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Sample records for caa um novo

  1. Software for CAA compliance

    SciTech Connect

    Elliott, T.C.

    1994-12-01

    Because of the enormous amount of emissions data that must be collected and reported quarterly to EPA, software is becoming as essential as hardware in the compliance procedure. This article reports on some problems being encountered and their solutions. By November 15, 1993, 50 some electric utilities affected by Phase 1 of the Clean Air Act Amendments of 1990 (CAA) Title 4 had begun continuous emissions monitoring (CEM) to meet the requirements of 40CFR75. By January 1, 1995, roughly 100 Phase 2-affected utilities must implement their CEM programs to comply with the same regulations. In both cases, software for the data-acquisition and handling system (DAHS) is the overarching challenge. The quantity of CEM data that must be reported quarterly by a DAHS, in computer-readable form, is enormous. Each day, the DAHS for a typical Phase 1 unit generates 225 records of CEM data in EPA's prescribed format, consisting of 690 critical data fields. Thus, in an average quarter, a utility with five units will submit to EPA a quarterly report comprising over 100,000 records and 310,000 critical data fields. Only with quality DAHS software can these reports be generated.

  2. OV-Wav: um novo pacote para análise multiescalar em astronomia

    NASA Astrophysics Data System (ADS)

    Pereira, D. N. E.; Rabaça, C. R.

    2003-08-01

    Wavelets e outras formas de análise multiescalar têm sido amplamente empregadas em diversas áreas do conhecimento, sendo reconhecidamente superiores a técnicas mais tradicionais, como as análises de Fourier e de Gabor, em certas aplicações. Embora a teoria dos wavelets tenha começado a ser elaborada há quase trinta anos, seu impacto no estudo de imagens astronômicas tem sido pequeno até bem recentemente. Apresentamos um conjunto de programas desenvolvidos ao longo dos últimos três anos no Observatório do Valongo/UFRJ que possibilitam aplicar essa poderosa ferramenta a problemas comuns em astronomia, como a remoção de ruído, a detecção hierárquica de fontes e a modelagem de objetos com perfis de brilho arbitrários em condições não ideais. Este pacote, desenvolvido para execução em plataforma IDL, teve sua primeira versão concluída recentemente e está sendo disponibilizado à comunidade científica de forma aberta. Mostramos também resultados de testes controlados ao quais submetemos os programas, com a sua aplicação a imagens artificiais, com resultados satisfatórios. Algumas aplicações astrofísicas foram estudadas com o uso do pacote, em caráter experimental, incluindo a análise da componente de luz difusa em grupos compactos de galáxias de Hickson e o estudo de subestruturas de nebulosas planetárias no espaço multiescalar.

  3. CAA for Jet Noise Physics

    NASA Technical Reports Server (NTRS)

    Mankbadi, Reda

    2001-01-01

    Dr. Mankbadi summarized recent CAA results. Examples of the effect of various boundary condition schemes on the computed acoustic field, for a point source in a uniform flow, were shown. Solutions showing the impact of inflow excitations on the result were also shown. Results from a large eddy simulation, using a fourth-order MacCormack scheme with a Smagorinsky sub-grid turbulence model, were shown for a Mach 2.1 unheated jet. The results showed that the results were free from spurious modes. Results were shown for a Mach 1.4 jet using LES in the near field and the Kirchhoff method for the far field. Predicted flow field characteristics were shown to be in good agreement with data and predicted far field directivities were shown to be in qualitative agree with experimental measurements.

  4. BUDDA (Bulge/Disk Decomposition Analysis) - um novo programa para análise estrutural de galáxias

    NASA Astrophysics Data System (ADS)

    Gadotti, D. A.; de Souza, R. E.; Dos Anjos, S.

    2003-08-01

    Tem sido prática comum nos últimos anos estudar a distribuição de luminosidade em galáxias fazendo uso da informação contida em toda a imagem da galáxia, já que esta técnica tem se mostrado muito mais confiável do que o simples ajuste de perfis radiais de luminosidade. Através destes estudos bidimensionais, melhores resultados tem sido obtidos na análise e.g. do Plano Fundamental, de correlações entre os parâmetros estruturais de galáxias, de sub-estruturas como barras e anéis nucleares etc. Apresentamos um novo código bidimensional, o BUDDA, de análise estrutural de galáxias, que será disponibilizado para a comunidade. Desenvolvido por nós, o código determina os parâmetros estruturais de galáxias de forma prática e robusta, e pode ser aplicado genericamente em qualquer estudo sobre a formação, evolução e estrutura de galáxias. O programa ainda permite a avaliação direta de sub-estruturas, através de imagens residuais que são obtidas ao se subtrair, das imagens originais, bojo e disco sintéticos que melhor representam essas componentes da galáxia sob consideração. Será apresentada a forma de utilização do código, bem como séries de testes que atestam a sua funcionalidade. Além disso, os resultados da aplicação do código em uma amostra de 51 galáxias serão expostos como exemplo prático, e do seu enorme potencial de uso.

  5. CEM system: Lynchpin holding CAA compliance together

    SciTech Connect

    Elliott, T.C.

    1995-05-01

    Continuous emissions monitoring (CEM) and associated reporting systems promise to be among the most important subjects in the electric power industry this year. With the first major deadline stipulated by the Clean Air Act amendments of 1990 (CAA) now past, viable CEM/reporting systems are absolutely essential to the compliance and allowance-tracking of many powerplants. The implications and challenges of meeting CAA`s Title 5, which went into effect on January 1, 1995, are discussed here. Title 5 consolidates all existing air-pollution regulations into one comprehensive but ungainly operating-permit program. It stipulates that powerplant operators must file their permit applications; that is, estimate all point-source and fugitive emissions, specify all regulations that apply to them, and show how each rule will be met.

  6. Cluster CAA Module for PaPCo

    NASA Astrophysics Data System (ADS)

    Faden, J.; Åsnes, A.; Friedel, R.; Taylor, M.; McCaffrey, S.; Perry, C.; Goldstein, M. L.

    A PaPCo module for visualization of data from the CAA has been developed. This module retrieves data from the CAA web interface, and allows for discovery and plotting of new datasets. PaPCo is modular, open source IDL software that uses plug-in modules to bring new datasets on to a stack of time series plots (www.papco.org). PaPCo includes modules for plotting data from Cluster/PEACE and Cluster/RAPID, CDA Web data which includes Cluster Prime Parameters, and various modules from CRRES, POLAR, GPS, and many other spacecraft. The Cluster CAA module is presented, as well as a brief description of PaPCo's use and installation procedure.

  7. CAA broadband noise prediction for aeroacoustic design

    NASA Astrophysics Data System (ADS)

    Ewert, R.; Dierke, J.; Siebert, J.; Neifeld, A.; Appel, C.; Siefert, M.; Kornow, O.

    2011-08-01

    The current status of a computational aeroacoustics (CAA) approach to simulate broadband noise is reviewed. The method rests on the use of steady Reynolds averaged Navier-Stokes (RANS) simulation to describe the time-averaged motion of turbulent flow. By means of synthetic turbulence the steady one-point statistics (e.g. turbulence kinetic energy) and turbulent length- and time-scales of RANS are translated into fluctuations having statistics that very accurately reproduce the initial RANS target-setting. The synthetic fluctuations are used to prescribe sound sources which drive linear perturbation equations. The whole approach represents a methodology to solve statistical noise theory with state-of-the-art CAA tools in the time-domain. A brief overview of the synthetic turbulence model and its numerical discretization in terms of the random particle-mesh (RPM) and fast random particle-mesh (FRPM) method is given. Results are presented for trailing-edge noise, slat noise, and jet noise. Some problems related to the formulation of vortex sound sources are discussed.

  8. Second Computational Aeroacoustics (CAA) Workshop on Benchmark Problems

    NASA Technical Reports Server (NTRS)

    Tam, C. K. W. (Editor); Hardin, J. C. (Editor)

    1997-01-01

    The proceedings of the Second Computational Aeroacoustics (CAA) Workshop on Benchmark Problems held at Florida State University are the subject of this report. For this workshop, problems arising in typical industrial applications of CAA were chosen. Comparisons between numerical solutions and exact solutions are presented where possible.

  9. Quick Win or Slow Burn: Modelling UK HE CAA Uptake

    ERIC Educational Resources Information Center

    Warburton, Bill

    2009-01-01

    The uptake of CAA in UK higher education (HE) on a large scale lags behind the expectations of CAA specialists. A research project was undertaken with the aim of discovering and addressing the underlying reasons for this. The research was conducted according to Strauss and Corbin's (1998) prescription for grounded theory (GT) research. During…

  10. Beta test results for the CAA mini-SAM system

    SciTech Connect

    Johnson, R.C.; Monagle, M.

    1997-04-01

    The mission of the Chemical Analysis Automation (CAA) Program is to automate methods for chemical analysis of environmental samples. To accomplish this mission, the CAA team has developed automated laboratory systems based on a plug-and-work strategy for integrating components. Realizing that standardization is the key to implementing this strategy, CAA has developed, demonstrated, and encouraged commercialization of standards for laboratory automation. While the CAA mission is driven by the analyses in support of the extensive remediation programs of the Departments of Energy and Defense, it also impacts any industry that depends upon high volumes of repetitive chemical analysis. A Standard Analysis Method (SAM) is any collection of hardware and software used to automate part or all of a method. The method automated for the Mini-SAM testing is EPA Method 3550, which outlines semivolatiles extraction by sonication. The list of semivolatiles includes the polychlorinated biphenyl (PCB) analytes of interest. The basic building block of a SAM is the Standard Laboratory Module (SLM). For the Mini-SAM test an automated sonication SLM and an automated concentration SLM were configured to perform the extraction and concentration processes. The Mini-SAM differs from the Full-SAM in that a fully automated delivery of materials, samples, and extracts is not required. The intent of the Beta Test of the Mini-SAM was threefold. Firstly, the Mini-SAM Beta Test met a milestone mandated by the Department of Energy in the course of the program effort. Secondly, the CAA Program secured an independent assessment of the equipment and its capabilities from Assagai Analytical Laboratory. Lastly, the Program captured real-world sample data. The independent assessment, coupled with CAA observation of equipment performance, was used to determine strengths and weaknesses of the Mini-SAM and to compile possible modifications for CAA engineers to address.

  11. Benchmark Solutions for Computational Aeroacoustics (CAA) Code Validation

    NASA Technical Reports Server (NTRS)

    Scott, James R.

    2004-01-01

    NASA has conducted a series of Computational Aeroacoustics (CAA) Workshops on Benchmark Problems to develop a set of realistic CAA problems that can be used for code validation. In the Third (1999) and Fourth (2003) Workshops, the single airfoil gust response problem, with real geometry effects, was included as one of the benchmark problems. Respondents were asked to calculate the airfoil RMS pressure and far-field acoustic intensity for different airfoil geometries and a wide range of gust frequencies. This paper presents the validated that have been obtained to the benchmark problem, and in addition, compares them with classical flat plate results. It is seen that airfoil geometry has a strong effect on the airfoil unsteady pressure, and a significant effect on the far-field acoustic intensity. Those parts of the benchmark problem that have not yet been adequately solved are identified and presented as a challenge to the CAA research community.

  12. Fourth Computational Aeroacoustics (CAA) Workshop on Benchmark Problems

    NASA Technical Reports Server (NTRS)

    Dahl, Milo D. (Editor)

    2004-01-01

    This publication contains the proceedings of the Fourth Computational Aeroacoustics (CAA) Workshop on Benchmark Problems. In this workshop, as in previous workshops, the problems were devised to gauge the technological advancement of computational techniques to calculate all aspects of sound generation and propagation in air directly from the fundamental governing equations. A variety of benchmark problems have been previously solved ranging from simple geometries with idealized acoustic conditions to test the accuracy and effectiveness of computational algorithms and numerical boundary conditions; to sound radiation from a duct; to gust interaction with a cascade of airfoils; to the sound generated by a separating, turbulent viscous flow. By solving these and similar problems, workshop participants have shown the technical progress from the basic challenges to accurate CAA calculations to the solution of CAA problems of increasing complexity and difficulty. The fourth CAA workshop emphasized the application of CAA methods to the solution of realistic problems. The workshop was held at the Ohio Aerospace Institute in Cleveland, Ohio, on October 20 to 22, 2003. At that time, workshop participants presented their solutions to problems in one or more of five categories. Their solutions are presented in this proceedings along with the comparisons of their solutions to the benchmark solutions or experimental data. The five categories for the benchmark problems were as follows: Category 1:Basic Methods. The numerical computation of sound is affected by, among other issues, the choice of grid used and by the boundary conditions. Category 2:Complex Geometry. The ability to compute the sound in the presence of complex geometric surfaces is important in practical applications of CAA. Category 3:Sound Generation by Interacting With a Gust. The practical application of CAA for computing noise generated by turbomachinery involves the modeling of the noise source mechanism as a

  13. Third Computational Aeroacoustics (CAA) Workshop on Benchmark Problems

    NASA Technical Reports Server (NTRS)

    Dahl, Milo D. (Editor)

    2000-01-01

    The proceedings of the Third Computational Aeroacoustics (CAA) Workshop on Benchmark Problems cosponsored by the Ohio Aerospace Institute and the NASA Glenn Research Center are the subject of this report. Fan noise was the chosen theme for this workshop with representative problems encompassing four of the six benchmark problem categories. The other two categories were related to jet noise and cavity noise. For the first time in this series of workshops, the computational results for the cavity noise problem were compared to experimental data. All the other problems had exact solutions, which are included in this report. The Workshop included a panel discussion by representatives of industry. The participants gave their views on the status of applying computational aeroacoustics to solve practical industry related problems and what issues need to be addressed to make CAA a robust design tool.

  14. Preparing the CAA Title V operating permit application

    SciTech Connect

    Wyles, T.R. )

    1994-01-01

    The CAA amendments contain 11 new and amended titles, including enhanced non-attainment area provisions, additional conditions for controlling hazardous air pollutants, expanded monitoring and record keeping requirements, and increased enforcement authority. The cornerstone of the regulation is the operating permits program (Title V). In the past, permits have been issued to construct or modify sources, and some sources have been permitted in states with operating permit programs. Such programs will remain in effect. However, under the new CAA, most emissions sources will be required to have an operating permit. Title V's permit provision initially affects about 34,000 major facilities and may affect another 350,000 smaller sources in the future. The amendments also increase the number of regulated pollutants from 21 to about 200. Operating permits limit emissions from manufacturing operations, and place further restrictions on raw materials and products.

  15. Nitric oxide activation by caa3 oxidoreductase from Thermus thermophilus.

    PubMed

    Ohta, Takehiro; Soulimane, Tewfik; Kitagawa, Teizo; Varotsis, Constantinos

    2015-04-28

    Visible and UV-resonance Raman spectroscopy was employed to investigate the reaction of NO with cytochrome caa3 from Thermus thermophilus. We show the formation of the hyponitrite (HO-N=N-O)(-) bound to the heme a3 species (νN=N = 1330 cm(-1)) forming a high spin complex in the oxidized heme a3 Fe/CuB binuclear center of caa3-oxidoreductase. In the absence of heme a3 Fe(2+)-NO formation, the electron required for the formation of the N=N bond originates from the autoreduction of CuB by NO, producing nitrite. With the identification of the hyponitrite intermediate the hypothesis of a common phylogeny of aerobic respiration and bacterial denitrification is fully supported and the mechanism for the 2e(-)/2H(+) reduction of NO to N2O can be described with more certainty. PMID:25820937

  16. Hybrid CFD/CAA Modeling for Liftoff Acoustic Predictions

    NASA Technical Reports Server (NTRS)

    Strutzenberg, Louise L.; Liever, Peter A.

    2011-01-01

    This paper presents development efforts at the NASA Marshall Space flight Center to establish a hybrid Computational Fluid Dynamics and Computational Aero-Acoustics (CFD/CAA) simulation system for launch vehicle liftoff acoustics environment analysis. Acoustic prediction engineering tools based on empirical jet acoustic strength and directivity models or scaled historical measurements are of limited value in efforts to proactively design and optimize launch vehicles and launch facility configurations for liftoff acoustics. CFD based modeling approaches are now able to capture the important details of vehicle specific plume flow environment, identifY the noise generation sources, and allow assessment of the influence of launch pad geometric details and sound mitigation measures such as water injection. However, CFD methodologies are numerically too dissipative to accurately capture the propagation of the acoustic waves in the large CFD models. The hybrid CFD/CAA approach combines the high-fidelity CFD analysis capable of identifYing the acoustic sources with a fast and efficient Boundary Element Method (BEM) that accurately propagates the acoustic field from the source locations. The BEM approach was chosen for its ability to properly account for reflections and scattering of acoustic waves from launch pad structures. The paper will present an overview of the technology components of the CFD/CAA framework and discuss plans for demonstration and validation against test data.

  17. Cluster Ion Spectrometry (CIS) Data Archiving in the CAA

    NASA Astrophysics Data System (ADS)

    Dandouras, I. S.; Barthe, A.; Penou, E.; Brunato, S.; Reme, H.; Kistler, L. M.; Blagau, A.; Facsko, G.; Kronberg, E.; Laakso, H. E.

    2009-12-01

    The Cluster Active Archive (CAA) aims at preserving the four Cluster spacecraft data, so that they are usable in the long-term by the scientific community as well as by the instrument team PIs and Co-Is. This implies that the data are filed together with the descriptive and documentary elements making it possible to select and interpret them. The CIS (Cluster Ion Spectrometry) experiment is a comprehensive ionic plasma spectrometry package onboard the four Cluster spacecraft, capable of obtaining full three-dimensional ion distributions (about 0 to 40 keV/e) with a time resolution of one spacecraft spin (4 sec) and with mass-per-charge composition determination. The CIS package consists of two different instruments, a Hot Ion Analyser (HIA) and a time-of-flight ion Composition Distribution Function (CODIF) analyser. For the archival of the CIS data a multi-level approach has been adopted. The CAA archival includes processed raw data (Level 1 data), moments of the ion distribution functions (Level 2 data), and calibrated high-resolution data in a variety of physical units (Level 3 data). The latter are 3-D ion distribution functions and 2-D pitch-angle distributions. In addition, a software package has been developed to allow the CAA user to interactively calculate partial or total moments of the ion distributions. Instrument cross-calibration has been an important activity in preparing the data for archival. The CIS data archive includes also experiment documentation, graphical products for browsing through the data, and data caveats. In addition, data quality indexes are under preparation, to help the user. Given the complexity of an ion spectrometer, and the variety of its operational modes, each one being optimised for a different magnetospheric region or measurement objective, consultation of the data caveats by the end user will always be a necessary step in the data analysis.

  18. Many new CAA requirements, deadlines scheduled during next five years

    SciTech Connect

    Iwanchuk, R. )

    1993-06-01

    Since the CAA Amendments were signed into law, EPA's rulemaking process has been underway, delineating specific compliance regulations. Many of the legislation's requirements and deadlines will be finalized over the next five years. The following list summarizes upcoming regulations and anticipated compliance deadlines. Title I applies to VOC and NOx controls in ozone non-attainment areas. Title III contains the Hazardous Organic National Emission Standard for Hazardous Air Pollutants. Title V consists of the operating permit rule. Title VII applies to the enhanced monitoring rule. The rule will require major sources to enhance monitoring systems to determine whether compliance is continuous or intermittent.

  19. CAA for Jet Noise Physics: Issues and Recent Progress

    NASA Technical Reports Server (NTRS)

    Mankbadi, Reda

    2001-01-01

    Dr. Mankbadi summarized recent CAA results. Examples of the effect of various boundary condition schemes on the computed acoustic field, for a point source in a uniform flow, were shown. Solutions showing the impact of inflow excitations on the result were also shown. Results from a large eddy simulation, using a fourth-order MacCormack scheme with a Smagorinsky sub-grid turbulence model, were shown for a Mach 2.1 unheated jet. The results showed that the results were free from spurious modes. Results were shown for a Mach 1.4 jet using LES in the near field and the Kirchhoff method for the far field. Predicted flow field characteristics were shown to be in good agreement with data and predicted far field directivities were shown to be in qualitative agree with experimental measurements.

  20. 40 CFR 59.1 - Final determinations under Section 183(e)(3)(C) of the CAA.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... furniture coatings; (b) Aerospace coatings; (c) Shipbuilding and repair coatings; (d) Lithographic printing...(e)(3)(C) of the CAA. 59.1 Section 59.1 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... COMMERCIAL PRODUCTS General § 59.1 Final determinations under Section 183(e)(3)(C) of the CAA. This...

  1. 40 CFR 59.1 - Final determinations under Section 183(e)(3)(C) of the CAA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... furniture coatings; (b) Aerospace coatings; (c) Shipbuilding and repair coatings; (d) Lithographic printing...(e)(3)(C) of the CAA. 59.1 Section 59.1 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... COMMERCIAL PRODUCTS General § 59.1 Final determinations under Section 183(e)(3)(C) of the CAA. This...

  2. 40 CFR 59.1 - Final determinations under Section 183(e)(3)(C) of the CAA.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... furniture coatings; (b) Aerospace coatings; (c) Shipbuilding and repair coatings; (d) Lithographic printing...(e)(3)(C) of the CAA. 59.1 Section 59.1 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... COMMERCIAL PRODUCTS General § 59.1 Final determinations under Section 183(e)(3)(C) of the CAA. This...

  3. 40 CFR 59.1 - Final determinations under Section 183(e)(3)(C) of the CAA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...(e)(3)(C) of the CAA. 59.1 Section 59.1 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... COMMERCIAL PRODUCTS General § 59.1 Final determinations under Section 183(e)(3)(C) of the CAA. This section... materials; (e) Letterpress printing materials; (f) Flexible packaging printing materials; (g) Flat...

  4. Using Focus Groups to Investigate the Presence of Formative Feedback in CAA

    ERIC Educational Resources Information Center

    Broughton, Stephen; Hernandez-Martinez, Paul; Robinson, Carol L.

    2012-01-01

    The aim of this project was to examine the effectiveness of feedback offered by computer-aided assessment (CAA). CAA provides practice tests for undergraduates, and feedback to help them improve their scores and mathematical understanding. However, there is a lack of evidence-based literature on the effect of formative feedback in mathematics…

  5. An optimized spectral difference scheme for CAA problems

    NASA Astrophysics Data System (ADS)

    Gao, Junhui; Yang, Zhigang; Li, Xiaodong

    2012-05-01

    In the implementation of spectral difference (SD) method, the conserved variables at the flux points are calculated from the solution points using extrapolation or interpolation schemes. The errors incurred in using extrapolation and interpolation would result in instability. On the other hand, the difference between the left and right conserved variables at the edge interface will introduce dissipation to the SD method when applying a Riemann solver to compute the flux at the element interface. In this paper, an optimization of the extrapolation and interpolation schemes for the fourth order SD method on quadrilateral element is carried out in the wavenumber space through minimizing their dispersion error over a selected band of wavenumbers. The optimized coefficients of the extrapolation and interpolation are presented. And the dispersion error of the original and optimized schemes is plotted and compared. An improvement of the dispersion error over the resolvable wavenumber range of SD method is obtained. The stability of the optimized fourth order SD scheme is analyzed. It is found that the stability of the 4th order scheme with Chebyshev-Gauss-Lobatto flux points, which is originally weakly unstable, has been improved through the optimization. The weak instability is eliminated completely if an additional second order filter is applied on selected flux points. One and two dimensional linear wave propagation analyses are carried out for the optimized scheme. It is found that in the resolvable wavenumber range the new SD scheme is less dispersive and less dissipative than the original scheme, and the new scheme is less anisotropic for 2D wave propagation. The optimized SD solver is validated with four computational aeroacoustics (CAA) workshop benchmark problems. The numerical results with optimized schemes agree much better with the analytical data than those with the original schemes.

  6. 2 CFR 1532.1120 - What is the purpose of CAA or CWA disqualification?

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... and Reinstatement Under the Clean Air Act and Clean Water Act § 1532.1120 What is the purpose of CAA or CWA disqualification? As provided for in Executive Order 11738 (3 CFR, 1973 Comp., p. 799),...

  7. 2 CFR 1532.1120 - What is the purpose of CAA or CWA disqualification?

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... and Reinstatement Under the Clean Air Act and Clean Water Act § 1532.1120 What is the purpose of CAA or CWA disqualification? As provided for in Executive Order 11738 (3 CFR, 1973 Comp., p. 799),...

  8. 2 CFR 1532.1120 - What is the purpose of CAA or CWA disqualification?

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... and Reinstatement Under the Clean Air Act and Clean Water Act § 1532.1120 What is the purpose of CAA or CWA disqualification? As provided for in Executive Order 11738 (3 CFR, 1973 Comp., p. 799),...

  9. 2 CFR 1532.1120 - What is the purpose of CAA or CWA disqualification?

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... and Reinstatement Under the Clean Air Act and Clean Water Act § 1532.1120 What is the purpose of CAA or CWA disqualification? As provided for in Executive Order 11738 (3 CFR, 1973 Comp., p. 799),...

  10. Multi centric origin of Hb D-Punjab [beta121(GH4)Glu-->Gln, GAA>CAA].

    PubMed

    Yavarian, Majid; Karimi, Mehran; Paran, Farideh; Neven, Catherine; Harteveld, Cornelis L; Giordano, Piero C

    2009-01-01

    Hb D-Punjab [beta121(GH4)Glu-->Gln, GAA>CAA], common in the northern Indian province, is often unexpectedly found in other populations. To study the multi centric origin of this variant which is causing sickle cell disease in association with Hb S [beta6(A3)Glu-->Val, GAG>GTG], we have examined the haplotype of the Hb D allele in different populations. We studied 43 alleles from south Iran (Hormozgan and Fars provinces) and 14 from Holland and Belgium using high performance liquid chromatography (HPLC), capillary electrophoresis, direct sequencing and/or restriction enzyme analysis. In Iranians, four haplotypes were observed at different frequencies: haplotype I [+ - - - -,+ +] at 67.5%, subhaplotype I' [+ - - - -,- +] at 17.5%, haplotype V [- + - - +,+ +] at 10.0% and haplotype III [- + - + +,+ +] at 5.0%. All European cases were on haplotype I. The occurrence of high Hb D frequencies on a single haplotype in specific regions can be expected if we consider founder effect and genetic drift mechanisms. However, considering that haplotype I is the most common haplotype worldwide, that Hb D-Punjab is reported in different populations on different haplotypes, and that codon beta121 is a site on which six different mutations are reported, we may expect to observe Hb D-Punjab in different populations, possibly because of a relatively higher occurrence of de novo mutations, generating unexpected risk from mixtures of allochtonous Hb S and indigenous Hb D-Punjab or vice versa. PMID:19958184

  11. CFD-CAA Coupled Calculations of a Tandem Cylinder Configuration to Assess Facility Installation Effects

    NASA Technical Reports Server (NTRS)

    Redonnet, Stephane; Lockard, David P.; Khorrami, Mehdi R.; Choudhari, Meelan M.

    2011-01-01

    This paper presents a numerical assessment of acoustic installation effects in the tandem cylinder (TC) experiments conducted in the NASA Langley Quiet Flow Facility (QFF), an open-jet, anechoic wind tunnel. Calculations that couple the Computational Fluid Dynamics (CFD) and Computational Aeroacoustics (CAA) of the TC configuration within the QFF are conducted using the CFD simulation results previously obtained at NASA LaRC. The coupled simulations enable the assessment of installation effects associated with several specific features in the QFF facility that may have impacted the measured acoustic signature during the experiment. The CFD-CAA coupling is based on CFD data along a suitably chosen surface, and employs a technique that was recently improved to account for installed configurations involving acoustic backscatter into the CFD domain. First, a CFD-CAA calculation is conducted for an isolated TC configuration to assess the coupling approach, as well as to generate a reference solution for subsequent assessments of QFF installation effects. Direct comparisons between the CFD-CAA calculations associated with the various installed configurations allow the assessment of the effects of each component (nozzle, collector, etc.) or feature (confined vs. free jet flow, etc.) characterizing the NASA LaRC QFF facility.

  12. 40 CFR 59.1 - Final determinations under Section 183(e)(3)(C) of the CAA.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 6 2013-07-01 2013-07-01 false Final determinations under Section 183(e)(3)(C) of the CAA. 59.1 Section 59.1 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL VOLATILE ORGANIC COMPOUND EMISSION STANDARDS FOR CONSUMER AND COMMERCIAL PRODUCTS General § 59.1...

  13. The caa3 terminal oxidase of Bacillus stearothermophilus. Transient spectroscopy of electron transfer and ligand binding.

    PubMed

    Giuffrè, A; D'Itri, E; Giannini, S; Brunori, M; Ubbink-Kok, T; Konings, W N; Antonini, G

    1996-06-14

    The thermophilic bacterium Bacillus stearothermophilus possesses a caa3-type terminal oxidase, which was previously purified (De Vrij, W., Heyne, R. I. R., and Konings, W. N. (1989) Eur. J. Biochem. 178, 763-770). We have carried out extensive kinetic experiments on the purified enzyme by stopped-flow time-resolved optical spectroscopy combined with singular value decomposition analysis. The results indicate a striking similarity of behavior between this enzyme and the electrostatic complex between mammalian cytochrome c and cytochrome c oxidase. CO binding to fully reduced caa3 occurs with a second order rate constant (k = 7.8 x 10(4)M-1 s-1) and an activation energy (E* = 6.1 kcal mol-1) similar to those reported for beef heart cytochrome c oxidase. Dithionite reduces cytochrome a with bimolecular kinetics, while cytochrome a3 (and CuB) is reduced via intramolecular electron transfer. When the fully reduced enzyme is mixed with O2, cytochrome a3, and cytochrome c are rapidly oxidized, whereas cytochrome a remains largely reduced in the first few milliseconds. When cyanide-bound caa3 is mixed with ascorbate plus TMPD, cytochrome c and cytochrome a are synchronously reduced; the value of the second order rate constant (k = 3 x 10(5) M-1 s-1 at 30 degrees C) suggests that cytochrome c is the electron entry site. Steady-state experiments indicate that cytochrome a has a redox potential higher than cytochrome c. The data from the reaction with O2 reveal a remarkable similarity in the kinetic, equilibrium, and optical properties of caa3 and the electrostatic complex cytochrome c/cytochrome c oxidase. PMID:8662862

  14. Electron transfer kinetics of caa3 oxidase from Bacillus stearothermophilus: a hypothesis for thermophilicity.

    PubMed Central

    Giuffrè, A; Watmough, N J; Giannini, S; Brunori, M; Konings, W N; Greenwood, C

    1999-01-01

    The O2 reaction and the reverse electron transfer of the thermophilic caa3 terminal oxidase of Bacillus stearothermophilus have been studied by laser flash-photolysis. The results show that both reactions, although studied at a temperature of 20 degreesC, far from the optimal temperature of > 60 degreesC for caa3, follow a kinetic behavior essentially identical to that observed with the electrostatic complex between mammalian cyt c and cyt c oxidase. In the O2 reaction cyt a and cyt a3 are very quickly oxidized; cyt a is then re-reduced via CuA, whereas cyt c oxidation is apparently rate-limited by the oxidation of CuA. Upon photodissociation of the mixed valence-CO caa3, reverse electron transfer from the binuclear center to cyt a3+ (tau1 = 3 micros) and CuA2+ (tau2 = 64 micros) is observed, while cyt c is not reduced by any detectable level. These results seem to rule out accounting for enzymatic thermophilicity by altered kinetics of intramolecular electron transfer involving the cyt center in the reduced configuration, which is very fast. On the basis of these results and previous data, we propose that thermophilicity involves an increased activation barrier for the reduction of cyt a3-CuB in the configuration typical of the oxidized site. PMID:9876155

  15. {sup 129}Xe nuclear magnetic resonance studies of xenon in zeolite CaA.

    SciTech Connect

    Jameson, C. J.; Jameson, A. K.; Gerald, R. E., II; de Dios, A. C.; Chemical Engineering; Univ. of Illinois at Chicago; Loyola Univ.

    1992-02-01

    The average {sup 129}Xe nuclear magnetic resonance (NMR) chemical shift for xenon atoms in alpha cages of zeolite CaA is observed in a single peak dependent on xenon loading ({l_angle}n{r_angle} = 0.5-8.9 Xe atoms/alpha cage) and temperature (240-360 K). The general increase of the shift with increasing average number of xenon atoms per alpha cage is shown to be due largely to the changing distribution of occupancies with increasing {l_angle}n{r_angle}, coupled with increasing increments in the chemical shifts of Xe{sub n} with increasing n. Except at the highest loadings, the results obtained for xenon in CaA are predicted nicely on the basis of {delta}{sub av}(T) = (1/{l_angle}n{r_angle}){Sigma}{sub n}n{delta}{sub n}(T)P{sub n}({l_angle}n{r_angle},T), where the fractions P{sub n} of alpha cages containing n Xe atoms are imported from the P{sub n} measured in xenon in zeolite NaA. The high loading data in CaA are interpreted in terms of contributions to the average {sup 129}Xe chemical shifts associated with xenon atoms in the window positions.

  16. Severe hepatocellular disease in mice lacking one or both CaaX prenyltransferases[S

    PubMed Central

    Yang, Shao H.; Chang, Sandy Y.; Tu, Yiping; Lawson, Gregory W.; Bergo, Martin O.; Fong, Loren G.; Young, Stephen G.

