymorphism patterns in intraspecific genome alignments. In the last decade, a plethora of algorithms for identifying selective sweeps have been developed. However, the majority of these algorithms have not been designed for analyzing whole-genome data. We present SweeD (Sweep Detector), an open-source tool for the rapid detection of selective sweeps in whole genomes. It analyzes site frequency spectra and represents a substantial extension of the widely used SweepFinder program. The sequential version of SweeD is up to 22 times faster than SweepFinder and, more importantly, is able to analyze thousands of sequences. We also provide a parallel implementation of SweeD for multi-core processors. Furthermore, we implemented a checkpointing mechanism that allows to deploy SweeD on cluster systems with queue execution time restrictions, as well as to resume long-running analyses after processor failures. In addition, the user can specify various demographic models via the command-line to calculate their theoretically expected site frequency spectra. Therefore, (in contrast to SweepFinder) the neutral site frequencies can optionally be directly calculated from a given demographic model. We show that an increase of sample size results in more precise detection of positive selection. Thus, the ability to analyze substantially larger sample sizes by using SweeD leads to more accurate sweep detection. We validate SweeD via simulations and by scanning the first chromosome from the 1000 human Genomes project for selective sweeps. We compare SweeD results with results from a linkage-disequilibrium-based approach and identify common outliers.

An insulated isothermal PCR method on a field-deployable device for rapid and sensitive detection of canine parvovirus type 2 at points of need.

PubMed

Wilkes, Rebecca P; Lee, Pei-Yu A; Tsai, Yun-Long; Tsai, Chuan-Fu; Chang, Hsiu-Hui; Chang, Hsiao-Fen G; Wang, Hwa-Tang T

2015-08-01

Canine parvovirus type 2 (CPV-2), including subtypes 2a, 2b and 2c, causes an acute enteric disease in both domestic and wild animals. Rapid and sensitive diagnosis aids effective disease management at points of need (PON). A commercially available, field-deployable and user-friendly system, designed with insulated isothermal PCR (iiPCR) technology, displays excellent sensitivity and specificity for nucleic acid detection. An iiPCR method was developed for on-site detection of all circulating CPV-2 strains. Limit of detection was determined using plasmid DNA. CPV-2a, 2b and 2c strains, a feline panleukopenia virus (FPV) strain, and nine canine pathogens were tested to evaluate assay specificity. Reaction sensitivity and performance were compared with an in-house real-time PCR using serial dilutions of a CPV-2b strain and 100 canine fecal clinical samples collected from 2010 to 2014, respectively. The 95% limit of detection of the iiPCR method was 13 copies of standard DNA and detection limits for CPV-2b DNA were equivalent for iiPCR and real-time PCR. The iiPCR reaction detected CPV-2a, 2b and 2c and FPV. Non-targeted pathogens were not detected. Test results of real-time PCR and iiPCR from 99 fecal samples agreed with each other, while one real-time PCR-positive sample tested negative by iiPCR. Therefore, excellent agreement (k = 0.98) with sensitivity of 98.41% and specificity of 100% in detecting CPV-2 in feces was found between the two methods. In conclusion, the iiPCR system has potential to serve as a useful tool for rapid and accurate PON, molecular detection of CPV-2. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Enrichment of methylated molecules using enhanced-ice-co-amplification at lower denaturation temperature-PCR (E-ice-COLD-PCR) for the sensitive detection of disease-related hypermethylation.

PubMed

Mauger, Florence; Kernaleguen, Magali; Lallemand, Céline; Kristensen, Vessela N; Deleuze, Jean-François; Tost, Jörg

2018-05-01

The detection of specific DNA methylation patterns bears great promise as biomarker for personalized management of cancer patients. Co-amplification at lower denaturation temperature-PCR (COLD-PCR) assays are sensitive methods, but have previously only been able to analyze loss of DNA methylation. Enhanced (E)-ice-COLD-PCR reactions starting from 2 ng of bisulfite-converted DNA were developed to analyze methylation patterns in two promoters with locked nucleic acid (LNA) probes blocking amplification of unmethylated CpGs. The enrichment of methylated molecules was compared to quantitative (q)PCR and quantified using serial dilutions. E-ice-COLD-PCR allowed the multiplexed enrichment and quantification of methylated DNA. Assays were validated in primary breast cancer specimens and circulating cell-free DNA from cancer patients. E-ice-COLD-PCR could prove a useful tool in the context of DNA methylation analysis for personalized medicine.

Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches.

PubMed

Yahr, Rebecca; Schoch, Conrad L; Dentinger, Bryn T M

2016-09-05

The fungal kingdom is a hyperdiverse group of multicellular eukaryotes with profound impacts on human society and ecosystem function. The challenge of documenting and describing fungal diversity is exacerbated by their typically cryptic nature, their ability to produce seemingly unrelated morphologies from a single individual and their similarity in appearance to distantly related taxa. This multiplicity of hurdles resulted in the early adoption of DNA-based comparisons to study fungal diversity, including linking curated DNA sequence data to expertly identified voucher specimens. DNA-barcoding approaches in fungi were first applied in specimen-based studies for identification and discovery of taxonomic diversity, but are now widely deployed for community characterization based on sequencing of environmental samples. Collectively, fungal barcoding approaches have yielded important advances across biological scales and research applications, from taxonomic, ecological, industrial and health perspectives. A major outstanding issue is the growing problem of 'sequences without names' that are somewhat uncoupled from the traditional framework of fungal classification based on morphology and preserved specimens. This review summarizes some of the most significant impacts of fungal barcoding, its limitations, and progress towards the challenge of effective utilization of the exponentially growing volume of data gathered from high-throughput sequencing technologies.This article is part of the themed issue 'From DNA barcodes to biomes'. © 2016 The Authors.

The Clinical Utilization of Circulating Cell Free DNA (CCFDNA) in Blood of Cancer Patients

PubMed Central

Elshimali, Yahya I.; Khaddour, Husseina; Sarkissyan, Marianna; Wu, Yanyuan; Vadgama, Jaydutt V.

2013-01-01

Qualitative and quantitative testing of circulating cell free DNA (CCFDNA) can be applied for the management of malignant and benign neoplasms. Detecting circulating DNA in cancer patients may help develop a DNA profile for early stage diagnosis in malignancies. The technical issues of obtaining, using, and analyzing CCFDNA from blood will be discussed. PMID:24065096

Genetic relationships within the genus Prevotella analyzed by multilocus enzyme electrophoresis and DNA-DNA hybridization.

PubMed

Combe, M L; Pons, J L

1999-12-01

The genetic diversity and relationships within the genus Prevotella were studied by analyzing twenty-five strains by multilocus enzyme electrophoresis (MLEE) at nine metabolic enzyme loci and DNA-DNA hybridization. MLEE revealed a high genetic diversity with 25 electrophoretic types (ETs) for the 25 strains studied, a mean number of alleles per enzyme locus of 6.8 and a mean genetic diversity per locus of 0.786. The index of association described by Maynard Smith et al. (1993) revealed a clonal structure within the genus Prevotella. A dendrogram generated by cluster analysis of a matrix of ETs showed that species like P. bivia, P. buccae, P. oris, P. oralis, P. nigrescens, and P. denticola form clusters that are consistent with DNA homologies. However, strains identified as P. melaninogenica or P. loescheii by DNA-DNA hybridization did not constitute distinct subpopulations in MLEE. MLEE analysis demonstrated its high power in differentiating closely related strains. It provides an alternative to 16S rRNA analysis for the study of phylogenetic relationships within the genus Prevotella, especially for differentiating strains with high DNA homology or high rRNA homology.

A Mutation in UL15 of Herpes Simplex Virus 1 That Reduces Packaging of Cleaved Genomes▿

PubMed Central

Yang, Kui; Wills, Elizabeth G.; Baines, Joel D.

2011-01-01

Herpesvirus genomic DNA is cleaved from concatemers that accumulate in infected cell nuclei. Genomic DNA is inserted into preassembled capsids through a unique portal vertex. Extensive analyses of viral mutants have indicated that intact capsids, the portal vertex, and all components of a tripartite terminase enzyme are required to both cleave and package viral DNA, suggesting that DNA cleavage and packaging are inextricably linked. Because the processes have not been functionally separable, it has been difficult to parse the roles of individual proteins in the DNA cleavage/packaging reaction. In the present study, a virus bearing the deletion of codons 400 to 420 of UL15, encoding a terminase component, was analyzed. This virus, designated vJB27, failed to replicate on noncomplementing cells but cleaved concatemeric DNA to ca. 35 to 98% of wild-type levels. No DNA cleavage was detected in cells infected with a UL15-null virus or a virus lacking UL15 codons 383 to 385, comprising a motif proposed to couple ATP hydrolysis to DNA translocation. The amount of vJB27 DNA protected from DNase I digestion was reduced compared to the wild-type virus by 6.5- to 200-fold, depending on the DNA fragment analyzed, thus indicating a profound defect in DNA packaging. Capsids containing viral DNA were not detected in vJB27-infected cells, as determined by electron microscopy. These data suggest that pUL15 plays an essential role in DNA translocation into the capsid and indicate that this function is separable from its role in DNA cleavage. PMID:21880766

Geometric design and mechanical behavior of a deployable cylinder with Miura origami

NASA Astrophysics Data System (ADS)

Cai, Jianguo; Deng, Xiaowei; Feng, Jian; Zhou, Ya

2015-12-01

The folding and deployment of a cylinder with Miura origami patterns are studied in this paper. First, the geometric formulation of the design problem is discussed. Then the loading case of the axial strains and corresponding external nodal loads applied on the vertices of the top polygon during the motion is investigated analytically. The influence of the angle between the diagonal and horizontal fold lines α and β and the number of Miura origami elements n on the dynamic behavior of the basic segment is also discussed. Then the dynamic behavior is analyzed using numerical simulations. Finally, the deployment process of a cylinder with multi-stories is discussed. The numerical results agree well with the analytical predictions. The results show that the range of motion, i.e. the maximal displacement of top nodes, will also increase with the increase of angles α and β. This cylinder, with a smaller n, may have a bistable behavior. When n is larger, the influence of n on the axial strains and external nodal loads is slight. The numerical results agree well with the analytical predictions. Moreover, the deployment of the cylinder with multi-stories is non-uniform, which deploys from the upper story to the lower story.

Recent Experiences and Challenges of Military Physiotherapists Deployed to Afghanistan: A Qualitative Study

PubMed Central

Carpenter, Christine

2011-01-01

ABSTRACT Purpose: Military physiotherapists in the Canadian Forces meet the unique rehabilitation needs of military personnel. Recently, the physiotherapy officer role has evolved in response to the Canadian Forces' involvement in the combat theatre of operations of Afghanistan, and this has created new and unique challenges and demands. The purpose of this study was to describe the experiences and challenges of military physiotherapists deployed to Afghanistan. Methods: A qualitative research design guided by descriptive phenomenology involved recruitment of key informants and in-depth interviews as the data collection method. The interviews were transcribed verbatim and the data analyzed using a foundational thematic analysis approach. Strategies of peer review and member checking were incorporated into the study design. Results: Six military physiotherapists were interviewed. They described rewarding experiences that were stressful yet highly career-satisfying. Main challenges revolved around heavy workloads, an expanded scope of practice as sole-charge practitioners, and the consequences and criticality of their clinical decisions. Conclusions: Our findings suggest that enhanced pre-deployment training and the implementation of a stronger support network will improve the capabilities of military physiotherapists deployed to difficult theatres of operations. This type of systematic and comprehensive research is needed to assist the Canadian Forces in proactively preparing and supporting physiotherapists deployed on future missions. PMID:22942524

Large Scale eHealth Deployment in Europe: Insights from Concurrent Use of Standards.

PubMed

Eichelberg, Marco; Chronaki, Catherine

2016-01-01

Large-scale eHealth deployment projects face a major challenge when called to select the right set of standards and tools to achieve sustainable interoperability in an ecosystem including both legacy systems and new systems reflecting technological trends and progress. There is not a single standard that would cover all needs of an eHealth project, and there is a multitude of overlapping and perhaps competing standards that can be employed to define document formats, terminology, communication protocols mirroring alternative technical approaches and schools of thought. eHealth projects need to respond to the important question of how alternative or inconsistently implemented standards and specifications can be used to ensure practical interoperability and long-term sustainability in large scale eHealth deployment. In the eStandards project, 19 European case studies reporting from R&D and large-scale eHealth deployment and policy projects were analyzed. Although this study is not exhaustive, reflecting on the concepts, standards, and tools for concurrent use and the successes, failures, and lessons learned, this paper offers practical insights on how eHealth deployment projects can make the most of the available eHealth standards and tools and how standards and profile developing organizations can serve the users embracing sustainability and technical innovation.

RadNet Sampling and Analyses Schedules

EPA Pesticide Factsheets

RadNet air monitors operate continuously and samples of air, precipitation and drinking water and analyzed on a routine schedule. RadNet can send deployable monitors to any U.S. location in the case of a radiological emergency.

Studies of potential intelligent transportation systems benefits using traffic simulation modeling

DOT National Transportation Integrated Search

1996-06-01

This report documents five studies performed by Mitretek Systems, Inc. to analyze potential : benefits of Intelligent Transportation Systems (ITS) deployment, in support of the ITS : Architecture Development Program. The studies explore the operation...

RivGen, Igiugig Deployment, Control System Specifications and Models

DOE Data Explorer

Forbush, Dominic; Cavagnaro, Robert J.; Guerra, Maricarmen; Donegan, James; McEntee, Jarlath; Thomson, Jim; Polagye, Brian; Fabien, Brian; Kilcher, Levi

2016-03-21

Control System simulation models, case studies, and processing codes for analyzing field data. Raw data files included from VFD and SCADA. MatLab and Simulink are required to open some data files and all model files.

A Preliminary Study: Human Fibroid Stro-1+/CD44+ Stem Cells Isolated From Uterine Fibroids Demonstrate Decreased DNA Repair and Genomic Integrity Compared to Adjacent Myometrial Stro-1+/CD44+ Cells.

PubMed

Prusinski Fernung, Lauren E; Al-Hendy, Ayman; Yang, Qiwei

2018-01-01

Although uterine fibroids (UFs) continue to place a major burden on female reproductive health, the mechanisms behind their origin remain undetermined. Normal myometrial stem cells may be transformed into tumor-initiating stem cells, causing UFs, due to unknown causes of somatic mutations in MED12, found in up to 85% of sporadically formed UFs. It is well established in other tumor types that defective DNA repair increases the risk of such tumorigenic somatic mutations, mechanisms not yet studied in UFs. To examine the putative cause(s) of this stem cell transformation, we analyzed DNA repair within stem cells from human UFs compared to those from adjacent myometrium to determine whether DNA repair in fibroid stem cells is compromised. Human fibroid (F) and adjacent myometrial (Myo) stem cells were isolated from fresh tissues, and gene expression relating to DNA repair was analyzed. Fibroid stem cells differentially expressed DNA repair genes related to DNA double- (DSBs) and single-strand breaks. DNA damage was measured using alkaline comet assay. Additionally, DNA DSBs were induced in these stem cells and DNA DSB repair evaluated (1) by determining changes in phosphorylation of DNA DSB-related proteins and (2) by determining differences in γ-H2AX foci formation and relative DNA repair protein RAD50 expression. Overall, F stem cells demonstrated increased DNA damage and altered DNA repair gene expression and signaling, suggesting that human F stem cells demonstrate impaired DNA repair. Compromised F stem cell DNA repair may contribute to further mutagenesis and, consequently, further growth and propagation of UF tumors.

Gender differences in substance use treatment utilization in the year prior to deployment in Army service members.

PubMed

Wooten, Nikki R; Mohr, Beth A; Lundgren, Lena M; Adams, Rachel Sayko; Merrick, Elizabeth L; Williams, Thomas V; Larson, Mary Jo

2013-09-01

Although military men have heavier drinking patterns, military women experience equal or higher rates of dependence symptoms and similar rates of alcohol-related problems as men at lower levels of consumption. Thus, gender may be important for understanding substance use treatment (SUT) utilization before deployment. Military health system data were analyzed to examine gender differences in both substance use diagnosis (SUDX) and SUT in 152,447 Army service members returning from deployments in FY2010. Propensity score analysis of probability of SUDX indicated that women had lower odds (AOR: 0.91, 95% CI: 0.86-0.96) of military lifetime SUDX. After adjusting for lifetime SUDX using propensity score analysis, multivariate regression found women had substantially lower odds (AOR: 0.61; 95% CI: 0.54-0.70) of using SUT the year prior to deployment. Findings suggest gender disparities in military-provided SUT and a need to consider whether military substance use assessment protocols are sensitive to gender differences. Copyright © 2013 Elsevier Inc. All rights reserved.

Quantification of HIV-1 DNA using real-time recombinase polymerase amplification.

PubMed

Crannell, Zachary Austin; Rohrman, Brittany; Richards-Kortum, Rebecca

2014-06-17

Although recombinase polymerase amplification (RPA) has many advantages for the detection of pathogenic nucleic acids in point-of-care applications, RPA has not yet been implemented to quantify sample concentration using a standard curve. Here, we describe a real-time RPA assay with an internal positive control and an algorithm that analyzes real-time fluorescence data to quantify HIV-1 DNA. We show that DNA concentration and the onset of detectable amplification are correlated by an exponential standard curve. In a set of experiments in which the standard curve and algorithm were used to analyze and quantify additional DNA samples, the algorithm predicted an average concentration within 1 order of magnitude of the correct concentration for all HIV-1 DNA concentrations tested. These results suggest that quantitative RPA (qRPA) may serve as a powerful tool for quantifying nucleic acids and may be adapted for use in single-sample point-of-care diagnostic systems.

Analysis of 4-hydroxy-1-(-3-pyridyl)-1-butanone (HPB)-releasing DNA adducts in human exfoliated oral mucosa cells by liquid chromatography-electrospray ionization-tandem mass spectrometry

PubMed Central

Stepanov, Irina; Muzic, John; Le, Chap T.; Sebero, Erin; Villalta, Peter; Ma, Bin; Jensen, Joni; Hatsukami, Dorothy; Hecht, Stephen S.

2013-01-01

Quantitation of DNA adducts could provide critical information on the relationship between exposure to tobacco smoke and cancer risk in smokers. In this study, we developed a robust and sensitive liquid chromatography-tandem mass spectrometry method for the analysis of 4-hydroxy-1-(3-pyridyl)-1-butanone (HPB1)-releasing DNA adducts in human oral cells, a non-invasive source of DNA for biomarker studies. Isolated DNA undergoes acid hydrolysis, after which samples are purified by solid-phase extraction and analyzed by LC-ESI-MS/MS. The developed method was applied for analysis of samples obtained via collection with a commercial mouthwash from 30 smokers and 15 nonsmokers. In smokers, the levels of HPB-releasing DNA adducts averaged 12.0 pmol HPB/mg DNA (detected in 20 out of 28 samples with quantifiable DNA yield) and in nonsmokers, the levels of adducts averaged 0.23 pmol/mg DNA (detected in 3 out of 15 samples). For the 30 smoking subjects, matching buccal brushings were also analyzed and HPB-releasing DNA adducts were detected in 24 out of 27 samples with quantifiable DNA yield, averaging 44.7 pmol HPB/mg DNA. The levels of adducts in buccal brushings correlated with those in mouthwash samples of smokers (R = 0.73, p < 0.0001). Potentially the method can be applied in studies of individual susceptibility to tobacco-induced cancers in humans. PMID:23252610

Geokinetic environment investigations

NASA Astrophysics Data System (ADS)

Hartnett, E. B.; Carleen, E. D.; Blaney, J. I.

1981-03-01

This report covers the development and implementation of special concepts, techniques and instrumentation for the collection, analysis and application of geokinetic data. The Geokinetic Data Acquisition System (GDAS) was modified, maintained and operationally deployed to various sites designated by AFGL. Tests were conducted at the Defense Nuclear Agency (DNA) CASINO Facility in Maryland; Central Inertial Guidance Test Facility (CIGTF), Holloman AFB, N.M.; Space Transportation System (STS) Launch Complex, Vandenberg AFB, Ca. and the SAC Wing V Minuteman Complex at Cheyenne, Wy. The CASINO data contributed to SAMSO's MX/TGG Advanced Development Bridge II Program for radiation hardening of third generation hardware. The CIGTF investigation supported USAF requirements for highly precise azimuth reference. The Hill AFB the performance of a minuteman III missile guidance system in an engineering silo. The STS program at Vandenberg AFB was to assist in determining the nature of a Titan III-D pressure load. The SAC Wing V deployment was to investigate plateau/valley basin geologic characteristics in respect to motion response.

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline

PubMed Central

2014-01-01

Background Massively parallel DNA sequencing generates staggering amounts of data. Decreasing cost, increasing throughput, and improved annotation have expanded the diversity of genomics applications in research and clinical practice. This expanding scale creates analytical challenges: accommodating peak compute demand, coordinating secure access for multiple analysts, and sharing validated tools and results. Results To address these challenges, we have developed the Mercury analysis pipeline and deployed it in local hardware and the Amazon Web Services cloud via the DNAnexus platform. Mercury is an automated, flexible, and extensible analysis workflow that provides accurate and reproducible genomic results at scales ranging from individuals to large cohorts. Conclusions By taking advantage of cloud computing and with Mercury implemented on the DNAnexus platform, we have demonstrated a powerful combination of a robust and fully validated software pipeline and a scalable computational resource that, to date, we have applied to more than 10,000 whole genome and whole exome samples. PMID:24475911

Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification.

PubMed

Calacal, Gayvelline C; Apaga, Dame Loveliness T; Salvador, Jazelyn M; Jimenez, Joseph Andrew D; Lagat, Ludivino J; Villacorta, Renato Pio F; Lim, Maria Cecilia F; Fortun, Raquel D R; Datar, Francisco A; De Ungria, Maria Corazon A

2015-11-01

The capability of DNA laboratories to perform genotyping procedures from post-mortem remains, including those that had undergone putrefaction, continues to be a challenge in the Philippines, a country characterized by very humid and warm conditions all year round. These environmental conditions accelerate the decomposition of human remains that were recovered after a disaster and those that were left abandoned after a crime. When considerable tissue decomposition of human remains has taken place, there is no other option but to extract DNA from bone and/or teeth samples. Routinely, femur shafts are obtained from recovered bodies for human identification because the calcium matrix protects the DNA contained in the osteocytes. In the Philippines, there is difficulty in collecting femur samples after natural disasters or even human-made disasters, because these events are usually characterized by a large number of fatalities. Identification of casualties is further delayed by limitation in human and material resources. Hence, it is imperative to test other types of biological samples that are easier to collect, transport, process and store. We analyzed DNA that were obtained from body fluid, bone marrow, muscle tissue, clavicle, femur, metatarsal, patella, rib and vertebral samples from five recently deceased untreated male cadavers and seven male human remains that were embalmed, buried for ∼ 1 month and then exhumed. The bodies had undergone different environmental conditions and were in various stages of putrefaction. A DNA extraction method utilizing a detergent-washing step followed by an organic procedure was used. The utility of bone marrow and vitreous fluid including bone marrow and vitreous fluid that was transferred on FTA(®) cards and subjected to autosomal STR and Y-STR DNA typing were also evaluated. DNA yield was measured and the presence or absence of PCR inhibitors in DNA extracts was assessed using Plexor(®)HY. All samples were amplified using PowerPlex(®)21 and PowerPlexY(®)23 systems and analyzed using the AB3500 Genetic Analyzer and the GeneMapper(®) ID-X v.1.2 software. PCR inhibitors were consistently detected in bone marrow, muscle tissue, rib and vertebra samples. Amplifiable DNA was obtained in a majority of the samples analyzed. DNA recovery from 0.1g biological material was adequate for successful genotyping of most of the non-bone and bone samples. Complete DNA profiles were generated from bone marrow, femur, metatarsal and patella with 0.1 ng DNA template. Using 0.5 ng DNA template resulted in increased allele recovery and improved intra- and inter-locus peak balance. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Physical training, smoking, and injury during deployment: a comparison of men and women in the US Army.

PubMed

Anderson, Morgan K; Grier, Tyson; Canham-Chervak, Michelle; Bushman, Timothy T; Jones, Bruce H

2015-01-01

To investigate changes in physical training (PT), fitness, and injury during deployment and identify differences between men and women. Data were collected on male and female US Army Soldiers through self-reported surveys completed before and after deployment to Afghanistan. Changes in physical training activities, physical fitness, injury incidence, BMI, and smoking status were analyzed. Descriptive statistics were used to compare before deployment and deployment results and differences between men and women. Surveys were completed by 727 men and 43 women. The percentage of Soldiers engaging in unit PT running of 5 miles or more per week decreased by almost half for men and women. The percentage of Soldiers doing personal PT running of 5 miles or more per week and engaged in resistance training 3 or more days per week more than doubled for men and women during deployment. Cardiorespiratory endurance for women improved by 50 seconds (P=.06) and for men declined by 29 seconds (P<.01), while muscular endurance increased by 0.6 repetitions (P<.01) during deployment. Injury rates for men decreased, on average, 36.2 to 19.0 injuries per 1,000 Soldiers per month (P=.01). Injury rates for women decreased on average from 42.6 to 14.0 injuries per 1,000 Soldiers per month (P=.02). During deployment, BMI did not change for men or women and smoking increased 19% for men (P<.01), but did not increase for women. Comparisons of physical training activities and health behavior among men and women before and during deployment suggests that increased resistance training could be recommended for women and smoking cessation for men. Given the potentially important role of personal PT in maintaining physical fitness in the deployment environment, future work should support provision of the necessary environment and equipment for Soldiers to perform personal PT effectively and safely on their own. Further, the physical training gaps between men and women should be addressed, with suggestions regarding where improvements can be made, especially for women interested in seeking combat positions with high physical demands.

Monte Carlo Analysis of Molecule Absorption Probabilities in Diffusion-Based Nanoscale Communication Systems with Multiple Receivers.

PubMed

Arifler, Dogu; Arifler, Dizem

2017-04-01

For biomedical applications of nanonetworks, employing molecular communication for information transport is advantageous over nano-electromagnetic communication: molecular communication is potentially biocompatible and inherently energy-efficient. Recently, several studies have modeled receivers in diffusion-based molecular communication systems as "perfectly monitoring" or "perfectly absorbing" spheres based on idealized descriptions of chemoreception. In this paper, we focus on perfectly absorbing receivers and present methods to improve the accuracy of simulation procedures that are used to analyze these receivers. We employ schemes available from the chemical physics and biophysics literature and outline a Monte Carlo simulation algorithm that accounts for the possibility of molecule absorption during discrete time steps, leading to a more accurate analysis of absorption probabilities. Unlike most existing studies that consider a single receiver, this paper analyzes absorption probabilities for multiple receivers deterministically or randomly deployed in a region. For random deployments, the ultimate absorption probabilities as a function of transmitter-receiver distance are shown to fit well to power laws; the exponents derived become more negative as the number of receivers increases up to a limit beyond which no additional receivers can be "packed" in the deployment region. This paper is expected to impact the design of molecular nanonetworks with multiple absorbing receivers.

Impact of High Power Interference Sources in Planning and Deployment of Wireless Sensor Networks and Devices in the 2.4 GHz Frequency Band in Heterogeneous Environments

PubMed Central

Iturri, Peio López; Nazábal, Juan Antonio; Azpilicueta, Leire; Rodriguez, Pablo; Beruete, Miguel; Fernández-Valdivielso, Carlos; Falcone, Francisco

2012-01-01

In this work, the impact of radiofrequency radiation leakage from microwave ovens and its effect on 802.15.4 ZigBee-compliant wireless sensor networks operating in the 2.4 GHz Industrial Scientific Medical (ISM) band is analyzed. By means of a novel radioplanning approach, based on electromagnetic field simulation of a microwave oven and determination of equivalent radiation sources applied to an in-house developed 3D ray launching algorithm, estimation of the microwave oven's power leakage is obtained for the complete volume of an indoor scenario. The magnitude and the variable nature of the interference is analyzed and the impact in the radio link quality in operating wireless sensors is estimated and compared with radio channel measurements as well as packet measurements. The measurement results reveal the importance of selecting an adequate 802.15.4 channel, as well as the Wireless Sensor Network deployment strategy within this type of environment, in order to optimize energy consumption and increase the overall network performance. The proposed method enables one to estimate potential interference effects in devices operating within the 2.4 GHz band in the complete scenario, prior to wireless sensor network deployment, which can aid in achieving the most optimal network topology. PMID:23202228

TQM and lean strategy deployment in Italian hospitals.

PubMed

Chiarini, Andrea; Baccarani, Claudio

2016-10-03

Purpose This paper aims to contribute to the debate concerning total quality management (TQM)-Lean strategy in public healthcare by analyzing the deployment path for implementation, the possible benefits that can be achieved and the encountered pitfalls. Design/methodology/approach Three case studies are drawn from three large Italian hospitals with more than 500 beds each and structured with many departments. The hospitals are located in Tuscany, Italy. These three hospitals have embraced TQM and Lean, starting from strategic objectives and their deployment. At the same time, they have also implemented many TQM-Lean tools. The case studies are based on interviews held with four managers in each of these three public hospitals. Findings Results from the interviews show that there is a specific deployment path for TQM-Lean implementation. The hospitals have also achieved benefits linked to patient satisfaction and improved organizational performances. Problems related to organizational and cultural issues, such as senior managers' commitment, staff management, manufacturing culture and tools adaptation, could affect the benefits. Research limitations/implications The research has been carried out in just three Italian public hospitals. Hence, similar investigations could be managed in other countries. Researchers could also use a larger sample and investigate these issues by means of quantitative inquiry. Practical implications Practitioners could try to apply the deployment path revealed by these case studies in other public and private hospitals. Originality/value The results of this research show that there is a specific, new deployment path for implementing TQM-Lean strategy in some public hospitals.

Millstone: software for multiplex microbial genome analysis and engineering

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

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering.

PubMed

Goodman, Daniel B; Kuznetsov, Gleb; Lajoie, Marc J; Ahern, Brian W; Napolitano, Michael G; Chen, Kevin Y; Chen, Changping; Church, George M

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Millstone: software for multiplex microbial genome analysis and engineering

DOE PAGES

Goodman, Daniel B.; Kuznetsov, Gleb; Lajoie, Marc J.; ...

2017-05-25

Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. Here, we describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab.

Constrained VPH+: a local path planning algorithm for a bio-inspired crawling robot with customized ultrasonic scanning sensor.

PubMed

Rao, Akshay; Elara, Mohan Rajesh; Elangovan, Karthikeyan

This paper aims to develop a local path planning algorithm for a bio-inspired, reconfigurable crawling robot. A detailed description of the robotic platform is first provided, and the suitability for deployment of each of the current state-of-the-art local path planners is analyzed after an extensive literature review. The Enhanced Vector Polar Histogram algorithm is described and reformulated to better fit the requirements of the platform. The algorithm is deployed on the robotic platform in crawling configuration and favorably compared with other state-of-the-art local path planning algorithms.

Analysis of a Single Year of Performance Data for Thin Film Modules Deployed at NREL and NISE

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

MacAlpine, Sara; Deceglie, Michael; Kurtz, Sarah

2016-08-01

The National Renewable Energy Laboratory (NREL) and National Institute of Solar Energy (NISE), located in the United States and India, respectively, have partnered to deploy and monitor modules of three different thin film technologies, to compare the performance and/or degradation between the two sites. This report analyzes a single year of performance data (May 2014 -- May 2015) for the three thin film technologies, exploring the modules' performance under standard test conditions and monthly performance ratios, as well as fill factors varying season, light level, and temperature.

A novel approach to spacecraft re-entry and recovery

NASA Astrophysics Data System (ADS)

Patten, Richard; Hedgecock, Judson C.

1990-01-01

A deployable radiative heat shield design for spacecraft reentry is discussed. The design would allow the spacecraft to be cylindrical instead of the the traditional conical shape, providing a greater internal volume and thus enhancing mission capabilities. The heat shield uses a flexible thermal blanket material which is deployed in a manner similar to an umbrella. Based on the radiative properties of this blanket material, heating constraints have been established which allow a descent trajectory to be designed. The heat shield and capsule configuration are analyzed for resistance to heat flux and aerodynamic stability based on reentry trajectory. Experimental tests are proposed.

mtDNA-Server: next-generation sequencing data analysis of human mitochondrial DNA in the cloud.

PubMed

Weissensteiner, Hansi; Forer, Lukas; Fuchsberger, Christian; Schöpf, Bernd; Kloss-Brandstätter, Anita; Specht, Günther; Kronenberg, Florian; Schönherr, Sebastian

2016-07-08

Next generation sequencing (NGS) allows investigating mitochondrial DNA (mtDNA) characteristics such as heteroplasmy (i.e. intra-individual sequence variation) to a higher level of detail. While several pipelines for analyzing heteroplasmies exist, issues in usability, accuracy of results and interpreting final data limit their usage. Here we present mtDNA-Server, a scalable web server for the analysis of mtDNA studies of any size with a special focus on usability as well as reliable identification and quantification of heteroplasmic variants. The mtDNA-Server workflow includes parallel read alignment, heteroplasmy detection, artefact or contamination identification, variant annotation as well as several quality control metrics, often neglected in current mtDNA NGS studies. All computational steps are parallelized with Hadoop MapReduce and executed graphically with Cloudgene. We validated the underlying heteroplasmy and contamination detection model by generating four artificial sample mix-ups on two different NGS devices. Our evaluation data shows that mtDNA-Server detects heteroplasmies and artificial recombinations down to the 1% level with perfect specificity and outperforms existing approaches regarding sensitivity. mtDNA-Server is currently able to analyze the 1000G Phase 3 data (n = 2,504) in less than 5 h and is freely accessible at https://mtdna-server.uibk.ac.at. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The BioSentinel Bioanalytical Microsystem: Characterizing DNA Radiation Damage in Living Organisms Beyond Earth Orbit

NASA Technical Reports Server (NTRS)

Ricco, A. J.; Hanel, R.; Bhattacharya, S.; Boone, T.; Tan, M.; Mousavi, A.; Rademacher, A.; Schooley, A.; Klamm, B.; Benton, J.;

Computational method and system for modeling, analyzing, and optimizing DNA amplification and synthesis

DOEpatents

Vandersall, Jennifer A.; Gardner, Shea N.; Clague, David S.

2010-05-04

A computational method and computer-based system of modeling DNA synthesis for the design and interpretation of PCR amplification, parallel DNA synthesis, and microarray chip analysis. The method and system include modules that address the bioinformatics, kinetics, and thermodynamics of DNA amplification and synthesis. Specifically, the steps of DNA selection, as well as the kinetics and thermodynamics of DNA hybridization and extensions, are addressed, which enable the optimization of the processing and the prediction of the products as a function of DNA sequence, mixing protocol, time, temperature and concentration of species.

Preanalytical blood sample workup for cell-free DNA analysis using Droplet Digital PCR for future molecular cancer diagnostics.

PubMed

van Ginkel, Joost H; van den Broek, Daan A; van Kuik, Joyce; Linders, Dorothé; de Weger, Roel; Willems, Stefan M; Huibers, Manon M H

2017-10-01

In current molecular cancer diagnostics, using blood samples of cancer patients for the detection of genetic alterations in plasma (cell-free) circulating tumor DNA (ctDNA) is an emerging practice. Since ctDNA levels in blood are low, highly sensitive Droplet Digital PCR (ddPCR) can be used for detecting rare mutational targets. In order to perform ddPCR on blood samples, a standardized procedure for processing and analyzing blood samples is necessary to facilitate implementation into clinical practice. Therefore, we assessed the technical sample workup procedure for ddPCR on blood plasma samples. Blood samples from healthy individuals, as well as lung cancer patients were analyzed. We compared different methods and protocols for sample collection, storage, centrifugation, isolation, and quantification. Cell-free DNA (cfDNA) concentrations of several wild-type targets and BRAF and EGFR-mutant ctDNA concentrations quantified by ddPCR were primary outcome measurements. Highest cfDNA concentrations were measured in blood collected in serum tubes. No significant differences in cfDNA concentrations were detected between various time points of up to 24 h until centrifugation. Highest cfDNA concentrations were detected after DNA isolation with the Quick cfDNA Serum & Plasma Kit, while plasma isolation using the QIAamp Circulating Nucleic Acid Kit yielded the most consistent results. DdPCR results on cfDNA are highly dependent on multiple factors during preanalytical sample workup, which need to be addressed during the development of this diagnostic tool for cancer diagnostics in the future. © 2017 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

Sequence periodicity in nucleosomal DNA and intrinsic curvature.

PubMed

Nair, T Murlidharan

2010-05-17

Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA.

APPLICATION OF DNA MICROARRAYS TO REPRODUCTIVE TOXICOLOGY AND THE DEVELOPMENT OF A TESTIS ARRAY

EPA Science Inventory

With the advent of sequence information for entire mammalian genomes, it is now possible to analyze gene expression and gene polymorphisms on a genomic scale. The primary tool for analysis of gene expression is the DNA microarray. We have used commercially available cDNA micro...

Aspergillus section Versicolores: nine new species and multilocus DNA sequence based phylogeny

USDA-ARS?s Scientific Manuscript database

ß-tubulin, calmodulin, internal transcribed spacer and partial lsu-rDNA, RNA polymerase, DNA replication licensing factor Mcm7, and pre-rRNA processing protein Tsr1 were amplified and sequenced from 62 A. versicolor clade isolates and analyzed phylogenetically using the concordance model to establis...

Aspergillus section Versicolores, nine new species and multilocus DNA sequence based phylogeny

USDA-ARS?s Scientific Manuscript database

ß-tubulin, calmodulin, internal transcribed spacer and partial lsu-rDNA, RNA polymerase, DNA replication licensing factor Mcm7, and pre-rRNA processing protein Tsr1 were amplified and sequenced from 62 A. versicolor clade isolates and analyzed phylogenetically using the concordance model to establis...

Attitude stability of a spinning spacecraft during appendage deployment/retraction

NASA Technical Reports Server (NTRS)

Fitz-Coy, Norman; Fullerton, Wayne

1994-01-01

The work presented is motivated by the need for a national satellite rescue policy, not the ad hoc policy now in place. In studying different approaches for a national policy, the issue of capture and stabilization of a tumbling spacecraft must be addressed. For a rescue mission involving a tumbling spacecraft, it may be advantageous to have a rescue vehicle which is compact and 'rigid' during the rendezvous/capture phase. After capture, passive stabilization techniques could be utilized as an efficient means of detumbling the resulting system (i.e., both the rescue vehicle and captures spacecraft). Since the rescue vehicle is initially compact and 'rigid,' significant passive stabilization through energy dissipation can only be achieved through the deployment of flexible appendages. Once stabilization is accomplished, retraction of the appendages before maneuvering the system to its final destination may also prove advantageous. It is therefore of paramount interest that we study the effect of appendage deployment/retraction on the attitude stability of a spacecraft. Particular interest should be paid to appendage retraction, since if this process is destabilizing, passive stabilization as proposed may not be useful. Over the past three decades, it has been an 'on-again-off-again affair' with the problem of spacecraft appendage deployment. In most instances, these studies have been numerical simulations of specific spacecraft configurations for which there were specific concerns. The primary focus of these studies was the behavior of the appendage during deployment; the effects of appendage retraction was considered only in one of these studies. What is missing in the literature is a thorough study of the effects of appendage deployment/retraction on the attitude stability of a spacecraft. This paper presents a rigorous analysis of the stability of a spinning spacecraft during the deployment or the retraction of an appendage. The analysis is simplified such that meaningful insights into the problem can be inferred; it is not overly simplified such that critical dynamical behavior is neglected. The system is analyzed assuming that the spacecraft hub is rigid. The appendage deployment mechanism is modeled as a point mass on a massless rod whose length undergoes prescribed changes. Simplified flexibility effects of the appendage are included. The system is examined for stability by linearizing the equations in terms of small deviations from steady, noninterfering coning motion. Routh's procedure for analyzing small deviations from steady motion in dynamical systems is utilized in the analysis. The system of equations are nondimensionalized to facilitate parametric studies. The results are presented in terms of a reduced number of nondimensional parameters so that some general conclusions may be drawn. Verification of the linear analysis is presented through numerical simulations of the complete nonlinear, nonautonomous, coupled equations.

Public transportation's role in responding to climate change

DOT National Transportation Integrated Search

2010-01-01

This paper details the role public transportation has in responding to the challenge of climate change. It collects and analyzes data from across the country on public transportation fuel use, vehicles deployed, rides taken, and other key metrics, dr...

Medical impulsive therapy (MIT): the impact of 1 week of preoperative tamsulosin on deployment of 16-French ureteral access sheaths without preoperative ureteral stent placement.

PubMed

Kaler, Kamaljot S; Safiullah, Shoaib; Lama, Daniel J; Parkhomenko, Egor; Okhunov, Zhamshid; Ko, Young H; Huynh, Linda; Patel, Roshan M; Landman, Jaime; Clayman, Ralph V

2018-05-25

Medical expulsive therapy is based on pharmacologic ureteral relaxation. We hypothesized this concept may facilitate the deployment of the large 16 French (F) ureteral access sheath (UAS) when patients are intentionally pre-treated with oral tamsulosin, i.e., medical impulsive therapy. We retrospectively analyzed our experience with UAS deployment during endoscopic-guided percutaneous nephrolithotomy in prone position in patients pre-treated for 1 week with oral tamsulosin with a contemporary untreated cohort. Between January 2015 and September 2016, seventy-seven patients without a pre-existing ureteral stent met inclusion criteria. Demographic data, tamsulosin usage, UAS size, deployment failure, ureteral injuries, stone-free rates, and complications were recorded. Univariate and multivariate analysis was conducted to assess the impact of tamsulosin on deployment of the 16F UAS. There was no statistical difference between the tamsulosin (n = 40) group and non-tamsulosin (n = 37) group in regard to demographic data. The tamsulosin group had a significantly higher percentage of 16F UAS deployment, 87 vs. 43% (p < 0.001), and no significant difference in ureteral injuries (p = 0.228). Univariate and multivariate analysis revealed that tamsulosin significantly increased the odds ratio (9.3 and 19.4, respectively) for successful passage of a 16F UAS. Despite a larger stone volume, there was no significant difference in computed tomography scan complete stone-free rates (29 vs. 42%; p = 0.277) at median post-operative time of only 3 days. In this retrospective study, 1 week of preoperative tamsulosin was associated with an increase in the deployment of a 16F UAS in patients without preoperative ureteral stent placement.

