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Sample records for intact coding region

  1. Intact coding region of the serotonin transporter gene in obsessive-compulsive disorder

    SciTech Connect

    Altemus, M.; Murphy, D.L.; Greenberg, B.; Lesch, K.P.

    1996-07-26

    Epidemiologic studies indicate that obsessive-compulsive disorder is genetically transmitted in some families, although no genetic abnormalities have been identified in individuals with this disorder. The selective response of obsessive-compulsive disorder to treatment with agents which block serotonin reuptake suggests the gene coding for the serotonin transporter as a candidate gene. The primary structure of the serotonin-transporter coding region was sequenced in 22 patients with obsessive-compulsive disorder, using direct PCR sequencing of cDNA synthesized from platelet serotonin-transporter mRNA. No variations in amino acid sequence were found among the obsessive-compulsive disorder patients or healthy controls. These results do not support a role for alteration in the primary structure of the coding region of the serotonin-transporter gene in the pathogenesis of obsessive-compulsive disorder. 27 refs.

  2. 46 CFR 170.165 - International Code on Intact Stability.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 7 2013-10-01 2013-10-01 false International Code on Intact Stability. 170.165 Section... STABILITY REQUIREMENTS FOR ALL INSPECTED VESSELS Intact Stability Criteria § 170.165 International Code on...) through (4) of this section, must comply with the Introduction and Part A of the International Code...

  3. 46 CFR 170.165 - International Code on Intact Stability.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 7 2014-10-01 2014-10-01 false International Code on Intact Stability. 170.165 Section... STABILITY REQUIREMENTS FOR ALL INSPECTED VESSELS Intact Stability Criteria § 170.165 International Code on...) through (4) of this section, must comply with the Introduction and Part A of the International Code...

  4. 46 CFR 170.165 - International Code on Intact Stability.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 7 2011-10-01 2011-10-01 false International Code on Intact Stability. 170.165 Section... STABILITY REQUIREMENTS FOR ALL INSPECTED VESSELS Intact Stability Criteria § 170.165 International Code on...) through (4) of this section, must comply with the Introduction and Part A of the International Code...

  5. 46 CFR 170.165 - International Code on Intact Stability.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 7 2012-10-01 2012-10-01 false International Code on Intact Stability. 170.165 Section... STABILITY REQUIREMENTS FOR ALL INSPECTED VESSELS Intact Stability Criteria § 170.165 International Code on...) through (4) of this section, must comply with the Introduction and Part A of the International Code...

  6. A mechanistic code for intact and defective nuclear fuel element performance

    NASA Astrophysics Data System (ADS)

    Shaheen, Khaled

    During reactor operation, nuclear fuel elements experience an environment featuring high radiation, temperature, and pressure. Predicting in-reactor performance of nuclear fuel elements constitutes a complex multi-physics problem, one that requires numerical codes to be solved. Fuel element performance codes have been developed for different reactor and fuel designs. Most of these codes simulate fuel elements using one-or quasi-two-dimensional geometries, and some codes are only applicable to steady state but not transient behaviour and vice versa. Moreover, while many conceptual and empirical separate-effects models exist for defective fuel behaviour, wherein the sheath is breached allowing coolant ingress and fission gas escape, there have been few attempts to predict defective fuel behaviour in the context of a mechanistic fuel performance code. Therefore, a mechanistic fuel performance code, called FORCE (Fuel Operational peRformance Computations in an Element) is proposed for the time-dependent behaviour of intact and defective CANDU nuclear fuel elements. The code, which is implemented in the COMSOL Multiphysics commercial software package, simulates the fuel, sheath, and fuel-to-sheath gap in a radial-axial geometry. For intact fuel performance, the code couples models for heat transport, fission gas production and diffusion, and structural deformation of the fuel and sheath. The code is extended to defective fuel performance by integrating an adapted version of a previously developed fuel oxidation model, and a model for the release of radioactive fission product gases from the fuel to the coolant. The FORCE code has been verified against the ELESTRES-IST and ELESIM industrial code for its predictions of intact fuel performance. For defective fuel behaviour, the code has been validated against coulometric titration data for oxygen-to-metal ratio in defective fuel elements from commercial reactors, while also being compared to a conceptual oxidation model

  7. Deleting the Redundant TSH Receptor C-Peptide Region Permits Generation of the Conformationally Intact Extracellular Domain by Insect Cells.

    PubMed

    Chen, Chun-Rong; Salazar, Larry M; McLachlan, Sandra M; Rapoport, Basil

    2015-07-01

    The TSH receptor (TSHR) extracellular domain (ECD) comprises a N-terminal leucine-rich repeat domain and an hinge region (HR), the latter contributing to ligand binding and critical for receptor activation. The crystal structure of the leucine-rich repeat domain component has been solved, but previous attempts to generate conformationally intact complete ECD or the isolated HR component for structural analysis have failed. The TSHR HR contains a C-peptide segment that is removed during spontaneous TSHR intramolecular cleavage into disulfide linked A- and B-subunits. We hypothesized that deletion of the redundant C-peptide would overcome the obstacle to generating conformationally intact TSHR ECD protein. Indeed, lacking the C-peptide region, the TSHR ECD (termed ECD-D1) and the isolated HR (termed HR-D1) were secreted into medium of insect cells infected with baculoviruses coding for these modified proteins. The identities of TSHR ECD-D1 and HR-D1 were confirmed by ELISA and immunoblotting using TSHR-specific monoclonal antibodies. The TSHR-ECD-D1 in conditioned medium was folded correctly, as demonstrated by its ability to inhibit radiolabeled TSH binding to the TSH holoreceptor. The TSHR ECD-D1 purification was accomplished in a single step using a TSHR monoclonal antibody affinity column, whereas the HR-D1 required a multistep protocol with a low yield. In conclusion, we report a novel approach to generate the TSHR ECD, as well as the isolated HR in insect cells, the former in sufficient amounts for structural studies. However, such studies will require previous complexing of the ECD with a ligand such as TSH or a thyroid-stimulating antibody. PMID:25860033

  8. Characterization of microsatellites in the coding regions

    SciTech Connect

    Tuskan, Gerald A; Li, Shuxian; Yin, Tongming; Wang, Prof. Mingxiu

    2009-01-01

    With the development of high-throughput sequencing techniques, transcriptome sequencing projects which provide valuable resources for designing simple sequence repeat (SSR) primers have been carried out for many plants. However, the utility of SSRs for molecular breeding depends on genomewide distribution and coverage, as well as moderately high allelic variability, in the available SSR library. In this study, we characterized the exonic SSRs developed from the publicly available Populus genome as a case study to determine their value for molecular breeding. As expected, our results confirmed that microsatellites occurred approximately three times less often in coding regions than in non-coding regions. Mutability test also showed that exonic SSRs contained less allelic variability than intronic SSRs. More importantly, exonic SSRs were unevenly distributed both among and within chromosomes. Large exonic SSRs deserts were observed on several chromosomes. Differential selection between paralogous chromosomes, at the gene level, appears to be responsible for these SSR deserts, though the mechanisms that cause chromosome-specific SSR deserts are not known. This work provides ample evidence that the candidate gene approach based on unigenes identified from transcribed sequences may not be the best strategy to identify highly polymorphic SSRs.

  9. Correlation approach to identify coding regions in DNA sequences

    NASA Technical Reports Server (NTRS)

    Ossadnik, S. M.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1994-01-01

    Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.

  10. Tricyclic antidepressant treatment evokes regional changes in neurotrophic factors over time within the intact and degenerating nigrostriatal system

    PubMed Central

    Paumier, Katrina L.; Sortwell, Caryl E.; Madhavan, Lalitha; Terpstra, Brian; Daley, Brian F.; Collier, Timothy J.

    2015-01-01

    In addition to alleviating depression, trophic responses produced by antidepressants may regulate neural plasticity in the diseased brain, providing not only symptomatic benefit but potentially slowing the rate of disease progression in Parkinson’s disease (PD). Recent in vitro and in vivo data provide evidence that neurotrophic factors such as brain derived-neurotrophic factor (BDNF) and glial cell line-derived neurotrophic factor (GDNF) may be key mediators of the therapeutic response to antidepressants. As such, we conducted a cross-sectional time-course study to determine whether antidepressant-mediated changes in neurotrophic factors occur in relevant brain regions in response to amitriptyline (AMI) treatment before and after intrastriatal 6-hydroxydopamine (6OHDA). Adult male Wistar rats were divided into seven cohorts and given daily injections (i.p.) of AMI (5mg/kg) or saline throughout the duration of the study. In parallel, various cohorts of intact or parkinsonian animals were sacrificed at specific time points to determine the impact of AMI treatment on trophic factor levels in the intact and degenerating nigrostriatal system. The left and right hemispheres of the substantia nigra, striatum, frontal cortex, piriform cortex, hippocampus and anterior cingulate cortex were dissected and BDNF and GDNF levels were measured with ELISA. Results show that chronic AMI treatment elicits effects in multiple brain regions and differentially regulates levels of BDNF and GDNF depending on the region. Additionally, AMI halts the progressive degeneration of dopamine (DA) neurons elicited by an intrastriatal 6-OHDA lesion. Taken together, these results suggest that AMI treatment elicits significant trophic changes important to DA neuron survival within both the intact and degenerating nigrostriatal system. PMID:25681575

  11. A gridded global data set of soil, intact regolith, and sedimentary deposit thicknesses for regional and global land surface modeling

    NASA Astrophysics Data System (ADS)

    Pelletier, Jon D.; Broxton, Patrick D.; Hazenberg, Pieter; Zeng, Xubin; Troch, Peter A.; Niu, Guo-Yue; Williams, Zachary; Brunke, Michael A.; Gochis, David

    2016-03-01

    Earth's terrestrial near-subsurface environment can be divided into relatively porous layers of soil, intact regolith, and sedimentary deposits above unweathered bedrock. Variations in the thicknesses of these layers control the hydrologic and biogeochemical responses of landscapes. Currently, Earth System Models approximate the thickness of these relatively permeable layers above bedrock as uniform globally, despite the fact that their thicknesses vary systematically with topography, climate, and geology. To meet the need for more realistic input data for models, we developed a high-resolution gridded global data set of the average thicknesses of soil, intact regolith, and sedimentary deposits within each 30 arcsec (˜1 km) pixel using the best available data for topography, climate, and geology as input. Our data set partitions the global land surface into upland hillslope, upland valley bottom, and lowland landscape components and uses models optimized for each landform type to estimate the thicknesses of each subsurface layer. On hillslopes, the data set is calibrated and validated using independent data sets of measured soil thicknesses from the U.S. and Europe and on lowlands using depth to bedrock observations from groundwater wells in the U.S. We anticipate that the data set will prove useful as an input to regional and global hydrological and ecosystems models. This article was corrected on 2 FEB 2016. See the end of the full text for details.

  12. Code for Calculating Regional Seismic Travel Time

    SciTech Connect

    BALLARD, SANFORD; HIPP, JAMES; & BARKER, GLENN

    2009-07-10

    The RSTT software computes predictions of the travel time of seismic energy traveling from a source to a receiver through 2.5D models of the seismic velocity distribution within the Earth. The two primary applications for the RSTT library are tomographic inversion studies and seismic event location calculations. In tomographic inversions studies, a seismologist begins with number of source-receiver travel time observations and an initial starting model of the velocity distribution within the Earth. A forward travel time calculator, such as the RSTT library, is used to compute predictions of each observed travel time and all of the residuals (observed minus predicted travel time) are calculated. The Earth model is then modified in some systematic way with the goal of minimizing the residuals. The Earth model obtained in this way is assumed to be a better model than the starting model if it has lower residuals. The other major application for the RSTT library is seismic event location. Given an Earth model, an initial estimate of the location of a seismic event, and some number of observations of seismic travel time thought to have originated from that event, location codes systematically modify the estimate of the location of the event with the goal of minimizing the difference between the observed and predicted travel times. The second application, seismic event location, is routinely implemented by the military as part of its effort to monitor the Earth for nuclear tests conducted by foreign countries.

  13. Code for Calculating Regional Seismic Travel Time

    Energy Science and Technology Software Center (ESTSC)

    2009-07-10

    The RSTT software computes predictions of the travel time of seismic energy traveling from a source to a receiver through 2.5D models of the seismic velocity distribution within the Earth. The two primary applications for the RSTT library are tomographic inversion studies and seismic event location calculations. In tomographic inversions studies, a seismologist begins with number of source-receiver travel time observations and an initial starting model of the velocity distribution within the Earth. A forwardmore » travel time calculator, such as the RSTT library, is used to compute predictions of each observed travel time and all of the residuals (observed minus predicted travel time) are calculated. The Earth model is then modified in some systematic way with the goal of minimizing the residuals. The Earth model obtained in this way is assumed to be a better model than the starting model if it has lower residuals. The other major application for the RSTT library is seismic event location. Given an Earth model, an initial estimate of the location of a seismic event, and some number of observations of seismic travel time thought to have originated from that event, location codes systematically modify the estimate of the location of the event with the goal of minimizing the difference between the observed and predicted travel times. The second application, seismic event location, is routinely implemented by the military as part of its effort to monitor the Earth for nuclear tests conducted by foreign countries.« less

  14. Fast functional imaging of multiple brain regions in intact zebrafish larvae using selective plane illumination microscopy.

    PubMed

    Panier, Thomas; Romano, Sebastián A; Olive, Raphaël; Pietri, Thomas; Sumbre, Germán; Candelier, Raphaël; Debrégeas, Georges

    2013-01-01

    The optical transparency and the small dimensions of zebrafish at the larval stage make it a vertebrate model of choice for brain-wide in-vivo functional imaging. However, current point-scanning imaging techniques, such as two-photon or confocal microscopy, impose a strong limit on acquisition speed which in turn sets the number of neurons that can be simultaneously recorded. At 5 Hz, this number is of the order of one thousand, i.e., approximately 1-2% of the brain. Here we demonstrate that this limitation can be greatly overcome by using Selective-plane Illumination Microscopy (SPIM). Zebrafish larvae expressing the genetically encoded calcium indicator GCaMP3 were illuminated with a scanned laser sheet and imaged with a camera whose optical axis was oriented orthogonally to the illumination plane. This optical sectioning approach was shown to permit functional imaging of a very large fraction of the brain volume of 5-9-day-old larvae with single- or near single-cell resolution. The spontaneous activity of up to 5,000 neurons was recorded at 20 Hz for 20-60 min. By rapidly scanning the specimen in the axial direction, the activity of 25,000 individual neurons from 5 different z-planes (approximately 30% of the entire brain) could be simultaneously monitored at 4 Hz. Compared to point-scanning techniques, this imaging strategy thus yields a ≃20-fold increase in data throughput (number of recorded neurons times acquisition rate) without compromising the signal-to-noise ratio (SNR). The extended field of view offered by the SPIM method allowed us to directly identify large scale ensembles of neurons, spanning several brain regions, that displayed correlated activity and were thus likely to participate in common neural processes. The benefits and limitations of SPIM for functional imaging in zebrafish as well as future developments are briefly discussed. PMID:23576959

  15. Characterization of regional deformation and material properties of the intact explanted vein by microCT and computational analysis

    PubMed Central

    Gomez, Arnold David; Zou, Huashan; Shiu, Yan-Ting; Hsu, Edward W.

    2014-01-01

    Purpose Detailed mechanical information of the vein is important to better understand remodeling of the vessel in disease states, but has been difficult to obtain due to its thinness, unique geometry, and limitations of mechanical testing. This study presents a novel method for characterizing deformation of the intact explanted vein under physiological loads and determining its material properties by combining high-resolution imaging and computational analysis. Methods High-resolution CT (microCT) was used to image an iodine-stained, excised porcine internal jugular vein sample under extension to 100% and 120% of in situ length, and inflation and 2, 10, 20 mmHg of pressure, inside a microCT-compatible hydrostatic loading chamber. Regional strains were measured with the finite element (FE) image registration method known as Hyperelastic Warping. Material properties were approximated with inverse FE characterization by optimizing stiffness-related coefficients so to match simulated strains to the experimental measurements. Results The observed morphology and regional strain of the vein were found to be relatively heterogeneous. The regional variability in the measured strain was primarily driven by geometry. Although iodine treatment may result in tissue stiffening, which requires additional investigation, it is effective in allowing detailed detection of vein geometry. Conclusions The feasibility and utility of using microCT and computational analysis to characterize mechanical responses and material properties of the vein were demonstrated. The presented method is a promising alternative or addition to mechanical testing for characterizing veins or other similarly delicate vessels in their native anatomical configuration under a wide range of realistic or simulated environmental and loading conditions. PMID:25541587

  16. CRITICA: coding region identification tool invoking comparative analysis

    NASA Technical Reports Server (NTRS)

    Badger, J. H.; Olsen, G. J.; Woese, C. R. (Principal Investigator)

    1999-01-01

    Gene recognition is essential to understanding existing and future DNA sequence data. CRITICA (Coding Region Identification Tool Invoking Comparative Analysis) is a suite of programs for identifying likely protein-coding sequences in DNA by combining comparative analysis of DNA sequences with more common noncomparative methods. In the comparative component of the analysis, regions of DNA are aligned with related sequences from the DNA databases; if the translation of the aligned sequences has greater amino acid identity than expected for the observed percentage nucleotide identity, this is interpreted as evidence for coding. CRITICA also incorporates noncomparative information derived from the relative frequencies of hexanucleotides in coding frames versus other contexts (i.e., dicodon bias). The dicodon usage information is derived by iterative analysis of the data, such that CRITICA is not dependent on the existence or accuracy of coding sequence annotations in the databases. This independence makes the method particularly well suited for the analysis of novel genomes. CRITICA was tested by analyzing the available Salmonella typhimurium DNA sequences. Its predictions were compared with the DNA sequence annotations and with the predictions of GenMark. CRITICA proved to be more accurate than GenMark, and moreover, many of its predictions that would seem to be errors instead reflect problems in the sequence databases. The source code of CRITICA is freely available by anonymous FTP (rdp.life.uiuc.edu in/pub/critica) and on the World Wide Web (http:/(/)rdpwww.life.uiuc.edu).

  17. New gene coding regions from the horn fly, Haematobia irritans

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We used an EST approach to isolate new gene coding regions from the horn fly, Haematobia irritans. Two sources of expressed gene sequences were utilized. First, a subtracted library was synthesized from adult mixed sex fly cDNA of an organophosphate and pyrethroid resistant population of flies subtr...

  18. Internalin of Listeria monocytogenes with an intact leucine-rich repeat region is sufficient to promote internalization.

    PubMed Central

    Lecuit, M; Ohayon, H; Braun, L; Mengaud, J; Cossart, P

    1997-01-01

    Listeria monocytogenes can use two different surface proteins, internalin (InlA) and InlB, to invade mammalian cells. The exact role of these invasiveness factors in vivo remains to be determined. In cultured cells, InlA is necessary to promote Listeria entry into human epithelial cells, such as Caco-2 cells, whereas InlB is necessary to promote Listeria internalization in several other cell types, including hepatocytes, fibroblasts, and epithelioid cells, such as Vero, HeLa, CHO, or Hep-2 cells. We have recently reported that the InlA receptor on Caco-2 cells is the cell adhesion molecule E-cadherin and demonstrated that nonpermissive fibroblasts become permissive for internalin-mediated entry when transfected with the gene coding for LCAM, the chicken homolog of the human E-cadherin gene. In this study, we demonstrate for the first time that the internalin protein alone is sufficient to promote internalization into cells expressing its receptor. Indeed, internalin confers invasiveness to both Enterococcus faecalis and internalin-coated latex beads. As shown by transmission electron microscopy, these beads were phagocytosed via a "zipper" mechanism similar to that observed during the internalin-E-cadherin-mediated entry of Listeria. Moreover, a functional analysis of internalin demonstrates that its amino-terminal region, encompassing the leucine-rich repeat (LRR) region and the inter-repeat (IR) region, is necessary and sufficient to promote bacterial entry into cells expressing its receptor. Several lines of evidence suggest that the LRR region would interact directly with E-cadherin, whereas the IR region would be required for a proper folding of the LRR region. PMID:9393831

  19. Techniques for region coding in object-based image compression

    NASA Astrophysics Data System (ADS)

    Schmalz, Mark S.

    2004-01-01

    Object-based compression (OBC) is an emerging technology that combines region segmentation and coding to produce a compact representation of a digital image or video sequence. Previous research has focused on a variety of segmentation and representation techniques for regions that comprise an image. The author has previously suggested [1] partitioning of the OBC problem into three steps: (1) region segmentation, (2) region boundary extraction and compression, and (3) region contents compression. A companion paper [2] surveys implementationally feasible techniques for boundary compression. In this paper, we analyze several strategies for region contents compression, including lossless compression, lossy VPIC, EPIC, and EBLAST compression, wavelet-based coding (e.g., JPEG-2000), as well as texture matching approaches. This paper is part of a larger study that seeks to develop highly efficient compression algorithms for still and video imagery, which would eventually support automated object recognition (AOR) and semantic lookup of images in large databases or high-volume OBC-format datastreams. Example applications include querying journalistic archives, scientific or medical imaging, surveillance image processing and target tracking, as well as compression of video for transmission over the Internet. Analysis emphasizes time and space complexity, as well as sources of reconstruction error in decompressed imagery.

  20. Identification of protein coding regions in RNA transcripts

    PubMed Central

    Tang, Shiyuyun; Lomsadze, Alexandre; Borodovsky, Mark

    2015-01-01

    Massive parallel sequencing of RNA transcripts by next-generation technology (RNA-Seq) generates critically important data for eukaryotic gene discovery. Gene finding in transcripts can be done by statistical (alignment-free) as well as by alignment-based methods. We describe a new tool, GeneMarkS-T, for ab initio identification of protein-coding regions in RNA transcripts. The algorithm parameters are estimated by unsupervised training which makes unnecessary manually curated preparation of training sets. We demonstrate that (i) the unsupervised training is robust with respect to the presence of transcripts assembly errors and (ii) the accuracy of GeneMarkS-T in identifying protein-coding regions and, particularly, in predicting translation initiation sites in modelled as well as in assembled transcripts compares favourably to other existing methods. PMID:25870408

  1. EXTENSION OF THE EMPIRE CODE TO THE RESONANCE REGION.

    SciTech Connect

    CHO,Y.S.; HERMAN, M.; MUGHABGHAB, S.F.; OBLOZINSKY, P.; ROCHMAN, D.; LEE, Y.O.

    2007-04-22

    The preliminary version of a new module has been developed to be added to a nuclear reaction model code EMPIRE to allow for an evaluation of neutron cross sections in a resonance region. It automates most of the evaluation procedures and can be executed within EMPIRE or as a stand-alone program. The module includes a graphic user interface (GUI) and a number of codes and scripts that read individual, as well as average, resonance parameters from the Atlas of Neutron Resonances and other physical constants from RIPL-2, perform an analysis of the available resonances, carry out statistical distributions, and compute cross sections in resolved and unresolved resonance regions which are then compared with experimental data. The module also provides an ENDF-formatted file for a resonance region and various plots allowing for a verification of the procedure. The formatted file can be integrated later into the final ENDF-6 file as generated by the EMPIRE code. However, as a preliminary version, extensive testing and further improvements are needed before this new capability can be incorporated into the production version of EMPIRE.

  2. OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations.

    PubMed

    Mularoni, Loris; Sabarinathan, Radhakrishnan; Deu-Pons, Jordi; Gonzalez-Perez, Abel; López-Bigas, Núria

    2016-01-01

    Distinguishing the driver mutations from somatic mutations in a tumor genome is one of the major challenges of cancer research. This challenge is more acute and far from solved for non-coding mutations. Here we present OncodriveFML, a method designed to analyze the pattern of somatic mutations across tumors in both coding and non-coding genomic regions to identify signals of positive selection, and therefore, their involvement in tumorigenesis. We describe the method and illustrate its usefulness to identify protein-coding genes, promoters, untranslated regions, intronic splice regions, and lncRNAs-containing driver mutations in several malignancies. PMID:27311963

  3. BioCode: Two biologically compatible Algorithms for embedding data in non-coding and coding regions of DNA

    PubMed Central

    2013-01-01

    Background In recent times, the application of deoxyribonucleic acid (DNA) has diversified with the emergence of fields such as DNA computing and DNA data embedding. DNA data embedding, also known as DNA watermarking or DNA steganography, aims to develop robust algorithms for encoding non-genetic information in DNA. Inherently DNA is a digital medium whereby the nucleotide bases act as digital symbols, a fact which underpins all bioinformatics techniques, and which also makes trivial information encoding using DNA straightforward. However, the situation is more complex in methods which aim at embedding information in the genomes of living organisms. DNA is susceptible to mutations, which act as a noisy channel from the point of view of information encoded using DNA. This means that the DNA data embedding field is closely related to digital communications. Moreover it is a particularly unique digital communications area, because important biological constraints must be observed by all methods. Many DNA data embedding algorithms have been presented to date, all of which operate in one of two regions: non-coding DNA (ncDNA) or protein-coding DNA (pcDNA). Results This paper proposes two novel DNA data embedding algorithms jointly called BioCode, which operate in ncDNA and pcDNA, respectively, and which comply fully with stricter biological restrictions. Existing methods comply with some elementary biological constraints, such as preserving protein translation in pcDNA. However there exist further biological restrictions which no DNA data embedding methods to date account for. Observing these constraints is key to increasing the biocompatibility and in turn, the robustness of information encoded in DNA. Conclusion The algorithms encode information in near optimal ways from a coding point of view, as we demonstrate by means of theoretical and empirical (in silico) analyses. Also, they are shown to encode information in a robust way, such that mutations have isolated

  4. HLA-G coding region and 3'untranslated region (3'UTR) in two Chinese Han populations.

    PubMed

    Wang, Wen Yi; Tian, Wei; Liu, Xue Xiang; Li, Li Xin

    2016-08-01

    In this study, exons 2-4 and 3'untranslated region (3'UTR) of human leukocyte antigen (HLA)-G gene were investigated for 201 and 104 healthy unrelated Han samples recruited from Hunan Province, southern China and central Inner Mongolia Autonomous Region, northern China, respectively, using sequence-based typing and cloning methods. Totally 12 HLA-G alleles in the coding region, 9 variable sites in 3'UTR, 8 3'UTR haplotypes and 15 HLA-G extended haplotypes (EHs) incorporating the coding region and 3'UTR were observed. Very strong linkage disequilibrium (LD) was observed between HLA-A and HLA-G, and between HLA-G coding region and 3'UTR in each population (all global P=0.0000). Seven HLA-A-G haplotypes showed significant LD in both populations. Three HLA-G alleles in the coding region, 4 polymorphic sites in the 3'UTR, 3 3'UTR haplotypes and 4 HLA-G EHs differed significantly in their distributions between the 2 Chinese Han populations (all P≤0.0001). There was evidence for balancing selection acting on HLA-G 3'UTR positions +3010, +3142 and +3187 in the two populations. The NJ dendrograms demonstrated the existence of two basic HLA-G lineages and indicated that, HLA-G*01:01:01, the most common HLA-G allele, formed a separate lineage from other alleles. Our results shed new lights into HLA-G genetics among Chinese Han populations. The findings reported here are of importance for future studies related to post-transcriptional regulation of HLA-G allelic expression and the potential role of HLA-G in disease association in populations of Chinese ancestry. PMID:27262928

  5. [Comparison study on the methods for finding borders between coding and non-coding DNA regions in rice].

    PubMed

    Sun, Yi-Gang; Gao, Lei; Zhang, Zhong-Hua; Xue, Qing-Zhong

    2005-07-01

    Entropy-based divergence measures have provided an impelling tool in evaluating sequence complexity, predicting CpG island, and detecting borders between coding and non-coding DNA regions etc. In this paper, two new divergence measures: the alpha-KL divergence and the alpha-Jensen-Shannon divergence were defined and a coarse-graining vector of amino acids- corresponding codons was proposed according to codons GC-content, in order to improve the computational approach to finding borders between coding and non-coding in rice. A comparison of the accuracies gained by different vectors (the Jensen-Shannon divergence, the Jensen-Renyi divergence, the alpha-KL divergence and the alpha-Jensen -Shannon divergence) showed that recognition efficiency based on the new information measures with the vector coarse-graining increase by 4-5 times than that of Bernaola's method in the 'stop codon' of coding regions in rice. PMID:16120591

  6. Spectrum of small mutations in the dystrophin coding region

    SciTech Connect

    Prior, T.W.; Bartolo, C.; Pearl, D.K.

    1995-07-01

    Duchenne and Becker muscular dystrophies (DMD and BMD) are caused by defects in the dystrophin gene. About two-thirds of the affected patients have large deletions or duplications, which occur in the 5` and central portion of the gene. The nondeletion/duplication cases are most likely the result of smaller mutations that cannot be identified by current diagnostic screening strategies. We screened {approximately} 80% of the dystrophin coding sequence for small mutations in 158 patients without deletions or duplications and identified 29 mutations. The study indicates that many of the DMD and the majority of the BMD small mutations lie in noncoding regions of the gene. All of the mutations identified were unique to single patients, and most of the mutations resulted in protein truncation. We did not find a clustering of small mutations similar to the deletion distribution but found > 40% of the small mutations 3` of exon 55. The extent of protein truncation caused by the 3` mutations did not determine the phenotype, since even the exon 76 nonsense mutation resulted in the severe DMD phenotype. Our study confirms that the dystrophin gene is subject to a high rate of mutation in CpG sequences. As a consequence of not finding any hotspots or prevalent small mutations, we conclude that it is presently not possible to perform direct carrier and prenatal diagnostics for many families without deletions or duplications. 71 refs., 2 figs., 2 tabs.

  7. Discrete Ramanujan transform for distinguishing the protein coding regions from other regions.

    PubMed

    Hua, Wei; Wang, Jiasong; Zhao, Jian

    2014-01-01

    Based on the study of Ramanujan sum and Ramanujan coefficient, this paper suggests the concepts of discrete Ramanujan transform and spectrum. Using Voss numerical representation, one maps a symbolic DNA strand as a numerical DNA sequence, and deduces the discrete Ramanujan spectrum of the numerical DNA sequence. It is well known that of discrete Fourier power spectrum of protein coding sequence has an important feature of 3-base periodicity, which is widely used for DNA sequence analysis by the technique of discrete Fourier transform. It is performed by testing the signal-to-noise ratio at frequency N/3 as a criterion for the analysis, where N is the length of the sequence. The results presented in this paper show that the property of 3-base periodicity can be only identified as a prominent spike of the discrete Ramanujan spectrum at period 3 for the protein coding regions. The signal-to-noise ratio for discrete Ramanujan spectrum is defined for numerical measurement. Therefore, the discrete Ramanujan spectrum and the signal-to-noise ratio of a DNA sequence can be used for distinguishing the protein coding regions from the noncoding regions. All the exon and intron sequences in whole chromosomes 1, 2, 3 and 4 of Caenorhabditis elegans have been tested and the histograms and tables from the computational results illustrate the reliability of our method. In addition, we have analyzed theoretically and gotten the conclusion that the algorithm for calculating discrete Ramanujan spectrum owns the lower computational complexity and higher computational accuracy. The computational experiments show that the technique by using discrete Ramanujan spectrum for classifying different DNA sequences is a fast and effective method. PMID:24787059

  8. JJ1017 image examination order codes: standardized codes supplementary to DICOM for imaging modality, region, and direction

    NASA Astrophysics Data System (ADS)

    Kimura, Michio; Kuranishi, Makoto; Sukenobu, Yoshiharu; Watanabe, Hiroki; Nakajima, Takashi; Morimura, Shinya; Kabata, Shun

    2002-05-01

    The DICOM standard includes non-image data information such as image study ordering data and performed procedure data, which are used for sharing information between HIS/RIS/PACS/modalities, which is essential for IHE. In order to bring such parts of the DICOM standard into force in Japan, a joint committee of JIRA and JAHIS (vendor associations) established JJ1017 management guideline. It specifies, for example, which items are legally required in Japan while remaining optional in the DICOM standard. Then, what should be used for the examination type, regional, and directional codes? Our investigation revealed that DICOM tables do not include items that are sufficiently detailed for use in Japan. This is because radiology departments (radiologists) in the US exercise greater discretion in image examination than in Japan, and the contents of orders from requesting physicians do not include the extra details used in Japan. Therefore, we have generated the JJ1017 code for these 3 codes for use based on the JJ1017 guidelines. The stem part of the JJ1017 code partially employs the DICOM codes in order to remain in line with the DICOM standard. JJ1017 codes are to be included not only in IHE-J specifications, also in Ministry recommendations of health data exchange.

  9. A Hydrochemical Hybrid Code for Astrophysical Problems. I. Code Verification and Benchmarks for a Photon-dominated Region (PDR)

    NASA Astrophysics Data System (ADS)

    Motoyama, Kazutaka; Morata, Oscar; Shang, Hsien; Krasnopolsky, Ruben; Hasegawa, Tatsuhiko

    2015-07-01

    A two-dimensional hydrochemical hybrid code, KM2, is constructed to deal with astrophysical problems that would require coupled hydrodynamical and chemical evolution. The code assumes axisymmetry in a cylindrical coordinate system and consists of two modules: a hydrodynamics module and a chemistry module. The hydrodynamics module solves hydrodynamics using a Godunov-type finite volume scheme and treats included chemical species as passively advected scalars. The chemistry module implicitly solves nonequilibrium chemistry and change of energy due to thermal processes with transfer of external ultraviolet radiation. Self-shielding effects on photodissociation of CO and H2 are included. In this introductory paper, the adopted numerical method is presented, along with code verifications using the hydrodynamics module and a benchmark on the chemistry module with reactions specific to a photon-dominated region (PDR). Finally, as an example of the expected capability, the hydrochemical evolution of a PDR is presented based on the PDR benchmark.

  10. Annotation of the Protein Coding Regions of the Equine Genome

    PubMed Central

    Hestand, Matthew S.; Kalbfleisch, Theodore S.; Coleman, Stephen J.; Zeng, Zheng; Liu, Jinze; Orlando, Ludovic; MacLeod, James N.