    2012-01-01

    Protein farnesyltransferase (FTase) and protein geranylgeranyltransferase-I (GGTase-I) add 15- or 20-carbon lipids, respectively, to proteins that terminate with a CaaX motif. These posttranslational modifications of proteins with lipids promote protein interactions with membrane surfaces in cells, but the in vivo importance of the CaaX prenyltransferases and the protein lipidation reactions they catalyze remain incompletely defined. One study concluded that a deficiency of FTase was inconsequential in adult mice and led to little or no tissue pathology. To assess the physiologic importance of the CaaX prenyltransferases, we used conditional knockout alleles and an albumin–Cre transgene to produce mice lacking FTase, GGTase-I, or both enzymes in hepatocytes. The hepatocyte-specific FTase knockout mice survived but exhibited hepatocellular disease and elevated transaminases. Mice lacking GGTase-I not only had elevated transaminases but also had dilated bile cannaliculi, hyperbilirubinemia, hepatosplenomegaly, and reduced survival. Of note, GGTase-I–deficient hepatocytes had a rounded shape and markedly reduced numbers of actin stress fibers. Hepatocyte-specific FTase/GGTase-I double-knockout mice closely resembled mice lacking GGTase-I alone, but the disease was slightly more severe. Our studies refute the notion that FTase is dispensable and demonstrate that GGTase-I is crucial for the vitality of hepatocytes. PMID:22039581

  17. NN-414. Novo Nordisk.

    PubMed

    Choi, Joong-Kwon

    2003-04-01

    Novo Nordisk is developing NN-414, an orally active beta-cell-selective regulator of insulin release, for the potential treatment of type 1 and type 2 diabetes. Phase 1 efficacy trials were underway by November 2000; these trials were ongoing in February 2002 and had been concluded by February 2003. PMID:12808887

  18. A Novel Role of the Yeast CaaX Protease Ste24 in Chitin Synthesis

    PubMed Central

    Meissner, Derek; Odman-Naresh, Jothini; Vogelpohl, Inga

    2010-01-01

    Ste24 is a membrane-integral CaaX metalloprotease residing in the endoplasmic reticulum (ER). In yeast, the only known substrate of Ste24 is the mating factor a precursor. A global screening for protein–protein interactions indicated that Ste24 interacts with chitin synthesis deficient (Chs)3, an enzyme required for chitin synthesis. We confirmed this interaction by yeast two-hybrid analyses and mapped the interacting cytoplasmic domains. Next, we investigated the influence of Ste24 on chitin synthesis. In sterile (ste)24Δ mutants, we observed resistance to calcofluor white (CFW), which was also apparent when the cells expressed a catalytically inactive version of Ste24. In addition, ste24Δ cells showed a decrease in chitin levels and Chs3-green fluorescent protein localized less frequently at the bud neck. Overexpression of STE24 resulted in hypersensitivity to CFW and a slight increase in chitin levels. The CFW phenotype of ste24Δ cells could be rescued by its human and insect orthologues. Although Chs3 binds to Ste24, it seems not to be a substrate for this protease. Instead, our data suggest that Chs3 and Ste24 form a complex in the ER that facilitates protease action on prenylated Chs4, a known activator of Chs3 with a C-terminal CaaX motif, leading to a more efficient localization of Chs3 at the plasma membrane. PMID:20505074

  19. CAA amendments` Title III could mean `future shock` to U.S. industry competitiveness

    SciTech Connect

    Rocco, V.A.

    1995-06-01

    While the regulated community awaits congressional action that could alter the government`s role in environmental protection and enforcement, the stipulations of existing regulations continue to unfold. Attention is focused on upcoming permitting deadlines imposed by the Clean Air Act Amendments of 1990, due by November for most facilities, and on products and strategies for air pollution control. Unless Congress adopts the unlikely strategy of rolling back all environmental regulations, the obligations on industry imposed by the CAA Amendments will continue to set forth a formidable compliance task. The Amendments ``created a complex maze of new and dramatically altered regulatory programs that will influence how US industry must operate well into the next century.`` This article provides an overview and guidelines for complying with the new rules.

  20. Rocky Flats CAAS System Recalibrated, Retested, and Analyzed to Install in the Criticality Experiments Facility at the Nevada Test Site

    SciTech Connect

    Kim, S; Heinrichs, D; Biswas, D; Huang, S; Dulik, G; Scorby, J; Boussoufi, M; Liu, B; Wilson, R

    2009-05-27

    Neutron detectors and control panels transferred from the Rocky Flats Plant (RFP) were recalibrated and retested for redeployment to the CEF. Testing and calibration were successful with no failure to any equipment. Detector sensitivity was tested at a TRIGA reactor, and the response to thermal neutron flux was satisfactory. MCNP calculated minimum fission yield ({approx} 2 x 10{sup 15} fissions) was applied to determine the thermal flux at selected detector positions at the CEF. Thermal flux levels were greater than 6.39 x 10{sup 6} (n/cm{sup 2}-sec), which was about four orders of magnitude greater than the minimum alarm flux. Calculations of detector survivable distances indicate that, to be out of lethal area, a detector needs to be placed greater than 15 ft away from a maximum credible source. MCNP calculated flux/dose results were independently verified by COG. CAAS calibration and the testing confirmed that the RFP CAAS system is performing its functions as expected. New criteria for the CAAS detector placement and 12-rad zone boundaries at the CEF are established. All of the CAAS related documents and hardware have been transferred from LLNL to NSTec for installation at the CEF high bay areas.

  1. 2 CFR 1532.1110 - How will a CAA or CWA conviction affect my eligibility to participate in Federal contracts...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... the Clean Air Act and Clean Water Act § 1532.1110 How will a CAA or CWA conviction affect my... debarment and suspension system (i.e. covered transactions under subpart A through I of 2 CFR part 180, or prohibited awards under 48 CFR part 9, subpart 9.4), if you: (a) Will perform any part of the transaction...

  2. 2 CFR 1532.1110 - How will a CAA or CWA conviction affect my eligibility to participate in Federal contracts...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... the Clean Air Act and Clean Water Act § 1532.1110 How will a CAA or CWA conviction affect my... debarment and suspension system (i.e. covered transactions under subpart A through I of 2 CFR part 180, or prohibited awards under 48 CFR part 9, subpart 9.4), if you: (a) Will perform any part of the transaction...

  3. 2 CFR 1532.1110 - How will a CAA or CWA conviction affect my eligibility to participate in Federal contracts...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... the Clean Air Act and Clean Water Act § 1532.1110 How will a CAA or CWA conviction affect my... debarment and suspension system (i.e. covered transactions under subpart A through I of 2 CFR part 180, or prohibited awards under 48 CFR part 9, subpart 9.4), if you: (a) Will perform any part of the transaction...

  4. 2 CFR 1532.1130 - How does disqualification under the CAA or CWA differ from a Federal discretionary suspension or...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Clean Air Act and Clean Water Act § 1532.1130 How does disqualification under the CAA or CWA differ from... 2 CFR part 180 or under 48 CFR part 9, subpart 9.4, are exclusions imposed at the discretion of... I of 2 CFR part 180, or under 48 CFR part 9, subpart 9.4....

  5. 2 CFR 1532.1130 - How does disqualification under the CAA or CWA differ from a Federal discretionary suspension or...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Clean Air Act and Clean Water Act § 1532.1130 How does disqualification under the CAA or CWA differ from... 2 CFR part 180 or under 48 CFR part 9, subpart 9.4, are exclusions imposed at the discretion of... I of 2 CFR part 180, or under 48 CFR part 9, subpart 9.4....

  6. 2 CFR 1532.1110 - How will a CAA or CWA conviction affect my eligibility to participate in Federal contracts...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... the Clean Air Act and Clean Water Act § 1532.1110 How will a CAA or CWA conviction affect my... debarment and suspension system (i.e. covered transactions under subpart A through I of 2 CFR part 180, or prohibited awards under 48 CFR part 9, subpart 9.4), if you: (a) Will perform any part of the transaction...

  7. 2 CFR 1532.1130 - How does disqualification under the CAA or CWA differ from a Federal discretionary suspension or...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... Clean Air Act and Clean Water Act § 1532.1130 How does disqualification under the CAA or CWA differ from... 2 CFR part 180 or under 48 CFR part 9, subpart 9.4, are exclusions imposed at the discretion of... I of 2 CFR part 180, or under 48 CFR part 9, subpart 9.4....

  8. 2 CFR 1532.1130 - How does disqualification under the CAA or CWA differ from a Federal discretionary suspension or...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Clean Air Act and Clean Water Act § 1532.1130 How does disqualification under the CAA or CWA differ from... 2 CFR part 180 or under 48 CFR part 9, subpart 9.4, are exclusions imposed at the discretion of... I of 2 CFR part 180, or under 48 CFR part 9, subpart 9.4....

  9. 40 CFR 51.902 - Which classification and nonattainment area planning provisions of the CAA shall apply to areas...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Implementation of 8-hour Ozone National Ambient Air Quality Standard § 51.902 Which classification and... with a 1-hour ozone design value equal to or greater than 0.121 ppm at the time the Administrator signs...) Covered under subpart 1 (CAA). An area designated nonattainment for the 8-hour ozone NAAQS with a...

  10. 40 CFR 51.902 - Which classification and nonattainment area planning provisions of the CAA shall apply to areas...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Implementation of 8-hour Ozone National Ambient Air Quality Standard § 51.902 Which classification and... with a 1-hour ozone design value equal to or greater than 0.121 ppm at the time the Administrator signs...) Covered under subpart 1 (CAA). An area designated nonattainment for the 8-hour ozone NAAQS with a...

  11. 40 CFR 51.902 - Which classification and nonattainment area planning provisions of the CAA shall apply to areas...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... area planning provisions of the CAA shall apply to areas designated nonattainment for the 1997 8-hour NAAQS? 51.902 Section 51.902 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Implementation of 8-hour Ozone National Ambient Air Quality Standard § 51.902 Which classification...

  12. 40 CFR 51.902 - Which classification and nonattainment area planning provisions of the CAA shall apply to areas...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... area planning provisions of the CAA shall apply to areas designated nonattainment for the 1997 8-hour NAAQS? 51.902 Section 51.902 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR... Implementation of 8-hour Ozone National Ambient Air Quality Standard § 51.902 Which classification...

  13. 40 CFR 51.1103 - Application of classification and attainment date provisions in CAA section 181 of subpart 2 to...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Ozone NAAQS (0.075 ppm) for Areas Subject to Section 51.1102(a) Area class 8-hour design value(ppm ozone... attainment date provisions in CAA section 181 of subpart 2 to areas subject to § 51.1102(a). 51.1103 Section 51.1103 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR...

  14. 40 CFR 51.126 - Determination of widespread use of ORVR and waiver of CAA section 182(b)(3) Stage II gasoline...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 2 2012-07-01 2012-07-01 false Determination of widespread use of ORVR and waiver of CAA section 182(b)(3) Stage II gasoline vapor recovery requirements. 51.126 Section 51... Determination of widespread use of ORVR and waiver of CAA section 182(b)(3) Stage II gasoline vapor...

  15. Multidentate 18F-polypegylated styrylpyridines as imaging agents for Aβ plaques in cerebral amyloid angiopathy (CAA)

    PubMed Central

    Zha, Zhihao; Choi, Seok Rye; Ploessl, Karl; Lieberman, Brian P.; Qu, Wenchao; Hefti, Franz; Mintun, Mark; Skovronsky, Daniel; Kung, Hank F.

    2011-01-01

    Beta-amyloid plaques (Aβ plaques) in the brain are associated with cerebral amyloid angiopathy (CAA). Imaging agents that could target the Aβ plaques in the living human brain would be potentially valuable as biomarkers in patients with CAA. A new series of 18F styrylpyridine derivatives with high molecular weights for selectively targeting Aβ plaques in the blood vessels of the brain, but excluded from the brain parenchyma is reported. The styrylpyridine derivatives, 8a–c, display high binding affinities and specificity to Aβ plaques (Ki = 2.87 nM, 3.24 and 7.71 nM, respectively). In vitro autoradiography of [18F]8a shows labeling of β-amyloid plaques associated with blood vessel walls in human brain sections of subjects with CAA, and also in the tissue of AD brain sections. The results suggest that [18F]8a may be a useful PET imaging agent for selectively detecting Aβ plaques associated with cerebral vessels in the living human brain. PMID:22011144

  16. 40 CFR 51.903 - How do the classification and attainment date provisions in section 181 of subpart 2 of the CAA...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... accordance with section 181(a)(1) of the CAA, each area subject to § 51.902(a) shall be classified by... for 8-Hour Ozone NAAQS for Areas Subject to § 51.902(a) Area class 8-hourdesign value (ppm ozone... attainment date provisions in section 181 of subpart 2 of the CAA apply to areas subject to § 51.902(a)?...

  17. Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif.

    PubMed

    Sousa, Sérgio F; Coimbra, João T S; Paramos, Diogo; Pinto, Rita; Guimarães, Rodrigo S; Teixeira, Vitor; Fernandes, Pedro A; Ramos, Maria J

    2013-02-01

    Protein farnesyltransferase (FTase) is an important target in many research fields, more markedly so in cancer investigation since several proteins known to be involved in human cancer development are thought to serve as substrates for FTase and to require farnesylation for proper biological activity. Several FTase inhibitors (FTIs) have advanced into clinical testing. Nevertheless, despite the progress in the field several functional and mechanistic doubts on the FTase catalytic activity have persisted. This work provides some crucial information on this important enzyme by describing the application of molecular dynamics simulations using specifically designed molecular mechanical parameters for a variety of 22 CaaX peptides known to work as natural substrates or inhibitors for this enzyme. The study involves a comparative analysis of several important molecular aspects, at the mechanistic level, of the behavior of substrates and inhibitors at the dynamic level, including the behavior of the enzyme and peptides, as well as their interaction, together with the effect of the solvent. Properties evaluated include the radial distribution function of the water molecules around the catalytically important zinc metal atom and cysteine sulfur of CaaX, the conformations of the substrate and inhibitor and the corresponding RMSF values, critical hydrogen bonds, and several catalytically relevant distances. These results are discussed in light of recent experimental and computational evidence that provides new insights into the activity of this enzyme. PMID:23011608

  18. A shunt pathway limits the CaaX processing of Hsp40 Ydj1p and regulates Ydj1p-dependent phenotypes

    PubMed Central

    Hildebrandt, Emily R; Cheng, Michael; Zhao, Peng; Kim, June H; Wells, Lance; Schmidt, Walter K

    2016-01-01

    The modifications occurring to CaaX proteins have largely been established using few reporter molecules (e.g. Ras, yeast a-factor mating pheromone). These proteins undergo three coordinated COOH-terminal events: isoprenylation of the cysteine, proteolytic removal of aaX, and COOH-terminal methylation. Here, we investigated the coupling of these modifications in the context of the yeast Ydj1p chaperone. We provide genetic, biochemical, and biophysical evidence that the Ydj1p CaaX motif is isoprenylated but not cleaved and carboxylmethylated. Moreover, we demonstrate that Ydj1p-dependent thermotolerance and Ydj1p localization are perturbed when alternative CaaX motifs are transplanted onto Ydj1p. The abnormal phenotypes revert to normal when post-isoprenylation events are genetically interrupted. Our findings indicate that proper Ydj1p function requires an isoprenylatable CaaX motif that is resistant to post-isoprenylation events. These results expand on the complexity of protein isoprenylation and highlight the impact of post-isoprenylation events in regulating the function of Ydj1p and perhaps other CaaX proteins. DOI: http://dx.doi.org/10.7554/eLife.15899.001 PMID:27525482

  19. Early detection of circulating anodic antigen (CAA) in a case of acute schistosomiasis mansoni with Katayama fever.

    PubMed

    Gundersen, S G; Ravn, J; Haagensen, I

    1992-01-01

    A 34-year-old male developed acute Katayama fever with fever, diarrhoea, joint pains, headache, urticarial rash and eosinophilia 18 days after falling into and spending 15 min in the water during water-skiing in the outlet of the Volta river. Low anti-schistosomal antibody titres were found by the immunofluorescence assay after 4 weeks, and the first Schistosoma mansoni eggs were found in faeces after 6 weeks. Both symptoms and eosinophilia increased the first days after treatment with oxamniquine, after which he improved gradually. Examination of frozen sera by the newly developed Magnetic Beads Antigen Capture-EIA (MBAC-EIA) later demonstrated a peak in schistosomal circulating anodic antigen (CAA) levels of diagnostic significance already 4 weeks after he was infected. PMID:1411323

  20. De novo trisomy 16p

    SciTech Connect

    Juan, J.L.C.; Cigudosa, J.C.; Gomez, A.O.

    1997-01-20

    We report on a patient with psychomotor retardation and a pattern of malformations comprising single umbilical artery, craniofacial anomalies, severe truncal hypotonia, and lower-limb hyporreflexia. G-banding cytogenetics demonstrated a 16p+ chromosome. Parental chromosomes were normal. The use of fluorescent in situ hybridization (FISH) showed that this extra material derived from chromosome 16. High-resolution G-banding demonstrated a duplicated segment on the 16p arm, confirming our suspicion of a de novo tandem duplication; hence, the cytogenetic diagnosis was given as 46,XY,dir dup(16)(p11.2{r_arrow}p12). 9 refs., 3 figs.

  1. De novo mammalian prion synthesis

    PubMed Central

    Benetti, Federico

    2009-01-01

    Prions are responsible for a heterogeneous group of fatal neurodegenerative diseases. They can be sporadic, genetic, or infectious disorders involving post-translational modifications of the cellular prion protein (PrPC). Prions (PrPSc) are characterized by their infectious property and intrinsic ability to convert the physiological PrPC into the pathological form, acting as a template. The “protein-only” hypothesis, postulated by Stanley B. Prusiner, implies the possibility to generate de novo prions in vivo and in vitro. Here we describe major milestones towards proving this hypothesis, taking into account physiological environment/s, biochemical properties and interactors of the PrPC. PMID:19887900

  2. Relationship of cytochrome caa sub 3 from Thermus thermophilus to other heme- and copper-containing terminal oxidases

    SciTech Connect

    Mather, M.W.; Springer, P.; Fee, J.A.

    1990-01-01

    Cytochrome oxidases are a key component of the energy metabolism of most aerobic organisms from mammals to bacteria. They are the final enzyme of the membrane associated respiratory chain responsible for converting the chemical energy of reduced substrates to a transmembrane electrochemical potential, which issused by the cell for a wide variety of energy-requiring processes. The most widely studied oxidase is the cytochrome c oxidase of the mammalian mitochondrion. This complex, integral membrane protein contains 13 subunits and four canonical metal centers: heme center a and a{sub 3}; copper centers CU{sub A} and CU{sub B}. It is responsible for electron transfer from reduced chytochrome c to dioxygen with the concomitant reduction of dioxygen to water and the coupled vectorial transfer of protons across the mitochondrial membrane. In this communication we will describe preliminary results of DNA sequencing experiments with the cytochrome caa{sub 3} oxidase, initially undertaken to determine the nature of the subunits of this oxidase and shed light on the distribution of the metal centers. We will speculate on oxidase gene and protein structures and evolutionary relationships in the light of these results and recent sequencing results from other groups. 47 refs., 4 figs., 1 tab.

  3. Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue.

    PubMed

    Strickland, C L; Windsor, W T; Syto, R; Wang, L; Bond, R; Wu, Z; Schwartz, J; Le, H V; Beese, L S; Weber, P C

    1998-11-24

    The crystallographic structure of acetyl-Cys-Val-Ile-selenoMet-COOH and alpha-hydroxyfarnesylphosphonic acid (alphaHFP) complexed with rat farnesyl protein transferase (FPT) (space group P61, a = b = 174. 13 A, c = 69.71 A, alpha = beta = 90 degrees, gamma = 120 degrees, Rfactor = 21.8%, Rfree = 29.2%, 2.5 A resolution) is reported. In the ternary complex, the bound substrates are within van der Waals contact of each other and the FPT enzyme. alphaHFP binds in an extended conformation in the active-site cavity where positively charged side chains and solvent molecules interact with the phosphate moiety and aromatic side chains pack adjacent to the isoprenoid chain. The backbone of the bound CaaX peptide adopts an extended conformation, and the side chains interact with both FPT and alphaHFP. The cysteine sulfur of the bound peptide coordinates the active-site zinc. Overall, peptide binding and recognition appear to be dominated by side-chain interactions. Comparison of the structures of the ternary complex and unliganded FPT [Park, H., Boduluri, S., Moomaw, J., Casey, P., and Beese, L. (1997) Science 275, 1800-1804] shows that major rearrangements of several active site side chains occur upon substrate binding. PMID:9843427

  4. De novo mutations in epileptic encephalopathies.

    PubMed

    Allen, Andrew S; Berkovic, Samuel F; Cossette, Patrick; Delanty, Norman; Dlugos, Dennis; Eichler, Evan E; Epstein, Michael P; Glauser, Tracy; Goldstein, David B; Han, Yujun; Heinzen, Erin L; Hitomi, Yuki; Howell, Katherine B; Johnson, Michael R; Kuzniecky, Ruben; Lowenstein, Daniel H; Lu, Yi-Fan; Madou, Maura R Z; Marson, Anthony G; Mefford, Heather C; Esmaeeli Nieh, Sahar; O'Brien, Terence J; Ottman, Ruth; Petrovski, Slavé; Poduri, Annapurna; Ruzzo, Elizabeth K; Scheffer, Ingrid E; Sherr, Elliott H; Yuskaitis, Christopher J; Abou-Khalil, Bassel; Alldredge, Brian K; Bautista, Jocelyn F; Berkovic, Samuel F; Boro, Alex; Cascino, Gregory D; Consalvo, Damian; Crumrine, Patricia; Devinsky, Orrin; Dlugos, Dennis; Epstein, Michael P; Fiol, Miguel; Fountain, Nathan B; French, Jacqueline; Friedman, Daniel; Geller, Eric B; Glauser, Tracy; Glynn, Simon; Haut, Sheryl R; Hayward, Jean; Helmers, Sandra L; Joshi, Sucheta; Kanner, Andres; Kirsch, Heidi E; Knowlton, Robert C; Kossoff, Eric H; Kuperman, Rachel; Kuzniecky, Ruben; Lowenstein, Daniel H; McGuire, Shannon M; Motika, Paul V; Novotny, Edward J; Ottman, Ruth; Paolicchi, Juliann M; Parent, Jack M; Park, Kristen; Poduri, Annapurna; Scheffer, Ingrid E; Shellhaas, Renée A; Sherr, Elliott H; Shih, Jerry J; Singh, Rani; Sirven, Joseph; Smith, Michael C; Sullivan, Joseph; Lin Thio, Liu; Venkat, Anu; Vining, Eileen P G; Von Allmen, Gretchen K; Weisenberg, Judith L; Widdess-Walsh, Peter; Winawer, Melodie R

    2013-09-12

    Epileptic encephalopathies are a devastating group of severe childhood epilepsy disorders for which the cause is often unknown. Here we report a screen for de novo mutations in patients with two classical epileptic encephalopathies: infantile spasms (n = 149) and Lennox-Gastaut syndrome (n = 115). We sequenced the exomes of 264 probands, and their parents, and confirmed 329 de novo mutations. A likelihood analysis showed a significant excess of de novo mutations in the ∼4,000 genes that are the most intolerant to functional genetic variation in the human population (P = 2.9 × 10(-3)). Among these are GABRB3, with de novo mutations in four patients, and ALG13, with the same de novo mutation in two patients; both genes show clear statistical evidence of association with epileptic encephalopathy. Given the relevant site-specific mutation rates, the probabilities of these outcomes occurring by chance are P = 4.1 × 10(-10) and P = 7.8 × 10(-12), respectively. Other genes with de novo mutations in this cohort include CACNA1A, CHD2, FLNA, GABRA1, GRIN1, GRIN2B, HNRNPU, IQSEC2, MTOR and NEDD4L. Finally, we show that the de novo mutations observed are enriched in specific gene sets including genes regulated by the fragile X protein (P < 10(-8)), as has been reported previously for autism spectrum disorders. PMID:23934111

  5. CAA: Computer Assisted Athletics.

    ERIC Educational Resources Information Center

    Hall, John H.

    Computers have been used in a variety of applications for athletics since the late 1950's. These have ranged from computer-controlled electric scoreboards to computer-designed pole vaulting poles. Described in this paper are a computer-based athletic injury reporting system and a computer-assisted football scouting system. The injury reporting…

  6. De Novo Genesis of Enhancers in Vertebrates

    PubMed Central

    Eichenlaub, Michael P.; Ettwiller, Laurence

    2011-01-01

    Evolutionary innovation relies partially on changes in gene regulation. While a growing body of evidence demonstrates that such innovation is generated by functional changes or translocation of regulatory elements via mobile genetic elements, the de novo generation of enhancers from non-regulatory/non-mobile sequences has, to our knowledge, not previously been demonstrated. Here we show evidence for the de novo genesis of enhancers in vertebrates. For this, we took advantage of the massive gene loss following the last whole genome duplication in teleosts to systematically identify regions that have lost their coding capacity but retain sequence conservation with mammals. We found that these regions show enhancer activity while the orthologous coding regions have no regulatory activity. These results demonstrate that these enhancers have been de novo generated in fish. By revealing that minor changes in non-regulatory sequences are sufficient to generate new enhancers, our study highlights an important playground for creating new regulatory variability and evolutionary innovation. PMID:22069375

  7. Cobalamin deficiency triggering de novo status epilepticus.

    PubMed

    Anastogiannis, Haralabos; Karanasios, Panagiotis; Makridou, Alexandra; Makris, Nicolaos; Argyriou, Andreas A

    2014-03-01

    Cobalamin deficiency is included in the spectrum of very uncommon underlying causes of status epilepticus (SE) and the literature contains very few such cases. We herein report a case of unusual presentation of cobalamin (vitamin B12) deficiency with de novo SE with the intention to bolster the argument that a de novo manifestation of SE due to cobalamin deficiency might not be that uncommon. We also support the importance of prompt identification and treatment of the underlying causes of SE, particularly those which are uncommon. PMID:24659635

  8. Decoding germline de novo point mutations.

    PubMed

    Goriely, Anne

    2016-07-27

    Analysis of a large whole-genome sequencing data set of 36,441 high-quality de novo mutations (DNMs) that arose in 816 family trios provides an unprecedented view into the landscape of DNMs in the germ line. This work both refines and challenges some of the views previously held on the nature and origin of DNMs. PMID:27463396

  9. Proteomics-grade de novo sequencing approach.

    PubMed

    Savitski, Mikhail M; Nielsen, Michael L; Kjeldsen, Frank; Zubarev, Roman A

    2005-01-01

    The conventional approach in modern proteomics to identify proteins from limited information provided by molecular and fragment masses of their enzymatic degradation products carries an inherent risk of both false positive and false negative identifications. For reliable identification of even known proteins, complete de novo sequencing of their peptides is desired. The main problems of conventional sequencing based on tandem mass spectrometry are incomplete backbone fragmentation and the frequent overlap of fragment masses. In this work, the first proteomics-grade de novo approach is presented, where the above problems are alleviated by the use of complementary fragmentation techniques CAD and ECD. Implementation of a high-current, large-area dispenser cathode as a source of low-energy electrons provided efficient ECD of doubly charged peptides, the most abundant species (65-80%), in a typical trypsin-based proteomics experiment. A new linear de novo algorithm is developed combining efficiency and speed, processing on a conventional 3 GHz PC, 1000 MS/MS data sets in 60 s. More than 6% of all MS/MS data for doubly charged peptides yielded complete sequences, and another 13% gave nearly complete sequences with a maximum gap of two amino acid residues. These figures are comparable with the typical success rates (5-15%) of database identification. For peptides reliably found in the database (Mowse score > or = 34), the agreement with de novo-derived full sequences was >95%. Full sequences were derived in 67% of the cases when full sequence information was present in MS/MS spectra. Thus the new de novo sequencing approach reached the same level of efficiency and reliability as conventional database-identification strategies. PMID:16335984

  10. Nanomedicine: de novo design of nanodrugs.

    PubMed

    Yang, Zaixing; Kang, Seung-gu; Zhou, Ruhong

    2014-01-21

    Phenomenal advances in nanotechnology and nanoscience have been accompanied by exciting progress in de novo design of nanomedicines. Nanoparticles with their large space of structural amenability and excellent mechanical and electrical properties have become ideal candidates for high efficacy nanomedicines in both diagnostics and therapeutics. The therapeutic nanomedicines can be further categorized into nanocarriers for conventional drugs and nanodrugs with direct curing of target diseases. Here we review some of the recent advances in de novo design of nanodrugs, with an emphasis on the molecular level understanding of their interactions with biological systems including key proteins and cell membranes. We also include some of the latest advances in the development of nanocarriers with both passive and active targeting for completeness. These studies may shed light on a better understanding of the molecular mechanisms behind these nanodrugs, and also provide new insights and direction for the future design of nanomedicines. PMID:24305636

  11. Nanomedicine: de novo design of nanodrugs

    NASA Astrophysics Data System (ADS)

    Yang, Zaixing; Kang, Seung-Gu; Zhou, Ruhong

    2013-12-01

    Phenomenal advances in nanotechnology and nanoscience have been accompanied by exciting progress in de novo design of nanomedicines. Nanoparticles with their large space of structural amenability and excellent mechanical and electrical properties have become ideal candidates for high efficacy nanomedicines in both diagnostics and therapeutics. The therapeutic nanomedicines can be further categorized into nanocarriers for conventional drugs and nanodrugs with direct curing of target diseases. Here we review some of the recent advances in de novo design of nanodrugs, with an emphasis on the molecular level understanding of their interactions with biological systems including key proteins and cell membranes. We also include some of the latest advances in the development of nanocarriers with both passive and active targeting for completeness. These studies may shed light on a better understanding of the molecular mechanisms behind these nanodrugs, and also provide new insights and direction for the future design of nanomedicines.

  12. Overcoming Geometry-Induced Stiffness with IMplicit-Explicit (IMEX) Runge-Kutta Algorithms on Unstructured Grids with Applications to CEM, CFD, and CAA

    NASA Technical Reports Server (NTRS)

    Kanevsky, Alex

    2004-01-01

    My goal is to develop and implement efficient, accurate, and robust Implicit-Explicit Runge-Kutta (IMEX RK) methods [9] for overcoming geometry-induced stiffness with applications to computational electromagnetics (CEM), computational fluid dynamics (CFD) and computational aeroacoustics (CAA). IMEX algorithms solve the non-stiff portions of the domain using explicit methods, and isolate and solve the more expensive stiff portions using implicit methods. Current algorithms in CEM can only simulate purely harmonic (up to lOGHz plane wave) EM scattering by fighter aircraft, which are assumed to be pure metallic shells, and cannot handle the inclusion of coatings, penetration into and radiation out of the aircraft. Efficient MEX RK methods could potentially increase current CEM capabilities by 1-2 orders of magnitude, allowing scientists and engineers to attack more challenging and realistic problems.