Visualization and quantitative analysis of extrachromosomal telomere-repeat DNA in individual human cells by Halo-FISH

PubMed Central

Komosa, Martin; Root, Heather; Meyn, M. Stephen

2015-01-01

Current methods for characterizing extrachromosomal nuclear DNA in mammalian cells do not permit single-cell analysis, are often semi-quantitative and frequently biased toward the detection of circular species. To overcome these limitations, we developed Halo-FISH to visualize and quantitatively analyze extrachromosomal DNA in single cells. We demonstrate Halo-FISH by using it to analyze extrachromosomal telomere-repeat (ECTR) in human cells that use the Alternative Lengthening of Telomeres (ALT) pathway(s) to maintain telomere lengths. We find that GM847 and VA13 ALT cells average ∼80 detectable G/C-strand ECTR DNA molecules/nucleus, while U2OS ALT cells average ∼18 molecules/nucleus. In comparison, human primary and telomerase-positive cells contain <5 ECTR DNA molecules/nucleus. ECTR DNA in ALT cells exhibit striking cell-to-cell variations in number (<20 to >300), range widely in length (<1 to >200 kb) and are composed of primarily G- or C-strand telomere-repeat DNA. Halo-FISH enables, for the first time, the simultaneous analysis of ECTR DNA and chromosomal telomeres in a single cell. We find that ECTR DNA comprises ∼15% of telomere-repeat DNA in GM847 and VA13 cells, but <4% in U2OS cells. In addition to its use in ALT cell analysis, Halo-FISH can facilitate the study of a wide variety of extrachromosomal DNA in mammalian cells. PMID:25662602

Evaluation of digital PCR for detecting low-level EGFR mutations in advanced lung adenocarcinoma patients: a cross-platform comparison study

PubMed Central

Liu, Bing; Li, Lei; Huang, Lixia; Li, Shaoli; Rao, Guanhua; Yu, Yang; Zhou, Yanbin

2017-01-01

Emerging evidence has indicated that circulating tumor DNA (ctDNA) from plasma could be used to analyze EGFR mutation status for NSCLC patients; however, due to the low level of ctDNA in plasma, highly sensitive approaches are required to detect low frequency mutations. In addition, the cutoff for the mutation abundance that can be detected in tumor tissue but cannot be detected in matched ctDNA is still unknown. To assess a highly sensitive method, we evaluated the use of digital PCR in the detection of EGFR mutations in tumor tissue from 47 advanced lung adenocarcinoma patients through comparison with NGS and ARMS. We determined the degree of concordance between tumor tissue DNA and paired ctDNA and analyzed the mutation abundance relationship between them. Digital PCR and Proton had a high sensitivity (96.00% vs. 100%) compared with that of ARMS in the detection of mutations in tumor tissue. Digital PCR outperformed Proton in identifying more low abundance mutations. The ctDNA detection rate of digital PCR was 87.50% in paired tumor tissue with a mutation abundance above 5% and 7.59% in paired tumor tissue with a mutation abundance below 5%. When the DNA mutation abundance of tumor tissue was above 3.81%, it could identify mutations in paired ctDNA with a high sensitivity. Digital PCR will help identify alternative methods for detecting low abundance mutations in tumor tissue DNA and plasma ctDNA. PMID:28978074

A small spacecraft for multipoint measurement of ionospheric plasma.

PubMed

Roberts, T M; Lynch, K A; Clayton, R E; Weiss, J; Hampton, D L

2017-07-01

Measurement of ionospheric plasma is often performed by a single in situ device or remotely using cameras and radar. This article describes a small, low-resource, deployed spacecraft used as part of a local, multipoint measurement network. A B-field aligned sounding rocket ejects four of these spin-stabilized spacecraft in a cross pattern. In this application, each spacecraft carries two retarding potential analyzers which are used to determine plasma density, flow, and ion temperature. An inertial measurement unit and a light-emitting diode array are used to determine the position and orientation of the devices after deployment. The design of this spacecraft is first described, and then results from a recent test flight are discussed. This flight demonstrated the successful operation of the deployment mechanism and telemetry systems, provided some preliminary plasma measurements in a simple mid-latitude environment, and revealed several design issues.

A small spacecraft for multipoint measurement of ionospheric plasma

NASA Astrophysics Data System (ADS)

Roberts, T. M.; Lynch, K. A.; Clayton, R. E.; Weiss, J.; Hampton, D. L.

2017-07-01

Measurement of ionospheric plasma is often performed by a single in situ device or remotely using cameras and radar. This article describes a small, low-resource, deployed spacecraft used as part of a local, multipoint measurement network. A B-field aligned sounding rocket ejects four of these spin-stabilized spacecraft in a cross pattern. In this application, each spacecraft carries two retarding potential analyzers which are used to determine plasma density, flow, and ion temperature. An inertial measurement unit and a light-emitting diode array are used to determine the position and orientation of the devices after deployment. The design of this spacecraft is first described, and then results from a recent test flight are discussed. This flight demonstrated the successful operation of the deployment mechanism and telemetry systems, provided some preliminary plasma measurements in a simple mid-latitude environment, and revealed several design issues.

Health Care Provider Burnout in a United States Military Medical Center During a Period of War.

PubMed

Sargent, Paul; Millegan, Jeffrey; Delaney, Eileen; Roesch, Scott; Sanders, Martha; Mak, Heather; Mallahan, Leonard; Raducha, Stephanie; Webb-Murphy, Jennifer

2016-02-01

Provider burnout can impact efficiency, empathy, and medical errors. Our study examines burnout in a military medical center during a period of war. A survey including the Maslach Burnout Inventory (MBI), deployment history, and work variables was distributed to health care providers. MBI subscale means were calculated and associations between variables were analyzed. Approximately 60% of 523 respondents were active duty and 34% had deployed. MBI subscale means were 19.99 emotional exhaustion, 4.84 depersonalization, and 40.56 personal accomplishment. Frustration over administrative support was associated with high emotional exhaustion and depersonalization; frustration over life/work balance was associated with high emotional exhaustion. Levels of burnout in our sample were similar to civilian medical centers. Sources of frustration were related to administrative support and life/work balance. Deployment had no effect on burnout levels. Reprint & Copyright © 2016 Association of Military Surgeons of the U.S.

The front line health worker: selection, training, and performance.

PubMed

Ronaghy, H A; Najarzadeh, E; Schwartz, T A; Russel, S S; Solter, S; Zeighami, B

1976-03-01

Iranian villagers with basic literacy were recruited, selected, trained, and deployed as Village Health Workers (VHWs) to rural areas of Iran. VHW clinical visit records and activities logs were analyzed to determine levels and nature of effort achieved in the field. Within six months of deployment, the number of patient visits to VHW treatment services constituted 53% of the target population. Within ten months of deployment, the number of family planning acceptors rose from 8% to 21% of the population at risk. Improvements to water supplies have been effected in 50% of target villages. Sanitary improvements have been made to 35% of the houses and 88% of toilets in those villages. Demographic characteristics, class rank, and place of residence of VHWs appear unassociated with village differences in levels of achievement. However, availability of material resources and actual time spent by VHWs on the job may be factors influencing the differences in outcome between villages.

Application of the actor model to large scale NDE data analysis

NASA Astrophysics Data System (ADS)

Coughlin, Chris

2018-03-01

The Actor model of concurrent computation discretizes a problem into a series of independent units or actors that interact only through the exchange of messages. Without direct coupling between individual components, an Actor-based system is inherently concurrent and fault-tolerant. These traits lend themselves to so-called "Big Data" applications in which the volume of data to analyze requires a distributed multi-system design. For a practical demonstration of the Actor computational model, a system was developed to assist with the automated analysis of Nondestructive Evaluation (NDE) datasets using the open source Myriad Data Reduction Framework. A machine learning model trained to detect damage in two-dimensional slices of C-Scan data was deployed in a streaming data processing pipeline. To demonstrate the flexibility of the Actor model, the pipeline was deployed on a local system and re-deployed as a distributed system without recompiling, reconfiguring, or restarting the running application.

Discursive Deployments: Mobilizing Support for Municipal and Community Wireless Networks in the U.S.

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

Alvarez, Rosio; Rodriguez, Juana Maria

2008-08-16

This paper examines Municipal Wireless (MW) deployments in the United States. In particular, the interest is in understanding how discourse has worked to mobilize widespread support for MW networks. We explore how local governments discursively deploy the language of social movements to create a shared understanding of the networking needs of communities. Through the process of"framing" local governments assign meaning to the MW networks in ways intended to mobilize support anddemobilize opposition. The mobilizing potential of a frame varies and is dependent on its centrality and cultural resonance. We examine the framing efforts of MW networks by using a samplemore » of Request for Proposals for community wireless networks, semi-structured interviews and local media sources. Prominent values that are central to a majority of the projects and others that are culturally specific are identified and analyzed for their mobilizing potency.« less

Design and analysis of morphing wing based on SMP composite

NASA Astrophysics Data System (ADS)

Yu, Kai; Yin, Weilong; Sun, Shouhua; Liu, Yanju; Leng, Jinsong

2009-03-01

A new concept of a morphing wing based on shape memory polymer (SMP) and its reinforced composites is proposed in this paper. SMP used in this study is a thermoset styrene-based resin in contrast to normal thermoplastic SMP. During heating, the wing curled on the aircraft can be deployed, providing main lift for a morphing aircraft to realize the stable flight. Aerodynamic characteristics of the deployed morphing wing are calculated by using CFD software. The static deformation of the wing under the air loads is also analyzed by using the finite element method. The results show that the used SMP material can provide enough strength and stiffness for the application. Finally, preliminary testing is conducted to investigate the recovery performances of SMP and its reinforced composites. During the test, the deployment and the wind-resistant ability of the morphing wing are dramatically improved by adding reinforced phase to the SMP.

Financial Well-Being and Post-Deployment Adjustment among Iraq and Afghanistan War Veterans

PubMed Central

Elbogen, Eric B.; Johnson, CAPT Sally C.; Wagner, H. Ryan; Newton, Virginia M.; Beckham, Jean C.

2012-01-01

Research has yet to examine the relationship between financial well-being and community reintegration of veterans. To address this, we analyzed data from n=1,388 Iraq and Afghanistan War Era Veterans who completed a national survey on post-deployment adjustment. The results indicated that probable major depressive disorder, posttraumatic stress disorder, and traumatic brain injury were associated with financial difficulties. However, regardless of diagnosis, veterans who reported having money to cover basic needs were significantly less likely to have post-deployment adjustment problems such as criminal arrest, homelessness, substance abuse, suicidal behavior, and aggression. Statistical analyses also indicated that poor money management (e.g. incurring significant debt or writing bad checks) was related to maladjustment, even among veterans at higher income levels. Given these findings, efforts aimed at enhancing financial literacy and promoting meaningful employment may have promise to enhance outcomes and improve quality of life among returning veterans. PMID:22730842

A census of marine zooplankton in the tropical/subtropical Atlantic from the surface to 5000 m.

NASA Astrophysics Data System (ADS)

Wiebe, P. H.; Bucklin, A.; Madin, L.; Angel, M. V.; Sutton, T.; Pages, F.; Hopcroft, R. R.

2006-12-01

Zooplankton from tropical/subtropical waters in the Atlantic Ocean were sampled from the surface to 5000 m, with a particular focus on the mesopelagic, bathypelagic, abyssopelagic zones. Sampling, on a cruise sponsored by the NOAA Ocean Exploration Program and the Census of Marine Life, was conducted at five stations from the northern Sargasso Sea to the equatorial waters northeast of Brazil. Environmental data and zooplankton samples were collected using three Multiple Opening/Closing Nets and Environmental Sensing Systems (MOCNESS): a 10-m opening/closing trawl with 335-um mesh nets sampled from 5000 to 1000 m and two smaller MOCNESS with similar or smaller mesh sampled the upper 1000 m. Ring net and water bottle casts, and blue-water SCUBA diving were also carried out. Samples were analyzed at sea using traditional morphological taxonomic approaches by a team of experts, followed by molecular systematic analysis, including determination of a DNA barcode (i.e., short DNA sequence for species recognition) for each species. Over 500 species were identified onboard ship; more than 1000 specimens were placed in a queue for barcoding; 87 species were barcoded at sea. For several taxonomic groups, a significant fraction of the region's species were collected and identified. Sixty-five species of planktonic ostracods were identified at sea out of the 140 known for the North Atlantic Ocean, with at least six undescribed species collected and the first DNA barcode for a planktonic ostracod obtained. At-sea analysis of samples also yielded identified specimens for more than 40 species of molluscs (pteropods, heteropods, etc.), more than 100 species of jellyfish, several hundred species of copepods, and more than 100 species of fish. In all, taxonomists estimated that at least 12 - 15 new species will be described from this effort. The special deployment of trawls to sample large volumes at great depths for small zooplankton yielded preliminary confirmation that species diversity is high (with many more species yet to be captured and studied), but abundance is low.

Hypothermia modulates the DNA damage response to ionizing radiation in human peripheral blood lymphocytes.

PubMed

Lisowska, Halina; Cheng, Lei; Sollazzo, Alice; Lundholm, Lovisa; Wegierek-Ciuk, Aneta; Sommer, Sylwester; Lankoff, Anna; Wojcik, Andrzej

2018-06-01

Low temperature at exposure has been shown to act in a radioprotective manner at the level of cytogenetic damage. It was suggested to be due to an effective transformation of DNA damage to chromosomal damage at low temperature. The purpose of the study was to analyze the kinetics of aberration formation during the first hours after exposing human peripheral blood lymphocytes to ionizing radiation at 0.8 °C and 37 °C. To this end, we applied the technique of premature chromosome condensation. In addition, DNA damage response was analyzed by measuring the levels of phosphorylated DNA damage responsive proteins ATM, DNA-PK and p53 and mRNA levels of the radiation-responsive genes BBC3, FDXR, GADD45A, XPC, MDM2 and CDKN1A. A consistently lower frequency of chromosomal breaks was observed in cells exposed at 0.8 °C as compared to 37 °C already after 30 minutes postexposure. This effect was accompanied by elevated levels of phosphorylated ATM and DNA-PK proteins and a reduced immediate level of phosphorylated p53 and of the responsive genes. Low temperature at exposure appears to promote DNA repair leading to reduced transformation of DNA damage to chromosomal aberrations.

Analysis of radio wave propagation for ISM 2.4 GHz Wireless Sensor Networks in inhomogeneous vegetation environments.

PubMed

Azpilicueta, Leire; López-Iturri, Peio; Aguirre, Erik; Mateo, Ignacio; Astrain, José Javier; Villadangos, Jesús; Falcone, Francisco

2014-12-10

The use of wireless networks has experienced exponential growth due to the improvements in terms of battery life and low consumption of the devices. However, it is compulsory to conduct previous radio propagation analysis when deploying a wireless sensor network. These studies are necessary to perform an estimation of the range coverage, in order to optimize the distance between devices in an actual network deployment. In this work, the radio channel characterization for ISM 2.4 GHz Wireless Sensor Networks (WSNs) in an inhomogeneous vegetation environment has been analyzed. This analysis allows designing environment monitoring tools based on ZigBee and WiFi where WSN and smartphones cooperate, providing rich and customized monitoring information to users in a friendly manner. The impact of topology as well as morphology of the environment is assessed by means of an in-house developed 3D Ray Launching code, to emulate the realistic operation in the framework of the scenario. Experimental results gathered from a measurement campaign conducted by deploying a ZigBee Wireless Sensor Network, are analyzed and compared with simulations in this paper. The scenario where this network is intended to operate is a combination of buildings and diverse vegetation species. To gain insight in the effects of radio propagation, a simplified vegetation model has been developed, considering the material parameters and simplified geometry embedded in the simulation scenario. An initial location-based application has been implemented in a real scenario, to test the functionality within a context aware scenario. The use of deterministic tools can aid to know the impact of the topological influence in the deployment of the optimal Wireless Sensor Network in terms of capacity, coverage and energy consumption, making the use of these systems attractive for multiple applications in inhomogeneous vegetation environments.

An economic analysis on optical Ethernet in the access network

NASA Astrophysics Data System (ADS)

Kim, Sung Hwi; Nam, Dohyun; Yoo, Gunil; Kim, WoonHa

2004-04-01

Nowadays, Broadband service subscribers have increased exponentially and have almost saturated in Korea. Several types of solutions for broadband service applied to the field. Among several types of broadband services, most of subscribers provided xDSL service like ADSL or VDSL. Usually, they who live in an apartment provided Internet service by Ntopia network as FTTC structure that is a dormant network in economical view at KT. Under competitive telecom environment for new services like video, we faced with needing to expand or rebuild portions of our access networks, are looking for ways to provide any service that competitors might offer presently or in the near future. In order to look for new business model like FTTH service, we consider deploying optical access network. In spite of numerous benefits of PON until now, we cannot believe that PON is the best solution in Korea. Because we already deployed optical access network of ring type feeder cable and have densely population of subscribers that mainly distributed inside 6km from central office. So we try to utilize an existing Ntopia network for FTTH service under optical access environment. Despite of such situations, we try to deploy PON solution in the field as FTTC or FTTH architecture. Therefore we analyze PON structure in comparison with AON structure in order to look for optimized structure in Korea. At first, we describe the existing optical access networks and network architecture briefly. Secondly we investigate the cost of building optical access networks by modeling cost functions on AON and PON structure which based on Ethernet protocol, and analyze two different network architectures according to different deployment scenarios: Urban, small town, rural. Finally we suggest the economic and best solution with PON structure to optimize to optical access environment of KT.

Installed Cost Benchmarks and Deployment Barriers for Residential Solar Photovoltaics with Energy Storage: Q1 2016

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

Ardani, Kristen; O'Shaughnessy, Eric; Fu, Ran

2016-12-01

In this report, we fill a gap in the existing knowledge about PV-plus-storage system costs and value by providing detailed component- and system-level installed cost benchmarks for residential systems. We also examine other barriers to increased deployment of PV-plus-storage systems in the residential sector. The results are meant to help technology manufacturers, installers, and other stakeholders identify cost-reduction opportunities and inform decision makers about regulatory, policy, and market characteristics that impede solar plus storage deployment. In addition, our periodic cost benchmarks will document progress in cost reductions over time. To analyze costs for PV-plus-storage systems deployed in the first quartermore » of 2016, we adapt the National Renewable Energy Laboratory's component- and system-level cost-modeling methods for standalone PV. In general, we attempt to model best-in-class installation techniques and business operations from an installed-cost perspective. In addition to our original analysis, model development, and review of published literature, we derive inputs for our model and validate our draft results via interviews with industry and subject-matter experts. One challenge to analyzing the costs of PV-plus-storage systems is choosing an appropriate cost metric. Unlike standalone PV, energy storage lacks universally accepted cost metrics, such as dollars per watt of installed capacity and lifetime levelized cost of energy. We explain the difficulty of arriving at a standard approach for reporting storage costs and then provide the rationale for using the total installed costs of a standard PV-plus-storage system as our primary metric, rather than using a system-size-normalized metric.« less

The scientists' opposition to SDI: How political views affect technical analysis

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

Tait, G.E.

1989-01-01

This study examines the scientists' opposition to President Reagan's Strategic Defense Initiative (1983-1989) with a focus on the relationship between the scientists' political and strategic opposition to ballistic missile defenses (BMD) and their technical doubts about BMD technologies. The study begins with a review of the scientists' increased influence in United State's national security decision making because of the development of atomic weapons. The study then examines the scientists' role in developing and promoting a theory of arms control based upon mutual societal vulnerability. Because of this theory, a large segment of the American scientific community came to believe thatmore » the development of ballistic missile defenses would destabilize the strategic balance and therefore took the lead in arguing against BMD deployments. These background chapters conclude with an analysis of the scientists' involvement in the political campaign to stop the proposed Sentinel and Safeguard Anti-Ballistic Missile defense. The study then turns to the contemporary scientific opposition to BMD deployments and the SDI research program. After examining the polls and petitions that identify the scientists opposed to SDI, the study analyzes the tactics that three scientists use in their political effort to prevent BMD deployments. Next, an examination of the political and strategic assumptions behind the scientists' opposition to BMD reveals that a belief in the arms control process and deterrence by punishment, especially Assured Destruction deterrence, with a fear of an action-reaction arms race inspires much of the contemporary opposition to BMD. Finally, the scientists' technical doubts about BMD technologies are analyzed through the prism of peer critique. These critiques show that the scientists opposed to BMD deployments us pessimistic and unrealistic assumptions to skew their technical analysis of BMD technologies.« less

TRANSGENE ESCAPE MONITORING, POPULATION GENETICS, AND THE LAW

EPA Science Inventory

There has been little discussion about how to apply population genetics methods to monitor the spread of transgenes that are detected outside the agricultural populations where they are deployed. Population geneticists have developed tools for analyzing the genetic makeup of indi...

Microarrays (DNA Chips) for the Classroom Laboratory

ERIC Educational Resources Information Center

Barnard, Betsy; Sussman, Michael; BonDurant, Sandra Splinter; Nienhuis, James; Krysan, Patrick

2006-01-01

We have developed and optimized the necessary laboratory materials to make DNA microarray technology accessible to all high school students at a fraction of both cost and data size. The primary component is a DNA chip/array that students "print" by hand and then analyze using research tools that have been adapted for classroom use. The…

Down Syndrome (For Parents)

MedlinePlus

... Infections Diseases & Conditions Pregnancy & Baby Nutrition & Fitness Emotions & Behavior School & Family Life First Aid & Safety Doctors & Hospitals ... traits abnormalities associated with Down syndrome. Cell free DNA. This test analyzes fetal DNA found in the ...

Liquid biopsy in the diagnosis of HPV DNA in breast lesions.

PubMed

Carolis, Sabrina De; Pellegrini, Alice; Santini, Donatella; Ceccarelli, Claudio; De Leo, Antonio; Alessandrini, Federica; Arienti, Chiara; Pignatta, Sara; Tesei, Anna; Mantovani, Vilma; Zamagni, Claudio; Taffurelli, Mario; Sansone, Pasquale; Bonafé, Massimiliano; Cricca, Monica

2018-02-01

HPV DNA has never been investigated in nipple discharges (ND) and serum-derived extracellular vesicles, although its presence has been reported in ductal lavage fluids and blood specimens. We analyzed 50 ND, 22 serum-derived extracellular vesicles as well as 51 pathologic breast tissues for the presence of 16 HPV DNA types. We show that the presence of HPV DNA in the ND is predictive of HPV DNA-positive breast lesions and that HPV DNA is more represented in intraductal papillomas. We also show the presence of HPV DNA in the serum-derived extracellular vesicles. Our data supports the use of liquid biopsy to detect HPV DNA in breast pathology.

DNA Nanotechnology for Cancer Therapy

PubMed Central

Kumar, Vinit; Palazzolo, Stefano; Bayda, Samer; Corona, Giuseppe; Toffoli, Giuseppe; Rizzolio, Flavio

2016-01-01

DNA nanotechnology is an emerging and exciting field, and represents a forefront frontier for the biomedical field. The specificity of the interactions between complementary base pairs makes DNA an incredible building material for programmable and very versatile two- and three-dimensional nanostructures called DNA origami. Here, we analyze the DNA origami and DNA-based nanostructures as a drug delivery system. Besides their physical-chemical nature, we dissect the critical factors such as stability, loading capability, release and immunocompatibility, which mainly limit in vivo applications. Special attention was dedicated to highlighting the boundaries to be overcome to bring DNA nanostructures closer to the bedside of patients. PMID:27022418

Performance of Identifiler Direct and PowerPlex 16 HS on the Applied Biosystems 3730 DNA Analyzer for processing biological samples archived on FTA cards.

PubMed

Laurin, Nancy; DeMoors, Anick; Frégeau, Chantal

2012-09-01

Direct amplification of STR loci from biological samples collected on FTA cards without prior DNA purification was evaluated using Identifiler Direct and PowerPlex 16 HS in conjunction with the use of a high throughput Applied Biosystems 3730 DNA Analyzer. In order to reduce the overall sample processing cost, reduced PCR volumes combined with various FTA disk sizes were tested. Optimized STR profiles were obtained using a 0.53 mm disk size in 10 μL PCR volume for both STR systems. These protocols proved effective in generating high quality profiles on the 3730 DNA Analyzer from both blood and buccal FTA samples. Reproducibility, concordance, robustness, sample stability and profile quality were assessed using a collection of blood and buccal samples on FTA cards from volunteer donors as well as from convicted offenders. The new developed protocols offer enhanced throughput capability and cost effectiveness without compromising the robustness and quality of the STR profiles obtained. These results support the use of these protocols for processing convicted offender samples submitted to the National DNA Data Bank of Canada. Similar protocols could be applied to the processing of casework reference samples or in paternity or family relationship testing. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Sequence periodicity in nucleosomal DNA and intrinsic curvature

PubMed Central

2010-01-01

Background Most eukaryotic DNA contained in the nucleus is packaged by wrapping DNA around histone octamers. Histones are ubiquitous and bind most regions of chromosomal DNA. In order to achieve smooth wrapping of the DNA around the histone octamer, the DNA duplex should be able to deform and should possess intrinsic curvature. The deformability of DNA is a result of the non-parallelness of base pair stacks. The stacking interaction between base pairs is sequence dependent. The higher the stacking energy the more rigid the DNA helix, thus it is natural to expect that sequences that are involved in wrapping around the histone octamer should be unstacked and possess intrinsic curvature. Intrinsic curvature has been shown to be dictated by the periodic recurrence of certain dinucleotides. Several genome-wide studies directed towards mapping of nucleosome positions have revealed periodicity associated with certain stretches of sequences. In the current study, these sequences have been analyzed with a view to understand their sequence-dependent structures. Results Higher order DNA structures and the distribution of molecular bend loci associated with 146 base nucleosome core DNA sequence from C. elegans and chicken have been analyzed using the theoretical model for DNA curvature. The curvature dispersion calculated by cyclically permuting the sequences revealed that the molecular bend loci were delocalized throughout the nucleosome core region and had varying degrees of intrinsic curvature. Conclusions The higher order structures associated with nucleosomes of C.elegans and chicken calculated from the sequences revealed heterogeneity with respect to the deviation of the DNA axis. The results points to the possibility of context dependent curvature of varying degrees to be associated with nucleosomal DNA. PMID:20487515

Towards understanding the breast cancer epigenome: a comparison of genome-wide DNA methylation and gene expression data

PubMed Central

Michiels, Stefan; Metzger-Filho, Otto; Saini, Kamal S.

2016-01-01

Until recently, an elevated disease risk has been ascribed to a genetic predisposition, however, exciting progress over the past years has discovered alternate elements of inheritance that involve epigenetic regulation. Epigenetic changes are heritably stable alterations that include DNA methylation, histone modifications and RNA-mediated silencing. Aberrant DNA methylation is a common molecular basis for a number of important human diseases, including breast cancer. Changes in DNA methylation profoundly affect global gene expression patterns. What is emerging is a more dynamic and complex association between DNA methylation and gene expression than previously believed. Although many tools have already been developed for analyzing genome-wide gene expression data, tools for analyzing genome-wide DNA methylation have not yet reached the same level of refinement. Here we provide an in-depth analysis of DNA methylation in parallel with gene expression data characteristics and describe the particularities of low-level and high-level analyses of DNA methylation data. Low-level analysis refers to pre-processing of methylation data (i.e. normalization, transformation and filtering), whereas high-level analysis is focused on illustrating the application of the widely used class comparison, class prediction and class discovery methods to DNA methylation data. Furthermore, we investigate the influence of DNA methylation on gene expression by measuring the correlation between the degree of CpG methylation and the level of expression and to explore the pattern of methylation as a function of the promoter region. PMID:26657508

Towards understanding the breast cancer epigenome: a comparison of genome-wide DNA methylation and gene expression data.

PubMed

Singhal, Sandeep K; Usmani, Nawaid; Michiels, Stefan; Metzger-Filho, Otto; Saini, Kamal S; Kovalchuk, Olga; Parliament, Matthew

2016-01-19

Until recently, an elevated disease risk has been ascribed to a genetic predisposition, however, exciting progress over the past years has discovered alternate elements of inheritance that involve epigenetic regulation. Epigenetic changes are heritably stable alterations that include DNA methylation, histone modifications and RNA-mediated silencing. Aberrant DNA methylation is a common molecular basis for a number of important human diseases, including breast cancer. Changes in DNA methylation profoundly affect global gene expression patterns. What is emerging is a more dynamic and complex association between DNA methylation and gene expression than previously believed. Although many tools have already been developed for analyzing genome-wide gene expression data, tools for analyzing genome-wide DNA methylation have not yet reached the same level of refinement. Here we provide an in-depth analysis of DNA methylation in parallel with gene expression data characteristics and describe the particularities of low-level and high-level analyses of DNA methylation data. Low-level analysis refers to pre-processing of methylation data (i.e. normalization, transformation and filtering), whereas high-level analysis is focused on illustrating the application of the widely used class comparison, class prediction and class discovery methods to DNA methylation data. Furthermore, we investigate the influence of DNA methylation on gene expression by measuring the correlation between the degree of CpG methylation and the level of expression and to explore the pattern of methylation as a function of the promoter region.

Analysis of particles produced during airbag deployment by scanning electron microscopy with energy dispersive x-ray spectroscopy and their deposition on surrounding surfaces: a mid-research summary

NASA Astrophysics Data System (ADS)

Wyatt, J. Matney

2011-06-01

Airbags can be encountered in forensic work when investigating a car crash and are typically constructed with primerlike material to begin the deployment apparatus. The mechanisms of airbag deployment can produce particles ideal for scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM/EDS) analysis. A recent study published by Berk studied airbags with vents and showed that it is possible for particles generated from the deployment of these airbags to deposit on surfaces in the vehicle as the airbags deflate.1 Another paper published by Berk reported particles similar in morphology and composition to primer gunshot residue (GSR) are produced by side impact airbags.2 This paper's aim will be to show mid-point results of a study still in progress in which non-vented airbags were analyzed to determine if they exhibited the same particle depositing features as their vented airbag counterparts. Further investigation in this study is being performed to find more airbags which produce primer gunshot residue-like particles containing lead, barium, and antimony from airbag deployment. To date, the study has resulted in (1) non-vented airbags exhibiting deposition of particles suitable for SEM/EDS analysis and (2) no gunshot residue-like particles being detected from the airbag residues studied thus far.

Effects of war exposure on Air Force personnel’s mental health, job burnout and other organizational related outcomes

PubMed Central

Vinokur, Amiram D.; Pierce, Penny F.; Lewandowski-Romps, Lisa; Hobfoll, Stevan E.; Galea, Sandro

2011-01-01

Longitudinal data from a stratified representative sample of U.S. Air Force personnel (N = 1009) deployed to the wars in Iraq, Afghanistan, and other locations were analyzed in this study. Using structural equation models, we examined the effects of war exposure on traumatic experiences, Post Traumatic Stress (PTS) symptoms, resource loss, and on subsequent functioning, perceived health, and on job and organizationally relevant outcomes. The job and organizational outcomes included job burnout, job involvement, job strain, job satisfaction, work-family conflict, organizational commitment, deployment readiness, and intention to reenlist. We found that deployment to the theater of the war increased risk of exposure to trauma, which in turn, predicted elevated PTS symptoms and resource loss. PTS symptoms predicted later loss of resources and deterioration in perceived health and functioning. In turn, resource loss predicted negative job and organizational outcomes. Exposure to trauma fully mediated the effects of deployment to the theater of war on PTS symptoms and resource loss and had additional significant indirect effects on several job and organizational relevant outcomes. For returning veterans, deployment to the theater of war, exposure to trauma, PTS symptoms, and resource loss represents a ‘cascading’ chain of events that over time results in a decline of health and functioning as well as in adverse job and organizationally relevant outcomes that may affect organizational effectiveness. PMID:21280941

Human Parvovirus B19 Utilizes Cellular DNA Replication Machinery for Viral DNA Replication.

PubMed

Zou, Wei; Wang, Zekun; Xiong, Min; Chen, Aaron Yun; Xu, Peng; Ganaie, Safder S; Badawi, Yomna; Kleiboeker, Steve; Nishimune, Hiroshi; Ye, Shui Qing; Qiu, Jianming

2018-03-01

Human parvovirus B19 (B19V) infection of human erythroid progenitor cells (EPCs) induces a DNA damage response and cell cycle arrest at late S phase, which facilitates viral DNA replication. However, it is not clear exactly which cellular factors are employed by this single-stranded DNA virus. Here, we used microarrays to systematically analyze the dynamic transcriptome of EPCs infected with B19V. We found that DNA metabolism, DNA replication, DNA repair, DNA damage response, cell cycle, and cell cycle arrest pathways were significantly regulated after B19V infection. Confocal microscopy analyses revealed that most cellular DNA replication proteins were recruited to the centers of viral DNA replication, but not the DNA repair DNA polymerases. Our results suggest that DNA replication polymerase δ and polymerase α are responsible for B19V DNA replication by knocking down its expression in EPCs. We further showed that although RPA32 is essential for B19V DNA replication and the phosphorylated forms of RPA32 colocalized with the replicating viral genomes, RPA32 phosphorylation was not necessary for B19V DNA replication. Thus, this report provides evidence that B19V uses the cellular DNA replication machinery for viral DNA replication. IMPORTANCE Human parvovirus B19 (B19V) infection can cause transient aplastic crisis, persistent viremia, and pure red cell aplasia. In fetuses, B19V infection can result in nonimmune hydrops fetalis and fetal death. These clinical manifestations of B19V infection are a direct outcome of the death of human erythroid progenitors that host B19V replication. B19V infection induces a DNA damage response that is important for cell cycle arrest at late S phase. Here, we analyzed dynamic changes in cellular gene expression and found that DNA metabolic processes are tightly regulated during B19V infection. Although genes involved in cellular DNA replication were downregulated overall, the cellular DNA replication machinery was tightly associated with the replicating single-stranded DNA viral genome and played a critical role in viral DNA replication. In contrast, the DNA damage response-induced phosphorylated forms of RPA32 were dispensable for viral DNA replication. Copyright © 2018 American Society for Microbiology.

Isolation and bioinformatics analysis of differentially methylated genomic fragments in human gastric cancer

PubMed Central

Liao, Ai-Jun; Su, Qi; Wang, Xun; Zeng, Bin; Shi, Wei

2008-01-01

AIM: To isolate and analyze the DNA sequences which are methylated differentially between gastric cancer and normal gastric mucosa. METHODS: The differentially methylated DNA sequences between gastric cancer and normal gastric mucosa were isolated by methylation-sensitive representational difference analysis (MS-RDA). Similarities between the separated fragments and the human genomic DNA were analyzed with Basic Local Alignment Search Tool (BLAST). RESULTS: Three differentially methylated DNA sequences were obtained, two of which have been accepted by GenBank. The accession numbers are AY887106 and AY887107. AY887107 was highly similar to the 11th exon of LOC440683 (98%), 3’ end of LOC440887 (99%), and promoter and exon regions of DRD5 (94%). AY887106 was consistent (98%) with a CpG island in ribosomal RNA isolated from colorectal cancer by Minoru Toyota in 1999. CONCLUSION: The methylation degree is different between gastric cancer and normal gastric mucosa. The differentially methylated DNA sequences can be isolated effectively by MS-RDA. PMID:18322944

MiniX-STR multiplex system population study in Japan and application to degraded DNA analysis.

PubMed

Asamura, H; Sakai, H; Kobayashi, K; Ota, M; Fukushima, H

2006-05-01

We sought to evaluate a more effective system for analyzing X-chromosomal short tandem repeats (X-STRs) in highly degraded DNA. To generate smaller amplicon lengths, we designed new polymerase chain reaction (PCR) primers for DXS7423, DXS6789, DXS101, GATA31E08, DXS8378, DXS7133, DXS7424, and GATA165B12 at X-linked short tandem repeat (STR) loci, devising two miniX-multiplex PCR systems. Among 333 Japanese individuals, these X-linked loci were detected in amplification products ranging in length from 76 to 169 bp, and statistical analyses of the eight loci indicated a high usefulness for the Japanese forensic practice. Results of tests on highly degraded DNA indicated the miniX-STR multiplex strategies to be an effective system for analyzing degraded DNA. We conclude that analysis by the current miniX-STR multiplex systems offers high effectiveness for personal identification from degraded DNA samples.

Cost assessment of the automated VERSANT 440 Molecular System versus the semi-automated System 340 bDNA Analyzer platforms.

PubMed

Elbeik, Tarek; Loftus, Richard A; Beringer, Scott

2007-11-01

Labor, supply and waste were evaluated for HIV-1 and HCV bDNA on the semi-automated System 340 bDNA Analyzer and the automated VERSANT 440 Molecular System (V440). HIV-1 sample processing was evaluated using a 24- and 48-position centrifuge rotor. Vigilance time (hands-on manipulations plus incubation time except initial target hybridization) and disposables were approximately 37 and 12% lower for HIV-1, and 64 and 31% lower for HCV bDNA, respectively, with V440. Biohazardous solid waste was approximately twofold lower for both assays and other waste types were the same for either assay on both platforms. HIV-1 sample processing vigilance time for the 48-position rotor was reduced by 2 h. V440 provides cost savings and improved workflow.

The Ins and Outs of DNA Fingerprinting the Infectious Fungi

PubMed Central

Soll, David R.

2000-01-01

DNA fingerprinting methods have evolved as major tools in fungal epidemiology. However, no single method has emerged as the method of choice, and some methods perform better than others at different levels of resolution. In this review, requirements for an effective DNA fingerprinting method are proposed and procedures are described for testing the efficacy of a method. In light of the proposed requirements, the most common methods now being used to DNA fingerprint the infectious fungi are described and assessed. These methods include restriction fragment length polymorphisms (RFLP), RFLP with hybridization probes, randomly amplified polymorphic DNA and other PCR-based methods, electrophoretic karyotyping, and sequencing-based methods. Procedures for computing similarity coefficients, generating phylogenetic trees, and testing the stability of clusters are then described. To facilitate the analysis of DNA fingerprinting data, computer-assisted methods are described. Finally, the problems inherent in the collection of test and control isolates are considered, and DNA fingerprinting studies of strain maintenance during persistent or recurrent infections, microevolution in infecting strains, and the origin of nosocomial infections are assessed in light of the preceding discussion of the ins and outs of DNA fingerprinting. The intent of this review is to generate an awareness of the need to verify the efficacy of each DNA fingerprinting method for the level of genetic relatedness necessary to answer the epidemiological question posed, to use quantitative methods to analyze DNA fingerprint data, to use computer-assisted DNA fingerprint analysis systems to analyze data, and to file data in a form that can be used in the future for retrospective and comparative studies. PMID:10756003

Adapting to Environmental Jolts.

ERIC Educational Resources Information Center

Meyer, Alan D.

1982-01-01

Examines the reactions of three San Francisco (California) hospitals to the 1975 doctors' strike. Analyzes the anticipatory, responsive, and readjustment phases of the hospitals' adaptations in terms of each hospital's previous market strategy, organizational structure and ideology, and deployment of slack resources, including financial, human,…

A Dual-Mode Large-Arrayed CMOS ISFET Sensor for Accurate and High-Throughput pH Sensing in Biomedical Diagnosis.

PubMed

Huang, Xiwei; Yu, Hao; Liu, Xu; Jiang, Yu; Yan, Mei; Wu, Dongping

2015-09-01

The existing ISFET-based DNA sequencing detects hydrogen ions released during the polymerization of DNA strands on microbeads, which are scattered into microwell array above the ISFET sensor with unknown distribution. However, false pH detection happens at empty microwells due to crosstalk from neighboring microbeads. In this paper, a dual-mode CMOS ISFET sensor is proposed to have accurate pH detection toward DNA sequencing. Dual-mode sensing, optical and chemical modes, is realized by integrating a CMOS image sensor (CIS) with ISFET pH sensor, and is fabricated in a standard 0.18-μm CIS process. With accurate determination of microbead physical locations with CIS pixel by contact imaging, the dual-mode sensor can correlate local pH for one DNA slice at one location-determined microbead, which can result in improved pH detection accuracy. Moreover, toward a high-throughput DNA sequencing, a correlated-double-sampling readout that supports large array for both modes is deployed to reduce pixel-to-pixel nonuniformity such as threshold voltage mismatch. The proposed CMOS dual-mode sensor is experimentally examined to show a well correlated pH map and optical image for microbeads with a pH sensitivity of 26.2 mV/pH, a fixed pattern noise (FPN) reduction from 4% to 0.3%, and a readout speed of 1200 frames/s. A dual-mode CMOS ISFET sensor with suppressed FPN for accurate large-arrayed pH sensing is proposed and demonstrated with state-of-the-art measured results toward accurate and high-throughput DNA sequencing. The developed dual-mode CMOS ISFET sensor has great potential for future personal genome diagnostics with high accuracy and low cost.