    2015-01-01

    Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From these, we derived the structures of 68,594 transcripts. In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2. Interestingly, 780 variants extend the open reading frame of the transcript and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons. PMID:26107351

  11. OrfPredictor: predicting protein-coding regions in EST-derived sequences.

    PubMed

    Min, Xiang Jia; Butler, Gregory; Storms, Reginald; Tsang, Adrian

    2005-07-01

    OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. OrfPredictor is available at https://fungalgenome.concordia.ca/tools/OrfPredictor.html. PMID:15980561

  12. Specific gene hypomethylation and cancer: New insights into coding region feature trends

    PubMed Central

    Daura-Oller, Elias; Cabre, Maria; Montero, Miguel A; Paternain, Jose L; Romeu, Antoni

    2009-01-01

    Giving coding region structural features a role in the hypomethylation of specific genes, the occurrence of G+C content, CpG islands, repeat and retrotransposable elements in demethylated genes related to cancer has been evaluated. A comparative analysis among different cancer types has also been performed. In this work, the inter-cancer coding region features comparative analysis carried out, show insights into what structural trends/patterns are present in the studied cancers. PMID:19707296

  13. Nearest-neighbor doublets in protein-coding regions of MS2 RNA. [coliphage virus

    NASA Technical Reports Server (NTRS)

    Jukes, T. H.

    1977-01-01

    'Nearest neighbor' base pairs ('doublets') in the protein-coding regions of MS2 RNA have been tabulated with respect to their positions in the first two bases of amino acid codons, in the second two bases, or paired by contact between adjoining codons. Considerable variation is evident between numbers of doublets in each of these three possible positions, but the totals of each of the 16 doublets in the coding regions of the MS2 RNA molecule show much less variation. Compilations of doublets in nucleic acid strands have no predictive value for the amino acid composition of proteins coded by such strands.

  14. Regional Atmospheric Transport Code for Hanford Emission Tracking, Version 2(RATCHET2)

    SciTech Connect

    Ramsdell, James V.; Rishel, Jeremy P.

    2006-07-01

    This manual describes the atmospheric model and computer code for the Atmospheric Transport Module within SAC. The Atmospheric Transport Module, called RATCHET2, calculates the time-integrated air concentration and surface deposition of airborne contaminants to the soil. The RATCHET2 code is an adaptation of the Regional Atmospheric Transport Code for Hanford Emissions Tracking (RATCHET). The original RATCHET code was developed to perform the atmospheric transport for the Hanford Environmental Dose Reconstruction Project. Fundamentally, the two sets of codes are identical; no capabilities have been deleted from the original version of RATCHET. Most modifications are generally limited to revision of the run-specification file to streamline the simulation process for SAC.

  15. Achievable Region in Slotted ALOHA Throughput for One-Relay Two-Hop Wireless Network Coding

    NASA Astrophysics Data System (ADS)

    Umehara, Daisuke; Denno, Satoshi; Morikura, Masahiro; Sugiyama, Takatoshi

    This paper presents achievable regions in slotted ALOHA throughput both without and with network coding for one-relay two-hop wireless networks between two end node groups. In this paper, there are no restrictions on the total traffic and the number of end nodes per group. It follows that the relay node will be generally involved with asymmetric bidirectional traffic. This paper derives closed-form expressions of the throughput and packet delay per group both without and with network coding from a theoretical perspective regardless of whether the buffer on the relay node is saturated or not. Furthermore, we show that the maximum throughput per group with network coding can be achieved at the boundary of the relay buffer saturation and unsaturation which is expressed as the solution of a polynomial equation in two group node traffics. As a result, we clarify the enhancement of the achievable region in slotted ALOHA throughput by applying network coding.

  16. Self-identification of protein-coding regions in microbial genomes.

    PubMed

    Audic, S; Claverie, J M

    1998-08-18

    A new method for predicting protein-coding regions in microbial genomic DNA sequences is presented. It uses an ab initio iterative Markov modeling procedure to automatically perform the partition of genomic sequences into three subsets shown to correspond to coding, coding on the opposite strand, and noncoding segments. In contrast to current methods, such as GENEMARK [Borodovsky, M. & McIninch, J. D. (1993) Comput. Chem. 17, 123-133], no training set or prior knowledge of the statistical properties of the studied genome are required. This new method tolerates error rates of 1-2% and can process unassembled sequences. It is thus ideal for the analysis of genome survey and/or fragmented sequence data from uncharacterized microorganisms. The method was validated on 10 complete bacterial genomes (from four major phylogenetic lineages). The results show that protein-coding regions can be identified with an accuracy of up to 90% with a totally automated and objective procedure. PMID:9707594

  17. TORUS-3DPDR: a self-consistent code treating three-dimensional photoionization and photodissociation regions

    NASA Astrophysics Data System (ADS)

    Bisbas, T. G.; Haworth, T. J.; Barlow, M. J.; Viti, S.; Harries, T. J.; Bell, T.; Yates, J. A.

    2015-12-01

    The interaction of ionizing and far-ultraviolet radiation with the interstellar medium is of great importance. It results in the formation of regions in which the gas is ionized, beyond which are photodissociation regions (PDRs) in which the gas transitions to its atomic and molecular form. Several numerical codes have been implemented to study these two main phases of the interstellar medium either dynamically or chemically. In this paper we present TORUS-3DPDR, a new self-consistent code for treating the chemistry of three-dimensional photoionization and photodissociation regions. It is an integrated code coupling the two codes TORUS, a hydrodynamics and Monte Carlo radiation transport code, and 3D-PDR, a PDRs code. The new code uses a Monte Carlo radiative transfer scheme to account for the propagation of the ionizing radiation including the diffusive component as well as a ray-tracing scheme based on the HEALPIX package in order to account for the escape probability and column density calculations. Here, we present the numerical techniques we followed and we show the capabilities of the new code in modelling three-dimensional objects including single or multiple sources. We discuss the effects introduced by the diffusive component of the ultraviolet field in determining the thermal balance of PDRs as well as the effects introduced by a multiple sources treatment of the radiation field. With this new code, three-dimensional synthetic observations for the major cooling lines are possible, for making feasible a detailed comparison between hydrodynamical simulations and observations.

  18. Inter-STOP symbol distances for the identification of coding regions.

    PubMed

    Bastos, Carlos A C; Afreixo, Vera; Garcia, Sara P; Pinho, Armando J

    2013-01-01

    In this study we explore the potential of inter-STOP symbol distances for finding coding regions in DNA sequences. We use the distance between STOP symbols in the DNA sequence and a chi-square statistic to evaluate the nonhomogeneity of the three possible reading frames and the occurrence of one long distance in one of the frames. The results of this exploratory study suggest that inter-STOP symbol distances have strong ability to discriminate coding regions in prokaryotes and simple eukaryotes. PMID:24231144

  19. [The code of ethics and conduct of nursing of the Valencian region: background and content].

    PubMed

    Gordo Casañ, Ma Eugenia; Bellver Capella, Vicente; Avila Olivares, José Antonio; Castelló López, María Isabel

    2013-09-01

    TIn order to provide to the nursing professionals in the Valencian Region a code of professional conduct to help them deal with new situations that arise in their daily clinical practice, derived from social changes produced, the Board of Nursing of Valencian Region/ Consejo de Enfermería de la Comunidad Valenciana (CECOVA) approved in May2010, the Code of Ethics and Conduct of Nursing of Valencia. This work is as much about the reasons that led to propel it, and the way they was developed and the most important aspects of your content. PMID:24245416

  20. Human phosphoribosylformylglycineamide amidotransferase (FGARAT): regional mapping, complete coding sequence, isolation of a functional genomic clone, and DNA sequence analysis.

    PubMed

    Patterson, D; Bleskan, J; Gardiner, K; Bowersox, J

    1999-11-01

    Purines play essential roles in many cellular functions, including DNA replication, transcription, intra- and extra-cellular signaling, energy metabolism, and as coenzymes for many biochemical reactions. The de-novo synthesis of purines requires 10 enzymatic steps for the production of inosine monophosphate (IMP). Defects in purine metabolism are associated with human diseases. Further, many anticancer agents function as inhibitors of the de-novo biosynthetic pathway. Genes or cDNAs for most of the enzymes comprising this pathway have been isolated from humans or other mammals. One notable exception is the phosphoribosylformylglycineamide amidotransferase (FGARAT) gene, which encodes the fourth step of this pathway. This gene has been cloned from numerous microorganisms and from Drosophila melanogaster and C. elegans. We report here the identification of a human cDNA containing the coding region of the FGARAT mRNA and the isolation of a P1 clone that contains an intact human FGARAT gene. The P1 clone corrects the purine auxotrophy and protein deficiency of Chinese hamster ovary (CHO) cell mutants (AdeB) deficient in both the activity and the protein for FGARAT. The P1 clone was used to regionally map the FGARAT gene to chromosome region 17p13, a location consistent with our prior assignment of this gene to chromosome 17. A comparison of the DNA sequence of the human FGARAT and FGARAT DNA sequence from 17 other organisms is reported. The isolation of this gene means that DNA clones for all the 10 steps of IMP synthesis have been isolated from humans or other mammals. PMID:10548741

  1. Relative rates of evolution in the coding and control regions of African mtDNAs.

    PubMed

    Howell, Neil; Elson, Joanna L; Howell, Corinna; Turnbull, Douglass M

    2007-10-01

    Reduced median networks of African haplogroup L mitochondrial DNA (mtDNA) sequences were analyzed to determine the pattern of substitutions in both the noncoding control and coding regions. In particular, we attempted to determine the causes of the previously reported (Howell et al. 2004) violation of the molecular clock during the evolution of these sequences. In the coding region, there was a significantly higher rate of substitution at synonymous sites than at nonsynonymous sites as well as in the tRNA and rRNA genes. This is further evidence for the operation of purifying selection during human mtDNA evolution. For most sites in the control region, the relative rate of substitution was similar to the rate of neutral evolution (assumed to be most closely approximated by the substitution rate at 4-fold degenerate sites). However, there are a number of mutational hot spots in the control region, approximately 3% of the total sites, that have a rate of substitution greater than the neutral rate, at some sites by more than an order of magnitude. It is possible either that these sites are evolving under conditions of positive selection or that the substitution rate at some sites in the control region is strongly dependent upon sequence context. Finally, we obtained preliminary evidence for "nonideal" evolution in the control region, including haplogroup-specific substitution patterns and a decoupling between relative rates of substitution in the control and coding regions. PMID:17642471

  2. A search for conserved sequences in coding regions reveals that the let-7 microRNA targets Dicer within its coding sequence

    PubMed Central

    Forman, Joshua J.; Legesse-Miller, Aster; Coller, Hilary A.

    2008-01-01

    Recognition sites for microRNAs (miRNAs) have been reported to be located in the 3′ untranslated regions of transcripts. In a computational screen for highly conserved motifs within coding regions, we found an excess of sequences conserved at the nucleotide level within coding regions in the human genome, the highest scoring of which are enriched for miRNA target sequences. To validate our results, we experimentally demonstrated that the let-7 miRNA directly targets the miRNA-processing enzyme Dicer within its coding sequence, thus establishing a mechanism for a miRNA/Dicer autoregulatory negative feedback loop. We also found computational evidence to suggest that miRNA target sites in coding regions and 3′ UTRs may differ in mechanism. This work demonstrates that miRNAs can directly target transcripts within their coding region in animals, and it suggests that a complete search for the regulatory targets of miRNAs should be expanded to include genes with recognition sites within their coding regions. As more genomes are sequenced, the methodological approach that we used for identifying motifs with high sequence conservation will be increasingly valuable for detecting functional sequence motifs within coding regions. PMID:18812516

  3. POLYMORPHISM IN THE CODING REGION SEQUENCE OF GDF8 GENE IN INDIAN SHEEP.

    PubMed

    Pothuraju, M; Mishra, S K; Kumar, S N; Mohamed, N F; Kataria, R S; Yadav, D K; Arora, R

    2015-11-01

    The present study was undertaken to identify polymorphism in the coding sequence of GDF8gene across indigenous meat type sheep breeds. A 1647 bp sequence was generated, encompassing 208 bp of the 5'UTR, 1128 bp of coding region (exon1, 2 and 3) as well as 311 bp of 3'UTR. The sheep and goat GDF8 gene sequences were observed to be highly conserved as compared to cattle, buffalo, horse and pig. Several nucleotide variations were observed across coding sequence of GDF8 gene in Indian sheep. Three polymorphic sites were identified in the 5'UTR, one in exon 1 and one in the exon 2 regions. Both SNPs in the exonic region were found to be non-synonymous. The mutations c.539T > G and c.821T > A discovered in this study in the exon 1 and exon 2, respectively, have not been previously reported. The information generated provides preliminary indication of the functional diversity present in Indian sheep at the coding region of GDF8gene. The novel as well as the previously reported SNPs discovered in the Indian sheep warrant further analysis to see whether they affect the phenotype. Future studies will need to establish the affect of reported SNPs in the expression of the GDF8 gene in Indian sheep population. PMID:26845859

  4. Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences.

    PubMed

    Pang, Erli; Wu, Xiaomei; Lin, Kui

    2016-06-01

    Protein evolution plays an important role in the evolution of each genome. Because of their functional nature, in general, most of their parts or sites are differently constrained selectively, particularly by purifying selection. Most previous studies on protein evolution considered individual proteins in their entirety or compared protein-coding sequences with non-coding sequences. Less attention has been paid to the evolution of different parts within each protein of a given genome. To this end, based on PfamA annotation of all human proteins, each protein sequence can be split into two parts: domains or unassigned regions. Using this rationale, single nucleotide polymorphisms (SNPs) in protein-coding sequences from the 1000 Genomes Project were mapped according to two classifications: SNPs occurring within protein domains and those within unassigned regions. With these classifications, we found: the density of synonymous SNPs within domains is significantly greater than that of synonymous SNPs within unassigned regions; however, the density of non-synonymous SNPs shows the opposite pattern. We also found there are signatures of purifying selection on both the domain and unassigned regions. Furthermore, the selective strength on domains is significantly greater than that on unassigned regions. In addition, among all of the human protein sequences, there are 117 PfamA domains in which no SNPs are found. Our results highlight an important aspect of protein domains and may contribute to our understanding of protein evolution. PMID:26833483

  5. Video segmentation using spatial proximity, color, and motion information for region-based coding

    NASA Astrophysics Data System (ADS)

    Hong, Won H.; Kim, Nam Chul; Lee, Sang-Mi

    1994-09-01

    An efficient video segmentation algorithm with homogeneity measure to incorporate spatial proximity, color, and motion information simultaneously is presented for region-based coding. The procedure toward complete segmentation consists of two steps: primary segmentation, and secondary segmentation. In the primary segmentation, an input image is finely segmented by FSCL. In the secondary segmentation, a lot of small regions and similar regions generated in the preceding step are eliminated or merged by a fast RSST. Through some experiments, it is found that the proposed algorithm produces efficient segmentation results and the video coding system with this algorithm yields visually acceptable quality and PSNR equals 36 - 37 dB at a very low bitrate of about 13.2 kbits/s.

  6. Complete coding region of the mitochondrial genome of Monochamus alternatus hope (Coleoptera: Cerambycidae).

    PubMed

    Wang, Cheng-Ye; Feng, Ying; Chen, Xiao-Ming

    2013-07-01

    The Japanese pine sawyer, Monochamus alternatus Hope, 1842, an important forest pest, mainly occurs in Far East. It is the main vector of pine wood nematode Bursaphelenchus xylophilus, which causes pine wilt disease. We determined the complete mitochondrial genome coding region of M. alternatus using long PCR and conserved primer walking. Our results show that the entire mitogenome coding region is 14,649 bp long, with 78.22% A+T content [deposited in GenBank (JX987292)]. Positions and arrangement of the 37 genes encoded by the coding region are identical to those of two other longhorn beetles (Psacothea hilaris and Anoplophora glabripennis) for which the complete gene content and arrangement are known. All protein-coding genes start with a typical initiation codon ATN in insects. All tRNAs show standard clover-leaf structure, except the tRNA(Ser) (AGN), which lacks dihydrouridine (DHU) arm. The most unusual feature found is the use of TCT as tRNA(Ser) (AGN) anticodon instead of GCT, which is used in most other arthropods. This provides further insights into the diversity and evolution of the Cerambycidae family of long-horned beetles. PMID:23829217

  7. Riboswitches in unexpected places--a synthetic riboswitch in a protein coding region.

    PubMed

    Topp, Shana; Gallivan, Justin P

    2008-12-01

    In natural and engineered systems, cis-RNA regulatory elements such as riboswitches are typically found within untranslated regions rather than within the protein coding sequences of genes. However, RNA sequences with important regulatory roles can exist within translated regions. Here, we present a synthetic riboswitch that is encoded within the translated region of a gene and represses Escherichia coli gene expression greater than 25-fold in the presence of a small-molecule ligand. The ability to encode riboswitches within translated regions as well as untranslated regions provides additional opportunities for creating new genetic control elements. Furthermore, evidence that a riboswitch can function in the translated region of a gene suggests that future efforts to identify natural riboswitches should consider this possibility. PMID:18945803

  8. Mapping laboratory test codes to LOINC for a regional health information exchange.

    PubMed

    Porter, Jameson P; Starmer, Jack; King, Janet; Frisse, Mark E

    2007-01-01

    Fully mapping laboratory tests to LOINC greatly increases functionality within a regional data exchange, but it is a costly process. As an inexpensive approach, we defined 53 "clinically significant" labs to map within the Memphis, Tennessee RHIO. These tests comprised a small percentage of unique test codes but a large percentage of laboratory message volume. We propose mapping a few clinically significant laboratory tests can deliver a low cost increase in functionality for a RHIO. PMID:18694179

  9. Sequence analysis of the 3' non-coding region of mouse immunoglobulin light chain messenger RNA.

    PubMed Central

    Hamlyn, P H; Gillam, S; Smith, M; Milstein, C

    1977-01-01

    Using an oligonucleotide d(pT10-C-A) as primer, cDNA has been transcribed from the 3' non-coding region of mouse immunoglobulin light chain mRNA and sequenced by a modification1 of the 'plus-minus' gel method2. The sequence obtained has partially corrected and extended a previously obtained sequence3. The new data contains an unusual sequence in which a trinucleotide is repeated seven times. Images PMID:405661

  10. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast.

    PubMed

    Salinas, Francisco; de Boer, Carl G; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F; Martínez, Claudio; Cubillos, Francisco A

    2016-01-01

    Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype. PMID:26898953

  11. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast

    PubMed Central

    Salinas, Francisco; de Boer, Carl G.; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F.; Martínez, Claudio; Cubillos, Francisco A.

    2016-01-01

    Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype. PMID:26898953

  12. Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein‐Coding Regions

    PubMed Central

    Lelieveld, Stefan H.; Spielmann, Malte; Mundlos, Stefan; Veltman, Joris A.

    2015-01-01

    ABSTRACT For next‐generation sequencing technologies, sufficient base‐pair coverage is the foremost requirement for the reliable detection of genomic variants. We investigated whether whole‐genome sequencing (WGS) platforms offer improved coverage of coding regions compared with whole‐exome sequencing (WES) platforms, and compared single‐base coverage for a large set of exome and genome samples. We find that WES platforms have improved considerably in the last years, but at comparable sequencing depth, WGS outperforms WES in terms of covered coding regions. At higher sequencing depth (95x–160x), WES successfully captures 95% of the coding regions with a minimal coverage of 20x, compared with 98% for WGS at 87‐fold coverage. Three different assessments of sequence coverage bias showed consistent biases for WES but not for WGS. We found no clear differences for the technologies concerning their ability to achieve complete coverage of 2,759 clinically relevant genes. We show that WES performs comparable to WGS in terms of covered bases if sequenced at two to three times higher coverage. This does, however, go at the cost of substantially more sequencing biases in WES approaches. Our findings will guide laboratories to make an informed decision on which sequencing platform and coverage to choose. PMID:25973577

  13. Regional Atmospheric Transport Code for Hanford Emission Tracking (RATCHET). Hanford Environmental Dose Reconstruction Project

    SciTech Connect

    Ramsdell, J.V. Jr.; Simonen, C.A.; Burk, K.W.

    1994-02-01

    The purpose of the Hanford Environmental Dose Reconstruction (HEDR) Project is to estimate radiation doses that individuals may have received from operations at the Hanford Site since 1944. This report deals specifically with the atmospheric transport model, Regional Atmospheric Transport Code for Hanford Emission Tracking (RATCHET). RATCHET is a major rework of the MESOILT2 model used in the first phase of the HEDR Project; only the bookkeeping framework escaped major changes. Changes to the code include (1) significant changes in the representation of atmospheric processes and (2) incorporation of Monte Carlo methods for representing uncertainty in input data, model parameters, and coefficients. To a large extent, the revisions to the model are based on recommendations of a peer working group that met in March 1991. Technical bases for other portions of the atmospheric transport model are addressed in two other documents. This report has three major sections: a description of the model, a user`s guide, and a programmer`s guide. These sections discuss RATCHET from three different perspectives. The first provides a technical description of the code with emphasis on details such as the representation of the model domain, the data required by the model, and the equations used to make the model calculations. The technical description is followed by a user`s guide to the model with emphasis on running the code. The user`s guide contains information about the model input and output. The third section is a programmer`s guide to the code. It discusses the hardware and software required to run the code. The programmer`s guide also discusses program structure and each of the program elements.

  14. Coding region SNP analysis to enhance dog mtDNA discrimination power in forensic casework.

    PubMed

    Verscheure, Sophie; Backeljau, Thierry; Desmyter, Stijn

    2015-01-01

    The high population frequencies of three control region haplotypes contribute to the low discrimination power of the dog mtDNA control region. It also diminishes the evidential power of a match with one of these haplotypes in forensic casework. A mitochondrial genome study of 214 Belgian dogs suggested 26 polymorphic coding region sites that successfully resolved dogs with the three most frequent control region haplotypes. In this study, three SNP assays were developed to determine the identity of the 26 informative sites. The control region of 132 newly sampled dogs was sequenced and added to the study of 214 dogs. The assays were applied to 58 dogs of the haplotypes of interest, which confirmed their suitability for enhancing dog mtDNA discrimination power. In the Belgian population study of 346 dogs, the set of 26 sites divided the dogs into 25 clusters of mtGenome sequences with substantially lower population frequency estimates than their control region sequences. In case of a match with one of the three control region haplotypes, using these three SNP assays in conjunction with control region sequencing would augment the exclusion probability of dog mtDNA analysis from 92.9% to 97.0%. PMID:25299153

  15. An unusually long non-coding region in rat lens alpha-crystallin messenger RNA.

    PubMed Central

    Moormann, R J; van der Velden, H M; Dodemont, H J; Andreoli, P M; Bloemendal, H; Schoenmakers, J G

    1981-01-01

    Most of the mRNA sequence coding for the alpha A2 chain of the ocular lens protein alpha-crystallin from rat, has been determined by sequencing cloned DNA copies of this mRNA. The 892-base pair cDNA sequence encompasses all but 52 N-terminal amino acids of the alpha A2 chain. It lacks the sequence characteristic for the 22 extra amino acids inserted in the alpha A2 -like chain, named alpha AIns. A stretch of 583 nuceotides, representing more than 50% of the entire mRNA sequence, is located 3' wards of the alpha A2 coding sequence. It contains the characteristic AAUAAA signal involved in poly(A) -addition and represents an unexpectedly long non-coding region. Examination of the total cytoplasmic poly(A) RNA of rat lens by filter-hybridization and subsequent translation of the electrophoretically separated mRNA fractions shows that the alpha A2 chain is encoded by mRNA species which are distinct from the alpha AIns encoding mRNA. No evidence is obtained for an extensive size heterogeneity in the 3' untranslated regions of these two different rat lens mRNAs. Images PMID:6171772

  16. Region-of-interest based rate control for UAV video coding

    NASA Astrophysics Data System (ADS)

    Zhao, Chun-lei; Dai, Ming; Xiong, Jing-ying

    2016-05-01

    To meet the requirement of high-quality transmission of videos captured by unmanned aerial vehicles (UAV) with low bandwidth, a novel rate control (RC) scheme based on region-of-interest (ROI) is proposed. First, the ROI information is sent to the encoder with the latest high efficient video coding (HEVC) standard to generate an ROI map. Then, by using the ROI map, bit allocation methods are developed at frame level and large coding unit (LCU) level, to avoid inaccurate bit allocation produced by camera movement. At last, by using a better robustness R- λ model, the quantization parameter ( QP) for each LCU is calculated. The experimental results show that the proposed RC method can get a lower bitrate error and a higher quality for reconstructed video by choosing appropriate pixel weight on the HEVC platform.

  17. Blind Detection of Region Duplication Forgery Using Fractal Coding and Feature Matching.

    PubMed

    Jenadeleh, Mohsen; Ebrahimi Moghaddam, Mohsen

    2016-05-01

    Digital image forgery detection is important because of its wide use in applications such as medical diagnosis, legal investigations, and entertainment. Copy-move forgery is one of the famous techniques, which is used in region duplication. Many of the existing copy-move detection algorithms cannot effectively blind detect duplicated regions that are made by powerful image manipulation software like Photoshop. In this study, a new method is proposed for blind detecting manipulations in digital images based on modified fractal coding and feature vector matching. The proposed method not only detects typical copy-move forgery, but also finds multiple copied forgery regions for images that are subjected to rotation, scaling, reflection, and a mixture of these postprocessing operations. The proposed method is robust against tampered images undergoing attacks such as Gaussian blurring, contrast scaling, and brightness adjustment. The experimental results demonstrated the validity and efficiency of the method. PMID:27122398

  18. New complete mitochondrial genome of the Perccottus glenii (Perciformes, Odontobutidae): additional non-coding region.

    PubMed

    Chen, Xiaohui; Shi, Yangbai; Zhong, Liqiang; Wang, Minghua; Sun, Lihui; Yang, Guoliang

    2016-05-01

    Perccottus glenii is a species of freshwater sleeper native to the Russian Far East, north-eastern China, and the northern part of the Korean Penninsula with introduced populations in other regions of Eurasia. In this study, a new complete mitochondrial genome of Perccottus glenii was reported. The circular genome is 16,510 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, and 1 control region. Except the origin of the light strand replication (OL), an additional non-coding region was present between ND6 and tRNA-Glu in the Light strand. The overall nucleotide composition was 30.5% A, 29.2% T, 24.4% C and 15.9% G, with an A + T bias of 59.7%. The gene composition and the structural arrangement of the P. glenii complete mtDNA were identical to most of the other vertebrates. The molecular data here we presented could play a useful role to study the evolutionary relationships and population genetics of Odontobutidae fish. PMID:25329281

  19. Development of a code for wall contour design in the transonic region of axisymmetric and square nozzles

    NASA Technical Reports Server (NTRS)

    Alcenius, Timothy; Schneider, Steven P.

    1994-01-01

    Nozzle design codes developed earlier under NAG1-1133 were modified and used in order to design a supersonic wind tunnel nozzle with square cross sections. As part of the design process, a computer code was written to implement the Hopkins and Hill perturbation solution for the flow in the transonic region of axisymmetric nozzles. This technique is used to design the bleed slot of quiet-flow nozzles. This new design code is documented in this report.

  20. One-dimensional transport code modelling of the limiter-divertor region in tokamaks

    SciTech Connect

    Ogden, J.M.; Post, D.E.; Jensen, R.V.; Seidl, F.G.P.

    1980-02-01

    A model of the limiter-divertor scrape-off region has been incorporated into the BALDUR one-dimensional tokamak transport code. Simulations of PDX and ALCATOR have been carried out for ohmic and neutral beam heated cases. In particular, we have studied how the edge conditions and energy loss mechanisms of PDX depend upon plasma density, and compared our results with analytic estimates. The sensitivity of the results to changes in the transport coefficients and scrape-off model is also discussed.

  1. Intronic miR-932 targets the coding region of its host gene, Drosophila neuroligin2.

    PubMed

    Qian, Jinjun; Tu, Renjun; Yuan, Liudi; Xie, Wei

    2016-06-10

    Despite great progress for two decades in microRNAs (miRNAs), the direct regulation of host gene by intragenic (mostly intronic) miRNA is conceptually plausible but evidence-limited. Here, we report that intronic miR-932 could target its host gene via binding with coding sequence (CDS) region rather than regular 3'UTR. The conserved miR-932 is embedded in the fourth intron of Drosophila neuroligin2 (dnlg2), which encodes a synaptic cell adhesion molecule, DNlg2. In silico analysis predicted two putative miR-932 target sites locate in the CDS region of dnlg2 instead of regular 3'-UTR miRNA binding sites. Employing luciferase reporter assay, we further proved that the miR-932 regulates expression of its host gene dnlg2 via the binding CDS region of dnlg2. Consistently, we observed miR-932 downregulated expression of dnlg2 in S2 cell, and the repression of dnlg2 by miR-932 at both protein and RNA level. Furthermore, we found CDS-located site1 is dominant for regulating expression of host dnlg2 by miR-932. In addition to providing thorough examination of one intronic miRNA targeting the CDS region of its host gene, our genome-wide analysis indicated that nearly half of fruitfly and human intronic miRNAs may target their own host gene at coding region. This study would be valuable in elucidating the regulation of intronic miRNA on host gene, and provide new information about the biological context of their genomic arrangements and functions. PMID:26844630

  2. (Photosynthesis in intact plants)

    SciTech Connect

    Not Available

    1990-01-01

    Progress in the two years since the last renewal application has been excellent. We have made substantial contributions on both main fronts of the projects, and are particularly happy with the progress of our research on intact plants. The approach of basing our field work on a sound foundation of laboratory studies has enabled is to use methods which provide unambiguous assays of well characterized reactions. We have also made excellent progress in several laboratory studies which will have direct applications in future field work, and have introduced to the laboratory a range of molecular genetics techniques which will allow us to explore new options in the attempt to understand function at the level of molecular structure.

  3. Stereoscopic Visual Attention-Based Regional Bit Allocation Optimization for Multiview Video Coding

    NASA Astrophysics Data System (ADS)

    Zhang, Yun; Jiang, Gangyi; Yu, Mei; Chen, Ken; Dai, Qionghai

    2010-12-01

    We propose a Stereoscopic Visual Attention- (SVA-) based regional bit allocation optimization for Multiview Video Coding (MVC) by the exploiting visual redundancies from human perceptions. We propose a novel SVA model, where multiple perceptual stimuli including depth, motion, intensity, color, and orientation contrast are utilized, to simulate the visual attention mechanisms of human visual system with stereoscopic perception. Then, a semantic region-of-interest (ROI) is extracted based on the saliency maps of SVA. Both objective and subjective evaluations of extracted ROIs indicated that the proposed SVA model based on ROI extraction scheme outperforms the schemes only using spatial or/and temporal visual attention clues. Finally, by using the extracted SVA-based ROIs, a regional bit allocation optimization scheme is presented to allocate more bits on SVA-based ROIs for high image quality and fewer bits on background regions for efficient compression purpose. Experimental results on MVC show that the proposed regional bit allocation algorithm can achieve over [InlineEquation not available: see fulltext.]% bit-rate saving while maintaining the subjective image quality. Meanwhile, the image quality of ROIs is improved by [InlineEquation not available: see fulltext.] dB at the cost of insensitive image quality degradation of the background image.

  4. Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium

    SciTech Connect

    Ansong, Charles; Tolic, Nikola; Purvine, Samuel O.; Porwollik, Steffen; Jones, Marcus B.; Yoon, Hyunjin; Payne, Samuel H.; Martin, Jessica L.; Burnet, Meagan C.; Monroe, Matthew E.; Venepally, Pratap; Smith, Richard D.; Peterson, Scott; Heffron, Fred; Mcclelland, Michael; Adkins, Joshua N.

    2011-08-25

    Complete and accurate genome annotation is crucial for comprehensive and systematic studies of biological systems. For example systems biology-oriented genome scale modeling efforts greatly benefit from accurate annotation of protein-coding genes to develop proper functioning models. However, determining protein-coding genes for most new genomes is almost completely performed by inference, using computational predictions with significant documented error rates (> 15%). Furthermore, gene prediction programs provide no information on biologically important post-translational processing events critical for protein function. With the ability to directly measure peptides arising from expressed proteins, mass spectrometry-based proteomics approaches can be used to augment and verify coding regions of a genomic sequence and importantly detect post-translational processing events. In this study we utilized “shotgun” proteomics to guide accurate primary genome annotation of the bacterial pathogen Salmonella Typhimurium 14028 to facilitate a systems-level understanding of Salmonella biology. The data provides protein-level experimental confirmation for 44% of predicted protein-coding genes, suggests revisions to 48 genes assigned incorrect translational start sites, and uncovers 13 non-annotated genes missed by gene prediction programs. We also present a comprehensive analysis of post-translational processing events in Salmonella, revealing a wide range of complex chemical modifications (70 distinct modifications) and confirming more than 130 signal peptide and N-terminal methionine cleavage events in Salmonella. This study highlights several ways in which proteomics data applied during the primary stages of annotation can improve the quality of genome annotations, especially with regards to the annotation of mature protein products.

  5. A First-Stage Approximation to Identify New Imprinted Genes through Sequence Analysis of Its Coding Regions

    PubMed Central

    Daura-Oller, Elias; Cabré, Maria; Montero, Miguel A.; Paternáin, José L.; Romeu, Antoni

    2009-01-01

    In the present study, a positive training set of 30 known human imprinted gene coding regions are compared with a set of 72 randomly sampled human nonimprinted gene coding regions (negative training set) to identify genomic features common to human imprinted genes. The most important feature of the present work is its ability to use multivariate analysis to look at variation, at coding region DNA level, among imprinted and non-imprinted genes. There is a force affecting genomic parameters that appears through the use of the appropriate multivariate methods (principle components analysis (PCA) and quadratic discriminant analysis (QDA)) to analyse quantitative genomic data. We show that variables, such as CG content, [bp]% CpG islands, [bp]% Large Tandem Repeats, and [bp]% Simple Repeats, are able to distinguish coding regions of human imprinted genes. PMID:19360135

  6. Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within HIV Coding Regions.

    PubMed

    Goz, Eli; Tuller, Tamir

    2016-08-01

    A large number of studies demonstrated the importance of different HIV RNA structural elements at all stages of the viral life cycle. Nevertheless, the significance of many of these structures is unknown, and plausibly new regions containing RNA structure-mediated regulatory signals remain to be identified. An important characteristic of genomic regions carrying functionally significant secondary structures is their mutational robustness, that is, the extent to which a sequence remains constant in spite of despite mutations in terms of its underlying secondary structure. Structural robustness to mutations is expected to be important in the case of functional RNA structures in viruses with high mutation rate; it may prevent fitness loss due to disruption of possibly functional conformations, pointing to the specific significance of the corresponding genomic region. In the current work, we perform a genome-wide computational analysis to detect signals of a direct evolutionary selection for strong folding and RNA structure-based mutational robustness within HIV coding sequences. We provide evidence that specific regions of HIV structural genes undergo an evolutionary selection for strong folding; in addition, we demonstrate that HIV Rev responsive element seems to undergo a direct evolutionary selection for increased secondary structure robustness to point mutations. We believe that our analysis may enable a better understanding of viral evolutionary dynamics at the RNA structural level and may benefit to practical efforts of engineering antiviral vaccines and novel therapeutic approaches. PMID:27347769

  7. The physics of intact capture

    NASA Technical Reports Server (NTRS)

    Tsou, Peter; Griffiths, D. J.; Albee, A. L.