  13. Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

    PubMed Central

    Besenbacher, Søren; Liu, Siyang; Izarzugaza, José M. G.; Grove, Jakob; Belling, Kirstine; Bork-Jensen, Jette; Huang, Shujia; Als, Thomas D.; Li, Shengting; Yadav, Rachita; Rubio-García, Arcadio; Lescai, Francesco; Demontis, Ditte; Rao, Junhua; Ye, Weijian; Mailund, Thomas; Friborg, Rune M.; Pedersen, Christian N. S.; Xu, Ruiqi; Sun, Jihua; Liu, Hao; Wang, Ou; Cheng, Xiaofang; Flores, David; Rydza, Emil; Rapacki, Kristoffer; Damm Sørensen, John; Chmura, Piotr; Westergaard, David; Dworzynski, Piotr; Sørensen, Thorkild I. A.; Lund, Ole; Hansen, Torben; Xu, Xun; Li, Ning; Bolund, Lars; Pedersen, Oluf; Eiberg, Hans; Krogh, Anders; Børglum, Anders D.; Brunak, Søren; Kristiansen, Karsten; Schierup, Mikkel H.; Wang, Jun; Gupta, Ramneek; Villesen, Palle; Rasmussen, Simon

    2015-01-01

    Building a population-specific catalogue of single nucleotide variants (SNVs), indels and structural variants (SVs) with frequencies, termed a national pan-genome, is critical for further advancing clinical and public health genetics in large cohorts. Here we report a Danish pan-genome obtained from sequencing 10 trios to high depth (50 × ). We report 536k novel SNVs and 283k novel short indels from mapping approaches and develop a population-wide de novo assembly approach to identify 132k novel indels larger than 10 nucleotides with low false discovery rates. We identify a higher proportion of indels and SVs than previous efforts showing the merits of high coverage and de novo assembly approaches. In addition, we use trio information to identify de novo mutations and use a probabilistic method to provide direct estimates of 1.27e−8 and 1.5e−9 per nucleotide per generation for SNVs and indels, respectively. PMID:25597990

  14. De Novo Lipogenesis Products and Endogenous Lipokines.

    PubMed

    Yilmaz, Mustafa; Claiborn, Kathryn C; Hotamisligil, Gökhan S

    2016-07-01

    Recent studies have shown that in addition to their traditionally recognized functions as building blocks, energy stores, or hazardous intermediates, lipids also have the ability to act as signaling molecules with potent effects on systemic metabolism and metabolic diseases. This Perspective highlights this somewhat less apparent biology of lipids, especially focusing on de novo lipogenesis as a process that gives rise to key messenger molecules mediating interorgan communication. Elucidating the mechanisms of lipid-dependent coordination of metabolism promises invaluable insights into the understanding of metabolic diseases and may contribute to the development of a new generation of preventative and therapeutic approaches. PMID:27288005

  15. Comparative analysis of de novo transcriptome assembly.

    PubMed

    Clarke, Kaitlin; Yang, Yi; Marsh, Ronald; Xie, Linglin; Zhang, Ke K

    2013-02-01

    The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis. A fast algorithm, de Bruijn graph has been successfully used for genome DNA de novo assembly; nevertheless, its performance for transcriptome assembly is unclear. In this study, we used both simulated and real RNA-Seq data, from either artificial RNA templates or human transcripts, to evaluate five de novo assemblers, ABySS, Mira, Trinity, Velvet and Oases. Of these assemblers, ABySS, Trinity, Velvet and Oases are all based on de Bruijn graph, and Mira uses an overlap graph algorithm. Various numbers of RNA short reads were selected from the External RNA Control Consortium (ERCC) data and human chromosome 22. A number of statistics were then calculated for the resulting contigs from each assembler. Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate. Trinity had relative good performance for both ERCC and human data, but it may not consistently generate full length transcripts. ABySS was the fastest method but its assembly quality was low. Mira gave a good rate for mapping its contigs onto human chromosome 22, but its computational speed is not satisfactory. Our results suggest that transcript assembly remains a challenge problem for bioinformatics society. Therefore, a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique. PMID:23393031

  16. De Novo Construction of Redox Active Proteins.

    PubMed

    Moser, C C; Sheehan, M M; Ennist, N M; Kodali, G; Bialas, C; Englander, M T; Discher, B M; Dutton, P L

    2016-01-01

    Relatively simple principles can be used to plan and construct de novo proteins that bind redox cofactors and participate in a range of electron-transfer reactions analogous to those seen in natural oxidoreductase proteins. These designed redox proteins are called maquettes. Hydrophobic/hydrophilic binary patterning of heptad repeats of amino acids linked together in a single-chain self-assemble into 4-alpha-helix bundles. These bundles form a robust and adaptable frame for uncovering the default properties of protein embedded cofactors independent of the complexities introduced by generations of natural selection and allow us to better understand what factors can be exploited by man or nature to manipulate the physical chemical properties of these cofactors. Anchoring of redox cofactors such as hemes, light active tetrapyrroles, FeS clusters, and flavins by His and Cys residues allow cofactors to be placed at positions in which electron-tunneling rates between cofactors within or between proteins can be predicted in advance. The modularity of heptad repeat designs facilitates the construction of electron-transfer chains and novel combinations of redox cofactors and new redox cofactor assisted functions. Developing de novo designs that can support cofactor incorporation upon expression in a cell is needed to support a synthetic biology advance that integrates with natural bioenergetic pathways. PMID:27586341

  17. De novo CNVs in bipolar affective disorder and schizophrenia

    PubMed Central

    Georgieva, Lyudmila; Rees, Elliott; Moran, Jennifer L.; Chambert, Kimberly D.; Milanova, Vihra; Craddock, Nicholas; Purcell, Shaun; Sklar, Pamela; McCarroll, Steven; Holmans, Peter; O'Donovan, Michael C.; Owen, Michael J.; Kirov, George

    2014-01-01

    An increased rate of de novo copy number variants (CNVs) has been found in schizophrenia (SZ), autism and developmental delay. An increased rate has also been reported in bipolar affective disorder (BD). Here, in a larger BD sample, we aimed to replicate these findings and compare de novo CNVs between SZ and BD. We used Illumina microarrays to genotype 368 BD probands, 76 SZ probands and all their parents. Copy number variants were called by PennCNV and filtered for frequency (<1%) and size (>10 kb). Putative de novo CNVs were validated with the z-score algorithm, manual inspection of log R ratios (LRR) and qPCR probes. We found 15 de novo CNVs in BD (4.1% rate) and 6 in SZ (7.9% rate). Combining results with previous studies and using a cut-off of >100 kb, the rate of de novo CNVs in BD was intermediate between controls and SZ: 1.5% in controls, 2.2% in BD and 4.3% in SZ. Only the differences between SZ and BD and SZ and controls were significant. The median size of de novo CNVs in BD (448 kb) was also intermediate between SZ (613 kb) and controls (338 kb), but only the comparison between SZ and controls was significant. Only one de novo CNV in BD was in a confirmed SZ locus (16p11.2). Sporadic or early onset cases were not more likely to have de novo CNVs. We conclude that de novo CNVs play a smaller role in BD compared with SZ. Patients with a positive family history can also harbour de novo mutations. PMID:25055870

  18. De Novo Kidney Regeneration with Stem Cells

    PubMed Central

    Yokote, Shinya; Yamanaka, Shuichiro; Yokoo, Takashi

    2012-01-01

    Recent studies have reported on techniques to mobilize and activate endogenous stem-cells in injured kidneys or to introduce exogenous stem cells for tissue repair. Despite many recent advantages in renal regenerative therapy, chronic kidney disease (CKD) remains a major cause of morbidity and mortality and the number of CKD patients has been increasing. When the sophisticated structure of the kidneys is totally disrupted by end stage renal disease (ESRD), traditional stem cell-based therapy is unable to completely regenerate the damaged tissue. This suggests that whole organ regeneration may be a promising therapeutic approach to alleviate patients with uncured CKD. We summarize here the potential of stem-cell-based therapy for injured tissue repair and de novo whole kidney regeneration. In addition, we describe the hurdles that must be overcome and possible applications of this approach in kidney regeneration. PMID:23251079

  19. A standard analysis method (SAM) for the automated analysis of polychlorinated biphenyls (PCBs) in soils using the chemical analysis automation (CAA) paradigm: validation and performance

    SciTech Connect

    Rzeszutko, C.; Johnson, C.R.; Monagle, M.; Klatt, L.N.

    1997-10-01

    The Chemical Analysis Automation (CAA) program is developing a standardized modular automation strategy for chemical analysis. In this automation concept, analytical chemistry is performed with modular building blocks that correspond to individual elements of the steps in the analytical process. With a standardized set of behaviors and interactions, these blocks can be assembled in a `plug and play` manner into a complete analysis system. These building blocks, which are referred to as Standard Laboratory Modules (SLM), interface to a host control system that orchestrates the entire analytical process, from sample preparation through data interpretation. The integrated system is called a Standard Analysis Method (SAME). A SAME for the automated determination of Polychlorinated Biphenyls (PCB) in soils, assembled in a mobile laboratory, is undergoing extensive testing and validation. The SAME consists of the following SLMs: a four channel Soxhlet extractor, a High Volume Concentrator, column clean up, a gas chromatograph, a PCB data interpretation module, a robot, and a human- computer interface. The SAME is configured to meet the requirements specified in U.S. Environmental Protection Agency`s (EPA) SW-846 Methods 3541/3620A/8082 for the analysis of pcbs in soils. The PCB SAME will be described along with the developmental test plan. Performance data obtained during developmental testing will also be discussed.

  20. A Standard Analysis Method (SAM) for the automated analysis of polychlorinated biphenyls (PCBs) in soils using the chemical analysis automation (CAA) paradigm: Validation and performance

    SciTech Connect

    Rzeszutko, C.; Johnson, C.R.; Monagle, M.; Klatt, L.N.

    1997-11-01

    The Chemical Analysis Automation (CAA) program is developing a standardized modular automation strategy for chemical analysis. In this automation concept, analytical chemistry is performed with modular building blocks that correspond to individual elements of the steps in the analytical process. With a standardized set of behaviors and interactions, these blocks can be assembled in a plug-and-play manner into a complete analysis system. These building blocks, which are referred to as Standard laboratory Modules (SLM), interface to a host control system that orchestrates the entire analytical process, from sample preparation through data interpretation. The integrated system is called a Standard Analysis Method (SAM). A SAM for the automated determination of polychlorinated biphenyls (PCBs) in soils, assembled in a mobile laboratory, is undergoing extensive testing and validation. The SAM consists of the following SLMs: a four-channel Soxhlet extractor, a high-volume concentration, a column clean-up, a gas chromatography, a PCB data-interpretation module, a robot, and a human-computer interface. The SAM is configured to meet the requirements specified in the US Environmental Protection Agency`s (EPA) SW-846 methods 3541/3620A/8082 for the analysis of PCBs in soils. The PCB SAM will be described along with the developmental test plan. Performance data obtained during developmental testing will also be discussed.

  1. Length Variation of Cag/Caa Trinucleotide Repeats in Natural Populations of Drosophila Melanogaster and Its Relation to the Recombination Rate

    PubMed Central

    Michalakis, Y.; Veuille, M.

    1996-01-01

    Eleven genes distributed along the Drosophila melanogaster chromosome 2 and showing exonic tandem repeats of glutamine codons (CAG or CAA) were surveyed for length variation in a sample of four European and African populations. Only one gene was monomorphic. Eight genes were polymorphic in all populations, with a total number of alleles varying between five and 12 for 120 chromosomes. The average heterozygozity per locus and population was 0.41. Selective neutrality in length variation could not be rejected under the assumptions of the infinite allele model. Significant population subdivision was found though no geographical pattern emerged, all populations being equally different. Significant linkage disequilibrium was found in four out of seven cases where the genetic distance between loci was <1 cM and was negligible when the distance was larger. There is evidence that these associations were established after the populations separated. An unexpected result was that variation at each locus was independent of the coefficient of exchange, although the latter ranged from zero to the relatively high value of 6.7%. This would indicate that background selection and selective hitchhiking, which are thought to affect levels of nucleotide substitution polymorphism, have no effect on trinucleotide repeat variation. PMID:8844158

  2. De Novo Gastric Cancer After Liver Transplantation.

    PubMed

    Gong, Chung-Sik; Yoo, Moon-Won; Kim, Beom-Su; Hwang, Shin; Kim, Ki-Hun; Yook, Jeong-Hwan; Kim, Byung-Sik; Lee, Sung-Gyu

    2016-01-01

    BACKGROUND In South Korea, which has a high incidence of gastric cancer, the most common de novo malignancy associated with liver transplantation is gastric cancer. This study sought to identify clinicopathologic characteristics in gastric cancer patients after liver transplantation, and to help manage these cases. MATERIAL AND METHODS We investigated gastric cancer patients after liver transplantation at Asan Medical Center. We analyzed sex, age, cause of liver transplantation, initiating immunosuppressant, pre-transplantation gastric fibroscopy findings, time interval between transplantation and gastric cancer occurrence, follow-up period, existence of gastric cancer screening, Helicobacter pylori infection, family cancer history, gastric cancer treatment, cancer location, size of tumor, macroscopic gross type, WHO histologic type, Lauren's classification, TNM stage, and survival. RESULTS Of 2968 adult liver transplantation patients at our hospital, 19 were diagnosed with gastric cancer. The mean age at the time of gastric cancer diagnosis was 60.2±6.8 (46-71) years and mean time interval between liver transplantation and diagnosis of gastric cancer was 56.0±30.7 (3.20-113) months. Endoscopic submucosal dissection was done for 10 patients, 4 of whom underwent surgical resection. Surgical resection as an initial treatment was done in 8 patients. One patient received chemotherapy first. The standard incidence ratio of gastric cancer in these patients was 1036 per 100 000 persons (95% CI, 623.7-1,619) in men and 318.9 per 100 000 (95% CI, 4.170-1,774) in women. CONCLUSIONS For long-term survival of liver transplant patients, early detection of de novo cancer is necessary. Therefore, annual screening for gastric cancer after liver transplantation is needed, especially in areas where the incidence of gastric cancer is high, such as South Korea. PMID:27334929

  3. De novo mutations in the classic epileptic encephalopathies

    PubMed Central

    2013-01-01

    Epileptic encephalopathies (EE) are a devastating group of severe childhood epilepsy disorders for which the cause is often unknown. Here, we report a screen for de novo mutations in patients with two classical EE: infantile spasms (IS, n=149) and Lennox-Gastaut Syndrome (LGS, n=115). We sequenced the exomes of 264 probands, and their parents, and confirmed 329 de novo mutations. A likelihood analysis showed a significant excess of de novo mutations in the ~4,000 genes that are the most intolerant to functional genetic variation in the human population (p=2.9 × 10−3). Among these are GABRB3 with de novo mutations in four patients and ALG13 with the same de novo mutation in two patients; both genes show clear statistical evidence of association. Given the relevant site-specific mutation rates, the probabilities of these outcomes occurring by chance are p=4.1 × 10−10 and p=7.8 × 10−12, respectively. Other genes with de novo mutations in this cohort include: CACNA1A, CHD2, FLNA, GABRA1, GRIN1, GRIN2B, HDAC4, HNRNPU, IQSEC2, MTOR, and NEDD4L. Finally, we show that the de novo mutations observed are enriched in specific gene sets including genes regulated by the Fragile X protein (p<10−8), as was reported for autism spectrum disorders (ASD)1. PMID:23934111

  4. Current challenges in de novo plant genome sequencing and assembly

    PubMed Central

    2012-01-01

    Genome sequencing is now affordable, but assembling plant genomes de novo remains challenging. We assess the state of the art of assembly and review the best practices for the community. PMID:22546054

  5. Genovo: De Novo Assembly for Metagenomes

    NASA Astrophysics Data System (ADS)

    Laserson, Jonathan; Jojic, Vladimir; Koller, Daphne

    Next-generation sequencing technologies produce a large number of noisy reads from the DNA in a sample. Metagenomics and population sequencing aim to recover the genomic sequences of the species in the sample, which could be of high diversity. Methods geared towards single sequence reconstruction are not sensitive enough when applied in this setting. We introduce a generative probabilistic model of read generation from environmental samples and present Genovo, a novel de novo sequence assembler that discovers likely sequence reconstructions under the model. A Chinese restaurant process prior accounts for the unknown number of genomes in the sample. Inference is made by applying a series of hill-climbing steps iteratively until convergence. We compare the performance of Genovo to three other short read assembly programs across one synthetic dataset and eight metagenomic datasets created using the 454 platform, the largest of which has 311k reads. Genovo's reconstructions cover more bases and recover more genes than the other methods, and yield a higher assembly score.

  6. The CAA Permit Review Process

    SciTech Connect

    Hyre, R.A.

    1995-06-01

    In the near future, all existing major sources will be required to submit an air permit application to the state or the Environmental Protection Agency (EPA) for review. This report details the permit review process, including information on state, EPA, affected states, judicial, and public review. It will also describe permit renewal, operational flexibility, off-permit changes, permit revisions, and permit reopenings.

  7. Novor: Real-Time Peptide de Novo Sequencing Software

    NASA Astrophysics Data System (ADS)

    Ma, Bin

    2015-11-01

    De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today's peptide de novo sequencing analyses. To improve the accuracy, Novor's scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%-37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today's mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data.

  8. De novo variants in sporadic cases of childhood onset schizophrenia.

    PubMed

    Ambalavanan, Amirthagowri; Girard, Simon L; Ahn, Kwangmi; Zhou, Sirui; Dionne-Laporte, Alexandre; Spiegelman, Dan; Bourassa, Cynthia V; Gauthier, Julie; Hamdan, Fadi F; Xiong, Lan; Dion, Patrick A; Joober, Ridha; Rapoport, Judith; Rouleau, Guy A

    2016-06-01

    Childhood-onset schizophrenia (COS), defined by the onset of illness before age 13 years, is a rare severe neurodevelopmental disorder of unknown etiology. Recently, sequencing studies have identified rare, potentially causative de novo variants in sporadic cases of adult-onset schizophrenia and autism. In this study, we performed exome sequencing of 17 COS trios in order to test whether de novo variants could contribute to this disease. We identified 20 de novo variants in 17 COS probands, which is consistent with the de novo mutation rate reported in the adult form of the disease. Interestingly, the missense de novo variants in COS have a high likelihood for pathogenicity and were enriched for genes that are less tolerant to variants. Among the genes found disrupted in our study, SEZ6, RYR2, GPR153, GTF2IRD1, TTBK1 and ITGA6 have been previously linked to neuronal function or to psychiatric disorders, and thus may be considered as COS candidate genes. PMID:26508570

  9. Genetic variation and the de novo assembly of human genomes

    PubMed Central

    Chaisson, Mark J. P.; Wilson, Richard K.; Eichler, Evan E.

    2016-01-01

    The discovery of genetic variation and the assembly of genome sequences are both inextricably linked to advances in DNA-sequencing technology. Short-read massively parallel sequencing has revolutionized our ability to discover genetic variation but is insufficient to generate high-quality genome assemblies or resolve most structural variation. Full resolution of variation is only guaranteed by complete de novo assembly of a genome. Here, we review approaches to genome assembly, the nature of gaps or missing sequences, and biases in the assembly process. We describe the challenges of generating a complete de novo genome assembly using current technologies and the impact that being able to perfectly sequence the genome would have on understanding human disease and evolution. Finally, we summarize recent technological advances that improve both contiguity and accuracy and emphasize the importance of complete de novo assembly as opposed to read mapping as the primary means to understanding the full range of human genetic variation. PMID:26442640

  10. A model of random sequences for de novo peptide sequencing

    SciTech Connect

    Jarman, Kenneth D.; Cannon, William R.; Jarman, Kristin H.; Heredia-Langner, Alejandro

    2003-04-15

    We present a model for the probability of random sequences appearing in product ion spectra obtained from tandem mass spectrometry experiments using collision-induced dissociation. We demonstrate the use of these probabilities for ranking candidate peptide sequences obtained using a de novo algorithm. Sequence candidates are obtained from a spectrum graph that is greatly reduced in size from those in previous graph-theoretical de novo approaches. Evidence of multiple instances of subsequences of each candidate, due to different fragment ion type series as well as isotopic peaks, is incorporated in a hierarchical scoring scheme. This approach is shown to be useful for confirming results from database search and as a first step towards a statistically rigorous de novo algorithm.

  11. Complete De Novo Assembly of Monoclonal Antibody Sequences.

    PubMed

    Tran, Ngoc Hieu; Rahman, M Ziaur; He, Lin; Xin, Lei; Shan, Baozhen; Li, Ming

    2016-01-01

    De novo protein sequencing is one of the key problems in mass spectrometry-based proteomics, especially for novel proteins such as monoclonal antibodies for which genome information is often limited or not available. However, due to limitations in peptides fragmentation and coverage, as well as ambiguities in spectra interpretation, complete de novo assembly of unknown protein sequences still remains challenging. To address this problem, we propose an integrated system, ALPS, which for the first time can automatically assemble full-length monoclonal antibody sequences. Our system integrates de novo sequencing peptides, their quality scores and error-correction information from databases into a weighted de Bruijn graph to assemble protein sequences. We evaluated ALPS performance on two antibody data sets, each including a heavy chain and a light chain. The results show that ALPS was able to assemble three complete monoclonal antibody sequences of length 216-441 AA, at 100% coverage, and 96.64-100% accuracy. PMID:27562653

  12. Complete De Novo Assembly of Monoclonal Antibody Sequences

    PubMed Central

    Tran, Ngoc Hieu; Rahman, M. Ziaur; He, Lin; Xin, Lei; Shan, Baozhen; Li, Ming

    2016-01-01

    De novo protein sequencing is one of the key problems in mass spectrometry-based proteomics, especially for novel proteins such as monoclonal antibodies for which genome information is often limited or not available. However, due to limitations in peptides fragmentation and coverage, as well as ambiguities in spectra interpretation, complete de novo assembly of unknown protein sequences still remains challenging. To address this problem, we propose an integrated system, ALPS, which for the first time can automatically assemble full-length monoclonal antibody sequences. Our system integrates de novo sequencing peptides, their quality scores and error-correction information from databases into a weighted de Bruijn graph to assemble protein sequences. We evaluated ALPS performance on two antibody data sets, each including a heavy chain and a light chain. The results show that ALPS was able to assemble three complete monoclonal antibody sequences of length 216–441 AA, at 100% coverage, and 96.64–100% accuracy. PMID:27562653

  13. Installing hydrolytic activity into a completely de novo protein framework.

    PubMed

    Burton, Antony J; Thomson, Andrew R; Dawson, William M; Brady, R Leo; Woolfson, Derek N

    2016-09-01

    The design of enzyme-like catalysts tests our understanding of sequence-to-structure/function relationships in proteins. Here we install hydrolytic activity predictably into a completely de novo and thermostable α-helical barrel, which comprises seven helices arranged around an accessible channel. We show that the lumen of the barrel accepts 21 mutations to functional polar residues. The resulting variant, which has cysteine-histidine-glutamic acid triads on each helix, hydrolyses p-nitrophenyl acetate with catalytic efficiencies that match the most-efficient redesigned hydrolases based on natural protein scaffolds. This is the first report of a functional catalytic triad engineered into a de novo protein framework. The flexibility of our system also allows the facile incorporation of unnatural side chains to improve activity and probe the catalytic mechanism. Such a predictable and robust construction of truly de novo biocatalysts holds promise for applications in chemical and biochemical synthesis. PMID:27554410

  14. De Novo Fragment Design for Drug Discovery and Chemical Biology.

    PubMed

    Rodrigues, Tiago; Reker, Daniel; Welin, Martin; Caldera, Michael; Brunner, Cyrill; Gabernet, Gisela; Schneider, Petra; Walse, Björn; Schneider, Gisbert

    2015-12-01

    Automated molecular de novo design led to the discovery of an innovative inhibitor of death-associated protein kinase 3 (DAPK3). An unprecedented crystal structure of the inactive DAPK3 homodimer shows the fragment-like hit bound to the ATP pocket. Target prediction software based on machine learning models correctly identified additional macromolecular targets of the computationally designed compound and the structurally related marketed drug azosemide. The study validates computational de novo design as a prime method for generating chemical probes and starting points for drug discovery. PMID:26486226

  15. Airline Maintenance Manpower Optimization from the De Novo Perspective

    NASA Astrophysics Data System (ADS)

    Liou, James J. H.; Tzeng, Gwo-Hshiung

    Human resource management (HRM) is an important issue for today’s competitive airline marketing. In this paper, we discuss a multi-objective model designed from the De Novo perspective to help airlines optimize their maintenance manpower portfolio. The effectiveness of the model and solution algorithm is demonstrated in an empirical study of the optimization of the human resources needed for airline line maintenance. Both De Novo and traditional multiple objective programming (MOP) methods are analyzed. A comparison of the results with those of traditional MOP indicates that the proposed model and solution algorithm does provide better performance and an improved human resource portfolio.

  16. DE NOVO DESIGN OF LIGANDS FOR METAL SEPARATION

    EPA Science Inventory

    This application focuses on the development of appropriate computation tools and parameters for the de novo design of selective metal ligands. We have developed a successful suite of tools for computer-aided design of ligands for receptors of known three-dimensional structure (st...

  17. De novo transcriptome of the hemimetabolous German cockroach (Blattella germanica)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A total of 1,365,609 raw reads with an average length of 529 bp, which were de novo assembled into 48,800 contigs and 3,961 singletons for a total of 52,761 high-quality unique sequences are generated. These sequences are annotated in terms of GO and KEGG, and the results reveal putative genes of va...

  18. Direct Visualization of De novo Lipogenesis in Single Living Cells

    NASA Astrophysics Data System (ADS)

    Li, Junjie; Cheng, Ji-Xin

    2014-10-01

    Increased de novo lipogenesis is being increasingly recognized as a hallmark of cancer. Despite recent advances in fluorescence microscopy, autoradiography and mass spectrometry, direct observation of de novo lipogenesis in living systems remains to be challenging. Here, by coupling stimulated Raman scattering (SRS) microscopy with isotope labeled glucose, we were able to trace the dynamic metabolism of glucose in single living cells with high spatial-temporal resolution. As the first direct visualization, we observed that glucose was largely utilized for lipid synthesis in pancreatic cancer cells, which occurs at a much lower rate in immortalized normal pancreatic epithelial cells. By inhibition of glycolysis and fatty acid synthase (FAS), the key enzyme for fatty acid synthesis, we confirmed the deuterium labeled lipids in cancer cells were from de novo lipid synthesis. Interestingly, we also found that prostate cancer cells exhibit relatively lower level of de novo lipogenesis, but higher fatty acid uptake compared to pancreatic cancer cells. Together, our results demonstrate a valuable tool to study dynamic lipid metabolism in cancer and other disorders.

  19. Measurement of de novo lipogenesis in humans during lactation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Milk fat is composed of 98% triglycerides (TG) and provides infants with approximately 50% of their calories. Mammary gland de novo lipogenesis contributes significantly to milk fat in animals. However, there are no data regarding this process in humans. Incorporation of 13C carbons from [U-13C]gluc...

  20. De novo synthesis of milk triglycerides in humans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mammary gland (MG) de novo lipogenesis contributes significantly to milk fat in animals but little is known in humans. Objective: To test the hypothesis that the incorporation of 13C carbons from [U-13C]glucose into fatty acids (FA) and glycerol in triglycerides (TG) will be greater: 1) in milk tha...

  1. A Public Trial De Novo: Rethinking "Industrial Interests"

    ERIC Educational Resources Information Center

    Vedel, Jane Bjorn; Gad, Christopher

    2011-01-01

    This article addresses the concept of "industrial interests" and examines its role in a topical controversy about a large research grant from a private foundation, the Novo Nordisk Foundation, to the University of Copenhagen. The authors suggest that the debate took the form of a "public trial" where the grant and close(r) intermingling between…

  2. 43 CFR 30.206 - What happens after I file a request for de novo review?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false What happens after I file a request for de... request for de novo review? (a) Within 10 days of receiving a request for de novo review, OHA will notify... the de novo review, and assign the case to a judge. (b) The judge will review the merits of the...

  3. 12 CFR 925.14 - De novo insured depository institution applicants.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 7 2010-01-01 2010-01-01 false De novo insured depository institution... MEMBERS AND HOUSING ASSOCIATES MEMBERS OF THE BANKS Eligibility Requirements § 925.14 De novo insured... application for membership in the Bank (de novo applicant) is deemed to meet the requirements of §§ 925.7,...

  4. 43 CFR 30.207 - What happens if nobody files for de novo review?

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false What happens if nobody files for de novo... PROBATE HEARINGS PROCEDURES Summary Probate Proceedings § 30.207 What happens if nobody files for de novo review? If no interested party requests de novo review within 30 days of the date of the written...

  5. Comparison of sodium naphthenate and air-ionization corona discharge as surface treatments for the ethylene-tetrafluoroethylene polymer (ETFE) to improve adhesion between ETFE and acrylonitrile-butadiene-styrene polymer (ABS) in the presence of a cyanoacrylate adhesive (CAA)

    NASA Astrophysics Data System (ADS)

    Lucía Johanning-Solís, Ana; Stradi-Granados, Benito A.

    2014-09-01

    This study compares two ethylene-tetrafluoroethylene (ETFE) surface activation treatments, namely chemical attack with a solution of sodium naphthenate and plasma erosion via air-ionization corona discharge in order to improve the adhesive properties of the ETFE. An experimental design was prepared for both treatments in order to assess the effect of the treatment characteristics on the tensile load needed to break the bond between the ETFE and the acrylonitrile-butadiene-styrene polymer (ABS) formed with a cyanoacrylate adhesive (CAA) applied between them. The reason for the selection of this problem is that both polymers are frequently used in the biomedical industry for their properties, and they need to be joined firmly in biomedical devices, and the cyanoacrylate adhesive is the adhesive traditionally used for fluoropolymers, in this case the ETFE, and the same CAA has also shown good adhesion with ABS. However, the strength of the bond for the triplet ETFE-CAA-ABS has not been reported and the improvement of the strength of the bond with surface treatments is not found in scholarly journals for modern medical devices such as stents and snares. Both treatments were compared based on the aforementioned design of experiments. The case where ETFE receives no surface treatment serves as the reference. The results indicated that the three factors evaluated (initial drying of the material, temperature of the chemical bath, and immersion time), and their interactions have no significant effect over the tensile load at failure (tensile strength) of the adhesive bond being evaluated. For the air-ionization corona discharge treatment, two factors were evaluated: discharge exposition time and air pressure. The results obtained from this experimental design indicate that there is no significant difference between the levels of the factors evaluated. These results were unexpected as the ranges used were representative of the maximum ranges permissible in manufacturing

  6. De Novo Gene Disruptions in Children on the Autistic Spectrum

    PubMed Central

    Iossifov, Ivan; Ronemus, Michael; Levy, Dan; Wang, Zihua; Hakker, Inessa; Rosenbaum, Julie; Yamrom, Boris; Lee, Yoon-ha; Narzisi, Giuseppe; Leotta, Anthony; Kendall, Jude; Grabowska, Ewa; Ma, Beicong; Marks, Steven; Rodgers, Linda; Stepansky, Asya; Troge, Jennifer; Andrews, Peter; Bekritsky, Mitchell; Pradhan, Kith; Ghiban, Elena; Kramer, Melissa; Parla, Jennifer; Demeter, Ryan; Fulton, Lucinda L.; Fulton, Robert S.; Magrini, Vincent J.; Ye, Kenny; Darnell, Jennifer C.; Darnell, Robert B.; Mardis, Elaine R.; Wilson, Richard K.; Schatz, Michael C.; McCombie, W. Richard; Wigler, Michael

    2012-01-01

    SUMMARY Exome sequencing of 343 families, each with a single child on the autism spectrum and at least one unaffected sibling, reveal de novo small indels and point substitutions, which come mostly from the paternal line in an age-dependent manner. We do not see significantly greater numbers of de novo missense mutations in affected versus unaffected children, but gene-disrupting mutations (nonsense, splice site, and frame shifts) are twice as frequent, 59 to 28. Based on this differential and the number of recurrent and total targets of gene disruption found in our and similar studies, we estimate between 350 and 400 autism susceptibility genes. Many of the disrupted genes in these studies are associated with the fragile X protein, FMRP, reinforcing links between autism and synaptic plasticity. We find FMRP-associated genes are under greater purifying selection than the remainder of genes and suggest they are especially dosage-sensitive targets of cognitive disorders. PMID:22542183

  7. Evolution of new functions de novo and from preexisting genes.

    PubMed

    Andersson, Dan I; Jerlström-Hultqvist, Jon; Näsvall, Joakim

    2015-06-01

    How the enormous structural and functional diversity of new genes and proteins was generated (estimated to be 10(10)-10(12) different proteins in all organisms on earth [Choi I-G, Kim S-H. 2006. Evolution of protein structural classes and protein sequence families. Proc Natl Acad Sci 103: 14056-14061] is a central biological question that has a long and rich history. Extensive work during the last 80 years have shown that new genes that play important roles in lineage-specific phenotypes and adaptation can originate through a multitude of different mechanisms, including duplication, lateral gene transfer, gene fusion/fission, and de novo origination. In this review, we focus on two main processes as generators of new functions: evolution of new genes by duplication and divergence of pre-existing genes and de novo gene origination in which a whole protein-coding gene evolves from a noncoding sequence. PMID:26032716

  8. A de novo peptide hexamer with a mutable channel

    PubMed Central

    Zaccai, Nathan R.; Chi, Bertie; Thomson, Andrew R.; Boyle, Aimee L.; Bartlett, Gail J.; Bruning, Marc; Linden, Noah; Sessions, Richard B.; Booth, Paula J.; Brady, R. Leo; Woolfson, Derek N.