Molecular Diagnosis of Infantile Mitochondrial Disease with Targeted Next-Generation Sequencing

PubMed Central

Calvo, Sarah E.; Compton, Alison G.; Hershman, Steven G.; Lim, Sze Chern; Lieber, Daniel S.; Tucker, Elena J.; Laskowski, Adrienne; Garone, Caterina; Liu, Shangtao; Jaffe, David B.; Christodoulou, John; Fletcher, Janice M.; Bruno, Damien L; Goldblatt, Jack; DiMauro, Salvatore; Thorburn, David R.; Mootha, Vamsi K.

2012-01-01

Advances in next-generation sequencing (NGS) promise to facilitate diagnosis of inherited disorders. While in research settings NGS has pinpointed causal alleles using segregation in large families, the key challenge for clinical diagnosis is application to single individuals. To explore its diagnostic utility, we performed targeted NGS in 42 unrelated infants with clinical and biochemical evidence of mitochondrial oxidative phosphorylation disease, who were refractory to traditional molecular diagnosis. These devastating mitochondrial disorders are characterized by phenotypic and genetic heterogeneity, with over 100 causal genes identified to date. We performed “MitoExome” sequencing of the mitochondrial DNA (mtDNA) and exons of ~1000 nuclear genes encoding mitochondrial proteins and prioritized rare mutations predicted to disrupt function. Since patients and controls harbored a comparable number of such heterozygous alleles, we could not prioritize dominant acting genes. However, patients showed a five-fold enrichment of genes with two such mutations that could underlie recessive disease. In total, 23/42 (55%) patients harbored such recessive genes or pathogenic mtDNA variants. Firm diagnoses were enabled in 10 patients (24%) who had mutations in genes previously linked to disease. 13 patients (31%) had mutations in nuclear genes never linked to disease. The pathogenicity of two such genes, NDUFB3 and AGK, was supported by cDNA complementation and evidence from multiple patients, respectively. The results underscore the immediate potential and challenges of deploying NGS in clinical settings. PMID:22277967

DeviceEditor visual biological CAD canvas

PubMed Central

2012-01-01

Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. PMID:22373390

[Application of new technologies in the design, manufacture and use of technology deployment of field medical units and establishments].

PubMed

Iakovlev, S V; Sidorov, V A; Korniushko, I G; Medvedev, V R; Matveev, A G

2011-11-01

Presented data is about attendance means of deployment of field medical units and pieces of army-level medical services and disaster medicine Defense Ministry did not ensure compliance with requirements to create optimal conditions for highly effective work of the medical staff, placing the wounded, the use of modern aids and appliances. The prospects of creation of mobile unit for high-availability modular pre-fabricated on the basis of tent structures, pneumoconstructions and removable habitable bodies, containers, tents, pneumocovers till 2020 are analyzed. Livelihood systems provide armor protection against fragments, bullets, flames, damaging factors of chemical and biological weapons.

Design and optimization of a self-deploying PV tent array

NASA Astrophysics Data System (ADS)

Colozza, Anthony J.

A study was performed to design a self-deploying tent shaped PV (photovoltaic) array and optimize the design for maximum specific power. Each structural component of the design was analyzed to determine the size necessary to withstand the various forces it would be subjected to. Through this analysis the component weights were determined. An optimization was performed to determine the array dimensions and blanket geometry which produce the maximum specific power for a given PV blanket. This optimization was performed for both Lunar and Martian environmental conditions. The performance specifications for the array at both locations and with various PV blankets were determined.

Payload vehicle aerodynamic reentry analysis

NASA Astrophysics Data System (ADS)

Tong, Donald

An approach for analyzing the dynamic behavior of a cone-cylinder payload vehicle during reentry to insure proper deployment of the parachute system and recovery of the payload is presented. This analysis includes the study of an aerodynamic device that is useful in extending vehicle axial rotation through the maximum dynamic pressure region. Attention is given to vehicle configuration and reentry trajectory, the derivation of pitch static aerodynamics, the derivation of the pitch damping coefficient, pitching moment modeling, aerodynamic roll device modeling, and payload vehicle reentry dynamics. It is shown that the vehicle dynamics at parachute deployment are well within the design limit of the recovery system, thus ensuring successful payload recovery.

The impact of war on Puerto Rican families: challenges and strengthened family relationships.

PubMed

Magaly Freytes, I; Hannold, Elizabeth M; Resende, Rosana; Wing, Kristen; Uphold, Constance R

2013-08-01

We describe the impact of war on Puerto Rican Veterans and family members. We used qualitative research methods to collect and analyze data. We interviewed 8 Veterans and 8 family members. We used the constant comparison method to review data to identify prominent themes. Two categories emerged: (1) Challenges associated with post-deployment family reintegration, and (2) A positive aftermath of war on the family. Overall, findings indicate that OEF/OIF Veterans and family members were not prepared for the changes they encounter post-deployment. Despite these challenges, some Veterans and family members strengthened their relationships and renewed their appreciation for one another.

The Potential for Energy Storage to Provide Peaking Capacity in California Under Increased Penetration of Solar Photovoltaics

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

Denholm, Paul L; Margolis, Robert M

In this report, we examine the potential for replacing conventional peaking capacity in California with energy storage, including analysis of the changing technical potential with increased storage deployment and the effect of PV deployment. We examine nine years of historic load data, a range of storage durations (2-8 hours), and a range of PV penetration levels (0%-30%). We demonstrate how PV increases the ability of storage to reduce peak net demand. In the scenarios analyzed, the expected penetration of PV in California in 2020 could more than double the potential for 4-hour energy storage to provide capacity services.

Diurnal vocal activity of gray whales in Laguna San Ignacio, BCS, Mexico

NASA Astrophysics Data System (ADS)

Guerra, Melania; Thode, Aaron; Wisdom, Sheyna; Gonzalez, Sergio; Urban, Jorge; Sumich, James

2005-09-01

Three sets of portable horizontal acoustic arrays were deployed during a week in February 2005 to gather acoustic recordings of gray whales (Eschrichtius robustus) in Laguna San Ignacio, one of the three major breeding/calving lagoons in Baja California, Mexico. These arrays, which were constructed by attaching a pair of autonomous flash-memory acoustic sensors to a rope, were deployed for 36 consecutive hours on two occasions, spatially covering the narrowest point of the lagoon near Punta Piedra, the area of the highest concentration of whales. Additionally a single hydrophone was deployed off a small boat to record during friendly encounters with single whales and cow/calf pairs. Each recorder's time series was analyzed for Type 1 gray whale sounds (called pops), which are pulsive, broadband, and have substantial acoustic energy between 100 and 600 Hz. The number of automated acoustic detections per hour can be compared with population sizes estimated by two visual surveys conducted by scientists of the Autonomous University of Baja California Sur, La Paz. The results of several automated analyses of both the bottom-mounted and boat-deployed recordings will be presented, with a focus on potential diurnal patterns in the vocal activity.

A Method for Assessing the Accuracy of a Photogrammetry System for Precision Deployable Structures

NASA Technical Reports Server (NTRS)

Moore, Ashley

2005-01-01

The measurement techniques used to validate analytical models of large deployable structures are an integral Part of the technology development process and must be precise and accurate. Photogrammetry and videogrammetry are viable, accurate, and unobtrusive methods for measuring such large Structures. Photogrammetry uses Software to determine the three-dimensional position of a target using camera images. Videogrammetry is based on the same principle, except a series of timed images are analyzed. This work addresses the accuracy of a digital photogrammetry system used for measurement of large, deployable space structures at JPL. First, photogrammetry tests are performed on a precision space truss test article, and the images are processed using Photomodeler software. The accuracy of the Photomodeler results is determined through, comparison with measurements of the test article taken by an external testing group using the VSTARS photogrammetry system. These two measurements are then compared with Australis photogrammetry software that simulates a measurement test to predict its accuracy. The software is then used to study how particular factors, such as camera resolution and placement, affect the system accuracy to help design the setup for the videogrammetry system that will offer the highest level of accuracy for measurement of deploying structures.

Casualty Profile of the United States Army in Afghanistan and Iraq

DTIC Science & Technology

2012-06-01

sex, race, and ethnicity. They constructed death rates for members of the United States military deployed to Iraq between March 2003 and September...country. The authors first analyzed differences in death rates according to branch of service and concluded that there was a huge difference among...2003-2006 Second, the authors analyzed death rates according to component of service. Their study showed that the active-Army risk of death was three

Using Playing Cards to Simulate a Molecular Clock

ERIC Educational Resources Information Center

Westerling, Karin E.

2008-01-01

Changes in DNA base-repair may serve as an indicator of the time elapsed since divergence from a common ancestor. DNA sequences can now be analyzed. The simulation presented in this article allows students to observe the accumulation of changes in a randomly mutating sequence of playing cards. The cards are analogous to DNA nucleotide or protein…

DNA methyltransferase expressions in Japanese rice fish (Oryzias latipes) embryogenesis is developmentally regulated and modulated by ethanol and 5-azacytidine

USDA-ARS?s Scientific Manuscript database

We aimed to investigate the impact of the epigenome in inducting fetal alcohol spectrum disorder (FASD) phenotypes in Japanese rice fish embryogenesis. One of the significant events in epigenome is DNA methylation which is catalyzed by DNA methyl transferase (DNMT) enzymes. We analyzed DNMT enzyme m...

Analyzing Exonuclease-Induced Hyperchromicity by Uv Spectroscopy: An Undergraduate Biochemistry Laboratory Experiment

ERIC Educational Resources Information Center

Ackerman, Megan M.; Ricciardi, Christopher; Weiss, David; Chant, Alan; Kraemer-Chant, Christina M.

2016-01-01

An undergraduate biochemistry laboratory experiment is described that utilizes free online bioinformatics tools along with readily available exonucleases to study the effects of base stacking and hydrogen bonding on the UV absorbance of DNA samples. UV absorbance of double-stranded DNA at the ?[subscript max] is decreased when the DNA bases are…

16S rRNA Gene Sequence Analysis of Drinking Water Using RNA and DNA Extracts as Targets for Clone Library Development

EPA Science Inventory

The bacterial composition of chlorinated drinking water was analyzed using 16S rRNA gene clone libraries derived from DNA extracts of 12 samples and compared to clone libraries previously generated using RNA extracts from the same samples. Phylogenetic analysis of 761 DNA-based ...

Uplink Scheduling and Adjacent-Channel Coupling Loss Analysis for TD-LTE Deployment

PubMed Central

Yeo, Woon-Young; Moon, Sung Ho

2014-01-01

TD-LTE, one of the two duplexing modes in LTE, operates in unpaired spectrum and has the advantages of TDD-based technologies. It is expected that TD-LTE will be more rapidly deployed in near future and most of WiMax operators will upgrade their networks to TD-LTE gradually. Before completely upgrading to TD-LTE, WiMax may coexist with TD-LTE in an adjacent frequency band. In addition, multiple TD-LTE operators may deploy their networks in adjacent bands. When more than one TDD network operates in adjacent frequency bands, severe interference may happen due to adjacent channel interference (ACI) and unsynchronized operations. In this paper, coexistence issues between TD-LTE and other systems are analyzed and coexistence requirements are provided. This paper has three research objectives. First, frame synchronization between TD-LTE and WiMax is discussed by investigating possible combinations of TD-LTE and WiMax configurations. Second, an uplink scheduling algorithm is proposed to utilize a leakage pattern of ACI in synchronized operations. Third, minimum requirements for coexistence in unsynchronized operations are analyzed by introducing a concept of adjacent-channel coupling loss. From the analysis and simulation results, we can see that coexistence of TD-LTE with other TDD systems is feasible if the two networks are synchronized. For the unsynchronized case, some special cell-site engineering techniques may be required to reduce the ACI. PMID:24707214

Uplink scheduling and adjacent-channel coupling loss analysis for TD-LTE deployment.

PubMed

Yeo, Woon-Young; Moon, Sung Ho; Kim, Jae-Hoon

2014-01-01

TD-LTE, one of the two duplexing modes in LTE, operates in unpaired spectrum and has the advantages of TDD-based technologies. It is expected that TD-LTE will be more rapidly deployed in near future and most of WiMax operators will upgrade their networks to TD-LTE gradually. Before completely upgrading to TD-LTE, WiMax may coexist with TD-LTE in an adjacent frequency band. In addition, multiple TD-LTE operators may deploy their networks in adjacent bands. When more than one TDD network operates in adjacent frequency bands, severe interference may happen due to adjacent channel interference (ACI) and unsynchronized operations. In this paper, coexistence issues between TD-LTE and other systems are analyzed and coexistence requirements are provided. This paper has three research objectives. First, frame synchronization between TD-LTE and WiMax is discussed by investigating possible combinations of TD-LTE and WiMax configurations. Second, an uplink scheduling algorithm is proposed to utilize a leakage pattern of ACI in synchronized operations. Third, minimum requirements for coexistence in unsynchronized operations are analyzed by introducing a concept of adjacent-channel coupling loss. From the analysis and simulation results, we can see that coexistence of TD-LTE with other TDD systems is feasible if the two networks are synchronized. For the unsynchronized case, some special cell-site engineering techniques may be required to reduce the ACI.

Evaluation and Comparison of Methods for Measuring Ozone ...

EPA Pesticide Factsheets

Ambient evaluations of the various ozone and NO2 methods were conducted during field intensive studies as part of the NASA DISCOVER-AQ project conducted during July 2011 near Baltimore, MD; January – February 2013 in the San Juaquin valley, CA; September 2013 in Houston, TX; and July – August 2014 near Denver, CO. During field intensive studies, instruments were calibrated according to manufacturers’ operation manuals and in accordance with FRM requirements listed in 40 CFR 50. During the ambient evaluation campaigns, nightly automated zero and span checks were performed to monitor the validity of the calibration and control for drifts or variations in the span and/or zero response. Both the calibration gas concentrations and the nightly zero and span gas concentrations were delivered using a dynamic dilution calibration system (T700U/T701H, Teledyne API). The analyzers were housed within a temperature-controlled shelter during the sampling campaigns. A glass inlet with sampling height located approximately 5 m above ground level and a subsequent sampling manifold were shared by all instruments. Data generated by all analyzers were collected and logged using a field deployable data acquisition system (Envidas Ultimate). A summary of instruments used during DISCOVER-AQ deployment are listed in Table 1. Figure 1 shows a typical DISCOVER-AQ site (Houston 2013) where EPA (and others) instrumentation was deployed. Under the Clean Air Act, the U.S. EPA has estab

In Situ Analysis of DNA Methylation in Plants.

PubMed

Kathiria, Palak; Kovalchuk, Igor

2017-01-01

Epigenetic regulation in the plant genome is associated with the determination of expression patterns of various genes. Methylation of DNA at cytosine residues is one of the mechanisms of epigenetic regulation and has been a subject of various studies. Various techniques have been developed to analyze DNA methylation, most of which involve isolation of chromatin from cells and further in vitro studies. Limited techniques are available for in situ study of DNA methylation in plants. Here, we present such an in situ method for DNA methylation analysis which has high sensitivity and good reproducibility.

Detection of DNA polymerase λ activity during seed germination and enhancement after salinity stress and dehydration in the plumules of indica rice (Oryza sativa L.

PubMed

Sihi, Sayantani; Bakshi, Sankar; Sengupta, Dibyendu Narayan

2015-02-01

DNA polymerase λ (DNA pol λ) is the only reported X-family DNA polymerases in plants and has been shown to play a significant role in dry quiescent seeds, growth, development and nuclear DNA repair. cDNA for DNA pol λ has been reported in Arabidopsis and japonica rice cultivar and has been characterized from E. coli expressed protein, but very little is known about its activity at protein level in plants. The enzymatic activity of DNA pol λ was studied in dry, imbibed and during different germination stages of indica rice IR-8 (salt sensitive) by in-gel activity assay to determine its physiological role in important stages of growth and development. The upstream sequence was also analyzed using plantCARE database and was found to contain several cis-acting elements, including light responsive elements, dehydration responsive elements, Myb binding sites, etc. Hence, 4-day-old germinating seedlings of IR29, a salt-sensitive, but high yielding indica rice cultivar and Nonabokra, a salt-tolerant, but low yielding cultivar were treated with water (control) or 250 mM NaCl or 20% polyethyleneglycol-6000 for 4 and 8 h. The protein was analyzed by in vitro DNA pol λ activity assay, in-gel activity assay and Western blot analysis. DNA pol λ was not detected in dry seeds, but enhanced after imbibition and detectable from low level to high level during subsequent germination steps. Both salinity and dehydration stress led to the enhancement of the activity and protein level of DNA pol λ, as compared to control tissues. This is the first evidence of the salinity or dehydration stress induced enhancement of DNA pol λ activity in the plumules of rice (Oryza sativa L.) cultivars.

DNA methyltransferase-3 like protein expression in various histological types of testicular germ cell tumor.

PubMed

Matsuoka, Taeko; Kawai, Koji; Ando, Satoshi; Sugita, Shintaro; Kandori, Shuya; Kojima, Takahiro; Miyazaki, Jun; Nishiyama, Hiroyuki

2016-05-01

DNA methyltransferase 3-like plays an important role in germ cell development. The aim of this study was to analyse the DNA methyltransferase 3-like protein expression in testicular germ cell tumors. The immunohistochemical expression of DNA methyltransferase 3-like was examined in 86 testicular germ cell tumor specimens in various clinical settings. The association between DNA methyltransferase 3-like expression and disease stage was analyzed. DNA methyltransferase 3-like was strongly expressed in seven of the eight pure embryonal carcinomas (87.5%). Partial DNA methyltransferase 3-like expression was observed in 6 of 23 (26.1%) pure seminomas. Various degrees of DNA methyltransferase 3-like expression was observed in all four pure yolk sac tumors, of which three were prepubertal yolk sac tumors. In mixed germ cell tumors, DNA methyltransferase 3-like protein was expressed in various degrees in elements of the embryonal carcinoma (14/18, 77.8%), seminoma (4/11, 36.4%), teratoma (4/7, 57.1%) and choriocarcinoma (3/3, 100%) but not in the yolk sac tumors (0/4). When DNA methyltransferase 3-like expression was analyzed according to disease stages, it was significantly correlated with advanced seminoma rather than Stage I seminoma (46.2 vs. 0%, P = 0.019), whereas there was no significant difference in the DNA methyltransferase 3-like-positive proportion between Stage I and advanced disease in the mixed germ cell tumors. Our findings suggest that DNA methyltransferase 3-like protein may play roles not only in the development of embryonal carcinoma but also in the development of advanced pure seminoma and pure yolk sac tumor. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Characterization of environmental chemicals with potential for DNA damage using isogenic DNA repair-deficient chicken DT40 cell lines.

PubMed

Yamamoto, Kimiyo N; Hirota, Kouji; Kono, Koichi; Takeda, Shunichi; Sakamuru, Srilatha; Xia, Menghang; Huang, Ruili; Austin, Christopher P; Witt, Kristine L; Tice, Raymond R

2011-08-01

Included among the quantitative high throughput screens (qHTS) conducted in support of the US Tox21 program are those being evaluated for the detection of genotoxic compounds. One such screen is based on the induction of increased cytotoxicity in seven isogenic chicken DT40 cell lines deficient in DNA repair pathways compared to the parental DNA repair-proficient cell line. To characterize the utility of this approach for detecting genotoxic compounds and identifying the type(s) of DNA damage induced, we evaluated nine of 42 compounds identified as positive for differential cytotoxicity in qHTS (actinomycin D, adriamycin, alachlor, benzotrichloride, diglycidyl resorcinol ether, lovastatin, melphalan, trans-1,4-dichloro-2-butene, tris(2,3-epoxypropyl)isocyanurate) and one non-cytotoxic genotoxic compound (2-aminothiamine) for (1) clastogenicity in mutant and wild-type cells; (2) the comparative induction of γH2AX positive foci by melphalan; (3) the extent to which a 72-hr exposure duration increased assay sensitivity or specificity; (4) the use of 10 additional DT40 DNA repair-deficient cell lines to better analyze the type(s) of DNA damage induced; and (5) the involvement of reactive oxygen species in the induction of DNA damage. All compounds but lovastatin and 2-aminothiamine were more clastogenic in at least one DNA repair-deficient cell line than the wild-type cells. The differential responses across the various DNA repair-deficient cell lines provided information on the type(s) of DNA damage induced. The results demonstrate the utility of this DT40 screen for detecting genotoxic compounds, for characterizing the nature of the DNA damage, and potentially for analyzing mechanisms of mutagenesis. Copyright © 2011 Wiley-Liss, Inc.

Characterization of environmental chemicals with potential for DNA damage using isogenic DNA repair-deficient chicken DT40 cell lines

PubMed Central

Yamamoto, Kimiyo N.; Hirota, Kouji; Kono, Koichi; Takeda, Shunichi; Sakamuru, Srilatha; Xia, Menghang; Huang, Ruili; Austin, Christopher P.; Witt, Kristine L.; Tice, Raymond R.

2012-01-01

Included among the quantitative high throughput screens (qHTS) conducted in support of the U.S. Tox21 program are those being evaluated for the detection of genotoxic compounds. One such screen is based on the induction of increased cytotoxicity in 7 isogenic chicken DT40 cell lines deficient in DNA repair pathways compared to the parental DNA repair-proficient cell line. To characterize the utility of this approach for detecting genotoxic compounds and identifying the type(s) of DNA damage induced, we evaluated nine of 42 compounds identified as positive for differential cytotoxicity in qHTS (actinomycin D, adriamycin, alachlor, benzotrichloride, diglycidyl resorcinol ether, lovastatin, melphalan, trans-1,4-dichloro-2-butene, tris(2,3-epoxypropyl)isocyanurate) and one non-cytotoxic genotoxic compound (2-aminothiamine) for (1) clastogenicity in mutant and wild-type cells; (2) the comparative induction of γH2AX positive foci by melphalan; (3) the extent to which a 72-hr exposure duration increased assay sensitivity or specificity; (4) the use of 10 additional DT40 DNA repair-deficient cell lines to better analyze the type(s) of DNA damage induced; and (5) the involvement of reactive oxygen species in the induction of DNA damage. All compounds but lovastatin and 2-aminothiamine were more clastogenic in at least one DNA repair-deficient cell line than the wild-type cells. The differential responses across the various DNA repair-deficient cell lines provided information on the type(s) of DNA damage induced. The results demonstrate the utility of this DT40 screen for detecting genotoxic compounds, for characterizing the nature of the DNA damage, and potentially for analyzing mechanisms of mutagenesis. PMID:21538559

Constructing DNA Barcode Sets Based on Particle Swarm Optimization.

PubMed

Wang, Bin; Zheng, Xuedong; Zhou, Shihua; Zhou, Changjun; Wei, Xiaopeng; Zhang, Qiang; Wei, Ziqi

2018-01-01

Following the completion of the human genome project, a large amount of high-throughput bio-data was generated. To analyze these data, massively parallel sequencing, namely next-generation sequencing, was rapidly developed. DNA barcodes are used to identify the ownership between sequences and samples when they are attached at the beginning or end of sequencing reads. Constructing DNA barcode sets provides the candidate DNA barcodes for this application. To increase the accuracy of DNA barcode sets, a particle swarm optimization (PSO) algorithm has been modified and used to construct the DNA barcode sets in this paper. Compared with the extant results, some lower bounds of DNA barcode sets are improved. The results show that the proposed algorithm is effective in constructing DNA barcode sets.

Modulating DNA configuration by interfacial traction: an elastic rod model to characterize DNA folding and unfolding.

PubMed

Huang, Zaixing

2011-01-01

As a continuum model of DNA, a thin elastic rod subjected to interfacial interactions is used to investigate the equilibrium configuration of DNA in intracellular solution. The interfacial traction between the rod and the solution environment is derived in detail. Kirchhoff's theory of elastic rods is used to analyze the equilibrium configuration of a DNA segment under the action of the interfacial traction. The influences of the interfacial energy factor and bending stiffness on the toroidal spool formation of the DNA segment are discussed. The results show that the equilibrium configuration of DNA is mainly determined by competition between the interfacial energy and elastic strain energy of the DNA itself, and the interfacial traction is one of the forces that drives DNA folding and unfolding.

Oxidative Stress, DNA Damage and DNA Repair in Female Patients with Diabetes Mellitus Type 2

PubMed Central

Grindel, Annemarie; Guggenberger, Bianca; Eichberger, Lukas; Pöppelmeyer, Christina; Gschaider, Michaela; Tosevska, Anela; Mare, George; Briskey, David; Brath, Helmut; Wagner, Karl-Heinz

2016-01-01

Background Diabetes mellitus type 2 (T2DM) is associated with oxidative stress which in turn can lead to DNA damage. The aim of the present study was to analyze oxidative stress, DNA damage and DNA repair in regard to hyperglycemic state and diabetes duration. Methods Female T2DM patients (n = 146) were enrolled in the MIKRODIAB study and allocated in two groups regarding their glycated hemoglobin (HbA1c) level (HbA1c≤7.5%, n = 74; HbA1c>7.5%, n = 72). In addition, tertiles according to diabetes duration (DD) were created (DDI = 6.94±3.1 y, n = 49; DDII = 13.35±1.1 y, n = 48; DDIII = 22.90±7.3 y, n = 49). Oxidative stress parameters, including ferric reducing ability potential, malondialdehyde, oxidized and reduced glutathione, reduced thiols, oxidized LDL and F2-Isoprostane as well as the activity of antioxidant enzymes superoxide dismutase, catalase and glutathione peroxidase were measured. Damage to DNA was analyzed in peripheral blood mononuclear cells and whole blood with single cell gel electrophoresis. DNA base excision repair capacity was tested with the modified comet repair assay. Additionally, mRNA expressions of nine genes related to base excision repair were analyzed in a subset of 46 matched individuals. Results No significant differences in oxidative stress parameters, antioxidant enzyme activities, damage to DNA and base excision repair capacity, neither between a HbA1c cut off />7.5%, nor between diabetes duration was found. A significant up-regulation in mRNA expression was found for APEX1, LIG3 and XRCC1 in patients with >7.5% HbA1c. Additionally, we observed higher total cholesterol, LDL-cholesterol, LDL/HDL-cholesterol, triglycerides, Framingham risk score, systolic blood pressure, BMI and lower HDL-cholesterol in the hyperglycemic group. Conclusion BMI, blood pressure and blood lipid status were worse in hyperglycemic individuals. However, no major disparities regarding oxidative stress, damage to DNA and DNA repair were present which might be due to good medical treatment with regular health checks in T2DM patients in Austria. PMID:27598300

Oxidative Stress, DNA Damage and DNA Repair in Female Patients with Diabetes Mellitus Type 2.

PubMed

Grindel, Annemarie; Guggenberger, Bianca; Eichberger, Lukas; Pöppelmeyer, Christina; Gschaider, Michaela; Tosevska, Anela; Mare, George; Briskey, David; Brath, Helmut; Wagner, Karl-Heinz

2016-01-01

Diabetes mellitus type 2 (T2DM) is associated with oxidative stress which in turn can lead to DNA damage. The aim of the present study was to analyze oxidative stress, DNA damage and DNA repair in regard to hyperglycemic state and diabetes duration. Female T2DM patients (n = 146) were enrolled in the MIKRODIAB study and allocated in two groups regarding their glycated hemoglobin (HbA1c) level (HbA1c≤7.5%, n = 74; HbA1c>7.5%, n = 72). In addition, tertiles according to diabetes duration (DD) were created (DDI = 6.94±3.1 y, n = 49; DDII = 13.35±1.1 y, n = 48; DDIII = 22.90±7.3 y, n = 49). Oxidative stress parameters, including ferric reducing ability potential, malondialdehyde, oxidized and reduced glutathione, reduced thiols, oxidized LDL and F2-Isoprostane as well as the activity of antioxidant enzymes superoxide dismutase, catalase and glutathione peroxidase were measured. Damage to DNA was analyzed in peripheral blood mononuclear cells and whole blood with single cell gel electrophoresis. DNA base excision repair capacity was tested with the modified comet repair assay. Additionally, mRNA expressions of nine genes related to base excision repair were analyzed in a subset of 46 matched individuals. No significant differences in oxidative stress parameters, antioxidant enzyme activities, damage to DNA and base excision repair capacity, neither between a HbA1c cut off />7.5%, nor between diabetes duration was found. A significant up-regulation in mRNA expression was found for APEX1, LIG3 and XRCC1 in patients with >7.5% HbA1c. Additionally, we observed higher total cholesterol, LDL-cholesterol, LDL/HDL-cholesterol, triglycerides, Framingham risk score, systolic blood pressure, BMI and lower HDL-cholesterol in the hyperglycemic group. BMI, blood pressure and blood lipid status were worse in hyperglycemic individuals. However, no major disparities regarding oxidative stress, damage to DNA and DNA repair were present which might be due to good medical treatment with regular health checks in T2DM patients in Austria.

Reliability analysis for the smart grid : from cyber control and communication to physical manifestations of failure.

DOT National Transportation Integrated Search

2010-01-01

The Smart Grid is a cyber-physical system comprised of physical components, such as transmission lines and generators, and a : network of embedded systems deployed for their cyber control. Our objective is to qualitatively and quantitatively analyze ...

Australian Red Dune Sand: A Potential Martian Regolith Analog

NASA Technical Reports Server (NTRS)

Kuhlman, K. R.; Marshall, J.; Evans, N. D.; Luttge, A.

2001-01-01

To demonstrate the potential scientific and technical merits of in situ microscopy on Mars, we analyzed a possible Martian regolith analog - an acolian red dune sand from the central Australian desert (near Mt. Olga). This sand was chosen for its ubiquitous red coating and the desert environment in which is it found. Grains of this sand were analyzed using a variety of microanalytical techniques. A database of detailed studies of such terrestrial analogs would assist the study of geological and astrobiological specimens in future missions to Mars. Potential instrument concepts for in situ deployment on Mars include local electrode atom probe nanoanalysis (LEAP), vertical scanning white light interferometry (VSWLI), scanning electron microscopies, energy dispersive x-ray microanalysis (EDX), atomic force microscopy (AFM) and X-ray diffraction (XRD). While in situ deployment of these techniques is many years away, ground-based studies using these analytical techniques extend our understanding of the data obtained from instruments to be flown in the near future.

Pivoting the Plant Immune System from Dissection to Deployment

PubMed Central

Dangl, Jeffery L.; Horvath, Diana M.; Staskawicz, Brian J.

2013-01-01

Diverse and rapidly evolving pathogens cause plant diseases and epidemics that threaten crop yield and food security around the world. Research over the last 25 years has led to an increasingly clear conceptual understanding of the molecular components of the plant immune system. Combined with ever-cheaper DNA-sequencing technology and the rich diversity of germ plasm manipulated for over a century by plant breeders, we now have the means to begin development of durable (long-lasting) disease resistance beyond the limits imposed by conventional breeding and in a manner that will replace costly and unsustainable chemical controls. PMID:23950531

Implementing Genome-Driven Oncology

PubMed Central

Hyman, David M.; Taylor, Barry S.; Baselga, José

2017-01-01

Early successes in identifying and targeting individual oncogenic drivers, together with the increasing feasibility of sequencing tumor genomes, have brought forth the promise of genome-driven oncology care. As we expand the breadth and depth of genomic analyses, the biological and clinical complexity of its implementation will be unparalleled. Challenges include target credentialing and validation, implementing drug combinations, clinical trial designs, targeting tumor heterogeneity, and deploying technologies beyond DNA sequencing, among others. We review how contemporary approaches are tackling these challenges and will ultimately serve as an engine for biological discovery and increase our insight into cancer and its treatment. PMID:28187282

A vision for ubiquitous sequencing

PubMed Central

Erlich, Yaniv

2015-01-01

Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors—miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors. PMID:26430149

Investigating the transcriptional control of cardiovascular development

PubMed Central

Kathiriya, Irfan S.; Nora, Elphege P.; Bruneau, Benoit G.

2015-01-01

Transcriptional regulation of thousands of genes instructs complex morphogenetic and molecular events for heart development. Cardiac transcription factors (TFs) choreograph gene expression at each stage of differentiation by interacting with co-factors, including chromatin-modifying enzymes, and by binding to a constellation of regulatory DNA elements. Here, we present salient examples relevant to cardiovascular development and heart disease and review techniques that can sharpen our understanding of cardiovascular biology. We discuss the interplay between cardiac TFs, cis-regulatory elements and chromatin as dynamic regulatory networks, to orchestrate sequential deployment of the cardiac gene expression program. PMID:25677518

The contribution of transient counterion imbalances to DNA bending fluctuations.

PubMed

Manning, Gerald S

2006-05-01

A two-sided model for DNA is employed to analyze fluctuations of the spatial distribution of condensed counterions and the effect of these fluctuations on transient bending. We analyze two classes of fluctuations. In the first, the number of condensed counterions on one side of the DNA remains at its average value, while on the other side, counterions are lost to bulk solution or gained from it. The second class of fluctuations is characterized by movement of some counterions from one side of the DNA to the other. The root-mean-square fluctuation for each class is calculated from counterion condensation theory. The amplitude of the root-mean-square fluctuation depends on the ionic strength as well as the length of the segment considered and is of the order 5-10%. Both classes of fluctuation result in transient bends toward the side of greater counterion density. The bending amplitudes are approximately 15% of the total root-mean-square bends associated with the persistence length of DNA. We are thus led to suggest that asymmetric fluctuations of counterion density contribute modestly but significantly toward the aggregate of thermalized solvent fluctuations that cause bending deformations of DNA free in solution. The calculations support the idea that counterions may exert some modulating influence on the fine structure of DNA.

Is radon emission in caves causing deletions in satellite DNA sequences of cave-dwelling crickets?

PubMed

Allegrucci, Giuliana; Sbordoni, Valerio; Cesaroni, Donatella

2015-01-01

The most stable isotope of radon, 222Rn, represents the major source of natural radioactivity in confined environments such as mines, caves and houses. In this study, we explored the possible radon-related effects on the genome of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae) sampled in caves with different concentrations of radon. We analyzed specimens from ten populations belonging to two genetically closely related species, D. geniculata and D. laetitiae, and explored the possible association between the radioactivity dose and the level of genetic polymorphism in a specific family of satellite DNA (pDo500 satDNA). Radon concentration in the analyzed caves ranged from 221 to 26,000 Bq/m3. Specimens coming from caves with the highest radon concentration showed also the highest variability estimates in both species, and the increased sequence heterogeneity at pDo500 satDNA level can be explained as an effect of the mutation pressure induced by radon in cave. We discovered a specific category of nuclear DNA, the highly repetitive satellite DNA, where the effects of the exposure at high levels of radon-related ionizing radiation are detectable, suggesting that the satDNA sequences might be a valuable tool to disclose harmful effects also in other organisms exposed to high levels of radon concentration.

Effect of Amalaki rasayana on DNA damage and repair in randomized aged human individuals.

PubMed

Vishwanatha, Udupi; Guruprasad, Kanive P; Gopinath, Puthiya M; Acharya, Raviraj V; Prasanna, Bokkasa V; Nayak, Jayakrishna; Ganesh, Rajeshwari; Rao, Jayalaxmi; Shree, Rashmi; Anchan, Suchitra; Raghu, Kothanahalli S; Joshi, Manjunath B; Paladhi, Puspendu; Varier, Panniampilly M; Muraleedharan, Kollath; Muraleedharan, Thrikovil S; Satyamoorthy, Kapaettu

2016-09-15

Preparations from Phyllanthus emblica called Amalaki rasayana is used in the Indian traditional medicinal system of Ayurveda for healthy living in elderly. The biological effects and its mechanisms are not fully understood. Since the diminishing DNA repair is the hallmark of ageing, we tested the influence of Amalaki rasayana on recognized DNA repair activities in healthy aged individuals. Amalaki rasayana was prepared fresh and healthy aged randomized human volunteers were administrated with either rasayana or placebo for 45 days strictly as per the traditional text. The DNA repair was analyzed in peripheral blood mononuclear cells before and after rasayana administration and after 45 days post-rasayana treatment regimen. UVC-induced DNA strand break repair (DSBR) based on extent of DNA unwinding by fluorometric analysis, nucleotide excision repair (NER) by flow cytometry and constitutive base excision repair (BER) by gap filling method were analyzed. Amalaki rasayana administration stably maintained/enhanced the DSBR in aged individuals. There were no adverse side effects. Further, subjects with different body mass index showed differential DNA strand break repair capacity. No change in unscheduled DNA synthesis during NER and BER was observed between the groups. Intake of Amalaki rasayana by aged individuals showed stable maintenance of DNA strand break repair without toxic effects. However, there was no change in nucleotide and base excision repair activities. Results warrant further studies on the effects of Amalaki rasayana on DSBR activities. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Comet assay: a prognostic tool for DNA integrity assessment in infertile men opting for assisted reproduction.

PubMed

Shamsi, M B; Venkatesh, S; Tanwar, M; Singh, G; Mukherjee, S; Malhotra, N; Kumar, R; Gupta, N P; Mittal, S; Dada, R

2010-05-01

The growing concern on transmission of genetic diseases in assisted reproduction technique (ART) and the lacunae in the conventional semen analysis to accurately predict the semen quality has led to the need for new techniques to identify the best quality sperm that can be used in assisted procreation techniques. This study analyzes the sperm parameters in the context of DNA damage in cytogenetically normal, AZF non deleted infertile men for DNA damage by comet assay. Seventy infertile men and 40 fertile controls were evaluated for the semen quality by conventional semen parameters and the sperms were also analyzed for DNA integrity by comet assay. The patients were classified into oligozoospermic (O), asthenozoospermic (A), teratozoospermic (T), oligoasthenoteratozoospermic (OAT) categories and infertile men with normal semen profile. The extent of DNA damage was assessed by visual scoring method of comets. Idiopathic infertile men with normal semen profile (n=18) according to conventional method and patients with history of spontaneous abortions and normal semen profile (n=10) had high degree of DNA damage (29 and 47% respectively) as compared to fertile controls (7%). The O, A, T and OAT categories of patients had a variably higher DNA damage load as compared to fertile controls. The normal range and threshold for DNA damage as a predictor of male fertility potential and technique which could assess the sperm DNA damage are necessary to lower the trauma of couples experiencing recurrent spontaneous abortion or failure in ART.

Cigarette smoking and hOGG1 Ser326Cys polymorphism are associated with 8-OHdG accumulation on mitochondrial DNA in thoracic esophageal squamous cell carcinoma.

PubMed

Lin, Chen-Sung; Wang, Liang-Shun; Chou, Teh-Ying; Hsu, Wen-Hu; Lin, Hui-Chen; Lee, Shu-Yu; Lee, Mau-Hua; Chang, Shi-Chuan; Wei, Yau-Huei

2013-12-01

We examined whether cigarette smoking affects the degrees of oxidative damage (8-hydroxyl-2'-deoxyguanosine [8-OHdG]) on mitochondrial DNA (mtDNA), whether the degree of 8-OHdG accumulation on mtDNA is related to the increased total mtDNA copy number, and whether human 8-oxoguanine DNA glycosylase 1 (hOGG1) Ser326Cys polymorphisms affect the degrees of 8-OHdG accumulation on mtDNA in thoracic esophageal squamous cell carcinoma (TESCC). DNA extracted from microdissected tissues of paired noncancerous esophageal muscles, noncancerous esophageal mucosa, and cancerous TESCC nests (n = 74) along with metastatic lymph nodes (n = 38) of 74 TESCC patients was analyzed. Both the mtDNA copy number and mtDNA integrity were analyzed by quantitative real-time polymerase chain reaction (PCR). The hOGG1 Ser326Cys polymorphisms were identified by restriction fragment length polymorphism PCR and PCR-based direct sequencing. Among noncancerous esophageal mucosa, cancerous TESCC nests, and metastatic lymph nodes, the mtDNA integrity decreased (95.2 to 47.9 to 18.6 %; P < 0.001) and the mtDNA copy number disproportionally increased (0.163 to 0.204 to 0.207; P = 0.026). In TESCC, higher indexes of cigarette smoking (0, 0-20, 20-40, and >40 pack-years) were related to an advanced pathologic N category (P = 0.038), elevated mtDNA copy number (P = 0.013), higher mtDNA copy ratio (P = 0.028), and increased mtDNA integrity (P = 0.069). The TESCC mtDNA integrity in patients with Ser/Ser, Ser/Cys, and Cys/Cys hOGG1 variants decreased stepwise from 65.2 to 52.1 to 41.3 % (P = 0.051). Elevated 8-OHdG accumulations on mtDNA in TESCC were observed. Such accumulations were associated with a compensatory increase in total mtDNA copy number, indexes of cigarette smoking, and hOGG1 Ser326Cys polymorphisms.

Translesion synthesis across the (6-4) photoproduct and its Dewar valence isomer by the Y-family and engineered DNA polymerases.

PubMed

Yamamoto, Junpei; Loakes, David; Masutani, Chikahide; Simmyo, Shizu; Urabe, Kumiko; Hanaoka, Fumio; Holliger, Philipp; Iwai, Shigenori

2008-01-01

We analyzed the translesion synthesis across the UV-induced lesions, the (6-4) photoproduct and its Dewar valence isomer, by using human DNA polymerases eta and iota in vitro. The primer extension experiments revealed that pol eta tended to incorporate dG opposite the 3' component of both lesions, but the incorporation efficiency for the Dewar isomer was higher than that for the (6-4) photoproduct. On the other hand, pol iota was likely to incorporate dA opposite the 3' components of the (6-4) photoproduct and its Dewar isomer with a similar efficiency. Elongation after the incorporation opposite the UV lesions was not observed for these Y-family polymerases. We further analyzed the bypass ability of an engineered polymerase developed from Thermus DNA polymerase for the amplification of ancient DNA. This polymerase could bypass the Dewar isomer more efficiently than the (6-4) photoproduct.