    1994-01-01

    The ability to capture projectiles intact at hypervelocities in underdense media open a new area of study in physics. Underdense material behaves markedly different than solid, liquid, or gas upon hypervelocity impact. This new phenomenon enables applications in science that would either not be possible or would be very costly by other means. This phenomenon has been fully demonstrated in the laboratory and validated in space. Even more interesting is the fact that this hypervelocity intact capture was accomplished passively. A better understanding of the physics of intact capture will lead to improvements in intact capture. A collection of physical observations of this phenomenon is presented here.

  8. Mutational analysis of the promoter and the coding region of the 5-HT1A gene

    SciTech Connect

    Erdmann, J.; Noethen, M.M.; Shimron-Abarbanell, D.

    1994-09-01

    Disturbances of serotonergic pathways have been implicated in many neuropsychiatric disorders. Serotonin (5HT) receptors can be subdivided into at least three major families (5HT1, 5HT2, and 5HT3). Five human 5HT1 receptor subtypes have been cloned, namely 1A, 1D{alpha}, 1D{beta}, 1E, and 1F. Of these, the 5HT1A receptor is the best characterized subtype. In the present study we sought to identify genetic variation in the 5HT1A receptor gene which through alteration of protein function or level of expression might contribute to the genetics of neuropsychiatric diseases. The coding region and the 5{prime} promoter region of the 5HT1A gene from 159 unrelated subjects (45 schizophrenic, 46 bipolar affective, and 43 patients with Tourette`s syndrome, as well as 25 controls) were analyzed using SSCA. SSCA revealed the presence of two mutations both located in the coding region of the 5HT1A receptor gene. The first mutation is a rare silent C{r_arrow}T substitution at nucleotide position 549. The second mutation is characterized by a base pair substitution (A{r_arrow}G) at the first position of codon 28 and results in an amino acid exchange (Ile{r_arrow}Val). Since Val28 was found only in a single schizophrenic patient and in none of the other patients or controls, we decided to extend our samples and to use a restriction assay for screening a further 74 schizophrenic, 95 bipolar affective, and 49 patients with Tourette`s syndrome, as well as 185 controls, for the presence of the mutation. In total, the mutation was found in 2 schizophrenic patients, in 3 bipolars, in 1 Tourette patient, and in 5 controls. To our knowledge the Ile-28-Val substitution reported here is the first natural occuring molecular variant which has been identified for a serotonin receptor so far.

  9. 50 CFR 622.247 - Landing golden crab intact.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 12 2013-10-01 2013-10-01 false Landing golden crab intact. 622.247... ATLANTIC Golden Crab Fishery of the South Atlantic Region § 622.247 Landing golden crab intact. The operator of a vessel that fishes in the EEZ is responsible for ensuring that golden crab on that vessel...

  10. 50 CFR 622.247 - Landing golden crab intact.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 12 2014-10-01 2014-10-01 false Landing golden crab intact. 622.247... ATLANTIC Golden Crab Fishery of the South Atlantic Region § 622.247 Landing golden crab intact. The operator of a vessel that fishes in the EEZ is responsible for ensuring that golden crab on that vessel...

  11. 50 CFR 622.186 - Landing fish intact.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 12 2014-10-01 2014-10-01 false Landing fish intact. 622.186 Section 622...-Grouper Fishery of the South Atlantic Region § 622.186 Landing fish intact. (a) South Atlantic snapper... specified in paragraph (b) of this section. Such fish may be eviscerated, gilled, and scaled, but...

  12. 50 CFR 622.186 - Landing fish intact.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 12 2013-10-01 2013-10-01 false Landing fish intact. 622.186 Section 622...-Grouper Fishery of the South Atlantic Region § 622.186 Landing fish intact. (a) South Atlantic snapper... specified in paragraph (b) of this section. Such fish may be eviscerated, gilled, and scaled, but...

  13. A Unified Mathematical Framework for Coding Time, Space, and Sequences in the Hippocampal Region

    PubMed Central

    MacDonald, Christopher J.; Tiganj, Zoran; Shankar, Karthik H.; Du, Qian; Hasselmo, Michael E.; Eichenbaum, Howard

    2014-01-01

    The medial temporal lobe (MTL) is believed to support episodic memory, vivid recollection of a specific event situated in a particular place at a particular time. There is ample neurophysiological evidence that the MTL computes location in allocentric space and more recent evidence that the MTL also codes for time. Space and time represent a similar computational challenge; both are variables that cannot be simply calculated from the immediately available sensory information. We introduce a simple mathematical framework that computes functions of both spatial location and time as special cases of a more general computation. In this framework, experience unfolding in time is encoded via a set of leaky integrators. These leaky integrators encode the Laplace transform of their input. The information contained in the transform can be recovered using an approximation to the inverse Laplace transform. In the temporal domain, the resulting representation reconstructs the temporal history. By integrating movements, the equations give rise to a representation of the path taken to arrive at the present location. By modulating the transform with information about allocentric velocity, the equations code for position of a landmark. Simulated cells show a close correspondence to neurons observed in various regions for all three cases. In the temporal domain, novel secondary analyses of hippocampal time cells verified several qualitative predictions of the model. An integrated representation of spatiotemporal context can be computed by taking conjunctions of these elemental inputs, leading to a correspondence with conjunctive neural representations observed in dorsal CA1. PMID:24672015

  14. Functional non-coding RNAs derived from the flavivirus 3' untranslated region.

    PubMed

    Clarke, B D; Roby, J A; Slonchak, A; Khromykh, A A

    2015-08-01

    Flaviviruses are single-stranded positive sense RNA enveloped viruses. The flavivirus genus includes important human pathogens such as dengue virus (DENV), West Nile virus (WNV), yellow fever virus (YFV), Japanese encephalitis virus (JEV), tick-borne encephalitis virus (TBEV), and Murray Valley encephalitis virus (MVEV). In addition to the viral proteins and viral genomic RNA, flaviviruses produce at least two functional non-coding RNAs derived from the 3' untranslated region (3'UTR), the subgenomic flavivirus RNA (sfRNA) and a putative WNV miRNA (KUN-miR-1). In this review we summarize published data from studies with WNV, YFV, DENV, JEV, and MVEV on sfRNA production following incomplete degradation of the viral genomic RNA by the cellular 5'-3' exoribonuclease 1 (XRN1), RNA structural elements involved in stalling XRN1 to generate sfRNA, and functions of sfRNA in modulating cellular mRNA decay and RNAi pathways as well as in modulating anti-viral type I interferon response. In addition, we also summarize data on the mechanisms of biogenesis of 3'UTR-derived KUN-miR-1 and its function in WNV replication in mosquito host, along with recent findings on a discovery of a second potential flaviviral miRNA vsRNA5, derived from the 3'UTR of DENV. This review thus summarizes the known mechanisms of generation and the functions of flaviviral 3'UTR-derived non-coding RNAs. PMID:25660582

  15. Divergent protein coding regions in otherwise closely related androgen-regulated mRNAs.

    PubMed Central

    McDonald, C J; Eliopoulos, E; Higgins, S J

    1984-01-01

    Rat seminal vesicles serve as a model system for studying androgen action. We have sequenced and compared full length cDNAs for two major proteins (S and F) synthesised and secreted under hormonal control. Overall, mRNAS and mRNAF share 57% nucleotide sequence homology suggesting that their genes arose by duplication of a common ancestor. However, the mRNAs display a highly unusual regional distribution of sequence homology, with the untranslated regions (UTRs) being substantially more homologous than the protein-coding regions (PCRs). Detailed analysis of nucleotide substitutions at synonymous and replacement sites shows that the PCRs have evolved very rapidly. Evolutionary conservation of the UTRs is no higher than that of UTRs generally and thus provides no evidence of a specific regulatory role for the UTRs in androgen action. The primary sequences of proteins S and F have diverged so rapidly that they are the best examples of neutrally evolving proteins for which comparative nucleotide sequence data are available. However, despite their rapid divergence, the predicted higher order structures for both proteins consist largely of non-regular conformation. This is discussed in terms of their roles as structural components of the rodent copulatory plug. PMID:6548962

  16. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach

    SciTech Connect

    Uberbacher, E.C.; Mural, R.J. Univ. of Tennessee, Oak Ridge )

    1991-12-15

    Genes in higher eukaryotes may span tens or hundreds of kilobases with the protein-coding regions accounting for only a few percent of the total sequence. Identifying genes within large regions of uncharacterized DNA is a difficult undertaking and is currently the focus of many research efforts. The authors describe a reliable computational approach for locating protein-coding portions of genes in anonymous DNA sequence. Using a concept suggested by robotic environmental sensing, the authors method combines a set of sensor algorithms and a neural network to localize the coding regions. Several algorithms that report local characteristics of the DNA sequence, and therefore act as sensors, are also described. In its current configuration the coding recognition module identifies 90% of coding exons of length 100 bases or greater with less than one false positive coding exon indicated per five coding exons indicated. This is a significantly lower false positive rate than any method of which the authors are aware. This module demonstrates a method with general applicability to sequence-pattern recognition problems and is available for current research efforts.

  17. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach.

    PubMed Central

    Uberbacher, E C; Mural, R J

    1991-01-01

    Genes in higher eukaryotes may span tens or hundreds of kilobases with the protein-coding regions accounting for only a few percent of the total sequence. Identifying genes within large regions of uncharacterized DNA is a difficult undertaking and is currently the focus of many research efforts. We describe a reliable computational approach for locating protein-coding portions of genes in anonymous DNA sequence. Using a concept suggested by robotic environmental sensing, our method combines a set of sensor algorithms and a neural network to localize the coding regions. Several algorithms that report local characteristics of the DNA sequence, and therefore act as sensors, are also described. In its current configuration the "coding recognition module" identifies 90% of coding exons of length 100 bases or greater with less than one false positive coding exon indicated per five coding exons indicated. This is a significantly lower false positive rate than any method of which we are aware. This module demonstrates a method with general applicability to sequence-pattern recognition problems and is available for current research efforts. PMID:1763041

  18. Space research with intact organisms

    NASA Technical Reports Server (NTRS)

    Phillips, Robert W.; Haddy, Francis J.

    1992-01-01

    Effects of space exposure on intact organisms are briefly reviewed, and examples of future experiments that might provide new information on the role of gravity in the evolution of life are suggested. It is noted that long term experiments with intact plant and animals for studying gravitational thresholds will provide important new insights.

  19. Inhibition of Human Methionine Adenosyltransferase 1A Transcription by Coding Region Methylation

    PubMed Central

    Tomasi, Maria Lauda; Li, Tony W. H.; Li, Mei; Mato, José M.; Lu, Shelly C.

    2011-01-01

    Two genes (MAT1A and MAT2A) encode for the essential enzyme methionine adenosyltransferase (MAT). MAT1A is silenced in hepatocellular carcinoma (HCC), and absence of MAT1A leads to spontaneous development of HCC in mice. Previous report correlated promoter methylation to silencing of MAT1A but definitive proof was lacking. Here we investigated the role of methylation in regulating MAT1A expression. There are three MspI/HpaII sites from −1913 to +160 of the human MAT1A gene (numbered relative to the translational start site) at position −977, +10, and +88. Bisulfite treatment and DNA sequencing, and Southern blot analysis showed that methylation at +10 and +88, but not −977, correlated with lack of MAT1A expression. MAT1A promoter construct methylated at −977, +10 or +88 position has 0.7-fold, 3-fold, and 1.6-fold lower promoter activity, respectively. Methylation at −977 and +10 did not inhibit the promoter more than methylation at +10 alone; while methylation at +10 and +88 reduced promoter activity by 60%. Mutation of +10 and +88 sites also resulted in 40% reduction of promoter activity. Reactivation of MAT1A correlated with demethylation of +10 and +88. In vitro transcription assay showed that methylation or mutation of +10 and +88 sites reduced transcription. In conclusion, our data support the novel finding that methylation of the MAT1A coding region can inhibit gene transcription. This represents a key mechanism for decreased MAT1A expression in HCC and a target for therapy. To our knowledge, this is the first example of coding region methylation inhibiting transcription of a mammalian gene. PMID:21678410

  20. Molecular analysis of human argininosuccinate lyase: mutant characterization and alternative splicing of the coding region.

    PubMed Central

    Walker, D C; McCloskey, D A; Simard, L R; McInnes, R R

    1990-01-01

    Argininosuccinic acid lyase (ASAL) deficiency is a clinically heterogeneous autosomal recessive urea cycle disorder. We previously established by complementation analysis that 28 ASAL-deficient patients have heterogeneous mutations in a single gene. To prove that the ASAL structural gene is the affected locus, we sequenced polymerase chain reaction-amplified ASAL cDNA of a representative mutant from the single complementation group. Fibroblast strain 944 (approximately 1% of residual ASAL activity), from a late-onset patient who was the product of a consanguineous mating, had only a single base-pair change in the coding region, a C-283----T transition at a CpG dinucleotide in exon 3. This substitution converts Arg-95 to Cys (R95C), occurs in a stretch of 13 residues that is identical in yeast and human ASAL, and was present in both of the patient's alleles but not in 14 other mutant or 10 normal alleles. Expression in COS cells demonstrated that the R95C mutation produces normal amounts of ASAL mRNA but little protein and less than 1% ASAL activity. We observed that amplified cDNA from mutant 944 and normal cells (liver, keratinocytes, lymphoblasts, and fibroblasts) contained, in addition to the expected 5' 513-base-pair band, a prominent 318-base-pair ASAL band formed by the splicing of exon 2 from the transcript. The short transcript maintains the ASAL reading frame but removes Lys-51, a residue that may be essential for catalysis, since it binds the argininosuccinate substrate. We conclude (i) that the identification of the R95C mutation in strain 944 demonstrates that virtually all ASAL deficiency results from defects in the ASAL structural gene and (ii) that minor alternative splicing of the coding region occurs at the ASAL locus. Images PMID:2263616

  1. Molecular analysis of human argininosuccinate lyase: Mutant characterization and alternative splicing of the coding region

    SciTech Connect

    Walker, D.C. ); McCloskey, D.A.; Simard, L.R.; McInnes, R.R. )

    1990-12-01

    Argininosuccinic acid lyase (ASAL) deficiency is a clinically heterogeneous autosomal recessive urea cycle disorder. The authors previously established by complementation analysis that 29 ASAL-deficient patients have heterogeneous mutations in a single gene. To prove that the ASAL structural gene is the affected locus, they sequenced polymerase chain reaction-amplified ASAL cDNA of a representative mutant from the single complementation group. Fibroblast strain 944 from a late-onset patient who was the product of a consanguineous mating, had only a single base-pair change in the coding region, a C-283{r arrow} T transition at a CpG dinucleotide in exon 3. This substitution converts Arg-95 to Cys (R95C), occurs in a stretch of 13 residues that is identical in yeast and human ASAL, and was present in both of the patient's alleles but not in 14 other mutant or 10 normal alleles. They observed that amplified cDNA from mutant 944 and normal cells (liver, keratinocytes, lymphoblasts, and fibroblasts) contained, in addition to the expected 5{prime} 513-base-pair band, a prominent 318-base-pair ASAL band formed by the splicing of exon 2 from the transcript. The short transcript maintains the ASAL reading frame but removes Lys-51, a residue that may be essential for catalysis, since it binds the argininosuccinate substrate. They conclude (i) that the identification of the R95C mutation in strain 944 demonstrates that virtually all ASAL deficiency results from defects in the ASAL structural gene and (ii) that minor alternative splicing of the coding region occurs at the ASAL locus.

  2. A Two-Locus Global DNA Barcode for Land Plants: The Coding rbcL Gene Complements the Non-Coding trnH-psbA Spacer Region

    PubMed Central

    Kress, W. John; Erickson, David L.

    2007-01-01

    Background A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Methodology/Principal Findings Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. Conclusions/Significance A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination. PMID:17551588

  3. INTERFROST: a benchmark of Thermo-Hydraulic codes for cold regions hydrology

    NASA Astrophysics Data System (ADS)

    Grenier, C. F.; Roux, N.; Costard, F.; Pessel, M.

    2013-12-01

    Large focus was put recently on the impact of climate changes in boreal regions due to the large temperature amplitudes expected. Large portions of these regions, corresponding to permafrost areas, are covered by water bodies (lakes, rivers) with very specific evolution and water budget. These water bodies generate taliks (unfrozen zones below) that may play a key role in the context of climate change. Recent studies and modeling exercises showed that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is a minimal requirement to model and understand the evolution of the river and lake - soil continuum in a changing climate (e.g. Mc Kenzie et al., 2007; Bense et al 2009, Rowland et al 2011; Painter 2011; Grenier et al 2012; Painter et al 2012 and others from the 2012 special issue Hydrogeology Journal: 'Hydrogeology of cold regions'). However, 3D studies are still scarce while numerical approaches can only be validated against analytical solutions for the purely thermal equation with conduction and phase change (e.g. Neumann, Lunardini). When it comes to the coupled TH system (coupling two highly non-linear equations), the only possible approach is to compare different codes on provided test cases and/or to have controlled experiments for validation. We propose here to initiate a benchmark exercise, detail some of its planned test cases (phase I) and invite other research groups to join. This initial phase of the benchmark will consist of some test cases inspired by existing literature (e.g. Mc Kenzie et al., 2007) as well as new ones. Some experimental cases in cold room will complement the validation approach. In view of a Phase II, the project is open as well to other test cases reflecting a numerical or a process oriented interest or answering a more general concern among the cold region community. A further purpose of the benchmark exercise is to propel discussions for the optimization of codes and numerical approaches in order to develop validated and

  4. INTERFROST: a benchmark of Thermo-Hydraulic codes for cold regions hydrology

    NASA Astrophysics Data System (ADS)

    Grenier, Christophe; Roux, Nicolas; Costard, François; Pessel, Marc

    2014-05-01

    Large focus was put recently on the impact of climate changes in boreal regions due to the large temperature amplitudes expected. Large portions of these regions, corresponding to permafrost areas, are covered by water bodies (lakes, rivers) with very specific evolution and water budget. These water bodies generate taliks (unfrozen zones below) that may play a key role in the context of climate change. Recent studies and modeling exercises showed that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is a minimal requirement to model and understand the evolution of the river and lake - soil continuum in a changing climate (e.g. Mc Kenzie et al., 2007; Bense et al 2009, Rowland et al 2011; Painter 2011; Grenier et al 2012; Painter et al 2012 and others from the 2012 special issue Hydrogeology Journal: "Hydrogeology of cold regions"). However, 3D studies are still scarce while numerical approaches can only be validated against analytical solutions for the purely thermal equation with conduction and phase change (e.g. Neumann, Lunardini). When it comes to the coupled TH system (coupling two highly non-linear equations), the only possible approach is to compare different codes on provided test cases and/or to have controlled experiments for validation. We propose here to join the INTERFROST benchmark exercise addressing these issues. We give an overview of some of its test cases (phase I) as well as provide the present stand of the exercise and invite other research groups to join. This initial phase of the benchmark consists of some test cases inspired by existing literature (e.g. Mc Kenzie et al., 2007) as well as new ones. Some experimental cases in cold room complement the validation approach. In view of a Phase II, the project is open as well to other test cases reflecting a numerical or a process oriented interest or answering a more general concern among the cold region community. A further purpose of the benchmark exercise is to propel discussions for the

  5. High frequency oscillations in the intact brain

    PubMed Central

    Buzsáki, György; da Silva, Fernando Lopes

    2016-01-01

    High frequency oscillations (HFOs) constitute a novel trend in neurophysiology that is fascinating neuroscientists in general, and epileptologists in particular. But what are HFOs? What is the frequency range of HFOs? Are there different types of HFOs, physiological and pathological? How are HFOs generated? Can HFOs represent temporal codes for cognitive processes? These questions are pressing and this symposium volume attempts to give constructive answers. As a prelude to this exciting discussion, we summarize the physiological high frequency patterns in the intact brain, concentrating mainly on hippocampal patterns, where the mechanisms of high frequency oscillations are perhaps best understood. PMID:22449727

  6. Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: Evolutionary footprints of RNA silencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pyknons are non-random sequence patterns significantly repeated throughout non-coding genomic DNA that also appear at least once among genes. They are interesting because they portend an unforeseen connection between coding and non-coding DNA. Pyknons have only been discovered in the human genome,...

  7. Sequence Variability in Viral Genome Non-coding Regions Likely Contribute to Observed Differences in Viral Replication Amongst MARV Strains

    PubMed Central

    ALONSO, JESUS A.; PATTERSON, JEAN L.

    2013-01-01

    The Marburg viruses Musoke (MARV-Mus) and Angola (MARV-Ang) have highly similar genomic sequences. Analysis of viral replication using various assays consistently identified MARV-Ang as the faster replicating virus. Non-coding genomic regions of negative sense RNA viruses are known to play a role in viral gene expression. A comparison of the six non-coding regions using bicistronic minigenomes revealed that the first two non-coding regions (NP / VP35 and VP35 / VP40) differed significantly in their transcriptional regulation. Deletion mutation analysis of the MARV-Mus NP / VP35 region further revealed that the MARV polymerase (L) is able to initiate production of the downstream gene without the presence of highly conserved regulatory signals. Bicistronic minigenome assays also identified the VP30 mRNA 5′ untranslated region as an rZAP-targeted RNA motif. Overall, our studies indicate that the high variation of MARV non-coding regions may play a significant role in observed differences in transcription and/or replication. PMID:23510675

  8. Long non-coding RNA containing ultraconserved genomic region 8 promotes bladder cancer tumorigenesis.

    PubMed

    Olivieri, Michele; Ferro, Matteo; Terreri, Sara; Durso, Montano; Romanelli, Alessandra; Avitabile, Concetta; De Cobelli, Ottavio; Messere, Anna; Bruzzese, Dario; Vannini, Ivan; Marinelli, Luciana; Novellino, Ettore; Zhang, Wei; Incoronato, Mariarosaria; Ilardi, Gennaro; Staibano, Stefania; Marra, Laura; Franco, Renato; Perdonà, Sisto; Terracciano, Daniela; Czerniak, Bogdan; Liguori, Giovanna L; Colonna, Vincenza; Fabbri, Muller; Febbraio, Ferdinando; Calin, George A; Cimmino, Amelia

    2016-04-12

    Ultraconserved regions (UCRs) have been shown to originate non-coding RNA transcripts (T-UCRs) that have different expression profiles and play functional roles in the pathophysiology of multiple cancers. The relevance of these functions to the pathogenesis of bladder cancer (BlCa) is speculative. To elucidate this relevance, we first used genome-wide profiling to evaluate the expression of T-UCRs in BlCa tissues. Analysis of two datasets comprising normal bladder tissues and BlCa specimens with a custom T-UCR microarray identified ultraconserved RNA (uc.) 8+ as the most upregulated T-UCR in BlCa tissues, although its expression was lower than in pericancerous bladder tissues. These results were confirmed on BlCa tissues by real-time PCR and by in situ hybridization. Although uc.8+ is located within intron 1 of CASZ1, a zinc-finger transcription factor, the transcribed non-coding RNA encoding uc.8+ is expressed independently of CASZ1. In vitro experiments evaluating the effects of uc.8+ silencing, showed significantly decreased capacities for cancer cell invasion, migration, and proliferation. From this, we proposed and validated a model of interaction in which uc.8+ shuttles from the nucleus to the cytoplasm of BlCa cells, interacts with microRNA (miR)-596, and cooperates in the promotion and development of BlCa. Using computational analysis, we investigated the miR-binding domain accessibility, as determined by base-pairing interactions within the uc.8+ predicted secondary structure, RNA binding affinity, and RNA species abundance in bladder tissues and showed that uc.8+ is a natural decoy for miR-596. Thus uc.8+ upregulation results in increased expression of MMP9, increasing the invasive potential of BlCa cells. These interactions between evolutionarily conserved regions of DNA suggest that natural selection has preserved this potentially regulatory layer that uses RNA to modulate miR levels, opening up the possibility for development of useful markers for

  9. Long non-coding RNA containing ultraconserved genomic region 8 promotes bladder cancer tumorigenesis

    PubMed Central

    Durso, Montano; Romanelli, Alessandra; Avitabile, Concetta; De Cobelli, Ottavio; Messere, Anna; Bruzzese, Dario; Vannini, Ivan; Marinelli, Luciana; Novellino, Ettore; Zhang, Wei; Incoronato, Mariarosaria; Ilardi, Gennaro; Staibano, Stefania; Marra, Laura; Franco, Renato; Perdonà, Sisto; Terracciano, Daniela; Czerniak, Bogdan; Liguori, Giovanna L.; Colonna, Vincenza; Fabbri, Muller; Febbraio, Ferdinando

    2016-01-01

    Ultraconserved regions (UCRs) have been shown to originate non-coding RNA transcripts (T-UCRs) that have different expression profiles and play functional roles in the pathophysiology of multiple cancers. The relevance of these functions to the pathogenesis of bladder cancer (BlCa) is speculative. To elucidate this relevance, we first used genome-wide profiling to evaluate the expression of T-UCRs in BlCa tissues. Analysis of two datasets comprising normal bladder tissues and BlCa specimens with a custom T-UCR microarray identified ultraconserved RNA (uc.) 8+ as the most upregulated T-UCR in BlCa tissues, although its expression was lower than in pericancerous bladder tissues. These results were confirmed on BlCa tissues by real-time PCR and by in situ hybridization. Although uc.8+ is located within intron 1 of CASZ1, a zinc-finger transcription factor, the transcribed non-coding RNA encoding uc.8+ is expressed independently of CASZ1. In vitro experiments evaluating the effects of uc.8+ silencing, showed significantly decreased capacities for cancer cell invasion, migration, and proliferation. From this, we proposed and validated a model of interaction in which uc.8+ shuttles from the nucleus to the cytoplasm of BlCa cells, interacts with microRNA (miR)-596, and cooperates in the promotion and development of BlCa. Using computational analysis, we investigated the miR-binding domain accessibility, as determined by base-pairing interactions within the uc.8+ predicted secondary structure, RNA binding affinity, and RNA species abundance in bladder tissues and showed that uc.8+ is a natural decoy for miR-596. Thus uc.8+ upregulation results in increased expression of MMP9, increasing the invasive potential of BlCa cells. These interactions between evolutionarily conserved regions of DNA suggest that natural selection has preserved this potentially regulatory layer that uses RNA to modulate miR levels, opening up the possibility for development of useful markers for

  10. Performance Improvement of the Goertzel Algorithm in Estimating of Protein Coding Regions Using Modified Anti-notch Filter and Linear Predictive Coding Model

    PubMed Central

    Farsani, Mahsa Saffari; Sahhaf, Masoud Reza Aghabozorgi; Abootalebi, Vahid

    2016-01-01

    The aim of this paper is to improve the performance of the conventional Goertzel algorithm in determining the protein coding regions in deoxyribonucleic acid (DNA) sequences. First, the symbolic DNA sequences are converted into numerical signals using electron ion interaction potential method. Then by combining the modified anti-notch filter and linear predictive coding model, we proposed an efficient algorithm to achieve the performance improvement in the Goertzel algorithm for estimating genetic regions. Finally, a thresholding method is applied to precisely identify the exon and intron regions. The proposed algorithm is applied to several genes, including genes available in databases BG570 and HMR195 and the results are compared to other methods based on the nucleotide level evaluation criteria. Results demonstrate that our proposed method reduces the number of incorrect nucleotides which are estimated to be in the noncoding region. In addition, the area under the receiver operating characteristic curve has improved by the factor of 1.35 and 1.12 in HMR195 and BG570 datasets respectively, in comparison with the conventional Goertzel algorithm. PMID:27563569

  11. Performance Improvement of the Goertzel Algorithm in Estimating of Protein Coding Regions Using Modified Anti-notch Filter and Linear Predictive Coding Model.

    PubMed

    Farsani, Mahsa Saffari; Sahhaf, Masoud Reza Aghabozorgi; Abootalebi, Vahid

    2016-01-01

    The aim of this paper is to improve the performance of the conventional Goertzel algorithm in determining the protein coding regions in deoxyribonucleic acid (DNA) sequences. First, the symbolic DNA sequences are converted into numerical signals using electron ion interaction potential method. Then by combining the modified anti-notch filter and linear predictive coding model, we proposed an efficient algorithm to achieve the performance improvement in the Goertzel algorithm for estimating genetic regions. Finally, a thresholding method is applied to precisely identify the exon and intron regions. The proposed algorithm is applied to several genes, including genes available in databases BG570 and HMR195 and the results are compared to other methods based on the nucleotide level evaluation criteria. Results demonstrate that our proposed method reduces the number of incorrect nucleotides which are estimated to be in the noncoding region. In addition, the area under the receiver operating characteristic curve has improved by the factor of 1.35 and 1.12 in HMR195 and BG570 datasets respectively, in comparison with the conventional Goertzel algorithm. PMID:27563569

  12. Deep sequencing of the tobacco mitochondrial transcriptome reveals expressed ORFs and numerous editing sites outside coding regions

    PubMed Central

    2014-01-01

    Background The purpose of this study was to sequence and assemble the tobacco mitochondrial transcriptome and obtain a genomic-level view of steady-state RNA abundance. Plant mitochondrial genomes have a small number of protein coding genes with large and variably sized intergenic spaces. In the tobacco mitogenome these intergenic spaces contain numerous open reading frames (ORFs) with no clear function. Results The assembled transcriptome revealed distinct monocistronic and polycistronic transcripts along with large intergenic spaces with little to no detectable RNA. Eighteen of the 117 ORFs were found to have steady-state RNA amounts above background in both deep-sequencing and qRT-PCR experiments and ten of those were found to be polysome associated. In addition, the assembled transcriptome enabled a full mitogenome screen of RNA C→U editing sites. Six hundred and thirty five potential edits were found with 557 occurring within protein-coding genes, five in tRNA genes, and 73 in non-coding regions. These sites were found in every protein-coding transcript in the tobacco mitogenome. Conclusion These results suggest that a small number of the ORFs within the tobacco mitogenome may produce functional proteins and that RNA editing occurs in coding and non-coding regions of mitochondrial transcripts. PMID:24433288

  13. The PPAR{gamma} coding region and its role in visceral obesity

    SciTech Connect

    Boon Yin, Khoo Najimudin, Nazalan; Muhammad, Tengku Sifzizul Tengku

    2008-06-27

    Peroxisome proliferator-activated receptor gamma (PPAR{gamma}) is a ligand activated transcription factor, plays many essential roles of biological function in higher organisms. The PPAR{gamma} is mainly expressed in adipose tissue. It regulates the transcriptional activity of genes by binding with other transcription factor. The PPAR{gamma} coding region has been found to be closest to that of monkey in ours and other research groups. Thus, monkey is a more suitable animal model for future PPAR{gamma} studying, although mice and rat are frequently being used. The PPAR{gamma} is involved in regulating alterations of adipose tissue masses result from changes in mature adipocyte size and/or number through a complex interplay process called adipogenesis. However, the role of PPAR{gamma} in negatively regulating the process of adipogenesis remains unclear. This review may help we investigate the differential expression of key transcription factor in adipose tissue in response to visceral obesity-induced diet in vivo. The study may also provide valuable information to define a more appropriate physiological condition in adipogenesis which may help to prevent diseases cause by negative regulation of the transcription factors in adipose tissue.

  14. Detection of short protein coding regions within the cyanobacterium genome: application of the hidden Markov model.

    PubMed

    Yada, T; Hirosawa, M

    1996-12-31

    The gene-finding programs developed so far have not paid much attention to the detection of short protein coding regions (CDSs). However, the detection of short CDSs is important for the study of photosynthesis. We utilized GeneHacker, a gene-finding program based on the hidden Markov model (HMM), to detect short CDSs (from 90 to 300 bases) in a 1.0 mega contiguous sequence of cyanobacterium Synechocystis sp. strain PCC6803 which carries a complete set of genes for oxygenic photosynthesis. GeneHacker differs from other gene-finding programs based on the HMM in that it utilizes di-codon statistics as well. GeneHacker successfully detected seven out of the eight short CDSs annotated in this sequence and was clearly superior to GeneMark in this range of length. GeneHacker detected 94 potentially new CDSs, 9 of which have counterparts in the genetic databases. Four of the nine CDSs were less than 150 bases and were photosynthesis-related genes. The results show the effectiveness of GeneHacker in detecting very short CDSs corresponding to genes. PMID:9097038

  15. A 5'-regulatory region and two coding region polymorphisms modulate promoter activity and gene expression of the growth suppressor gene ZBED6 in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Zinc finger, BED-type containing 6 (ZBED6) is an important transcription factor in placental mammals, affecting development, cell proliferation, and growth. Polymorphisms in its promoter and coding regions are likely to impact ZBED6 transcription and growth traits. In this study, a total of three no...

  16. In silico screening of the chicken genome for overlaps between genomic regions: microRNA genes, coding and non-coding transcriptional units, QTL, and genetic variations.

    PubMed

    Zorc, Minja; Kunej, Tanja

    2016-05-01

    MicroRNAs (miRNAs) are a class of non-coding RNAs involved in posttranscriptional regulation of target genes. Regulation requires complementarity between target mRNA and the mature miRNA seed region, responsible for their recognition and binding. It has been estimated that each miRNA targets approximately 200 genes, and genetic variability of miRNA genes has been reported to affect phenotypic variability and disease susceptibility in humans, livestock species, and model organisms. Polymorphisms in miRNA genes could therefore represent biomarkers for phenotypic traits in livestock animals. In our previous study, we collected polymorphisms within miRNA genes in chicken. In the present study, we identified miRNA-related genomic overlaps to prioritize genomic regions of interest for further functional studies and biomarker discovery. Overlapping genomic regions in chicken were analyzed using the following bioinformatics tools and databases: miRNA SNiPer, Ensembl, miRBase, NCBI Blast, and QTLdb. Out of 740 known pre-miRNA genes, 263 (35.5 %) contain polymorphisms; among them, 35 contain more than three polymorphisms The most polymorphic miRNA genes in chicken are gga-miR-6662, containing 23 single nucleotide polymorphisms (SNPs) within the pre-miRNA region, including five consecutive SNPs, and gga-miR-6688, containing ten polymorphisms including three consecutive polymorphisms. Several miRNA-related genomic hotspots have been revealed in chicken genome; polymorphic miRNA genes are located within protein-coding and/or non-coding transcription units and quantitative trait loci (QTL) associated with production traits. The present study includes the first description of an exonic miRNA in a chicken genome, an overlap between the miRNA gene and the exon of the protein-coding gene (gga-miR-6578/HADHB), and the first report of a missense polymorphism located within a mature miRNA seed region. Identified miRNA-related genomic hotspots in chicken can serve researchers as a

  17. Modeling the physical structure of star-forming regions with LIME, a 3D radiative transfer code

    NASA Astrophysics Data System (ADS)

    Quénard, D.; Bottinelli, S.; Caux, E.