    2011-01-01

    The design of new proteins that expand the repertoire of natural protein structures represents a formidable challenge. Success in this area would increase understanding of protein structure, and present new scaffolds that could be exploited in biotechnology and synthetic biology. Here we describe the design, characterisation and X-ray crystal structure of a new coiled-coil protein. The de novo sequence forms a stand-alone, parallel, 6-helix bundle with a channel running through it. Although lined exclusively by hydrophobic leucine and isoleucine side chains, the 6 Å channel is permeable to water. One layer of leucine residues within the channel is mutable accepting polar aspartic acid (Asp) and histidine (His) side chains, and leading to subdivision and organization of solvent within the lumen. Moreover, these mutants can be combined to form a stable and unique (Asp-His)3 heterohexamer. These new structures provide a basis for engineering de novo proteins with new functions. PMID:22037471

  9. RNA-template dependent de novo telomere addition.

    PubMed

    Fuhrmann, Gloria; Jönsson, Franziska; Weil, Patrick Philipp; Postberg, Jan; Lipps, Hans J

    2016-08-01

    De novo addition of telomeric sequences can occur at broken chromosomes and must be well controlled, which is essential during programmed DNA reorganization processes. In ciliated protozoa an extreme form of DNA-reorganization is observed during macronuclear differentiation after sexual reproduction leading to the elimination of specific parts of the germline genome. Regulating these processes involves small noncoding RNAs, but in addition DNA-reordering, excision and amplification require RNA templates deriving from the parental macronucleus. We show that these putative RNA templates can carry telomeric repeats. Microinjection of RNA templates carrying modified telomeres into the developing macronucleus leads to modified telomeres in vegetative cells, providing strong evidence, that de novo addition of telomeres depends on a telomere-containing transcript from the parental macronucleus. PMID:26786510

  10. De Novo Mutations in Ataxin-2 Gene and ALS Risk

    PubMed Central

    Laffita-Mesa, José Miguel; Rodríguez Pupo, Jorge Michel; Moreno Sera, Raciel; Vázquez Mojena, Yaimee; Kourí, Vivian; Laguna-Salvia, Leonides; Martínez-Godales, Michael; Valdevila Figueira, José A.; Bauer, Peter O.; Rodríguez-Labrada, Roberto; Zaldívar, Yanetza González; Paucar, Martin; Svenningsson, Per; Pérez, Luís Velázquez

    2013-01-01

    Pathogenic CAG repeat expansion in the ataxin-2 gene (ATXN2) is the genetic cause of spinocerebellar ataxia type 2 (SCA2). Recently, it has been associated with Parkinsonism and increased genetic risk for amyotrophic lateral sclerosis (ALS). Here we report the association of de novo mutations in ATXN2 with autosomal dominant ALS. These findings support our previous conjectures based on population studies on the role of large normal ATXN2 alleles as the source for new mutations being involved in neurodegenerative pathologies associated with CAG expansions. The de novo mutations expanded from ALS/SCA2 non-risk alleles as proven by meta-analysis method. The ALS risk was associated with SCA2 alleles as well as with intermediate CAG lengths in the ATXN2. Higher risk for ALS was associated with pathogenic CAG repeat as revealed by meta-analysis. PMID:23936447

  11. From de novo mutations to personalized therapeutic interventions in autism.

    PubMed

    Brandler, William M; Sebat, Jonathan

    2015-01-01

    The high heritability, early age at onset, and reproductive disadvantages of autism spectrum disorders (ASDs) are consistent with an etiology composed of dominant-acting de novo (spontaneous) mutations. Mutation detection by microarray analysis and DNA sequencing has confirmed that de novo copy-number variants or point mutations in protein-coding regions of genes contribute to risk, and some of the underlying causal variants and genes have been identified. As our understanding of autism genes develops, the spectrum of autism is breaking up into quanta of many different genetic disorders. Given the diversity of etiologies and underlying biochemical pathways, personalized therapy for ASDs is logical, and clinical genetic testing is a prerequisite. PMID:25587659

  12. NovoPen Echo(®) insulin delivery device.

    PubMed

    Hyllested-Winge, Jacob; Sparre, Thomas; Pedersen, Line Kynemund

    2016-01-01

    The introduction of insulin pen devices has provided easier, well-tolerated, and more convenient treatment regimens for patients with diabetes mellitus. When compared with vial and syringe regimens, insulin pens offer a greater clinical efficacy, improved quality of life, and increased dosing accuracy, particularly at low doses. The portable and discreet nature of pen devices reduces the burden on the patient, facilitates adherence, and subsequently contributes to the improvement in glycemic control. NovoPen Echo(®) is one of the latest members of the NovoPen(®) family that has been specifically designed for the pediatric population and is the first to combine half-unit increment (=0.5 U of insulin) dosing with a simple memory function. The half-unit increment dosing amendments and accurate injection of 0.5 U of insulin are particularly beneficial for children (and insulin-sensitive adults/elders), who often require small insulin doses. The memory function can be used to record the time and amount of the last dose, reducing the fear of double dosing or missing a dose. The memory function also provides parents with extra confidence and security that their child is taking insulin at the correct doses and times. NovoPen Echo is a lightweight, durable insulin delivery pen; it is available in two different colors, which may help to distinguish between different types of insulin, providing more confidence for both users and caregivers. Studies have demonstrated a high level of patient satisfaction, with 80% of users preferring NovoPen Echo to other pediatric insulin pens. PMID:26793007

  13. Effective de novo assembly of fish genome using haploid larvae.

    PubMed

    Iwasaki, Yuki; Nishiki, Issei; Nakamura, Yoji; Yasuike, Motoshige; Kai, Wataru; Nomura, Kazuharu; Yoshida, Kazunori; Nomura, Yousuke; Fujiwara, Atushi; Kobayashi, Takanori; Ototake, Mitsuru

    2016-02-01

    Recent improvements in next-generation sequencing technology have made it possible to do whole genome sequencing, on even non-model eukaryote species with no available reference genomes. However, de novo assembly of diploid genomes is still a big challenge because of allelic variation. The aim of this study was to determine the feasibility of utilizing the genome of haploid fish larvae for de novo assembly of whole-genome sequences. We compared the efficiency of assembly using the haploid genome of yellowtail (Seriola quinqueradiata) with that using the diploid genome obtained from the dam. De novo assembly from the haploid and the diploid sequence reads (100 million reads per each datasets) generated by the Ion Proton sequencer (200 bp) was done under two different assembly algorithms, namely overlap-layout-consensus (OLC) and de Bruijn graph (DBG). This revealed that the assembly of the haploid genome significantly reduced (approximately 22% for OLC, 9% for DBG) the total number of contigs (with longer average and N50 contig lengths) when compared to the diploid genome assembly. The haploid assembly also improved the quality of the scaffolds by reducing the number of regions with unassigned nucleotides (Ns) (total length of Ns; 45,331,916 bp for haploids and 67,724,360 bp for diploids) in OLC-based assemblies. It appears clear that the haploid genome assembly is better because the allelic variation in the diploid genome disrupts the extension of contigs during the assembly process. Our results indicate that utilizing the genome of haploid larvae leads to a significant improvement in the de novo assembly process, thus providing a novel strategy for the construction of reference genomes from non-model diploid organisms such as fish. PMID:26478467

  14. NovoPen Echo® insulin delivery device

    PubMed Central

    Hyllested-Winge, Jacob; Sparre, Thomas; Pedersen, Line Kynemund

    2016-01-01

    The introduction of insulin pen devices has provided easier, well-tolerated, and more convenient treatment regimens for patients with diabetes mellitus. When compared with vial and syringe regimens, insulin pens offer a greater clinical efficacy, improved quality of life, and increased dosing accuracy, particularly at low doses. The portable and discreet nature of pen devices reduces the burden on the patient, facilitates adherence, and subsequently contributes to the improvement in glycemic control. NovoPen Echo® is one of the latest members of the NovoPen® family that has been specifically designed for the pediatric population and is the first to combine half-unit increment (=0.5 U of insulin) dosing with a simple memory function. The half-unit increment dosing amendments and accurate injection of 0.5 U of insulin are particularly beneficial for children (and insulin-sensitive adults/elders), who often require small insulin doses. The memory function can be used to record the time and amount of the last dose, reducing the fear of double dosing or missing a dose. The memory function also provides parents with extra confidence and security that their child is taking insulin at the correct doses and times. NovoPen Echo is a lightweight, durable insulin delivery pen; it is available in two different colors, which may help to distinguish between different types of insulin, providing more confidence for both users and caregivers. Studies have demonstrated a high level of patient satisfaction, with 80% of users preferring NovoPen Echo to other pediatric insulin pens. PMID:26793007

  15. Um Infixation and Prefixation in Toba Batak.

    ERIC Educational Resources Information Center

    Crowhurst, Megan J.

    1998-01-01

    Examines the behavior of the morpheme, um, in Toba Batak and Tagalog, which alternates as a prefix or an infix, arguing that the variation is conditioned by constraints on consonant clusters. Three patterns of variation that occur with um are described, noting that the stages involved in changing from infixed to prefixed positions over time are…

  16. Infant Mortality in Novo Hamburgo: Associated Factors and Cardiovascular Causes

    PubMed Central

    Brum, Camila de Andrade; Stein, Airton Tetelbom; Pellanda, Lucia Campos

    2015-01-01

    Background Infant mortality has decreased in Brazil, but remains high as compared to that of other developing countries. In 2010, the Rio Grande do Sul state had the lowest infant mortality rate in Brazil. However, the municipality of Novo Hamburgo had the highest infant mortality rate in the Porto Alegre metropolitan region. Objective To describe the causes of infant mortality in the municipality of Novo Hamburgo from 2007 to 2010, identifying which causes were related to heart diseases and if they were diagnosed in the prenatal period, and to assess the access to healthcare services. Methods This study assessed infants of the municipality of Novo Hamburgo, who died, and whose data were collected from the infant death investigation records. Results Of the 157 deaths in that period, 35.3% were reducible through diagnosis and early treatment, 25% were reducible through partnership with other sectors, 19.2% were non-preventable, 11.5% were reducible by means of appropriate pregnancy monitoring, 5.1% were reducible through appropriate delivery care, and 3.8% were ill defined. The major cause of death related to heart disease (13.4%), which was significantly associated with the variables ‘age at death’, ‘gestational age’ and ‘birth weight’. Regarding access to healthcare services, 60.9% of the pregnant women had a maximum of six prenatal visits. Conclusion It is mandatory to enhance prenatal care and newborn care at hospitals and basic healthcare units to prevent infant mortality. PMID:25993588

  17. The Recent De Novo Origin of Protein C-Termini

    PubMed Central

    Andreatta, Matthew E.; Levine, Joshua A.; Foy, Scott G.; Guzman, Lynette D.; Kosinski, Luke J.; Cordes, Matthew H.J.; Masel, Joanna

    2015-01-01

    Protein-coding sequences can arise either from duplication and divergence of existing sequences, or de novo from noncoding DNA. Unfortunately, recently evolved de novo genes can be hard to distinguish from false positives, making their study difficult. Here, we study a more tractable version of the process of conversion of noncoding sequence into coding: the co-option of short segments of noncoding sequence into the C-termini of existing proteins via the loss of a stop codon. Because we study recent additions to potentially old genes, we are able to apply a variety of stringent quality filters to our annotations of what is a true protein-coding gene, discarding the putative proteins of unknown function that are typical of recent fully de novo genes. We identify 54 examples of C-terminal extensions in Saccharomyces and 28 in Drosophila, all of them recent enough to still be polymorphic. We find one putative gene fusion that turns out, on close inspection, to be the product of replicated assembly errors, further highlighting the issue of false positives in the study of rare events. Four of the Saccharomyces C-terminal extensions (to ADH1, ARP8, TPM2, and PIS1) that survived our quality filters are predicted to lead to significant modification of a protein domain structure. PMID:26002864

  18. De novo isochromosome 18p in a female dysmorphic child.

    PubMed

    Ramegowda, Smitha; Gawde, Harshavardhan M; Hyderi, Abbas; Savitha, Mysore R; Patel, Zareen M; Krishnamurthy, Balasundaram; Ramachandra, Nallur B

    2006-01-01

    Isochromosome 18p results in tetrasomy 18p. Most of the i(18p) cases reported so far in the literature are sporadic due to de novo formation, while familial and mosaic cases are infrequent. It is a rare chromosomal abnormality, occurring once in every 140,000 livebirths, affecting males and females equally. In the present investigation, we report a de novo i(18p) in a female dysmorphic child. The small metacentric marker chromosome was confirmed as i(18p) in the proband by cytogenetic and FISH analysis [47,XX+i(18p)]. Cytogenetic investigations in the family members revealed normal chromosome numbers, indicating the case as a de novo event of i(18p) formation. It could be due to the somewhat advanced maternal age (32 years) and/or expression of recessive genes in the proband, who is the progeny of consanguineous marriage, which could have led to misdivision and nondisjunction of chromosome 18 in meiosis I, followed by failure in the chromatid separation of 18p in meiosis II and by inverted duplication. PMID:17132906

  19. Pleiotropy of the de novo-originated gene MDF1

    PubMed Central

    Li, Dan; Yan, Zhihui; Lu, Lina; Jiang, Huifeng; Wang, Wen

    2014-01-01

    MDF1 is a young de novo-originated gene from a non-coding sequence in baker's yeast, S. cerevisiae, which can suppress mating and promote vegetative growth. Our previous experiments successfully demonstrated how Mdf1p binds to the key mating pathway determinant MATα2 to suppress mating. However, how Mdf1p promotes growth and fulfills the crosstalk between the yeast mating and growth pathways are still open questions. Thus, the adaptive significance of this new de novo gene remains speculative. Here, we show that Mdf1p shortens the lag phase of S. cerevisiae by physically interacting with SNF1, the governing factor for nonfermentable carbon source utilization, and thereby confers a selective advantage on yeasts through the rapid consumption of glucose in the early generational stage in rich medium. Therefore, MDF1 functions in two important molecular pathways, mating and fermentation, and mediates the crosstalk between reproduction and vegetative growth. Together, our results provide a comprehensive example of how a de novo-originated gene organizes new regulatory circuits and thereby confers a selective advantage on S. cerevisiae to allow exquisite adaptation to the changing environment. PMID:25452167

  20. Recurrent and de novo disease after renal transplantation: a report from the Renal Allograft Disease Registry.

    PubMed

    Hariharan, Sundaram; Savin, Virginia J

    2004-08-01

    Recurrent and de novo disease is an increasing problem and is known to negatively impact transplant graft survival. Immunosuppressive medications have not had an impact on the prevalence of recurrent and de novo disease. Renal Allograft Disease Registry (RADR) was established to study the prevalence, impact and risk factors for the development of recurrent and de novo disease. Retrospective and prospective study on recurrent disease is discussed in this manuscript. PMID:15265160

  1. Open questions in the study of de novo genes: what, how and why.

    PubMed

    McLysaght, Aoife; Hurst, Laurence D

    2016-09-01

    The study of de novo protein-coding genes is maturing from the ad hoc reporting of individual cases to the systematic analysis of extensive genomic data from several species. We identify three key challenges for this emerging field: understanding how best to identify de novo genes, how they arise and why they spread. We highlight the intellectual challenges of understanding how a de novo gene becomes integrated into pre-existing functions and becomes essential. We suggest that, as with protein sequence evolution, antagonistic co-evolution may be key to de novo gene evolution, particularly for new essential genes and new cancer-associated genes. PMID:27452112

  2. De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins

    SciTech Connect

    Shen, Yufeng; Tolic, Nikola; Hixson, Kim K.; Purvine, Samuel O.; Anderson, Gordon A.; Smith, Richard D.

    2008-10-15

    De novo sequencing has a promise to discover the protein post-translation modifications; however, such approach is still in their infancy and not widely applied for proteomics practices due to its limited reliability. In this work, we describe a de novo sequencing approach for discovery of protein modifications through identification of the UStags (Anal. Chem. 2008, 80, 1871-1882). The de novo information was obtained from Fourier-transform tandem mass spectrometry for peptides and polypeptides in a yeast lysate, and the de novo sequences obtained were filtered to define a more limited set of UStags. The DNA-predicted database protein sequences were then compared to the UStags, and the differences observed across or in the UStags (i.e., the UStags’ prefix and suffix sequences and the UStags themselves) were used to infer the possible sequence modifications. With this de novo-UStag approach, we uncovered some unexpected variances of yeast protein sequences due to amino acid mutations and/or multiple modifications to the predicted protein sequences. Random matching of the de novo sequences to the predicted sequences were examined with use of two random (false) databases, and ~3% false discovery rates were estimated for the de novo-UStag approach. The factors affecting the reliability (e.g., existence of de novo sequencing noise residues and redundant sequences) and the sensitivity are described. The de novo-UStag complements the UStag method previously reported by enabling discovery of new protein modifications.

  3. Informed kmer selection for de novo transcriptome assembly

    PubMed Central

    Durai, Dilip A.; Schulz, Marcel H.

    2016-01-01

    Motivation: De novo transcriptome assembly is an integral part for many RNA-seq workflows. Common applications include sequencing of non-model organisms, cancer or meta transcriptomes. Most de novo transcriptome assemblers use the de Bruijn graph (DBG) as the underlying data structure. The quality of the assemblies produced by such assemblers is highly influenced by the exact word length k. As such no single kmer value leads to optimal results. Instead, DBGs over different kmer values are built and the assemblies are merged to improve sensitivity. However, no studies have investigated thoroughly the problem of automatically learning at which kmer value to stop the assembly. Instead a suboptimal selection of kmer values is often used in practice. Results: Here we investigate the contribution of a single kmer value in a multi-kmer based assembly approach. We find that a comparative clustering of related assemblies can be used to estimate the importance of an additional kmer assembly. Using a model fit based algorithm we predict the kmer value at which no further assemblies are necessary. Our approach is tested with different de novo assemblers for datasets with different coverage values and read lengths. Further, we suggest a simple post processing step that significantly improves the quality of multi-kmer assemblies. Conclusion: We provide an automatic method for limiting the number of kmer values without a significant loss in assembly quality but with savings in assembly time. This is a step forward to making multi-kmer methods more reliable and easier to use. Availability and Implementation:A general implementation of our approach can be found under: https://github.com/SchulzLab/KREATION. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: mschulz@mmci.uni-saarland.de PMID:27153653

  4. RNAbrowse: RNA-Seq de novo assembly results browser.

    PubMed

    Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

    2014-01-01

    Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse. PMID:24823498

  5. RNAbrowse: RNA-Seq De Novo Assembly Results Browser

    PubMed Central

    Mariette, Jérôme; Noirot, Céline; Nabihoudine, Ibounyamine; Bardou, Philippe; Hoede, Claire; Djari, Anis; Cabau, Cédric; Klopp, Christophe

    2014-01-01

    Transcriptome analysis based on a de novo assembly of next generation RNA sequences is now performed routinely in many laboratories. The generated results, including contig sequences, quantification figures, functional annotations and variation discovery outputs are usually bulky and quite diverse. This article presents a user oriented storage and visualisation environment permitting to explore the data in a top-down manner, going from general graphical views to all possible details. The software package is based on biomart, easy to install and populate with local data. The software package is available under the GNU General Public License (GPL) at http://bioinfo.genotoul.fr/RNAbrowse. PMID:24823498

  6. De Novo Designed Imaging Agents Based on Lanthanide Peptides Complexes.

    PubMed

    Peacock, A F A

    2016-01-01

    Herein are discussed a selection of lanthanide peptide/protein complexes in view of their potential applications as imaging agents, both in terms of luminescence detection and magnetic resonance imaging. Though this chapter covers a range of different peptides and protein, if focuses specifically on the opportunities afforded by the de novo design of coiled coils, miniature protein scaffolds, and the development on lanthanide-binding sites into these architectures. The requirements for lanthanide coordination and the challenges that need to be addressed when preparing lanthanide peptides with a view to their potential adoption as clinical imaging applications, will be highlighted. PMID:27586349

  7. The carbon isotopic composition of Novo Urei diamonds

    NASA Technical Reports Server (NTRS)

    Fisenko, A. V.; Semjenova, L. F.; Verchovsky, A. B.; Russell, S. S.; Pillinger, C. T.

    1993-01-01

    The carbon isotopic composition of diamond grains isolated from the Novo Urei meteorite are discussed. A diamond separate was obtained from 2g of whole rock using the chemical treatments described aimed at obtaining very pure diamond. X ray diffraction of the residue, which represented 5000 ppm of the parent mass, indicated only the presence of the desired mineral. The diamond crystals were 1-30 microns in diameter, and some grains had a yellow color. The chemical treatments were followed by a size separation to give a 1-10 microns and a 5-30 microns fraction, which were named DNU-1 and DNU-2, respectively.

  8. De novo periaortic fibrosis after endovascular aortic repair.

    PubMed

    Alomran, Faris; de Blic, Romain; Mallios, Alexandros; Costanzo, Alessandro; Boura, Benoit; Combes, Myriam

    2014-02-01

    We report a case of a 63-year-old man presenting with abdominal pain and hydronephrosis secondary to periaortic fibrosis (PAF) 8 months after an endovascular aortic repair (EVAR) using a woven polyester bifurcated graft. De novo delayed PAF after open repair is rare and even more infrequent after EVAR. All 3 previously reported cases occurred after woven polyester grafts and no reported cases after polytetrafluorethylene grafts. Management included steroidal anti-inflammatory treatment and bilateral double J tube placement. Satisfactory results were obtained. PMID:24275428

  9. De Novo Design at the Edge of Chaos.

    PubMed

    Schneider, Petra; Schneider, Gisbert

    2016-05-12

    Computational medicinal chemistry offers viable strategies for finding, characterizing, and optimizing innovative pharmacologically active compounds. Technological advances in both computer hardware and software as well as biological chemistry have enabled a renaissance of computer-assisted "de novo" design of molecules with desired pharmacological properties. Here, we present our current perspective on the concept of automated molecule generation by highlighting chemocentric methods that may capture druglike chemical space, consider ligand promiscuity for hit and lead finding, and provide fresh ideas for the rational design of customized screening of compound libraries. PMID:26881908

  10. De novo transcriptome assembly of two different apricot cultivars.

    PubMed

    Jo, Yeonhwa; Lian, Sen; Cho, Jin Kyong; Choi, Hoseong; Chu, Hyosub; Cho, Won Kyong

    2015-12-01

    Apricot (Prunus armeniaca) belonging to the Prunus species is a popular kind of stone fruit tree. Apricot is native to Armenia and is currently cultivated in many countries with climates adaptable for apricot growth. In general, fresh fruits as well as dried apricot are produced. However, the information associated with genes and genetic markers for apricot is very limited. In this study, we carried out de novo transcriptome assembly for two selected apricot cultivars referred to as Harcot and Ungarische Beste, which are commercially important apricot cultivars in the world, using next generation sequencing. We obtained a total of 9.31 GB and 8.88 GB raw data from Harcot and Ungarische Beste (NCBI accession numbers: SRX1186946 and SRX1186893), respectively. De novo transcriptome assembly using Trinity identified 147,501 and 152,235 transcripts for Harcot and Ungarische Beste, respectively. Next, we identified 113,565 and 126,444 proteins from Harcot and Ungarische Beste using the TransDecoder program. We performed BLASTP against an NCBI non-redundant (nr) dataset to annotate identified proteins. Taken together, we provide transcriptomes of two different apricot cultivars by RNA-Seq. PMID:26697397

  11. De novo transcriptome assembly of Setatria italica variety Taejin.

    PubMed

    Jo, Yeonhwa; Lian, Sen; Cho, Jin Kyong; Choi, Hoseong; Kim, Sang-Min; Kim, Sun-Lim; Lee, Bong Choon; Cho, Won Kyong

    2016-06-01

    Foxtail millet (Setaria italica) belonging to the family Poaceae is an important millet that is widely cultivated in East Asia. Of the cultivated millets, the foxtail millet has the longest history and is one of the main food crops in South India and China. Moreover, foxtail millet is a model plant system for biofuel generation utilizing the C4 photosynthetic pathway. In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676 GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins. Taken together, this study provides transcriptome data for the foxtail millet variety Taejin by RNA-Seq. PMID:27257606

  12. Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes

    PubMed Central

    Moreton, Joanna; Izquierdo, Abril; Emes, Richard D.

    2016-01-01

    De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome. Transcriptomics allows the understanding and comparison of spatial and temporal samples within an organism, and allows surveying of multiple individuals or closely related species. De novo assembly in theory allows the building of a complete transcriptome without any prior knowledge of the genome. It also allows the discovery of alternate splice forms of coding RNAs and also non-coding RNAs, which are often missed by proteomic approaches, or are incompletely annotated in genome studies. The limitations of the method are that the generation of a truly complete assembly is unlikely, and so we require some methods for the assessment of the quality and appropriateness of a generated transcriptome. Whilst no single consensus pipeline or tool is agreed as optimal, various algorithms, and easy to use software do exist making transcriptome generation a more common approach. With this expansion of data, questions still exist relating to how do we make these datasets fully discoverable, comparable and most useful to understand complex biological systems? PMID:26793234

  13. Tea consumption reduces the risk of de novo myelodysplastic syndromes.

    PubMed

    Liu, Ping; Zhang, Min; Jin, Jie; Holman, C D'Arcy J

    2015-02-01

    Epidemiologic data suggest that green tea consumption may protect against certain cancers, but no previous study has examined myelodysplastic syndromes (MDS). A hospital-based case-control study was conducted in China in 2012-2013 to investigate the association between tea intake and the risk of de novo MDS in adults. The study included 208 cases aged 19-85 years with MDS and 208 controls individually matched to the cases by gender, 5-year age group and residential locality. Odds ratios (ORs) were estimated using conditional logistic regression. Compared with non-tea drinkers, the adjusted ORs (95% confidence intervals) for all MDS combined were 0.39 (0.20-0.74), 0.45 (0.25-0.79), and 0.40 (0.21-0.77) for those who consumed tea >20 years, ≥2 cups daily, and dried tealeaves ≥750g per annum, respectively. Significant dose-response trends were observed across all the measures. The inverse association existed in both genders, in the refractory anemia with excessive blasts subtype, in cytogenetic 'good' and 'intermediated/poor' prognosis groups, and in the International Prognostic Scoring System lower and higher risk groups, but not in the refractory cytopenia with multilineage dysplasia subtype. The study suggests that regular tea consumption reduces the risk of de novo MDS in the Chinese population. PMID:25529769

  14. Origins of De Novo Genes in Human and Chimpanzee.

    PubMed

    Ruiz-Orera, Jorge; Hernandez-Rodriguez, Jessica; Chiva, Cristina; Sabidó, Eduard; Kondova, Ivanela; Bontrop, Ronald; Marqués-Bonet, Tomàs; Albà, M Mar

    2015-12-01

    The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species--human, chimpanzee, macaque, and mouse--and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins. PMID:26720152

  15. Origins of De Novo Genes in Human and Chimpanzee

    PubMed Central

    Ruiz-Orera, Jorge; Hernandez-Rodriguez, Jessica; Chiva, Cristina; Sabidó, Eduard; Kondova, Ivanela; Bontrop, Ronald; Marqués-Bonet, Tomàs; Albà, M.Mar

    2015-01-01

    The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process, we have performed in-depth sequencing of the transcriptomes of four mammalian species—human, chimpanzee, macaque, and mouse—and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new multiexonic transcriptional events in human and/or chimpanzee that are not observed in the rest of species. Using comparative genomics, we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. In general, these transcripts show little evidence of purifying selection, suggesting that many of them are not functional. However, we find signatures of selection in a subset of de novo genes which have evidence of protein translation. Taken together, the data support a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins. PMID:26720152

  16. Ethanol enhances de novo synthesis of high density lipoprotein cholesterol

    SciTech Connect

    Cluette, J.E.; Mulligan, J.J.; Noring, R.; Doyle, K.; Hojnacki, J.

    1984-05-01

    Male squirrel monkeys fed ethanol at variable doses were used to assess whether alcohol enhances de novo synthesis of high density lipoprotein (HDL) cholesterol in vivo. Monkeys were divided into three groups: 1) controls fed isocaloric liquid diet; 2) low ethanol monkeys fed liquid diet with vodka substituted isocalorically for carbohydrate at 12% of calories; and 3) High Ethanol animals fed diet plus vodka at 24% of calories. High Ethanol primates had significantly higher levels of HDL nonesterified cholesterol than Control and Low Ethanol animals while serum glutamate oxaloacetate transaminase was similar for the three treatments. There were no significant differences between the groups in HDL cholesteryl ester mass or specific activity following intravenous injection of labeled mevalonolactone. By contrast, High Ethanol monkeys had significantly greater HDL nonesterified cholesterol specific activity with approximately 60% of the radioactivity distributed in the HDL/sub 3/ subfraction. This report provides the first experimental evidence that ethanol at 24% of calories induces elevations in HDL cholesterol in primates through enhanced de novo synthesis without adverse effects on liver function.

  17. Molecular characterization of de novo secondary trisomy 13.

    PubMed Central

    Shaffer, L. G.; McCaskill, C.; Han, J. Y.; Choo, K. H.; Cutillo, D. M.; Donnenfeld, A. E.; Weiss, L.; Van Dyke, D. L.

    1994-01-01

    Unbalanced Robertsonian translocations are a significant cause of mental retardation and fetal wastage. The majority of homologous rearrangements of chromosome 21 in Down syndrome have been shown to be isochromosomes. Aside from chromosome 21, very little is known about other acrocentric homologous rearrangements. In this study, four cases of de novo secondary trisomy 13 are presented. FISH using alpha-satellite sequences, rDNA, and a pTRI-6 satellite I sequence specific to the short arm of chromosome 13 showed all four rearrangements to be dicentric and apparently devoid of ribosomal genes. Three of four rearrangements retained the pTRI-6 satellite I sequence. Case 1 was the exception, showing a deletion of this sequence in the rearrangement, although both parental chromosomes 13 had strong positive hybridization signals. Eleven microsatellite markers from chromosome 13 were also used to characterize the rearrangements. Of the four possible outcomes, one maternal Robertsonian translocation, two paternal isochromosomes, and one maternal isochromosome were observed. A double recombination was observed in the maternally derived rob(13q13q). No recombination events were detected in any isochromosome. The parental origins and molecular chromosomal structure of these cases are compared with previous studies of de novo acrocentric rearrangements. Images Figure 1 Figure 2 Figure 3 PMID:7977360

  18. Heavy-metal complexation by de novo peptide design.

    PubMed

    Farrer, Brian T; Pecoraro, Vincent L

    2002-11-01

    From poisoning caused by lead-based paint on domestic buildings to groundwater contamination by naturally occurring arsenic deposits in India, heavy-metal toxicity is a global health problem. Contaminated ground water and acute cases of heavy-metal poisoning are treated with chelators to remove the heavy metals from the contaminated site or person. This review discusses the effort to generate heavy-metal chelators through peptide de novo design. De novo design entails the design of a primary sequence that will precisely fold into a predetermined secondary and tertiary protein structure. The first-generation peptide chelator used to initiate this investigation is the three-stranded coild coil containing Cys. Cys provides a potential trigonal binding site with soft thiolate ligands, which has been proposed to provide specific interactions with heavy metals. This hypothesis derives from the observation that similar sites on natural proteins show selectivity for heavy metals over other essential metals, such as Zn or Mg. A description of two systems, the TRI series and the IZ-AC peptide, is given, highlighting the interaction of these peptides with Hg, Cd, As and Pb. Arguments are also presented for the potential use of three-helix bundles as a second-generation design. PMID:12478724

  19. Molecular characterization of de novo secondary trisomy 13

    SciTech Connect

    Shaffer, L.G.; McCaskill, C.; Han, Jin-Yeong; Choo, K.H.A.; Cutillo, D.M.; Donnenfeld, A.E.; Weiss, L.; Van Dyke, D.L.

    1994-11-01

    Unbalanced Robertsonian translocations are a significant cause of mental retardation and fetal wastage. The majority of homologous rearrangements of chromosome 21 in Down syndrome have been shown to be isochromosomes. Aside from chromosome 21, very little is known about other acrocentric homologous rearrangements. In this study, four cases of de novo secondary trisomy 13 are presented. FISH using alpha-satellite sequences, rDNA, and a pTRI-6 satellite I sequence specific to the short arm of chromosome 13 showed all four rearrangements to be dicentric an apparently devoid of ribosomal genes. Three of four rearrangements retained the pTRI-6 satellite I sequence. Case 1 was the exception, showing a deletion of this sequence in the rearrangement, although both parental chromosomes 13 had strong positive hybridization signals. Eleven microsatellite markers from chromosome 13 were also used to characterize the rearrangements. Of the four possible outcomes, one maternal Robertsonian translocation, two paternal isochromosomes, and one maternal isochromosomes were observed. A double recombination was observed in the maternally derived rob(13q13q). No recombination events were detected in any isochromosome. The parental origins and molecular chromosomal structure of these cases are compared with previous studies of de novo acrocentric rearrangements. 20 refs., 3 figs., 2 tabs.

  20. Extensive Natural Epigenetic Variation at a De Novo Originated Gene

    PubMed Central

    Silveira, Amanda Bortolini; Trontin, Charlotte; Cortijo, Sandra; Barau, Joan; Del Bem, Luiz Eduardo Vieira; Loudet, Olivier; Colot, Vincent; Vincentz, Michel

    2013-01-01

    Epigenetic variation, such as heritable changes of DNA methylation, can affect gene expression and thus phenotypes, but examples of natural epimutations are few and little is known about their stability and frequency in nature. Here, we report that the gene Qua-Quine Starch (QQS) of Arabidopsis thaliana, which is involved in starch metabolism and that originated de novo recently, is subject to frequent epigenetic variation in nature. Specifically, we show that expression of this gene varies considerably among natural accessions as well as within populations directly sampled from the wild, and we demonstrate that this variation correlates negatively with the DNA methylation level of repeated sequences located within the 5′end of the gene. Furthermore, we provide extensive evidence that DNA methylation and expression variants can be inherited for several generations and are not linked to DNA sequence changes. Taken together, these observations provide a first indication that de novo originated genes might be particularly prone to epigenetic variation in their initial stages of formation. PMID:23593031

  1. DOGS: Reaction-Driven de novo Design of Bioactive Compounds

    PubMed Central

    Hartenfeller, Markus; Zettl, Heiko; Walter, Miriam; Rupp, Matthias; Reisen, Felix; Proschak, Ewgenij; Weggen, Sascha; Stark, Holger; Schneider, Gisbert

    2012-01-01

    We present a computational method for the reaction-based de novo design of drug-like molecules. The software DOGS (Design of Genuine Structures) features a ligand-based strategy for automated ‘in silico’ assembly of potentially novel bioactive compounds. The quality of the designed compounds is assessed by a graph kernel method measuring their similarity to known bioactive reference ligands in terms of structural and pharmacophoric features. We implemented a deterministic compound construction procedure that explicitly considers compound synthesizability, based on a compilation of 25'144 readily available synthetic building blocks and 58 established reaction principles. This enables the software to suggest a synthesis route for each designed compound. Two prospective case studies are presented together with details on the algorithm and its implementation. De novo designed ligand candidates for the human histamine H4 receptor and γ-secretase were synthesized as suggested by the software. The computational approach proved to be suitable for scaffold-hopping from known ligands to novel chemotypes, and for generating bioactive molecules with drug-like properties. PMID:22359493

  2. 76 FR 61103 - Draft Guidance for Industry and Food and Drug Administration Staff; De Novo Classification...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-03

    ... Staff; De Novo Classification Process (Evaluation of Automatic Class III Designation); Availability...) is announcing the availability of the draft guidance entitled ``De Novo Classification Process... staff and industry on the process for the submission and review of petitions submitted under the...

  3. De Novo duplication in Charcot-Marie-Tooth Type 1A

    SciTech Connect

    Mandich, P.; Bellone, E.; Ajmar, F.

    1996-09-01

    We read with interest the paper on {open_quotes}Prevalence and Origin of De Novo Duplications in Charcot-Marie-Tooth Disease Type 1A: First Report of a De Novo Duplication with a Maternal Origin,{close_quotes}. They reported their experience with 10 sporadic cases of Charcot-Marie-Tooth type 1A (CMT1A) in which it was demonstrated that the disease had arisen as the result of a de novo duplication. They analyzed the de novo-duplication families by using microsatellite markers and identified the parental origin of the duplication in eight cases. In one family the duplication was of maternal origin, whereas in the remaining seven cases it was of paternal origin. The authors concluded that their report was the first evidence of a de novo duplication of maternal origin, suggesting that this is not a phenomenon associated solely with male meiosis. 7 refs.

  4. Sm-Nd Isotopic Studies of Ureilite Novo Urei

    NASA Technical Reports Server (NTRS)

    Shih, C.-Y.; Nyquist, L. E.; Reese, Y.; Goodrich, C. A.