[Molecular identification of medicinal plant genus Uncaria in Guizhou].

PubMed

Gang, Tao; Liu, Tao; Zhu, Ying; Liu, Zuo-Yi

2008-06-01

To analyze rDNA ITS regions of the Medicinal Plant Genus Uncaria in Guizhou and construct their phylogenetic tree in order to supply molecular evidence of taxonomy and identification of these Medicinal Plants in genetic level. The ITS gene fragments of the 4 Medicinal Plants were PCR amplified and sequenced. The rDNA ITS regions were analyzed by means of the software of ClustalX, BioEdit and PAUP* 4.0 beta 10. The entire sequences of rDNA ITS1, ITS2, and 5.8S rDNA were obtained, The Maximum-parsimony tree of four ITS regions together with those of similar sequences from GenBank were found, as Mitrayna rubrostipulata (AJ492621 ) and Mitragyna rubrostipulata (AJ605988) were designated as outgroup. The 4 medicinal plants are the 4 species in the genus Uncaria, and are mostly similar to the Uncaria rhynhcophylla.

Investigations of Escherichia coli promoter sequences with artificial neural networks: New signals discovered upstream of the transcriptional startpoint

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

Pedersen, A.G.; Engelbrecht, J.

1995-12-31

In this paper we present a novel method for using the learning ability of a neural network as a measure of information in local regions of input data. Using the method to analyze Escherichia coli promoters, we discover all previously described signals, and furthermore find new signals that are regularly spaced along the promoter region. The spacing of all signals correspond to the helical periodicity of DNA, meaning that the signals are all present on the same face of the DNA helix in the promoter region. This is consistent with a model where the RNA polymerase contacts the promoter onmore » one side of the DNA, and suggests that the regions important for promoter recognition may include more positions on the DNA than usually assumed. We furthermore analyze the E.coli promoters by calculating the Kullback Leibler distance, and by constructing sequence logos.« less

Association between mitochondrial DNA variations and schizophrenia in the northern Chinese Han population.

PubMed

Xu, Feng-Ling; Ding, Mei; Yao, Jun; Shi, Zhang-Sen; Wu, Xue; Zhang, Jing-Jing; Pang, Hao; Xing, Jia-Xin; Xuan, Jin-Feng; Wang, Bao-Jie

2017-01-01

To determine whether mitochondrial DNA (mtDNA) variations are associated with schizophrenia, 313 patients with schizophrenia and 326 unaffected participants of the northern Chinese Han population were included in a prospective study. Single-nucleotide polymorphisms (SNPs) including C5178A, A10398G, G13708A, and C13928G were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Hypervariable regions I and II (HVSI and HVSII) were analyzed by sequencing. The results showed that the 4 SNPs and 11 haplotypes, composed of the 4 SNPs, did not differ significantly between patient and control groups. No significant association between haplogroups and the risk of schizophrenia was ascertained after Bonferroni correction. Drawing a conclusion, there was no evidence of an association between mtDNA (the 4 SNPs and the control region) and schizophrenia in the northern Chinese Han population.

Using FRET to Measure the Angle at Which a Protein Bends DNA: TBP Binding a TATA Box as a Model System

ERIC Educational Resources Information Center

Kugel, Jennifer F.

2008-01-01

An undergraduate biochemistry laboratory experiment that will teach the technique of fluorescence resonance energy transfer (FRET) while analyzing protein-induced DNA bending is described. The experiment uses the protein TATA binding protein (TBP), which is a general transcription factor that recognizes and binds specific DNA sequences known as…

Genome sizes of cranes (Aves: Gruiformes).

PubMed

Rasch, Ellen M

2006-12-01

The DNA content of blood cell nuclei of 15 species of cranes was determined by Feulgen-DNA cytophotometry. Genome sizes agree with values reported elsewhere for several crane species analyzed by flow cytometry. Males have more DNA per cell than females in several species. A karyotype where 2n = 80 is reported for a male greater sandhill crane. Copyright 2006 Wiley-Liss, Inc.

GENETIC STRUCTURE OF CREEK CHUB (SEMOTILUS ATROMACULATUS) POPULATIONS IN COAL MINING-IMPACTED AREAS OF THE EASTERN UNITED STATES, AS DETERMINED BY MTDNA SEQUENCING AND AFLP ANALYSIS

EPA Science Inventory

Analysis of intraspecific patterns in genetic diversity of stream fishes provides a potentially powerful method for assessing the status and trends in the condition of aquatic ecosystems. We analyzed mitochondrial DNA (mtDNA) sequences (590 bases of cytochrome B) and nuclear DNA...

Effects of cyanoacrylate fuming, time after recovery, and location of biological material on the recovery and analysis of DNA from post-blast pipe bomb fragments*.

PubMed

Bille, Todd W; Cromartie, Carter; Farr, Matthew

2009-09-01

This study investigated the effects of time, cyanoacrylate fuming, and location of the biological material on DNA analysis of post-blast pipe bomb fragments. Multiple aliquots of a cell suspension (prepared by soaking buccal swabs in water) were deposited on components of the devices prior to assembly. The pipe bombs were then deflagrated and the fragments recovered. Fragments from half of the devices were cyanoacrylate fumed. The cell spots on the fragments were swabbed and polymerase chain reaction/short tandem repeat analysis was performed 1 week and 3 months after deflagration. A significant decrease in the amount of DNA recovered was observed between samples collected and analyzed within 1 week compared with the samples collected and analyzed 3 months after deflagration. Cyanoacrylate fuming did not have a measurable effect on the success of the DNA analysis at either time point. Greater quantities of DNA were recovered from the pipe nipples than the end caps. Undeflagrated controls showed that the majority (>95%) of the DNA deposited on the devices was not recovered at a week or 3 months.

A vertically-stacked, polymer, microfluidic point mutation analyzer: Rapid, high accuracy detection of low-abundance K-ras mutations

PubMed Central

Han, Kyudong; Lee, Tae Yoon; Nikitopoulos, Dimitris E.; Soper, Steven A.; Murphy, Michael C.

2011-01-01

Recognition of point mutations in the K-ras gene can be used for the clinical management of several types of cancers. Unfortunately, several assay and hardware concerns must be addressed to allow users not well-trained in performing molecular analyses the opportunity to undertake these measurements. To provide for a larger user-base for these types of molecular assays, a vertically-stacked microfluidic analyzer with a modular architecture and process automation was developed. The analyzer employed a primary PCR coupled to an allele-specific ligase detection reaction (LDR). Each functional device, including continuous flow thermal reactors for the PCR and LDR, passive micromixers and ExoSAP-IT® purification, was designed and tested. Individual devices were fabricated in polycarbonate using hot embossing and assembled using adhesive bonding for system assembly. The system produced LDR products from a DNA sample in ~1 h, an 80% reduction in time compared to conventional bench-top instrumentation. Purifying the post-PCR products with the ExoSAP-IT® enzyme led to optimized LDR performance minimizing false positive signals and producing reliable results. Mutant alleles in genomic DNA were quantified to the level of 0.25 ng of mutant DNA in 50 ng of wild-type DNA for a 25 μL sample, equivalent to DNA from 42 mutant cells. PMID:21771577

Evaluation of optimal DNA staining for triggering by scanning fluorescence microscopy (SFM)

NASA Astrophysics Data System (ADS)

Mittag, Anja; Marecka, Monika; Pierzchalski, Arkadiusz; Malkusch, Wolf; Bocsi, József; Tárnok, Attila

2009-02-01

In imaging and flow cytometry, DNA staining is a common trigger signal for cell identification. Selection of the proper DNA dye is restricted by the hardware configuration of the instrument. The Zeiss Imaging Solutions GmbH (München, Germany) introduced a new automated scanning fluorescence microscope - SFM (Axio Imager.Z1) which combines fluorescence imaging with cytometric parameters measurement. The aim of the study was to select optimal DNA dyes as trigger signal in leukocyte detection and subsequent cytometric analysis of double-labeled leukocytes by SFM. Seven DNA dyes (DAPI, Hoechst 33258, Hoechst 33342, POPO-3, PI, 7-AAD, and TOPRO-3) were tested and found to be suitable for the implemented filtersets (fs) of the SFM (fs: 49, fs: 44, fs: 20). EDTA blood was stained after erythrocyte lysis with DNA dye. Cells were transferred on microscopic slides and embedded in fluorescent mounting medium. Quality of DNA fluorescence signal as well as spillover signals were analyzed by SFM. CD45-APC and CD3-PE as well as CD4-FITC and CD8-APC were selected for immunophenotyping and used in combination with Hoechst. Within the tested DNA dyes DAPI showed relatively low spillover and the best CV value. Due to the low spillover of UV DNA dyes a triple staining of Hoechst and APC and PE (or APC and FITC, respectively) could be analyzed without difficulty. These results were confirmed by FCM measurements. DNA fluorescence is applicable for identifying and triggering leukocytes in SFM analyses. Although some DNA dyes exhibit strong spillover in other fluorescence channels, it was possible to immunophenotype leukocytes. DAPI seems to be best suitable for use in the SFM system and will be used in protocol setups as primary parameter.

Enhanced GSH synthesis by Bisphenol A exposure promoted DNA methylation process in the testes of adult rare minnow Gobiocypris rarus.

PubMed

Yuan, Cong; Zhang, Yingying; Liu, Yan; Zhang, Ting; Wang, Zaizhao

2016-09-01

DNA methylation is a commonly studied epigenetic modification. The mechanism of BPA on DNA methylation is poorly understood. The present study aims to explore whether GSH synthesis affects DNA methylation in the testes of adult male rare minnow Gobiocypris rarus in response to Bisphenol A (BPA). Male G. rarus was exposed to 1, 15 and 225μgL(-1) BPA for 7 days. The levels of global DNA methylation, hydrogen peroxide (H2O2) and glutathione (GSH) in the testes were analyzed. Meanwhile, the levels of enzymes involved in DNA methylation and de novo GSH synthesis, and the substrate contents for GSH production were measured. Furthermore, gene expression profiles of the corresponding genes of all studied enzymes were analyzed. Results indicated that BPA at 15 and 225μgL(-1) caused hypermethylation of global DNA in the testes. The 15μgL(-1) BPA resulted in significant decrease of ten-eleven translocation proteins (TETs) while 225μgL(-1) BPA caused significant increase of DNA methyltransferase proteins (DNMTs). Moreover, 225μgL(-1) BPA caused significant increase of H2O2 and GSH levels, and the de novo GSH synthesis was enhanced. These results indicated that the significant decrease of the level of TETs may be sufficient to cause the DNA hypermethylation by 15μgL(-1) BPA. However, the significantly increased of DNMTs contributed to the significant increase of DNA methylation levels by 225μgL(-1) BPA. Moreover, the elevated de novo GSH synthesis may promote the DNA methylation process. Copyright © 2016 Elsevier B.V. All rights reserved.

Automation of complex assays: pharmacogenetics of warfarin dosing.

PubMed

Wu, Whei-Kuo; Hujsak, Paul G; Kureshy, Fareed

2007-10-01

AutoGenomics, Inc. (Carlsbad, CA, USA) have developed a multiplex microarray assay for genotyping both VKORC1 and CYP2C9 using the INFINITI(™) Analyzer. Multiple alleles in each DNA sample are analyzed by polymerase chain reaction amplification, followed by detection primer extension using the INFINITI Analyzer. The INFINITI Analyzer performs single-nucleotide polymorphism (SNP) analysis using universal oligonucleotides immobilized on the biochip. To genotype broader ethnic groups, genomic DNA from whole blood was tested for nine SNPs for VKORC1 and six for CYP2C9 genotypes. Information related to all 15 SNPs is needed to determine dosing of population of diverse ethnic origin. The INFINITI system provides genotyping information for same day dosing of warfarin.

DNA Origami-Graphene Hybrid Nanopore for DNA Detection.

PubMed

Barati Farimani, Amir; Dibaeinia, Payam; Aluru, Narayana R

2017-01-11

DNA origami nanostructures can be used to functionalize solid-state nanopores for single molecule studies. In this study, we characterized a nanopore in a DNA origami-graphene heterostructure for DNA detection. The DNA origami nanopore is functionalized with a specific nucleotide type at the edge of the pore. Using extensive molecular dynamics (MD) simulations, we computed and analyzed the ionic conductivity of nanopores in heterostructures carpeted with one or two layers of DNA origami on graphene. We demonstrate that a nanopore in DNA origami-graphene gives rise to distinguishable dwell times for the four DNA base types, whereas for a nanopore in bare graphene, the dwell time is almost the same for all types of bases. The specific interactions (hydrogen bonds) between DNA origami and the translocating DNA strand yield different residence times and ionic currents. We also conclude that the speed of DNA translocation decreases due to the friction between the dangling bases at the pore mouth and the sequencing DNA strands.

Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties

PubMed Central

2011-01-01

Background Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome problem for designers that some different physicochemical properties have similar vectors of representing 20 amino acids and some closely related physicochemical properties have dissimilar vectors. Results This study proposes a systematic approach (named Auto-IDPCPs) to automatically identify a set of physicochemical and biochemical properties in the AAindex database to design SVM-based classifiers for predicting and analyzing DNA-binding domains/proteins. Auto-IDPCPs consists of 1) clustering 531 amino acid indices in AAindex into 20 clusters using a fuzzy c-means algorithm, 2) utilizing an efficient genetic algorithm based optimization method IBCGA to select an informative feature set of size m to represent sequences, and 3) analyzing the selected features to identify related physicochemical properties which may affect the binding mechanism of DNA-binding domains/proteins. The proposed Auto-IDPCPs identified m=22 features of properties belonging to five clusters for predicting DNA-binding domains with a five-fold cross-validation accuracy of 87.12%, which is promising compared with the accuracy of 86.62% of the existing method PSSM-400. For predicting DNA-binding sequences, the accuracy of 75.50% was obtained using m=28 features, where PSSM-400 has an accuracy of 74.22%. Auto-IDPCPs and PSSM-400 have accuracies of 80.73% and 82.81%, respectively, applied to an independent test data set of DNA-binding domains. Some typical physicochemical properties discovered are hydrophobicity, secondary structure, charge, solvent accessibility, polarity, flexibility, normalized Van Der Waals volume, pK (pK-C, pK-N, pK-COOH and pK-a(RCOOH)), etc. Conclusions The proposed approach Auto-IDPCPs would help designers to investigate informative physicochemical and biochemical properties by considering both prediction accuracy and analysis of binding mechanism simultaneously. The approach Auto-IDPCPs can be also applicable to predict and analyze other protein functions from sequences. PMID:21342579

Comparative genomic analysis of Genlisea (corkscrew plants—Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes

PubMed Central

Silva, Saura R.; Michael, Todd P.; Meer, Elliott J.; Pinheiro, Daniel G.; Miranda, Vitor F. O.

2018-01-01

In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structurally conserved except for deletion and/or pseudogenization of the NAD(P)H-dehydrogenase complex (ndh) genes known to be involved in stress conditions of low light or CO2 concentrations. In order to determine how the cpDNA are changing, and to better understand the evolutionary history within the Genlisea genus, we sequenced, assembled and analyzed complete cpDNA from six species (G. aurea, G. filiformis, G. pygmaea, G. repens, G. tuberosa and G. violacea) together with the publicly available G. margaretae cpDNA. In general, the cpDNA structure among the analyzed Genlisea species is highly similar. However, we found that the plastidial ndh genes underwent a progressive process of degradation similar to the other terrestrial Lentibulariaceae cpDNA analyzed to date, but in contrast to the aquatic species. Contrary to current thinking that the terrestrial environment is a more stressful environment and thus requiring the ndh genes, we provide evidence that in the Lentibulariaceae the terrestrial forms have progressive loss while the aquatic forms have the eleven plastidial ndh genes intact. Therefore, the Lentibulariaceae system provides an important opportunity to understand the evolutionary forces that govern the transition to an aquatic environment and may provide insight into how plants manage water stress at a genome scale. PMID:29293597

Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes.

PubMed

Silva, Saura R; Michael, Todd P; Meer, Elliott J; Pinheiro, Daniel G; Varani, Alessandro M; Miranda, Vitor F O

2018-01-01

In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structurally conserved except for deletion and/or pseudogenization of the NAD(P)H-dehydrogenase complex (ndh) genes known to be involved in stress conditions of low light or CO2 concentrations. In order to determine how the cpDNA are changing, and to better understand the evolutionary history within the Genlisea genus, we sequenced, assembled and analyzed complete cpDNA from six species (G. aurea, G. filiformis, G. pygmaea, G. repens, G. tuberosa and G. violacea) together with the publicly available G. margaretae cpDNA. In general, the cpDNA structure among the analyzed Genlisea species is highly similar. However, we found that the plastidial ndh genes underwent a progressive process of degradation similar to the other terrestrial Lentibulariaceae cpDNA analyzed to date, but in contrast to the aquatic species. Contrary to current thinking that the terrestrial environment is a more stressful environment and thus requiring the ndh genes, we provide evidence that in the Lentibulariaceae the terrestrial forms have progressive loss while the aquatic forms have the eleven plastidial ndh genes intact. Therefore, the Lentibulariaceae system provides an important opportunity to understand the evolutionary forces that govern the transition to an aquatic environment and may provide insight into how plants manage water stress at a genome scale.

Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm.

PubMed

Seol, Yeonee; Li, Jinyu; Nelson, Philip C; Perkins, Thomas T; Betterton, M D

2007-12-15

The wormlike chain (WLC) model currently provides the best description of double-stranded DNA elasticity for micron-sized molecules. This theory requires two intrinsic material parameters-the contour length L and the persistence length p. We measured and then analyzed the elasticity of double-stranded DNA as a function of L (632 nm-7.03 microm) using the classic solution to the WLC model. When the elasticity data were analyzed using this solution, the resulting fitted value for the persistence length p(wlc) depended on L; even for moderately long DNA molecules (L = 1300 nm), this apparent persistence length was 10% smaller than its limiting value for long DNA. Because p is a material parameter, and cannot depend on length, we sought a new solution to the WLC model, which we call the "finite wormlike chain (FWLC)," to account for effects not considered in the classic solution. Specifically we accounted for the finite chain length, the chain-end boundary conditions, and the bead rotational fluctuations inherent in optical trapping assays where beads are used to apply the force. After incorporating these corrections, we used our FWLC solution to generate force-extension curves, and then fit those curves with the classic WLC solution, as done in the standard experimental analysis. These results qualitatively reproduced the apparent dependence of p(wlc) on L seen in experimental data when analyzed with the classic WLC solution. Directly fitting experimental data to the FWLC solution reduces the apparent dependence of p(fwlc) on L by a factor of 3. Thus, the FWLC solution provides a significantly improved theoretical framework in which to analyze single-molecule experiments over a broad range of experimentally accessible DNA lengths, including both short (a few hundred nanometers in contour length) and very long (microns in contour length) molecules.

Outcomes of Prosthetic Hemodialysis Grafts after Deployment of Bare Metal versus Covered Stents at the Venous Anastomosis

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

Kim, Charles Y., E-mail: charles.kim@duke.edu; Tandberg, Daniel J.; Rosenberg, Michael D.

2012-08-15

Purpose: To compare postintervention patency rates after deployment of bare metal versus covered stents across the venous anastomosis of prosthetic arteriovenous (AV) grafts. Methods: Review of our procedural database over a 6 year period revealed 377 procedures involving stent deployment in an AV access circuit. After applying strict inclusion criteria, our study group consisted of 61 stent deployments in 58 patients (median age 58 years, 25 men, 33 women) across the venous anastomosis of an upper extremity AV graft circuit that had never been previously stented. Both patent and thrombosed AV access circuits were retrospectively analyzed. Within the bare metalmore » stent group, 20 of 32 AV grafts were thrombosed at initial presentation compared to 18 of 29 AV grafts in the covered stent group. Results: Thirty-two bare metal stents and 29 covered stents were deployed across the venous anastomosis. The 3, 6, and 12 months primary access patency rates for bare metal stents were not significantly different than for covered stents: 50, 41, and 22 % compared to 59, 52, and 29 %, respectively (p = 0.21). The secondary patency rates were also not significantly different: 78, 78, and 68 % for bare metal stents compared to 76, 69, and 61 % for covered stents, respectively (p = 0.85). However, covered stents demonstrated a higher primary stent patency rate than bare metal stents: 100, 85, and 70 % compared to 75, 67, and 49 % at 3, 6, and 12 months (p < 0.01). Conclusion: The primary and secondary access patency rates after deployment of bare metal versus covered stents at the venous anastomosis were not significantly different. However, bare metal stents developed in-stent stenoses significantly sooner.« less

More Than 1,000 Fuel Cell Units Deployed Through DOE ARRA Funding (Fact Sheet)

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

Not Available

This NREL Hydrogen and Fuel Cell Technical Highlight describes how early market end users are operating 1,111 fuel cell units at 301 sites in 20 states with funding from the U.S. Department of Energy Fuel Cell Technologies Program and analysis by NREL. The American Recovery and Reinvestment Act (ARRA) funded the deployment of approximately 1,000 fuel cell systems in key early markets to accelerate the commercialization and deployment of fuel cells and fuel cell manufacturing, installation, maintenance, and support services. In support of the ARRA fuel cell deployment objectives, NREL analyzes and validates the technology in real-world applications, reports onmore » the technology status, and facilitates the development of fuel cell technologies, manufacturing, and operations in strategic markets-including material handling equipment, backup power, and stationary power-where fuel cells can compete with conventional technologies. NREL is validating hydrogen and fuel cell systems in real-world settings through data collection, analysis, and reporting. The fuel cell and infrastructure analysis provides an independent, third-party assessment that focuses on fuel cell system and hydrogen infrastructure performance, operation, maintenance, use, and safety. An objective of the ARRA fuel cell project-to deploy approximately 1,000 fuel cell systems in key early markets - has been met in two years. By the end of 2011, 504 material handling equipment (MHE) fuel cell units were operating at 8 facilities and 607 backup power fuel cell units were operating at 293 sites. MHE and backup power are two markets where fuel cells are capable of meeting the operating demands, and deployments can be leveraged to accelerate fuel cell commercialization.« less

A simple modification to the luminometric methylation assay to control for the effects of DNA fragmentation.

PubMed

Duman, Elif Aysimi; Kriaucionis, Skirmantas; Dunn, John J; Hatchwell, Eli

2015-05-01

Variations in DNA methylation have been implicated in a number of disorders. Changes in global DNA methylation levels have long been associated with various types of cancer. One of the recently described methods for determining global DNA methylation levels is the LUminometric Methylation Assay (LUMA), which utilizes methylation sensitive and insensitive restriction endonucleases and pyrosequencing technology for quantification. Here we provide evidence suggesting that the global methylation level reported by LUMA is affected by the integrity of the DNA being analyzed. The less intact the DNA, the lower the global methylation levels reported by LUMA. In order to overcome this problem, we propose the use of undigested DNA alongside digested samples. Finally, we demonstrate that this results in a more accurate assessment of global DNA methylation levels.

Design Validation Methodology Development for an Aircraft Sensor Deployment System

NASA Astrophysics Data System (ADS)

Wowczuk, Zenovy S.

The OCULUS 1.0 Sensor Deployment concept design, was developed in 2004 at West Virginia University (WVU), outlined the general concept of a deployment system to be used on a C-130 aircraft. As a sequel, a new system, OCULUS 1.1, has been developed and designed. The new system transfers the concept system design to a safety of flight design, and also enhanced to a pre-production system to be used as the test bed to gain full military certification approval. The OCULUS 1.1 system has an implemented standard deployment system/procedure to go along with a design suited for military certification and implementation. This design process included analysis of the system's critical components and the generation of a critical component holistic model to be used as an analysis tool for future payload modification made to the system. Following the completion of the OCULUS 1.1 design, preparations and procedures for obtaining military airworthiness certification are described. The airworthiness process includes working with the agency overseeing all modifications to the normal operating procedures made to military C-130 aircraft and preparing the system for an experimental flight test. The critical steps in his process include developing a complete documentation package that details the analysis performed on the OCULUS 1.1 system and also the design of experiment flight test plan to analyze the system. Following the approval of the documentation and design of experiment an experimental flight test of the OCULUS 1.1 system was performed to verify the safety and airworthiness of the system. This test proved successfully that the OCULUS 1.1 system design was airworthy and approved for military use. The OCULUS 1.1 deployment system offers an open architecture design that is ideal for use as a sensor testing platform for developmental airborne sensors. The system's patented deployment methodology presents a simplistic approach to reaching the systems final operating position which offers the most robust field of view area of rear ramp deployment systems.

Performance of 3-Component Nodes in the IRIS Community Wavefield Demonstration Experiment

NASA Astrophysics Data System (ADS)

Sweet, J. R.; Anderson, K. R.; Woodward, R.

2017-12-01

In June 2016, a field crew of 50 students, faculty, industry personnel, and IRIS staff deployed a total of 390 stations as part of a community seismic experiment above an active seismic lineament in north-central Oklahoma. The goals of the experiment were to test new instrumentation and deployment strategies that record the full seismic wavefield, and to advance understanding of earthquake source processes and regional lithospheric structure. The crew deployed 363 3-component, 5Hz Generation 2 Fairfield Z-Land nodes along three seismic lines and in a seven-layer nested gradiometer array. The seismic lines spanned a region 13 km long by 5 km wide. A broadband, 18 station "Golay 3x6" array with an aperture of approximately 5 km was deployed around the gradiometer and seismic lines to collect waveform data from local and regional events. In addition, 9 infrasound stations were deployed in order to capture and identify acoustic events that might be recorded by the seismic array. The variety and geometry of instrumentation deployed was intended to capture the full seismic wavefield generated by the local and regional seismicity beneath the array and the surrounding region. Additional details on the instrumentation and how it was deployed can be found by visiting our website www.iris.edu/wavefields. We present a detailed analysis of noise across the array—including station performance, as well as noise from nearby sources (wind turbines, automobiles, etc.). We report a clear reduction in noise for buried 3-component nodes compared to co-located surface nodes (see Figure). Using the IRIS DMC's ISPAQ client, we present a variety of metrics to evaluate the network's performance. We also present highlights from student projects at the recently-held IRIS advanced data processing short course, which focused on analyzing the wavefield dataset using array processing techniques.

Surface shapes and surrounding environment analysis of single- and double-stranded DNA-binding proteins in protein-DNA interface.

PubMed

Wang, Wei; Liu, Juan; Sun, Lin

2016-07-01

Protein-DNA bindings are critical to many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. Here, we analyzed the residues shape (peak, flat, or valley) and the surrounding environment of double-stranded DNA-binding proteins (DSBs) and single-stranded DNA-binding proteins (SSBs) in protein-DNA interfaces. In the results, we found that the interface shapes, hydrogen bonds, and the surrounding environment present significant differences between the two kinds of proteins. Built on the investigation results, we constructed a random forest (RF) classifier to distinguish DSBs and SSBs with satisfying performance. In conclusion, we present a novel methodology to characterize protein interfaces, which will deepen our understanding of the specificity of proteins binding to ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA). Proteins 2016; 84:979-989. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A role for recombination junctions in the segregation of mitochondrial DNA in yeast.

PubMed

Lockshon, D; Zweifel, S G; Freeman-Cook, L L; Lorimer, H E; Brewer, B J; Fangman, W L

1995-06-16

In S. cerevisiae, mitochondrial DNA (mtDNA) molecules, in spite of their high copy number, segregate as if there were a small number of heritable units. The rapid segregation of mitochondrial genomes can be analyzed using mtDNA deletion variants. These small, amplified genomes segregate preferentially from mixed zygotes relative to wild-type mtDNA. This segregation advantage is abolished by mutations in a gene, MGT1, that encodes a recombination junction-resolving enzyme. We show here that resolvase deficiency causes a larger proportion of molecules to be linked together by recombination junctions, resulting in the aggregation of mtDNA into a small number of cytological structures. This change in mtDNA structure can account for the increased mitotic loss of mtDNA and the altered pattern of mtDNA segregation from zygotes. We propose that the level of unresolved recombination junctions influences the number of heritable units of mtDNA.

Impact of Federal Tax Policy on Utility-Scale Solar Deployment Given Financing Interactions

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

Mai, Trieu; Cole, Wesley; Krishnan, Venkat

In this study, the authors conducted a literature review of approaches and assumptions used by other modeling teams and consultants with respect to solar project financing; developed and incorporated an ability to model the likely financing shift away from more expensive sources of capital and toward cheaper sources as the investment tax credit declines in the ReEDS model; and used the 'before and after' versions of the ReEDS model to isolate and analyze the deployment impact of the financing shift under a range of conditions. Using ReEDS scenarios with this improved capability, we find that this 'financing' shift would softenmore » the blow of the ITC reversion; however, the overall impacts of such a shift in capital structure are estimated to be small and near-term utility-scale PV deployment is found to be much more sensitive to other factors that might drive down utility-scale PV prices.« less

[Validation of Differential Extraction Kit in forensic sexual assault cases].

PubMed

Wu, Dan; Cao, Yu; Xu, Yan; He, Bai-Fang; Bi, Gang; Zhou, Huai-Gu

2009-12-01

To evaluate the validity of Differential Extraction Kit in isolating spermatozoa and epithelial cell DNA from mixture samples. Selective lysis of spermatid and epithelial cells combined with paramagnetic particle method were applied to extract the DNA from the mock samples under controlled conditions and forensic case samples, and template DNA were analyzed by STR genotype method. This Differential Extraction Kit is efficient to obtain high quality spermatid and epithelial cell DNA from the mixture samples with different proportion of sperm to epithelial cell. The Differential Extraction Kit can be applied in DNA extraction for mixed stain from forensic sexual assault samples.

Utilizing DNA analysis to combat the world wide plague of present day slavery – trafficking in persons

PubMed Central

Palmbach, Timothy; Blom, Jeffrey; Hoynes, Emily; Primorac, Dragan; Gaboury, Mario

2014-01-01

A study was conducted to determine if modern forensic DNA typing methods can be properly employed throughout the world with a final goal of increasing arrests, prosecutions, and convictions of perpetrators of modern day trafficking in persons while concurrently reducing the burden of victim testimony in legal proceedings. Without interruption of investigations, collection of samples containing DNA was conducted in a variety of settings. Evidentiary samples were analyzed on the ANDE Rapid DNA system. Many of the collected swabs yielded informative short tandem repeat profiles with Rapid DNA technology. PMID:24577820

Utilizing DNA analysis to combat the world wide plague of present day slavery--trafficking in persons.

PubMed

Palmbach, Timothy M; Blom, Jeffrey; Hoynes, Emily; Primorac, Dragan; Gaboury, Mario

2014-02-01

A study was conducted to determine if modern forensic DNA typing methods can be properly employed throughout the world with a final goal of increasing arrests, prosecutions, and convictions of perpetrators of modern day trafficking in persons while concurrently reducing the burden of victim testimony in legal proceedings. Without interruption of investigations, collection of samples containing DNA was conducted in a variety of settings. Evidentiary samples were analyzed on the ANDE Rapid DNA system. Many of the collected swabs yielded informative short tandem repeat profiles with Rapid DNA technology.

Trends in brain cancer mortality among U.S. Gulf War veterans: 21 year follow-up.

PubMed

Barth, Shannon K; Dursa, Erin K; Bossarte, Robert M; Schneiderman, Aaron I

2017-10-01

Previous mortality studies of U.S. Gulf War veterans through 2000 and 2004 have shown an increased risk of brain cancer mortality among some deployed individuals. When veterans possibly exposed to environmental contaminants associated with demolition of the Khamisiyah Ammunition Storage Facility at Khamisiyah, Iraq, have been compared to contemporaneously deployed unexposed veterans, the results have suggested increased risk for mortality from brain cancer among the exposed. Brain cancer mortality risk in this cohort has not been updated since 2004. This study analyzes the risk for brain cancer mortality between 1991-2011 through two series of comparisons: U.S. Gulf War deployed and non-deployed veterans from the same era; and veterans possibly exposed to environmental contaminants at Khamisiyah compared to contemporaneously deployed but unexposed U.S. Gulf War veterans. Risk of brain cancer mortality was determined using logistic regression. Life test hazard models were created to plot comparisons of annual hazard rates. Joinpoint regression models were applied to assess trends in hazard rates for brain cancer mortality. U.S. Army veterans possibly exposed at Khamisiyah had similar rates of brain cancer mortality compared to those not possibly exposed; however, veterans possibly exposed had a higher risk of brain cancer in the time period immediately following the Gulf War. Results from these analyses suggest that veterans possibly exposed at Khamisiyah experienced different patterns of brain cancer mortality risk compared to the other groups. Published by Elsevier Ltd.

Relay NBS Graft with the Plus Delivery System to Improve Deployment in Aortic Arch with Small Radius Curve

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

Ferro, Carlo; Rossi, Umberto G., E-mail: urossi76@hotmail.com; Seitun, Sara

The purpose of this report is to describe deployment of the Relay NBS Thoracic Stent Graft with the Plus Delivery System (Bolton Medical, Sunrise, FL) in a flexible resin arch model with a 15-mm radius curve as well as our preliminary clinical results. The Relay NBS graft with the Plus Delivery System was evaluated by way of bench testing, which was performed with stent grafts with diameters ranging from 24 to 46 mm and lengths ranging from 100 to 250 mm in flexible resin arch models with a 15-mm arch radius of curvature. The deployment sequence was analyzed. The Relaymore » NBS graft with the Plus Delivery System was deployed in two patients, respectively, having a 6.5-cm penetrating aortic ulcer of the proximal third of the descending thoracic aorta and a DeBakey type-I aortic dissection with chronic false lumen dilatation after surgery due to an entry site at the distal thoracic aorta. Bench tests showed proper conformation and apposition of the Relay NBS graft with the Plus Delivery System in the flexible resin model. This stent graft was deployed successfully into the two patients with a correct orientation of the first stent and without early or late complications. The Relay NBS graft with the Plus Delivery System ensures an optimal conformation and apposition of the first stent in the aortic arch with a small radius of curvature.« less

On the Path to SunShot. Emerging Issues and Challenges in Integrating Solar with the Distribution System

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

Palmintier, Bryan; Broderick, Robert; Mather, Barry

2016-05-01

This report analyzes distribution-integration challenges, solutions, and research needs in the context of distributed generation from PV (DGPV) deployment to date and the much higher levels of deployment expected with achievement of the U.S. Department of Energy's SunShot targets. Recent analyses have improved estimates of the DGPV hosting capacities of distribution systems. This report uses these results to statistically estimate the minimum DGPV hosting capacity for the contiguous United States using traditional inverters of approximately 170 GW without distribution system modifications. This hosting capacity roughly doubles if advanced inverters are used to manage local voltage and additional minor, low-cost changesmore » could further increase these levels substantially. Key to achieving these deployment levels at minimum cost is siting DGPV based on local hosting capacities, suggesting opportunities for regulatory, incentive, and interconnection innovation. Already, pre-computed hosting capacity is beginning to expedite DGPV interconnection requests and installations in select regions; however, realizing SunShot-scale deployment will require further improvements to DGPV interconnection processes, standards and codes, and compensation mechanisms so they embrace the contributions of DGPV to system-wide operations. SunShot-scale DGPV deployment will also require unprecedented coordination of the distribution and transmission systems. This includes harnessing DGPV's ability to relieve congestion and reduce system losses by generating closer to loads; minimizing system operating costs and reserve deployments through improved DGPV visibility; developing communication and control architectures that incorporate DGPV into system operations; providing frequency response, transient stability, and synthesized inertia with DGPV in the event of large-scale system disturbances; and potentially managing reactive power requirements due to large-scale deployment of advanced inverter functions. Finally, additional local and system-level value could be provided by integrating DGPV with energy storage and 'virtual storage,' which exploits improved management of electric vehicle charging, building energy systems, and other large loads. Together, continued innovation across this rich distribution landscape can enable the very-high deployment levels envisioned by SunShot.« less

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

PubMed Central

Zhabinskaya, Dina; Benham, Craig J.

2012-01-01

We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence. Since DNA superhelicity topologically couples together the transition behaviors of all base pairs, a unified model is required to analyze all the transitions to which the DNA sequence is susceptible. Here we present a first model of this type. Our numerical approach generalizes the strategy of previously developed algorithms, which studied superhelical transitions to a single alternate conformation. We apply our multi-state model to study the competition between strand separation and B-Z transitions in superhelical DNA. We show this competition to be highly sensitive to temperature and to the imposed level of supercoiling. Comparison of our results with experimental data shows that, when the energetics appropriate to the experimental conditions are used, the competition between these two transitions is accurately captured by our algorithm. We analyze the superhelical competition between B-Z transitions and denaturation around the c-myc oncogene, where both transitions are known to occur when this gene is transcribing. We apply our model to explore the correlation between stress-induced transitions and transcriptional activity in various organisms. In higher eukaryotes we find a strong enhancement of Z-forming regions immediately 5′ to their transcription start sites (TSS), and a depletion of strand separating sites in a broad region around the TSS. The opposite patterns occur around transcript end locations. We also show that susceptibility to each type of transition is different in eukaryotes and prokaryotes. By analyzing a set of untranscribed pseudogenes we show that the Z-susceptibility just downstream of the TSS is not preserved, suggesting it may be under selection pressure. PMID:22570598

Dissecting DNA damage response pathways by analyzing protein localization and abundance changes during DNA replication stress

PubMed Central

Tkach, Johnny M.; Yimit, Askar; Lee, Anna Y.; Riffle, Michael; Costanzo, Michael; Jaschob, Daniel; Hendry, Jason A.; Ou, Jiongwen; Moffat, Jason; Boone, Charles; Davis, Trisha N.; Nislow, Corey; Brown, Grant W.

2012-01-01

Re-localization of proteins is a hallmark of the DNA damage response. We use high-throughput microscopic screening of the yeast GFP fusion collection to develop a systems-level view of protein re-organization following drug-induced DNA replication stress. Changes in protein localization and abundance reveal drug-specific patterns of functional enrichments. Classification of proteins by sub-cellular destination allows the identification of pathways that respond to replication stress. We analyzed pairwise combinations of GFP fusions and gene deletion mutants to define and order two novel DNA damage responses. In the first, Cmr1 forms subnuclear foci that are regulated by the histone deacetylase Hos2 and are distinct from the typical Rad52 repair foci. In a second example, we find that the checkpoint kinases Mec1/Tel1 and the translation regulator Asc1 regulate P-body formation. This method identifies response pathways that were not detected in genetic and protein interaction screens, and can be readily applied to any form of chemical or genetic stress to reveal cellular response pathways. PMID:22842922

Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas

PubMed Central

Hou, Yu; Guo, Huahu; Cao, Chen; Li, Xianlong; Hu, Boqiang; Zhu, Ping; Wu, Xinglong; Wen, Lu; Tang, Fuchou; Huang, Yanyi; Peng, Jirun

2016-01-01

Single-cell genome, DNA methylome, and transcriptome sequencing methods have been separately developed. However, to accurately analyze the mechanism by which transcriptome, genome and DNA methylome regulate each other, these omic methods need to be performed in the same single cell. Here we demonstrate a single-cell triple omics sequencing technique, scTrio-seq, that can be used to simultaneously analyze the genomic copy-number variations (CNVs), DNA methylome, and transcriptome of an individual mammalian cell. We show that large-scale CNVs cause proportional changes in RNA expression of genes within the gained or lost genomic regions, whereas these CNVs generally do not affect DNA methylation in these regions. Furthermore, we applied scTrio-seq to 25 single cancer cells derived from a human hepatocellular carcinoma tissue sample. We identified two subpopulations within these cells based on CNVs, DNA methylome, or transcriptome of individual cells. Our work offers a new avenue of dissecting the complex contribution of genomic and epigenomic heterogeneities to the transcriptomic heterogeneity within a population of cells. PMID:26902283

Day and night variations in the repair of ionizing-radiation-induced DNA damage in mouse splenocytes.

PubMed

Palombo, Philipp; Moreno-Villanueva, Maria; Mangerich, Aswin

2015-04-01

In mammals, biological rhythms synchronize physiological and behavioral processes to the 24-h light-dark (LD) cycle. At the molecular level, self-sustaining processes, such as oscillations of transcription-translation feedback loops, control the circadian clock, which in turn regulates a wide variety of cellular processes, including gene expression and cell cycle progression. Furthermore, previous studies reported circadian oscillations in the repair capacity of DNA lesions specifically repaired by nucleotide excision repair (NER). However, it is so far only poorly understood if DNA repair pathways other than NER are under circadian control, in particular base excision and DNA strand break repair. In the present study, we analyzed potential day and night variations in the repair of DNA lesions induced by ionizing radiation (i.e., mainly oxidative damage and DNA strand breaks) in living mouse splenocytes using a modified protocol of the automated FADU assay. Our results reveal that splenocytes isolated from mice during the light phase (ZT06) displayed higher DNA repair activity than those of the dark phase (ZT18). As analyzed by highly sensitive and accurate qPCR arrays, these alterations were accompanied by significant differences in expression profiles of genes involved in the circadian clock and DNA repair. Notably, the majority of the DNA repair genes were expressed at higher levels during the light phase (ZT06). This included genes of all major DNA repair pathways with the strongest differences observed for genes of base excision and DNA double strand break repair. In conclusion, here we provide novel evidence that mouse splenocytes exhibit significant differences in the repair of IR-induced DNA damage during the LD cycle, both on a functional and on a gene expression level. It will be interesting to test if these findings could be exploited for therapeutic purposes, e.g. time-of-the-day-specific application of DNA-damaging treatments used against blood malignancies. Copyright © 2015 Elsevier B.V. All rights reserved.