    2016-05-01

    The ability to predict line emission is crucial in order to make a comparison with observations. From LTE to full radiative transfer codes, the goal is always to derive the most accurately possible the physical properties of the source. Non-LTE calculations can be very time consuming but are needed in most of the cases since many studied regions are far from LTE.

  18. The destabilizing elements in the coding region of c-fos mRNA are recognized as RNA.

    PubMed Central

    Wellington, C L; Greenberg, M E; Belasco, J G

    1993-01-01

    The protein-coding region of the c-fos proto-oncogene transcript contains elements that direct the rapid deadenylation and decay of this mRNA in mammalian cells. The function of these coding region instability determinants requires movement of ribosomes across mRNAs containing them. Three types of mechanisms could account for this translational requirement. Two of these possibilities, (i) that rapid mRNA decay might be mediated by the nascent polypeptide chain and (ii) that it might result from an unusual codon usage, have experimental precedent. Here, we present evidence that the destabilizing elements in the c-fos coding region are not recognized in either of these two ways. Instead, the ability of the c-fos coding region to function as a potent mRNA destabilizer when translated in the +1 reading frame indicates that the signals for rapid deadenylation and decay reside in the sequence or structure of the RNA comprising this c-fos domain. Images PMID:8336733

  19. Intact capture of hypervelocity particles

    NASA Technical Reports Server (NTRS)

    Tsou, P.; Brownlee, D. E.; Albee, A. L.

    1986-01-01

    Knowledge of the phase, structure, and crystallography of cosmic particles, as well as their elemental and isotopic compositions, would be very valuable information toward understanding the nature of our solar system. This information can be obtained from the intact capture of large mineral grains of cosmic particles from hypervelocity impacts. Hypervelocity experiments of intact capture in underdense media have indicated realistic potential in this endeaver. The recovery of the thermal blankets and louvers from the Solar Max spacecraft have independently verified this potential in the unintended capture of cosmic materials from hypervelocity impacts. Passive underdense media will permit relatively simple and inexpensive missions to capture cosmic particles intact, either by going to a planetary body or by waiting for the particles to come to the Shuttle or the Space Station. Experiments to explore the potential of using various underdense media for an intact comet sample capture up to 6.7 km/s were performed at NASA Ames Research Center Vertical Gun Range. Explorative hypervelocity experiments up to 7.9 km/s were also made at the Ernst Mach Institute. These experiments have proven that capturing intact particles at hypervelocity impacts is definitely possible. Further research is being conducted to achieve higher capture ratios at even higher hypervelocities for even smaller projectiles.

  20. Intact capture of hypervelocity particles

    NASA Astrophysics Data System (ADS)

    Tsou, P.; Brownlee, D. E.; Albee, A. L.

    Knowledge of the phase, structure, and crystallography of cosmic particles, as well as their elemental and isotopic compositions, would be very valuable information toward understanding the nature of our solar system. This information can be obtained from the intact capture of large mineral grains of cosmic particles from hypervelocity impacts. Hypervelocity experiments of intact capture in underdense media have indicated realistic potential in this endeaver. The recovery of the thermal blankets and louvers from the Solar Max spacecraft have independently verified this potential in the unintended capture of cosmic materials from hypervelocity impacts. Passive underdense media will permit relatively simple and inexpensive missions to capture cosmic particles intact, either by going to a planetary body or by waiting for the particles to come to the Shuttle or the Space Station. Experiments to explore the potential of using various underdense media for an intact comet sample capture up to 6.7 km/s were performed at NASA Ames Research Center Vertical Gun Range. Explorative hypervelocity experiments up to 7.9 km/s were also made at the Ernst Mach Institute. These experiments have proven that capturing intact particles at hypervelocity impacts is definitely possible. Further research is being conducted to achieve higher capture ratios at even higher hypervelocities for even smaller projectiles.

  1. Roles of DNA mutation in the coding region and DNA methylation in the 5' flanking region of BRCA1 in canine mammary tumors.

    PubMed

    Qiu, Hengbin; Lin, Deigui

    2016-07-01

    The Breast cancer 1, early onset gene (BRCA1) is known to be significantly associated with human familial breast cancer and is identified to play an important role in canine mammary tumors. Here, genetic variations in the coding region and DNA methylation in the 5' flanking region of BRCA1 in canine mammary tumor samples, 15 each of benign and malignant against 10 normal canine mammary tissue samples, were analyzed using the direct sequencing method. The results indicated two point mutations each in the coding region of canine BRCA1 in one benign mammary tumor sample (4702G >T and 4765G >T) and in one malignant canine mammary tumor sample (3619A >G and 4006G >A). No mutations were detected in the normal canine mammary tissue samples. The 4702G >T mutation was found to terminate further translation. The physical effect of the 4765G >T mutation was found to be the repalacement of the glutamate residue with glutamine. The physical effect of the 3619A >G mutation was found to be the replacement of the threonine residue with alanine, and that of mutation 4006G >A was the replacement of the valine residue with isoleucine in the BRCA1 protein. Bisulfite sequencing detected methylated CpG sites in one canine malignant mammary tumor sample. In conclusion, the present study elucidated the mutational status of the BRCA1 coding region and methylation status of the 5' flanking region of BRCA1 in canine mammary tumors. PMID:26888582

  2. Roles of DNA mutation in the coding region and DNA methylation in the 5′ flanking region of BRCA1 in canine mammary tumors

    PubMed Central

    QIU, Hengbin; LIN, Deigui

    2016-01-01

    The Breast cancer 1, early onset gene (BRCA1) is known to be significantly associated with human familial breast cancer and is identified to play an important role in canine mammary tumors. Here, genetic variations in the coding region and DNA methylation in the 5′ flanking region of BRCA1 in canine mammary tumor samples, 15 each of benign and malignant against 10 normal canine mammary tissue samples, were analyzed using the direct sequencing method. The results indicated two point mutations each in the coding region of canine BRCA1 in one benign mammary tumor sample (4702G >T and 4765G >T) and in one malignant canine mammary tumor sample (3619A >G and 4006G >A). No mutations were detected in the normal canine mammary tissue samples. The 4702G >T mutation was found to terminate further translation. The physical effect of the 4765G >T mutation was found to be the repalacement of the glutamate residue with glutamine. The physical effect of the 3619A >G mutation was found to be the replacement of the threonine residue with alanine, and that of mutation 4006G >A was the replacement of the valine residue with isoleucine in the BRCA1 protein. Bisulfite sequencing detected methylated CpG sites in one canine malignant mammary tumor sample. In conclusion, the present study elucidated the mutational status of the BRCA1 coding region and methylation status of the 5′ flanking region of BRCA1 in canine mammary tumors. PMID:26888582

  3. Evolutionary connections between coding and splicing regulatory regions in the fibronectin EDA exon.

    PubMed

    Zago, Paola; Buratti, Emanuele; Stuani, Cristiana; Baralle, Francisco E

    2011-08-01

    Research on exonic coding sequences has demonstrated that many substitutions at the amino acid level may also reflect profound changes at the level of splicing regulatory regions. These results have revealed that, for many alternatively spliced exons, there is considerable pressure to strike a balance between two different and sometimes conflicting forces: the drive to improve the quality and production efficiency of proteins and the maintenance of proper exon recognition by the splicing machinery. Up to now, the systems used to investigate these connections have mostly focused on short alternatively spliced exons that contain a high density of splicing regulatory elements. Although this is obviously a desirable feature in order to maximize the chances of spotting connections, it also complicates the process of drawing straightforward evolutionary pathways between different species (because of the numerous alternative pathways through which the same end point can be achieved). The alternatively spliced fibronectin extra domain A exon (also referred to as EDI or EIIIA) does not have these limitations, as its inclusion is already known to depend on a single exonic splicing enhancer element within its sequence. In this study, we have compared the rat and human fibronectin EDA exons with regard to RNA structure, exonic splicing enhancer strengths, and SR protein occupancy. The results gained from these analyses have then been used to perform an accurate evaluation of EDA sequences observed in a wide range of animal species. This comparison strongly suggests the existence of an evolutionary connection between changes at the nucleotide levels and the need to maintain efficient EDA recognition in different species. PMID:21663748

  4. Intact capture of cosmic dust

    NASA Technical Reports Server (NTRS)

    Tsou, P.

    1991-01-01

    The focus of this development effort is to capture dust particles at hypervelocities intact and unmelted in order to preserve volatile organics. At the same time, the capture process must minimize any organic elemental or compound contamination to prevent any compromise of exobiological analyses. Inorganic silicate aerogel has been developed as a successful capture medium to satisfy both requirements of intact capture and minimal organic contamination. Up to 6 km/s, silicate projectiles from a few microns up to 100 microns have been captured intact without any melting and with minimal loss of mass. Carbon in silicate aerogel can be reduced to less than 1 part in 1000 and hydrogen 3 parts in 1000 when baked in air. Under controlled inert gas environments, additional hydrocarbon reduction can be achieved.

  5. Transcriptional activator elements for curtovirus C1 expression reside in the 3' coding region of ORF C1.

    PubMed

    Hur, Jingyung; Buckley, Kenneth; Lee, Sukchan; Davis, Keith

    2007-02-28

    Beet curly top virus (BCTV) and Beet severe curly top virus (BSCTV), members of curtoviruses, encode seven open reading frames (ORFs) within a approximately 3 kb genome. One of these viral ORFs, C1, is known to play an important role in the early stage of viral infection in plants during initiation of viral DNA replication. We used promoter:: reporter (beta-glucuronidase) gene fusions in transgenic Ara-bidopsis to identify the putative promoter region of BCTV ORF C1. Unlike other geminiviruses, the intergenic region of BCTV was not sufficient to promote C1 expression in transgenic plants. When sequences extending into the coding region of C1 were tested, strong expression of the reporter protein was observed in vascular tissues of transgenic plants. This expression was not dependent on the presence of the intergenic regions or proximal 5' portions of the C1 coding region. Transgenic plants expressing a reporter gene under control of the putative complete C1 promoter were inoculated with virus to determine if any viral transcript affected C1 expression. Virus inoculated plants did not show any altered pattern or change in of reporter gene expression level. These results suggest that (1) important transcriptional activator elements for C1 expression reside in the 3' portion of C1 coding area itself, (2) C1 protein does not auto-regulate its own expression and (3) C1 expression of two curtoviruses is controlled differently compared to other geminiviruses. PMID:17464215

  6. NHEXAS PHASE I REGION 5 STUDY--STANDARD OPERATING PROCEDURE--SAMPLE CODING, LABELING, AND FIELD TRACKING PROCEDURES (RTI/ACS-AP-209-070)

    EPA Science Inventory

    This protocol defines the coding scheme, labeling procedures, and field tracking for samples collected in the NHEXAS Region 5 study. Unique sample codes were assigned to all personal, environmental, biological, and quality control samples. A label bearing the code in both bar cod...

  7. Suppression of adult neurogenesis impairs population coding of similar contexts in hippocampal CA3 region

    PubMed Central

    Niibori, Yosuke; Yu, Tzong-Shiue; Epp, Jonathan R.; Akers, Katherine G.; Josselyn, Sheena A.; Frankland, Paul W.

    2016-01-01

    Different places may share common features, but are coded by distinct populations of CA3 neurons in the hippocampus. Here we show that chemical or genetic suppression of adult neurogenesis in the hippocampus impairs this population-based coding of similar (but not dissimilar) contexts. These data provide a neural basis for impaired spatial discrimination following ablation of adult neurogenesis, and support the proposal that adult neurogenesis regulates the efficiency of a pattern separation process in the hippocampus. PMID:23212382

  8. Fast Mode Decision in the HEVC Video Coding Standard by Exploiting Region with Dominated Motion and Saliency Features

    PubMed Central

    Podder, Pallab Kanti; Paul, Manoranjan; Murshed, Manzur

    2016-01-01

    The emerging High Efficiency Video Coding (HEVC) standard introduces a number of innovative and powerful coding tools to acquire better compression efficiency compared to its predecessor H.264. The encoding time complexities have also increased multiple times that is not suitable for realtime video coding applications. To address this limitation, this paper employs a novel coding strategy to reduce the time complexity in HEVC encoder by efficient selection of appropriate block-partitioning modes based on human visual features (HVF). The HVF in the proposed technique comprise with human visual attention modelling-based saliency feature and phase correlation-based motion features. The features are innovatively combined through a fusion process by developing a content-based adaptive weighted cost function to determine the region with dominated motion/saliency (RDMS)- based binary pattern for the current block. The generated binary pattern is then compared with a codebook of predefined binary pattern templates aligned to the HEVC recommended block-paritioning to estimate a subset of inter-prediction modes. Without exhaustive exploration of all modes available in the HEVC standard, only the selected subset of modes are motion estimated and motion compensated for a particular coding unit. The experimental evaluation reveals that the proposed technique notably down-scales the average computational time of the latest HEVC reference encoder by 34% while providing similar rate-distortion (RD) performance for a wide range of video sequences. PMID:26963813

  9. High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region.

    PubMed

    Sati, Satish; Tanwar, Vinay Singh; Kumar, K Anand; Patowary, Ashok; Jain, Vaibhav; Ghosh, Sourav; Ahmad, Shadab; Singh, Meghna; Reddy, S Umakar; Chandak, Giriraj Ratan; Raghunath, Manchala; Sivasubbu, Sridhar; Chakraborty, Kausik; Scaria, Vinod; Sengupta, Shantanu

    2012-01-01

    DNA methylation is crucial for gene regulation and maintenance of genomic stability. Rat has been a key model system in understanding mammalian systemic physiology, however detailed rat methylome remains uncharacterized till date. Here, we present the first high resolution methylome of rat liver generated using Methylated DNA immunoprecipitation and high throughput sequencing (MeDIP-Seq) approach. We observed that within the DNA/RNA repeat elements, simple repeats harbor the highest degree of methylation. Promoter hypomethylation and exon hypermethylation were common features in both RefSeq genes and expressed genes (as evaluated by proteomic approach). We also found that although CpG islands were generally hypomethylated, about 6% of them were methylated and a large proportion (37%) of methylated islands fell within the exons. Notably, we obeserved significant differences in methylation of terminal exons (UTRs); methylation being more pronounced in coding/partially coding exons compared to the non-coding exons. Further, events like alternate exon splicing (cassette exon) and intron retentions were marked by DNA methylation and these regions are retained in the final transcript. Thus, we suggest that DNA methylation could play a crucial role in marking coding regions thereby regulating alternative splicing. Apart from generating the first high resolution methylome map of rat liver tissue, the present study provides several critical insights into methylome organization and extends our understanding of interplay between epigenome, gene expression and genome stability. PMID:22355382

  10. Overexpression of KLC2 due to a homozygous deletion in the non-coding region causes SPOAN syndrome.

    PubMed

    Melo, Uirá S; Macedo-Souza, Lucia I; Figueiredo, Thalita; Muotri, Alysson R; Gleeson, Joseph G; Coux, Gabriela; Armas, Pablo; Calcaterra, Nora B; Kitajima, João P; Amorim, Simone; Olávio, Thiago R; Griesi-Oliveira, Karina; Coatti, Giuliana C; Rocha, Clarissa R R; Martins-Pinheiro, Marinalva; Menck, Carlos F M; Zaki, Maha S; Kok, Fernando; Zatz, Mayana; Santos, Silvana

    2015-12-15

    SPOAN syndrome is a neurodegenerative disorder mainly characterized by spastic paraplegia, optic atrophy and neuropathy (SPOAN). Affected patients are wheelchair bound after 15 years old, with progressive joint contractures and spine deformities. SPOAN patients also have sub normal vision secondary to apparently non-progressive congenital optic atrophy. A potential causative gene was mapped at 11q13 ten years ago. Here we performed next-generation sequencing in SPOAN-derived samples. While whole-exome sequencing failed to identify the causative mutation, whole-genome sequencing allowed to detect a homozygous 216-bp deletion (chr11.hg19:g.66,024,557_66,024,773del) located at the non-coding upstream region of the KLC2 gene. Expression assays performed with patient's fibroblasts and motor neurons derived from SPOAN patients showed KLC2 overexpression. Luciferase assay in constructs with 216-bp deletion confirmed the overexpression of gene reporter, varying from 48 to 74%, as compared with wild-type. Knockdown and overexpression of klc2 in Danio rerio revealed mild to severe curly-tail phenotype, which is suggestive of a neuromuscular disorder. Overexpression of a gene caused by a small deletion in the non-coding region is a novel mechanism, which to the best of our knowledge, was never reported before in a recessive condition. Although the molecular mechanism of KLC2 up-regulation still remains to be uncovered, such example adds to the importance of non-coding regions in human pathology. PMID:26385635

  11. Development of an efficient entire-capsid-coding-region amplification method for direct detection of poliovirus from stool extracts.

    PubMed

    Arita, Minetaro; Kilpatrick, David R; Nakamura, Tomofumi; Burns, Cara C; Bukbuk, David; Oderinde, Soji B; Oberste, M Steven; Kew, Olen M; Pallansch, Mark A; Shimizu, Hiroyuki

    2015-01-01

    Laboratory diagnosis has played a critical role in the Global Polio Eradication Initiative since 1988, by isolating and identifying poliovirus (PV) from stool specimens by using cell culture as a highly sensitive system to detect PV. In the present study, we aimed to develop a molecular method to detect PV directly from stool extracts, with a high efficiency comparable to that of cell culture. We developed a method to efficiently amplify the entire capsid coding region of human enteroviruses (EVs) including PV. cDNAs of the entire capsid coding region (3.9 kb) were obtained from as few as 50 copies of PV genomes. PV was detected from the cDNAs with an improved PV-specific real-time reverse transcription-PCR system and nucleotide sequence analysis of the VP1 coding region. For assay validation, we analyzed 84 stool extracts that were positive for PV in cell culture and detected PV genomes from 100% of the extracts (84/84 samples) with this method in combination with a PV-specific extraction method. PV could be detected in 2/4 stool extract samples that were negative for PV in cell culture. In PV-positive samples, EV species C viruses were also detected with high frequency (27% [23/86 samples]). This method would be useful for direct detection of PV from stool extracts without using cell culture. PMID:25339406

  12. German Minority Children in the Danish Border Region: Code-Switching and Interference.

    ERIC Educational Resources Information Center

    Pedersen, Karen Margrethe

    1987-01-01

    Children from the German minority in Denmark were studied as part of a longitudinal sociolinguistic research project. Most spoke the Jutland (a Danish) dialect and picked up German as a second language when they started preschool, resulting in code-switching and interference in some cases, which appear to be manifestations of linguistic creativity…

  13. Monitoring Intact Viruses Using Aptamers.

    PubMed

    Kumar, Penmetcha K R

    2016-01-01

    Viral diagnosis and surveillance are necessary steps in containing the spread of viral diseases, and they help in the deployment of appropriate therapeutic interventions. In the past, the commonly employed viral detection methods were either cell-culture or molecule-level assays. Most of these assays are laborious and expensive, require special facilities, and provide a slow diagnosis. To circumvent these limitations, biosensor-based approaches are becoming attractive, especially after the successful commercialization of glucose and other biosensors. In the present article, I have reviewed the current progress using the biosensor approach for detecting intact viruses. At the time of writing this review, three types of bioreceptor surfaces (antibody-, glycan-, and aptamer-based) have been explored on different sensing platforms for detecting intact viruses. Among these bioreceptors, aptamer-based sensors have been increasingly explored for detecting intact viruses using surface plasmon resonance (SPR) and other platforms. Special emphasis is placed on the aptamer-based SPR platform in the present review. PMID:27527230

  14. Systematic screening for mutations in the promoter and the coding region of the 5-HT{sub 1A} gene

    SciTech Connect

    Erdmann, J.; Shimron-Abarbanell, D.; Cichon, S.

    1995-10-09

    In the present study we sought to identify genetic variation in the 5-HT{sub 1A} receptor gene which through alteration of protein function or level of expression might contribute to the genetic predisposition to neuropsychiatric diseases. Genomic DNA samples from 159 unrelated subjects (including 45 schizophrenic, 46 bipolar affective, and 43 patients with Tourette`s syndrome, as well as 25 healthy controls) were investigated by single-strand conformation analysis. Overlapping PCR (polymerase chain reaction) fragments covered the whole coding sequence as well as the 5{prime} untranslated region of the 5-HT{sub 1A} gene. The region upstream to the coding sequence we investigated contains a functional promoter. We found two rare nucleotide sequence variants. Both mutations are located in the coding region of the gene: a coding mutation (A{yields}G) in nucleotide position 82 which leads to an amino acid exchange (Ile{yields}Val) in position 28 of the receptor protein and a silent mutation (C{yields}T) in nucleotide position 549. The occurrence of the Ile-28-Val substitution was studied in an extended sample of patients (n = 352) and controls (n = 210) but was found in similar frequencies in all groups. Thus, this mutation is unlikely to play a significant role in the genetic predisposition to the diseases investigated. In conclusion, our study does not provide evidence that the 5-HT{sub 1A} gene plays either a major or a minor role in the genetic predisposition to schizophrenia, bipolar affective disorder, or Tourette`s syndrome. 29 refs., 4 figs., 1 tab.

  15. Modeling Star-Forming Regions using a 3D Molecular Transport Code

    NASA Astrophysics Data System (ADS)

    Loughnane, R. M.; Redman, M. P.; Keto, E. R.

    2012-07-01

    This paper presents the 3-dimensional non-LTE radiative transfer code, MOLLIE (MOLelcular LIne Explorer), for solving molecular and atomic excitation and radiation transfer in a molecular gas and predicting emergent spectra. The code implementation makes use of the Accelerated Lambda Iteration (ALI) method of Rybicki & Hummer (1991) to solve the radiative transfer equation along rays passing through a spherical model cloud. When convergence between level populations, the radiation field, and the point separation has been obtained, the grid is ray-traced to produce images that can be readily compared to observations. The optimization technique, Fast Simulated Annealing (FSA), adopted by MOLLIE to increase the probability of arriving at a satisfactory output in a timely fashion, is briefly considered.

  16. Language and Williams syndrome: how intact is "intact"?

    PubMed

    Karmiloff-Smith, A; Grant, J; Berthoud, I; Davies, M; Howlin, P; Udwin, O

    1997-04-01

    It has been claimed that Williams syndrome (WS), a rare neurodevelopmental disorder, is characterized by serious cognitive deficits alongside intact language. The syndrome is often used as a prime example of the modularity of an innate faculty for morphosyntactic rules. We challenge this claim and hypothesize that morphosyntax, although surprisingly good given WS level of mental retardation, is by no means intact. We make an initial test of this hypothesis through an analysis of the receptive language of a group of English-speaking WS individuals on a standardized morphosyntactic test. We then present an experimental study of expressive language that examines grammatical gender assignment in French-speaking WS patients. Despite a Verbal Mental Age selected to be higher than the chronological age of the young control group, these people with WS continue even in adulthood to show clear-cut deficits in their production of an aspect of morphosyntax that normal children acquire effortlessly very early. The results of the 2 studies, one focusing on receptive language and the other on expressive language, challenge the notion that comprehension and use of morphosyntactic rules in WS individuals are intact. The Within-domain dissociations regarding the use of grammatical gender assignment across several sentence clements and their difficulties in understanding embedded sentences-two quintessentially linguistic skills-suggest that we must rethink the notion of spared, modular, language capacities in Williams syndrome. We conclude that WS language follows a different path to normal acquisition and may turn out to be more like second language learning. PMID:9180000

  17. Enhanced translation by Nucleolin via G-rich elements in coding and non-coding regions of target mRNAs.

    PubMed

    Abdelmohsen, Kotb; Tominaga, Kumiko; Lee, Eun Kyung; Srikantan, Subramanya; Kang, Min-Ju; Kim, Mihee M; Selimyan, Roza; Martindale, Jennifer L; Yang, Xiaoling; Carrier, France; Zhan, Ming; Becker, Kevin G; Gorospe, Myriam

    2011-10-01

    RNA-binding proteins (RBPs) regulate gene expression at many post-transcriptional levels, including mRNA stability and translation. The RBP nucleolin, with four RNA-recognition motifs, has been implicated in cell proliferation, carcinogenesis and viral infection. However, the subset of nucleolin target mRNAs and the influence of nucleolin on their expression had not been studied at a transcriptome-wide level. Here, we globally identified nucleolin target transcripts, many of which encoded cell growth- and cancer-related proteins, and used them to find a signature motif on nucleolin target mRNAs. Surprisingly, this motif was very rich in G residues and was not only found in the 3'-untranslated region (UTR), but also in the coding region (CR) and 5'-UTR. Nucleolin enhanced the translation of mRNAs bearing the G-rich motif, since silencing nucleolin did not change target mRNA stability, but decreased the size of polysomes forming on target transcripts and lowered the abundance of the encoded proteins. In summary, nucleolin binds G-rich sequences in the CR and UTRs of target mRNAs, many of which encode cancer proteins, and enhances their translation. PMID:21737422

  18. Enhanced translation by Nucleolin via G-rich elements in coding and non-coding regions of target mRNAs

    PubMed Central

    Abdelmohsen, Kotb; Tominaga, Kumiko; Lee, Eun Kyung; Srikantan, Subramanya; Kang, Min-Ju; Kim, Mihee M.; Selimyan, Roza; Martindale, Jennifer L.; Yang, Xiaoling; Carrier, France; Zhan, Ming; Becker, Kevin G.; Gorospe, Myriam

    2011-01-01

    RNA-binding proteins (RBPs) regulate gene expression at many post-transcriptional levels, including mRNA stability and translation. The RBP nucleolin, with four RNA-recognition motifs, has been implicated in cell proliferation, carcinogenesis and viral infection. However, the subset of nucleolin target mRNAs and the influence of nucleolin on their expression had not been studied at a transcriptome-wide level. Here, we globally identified nucleolin target transcripts, many of which encoded cell growth- and cancer-related proteins, and used them to find a signature motif on nucleolin target mRNAs. Surprisingly, this motif was very rich in G residues and was not only found in the 3′-untranslated region (UTR), but also in the coding region (CR) and 5′-UTR. Nucleolin enhanced the translation of mRNAs bearing the G-rich motif, since silencing nucleolin did not change target mRNA stability, but decreased the size of polysomes forming on target transcripts and lowered the abundance of the encoded proteins. In summary, nucleolin binds G-rich sequences in the CR and UTRs of target mRNAs, many of which encode cancer proteins, and enhances their translation. PMID:21737422

  19. Detection of spurious interruptions of protein-coding regions in cloned cDNA sequences by GeneMark analysis.

    PubMed

    Hirosawa, M; Ishikawa, K; Nagase, T; Ohara, O

    2000-09-01

    cDNA is an artificial copy of mRNA and, therefore, no cDNA can be completely free from suspicion of cloning errors. Because overlooking these cloning errors results in serious misinterpretation of cDNA sequences, development of an alerting system targeting spurious sequences in cloned cDNAs is an urgent requirement for massive cDNA sequence analysis. We describe here the application of a modified GeneMark program, originally designed for prokaryotic gene finding, for detection of artifacts in cDNA clones. This program serves to provide a warning when any spurious split of protein-coding regions is detected through statistical analysis of cDNA sequences based on Markov models. In this study, 817 cDNA sequences deposited in public databases by us were subjected to analysis using this alerting system to assess its sensitivity and specificity. The results indicated that any spurious split of protein-coding regions in cloned cDNAs could be sensitively detected and systematically revised by means of this system after the experimental validation of the alerts. Furthermore, this study offered us, for the first time, statistical data regarding the rates and types of errors causing protein-coding splits in cloned cDNAs obtained by conventional cloning methods. PMID:10984451

  20. Development of a multi-region orthogonal curvilinear CFD code for gas turbine combustors

    NASA Astrophysics Data System (ADS)

    Syed, S. A.; Siddons, W. D., Jr.

    1986-06-01

    In the present multiregion curvilinear code for accurately and economically modeling modern gas turbine combustor geometries, the mesh generator and the flow solver are flexible, robust, and economical. Because of the unavoidable presence of sharp corners and the finite area of the computational cells, however, perfect orthogonality cannot be achieved even with this multiregion treatment. Illustrative cases are presented, including constant property flow in an inclined plane channel, turbulent flow in a suddently expanded pipe, a hydrogen horizontal diffusion flame, and an annular dump diffuser with a centerbody.

  1. Massively parallel sequencing of the entire control region and targeted coding region SNPs of degraded mtDNA using a simplified library preparation method.

    PubMed

    Lee, Eun Young; Lee, Hwan Young; Oh, Se Yoon; Jung, Sang-Eun; Yang, In Seok; Lee, Yang-Han; Yang, Woo Ick; Shin, Kyoung-Jin

    2016-05-01

    The application of next-generation sequencing (NGS) to forensic genetics is being explored by an increasing number of laboratories because of the potential of high-throughput sequencing for recovering genetic information from multiple markers and multiple individuals in a single run. A cumbersome and technically challenging library construction process is required for NGS. In this study, we propose a simplified library preparation method for mitochondrial DNA (mtDNA) analysis that involves two rounds of PCR amplification. In the first-round of multiplex PCR, six fragments covering the entire mtDNA control region and 22 fragments covering interspersed single nucleotide polymorphisms (SNPs) in the coding region that can be used to determine global haplogroups and East Asian haplogroups were amplified using template-specific primers with read sequences. In the following step, indices and platform-specific sequences for the MiSeq(®) system (Illumina) were added by PCR. The barcoded library produced using this simplified workflow was successfully sequenced on the MiSeq system using the MiSeq Reagent Nano Kit v2. A total of 0.4 GB of sequences, 80.6% with base quality of >Q30, were obtained from 12 degraded DNA samples and mapped to the revised Cambridge Reference Sequence (rCRS). A relatively even read count was obtained for all amplicons, with an average coverage of 5200 × and a less than three-fold read count difference between amplicons per sample. Control region sequences were successfully determined, and all samples were assigned to the relevant haplogroups. In addition, enhanced discrimination was observed by adding coding region SNPs to the control region in in silico analysis. Because the developed multiplex PCR system amplifies small-sized amplicons (<250 bp), NGS analysis using the library preparation method described here allows mtDNA analysis using highly degraded DNA samples. PMID:26844917

  2. Worldwide HLA-E nucleotide and haplotype variability reveals a conserved gene for coding and 3' untranslated regions.

    PubMed

    Felício, L P; Porto, I O P; Mendes-Junior, C T; Veiga-Castelli, L C; Santos, K E; Vianello-Brondani, R P; Sabbagh, A; Moreau, P; Donadi, E A; Castelli, E C

    2014-02-01

    The human leukocyte antigen-E (HLA-E) locus is a human major histocompatibility complex (MHC) gene associated with immune-modulation and suppression of the immune response by the interaction with specific natural killer (NK) and T cell receptors (TCRs). It is considered one of the most conserved genes of the human MHC; however, this low nucleotide variability seems to be a consequence of the scarce number of studies focusing on this subject. In this manuscript we assessed the nucleotide variability at the HLA-E coding and 3' untranslated regions (3'UTRs) in Brazil and in the populations from the 1000Genomes Consortium. Twenty-eight variable sites arranged into 33 haplotypes were detected and most of these haplotypes (98.2%) are encoding one of the two HLA-E molecules found worldwide, E*01:01 and E*01:03. Moreover, three worldwide spread haplotypes, associated with the coding alleles E*01:01:01, E*01:03:01 and E*01:03:02, account for 85% of all HLA-E haplotypes, suggesting that they arose early before human speciation. In addition, the low nucleotide diversity found for the HLA-E coding and 3'UTR in worldwide populations suggests that the HLA-E gene is in fact a conserved gene, which might be a consequence of its key role in the modulation of the immune system. PMID:24400773

  3. Widespread Differential Expression of Coding Region and 3' UTR Sequences in Neurons and Other Tissues.

    PubMed

    Kocabas, Arif; Duarte, Terence; Kumar, Saranya; Hynes, Mary A

    2015-12-16

    Mature messenger RNAs (mRNAs) consist of coding sequence (CDS) and 5' and 3' UTRs, typically expected to show similar abundance within a given neuron. Examining mRNA from defined neurons, we unexpectedly show extremely common unbalanced expression of cognate 3' UTR and CDS sequences; many genes show high 3' UTR relative to CDS, others show high CDS to 3' UTR. In situ hybridization (19 of 19 genes) shows a broad range of 3' UTR-to-CDS expression ratios across neurons and tissues. Ratios may be spatially graded or change with developmental age but are consistent across animals. Further, for two genes examined, a 3' UTR-to-CDS ratio above a particular threshold in any given neuron correlated with reduced or undetectable protein expression. Our findings raise questions about the role of isolated 3' UTR sequences in regulation of protein expression and highlight the importance of separately examining 3' UTR and CDS sequences in gene expression analyses. PMID:26687222

  4. Histone acetylation: from code to web and router via intrinsically disordered regions.

    PubMed

    Horikoshi, Masami

    2013-01-01

    Structural changes of chromatin, which consists of nucleosomes and nucleosome-associated factors, lead to functional changes that are important determinants of eukaryotic gene regulation. These structural changes are regulated by modifications of histones and DNA, both of which are components of nucleosomes, as well as by replacement of histone variants and the actions of noncoding RNAs. In studies of chromatin modifications, a great deal of attention has been paid to histone acetylation. Progress in understanding this subject has been extensive, including i) elucidation of the relationship of histone acetylation and gene activity; ii) the first isolation of a histonemodifying enzyme; iii) the first identification of a factor that recognizes a modified site; iv) elucidation of the mechanism by which histone modification leads to structural changes in nucleosomes; and v) elucidation of the mechanism of border formation between euchromatin and heterochromatin. Histone acetylation is considered to be fundamental in several fields, including studies of a) the role of chromatin and epigenetics in higher-order biochemical systems such as transcription, DNA replication, and repair; b) biological phenomena such as cell proliferation and differentiation; and c) cancer and aging, potentially leading to clinical applications. In this review, I will discuss the histone code hypothesis, at one time believed to represent a unified theory regarding the functions of histone modification. In addition, I will describe the "modification web theory, " by which the problems in the histone code hypothesis can be overcome, as well as the "signal router theory, " which explains the mechanisms of formation, development, and evolution of the modification web from a structural viewpoint. Lastly, I will illustrate how these novel theories partially explain the robustness of biological systems against various perturbations, and elucidate the strategy that a cell employs to avoid fatal