    2011-01-01

    Ureilites are ultramafic (harzburgitic) achondrites composed predominantly of olivine and pyroxenes, abundant carbon (graphites and shock-produced diamonds), some metal and sulfides. These rocks probably represent ultramafic mantles of differentiated parent asteroidal bodies. Age determinations of these rocks by Rb-Sr and Sm-Nd methods have been difficult because of their extremely low abundances of these parent-daughter elements. Nevertheless, Sm-Nd isochron ages were reported for Kenna, Goalpara, MET 78008 and PCA 82506 yielding ages of 3.74+/-0.02 Ga, approx.3.7 Ga, 4.09+/-0.08 Ga, 4.23+/-0.06 Ga, respectively [1-4]. These "young" Sm-Nd ages may represent secondary metasomatism events [1] related to impacts [5], as indicated by the similarly young Ar-39-Ar-40 degassing ages of 3.3-4.1 Ga for ureilites Kenna, Novo Urei and Havero [6]. Alternatively, it has been suggested that these rocks may have been contaminated with terrestrial crustal materials and the isochrons do not have any age significance [2,7]. Indications of old approx.4.56 Ga ages for ureilites were reported from the U-Pb and Sm-Nd model ages for MET 78008 [8]. More reliable evidences for old formation ages of ureilites were reported recently using the short-lived chronometers Hf-182-W-182, Al-26-Mg-26 and Mn-53-Cr-53. The deficits of 182W in ureilites suggest the metal-silicate segregation occurred very early, approx.1-2 Ma after CAI [9]. The Al-26-Mg-26 and Mn-53-Cr-53 studies for a feldspathic lithology [10] and the Mn-53-Cr-53 for olivine- and pyroxene-dominant lithologies [11] in ureilites revealed that they crystallized approx.5.4 Ma after CAI, i.e., at 4563.8+/-0.5 Ma relative to D.Orbigny. In this report, we present Sm-Nd isotopic data for a relatively fresh ureilite, Novo Urei, a rare ureilite fall (1886). We compare these data to Sm-Nd data for other ureilites, and discuss Novo Urei's petrogenesis

  5. A gradient-boosting approach for filtering de novo mutations in parent–offspring trios

    PubMed Central

    Liu, Yongzhuang; Li, Bingshan; Tan, Renjie; Zhu, Xiaolin; Wang, Yadong

    2014-01-01

    Motivation: Whole-genome and -exome sequencing on parent–offspring trios is a powerful approach to identifying disease-associated genes by detecting de novo mutations in patients. Accurate detection of de novo mutations from sequencing data is a critical step in trio-based genetic studies. Existing bioinformatic approaches usually yield high error rates due to sequencing artifacts and alignment issues, which may either miss true de novo mutations or call too many false ones, making downstream validation and analysis difficult. In particular, current approaches have much worse specificity than sensitivity, and developing effective filters to discriminate genuine from spurious de novo mutations remains an unsolved challenge. Results: In this article, we curated 59 sequence features in whole genome and exome alignment context which are considered to be relevant to discriminating true de novo mutations from artifacts, and then employed a machine-learning approach to classify candidates as true or false de novo mutations. Specifically, we built a classifier, named De Novo Mutation Filter (DNMFilter), using gradient boosting as the classification algorithm. We built the training set using experimentally validated true and false de novo mutations as well as collected false de novo mutations from an in-house large-scale exome-sequencing project. We evaluated DNMFilter’s theoretical performance and investigated relative importance of different sequence features on the classification accuracy. Finally, we applied DNMFilter on our in-house whole exome trios and one CEU trio from the 1000 Genomes Project and found that DNMFilter could be coupled with commonly used de novo mutation detection approaches as an effective filtering approach to significantly reduce false discovery rate without sacrificing sensitivity. Availability: The software DNMFilter implemented using a combination of Java and R is freely available from the website at http

  6. Response assessment of NovoTTF-100A versus best physician's choice chemotherapy in recurrent glioblastoma.

    PubMed

    Wong, Eric T; Lok, Edwin; Swanson, Kenneth D; Gautam, Shiva; Engelhard, Herbert H; Lieberman, Frank; Taillibert, Sophie; Ram, Zvi; Villano, John L

    2014-06-01

    The NovoTTF-100A device emits frequency-tuned alternating electric fields that interfere with tumor cell mitosis. In phase III trial for recurrent glioblastomas, NovoTTF-100A was shown to have equivalent efficacy and less toxicity when compared to Best Physician's Choice (BPC) chemotherapy. We analyzed the characteristics of responders and nonresponders in both cohorts to determine the characteristics of response and potential predictive factors. Tumor response and progression were determined by Macdonald criteria. Time to response, response duration, progression-free survival (PFS) ± Simon-Makuch correction, overall survival (OS), prognostic factors, and relative hazard rates were compared between responders and nonresponders. Median response duration was 7.3 versus 5.6 months for NovoTTF-100A and BPC chemotherapy, respectively (P = 0.0009). Five of 14 NovoTTF-100A responders but none of seven BPC responders had prior low-grade histology. Mean cumulative dexamethasone dose was 35.9 mg for responders versus 485.6 mg for nonresponders in the NovoTTF-100A cohort (P < 0.0001). Hazard analysis showed delayed tumor progression in responders compared to nonresponders. Simon-Makuch-adjusted PFS was longer in responders than in nonresponders treated with NovoTTF-100A (P = 0.0007) or BPC chemotherapy (P = 0.0222). Median OS was longer for responders than nonresponders treated with NovoTTF-100A (P < 0.0001) and BPC chemotherapy (P = 0.0235). Pearson analysis showed strong correlation between response and OS in NovoTTF-100A (P = 0.0002) but not in BPC cohort (P = 0.2900). Our results indicate that the response characteristics favor NovoTTF-100A and data on prior low-grade histology and dexamethasone suggest potential genetic and epigenetic determinants of NovoTTF-100A response. PMID:24574359

  7. Ray Meta: scalable de novo metagenome assembly and profiling

    PubMed Central

    2012-01-01

    Voluminous parallel sequencing datasets, especially metagenomic experiments, require distributed computing for de novo assembly and taxonomic profiling. Ray Meta is a massively distributed metagenome assembler that is coupled with Ray Communities, which profiles microbiomes based on uniquely-colored k-mers. It can accurately assemble and profile a three billion read metagenomic experiment representing 1,000 bacterial genomes of uneven proportions in 15 hours with 1,024 processor cores, using only 1.5 GB per core. The software will facilitate the processing of large and complex datasets, and will help in generating biological insights for specific environments. Ray Meta is open source and available at http://denovoassembler.sf.net. PMID:23259615

  8. Parent-of-origin-specific signatures of de novo mutations.

    PubMed

    Goldmann, Jakob M; Wong, Wendy S W; Pinelli, Michele; Farrah, Terry; Bodian, Dale; Stittrich, Anna B; Glusman, Gustavo; Vissers, Lisenka E L M; Hoischen, Alexander; Roach, Jared C; Vockley, Joseph G; Veltman, Joris A; Solomon, Benjamin D; Gilissen, Christian; Niederhuber, John E

    2016-08-01

    De novo mutations (DNMs) originating in gametogenesis are an important source of genetic variation. We use a data set of 7,216 autosomal DNMs with resolved parent of origin from whole-genome sequencing of 816 parent-offspring trios to investigate differences between maternally and paternally derived DNMs and study the underlying mutational mechanisms. Our results show that the number of DNMs in offspring increases not only with paternal age, but also with maternal age, and that some genome regions show enrichment for maternally derived DNMs. We identify parent-of-origin-specific mutation signatures that become more pronounced with increased parental age, pointing to different mutational mechanisms in spermatogenesis and oogenesis. Moreover, we find DNMs that are spatially clustered to have a unique mutational signature with no significant differences between parental alleles, suggesting a different mutational mechanism. Our findings provide insights into the molecular mechanisms that underlie mutagenesis and are relevant to disease and evolution in humans. PMID:27322544

  9. De-Novo Design of Antimicrobial Peptides for Plant Protection

    PubMed Central

    Zeitler, Benjamin; Herrera Diaz, Areli; Dangel, Alexandra; Thellmann, Martha; Meyer, Helge; Sattler, Michael; Lindermayr, Christian

    2013-01-01

    This work describes the de-novo design of peptides that inhibit a broad range of plant pathogens. Four structurally different groups of peptides were developed that differ in size and position of their charged and hydrophobic clusters and were assayed for their ability to inhibit bacterial growth and fungal spore germination. Several peptides are highly active at concentrations between 0,1 and 1 µg/ml against plant pathogenic bacteria, such as Pseudomonas syringae, Pectobacterium carotovorum, and Xanthomonas vesicatoria. Importantly, no hemolytic activity could be detected for these peptides at concentrations up to 200 µg/ml. Moreover, the peptides are also active after spraying on the plant surface demonstrating a possible way of application. In sum, our designed peptides represent new antimicrobial agents and with the increasing demand for antimicrobial compounds for production of “healthy” food, these peptides might serve as templates for novel antibacterial and antifungal agents. PMID:23951222

  10. De novo gene synthesis design using TmPrime software.

    PubMed

    Li, Mo-Huang; Bode, Marcus; Huang, Mo Chao; Cheong, Wai Chye; Lim, Li Shi

    2012-01-01

    This chapter presents TmPrime, a computer program to design oligonucleotide for both ligase chain reaction (LCR)- and polymerase chain reaction (PCR)-based de novo gene synthesis. The program divides a long input DNA sequence based on user-specified melting temperatures and assembly conditions, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences, and potential formation of secondary structures in a PDF file, which will be sent to the user via e-mail. The program also provides functions on sequence pooling to separate long genes into smaller pieces for multipool assembly and codon optimization for expression based on the highest organism-specific codon frequency. This software has been successfully used in the design and synthesis of various genes with total length >20 kbp. This program is freely available at http://prime.ibn.a-star.edu.sg. PMID:22328437

  11. De novo development of artistic creativity in Alzheimer's disease

    PubMed Central

    Chakravarty, Ambar

    2011-01-01

    The case of an 82-year-old female with probable Alzheimer's disease (AD), who developed unusual artistic creativity after development of her disease, is described. The possible pathogenetic mechanism is discussed. The patient showed no inclination toward visual arts during her premorbid years. However, 4 years after development of AD suggestive symptoms she started painting beautiful pictures rather impulsively. Some such paintings have been appreciated even by a qualified art expert. Such de novo development of artistic creativity had been described earlier in subjects with the semantic form of fronto-temporal dementia (FTD), but not in AD. The prevailing concept of lateralized compromise and paradoxical functional facilitation, proposed in connection with FTD subjects, may not be applicable in AD subjects where the affection is more diffuse and more posterior in the brain. Hence, the likely pathogenetic mechanism involved in the case described may remain uncertain. Possibilities are discussed. PMID:22346020

  12. De novo assembly of a haplotype-resolved human genome.

    PubMed

    Cao, Hongzhi; Wu, Honglong; Luo, Ruibang; Huang, Shujia; Sun, Yuhui; Tong, Xin; Xie, Yinlong; Liu, Binghang; Yang, Hailong; Zheng, Hancheng; Li, Jian; Li, Bo; Wang, Yu; Yang, Fang; Sun, Peng; Liu, Siyang; Gao, Peng; Huang, Haodong; Sun, Jing; Chen, Dan; He, Guangzhu; Huang, Weihua; Huang, Zheng; Li, Yue; Tellier, Laurent C A M; Liu, Xiao; Feng, Qiang; Xu, Xun; Zhang, Xiuqing; Bolund, Lars; Krogh, Anders; Kristiansen, Karsten; Drmanac, Radoje; Drmanac, Snezana; Nielsen, Rasmus; Li, Songgang; Wang, Jian; Yang, Huanming; Li, Yingrui; Wong, Gane Ka-Shu; Wang, Jun

    2015-06-01

    The human genome is diploid, and knowledge of the variants on each chromosome is important for the interpretation of genomic information. Here we report the assembly of a haplotype-resolved diploid genome without using a reference genome. Our pipeline relies on fosmid pooling together with whole-genome shotgun strategies, based solely on next-generation sequencing and hierarchical assembly methods. We applied our sequencing method to the genome of an Asian individual and generated a 5.15-Gb assembled genome with a haplotype N50 of 484 kb. Our analysis identified previously undetected indels and 7.49 Mb of novel coding sequences that could not be aligned to the human reference genome, which include at least six predicted genes. This haplotype-resolved genome represents the most complete de novo human genome assembly to date. Application of our approach to identify individual haplotype differences should aid in translating genotypes to phenotypes for the development of personalized medicine. PMID:26006006

  13. Toehold Switches: De-Novo-Designed Regulators of Gene Expression

    PubMed Central

    Green, Alexander A.; Silver, Pamela A.; Collins, James J.; Yin, Peng

    2014-01-01

    SUMMARY Efforts to construct synthetic networks in living cells have been hindered by the limited number of regulatory components that provide wide dynamic range and low crosstalk. Here, we report a new class of de-novo-designed prokaryotic riboregulators called toehold switches that activate gene expression in response to cognate RNAs with arbitrary sequences. Toehold switches provide a high level of orthogonality and can be forward-engineered to provide average dynamic range above 400. We show that switches can be integrated into the genome to regulate endogenous genes and use them as sensors that respond to endogenous RNAs. We exploit the orthogonality of toehold switches to regulate 12 genes independently and to construct a genetic circuit that evaluates 4-input AND logic. Toehold switches, with their wide dynamic range, orthogonality, and programmability, represent a versatile and powerful platform for regulation of translation, offering diverse applications in molecular biology, synthetic biology, and biotechnology. PMID:25417166

  14. Neoplastic disease after liver transplantation: Focus on de novo neoplasms

    PubMed Central

    Burra, Patrizia; Rodriguez-Castro, Kryssia I

    2015-01-01

    De novo neoplasms account for almost 30% of deaths 10 years after liver transplantation and are the most common cause of mortality in patients surviving at least 1 year after transplant. The risk of malignancy is two to four times higher in transplant recipients than in an age- and sex-matched population, and cancer is expected to surpass cardiovascular complications as the primary cause of death in transplanted patients within the next 2 decades. Since exposure to immunosuppression is associated with an increased frequency of developing neoplasm, long-term immunosuppression should be therefore minimized. Promising results in the prevention of hepatocellular carcinoma (HCC) recurrence have been reported with the use of mTOR inhibitors including everolimus and sirolimus and the ongoing open-label prospective randomized controlled SILVER. Study will provide more information on whether sirolimus-containing vs mTOR-inhibitor-free immunosuppression is more efficacious in reducing HCC recurrence. PMID:26269665

  15. Herpes simplex virus 1 induces de novo phospholipid synthesis

    SciTech Connect

    Sutter, Esther; Oliveira, Anna Paula de; Tobler, Kurt; Schraner, Elisabeth M.; Sonda, Sabrina; Kaech, Andres; Lucas, Miriam S.; Ackermann, Mathias; Wild, Peter

    2012-08-01

    Herpes simplex virus type 1 capsids bud at nuclear membranes and Golgi membranes acquiring an envelope composed of phospholipids. Hence, we measured incorporation of phospholipid precursors into these membranes, and quantified changes in size of cellular compartments by morphometric analysis. Incorporation of [{sup 3}H]-choline into both nuclear and cytoplasmic membranes was significantly enhanced upon infection. [{sup 3}H]-choline was also part of isolated virions even grown in the presence of brefeldin A. Nuclei expanded early in infection. The Golgi complex and vacuoles increased substantially whereas the endoplasmic reticulum enlarged only temporarily. The data suggest that HSV-1 stimulates phospholipid synthesis, and that de novo synthesized phospholipids are inserted into nuclear and cytoplasmic membranes to i) maintain membrane integrity in the course of nuclear and cellular expansion, ii) to supply membrane constituents for envelopment of capsids by budding at nuclear membranes and Golgi membranes, and iii) to provide membranes for formation of transport vacuoles.

  16. De novo synthesis of a sunscreen compound in vertebrates.

    PubMed

    Osborn, Andrew R; Almabruk, Khaled H; Holzwarth, Garrett; Asamizu, Shumpei; LaDu, Jane; Kean, Kelsey M; Karplus, P Andrew; Tanguay, Robert L; Bakalinsky, Alan T; Mahmud, Taifo

    2015-01-01

    Ultraviolet-protective compounds, such as mycosporine-like amino acids (MAAs) and related gadusols produced by some bacteria, fungi, algae, and marine invertebrates, are critical for the survival of reef-building corals and other marine organisms exposed to high-solar irradiance. These compounds have also been found in marine fish, where their accumulation is thought to be of dietary or symbiont origin. In this study, we report the unexpected discovery that fish can synthesize gadusol de novo and that the analogous pathways are also present in amphibians, reptiles, and birds. Furthermore, we demonstrate that engineered yeast containing the fish genes can produce and secrete gadusol. The discovery of the gadusol pathway in vertebrates provides a platform for understanding its role in these animals, and the possibility of engineering yeast to efficiently produce a natural sunscreen and antioxidant presents an avenue for its large-scale production for possible use in pharmaceuticals and cosmetics. PMID:25965179

  17. FEIBA versus NovoSeven in hemophilia patients with inhibitors.

    PubMed

    Franchini, Massimo; Coppola, Antonio; Tagliaferri, Annarita; Lippi, Giuseppe

    2013-10-01

    The management of patients with congenital hemophilia who develop alloantibodies that neutralize coagulation factor activity is the most important challenge for hemophilia care providers because this complication renders replacement treatment with factor concentrates partially or completely ineffective, exposing the patients to an increased risk of morbidity and mortality. Development of inhibitors complicates the clinical course of severe hemophilia in up to 30% of patients with hemophilia A and up to 5% of those with hemophilia B. Although the ultimate goal of treatment of patients with alloantibodies against factors VIII and IX is eradication of the inhibitor, the control of bleeding through high doses of factor concentrates (low titer inhibitors) or bypassing agents (high titer inhibitors) is the mainstay of management of these patients. In this review, we summarize the main characteristics of the bypassing agents FEIBA and NovoSeven, briefly discussing available literature data, and in particular, focusing on comparative studies. PMID:24014071

  18. Genome-wide characteristics of de novo mutations in autism

    PubMed Central

    Yuen, Ryan K C; Merico, Daniele; Cao, Hongzhi; Pellecchia, Giovanna; Alipanahi, Babak; Thiruvahindrapuram, Bhooma; Tong, Xin; Sun, Yuhui; Cao, Dandan; Zhang, Tao; Wu, Xueli; Jin, Xin; Zhou, Ze; Liu, Xiaomin; Nalpathamkalam, Thomas; Walker, Susan; Howe, Jennifer L.; Wang, Zhuozhi; MacDonald, Jeffrey R.; Chan, Ada; D’Abate, Lia; Deneault, Eric; Siu, Michelle T.; Tammimies, Kristiina; Uddin, Mohammed; Zarrei, Mehdi; Wang, Mingbang; Li, Yingrui; Wang, Jun; Wang, Jian; Yang, Huanming; Bookman, Matt; Bingham, Jonathan; Gross, Samuel S.; Loy, Dion; Pletcher, Mathew; Marshall, Christian R.; Anagnostou, Evdokia; Zwaigenbaum, Lonnie; Weksberg, Rosanna; Fernandez, Bridget A; Roberts, Wendy; Szatmari, Peter; Glazer, David; Frey, Brendan J.; Ring, Robert H.; Xu, Xun; Scherer, Stephen W.

    2016-01-01

    De novo mutations (DNMs) are important in Autism Spectrum Disorder (ASD), but so far analyses have mainly been on the ~1.5% of the genome encoding genes. Here, we performed whole genome sequencing (WGS) of 200 ASD parent-child trios and characterized germline and somatic DNMs. We confirmed that the majority of germline DNMs (75.6%) originated from the father, and these increased significantly with paternal age only (p=4.2×10−10). However, when clustered DNMs (those within 20kb) were found in ASD, not only did they mostly originate from the mother (p=7.7×10−13), but they could also be found adjacent to de novo copy number variations (CNVs) where the mutation rate was significantly elevated (p=2.4×10−24). By comparing DNMs detected in controls, we found a significant enrichment of predicted damaging DNMs in ASD cases (p=8.0×10−9; OR=1.84), of which 15.6% (p=4.3×10−3) and 22.5% (p=7.0×10−5) were in the non-coding or genic non-coding, respectively. The non-coding elements most enriched for DNM were untranslated regions of genes, boundaries involved in exon-skipping and DNase I hypersensitive regions. Using microarrays and a novel outlier detection test, we also found aberrant methylation profiles in 2/185 (1.1%) of ASD cases. These same individuals carried independently identified DNMs in the ASD risk- and epigenetic- genes DNMT3A and ADNP. Our data begins to characterize different genome-wide DNMs, and highlight the contribution of non-coding variants, to the etiology of ASD. PMID:27525107

  19. De novo design of the hydrophobic cores of proteins.

    PubMed Central

    Desjarlais, J. R.; Handel, T. M.

    1995-01-01

    We have developed and experimentally tested a novel computational approach for the de novo design of hydrophobic cores. A pair of computer programs has been written, the first of which creates a "custom" rotamer library for potential hydrophobic residues, based on the backbone structure of the protein of interest. The second program uses a genetic algorithm to globally optimize for a low energy core sequence and structure, using the custom rotamer library as input. Success of the programs in predicting the sequences of native proteins indicates that they should be effective tools for protein design. Using these programs, we have designed and engineered several variants of the phage 434 cro protein, containing five, seven, or eight sequence changes in the hydrophobic core. As controls, we have produced a variant consisting of a randomly generated core with six sequence changes but equal volume relative to the native core and a variant with a "minimalist" core containing predominantly leucine residues. Two of the designs, including one with eight core sequence changes, have thermal stabilities comparable to the native protein, whereas the third design and the minimalist protein are significantly destabilized. The randomly designed control is completely unfolded under equivalent conditions. These results suggest that rational de novo design of hydrophobic cores is feasible, and stress the importance of specific packing interactions for the stability of proteins. A surprising aspect of the results is that all of the variants display highly cooperative thermal denaturation curves and reasonably dispersed NMR spectra. This suggests that the non-core residues of a protein play a significant role in determining the uniqueness of the folded structure. PMID:8535237

  20. Myocardial ischemic reperfusion induces de novo Nrf2 protein translation

    PubMed Central

    Xu, Beibei; Zhang, Jack; Strom, Joshua; Lee, Sang; Chen, Qin M.

    2016-01-01

    Nrf2 is a bZIP transcription factor regulating the expression of antioxidant and detoxification genes. We have found that Nrf2 knockout mice have an increased infarction size in response to regional ischemic reperfusion and have a reduced degree of cardiac protection by means of ischemic preconditioning. With cycles of brief ischemia and reperfusion (5′I/5′R) that induce cardiac protection in wild type mice, an elevated Nrf2 protein was observed without prior increases of Nrf2 mRNA. When an mRNA species is being translated into a protein, it is occupied by multiple ribosomes. The level of ribosome-associated Nrf2 mRNA increased following cycles of 5′I/5′R, supporting de novo Nrf2 protein translation. A dicistronic reporter assay indicated a role of the 5′ untranslated region (5′ UTR) of Nrf2 mRNA in oxidative stress induced Nrf2 protein translation in isolated cardiomyocytes. Western blot analyses after isolation of proteins binding to biotinylated Nrf2 5′ UTR from the myocardium or cultured cardiomyocytes demonstrated that cycles of 5′I/5′R or oxidants caused an increased association of La protein with Nrf2 5′ UTR. Ribonucleoprotein complex immunoprecipitation assays confirmed such association indeed occurring in vivo. Knocking down La using siRNA was able to prevent Nrf2 protein elevation by oxidants in cultured cardiomyocytes and by cycles of 5′I/5′R in the myocardium. Our data point out a novel mechanism of cardiac protection by de novo Nrf2 protein translation involving interaction of La protein with 5′ UTR of Nrf2 mRNA in cardiomyocytes. PMID:24915518

  1. De novo mutations in moderate or severe intellectual disability.

    PubMed

    Hamdan, Fadi F; Srour, Myriam; Capo-Chichi, Jose-Mario; Daoud, Hussein; Nassif, Christina; Patry, Lysanne; Massicotte, Christine; Ambalavanan, Amirthagowri; Spiegelman, Dan; Diallo, Ousmane; Henrion, Edouard; Dionne-Laporte, Alexandre; Fougerat, Anne; Pshezhetsky, Alexey V; Venkateswaran, Sunita; Rouleau, Guy A; Michaud, Jacques L

    2014-10-01

    Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband). We observed a significant excess of de novo single nucleotide substitutions and loss-of-function mutations in these cases compared to control subjects, suggesting that at least a subset of these variations are pathogenic. A total of 12 likely pathogenic DNMs were identified in genes previously associated with ID (ARID1B, CHD2, FOXG1, GABRB3, GATAD2B, GRIN2B, MBD5, MED13L, SETBP1, TBR1, TCF4, WDR45), resulting in a diagnostic yield of ∼29%. We also identified 12 possibly pathogenic DNMs in genes (HNRNPU, WAC, RYR2, SET, EGR1, MYH10, EIF2C1, COL4A3BP, CHMP2A, PPP1CB, VPS4A, PPP2R2B) that have not previously been causally linked to ID. Interestingly, no case was explained by inherited mutations. Protein network analysis indicated that the products of many of these known and candidate genes interact with each other or with products of other ID-associated genes further supporting their involvement in ID. We conclude that DNMs represent a major cause of moderate or severe ID. PMID:25356899

  2. De Novo Mutations in Moderate or Severe Intellectual Disability

    PubMed Central

    Hamdan, Fadi F.; Srour, Myriam; Capo-Chichi, Jose-Mario; Daoud, Hussein; Nassif, Christina; Patry, Lysanne; Massicotte, Christine; Ambalavanan, Amirthagowri; Spiegelman, Dan; Diallo, Ousmane; Henrion, Edouard; Dionne-Laporte, Alexandre; Fougerat, Anne; Pshezhetsky, Alexey V.; Venkateswaran, Sunita; Rouleau, Guy A.; Michaud, Jacques L.

    2014-01-01

    Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband). We observed a significant excess of de novo single nucleotide substitutions and loss-of-function mutations in these cases compared to control subjects, suggesting that at least a subset of these variations are pathogenic. A total of 12 likely pathogenic DNMs were identified in genes previously associated with ID (ARID1B, CHD2, FOXG1, GABRB3, GATAD2B, GRIN2B, MBD5, MED13L, SETBP1, TBR1, TCF4, WDR45), resulting in a diagnostic yield of ∼29%. We also identified 12 possibly pathogenic DNMs in genes (HNRNPU, WAC, RYR2, SET, EGR1, MYH10, EIF2C1, COL4A3BP, CHMP2A, PPP1CB, VPS4A, PPP2R2B) that have not previously been causally linked to ID. Interestingly, no case was explained by inherited mutations. Protein network analysis indicated that the products of many of these known and candidate genes interact with each other or with products of other ID-associated genes further supporting their involvement in ID. We conclude that DNMs represent a major cause of moderate or severe ID. PMID:25356899

  3. Donor transmitted and de novo cancer after liver transplantation.

    PubMed

    Desai, Rajeev; Neuberger, James

    2014-05-28

    Cancers in solid organ recipients may be classified as donor transmitted, donor derived, de novo or recurrent. The risk of donor-transmitted cancer is very low and can be reduced by careful screening of the donor but cannot be abolished and, in the United Kingdom series is less than 0.03%. For donors with a known history of cancer, the risks will depend on the nature of the cancer, the interventions given and the interval between diagnosis and organ donation. The risks of cancer transmission must be balanced against the risks of death awaiting a new graft and strict adherence to current guidelines may result increased patient death. Organs from selected patients, even with high-grade central nervous system (CNS) malignancy and after a shunt, can, in some circumstances, be considered. Of potential donors with non-CNS cancers, whether organs may be safely used again depends on the nature of the cancer, the treatment and interval. Data are scarce about the most appropriate treatment when donor transmitted cancer is diagnosed: sometimes substitution of agents and reduction of the immunosuppressive load may be adequate and the impact of graft removal should be considered but not always indicated. Liver allograft recipients are at increased risk of some de novo cancers, especially those grafted for alcohol-related liver disease and hepatitis C virus infection. The risk of lymphoproliferative disease and cancers of the skin, upper airway and bowel are increased but not breast. Recipients should be advised to avoid risk behavior and monitored appropriately. PMID:24876738

  4. Post-zygotic Point Mutations Are an Underrecognized Source of De Novo Genomic Variation

    PubMed Central

    Acuna-Hidalgo, Rocio; Bo, Tan; Kwint, Michael P.; van de Vorst, Maartje; Pinelli, Michele; Veltman, Joris A.; Hoischen, Alexander; Vissers, Lisenka E.L.M.; Gilissen, Christian

    2015-01-01

    De novo mutations are recognized both as an important source of genetic variation and as a prominent cause of sporadic disease in humans. Mutations identified as de novo are generally assumed to have occurred during gametogenesis and, consequently, to be present as germline events in an individual. Because Sanger sequencing does not provide the sensitivity to reliably distinguish somatic from germline mutations, the proportion of de novo mutations that occur somatically rather than in the germline remains largely unknown. To determine the contribution of post-zygotic events to de novo mutations, we analyzed a set of 107 de novo mutations in 50 parent-offspring trios. Using four different sequencing techniques, we found that 7 (6.5%) of these presumed germline de novo mutations were in fact present as mosaic mutations in the blood of the offspring and were therefore likely to have occurred post-zygotically. Furthermore, genome-wide analysis of “de novo” variants in the proband led to the identification of 4/4,081 variants that were also detectable in the blood of one of the parents, implying parental mosaicism as the origin of these variants. Thus, our results show that an important fraction of de novo mutations presumed to be germline in fact occurred either post-zygotically in the offspring or were inherited as a consequence of low-level mosaicism in one of the parents. PMID:26054435

  5. Role of de novo biosynthesis in ecosystem scale monoterpene emissions from a boreal Scots pine forest

    NASA Astrophysics Data System (ADS)

    Taipale, R.; Kajos, M. K.; Patokoski, J.; Rantala, P.; Ruuskanen, T. M.; Rinne, J.

    2011-08-01

    Monoterpene emissions from Scots pine have traditionally been assumed to originate as evaporation from specialized storage pools. More recently, the significance of de novo emissions, originating directly from monoterpene biosynthesis, has been recognized. To study the role of biosynthesis at the ecosystem scale, we measured monoterpene emissions from a Scots pine dominated forest in southern Finland using the disjunct eddy covariance method combined with proton transfer reaction mass spectrometry. The interpretation of the measurements was based on a correlation analysis and a hybrid emission algorithm describing both de novo and pool emissions. During the measurement period May-August 2007, the monthly medians of daytime emissions were 200, 290, 180, and 200 μg m-2 h-1. The emissions were partly light dependent, probably due to de novo biosynthesis. The emission potential for both de novo and pool emissions exhibited a decreasing summertime trend. The ratio of the de novo emission potential to the total emission potential varied between 30 % and 46 %. Although the monthly changes were not significant, the ratio always differed statistically from zero, suggesting that the role of de novo biosynthesis was observable. Given the uncertainties in this study, we conclude that more accurate estimates of the contribution of de novo emissions are required for improving monoterpene emission algorithms for Scots pine dominated forests.

  6. On the Origin of De Novo Genes in Arabidopsis thaliana Populations.

    PubMed

    Li, Zi-Wen; Chen, Xi; Wu, Qiong; Hagmann, Jörg; Han, Ting-Shen; Zou, Yu-Pan; Ge, Song; Guo, Ya-Long

    2016-01-01

    De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications (DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process. PMID:27401176

  7. On the Origin of De Novo Genes in Arabidopsis thaliana Populations

    PubMed Central

    Li, Zi-Wen; Chen, Xi; Wu, Qiong; Hagmann, Jörg; Han, Ting-Shen; Zou, Yu-Pan; Ge, Song; Guo, Ya-Long

    2016-01-01

    De novo genes, which originate from ancestral nongenic sequences, are one of the most important sources of protein-coding genes. This origination process is crucial for the adaptation of organisms. However, how de novo genes arise and become fixed in a population or species remains largely unknown. Here, we identified 782 de novo genes from the model plant Arabidopsis thaliana and divided them into three types based on the availability of translational evidence, transcriptional evidence, and neither transcriptional nor translational evidence for their origin. Importantly, by integrating multiple types of omics data, including data from genomes, epigenomes, transcriptomes, and translatomes, we found that epigenetic modifications (DNA methylation and histone modification) play an important role in the origination process of de novo genes. Intriguingly, using the transcriptomes and methylomes from the same population of 84 accessions, we found that de novo genes that are transcribed in approximately half of the total accessions within the population are highly methylated, with lower levels of transcription than those transcribed at other frequencies within the population. We hypothesized that, during the origin of de novo gene alleles, those neutralized to low expression states via DNA methylation have relatively high probabilities of spreading and becoming fixed in a population. Our results highlight the process underlying the origin of de novo genes at the population level, as well as the importance of DNA methylation in this process. PMID:27401176

  8. De novo arteriovenous malformation in a patient with hereditary hemorrhagic telangiectasia.

    PubMed

    Shimoda, Yusuke; Osanai, Toshiya; Nakayama, Naoki; Ushikoshi, Satoshi; Hokari, Masaaki; Shichinohe, Hideo; Abumiya, Takeo; Kazumata, Ken; Houkin, Kiyohiro

    2016-03-01

    Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant systemic disorder characterized by the enlargement of capillaries, recurrent nosebleeds, and multiple arteriovenous malformations (AVMs). Although cerebral AVMs are traditionally considered to be congenital lesions, some reports have described de novo AVMs, which suggests that the authors believed them to be dynamic conditions. In this article, the authors describe the case of a 5-year-old boy with HHT in whom a de novo cerebral AVM was detected after a negative MRI result at 5 months. To the authors' knowledge, this is the first report of a de novo AVM in a patient with HHT. In patients with a family history of HHT, de novo AVMs are possible, even when no lesions are detected at the first screening. Therefore, regular screenings need to be performed, and the family should be informed that AVMs could still develop despite normal MRI results. PMID:26613274

  9. Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler

    PubMed Central

    Bankar, Kiran Gopinath; Todur, Vivek Nagaraj; Shukla, Rohit Nandan; Vasudevan, Madavan

    2015-01-01

    Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays. PMID:26484285

  10. De novo sequencing of unique sequence tags for discovery of post-translational modifications of proteins.

    PubMed

    Shen, Yufeng; Tolić, Nikola; Hixson, Kim K; Purvine, Samuel O; Anderson, Gordon A; Smith, Richard D

    2008-10-15

    De novo sequencing is a spectrum analysis approach for mass spectrometry data to discover post-translational modifications in proteins; however, such an approach is still in its infancy and is still not widely applied to proteomic practices due to its limited reliability. In this work, we describe a de novo sequencing approach for the discovery of protein modifications based on identification of the proteome UStags (Shen, Y.; Tolić, N.; Hixson, K. K.; Purvine, S. O.; Pasa-Tolić, L.; Qian, W. J.; Adkins, J. N.; Moore, R. J.; Smith, R. D. Anal. Chem. 2008, 80, 1871-1882). The de novo information was obtained from Fourier-transform tandem mass spectrometry data for peptides and polypeptides from a yeast lysate, and the de novo sequences obtained were selected based on filter levels designed to provide a limited yet high quality subset of UStags. The DNA-predicted database protein sequences were then compared to the UStags, and the differences observed across or in the UStags (i.e., the UStags' prefix and suffix sequences and the UStags themselves) were used to infer possible sequence modifications. With this de novo-UStag approach, we uncovered some unexpected variances within several yeast protein sequences due to amino acid mutations and/or multiple modifications to the predicted protein sequences. To determine false discovery rates, two random (false) databases were independently used for sequence matching, and ~3% false discovery rates were estimated for the de novo-UStag approach. The factors affecting the reliability (e.g., existence of de novo sequencing noise residues and redundant sequences) and the sensitivity of the approach were investigated and described. The combined de novo-UStag approach complements the UStag method previously reported by enabling the discovery of new protein modifications. PMID:18783246

  11. Patterns and rates of exonic de novo mutations in autism spectrum disorders

    PubMed Central

    Neale, Benjamin M.; Kou, Yan; Liu, Li; Ma'ayan, Avi; Samocha, Kaitlin E.; Sabo, Aniko; Lin, Chiao-Feng; Stevens, Christine; Wang, Li-San; Makarov, Vladimir; Polak, Paz; Yoon, Seungtai; Maguire, Jared; Crawford, Emily L.; Campbell, Nicholas G.; Geller, Evan T.; Valladares, Otto; Shafer, Chad; Liu, Han; Zhao, Tuo; Cai, Guiqing; Lihm, Jayon; Dannenfelser, Ruth; Jabado, Omar; Peralta, Zuleyma; Nagaswamy, Uma; Muzny, Donna; Reid, Jeffrey G.; Newsham, Irene; Wu, Yuanqing; Lewis, Lora; Han, Yi; Voight, Benjamin F.; Lim, Elaine; Rossin, Elizabeth; Kirby, Andrew; Flannick, Jason; Fromer, Menachem; Shakir, Khalid; Fennell, Tim; Garimella, Kiran; Banks, Eric; Poplin, Ryan; Gabriel, Stacey; DePristo, Mark; Wimbish, Jack R.; Boone, Braden E.; Levy, Shawn E.; Betancur, Catalina; Sunyaev, Shamil; Boerwinkle, Eric; Buxbaum, Joseph D.; Cook, Edwin H.; Devlin, Bernie; Gibbs, Richard A.; Roeder, Kathryn; Schellenberg, Gerard D.; Sutcliffe, James S.; Daly, Mark J.