Bacterial growth and the decomposition of particulate organic carbon collected in sediment traps

NASA Astrophysics Data System (ADS)

Ducklow, Hugh W.; Hill, Suzanne M.; Gardner, Wilford D.

We have studied bacterial abundance and production in samples from sediment traps deployed for 1 and 100 days in several areas of the shelf and slope regions of the Middle Atlantic Bight, U.S.A. By making a series of assumptions about bacterial growth at the expense of POC in traps, we have estimated that the turnover time of organic particles collected in traps during long deployments is slow (mean 1500 ± 300 days), if only bacterial activity is considered. However the abundance and biomass of bacteria in traps is very high, ranging from 3 to 30 × 10 11 cells gC -1, i.e., 0.3 to 3% of the POC is bacterial carbon. Fifteen to 88% of the particles in traps were colonized by bacteria, but usually about half the particles had only 0 to 1 cell attached. Growth of bacteria was observed at all scales relevant to these trap deployments; over periods ranging from hours to weeks, at rates of 0.01 to 0.3 d -1. In spite of slow growth, bacteria appeared to be physiologically active in that [ 3H]adenine and [ 3H]thymidine were incorporated more rapidly into RNA and protein than into DNA. Total incorporation rates were high. We conclude that even relatively old (ca. 1 y) POC in sediment traps supports high levels of active bacterial biomass, but that POC decomposition is slow, so that bacteria may not be the principal agents of POC turnover following collection.

A fusion of minicircle DNA and nanoparticle delivery technologies facilitates therapeutic genetic engineering of autologous canine olfactory mucosal cells.

PubMed

Delaney, Alexander M; Adams, Christopher F; Fernandes, Alinda R; Al-Shakli, Arwa F; Sen, Jon; Carwardine, Darren R; Granger, Nicolas; Chari, Divya M

2017-06-29

Olfactory ensheathing cells (OECs) promote axonal regeneration and improve locomotor function when transplanted into the injured spinal cord. A recent clinical trial demonstrated improved motor function in domestic dogs with spinal injury following autologous OEC transplantation. Their utility in canines offers promise for human translation, as dogs are comparable to humans in terms of clinical management and genetic/environmental variation. Moreover, the autologous, minimally invasive derivation of OECs makes them viable for human spinal injury investigation. Genetic engineering of transplant populations may augment their therapeutic potential, but relies heavily on viral methods which have several drawbacks for clinical translation. We present here the first proof that magnetic particles deployed with applied magnetic fields and advanced DNA minicircle vectors can safely bioengineer OECs to secrete a key neurotrophic factor, with an efficiency approaching that of viral vectors. We suggest that our alternative approach offers high translational potential for the delivery of augmented clinical cell therapies.

High-throughput automated microfluidic sample preparation for accurate microbial genomics

PubMed Central

Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B.; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P.; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C.

2017-01-01

Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications. PMID:28128213

Slab-plume interaction beneath the Pacific Northwest

NASA Astrophysics Data System (ADS)

Obrebski, Mathias; Allen, Richard M.; Xue, Mei; Hung, Shu-Huei

2010-07-01

The Pacific Northwest has undergone complex plate reorganization and intense tectono-volcanic activity to the east during the Cenozoic (last 65 Ma). Here we show new high-resolution tomographic images obtained using shear and compressional data from the ongoing USArray deployment that demonstrate first that there is a continuous, whole-mantle plume beneath the Yellowstone Snake River Plain (YSRP) and second, that the subducting Juan de Fuca (JdF) slab is fragmented and even absent beneath Oregon. The analysis of the geometry of our tomographic models suggests that the arrival and emplacement of the large Yellowstone plume had a substantial impact on the nearby Cascadia subduction zone, promoting the tearing and weakening of the JdF slab. This interpretation also explains several intriguing geophysical properties of the Cascadia trench that contrast with most other subduction zones, such as the absence of deep seismicity and the trench-normal fast direction of mantle anisotropy. The DNA velocity models are available for download and slicing at http://dna.berkeley.edu.

Method for analyzing microbial communities

DOEpatents

Zhou, Jizhong [Oak Ridge, TN; Wu, Liyou [Oak Ridge, TN

2010-07-20

The present invention provides a method for quantitatively analyzing microbial genes, species, or strains in a sample that contains at least two species or strains of microorganisms. The method involves using an isothermal DNA polymerase to randomly and representatively amplify genomic DNA of the microorganisms in the sample, hybridizing the resultant polynucleotide amplification product to a polynucleotide microarray that can differentiate different genes, species, or strains of microorganisms of interest, and measuring hybridization signals on the microarray to quantify the genes, species, or strains of interest.

Tissue-based standoff biosensors for detecting chemical warfare agents

DOEpatents

Greenbaum, Elias; Sanders, Charlene A.

2003-11-18

A tissue-based, deployable, standoff air quality sensor for detecting the presence of at least one chemical or biological warfare agent, includes: a cell containing entrapped photosynthetic tissue, the cell adapted for analyzing photosynthetic activity of the entrapped photosynthetic tissue; means for introducing an air sample into the cell and contacting the air sample with the entrapped photosynthetic tissue; a fluorometer in operable relationship with the cell for measuring photosynthetic activity of the entrapped photosynthetic tissue; and transmitting means for transmitting analytical data generated by the fluorometer relating to the presence of at least one chemical or biological warfare agent in the air sample, the sensor adapted for deployment into a selected area.

Peace umbrella, a vague policy and checkered past. Research report

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

Biszak, G.A.

1997-03-01

With the break-up of the former Soviet Union, the United Nations Security Council enjoyed a greater consensus among its members in confronting aggression and participation in humanitarian and peace operations. Deploying significant military forces under the peace umbrella at the beginning of this decade was highly unlikely. However, since 1990, 25 deployments have been conducted with the majority falling under the peace umbrella. This paper analyzes current national and military strategy in regards to the peace umbrella, specifically peace enforcement, military doctrine, and the case of Somalia. In addition, this paper looks at doctrine and directives that currently guide deploymentmore » of forces and the potential for future peace operations.« less

Application of SMP composite in designing a morphing wing

NASA Astrophysics Data System (ADS)

Yu, Kai; Yin, Weilong; Liu, Yanju; Leng, Jinsong

2008-11-01

A new concept of a morphing wing based on shape memory polymer (SMP) and its reinforced composite is proposed in this paper. SMP used in this study is a thermoset styrene-based resin in contrast to normal thermoplastic SMP. In our design, the wing winded on the airframe can be deployed during heating, which provides main lift for a morphing aircraft to realize stable flight. Aerodynamic characteristics of the deployed morphing wing are calculated by using CFD software. The static deformation of the wing under the air loads is also analyzed by using the finite element method. The results show that the used SMP material can provide enough strength and stiffness for the application.

Quantitative Method of Measuring Metastatic Activity

NASA Technical Reports Server (NTRS)

Morrison, Dennis R. (Inventor)

1999-01-01

The metastatic potential of tumors can be evaluated by the quantitative detection of urokinase and DNA. The cell sample selected for examination is analyzed for the presence of high levels of urokinase and abnormal DNA using analytical flow cytometry and digital image analysis. Other factors such as membrane associated uroldnase, increased DNA synthesis rates and certain receptors can be used in the method for detection of potentially invasive tumors.

Enhanced Reliability and Accuracy for Field Deployable Bioforensic Detection and Discrimination of Xylella fastidiosa subsp. pauca, Causal Agent of Citrus Variegated Chlorosis Using Razor Ex Technology and TaqMan Quantitative PCR

PubMed Central

Fletcher, Jacqueline; Melcher, Ulrich; Ochoa Corona, Francisco Manuel

2013-01-01

A reliable, accurate and rapid multigene-based assay combining real time quantitative PCR (qPCR) and a Razor Ex BioDetection System (Razor Ex) was validated for detection of Xylella fastidiosa subsp. pauca (Xfp, a xylem-limited bacterium that causes citrus variegated chlorosis [CVC]). CVC, which is exotic to the United States, has spread through South and Central America and could significantly impact U.S. citrus if it arrives. A method for early, accurate and sensitive detection of Xfp in plant tissues is needed by plant health officials for inspection of products from quarantined locations, and by extension specialists for detection, identification and management of disease outbreaks and reservoir hosts. Two sets of specific PCR primers and probes, targeting Xfp genes for fimbrillin and the periplasmic iron-binding protein were designed. A third pair of primers targeting the conserved cobalamin synthesis protein gene was designed to detect all possible X. fastidiosa (Xf) strains. All three primer sets detected as little as 1 fg of plasmid DNA carrying X. fastidiosa target sequences and genomic DNA of Xfp at as little as 1 - 10 fg. The use of Razor Ex facilitates a rapid (about 30 min) in-field assay capability for detection of all Xf strains, and for specific detection of Xfp. Combined use of three primer sets targeting different genes increased the assay accuracy and broadened the range of detection. To our knowledge, this is the first report of a field-deployable rapid and reliable bioforensic detection and discrimination method for a bacterial phytopathogen based on multigene targets. PMID:24312333

Enhanced reliability and accuracy for field deployable bioforensic detection and discrimination of Xylella fastidiosa subsp. pauca, causal agent of citrus variegated chlorosis using razor ex technology and TaqMan quantitative PCR.

PubMed

Ouyang, Ping; Arif, Mohammad; Fletcher, Jacqueline; Melcher, Ulrich; Ochoa Corona, Francisco Manuel

2013-01-01

A reliable, accurate and rapid multigene-based assay combining real time quantitative PCR (qPCR) and a Razor Ex BioDetection System (Razor Ex) was validated for detection of Xylella fastidiosa subsp. pauca (Xfp, a xylem-limited bacterium that causes citrus variegated chlorosis [CVC]). CVC, which is exotic to the United States, has spread through South and Central America and could significantly impact U.S. citrus if it arrives. A method for early, accurate and sensitive detection of Xfp in plant tissues is needed by plant health officials for inspection of products from quarantined locations, and by extension specialists for detection, identification and management of disease outbreaks and reservoir hosts. Two sets of specific PCR primers and probes, targeting Xfp genes for fimbrillin and the periplasmic iron-binding protein were designed. A third pair of primers targeting the conserved cobalamin synthesis protein gene was designed to detect all possible X. fastidiosa (Xf) strains. All three primer sets detected as little as 1 fg of plasmid DNA carrying X. fastidiosa target sequences and genomic DNA of Xfp at as little as 1 - 10 fg. The use of Razor Ex facilitates a rapid (about 30 min) in-field assay capability for detection of all Xf strains, and for specific detection of Xfp. Combined use of three primer sets targeting different genes increased the assay accuracy and broadened the range of detection. To our knowledge, this is the first report of a field-deployable rapid and reliable bioforensic detection and discrimination method for a bacterial phytopathogen based on multigene targets.

Properties of internalization factors contributing to the uptake of extracellular DNA into tumor-initiating stem cells of mouse Krebs-2 cell line.

PubMed

Dolgova, Evgeniya V; Potter, Ekaterina A; Proskurina, Anastasiya S; Minkevich, Alexandra M; Chernych, Elena R; Ostanin, Alexandr A; Efremov, Yaroslav R; Bayborodin, Sergey I; Nikolin, Valeriy P; Popova, Nelly A; Kolchanov, Nikolay A; Bogachev, Sergey S

2016-05-25

Previously, we demonstrated that poorly differentiated cells of various origins, including tumor-initiating stem cells present in the ascites form of mouse cancer cell line Krebs-2, are capable of naturally internalizing both linear double-stranded DNA and circular plasmid DNA. The method of co-incubating Krebs-2 cells with extracellular plasmid DNA (pUC19) or TAMRA-5'-dUTP-labeled polymerase chain reaction (PCR) product was used. It was found that internalized plasmid DNA isolated from Krebs-2 can be transformed into competent Escherichia coli cells. Thus, the internalization processes taking place in the Krebs-2 cell subpopulation have been analyzed and compared, as assayed by E. coli colony formation assay (plasmid DNA) and cytofluorescence (TAMRA-DNA). We showed that extracellular DNA both in the form of plasmid DNA and a PCR product is internalized by the same subpopulation of Krebs-2 cells. We found that the saturation threshold for Krebs-2 ascites cells is 0.5 μg DNA/10(6) cells. Supercoiled plasmid DNA, human high-molecular weight DNA, and 500 bp PCR fragments are internalized into the Krebs-2 tumor-initiating stem cells via distinct, non-competing internalization pathways. Under our experimental conditions, each cell may harbor 340-2600 copies of intact plasmid material, or up to 3.097 ± 0.044×10(6) plasmid copies (intact or not), as detected by quantitative PCR. The internalization dynamics of extracellular DNA, copy number of the plasmids taken up by the cells, and competition between different types of double-stranded DNA upon internalization into tumor-initiating stem cells of mouse ascites Krebs-2 have been comprehensively analyzed. Investigation of the extracellular DNA internalization into tumor-initiating stem cells is an important part of understanding their properties and possible destruction mechanisms. For example, a TAMRA-labeled DNA probe may serve as an instrument to develop a target for the therapy of cancer, aiming at elimination of tumor stem cells, as well as developing a straightforward test system for the quantification of poorly differentiated cells, including tumor-initiating stem cells, in the bulk tumor sample (biopsy or surgery specimen).

Irradiation influence on the detection of genetic-modified soybeans

NASA Astrophysics Data System (ADS)

Villavicencio, A. L. C. H.; Araújo, M. M.; Baldasso, J. G.; Aquino, S.; Konietzny, U.; Greiner, R.

2004-09-01

Three soybean varieties were analyzed to evaluate the irradiation influence on the detection of genetic modification. Samples were treated in a 60Co facility at dose levels of 0, 500, 800, and 1000Gy. The seeds were at first analyzed by Comet Assay as a rapid screening irradiation detection method. Secondly, germination test was performed to detect the viability of irradiated soybeans. Finally, because of its high sensitivity, its specificity and rapidity the polimerase chain reaction was the method applied for genetic modified organism detection. The analysis of DNA by the single technique of microgel electrophoresis of single cells (DNA Comet Assay) showed that DNA damage increased with increasing radiation doses. No negative influence of irradiation on the genetic modification detection was found.

A Structured Decision Approach for Integrating and Analyzing Community Perspectives in Re-Use Planning of Vacant Properties in Cleveland, Ohio

EPA Science Inventory

An integrated GIS-based, multi-attribute decision model deployed in a web-based platform is presented enabling an iterative, spatially explicit and collaborative analysis of relevant and available information for repurposing vacant land. The process incorporated traditional and ...

Improving adaptive/responsive signal control performance : implications of non-invasive detection and legacy timing practices : final report.

DOT National Transportation Integrated Search

2017-02-01

This project collected and analyzed event based vehicle detection data from multiple technologies at four different sites across Oregon to provide guidance for deployment of non-invasive detection for use in adaptive control, as well as develop a tru...

Extending Item Response Theory to Online Homework

ERIC Educational Resources Information Center

Kortemeyer, Gerd

2014-01-01

Item response theory (IRT) becomes an increasingly important tool when analyzing "big data" gathered from online educational venues. However, the mechanism was originally developed in traditional exam settings, and several of its assumptions are infringed upon when deployed in the online realm. For a large-enrollment physics course for…

Building a Virtual Learning Network for Teachers in a Suburban School District

ERIC Educational Resources Information Center

Kurtzworth-Keen, Kristin A.

2011-01-01

Emerging research indicates that learning management systems such as Moodle can function as virtual, collaborative environments, where collegial interactions promote professional learning opportunities. This study deployed a mixed methods design in order to describe and analyze teacher participation in a virtual learning network (VLN) that was…

ENVIRONMENTAL TECHNOLOGY VERIFICATION REPORT, LEAD IN DUST WIPE MEASUREMENT TECHNOLOGY, NITON LLC, X-RAY FLUORESCENCE SPECTRUM ANALYZER, XLT-700

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) design efficient processes for conducting has created the Environmental Technology perfofl1lance tests of innovative technologies. Verification Program (E TV) to facilitate the deployment of innovative or improved environmental techn...

DNApod: DNA polymorphism annotation database from next-generation sequence read archives.

PubMed

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information.

DNApod: DNA polymorphism annotation database from next-generation sequence read archives

PubMed Central

Mochizuki, Takako; Tanizawa, Yasuhiro; Fujisawa, Takatomo; Ohta, Tazro; Nikoh, Naruo; Shimizu, Tokurou; Toyoda, Atsushi; Fujiyama, Asao; Kurata, Nori; Nagasaki, Hideki; Kaminuma, Eli; Nakamura, Yasukazu

2017-01-01

With the rapid advances in next-generation sequencing (NGS), datasets for DNA polymorphisms among various species and strains have been produced, stored, and distributed. However, reliability varies among these datasets because the experimental and analytical conditions used differ among assays. Furthermore, such datasets have been frequently distributed from the websites of individual sequencing projects. It is desirable to integrate DNA polymorphism data into one database featuring uniform quality control that is distributed from a single platform at a single place. DNA polymorphism annotation database (DNApod; http://tga.nig.ac.jp/dnapod/) is an integrated database that stores genome-wide DNA polymorphism datasets acquired under uniform analytical conditions, and this includes uniformity in the quality of the raw data, the reference genome version, and evaluation algorithms. DNApod genotypic data are re-analyzed whole-genome shotgun datasets extracted from sequence read archives, and DNApod distributes genome-wide DNA polymorphism datasets and known-gene annotations for each DNA polymorphism. This new database was developed for storing genome-wide DNA polymorphism datasets of plants, with crops being the first priority. Here, we describe our analyzed data for 679, 404, and 66 strains of rice, maize, and sorghum, respectively. The analytical methods are available as a DNApod workflow in an NGS annotation system of the DNA Data Bank of Japan and a virtual machine image. Furthermore, DNApod provides tables of links of identifiers between DNApod genotypic data and public phenotypic data. To advance the sharing of organism knowledge, DNApod offers basic and ubiquitous functions for multiple alignment and phylogenetic tree construction by using orthologous gene information. PMID:28234924

Base excision DNA repair in the embryonic development of the sea urchin, Strongylocentrotus intermedius.

PubMed

Torgasheva, Natalya A; Menzorova, Natalya I; Sibirtsev, Yurii T; Rasskazov, Valery A; Zharkov, Dmitry O; Nevinsky, Georgy A

2016-06-21

In actively proliferating cells, such as the cells of the developing embryo, DNA repair is crucial for preventing the accumulation of mutations and synchronizing cell division. Sea urchin embryo growth was analyzed and extracts were prepared. The relative activity of DNA polymerase, apurinic/apyrimidinic (AP) endonuclease, uracil-DNA glycosylase, 8-oxoguanine-DNA glycosylase, and other glycosylases was analyzed using specific oligonucleotide substrates of these enzymes; the reaction products were resolved by denaturing 20% polyacrylamide gel electrophoresis. We have characterized the profile of several key base excision repair activities in the developing embryos (2 blastomers to mid-pluteus) of the grey sea urchin, Strongylocentrotus intermedius. The uracil-DNA glycosylase specific activity sharply increased after blastula hatching, whereas the specific activity of 8-oxoguanine-DNA glycosylase steadily decreased over the course of the development. The AP-endonuclease activity gradually increased but dropped at the last sampled stage (mid-pluteus 2). The DNA polymerase activity was high at the first cleavage division and then quickly decreased, showing a transient peak at blastula hatching. It seems that the developing sea urchin embryo encounters different DNA-damaging factors early in development within the protective envelope and later as a free-floating larva, with hatching necessitating adaptation to the shift in genotoxic stress conditions. No correlation was observed between the dynamics of the enzyme activities and published gene expression data from developing congeneric species, S. purpuratus. The results suggest that base excision repair enzymes may be regulated in the sea urchin embryos at the level of covalent modification or protein stability.

Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses.

PubMed

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y F; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie; Martin, Darren Patrick

2014-02-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here.

Evidence of Pervasive Biologically Functional Secondary Structures within the Genomes of Eukaryotic Single-Stranded DNA Viruses

PubMed Central

Muhire, Brejnev Muhizi; Golden, Michael; Murrell, Ben; Lefeuvre, Pierre; Lett, Jean-Michel; Gray, Alistair; Poon, Art Y. F.; Ngandu, Nobubelo Kwanele; Semegni, Yves; Tanov, Emil Pavlov; Monjane, Adérito Luis; Harkins, Gordon William; Varsani, Arvind; Shepherd, Dionne Natalie

2014-01-01

Single-stranded DNA (ssDNA) viruses have genomes that are potentially capable of forming complex secondary structures through Watson-Crick base pairing between their constituent nucleotides. A few of the structural elements formed by such base pairings are, in fact, known to have important functions during the replication of many ssDNA viruses. Unknown, however, are (i) whether numerous additional ssDNA virus genomic structural elements predicted to exist by computational DNA folding methods actually exist and (ii) whether those structures that do exist have any biological relevance. We therefore computationally inferred lists of the most evolutionarily conserved structures within a diverse selection of animal- and plant-infecting ssDNA viruses drawn from the families Circoviridae, Anelloviridae, Parvoviridae, Nanoviridae, and Geminiviridae and analyzed these for evidence of natural selection favoring the maintenance of these structures. While we find evidence that is consistent with purifying selection being stronger at nucleotide sites that are predicted to be base paired than at sites predicted to be unpaired, we also find strong associations between sites that are predicted to pair with one another and site pairs that are apparently coevolving in a complementary fashion. Collectively, these results indicate that natural selection actively preserves much of the pervasive secondary structure that is evident within eukaryote-infecting ssDNA virus genomes and, therefore, that much of this structure is biologically functional. Lastly, we provide examples of various highly conserved but completely uncharacterized structural elements that likely have important functions within some of the ssDNA virus genomes analyzed here. PMID:24284329

Reservoir-Scale Biological Community Response to Trace Element Additions in a Northern Montana Oil Field

NASA Astrophysics Data System (ADS)

Connors, D. E.; Bradfish, J.; DeBruyn, R. P.; Zemetra, J.; Mitchell, H.

2017-12-01

In subsurface oil bearing formations, microbial growth and metabolism is restricted due to a lack of elements other than carbon, hydrogen, and oxygen required for cell structure and as cofactors. A chemical treatment that adds these elements back into the formation was deployed into an oil reservoir in Northern Montana, with the intent of increasing biogenic methane generation. Samples of water from producing wells in the reservoir were collected anaerobically, and analyzed for geochemical content, and cells from the water were collected and analyzed via 16S rRNA gene DNA sequencing to determine the makeup of the microbial community over the course of twelve months of treatment, and for two years after. Prior to chemical treatment, this reservoir was depleted in elements required for enzyme co-factors in the methanogenesis metabolic pathway (Co, Mo, Ni, W, Zn) as well as nitrogen and phosphorus. Most the microbial community was composed of chemoheterotrophic bacteria associated with the biodegradation of large carbon molecules, with a small community of acetoclastic methanogens. During and after additions of the depleted elements, the metabolism of the community in the reservoir shifted towards chemoautotrophs and hydrogenotrophic methanogens, and the cell density increased. After treatment was ended, cell counts stabilized at a new equilibrium concentration, and the autotrophic metabolism was maintained. The pre-treatment community was dependent on energy input from solubilized oil molecules, whereas the post-treatment community more effectively utilized dissolved organics and carbon dioxide as carbon sources for fixation and respiration. This study demonstrates the capability of microbial communities to rapidly reorganize in the environment when provided with an influx of the elements required for growth and metabolism.

A genetic investigation of Korean mummies from the Joseon Dynasty.

PubMed

Kim, Na Young; Lee, Hwan Young; Park, Myung Jin; Yang, Woo Ick; Shin, Kyoung-Jin

2011-01-01

Two Korean mummies (Danwoong-mirra and Yoon-mirra) found in medieval tombs in the central region of the Korean peninsula were genetically investigated by analysis of mitochondrial DNA (mtDNA), Y-chromosomal short tandem repeat (Y-STR) and the ABO gene. Danwoong-mirra is a male child mummy and Yoon-mirra is a pregnant female mummy, dating back about 550 and 450 years, respectively. DNA was extracted from soft tissues or bones. mtDNA, Y-STR and the ABO gene were amplified using a small size amplicon strategy and were analyzed according to the criteria of ancient DNA analysis to ensure that authentic DNA typing results were obtained from these ancient samples. Analysis of mtDNA hypervariable region sequence and coding region single nucleotide polymorphism (SNP) information revealed that Danwoong-mirra and Yoon-mirra belong to the East Asian mtDNA haplogroups D4 and M7c, respectively. The Y-STRs were analyzed in the male child mummy (Danwoong-mirra) using the AmpFlSTR® Yfiler PCR Amplification Kit and an in-house Y-miniplex plus system, and could be characterized in 4 loci with small amplicon size. The analysis of ABO gene SNPs using multiplex single base extension methods revealed that the ABO blood types of Danwoong-mirra and Yoon-mirra are AO01 and AB, respectively. The small size amplicon strategy and the authentication process in the present study will be effectively applicable to future genetic analyses of various forensic and ancient samples.

Effect of the one‑carbon unit cycle on overall DNA methylation in children with Down's syndrome.

PubMed

Song, Cui; He, Jingyi; Chen, Jie; Liu, Youxue; Xiong, Feng; Wang, Yutian; Li, Tingyu

2015-12-01

DNA methylation is a major epigenetic mechanism regulating gene expression. In order to analyze the impact of the one‑carbon unit cycle on the overall level of DNA methylation in children with Down's syndrome (DS), the levels of indicators associated with the one‑carbon unit cycle, including folic acid (FA), vitamin B12 (VB12) and homocysteine (Hcy), and the overall DNA methylation level of DS and healthy controls (HCs) were determined in the present study. A total of 36 DS children and 40 age‑ and gender‑matched HCs were included in the present study to determine the levels of FA, VB12, Hcy and overall DNA methylation. The effect of the one‑carbon unit cycle on the overall level of DNA methylation within the DS group was analyzed. The results demonstrated that the level of VB12 was decreased (P=0.008), while the Hcy level was increased (P=0.000) in DS patients compared with the HCs. FA and VB12 levels decreased with increasing age in DS patients (P<0.05). DNA hypermethylation and hypomethylation were observed in DS patients with VB12 deficiency and hyperhomocysteinemia, respectively (P=0.031, P=0.021). Abnormalities in the one‑carbon unit cycle tend to worsen with increasing age in DS children. Thus, one‑carbon unit cycle‑associated alterations in DNA methylation may be important in the neuropathological alterations observed in DS.

The effect of different methods and image analyzers on the results of the in vivo comet assay.

PubMed

Kyoya, Takahiro; Iwamoto, Rika; Shimanura, Yuko; Terada, Megumi; Masuda, Shuichi

2018-01-01

The in vivo comet assay is a widely used genotoxicity test that can detect DNA damage in a range of organs. It is included in the Organisation for Economic Co-operation and Development Guidelines for the Testing of Chemicals. However, various protocols are still used for this assay, and several different image analyzers are used routinely to evaluate the results. Here, we verified a protocol that largely contributes to the equivalence of results, and we assessed the effect on the results when slides made from the same sample were analyzed using two different image analyzers (Comet Assay IV vs Comet Analyzer). Standardizing the agarose concentrations and DNA unwinding and electrophoresis times had a large impact on the equivalence of the results between the different methods used for the in vivo comet assay. In addition, there was some variation in the sensitivity of the two different image analyzers tested; however this variation was considered to be minor and became negligible when the test conditions were standardized between the two different methods. By standardizing the concentrations of low melting agarose and DNA unwinding and electrophoresis times between both methods used in the current study, the sensitivity to detect the genotoxicity of a positive control substance in the in vivo comet assay became generally comparable, independently of the image analyzer used. However, there may still be the possibility that other conditions, except for the three described here, could affect the reproducibility of the in vivo comet assay.

Targeting of >1.5 Mb of Human DNA into the Mouse X Chromosome Reveals Presence of cis-Acting Regulators of Epigenetic Silencing

PubMed Central

Yang, Christine; McLeod, Andrea J.; Cotton, Allison M.; de Leeuw, Charles N.; Laprise, Stéphanie; Banks, Kathleen G.; Simpson, Elizabeth M.; Brown, Carolyn J.

2012-01-01

Regulatory sequences can influence the expression of flanking genes over long distances, and X chromosome inactivation is a classic example of cis-acting epigenetic gene regulation. Knock-ins directed to the Mus musculus Hprt locus offer a unique opportunity to analyze the spread of silencing into different human DNA sequences in the identical genomic environment. X chromosome inactivation of four knock-in constructs, including bacterial artificial chromosome (BAC) integrations of over 195 kb, was demonstrated by both the lack of expression from the inactive X chromosome in females with nonrandom X chromosome inactivation and promoter DNA methylation of the human transgene in females. We further utilized promoter DNA methylation to assess the inactivation status of 74 human reporter constructs comprising >1.5 Mb of DNA. Of the 47 genes examined, only the PHB gene showed female DNA hypomethylation approaching the level seen in males, and escape from X chromosome inactivation was verified by demonstration of expression from the inactive X chromosome. Integration of PHB resulted in lower DNA methylation of the flanking HPRT promoter in females, suggesting the action of a dominant cis-acting escape element. Female-specific DNA hypermethylation of CpG islands not associated with promoters implies a widespread imposition of DNA methylation during X chromosome inactivation; yet transgenes demonstrated differential capacities to accumulate DNA methylation when integrated into the identical location on the inactive X chromosome, suggesting additional cis-acting sequence effects. As only one of the human transgenes analyzed escaped X chromosome inactivation, we conclude that elements permitting ongoing expression from the inactive X are rare in the human genome. PMID:23023002

Entry Dispersion Analysis for the Stardust Comet Sample Return Capsule

NASA Technical Reports Server (NTRS)

Desai, Prasun N.; Mitcheltree, Robert A.; Cheatwood, F. McNeil

1997-01-01

Stardust will be the first mission to return samples from beyond the Earth-Moon system. The sample return capsule, which is passively controlled during the fastest Earth entry ever, will land by parachute in Utah. The present study analyzes the entry, descent, and landing of the returning sample capsule. The effects of two aerodynamic instabilities are revealed (one in the high altitude free molecular regime and the other in the transonic/subsonic flow regime). These instabilities could lead to unacceptably large excursions in the angle-of-attack near peak heating and main parachute deployment, respectively. To reduce the excursions resulting from the high altitude instability, the entry spin rate of the capsule is increased. To stabilize the excursions from the transonic/subsonic instability, a drogue chute with deployment triggered by an accelerometer and timer is added prior to main parachute deployment. A Monte Carlo dispersion analysis of the modified entry (from which the impact of off-nominal conditions during the entry is ascertained) shows that the capsule attitude excursions near peak heating and drogue chute deployment are within Stardust program limits. Additionally, the size of the resulting 3-sigma landing ellipse is 83.5 km in downrange by 29.2 km in crossrange, which is within the Utah Test and Training Range boundaries.

Past Trends and Current Status of Self-Reported Incidence and Impact of Disease and Nonbattle Injury in Military Operations in Southwest Asia and the Middle East

PubMed Central

Tribble, David R.; Putnam, Shannon D.; Mostafa, Manal; Brown, Theodore R.; Letizia, Andrew; Armstrong, Adam W.; Sanders, John W.

2008-01-01

Objectives. To evaluate the evolutional changes in disease and nonbattle injury in a long-term deployment setting, we investigated trends of selected disease and nonbattle injury (NBI) incidence among US military personnel deployed in ongoing military operations in Southwest Asia and the Middle East. Methods. Participants completed an anonymous questionnaire concerning diarrhea, acute respiratory illness (ARI), and NBIs. We compared incidence, morbidity, and risk associations of disease and NBI incidence with historical data. We analyzed a clinic screening form to describe trends in diarrhea incidence over a 3-year period. Results. Between April 2006 and March 2007, 3374 troops completed deployment questionnaires. Incidence of diarrhea was higher than that of ARI and NBI (12.1, 7.1, and 2.5 episodes per 100 person-months, respectively), but ARI and NBI resulted in more-frequent health system utilization (both P < .001) and decreased work performance (P < .001 and P = .05, respectively) than did diarrhea. Compared with historical disease and NBI incidence rates, diarrhea and NBI incidence declined over a 4-year period, whereas ARI remained relatively constant. Conclusions. Diarrhea, ARI, and NBI are important health concerns among deployed military personnel. Public health and preventive measures are needed to mitigate this burden. PMID:18923114

Assessment of a Post-deployment Yellow Ribbon Reintegration Program for National Guard Members and Supporters

PubMed Central

Scherrer, Jeffrey F.; Widner, Greg; Shroff, Manan; Matthieu, Monica; Balan, Sundari; van den Berk-Clark, Carissa; Price, Rumi Kato

2014-01-01

The Yellow Ribbon Reintegration Program (YRRP) was created to meet the needs of National Guard members and their families throughout the deployment cycle. This study examined the perceived utility of the YRRP’s delivery of information and assistance during the post-deployment reintegration period by National Guard members and accompanying supporters who were mostly spouses. Over 22 months, from 10 YRRP events, 683 service members and 411 supporters completed questionnaires immediately after the YRRP. We analyzed questions on information and help provision, timeliness and concerns related to education, employment, legal, family, and health. Service members and supporters most often endorsed education needs being met (76.8% and 78.2% respectively) and were least likely to endorse legal needs being met (63.5% and 60% respectively). Significantly more supporters than service members (p < 0.0001) reported that the YRRP was the first time they learned of available services across all domains. Service members were significantly more likely than supporters to report concerns about education, employment, and health; while supporters were significantly more likely to report concerns about family. Results suggest the YRRP fills gaps in supporter knowledge and provides needed information and resources to most National Guard families 2-4 months after a deployment. PMID:25373071

Methods for Analyzing the Economic Value of Concentrating Solar Power with Thermal Energy Storage

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

Denholm, Paul; Jorgenson, Jennie; Miller, Mackay

2015-07-20

Concentrating solar power with thermal energy storage (CSP-TES) provides multiple quantifiable benefits compared to CSP without storage or to solar photovoltaic (PV) technology, including higher energy value, ancillary services value, and capacity value. This report describes modeling approaches to quantifying these benefits that have emerged through state-level policymaking in the United States as well as the potential applicability of these methods in China. The technical potential for CSP-TES in China is significant, but deployment has not yet achieved the targets established by the Chinese government. According to the 12th Five Year Plan for Renewable Energy (2011-2015), CSP was expected tomore » reach 1 GW by 2015 and 3 GW by 2020 in China, yet as of December 2014, deployment totaled only 13.8 MW. One barrier to more rapid deployment is the lack of an incentive specific to CSP, such as a feed-in tariff. The 13th Five Year Plan for Solar Generation (2016-2020), which is under development, presents an opportunity to establish a feed-in tariff specific to CSP. This report, produced under the auspices of the U.S.-China Renewable Energy Partnership, aims to support the development of Chinese incentives that advance CSP deployment goals.« less

Pilot Deployment of the LDSD Parachute via a Supersonic Ballute

NASA Technical Reports Server (NTRS)

Tanner, Christopher L.; O'Farrell, Clara; Gallon, John C.; Clark, Ian G.; Witkowski, Allen; Woodruff, Paul

2015-01-01

The Low Density Supersonic Decelerator (LDSD) Project required the use of a pilot system due to the inability to mortar deploy its main supersonic parachute. A mortar deployed 4.4 m diameter supersonic ram-air ballute was selected as the pilot system for its high drag coefficient and stability relative to candidate supersonic parachutes at the targeted operational Mach number of 3. The ballute underwent a significant development program that included the development of a new liquid methanol-based pre-inflation system to assist the ballute inflation process. Both pneumatic and pyrotechnic mortar tests were conducted to verify orderly rigging deployment, bag strip, inflation aid activation, and proper mortar performance. The ballute was iteratively analyzed between fluid and structural analysis codes to obtain aerodynamic and aerothermodynamic estimates as well as estimates of the ballute's structural integrity and shape. The ballute was successfully flown in June 2014 at a Mach number of 2.73 as part of the first LDSD supersonic flight test and performed beyond expectations. Recovery of the ballute indicated that it did not exceed its structural or thermal capabilities. This flight set a historical precedent as it represented the largest ballute to have ever been successfully flown at this Mach number by a NASA entity.

Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania.

PubMed

Nagle, Nano; Ballantyne, Kaye N; van Oven, Mannis; Tyler-Smith, Chris; Xue, Yali; Wilcox, Stephen; Wilcox, Leah; Turkalov, Rust; van Oorschot, Roland A H; van Holst Pellekaan, Sheila; Schurr, Theodore G; McAllister, Peter; Williams, Lesley; Kayser, Manfred; Mitchell, R John

2017-03-01

Aboriginal Australians are one of the more poorly studied populations from the standpoint of human evolution and genetic diversity. Thus, to investigate their genetic diversity, the possible date of their ancestors' arrival and their relationships with neighboring populations, we analyzed mitochondrial DNA (mtDNA) diversity in a large sample of Aboriginal Australians. Selected mtDNA single-nucleotide polymorphisms and the hypervariable segment haplotypes were analyzed in 594 Aboriginal Australians drawn from locations across the continent, chiefly from regions not previously sampled. Most (~78%) samples could be assigned to mtDNA haplogroups indigenous to Australia. The indigenous haplogroups were all ancient (with estimated ages >40 000 years) and geographically widespread across the continent. The most common haplogroup was P (44%) followed by S (23%) and M42a (9%). There was some geographic structure at the haplotype level. The estimated ages of the indigenous haplogroups range from 39 000 to 55 000 years, dates that fit well with the estimated date of colonization of Australia based on archeological evidence (~47 000 years ago). The distribution of mtDNA haplogroups in Australia and New Guinea supports the hypothesis that the ancestors of Aboriginal Australians entered Sahul through at least two entry points. The mtDNA data give no support to the hypothesis of secondary gene flow into Australia during the Holocene, but instead suggest long-term isolation of the continent.

[Synthesis of Circular DNA Templates with T4 RNA Ligase for Rolling Circle Amplification].

PubMed

Sakhabutdinova, A R; Maksimova, M A; Garafutdinov, R R

2017-01-01

Currently, isothermal methods of nucleic acid amplification have been well established; in particular, rolling circle amplification is of great interest. In this approach, circular ssDNA molecules have been used as a target that can be obtained by the intramolecular template-dependent ligation of an oligonucleotide C-probe. Here, a new method of synthesizing small circular DNA molecules via the cyclization of ssDNA based on T4 RNA ligase has been proposed. Circular ssDNA is further used as the template for the rolling circle amplification. The maximum yield of the cyclization products was observed in the presence of 5-10% polyethylene glycol 4000, and the optimum DNA length for the cyclization constituted 50 nucleotides. This highly sensitive method was shown to detect less than 10^(2) circular DNA molecules. The method reliability was proved based on artificially destroyed dsDNA, which suggests its implementation for analyzing any significantly fragmented dsDNA.

DNA typing for the identification of old skeletal remains from Korean War victims.

PubMed

Lee, Hwan Young; Kim, Na Young; Park, Myung Jin; Sim, Jeong Eun; Yang, Woo Ick; Shin, Kyoung-Jin

2010-11-01

The identification of missing casualties of the Korean War (1950-1953) has been performed using mitochondrial DNA (mtDNA) profiles, but recent advances in DNA extraction techniques and approaches using smaller amplicons have significantly increased the possibility of obtaining DNA profiles from highly degraded skeletal remains. Therefore, 21 skeletal remains of Korean War victims and 24 samples from biological relatives of the supposed victims were selected based on circumstantial evidence and/or mtDNA-matching results and were analyzed to confirm the alleged relationship. Cumulative likelihood ratios were obtained from autosomal short tandem repeat, Y-chromosomal STR, and mtDNA-genotyping results, and mainly confirmed the alleged relationship with values over 10⁵. The present analysis emphasizes the value of mini- and Y-STR systems as well as an efficient DNA extraction method in DNA testing for the identification of old skeletal remains. © 2010 American Academy of Forensic Sciences.

Comprehensive GMO detection using real-time PCR array: single-laboratory validation.

PubMed

Mano, Junichi; Harada, Mioko; Takabatake, Reona; Furui, Satoshi; Kitta, Kazumi; Nakamura, Kosuke; Akiyama, Hiroshi; Teshima, Reiko; Noritake, Hiromichi; Hatano, Shuko; Futo, Satoshi; Minegishi, Yasutaka; Iizuka, Tayoshi

2012-01-01

We have developed a real-time PCR array method to comprehensively detect genetically modified (GM) organisms. In the method, genomic DNA extracted from an agricultural product is analyzed using various qualitative real-time PCR assays on a 96-well PCR plate, targeting for individual GM events, recombinant DNA (r-DNA) segments, taxon-specific DNAs, and donor organisms of the respective r-DNAs. In this article, we report the single-laboratory validation of both DNA extraction methods and component PCR assays constituting the real-time PCR array. We selected some DNA extraction methods for specified plant matrixes, i.e., maize flour, soybean flour, and ground canola seeds, then evaluated the DNA quantity, DNA fragmentation, and PCR inhibition of the resultant DNA extracts. For the component PCR assays, we evaluated the specificity and LOD. All DNA extraction methods and component PCR assays satisfied the criteria set on the basis of previous reports.