  5. Discovery of functional non-coding conserved regions in the α-synuclein gene locus

    PubMed Central

    Sterling, Lori; Walter, Michael; Ting, Dennis; Schüle, Birgitt

    2014-01-01

    Several single nucleotide polymorphisms (SNPs) and the Rep-1 microsatellite marker of the α-synuclein ( SNCA) gene have consistently been shown to be associated with Parkinson’s disease, but the functional relevance is unclear. Based on these findings we hypothesized that conserved cis-regulatory elements in the SNCA genomic region regulate expression of SNCA, and that SNPs in these regions could be functionally modulating the expression of SNCA, thus contributing to neuronal demise and predisposing to Parkinson’s disease. In a pair-wise comparison of a 206kb genomic region encompassing the SNCA gene, we revealed 34 evolutionary conserved DNA sequences between human and mouse. All elements were cloned into reporter vectors and assessed for expression modulation in dual luciferase reporter assays.  We found that 12 out of 34 elements exhibited either an enhancement or reduction of the expression of the reporter gene. Three elements upstream of the SNCA gene displayed an approximately 1.5 fold (p<0.009) increase in expression. Of the intronic regions, three showed a 1.5 fold increase and two others indicated a 2 and 2.5 fold increase in expression (p<0.002). Three elements downstream of the SNCA gene showed 1.5 fold and 2.5 fold increase (p<0.0009). One element downstream of SNCA had a reduced expression of the reporter gene of 0.35 fold (p<0.0009) of normal activity. Our results demonstrate that the SNCA gene contains cis-regulatory regions that might regulate the transcription and expression of SNCA. Further studies in disease-relevant tissue types will be important to understand the functional impact of regulatory regions and specific Parkinson’s disease-associated SNPs and its function in the disease process. PMID:25566351

  6. Vulnerability of ecosystems to climate change moderated by habitat intactness.

    PubMed

    Eigenbrod, Felix; Gonzalez, Patrick; Dash, Jadunandan; Steyl, Ilse

    2015-01-01

    The combined effects of climate change and habitat loss represent a major threat to species and ecosystems around the world. Here, we analyse the vulnerability of ecosystems to climate change based on current levels of habitat intactness and vulnerability to biome shifts, using multiple measures of habitat intactness at two spatial scales. We show that the global extent of refugia depends highly on the definition of habitat intactness and spatial scale of the analysis of intactness. Globally, 28% of terrestrial vegetated area can be considered refugia if all natural vegetated land cover is considered. This, however, drops to 17% if only areas that are at least 50% wilderness at a scale of 48×48 km are considered and to 10% if only areas that are at least 50% wilderness at a scale of 4.8×4.8 km are considered. Our results suggest that, in regions where relatively large, intact wilderness areas remain (e.g. Africa, Australia, boreal regions, South America), conservation of the remaining large-scale refugia is the priority. In human-dominated landscapes, (e.g. most of Europe, much of North America and Southeast Asia), focusing on finer scale refugia is a priority because large-scale wilderness refugia simply no longer exist. Action to conserve such refugia is particularly urgent since only 1 to 2% of global terrestrial vegetated area is classified as refugia and at least 50% covered by the global protected area network. PMID:25059822

  7. Efficient random access high resolution region-of-interest (ROI) image retrieval using backward coding of wavelet trees (BCWT)

    NASA Astrophysics Data System (ADS)

    Corona, Enrique; Nutter, Brian; Mitra, Sunanda; Guo, Jiangling; Karp, Tanja

    2008-03-01

    Efficient retrieval of high quality Regions-Of-Interest (ROI) from high resolution medical images is essential for reliable interpretation and accurate diagnosis. Random access to high quality ROI from codestreams is becoming an essential feature in many still image compression applications, particularly in viewing diseased areas from large medical images. This feature is easier to implement in block based codecs because of the inherent spatial independency of the code blocks. This independency implies that the decoding order of the blocks is unimportant as long as the position for each is properly identified. In contrast, wavelet-tree based codecs naturally use some interdependency that exploits the decaying spectrum model of the wavelet coefficients. Thus one must keep track of the decoding order from level to level with such codecs. We have developed an innovative multi-rate image subband coding scheme using "Backward Coding of Wavelet Trees (BCWT)" which is fast, memory efficient, and resolution scalable. It offers far less complexity than many other existing codecs including both, wavelet-tree, and block based algorithms. The ROI feature in BCWT is implemented through a transcoder stage that generates a new BCWT codestream containing only the information associated with the user-defined ROI. This paper presents an efficient technique that locates a particular ROI within the BCWT coded domain, and decodes it back to the spatial domain. This technique allows better access and proper identification of pathologies in high resolution images since only a small fraction of the codestream is required to be transmitted and analyzed.

  8. The functional half-life of an mRNA depends on the ribosome spacing in an early coding region.

    PubMed

    Pedersen, Margit; Nissen, Søren; Mitarai, Namiko; Lo Svenningsen, Sine; Sneppen, Kim; Pedersen, Steen

    2011-03-18

    Bacterial mRNAs are translated by closely spaced ribosomes and degraded from the 5'-end, with half-lives of around 2 min at 37 °C in most cases. Ribosome-free or "naked" mRNA is known to be readily degraded, but the initial event that inactivates the mRNA functionally has not been fully described. Here, we characterize a determinant of the functional stability of an mRNA, which is located in the early coding region. Using literature values for the mRNA half-lives of variant lacZ mRNAs in Escherichia coli, we modeled how the ribosome spacing is affected by the translation rate of the individual codons. When comparing the ribosome spacing at various segments of the mRNA to its functional half-life, we found a clear correlation between the functional mRNA half-life and the ribosome spacing in the mRNA region approximately between codon 20 and codon 45. From this finding, we predicted that inserts of slowly translated codons before codon 20 or after codon 45 should shorten or prolong, respectively, the functional mRNA half-life by altering the ribosome density in the important region. These predictions were tested on eight new lacZ variants, and their experimentally determined mRNA half-lives all supported the model. We thus suggest that translation-rate-mediated differences in the spacing between ribosomes in this early coding region is a parameter that determines the mRNAs functional half-life. We present a model that is in accordance with many earlier observations and that allows a prediction of the functional half-life of a given mRNA sequence. PMID:21255584

  9. Segmentation of DNA into Coding and Noncoding Regions Based on Recursive Entropic Segmentation and Stop-Codon Statistics

    NASA Astrophysics Data System (ADS)

    Nicorici, Daniel; Astola, Jaakko

    2004-12-01

    Heterogeneous DNA sequences can be partitioned into homogeneous domains that are comprised of the four nucleotides A, C, G, and T and the stop-codons. Recursively, we apply a new entropic segmentation method on DNA sequences using Jensen-Shannon and Jensen-Rényi divergences in order to find the borders between coding and noncoding DNA regions. We have chosen 12- and 18-symbol alphabets that capture (i) the differential nucleotide composition in codons, and (ii) the differential stop-codon composition along all the three phases in both strands of the DNA. The new segmentation method is based on the Jensen-Rényi divergence measure, nucleotide statistics, and stop-codon statistics in both DNA strands. The recursive segmentation process requires no prior training on known datasets. Consequently, for three entire genomes of bacteria, we find that the use of nucleotide composition, stop-codon composition, and Jensen-Rényi divergence improve the accuracy of finding the borders between coding and noncoding regions in DNA sequences.

  10. Maternal transcription of non-protein coding RNAs from the PWS-critical region rescues growth retardation in mice.

    PubMed

    Rozhdestvensky, Timofey S; Robeck, Thomas; Galiveti, Chenna R; Raabe, Carsten A; Seeger, Birte; Wolters, Anna; Gubar, Leonid V; Brosius, Jürgen; Skryabin, Boris V

    2016-01-01

    Prader-Willi syndrome (PWS) is a neurogenetic disorder caused by loss of paternally expressed genes on chromosome 15q11-q13. The PWS-critical region (PWScr) contains an array of non-protein coding IPW-A exons hosting intronic SNORD116 snoRNA genes. Deletion of PWScr is associated with PWS in humans and growth retardation in mice exhibiting ~15% postnatal lethality in C57BL/6 background. Here we analysed a knock-in mouse containing a 5'HPRT-LoxP-Neo(R) cassette (5'LoxP) inserted upstream of the PWScr. When the insertion was inherited maternally in a paternal PWScr-deletion mouse model (PWScr(p-/m5'LoxP)), we observed compensation of growth retardation and postnatal lethality. Genomic methylation pattern and expression of protein-coding genes remained unaltered at the PWS-locus of PWScr(p-/m5'LoxP) mice. Interestingly, ubiquitous Snord116 and IPW-A exon transcription from the originally silent maternal chromosome was detected. In situ hybridization indicated that PWScr(p-/m5'LoxP) mice expressed Snord116 in brain areas similar to wild type animals. Our results suggest that the lack of PWScr RNA expression in certain brain areas could be a primary cause of the growth retardation phenotype in mice. We propose that activation of disease-associated genes on imprinted regions could lead to general therapeutic strategies in associated diseases. PMID:26848093

  11. Maternal transcription of non-protein coding RNAs from the PWS-critical region rescues growth retardation in mice

    PubMed Central

    Rozhdestvensky, Timofey S.; Robeck, Thomas; Galiveti, Chenna R.; Raabe, Carsten A.; Seeger, Birte; Wolters, Anna; Gubar, Leonid V.; Brosius, Jürgen; Skryabin, Boris V.

    2016-01-01

    Prader-Willi syndrome (PWS) is a neurogenetic disorder caused by loss of paternally expressed genes on chromosome 15q11-q13. The PWS-critical region (PWScr) contains an array of non-protein coding IPW-A exons hosting intronic SNORD116 snoRNA genes. Deletion of PWScr is associated with PWS in humans and growth retardation in mice exhibiting ~15% postnatal lethality in C57BL/6 background. Here we analysed a knock-in mouse containing a 5′HPRT-LoxP-NeoR cassette (5′LoxP) inserted upstream of the PWScr. When the insertion was inherited maternally in a paternal PWScr-deletion mouse model (PWScrp−/m5′LoxP), we observed compensation of growth retardation and postnatal lethality. Genomic methylation pattern and expression of protein-coding genes remained unaltered at the PWS-locus of PWScrp−/m5′LoxP mice. Interestingly, ubiquitous Snord116 and IPW-A exon transcription from the originally silent maternal chromosome was detected. In situ hybridization indicated that PWScrp−/m5′LoxP mice expressed Snord116 in brain areas similar to wild type animals. Our results suggest that the lack of PWScr RNA expression in certain brain areas could be a primary cause of the growth retardation phenotype in mice. We propose that activation of disease-associated genes on imprinted regions could lead to general therapeutic strategies in associated diseases. PMID:26848093

  12. Absence of Novel CYP4F2 and VKORC1 Coding Region DNA Variants in Patients Requiring High Warfarin Doses

    PubMed Central

    Burmester, James K.; Berg, Richard L.; Glurich, Ingrid; Yale, Steven H.; Schmelzer, John R.; Caldwell, Michael D.

    2011-01-01

    Objective Warfarin is an FDA-approved oral anticoagulant for long-term prevention of thromboembolism. Substantial inter-individual variation in dosing requirements and the narrow therapeutic index of this widely-prescribed drug make safe initiation and dose stabilization challenging. Single nucleotide polymorphisms (SNPs) occurring in CYP2C9, VKORC1, and CYP4F2 genes are known to impact dose, and VKORC1 and CYP4F2 polymorphisms are associated with higher therapeutic dose requirements in our cohort. However, the most advanced regression models using personal, clinical, and genetic factors to predict individual stable dose account for only 50% to 60% of the observed variability in stable theapeutic dose in Caucasians. Design and Methods In this study, we used DNA sequence analysis to determine whether additional variants in CYP4F2 and VKORC1 gene coding regions contribute to variable dosing requirements among individuals for whom the actual dose was the highest relative to regression model- predicted dose. Results and Conclusions No novel DNA variants in the coding regions of these genes were identified among subjects requiring high warfarin doses, suggesting that other factors yet to be defined contribute to variability in warfarin dose requirements in this subset of our cohort. PMID:21562135

  13. Molecular evolution of duplicated amylase gene regions in Drosophila melanogaster: evidence of positive selection in the coding regions and selective constraints in the cis-regulatory regions.

    PubMed Central

    Araki, H; Inomata, N; Yamazaki, T

    2001-01-01

    In this study, we randomly sampled Drosophila melanogaster from Japanese and Kenyan natural populations. We sequenced duplicated (proximal and distal) Amy gene regions to test whether the patterns of polymorphism were consistent with neutral molecular evolution. F(st) between the two geographically distant populations, estimated from Amy gene regions, was 0.084, smaller than reported values for other loci, comparing African and Asian populations. Furthermore, little genetic differentiation was found at a microsatellite locus (DROYANETSB) in these samples (G'st = -0.018). The results of several tests (Tajima's, Fu and Li's, and Wall's tests) were not significantly different from neutrality. However, a significantly higher level of fixed replacement substitutions was detected by a modified McDonald and Kreitman test for both populations. This indicates that positive selection occurred during or immediately after the speciation of D. melanogaster. Sliding-window analysis showed that the proximal region 1, a part of the proximal 5' flanking region, was conserved between D. melanogaster and its sibling species, D. simulans. An HKA test was significant when the proximal region 1 was compared with the 5' flanking region of Alcohol dehydrogenase (Adh), indicating a severe selective constraint on the Amy proximal region 1. These results suggest that natural selection has played an important role in the molecular evolution of Amy gene regions in D. melanogaster. PMID:11156987

  14. Intact capture of hypervelocity projectiles.

    PubMed

    Tsou, P

    1990-01-01

    The ability to capture projectiles intact at hypervelocities opens new applications in science and technology that would either not be possible or would be very costly by other means. This capability has been demonstrated in the laboratory for aluminum projectiles of 1.6 mm diameter, captured at 6 km/s, in one unmelted piece, and retaining up to 95% of the original mass. Furthermore, capture was accomplished passively using microcellular underdense polymer foam. Another advantage of capturing projectiles in an underdense medium is the ability of such a medium to preserve a record of the projectile's original velocity components of speed and direction. A survey of these experimental results is described in terms of a dozen parameters which characterize the amount of capture and the effect on the projectile due to different capture media. PMID:11538362

  15. TREND code for reconstruction of neutron reaction cross sections and calculation of the Doppler broadening in the region of resolved resonances

    SciTech Connect

    Chichulin, N. L. Kulakov, A. S.

    2010-12-15

    The TREND code is developed for reconstruction of neutron cross sections in the region of resolved resonances from the data of the international evaluated nuclear data libraries using the Reich-Moore, Adler-Adler, and Breit-Wigner formalisms and for calculation of the Doppler broadening of the resulting cross sections within the classical approximation. The TREND code is incorporated into the MCU code package for Monte Carlo reactor calculations. The TREND and MCU codes have been used to evaluate the data of the ROSFOND data bank on uranium and plutonium isotopes in comparison with the data of the ICSBEP data bank.

  16. DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome

    PubMed Central

    Beh, Leslie Y.; Müller, Manuel M.; Muir, Tom W.; Kaplan, Noam; Landweber, Laura F.

    2015-01-01

    A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream from transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes and affects codon usage and amino acid composition in genes. Given that the AT-rich Tetrahymena genome is intrinsically unfavorable for nucleosome formation, we propose that these “seed” nucleosomes—together with trans-acting factors—may facilitate the establishment of nucleosome arrays within genes in vivo, while minimizing changes to the underlying coding sequences. PMID:26330564

  17. Population Genomic Analysis of 962 Whole Genome Sequences of Humans Reveals Natural Selection in Non-Coding Regions

    PubMed Central

    Gazave, Elodie; Chang, Diana; Raj, Srilakshmi; Hunter-Zinck, Haley; Blekhman, Ran; Arbiza, Leonardo; Van Hout, Cris; Morrison, Alanna; Johnson, Andrew D.; Bis, Joshua; Cupples, L. Adrienne; Psaty, Bruce M.; Muzny, Donna; Yu, Jin; Gibbs, Richard A.; Keinan, Alon; Clark, Andrew G.; Boerwinkle, Eric

    2015-01-01

    Whole genome analysis in large samples from a single population is needed to provide adequate power to assess relative strengths of natural selection across different functional components of the genome. In this study, we analyzed next-generation sequencing data from 962 European Americans, and found that as expected approximately 60% of the top 1% of positive selection signals lie in intergenic regions, 33% in intronic regions, and slightly over 1% in coding regions. Several detailed functional annotation categories in intergenic regions showed statistically significant enrichment in positively selected loci when compared to the null distribution of the genomic span of ENCODE categories. There was a significant enrichment of purifying selection signals detected in enhancers, transcription factor binding sites, microRNAs and target sites, but not on lincRNA or piRNAs, suggesting different evolutionary constraints for these domains. Loci in “repressed or low activity regions” and loci near or overlapping the transcription start site were the most significantly over-represented annotations among the top 1% of signals for positive selection. PMID:25807536

  18. Characterization of the Burkholderia pseudomallei K96243 Capsular Polysaccharide I Coding Region

    PubMed Central

    Cuccui, Jon; Milne, Timothy S.; Harmer, Nicholas; George, Alison J.; Harding, Sarah V.; Dean, Rachel E.; Scott, Andrew E.; Sarkar-Tyson, Mitali; Wren, Brendan W.; Prior, Joann L.

    2012-01-01

    Burkholderia pseudomallei is the causative agent of melioidosis, a disease endemic to regions of Southeast Asia and Northern Australia. Both humans and a range of other animal species are susceptible to melioidosis, and the production of a group 3 polysaccharide capsule in B. pseudomallei is essential for virulence. B. pseudomallei capsular polysaccharide (CPS) I comprises unbranched manno-heptopyranose residues and is encoded by a 34.5-kb locus on chromosome 1. Despite the importance of this locus, the role of all of the genes within this region is unclear. We inactivated 18 of these genes and analyzed their phenotype using Western blotting and immunofluorescence staining. Furthermore, by combining this approach with bioinformatic analysis, we were able to develop a model for CPS I biosynthesis and export. We report that inactivating gmhA, wcbJ, and wcbN in B. pseudomallei K96243 retains the immunogenic integrity of the polysaccharide despite causing attenuation in the BALB/c murine infection model. Mice immunized with the B. pseudomallei K96243 mutants lacking a functional copy of either gmhA or wcbJ were afforded significant levels of protection against a wild-type B. pseudomallei K96243 challenge. PMID:22252864

  19. Bean yellow mosaic, clover yellow vein, and pea mosaic are distinct potyviruses: evidence from coat protein gene sequences and molecular hybridization involving the 3' non-coding regions.

    PubMed

    Tracy, S L; Frenkel, M J; Gough, K H; Hanna, P J; Shukla, D D

    1992-01-01

    The sequences of the 3' 1019 nucleotides of the genome of an atypical strain of bean yellow mosaic virus (BYMV-S) and of the 3' 1018 nucleotides of the clover yellow vein virus (CYVV-B) genome have been determined. These sequences contain the complete coding region of the viral coat protein followed by a 3' non-coding region of 173 and 178 nucleotides for BYMV-S and CYVV-B, respectively. When the deduced amino acid sequences of the coat protein coding regions were compared, a sequence identity of 77% was found between the two viruses, and optimal alignment of the 3' untranslated regions of BYMV-S and CYVV-B gave a 65% identity. However, the degree of homology of the amino acid sequences of coat proteins of BYMV-S with the published sequences for three other strains of BYMV ranged from 88% to 94%, while the sequence homology of the 3' untranslated regions between the four strains of BYMV ranged between 86% and 95%. Amplified DNA probes corresponding to the 3' non-coding regions of BYMV-S and CYVV-B showed strong hybridization only with the strains of their respective viruses and not with strains of other potyviruses, including pea mosaic virus (PMV). The relatively low sequence identities between the BYMV-S and CYVV-B coat proteins and their 3' non-coding regions, together with the hybridization results, indicate that BYMV, CYVV, and PMV are distinct potyviruses. PMID:1731696

  20. Uranium migration through intact sandstone cores

    NASA Astrophysics Data System (ADS)

    Read, D.; Lawless, T. A.; Sims, R. J.; Butter, K. R.

    1993-06-01

    Uranium is often considered to be a mobile radioelement in the natural environment owing to its tendency to form stable complexes with a number of aqueous anions, particularly in oxidising milieu. A series of infiltration experiments were devised to investigate this migration behaviour under rigidly controlled laboratory conditions. Intact cores of Permo-Triassic Clashach Sandstone were pre-equilibrated with synthetic groundwater solutions and continuous flow-through of uranium monitored together with pH and concentrations of other ions. Prior to performing each experiment a simulation was carried out using a one-dimensional coupled chemical transport code, encompassing a thermodynamic description of the electrical double layer. These calculations together with electron microscopy indicated the potential role played by iron oxyhydroxide grain coatings in retarding the uranium plume. Thus, a second series of experiments was initiated on pre-acidified cores from which all surface exposed iron had been removed, allowing an assessment of the retention capacity of non-ferric components. Taken together, the data clearly illustrate the strong affinity of aqueous uranium species for natural surfaces even under strongly oxidising conditions. The success of the model in predicting a priori the dominant trends in uranium migration behaviour is encouraging and may aid in prioritising analytical requirements for investigations in more complex geochemical situations than those studied here.

  1. Identification of a positive transcription regulatory element within the coding region of the nifLA operon in Azotobacter vinelandii.

    PubMed

    Mitra, Ranjana; Das, Hirendra K; Dixit, Aparna

    2005-07-01

    Nitrogen fixation in Azotobacter vinelandii is regulated by the nifLA operon. NifA activates the transcription of nif genes, while NifL antagonizes the transcriptional activator NifA in response to fixed nitrogen and molecular oxygen levels. However, transcriptional regulation of the nifLA operon of A. vinelandii itself is not fully understood. Using the S1 nuclease assay, we mapped the transcription start site of the nifLA operon, showing it to be similar to the sigma54-dependent promoters. We also identified a positive cis-acting regulatory element (+134 to +790) of the nifLA operon within the coding region of the nifL gene of A. vinelandii. Deletion of this element results in complete loss of promoter activity. Several protein factors bind to this region, and the specific binding sites have been mapped by DNase I foot printing. Two of these sites, namely dR1 (+134 to +204) and dR2 (+745 to +765), are involved in regulating the nifLA promoter activity. The absence of NtrC-like binding sites in the upstream region of the nifLA operon in A. vinelandii makes the identification of these downstream elements a highly significant finding. The interaction of the promoter with the proteins binding to the dR2 region spanning +745 to +765 appears to be dependent on the face of the helix as introduction of 4 bases just before this region completely disrupts promoter activity. Thus, the positive regulatory element present within the BglII-BglII fragment may play, in part; an important role in nifLA regulation in A. vinelandii. PMID:16000781

  2. Virtual screening of gene expression regulatory sites in non-coding regions of the infectious salmon anemia virus

    PubMed Central

    2014-01-01

    Background Members of the Orthomyxoviridae family, which contains an important fish pathogen called the infectious salmon anemia virus (ISAV), have a genome consisting of eight segments of single-stranded RNA that encode different viral proteins. Each of these segments is flanked by non-coding regions (NCRs). In other Orthomyxoviruses, sequences have been shown within these NCRs that regulate gene expression and virulence; however, only the sequences of these regions are known in ISAV, and a biological role has not yet been attributed to these regions. This study aims to determine possible functions of the NCRs of ISAV. Results The results suggested an association between the molecular architecture of NCR regions and their role in the viral life cycle. The available NCR sequences from ISAV isolates were compiled, alignments were performed to obtain a consensus sequence, and conserved regions were identified in this consensus sequence. To determine the molecular structure adopted by these NCRs, various bioinformatics tools, including RNAfold, RNAstructure, Sfold, and Mfold, were used. This hypothetical structure, together with a comparison with influenza, yielded reliable secondary structure models that lead to the identification of conserved nucleotide positions on an intergenus level. These models determined which nucleotide positions are involved in the recognition of the vRNA/cRNA by RNA-dependent RNA polymerase (RdRp) or mRNA by the ribosome. Conclusions The information obtained in this work allowed the proposal of previously unknown sites that are involved in the regulation of different stages of the viral cycle, leading to the identification of new viral targets that may assist future antiviral strategies. PMID:25069483

  3. Stacked Predictive Sparse Coding for Classification of Distinct Regions of Tumor Histopathology.

    PubMed

    Chang, Hang; Zhou, Yin; Spellman, Paul; Parvin, Bahram

    2013-01-01

    Image-based classification of tissue histology, in terms of distinct histopathology (e.g., tumor or necrosis regions), provides a series of indices for tumor composition. Furthermore, aggregation of these indices from each whole slide image (WSI) in a large cohort can provide predictive models of clinical outcome. However, the performance of the existing techniques is hindered as a result of large technical variations (e.g., fixation, staining) and biological heterogeneities (e.g., cell type, cell state) that are always present in a large cohort. We suggest that, compared with human engineered features widely adopted in existing systems, unsupervised feature learning is more tolerant to batch effect (e.g., technical variations associated with sample preparation) and pertinent features can be learned without user intervention. This leads to a novel approach for classification of tissue histology based on unsupervised feature learning and spatial pyramid matching (SPM), which utilize sparse tissue morphometric signatures at various locations and scales. This approach has been evaluated on two distinct datasets consisting of different tumor types collected from The Cancer Genome Atlas (TCGA), and the experimental results indicate that the proposed approach is (i) extensible to different tumor types; (ii) robust in the presence of wide technical variations and biological heterogeneities; and (iii) scalable with varying training sample sizes. PMID:24770492

  4. Genome analysis: Assigning protein coding regions to three-dimensional structures.

    PubMed Central

    Salamov, A. A.; Suwa, M.; Orengo, C. A.; Swindells, M. B.

    1999-01-01

    We describe the results of a procedure for maximizing the number of sequences that can be reliably linked to a protein of known three-dimensional structure. Unlike other methods, which try to increase sensitivity through the use of fold recognition software, we only use conventional sequence alignment tools, but apply them in a manner that significantly increases the number of relationships detected. We analyzed 11 genomes and found that, depending on the genome, between 23 and 32% of the ORFs had significant matches to proteins of known structure. In all cases, the aligned region consisted of either >100 residues or >50% of the smaller sequence. Slightly higher percentages could be attained if smaller motifs were also included. This is significantly higher than most previously reported methods, even those that have a fold-recognition component. We survey the biochemical and structural characteristics of the most frequently occurring proteins, and discuss the extent to which alignment methods can realistically assign function to gene products. PMID:10211823

  5. Mechanics of intact bone marrow.

    PubMed

    Jansen, Lauren E; Birch, Nathan P; Schiffman, Jessica D; Crosby, Alfred J; Peyton, Shelly R

    2015-10-01

    The current knowledge of bone marrow mechanics is limited to its viscous properties, neglecting the elastic contribution of the extracellular matrix. To get a more complete view of the mechanics of marrow, we characterized intact yellow porcine bone marrow using three different, but complementary techniques: rheology, indentation, and cavitation. Our analysis shows that bone marrow is elastic, and has a large amount of intra- and inter-sample heterogeneity, with an effective Young׳s modulus ranging from 0.25 to 24.7 kPa at physiological temperature. Each testing method was consistent across matched tissue samples, and each provided unique benefits depending on user needs. We recommend bulk rheology to capture the effects of temperature on tissue elasticity and moduli, indentation for quantifying local tissue heterogeneity, and cavitation rheology for mitigating destructive sample preparation. We anticipate the knowledge of bone marrow elastic properties for building in vitro models will elucidate mechanisms involved in disease progression and regenerative medicine. PMID:26189198

  6. Allelic variations in coding regions of the vitamin D receptor gene in dairy cows and potential susceptibility to periparturient hypocalcaemia.

    PubMed

    Deiner, Carolin; Reiche, Maria; Lassner, Dirk; Grienitz, Desirée; Twardziok, Sven; Moesch, Anne; Wenning, Peter; Martens, Holger

    2012-11-01

    Periparturient hypocalcaemia (milk fever) is a disorder of Ca metabolism in dairy cattle primarily affecting multiparous cows. The major reasons for the rapid decrease of blood Ca concentration after calving are the prompt increase of Ca secretion into the colostrum and the delayed activation of Ca regulation mechanisms including calcitriol, a metabolite of vitamin D. In man, vitamin D receptor (VDR) gene polymorphisms are reported to be associated with disturbances of Ca metabolism, whereas data confirming the same in dairy cows are still missing. Moreover, polymorphisms that only affect non-coding regions are sometimes difficult to ascribe to a specific disorder as pathways and unequivocal links remain elusive. Therefore, the idea of the present study was to investigate in a small group of dairy cows with documented clinical records whether polymorphisms in the coding regions of the VDR gene existed and whether these potentially found variations were correlated with the incidence of periparturient hypocalcaemia. For this purpose, blood DNA was isolated from 26 dairy cows in their 4th to 6th lactation, out of which 17 had experienced hypocalcaemia at least once, whereas 9 cows had never undergone periparturient hypocalcaemia in their lifetime. The 10 VDR exons and small parts of adjacent introns were sequenced and compared with the Bos taurus VDR sequence published on NCBI based on the DNA of one Hereford cow. In total, 8 sequence alterations were detected in the fragments, which were primarily heterozygous. However, only 4 of them were really located on exons thereby potentially causing changes of the encoded amino acid of the VDR protein, but were not correlated with the incidence of periparturient hypocalcaemia. Certainly, this lack of statistical correlation could be due to the small number of animals included; anyhow, it was not encouraging enough to initiate a larger study with hundreds of cows and document blood Ca levels post partum for at least four

  7. Novel exon 1 protein-coding regions N-terminally extend human KCNE3 and KCNE4.

    PubMed

    Abbott, Geoffrey W

    2016-08-01

    The 5 human (h)KCNE β subunits each regulate various cation channels and are linked to inherited cardiac arrhythmias. Reported here are previously undiscovered protein-coding regions in exon 1 of hKCNE3 and hKCNE4 that extend their encoded extracellular domains by 44 and 51 residues, which yields full-length proteins of 147 and 221 residues, respectively. Full-length hKCNE3 and hKCNE4 transcript and protein are expressed in multiple human tissues; for hKCNE4, only the longer protein isoform is detectable. Two-electrode voltage-clamp electrophysiology revealed that, when coexpressed in Xenopus laevis oocytes with various potassium channels, the newly discovered segment preserved conversion of KCNQ1 by hKCNE3 to a constitutively open channel, but prevented its inhibition of Kv4.2 and KCNQ4. hKCNE4 slowing of Kv4.2 inactivation and positive-shifted steady-state inactivation were also preserved in the longer form. In contrast, full-length hKCNE4 inhibition of KCNQ1 was limited to 40% at +40 mV vs. 80% inhibition by the shorter form, and augmentation of KCNQ4 activity by hKCNE4 was entirely abolished by the additional segment. Among the genome databases analyzed, the longer KCNE3 is confined to primates; full-length KCNE4 is widespread in vertebrates but is notably absent from Mus musculus Findings highlight unexpected KCNE gene diversity, raise the possibility of dynamic regulation of KCNE partner modulation via splice variation, and suggest that the longer hKCNE3 and hKCNE4 proteins should be adopted in future mechanistic and genetic screening studies.-Abbott, G. W. Novel exon 1 protein-coding regions N-terminally extend human KCNE3 and KCNE4. PMID:27162025

  8. Synonymous deoptimization of the foot-and-mouth disease virus P1 coding region causes attenuation in vivo while inducing a strong neutralizing antibody response

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Codon bias deoptimization has been previously used to successfully attenuate human pathogens including polio, respiratory syncytial and influenza viruses. We have applied a similar technology to deoptimize the capsid coding region (P1 region) of the cDNA infectious clone of foot-and-mouth disease vi...

  9. The mitochondrial genome of the banded guitarfish, Zapteryx exasperata (Jordan and Gilbert, 1880), possesses a non-coding duplication remnant region.

    PubMed

    Castillo-Páez, Ana; Del Río-Portilla, Miguel Angel; Oñate-González, Erick; Rocha-Olivares, Axayácatl

    2016-05-01

    The complete mitochondrial genome of the banded guitarfish is 17,310 bp long and includes 2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes, a replication origin and a control region (GenBank accession number KM370325). Gene arrangement is similar to that found in other batoids. An extra non-coding region was found between the genes coding for transfer RNA proline and threonine possessing a set of tandem repeat motifs pointing to its origin as a duplication remnant. Start codon ATG and stop codon TAA/T were found in most protein-coding genes. The base composition of the genome is 32.3% A, 30.2% T, 24.3% C and 13.1% G. PMID:25208175

  10. Tongue sole (Cynoglossus semilaevis) prothymosin alpha: Cytokine-like activities associated with the intact protein and the C-terminal region that lead to antiviral immunity via Myd88-dependent and -independent pathways respectively.

    PubMed

    Zhang, Bao-cun; Sun, Li

    2015-11-01

    Prothymosin alpha (ProTα) is a small protein that in mammals is known to participate in diverse biological processes including immunomodulation. In teleost, the immunological function of ProTα is unknown. In the current study, we investigated the expression and function of the ProTα (named CsProTα) from the teleost fish tongue sole (Cynoglossus semilaevis). We found that CsProTα expression was abundant in immune relevant tissues and upregulated by megalocytivirus infection. Immunoblot detected secretion of CsProTα by peripheral blood leukocytes. Recombinant CsProTα (rCsProTα) as well as the C-terminal 11-residue (Ct11) were able to bind head kidney monocytes (HKM) and induce immune gene expression; however, the induction patterns caused by rCsProTα and Ct11 differed considerably. When introduced in vivo, rCsProTα and Ct11 significantly reduced megalocytivirus infection in fish tissues, whereas rCsProTα antibody significantly promoted viral replication. Blocking of Myd88 activity abolished the virus-inhibitory effect of rCsProTα but not Ct11. Taken together, these results demonstrate for the first time that both the intact protein and the C-terminal segment of a teleost ProTα can act like cytokines and induce antiviral immunity via, however, distinct signaling pathways that differ in the requirement of Myd88. PMID:26162512

  11. Features of a leader peptide coding region that regulate translation initiation for the anti-TRAP protein of B. subtilis.