    2013-01-01

    Autism spectrum disorders (ASD) are believed to have genetic and environmental origins, yet in only a modest fraction of individuals can specific causes be identified1,2. To identify further genetic risk factors, we assess the role of de novo mutations in ASD by sequencing the exomes of ASD cases and their parents (n= 175 trios). Fewer than half of the cases (46.3%) carry a missense or nonsense de novo variant and the overall rate of mutation is only modestly higher than the expected rate. In contrast, there is significantly enriched connectivity among the proteins encoded by genes harboring de novo missense or nonsense mutations, and excess connectivity to prior ASD genes of major effect, suggesting a subset of observed events are relevant to ASD risk. The small increase in rate of de novo events, when taken together with the connections among the proteins themselves and to ASD, are consistent with an important but limited role for de novo point mutations, similar to that documented for de novo copy number variants. Genetic models incorporating these data suggest that the majority of observed de novo events are unconnected to ASD, those that do confer risk are distributed across many genes and are incompletely penetrant (i.e., not necessarily causal). Our results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5 to 20-fold. Despite the challenge posed by such models, results from de novo events and a large parallel case-control study provide strong evidence in favor of CHD8 and KATNAL2 as genuine autism risk factors. PMID:22495311

  12. 12 CFR 1263.14 - De novo insured depository institution applicants.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ...)(A) of the Bank Act (12 U.S.C. 1424(a)(2)(A)) and § 1263.6(b) shall have until one year after... 12 Banks and Banking 9 2012-01-01 2012-01-01 false De novo insured depository institution... (de novo applicant) is deemed to meet the requirements of §§ 1263.7, 1263.8, 1263.11 and 1263.12....

  13. De Novo Histoid Leprosy: A Case Report from a Post-Elimination Area

    PubMed Central

    Bhat, Yasmeen J; Hassan, Iffat; Yaseen, Atiya; Wani, Rohi

    2015-01-01

    Histoid leprosy is an uncommon variant of lepromatous leprosy that usually follows treatment failure. Occasionally it occurs de novo without any history of previous inadequate or irregular treatment. We, hereby, report a case of de novo histoid leprosy in a 25-year-old man from the post-elimination area of Kashmir, where the prevalence rate of the disease was reported to be 0.17/10000 in March, 2013 (NLEP). PMID:25814742

  14. Paternal Factors and Schizophrenia Risk: De Novo Mutations and Imprinting

    PubMed Central

    Malaspina, Dolores

    2010-01-01

    There is a strong genetic component for schizophrenia risk, but it is unclear how the illness is maintained in the population given the significantly reduced fertility of those with the disorder. One possibility is that new mutations occur in schizophrenia vulnerability genes. If so, then those with schizophrenia may have older fathers, because advancing paternal age is the major source of new mutations in humans. This review describes several neurodevelopmental disorders that have been associated with de novo mutations in the paternal germ line and reviews data linking increased schizophrenia risk with older fathers. Several genetic mechanisms that could explain this association are proposed, including paternal germ line mutations, trinucleotide repeat expansions, and alterations in genetic imprinting in one or several genes involved in neurodevelopment. Animal models may be useful in exploring these and other explanations for the paternal age effect and they may provide a novel approach for gene identification. Finally, it is proposed that environmental exposures of the father, as well as those of the mother and developing fetus, may be relevant to the etiology of schizophrenia. PMID:11596842

  15. Spaced Seed Data Structures for De Novo Assembly.

    PubMed

    Birol, Inanç; Chu, Justin; Mohamadi, Hamid; Jackman, Shaun D; Raghavan, Karthika; Vandervalk, Benjamin P; Raymond, Anthony; Warren, René L

    2015-01-01

    De novo assembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads. Here, we revisit the DBG paradigm to adapt it to the changing sequencing technology landscape and introduce three data structure designs for spaced seeds in the form of paired subsequences. These data structures address memory and run time constraints imposed by longer reads. We observe that when a fixed distance separates seed pairs, it provides increased sequence specificity with increased gap length. Further, we note that Bloom filters would be suitable to implicitly store spaced seeds and be tolerant to sequencing errors. Building on this concept, we describe a data structure for tracking the frequencies of observed spaced seeds. These data structure designs will have applications in genome, transcriptome and metagenome assemblies, and read error correction. PMID:26539459

  16. Spaced Seed Data Structures for De Novo Assembly

    PubMed Central

    Birol, Inanç; Chu, Justin; Mohamadi, Hamid; Jackman, Shaun D.; Raghavan, Karthika; Vandervalk, Benjamin P.; Raymond, Anthony; Warren, René L.

    2015-01-01

    De novo assembly of the genome of a species is essential in the absence of a reference genome sequence. Many scalable assembly algorithms use the de Bruijn graph (DBG) paradigm to reconstruct genomes, where a table of subsequences of a certain length is derived from the reads, and their overlaps are analyzed to assemble sequences. Despite longer subsequences unlocking longer genomic features for assembly, associated increase in compute resources limits the practicability of DBG over other assembly archetypes already designed for longer reads. Here, we revisit the DBG paradigm to adapt it to the changing sequencing technology landscape and introduce three data structure designs for spaced seeds in the form of paired subsequences. These data structures address memory and run time constraints imposed by longer reads. We observe that when a fixed distance separates seed pairs, it provides increased sequence specificity with increased gap length. Further, we note that Bloom filters would be suitable to implicitly store spaced seeds and be tolerant to sequencing errors. Building on this concept, we describe a data structure for tracking the frequencies of observed spaced seeds. These data structure designs will have applications in genome, transcriptome and metagenome assemblies, and read error correction. PMID:26539459

  17. A de novo redesign of the WW domain.

    PubMed

    Kraemer-Pecore, Christina M; Lecomte, Juliette T J; Desjarlais, John R

    2003-10-01

    We have used a sequence prediction algorithm and a novel sampling method to design protein sequences for the WW domain, a small beta-sheet motif. The procedure, referred to as SPANS, designs sequences to be compatible with an ensemble of closely related polypeptide backbones, mimicking the inherent flexibility of proteins. Two designed sequences (termed SPANS-WW1 and SPANS-WW2), using only naturally occurring L-amino acids, were selected for study and the corresponding polypeptides were prepared in Escherichia coli. Circular dichroism data suggested that both purified polypeptides adopted secondary structure features related to those of the target without the aid of disulfide bridges or bound cofactors. The structure exhibited by SPANS-WW2 melted cooperatively by raising the temperature of the solution. Further analysis of this polypeptide by proton nuclear magnetic resonance spectroscopy demonstrated that at 5 degrees C, it folds into a structure closely resembling a natural WW domain. This achievement constitutes one of a small number of successful de novo protein designs through fully automated computational methods and highlights the feasibility of including backbone flexibility in the design strategy. PMID:14500877

  18. Dominant de novo DSP mutations cause erythrokeratodermia-cardiomyopathy syndrome.

    PubMed

    Boyden, Lynn M; Kam, Chen Y; Hernández-Martín, Angela; Zhou, Jing; Craiglow, Brittany G; Sidbury, Robert; Mathes, Erin F; Maguiness, Sheilagh M; Crumrine, Debra A; Williams, Mary L; Hu, Ronghua; Lifton, Richard P; Elias, Peter M; Green, Kathleen J; Choate, Keith A

    2016-01-15

    Disorders of keratinization (DOK) show marked genotypic and phenotypic heterogeneity. In most cases, disease is primarily cutaneous, and further clinical evaluation is therefore rarely pursued. We have identified subjects with a novel DOK featuring erythrokeratodermia and initially-asymptomatic, progressive, potentially fatal cardiomyopathy, a finding not previously associated with erythrokeratodermia. We show that de novo missense mutations clustered tightly within a single spectrin repeat of DSP cause this novel cardio-cutaneous disorder, which we term erythrokeratodermia-cardiomyopathy (EKC) syndrome. We demonstrate that DSP mutations in our EKC syndrome subjects affect localization of desmosomal proteins and connexin 43 in the skin, and result in desmosome aggregation, widening of intercellular spaces, and lipid secretory defects. DSP encodes desmoplakin, a primary component of desmosomes, intercellular adhesion junctions most abundant in the epidermis and heart. Though mutations in DSP are known to cause other disorders, our cohort features the unique clinical finding of severe whole-body erythrokeratodermia, with distinct effects on localization of desmosomal proteins and connexin 43. These findings add a severe, previously undescribed syndrome featuring erythrokeratodermia and cardiomyopathy to the spectrum of disease caused by mutation in DSP, and identify a specific region of the protein critical to the pathobiology of EKC syndrome and to DSP function in the heart and skin. PMID:26604139

  19. De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa

    PubMed Central

    Kim, Hyun A; Shin, Ah-Young; Lee, Min-Seon; Lee, Hee-Jeong; Lee, Heung-Ryul; Ahn, Jongmoon; Nahm, Seokhyeon; Jo, Sung-Hwan; Park, Jeong Mee; Kwon, Suk-Yoon

    2016-01-01

    Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family. PMID:26743902

  20. De novo cerebellar malignant glioma: A case report

    PubMed Central

    Matsumoto, Hiroaki; Yoshida, Yasuhisa

    2016-01-01

    Introduction Gliomas of the cerebellum are rare in adults, and their natural history and clinical behavior are not well known. Because cerebellar glioma is not usually diagnosed until clinical symptoms have appeared, no reports have described the developmental process of new cerebellar gliomas. We describe a case of de novo cerebellar anaplastic astrocytoma in which the developmental process was detected on magnetic resonance imaging (MRI). Presentation of case A 78-year-old man with a history of cerebral infarction was undergoing follow-up MRI every 6 months. This follow-up revealed a small abnormality in the left cerebellar hemisphere without clinical symptoms. Subsequent MRI showed lesion growth accompanying clinical symptoms. As cerebellar tumor was suspected, the lesion was extirpated. The histological diagnosis was anaplastic astrocytoma. Local recurrence developed and the patient died 20 months postoperatively. Discussion Cerebellar gliomas sometimes do not exhibit the common MRI findings of supratentorial gliomas, leading to difficulty with preoperative diagnosis. In this case, we initially diagnosed asymptomatic cerebellar infarction because the lesion was small and asymptomatic. The abnormal lesion gradually grew and clinical symptoms appeared. Cerebellar glioma may show few signs characteristic of tumor on MRI in the initial stages. Conclusion When MRI detects a new, faint abnormality in the cerebellum, close follow-up of clinical symptoms and MRI on suspicion of glioma is warranted PMID:27017277

  1. De Novo Methylation of Repeated Sequences in Coprinus Cinereus

    PubMed Central

    Freedman, T.; Pukkila, P. J.

    1993-01-01

    We have examined the stability of duplicated DNA sequences in the sexual phase of the life cycle of the basidiomycete fungus, Coprinus cinereus. We observed premeiotic de novo methylation in haploid nuclei containing either a triplication, a tandem duplication, or an ectopic duplication. Methylation changes were not observed in unique sequences. Repeated sequences underwent methylation changes during the dikaryotic stage. In one cross, 27% of the segregants exhibited methylation-directed gene inactivation. However, all auxotrophs eventually reverted to prototrophy. C to T transition mutations were not observed in this study. Our studies also revealed one inversion that occurred in 50% of the segregants in a single triplication cross, and a single pop-out event that occurred during vegetative growth. These alterations were similar to changes reported in experiments with duplicated sequences in Neurospora crassa and Ascobolus immersus. However, significant differences were also noted. First, the extent of methylation was much less in C. cinereus than in the other two fungi. Second, CpG sequences appeared to be the preferred targets of methylation. PMID:8244000

  2. De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa.

    PubMed

    Kim, Hyun A; Shin, Ah-Young; Lee, Min-Seon; Lee, Hee-Jeong; Lee, Heung-Ryul; Ahn, Jongmoon; Nahm, Seokhyeon; Jo, Sung-Hwan; Park, Jeong Mee; Kwon, Suk-Yoon

    2016-02-01

    Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family. PMID:26743902

  3. LESSONS IN DE NOVO PEPTIDE SEQUENCING BY TANDEM MASS SPECTROMETRY

    PubMed Central

    Medzihradszky, Katalin F.; Chalkley, Robert J.

    2015-01-01

    Mass spectrometry has become the method of choice for the qualitative and quantitative characterization of protein mixtures isolated from all kinds of living organisms. The raw data in these studies are MS/MS spectra, usually of peptides produced by proteolytic digestion of a protein. These spectra are “translated” into peptide sequences, normally with the help of various search engines. Data acquisition and interpretation have both been automated, and most researchers look only at the summary of the identifications without ever viewing the underlying raw data used for assignments. Automated analysis of data is essential due to the volume produced. However, being familiar with the finer intricacies of peptide fragmentation processes, and experiencing the difficulties of manual data interpretation allow a researcher to be able to more critically evaluate key results, particularly because there are many known rules of peptide fragmentation that are not incorporated into search engine scoring. Since the most commonly used MS/MS activation method is collision-induced dissociation (CID), in this article we present a brief review of the history of peptide CID analysis. Next, we provide a detailed tutorial on how to determine peptide sequences from CID data. Although the focus of the tutorial is de novo sequencing, the lessons learned and resources supplied are useful for data interpretation in general. PMID:25667941

  4. Activation and de novo synthesis of hydrogenase in Chlamydomonas

    SciTech Connect

    Roessler, P.G.; Lien, S.

    1984-12-01

    Two distinct processes are involved in the formation of active hydrogenase during anaerobic adaptation of Chlamydomonas reinhardtii cells. In the first 30 minutes of anaerobiosis, nearly all of the hydrogenase activity can be attributed to activation of constituitive polypeptide precursor, based on the insensitivity of the process to treatment with cycloheximide (15 micrograms per milliliter). This concentration of cycloheximide inhibits protein synthesis by greater than 98%. After the initial activation period, de novo protein synthesis plays a critical role in the adaptation process since cycloheximide inhibits the expression of hydrogenase in maximally adapted cells by 70%. Chloramphenicol (500 micrograms per milliliter) has a much lesser effect on the adaptation process. Incubation of cell-free extracts under anaerobic conditions in the presence of dithionite, dithiothreitol, NADH, NADP, ferredoxin, ATP, Mg/sup 2 +/, Ca/sup 2 +/, and iron does not lead to active hydrogenase formation. Furthermore, in vivo reactivation of oxygen-inactivated hydrogenase does not appear to take place. The adaptation process is very sensitive to the availability of iron. Iron-deficient cultures lose the ability to form active hydrogenase before growth, photosynthesis, and respiration are significantly affected. Preincubation of iron-deficient cells with iron 2 hours prior to the adaptation period fully restores the capacity of the cells to synthesize functional hydrogenase.

  5. De novo transcriptome assembly of Sorghum bicolor variety Taejin.

    PubMed

    Jo, Yeonhwa; Lian, Sen; Cho, Jin Kyong; Choi, Hoseong; Kim, Sang-Min; Kim, Sun-Lim; Lee, Bong Choon; Cho, Won Kyong

    2016-06-01

    Sorghum (Sorghum bicolor), also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers. PMID:27257604

  6. 8-oxoguanine causes spontaneous de novo germline mutations in mice

    NASA Astrophysics Data System (ADS)

    Ohno, Mizuki; Sakumi, Kunihiko; Fukumura, Ryutaro; Furuichi, Masato; Iwasaki, Yuki; Hokama, Masaaki; Ikemura, Toshimichi; Tsuzuki, Teruhisa; Gondo, Yoichi; Nakabeppu, Yusaku

    2014-04-01

    Spontaneous germline mutations generate genetic diversity in populations of sexually reproductive organisms, and are thus regarded as a driving force of evolution. However, the cause and mechanism remain unclear. 8-oxoguanine (8-oxoG) is a candidate molecule that causes germline mutations, because it makes DNA more prone to mutation and is constantly generated by reactive oxygen species in vivo. We show here that endogenous 8-oxoG caused de novo spontaneous and heritable G to T mutations in mice, which occurred at different stages in the germ cell lineage and were distributed throughout the chromosomes. Using exome analyses covering 40.9 Mb of mouse transcribed regions, we found increased frequencies of G to T mutations at a rate of 2 × 10-7 mutations/base/generation in offspring of Mth1/Ogg1/Mutyh triple knockout (TOY-KO) mice, which accumulate 8-oxoG in the nuclear DNA of gonadal cells. The roles of MTH1, OGG1, and MUTYH are specific for the prevention of 8-oxoG-induced mutation, and 99% of the mutations observed in TOY-KO mice were G to T transversions caused by 8-oxoG; therefore, we concluded that 8-oxoG is a causative molecule for spontaneous and inheritable mutations of the germ lineage cells.

  7. Activation and de novo synthesis of hydrogenase in chlamydomonas.

    PubMed

    Roessler, P G; Lien, S

    1984-12-01

    Two distinct processes are involved in the formation of active hydrogenase during anaerobic adaptation of Chlamydomonas reinhardtii cells. In the first 30 minutes of anaerobiosis, nearly all of the hydrogenase activity can be attributed to activation of a constituitive polypeptide precursor, based on the insensitivity of the process to treatment with cycloheximide (15 micrograms per milliliter). This concentration of cycloheximide inhibits protein synthesis by greater than 98%. After the initial activation period, de novo protein synthesis plays a critical role in the adaptation process since cycloheximide inhibits the expression of hydrogense in maximally adapted cells by 70%. Chloramphenicol (500 micrograms per milliliter) has a much lesser effect on the adaptation process.Incubation of cell-free extracts under anaerobic conditions in the presence of dithionite, dithiothreitol, NADH, NADP, ferredoxin, ATP, Mg(2+), Ca(2+), and iron does not lead to active hydrogenase formation. Futhermore, in vivo reactivation of oxygen-inactivated hydrogenase does not appear to take place.The adaptation process is very sensitive to the availability of iron. Iron-deficient cultures lose the ability to form active hydrogenase before growth, photosynthesis, and respiration are significantly affected. Preincubation of iron-deficient cells with iron 2 hours prior to the adaptation period fully restores the capacity of the cells to synthesize functional hydrogenase. PMID:16663954

  8. Considering Transposable Element Diversification in De Novo Annotation Approaches

    PubMed Central

    Flutre, Timothée; Duprat, Elodie; Feuillet, Catherine; Quesneville, Hadi

    2011-01-01

    Transposable elements (TEs) are mobile, repetitive DNA sequences that are almost ubiquitous in prokaryotic and eukaryotic genomes. They have a large impact on genome structure, function and evolution. With the recent development of high-throughput sequencing methods, many genome sequences have become available, making possible comparative studies of TE dynamics at an unprecedented scale. Several methods have been proposed for the de novo identification of TEs in sequenced genomes. Most begin with the detection of genomic repeats, but the subsequent steps for defining TE families differ. High-quality TE annotations are available for the Drosophila melanogaster and Arabidopsis thaliana genome sequences, providing a solid basis for the benchmarking of such methods. We compared the performance of specific algorithms for the clustering of interspersed repeats and found that only a particular combination of algorithms detected TE families with good recovery of the reference sequences. We then applied a new procedure for reconciling the different clustering results and classifying TE sequences. The whole approach was implemented in a pipeline using the REPET package. Finally, we show that our combined approach highlights the dynamics of well defined TE families by making it possible to identify structural variations among their copies. This approach makes it possible to annotate TE families and to study their diversification in a single analysis, improving our understanding of TE dynamics at the whole-genome scale and for diverse species. PMID:21304975

  9. De Novo Transcriptome of the Hemimetabolous German Cockroach (Blattella germanica)

    PubMed Central

    Zhou, Xiaojie; Qian, Kun; Tong, Ying; Zhu, Junwei Jerry; Qiu, Xinghui; Zeng, Xiaopeng

    2014-01-01

    Background The German cockroach, Blattella germanica, is an important insect pest that transmits various pathogens mechanically and causes severe allergic diseases. This insect has long served as a model system for studies of insect biology, physiology and ecology. However, the lack of genome or transcriptome information heavily hinder our further understanding about the German cockroach in every aspect at a molecular level and on a genome-wide scale. To explore the transcriptome and identify unique sequences of interest, we subjected the B. germanica transcriptome to massively parallel pyrosequencing and generated the first reference transcriptome for B. germanica. Methodology/Principal Findings A total of 1,365,609 raw reads with an average length of 529 bp were generated via pyrosequencing the mixed cDNA library from different life stages of German cockroach including maturing oothecae, nymphs, adult females and males. The raw reads were de novo assembled to 48,800 contigs and 3,961 singletons with high-quality unique sequences. These sequences were annotated and classified functionally in terms of BLAST, GO and KEGG, and the genes putatively coding detoxification enzyme systems, insecticide targets, key components in systematic RNA interference, immunity and chemoreception pathways were identified. A total of 3,601 SSRs (Simple Sequence Repeats) loci were also predicted. Conclusions/Significance The whole transcriptome pyrosequencing data from this study provides a usable genetic resource for future identification of potential functional genes involved in various biological processes. PMID:25265537

  10. Enzyme-like replication de novo in a microcontroller environment.

    PubMed

    Tangen, Uwe

    2010-01-01

    The desire to start evolution from scratch inside a computer memory is as old as computing. Here we demonstrate how viable computer programs can be established de novo in a Precambrian environment without supplying any specific instantiation, just starting with random bit sequences. These programs are not self-replicators, but act much more like catalysts. The microcontrollers used in the end are the result of a long series of simplifications. The objective of this simplification process was to produce universal machines with a human-readable interface, allowing software and/or hardware evolution to be studied. The power of the instruction set can be modified by introducing a secondary structure-folding mechanism, which is a state machine, allowing nontrivial replication to emerge with an instruction width of only a few bits. This state-machine approach not only attenuates the problems of brittleness and encoding functionality (too few bits available for coding, and too many instructions needed); it also enables the study of hardware evolution as such. Furthermore, the instruction set is sufficiently powerful to permit external signals to be processed. This information-theoretic approach forms one vertex of a triangle alongside artificial cell research and experimental research on the creation of life. Hopefully this work helps develop an understanding of how information—in a similar sense to the account of functional information described by Hazen et al.—is created by evolution and how this information interacts with or is embedded in its physico-chemical environment. PMID:20712511

  11. De novo design of protein mimics of B-DNA.

    PubMed

    Yüksel, Deniz; Bianco, Piero R; Kumar, Krishna

    2016-01-01

    Structural mimicry of DNA is utilized in nature as a strategy to evade molecular defences mounted by host organisms. One such example is the protein Ocr - the first translation product to be expressed as the bacteriophage T7 infects E. coli. The structure of Ocr reveals an intricate and deliberate arrangement of negative charges that endows it with the ability to mimic ∼24 base pair stretches of B-DNA. This uncanny resemblance to DNA enables Ocr to compete in binding the type I restriction modification (R/M) system, and neutralizes the threat of hydrolytic cleavage of viral genomic material. Here, we report the de novo design and biophysical characterization of DNA mimicking peptides, and describe the inhibitory action of the designed helical bundles on a type I R/M enzyme, EcoR124I. This work validates the use of charge patterning as a design principle for creation of protein mimics of DNA, and serves as a starting point for development of therapeutic peptide inhibitors against human pathogens that employ molecular camouflage as part of their invasion stratagem. PMID:26568416

  12. De novo synthesis of a sunscreen compound in vertebrates

    PubMed Central

    Osborn, Andrew R; Almabruk, Khaled H; Holzwarth, Garrett; Asamizu, Shumpei; LaDu, Jane; Kean, Kelsey M; Karplus, P Andrew; Tanguay, Robert L; Bakalinsky, Alan T; Mahmud, Taifo

    2015-01-01

    Ultraviolet-protective compounds, such as mycosporine-like amino acids (MAAs) and related gadusols produced by some bacteria, fungi, algae, and marine invertebrates, are critical for the survival of reef-building corals and other marine organisms exposed to high-solar irradiance. These compounds have also been found in marine fish, where their accumulation is thought to be of dietary or symbiont origin. In this study, we report the unexpected discovery that fish can synthesize gadusol de novo and that the analogous pathways are also present in amphibians, reptiles, and birds. Furthermore, we demonstrate that engineered yeast containing the fish genes can produce and secrete gadusol. The discovery of the gadusol pathway in vertebrates provides a platform for understanding its role in these animals, and the possibility of engineering yeast to efficiently produce a natural sunscreen and antioxidant presents an avenue for its large-scale production for possible use in pharmaceuticals and cosmetics. DOI: http://dx.doi.org/10.7554/eLife.05919.001 PMID:25965179

  13. Divergent evolution of a bifunctional de novo protein.

    PubMed

    Smith, Betsy A; Mularz, Ann E; Hecht, Michael H

    2015-02-01

    Primordial proteins, the evolutionary ancestors of modern sequences, are presumed to have been minimally active and nonspecific. Following eons of selective pressure, these early progenitors evolved into highly active and specific proteins. While evolutionary trajectories from poorly active and multifunctional generalists toward highly active specialists likely occurred many times in evolutionary history, such pathways are difficult to reconstruct in natural systems, where primordial sequences are lost to time. To test the hypothesis that selection for enhanced activity leads to a loss of promiscuity, we evolved a de novo designed bifunctional protein. The parental protein, denoted Syn-IF, was chosen from a library of binary patterned 4-helix bundles. Syn-IF was shown previously to rescue two different auxotrophic strains of E. coli: ΔilvA and Δfes. These two strains contain deletions for proteins with very different biochemical functions; IlvA is involved in isoleucine biosynthesis, while Fes is involved in iron assimilation. In two separate experiments, Syn-IF, was evolved for faster rescue of either ΔilvA or Δfes. Following multiple rounds of mutagenesis, two new proteins were selected, each capable of rescuing the selected function significantly faster than the parental protein. In each case, the evolved protein also lost the ability to rescue the unselected function. In both evolutionary trajectories, the original bifunctional generalist was evolved into a monofunctional specialist with enhanced activity. PMID:25420677

  14. De novo C3 glomerulonephritis in a renal allograft.

    PubMed

    Nahm, Ji Hae; Song, Seung Hwan; Kim, Yu Seun; Cheong, Hae-Il; Lim, Beom Jin; Kim, Beom Seok; Jeong, Hyeon Joo

    2016-01-01

    C3 glomerulonephritis (C3GN) is a recently described, rare glomerular disease characterized by predominant or sole glomerular C3 deposits. Morphologic features of C3GN are similar to those of dense deposit disease (DDD); however, ribbon-like intramembranous electron-dense deposits are absent in the former. We report a case of de novo C3GN in a renal allograft with morphologic transformation to DDD. A 6-year-old boy presented with congenital left renal agenesis and right ureteropelvic junction obstruction. The patient underwent pyeloplasty but experienced recurrent urinary tract infections. At the age of 22 years, he received a renal allograft from a living related donor. C3GN was diagnosed after 1 year of transplantation; initial histology showed minimal mesangiopathy and this progressed to mesangial proliferation and membranoproliferative features over the next 7 years. Serum creatinine levels were stabilized with anti-rejection treatments for combating repeated episodes of acute rejection; however, glomerular and tubular band-like electron-dense deposits became evident. PMID:26986539

  15. Growth Hormone Inhibits Hepatic De Novo Lipogenesis in Adult Mice.

    PubMed

    Cordoba-Chacon, Jose; Majumdar, Neena; List, Edward O; Diaz-Ruiz, Alberto; Frank, Stuart J; Manzano, Anna; Bartrons, Ramon; Puchowicz, Michelle; Kopchick, John J; Kineman, Rhonda D

    2015-09-01

    Patients with nonalcoholic fatty liver disease (NAFLD) are reported to have low growth hormone (GH) production and/or hepatic GH resistance. GH replacement can resolve the fatty liver condition in diet-induced obese rodents and in GH-deficient patients. However, it remains to be determined whether this inhibitory action of GH is due to direct regulation of hepatic lipid metabolism. Therefore, an adult-onset, hepatocyte-specific, GH receptor (GHR) knockdown (aLivGHRkd) mouse was developed to model hepatic GH resistance in humans that may occur after sexual maturation. Just 7 days after aLivGHRkd, hepatic de novo lipogenesis (DNL) was increased in male and female chow-fed mice, compared with GHR-intact littermate controls. However, hepatosteatosis developed only in male and ovariectomized female aLivGHRkd mice. The increase in DNL observed in aLivGHRkd mice was not associated with hyperactivation of the pathway by which insulin is classically considered to regulate DNL. However, glucokinase mRNA and protein levels as well as fructose-2,6-bisphosphate levels were increased in aLivGHRkd mice, suggesting that enhanced glycolysis drives DNL in the GH-resistant liver. These results demonstrate that hepatic GH actions normally serve to inhibit DNL, where loss of this inhibitory signal may explain, in part, the inappropriate increase in hepatic DNL observed in NAFLD patients. PMID:26015548

  16. Role of de novo biosynthesis in ecosystem scale monoterpene emissions from a boreal Scots pine forest

    NASA Astrophysics Data System (ADS)

    Taipale, R.; Kajos, M. K.; Patokoski, J.; Rantala, P.; Ruuskanen, T. M.; Rinne, J.

    2010-11-01

    Monoterpene emissions from Scots pine have traditionally been assumed to originate as evaporation from specialized storage pools. More recently, the significance of de novo emissions, originating directly from monoterpene biosynthesis, has been recognized. To study the role of biosynthesis in the ecosystem scale, we measured monoterpene emissions from a Scots pine dominated forest in southern Finland using the disjunct eddy covariance method combined with proton transfer reaction mass spectrometry. The interpretation of the measurements was based on a hybrid emission algorithm describing both de novo and pool emissions. During the measurement period May-August 2007, the monthly medians of daytime emissions were 170, 280, 180, and 180 μg m-2 h-1. The emission potential for both de novo and pool emissions exhibited a decreasing summertime trend. The ratio of the de novo emission potential to the total emission potential varied between 30% and 46%. Although the monthly changes were not significant, the ratio always differed statistically from zero, i.e., the role of de novo biosynthesis was evident. The hybrid approach showed promising potential for the improvement of the ecosystem scale emission modelling. Given this feature and the significant role of biosynthesis, we recommend incorporating both de novo and pool emissions into the monoterpene emission algorithms for Scots pine dominated forests.

  17. Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome.