Functional Role of Extranucleosomal DNA and the Entry Site of the Nucleosome in Chromatin Remodeling by ISW2

PubMed Central

Zofall, Martin; Persinger, Jim; Bartholomew, Blaine

2004-01-01

A minimal amount of extranucleosomal DNA was required for nucleosome mobilization by ISW2 as shown by using a photochemical histone mapping approach to analyze nucleosome movement on a set of nucleosomes with varied lengths of extranucleosomal DNA. ISW2 was ineffective in repositioning or mobilizing nucleosomes with ≤20 bp of extranucleosomal DNA. In addition, ISW2 was able to slide nucleosomes to within only 10 to 13 bp of the edge of DNA fragments. The nucleosome mobilization was promoted by extranucleosomal single-stranded DNA with modest strand preference. Gaps (10 bp) just inside the nucleosome and in the extranucleosomal DNA showed that the transfer of torsional strain (twist) into the nucleosomal DNA region was not required for mobilizing nucleosomes. However, indications are that the extranucleosomal DNA immediately adjacent to the nucleosome has an important role in the initial stage of nucleosome movement by ISW2. PMID:15509805

Importance of biometrics to addressing vulnerabilities of the U.S. infrastructure

NASA Astrophysics Data System (ADS)

Arndt, Craig M.; Hall, Nathaniel A.

2004-08-01

Human identification technologies are important threat countermeasures in minimizing select infrastructure vulnerabilities. Properly targeted countermeasures should be selected and integrated into an overall security solution based on disciplined analysis and modeling. Available data on infrastructure value, threat intelligence, and system vulnerabilities are carefully organized, analyzed and modeled. Prior to design and deployment of an effective countermeasure; the proper role and appropriateness of technology in addressing the overall set of vulnerabilities is established. Deployment of biometrics systems, as with other countermeasures, introduces potentially heightened vulnerabilities into the system. Heightened vulnerabilities may arise from both the newly introduced system complexities and an unfocused understanding of the set of vulnerabilities impacted by the new countermeasure. The countermeasure's own inherent vulnerabilities and those introduced by the system's integration with the existing system are analyzed and modeled to determine the overall vulnerability impact. The United States infrastructure is composed of government and private assets. The infrastructure is valued by their potential impact on several components: human physical safety, physical/information replacement/repair cost, potential contribution to future loss (criticality in weapons production), direct productivity output, national macro-economic output/productivity, and information integrity. These components must be considered in determining the overall impact of an infrastructure security breach. Cost/benefit analysis is then incorporated in the security technology deployment decision process. Overall security risks based on system vulnerabilities and threat intelligence determines areas of potential benefit. Biometric countermeasures are often considered when additional security at intended points of entry would minimize vulnerabilities.

Immunogenicity of a DNA-launched replicon-based canine parvovirus DNA vaccine expressing VP2 antigen in dogs.

PubMed

Dahiya, Shyam S; Saini, Mohini; Kumar, Pankaj; Gupta, Praveen K

2012-10-01

A replicon-based DNA vaccine encoding VP2 gene of canine parvovirus (CPV) was developed by cloning CPV-VP2 gene into a replicon-based DNA vaccine vector (pAlpha). The characteristics of a replicon-based DNA vaccine like, self-amplification of transcripts and induction of apoptosis were analyzed in transfected mammalian cells. When the pAlpha-CPV-VP2 was injected intradermal as DNA-launched replicon-based DNA vaccine in dogs, it induced CPV-specific humoral and cell mediated immune responses. The virus neutralization antibody and lymphocyte proliferative responses were higher than conventional CPV DNA vaccine and commercial CPV vaccine. These results indicated that DNA-launched replicon-based CPV DNA vaccine was effective in inducing both CPV-specific humoral and cellular immune responses and can be considered as effective alternative to conventional CPV DNA vaccine and commercial CPV vaccine. Crown Copyright © 2012. Published by Elsevier India Pvt Ltd. All rights reserved.

Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

PubMed Central

Ru, Sushan; Hardner, Craig; Carter, Patrick A; Evans, Kate; Main, Dorrie; Peace, Cameron

2016-01-01

Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. PMID:27148453

Large-scale molecular dynamics simulation of DNA: implementation and validation of the AMBER98 force field in LAMMPS.

PubMed

Grindon, Christina; Harris, Sarah; Evans, Tom; Novik, Keir; Coveney, Peter; Laughton, Charles

2004-07-15

Molecular modelling played a central role in the discovery of the structure of DNA by Watson and Crick. Today, such modelling is done on computers: the more powerful these computers are, the more detailed and extensive can be the study of the dynamics of such biological macromolecules. To fully harness the power of modern massively parallel computers, however, we need to develop and deploy algorithms which can exploit the structure of such hardware. The Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a scalable molecular dynamics code including long-range Coulomb interactions, which has been specifically designed to function efficiently on parallel platforms. Here we describe the implementation of the AMBER98 force field in LAMMPS and its validation for molecular dynamics investigations of DNA structure and flexibility against the benchmark of results obtained with the long-established code AMBER6 (Assisted Model Building with Energy Refinement, version 6). Extended molecular dynamics simulations on the hydrated DNA dodecamer d(CTTTTGCAAAAG)(2), which has previously been the subject of extensive dynamical analysis using AMBER6, show that it is possible to obtain excellent agreement in terms of static, dynamic and thermodynamic parameters between AMBER6 and LAMMPS. In comparison with AMBER6, LAMMPS shows greatly improved scalability in massively parallel environments, opening up the possibility of efficient simulations of order-of-magnitude larger systems and/or for order-of-magnitude greater simulation times.

Filtration recovery of extracellular DNA from environmental water samples

EPA Science Inventory

qPCR methods are able to analyze DNA from microbes within hours of collecting water samples, providing the promptest notification and public awareness possible when unsafe pathogenic levels are reached. Health risk, however, may be overestimated by the presence of extracellular ...

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma.

PubMed

Wrzeszczynski, Kazimierz O; Frank, Mayu O; Koyama, Takahiko; Rhrissorrakrai, Kahn; Robine, Nicolas; Utro, Filippo; Emde, Anne-Katrin; Chen, Bo-Juen; Arora, Kanika; Shah, Minita; Vacic, Vladimir; Norel, Raquel; Bilal, Erhan; Bergmann, Ewa A; Moore Vogel, Julia L; Bruce, Jeffrey N; Lassman, Andrew B; Canoll, Peter; Grommes, Christian; Harvey, Steve; Parida, Laxmi; Michelini, Vanessa V; Zody, Michael C; Jobanputra, Vaidehi; Royyuru, Ajay K; Darnell, Robert B

2017-08-01

To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each. Tumor DNA was analyzed by a commercial targeted panel. In addition, tumor-normal DNA was analyzed by whole-genome sequencing (WGS) and tumor RNA was analyzed by RNA sequencing (RNA-seq). The WGS and RNA-seq data were analyzed by a team of bioinformaticians and cancer oncologists, and separately by IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants and identifying drugs. More variants were identified by WGS/RNA analysis than by targeted panels. WGA completed a comparable analysis in a fraction of the time required by the human analysts. The development of an effective human-machine interface in the analysis of deep cancer genomic datasets may provide potentially clinically actionable calls for individual patients in a more timely and efficient manner than currently possible. NCT02725684.

Effect of cold atmospheric pressure He-plasma jet on DNA change and mutation

NASA Astrophysics Data System (ADS)

Yaopromsiri, C.; Yu, L. D.; Sarapirom, S.; Thopan, P.; Boonyawan, D.

2015-12-01

Cold atmospheric pressure plasma jet (CAPPJ) effect on DNA change was studied for assessment of its safety. The experiment utilized a home-developed CAPPJ using 100% helium to directly treat naked DNA plasmid pGFP (plasmid green fluorescent protein). A traversal electric field was applied to separate the plasma components and both dry and wet sample conditions were adopted to investigate various factor roles in changing DNA. Plasma species were measured by using optical emission spectroscopy. DNA topological form change was analyzed by gel electrophoresis. The plasma jet treated DNA was transferred into bacterial Escherichia coli cells for observing mutation. The results show that the He-CAPPJ could break DNA strands due to actions from charge, radicals and neutrals and potentially cause genetic modification of living cells.

DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta

PubMed Central

Kwon, Seulgi; Park, Da Hye; Kim, Tae Wan; Kang, Deok Gyeong; Yu, Go Eun; Kim, Il-Suk; Park, Hwa Chun; Ha, Jeongim; Kim, Chul Wook

2017-01-01

Increasing litter size is of great interest to the pig industry. DNA methylation is an important epigenetic modification that regulates gene expression, resulting in livestock phenotypes such as disease resistance, milk production, and reproduction. We classified Berkshire pigs into two groups according to litter size and estimated breeding value: smaller (SLG) and larger (LLG) litter size groups. Genome-wide DNA methylation and gene expression were analyzed using placenta genomic DNA and RNA to identify differentially methylated regions (DMRs) and differentially expressed genes (DEGs) associated with litter size. The methylation levels of CpG dinucleotides in different genomic regions were noticeably different between the groups, while global methylation pattern was similar, and excluding intergenic regions they were found the most frequently in gene body regions. Next, we analyzed RNA-Seq data to identify DEGs between the SLG and LLG groups. A total of 1591 DEGs were identified: 567 were downregulated and 1024 were upregulated in LLG compared to SLG. To identify genes that simultaneously exhibited changes in DNA methylation and mRNA expression, we integrated and analyzed the data from bisulfite-Seq and RNA-Seq. Nine DEGs positioned in DMRs were found. The expression of only three of these genes (PRKG2, CLCA4, and PCK1) was verified by RT-qPCR. Furthermore, we observed the same methylation patterns in blood samples as in the placental tissues by PCR-based methylation analysis. Together, these results provide useful data regarding potential epigenetic markers for selecting hyperprolific sows. PMID:28880934

Terahertz Characterization of DNA: Enabling a Novel Approach

DTIC Science & Technology

2015-11-01

DNA in a more reliable and less procedurally complicated manner. The method involves the use of terahertz surface plasmon generated on the surface of...advantages are due to overlapping resonance when the plasmon frequency generated by a foil coincides with that of the biological material. The...interference of the impinging terahertz wave and surface plasmon produces spectral graphs, which can be analyzed to identify and characterize a DNA sample

Quantitative method of measuring cancer cell urokinase and metastatic potential

NASA Technical Reports Server (NTRS)

Morrison, Dennis R. (Inventor)

1993-01-01

The metastatic potential of tumors can be evaluated by the quantitative detection of urokinase and DNA. The cell sample selected for examination is analyzed for the presence of high levels of urokinase and abnormal DNA using analytical flow cytometry and digital image analysis. Other factors such as membrane associated urokinase, increased DNA synthesis rates and certain receptors can be used in the method for detection of potentially invasive tumors.

In vitro characterization of DNA gyrase inhibition by microcin B17 analogs with altered bisheterocyclic sites

PubMed Central

Zamble, Deborah B.; Miller, Deborah A.; Heddle, Jonathan G.; Maxwell, Anthony; Walsh, Christopher T.; Hollfelder, Florian

2001-01-01

Microcin B17 (MccB17) is a 3.1-kDa Escherichia coli antibiotic that contains thiazole and oxazole heterocycles in a peptide backbone. MccB17 inhibits its cellular target, DNA gyrase, by trapping the enzyme in a complex that is covalently bound to double-strand cleaved DNA, in a manner similar to the well-known quinolone drugs. The identification of gyrase as the target of MccB17 provides an opportunity to analyze the relationship between the structure of this unusual antibiotic and its activity. In this report, steady-state parameters are used to describe the induction of the cleavable complex by MccB17 analogs containing modified bisheterocyclic sites. The relative potency of these analogs corresponds to the capacity of the compounds to prevent growth of sensitive cells. In contrast to previously reported experiments, inhibition of DNA gyrase supercoiling activity by wild-type MccB17 also was observed. These results suggest that DNA gyrase is the main intracellular target of MccB17. This study probes the structure-function relationship of a new class of gyrase inhibitors and demonstrates that these techniques could be used to analyze compounds in the search for clinically useful antibiotics that block DNA gyrase. PMID:11427730

Micromechanical study of protein-DNA interactions and chromosomes

NASA Astrophysics Data System (ADS)

Marko, John

I will discuss micromechanics experiments that our group has used to analyze protein-DNA interactions and chromosome organization. In single-DNA experiments we have found that a feature of protein-DNA complexes is that their dissociation rates can depend strikingly on bulk solution concentrations of other proteins and DNA segments; I will describe experiments which demonstrate this effect, which can involve tens-fold changes in off-rates with submicromolar changes in solution concentrations. Second, I will discuss experiments aimed at analyzing large-scale human chromosome structure; we isolate metaphase chromosomes, which in their native form behave as remarkably elastic networks of chromatin. Exposure to DNA-cutting restriction enzymes completely eliminates this elasticity, indicating that there is not a mechanically contiguous protein ''scaffold'' from which the chromosome gains its stability. I will show results of siRNA experiments indicating that depletion of condensin proteins leads to destabilization of chromosome mechanics, indicating condensin's role as the major chromatin ''cross-linker'' in metaphase chromosomes. Finally I will discuss similar experiments on human G1 nuclei, where we use genetic and chemical modifications to separate the contributions of the nuclear lamina and chromatin to the mechanical stiffness of the nucleus as a whole. Supported by the NSF (DMR-1206868, MCB-1022117) and the NIH (GM105847, CA193419).

Phylogenetic Information Content of Copepoda Ribosomal DNA Repeat Units: ITS1 and ITS2 Impact

PubMed Central

Zagoskin, Maxim V.; Lazareva, Valentina I.; Grishanin, Andrey K.; Mukha, Dmitry V.

2014-01-01

The utility of various regions of the ribosomal repeat unit for phylogenetic analysis was examined in 16 species representing four families, nine genera, and two orders of the subclass Copepoda (Crustacea). Fragments approximately 2000 bp in length containing the ribosomal DNA (rDNA) 18S and 28S gene fragments, the 5.8S gene, and the internal transcribed spacer regions I and II (ITS1 and ITS2) were amplified and analyzed. The DAMBE (Data Analysis in Molecular Biology and Evolution) software was used to analyze the saturation of nucleotide substitutions; this test revealed the suitability of both the 28S gene fragment and the ITS1/ITS2 rDNA regions for the reconstruction of phylogenetic trees. Distance (minimum evolution) and probabilistic (maximum likelihood, Bayesian) analyses of the data revealed that the 28S rDNA and the ITS1 and ITS2 regions are informative markers for inferring phylogenetic relationships among families of copepods and within the Cyclopidae family and associated genera. Split-graph analysis of concatenated ITS1/ITS2 rDNA regions of cyclopoid copepods suggested that the Mesocyclops, Thermocyclops, and Macrocyclops genera share complex evolutionary relationships. This study revealed that the ITS1 and ITS2 regions potentially represent different phylogenetic signals. PMID:25215300

[DNA prints instead of plantar prints in neonatal identification].

PubMed

Rodríguez-Alarcón Gómez, J; Martińez de Pancorbo Gómez, M; Santillana Ferrer, L; Castro Espido, A; Melchor Maros, J C; Linares Uribe, M A; Fernández-Llebrez del Rey, L; Aranguren Dúo, G

1996-06-22

To check the possible usefulness in studying DNA in dried blood spots taken on filter paper blotters for newborn identification. It set out to establish: 1. The validity of the method for analysis; 2. The validity of all stored samples (such as those kept in clinical records); 3. Guarantee of non-intrusion in the genetic code; 4. Acceptable price and execution time. Forty (40) anonymous 13-year-old samples of 20 subjects (2 per subject) were studied. DNA was extracted using Chelex resin and the STR ("small tandem repeat") of microsatellite DNA was studies using the "polimerase chain reaction method" (PCR). Three non coding DNA loci (CSF1PO, TPOX and THO1) were analyzed by Multiplex amplification. It was possible to type 39 samples, making it possible to match the 20 cases (one by exclusion). The complete procedure yielded the results within 24 hours in all cases. The estimated final cost was found to be a fifth of that conventional maternity/paternity tests. The study carried out made matching possible in all 20 cases (directly in 19 cases). It was not necessary to study DNA coding areas. The validity of the method for analyzing samples stored for 13 years without any special care was also demonstrated. The technic was fast, producing the results within 24 hours, and at reasonable cost.

Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome

PubMed Central

Kuznetsova, Inna S.; Thevasagayam, Natascha M.; Sridatta, Prakki S. R.; Komissarov, Aleksey S.; Saju, Jolly M.; Ngoh, Si Y.; Jiang, Junhui; Shen, Xueyan; Orbán, László

2014-01-01

As part of our Asian seabass genome project, we are generating an inventory of repeat elements in the genome and transcriptome. The karyotype showed a diploid number of 2n = 24 chromosomes with a variable number of B-chromosomes. The transcriptome and genome of Asian seabass were searched for repetitive elements with experimental and bioinformatics tools. Six different types of repeats constituting 8–14% of the genome were characterized. Repetitive elements were clustered in the pericentromeric heterochromatin of all chromosomes, but some of them were preferentially accumulated in pretelomeric and pericentromeric regions of several chromosomes pairs and have chromosomes specific arrangement. From the dispersed class of fish-specific non-LTR retrotransposon elements Rex1 and MAUI-like repeats were analyzed. They were wide-spread both in the genome and transcriptome, accumulated on the pericentromeric and peritelomeric areas of all chromosomes. Every analyzed repeat was represented in the Asian seabass transcriptome, some showed differential expression between the gonads. The other group of repeats analyzed belongs to the rRNA multigene family. FISH signal for 5S rDNA was located on a single pair of chromosomes, whereas that for 18S rDNA was found on two pairs. A BAC-derived contig containing rDNA was sequenced and assembled into a scaffold containing incomplete fragments of 18S rDNA. Their assembly and chromosomal position revealed that this part of Asian seabass genome is extremely rich in repeats containing evolutionarily conserved and novel sequences. In summary, transcriptome assemblies and cDNA data are suitable for the identification of repetitive DNA from unknown genomes and for comparative investigation of conserved elements between teleosts and other vertebrates. PMID:25120555

Recent progress on DNA based walkers.

PubMed

Pan, Jing; Li, Feiran; Cha, Tae-Gon; Chen, Haorong; Choi, Jong Hyun

2015-08-01

DNA based synthetic molecular walkers are reminiscent of biological protein motors. They are powered by hybridization with fuel strands, environment induced conformational transitions, and covalent chemistry of oligonucleotides. Recent developments in experimental techniques enable direct observation of individual walkers with high temporal and spatial resolution. The functionalities of state-of-the-art DNA walker systems can thus be analyzed for various applications. Herein we review recent progress on DNA walker principles and characterization methods, and evaluate various aspects of their functions for future applications. Copyright © 2014 Elsevier Ltd. All rights reserved.

Human papillomavirus hpv-16 DNA as an epitheliotropic virus that induces hyperproliferation in squamous penile tissue.

PubMed

Salazar, Edith L; Mercado, E; Calzada, L

2005-01-01

The prevalence of human papillomavirus HPV-16DNA sequences in 57 penile carcinoma biopsies was examined using the polymerase chain reaction (PCR) with type specific internal probes, employing HPV consensus primers from the L1 region. The cases comprised 39 typical squamous cell carcinoma and 18 specimens with different subtype. PCR products were analyzed and HPV-16DNA was detected in a high percentage of specimens. Thirty-eight biopsies were HPV-16DNA positive. This determination was correlated with cellular differentiation and growth pattern. Our data corroborates that squamous cell carcinoma was invariably associated with HPV-16DNA.

Hiding message into DNA sequence through DNA coding and chaotic maps.

PubMed

Liu, Guoyan; Liu, Hongjun; Kadir, Abdurahman

2014-09-01

The paper proposes an improved reversible substitution method to hide data into deoxyribonucleic acid (DNA) sequence, and four measures have been taken to enhance the robustness and enlarge the hiding capacity, such as encode the secret message by DNA coding, encrypt it by pseudo-random sequence, generate the relative hiding locations by piecewise linear chaotic map, and embed the encoded and encrypted message into a randomly selected DNA sequence using the complementary rule. The key space and the hiding capacity are analyzed. Experimental results indicate that the proposed method has a better performance compared with the competing methods with respect to robustness and capacity.

Label-free monitoring of interaction between DNA and oxaliplatin in aqueous solution by terahertz spectroscopy

NASA Astrophysics Data System (ADS)

Wu, Xiaojun; E, Yiwen; Xu, Xinlong; Wang, Li

2012-07-01

We demonstrated the feasibility of applying terahertz time-domain spectroscopy (THz-TDS) to monitor the molecular reactions in aqueous solutions of anticancer drug oxaliplatin with λ-DNA and macrophages DNA. The reaction time dependent refractive index and absorption coefficient were extracted and analyzed. The reaction half-decaying time of about 4.0 h for λ-DNA and 12.9 h for M-DNA was established. The results suggest that the THz-TDS detection could be an effective label-free technique to sense the molecular reaction in aqueous solutions and could be very useful in biology, medicine, and pharmacy industry.

Sensitive Detection of Xanthomonas oryzae Pathovars oryzae and oryzicola by Loop-Mediated Isothermal Amplification

PubMed Central

Lang, Jillian M.; Langlois, Paul; Nguyen, Marian Hanna R.; Triplett, Lindsay R.; Purdie, Laura; Holton, Timothy A.; Djikeng, Appolinaire; Vera Cruz, Casiana M.; Verdier, Valérie

2014-01-01

Molecular diagnostics for crop diseases can enhance food security by enabling the rapid identification of threatening pathogens and providing critical information for the deployment of disease management strategies. Loop-mediated isothermal amplification (LAMP) is a PCR-based tool that allows the rapid, highly specific amplification of target DNA sequences at a single temperature and is thus ideal for field-level diagnosis of plant diseases. We developed primers highly specific for two globally important rice pathogens, Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB) disease, and X. oryzae pv. oryzicola, the causal agent of bacterial leaf streak disease (BLS), for use in reliable, sensitive LAMP assays. In addition to pathovar distinction, two assays that differentiate X. oryzae pv. oryzae by African or Asian lineage were developed. Using these LAMP primer sets, the presence of each pathogen was detected from DNA and bacterial cells, as well as leaf and seed samples. Thresholds of detection for all assays were consistently 104 to 105 CFU ml−1, while genomic DNA thresholds were between 1 pg and 10 fg. Use of the unique sequences combined with the LAMP assay provides a sensitive, accurate, rapid, simple, and inexpensive protocol to detect both BB and BLS pathogens. PMID:24837384

Optimization of multiplexed PCR on an integrated microfluidic forensic platform for rapid DNA analysis.

PubMed

Estes, Matthew D; Yang, Jianing; Duane, Brett; Smith, Stan; Brooks, Carla; Nordquist, Alan; Zenhausern, Frederic

2012-12-07

This study reports the design, prototyping, and assay development of multiplexed polymerase chain reaction (PCR) on a plastic microfluidic device. Amplification of 17 DNA loci is carried out directly on-chip as part of a system for continuous workflow processing from sample preparation (SP) to capillary electrophoresis (CE). For enhanced performance of on-chip PCR amplification, improved control systems have been developed making use of customized Peltier assemblies, valve actuators, software, and amplification chemistry protocols. Multiple enhancements to the microfluidic chip design have been enacted to improve the reliability of sample delivery through the various on-chip modules. This work has been enabled by the encapsulation of PCR reagents into a solid phase material through an optimized Solid Phase Encapsulating Assay Mix (SPEAM) bead-based hydrogel fabrication process. SPEAM bead technology is reliably coupled with precise microfluidic metering and dispensing for efficient amplification and subsequent DNA short tandem repeat (STR) fragment analysis. This provides a means of on-chip reagent storage suitable for microfluidic automation, with the long shelf-life necessary for point-of-care (POC) or field deployable applications. This paper reports the first high quality 17-plex forensic STR amplification from a reference sample in a microfluidic chip with preloaded solid phase reagents, that is designed for integration with up and downstream processing.

New Fpg probe chemistry for direct detection of recombinase polymerase amplification on lateral flow strips.

PubMed

Powell, Michael L; Bowler, Frank R; Martinez, Aurore J; Greenwood, Catherine J; Armes, Niall; Piepenburg, Olaf

2018-02-15

Rapid, cost-effective and sensitive detection of nucleic acids has the ability to improve upon current practices employed for pathogen detection in diagnosis of infectious disease and food testing. Furthermore, if assay complexity can be reduced, nucleic acid amplification tests could be deployed in resource-limited and home use scenarios. In this study, we developed a novel Fpg (Formamidopyrimidine DNA glycosylase) probe chemistry, which allows lateral flow detection of amplification in undiluted recombinase polymerase amplification (RPA) reactions. The prototype nucleic acid lateral flow chemistry was applied to a human genomic target (rs1207445), Campylobacter jejuni 16S rDNA and two genetic markers of the important food pathogen E. coli O157:H7. All four assays have an analytical sensitivity between 10 and 100 copies DNA per amplification. Furthermore, the assay is performed with fewer hands-on steps than using the current RPA Nfo lateral flow method as dilution of amplicon is not required for lateral flow analysis. Due to the simplicity of the workflow, we believe that the lateral flow chemistry for direct detection could be readily adapted to a cost-effective single-use consumable, ideal for use in non-laboratory settings. Copyright © 2017. Published by Elsevier Inc.

Development and Deployment of Mobile Emissions Laboratory for Continuous Long-Term Unattended Measurements of Greenhouse Gases, Fluxes, Isotopes and Pollutants

NASA Astrophysics Data System (ADS)

Gardner, A.; Baer, D. S.; Owano, T. G.; Provencal, R. A.; Gupta, M.; Parsotam, V.; Graves, P.; Goldstein, A.; Guha, A.

2010-12-01

Development and Deployment of Mobile Emissions Laboratory for Continuous Long-Term Unattended Measurements of Greenhouse Gases, Fluxes, Isotopes and Pollutants A. Gardner(1), D. Baer (1), T. Owano (1), R. Provencal (1), V. Parsotam (1), P. Graves (1), M. Gupta (1), Allen Goldstein (2), Abhinav Guha (2) (1) Los Gatos Research, 67 East Evelyn Avenue, Suite 3, Mountain View, CA 94041-1529 (2) Department of Environmental Science, Policy, and Management, University of California at Berkeley Quantifying the Urban Fossil Fuel Plume: Convergence of top-down and bottom-up approaches (Session A54). We report on the design, development and deployment of a novel Mobile Emissions Laboratory, consisting of innovative laser-based gas analyzers, for rapid measurements of multiple greenhouse gases and pollutants. Designed for real-time mobile and stationery emissions monitoring, the Mobile Emissions Laboratory was deployed at several locations during 2010, including CalNEX 2010, Caldecott Tunnel (Oakland, CA), and Altamont Landfill (Livermore, CA), to record real-time continuous measurements of isotopic CO2 (δ13C, CO2), methane (CH4), acetylene (C2H2), nitrous oxide (N2O), carbon monoxide (CO), and isotopic water vapor (H2O; δ18O, δ2H). The commercial gas analyzers are based on novel cavity-enhanced laser absorption spectroscopy. The portable analyzers provide measurements in real time, require about 150 watts (each) of power and do not need liquid nitrogen to operate. These instruments have been applied in the field for applications that require high data rates (for eddy correlation flux), wide dynamic range (e.g., for chamber flux and other applications with concentrations that can be 10-1000 times higher than typical ambient levels) and highest accuracy (atmospheric monitoring stations). The Mobile Emissions Laboratory, which contains onboard batteries for long-term unattended measurements without access to mains power, can provide regulatory agencies, monitoring stations, scientists and researchers with temporally and spatially resolved data (including measurements of important greenhouse gases, isotopes and pollutants) necessary for compliance monitoring, hot-spot detection, as well as cap and trade, at any location. Details of extended measurement campaigns (including lessons learned) at the various field sites (urban and rural environments) will be presented.

A DNA Vaccine That Targets Hemagglutinin to Antigen-Presenting Cells Protects Mice against H7 Influenza

PubMed Central

Andersen, Tor Kristian; Zhou, Fan; Cox, Rebecca; Bogen, Bjarne

2017-01-01

ABSTRACT Zoonotic influenza H7 viral infections have a case fatality rate of about 40%. Currently, no or limited human to human spread has occurred, but we may be facing a severe pandemic threat if the virus acquires the ability to transmit between humans. Novel vaccines that can be rapidly produced for global distribution are urgently needed, and DNA vaccines may be the only type of vaccine that allows for the speed necessary to quench an emerging pandemic. Here, we constructed DNA vaccines encoding the hemagglutinin (HA) from influenza A/chicken/Italy/13474/99 (H7N1). In order to increase the efficacy of DNA vaccination, HA was targeted to either major histocompatibility complex class II molecules or chemokine receptors 1, 3, and 5 (CCR1/3/5) that are expressed on antigen-presenting cells (APC). A single DNA vaccination with APC-targeted HA significantly increased antibody levels in sera compared to nontargeted control vaccines. The antibodies were confirmed neutralizing in an H7 pseudotype-based neutralization assay. Furthermore, the APC-targeted vaccines increased the levels of antigen-specific cytotoxic T cells, and a single DNA vaccination could confer protection against a lethal challenge with influenza A/turkey/Italy/3889/1999 (H7N1) in mice. In conclusion, we have developed a vaccine that rapidly could contribute protection against a pandemic threat from avian influenza. IMPORTANCE Highly pathogenic avian influenza H7 constitute a pandemic threat that can cause severe illness and death in infected individuals. Vaccination is the main method of prophylaxis against influenza, but current vaccine strategies fall short in a pandemic situation due to a prolonged production time and insufficient production capabilities. In contrast, a DNA vaccine can be rapidly produced and deployed to prevent the potential escalation of a highly pathogenic influenza pandemic. We here demonstrate that a single DNA delivery of hemagglutinin from an H7 influenza could mediate full protection against a lethal challenge with H7N1 influenza in mice. Vaccine efficacy was contingent on targeting of the secreted vaccine protein to antigen-presenting cells. PMID:28931687

Comprehensive definition of genome features in Spirodela polyrhiza by high-depth physical mapping and short-read DNA sequencing strategies.

PubMed

Michael, Todd P; Bryant, Douglas; Gutierrez, Ryan; Borisjuk, Nikolai; Chu, Philomena; Zhang, Hanzhong; Xia, Jing; Zhou, Junfei; Peng, Hai; El Baidouri, Moaine; Ten Hallers, Boudewijn; Hastie, Alex R; Liang, Tiffany; Acosta, Kenneth; Gilbert, Sarah; McEntee, Connor; Jackson, Scott A; Mockler, Todd C; Zhang, Weixiong; Lam, Eric

2017-02-01

Spirodela polyrhiza is a fast-growing aquatic monocot with highly reduced morphology, genome size and number of protein-coding genes. Considering these biological features of Spirodela and its basal position in the monocot lineage, understanding its genome architecture could shed light on plant adaptation and genome evolution. Like many draft genomes, however, the 158-Mb Spirodela genome sequence has not been resolved to chromosomes, and important genome characteristics have not been defined. Here we deployed rapid genome-wide physical maps combined with high-coverage short-read sequencing to resolve the 20 chromosomes of Spirodela and to empirically delineate its genome features. Our data revealed a dramatic reduction in the number of the rDNA repeat units in Spirodela to fewer than 100, which is even fewer than that reported for yeast. Consistent with its unique phylogenetic position, small RNA sequencing revealed 29 Spirodela-specific microRNA, with only two being shared with Elaeis guineensis (oil palm) and Musa balbisiana (banana). Combining DNA methylation data and small RNA sequencing enabled the accurate prediction of 20.5% long terminal repeats (LTRs) that doubled the previous estimate, and revealed a high Solo:Intact LTR ratio of 8.2. Interestingly, we found that Spirodela has the lowest global DNA methylation levels (9%) of any plant species tested. Taken together our results reveal a genome that has undergone reduction, likely through eliminating non-essential protein coding genes, rDNA and LTRs. In addition to delineating the genome features of this unique plant, the methodologies described and large-scale genome resources from this work will enable future evolutionary and functional studies of this basal monocot family. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

DNA amount of X and B chromosomes in the grasshoppers Eyprepocnemis plorans and Locusta migratoria.

PubMed

Ruiz-Ruano, F J; Ruiz-Estévez, M; Rodríguez-Pérez, J; López-Pino, J L; Cabrero, J; Camacho, J P M

2011-01-01

We analyzed the DNA amount in X and B chromosomes of 2 XX/X0 grasshopper species (Eyprepocnemis plorans and Locusta migratoria), by means of Feulgen image analysis densitometry (FIAD), using previous estimates in L. migratoria as standard (5.89 pg). We first analyzed spermatids of 0B males and found a bimodal distribution of integrated optical densities (IODs), suggesting that one peak corresponded to +X and the other to -X spermatids. The difference between the 2 peaks corresponded to the X chromosome DNA amount, which was 1.28 pg in E. plorans and 0.80 pg in L. migratoria. In addition, the +X peak in E. plorans gave an estimate of the C-value in this species (10.39 pg). We next analyzed diplotene cells from 1B males in E. plorans and +B males in L. migratoria (a species where Bs are mitotically unstable and no integer B number can be defined for an individual) and measured B chromosome IOD relative to X chromosome IOD, within the same cell, taking advantage of the similar degree of condensation for both positively heteropycnotic chromosomes at this meiotic stage. From this proportion, we estimated the DNA amount for 3 different B chromosome variants found in individuals from 3 E. plorans Spanish populations (0.54 pg for B1 from Saladares, 0.51 pg for B2 from Salobreña and 0.64 for B24 from Torrox). Likewise, we estimated the DNA amount of the B chromosome in L. migratoria to be 0.15 pg. To automate measurements, we wrote a GPL3 licensed Python program (pyFIA). We discuss the utility of the present approach for estimating X and B chromosome DNA amount in a variety of situations, and the meaning of the DNA amount estimates for X and B chromosomes in these 2 species. Copyright © 2011 S. Karger AG, Basel.

Stochastic properties of radiation-induced DSB: DSB distributions in large scale chromatin loops, the HPRT gene and within the visible volumes of DNA repair foci.

PubMed

Ponomarev, Artem L; Costes, Sylvain V; Cucinotta, Francis A

2008-11-01

We computed probabilities to have multiple double-strand breaks (DSB), which are produced in DNA on a regional scale, and not in close vicinity, in volumes matching the size of DNA damage foci, of a large chromatin loop, and in the physical volume of DNA containing the HPRT (human hypoxanthine phosphoribosyltransferase) locus. The model is based on a Monte Carlo description of DSB formation by heavy ions in the spatial context of the entire human genome contained within the cell nucleus, as well as at the gene sequence level. We showed that a finite physical volume corresponding to a visible DNA repair focus, believed to be associated with one DSB, can contain multiple DSB due to heavy ion track structure and the DNA supercoiled topography. A corrective distribution was introduced, which was a conditional probability to have excess DSB in a focus volume, given that there was already one present. The corrective distribution was calculated for 19.5 MeV/amu N ions, 3.77 MeV/amu alpha-particles, 1000 MeV/amu Fe ions, and X-rays. The corrected initial DSB yield from the experimental data on DNA repair foci was calculated. The DSB yield based on the corrective function converts the focus yield into the DSB yield, which is comparable with the DSB yield based on the earlier PFGE experiments. The distribution of DSB within the physical limits of the HPRT gene was analyzed by a similar method as well. This corrective procedure shows the applicability of the model and empowers the researcher with a tool to better analyze focus statistics. The model enables researchers to analyze the DSB yield based on focus statistics in real experimental situations that lack one-to-one focus-to-DSB correspondance.

Sequencing cDNAs: An Introduction to DNA Sequence Analysis in the Undergraduate Molecular Genetics Course.

ERIC Educational Resources Information Center

Galewsky, Samuel

2000-01-01

Introduces a series of molecular genetics laboratories where students pick a single colony from a Drosophila melanogester embryo cDNA library and purify the plasmid, then analyze the insert through restriction digests and gel electrophoresis. (Author/YDS)

Radiation breakage of DNA: a model based on random-walk chromatin structure

NASA Technical Reports Server (NTRS)

Ponomarev, A. L.; Sachs, R. K.

2001-01-01

Monte Carlo computer software, called DNAbreak, has recently been developed to analyze observed non-random clustering of DNA double strand breaks in chromatin after exposure to densely ionizing radiation. The software models coarse-grained configurations of chromatin and radiation tracks, small-scale details being suppressed in order to obtain statistical results for larger scales, up to the size of a whole chromosome. We here give an analytic counterpart of the numerical model, useful for benchmarks, for elucidating the numerical results, for analyzing the assumptions of a more general but less mechanistic "randomly-located-clusters" formalism, and, potentially, for speeding up the calculations. The equations characterize multi-track DNA fragment-size distributions in terms of one-track action; an important step in extrapolating high-dose laboratory results to the much lower doses of main interest in environmental or occupational risk estimation. The approach can utilize the experimental information on DNA fragment-size distributions to draw inferences about large-scale chromatin geometry during cell-cycle interphase.

The Carpathian range represents a weak genetic barrier in South-East Europe

PubMed Central

2014-01-01

Background In the present study we have assessed whether the Carpathian Mountains represent a genetic barrier in East Europe. Therefore, we have analyzed the mtDNA of 128 native individuals of Romania: 62 of them from the North of Romania, and 66 from South Romania. Results We have analyzed their mtDNA variability in the context of other European and Near Eastern populations through multivariate analyses. The results show that regarding the mtDNA haplogroup and haplotype distributions the Romanian groups living outside the Carpathian range (South Romania) displayed some degree of genetic differentiation compared to those living within the Carpahian range (North Romania). Conclusion The main differentiation between the mtDNA variability of the groups from North and South Romania can be attributed to the demographic movements from East to West (prehistoric or historic) that differently affected in these regions, suggesting that the Carpathian mountain range represents a weak genetic barrier in South-East Europe. PMID:24885208

Efficient generation of transgenic cattle using the DNA transposon and their analysis by next-generation sequencing

PubMed Central

Yum, Soo-Young; Lee, Song-Jeon; Kim, Hyun-Min; Choi, Woo-Jae; Park, Ji-Hyun; Lee, Won-Wu; Kim, Hee-Soo; Kim, Hyeong-Jong; Bae, Seong-Hun; Lee, Je-Hyeong; Moon, Joo-Yeong; Lee, Ji-Hyun; Lee, Choong-Il; Son, Bong-Jun; Song, Sang-Hoon; Ji, Su-Min; Kim, Seong-Jin; Jang, Goo

2016-01-01

Here, we efficiently generated transgenic cattle using two transposon systems (Sleeping Beauty and Piggybac) and their genomes were analyzed by next-generation sequencing (NGS). Blastocysts derived from microinjection of DNA transposons were selected and transferred into recipient cows. Nine transgenic cattle have been generated and grown-up to date without any health issues except two. Some of them expressed strong fluorescence and the transgene in the oocytes from a superovulating one were detected by PCR and sequencing. To investigate genomic variants by the transgene transposition, whole genomic DNA were analyzed by NGS. We found that preferred transposable integration (TA or TTAA) was identified in their genome. Even though multi-copies (i.e. fifteen) were confirmed, there was no significant difference in genome instabilities. In conclusion, we demonstrated that transgenic cattle using the DNA transposon system could be efficiently generated, and all those animals could be a valuable resource for agriculture and veterinary science. PMID:27324781

Real-Time Analysis of Specific Protein-DNA Interactions with Surface Plasmon Resonance

PubMed Central

Ritzefeld, Markus; Sewald, Norbert

2012-01-01

Several proteins, like transcription factors, bind to certain DNA sequences, thereby regulating biochemical pathways that determine the fate of the corresponding cell. Due to these key positions, it is indispensable to analyze protein-DNA interactions and to identify their mode of action. Surface plasmon resonance is a label-free method that facilitates the elucidation of real-time kinetics of biomolecular interactions. In this article, we focus on this biosensor-based method and provide a detailed guide how SPR can be utilized to study binding of proteins to oligonucleotides. After a description of the physical phenomenon and the instrumental realization including fiber-optic-based SPR and SPR imaging, we will continue with a survey of immobilization methods. Subsequently, we will focus on the optimization of the experiment, expose pitfalls, and introduce how data should be analyzed and published. Finally, we summarize several interesting publications of the last decades dealing with protein-DNA and RNA interaction analysis by SPR. PMID:22500214

Identification of forensic samples by using an infrared-based automatic DNA sequencer.

PubMed

Ricci, Ugo; Sani, Ilaria; Klintschar, Michael; Cerri, Nicoletta; De Ferrari, Francesco; Giovannucci Uzielli, Maria Luisa

2003-06-01

We have recently introduced a new protocol for analyzing all core loci of the Federal Bureau of Investigation's (FBI) Combined DNA Index System (CODIS) with an infrared (IR) automatic DNA sequencer (LI-COR 4200). The amplicons were labeled with forward oligonucleotide primers, covalently linked to a new infrared fluorescent molecule (IRDye 800). The alleles were displayed as familiar autoradiogram-like images with real-time detection. This protocol was employed for paternity testing, population studies, and identification of degraded forensic samples. We extensively analyzed some simulated forensic samples and mixed stains (blood, semen, saliva, bones, and fixed archival embedded tissues), comparing the results with donor samples. Sensitivity studies were also performed for the four multiplex systems. Our results show the efficiency, reliability, and accuracy of the IR system for the analysis of forensic samples. We also compared the efficiency of the multiplex protocol with ultraviolet (UV) technology. Paternity tests, undegraded DNA samples, and real forensic samples were analyzed with this approach based on IR technology and with UV-based automatic sequencers in combination with commercially-available kits. The comparability of the results with the widespread UV methods suggests that it is possible to exchange data between laboratories using the same core group of markers but different primer sets and detection methods.

Flow cytometry reliability analysis and variations in sugarcane DNA content.