    PubMed

    Chen, Guangnan; Yanofsky, Charles

    2004-03-12

    The rtpA gene of Bacillus subtilis encodes the Anti-TRAP protein, AT. AT can bind and inhibit the TRAP regulatory protein, preventing TRAP from promoting transcription termination in the trpEDCFBA operon leader region. AT synthesis is upregulated transcriptionally and translationally in response to the accumulation of uncharged tRNA(Trp). Here we analyze AT's translational regulation by rtpLP, a 10 residue leader peptide coding region located immediately preceding the rtpA Shine-Dalgarno sequence. Our findings suggest that, whenever the charged tRNA(Trp) level is sufficient to allow the ribosome translating rtpLP to reach its stop codon, it blocks the adjacent rtpA Shine-Dalgarno sequence, inhibiting AT synthesis. However, when there is a charged tRNA(Trp) deficiency, the translating ribosome presumably stalls at one of three adjacent rtpLP Trp codons. This stalling exposes the rtpA Shine-Dalgarno sequence, permitting AT synthesis. RNA-RNA pairing may also influence AT synthesis. Production of AT would inactivate TRAP, thereby increasing trp operon expression. PMID:15023340

  12. Structure of the coding region and mRNA variants of the apyrase gene from pea (Pisum sativum)

    NASA Technical Reports Server (NTRS)

    Shibata, K.; Abe, S.; Davies, E.

    2001-01-01

    Partial amino acid sequences of a 49 kDa apyrase (ATP diphosphohydrolase, EC 3.6.1.5) from the cytoskeletal fraction of etiolated pea stems were used to derive oligonucleotide DNA primers to generate a cDNA fragment of pea apyrase mRNA by RT-PCR and these primers were used to screen a pea stem cDNA library. Two almost identical cDNAs differing in just 6 nucleotides within the coding regions were found, and these cDNA sequences were used to clone genomic fragments by PCR. Two nearly identical gene fragments containing 8 exons and 7 introns were obtained. One of them (H-type) encoded the mRNA sequence described by Hsieh et al. (1996) (DDBJ/EMBL/GenBank Z32743), while the other (S-type) differed by the same 6 nucleotides as the mRNAs, suggesting that these genes may be alleles. The six nucleotide differences between these two alleles were found solely in the first exon, and these mutation sites had two types of consensus sequences. These mRNAs were found with varying lengths of 3' untranslated regions (3'-UTR). There are some similarities between the 3'-UTR of these mRNAs and those of actin and actin binding proteins in plants. The putative roles of the 3'-UTR and alternative polyadenylation sites are discussed in relation to their possible role in targeting the mRNAs to different subcellular compartments.

  13. Codon usage, genetic code and phylogeny of Dictyostelium discoideum mitochondrial DNA as deduced from a 7.3-kb region.

    PubMed

    Angata, K; Kuroe, K; Yanagisawa, K; Tanaka, Y

    1995-02-01

    We have sequenced a region (7,376-bp) of the mitochondrial (mt) DNA (54 kb) of the cellular slime mold, Dictyostelium discoideum. From the DNA and amino-acid sequence comparisons with known sequences, genes for ATPase subunit 9 (ATP9), cytochrome b (CYTB), NADH dehydrogenase subunits 1, 3 and 6 (ND1, ND3 and ND6), small subunit rRNA (SSU rRNA) and seven tRNAs (Arg, Asn, Cys, Lys, f-Met, Met and Pro) have been identified. The sequenced region of the mtDNA has a high average A + T-content (70.8%). The A + T-content of protein-genes (73.6%) is considerably higher than that of RNA genes (61.3%). Even with the strong AT-bias, the genetic code employed is most probably the universal one. All seven tRNAs are able to form typical clover leaf structures. The molecular phylogenetic trees of CYTB and SSU rRNA suggest that D. discoideum is closer to green plants than to animals and fungi. PMID:7736610

  14. The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non-coding RNA and synonymous mutations.

    PubMed

    Diederichs, Sven; Bartsch, Lorenz; Berkmann, Julia C; Fröse, Karin; Heitmann, Jana; Hoppe, Caroline; Iggena, Deetje; Jazmati, Danny; Karschnia, Philipp; Linsenmeier, Miriam; Maulhardt, Thomas; Möhrmann, Lino; Morstein, Johannes; Paffenholz, Stella V; Röpenack, Paula; Rückert, Timo; Sandig, Ludger; Schell, Maximilian; Steinmann, Anna; Voss, Gjendine; Wasmuth, Jacqueline; Weinberger, Maria E; Wullenkord, Ramona

    2016-01-01

    Cancer is a disease of the genome caused by oncogene activation and tumor suppressor gene inhibition. Deep sequencing studies including large consortia such as TCGA and ICGC identified numerous tumor-specific mutations not only in protein-coding sequences but also in non-coding sequences. Although 98% of the genome is not translated into proteins, most studies have neglected the information hidden in this "dark matter" of the genome. Malignancy-driving mutations can occur in all genetic elements outside the coding region, namely in enhancer, silencer, insulator, and promoter as well as in 5'-UTR and 3'-UTR Intron or splice site mutations can alter the splicing pattern. Moreover, cancer genomes contain mutations within non-coding RNA, such as microRNA, lncRNA, and lincRNA A synonymous mutation changes the coding region in the DNA and RNA but not the protein sequence. Importantly, oncogenes such as TERT or miR-21 as well as tumor suppressor genes such as TP53/p53, APC, BRCA1, or RB1 can be affected by these alterations. In summary, coding-independent mutations can affect gene regulation from transcription, splicing, mRNA stability to translation, and hence, this largely neglected area needs functional studies to elucidate the mechanisms underlying tumorigenesis. This review will focus on the important role and novel mechanisms of these non-coding or allegedly silent mutations in tumorigenesis. PMID:26992833

  15. The InterFrost benchmark of Thermo-Hydraulic codes for cold regions hydrology - first inter-comparison results

    NASA Astrophysics Data System (ADS)

    Grenier, Christophe; Roux, Nicolas; Anbergen, Hauke; Collier, Nathaniel; Costard, Francois; Ferrry, Michel; Frampton, Andrew; Frederick, Jennifer; Holmen, Johan; Jost, Anne; Kokh, Samuel; Kurylyk, Barret; McKenzie, Jeffrey; Molson, John; Orgogozo, Laurent; Rivière, Agnès; Rühaak, Wolfram; Selroos, Jan-Olof; Therrien, René; Vidstrand, Patrik

    2015-04-01

    The impacts of climate change in boreal regions has received considerable attention recently due to the warming trends that have been experienced in recent decades and are expected to intensify in the future. Large portions of these regions, corresponding to permafrost areas, are covered by water bodies (lakes, rivers) that interact with the surrounding permafrost. For example, the thermal state of the surrounding soil influences the energy and water budget of the surface water bodies. Also, these water bodies generate taliks (unfrozen zones below) that disturb the thermal regimes of permafrost and may play a key role in the context of climate change. Recent field studies and modeling exercises indicate that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is required to understand and model the past and future evolution of landscapes, rivers, lakes and associated groundwater systems in a changing climate. However, there is presently a paucity of 3D numerical studies of permafrost thaw and associated hydrological changes, and the lack of study can be partly attributed to the difficulty in verifying multi-dimensional results produced by numerical models. Numerical approaches can only be validated against analytical solutions for a purely thermic 1D equation with phase change (e.g. Neumann, Lunardini). When it comes to the coupled TH system (coupling two highly non-linear equations), the only possible approach is to compare the results from different codes to provided test cases and/or to have controlled experiments for validation. Such inter-code comparisons can propel discussions to try to improve code performances. A benchmark exercise was initialized in 2014 with a kick-off meeting in Paris in November. Participants from USA, Canada, Germany, Sweden and France convened, representing altogether 13 simulation codes. The benchmark exercises consist of several test cases inspired by existing literature (e.g. McKenzie et al., 2007) as well as new ones. They

  16. Non-coding roX RNAs prevent the binding of the MSL-complex to heterochromatic regions.

    PubMed

    Figueiredo, Margarida L A; Kim, Maria; Philip, Philge; Allgardsson, Anders; Stenberg, Per; Larsson, Jan

    2014-12-01

    Long non-coding RNAs contribute to dosage compensation in both mammals and Drosophila by inducing changes in the chromatin structure of the X-chromosome. In Drosophila melanogaster, roX1 and roX2 are long non-coding RNAs that together with proteins form the male-specific lethal (MSL) complex, which coats the entire male X-chromosome and mediates dosage compensation by increasing its transcriptional output. Studies on polytene chromosomes have demonstrated that when both roX1 and roX2 are absent, the MSL-complex becomes less abundant on the male X-chromosome and is relocated to the chromocenter and the 4th chromosome. Here we address the role of roX RNAs in MSL-complex targeting and the evolution of dosage compensation in Drosophila. We performed ChIP-seq experiments which showed that MSL-complex recruitment to high affinity sites (HAS) on the X-chromosome is independent of roX and that the HAS sequence motif is conserved in D. simulans. Additionally, a complete and enzymatically active MSL-complex is recruited to six specific genes on the 4th chromosome. Interestingly, our sequence analysis showed that in the absence of roX RNAs, the MSL-complex has an affinity for regions enriched in Hoppel transposable elements and repeats in general. We hypothesize that roX mutants reveal the ancient targeting of the MSL-complex and propose that the role of roX RNAs is to prevent the binding of the MSL-complex to heterochromatin. PMID:25501352

  17. DNA sequence variation in a non-coding region of low recombination on the human X chromosome.

    PubMed

    Kaessmann, H; Heissig, F; von Haeseler, A; Pääbo, S

    1999-05-01

    DNA sequence variation has become a major source of insight regarding the origin and history of our species as well as an important tool for the identification of allelic variants associated with disease. Comparative sequencing of DNA has to date focused mainly on mitochondrial (mt) DNA, which due to its apparent lack of recombination and high evolutionary rate lends itself well to the study of human evolution. These advantages also entail limitations. For example, the high mutation rate of mtDNA results in multiple substitutions that make phylogenetic analysis difficult and, because mtDNA is maternally inherited, it reflects only the history of females. For the history of males, the non-recombining part of the paternally inherited Y chromosome can be studied. The extent of variation on the Y chromosome is so low that variation at particular sites known to be polymorphic rather than entire sequences are typically determined. It is currently unclear how some forms of analysis (such as the coalescent) should be applied to such data. Furthermore, the lack of recombination means that selection at any locus affects all 59 Mb of DNA. To gauge the extent and pattern of point substitutional variation in non-coding parts of the human genome, we have sequenced 10 kb of non-coding DNA in a region of low recombination at Xq13.3. Analysis of this sequence in 69 individuals representing all major linguistic groups reveals the highest overall diversity in Africa, whereas deep divergences also exist in Asia. The time elapsed since the most recent common ancestor (MRCA) is 535,000+/-119,000 years. We expect this type of nuclear locus to provide more answers about the genetic origin and history of humans. PMID:10319866

  18. Murine leukemia virus mutant with a frameshift in the reverse transcriptase coding region: implications for pol gene structure.

    PubMed Central

    Levin, J G; Hu, S C; Rein, A; Messer, L I; Gerwin, B I

    1984-01-01

    The molecular defect in the nonconditional B-tropic MuLV pol mutant, clone 23 (Gerwin et al., J. Virol. 31:741-751, 1979), has been characterized by recombinant DNA technology. The entire mutant genome was cloned from an EcoRI digest of integrated cellular DNA into bacteriophage lambda Charon 4A and then subcloned at the EcoRI site of pBR322. NIH-3T3 cells transfected with the plasmid clone, termed pRTM (RTM, reverse transcriptase mutant), reproduced the properties of clone 23 virus-infected cells. In vivo ligation experiments involving cotransfection of subclones of pRTM and wild-type murine leukemia virus localized the defect in the clone 23 genome to an approximately 400-base-pair region in the pol gene between the SalI and XhoI sites. Sequence analysis of this region in the wild-type and mutant genomes revealed that the mutant has one additional C residue located 231 bases downstream of the last base of the SalI recognition site. This 1-base insertion brings three TGA termination codons into phase. Thus, the mutation in clone 23 leads to premature termination of translation, explaining the presence in clone 23 virions of a truncated polymerase with low levels of enzymatic activity. It was previously shown that the gag precursor is cleaved normally in clone 23-infected cells; therefore, if a virus-coded protease is involved in this cleavage, it must be encoded by sequences upstream of the reverse transcriptase region of the pol gene. This consideration, coupled with the observed molecular weight of the mutant polymerase and our precise determination of its C terminus, have led to a proposal for the genetic organization of the murine leukemia virus pol gene. Images PMID:6205170

  19. Multiplexed Intact-Tissue Transcriptional Analysis at Cellular Resolution.

    PubMed

    Sylwestrak, Emily Lauren; Rajasethupathy, Priyamvada; Wright, Matthew Arnot; Jaffe, Anna; Deisseroth, Karl

    2016-02-11

    In recently developed approaches for high-resolution imaging within intact tissue, molecular characterization over large volumes has been largely restricted to labeling of proteins. But volumetric nucleic acid labeling may represent a far greater scientific and clinical opportunity, enabling detection of not only diverse coding RNA variants but also non-coding RNAs. Moreover, scaling immunohistochemical detection to large tissue volumes has limitations due to high cost, limited renewability/availability, and restricted multiplexing capability of antibody labels. With the goal of versatile, high-content, and scalable molecular phenotyping of intact tissues, we developed a method using carbodiimide-based chemistry to stably retain RNAs in clarified tissue, coupled with amplification tools for multiplexed detection. The resulting technology enables robust measurement of activity-dependent transcriptional signatures, cell-identity markers, and diverse non-coding RNAs in rodent and human tissue volumes. The growing set of validated probes is deposited in an online resource for nucleating related developments from across the scientific community. PMID:26871636

  20. The 5' non-coding region of the BCR/ABL oncogene augments its ability to stimulate the growth of immature lymphoid cells.

    PubMed

    Gishizky, M L; McLaughlin, J; Pendergast, A M; Witte, O N

    1991-08-01

    The Philadelphia chromosome (Ph1, t9:22;34:q11) is a reciprocal translocation between chromosome 22 and chromosome 9 which results in the formation of the chimeric BCR/ABL oncogene. Alternative forms of BCR/ABL are produced by splicing different sets of exons of the BCR gene to a common set of c-ABL sequences. This results in the formation of an 8.7 kilobase mRNA that encodes the P210 BCR/ABL gene product or a 7.0 kilobase mRNA that encodes the P185 BCR/ABL gene product. Both BCR/ABL transcripts derive their 5' non-coding sequences from the BCR gene locus. This 5' region is over 500 nucleotides in length, has a GC content greater than 75% and has a short open reading frame. To determine if this unusual 5' non-coding region plays a role in BCR/ABL transformation, we prepared retroviral vectors containing identical BCR/ABL coding regions but differing in the length of the BCR 5' non-coding region. Matched viral stocks were evaluated for their ability to transform bone marrow in vitro and for their ability to cause tumors when inoculated into 3- to 4-week-old mice. In this report we present the unexpected finding that the BCR/ABL 5' non-coding region augments the transforming activity of both P210 and P185 BCR/ABL in vitro. In vivo, BCR/ABL is a weak tumorigenic agent and its potency is enhanced by the presence of the 5' non-coding region. PMID:1886706

  1. Evolution of naturally occurring 5'non-coding region variants of Hepatitis C virus in human populations of the South American region

    PubMed Central

    Moratorio, Gonzalo; Martínez, Mariela; Gutiérrez, María F; González, Katiuska; Colina, Rodney; López-Tort, Fernando; López, Lilia; Recarey, Ricardo; Schijman, Alejandro G; Moreno, María P; García-Aguirre, Laura; Manascero, Aura R; Cristina, Juan

    2007-01-01

    Background Hepatitis C virus (HCV) has been the subject of intense research and clinical investigation as its major role in human disease has emerged. Previous and recent studies have suggested a diversification of type 1 HCV in the South American region. The degree of genetic variation among HCV strains circulating in Bolivia and Colombia is currently unknown. In order to get insight into these matters, we performed a phylogenetic analysis of HCV 5' non-coding region (5'NCR) sequences from strains isolated in Bolivia, Colombia and Uruguay, as well as available comparable sequences of HCV strains isolated in South America. Methods Phylogenetic tree analysis was performed using the neighbor-joining method under a matrix of genetic distances established under the Kimura-two parameter model. Signature pattern analysis, which identifies particular sites in nucleic acid alignments of variable sequences that are distinctly representative relative to a background set, was performed using the method of Korber & Myers, as implemented in the VESPA program. Prediction of RNA secondary structures was done by the method of Zuker & Turner, as implemented in the mfold program. Results Phylogenetic tree analysis of HCV strains isolated in the South American region revealed the presence of a distinct genetic lineage inside genotype 1. Signature pattern analysis revealed that the presence of this lineage is consistent with the presence of a sequence signature in the 5'NCR of HCV strains isolated in South America. Comparisons of these results with the ones found for Europe or North America revealed that this sequence signature is characteristic of the South American region. Conclusion Phylogentic analysis revealed the presence of a sequence signature in the 5'NCR of type 1 HCV strains isolated in South America. This signature is frequent enough in type 1 HCV populations circulating South America to be detected in a phylogenetic tree analysis as a distinct type 1 sub-population. The

  2. Sequencing the GRHL3 Coding Region Reveals Rare Truncating Mutations and a Common Susceptibility Variant for Nonsyndromic Cleft Palate.

    PubMed

    Mangold, Elisabeth; Böhmer, Anne C; Ishorst, Nina; Hoebel, Ann-Kathrin; Gültepe, Pinar; Schuenke, Hannah; Klamt, Johanna; Hofmann, Andrea; Gölz, Lina; Raff, Ruth; Tessmann, Peter; Nowak, Stefanie; Reutter, Heiko; Hemprich, Alexander; Kreusch, Thomas; Kramer, Franz-Josef; Braumann, Bert; Reich, Rudolf; Schmidt, Gül; Jäger, Andreas; Reiter, Rudolf; Brosch, Sibylle; Stavusis, Janis; Ishida, Miho; Seselgyte, Rimante; Moore, Gudrun E; Nöthen, Markus M; Borck, Guntram; Aldhorae, Khalid A; Lace, Baiba; Stanier, Philip; Knapp, Michael; Ludwig, Kerstin U

    2016-04-01

    Nonsyndromic cleft lip with/without cleft palate (nsCL/P) and nonsyndromic cleft palate only (nsCPO) are the most frequent subphenotypes of orofacial clefts. A common syndromic form of orofacial clefting is Van der Woude syndrome (VWS) where individuals have CL/P or CPO, often but not always associated with lower lip pits. Recently, ∼5% of VWS-affected individuals were identified with mutations in the grainy head-like 3 gene (GRHL3). To investigate GRHL3 in nonsyndromic clefting, we sequenced its coding region in 576 Europeans with nsCL/P and 96 with nsCPO. Most strikingly, nsCPO-affected individuals had a higher minor allele frequency for rs41268753 (0.099) than control subjects (0.049; p = 1.24 × 10(-2)). This association was replicated in nsCPO/control cohorts from Latvia, Yemen, and the UK (pcombined = 2.63 × 10(-5); ORallelic = 2.46 [95% CI 1.6-3.7]) and reached genome-wide significance in combination with imputed data from a GWAS in nsCPO triads (p = 2.73 × 10(-9)). Notably, rs41268753 is not associated with nsCL/P (p = 0.45). rs41268753 encodes the highly conserved p.Thr454Met (c.1361C>T) (GERP = 5.3), which prediction programs denote as deleterious, has a CADD score of 29.6, and increases protein binding capacity in silico. Sequencing also revealed four novel truncating GRHL3 mutations including two that were de novo in four families, where all nine individuals harboring mutations had nsCPO. This is important for genetic counseling: given that VWS is rare compared to nsCPO, our data suggest that dominant GRHL3 mutations are more likely to cause nonsyndromic than syndromic CPO. Thus, with rare dominant mutations and a common risk variant in the coding region, we have identified an important contribution for GRHL3 in nsCPO. PMID:27018475

  3. The InterFrost benchmark of Thermo-Hydraulic codes for cold regions hydrology - first inter-comparison phase results

    NASA Astrophysics Data System (ADS)

    Grenier, Christophe; Rühaak, Wolfram

    2016-04-01

    Climate change impacts in permafrost regions have received considerable attention recently due to the pronounced warming trends experienced in recent decades and which have been projected into the future. Large portions of these permafrost regions are characterized by surface water bodies (lakes, rivers) that interact with the surrounding permafrost often generating taliks (unfrozen zones) within the permafrost that allow for hydrologic interactions between the surface water bodies and underlying aquifers and thus influence the hydrologic response of a landscape to climate change. Recent field studies and modeling exercises indicate that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is required to understand and model past and future evolution such units (Kurylyk et al. 2014). However, there is presently a paucity of 3D numerical studies of permafrost thaw and associated hydrological changes, which can be partly attributed to the difficulty in verifying multi-dimensional results produced by numerical models. A benchmark exercise was initialized at the end of 2014. Participants convened from USA, Canada, Europe, representing 13 simulation codes. The benchmark exercises consist of several test cases inspired by existing literature (e.g. McKenzie et al., 2007) as well as new ones (Kurylyk et al. 2014; Grenier et al. in prep.; Rühaak et al. 2015). They range from simpler, purely thermal 1D cases to more complex, coupled 2D TH cases (benchmarks TH1, TH2, and TH3). Some experimental cases conducted in a cold room complement the validation approach. A web site hosted by LSCE (Laboratoire des Sciences du Climat et de l'Environnement) is an interaction platform for the participants and hosts the test case databases at the following address: https://wiki.lsce.ipsl.fr/interfrost. The results of the first stage of the benchmark exercise will be presented. We will mainly focus on the inter-comparison of participant results for the coupled cases TH2 & TH3. Both cases

  4. Androgen response element of the glycine N-methyltransferase gene is located in the coding region of its first exon.

    PubMed

    Lee, Cheng-Ming; Yen, Chia-Hung; Tzeng, Tsai-Yu; Huang, Yu-Zen; Chou, Kuan-Hsien; Chang, Tai-Jay; Arthur Chen, Yi-Ming

    2013-01-01

    Androgen plays an important role in the pathogenesis of PCa (prostate cancer). Previously, we identified GNMT (glycine N-methyltransferase) as a tumour susceptibility gene and characterized its promoter region. Besides, its enzymatic product-sarcosine has been recognized as a marker for prognosis of PCa. The goals of this study were to determine whether GNMT is regulated by androgen and to map its AREs (androgen response elements). Real-time PCR analyses showed that R1881, a synthetic AR (androgen receptor) agonist induced GNMT expression in AR-positive LNCaP cells, but not in AR-negative DU145 cells. In silico prediction showed that there are four putative AREs in GNMT-ARE1, ARE2 and ARE3 are located in the intron 1 and ARE4 is in the intron 2. Consensus ARE motif deduced from published AREs was used to identify the fifth ARE-ARE5 in the coding region of exon 1. Luciferase reporter assay found that only ARE5 mediated the transcriptional activation of R1881. ARE3 overlaps with a YY1 [Yin and Yang 1 (motif (CaCCATGTT, +1118/+1126)] that was further confirmed by antibody supershift and ChIP (chromatin immunoprecipitation) assays. EMSA (electrophoretic mobility shift assay) and ChIP assay confirmed that AR interacts with ARE5 in vitro and in vivo. In summary, GNMT is an AR-targeted gene with its functional ARE located at +19/+33 of the first exon. These results are valuable for the study of the influence of androgen on the gene expression of GNMT especially in the pathogenesis of cancer. PMID:23883094

  5. Phylogenetic analysis of the polyprotein coding region of an infectious South African bursal disease virus (IBDV) strain.

    PubMed

    Vukea, Phillia R; Willows-Munro, Sandi; Horner, Roger F; Coetzer, Theresa H T

    2014-01-01

    Infectious bursal disease virus (IBDV) causes Gumboro disease, which is highly contagious and immunosuppressive in young chickens. A virulent form of IBDV reached South Africa in 1989 and to date there has been little molecular information available for this strain. In this study, the polyprotein coding region of the South African strain SA-KZN95 was sequenced and analysed along with 52 representative sequences of other serotype I and II strains. We explored the relative impact of recombination on phylogenetic reconstruction using a multidimensional scaling approach. Phylogenetic analyses consistently placed the South African isolate within the very virulent IBDV clade. Selection analyses were also conducted to identify evolutionarily relevant amino acid residues. Previously, 19 residues in the polyprotein were shown to be potentially diagnostic for the different IBDV pathotypes. This study identified an additional two unique residues in the polyprotein which may be used as genetic signatures in future viral identifications. Better strain identification would aid in the development and application of vaccines. PMID:24291011

  6. Long non-coding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes.

    PubMed

    Ahadi, Alireza; Brennan, Samuel; Kennedy, Paul J; Hutvagner, Gyorgy; Tran, Nham

    2016-01-01

    Long non-coding RNAs (lncRNAs) form the largest transcript class in the human transcriptome. These lncRNA are expressed not only in the cells, but they are also present in the cell-derived extracellular vesicles such as exosomes. The function of these lncRNAs in cancer biology is not entirely clear, but they appear to be modulators of gene expression. In this study, we characterize the expression of lncRNAs in several prostate cancer exosomes and their parental cell lines. We show that certain lncRNAs are enriched in cancer exosomes with the overall expression signatures varying across cell lines. These exosomal lncRNAs are themselves enriched for miRNA seeds with a preference for let-7 family members as well as miR-17, miR-18a, miR-20a, miR-93 and miR-106b. The enrichment of miRNA seed regions in exosomal lncRNAs is matched with a concomitant high expression of the same miRNA. In addition, the exosomal lncRNAs also showed an over representation of RNA binding protein binding motifs. The two most common motifs belonged to ELAVL1 and RBMX. Given the enrichment of miRNA and RBP sites on exosomal lncRNAs, their interplay may suggest a possible function in prostate cancer carcinogenesis. PMID:27102850

  7. Long non-coding RNAs harboring miRNA seed regions are enriched in prostate cancer exosomes

    PubMed Central

    Ahadi, Alireza; Brennan, Samuel; Kennedy, Paul J.; Hutvagner, Gyorgy; Tran, Nham

    2016-01-01

    Long non-coding RNAs (lncRNAs) form the largest transcript class in the human transcriptome. These lncRNA are expressed not only in the cells, but they are also present in the cell-derived extracellular vesicles such as exosomes. The function of these lncRNAs in cancer biology is not entirely clear, but they appear to be modulators of gene expression. In this study, we characterize the expression of lncRNAs in several prostate cancer exosomes and their parental cell lines. We show that certain lncRNAs are enriched in cancer exosomes with the overall expression signatures varying across cell lines. These exosomal lncRNAs are themselves enriched for miRNA seeds with a preference for let-7 family members as well as miR-17, miR-18a, miR-20a, miR-93 and miR-106b. The enrichment of miRNA seed regions in exosomal lncRNAs is matched with a concomitant high expression of the same miRNA. In addition, the exosomal lncRNAs also showed an over representation of RNA binding protein binding motifs. The two most common motifs belonged to ELAVL1 and RBMX. Given the enrichment of miRNA and RBP sites on exosomal lncRNAs, their interplay may suggest a possible function in prostate cancer carcinogenesis. PMID:27102850

  8. Distinct BK polyomavirus non-coding control region (NCCR) variants in oral fluids of HIV- associated Salivary Gland Disease patients.

    PubMed

    Burger-Calderon, Raquel; Ramsey, Kathy J; Dolittle-Hall, Janet M; Seaman, William T; Jeffers-Francis, Liesl K; Tesfu, Daniel; Nickeleit, Volker; Webster-Cyriaque, Jennifer

    2016-06-01

    HIV-associated Salivary Gland Disease (HIVSGD) is among the most common salivary gland-associated complications in HIV positive individuals and was associated with the small DNA tumorvirus BK polyomavirus (BKPyV). The BKPyV non-coding control region (NCCR) is the main determinant of viral replication and rearranges readily. This study analyzed the BKPyV NCCR architecture and viral loads of 35 immunosuppressed individuals. Throatwash samples from subjects diagnosed with HIVSGD and urine samples from transplant patients were BKPyV positive and yielded BKPyV NCCR sequences. 94.7% of the BKPyV HIVSGD NCCRs carried a rearranged OPQPQQS block arrangement, suggesting a distinct architecture among this sample set. BKPyV from HIV positive individuals without HIVSGD harbored NCCR block sequences that were distinct from OPQPQQS. Cloned HIVSGD BKPyV isolates displayed active promoters and efficient replication capability in human salivary gland cells. The unique HIVSGD NCCR architecture may represent a potentially significant oral-tropic BKPyV substrain. PMID:27085139

  9. Genetic characterization of the complete coding regions of genotype 3 hepatitis E virus isolated from Spanish swine herds.

    PubMed

    Peralta, Bibiana; Mateu, Enric; Casas, Maribel; de Deus, Nilsa; Martín, Marga; Pina, Sonia

    2009-01-01

    The complete coding regions of five hepatitis E virus isolates of swine origin from two different pig farms and the complete genome sequence of two of these strains were obtained and compared to other full length or partial HEV sequences. Based on the nucleotide sequence, the examined Spanish isolates were 87.1-99.7% similar among them being the closest known strain a Mongolian porcine strain (swMN06-C1056) which shares 84.5-86.1% of the nucleotide sequence, and are also close to other HEV porcine strains from Japan. Two isolates from the same farm presented an 87 nucleotide insertion in the poly-proline hinge unique among all HEV isolates known so far. Comparison with partial HEV sequenced strains indicates that the isolates described in this study form a cluster containing human and porcine HEV strains from Europe, being the only representatives of the subtype 3f that were completely sequenced. Evolutive pressure analysis indicates that microevolution of HEV seems to be driven by negative selection. Further studies should be carried out in order to clarify the HEV origin and evolution. PMID:18977254

  10. A MARS-based method for estimating regional 2-D ionospheric VTEC and receiver differential code bias

    NASA Astrophysics Data System (ADS)

    Kao, Szu-Pyng; Chen, Yao-Chung; Ning, Fang-Shii

    2014-01-01

    The geometry-free linear combination of dual-frequency GNSS reference station ground observations are currently used to build the Vertical Total Electron Content (VTEC) model of the ionosphere. As it is known, besides ionospheric delays, there are differential code bias (DCB) of satellite (SDCB) and receiver (RDCB) in the geometry-free observation equation. The SDCB can be obtained using the International GNSS Service (IGS) analysis centers, but the RDCB for regional and local network receivers are not provided. Therefore, estimating the RDCB and VTEC model accurately and simultaneously is a critical factor investigated by researchers. This study uses Multivariate Adaptive Regression Splines (MARS) to estimate the VTEC approximate model and then substitutes this model in the observation equation to form the normal equation. The least squares method is used to solve the RDCB and VTEC model together. The research findings show that this method has good modeling effectiveness and the estimated RDCB has good reliability. The estimated VTEC model applied to GPS single-frequency precise point positioning has better positioning accuracy in comparison to the IGS global ionosphere map (GIM).

  11. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions.

    PubMed

    Kaneko, T; Sato, S; Kotani, H; Tanaka, A; Asamizu, E; Nakamura, Y; Miyajima, N; Hirosawa, M; Sugiura, M; Sasamoto, S; Kimura, T; Hosouchi, T; Matsuno, A; Muraki, A; Nakazaki, N; Naruo, K; Okumura, S; Shimpo, S; Takeuchi, C; Wada, T; Watanabe, A; Yamada, M; Yasuda, M; Tabata, S

    1996-06-30

    The sequence determination of the entire genome of the Synechocystis sp. strain PCC6803 was completed. The total length of the genome finally confirmed was 3,573,470 bp, including the previously reported sequence of 1,003,450 bp from map position 64% to 92% of the genome. The entire sequence was assembled from the sequences of the physical map-based contigs of cosmid clones and of lambda clones and long PCR products which were used for gap-filling. The accuracy of the sequence was guaranteed by analysis of both strands of DNA through the entire genome. The authenticity of the assembled sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA using the assembled sequence data. To predict the potential protein-coding regions, analysis of open reading frames (ORFs), analysis by the GeneMark program and similarity search to databases were performed. As a result, a total of 3,168 potential protein genes were assigned on the genome, in which 145 (4.6%) were identical to reported genes and 1,257 (39.6%) and 340 (10.8%) showed similarity to reported and hypothetical genes, respectively. The remaining 1,426 (45.0%) had no apparent similarity to any genes in databases. Among the potential protein genes assigned, 128 were related to the genes participating in photosynthetic reactions. The sum of the sequences coding for potential protein genes occupies 87% of the genome length. By adding rRNA and tRNA genes, therefore, the genome has a very compact arrangement of protein- and RNA-coding regions. A notable feature on the gene organization of the genome was that 99 ORFs, which showed similarity to transposase genes and could be classified into 6 groups, were found spread all over the genome, and at least 26 of them appeared to remain intact. The result implies that rearrangement of the genome occurred frequently during and after establishment of this species. PMID:8905231

  12. Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs

    PubMed Central

    Meyer, Irmtraud M.; Miklós, István

    2005-01-01

    Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes for evolutionarily conserved secondary structure elements using RNA-Decoder, a comparative secondary structure prediction program that is capable of explicitly taking the known protein-coding context of the mRNA sequences into account. We detect well-defined, conserved RNA secondary structure elements in the coding regions of the mRNA sequences and show that base-paired codons strongly correlate with sparse codons. We also investigate the role of repetitive elements in the formation of secondary structure and explain the use of alternate start codons in the caveolin-1 gene by a conserved secondary structure element overlapping the nominal start codon. We discuss the functional roles of our novel findings in regulating the gene expression on mRNA level. We also investigate the role of secondary structure on the correct splicing of the human CFTR gene. We study the wild-type version of the pre-mRNA as well as 29 variants with synonymous mutations in exon 12. By comparing our predicted secondary structures to the experimentally determined splicing efficiencies, we find with weak statistical significance that pre-mRNAs with high-splicing efficiencies have different predicted secondary structures than pre-mRNAs with low-splicing efficiencies. PMID:16275783

  13. The Fusion Protein Signal-Peptide-Coding Region of Canine Distemper Virus: A Useful Tool for Phylogenetic Reconstruction and Lineage Identification

    PubMed Central

    Sarute, Nicolás; Calderón, Marina Gallo; Pérez, Ruben; La Torre, José; Hernández, Martín; Francia, Lourdes; Panzera, Yanina

    2013-01-01

    Canine distemper virus (CDV; Paramyxoviridae, Morbillivirus) is the etiologic agent of a multisystemic infectious disease affecting all terrestrial carnivore families with high incidence and mortality in domestic dogs. Sequence analysis of the hemagglutinin (H) gene has been widely employed to characterize field strains, permitting the identification of nine CDV lineages worldwide. Recently, it has been established that the sequences of the fusion protein signal-peptide (Fsp) coding region are extremely variable, suggesting that analysis of its sequence might be useful for strain characterization studies. However, the divergence of Fsp sequences among worldwide strains and its phylogenetic resolution has not yet been evaluated. We constructed datasets containing the Fsp-coding region and H gene sequences of the same strains belonging to eight CDV lineages. Both datasets were used to evaluate their phylogenetic resolution. The phylogenetic analysis revealed that both datasets clustered the same strains into eight different branches, corresponding to CDV lineages. The inter-lineage amino acid divergence was fourfold greater for the Fsp peptide than for the H protein. The likelihood mapping revealed that both datasets display strong phylogenetic signals in the region of well-resolved topologies. These features indicate that Fsp-coding region sequence analysis is suitable for evolutionary studies as it allows for straightforward identification of CDV lineages. PMID:23675493

  14. The Chikungunya Virus Capsid Protein Contains Linear B Cell Epitopes in the N- and C-Terminal Regions that are Dependent on an Intact C-Terminus for Antibody Recognition

    PubMed Central

    Goh, Lucas Y. H.; Hobson-Peters, Jody; Prow, Natalie A.; Baker, Kelly; Piyasena, Thisun B. H.; Taylor, Carmel T.; Rana, Ashok; Hastie, Marcus L.; Gorman, Jeff J.; Hall, Roy A.