    PubMed

    Honaas, Loren A; Wafula, Eric K; Wickett, Norman J; Der, Joshua P; Zhang, Yeting; Edger, Patrick P; Altman, Naomi S; Pires, J Chris; Leebens-Mack, James H; dePamphilis, Claude W

    2016-01-01

    Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1) proportion of reads mapping to an assembly 2) recovery of conserved, widely expressed genes, 3) N50 length statistics, and 4) the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation. PMID:26731733

  18. De novo giant A2 aneurysm following anterior communicating artery occlusion

    PubMed Central

    Ibrahim, Tarik F.; Hafez, Ahmad; Andrade-Barazarte, Hugo; Raj, Rahul; Niemela, Mika; Lehto, Hanna; Numminen, Jussi; Jarvelainen, Juha; Hernesniemi, Juha

    2015-01-01

    Background: De novo intracranial aneurysms are reported to occur with varying incidence after intracranial aneurysm treatment. They are purported to be observed, however, with increased incidence after Hunterian ligation; particularly in cases of carotid artery occlusion for giant or complex aneurysms deemed unclippable. Case Description: We report a case of right-sided de novo giant A2 aneurysm 6 years after an anterior communicating artery (ACoA) aneurysm clipping. We believe this de novo aneurysm developed in part due to patient-specific risk factors but also a significant change in cerebral hemodynamics. The ACoA became occluded after surgery that likely altered the cerebral hemodynamics and contributed to the de novo aneurysm. We believe this to be the first reported case of a giant de novo aneurysm in this location. Following parent vessel occlusion (mostly of the carotid artery), there are no reports of any de novo aneurysms in the pericallosal arteries let alone a giant one. The patient had a dominant right A1 and the sudden increase in A2 blood flow likely resulted in increased wall shear stress, particularly in the medial wall of the A2 where the aneurysm occurred 2 mm distal to the A1-2 junction. Conclusion: ACoA preservation is a key element of aneurysm surgery in this location. Suspected occlusion of this vessel may warrant closer radiographic follow-up in patients with other risk factors for aneurysm development. PMID:26664872

  19. De novo mutations revealed by whole exome sequencing are strongly associated with autism

    PubMed Central

    Sanders, Stephan J.; Murtha, Michael T.; Gupta, Abha R.; Murdoch, John D.; Raubeson, Melanie J.; Willsey, A. Jeremy; Ercan-Sencicek, A. Gulhan; DiLullo, Nicholas M.; Parikshak, Neelroop N.; Stein, Jason L.; Walker, Michael F.; Ober, Gordon T.; Teran, Nicole A.; Song, Youeun; El-Fishawy, Paul; Murtha, Ryan C.; Choi, Murim; Overton, John D.; Bjornson, Robert D.; Carriero, Nicholas J.; Meyer, Kyle A.; Bilguvar, Kaya; Mane, Shrikant M.; Šestan, Nenad; Lifton, Richard P.; Günel, Murat; Roeder, Kathryn; Geschwind, Daniel H.; Devlin, Bernie; State, Matthew W.

    2013-01-01

    Multiple studies have confirmed the contribution of rare de novo copy number variations (CNVs) to the risk for Autism Spectrum Disorders (ASD).1-3 While de novo single nucleotide variants (SNVs) have been identified in affected individuals,4 their contribution to risk has yet to be clarified. Specifically, the frequency and distribution of these mutations has not been well characterized in matched unaffected controls, data that are vital to the interpretation of de novo coding mutations observed in probands. Here we show, via whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with ASD and carry large effects (OR=5.65; CI: 1.44-22.2; p=0.01 asymptotic test). Based on mutation rates in unaffected individuals, we demonstrate that multiple independent de novo SNVs in the same gene among unrelated probands reliably identifies risk alleles, providing a clear path forward for gene discovery. Among a total of 279 identified de novo coding mutations, there is a single instance in probands, and none in siblings, in which two independent nonsense variants disrupt the same gene, SCN2A (Sodium Channel, Voltage-Gated, Type II, Alpha Subunit), a result that is highly unlikely by chance (p=0.005). PMID:22495306

  20. Sequestration-Mediated Downregulation of de Novo Purine Biosynthesis by AMPK.

    PubMed

    Schmitt, Danielle L; Cheng, Yun-Ju; Park, Junyong; An, Songon

    2016-07-15

    Dynamic partitioning of de novo purine biosynthetic enzymes into multienzyme compartments, purinosomes, has been associated with increased flux of de novo purine biosynthesis in human cells. However, we do not know of a mechanism by which de novo purine biosynthesis would be downregulated in cells. We have investigated the functional role of AMP-activated protein kinase (AMPK) in the regulation of de novo purine biosynthesis because of its regulatory action on lipid and carbohydrate biosynthetic pathways. Using pharmacological AMPK activators, we have monitored subcellular localizations of six pathway enzymes tagged with green fluorescent proteins under time-lapse fluorescence single-cell microscopy. We revealed that only one out of six pathway enzymes, formylglycinamidine ribonucleotide synthase (FGAMS), formed spatially distinct cytoplasmic granules after treatment with AMPK activators, indicating the formation of single-enzyme self-assemblies. In addition, subsequent biophysical studies using fluorescence recovery after photobleaching showed that the diffusion kinetics of FGAMS were slower when it localized inside the self-assemblies than within the purinosomes. Importantly, high-performance liquid chromatographic studies revealed that the formation of AMPK-promoted FGAMS self-assembly caused the reduction of purine metabolites in HeLa cells, indicating the downregulation of de novo purine biosynthesis. Collectively, we demonstrate here that the spatial sequestration of FGAMS by AMPK is a mechanism by which de novo purine biosynthesis is downregulated in human cells. PMID:27128383

  1. TransRate: reference-free quality assessment of de novo transcriptome assemblies.

    PubMed

    Smith-Unna, Richard; Boursnell, Chris; Patro, Rob; Hibberd, Julian M; Kelly, Steven

    2016-08-01

    TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly, and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig, and these contig scores are integrated to evaluate whole assemblies. Thus, TransRate can be used for de novo assembly filtering and optimization as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published de novo transcriptome assemblies. Because TransRate is reference-free, it is suitable for assessment of assemblies of all types of RNA, including assemblies of long noncoding RNA, rRNA, mRNA, and mixed RNA samples. PMID:27252236

  2. Breast and ovarian cancer predisposition due to de novo BRCA1 and BRCA2 mutations.

    PubMed

    Golmard, L; Delnatte, C; Laugé, A; Moncoutier, V; Lefol, C; Abidallah, K; Tenreiro, H; Copigny, F; Giraudeau, M; Guy, C; Barbaroux, C; Amorim, G; Briaux, A; Guibert, V; Tarabeux, J; Caputo, S; Collet, A; Gesta, P; Ingster, O; Stern, M-H; Rouleau, E; de Pauw, A; Gauthier-Villars, M; Buecher, B; Bézieau, S; Stoppa-Lyonnet, D; Houdayer, C

    2016-03-10

    BRCA1 and BRCA2 are the two major genes predisposing to breast and ovarian cancer. Whereas high de novo mutation rates have been demonstrated for several genes, only 11 cases of de novo BRCA1/2 mutations have been reported to date and the BRCA1/2 de novo mutation rate remains unknown. The present study was designed to fill this gap based on a series of 12 805 consecutive unrelated patients diagnosed with breast and/or ovarian cancer who met the inclusion criteria for BRCA1/2 gene analysis according to French guidelines. BRCA1/2 mutations were detected in 1527 (12%) patients, and three BRCA1 mutations and one BRCA2 mutation were de novo. The BRCA1/2 de novo mutation rate was estimated to be 0.3% (0.1%; 0.7%). Although rare, it may be useful to take the possibility of de novo BRCA1/2 mutation into account in genetic counseling of relatives and to improve the understanding of complex family histories of breast and ovarian cancers. PMID:26028024

  3. Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome

    PubMed Central

    Honaas, Loren A.; Wafula, Eric K.; Wickett, Norman J.; Der, Joshua P.; Zhang, Yeting; Edger, Patrick P.; Altman, Naomi S.; Pires, J. Chris; Leebens-Mack, James H.; dePamphilis, Claude W.

    2016-01-01

    Whereas de novo assemblies of RNA-Seq data are being published for a growing number of species across the tree of life, there are currently no broadly accepted methods for evaluating such assemblies. Here we present a detailed comparison of 99 transcriptome assemblies, generated with 6 de novo assemblers including CLC, Trinity, SOAP, Oases, ABySS and NextGENe. Controlled analyses of de novo assemblies for Arabidopsis thaliana and Oryza sativa transcriptomes provide new insights into the strengths and limitations of transcriptome assembly strategies. We find that the leading assemblers generate reassuringly accurate assemblies for the majority of transcripts. At the same time, we find a propensity for assemblers to fail to fully assemble highly expressed genes. Surprisingly, the instance of true chimeric assemblies is very low for all assemblers. Normalized libraries are reduced in highly abundant transcripts, but they also lack 1000s of low abundance transcripts. We conclude that the quality of de novo transcriptome assemblies is best assessed through consideration of a combination of metrics: 1) proportion of reads mapping to an assembly 2) recovery of conserved, widely expressed genes, 3) N50 length statistics, and 4) the total number of unigenes. We provide benchmark Illumina transcriptome data and introduce SCERNA, a broadly applicable modular protocol for de novo assembly improvement. Finally, our de novo assembly of the Arabidopsis leaf transcriptome revealed ~20 putative Arabidopsis genes lacking in the current annotation. PMID:26731733

  4. TransRate: reference-free quality assessment of de novo transcriptome assemblies

    PubMed Central

    Smith-Unna, Richard; Boursnell, Chris; Patro, Rob; Hibberd, Julian M.; Kelly, Steven

    2016-01-01

    TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show that multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly, and base errors. TransRate evaluates these errors to produce a diagnostic quality score for each contig, and these contig scores are integrated to evaluate whole assemblies. Thus, TransRate can be used for de novo assembly filtering and optimization as well as comparison of assemblies generated using different methods from the same input reads. Applying the method to a data set of 155 published de novo transcriptome assemblies, we deconstruct the contribution that assembly method, read length, read quantity, and read quality make to the accuracy of de novo transcriptome assemblies and reveal that variance in the quality of the input data explains 43% of the variance in the quality of published de novo transcriptome assemblies. Because TransRate is reference-free, it is suitable for assessment of assemblies of all types of RNA, including assemblies of long noncoding RNA, rRNA, mRNA, and mixed RNA samples. PMID:27252236

  5. A Novel de novo Mutation in CEACAM16 Associated with Postlingual Hearing Impairment

    PubMed Central

    Hofrichter, Michaela A.H.; Nanda, Indrajit; Gräf, Jens; Schröder, Jörg; Shehata-Dieler, Wafaa; Vona, Barbara; Haaf, Thomas

    2015-01-01

    Mutations in CEACAM16 cause autosomal dominant nonsyndromic hearing loss (DFNA4B). So far, 2 families have been reported with segregating missense mutations, both in the immunoglobulin constant domain A of the CEACAM16 protein. In this study, we used the TruSight One panel to investigate a parent-child trio without familial history of hearing loss and one affected child. When filtering for recessive inheritance and de novo events, we discovered a de novo CEACAM16 mutation (c.1094T>G, p.Leu365Arg) as the sole likely pathogenic variant. The de novo mutation was confirmed by Sanger sequencing and STR analysis. The proband's hearing loss closely matches the described onset and severity for DFNA4B. We present the third CEACAM16 variant and the first de novo mutation in CEACAM16. This de novo mutation is robustly described as a pathogenic mutation according to in silico mutation prediction tools and affects a highly conserved amino acid in the most strongly conserved CEACAM16 N2 domain. Our strategy of screening family trios enhances de novo mutation discovery and the exclusion of other variants of potential interest through pedigree filtering. PMID:26648831

  6. De novo mutations in histone modifying genes in congenital heart disease

    PubMed Central

    Zaidi, Samir; Choi, Murim; Wakimoto, Hiroko; Ma, Lijiang; Jiang, Jianming; Overton, John D.; Romano-Adesman, Angela; Bjornson, Robert D.; Breitbart, Roger E.; Brown, Kerry K.; Carriero, Nicholas J.; Cheung, Yee Him; Deanfield, John; DePalma, Steve; Fakhro, Khalid A.; Glessner, Joseph; Hakonarson, Hakon; Italia, Michael; Kaltman, Jonathan R.; Kaski, Juan; Kim, Richard; Kline, Jennie K.; Lee, Teresa; Leipzig, Jeremy; Lopez, Alexander; Mane, Shrikant M.; Mitchell, Laura E.; Newburger, Jane W.; Parfenov, Michael; Pe'er, Itsik; Porter, George; Roberts, Amy; Sachidanandam, Ravi; Sanders, Stephan J.; Seiden, Howard S.; State, Mathew W.; Subramanian, Sailakshmi; Tikhonova, Irina R.; Wang, Wei; Warburton, Dorothy; White, Peter S.; Williams, Ismee A.; Zhao, Hongyu; Seidman, Jonathan G.; Brueckner, Martina; Chung, Wendy K.; Gelb, Bruce D.; Goldmuntz, Elizabeth; Seidman, Christine E.; Lifton, Richard P.

    2013-01-01

    Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births1. Many cases occur sporadically and impair reproductive fitness, suggesting a role for de novo mutations. By analysis of exome sequencing of parent-offspring trios, we compared the incidence of de novo mutations in 362 severe CHD cases and 264 controls. CHD cases showed a significant excess of protein-altering de novo mutations in genes expressed in the developing heart, with an odds ratio of 7.5 for damaging mutations. Similar odds ratios were seen across major classes of severe CHD. We found a marked excess of de novo mutations in genes involved in production, removal or reading of H3K4 methylation (H3K4me), or ubiquitination of H2BK120, which is required for H3K4 methylation2–4. There were also two de novo mutations in SMAD2; SMAD2 signaling in the embryonic left-right organizer induces demethylation of H3K27me5. H3K4me and H3K27me mark `poised' promoters and enhancers that regulate expression of key developmental genes6. These findings implicate de novo point mutations in several hundred genes that collectively contribute to ~10% of severe CHD. PMID:23665959

  7. De novo donor-specific anti-HLA antibodies mediated rejection in liver-transplant patients.

    PubMed

    Del Bello, Arnaud; Congy-Jolivet, Nicolas; Danjoux, Marie; Muscari, Fabrice; Lavayssière, Laurence; Esposito, Laure; Cardeau-Desangles, Isabelle; Guitard, Joëlle; Dörr, Gaëlle; Milongo, David; Suc, Bertrand; Duffas, Jean Pierre; Alric, Laurent; Bureau, Christophe; Guilbeau-Frugier, Céline; Rostaing, Lionel; Kamar, Nassim

    2015-12-01

    The incidence and consequences of de novo donor-specific anti-HLA antibodies (DSAs) after liver transplantation (LT) are not well known. We investigated the incidence, risk factors, and complications associated with de novo DSAs in this setting. A total of 152 de novo liver-transplant patients, without preformed anti-HLA DSAs, were tested for anti-HLA antibodies, with single-antigen bead technology, before, at transplantation, at 1, 3, 6 and 12 months after transplantation, and thereafter annually and at each time they presented with increased liver-enzyme levels until the last follow-up, that is, 34 (1.5-77) months. Twenty-one patients (14%) developed de novo DSAs. Of these, five patients had C1q-binding DSAs (24%). Younger age, low exposure to calcineurin inhibitors, and noncompliance were predictive factors for de novo DSA formation. Nine of the 21 patients (43%) with de novo DSAs experienced an acute antibody-mediated rejection (AMR). Positive C4d staining was more frequently observed in liver biopsies of patients with AMR (9/9 vs. 1/12, P < 0.0001). Eight patients received a B-cell targeting therapy, and one patient received polyclonal antibodies. Only one patient required retransplantation. Patient- and graft-survival rates did not differ between patients with and without DSAs. In conclusion, liver-transplant patients with liver abnormalities should be screened for DSAs and AMR. PMID:26303035

  8. Further Insights into Brevetoxin Metabolism by de Novo Radiolabeling

    PubMed Central

    Calabro, Kevin; Guigonis, Jean-Marie; Teyssié, Jean-Louis; Oberhänsli, François; Goudour, Jean-Pierre; Warnau, Michel; Dechraoui Bottein, Marie-Yasmine; Thomas, Olivier P.

    2014-01-01

    The toxic dinoflagellate Karenia brevis, responsible for early harmful algal blooms in the Gulf of Mexico, produces many secondary metabolites, including potent neurotoxins called brevetoxins (PbTx). These compounds have been identified as toxic agents for humans, and they are also responsible for the deaths of several marine organisms. The overall biosynthesis of these highly complex metabolites has not been fully ascertained, even if there is little doubt on a polyketide origin. In addition to gaining some insights into the metabolic events involved in the biosynthesis of these compounds, feeding studies with labeled precursors helps to discriminate between the de novo biosynthesis of toxins and conversion of stored intermediates into final toxic products in the response to environmental stresses. In this context, the use of radiolabeled precursors is well suited as it allows working with the highest sensitive techniques and consequently with a minor amount of cultured dinoflagellates. We were then able to incorporate [U-14C]-acetate, the renowned precursor of the polyketide pathway, in several PbTx produced by K. brevis. The specific activities of PbTx-1, -2, -3, and -7, identified by High-Resolution Electrospray Ionization Mass Spectrometer (HRESIMS), were assessed by HPLC-UV and highly sensitive Radio-TLC counting. We demonstrated that working at close to natural concentrations of acetate is a requirement for biosynthetic studies, highlighting the importance of highly sensitive radiolabeling feeding experiments. Quantification of the specific activity of the four, targeted toxins led us to propose that PbTx-1 and PbTx-2 aldehydes originate from oxidation of the primary alcohols of PbTx-7 and PbTx-3, respectively. This approach will open the way for a better comprehension of the metabolic pathways leading to PbTx but also to a better understanding of their regulation by environmental factors. PMID:24918358

  9. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis

    PubMed Central

    Pisithkul, Tippapha; Jacobson, Tyler B.; O'Brien, Thomas J.; Stevenson, David M.

    2015-01-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using 13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. PMID:26070680

  10. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis.

    PubMed

    Pisithkul, Tippapha; Jacobson, Tyler B; O'Brien, Thomas J; Stevenson, David M; Amador-Noguez, Daniel

    2015-09-01

    An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using (13)C-labeled sugars and [(15)N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals. PMID:26070680

  11. De Novo Mutations in Synaptic Transmission Genes Including DNM1 Cause Epileptic Encephalopathies

    PubMed Central

    Appenzeller, Silke; Balling, Rudi; Barisic, Nina; Baulac, Stéphanie; Caglayan, Hande; Craiu, Dana; De Jonghe, Peter; Depienne, Christel; Dimova, Petia; Djémié, Tania; Gormley, Padhraig; Guerrini, Renzo; Helbig, Ingo; Hjalgrim, Helle; Hoffman-Zacharska, Dorota; Jähn, Johanna; Klein, Karl Martin; Koeleman, Bobby; Komarek, Vladimir; Krause, Roland; Kuhlenbäumer, Gregor; Leguern, Eric; Lehesjoki, Anna-Elina; Lemke, Johannes R.; Lerche, Holger; Linnankivi, Tarja; Marini, Carla; May, Patrick; Møller, Rikke S.; Muhle, Hiltrud; Pal, Deb; Palotie, Aarno; Pendziwiat, Manuela; Robbiano, Angela; Roelens, Filip; Rosenow, Felix; Selmer, Kaja; Serratosa, Jose M.; Sisodiya, Sanjay; Stephani, Ulrich; Sterbova, Katalin; Striano, Pasquale; Suls, Arvid; Talvik, Tiina; von Spiczak, Sarah; Weber, Yvonne; Weckhuysen, Sarah; Zara, Federico; Abou-Khalil, Bassel; Alldredge, Brian K.; Andermann, Eva; Andermann, Frederick; Amron, Dina; Bautista, Jocelyn F.; Berkovic, Samuel F.; Bluvstein, Judith; Boro, Alex; Cascino, Gregory; Consalvo, Damian; Crumrine, Patricia; Devinsky, Orrin; Dlugos, Dennis; Epstein, Michael P.; Fiol, Miguel; Fountain, Nathan B.; French, Jacqueline; Friedman, Daniel; Geller, Eric B.; Glauser, Tracy; Glynn, Simon; Haas, Kevin; Haut, Sheryl R.; Hayward, Jean; Helmers, Sandra L.; Joshi, Sucheta; Kanner, Andres; Kirsch, Heidi E.; Knowlton, Robert C.; Kossoff, Eric H.; Kuperman, Rachel; Kuzniecky, Ruben; Lowenstein, Daniel H.; McGuire, Shannon M.; Motika, Paul V.; Novotny, Edward J.; Ottman, Ruth; Paolicchi, Juliann M.; Parent, Jack; Park, Kristen; Poduri, Annapurna; Sadleir, Lynette; Scheffer, Ingrid E.; Shellhaas, Renée A.; Sherr, Elliott; Shih, Jerry J.; Singh, Rani; Sirven, Joseph; Smith, Michael C.; Sullivan, Joe; Thio, Liu Lin; Venkat, Anu; Vining, Eileen P.G.; Von Allmen, Gretchen K.; Weisenberg, Judith L.; Widdess-Walsh, Peter; Winawer, Melodie R.; Allen, Andrew S.; Berkovic, Samuel F.; Cossette, Patrick; Delanty, Norman; Dlugos, Dennis; Eichler, Evan E.; Epstein, Michael P.; Glauser, Tracy; Goldstein, David B.; Han, Yujun; Heinzen, Erin L.; Johnson, Michael R.; Kuzniecky, Ruben; Lowenstein, Daniel H.; Marson, Anthony G.; Mefford, Heather C.; Nieh, Sahar Esmaeeli; O’Brien, Terence J.; Ottman, Ruth; Petrou, Stephen; Petrovski, Slavé; Poduri, Annapurna; Ruzzo, Elizabeth K.; Scheffer, Ingrid E.; Sherr, Elliott

    2014-01-01

    Emerging evidence indicates that epileptic encephalopathies are genetically highly heterogeneous, underscoring the need for large cohorts of well-characterized individuals to further define the genetic landscape. Through a collaboration between two consortia (EuroEPINOMICS and Epi4K/EPGP), we analyzed exome-sequencing data of 356 trios with the “classical” epileptic encephalopathies, infantile spasms and Lennox Gastaut syndrome, including 264 trios previously analyzed by the Epi4K/EPGP consortium. In this expanded cohort, we find 429 de novo mutations, including de novo mutations in DNM1 in five individuals and de novo mutations in GABBR2, FASN, and RYR3 in two individuals each. Unlike previous studies, this cohort is sufficiently large to show a significant excess of de novo mutations in epileptic encephalopathy probands compared to the general population using a likelihood analysis (p = 8.2 × 10−4), supporting a prominent role for de novo mutations in epileptic encephalopathies. We bring statistical evidence that mutations in DNM1 cause epileptic encephalopathy, find suggestive evidence for a role of three additional genes, and show that at least 12% of analyzed individuals have an identifiable causal de novo mutation. Strikingly, 75% of mutations in these probands are predicted to disrupt a protein involved in regulating synaptic transmission, and there is a significant enrichment of de novo mutations in genes in this pathway in the entire cohort as well. These findings emphasize an important role for synaptic dysregulation in epileptic encephalopathies, above and beyond that caused by ion channel dysfunction. PMID:25262651

  12. Prevalence and origin of De Novo duplications in Charcot-Marie-Tooth disease type 1A: First report of a De Novo duplication with a maternal origin

    SciTech Connect

    Blair, I.P.; Nash, J.; Gordon, M.J.; Nicholson, G.A.

    1996-03-01

    Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral neuropathy. Sporadic cases of CMT have been described since the earliest reports of the disease. The most frequent form of the disorder, CMT1A, is associated with a 1.5-Mb DNA duplication on chromosome 17p11.2, which segregates with the disease. In order to investigate the prevalence of de novo CMT1A duplications, this study examined 118 duplication-positive CMT1A families. In 10 of these families it was demonstrated that the disease had arisen as the result of a de novo mutation. By taking into account the ascertainment of families, it can be estimated that {>=}10% of autosomal dominant CMT1 families are due to de novo duplications. The CMT1A duplication is thought to be the product of unequal crossing over between parental chromosome 17 homologues during meiosis. Polymorphic markers from within the duplicated region were used to determine the parental origin of these de novo duplications in eight informative families. Seven were of paternal and one of maternal origin. This study represents the first report of a de novo duplication with a maternal origin and indicates that it is not a phenomenon associated solely with male meioses. Recombination fractions for the region duplicated in CMT1A are larger in females than in males. That suggests that oogenesis may be afforded greater protection from misalignment during synapsis, and/or that there may be lower activity of those factors or mechanisms that lead to unequal crossing over at the CMT1A locus. 41 refs., 2 figs.

  13. Cryptic genomic imbalances in patients with de novo or familial apparently balanced translocations and abnormal phenotype

    PubMed Central

    Sismani, Carolina; Kitsiou-Tzeli, Sofia; Ioannides, Marios; Christodoulou, Christodoulos; Anastasiadou, Violetta; Stylianidou, Goula; Papadopoulou, Eleftheria; Kanavakis, Emanuel; Kosmaidou-Aravidou, Zoe; Patsalis, Philippos C

    2008-01-01

    Background Carriers of apparently balanced translocations are usually phenotypically normal; however in about 6% of de novo cases, an abnormal phenotype is present. In the current study we investigated 12 patients, six de novo and six familial, with apparently balanced translocations and mental retardation and/or congenital malformations by applying 1 Mb resolution array-CGH. In all de novo cases, only the patient was a carrier of the translocation and had abnormal phenotype. In five out of the six familial cases, the phenotype of the patient was abnormal, although the karyotype appeared identical to other phenotypically normal carriers of the family. In the sixth familial case, all carriers of the translocations had an abnormal phenotype. Results Chromosomal and FISH analyses suggested that the rearrangements were "truly balanced" in all patients. However, array-CGH, revealed cryptic imbalances in three cases (3/12, 25%), two de novo (2/12, 33.3%) and one familial (1/12, 16.6%). The nature and type of abnormalities differed among the cases. In the first case, what was identified as a de novo t(9;15)(q31;q26.1), a complex rearrangement was revealed involving a ~6.1 Mb duplication on the long arm of chromosome 9, an ~10 Mb deletion and an inversion both on the long arm of chromosome 15. These imbalances were located near the translocation breakpoints. In the second case of a de novo t(4;9)(q25;q21.2), an ~6.6 Mb deletion was identified on the short arm of chromosome 7 which is unrelated to the translocation. In the third case, of a familial, t(4;7)(q13.3;p15.3), two deletions of ~4.3 Mb and ~2.3 Mb were found, each at one of the two translocation breakpoints. In the remaining cases the translocations appeared balanced at 1 Mb resolution. Conclusion This study investigated both de novo and familial apparently balanced translocations unlike other relatively large studies which are mainly focused on de novo cases. This study provides additional evidence that cryptic

  14. AMPK Activation via Modulation of De Novo Purine Biosynthesis with an Inhibitor of ATIC Homodimerization.

    PubMed

    Asby, Daniel J; Cuda, Francesco; Beyaert, Maxime; Houghton, Franchesca D; Cagampang, Felino R; Tavassoli, Ali

    2015-07-23

    5-Aminoimidazole-4-carboxamide ribonucleotide (known as ZMP) is a metabolite produced in de novo purine biosynthesis and histidine biosynthesis, but only utilized in the cell by a homodimeric bifunctional enzyme (called ATIC) that catalyzes the last two steps of de novo purine biosynthesis. ZMP is known to act as an allosteric activator of the cellular energy sensor adenosine monophosphate-activated protein kinase (AMPK), when exogenously administered as the corresponding cell-permeable ribonucleoside. Here, we demonstrate that endogenous ZMP, produced by the aforementioned metabolic pathways, is also capable of activating AMPK. Using an inhibitor of ATIC homodimerization to block the ninth step of de novo purine biosynthesis, we demonstrate that the subsequent increase in endogenous ZMP activates AMPK and its downstream signaling pathways. We go on to illustrate the viability of using this approach to AMPK activation as a therapeutic strategy with an in vivo mouse model for metabolic disorders. PMID:26144885

  15. Defining the maize transcriptome de novo using deep RNA-Seq

    SciTech Connect

    Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong

    2011-06-02

    De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.

  16. Defining the maize transcriptome de novo using deep RNA-Seq

    SciTech Connect

    Martin, Jeffrey; Gross, Stephen; Choi, Cindy; Zhang, Tao; Lindquist, Erika; Wei, Chia-Lin; Wang, Zhong

    2011-06-01

    De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.

  17. Dedifferentiated gastrointestinal stromal tumor arising de novo from the small intestine.

    PubMed

    Choi, Jacqueline J; Sinada-Bottros, Laura; Maker, Ajay V; Weisenberg, Elliot

    2014-04-01

    Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract and usually display monotonous cytologic features and immunoactivity for CD117. Anaplastic GIST, with pleomorphic cells and loss of CD117, until recently have only been reported in patients with chronic imatinib mesylate treatment. Dedifferentiated GISTs arising de novo is a newly identified entity that may prove to be difficult to diagnose. We present the case of a 52-year-old female found to have a dedifferentiated GIST without prior imatinib mesylate therapy. This case is the first reported dedifferentiated GIST arising de novo from the small bowel, and at 30cm in greatest diameter, the largest reported to date. Additionally, we demonstrate for the first time the loss of DOG1 in the anaplastic component of the tumor. De novo dedifferentiated GIST is a rare and diagnostically challenging tumor that may be mischaracterized unless considered in the differential diagnosis. PMID:24484970

  18. Rare De Novo Germline Copy-Number Variation in Testicular Cancer

    PubMed Central

    Stadler, Zsofia K.; Esposito, Diane; Shah, Sohela; Vijai, Joseph; Yamrom, Boris; Levy, Dan; Lee, Yoon-ha; Kendall, Jude; Leotta, Anthony; Ronemus, Michael; Hansen, Nichole; Sarrel, Kara; Rau-Murthy, Rohini; Schrader, Kasmintan; Kauff, Noah; Klein, Robert J.; Lipkin, Steven M.; Murali, Rajmohan; Robson, Mark; Sheinfeld, Joel; Feldman, Darren; Bosl, George; Norton, Larry; Wigler, Michael; Offit, Kenneth

    2012-01-01

    Although heritable factors are an important determinant of risk of early-onset cancer, the majority of these malignancies appear to occur sporadically without identifiable risk factors. Germline de novo copy-number variations (CNVs) have been observed in sporadic neurocognitive and cardiovascular disorders. We explored this mechanism in 382 genomes of 116 early-onset cancer case-parent trios and unaffected siblings. Unique de novo germline CNVs were not observed in 107 breast or colon cancer trios or controls but were indeed found in 7% of 43 testicular germ cell tumor trios; this percentage exceeds background CNV rates and suggests a rare de novo genetic paradigm for susceptibility to some human malignancies. PMID:22863192

  19. Genome-wide patterns and properties of de novo mutations in humans.

    PubMed

    Francioli, Laurent C; Polak, Paz P; Koren, Amnon; Menelaou, Androniki; Chun, Sung; Renkens, Ivo; van Duijn, Cornelia M; Swertz, Morris; Wijmenga, Cisca; van Ommen, Gertjan; Slagboom, P Eline; Boomsma, Dorret I; Ye, Kai; Guryev, Victor; Arndt, Peter F; Kloosterman, Wigard P; de Bakker, Paul I W; Sunyaev, Shamil R

    2015-07-01

    Mutations create variation in the population, fuel evolution and cause genetic diseases. Current knowledge about de novo mutations is incomplete and mostly indirect. Here we analyze 11,020 de novo mutations from the whole genomes of 250 families. We show that de novo mutations in the offspring of older fathers are not only more numerous but also occur more frequently in early-replicating, genic regions. Functional regions exhibit higher mutation rates due to CpG dinucleotides and show signatures of transcription-coupled repair, whereas mutation clusters with a unique signature point to a new mutational mechanism. Mutation and recombination rates independently associate with nucleotide diversity, and regional variation in human-chimpanzee divergence is only partly explained by heterogeneity in mutation rate. Finally, we provide a genome-wide mutation rate map for medical and population genetics applications. Our results provide new insights and refine long-standing hypotheses about human mutagenesis. PMID:25985141

  20. De Novo-Designed Enzymes as Small-Molecule-Regulated Fluorescence Imaging Tags and Fluorescent Reporters

    PubMed Central

    2015-01-01

    Enzyme-based tags attached to a protein-of-interest (POI) that react with a small molecule, rendering the conjugate fluorescent, are very useful for studying the POI in living cells. These tags are typically based on endogenous enzymes, so protein engineering is required to ensure that the small-molecule probe does not react with the endogenous enzyme in the cell of interest. Here we demonstrate that de novo-designed enzymes can be used as tags to attach to POIs. The inherent bioorthogonality of the de novo-designed enzyme–small-molecule probe reaction circumvents the need for protein engineering, since these enzyme activities are not present in living organisms. Herein, we transform a family of de novo-designed retroaldolases into variable-molecular-weight tags exhibiting fluorescence imaging, reporter, and electrophoresis applications that are regulated by tailored, reactive small-molecule fluorophores. PMID:25209927

  1. Integrated Model of De Novo and Inherited Genetic Variants Yields Greater Power to Identify Risk Genes

    PubMed Central

    He, Xin; Sanders, Stephan J.; Liu, Li; De Rubeis, Silvia; Lim, Elaine T.; Sutcliffe, James S.; Schellenberg, Gerard D.; Gibbs, Richard A.; Daly, Mark J.; Buxbaum, Joseph D.; State, Matthew W.; Devlin, Bernie; Roeder, Kathryn

    2013-01-01

    De novo mutations affect risk for many diseases and disorders, especially those with early-onset. An example is autism spectrum disorders (ASD). Four recent whole-exome sequencing (WES) studies of ASD families revealed a handful of novel risk genes, based on independent de novo loss-of-function (LoF) mutations falling in the same gene, and found that de novo LoF mutations occurred at a twofold higher rate than expected by chance. However successful these studies were, they used only a small fraction of the data, excluding other types of de novo mutations and inherited rare variants. Moreover, such analyses cannot readily incorporate data from case-control studies. An important research challenge in gene discovery, therefore, is to develop statistical methods that accommodate a broader class of rare variation. We develop methods that can incorporate WES data regarding de novo mutations, inherited variants present, and variants identified within cases and controls. TADA, for Transmission And De novo Association, integrates these data by a gene-based likelihood model involving parameters for allele frequencies and gene-specific penetrances. Inference is based on a Hierarchical Bayes strategy that borrows information across all genes to infer parameters that would be difficult to estimate for individual genes. In addition to theoretical development we validated TADA using realistic simulations mimicking rare, large-effect mutations affecting risk for ASD and show it has dramatically better power than other common methods of analysis. Thus TADA's integration of various kinds of WES data can be a highly effective means of identifying novel risk genes. Indeed, application of TADA to WES data from subjects with ASD and their families, as well as from a study of ASD subjects and controls, revealed several novel and promising ASD candidate genes with strong statistical support. PMID:23966865

  2. Optimization of de novo transcriptome assembly from next-generation sequencing data.

    PubMed

    Surget-Groba, Yann; Montoya-Burgos, Juan I

    2010-10-01

    Transcriptome analysis has important applications in many biological fields. However, assembling a transcriptome without a known reference remains a challenging task requiring algorithmic improvements. We present two methods for substantially improving transcriptome de novo assembly. The first method relies on the observation that the use of a single k-mer length by current de novo assemblers is suboptimal to assemble transcriptomes where the sequence coverage of transcripts is highly heterogeneous. We present the Multiple-k method in which various k-mer lengths are used for de novo transcriptome assembly. We demonstrate its good performance by assembling de novo a published next-generation transcriptome sequence data set of Aedes aegypti, using the existing genome to check the accuracy of our method. The second method relies on the use of a reference proteome to improve the de novo assembly. We developed the Scaffolding using Translation Mapping (STM) method that uses mapping against the closest available reference proteome for scaffolding contigs that map onto the same protein. In a controlled experiment using simulated data, we show that the STM method considerably improves the assembly, with few errors. We applied these two methods to assemble the transcriptome of the non-model catfish Loricaria gr. cataphracta. Using the Multiple-k and STM methods, the assembly increases in contiguity and in gene identification, showing that our methods clearly improve quality and can be widely used. The new methods were used to assemble successfully the transcripts of the core set of genes regulating tooth development in vertebrates, while classic de novo assembly failed. PMID:20693479

  3. De novo mutations in KIF1A cause progressive encephalopathy and brain atrophy

    PubMed Central

    Esmaeeli Nieh, Sahar; Madou, Maura R Z; Sirajuddin, Minhajuddin; Fregeau, Brieana; McKnight, Dianalee; Lexa, Katrina; Strober, Jonathan; Spaeth, Christine; Hallinan, Barbara E; Smaoui, Nizar; Pappas, John G; Burrow, Thomas A; McDonald, Marie T; Latibashvili, Mariam; Leshinsky-Silver, Esther; Lev, Dorit; Blumkin, Luba; Vale, Ronald D; Barkovich, Anthony James; Sherr, Elliott H

    2015-01-01

    Objective To determine the cause and course of a novel syndrome with progressive encephalopathy and brain atrophy in children. Methods Clinical whole-exome sequencing was performed for global developmental delay and intellectual disability; some patients also had spastic paraparesis and evidence of clinical regression. Six patients were identified with de novo missense mutations in the kinesin gene KIF1A. The predicted functional disruption of these mutations was assessed in silico to compare the calculated conformational flexibility and estimated efficiency of ATP binding to kinesin motor domains of wild-type (WT) versus mutant alleles. Additionally, an in vitro microtubule gliding assay was performed to assess the effects of de novo dominant, inherited recessive, and polymorphic variants on KIF1A motor function. Results All six subjects had severe developmental delay, hypotonia, and varying degrees of hyperreflexia and spastic paraparesis. Microcephaly, cortical visual impairment, optic neuropathy, peripheral neuropathy, ataxia, epilepsy, and movement disorders were also observed. All six patients had a degenerative neurologic course with progressive cerebral and cerebellar atrophy seen on sequential magnetic resonance imaging scans. Computational modeling of mutant protein structures when compared to WT kinesin showed substantial differences in conformational flexibility and ATP-binding efficiency. The de novo KIF1A mutants were nonmotile in the microtubule gliding assay. Interpretation De novo mutations in KIF1A cause a degenerative neurologic syndrome with brain atrophy. Computational and in vitro assays differentiate the severity of dominant de novo heterozygous versus inherited recessive KIF1A mutations. The profound effect de novo mutations have on axonal transport is likely related to the cause of progressive neurologic impairment in these patients. PMID:26125038

  4. Using linkage maps to correct and scaffold de novo genome assemblies: methods, challenges, and computational tools

    PubMed Central

    Fierst, Janna L.