PubMed

Oliveira, A C L; Pasqual, M; Bruzi, A T; Pio, L A S; Mendonça, P M S; Soares, J D R

2015-06-29

The aim of this study was to evaluate the reliability of flow cytometry analysis and the use of this technique to differentiate species and varieties of sugarcane (Saccharum spp) according to their relative DNA content. We analyzed 16 varieties and three species belonging to this genus. To determine a reliable protocol, we evaluated three extraction buffers (LB01, Marie, and Tris·MgCl2), the presence and absence of RNase, six doses of propidium iodide (10, 15, 20, 25, and 30 μg), four periods of exposure to propidium iodide (0, 5, 10, and 20 min), and seven external reference standards (peas, beans, corn, radish, rye, soybean, and tomato) with reference to the coefficient of variation and the DNA content. For statistical analyses, we used the programs Sisvar(®) and Xlstat(®). We recommend using the Marie extraction buffer and at least 15 μg propidium iodide. The samples should not be analyzed immediately after the addition of propidium iodide. The use of RNase is optional, and tomato should be used as an external reference standard. The results show that sugarcane has a variable genome size (8.42 to 12.12 pg/2C) and the individuals analyzed could be separated into four groups according to their DNA content with relative equality in the genome sizes of the commercial varieties.

Transgene and immune gene expression following intramuscular injection of Atlantic salmon (Salmo salar L.) with DNA-releasing PLGA nano- and microparticles.

PubMed

Hølvold, Linn Benjaminsen; Fredriksen, Børge N; Bøgwald, Jarl; Dalmo, Roy A

2013-09-01

The use of poly-(D,L-lactic-co-glycolic) acid (PLGA) particles as carriers for DNA delivery has received considerable attention in mammalian studies. DNA vaccination of fish has been shown to elicit durable transgene expression, but no reports exist on intramuscular administration of PLGA-encapsulated plasmid DNA (pDNA). We injected Atlantic salmon (Salmo salar L.) intramuscularly with a plasmid vector containing a luciferase (Photinus pyralis) reporter gene as a) naked pDNA, b) encapsulated into PLGA nano- (~320 nm) (NP) or microparticles (~4 μm) (MP), c) in an oil-based formulation, or with empty particles of both sizes. The ability of the different pDNA-treatments to induce transgene expression was analyzed through a 70-day experimental period. Anatomical distribution patterns and depot effects were determined by tracking isotope labeled pDNA. Muscle, head kidney and spleen from all treatment groups were analyzed for proinflammatory cytokines (TNF-α, IL-1β), antiviral genes (IFN-α, Mx) and cytotoxic T-cell markers (CD8, Eomes) at mRNA transcription levels at days 1, 2, 4 and 7. Histopathological examinations were performed on injection site samples from days 2, 7 and 30. Injection of either naked pDNA or the oil-formulation was superior to particle treatments for inducing transgene expression at early time-points. Empty particles of both sizes were able to induce proinflammatory immune responses as well as degenerative and inflammatory pathology at the injection site. Microparticles demonstrated injection site depots and an inflammatory pathology comparable to the oil-based formulation. In comparison, the distribution of NP-encapsulated pDNA resembled that of naked pDNA, although encapsulation into NPs significantly elevated the expression of antiviral genes in all tissues. Together the results indicate that while naked pDNA is most efficient for inducing transgene expression, the encapsulation of pDNA into NPs up-regulates antiviral responses that could be of benefit to DNA vaccination. Copyright © 2013 Elsevier Ltd. All rights reserved.

[Biomarkers of radiation-induced DNA repair processes].

PubMed

Vallard, Alexis; Rancoule, Chloé; Guy, Jean-Baptiste; Espenel, Sophie; Sauvaigo, Sylvie; Rodriguez-Lafrasse, Claire; Magné, Nicolas

2017-11-01

The identification of DNA repair biomarkers is of paramount importance. Indeed, it is the first step in the process of modulating radiosensitivity and radioresistance. Unlike tools of detection and measurement of DNA damage, DNA repair biomarkers highlight the variations of DNA damage responses, depending on the dose and the dose rate. The aim of the present review is to describe the main biomarkers of radiation-induced DNA repair. We will focus on double strand breaks (DSB), because of their major role in radiation-induced cell death. The most important DNA repair biomarkers are DNA damage signaling proteins, with ATM, DNA-PKcs, 53BP1 and γ-H2AX. They can be analyzed either using immunostaining, or using lived cell imaging. However, to date, these techniques are still time and money consuming. The development of "omics" technologies should lead the way to new (and usable in daily routine) DNA repair biomarkers. Copyright © 2017 Société Française du Cancer. Published by Elsevier Masson SAS. All rights reserved.

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures

PubMed Central

2010-01-01

Background An important focus of genomic science is the discovery and characterization of all functional elements within genomes. In silico methods are used in genome studies to discover putative regulatory genomic elements (called words or motifs). Although a number of methods have been developed for motif discovery, most of them lack the scalability needed to analyze large genomic data sets. Methods This manuscript presents WordSeeker, an enumerative motif discovery toolkit that utilizes multi-core and distributed computational platforms to enable scalable analysis of genomic data. A controller task coordinates activities of worker nodes, each of which (1) enumerates a subset of the DNA word space and (2) scores words with a distributed Markov chain model. Results A comprehensive suite of performance tests was conducted to demonstrate the performance, speedup and efficiency of WordSeeker. The scalability of the toolkit enabled the analysis of the entire genome of Arabidopsis thaliana; the results of the analysis were integrated into The Arabidopsis Gene Regulatory Information Server (AGRIS). A public version of WordSeeker was deployed on the Glenn cluster at the Ohio Supercomputer Center. Conclusion WordSeeker effectively utilizes concurrent computing platforms to enable the identification of putative functional elements in genomic data sets. This capability facilitates the analysis of the large quantity of sequenced genomic data. PMID:21210985

Patent data mining: a tool for accelerating HIV vaccine innovation.

PubMed

Clark, K; Cavicchi, J; Jensen, K; Fitzgerald, R; Bennett, A; Kowalski, S P

2011-05-31

Global access to advanced vaccine technologies is challenged by the interrelated components of intellectual property (IP) management strategies, technology transfer (legal and technical) capabilities and the capacity necessary for accelerating R&D, commercialization and delivery of vaccines. Due to a negative association with the management of IP, patents are often overlooked as a vast resource of freely available, information akin to scientific journals as well as business and technological information and trends fundamental for formulating policies and IP management strategies. Therefore, a fundamental step towards facilitating global vaccine access will be the assembly, organization and analysis of patent landscapes, to identify the amount of patenting, ownership (assignees) and fields of technology covered. This is critical for making informed decisions (e.g., identifying licensees, building research and product development collaborations, and ascertaining freedom to operate). Such information is of particular interest to the HIV vaccine community where the HIV Vaccine Enterprise, have voiced concern that IP rights (particularly patents and trade secrets) may prevent data and materials sharing, delaying progress in research and development of a HIV vaccine. We have compiled and analyzed a representative HIV vaccine patent landscape for a prime-boost, DNA/adenoviral vaccine platform, as an example for identifying obstacles, maximizing opportunities and making informed IP management strategy decisions towards the development and deployment of an efficacious HIV vaccine. Copyright © 2011 Elsevier Ltd. All rights reserved.

Image Analysis of DNA Fiber and Nucleus in Plants.

PubMed

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

2016-01-01

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

DNA Nanocarriers for Systemic Administration: Characterization and In Vivo Bioimaging in Healthy Mice

PubMed Central

David, Stephanie; Passirani, Catherine; Carmoy, Nathalie; Morille, Marie; Mevel, Mathieu; Chatin, Benoit; Benoit, Jean-Pierre; Montier, Tristan; Pitard, Bruno

2013-01-01

We hereby present different DNA nanocarriers consisting of new multimodular systems (MMS), containing the cationic lipid dioleylaminesuccinylparomomycin (DNA MMS DOSP), or bis (guanidinium)-tren-cholesterol (DNA MMS BGTC), and DNA lipid nanocapsules (DNA LNCs). Active targeting of the asialoglycoprotein receptor (ASGP-R) using galactose as a ligand for DNA MMS (GAL DNA MMS) and passive targeting using a polyethylene glycol coating for DNA LNCs (PEG DNA LNCs) should improve the properties of these DNA nanocarriers. All systems were characterized via physicochemical methods and the DNA payload of DNA LNCs was quantified for the first time. Afterwards, their biodistribution in healthy mice was analyzed after encapsulation of a fluorescent dye via in vivo biofluorescence imaging (BFI), revealing various distribution profiles depending on the cationic lipid used and their surface characteristics. Furthermore, the two vectors with the best prolonged circulation profile were administered twice in healthy mice revealing that the new DNA MMS DOSP vectors showed no toxicity and the same distribution profile for both injections, contrary to PEG DNA LNCs which showed a rapid clearance after the second injection, certainly due to the accelerated blood clearance phenomenon. PMID:23299832

Conjugated Polymers/DNA Hybrid Materials for Protein Inactivation.

PubMed

Zhao, Likun; Zhang, Jiangyan; Xu, Huiming; Geng, Hao; Cheng, Yongqiang

2016-09-07

Chromophore-assisted light inactivation (CALI) is a powerful tool for analyzing protein functions due to the high degree of spatial and temporal resolution. In this work, we demonstrate a CALI approach based on conjugated polymers (CPs)/DNA hybrid material for protein inactivation. The target protein is conjugated with single-stranded DNA in advance. Single-stranded DNA can form CPs/DNA hybrid material with cationic CPs via electrostatic and hydrophobic interactions. Through the formation of CPs/DNA hybrid material, the target protein that is conjugated with DNA is brought into close proximity to CPs. Under irradiation, CPs harvest light and generate reactive oxygen species (ROS), resulting in the inactivation of the adjacent target protein. This approach can efficiently inactivate any target protein which is conjugated with DNA and has good specificity and universality, providing a new strategy for studies of protein function and adjustment of protein activity.

Lessons Learned from Deploying an Analytical Task Management Database

NASA Technical Reports Server (NTRS)

O'Neil, Daniel A.; Welch, Clara; Arceneaux, Joshua; Bulgatz, Dennis; Hunt, Mitch; Young, Stephen

2007-01-01

Defining requirements, missions, technologies, and concepts for space exploration involves multiple levels of organizations, teams of people with complementary skills, and analytical models and simulations. Analytical activities range from filling a To-Be-Determined (TBD) in a requirement to creating animations and simulations of exploration missions. In a program as large as returning to the Moon, there are hundreds of simultaneous analysis activities. A way to manage and integrate efforts of this magnitude is to deploy a centralized database that provides the capability to define tasks, identify resources, describe products, schedule deliveries, and generate a variety of reports. This paper describes a web-accessible task management system and explains the lessons learned during the development and deployment of the database. Through the database, managers and team leaders can define tasks, establish review schedules, assign teams, link tasks to specific requirements, identify products, and link the task data records to external repositories that contain the products. Data filters and spreadsheet export utilities provide a powerful capability to create custom reports. Import utilities provide a means to populate the database from previously filled form files. Within a four month period, a small team analyzed requirements, developed a prototype, conducted multiple system demonstrations, and deployed a working system supporting hundreds of users across the aeros pace community. Open-source technologies and agile software development techniques, applied by a skilled team enabled this impressive achievement. Topics in the paper cover the web application technologies, agile software development, an overview of the system's functions and features, dealing with increasing scope, and deploying new versions of the system.

Trillium Horizon, A Small Portable Observatory Grade Seismometer For Direct Bury And Vault Use

NASA Astrophysics Data System (ADS)

Moores, A.; Parker, T.; Bainbridge, G.

2017-12-01

As of August 2017 almost 5 years of data have been collected from broadband seismic sensors designed for direct burial applications. These first posthole instruments have been deployed in a wide range of extremely challenging environments such as dynamic ice and snow environments, extreme wet and dry conditions in soils of high clay content, and steep creeping terrain. In all use cases the direct burial approach has consistently provided high quality data when compared to shallow vault installations. In this presentation we extract and analyze operational performance data, including tilt information from mass position time series recorded at direct burial installations and at temporary shallow vault deployments. This data shows that while higher tilt tolerance is required for data quality outcome certainty in some installations, the majority of installations can be addressed by a smaller instrument with a narrower tilt range hence reducing size and cost. The lessons learned from this real world field data have guided the development of a new smaller, less expensive instrument, Trillium Horizon.Based on this analysis and and user feedback from many direct burial deployments, the Trillium Horizon seismometer has been developed as a simple versatile instrument to span the majority of deployment scenarios and specific use cases including shallow direct bury deployments, traditional piers, and problematic wet vault installs. With its small size, robust waterproof case and connector, +/-1.5° tilt range, dual-purpose cable, and accessories for both posthole and vault installation, Trillium Horizon is optimized for usability as well as performance.

[Single-molecule detection and characterization of DNA replication based on DNA origami].

PubMed

Wang, Qi; Fan, Youjie; Li, Bin

2014-08-01

To investigate single-molecule detection and characterization of DNA replication. Single-stranded DNA (ssDNA) as the template of DNA replication was attached to DNA origami by a hybridization reaction based on the complementary base-pairing principle. DNA replication catalyzed by E.coli DNA polymerase I Klenow Fragment (KF) was detected using atomic force microscopy (AFM). The height variations between the ssDNA and the double-stranded DNA (dsDNA), the distribution of KF during DNA replication and biotin-streptavidin (BA) complexes on the DNA strand after replication were detected. Agarose gel electrophoresis was employed to analyze the changes in the DNA after replication. The designed ssDNA could be anchored on the target positions of over 50% of the DNA origami. The KF was capable of binding to the ssDNA fixed on DNA origami and performing its catalytic activities, and was finally dissociated from the DNA after replication. The height of DNA strand increased by about 0.7 nm after replication. The addition of streptavidin also resulted in an DNA height increase to about 4.9 nm due to the formation of BA complexes on the biotinylated dsDNA. The resulting dsDNA and BA complex were subsequently confirmed by agarose gel electrophoresis. The combination of AFM and DNA origami allows detection and characterization of DNA replication at the single molecule level, and this approach provides better insights into the mechanism of DNA polymerase and the factors affecting DNA replication.

The arbuscular mycorrhizal fungus Glomus intraradices is haploid and has a small genome size in the lower limit of eukaryotes.

PubMed

Hijri, Mohamed; Sanders, Ian R

2004-02-01

The genome size, complexity, and ploidy of the arbuscular mycorrhizal fungus (AMF) Glomus intraradices was determined using flow cytometry, reassociation kinetics, and genomic reconstruction. Nuclei of G. intraradices from in vitro culture, were analyzed by flow cytometry. The estimated average length of DNA per nucleus was 14.07+/-3.52 Mb. Reassociation kinetics on G. intraradices DNA indicated a haploid genome size of approximately 16.54 Mb, comprising 88.36% single copy DNA, 1.59% repetitive DNA, and 10.05% fold-back DNA. To determine ploidy, the DNA content per nucleus measured by flow cytometry was compared with the genome estimate of reassociation kinetics. G. intraradices was found to have a DNA index (DNA per nucleus per haploid genome size) of approximately 0.9, indicating that it is haploid. Genomic DNA of G. intraradices was also analyzed by genomic reconstruction using four genes (Malate synthase, RecA, Rad32, and Hsp88). Because we used flow cytometry and reassociation kinetics to reveal the genome size of G. intraradices and show that it is haploid, then a similar value for genome size should be found when using genomic reconstruction as long as the genes studied are single copy. The average genome size estimate was 15.74+/-1.69 Mb indicating that these four genes are single copy per haploid genome and per nucleus of G. intraradices. Our results show that the genome size of G. intraradices is much smaller than estimates of other AMF and that the unusually high within-spore genetic variation that is seen in this fungus cannot be due to high ploidy.

Genetic identification of missing persons: DNA analysis of human remains and compromised samples.

PubMed

Alvarez-Cubero, M J; Saiz, M; Martinez-Gonzalez, L J; Alvarez, J C; Eisenberg, A J; Budowle, B; Lorente, J A

2012-01-01

Human identification has made great strides over the past 2 decades due to the advent of DNA typing. Forensic DNA typing provides genetic data from a variety of materials and individuals, and is applied to many important issues that confront society. Part of the success of DNA typing is the generation of DNA databases to help identify missing persons and to develop investigative leads to assist law enforcement. DNA databases house DNA profiles from convicted felons (and in some jurisdictions arrestees), forensic evidence, human remains, and direct and family reference samples of missing persons. These databases are essential tools, which are becoming quite large (for example the US Database contains 10 million profiles). The scientific, governmental and private communities continue to work together to standardize genetic markers for more effective worldwide data sharing, to develop and validate robust DNA typing kits that contain the reagents necessary to type core identity genetic markers, to develop technologies that facilitate a number of analytical processes and to develop policies to make human identity testing more effective. Indeed, DNA typing is integral to resolving a number of serious criminal and civil concerns, such as solving missing person cases and identifying victims of mass disasters and children who may have been victims of human trafficking, and provides information for historical studies. As more refined capabilities are still required, novel approaches are being sought, such as genetic testing by next-generation sequencing, mass spectrometry, chip arrays and pyrosequencing. Single nucleotide polymorphisms offer the potential to analyze severely compromised biological samples, to determine the facial phenotype of decomposed human remains and to predict the bioancestry of individuals, a new focus in analyzing this type of markers. Copyright © 2012 S. Karger AG, Basel.

Forensic DNA data banking by state crime labortaories

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

McEwen, J.E.

This article reports the results of a survey of the responsible crime laboratories in the first 19 states with legislation establishing forensic DNA data banks. The survey inquired into the labs` policies and procedures regarding the collection, storage, and analysis of samples; the retention of samples and data; search protocols; access to samples and data by third parties; and related matters. The research suggests that (1) the number of samples collected from convicted offenders for DNA data banking has far surpassed the number that have been analyzed; (2) data banks have already been used in a small but growing numbermore » of cases, to locate suspects and to identify associations between unresolved cases; (3) crime labs currently plan to retain indefinitely the samples collected for their data banks; and (4) the nature and extent of security safeguards that crime labs have implemented for their data banks vary among states. The recently enacted DNA Identification Act (1994) will provide $40 million in federal matching grants to states for DNA analysis activities, so long as states comply with specified quality-assurance standards, submit to external proficiency testing, and limit access to DNA information. Although these additional funds should help to ease some sample backlogs, it remains unclear how labs will allocate the funds, as between analyzing samples for their data banks and testing evidence samples in cases without suspects. The DNA Identification Act provides penalties for the disclosure or obtaining of DNA data held by data banks that participate in CODIS, the FBI`s evolving national network of DNA data banks, but individual crime labs must also develop stringent internal safeguards to prevent breaches of data-bank security. 9 refs., 3 tabs.« less

Role of isolated and clustered DNA damage and the post-irradiating repair process in the effects of heavy ion beam irradiation.

PubMed

Tokuyama, Yuka; Furusawa, Yoshiya; Ide, Hiroshi; Yasui, Akira; Terato, Hiroaki

2015-05-01

Clustered DNA damage is a specific type of DNA damage induced by ionizing radiation. Any type of ionizing radiation traverses the target DNA molecule as a beam, inducing damage along its track. Our previous study showed that clustered DNA damage yields decreased with increased linear energy transfer (LET), leading us to investigate the importance of clustered DNA damage in the biological effects of heavy ion beam radiation. In this study, we analyzed the yield of clustered base damage (comprising multiple base lesions) in cultured cells irradiated with various heavy ion beams, and investigated isolated base damage and the repair process in post-irradiation cultured cells. Chinese hamster ovary (CHO) cells were irradiated by carbon, silicon, argon and iron ion beams with LETs of 13, 55, 90 and 200 keV µm(-1), respectively. Agarose gel electrophoresis of the cells with enzymatic treatments indicated that clustered base damage yields decreased as the LET increased. The aldehyde reactive probe procedure showed that isolated base damage yields in the irradiated cells followed the same pattern. To analyze the cellular base damage process, clustered DNA damage repair was investigated using DNA repair mutant cells. DNA double-strand breaks accumulated in CHO mutant cells lacking Xrcc1 after irradiation, and the cell viability decreased. On the other hand, mouse embryonic fibroblast (Mef) cells lacking both Nth1 and Ogg1 became more resistant than the wild type Mef. Thus, clustered base damage seems to be involved in the expression of heavy ion beam biological effects via the repair process. © The Author 2015. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

Outcomes-Based Education Integration in Home Economics Program: An Evaluative Study

ERIC Educational Resources Information Center

Limon, Mark Raguindin; Castillo Vallente, John Paul

2016-01-01

This study examined the factors that affect the integration of Outcomes-Based Education (OBE) in the Home Economics (HE) education curriculum of the Technology and Livelihood Education (TLE) program of a State University in the northern part of the Philippines. Descriptive survey and qualitative design were deployed to gather, analyze, and…

Children Interactions in Literacy Tutoring Situations: A Study with Urban Marginalized Populations in Argentina

ERIC Educational Resources Information Center

Rosemberg, Celia Renata; Alam, Florencia; Stein, Alejandra

2014-01-01

The study analyzed the conversational exchanges through which child tutors mediated literacy abilities and knowledge with young children in the framework of the project "From Child to Child: A Tutor-Child Literacy Program," that is being conducted in Buenos Aires, Argentina. The analysis considered the conversational moves deployed by…

Use of Passive Samplers to Determine the Source of Dissolved PAHs in the Ottawa River, Toledo, Ohio

EPA Science Inventory

As part of a larger study on the remedy effectiveness on the Ottawa River, (Ohio, USA), research was focused on the source of PAHs to water and sediment. Polyethylene passive samplers, or polyethylene devices (PEDs), were deployed and analyzed, along with whole water samples and...

Analysis of the Flight Motions of a Small Deployable Glider Configuration

NASA Technical Reports Server (NTRS)

Coe, Paul L., Jr.

1975-01-01

An investigation was conducted at the request of the U.S. Air Force Avionics Laboratory to analyze the flight characteristics of a small uncontrolled glider with folding wings. The study consisted of wind-tunnel tests of an actual glider and a theoretical analysis of the performance, stability, and trimmability of the configuration.

Subject-Specific Science Teachers' Views of Alternative Assessment

ERIC Educational Resources Information Center

Kolomuç, Ali

2017-01-01

This study aimed to discover subject-specific science teachers' views of alternative assessment. The questionnaire by Okur (2008) was adapted and deployed for data collection. The sample consisted of 80 subject-specific science teachers drawn from the cities of Trabzon, Rize and Erzurum in Turkey. In analyzing data, descriptive analysis was…

Reading Efficiency of Deaf and Hearing People in Spanish

ERIC Educational Resources Information Center

Moreno-Pérez, Francisco J.; Saldaña, David; Rodríguez-Ortiz, Isabel R.

2015-01-01

Different studies have showed poor reading performance in the deaf compared to the hearing population. This has overshadowed the fact that a minority of deaf children learns to read successfully and reaches levels similar to their hearing peers. We analyze whether deaf people deploy the same cognitive and learning processes in reading as their…

Gaming History: A Framework for What Video Games Teach about the Past

ERIC Educational Resources Information Center

Metzger, Scott Alan; Paxton, Richard J.

2016-01-01

This article offers a typological framework for analyzing how video games make use of historical elements, shaping the ways players engage with and think about the past. Phenomenologically induced labels are posited for identifying different deployments of and experiences with historical elements in video games, illustrated by examples drawn from…

Increasing temperature reduces wheat resistance mediated by major resistance genes to the gall midge Mayetiola destructor (Diptera: Cecidomyiidae)

USDA-ARS?s Scientific Manuscript database

Mayetiola destructor (Say) (Diptera: Cecidomyiidae) is a destructive pest of wheat and is mainly controlled by deploying resistant cultivars. Unfortunately, wheat resistance to Hessian fly is often lost when temperatures rise to a certain level. This study analyzed temperature sensitivity of 20 whea...

Discursive Obstruction and Elite Opposition to Environmental Activism in the Czech Republic

ERIC Educational Resources Information Center

Shriver, Thomas E.; Adams, Alison E.; Cable, Sherry

2013-01-01

Extant research on social movements has highlighted activists' discursive tactics to challenge the state, yet little analytical attention focuses on elite efforts to dominate the discourse arena through the deployment of oppositional frames. This paper analyzes elite oppositional framing surrounding the placement of a highway bypass in the Czech…

Perceptions of Open Source versus Commercial Software: Is Higher Education Still on the Fence?

ERIC Educational Resources Information Center

van Rooij, Shahron Williams

2007-01-01

This exploratory study investigated the perceptions of technology and academic decision-makers about open source benefits and risks versus commercial software applications. The study also explored reactions to a concept for outsourcing campus-wide deployment and maintenance of open source. Data collected from telephone interviews were analyzed,…

Extended System Operations Studies for Automated Guideway Transit Systems : Procedure for the Analysis of Representative AGT Deployments

DOT National Transportation Integrated Search

1981-12-01

The purpose of this report is to present a general procedure for using the SOS software to analyze AGT systems. Data to aid the analyst in specifying input information, required as input to the software, are summarized in the appendices. The data are...

Critical Realism and Realist Review: Analyzing Complexity in Educational Restructuring and the Limits of Generalizing Program Theories Across Borders

ERIC Educational Resources Information Center

De Souza, Denise E.

2016-01-01

This article focuses on the design of a critical realist review that deployed Bhaskar's resolution, redescribing, retroduction, eliminating, identifying, and correcting schema and Pawson and Tilley's Context-Mechanism-Outcome configuration underpinned by realist social theory. Methodologically, the review examined the relationship between…

Thermomechanical Analysis of Shape-Memory Composite Tape Spring

NASA Astrophysics Data System (ADS)

Yang, H.; Wang, L. Y.

2013-06-01

Intelligent materials and structures have been extensively applied for satellite designs in order to minimize the mass and reduce the cost in the launch of the spacecraft. Elastic memory composites (EMCs) have the ability of high-strain packaging and shape-memory effect, but increase the parts and total weight due to the additional heating system. Shape-memory sandwich structures Li and Wang (J. Intell. Mater. Syst. Struct. 22(14), 1605-1612, 2011) can overcome such disadvantage by using the metal skin acting as the heating element. However, the high strain in the micro-buckled metal skin decreases the deployment efficiency. This paper aims to present an insight into the folding and deployment behaviors of shape-memory composite (SMC) tape springs. A thermomechanical process was analyzed, including the packaging deformation at an elevated temperature, shape frozen at the low temperature and shape recovery after reheating. The result shows that SMC tape springs can significantly decrease the strain concentration in the metal skin, as well as exhibiting excellent shape frozen and recovery behaviors. Additionally, possible failure modes of SMC tape springs were also analyzed.

Evaluation of oxidative DNA damage promoted by storage in sperm from sex-reversed rainbow trout.

PubMed

Pérez-Cerezales, S; Martínez-Páramo, S; Cabrita, E; Martínez-Pastor, F; de Paz, P; Herráez, M P

2009-03-01

Short-term storage and cryopreservation of sperm are two common procedures in aquaculture, used for routine practices in artificial insemination reproduction and gene banking, respectively. Nevertheless, both procedures cause injuries affecting sperm motility, viability, cell structure and DNA stability, which diminish reproductive success. DNA modification is considered extremely important, especially when sperm storage is carried out with gene banking purposes. DNA damage caused by sperm storage is not well characterized and previous studies have reported simple and double strand breaks that have been attributed to oxidative events promoted by the generation of free radicals during storage. The objective of this study was to reveal DNA fragmentation and to explore the presence of oxidized bases that could be produced by oxidative events during short-term storage and cryopreservation in sex-reversed rainbow trout (Oncorhynchus mykiss) spermatozoa. Sperm from six males was analyzed separately. Different aliquots of the samples were stored 2h (fresh) or 5 days at 4 degrees C or were cryopreserved. Then spermatozoa were analyzed using the Comet assay, as well as combining this method with digestion with two endonucleases from Escherichia coli (Endonuclease III, that cut in oxidized cytosines, and FPG, cutting in oxidized guanosines). Both storage procedures yielded DNA fragmentation, but only short-term storage oxidative events were clearly detected, showing that oxidative processes affect guanosines rather than cytosines. Cryopreservation increases DNA fragmentation but the presence of oxidized bases was not noticed, suggesting that mechanisms other than oxidative stress could be involved in DNA fragmentation promoted by freezing.

Surveys of environmental DNA (eDNA): a new approach to estimate occurrence in Vulnerable manatee populations

USGS Publications Warehouse

Hunter, Margaret; Meigs-Friend, Gaia; Ferrante, Jason; Takoukam Kamla, Aristide; Dorazio, Robert; Keith Diagne, Lucy; Luna, Fabia; Lanyon, Janet M.; Reid, James P.

2018-01-01

Environmental DNA (eDNA) detection is a technique used to non-invasively detect cryptic, low density, or logistically difficult-to-study species, such as imperiled manatees. For eDNA measurement, genetic material shed into the environment is concentrated from water samples and analyzed for the presence of target species. Cytochrome bquantitative PCR and droplet digital PCR eDNA assays were developed for the 3 Vulnerable manatee species: African, Amazonian, and both subspecies of the West Indian (Florida and Antillean) manatee. Environmental DNA assays can help to delineate manatee habitat ranges, high use areas, and seasonal population changes. To validate the assay, water was analyzed from Florida’s east coast containing a high-density manatee population and produced 31564 DNA molecules l-1on average and high occurrence (ψ) and detection (p) estimates (ψ = 0.84 [0.40-0.99]; p = 0.99 [0.95-1.00]; limit of detection 3 copies µl-1). Similar occupancy estimates were produced in the Florida Panhandle (ψ = 0.79 [0.54-0.97]) and Cuba (ψ = 0.89 [0.54-1.00]), while occupancy estimates in Cameroon were lower (ψ = 0.49 [0.09-0.95]). The eDNA-derived detection estimates were higher than those generated using aerial survey data on the west coast of Florida and may be effective for population monitoring. Subsequent eDNA studies could be particularly useful in locations where manatees are (1) difficult to identify visually (e.g. the Amazon River and Africa), (2) are present in patchy distributions or are on the verge of extinction (e.g. Jamaica, Haiti), and (3) where repatriation efforts are proposed (e.g. Brazil, Guadeloupe). Extension of these eDNA techniques could be applied to other imperiled marine mammal populations such as African and Asian dugongs.

Cryopreservation of human blood for alkaline and Fpg-modified comet assay.

PubMed

Pu, Xinzhu; Wang, Zemin; Klaunig, James E

2016-01-01

The Comet assay is a reproducible and sensitive assay for the detection of DNA damage in eukaryotic cells and tissues. Incorporation of lesion specific, oxidative DNA damage repair enzymes (for example, Fpg, OGG1 and EndoIII) in the standard alkaline Comet assay procedure allows for the detection and measurement of oxidative DNA damage. The Comet assay using white blood cells (WBC) has proven useful in monitoring DNA damage from environmental agents in humans. However, it is often impractical to performance Comet assay immediately after blood sampling. Thus, storage of blood sample is required. In this study, we developed and tested a simple storage method for very small amount of whole blood for standard and Fpg-modified modified Comet assay. Whole blood was stored in RPMI 1640 media containing 10% FBS, 10% DMSO and 1 mM deferoxamine at a sample to media ratio of 1:50. Samples were stored at -20 °C and -80 °C for 1, 7, 14 and 28 days. Isolated lymphocytes from the same subjects were also stored under the same conditions for comparison. Direct DNA strand breakage and oxidative DNA damage in WBC and lymphocytes were analyzed using standard and Fpg-modified alkaline Comet assay and compared with freshly analyzed samples. No significant changes in either direct DNA strand breakage or oxidative DNA damage was seen in WBC and lymphocytes stored at -20 °C for 1 and 7 days compared to fresh samples. However, significant increases in both direct and oxidative DNA damage were seen in samples stored at -20 °C for 14 and 28 days. No changes in direct and oxidative DNA damage were observed in WBC and lymphocytes stored at -80 °C for up to 28 days. These results identified the proper storage conditions for storing whole blood or isolated lymphocytes to evaluate direct and oxidative DNA damage using standard and Fpg-modified alkaline Comet assay.

[The association between the DNA marker rs1842993 and risk for cardioembolic stroke in the Slavic population].

PubMed

Shetova, I M; Timofeev, D Iu; Shamalov, N A; Bondarenko, E A; Slominskiĭ, P A; Limborskaia, S A; Skvortsova, V I

2012-01-01

The analysis of association between DNA markers and total stroke risk was performed in 950 Slavonic patients. Patients with cardioembolic stroke were selected for a genome-wide association study. The HUMANCYTOSNP12 v.2 microchip was used to analyze all DNA samples on a panel of 301 000 single nucleotide polymorphisms. SNP rs1842993 on chromosome 7 was found to be associated with cardioembolic stroke risk.

Wireless Sensors Grouping Proofs for Medical Care and Ambient Assisted-Living Deployment

PubMed Central

Trček, Denis

2016-01-01

Internet of Things (IoT) devices are rapidly penetrating e-health and assisted living domains, and an increasing proportion among them goes on the account of computationally-weak devices, where security and privacy provisioning alone are demanding tasks, not to mention grouping proofs. This paper, therefore, gives an extensive analysis of such proofs and states lessons learnt to avoid possible pitfalls in future designs. It sticks with prudent engineering techniques in this field and deploys in a novel way the so called non-deterministic principle to provide not only grouping proofs, but (among other) also privacy. The developed solution is analyzed by means of a tangible metric and it is shown to be lightweight, and formally for security. PMID:26729131

Economically Sustainable Scaling of Photovoltaics to Meet Climate Targets

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

Needleman, David Berney; Poindexter, Jeremy R.; Kurchin, Rachel C.

To meet climate goals, photovoltaics (PV) deployment will have to grow rapidly over the next fifteen years. We identify two barriers to this growth: scale-up of manufacturing capacity and the cost of PV module production. We explore several technoeconomic approaches to overcoming these barriers and identify deep reductions in the capital intensity (capex) of PV module manufacturing and large increases in module efficiency as the most promising routes to rapid deployment. Given the lag inherent in rolling out new technology, we explore an approach where growth is fueled by debt or subsidies in the short-term and technological advances in themore » medium term. Finally, we analyze the current capex structure of crystalline silicon PV module manufacturing to identify potential savings.« less

Wireless Sensors Grouping Proofs for Medical Care and Ambient Assisted-Living Deployment.

PubMed

Trček, Denis

2016-01-02

Internet of Things (IoT) devices are rapidly penetrating e-health and assisted living domains, and an increasing proportion among them goes on the account of computationally-weak devices, where security and privacy provisioning alone are demanding tasks, not to mention grouping proofs. This paper, therefore, gives an extensive analysis of such proofs and states lessons learnt to avoid possible pitfalls in future designs. It sticks with prudent engineering techniques in this field and deploys in a novel way the so called non-deterministic principle to provide not only grouping proofs, but (among other) also privacy. The developed solution is analyzed by means of a tangible metric and it is shown to be lightweight, and formally for security.

Hydrodynamics Offshore of the North Beach of Indian River Inlet, DE

NASA Astrophysics Data System (ADS)

DiCosmo, N. R.; Puleo, J. A.

2014-12-01

The Indian River Inlet (IRI) on the east coast of Delaware, USA connects the Atlantic Ocean to the Indian River and Rehoboth Bays. Long-term and large-scale net alongshore sediment transport along this portion of coastline is from south to north. The north beach of IRI suffers from severe erosion due to interruption of the alongshore transport and current variability near the inlet. The magnitude of such erosion has increased over the past decade and questions have arisen as to the cause. The goal of this study is to quantify currents and wave patterns and estimate sediment transport rates at the north beach and near the inlet in an effort to determine the causes of persistent erosion. Data were obtained from October 2013 to March 2014 in the form of 3 separate 28-day deployments. Each deployment consisted of 4 proposed deployment sites. Data at each site were collected using a bottom mounted Nortek Aquadopp Acoustic Doppler Current Profiler (ADCP) and 2 Campbell Scientific Optical Backscatter Sensors (OBS). Currents and OBS data were sampled every 120 s. Waves were sampled for approximately 17 minutes at the beginning of every hour. Data analysis from the deployments indicates the presence of several interesting trends in currents that can be linked to the persistent erosion. Current data are filtered to quantify typical current speed and direction for a tidal cycle (peak flood to peak flood) at each deployment site. The typical currents off of the north beach and up to 800 m north of the north jetty are mostly directed southward over the entire tidal cycle. This consistent southward flow implies: 1) there is no flow reversal based on tide, contrary to what might be expected at an inlet adjacent beach, 2) the typical current direction is opposite of the expectations for the known long-term large-scale net alongshore transport and 3) the consistency of this atypical current may be responsible for transporting sediment southward and away from the north beach. Currents and waves will be further analyzed for storm and non-storm conditions in order to more completely quantify the hydrodynamics of the area. Sediment data will also be analyzed in conjunction with the hydrodynamic data in order to better understand the sediment transport process.

Development of Rapid Isothermal Amplification Assays for Detection of Phytophthora spp. in Plant Tissue.

PubMed

Miles, Timothy D; Martin, Frank N; Coffey, Michael D

2015-02-01

Several isothermal amplification techniques recently have been developed that are tolerant of inhibitors present in many plant extracts, which can reduce the need for obtaining purified DNA for running diagnostic assays. One such commercially available technique that has similarities with real-time polymerase chain reaction (PCR) for designing primers and a labeled probe is recombinase polymerase amplification (RPA). This technology was used to develop two simple and rapid approaches for detection of Phytophthora spp.: one genus-specific assay multiplexed with a plant internal control and the other species-specific assays for Phytophthora ramorum and P. kernoviae. All assays were tested for sensitivity (ranging from 3 ng to 1 fg of DNA) and specificity using DNA extracted from more than 136 Phytophthora taxa, 21 Pythium spp., 1 Phytopythium sp., and a wide range of plant species. The lower limit of linear detection using purified DNA was 200 to 300 fg of DNA in all pathogen RPA assays. Six different extraction buffers were tested for use during plant tissue maceration and the assays were validated in the field by collecting 222 symptomatic plant samples from over 50 different hosts. Only 56 samples were culture positive for Phytophthora spp. whereas 91 were positive using the Phytophthora genus-specific RPA test and a TaqMan real-time PCR assay. A technique for the generation of sequencing templates from positive RPA amplifications to confirm species identification was also developed. These RPA assays have added benefits over traditional technologies because they are rapid (results can be obtained in as little as 15 min), do not require DNA extraction or extensive training to complete, use less expensive portable equipment than PCR-based assays, and are significantly more specific than current immunologically based methods. This should provide a rapid, field-deployable capability for pathogen detection that will facilitate point-of-sample collection processing, thereby reducing the time necessary for accurate diagnostics and making management decisions.

Performance of Prototype High-Flow Inhalable Dust Sampler in a Livestock Production Facility

PubMed Central

Anthony, T. Renée; Cai, Changjie; Mehaffy, John; Sleeth, Darrah; Volckens, John

2017-01-01

A high-flow inhalable sampler, designed for operational flow rates up to 10 L/min using computer simulations and examined in wind tunnel experiments, was evaluated in the field. This prototype sampler was deployed in collocation with an IOM (the benchmark standard sampler) in a swine farrowing building to examine the sampling performance for assessing concentrations of inhalable particulate mass and endotoxin. Paired samplers were deployed for 24-hours on 19 days over a three-month period. On each sampling day, the paired samplers were deployed at three fixed locations and data were analyzed to identify agreement and to examine systematic biases between concentrations measured by these samplers. Thirty-six paired gravimetric samples were analyzed; insignificant, unsubstantial differences between concentrations were identified between the two samplers (p=0.16; mean difference 0.03 mg/m3). Forty-four paired samples were available for endotoxin analysis, and a significant (p=0.001) difference in endotoxin concentration was identified: the prototype sampler, on average, had 120 EU/m3 more endotoxin than did the IOM samples. Since the same gravimetric samples were analyzed for endotoxin content, the endotoxin difference is likely attributable to differences in endotoxin extraction. The prototype’s disposable thin-film polycarbonate capsule was included with the filter in the 1-hour extraction procedure while the internal plastic cassette of the IOM required a rinse procedure that is susceptible to dust losses. Endotoxin concentrations measured with standard plastic IOM inserts that follow this rinsing procedure may underestimate the true endotoxin exposure concentrations. The maximum concentrations in the study (1.55 mg/m3 gravimetric, 2328 EU/m3 endotoxin) were lower than other agricultural or industrial environments. Future work should explore the performance of the prototype sampler in dustier environments, where concentrations approach particulates not otherwise specified (PNOS) limits of 10 mg/m3, including using the prototype as a personal sampler. PMID:27792469

Performance of prototype high-flow inhalable dust sampler in a livestock production facility.

PubMed

Anthony, T Renée; Cai, Changjie; Mehaffy, John; Sleeth, Darrah; Volckens, John

2017-05-01

A high-flow inhalable sampler, designed for operational flow rates up to 10 L/min using computer simulations and examined in wind tunnel experiments, was evaluated in the field. This prototype sampler was deployed in collocation with an IOM (the benchmark standard sampler) in a swine farrowing building to examine the sampling performance for assessing concentrations of inhalable particulate mass and endotoxin. Paired samplers were deployed for 24 hr on 19 days over a 3-month period. On each sampling day, the paired samplers were deployed at three fixed locations and data were analyzed to identify agreement and to examine systematic biases between concentrations measured by these samplers. Thirty-six paired gravimetric samples were analyzed; insignificant, unsubstantial differences between concentrations were identified between the two samplers (p = 0.16; mean difference 0.03 mg/m 3 ). Forty-four paired samples were available for endotoxin analysis, and a significant (p = 0.001) difference in endotoxin concentration was identified: the prototype sampler, on average, had 120 EU/m 3 more endotoxin than did the IOM samples. Since the same gravimetric samples were analyzed for endotoxin content, the endotoxin difference is likely attributable to differences in endotoxin extraction. The prototype's disposable thin-film polycarbonate capsule was included with the filter in the 1-hr extraction procedure while the internal plastic cassette of the IOM required a rinse procedure that is susceptible to dust losses. Endotoxin concentrations measured with standard plastic IOM inserts that follow this rinsing procedure may underestimate the true endotoxin exposure concentrations. The maximum concentrations in the study (1.55 mg/m 3 gravimetric, 2328 EU/m 3 endotoxin) were lower than other agricultural or industrial environments. Future work should explore the performance of the prototype sampler in dustier environments, where concentrations approach particulates not otherwise specified (PNOS) limits of 10 mg/m 3 , including using the prototype as a personal sampler.