    2015-01-01

    Chikungunya virus (CHIKV) is an arthropod-borne agent that causes severe arthritic disease in humans and is considered a serious health threat in areas where competent mosquito vectors are prevalent. CHIKV has recently been responsible for several millions of cases of disease, involving over 40 countries. The recent re-emergence of CHIKV and its potential threat to human health has stimulated interest in better understanding of the biology and pathogenesis of the virus, and requirement for improved treatment, prevention and control measures. In this study, we mapped the binding sites of a panel of eleven monoclonal antibodies (mAbs) previously generated towards the capsid protein (CP) of CHIKV. Using N- and C-terminally truncated recombinant forms of the CHIKV CP, two putative binding regions, between residues 1–35 and 140–210, were identified. Competitive binding also revealed that five of the CP-specific mAbs recognized a series of overlapping epitopes in the latter domain. We also identified a smaller, N-terminally truncated product of native CP that may represent an alternative translation product of the CHIKV 26S RNA and have potential functional significance during CHIKV replication. Our data also provides evidence that the C-terminus of CP is required for authentic antigenic structure of CP. This study shows that these anti-CP mAbs will be valuable research tools for further investigating the structure and function of the CHIKV CP. PMID:26061335

  15. The Use and Effectiveness of Triple Multiplex System for Coding Region Single Nucleotide Polymorphism in Mitochondrial DNA Typing of Archaeologically Obtained Human Skeletons from Premodern Joseon Tombs of Korea

    PubMed Central

    Oh, Chang Seok; Lee, Soong Deok; Kim, Yi-Suk; Shin, Dong Hoon

    2015-01-01

    Previous study showed that East Asian mtDNA haplogroups, especially those of Koreans, could be successfully assigned by the coupled use of analyses on coding region SNP markers and control region mutation motifs. In this study, we tried to see if the same triple multiplex analysis for coding regions SNPs could be also applicable to ancient samples from East Asia as the complementation for sequence analysis of mtDNA control region. By the study on Joseon skeleton samples, we know that mtDNA haplogroup determined by coding region SNP markers successfully falls within the same haplogroup that sequence analysis on control region can assign. Considering that ancient samples in previous studies make no small number of errors in control region mtDNA sequencing, coding region SNP analysis can be used as good complimentary to the conventional haplogroup determination, especially of archaeological human bone samples buried underground over long periods. PMID:26345190

  16. Expression and characterization of full-length human heme oxygenase-1: the presence of intact membrane-binding region leads to increased binding affinity for NADPH cytochrome P450 reductase.

    PubMed

    Huber, Warren J; Backes, Wayne L

    2007-10-30

    Heme oxygenase-1 (HO-1) is the chief regulatory enzyme in the oxidative degradation of heme to biliverdin. In the process of heme degradation, HO-1 receives the electrons necessary for catalysis from the flavoprotein NADPH cytochrome P450 reductase (CPR), releasing free iron and carbon monoxide. Much of the recent research involving heme oxygenase has been done using a 30 kDa soluble form of the enzyme, which lacks the membrane binding region (C-terminal 23 amino acids). The goal of this study was to express and purify a full-length human HO-1 (hHO-1) protein; however, due to the lability of the full-length form, a rapid purification procedure was required. This was accomplished by use of a glutathione-s-transferase (GST)-tagged hHO-1 construct. Although the procedure permitted the generation of a full-length HO-1, this form was contaminated with a 30 kDa degradation product that could not be eliminated. Therefore, attempts were made to remove a putative secondary thrombin cleavage site by a conservative mutation of amino acid 254, which replaces arginine with lysine. This mutation allowed the expression and purification of a full-length hHO-1 protein. Unlike wild type (WT) HO-1, the R254K mutant could be purified to a single 32 kDa protein capable of degrading heme at the same rate as the WT enzyme. The R254K full-length form had a specific activity of approximately 200-225 nmol of bilirubin h-1 nmol-1 HO-1 as compared to approximately 140-150 nmol of bilirubin h-1 nmol-1 for the WT form, which contains the 30 kDa contaminant. This is a 2-3-fold increase from the previously reported soluble 30 kDa HO-1, suggesting that the C-terminal 23 amino acids are essential for maximal catalytic activity. Because the membrane-spanning domain is present, the full-length hHO-1 has the potential to incorporate into phospholipid membranes, which can be reconstituted at known concentrations, in combination with other endoplasmic reticulum resident enzymes. PMID:17915953

  17. Human growth hormone-related latrogenic Creutzfeldt-Jakob disease: Search for a genetic susceptibility by analysis of the PRNP coding region

    SciTech Connect

    Jaegly, A.; Boussin, F.; Deslys, J.P.

    1995-05-20

    The human PRNP gene encoding PrP is located on chromosome 20 and consists of two exons and a single intron. The open reading frame is entirely fitted into the second exon. Genetic studies indicate that all of the familial and several sporadic forms of TSSEs are associated with mutations in the PRNP 759-bp coding region. Moreover, homozygosity at codon 129, a locus harboring a polymorphism among the general population, was proposed as a genetic susceptibility marker for both sporadic and iatrogenic CJD. To assess whether additional genetic predisposition markers exist in the PRNP gene, the authors sequenced the PRNP coding region of 17 of the 32 French patients who developed a hGH-related CJD.

  18. RegSEM: a versatile code based on the spectral element method to compute seismic wave propagation at the regional scale

    NASA Astrophysics Data System (ADS)

    Cupillard, Paul; Delavaud, Elise; Burgos, Gaël.; Festa, Geatano; Vilotte, Jean-Pierre; Capdeville, Yann; Montagner, Jean-Paul

    2012-03-01

    The spectral element method, which provides an accurate solution of the elastodynamic problem in heterogeneous media, is implemented in a code, called RegSEM, to compute seismic wave propagation at the regional scale. By regional scale we here mean distances ranging from about 1 km (local scale) to 90° (continental scale). The advantage of RegSEM resides in its ability to accurately take into account 3-D discontinuities such as the sediment-rock interface and the Moho. For this purpose, one version of the code handles local unstructured meshes and another version manages continental structured meshes. The wave equation can be solved in any velocity model, including anisotropy and intrinsic attenuation in the continental version. To validate the code, results from RegSEM are compared to analytical and semi-analytical solutions available in simple cases (e.g. explosion in PREM, plane wave in a hemispherical basin). In addition, realistic simulations of an earthquake in different tomographic models of Europe are performed. All these simulations show the great flexibility of the code and point out the large influence of the shallow layers on the propagation of seismic waves at the regional scale. RegSEM is written in Fortran 90 but it also contains a couple of C routines. It is an open-source software which runs on distributed memory architectures. It can give rise to interesting applications, such as testing regional tomographic models, developing tomography using either passive (i.e. noise correlations) or active (i.e. earthquakes) data, or improving our knowledge on effects linked with sedimentary basins.

  19. Lipid diffusibility in the intact erythrocyte membrane.

    PubMed Central

    Bloom, J A; Webb, W W

    1983-01-01

    The lateral diffusion of fluorescent lipid analogues in the plasma membrane of intact erythrocytes from man, mouse, rabbit, and frog has been measured by fluorescence photobleaching recovery (FPR). Intact cells from dystrophic, normoblastic, hemolytic, and spherocytotic mouse mutants; from hypercholesterolemic rabbits and humans; and from prenatal, neonatal, and juvenile mice have been compared with corresponding normals. The lateral diffusion coefficient (D) for 3,3'-dioctadecylindodicarbocyanine iodide (DiI[5]) in intact normal human erythrocytes is D = 8.2 +/- 1.2 X 10(-9) cm2/s at 25 degrees C and D = 2.1 +/- 0.4 X 10(-8) cm2/s at 37 degrees C, and varies approximately 50-fold between 1 degree and 42 degrees C. The diffusion constants of lipid analogue rhodamine-B phosphatidylethanolamine (RBPE) are about twice those of DiI[5]. The temperature dependence and magnitude of D vary by up to a factor of 3 between species and are only influenced by donor age in prenatals. DiI[5] diffusibility is not perturbed by the presence of calcium or local anesthetics or by spectrin depletion (via mutation). However, lipid-analogue diffusibility in erythrocyte ghosts may differ from intact cells. Dietary hypercholesterolemia in rabbits reduces the diffusion coefficient and eliminates the characteristic break in Arrhenius plots of D found in all other cells studied except frog. PMID:6603237

  20. HYDROCARBON VAPOR DIFFUSION IN INTACT CORE SLEEVES

    EPA Science Inventory

    The diffusion of 2,2,4-trimethylpentane (TMP) and 2,2,5-trimethylhexane (TMH) vapors out of residually contaminated sandy soil from the U.S. Environmental Protection Agency (EPA) field research site at Traverse City, Michigan, was measured and modeled. he headspace of an intact c...

  1. HYDROCARBON VAPOR DIFFUSION IN INTACT CORE SLEEVES

    EPA Science Inventory

    The diffusion of 2,2,4-trimethylpentane (TMP) and 2,2,5-trimethylhexane (TMH) vapors put of residually contaminated sandy soil from the U.S. Environmental Protection Agency (EPA) field research site at Traverse City, Michigan, was measured and modeled. The headspace of an intact ...

  2. Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: a typical Hox structure for non-mammalian tetrapod vertebrates?

    PubMed Central

    2013-01-01

    Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding sequences. The potential for evolutionary changes in Hox cluster structure is thought to be low among vertebrates; however, recent studies of a few non-mammalian taxa suggest greater variation than originally thought. Using next generation sequencing of large genomic fragments (>100 kb) from the red spotted newt (Notophthalamus viridescens), we found that the arrangement of Hox cluster genes was conserved relative to orthologous regions from other vertebrates, but the length of introns and intergenic regions varied. In particular, the distance between hoxd13 and hoxd11 is longer in newt than orthologous regions from vertebrate species with expanded Hox clusters and is predicted to exceed the length of the entire HoxD clusters (hoxd13–hoxd4) of humans, mice, and frogs. Many repetitive DNA sequences were identified for newt Hox clusters, including an enrichment of DNA transposon-like sequences relative to non-coding genomic fragments. Our results suggest that Hox cluster expansion and transposon accumulation are common features of non-mammalian tetrapod vertebrates. PMID:23561734

  3. Analysis of the coding potential of the ORF in the control region of the female-transmitted Mytilus mtDNA.

    PubMed

    Minoiu, Ioana; Burzyński, Artur; Breton, Sophie

    2016-01-15

    Key elements in determining the sex-specific transmission of the female and male mitochondrial genomes in Mytilus species with doubly uniparental inheritance of mtDNA are suspected to be contained in the control region. A novel F genome-specific open reading frame (ORF) identified in this region has previously been hypothesized to be involved in the DUI mechanism. In their recent work Kyriakou et al. (2014a) questioned the functionality of this ORF. Here, we present evidence that this ORF is transcribed and may thus code for a functional product. PMID:26424598

  4. Transcripts of the MHM region on the chicken Z chromosome accumulate as non-coding RNA in the nucleus of female cells adjacent to the DMRT1 locus.

    PubMed

    Teranishi, M; Shimada, Y; Hori, T; Nakabayashi, O; Kikuchi, T; Macleod, T; Pym, R; Sheldon, B; Solovei, I; Macgregor, H; Mizuno, S

    2001-01-01

    The male hypermethylated (MHM) region, located near the middle of the short arm of the Z chromosome of chickens, consists of approximately 210 tandem repeats of a BamHI 2.2-kb sequence unit. Cytosines of the CpG dinucleotides of this region are extensively methylated on the two Z chromosomes in the male but much less methylated on the single Z chromosome in the female. The state of methylation of the MHM region is established after fertilization by about the 1-day embryonic stage. The MHM region is transcribed only in the female from the particular strand into heterogeneous, high molecular-mass, non-coding RNA, which is accumulated at the site of transcription, adjacent to the DMRT1 locus, in the nucleus. The transcriptional silence of the MHM region in the male is most likely caused by the CpG methylation, since treatment of the male embryonic fibroblasts with 5-azacytidine results in hypo-methylation and active transcription of this region. In ZZW triploid chickens, MHM regions are hypomethylated and transcribed on the two Z chromosomes, whereas MHM regions are hypermethylated and transcriptionally inactive on the three Z chromosomes in ZZZ triploid chickens, suggesting a possible role of the W chromosome on the state of the MHM region. PMID:11321370

  5. Molecular Evolution of the Duplicated Amy Locus in the Drosophila Melanogaster Species Subgroup: Concerted Evolution Only in the Coding Region and an Excess of Nonsynonymous Substitutions in Speciation

    PubMed Central

    Shibata, H.; Yamazaki, T.

    1995-01-01

    From the analysis of restriction maps of the Amy region in eight sibling species belonging to the Drosophila melanogaster species subgroup, we herein show that the patterns of duplication of the Amy gene are almost the same in all species. This indicates that duplication occurred before speciation within this species subgroup. From the nucleotide sequence data, we show a strong within-species similarity between the duplicated loci in the Amy coding region. This is in contrast to a strong similarity in the 5' and 3' flanking regions within each locus (proximal or distal) throughout the species subgroup. This means that concerted evolution occurred only in the Amy coding region and that differentiated evolution between the duplication occurred in the flanking regions. Moreover, when comparing the species, we also found a significant excess of nonsynonymous substitutions. In particular, all the fixed substitutions specific to D. erecta were found to be nonsynonymous. We thus conclude that adaptive protein evolution occurred in the lineage of D. erecta that is a ``specialist'' species for host plants and probably also occurs in the process of speciation in general. PMID:8536970

  6. Small Particles Intact Capture Experiment (SPICE)

    NASA Astrophysics Data System (ADS)

    Nishioka, Ken-Ji; Carle, G. C.; Bunch, T. E.; Mendez, David J.; Ryder, J. T.

    The Small Particles Intact Capture Experiment (SPICE) will develop technologies and engineering techniques necessary to capture nearly intact, uncontaminated cosmic and interplanetary dust particles (IDP's). Successful capture of such particles will benefit the exobiology and planetary science communities by providing particulate samples that may have survived unaltered since the formation of the solar system. Characterization of these particles may contribute fundamental data to our knowledge of how these particles could have formed into our planet Earth and, perhaps, contributed to the beginnings of life. The term 'uncontaminated' means that captured cosmic and IDP particles are free of organic contamination from the capture process and the term 'nearly intact capture' means that their chemical and elemental components are not materially altered during capture. The key to capturing cosmic and IDP particles that are organic-contamination free and nearly intact is the capture medium. Initial screening of capture media included organic foams, multiple thin foil layers, and aerogel (a silica gel); but, with the exception of aerogel, the requirements of no contamination or nearly intact capture were not met. To ensure no contamination of particles in the capture process, high-purity aerogel was chosen. High-purity aerogel results in high clarity (visual clearness), a useful quality in detection and recovery of embedded captured particles from the aerogel. P. Tsou at the Jet Propulsion Laboratory (JPL) originally described the use of aerogel for this purpose and reported laboratory test results. He has flown aerogel as a 'GAS-can Lid' payload on STS-47 and is evaluating the results. The Timeband Capture Cell Experiment (TICCE), a Eureca 1 experiment, is also flying aerogel and is scheduled for recovery in late April.

  7. Small Particles Intact Capture Experiment (SPICE)

    NASA Technical Reports Server (NTRS)

    Nishioka, Ken-Ji; Carle, G. C.; Bunch, T. E.; Mendez, David J.; Ryder, J. T.

    1994-01-01

    The Small Particles Intact Capture Experiment (SPICE) will develop technologies and engineering techniques necessary to capture nearly intact, uncontaminated cosmic and interplanetary dust particles (IDP's). Successful capture of such particles will benefit the exobiology and planetary science communities by providing particulate samples that may have survived unaltered since the formation of the solar system. Characterization of these particles may contribute fundamental data to our knowledge of how these particles could have formed into our planet Earth and, perhaps, contributed to the beginnings of life. The term 'uncontaminated' means that captured cosmic and IDP particles are free of organic contamination from the capture process and the term 'nearly intact capture' means that their chemical and elemental components are not materially altered during capture. The key to capturing cosmic and IDP particles that are organic-contamination free and nearly intact is the capture medium. Initial screening of capture media included organic foams, multiple thin foil layers, and aerogel (a silica gel); but, with the exception of aerogel, the requirements of no contamination or nearly intact capture were not met. To ensure no contamination of particles in the capture process, high-purity aerogel was chosen. High-purity aerogel results in high clarity (visual clearness), a useful quality in detection and recovery of embedded captured particles from the aerogel. P. Tsou at the Jet Propulsion Laboratory (JPL) originally described the use of aerogel for this purpose and reported laboratory test results. He has flown aerogel as a 'GAS-can Lid' payload on STS-47 and is evaluating the results. The Timeband Capture Cell Experiment (TICCE), a Eureca 1 experiment, is also flying aerogel and is scheduled for recovery in late April.

  8. Accelerate Implementation of the WHO Global Code of Practice on International Recruitment of Health Personnel: Experiences From the South East Asia Region

    PubMed Central

    Tangcharoensathien, Viroj; Travis, Phyllida

    2016-01-01

    Strengthening the health workforce and universal health coverage (UHC) are among key targets in the heath-related Sustainable Development Goals (SDGs) to be committed by the United Nations (UN) Member States in September 2015. The health workforce, the backbone of health systems, contributes to functioning delivery systems. Equitable distribution of functioning services is indispensable to achieve one of the UHC goals of equitable access. This commentary argues the World Health Organization (WHO) Global Code of Practice on International Recruitment of Health Personnel is relevant to the countries in the South East Asia Region (SEAR) as there is a significant outflow of health workers from several countries and a significant inflow in a few, increased demand for health workforce in high- and middle-income countries, and slow progress in addressing the "push factors." Awareness and implementation of the Code in the first report in 2012 was low but significantly improved in the second report in 2015. An inter-country workshop in 2015 convened by WHO SEAR to review progress in implementation of the Code was an opportunity for countries to share lessons on policy implementation, on retention of health workers, scaling up health professional education and managing in and out migration. The meeting noted that capturing outmigration of health personnel, which is notoriously difficult for source countries, is possible where there is an active recruitment management through government to government (G to G) contracts or licensing the recruiters and mandatory reporting requirement by them. According to the 2015 second report on the Code, the size and profile of outflow health workers from SEAR source countries is being captured and now also increasingly being shared by destination country professional councils. This is critical information to foster policy action and implementation of the Code in the Region. PMID:26673648

  9. A New Method for Computing Three-Dimensional Capture Fraction in Heterogeneous Regional Systems using the MODFLOW Adjoint Code

    NASA Astrophysics Data System (ADS)

    Clemo, T. M.; Ramarao, B.; Kelly, V. A.; Lavenue, M.

    2011-12-01

    Capture is a measure of the impact of groundwater pumping upon groundwater and surface water systems. The computation of capture through analytical or numerical methods has been the subject of articles in the literature for several decades (Bredehoeft et al., 1982). Most recently Leake et al. (2010) described a systematic way to produce capture maps in three-dimensional systems using a numerical perturbation approach in which capture from streams was computed using unit rate pumping at many locations within a MODFLOW model. The Leake et al. (2010) method advances the current state of computing capture. A limitation stems from the computational demand required by the perturbation approach wherein days or weeks of computational time might be required to obtain a robust measure of capture. In this paper, we present an efficient method to compute capture in three-dimensional systems based upon adjoint states. The efficiency of the adjoint method will enable uncertainty analysis to be conducted on capture calculations. The USGS and INTERA have collaborated to extend the MODFLOW Adjoint code (Clemo, 2007) to include stream-aquifer interaction and have applied it to one of the examples used in Leake et al. (2010), the San Pedro Basin MODFLOW model. With five layers and 140,800 grid blocks per layer, the San Pedro Basin model, provided an ideal example data set to compare the capture computed from the perturbation and the adjoint methods. The capture fraction map produced from the perturbation method for the San Pedro Basin model required significant computational time to compute and therefore the locations for the pumping wells were limited to 1530 locations in layer 4. The 1530 direct simulations of capture require approximately 76 CPU hours. Had capture been simulated in each grid block in each layer, as is done in the adjoint method, the CPU time would have been on the order of 4 years. The MODFLOW-Adjoint produced the capture fraction map of the San Pedro Basin model

  10. Xenopus egg cytoplasm with intact actin.

    PubMed

    Field, Christine M; Nguyen, Phuong A; Ishihara, Keisuke; Groen, Aaron C; Mitchison, Timothy J

    2014-01-01

    We report optimized methods for preparing Xenopus egg extracts without cytochalasin D, that we term "actin-intact egg extract." These are undiluted egg cytoplasm that contains abundant organelles, and glycogen which supplies energy, and represents the least perturbed cell-free cytoplasm preparation we know of. We used this system to probe cell cycle regulation of actin and myosin-II dynamics (Field et al., 2011), and to reconstitute the large, interphase asters that organize early Xenopus embryos (Mitchison et al., 2012; Wühr, Tan, Parker, Detrich, & Mitchison, 2010). Actin-intact Xenopus egg extracts are useful for analysis of actin dynamics, and interaction of actin with other cytoplasmic systems, in a cell-free system that closely mimics egg physiology, and more generally for probing the biochemistry and biophysics of the egg, zygote, and early embryo. Detailed protocols are provided along with assays used to check cell cycle state and tips for handling and storing undiluted egg extracts. PMID:24630119

  11. Silica Aerogel Captures Cosmic Dust Intact

    NASA Technical Reports Server (NTRS)

    Tsou, P.

    1994-01-01

    The mesostructure of silica aerogel resembles stings of grapes, ranging in size from 10 to 100 angstrom. This fine mesostructure transmits nearly 90 percent of incident light in the visible, while providing sufficiently gentle dissipation of the kinetric energy of hypervelocity cosmic dust particles to permit their intact capture. We introduced silica aerogel in 1987 as capture medium to take advantage of its low density, fine mesostruicture and most importantly, its transparency, allowing optical location of captured micron sized particles.

  12. The complete mitochondrial genome of the grand jackknife clam, Solen grandis (Bivalvia: Solenidae): a novel gene order and unusual non-coding region.

    PubMed

    Yuan, Yang; Li, Qi; Kong, Lingfeng; Yu, Hong

    2012-02-01

    Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. The complete mitochondrial genome of Solen grandis (Bivalvia: Solenidae) was determined using long-PCR and genome walking techniques. The entire mitochondrial genome sequence of S. grandis is 16,784 bp in length, and contains 36 genes including 12 protein-coding genes (atp8 is absent), 2 ribosomal RNAs, and 22 tRNAs. All genes are encoded on the same strand. Compared with other species, it bears a novel gene order. Besides these, we find a peculiar non-coding region of 435 bp with a microsatellite-like (TA)(12) element, poly-structures and many hairpin structures. In contrast to the available heterodont mitochondrial genomes from GenBank, the complete mtDNA of S. grandis has the shortest cox3 gene, and the longest atp6, nad4, nad5 genes. PMID:21598108

  13. Multi-View Intact Space Learning.

    PubMed

    Xu, Chang; Tao, Dacheng; Xu, Chao

    2015-12-01

    It is practical to assume that an individual view is unlikely to be sufficient for effective multi-view learning. Therefore, integration of multi-view information is both valuable and necessary. In this paper, we propose the Multi-view Intact Space Learning (MISL) algorithm, which integrates the encoded complementary information in multiple views to discover a latent intact representation of the data. Even though each view on its own is insufficient, we show theoretically that by combing multiple views we can obtain abundant information for latent intact space learning. Employing the Cauchy loss (a technique used in statistical learning) as the error measurement strengthens robustness to outliers. We propose a new definition of multi-view stability and then derive the generalization error bound based on multi-view stability and Rademacher complexity, and show that the complementarity between multiple views is beneficial for the stability and generalization. MISL is efficiently optimized using a novel Iteratively Reweight Residuals (IRR) technique, whose convergence is theoretically analyzed. Experiments on synthetic data and real-world datasets demonstrate that MISL is an effective and promising algorithm for practical applications. PMID:26539856

  14. Measuring mitochondrial function in intact cardiac myocytes

    PubMed Central

    Dedkova, Elena N.; Blatter, Lothar A.

    2011-01-01

    Mitochondria are involved in cellular functions that go beyond the traditional role of these organelles as the power plants of the cell. Mitochondria have been implicated in several human diseases, including cardiac dysfunction, and play a role in the aging process. Many aspects of our knowledge of mitochondria stem from studies performed on the isolated organelle. Their relative inaccessibility imposes experimental difficulties to study mitochondria in their natural environment – the cytosol of intact cells – and has hampered a comprehensive understanding of the plethora of mitochondrial functions. Here we review currently available methods to study mitochondrial function in intact cardiomyocytes. These methods primarily use different flavors of fluorescent dyes and genetically encoded fluorescent proteins in conjunction with high-resolution imaging techniques. We review methods to study mitochondrial morphology, mitochondrial membrane potential, Ca2+ and Na+ signaling, mitochondrial pH regulation, redox state and ROS production, NO signaling, oxygen consumption, ATP generation and the activity of the mitochondrial permeability transition pore. Where appropriate we complement this review on intact myocytes with seminal studies that were performed on isolated mitochondria, permeabilized cells, and in whole hearts. PMID:21964191

  15. Radioimmunoassay for intact Gross mouse leukemia virus.

    PubMed Central

    Yalow, R S; Gross, L

    1976-01-01

    A radioimmunoassay for intact Gross leukemia virus has been developed using 125I-labeled Gross virus grown in tissue culture and guinea pig antisera to Gross virus grown either in tissue culture or harvested from leukemic C3H(f) mice. Separation of bound from free labeled virus was effected using the double antibody method. The assay can detect fewer than 10(8) virus particles and has been used to measure the viral content of individual organs from inoculated leukemic C3H(f) mice and from Ak mice with spontaneous leukemia. Organs from noninoculated healthy C3H(f) mice crossreacted poorly in the system, virus generally being detectable only in the thymus and spleen and at low concentration. In some of the inoculated C3H(f) leukemic mice the viral content of as little as 0.5 mul of plasma is measurable. That this assay is for intact virus and not for soluble antigens of the viral envelope was proven by the observation that the immunoreactive material of plasma and extracts from thymus and liver of leukemic mice has a buoyant denisty in sucrose of 1.17-1.18 g/ml, corresponding to that of intact virus grown in tissue culture. With this sensitivity it may now be possible to quantitate viral concentrations in tissue and body fluids from the time of inoculation through the development of obvious pathology. PMID:1066697

  16. Normal D-region models for weapon-effects code. Technical report, 1 January-24 August 1985

    SciTech Connect

    Gambill

    1985-09-18

    This report examines several normal D-region models and their application to vlf/f propagation predictions. Special emphasis is placed on defining models that reproduce measured normal propagation data and also provide reasonable departure/recovery conditions after an ionospheric disturbance. An interim numerical model is described that provides for selection of a range of normal D-region electron profiles and also provides for a smooth transition to disturbed profiles. Requirements are also examined for defining prescribed D-region profiles using complex aero-chemistry models.

  17. Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups

    PubMed Central

    Herrnstadt, Corinna; Elson, Joanna L.; Fahy, Eoin; Preston, Gwen; Turnbull, Douglass M.; Anderson, Christen; Ghosh, Soumitra S.; Olefsky, Jerrold M.; Beal, M. Flint; Davis, Robert E.; Howell, Neil

    2002-01-01

    The evolution of the human mitochondrial genome is characterized by the emergence of ethnically distinct lineages or haplogroups. Nine European, seven Asian (including Native American), and three African mitochondrial DNA (mtDNA) haplogroups have been identified previously on the basis of the presence or absence of a relatively small number of restriction-enzyme recognition sites or on the basis of nucleotide sequences of the D-loop region. We have used reduced-median-network approaches to analyze 560 complete European, Asian, and African mtDNA coding-region sequences from unrelated individuals to develop a more complete understanding of sequence diversity both within and between haplogroups. A total of 497 haplogroup-associated polymorphisms were identified, 323 (65%) of which were associated with one haplogroup and 174 (35%) of which were associated with two or more haplogroups. Approximately one-half of these polymorphisms are reported for the first time here. Our results confirm and substantially extend the phylogenetic relationships among mitochondrial genomes described elsewhere from the major human ethnic groups. Another important result is that there were numerous instances both of parallel mutations at the same site and of reversion (i.e., homoplasy). It is likely that homoplasy in the coding region will confound evolutionary analysis of small sequence sets. By a linkage-disequilibrium approach, additional evidence for the absence of human mtDNA recombination is presented here. PMID:11938495

  18. Genetic analysis of the central untranslated genome region and the proximal coding part of the F gene of wild-type and vaccine canine distemper morbilliviruses.

    PubMed

    Liermann, H; Harder, T C; Löchelt, M; von Messling, V; Baumgärtner, W; Moennig, V; Haas, L

    1998-01-01

    Located between the open reading frames encoding the matrix (M) and the fusion (F) protein the morbillivirus genome contains an unusually large non-coding intercistronic region (M-F UTR) of up to 5.6% of the full length genome. Any function(s) of this region have largely remained obscure. Here, we analyze the M-F UTR and the proximal coding part of the downstream F gene of several recent canine distemper morbillivirus (CDV) wild-type (wt) isolates and vaccine strains. While the F gene coding part appeared to be highly conserved (about 93% homology), a considerable degree of strain-specific variation of up to 21.4% was evident when comparing the M-F UTR. Phylogenetic analysis revealed a co-circulation of several contemporary CDV genotypes within a close geographic range (central Europe). A remarkably distinct CDV wt lineage, so far detected only in mustelids, is displayed. A rather non-scattered pattern of mutations within the M-F UTR suggested superimposition of RNA sequence and/or secondary structure constraints. Extensive folding in the long (460 nt) and moderately GC-rich 5'-UTR of the F mRNA was evident, particularly around the putative F protein translation initiation codon (AUG461 of the Onderstepoort vaccine strain). The region immediately preceding the putative F initiation site also harbored the only mutation unique to both vaccine strains within the F-5'UTR (position 455: Awt vs. Cvac). The putative F protein start codon, AUG461, was found to be mutated to AUA or GUA in all wt isolates analyzed and in another vaccine strain (Rockborn). Possible consequences for F protein translation initiation in wt CDV are discussed. PMID:9926401

  19. Two isotocin genes are present in the white sucker Catostomus commersoni both lacking introns in their protein coding regions.

    PubMed Central

    Figueroa, J; Morley, S D; Heierhorst, J; Krentler, C; Lederis, K; Richter, D

    1989-01-01

    Two genes each encoding a distinct precursor protein to the hormone isotocin and a neurophysin-related protein are present in the teleost fish Catostomus commersoni. These precursors are referred to as isotocin 1 and 2. As shown by the polymerase chain reaction technique, both genes lack introns in their protein-coding sequences. Both genes are transcribed giving rise to mRNAs of 920 (isotocin 1) and 1020 (isotocin 2) bases, respectively. Based on the nucleotide sequences, the predicted isotocin precursors contain, besides the hormone moiety, a neurophysin-like protein that, in contrast to its mammalian counterpart, is extended at its C-terminus by a peptide which includes a leucine-rich core segment. This segment shows similarities to the copeptin of the mammalian vasopressin precursor that is known to possess prolactin-releasing activity. The data imply that the mammalian copeptin sequence was initially part of a larger ancestral neurophysin molecule. Images PMID:2583084

  20. A statistical framework to predict functional non-coding regions in the human genome through integrated analysis of annotation data.

    PubMed

    Lu, Qiongshi; Hu, Yiming; Sun, Jiehuan; Cheng, Yuwei; Cheung, Kei-Hoi; Zhao, Hongyu

    2015-01-01

    Identifying functional regions in the human genome is a major goal in human genetics. Great efforts have been made to functionally annotate the human genome either through computational predictions, such as genomic conservation, or high-throughput experiments, such as the ENCODE project. These efforts have resulted in a rich collection of functional annotation data of diverse types that need to be jointly analyzed for integrated interpretation and annotation. Here we present GenoCanyon, a whole-genome annotation method that performs unsupervised statistical learning using 22 computational and experimental annotations thereby inferring the functional potential of each position in the human genome. With GenoCanyon, we are able to predict many of the known functional regions. The ability of predicting functional regions as well as its generalizable statistical framework makes GenoCanyon a unique and powerful tool for whole-genome annotation. The GenoCanyon web server is available at http://genocanyon.med.yale.edu. PMID:26015273

  1. Neural activation differences in amputees during imitation of intact versus amputee movements

    PubMed Central

    Cusack, William F.; Cope, Michael; Nathanson, Sheryl; Pirouz, Nikta; Kistenberg, Robert; Wheaton, Lewis A.