    2015-01-01

    Modern high-throughput DNA sequencing has made it possible to inexpensively produce genome sequences, but in practice many of these draft genomes are fragmented and incomplete. Genetic linkage maps based on recombination rates between physical markers have been used in biology for over 100 years and a linkage map, when paired with a de novo sequencing project, can resolve mis-assemblies and anchor chromosome-scale sequences. Here, I summarize the methodology behind integrating de novo assemblies and genetic linkage maps, outline the current challenges, review the available software tools, and discuss new mapping technologies. PMID:26150829

  5. Genetic and metabolomic analysis of AdeD and AdeI mutants of de novo purine biosynthesis: cellular models of de novo purine biosynthesis deficiency disorders.

    PubMed

    Duval, Nathan; Luhrs, Kyleen; Wilkinson, Terry G; Baresova, Veronika; Skopova, Vaclava; Kmoch, Stanislav; Vacano, Guido N; Zikanova, Marie; Patterson, David

    2013-03-01

    Purines are molecules essential for many cell processes, including RNA and DNA synthesis, regulation of enzyme activity, protein synthesis and function, energy metabolism and transfer, essential coenzyme function, and cell signaling. Purines are produced via the de novo purine biosynthesis pathway. Mutations in purine biosynthetic genes, for example phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetase (PAICS, E.C. 6.3.2.6/E.C. 4.1.1.21), can lead to developmental anomalies in lower vertebrates. Alterations in PAICS expression in humans have been associated with various types of cancer. Mutations in adenylosuccinate lyase (ADSL, E.C. 4.3.2.2) or 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase (ATIC, E.C. 2.1.2.3/E.C. 3.5.4.10) lead to inborn errors of metabolism with a range of clinical symptoms, including developmental delay, severe neurological symptoms, and autistic features. The pathogenetic mechanism is unknown for these conditions, and no effective treatments exist. The study of cells carrying mutations in the various de novo purine biosynthesis pathway genes provides one approach to analysis of purine disorders. Here we report the characterization of AdeD Chinese hamster ovary (CHO) cells, which carry genetic mutations encoding p.E177K and p.W363* variants of PAICS. Both mutations impact PAICS structure and completely abolish its biosynthesis. Additionally, we describe a sensitive and rapid analytical method for detection of purine de novo biosynthesis intermediates based on high performance liquid chromatography with electrochemical detection. Using this technique we detected accumulation of AIR in AdeD cells. In AdeI cells, mutant for the ADSL gene, we detected accumulation of SAICAR and SAMP and, somewhat unexpectedly, accumulation of AIR. This method has great potential for metabolite profiling of de novo purine biosynthesis pathway mutants, identification of novel genetic

  6. A randomized, double-blind, cross-over, phase IV trial of oros-methylphenidate (CONCERTA®) and generic novo-methylphenidate ER-C (NOVO-generic)

    PubMed Central

    Fallu, Angelo; Dabouz, Farida; Furtado, Melissa; Anand, Leena; Katzman, Martin A.

    2016-01-01

    Objective: Attention-deficit/hyperactivity disorder (ADHD) is a common neurobehavioral disorder with onset during childhood. Multiple aspects of a child’s development are hindered, in both home and school settings, with negative impacts on social, emotional, and cognitive functioning. If left untreated, ADHD is commonly associated with poor academic achievement and low occupational status, as well as increased risk of substance abuse and delinquency. The objective of this study was to evaluate adult ADHD subject reported outcomes when switched from a stable dose of CONCERTA® to the same dose of generic Novo-methylphenidate ER-C®. Methods: Randomized, double-blind, cross-over, phase IV trial consisted of two phases in which participants with a primary diagnosis of ADHD were randomized in a 1:1 ratio to 3 weeks of treatment with CONCERTA or generic Novo-Methylphenidate ER-C. Following 3 weeks of treatment, participants were crossed-over to receive the other treatment for an additional 3 weeks. Primary efficacy was assessed through the use of the Treatment Satisfaction Questionnaire for Medication, Version II (TSQM-II). Results: Participants with ADHD treated with CONCERTA were more satisfied in terms of efficacy and side effects compared to those receiving an equivalent dose of generic Novo-Methylphenidate ER-C. All participants chose to continue with CONCERTA treatment at the conclusion of the study. Conclusion: Although CONCERTA and generic Novo-Methylphenidate ER-C have been deemed bioequivalent, however the present findings demonstrate clinically and statistically significant differences between generic and branded CONCERTA. Further investigation of these differences is warranted. PMID:27536342

  7. 78 FR 38027 - Novo BioPower LLC; Supplemental Notice That Initial Market-Based Rate Filing Includes Request for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-25

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF ENERGY Federal Energy Regulatory Commission Novo BioPower LLC; Supplemental Notice That Initial Market-Based Rate Filing...-referenced proceeding, of Novo BioPower LLC's application for market-based rate authority, with...

  8. Parylene supported 20um*20um uncooled thermoelectric infrared detector with high fill factor

    NASA Astrophysics Data System (ADS)

    Modarres-Zadeh, Mohammad J.; Carpenter, Zachary S.; Rockley, Mark G.; Abdolvand, Reza

    2012-06-01

    Presented is a novel design for an uncooled surface-micromachined thermoelectric (TE) infrared (IR) detector. The detector features a P-doped polysilicon/Nichrome (Cr20-Ni80) thermocouple, which is embedded into a thin layer of Parylene-N to provide structural support. The low thermal conductivity (~0.1W/m.K), chemical resistance, and ease of deposition/patterning of Parylene-N make it an excellent choice of material for use in MEMS thermal detectors. This detector also features an umbrella-like IR absorber composed of a three layer stack of NiCr/SiN/NiCr to optimize IR absorption. The total device area is 20 um * 20 um per pixel with an absorber area of ~19 um * 19 um resulting in a fill factor of 90%. At room temperature, a DC responsivity of ~170V/W with a rise time of less than 8 ms is measured from the fabricated devices in vacuum when viewing a 500K blackbody without any concentrating optics. The dominant source of noise in thermoelectric IR detectors is typically Johnson noise when the detectors are operating in an open circuit condition. The fabricated detectors have resistances about 85KOhm which results in Johnson noise of about 38nV/Hz^0.5. The D* is calculated to be 9 * 106 cm*Hz0.5/ W. Preliminary finite element analysis indicates that the thermal conduction from the hot junction to the substrate through the TE wires is dominant ( GTE >> Gparylene) considering the fabricated dimensions of the parylene film and the TE wires. Thus, by further reducing the size of the TE wires, GTE can be decreased and hence, responsivity can be improved while the parylene film sustains the structural integrity of the cell.

  9. Spectrum of De Novo Cancers and Predictors in Liver Transplantation: Analysis of the Scientific Registry of Transplant Recipients Database

    PubMed Central

    Zhou, Jie; Hu, Zhenhua; Zhang, Qijun; Li, Zhiwei; Xiang, Jie; Yan, Sheng; Wu, Jian; Zhang, Min; Zheng, Shusen

    2016-01-01

    Background De novo malignancies occur after liver transplantation because of immunosuppression and improved long-term survival. But the spectrums and associated risk factors remain unclear. Aims To describe the overall pattern of de novo cancers in liver transplant recipients. Methods Data from Scientific Registry of Transplant Recipients from October 1987 to December 2009 were analyzed. The spectrum of de novo cancer was analyzed and logistic-regression was used to identify predictors of do novo malignancies. Results Among 89,036 liver transplant recipients, 6,834 recipients developed 9,717 post-transplant malignancies. We focused on non-skin malignancies. A total of 3,845 recipients suffered from 4,854 de novo non-skin malignancies, including 1,098 de novo hematological malignancies, 38 donor-related cases, and 3,718 de novo solid-organ malignancies. Liver transplant recipients had more than 11 times elevated cancer risk compared with the general population. The long-term overall survival was better for recipients without de novo cancer. Multivariate analysis indicated that HCV, alcoholic liver disease, autoimmune liver disease, nonalcoholic steatohepatitis, re-transplantation, combined transplantation, hepatocellular carcinoma, immunosuppression regime of cellcept, cyclosporine, sirolimus, steroids and tacrolimus were independent predictors for the development of solid malignancies after liver transplantation. Conclusions De novo cancer risk was elevated in liver transplant recipients. Multiple factors including age, gender, underlying liver disease and immunosuppression were associated with the development of de novo cancer. This is useful in guiding recipient selection as well as post-transplant surveillance and prevention. PMID:27171501

  10. "Uh" and "Um" Revisited: Are They Interjections for Signaling Delay?

    ERIC Educational Resources Information Center

    O'Connell, Daniel C.; Kowal, Sabine

    2005-01-01

    Clark and Fox Tree (2002) have presented empirical evidence, based primarily on the London-Lund corpus (LL; Svartvik & Quirk, 1980), that the fillers "uh" and "um" are conventional English words that signal a speaker's intention to initiate a minor and a major delay, respectively. We present here empirical analyses of "uh" and "um" and of silent…

  11. Three families with 'de novo' m.3243A > G mutation.

    PubMed

    de Laat, Paul; Janssen, Mirian C H; Alston, Charlotte L; Taylor, Robert W; Rodenburg, Richard J T; Smeitink, Jan A M

    2016-12-01

    The m.3243A > G mutation is the most prevalent, disease-causing mitochondrial DNA (mtDNA) mutation. In a national cohort study of 48 families harbouring the m.3243A > G mutation, we identified three families in which the mutation appeared to occur sporadically within these families. In this report we describe these three families. Based on detailed mtDNA analysis of three different tissues using two different quantitative pyrosequencing assays with sensitivity to a level of 1% mutated mtDNA, we conclude that the m.3243A > G mutation has arisen de novo in each of these families. The symptomatic carriers presented with a variety of symptoms frequently observed in patients harbouring the m.3243A > G mutation. A more severe phenotype is seen in the de novo families compared to recent cohort studies, which might be due to reporting bias. The observation that de novo m.3243A > G mutations exist is of relevance for both diagnostic investigations and genetic counselling. Firstly, even where there is no significant (maternal) family history in patients with stroke-like episodes, diabetes and deafness or other unexplained organ dysfunction, the m.3243A > G mutation should be screened as a possible cause of the disease. Second, analysis of maternally-related family members is highly recommended to provide reliable counselling for these families, given that the m.3243A > G mutation may have arisen de novo. PMID:27331024

  12. De novo autoimmune hepatitis in liver transplant: State-of-the-art review.

    PubMed

    Vukotic, Ranka; Vitale, Giovanni; D'Errico-Grigioni, Antonia; Muratori, Luigi; Andreone, Pietro

    2016-03-14

    In the two past decades, a number of communications, case-control studies, and retrospective reports have appeared in the literature with concerns about the development of a complex set of clinical, laboratory and histological characteristics of a liver graft dysfunction that is compatible with autoimmune hepatitis. The de novo prefix was added to distinguish this entity from a pre-transplant primary autoimmune hepatitis, but the globally accepted criteria for the diagnosis of autoimmune hepatitis have been adopted in the diagnostic algorithm. Indeed, de novo autoimmune hepatitis is characterized by the typical liver necro-inflammation that is rich in plasma cells, the presence of interface hepatitis and the consequent laboratory findings of elevations in liver enzymes, increases in serum gamma globulin and the appearance of non-organ specific auto-antibodies. Still, the overall features of de novo autoimmune hepatitis appear not to be attributable to a univocal patho-physiological pathway because they can develop in the patients who have undergone liver transplantation due to different etiologies. Specifically, in subjects with hepatitis C virus recurrence, an interferon-containing antiviral treatment has been indicated as a potential inception of immune system derangement. Herein, we attempt to review the currently available knowledge about de novo liver autoimmunity and its clinical management. PMID:26973387

  13. De novo transcriptome assembly of the plant-parasitic nematode Rotylenchulus reniformis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rotylenchulus reniformis, commonly known as the reniform nematode, is a pathogen of cotton, soybean, and sweet potatoes in the Southeastern United States. An estimate of cotton production loss due to R. reniformis parasitism in the United States in 2011 was 279,000 bales. Here, we present a de novo...

  14. A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads.

    PubMed

    Mbandi, Stanley Kimbung; Hesse, Uljana; Rees, D Jasper G; Christoffels, Alan

    2014-01-01

    Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base quality scores to retain the read or a portion of it when the score is above a predefined threshold. It is difficult to differentiate sequencing error from biological variation without a reference using quality scores. The effects of quality score based trimming have not been systematically studied in de novo transcriptome assembly. Using RNA-Seq data produced from Illumina, we teased out the effects of quality score based filtering or trimming on de novo transcriptome reconstruction. We showed that assemblies produced from reads subjected to different quality score thresholds contain truncated and missing transfrags when compared to those from untrimmed reads. Our data supports the fact that de novo assembling of untrimmed data is challenging for de Bruijn graph assemblers. However, our results indicates that comparing the assemblies from untrimmed and trimmed read subsets can suggest appropriate filtering parameters and enable selection of the optimum de novo transcriptome assembly in non-model organisms. PMID:24575122

  15. Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution.

    PubMed

    Moyers, Bryan A; Zhang, Jianzhi

    2016-05-01

    The source of genetic novelty is an area of wide interest and intense investigation. Although gene duplication is conventionally thought to dominate the production of new genes, this view was recently challenged by a proposal of widespread de novo gene origination in eukaryotic evolution. Specifically, distributions of various gene properties such as coding sequence length, expression level, codon usage, and probability of being subject to purifying selection among groups of genes with different estimated ages were reported to support a model in which new protein-coding proto-genes arise from noncoding DNA and gradually integrate into cellular networks. Here we show that the genomic patterns asserted to support widespread de novo gene origination are largely attributable to biases in gene age estimation by phylostratigraphy, because such patterns are also observed in phylostratigraphic analysis of simulated genes bearing identical ages. Furthermore, there is no evidence of purifying selection on very young de novo genes previously claimed to show such signals. Together, these findings are consistent with the prevailing view that de novo gene birth is a relatively minor contributor to new genes in genome evolution. They also illustrate the danger of using phylostratigraphy in the study of new gene origination without considering its inherent bias. PMID:26758516

  16. De novo erectile dysfunction after anterior urethroplasty: a systematic review and meta-analysis

    PubMed Central

    Blaschko, Sarah D.; Sanford, Melissa T.; Cinman, Nadya M.; McAninch, Jack W.; Breyer, Benjamin N.

    2013-01-01

    Objective To evaluate the likelihood of developing de novo erectile dysfunction (ED) after anterior urethroplasty and to determine if this likelihood is influenced by age, stricture length, number of previous procedures or timing of evaluation. Materials and Methods PubMed, Embase, Cochrane, and Google Scholar databases were searched for the terms `urethroplasty', `urethral obstruction', `urethral stricture', `sexual function', `erection', `erectile function', `erectile dysfunction', `impotence' and `sexual dysfunction'. Two reviewers evaluated articles for inclusion based on predetermined criteria. Results In a meta-analysis of 36 studies with a total of 2323 patients, de novo ED was rare, with an incidence of 1%. In studies that assessed postoperative erectile function at more than one time point, ED was transient and resolved at between 6 and 12 months in 86% of cases. Conclusions Men should be counselled regarding the possibility of transient or permanent de novo ED after anterior urethroplasty procedures. Increasing mean age was associated with an increased likelihood of de novo ED, but this was not statistically significant. PMID:23924424

  17. De Novo Genome Assembly of Grapevine Yellow Speckle Viroid 1 from a Grapevine Transcriptome

    PubMed Central

    Jo, Yeonhwa; Choi, Hoseong; Yoon, Ju-Yeon; Choi, Seung-Kook

    2015-01-01

    Grapevine yellow speckle viroid 1 (GYSVd1), which is a member of the genus Apscaviroid, causes yellow speckle disease in grapevines. Here, we report the complete de novo genome assembly of GYSVd1 from the grapevine transcriptome and identified 10 single nucleotide polymorphisms of GYSVd1 across the grapevine populations. PMID:25999581

  18. De novo mutations from sporadic schizophrenia cases highlight important signaling genes in an independent sample.

    PubMed

    Kranz, Thorsten M; Harroch, Sheila; Manor, Orly; Lichtenberg, Pesach; Friedlander, Yechiel; Seandel, Marco; Harkavy-Friedman, Jill; Walsh-Messinger, Julie; Dolgalev, Igor; Heguy, Adriana; Chao, Moses V; Malaspina, Dolores

    2015-08-01

    Schizophrenia is a debilitating syndrome with high heritability. Genomic studies reveal more than a hundred genetic variants, largely nonspecific and of small effect size, and not accounting for its high heritability. De novo mutations are one mechanism whereby disease related alleles may be introduced into the population, although these have not been leveraged to explore the disease in general samples. This paper describes a framework to find high impact genes for schizophrenia. This study consists of two different datasets. First, whole exome sequencing was conducted to identify disruptive de novo mutations in 14 complete parent-offspring trios with sporadic schizophrenia from Jerusalem, which identified 5 sporadic cases with de novo gene mutations in 5 different genes (PTPRG, TGM5, SLC39A13, BTK, CDKN3). Next, targeted exome capture of these genes was conducted in 48 well-characterized, unrelated, ethnically diverse schizophrenia cases, recruited and characterized by the same research team in New York (NY sample), which demonstrated extremely rare and potentially damaging variants in three of the five genes (MAF<0.01) in 12/48 cases (25%); including PTPRG (5 cases), SCL39A13 (4 cases) and TGM5 (4 cases), a higher number than usually identified by whole exome sequencing. Cases differed in cognition and illness features based on which mutation-enriched gene they carried. Functional de novo mutations in protein-interaction domains in sporadic schizophrenia can illuminate risk genes that increase the propensity to develop schizophrenia across ethnicities. PMID:26091878

  19. De novo-synthesized ceramide is involved in cannabinoid-induced apoptosis.

    PubMed Central

    Gómez del Pulgar, Teresa; Velasco, Guillermo; Sánchez, Cristina; Haro, Amador; Guzmán, Manuel

    2002-01-01

    Delta(9)-Tetrahydrocannabinol (THC) and other cannabinoids have been shown to induce apoptosis of glioma cells via ceramide generation. In the present study, we investigated the metabolic origin of the ceramide responsible for this cannabinoid-induced apoptosis by using two subclones of C6 glioma cells: C6.9, which is sensitive to THC-induced apoptosis; and C6.4, which is resistant to THC-induced apoptosis. Pharmacological inhibition of ceramide synthesis de novo, but not of neutral and acid sphingomyelinases, prevented THC-induced apoptosis in C6.9 cells. The activity of serine palmitoyltransferase (SPT), which catalyses the rate-limiting step of ceramide synthesis de novo, was remarkably enhanced by THC in C6.9 cells, but not in C6.4 cells. However, no major changes in SPT mRNA and protein levels were evident. Changes in SPT activity paralleled changes in ceramide levels. Pharmacological inhibition of ceramide synthesis de novo also prevented the stimulation of extracellular-signal-regulated kinase and the inhibition of protein kinase B triggered by cannabinoids. These findings show that de novo-synthesized ceramide is involved in cannabinoid-induced apoptosis of glioma cells. PMID:11903061

  20. A framework for the interpretation of de novo mutation in human disease

    PubMed Central

    Samocha, Kaitlin E.; Robinson, Elise B.; Sanders, Stephan J.; Stevens, Christine; Sabo, Aniko; McGrath, Lauren M.; Kosmicki, Jack A.; Rehnström, Karola; Mallick, Swapan; Kirby, Andrew; Wall, Dennis P.; MacArthur, Daniel G.; Gabriel, Stacey B.; dePristo, Mark; Purcell, Shaun M.; Palotie, Aarno; Boerwinkle, Eric; Buxbaum, Joseph D.; Cook, Edwin H.; Gibbs, Richard A.; Schellenberg, Gerard D.; Sutcliffe, James S.; Devlin, Bernie; Roeder, Kathryn; Neale, Benjamin M.; Daly, Mark J.

    2014-01-01

    Spontaneously arising (‘de novo’) mutations play an important role in medical genetics. For diseases with extensive locus heterogeneity – such as autism spectrum disorders (ASDs) – the signal from de novo mutations (DNMs) is distributed across many genes, making it difficult to distinguish disease-relevant mutations from background variation. We provide a statistical framework for the analysis of DNM excesses per gene and gene set by calibrating a model of de novo mutation. We applied this framework to DNMs collected from 1,078 ASD trios and – while affirming a significant role for loss-of-function (LoF) mutations – found no excess of de novo LoF mutations in cases with IQ above 100, suggesting that the role of DNMs in ASD may reside in fundamental neurodevelopmental processes. We also used our model to identify ~1,000 genes that are significantly lacking functional coding variation in non-ASD samples and are enriched for de novo LoF mutations identified in ASD cases. PMID:25086666

  1. Quantitative analysis of purine nucleotides indicates that purinosomes increase de novo purine biosynthesis.

    PubMed

    Zhao, Hong; Chiaro, Christopher R; Zhang, Limin; Smith, Philip B; Chan, Chung Yu; Pedley, Anthony M; Pugh, Raymond J; French, Jarrod B; Patterson, Andrew D; Benkovic, Stephen J

    2015-03-13

    Enzymes in the de novo purine biosynthesis pathway are recruited to form a dynamic metabolic complex referred to as the purinosome. Previous studies have demonstrated that purinosome assembly responds to purine levels in culture medium. Purine-depleted medium or 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole (DMAT) treatment stimulates the purinosome assembly in HeLa cells. Here, several metabolomic technologies were applied to quantify the static cellular levels of purine nucleotides and measure the de novo biosynthesis rate of IMP, AMP, and GMP. Direct comparison of purinosome-rich cells (cultured in purine-depleted medium) and normal cells showed a 3-fold increase in IMP concentration in purinosome-rich cells and similar levels of AMP, GMP, and ratios of AMP/GMP and ATP/ADP for both. In addition, a higher level of IMP was also observed in HeLa cells treated with DMAT. Furthermore, increases in the de novo IMP/AMP/GMP biosynthetic flux rate under purine-depleted condition were observed. The synthetic enzymes, adenylosuccinate synthase (ADSS) and inosine monophosphate dehydrogenase (IMPDH), downstream of IMP were also shown to be part of the purinosome. Collectively, these results provide further evidence that purinosome assembly is directly related to activated de novo purine biosynthesis, consistent with the functionality of the purinosome. PMID:25605736

  2. Quantitative Analysis of Purine Nucleotides Indicates That Purinosomes Increase de Novo Purine Biosynthesis*♦

    PubMed Central

    Zhao, Hong; Chiaro, Christopher R.; Zhang, Limin; Smith, Philip B.; Chan, Chung Yu; Pedley, Anthony M.; Pugh, Raymond J.; French, Jarrod B.; Patterson, Andrew D.; Benkovic, Stephen J.

    2015-01-01

    Enzymes in the de novo purine biosynthesis pathway are recruited to form a dynamic metabolic complex referred to as the purinosome. Previous studies have demonstrated that purinosome assembly responds to purine levels in culture medium. Purine-depleted medium or 2-dimethylamino-4,5,6,7-tetrabromo-1H-benzimidazole (DMAT) treatment stimulates the purinosome assembly in HeLa cells. Here, several metabolomic technologies were applied to quantify the static cellular levels of purine nucleotides and measure the de novo biosynthesis rate of IMP, AMP, and GMP. Direct comparison of purinosome-rich cells (cultured in purine-depleted medium) and normal cells showed a 3-fold increase in IMP concentration in purinosome-rich cells and similar levels of AMP, GMP, and ratios of AMP/GMP and ATP/ADP for both. In addition, a higher level of IMP was also observed in HeLa cells treated with DMAT. Furthermore, increases in the de novo IMP/AMP/GMP biosynthetic flux rate under purine-depleted condition were observed. The synthetic enzymes, adenylosuccinate synthase (ADSS) and inosine monophosphate dehydrogenase (IMPDH), downstream of IMP were also shown to be part of the purinosome. Collectively, these results provide further evidence that purinosome assembly is directly related to activated de novo purine biosynthesis, consistent with the functionality of the purinosome. PMID:25605736

  3. De novo assembly of a bell pepper endornavirus genome sequence using RNA sequencing data.

    PubMed

    Jo, Yeonhwa; Choi, Hoseng; Cho, Won Kyong

    2015-01-01

    The genus Endornavirus is a double-stranded RNA virus that infects a wide range of hosts. In this study, we report on the de novo assembly of a bell pepper endornavirus genome sequence by RNA sequencing (RNA-Seq). Our result demonstrates the successful application of RNA-Seq to obtain a complete viral genome sequence from the transcriptome data. PMID:25792042

  4. Identification of a de novo DYNC1H1 mutation via WES according to published guidelines

    PubMed Central

    Ding, Dongxue; Chen, Zhao; Li, Kai; Long, Zhe; Ye, Wei; Tang, Zhaoli; Xia, Kun; Qiu, Rong; Tang, Beisha; Jiang, Hong

    2016-01-01

    De novo mutations that contribute to rare Mendelian diseases, including neurological disorders, have been recently identified. Whole-exome sequencing (WES) has become a powerful tool for the identification of inherited and de novo mutations in Mendelian diseases. Two important guidelines were recently published regarding the investigation of causality of sequence variant in human disease and the interpretation of novel variants identified in human genome sequences. In this study, a family with supposed movement disorders was sequenced via WES (including the proband and her unaffected parents), and a standard investigation and interpretation of the identified variants was performed according to the published guidelines. We identified a novel de novo mutation (c.2327C > T, p.P776L) in DYNC1H1 gene and confirmed that it was the causal variant. The phenotype of the affected twins included delayed motor milestones, pes cavus, lower limb weakness and atrophy, and a waddling gait. Electromyographic (EMG) recordings revealed typical signs of chronic denervation. Our study demonstrates the power of WES to discover the de novo mutations associated with a neurological disease on the whole exome scale, and guidelines to conduct WES studies and interpret of identified variants are a preferable option for the exploration of the pathogenesis of rare neurological disorders. PMID:26846447

  5. De novo synthesis of phenolic dihydroxanthene near-infrared emitting fluorophores.

    PubMed

    Richard, Jean-Alexandre

    2015-08-14

    We report a flexible de novo synthesis of phenolic dihydroxanthene fluorophores. The synthesis relies on a one-pot formation of an aldehyde intermediate which can be diversified in 60-70% overall yield, providing an efficient access to this family of near-infrared emitting fluorophores. PMID:26146358

  6. De novo reconstruction of plant RNA and DNA virus genomes from viral siRNAs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In antiviral defense, plants produce massive quantities of 21-24 nucleotide siRNAs. Here we demonstrate that the complete genomes of DNA and RNA viruses and viroids can be reconstructed by deep sequencing and de novo assembly of viral/viroid siRNAs from experimentally- and naturally-infected plants....

  7. KEY PARAMETERS FOR DE NOVO FORMATION OF POLYCHLORINATED DIBENZO-P-DIOXINS AND DIBENZOFURANS

    EPA Science Inventory

    De novo formation of polychlorinated- dibenzo-p-dioxins and dibenzofurans (PCDDs and PCDFs) was investigated in an Entrained Flow Reactor (EFR) to simulate combustion conditions. The parameters investigated were carbon content and nature in fly ash; type of gas- phase environment...

  8. Thermogravimetric desorption and de novo tests I: method development and validation.

    PubMed

    Tsytsik, Palina; Czech, Jan; Carleer, Robert; Reggers, Guy; Buekens, Alfons

    2008-08-01

    Thermogravimetric analysis (TGA) has been combined with evolved gas analysis (EGA) with the purpose of simulating the thermal behaviour of filter dust samples under inert (desorption) and de novo test oxidising conditions. Emphasis is on studying de novo formation of dioxins, surrogates and precursors arising from filter dust derived from thermal processes, such as municipal solid waste incineration and metallurgy. A new method is tested for sampling and analysing dioxin surrogates and precursors in the TGA effluent, which are collected on sampling tubes; the adsorbed compounds are eventually desorbed and quantified by TD-GC-MS. The major sources of error and losses are considered, including potential sorbent artefacts, possible breakthrough of volatiles through sampling tubes, or eventual losses of semi-volatiles due to their incomplete desorption or re-condensation inside the TG Analyser. The method is optimised and validated for di- to hexa-chlorinated benzenes in a range of 10-1000 ppb with average recovery exceeding 85%. The results are compared with data obtained in similar studies, performed by other research groups. As a result, the method provides the means for simulating de novo synthesis of dioxins in fly-ash and facilitates reliable and easy estimation of de novo activity, comparable with results of other studies, in combination with wide flexibility of testing conditions. PMID:18556042

  9. De novo transcript sequence reconstruction from RNA-Seq: reference generation and analysis with Trinity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol...

  10. Fragment-Based De Novo Design of Cyclin-Dependent Kinase 2 Inhibitors.

    PubMed

    Tripathi, Sunil Kumar; Singh, Poonam; Singh, Sanjeev Kumar

    2016-01-01

    Cyclin-dependent kinases (CDKs) are core components of the cell cycle machinery that govern the transition between phases during cell cycle progression. Abnormalities in CDKs activity and regulation are common features of cancer, making CDK family members attractive targets for the development of anticancer drugs. One of the main bottlenecks hampering the development of drugs for kinase is the difficulty to attain selectivity. A huge variety of small molecules have been reported as CDK inhibitors, as potential anticancer agents, but none of these has been approved for commercial use. Computer-based molecular design supports drug discovery by suggesting novel new chemotypes and compound modifications for lead candidate optimization. One of the methods known as de novo ligand design technique has emerged as a complementary approach to high-throughput screening. Several automated de novo software programs have been written, which automatically design novel structures to perfectly fit in known binding site. The de novo design supports drug discovery assignments by generating novel pharmaceutically active agents with desired properties in a cost as well as time efficient approach. This chapter describes procedure and an overview of computer-based molecular de novo design methods on a conceptual level with successful examples of CDKs inhibitors. PMID:26231707