Molecular traffic jams on DNA.

PubMed

Finkelstein, Ilya J; Greene, Eric C

2013-01-01

All aspects of DNA metabolism-including transcription, replication, and repair-involve motor enzymes that move along genomic DNA. These processes must all take place on chromosomes that are occupied by a large number of other proteins. However, very little is known regarding how nucleic acid motor proteins move along the crowded DNA substrates that are likely to exist in physiological settings. This review summarizes recent progress in understanding how DNA-binding motor proteins respond to the presence of other proteins that lie in their paths. We highlight recent single-molecule biophysical experiments aimed at addressing this question, with an emphasis placed on analyzing the single-molecule, ensemble biochemical, and in vivo data from a mechanistic perspective.

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

PubMed

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

2011-01-01

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

Methylation pattern of fish lymphocystis disease virus DNA.

PubMed

Wagner, H; Simon, D; Werner, E; Gelderblom, H; Darai, C; Flügel, R M

1985-03-01

The content and distribution of 5-methylcytosine in DNA from fish lymphocystis disease virus was analyzed by high-pressure liquid chromatography, nearest-neighbor analysis, and with restriction endonucleases. We found that 22% of all C residues were methylated, including methylation of the following dinucleotide sequences: CpG to 75%, CpC to ca. 1%, and CpA to 2 to 5%. Comparison of relative digestion of viral DNA with MspI and HpaII indicated that CCGG sequences were almost completely methylated at the inner C. The degree of methylation of GCGC was much lower. The methylation pattern of fish lymphocystis disease virus DNA differed from that of the host cell DNA.

Methylation pattern of fish lymphocystis disease virus DNA.

PubMed Central

Wagner, H; Simon, D; Werner, E; Gelderblom, H; Darai, C; Flügel, R M

1985-01-01

The content and distribution of 5-methylcytosine in DNA from fish lymphocystis disease virus was analyzed by high-pressure liquid chromatography, nearest-neighbor analysis, and with restriction endonucleases. We found that 22% of all C residues were methylated, including methylation of the following dinucleotide sequences: CpG to 75%, CpC to ca. 1%, and CpA to 2 to 5%. Comparison of relative digestion of viral DNA with MspI and HpaII indicated that CCGG sequences were almost completely methylated at the inner C. The degree of methylation of GCGC was much lower. The methylation pattern of fish lymphocystis disease virus DNA differed from that of the host cell DNA. Images PMID:3973962

An Optimized DNA Analysis Workflow for the Sampling, Extraction, and Concentration of DNA obtained from Archived Latent Fingerprints.

PubMed

Solomon, April D; Hytinen, Madison E; McClain, Aryn M; Miller, Marilyn T; Dawson Cruz, Tracey

2018-01-01

DNA profiles have been obtained from fingerprints, but there is limited knowledge regarding DNA analysis from archived latent fingerprints-touch DNA "sandwiched" between adhesive and paper. Thus, this study sought to comparatively analyze a variety of collection and analytical methods in an effort to seek an optimized workflow for this specific sample type. Untreated and treated archived latent fingerprints were utilized to compare different biological sampling techniques, swab diluents, DNA extraction systems, DNA concentration practices, and post-amplification purification methods. Archived latent fingerprints disassembled and sampled via direct cutting, followed by DNA extracted using the QIAamp® DNA Investigator Kit, and concentration with Centri-Sep™ columns increased the odds of obtaining an STR profile. Using the recommended DNA workflow, 9 of the 10 samples provided STR profiles, which included 7-100% of the expected STR alleles and two full profiles. Thus, with carefully selected procedures, archived latent fingerprints can be a viable DNA source for criminal investigations including cold/postconviction cases. © 2017 American Academy of Forensic Sciences.

The optical biomedical sensors for DNA detection and imaging based on two-photon excited luminescent styryl dyes: phototoxic influence on the DNA

NASA Astrophysics Data System (ADS)

Yashchuk, Valeriy M.; Kudrya, Vladislav Yu.; Losytskyy, Mykhaylo Yu.; Tokar, Valentyna P.; Yarmoluk, Sergiy M.; Dmytruk, Igor M.; Prokopets, Vadym M.; Kovalska, Vladyslava B.; Balanda, Anatoliy O.; Kryvorotenko, Dmytro V.; Ogul'chansky, Tymish Yu.

2007-06-01

The optical absorption, fluorescence and phosphorescence of the novel styryl dyes developed for the fluorescent detection of DNA were investigated. The energy structures of dye molecules as well as spectral manifestations of the dyes aggregate formation and interaction with DNA were studied. The dramatic increase (up to 1000 times) of the fluorescence intensity of dyes in the presence of DNA was observed. The photostability and phototoxic influence on the DNA of several styryl dyes were studied by analyzing absorption, fluorescence and phosphorescence spectra of these dyes and dye-DNA systems. Changes of the optical density value of dye-DNA solutions caused by the visible light irradiation were fixed in the wavelength regions of the DNA absorption and of the dye absorption. Fluorescence emission of dye-DNA complexes upon two-photon excitation (TPE) at wavelength 1064 nm with the 20 ns pulsed YAG: Nd3+ laser and at 840 nm with the 90 fs pulsed Ti:sapphire laser was registered. The values of two-photon absorption cross-sections of dye-DNA complexes were evaluated.

Recombination of mitochondrial DNA in skeletal muscle of individuals with multiple mitochondrial DNA heteroplasmy.

PubMed

Zsurka, Gábor; Kraytsberg, Yevgenia; Kudina, Tatiana; Kornblum, Cornelia; Elger, Christian E; Khrapko, Konstantin; Kunz, Wolfram S

2005-08-01

Experimental evidence for human mitochondrial DNA (mtDNA) recombination was recently obtained in an individual with paternal inheritance of mtDNA and in an in vitro cell culture system. Whether mtDNA recombination is a common event in humans remained to be determined. To detect mtDNA recombination in human skeletal muscle, we analyzed the distribution of alleles in individuals with multiple mtDNA heteroplasmy using single-cell PCR and allele-specific PCR. In all ten individuals who carried a heteroplasmic D-loop mutation and a distantly located tRNA point mutation or a large deletion, we observed a mixture of four allelic combinations (tetraplasmy), a hallmark of recombination. Twelve of 14 individuals with closely located heteroplasmic D-loop mutation pairs contained a mixture of only three types of mitochondrial genomes (triplasmy), consistent with the absence of recombination between adjacent markers. These findings indicate that mtDNA recombination is common in human skeletal muscle.

Binding mechanism of PicoGreen to DNA characterized by magnetic tweezers and fluorescence spectroscopy.

PubMed

Wang, Ying; Schellenberg, Helene; Walhorn, Volker; Toensing, Katja; Anselmetti, Dario

2017-09-01

Fluorescent dyes are broadly used in many biotechnological applications to detect and visualize DNA molecules. However, their binding to DNA alters the structural and nanomechanical properties of DNA and, thus, interferes with associated biological processes. In this work we employed magnetic tweezers and fluorescence spectroscopy to investigate the binding of PicoGreen to DNA at room temperature in a concentration-dependent manner. PicoGreen is an ultrasensitive quinolinium nucleic acid stain exhibiting hardly any background signal from unbound dye molecules. By means of stretching and overwinding single, torsionally constrained, nick-free double-stranded DNA molecules, we acquired force-extension and supercoiling curves which allow quantifying DNA contour length, persistence length and other thermodynamical binding parameters, respectively. The results of our magnetic tweezers single-molecule binding study were well supported through analyzing the fluorescent spectra of stained DNA. On the basis of our work, we could identify a concentration-dependent bimodal binding behavior, where, apparently, PicoGreen associates to DNA as an intercalator and minor-groove binder simultaneously.

DNA-directed mutations. Leading and lagging strand specificity

NASA Technical Reports Server (NTRS)

Sinden, R. R.; Hashem, V. I.; Rosche, W. A.

1999-01-01

The fidelity of replication has evolved to reproduce B-form DNA accurately, while allowing a low frequency of mutation. The fidelity of replication can be compromised, however, by defined order sequence DNA (dosDNA) that can adopt unusual or non B-DNA conformations. These alternative DNA conformations, including hairpins, cruciforms, triplex DNAs, and slipped-strand structures, may affect enzyme-template interactions that potentially lead to mutations. To analyze the effect of dosDNA elements on spontaneous mutagenesis, various mutational inserts containing inverted repeats or direct repeats were cloned in a plasmid containing a unidirectional origin of replication and a selectable marker for the mutation. This system allows for analysis of mutational events that are specific for the leading or lagging strands during DNA replication in Escherichia coli. Deletions between direct repeats, involving misalignment stabilized by DNA secondary structure, occurred preferentially on the lagging strand. Intermolecular strand switch events, correcting quasipalindromes to perfect inverted repeats, occurred preferentially during replication of the leading strand.

A high-throughput and quantitative method to assess the mutagenic potential of translesion DNA synthesis

PubMed Central

Taggart, David J.; Camerlengo, Terry L.; Harrison, Jason K.; Sherrer, Shanen M.; Kshetry, Ajay K.; Taylor, John-Stephen; Huang, Kun; Suo, Zucai

2013-01-01

Cellular genomes are constantly damaged by endogenous and exogenous agents that covalently and structurally modify DNA to produce DNA lesions. Although most lesions are mended by various DNA repair pathways in vivo, a significant number of damage sites persist during genomic replication. Our understanding of the mutagenic outcomes derived from these unrepaired DNA lesions has been hindered by the low throughput of existing sequencing methods. Therefore, we have developed a cost-effective high-throughput short oligonucleotide sequencing assay that uses next-generation DNA sequencing technology for the assessment of the mutagenic profiles of translesion DNA synthesis catalyzed by any error-prone DNA polymerase. The vast amount of sequencing data produced were aligned and quantified by using our novel software. As an example, the high-throughput short oligonucleotide sequencing assay was used to analyze the types and frequencies of mutations upstream, downstream and at a site-specifically placed cis–syn thymidine–thymidine dimer generated individually by three lesion-bypass human Y-family DNA polymerases. PMID:23470999

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.

PubMed

Howell, Kate Joanne; Kraiczy, Judith; Nayak, Komal M; Gasparetto, Marco; Ross, Alexander; Lee, Claire; Mak, Tim N; Koo, Bon-Kyoung; Kumar, Nitin; Lawley, Trevor; Sinha, Anupam; Rosenstiel, Philip; Heuschkel, Robert; Stegle, Oliver; Zilbauer, Matthias

2018-02-01

We analyzed DNA methylation patterns and transcriptomes of primary intestinal epithelial cells (IEC) of children newly diagnosed with inflammatory bowel diseases (IBD) to learn more about pathogenesis. We obtained mucosal biopsies (N = 236) collected from terminal ileum and ascending and sigmoid colons of children (median age 13 years) newly diagnosed with IBD (43 with Crohn's disease [CD], 23 with ulcerative colitis [UC]), and 30 children without IBD (controls). Patients were recruited and managed at a hospital in the United Kingdom from 2013 through 2016. We also obtained biopsies collected at later stages from a subset of patients. IECs were purified and analyzed for genome-wide DNA methylation patterns and gene expression profiles. Adjacent microbiota were isolated from biopsies and analyzed by 16S gene sequencing. We generated intestinal organoid cultures from a subset of samples and genome-wide DNA methylation analysis was performed. We found gut segment-specific differences in DNA methylation and transcription profiles of IECs from children with IBD vs controls; some were independent of mucosal inflammation. Changes in gut microbiota between IBD and control groups were not as large and were difficult to assess because of large amounts of intra-individual variation. Only IECs from patients with CD had changes in DNA methylation and transcription patterns in terminal ileum epithelium, compared with controls. Colon epithelium from patients with CD and from patients with ulcerative colitis had distinct changes in DNA methylation and transcription patterns, compared with controls. In IECs from patients with IBD, changes in DNA methylation, compared with controls, were stable over time and were partially retained in ex-vivo organoid cultures. Statistical analyses of epithelial cell profiles allowed us to distinguish children with CD or UC from controls; profiles correlated with disease outcome parameters, such as the requirement for treatment with biologic agents. We identified specific changes in DNA methylation and transcriptome patterns in IECs from pediatric patients with IBD compared with controls. These data indicate that IECs undergo changes during IBD development and could be involved in pathogenesis. Further analyses of primary IECs from patients with IBD could improve our understanding of the large variations in disease progression and outcomes. Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.

Factors associated with trace evidence analyses and DNA findings among police reported cases of rape.

PubMed

Forr, Camilla; Schei, Berit; Stene, Lise Eilin; Ormstad, Kari; Hagemann, Cecilie Therese

2018-02-01

The aim of this study was to examine the association between victim, suspect and assault characteristics and (1) forensic analysis of trace evidence, (2) detection of spermatozoa and (3) DNA match in police-reported cases of rape/attempted rape. In addition, we explored whether DNA findings were associated with legal outcome. We conducted a retrospective, descriptive study based on police-reported rapes and attempted rapes of women  ≥16 years of age in Sør-Trøndelag Police District throughout 1997-2010. Police data were merged with information from the Sexual Assault Centre (SAC) at St. Olavs University Hospital, Trondheim, Norway. We used binary and multivariable logistic regression for the comparisons. We identified 324 victims (mean age 24 years). The police requested analysis in 135 (45%) of the 299 collected victim samples. The police decision to analyze was after adjustment associated with the victim being employed or under education, and a public venue, but not with interval from assault to sampling. Spermatozoa were detected in 79 (61%) of the analyzed cases, of which 71 were collected from victims within 24h. Interval from assault being <24h and reporting a penetrative assault remained associated with the findings of spermatozoa after adjustments. Forensic analyses of trace evidence collected from victim, suspect and/or venue disclosed matching DNA profiles in 57 (40%) of a total of 143 analyzed cases. Matching DNA profiles were associated with suspect being known to the victim and with the venue being private. A higher proportion of cases with a DNA match were prosecuted in court: 20 of the 29 cases prosecuted. However, despite a DNA match 35 cases were anyway dismissed because of insufficient evidence. Although many of the associations in our study were expected, it is still important to report the actual numbers to gain insight into the importance of a DNA match in legal proceedings. A substantial proportion of cases with DNA match was dismissed because of insufficient evidence. To strengthen the justice response to sexual assault, it is essential to generate knowledge about the role of medico-legal evidence in such cases, and there are obviously other non-medical factors influencing the legal decisions. Copyright © 2017 Elsevier B.V. All rights reserved.

Genetic diversity analysis of nine chewing cane varieties (lines) and construction of their DNA fingerprints

USDA-ARS?s Scientific Manuscript database

In order to provide theoretical basis for variety identification and parental selection during sugarcane breeding process, the present study was conducted to analyze genetic diversity of nine chewing cane varieties (lines) and construct their DNA fingerprints. Combining twenty-one SSR molecular mark...

Efficient Deployment of Key Nodes for Optimal Coverage of Industrial Mobile Wireless Networks

PubMed Central

Li, Xiaomin; Li, Di; Dong, Zhijie; Hu, Yage; Liu, Chengliang

2018-01-01

In recent years, industrial wireless networks (IWNs) have been transformed by the introduction of mobile nodes, and they now offer increased extensibility, mobility, and flexibility. Nevertheless, mobile nodes pose efficiency and reliability challenges. Efficient node deployment and management of channel interference directly affect network system performance, particularly for key node placement in clustered wireless networks. This study analyzes this system model, considering both industrial properties of wireless networks and their mobility. Then, static and mobile node coverage problems are unified and simplified to target coverage problems. We propose a novel strategy for the deployment of clustered heads in grouped industrial mobile wireless networks (IMWNs) based on the improved maximal clique model and the iterative computation of new candidate cluster head positions. The maximal cliques are obtained via a double-layer Tabu search. Each cluster head updates its new position via an improved virtual force while moving with full coverage to find the minimal inter-cluster interference. Finally, we develop a simulation environment. The simulation results, based on a performance comparison, show the efficacy of the proposed strategies and their superiority over current approaches. PMID:29439439

Addressing critical issues in the development of an Oncology Information System.

PubMed

Urda, D; Ribelles, N; Subirats, J L; Franco, L; Alba, E; Jerez, J M

2013-05-01

This paper presents the experience on the design and implementation of a user-centered Oncology Information System developed for the Medical Oncology Department at the "Hospital Universitario Virgen de la Victoria", in Málaga, Spain. The project focused on the aspects considered in the literature as critical factors for a successful deployment and usage of a health information system. System usability, adequate technology, integration of clinical routines, real-time statistical analysis of data, information confidentiality and standard protocol-based external interconnection were the key aspects considered. The developed system is based on a web application with a modular and layered architecture accounting for usability, ease of maintenance and further system development. Evaluation of system usability was carried at three and fifteen months after system deployment to analyze the advantages/disadvantages experienced by the end-users. A thorough prior analysis of clinical activities and workflows, the use of the adequate technology, and the availability of data analysis tools will almost guarantee success in the deployment of an Oncology Information System. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Design and Analysis of Cost-Efficient Sensor Deployment for Tracking Small UAS with Agent-Based Modeling.

PubMed

Shin, Sangmi; Park, Seongha; Kim, Yongho; Matson, Eric T

2016-04-22

Recently, commercial unmanned aerial systems (UAS) have gained popularity. However, these UAS are potential threats to people in terms of safety in public places, such as public parks or stadiums. To reduce such threats, we consider a design, modeling, and evaluation of a cost-efficient sensor system that detects and tracks small UAS. In this research, we focus on discovering the best sensor deployments by simulating different types and numbers of sensors in a designated area, which provide reasonable detection rates at low costs. Also, the system should cover the crowded areas more thoroughly than vacant areas to reduce direct threats to people underneath. This research study utilized the Agent-Based Modeling (ABM) technique to model a system consisting of independent and heterogeneous agents that interact with each other. Our previous work presented the ability to apply ABM to analyze the sensor configurations with two types of radars in terms of cost-efficiency. The results from the ABM simulation provide a list of candidate configurations and deployments that can be referred to for applications in the real world environment.

OTEC modular experiment cold water pipe concept evaluation. Volume III. Appendices

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

Not Available

1979-04-01

The Cold Water Pipe System Design Study was undertaken to evaluate the diverse CWP concepts, recommend the most viable alternatives for a 1984 deployment of the 10 to 40 MWe MEP, and carry out preliminary designs of three concepts. The concept evaluation phase reported involved a systems analysis of design alternatives in the broad categories of rigid walled (with hinges), compliant walled, stockade and bottom mounted buoyant. Quantitative evaluations were made of concept performance, availability, deployment schedule, technical feasibility and cost. CWP concepts were analyzed to determine if they met or could be made to meet established system requirements andmore » could be deployed by 1984. Fabrication, construction and installation plans were developed for successful concepts, and costs were determined in a WBS format. Evaluations were performed on the basis of technical and cost risk. This volume includes the following appendices: (A) materials and associated design criteria; (B) summary of results of dynamic flow and transportation analysis; (C) CWP sizing analysis; (D) CWP thermal performance; and (E) investigation of the APL/ABAM CWP design. (WHK)« less

Dynamics of tether-assisted reentry vehicle systems

NASA Astrophysics Data System (ADS)

Zhu, Renzhang; Misra, A. K.; Lin, Huabao

The dynamics of tether-assisted reentry of a capsule is considered in this paper. A major advantage in tethered-assisted reentry is the ability to replace a retro-rocket by a tether. In this reentry procedure, a capsule is deployed down to a design altitude near the local vertical, and at an appropriate time the capsule is disconnected from the tether and enters into a reentry trajectory. In addition to static release, swing release is also considered in this paper. Three deployment schemes appropriate for swing release are considered. A two-stage accelerated-exponential/decelerated-exponential deployment appears to be the best of the three. In comparison with static release, for the same duration of return, this swing release can lead to about 22 percent reduction in tether length at the cost of an increase in tension in the tether by only 8 to 12 percent, and thus, it could decrease the tether mass launched into space. The paper analyzes the detailed dynamics of the tethered system before release as well as the reentry dynamics of the capsule after release along with the heat generated during reentry.

Design and Analysis of Cost-Efficient Sensor Deployment for Tracking Small UAS with Agent-Based Modeling

PubMed Central

Shin, Sangmi; Park, Seongha; Kim, Yongho; Matson, Eric T.

2016-01-01

Recently, commercial unmanned aerial systems (UAS) have gained popularity. However, these UAS are potential threats to people in terms of safety in public places, such as public parks or stadiums. To reduce such threats, we consider a design, modeling, and evaluation of a cost-efficient sensor system that detects and tracks small UAS. In this research, we focus on discovering the best sensor deployments by simulating different types and numbers of sensors in a designated area, which provide reasonable detection rates at low costs. Also, the system should cover the crowded areas more thoroughly than vacant areas to reduce direct threats to people underneath. This research study utilized the Agent-Based Modeling (ABM) technique to model a system consisting of independent and heterogeneous agents that interact with each other. Our previous work presented the ability to apply ABM to analyze the sensor configurations with two types of radars in terms of cost-efficiency. The results from the ABM simulation provide a list of candidate configurations and deployments that can be referred to for applications in the real world environment. PMID:27110790

Sampling Approaches for Multi-Domain Internet Performance Measurement Infrastructures

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

Calyam, Prasad

2014-09-15

The next-generation of high-performance networks being developed in DOE communities are critical for supporting current and emerging data-intensive science applications. The goal of this project is to investigate multi-domain network status sampling techniques and tools to measure/analyze performance, and thereby provide “network awareness” to end-users and network operators in DOE communities. We leverage the infrastructure and datasets available through perfSONAR, which is a multi-domain measurement framework that has been widely deployed in high-performance computing and networking communities; the DOE community is a core developer and the largest adopter of perfSONAR. Our investigations include development of semantic scheduling algorithms, measurement federationmore » policies, and tools to sample multi-domain and multi-layer network status within perfSONAR deployments. We validate our algorithms and policies with end-to-end measurement analysis tools for various monitoring objectives such as network weather forecasting, anomaly detection, and fault-diagnosis. In addition, we develop a multi-domain architecture for an enterprise-specific perfSONAR deployment that can implement monitoring-objective based sampling and that adheres to any domain-specific measurement policies.« less

The Potential of Different Concepts of Fast Breeder Reactor for the French Fleet Renewal

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

Massara, Simone; Tetart, Philippe; Lecarpentier, David

2006-07-01

The performances of different concepts of Fast Breeder Reactor (Na-cooled, He-cooled and Pb-cooled FBR) for the current French fleet renewal are analyzed in the framework of a transition scenario to a 100% FBR fleet at the end of the 21. century. Firstly, the modeling of these three FBR types by means of a semi-analytical approach in TIRELIRE - STRATEGIE, the EDF fuel cycle simulation code, is presented, together with some validation elements against ERANOS, the French reference code system for neutronic FBR analysis (CEA). Afterwards, performances comparisons are made in terms of maximum deployable power, natural uranium consumption and wastemore » production. The results show that the FBR maximum deployable capacity, independently from the FBR technology, is highly sensitive to the fuel cycle options, like the spent nuclear fuel cooling time or the Minor Actinides management strategy. Thus, some of the key parameters defining the dynamic of FBR deployment are highlighted, to inform the orientation of R and D in the development and optimization of these systems. (authors)« less

Integrated Canada-U.S. Power Sector Modeling with the Regional Energy Deployment System (ReEDS)

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

Martinez, A.; Eurek, K.; Mai, T.

2013-02-01

The electric power system in North America is linked between the United States and Canada. Canada has historically been a net exporter of electricity to the United States. The extent to which this remains true will depend on the future evolution of power markets, technology deployment, and policies. To evaluate these and related questions, we modify the Regional Energy Deployment System (ReEDS) model to include an explicit representation of the grid-connected power system in Canada to the continental United States. ReEDS is unique among long-term capacity expansion models for its high spatial resolution and statistical treatment of the impact ofmore » variable renewable generation on capacity planning and dispatch. These unique traits are extended to new Canadian regions. We present example scenario results using the fully integrated Canada-U.S. version of ReEDS to demonstrate model capabilities. The newly developed, integrated Canada-U.S. ReEDS model can be used to analyze the dynamics of electricity transfers and other grid services between the two countries under different scenarios.« less

Motion and ranging sensor system for through-the-wall surveillance system

NASA Astrophysics Data System (ADS)

Black, Jeffrey D.

2002-08-01

A portable Through-the-Wall Surveillance System is being developed for law enforcement, counter-terrorism, and military use. The Motion and Ranging Sensor is a radar that operates in a frequency band that allows for surveillance penetration of most non-metallic walls. Changes in the sensed radar returns are analyzed to detect the human motion that would typically be present during a hostage or barricaded suspect scenario. The system consists of a Sensor Unit, a handheld Remote Display Unit, and an optional laptop computer Command Display Console. All units are battery powered and a wireless link provides command and data communication between units. The Sensor Unit is deployed close to the wall or door through which the surveillance is to occur. After deploying the sensor the operator may move freely as required by the scenario. Up to five Sensor Units may be deployed at a single location. A software upgrade to the Command Display Console is also being developed. This software upgrade will combine the motion detected by multiple Sensor Units and determine and track the location of detected motion in two dimensions.

Genetic Homologies Among Streptomyces violaceoruber Strains

PubMed Central

Monson, A. M.; Bradley, S. G.; Enquist, L. W.; Cruces, Griselda

1969-01-01

Most of the genetic studies on streptomycetes have been done with cultures erroneously designated as Streptomyces coelicolor. To determine whether these cultures are genetically homologous with the S. violaceoruber nominifer, their deoxyribonucleic acids (DNA) were analyzed, and selected pairs of mutants were crossed. The four cultures used in genetic studies, and called S. coelicolor in the literature, were found to constitute a genospecies, based upon DNA hybridization and recombination tests. In addition, DNA from Actinopycnidium caeruleum formed extensive duplexes with S. violaceoruber DNA. S. violaceoruber cultures and A. caeruleum were distinctly different from the S. coelicolor nominifer. PMID:5370275

Visualizing biological reaction intermediates with DNA curtains

NASA Astrophysics Data System (ADS)

Zhao, Yiling; Jiang, Yanzhou; Qi, Zhi

2017-04-01

Single-molecule approaches have tremendous potential analyzing dynamic biological reaction with heterogeneity that cannot be effectively accessed via traditional ensemble-level biochemical approaches. The approach of deoxyribonucleic acid (DNA) curtains developed by Dr Eric Greene and his research team at Columbia University is a high-throughput single-molecule technique that utilizes fluorescent imaging to visualize protein-DNA interactions directly and allows the acquisition of statistically relevant information from hundreds or even thousands of individual reactions. This review aims to summarize the past, present, and future of DNA curtains, with an emphasis on its applications to solve important biological questions.

CloudDOE: a user-friendly tool for deploying Hadoop clouds and analyzing high-throughput sequencing data with MapReduce.

PubMed

Chung, Wei-Chun; Chen, Chien-Chih; Ho, Jan-Ming; Lin, Chung-Yen; Hsu, Wen-Lian; Wang, Yu-Chun; Lee, D T; Lai, Feipei; Huang, Chih-Wei; Chang, Yu-Jung

2014-01-01

Explosive growth of next-generation sequencing data has resulted in ultra-large-scale data sets and ensuing computational problems. Cloud computing provides an on-demand and scalable environment for large-scale data analysis. Using a MapReduce framework, data and workload can be distributed via a network to computers in the cloud to substantially reduce computational latency. Hadoop/MapReduce has been successfully adopted in bioinformatics for genome assembly, mapping reads to genomes, and finding single nucleotide polymorphisms. Major cloud providers offer Hadoop cloud services to their users. However, it remains technically challenging to deploy a Hadoop cloud for those who prefer to run MapReduce programs in a cluster without built-in Hadoop/MapReduce. We present CloudDOE, a platform-independent software package implemented in Java. CloudDOE encapsulates technical details behind a user-friendly graphical interface, thus liberating scientists from having to perform complicated operational procedures. Users are guided through the user interface to deploy a Hadoop cloud within in-house computing environments and to run applications specifically targeted for bioinformatics, including CloudBurst, CloudBrush, and CloudRS. One may also use CloudDOE on top of a public cloud. CloudDOE consists of three wizards, i.e., Deploy, Operate, and Extend wizards. Deploy wizard is designed to aid the system administrator to deploy a Hadoop cloud. It installs Java runtime environment version 1.6 and Hadoop version 0.20.203, and initiates the service automatically. Operate wizard allows the user to run a MapReduce application on the dashboard list. To extend the dashboard list, the administrator may install a new MapReduce application using Extend wizard. CloudDOE is a user-friendly tool for deploying a Hadoop cloud. Its smart wizards substantially reduce the complexity and costs of deployment, execution, enhancement, and management. Interested users may collaborate to improve the source code of CloudDOE to further incorporate more MapReduce bioinformatics tools into CloudDOE and support next-generation big data open source tools, e.g., Hadoop BigTop and Spark. CloudDOE is distributed under Apache License 2.0 and is freely available at http://clouddoe.iis.sinica.edu.tw/.

CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce

PubMed Central

Chung, Wei-Chun; Chen, Chien-Chih; Ho, Jan-Ming; Lin, Chung-Yen; Hsu, Wen-Lian; Wang, Yu-Chun; Lee, D. T.; Lai, Feipei; Huang, Chih-Wei; Chang, Yu-Jung

2014-01-01

Background Explosive growth of next-generation sequencing data has resulted in ultra-large-scale data sets and ensuing computational problems. Cloud computing provides an on-demand and scalable environment for large-scale data analysis. Using a MapReduce framework, data and workload can be distributed via a network to computers in the cloud to substantially reduce computational latency. Hadoop/MapReduce has been successfully adopted in bioinformatics for genome assembly, mapping reads to genomes, and finding single nucleotide polymorphisms. Major cloud providers offer Hadoop cloud services to their users. However, it remains technically challenging to deploy a Hadoop cloud for those who prefer to run MapReduce programs in a cluster without built-in Hadoop/MapReduce. Results We present CloudDOE, a platform-independent software package implemented in Java. CloudDOE encapsulates technical details behind a user-friendly graphical interface, thus liberating scientists from having to perform complicated operational procedures. Users are guided through the user interface to deploy a Hadoop cloud within in-house computing environments and to run applications specifically targeted for bioinformatics, including CloudBurst, CloudBrush, and CloudRS. One may also use CloudDOE on top of a public cloud. CloudDOE consists of three wizards, i.e., Deploy, Operate, and Extend wizards. Deploy wizard is designed to aid the system administrator to deploy a Hadoop cloud. It installs Java runtime environment version 1.6 and Hadoop version 0.20.203, and initiates the service automatically. Operate wizard allows the user to run a MapReduce application on the dashboard list. To extend the dashboard list, the administrator may install a new MapReduce application using Extend wizard. Conclusions CloudDOE is a user-friendly tool for deploying a Hadoop cloud. Its smart wizards substantially reduce the complexity and costs of deployment, execution, enhancement, and management. Interested users may collaborate to improve the source code of CloudDOE to further incorporate more MapReduce bioinformatics tools into CloudDOE and support next-generation big data open source tools, e.g., Hadoop BigTop and Spark. Availability: CloudDOE is distributed under Apache License 2.0 and is freely available at http://clouddoe.iis.sinica.edu.tw/. PMID:24897343

ChIP-chip.

PubMed

Kim, Tae Hoon; Dekker, Job

2018-05-01

ChIP-chip can be used to analyze protein-DNA interactions in a region-wide and genome-wide manner. DNA microarrays contain PCR products or oligonucleotide probes that are designed to represent genomic sequences. Identification of genomic sites that interact with a specific protein is based on competitive hybridization of the ChIP-enriched DNA and the input DNA to DNA microarrays. The ChIP-chip protocol can be divided into two main sections: Amplification of ChIP DNA and hybridization of ChIP DNA to arrays. A large amount of DNA is required to hybridize to DNA arrays, and hybridization to a set of multiple commercial arrays that represent the entire human genome requires two rounds of PCR amplifications. The relative hybridization intensity of ChIP DNA and that of the input DNA is used to determine whether the probe sequence is a potential site of protein-DNA interaction. Resolution of actual genomic sites bound by the protein is dependent on the size of the chromatin and on the genomic distance between the probes on the array. As with expression profiling using gene chips, ChIP-chip experiments require multiple replicates for reliable statistical measure of protein-DNA interactions. © 2018 Cold Spring Harbor Laboratory Press.

Multiplex APLP System for High-Resolution Haplogrouping of Extremely Degraded East-Asian Mitochondrial DNAs

PubMed Central

Kakuda, Tsuneo; Shojo, Hideki; Tanaka, Mayumi; Nambiar, Phrabhakaran; Minaguchi, Kiyoshi; Umetsu, Kazuo; Adachi, Noboru

2016-01-01

Mitochondrial DNA (mtDNA) serves as a powerful tool for exploring matrilineal phylogeographic ancestry, as well as for analyzing highly degraded samples, because of its polymorphic nature and high copy numbers per cell. The recent advent of complete mitochondrial genome sequencing has led to improved techniques for phylogenetic analyses based on mtDNA, and many multiplex genotyping methods have been developed for the hierarchical analysis of phylogenetically important mutations. However, few high-resolution multiplex genotyping systems for analyzing East-Asian mtDNA can be applied to extremely degraded samples. Here, we present a multiplex system for analyzing mitochondrial single nucleotide polymorphisms (mtSNPs), which relies on a novel amplified product-length polymorphisms (APLP) method that uses inosine-flapped primers and is specifically designed for the detailed haplogrouping of extremely degraded East-Asian mtDNAs. We used fourteen 6-plex polymerase chain reactions (PCRs) and subsequent electrophoresis to examine 81 haplogroup-defining SNPs and 3 insertion/deletion sites, and we were able to securely assign the studied mtDNAs to relevant haplogroups. Our system requires only 1×10−13 g (100 fg) of crude DNA to obtain a full profile. Owing to its small amplicon size (<110 bp), this new APLP system was successfully applied to extremely degraded samples for which direct sequencing of hypervariable segments using mini-primer sets was unsuccessful, and proved to be more robust than conventional APLP analysis. Thus, our new APLP system is effective for retrieving reliable data from extremely degraded East-Asian mtDNAs. PMID:27355212

Multiplex APLP System for High-Resolution Haplogrouping of Extremely Degraded East-Asian Mitochondrial DNAs.

PubMed

Kakuda, Tsuneo; Shojo, Hideki; Tanaka, Mayumi; Nambiar, Phrabhakaran; Minaguchi, Kiyoshi; Umetsu, Kazuo; Adachi, Noboru

2016-01-01

Mitochondrial DNA (mtDNA) serves as a powerful tool for exploring matrilineal phylogeographic ancestry, as well as for analyzing highly degraded samples, because of its polymorphic nature and high copy numbers per cell. The recent advent of complete mitochondrial genome sequencing has led to improved techniques for phylogenetic analyses based on mtDNA, and many multiplex genotyping methods have been developed for the hierarchical analysis of phylogenetically important mutations. However, few high-resolution multiplex genotyping systems for analyzing East-Asian mtDNA can be applied to extremely degraded samples. Here, we present a multiplex system for analyzing mitochondrial single nucleotide polymorphisms (mtSNPs), which relies on a novel amplified product-length polymorphisms (APLP) method that uses inosine-flapped primers and is specifically designed for the detailed haplogrouping of extremely degraded East-Asian mtDNAs. We used fourteen 6-plex polymerase chain reactions (PCRs) and subsequent electrophoresis to examine 81 haplogroup-defining SNPs and 3 insertion/deletion sites, and we were able to securely assign the studied mtDNAs to relevant haplogroups. Our system requires only 1×10-13 g (100 fg) of crude DNA to obtain a full profile. Owing to its small amplicon size (<110 bp), this new APLP system was successfully applied to extremely degraded samples for which direct sequencing of hypervariable segments using mini-primer sets was unsuccessful, and proved to be more robust than conventional APLP analysis. Thus, our new APLP system is effective for retrieving reliable data from extremely degraded East-Asian mtDNAs.

Stochastic sampling effects in STR typing: Implications for analysis and interpretation.

PubMed

Timken, Mark D; Klein, Sonja B; Buoncristiani, Martin R

2014-07-01

The analysis and interpretation of forensic STR typing results can become more complicated when reduced template amounts are used for PCR amplification due to increased stochastic effects. These effects are typically observed as reduced heterozygous peak-height balance and increased frequency of undetected alleles (allelic "dropout"). To investigate the origins of these effects, a study was performed using the AmpFlSTR(®) Identifiler Plus(®) and MiniFiler(®) kits to amplify replicates from a dilution series of NIST Human DNA Quantitation Standard (SRM(®) 2372A). The resulting amplicons were resolved and detected on two different genetic analyzer platforms, the Applied Biosystems 3130xL and 3500 analyzers. Results from our study show that the four different STR/genetic analyzer combinations exhibited very similar peak-height ratio statistics when normalized for the amount of template DNA in the PCR. Peak-height ratio statistics were successfully modeled using the Poisson distribution to simulate pre-PCR stochastic sampling of the alleles, confirming earlier explanations that sampling is the primary source for peak-height imbalance in reduced template dilutions. In addition, template-based pre-PCR sampling simulations also successfully predicted allelic dropout frequencies, as modeled by logistic regression methods, for the low-template DNA dilutions. We discuss the possibility that an accurately quantified DNA template might be used to characterize the linear signal response for data collected using different STR kits or genetic analyzer platforms, so as to provide a standardized approach for comparing results obtained from different STR/CE combinations and to aid in validation studies. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Challenges towards realization of health care sector goals of Tanzania development vision 2025: training and deployment of graduate human resource for health.

PubMed

Siril, Nathanael; Kiwara, Angwara; Simba, Daud

2013-06-01

Human resource for health (HRH) is an essential building block for effective and efficient health care system. In Tanzania this component is faced by many challenges which in synergy with others make the health care system inefficient. In vision 2025 the country recognizes the importance of the health care sector in attaining quality livelihood for its citizens. The vision is in its 13th year since its launch. Given the central role of HRH in attainment of this vision, how the HRH is trained and deployed deserves a deeper understanding. To analyze the factors affecting training and deployment process of graduate level HRH of three core cadres; Medical Doctors, Doctor of Dental Surgery and Bachelor of Pharmacy towards realization of development vision 2025. Explorative study design in five training institutions for health and Ministry of Health and Social Welfare (MoHSW) headquarters utilizing in-depth interviews, observations and review of available documents methodology. The training Institutions which are cornerstone for HRH training are understaffed, underfunded (donor dependent), have low admitting capacities and lack co-ordination with other key stakeholders dealing with health. The deployment of graduate level HRH is affected by; limited budget, decision on deployment handled by another ministry rather than MoHSW, competition between health care sector and other sectors and lack of co-ordination between employer, trainers and other key health care sector stakeholders. Awareness on vision 2025 is low in the training institutions. For the vision 2025 health care sector goals to be realized well devised strategies on raising its awareness in the training institutions is recommended. Quality livelihood as stated in vision 2025 will be a forgotten dream if the challenges facing the training and deployment of graduate level HRH will not be addressed timely. It is the authors' view that reduction of donor dependency syndrome, extension of retirement age for academic Staffs in the training institutions for health and synergizing the training and deployment of the graduate level HRH can be among the initial strategies towards addressing these challenges.

Integrating DNA barcode data and taxonomic practice: determination, discovery, and description.

PubMed

Goldstein, Paul Z; DeSalle, Rob

2011-02-01

DNA barcodes, like traditional sources of taxonomic information, are potentially powerful heuristics in the identification of described species but require mindful analytical interpretation. The role of DNA barcoding in generating hypotheses of new taxa in need of formal taxonomic treatment is discussed, and it is emphasized that the recursive process of character evaluation is both necessary and best served by understanding the empirical mechanics of the discovery process. These undertakings carry enormous ramifications not only for the translation of DNA sequence data into taxonomic information but also for our comprehension of the magnitude of species diversity and its disappearance. This paper examines the potential strengths and pitfalls of integrating DNA sequence data, specifically in the form of DNA barcodes as they are currently generated and analyzed, with taxonomic practice.

Non-homologous end joining mediated DNA repair is impaired in the NUP98-HOXD13 mouse model for myelodysplastic syndrome.

PubMed

Puthiyaveetil, Abdul Gafoor; Reilly, Christopher M; Pardee, Timothy S; Caudell, David L

2013-01-01

Chromosomal translocations typically impair cell differentiation and often require secondary mutations for malignant transformation. However, the role of a primary translocation in the development of collaborating mutations is debatable. To delineate the role of leukemic translocation NUP98-HOXD13 (NHD13) in secondary mutagenesis, DNA break and repair mechanisms in stimulated mouse B lymphocytes expressing NHD13 were analyzed. Our results showed significantly reduced expression of non-homologous end joining (NHEJ)-mediated DNA repair genes, DNA Pkcs, DNA ligase4, and Xrcc4 leading to cell cycle arrest at G2/M phase. Our results showed that expression of NHD13 fusion gene resulted in impaired NHEJ-mediated DNA break repair. Copyright © 2012 Elsevier Ltd. All rights reserved.