    2012-01-01

    The mirror neuron system (MNS) has been attributed with increased activation in motor-related cortical areas upon viewing of another's actions. Recent work suggests that limb movements that are similar and dissimilar in appearance to that of the viewer equivalently activate the MNS. It is unclear if this result can be observed in the action encoding areas in amputees who use prosthetic devices. Intact subjects and upper extremity amputee prosthesis users were recruited to view video demonstrations of tools being used by an intact actor and a prosthetic device user. All subjects pantomimed the movements seen in the video while recording electroencephalography (EEG). Intact subjects showed equivalent left parietofrontal activity during imitation planning after watching the intact or prosthetic arm. Likewise, when prosthesis users imitated prosthesis demonstrations, typical left parietofrontal activation was observed. When prosthesis users imitated intact actors, an additional pattern was revealed which showed greater activity in right parietal and occipital regions that are associated with the mentalizing system. This change may be required for prosthesis users to plan imitation movements in which the limb states between the observed and the observer do not match. The finding that prosthesis users imitating other prosthesis users showed typical left parietofrontal activation suggests that these subjects engage normal planning related activity when they are able to imitate a limb matching their own. This result has significant implications on rehabilitation, as standard therapy involves training with an intact occupational therapist, which could necessitate atypical planning mechanisms in amputees when learning to use their prosthesis. PMID:22754516

  2. Calcium Signaling in Intact Dorsal Root Ganglia

    PubMed Central

    Gemes, Geza; Rigaud, Marcel; Koopmeiners, Andrew S.; Poroli, Mark J.; Zoga, Vasiliki; Hogan, Quinn H.

    2013-01-01

    Background Ca2+ is the dominant second messenger in primary sensory neurons. In addition, disrupted Ca2+ signaling is a prominent feature in pain models involving peripheral nerve injury. Standard cytoplasmic Ca2+ recording techniques use high K+ or field stimulation and dissociated neurons. To compare findings in intact dorsal root ganglia, we used a method of simultaneous electrophysiologic and microfluorimetric recording. Methods Dissociated neurons were loaded by bath-applied Fura-2-AM and subjected to field stimulation. Alternatively, we adapted a technique in which neuronal somata of intact ganglia were loaded with Fura-2 through an intracellular microelectrode that provided simultaneous membrane potential recording during activation by action potentials (APs) conducted from attached dorsal roots. Results Field stimulation at levels necessary to activate neurons generated bath pH changes through electrolysis and failed to predictably drive neurons with AP trains. In the intact ganglion technique, single APs produced measurable Ca2+ transients that were fourfold larger in presumed nociceptive C-type neurons than in nonnociceptive Aβ-type neurons. Unitary Ca2+ transients summated during AP trains, forming transients with amplitudes that were highly dependent on stimulation frequency. Each neuron was tuned to a preferred frequency at which transient amplitude was maximal. Transients predominantly exhibited monoexponential recovery and had sustained plateaus during recovery only with trains of more than 100 APs. Nerve injury decreased Ca2+ transients in C-type neurons, but increased transients in Aβ-type neurons. Conclusions Refined observation of Ca2+ signaling is possible through natural activation by conducted APs in undissociated sensory neurons and reveals features distinct to neuronal types and injury state. PMID:20526180

  3. 50 CFR 622.38 - Landing fish intact.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 10 2011-10-01 2011-10-01 false Landing fish intact. 622.38 Section 622... § 622.38 Landing fish intact. The operator of a vessel that fishes in the EEZ is responsible for ensuring that fish on that vessel in the EEZ are maintained intact and, if taken from the EEZ,...

  4. 7 CFR 160.29 - Containers to remain intact.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Containers to remain intact. 160.29 Section 160.29... STANDARDS FOR NAVAL STORES Analysis, Inspection, and Grading on Request § 160.29 Containers to remain intact... the containers holding such naval stores remain intact as sampled until the analysis,...

  5. Formation of a unique cluster of G-quadruplex structures in the HIV-1 Nef coding region: implications for antiviral activity.

    PubMed

    Perrone, Rosalba; Nadai, Matteo; Poe, Jerrod A; Frasson, Ilaria; Palumbo, Manlio; Palù, Giorgio; Smithgall, Thomas E; Richter, Sara N

    2013-01-01

    G-quadruplexes are tetraplex structures of nucleic acids that can form in G-rich sequences. Their presence and functional role have been established in telomeres, oncogene promoters and coding regions of the human chromosome. In particular, they have been proposed to be directly involved in gene regulation at the level of transcription. Because the HIV-1 Nef protein is a fundamental factor for efficient viral replication, infectivity and pathogenesis in vitro and in vivo, we investigated G-quadruplex formation in the HIV-1 nef gene to assess the potential for viral inhibition through G-quadruplex stabilization. A comprehensive computational analysis of the nef coding region of available strains showed the presence of three conserved sequences that were uniquely clustered. Biophysical testing proved that G-quadruplex conformations were efficiently stabilized or induced by G-quadruplex ligands in all three sequences. Upon incubation with a G-quadruplex ligand, Nef expression was reduced in a reporter gene assay and Nef-dependent enhancement of HIV-1 infectivity was significantly repressed in an antiviral assay. These data constitute the first evidence of the possibility to regulate HIV-1 gene expression and infectivity through G-quadruplex targeting and therefore open a new avenue for viral treatment. PMID:24015290

  6. Karyopherin-Mediated Nuclear Import of the Homing Endonuclease VMA1-Derived Endonuclease Is Required for Self-Propagation of the Coding Region

    PubMed Central

    Nagai, Yuri; Nogami, Satoru; Kumagai-Sano, Fumi; Ohya, Yoshikazu

    2003-01-01

    VMA1-derived endonuclease (VDE), a site-specific endonuclease in Saccharomyces cerevisiae, enters the nucleus to generate a double-strand break in the VDE-negative allelic locus, mediating the self-propagating gene conversion called homing. Although VDE is excluded from the nucleus in mitotic cells, it relocalizes at premeiosis, becoming localized in both the nucleus and the cytoplasm in meiosis. The nuclear localization of VDE is induced by inactivation of TOR kinases, which constitute central regulators of cell differentiation in S. cerevisiae, and by nutrient depletion. A functional genomic approach revealed that at least two karyopherins, Srp1p and Kap142p, are required for the nuclear localization pattern. Genetic and physical interactions between Srp1p and VDE imply direct involvement of karyopherin-mediated nuclear transport in this process. Inactivation of TOR signaling or acquisition of an extra nuclear localization signal in the VDE coding region leads to artificial nuclear localization of VDE and thereby induces homing even during mitosis. These results serve as evidence that VDE utilizes the host systems of nutrient signal transduction and nucleocytoplasmic transport to ensure the propagation of its coding region. PMID:12588991

  7. A novel coding-region RNA element modulates infectious dengue virus particle production in both mammalian and mosquito cells and regulates viral replication in Aedes aegypti mosquitoes

    PubMed Central

    Groat-Carmona, Anna Maria; Orozco, Susana; Friebe, Peter; Payne, Anne; Kramer, Laura; Harris, Eva

    2013-01-01

    Dengue virus (DENV) is an enveloped flavivirus with a positive-sense RNA genome transmitted by Aedes mosquitoes, causing the most important arthropod-borne viral disease affecting humans. Relatively few cis-acting RNA regulatory elements have been described in the DENV coding-region. Here, by introducing silent mutations into a DENV-2 infectious clone, we identify the conserved capsid-coding region 1 (CCR1), an RNA sequence element that regulates viral replication in mammalian cells and to a greater extent in Ae. albopictus mosquito cells. These defects were confirmed in vivo, resulting in decreased replication in Ae. aegypti mosquito bodies and dissemination to the salivary glands. Furthermore, CCR1 does not regulate translation, RNA synthesis or virion retention but likely modulates assembly, as mutations resulted in the release of non-infectious viral particles from both cell types. Understanding the role of CCR1 could help characterize the poorly-defined stage of assembly in the DENV life cycle and uncover novel anti-viral targets. PMID:22840606

  8. Autosomal recessive retinitis pigmentosa with homozygous rhodopsin mutation E150K and non-coding cis-regulatory variants in CRX-binding regions of SAMD7

    PubMed Central

    Van Schil, Kristof; Karlstetter, Marcus; Aslanidis, Alexander; Dannhausen, Katharina; Azam, Maleeha; Qamar, Raheel; Leroy, Bart P.; Depasse, Fanny; Langmann, Thomas; De Baere, Elfride

    2016-01-01

    The aim of this study was to unravel the molecular pathogenesis of an unusual retinitis pigmentosa (RP) phenotype observed in a Turkish consanguineous family. Homozygosity mapping revealed two candidate genes, SAMD7 and RHO. A homozygous RHO mutation c.448G > A, p.E150K was found in two affected siblings, while no coding SAMD7 mutations were identified. Interestingly, four non-coding homozygous variants were found in two SAMD7 genomic regions relevant for binding of the retinal transcription factor CRX (CRX-bound regions, CBRs) in these affected siblings. Three variants are located in a promoter CBR termed CBR1, while the fourth is located more downstream in CBR2. Transcriptional activity of these variants was assessed by luciferase assays and electroporation of mouse retinal explants with reporter constructs of wild-type and variant SAMD7 CBRs. The combined CBR2/CBR1 variant construct showed significantly decreased SAMD7 reporter activity compared to the wild-type sequence, suggesting a cis-regulatory effect on SAMD7 expression. As Samd7 is a recently identified Crx-regulated transcriptional repressor in retina, we hypothesize that these SAMD7 variants might contribute to the retinal phenotype observed here, characterized by unusual, recognizable pigment deposits, differing from the classic spicular intraretinal pigmentation observed in other individuals homozygous for p.E150K, and typically associated with RP in general. PMID:26887858

  9. Formation of a Unique Cluster of G-Quadruplex Structures in the HIV-1 nef Coding Region: Implications for Antiviral Activity

    PubMed Central

    Perrone, Rosalba; Nadai, Matteo; Poe, Jerrod A.; Frasson, Ilaria; Palumbo, Manlio; Palù, Giorgio; Smithgall, Thomas E.; Richter, Sara N.

    2013-01-01

    G-quadruplexes are tetraplex structures of nucleic acids that can form in G-rich sequences. Their presence and functional role have been established in telomeres, oncogene promoters and coding regions of the human chromosome. In particular, they have been proposed to be directly involved in gene regulation at the level of transcription. Because the HIV-1 Nef protein is a fundamental factor for efficient viral replication, infectivity and pathogenesis invitro and invivo, we investigated G-quadruplex formation in the HIV-1 nef gene to assess the potential for viral inhibition through G-quadruplex stabilization. A comprehensive computational analysis of the nef coding region of available strains showed the presence of three conserved sequences that were uniquely clustered. Biophysical testing proved that G-quadruplex conformations were efficiently stabilized or induced by G-quadruplex ligands in all three sequences. Upon incubation with a G-quadruplex ligand, Nef expression was reduced in a reporter gene assay and Nef-dependent enhancement of HIV-1 infectivity was significantly repressed in an antiviral assay. These data constitute the first evidence of the possibility to regulate HIV-1 gene expression and infectivity through G-quadruplex targeting and therefore open a new avenue for viral treatment. PMID:24015290

  10. Cloning of human transketolase cDNAs and comparison of the nucleotide sequence of the coding region in Wernicke-Korsakoff and non-Wernicke-Korsakoff individuals.

    PubMed

    McCool, B A; Plonk, S G; Martin, P R; Singleton, C K

    1993-01-15

    Variants of the enzyme transketolase which possess reduced affinity for its cofactor thiamine pyrophosphate (high apparent Km) have been described in chronic alcoholic patients with Wernicke-Korsakoff syndrome. Since the syndrome has been shown to be directly related to thiamine deficiency, it has been hypothesized that such transketolase variants may represent a genetic predisposition to the development of this syndrome. To test this hypothesis, human transketolase cDNA clones were isolated, and their nucleotide and predicted amino acid sequence were determined. Transketolase was found to be a single copy gene which produces a single mRNA of approximately 2100 nucleotides. Additionally, the nucleotide sequence of the transketolase coding region in fibroblasts derived from two Wernicke-Korsakoff (WK) patients was compared to that of two nonalcoholic controls. Although nucleotide and predicted amino acid differences were detected between fibroblast cultures and the original cDNAs and among the cultures themselves, no specific nucleotide variations, which would encode a variant amino acid sequence, were associated exclusively with the coding region from WK patients. Thus, allelic variants of the transketolase gene cannot account for the biochemically distinct forms of the enzyme found in these patients nor be considered as a mechanism for genetic predisposition to the development of Wernicke-Korsakoff syndrome. Instead, the underlying mechanism must be extragenic and may be a result of differences in post-translational processing/modification of the transketolase polypeptide. PMID:8419340

  11. A search for intact lava tubes on the Moon: Possible lunar base habitats

    NASA Technical Reports Server (NTRS)

    Coombs, Cassandra R.; Hawke, B. Ray

    1992-01-01

    We have surveyed lunar sinuous rilles and other volcanic features in an effort to locate intact lava tubes that could be used to house an advanced lunar base. Criteria were established for identifying intact tube segments. Sixty-seven tube candidates within 20 rilles were identified on the lunar nearside. The rilles, located in four mare regions, varied in size and sinuosity. We identified four rilles that exhibited particularly strong evidence for the existence of intact lava tube segments. These are located in the following areas: (1) south of Gruithuisen K, (2) in the Marius Hills region, (3) in the southeastern Mare Serenitatis, and (4) in the eastern Mare Serenitatis. We rated each of the 67 probable tube segments for lunar base suitability based on its dimensions, stability, location, and access to lunar resources. Nine tube segments associated with three separate rilles are considered prime candidates for use as part of an advanced lunar base.

  12. Intact Protein Quantitation Using Pseudoisobaric Dimethyl Labeling.

    PubMed

    Fang, Houqin; Xiao, Kaijie; Li, Yunhui; Yu, Fan; Liu, Yan; Xue, Bingbing; Tian, Zhixin

    2016-07-19

    Protein structural and functional studies rely on complete qualitative and quantitative information on protein species (proteoforms); thus, it is important to quantify differentially expressed proteins at their molecular level. Here we report our development of universal pseudoisobaric dimethyl labeling (pIDL) of amino groups at both the N-terminal and lysine residues for relative quantitation of intact proteins. Initial proof-of-principle study was conducted on standard protein myoglobin and hepatocellular proteomes (HepG2 vs LO2). The amino groups from both the N-terminal and lysine were dimethylated with HXHO (X = (13)C or C) and NaBY3CN (Y = H or D). At the standard protein level, labeling efficiency, effect of product ion size, and mass resolution on quantitation accuracy were explored; and a good linear quantitation dynamic range up to 50-fold was obtained. For the hepatocellular proteome samples, 33 proteins were quantified with RSD ≤ 10% from one-dimensional reversed phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) analysis of the 1:1 mixed samples. The method in this study can be extended to quantitation of other intact proteome systems. The universal "one-pot" dimethyl labeling of all the amino groups in a protein without the need of preblocking of those on the lysine residues is made possible by protein identification and quantitation analysis using ProteinGoggle 2.0 with customized databases of both precursor and product ions containing heavy isotopes. PMID:27359340

  13. Common coding variants in the HLA-DQB1 region confer susceptibility to age-related macular degeneration.

    PubMed

    Jorgenson, Eric; Melles, Ronald B; Hoffmann, Thomas J; Jia, Xiaoming; Sakoda, Lori C; Kvale, Mark N; Banda, Yambazi; Schaefer, Catherine; Risch, Neil; Shen, Ling

    2016-07-01

    Age-related macular degeneration (AMD) risk variants in the complement system point to the important role of immune response and inflammation in the pathogenesis of AMD. Although the human leukocyte antigen (HLA) region has a central role in regulating immune response, previous studies of genetic variation in HLA genes and AMD have been limited by sample size or incomplete coverage of the HLA region by first-generation genotyping arrays and imputation panels. Here, we conducted a large-scale HLA fine-mapping study with 4841 AMD cases and 23 790 controls of non-Hispanic white ancestry from the Kaiser Permanente Genetic Epidemiology Research on Adult Health and Aging cohort. Genotyping was conducted using custom Affymetrix Axiom arrays, with dense coverage of the HLA region. Classic HLA polymorphisms were imputed using SNP2HLA, which utilizes a large reference panel to provide improved imputation accuracy of variants in this region. We examined a total of 6937 SNPs and 172 classical HLA alleles, conditioning on established AMD risk variants, which revealed novel associations with two non-synonymous SNPs in perfect linkage disequilibrium, rs9274390 and rs41563814 (odds ratio (OR)=1.21; P=1.4 × 10(-11)) corresponding to amino-acid changes at position 66 and 67 in HLA-DQB1, respectively, and the DQB1*02 classical HLA allele (OR=1.22; P=3.9 × 10(-10)) with the risk of AMD. We confirmed these association signals, again conditioning on established risk variants, in the MMAP data set of subjects with advanced AMD (rs9274390/rs41563814: OR=1.28; P=1.30 × 10(-3), DQB1*02: OR=1.32; P=9.00 × 10(-4)). These findings support a role of HLA class II alleles in the risk of AMD. PMID:26733291

  14. Recollections of Parent Characteristics and Attachment Patterns for College Women of Intact vs. Non-Intact Families

    ERIC Educational Resources Information Center

    Kilmann, Peter R.; Carranza, Laura V.; Vendemia, Jennifer M. C.

    2006-01-01

    This study contrasted offsprings' attachment patterns and recollections of parent characteristics in two college samples: 147 females from intact biological parents and 157 females of parental divorce. Secure females from intact or non-intact families rated parents positively, while insecure females rated parents as absent, distant, and demanding.…

  15. Vesta is not an intact protoplanet

    NASA Astrophysics Data System (ADS)

    Consolmagno, G.; Turrini, D.; Golabek, G.; Svetsov, V.; Sirono, S.; Tsiganis, K.

    2014-07-01

    The Dawn mission was designed to explore ''remnant intact protoplanets from the earliest epoch of solar system formation'' [1]. However, models of Vesta composed of an iron core, olivine mantle, and HED crust in chondritic proportions cannot match the joint constraints from Dawn [1] of Vesta's density, core size, and the extremely limited presence of exposed olivine on its surface. Vesta has a mean density of 3456 kg/m3 and its surface composition is well matched by howardites. The Dawn gravity data suggest a nickel-iron core of radius 110 km and density 7500--7800 kg/m3. The Rheasilvia impact basin, formed within a pre-existing large basin, Veneneia, should have excavated material from a depth of 50 km to 80 km or more below Vesta's surface [2]. If the howardite crust were thinner than 50--80 km, a significant amount of olivine-rich material, derived from depth, would have been exposed within this basin; models suggest that olivine would also be distributed both on Vesta's surface and in space as meteorite-source Vestoids. Such olivine is rare on Vesta, among the Vestoids, or in our meteorite collection. Vesta's density is similar to an L chondrite, but the Na and K abundances in Vesta are strongly depleted compared to chondrites and the average metal content of an L chondrite, 8.4% by mass, would give a core radius less than 90 km. A 110 km radius metallic core, via the Dawn data, represents 15% of Vesta's mass. The Mg/Al ratio in cosmic abundances is about 10:1, but roughly 1:1 within the eucrites; thus if Vesta started with cosmic abundances, the eucrites can only represent 10% of the parent body total mass. Likewise the 10 x chondritic rare earth trace elements (REE) abundance seen in most eucrites demands that, regardless of formation mechanism, these basalts were crystallized from a melt representing 10% of the mass of the source region [3]. Thus the howardite crust of a chondritic HED parent body, mixing all the available eucritic and diogenitic material

  16. Oligodeoxynucleotide Probes for Detecting Intact Cells

    NASA Technical Reports Server (NTRS)

    Rosson, Reinhardt A.; Maurina-Brunker, Julie; Langley, Kim; Pynnonen, Christine M.

    2004-01-01

    A rapid, sensitive test using chemiluminescent oligodeoxynucleotide probes has been developed for detecting, identifying, and enumerating intact cells. The test is intended especially for use in detecting and enumerating bacteria and yeasts in potable water. As in related tests that have been developed recently for similar purposes, the oligodeoxynucleotide probes used in this test are typically targeted at either singlecopy deoxyribonucleic acid (DNA) genes (such as virulence genes) or the multiple copies (10,000 to 50,000 copies per cell) of 16S ribosomal ribonucleic acids (rRNAs). Some of those tests involve radioisotope or fluorescent labeling of the probes for reporting hybridization of probes to target nucleic acids. Others of those tests involve labeling with enzymes plus the use of chemiluminescent or chromogenic substrates to report hybridization via color or the emission of light, respectively. The present test is of the last-mentioned type. The chemiluminescence in the present test can be detected easily with relatively simple instrumentation. In developing the present test, the hybridization approach was chosen because hybridization techniques are very specific. Hybridization detects stable, inheritable genetic targets within microorganisms. These targets are not dependent on products of gene expression that can vary with growth conditions or physiological states of organisms in test samples. Therefore, unique probes can be designed to detect and identify specific genera or species of bacteria or yeast (in terms of rRNA target sequences) or can be designed to detect and identify virulence genes (genomic target sequences). Because of the inherent specificity of this system, there are few problems of cross-reactivity. Hybridization tests are rapid, but hybridization tests now available commercially lack sensitivity; typically, between 10(exp 6) and 10(exp 7) cells of the target organism are needed to ensure a reliable test. Consequently, the numbers of

  17. Intact quasiparticles at an unconventional quantum critical point

    NASA Astrophysics Data System (ADS)

    Sutherland, M. L.; O'Farrell, E. C. T.; Toews, W. H.; Dunn, J.; Kuga, K.; Nakatsuji, S.; Machida, Y.; Izawa, K.; Hill, R. W.

    2015-07-01

    We report measurements of in-plane electrical and thermal transport properties in the limit T →0 near the unconventional quantum critical point in the heavy-fermion metal β -YbAlB4 . The high Kondo temperature TK≃200 K in this material allows us to probe transport extremely close to the critical point, at unusually small values of T /TK<5 ×10-4 . Here we find that the Wiedemann-Franz law is obeyed at the lowest temperatures, implying that the Landau quasiparticles remain intact in the critical region. At finite temperatures we observe a non-Fermi-liquid T -linear dependence of inelastic-scattering processes to energies lower than those previously accessed. These processes have a weaker temperature dependence than in comparable heavy fermion quantum critical systems, revealing a temperature scale of T ˜0.3 K which signals a sudden change in the character of the inelastic scattering.

  18. A polymorphism site in the pre‑miR‑34a coding region reduces miR‑34a expression and promotes osteosarcoma cell proliferation and migration.

    PubMed

    Lv, Honglin; Pei, Jingfang; Liu, Hongtao; Wang, Haiyan; Liu, Jun

    2014-12-01

    Osteosarcoma (OS) is the most prevalent primary malignant bone tumor in children and young adults, its complex etiology involving a combination of environmental and genetic factors. MicroRNA (miRNA) is a short, non‑coding regulatory RNA molecule that represses gene expression by imperfectly base‑pairing to the 3' untranslated region of target mRNAs. Evidence has shown that alterations in the expression of miRNA are involved in the initiation, progression, and metastasis of human cancers. It is believed that miRNAs function both as tumor suppressors and oncogenes during cancer development. In the present study, three tumor-associated miRNAs (miR‑21, miR‑34a and miR‑146a) coding regions were screened in Chinese‑Han OS patients. A G>A variation in the pre‑miR‑34a coding region was found to be associated with higher OS morbidity. By detecting the mature miR‑34a expression in cells transfected with pre‑miR‑34a expression vectors of different genotypes using quantitative polymerase chain reaction, it was demonstrated that the G>A variation reduced miR‑34a expression in vitro. This was in accordance with the data collected from tumor tissue and patient serum samples. Subsequently, a dual‑luciferase reporter assay and western blot analysis were used to detect the site variation effect on the expression of c‑Met, a target gene of miR‑34a. The G>A variation downregulated the suppression of c‑Met in two OS cell lines. Furthermore, it was found that reduced miR‑34a expression decreased the suppression of OS cell proliferation in vitro. In conclusion, the present study established the association between miR‑34a and the risk of suffering OS in a Chinese Han population by identifying one functional single nucleotide polymorphism site in pre‑miR‑34a. These findings may give insight into the mechanism of OS development and create an opportunity to approach the diagnosis and treatment of OS. PMID:25242229

  19. Drilling to gabbro in intact ocean crust.

    PubMed

    Wilson, Douglas S; Teagle, Damon A H; Alt, Jeffrey C; Banerjee, Neil R; Umino, Susumu; Miyashita, Sumio; Acton, Gary D; Anma, Ryo; Barr, Samantha R; Belghoul, Akram; Carlut, Julie; Christie, David M; Coggon, Rosalind M; Cooper, Kari M; Cordier, Carole; Crispini, Laura; Durand, Sedelia Rodriguez; Einaudi, Florence; Galli, Laura; Gao, Yongjun; Geldmacher, Jörg; Gilbert, Lisa A; Hayman, Nicholas W; Herrero-Bervera, Emilio; Hirano, Nobuo; Holter, Sara; Ingle, Stephanie; Jiang, Shijun; Kalberkamp, Ulrich; Kerneklian, Marcie; Koepke, Jürgen; Laverne, Christine; Vasquez, Haroldo L Lledo; Maclennan, John; Morgan, Sally; Neo, Natsuki; Nichols, Holly J; Park, Sung-Hyun; Reichow, Marc K; Sakuyama, Tetsuya; Sano, Takashi; Sandwell, Rachel; Scheibner, Birgit; Smith-Duque, Chris E; Swift, Stephen A; Tartarotti, Paola; Tikku, Anahita A; Tominaga, Masako; Veloso, Eugenio A; Yamasaki, Toru; Yamazaki, Shusaku; Ziegler, Christa

    2006-05-19

    Sampling an intact sequence of oceanic crust through lavas, dikes, and gabbros is necessary to advance the understanding of the formation and evolution of crust formed at mid-ocean ridges, but it has been an elusive goal of scientific ocean drilling for decades. Recent drilling in the eastern Pacific Ocean in Hole 1256D reached gabbro within seismic layer 2, 1157 meters into crust formed at a superfast spreading rate. The gabbros are the crystallized melt lenses that formed beneath a mid-ocean ridge. The depth at which gabbro was reached confirms predictions extrapolated from seismic experiments at modern mid-ocean ridges: Melt lenses occur at shallower depths at faster spreading rates. The gabbros intrude metamorphosed sheeted dikes and have compositions similar to the overlying lavas, precluding formation of the cumulate lower oceanic crust from melt lenses so far penetrated by Hole 1256D. PMID:16627698

  20. Mass Spectrometry of Intact Membrane Protein Complexes

    PubMed Central

    Laganowsky, Arthur; Reading, Eamonn; Hopper, Jonathan T.S.; Robinson, Carol V.

    2014-01-01

    Mass spectrometry of intact soluble protein complexes has emerged as a powerful technique to study the stoichiometry, structure-function and dynamics of protein assemblies. Recent developments have extended this technique to the study of membrane protein complexes where it has already revealed subunit stoichiometries and specific phospholipid interactions. Here, we describe a protocol for mass spectrometry of membrane protein complexes. The protocol begins with preparation of the membrane protein complex enabling not only the direct assessment of stoichiometry, delipidation, and quality of the target complex, but also evaluation of the purification strategy. A detailed list of compatible non-ionic detergents is included, along with a protocol for screening detergents to find an optimal one for mass spectrometry, biochemical and structural studies. This protocol also covers the preparation of lipids for protein-lipid binding studies and includes detailed settings for a Q-ToF mass spectrometer after introduction of complexes from gold-coated nanoflow capillaries. PMID:23471109

  1. Protein methylation reactions in intact pea chloroplasts

    SciTech Connect

    Niemi, K.J. )

    1989-04-01

    Post-translational protein methylation was investigated in Pisum sativum chloroplasts. Intact pea chloroplasts were incubated with ({sup 3}H-methyl)-S-adenosylmethionine under various conditions. The chloroplasts were then separated into stromal and thylakoid fractions and analyzed for radioactivity transferred to protein. Light enhanced the magnitude of labeling in both fractions. One thylakoid polypeptide with an apparent molecular mass of 43 kDa was labeled only in the light. Several other thylakoid and stromal proteins were labeled in both light and dark-labeling conditions. Both base-labile methylation, carboxy-methylesters and base-stable groups, N-methylations were found. Further characterization of the methyl-transfer reactions will be presented.

  2. A novel TaqI polymorphism in the coding region of the ovine TNXB gene in the MHC class III region: morphostructural and physiological influences.

    PubMed

    Ajayi, Oyeyemi O; Adefenwa, Mufliat A; Agaviezor, Brilliant O; Ikeobi, Christian O N; Wheto, Matthew; Okpeku, Moses; Amusan, Samuel A; Yakubu, Abdulmojeed; De Donato, Marcos; Peters, Sunday O; Imumorin, Ikhide G

    2014-02-01

    The tenascin-XB (TNXB) gene has antiadhesive effects, functions in matrix maturation in connective tissues, and localizes to the major histocompatibility complex class III region. We hypothesized that it may influence adaptive physiological response through an effect on blood vessel function. We identified a novel g.1324 A→G polymorphism at a TaqI recognition site in a 454 bp fragment of ovine TNXB and genotyped it in 150 Nigerian sheep using PCR-RFLP. The missense mutation changes glutamic acid (GAA) to glycine (GGA). Among SNP genotypes, significant differences (P < 0.05) were observed in body weight and fore cannon bone length. Interaction effects of breed, SNP genotype, and geographic location had a significant effect (P < 0.05) on chest girth. The SNP genotype was significantly (P < 0.05) associated with physiological traits of pulse rate and skin temperature. The observed effect of this novel polymorphism may be mediated through its role in connective tissue biology, requiring further association and functional studies. PMID:23877191

  3. Isolation and characterization of a cDNA clone for the complete protein coding region of the delta subunit of the mouse acetylcholine receptor.

    PubMed Central

    LaPolla, R J; Mayne, K M; Davidson, N

    1984-01-01

    A mouse cDNA clone has been isolated that contains the complete coding region of a protein highly homologous to the delta subunit of the Torpedo acetylcholine receptor (AcChoR). The cDNA library was constructed in the vector lambda 10 from membrane-associated poly(A)+ RNA from BC3H-1 mouse cells. Surprisingly, the delta clone was selected by hybridization with cDNA encoding the gamma subunit of the Torpedo AcChoR. The nucleotide sequence of the mouse cDNA clone contains an open reading frame of 520 amino acids. This amino acid sequence exhibits 59% and 50% sequence homology to the Torpedo AcChoR delta and gamma subunits, respectively. However, the mouse nucleotide sequence has several stretches of high homology with the Torpedo gamma subunit cDNA, but not with delta. The mouse protein has the same general structural features as do the Torpedo subunits. It is encoded by a 3.3-kilobase mRNA. There is probably only one, but at most two, chromosomal genes coding for this or closely related sequences. Images PMID:6096870

  4. Functional Anthology of Intrinsic Disorder. II. Cellular Components, Domains, Technical Terms, Developmental Processes and Coding Sequence Diversities Correlated with Long Disordered Regions

    PubMed Central

    Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

    2008-01-01

    Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes ~90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes and coding sequence diversities possessing strong positive and negative correlation with long disordered regions. PMID:17391015

  5. Clinical coding. Code breakers.

    PubMed

    Mathieson, Steve

    2005-02-24

    --The advent of payment by results has seen the role of the clinical coder pushed to the fore in England. --Examinations for a clinical coding qualification began in 1999. In 2004, approximately 200 people took the qualification. --Trusts are attracting people to the role by offering training from scratch or through modern apprenticeships. PMID:15768716

  6. Systematic comparison of gene expression through analysis of cDNA fragments within or near to the protein-coding region.

    PubMed

    Ke, Y; Jing, C; Rudland, P S; Smith, P H; Foster, C S

    1999-02-01

    Life is controlled by the timely and ordered expression of genes. Identification of important genes involved in specific physiological and pathological conditions requires efficient methods to analyse differential gene expression. We describe a novel strategy, namely complete comparison of gene expression (CCGE), for a systematic assessment of differentially expressed genes. Using the CCGE method, double-stranded cDNA is digested with two restriction enzymes that cut with different frequencies, the representative cDNA fragments are generated within or near to the protein-coding region. After being flanked by two different types of adapters, and amplified by a nested suppression PCR, the selected cDNA fragments, representing entire cDNA population, can be divided into 256 subsets; amplified and compared in a systematic manner. PMID:9889292

  7. Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions.

    PubMed

    Chen, Jin; Coakley, Arthur; O'Connor, Michelle; Petrov, Alexey; O'Leary, Seán E; Atkins, John F; Puglisi, Joseph D

    2015-11-19

    Nearly half of the ribosomes translating a particular bacteriophage T4 mRNA bypass a region of 50 nt, resuming translation 3' of this gap. How this large-scale, specific hop occurs and what determines whether a ribosome bypasses remain unclear. We apply single-molecule fluorescence with zero-mode waveguides to track individual Escherichia coli ribosomes during translation of T4's gene 60 mRNA. Ribosomes that bypass are characterized by a 10- to 20-fold longer pause in a non-canonical rotated state at the take-off codon. During the pause, mRNA secondary structure rearrangements are coupled to ribosome forward movement, facilitated by nascent peptide interactions that disengage the ribosome anticodon-codon interactions for slippage. Close to the landing site, the ribosome then scans mRNA in search of optimal base-pairing interactions. Our results provide a mechanistic and conformational framework for bypassing, highlighting a non-canonical ribosomal state to allow for mRNA structure refolding to drive large-scale ribosome movements. PMID:26590426

  8. A New Model for Real-Time Regional Vertical Total Electron Content and Differential Code Bias Estimation Using IGS Real-Time Service (IGS-RTS) Products

    NASA Astrophysics Data System (ADS)

    Abdelazeem, Mohamed; Çelik, Rahmi N.; El-Rabbany, Ahmed

    2016-04-01

    The international global navigation satellite system (GNSS) real-time service (IGS-RTS) products have been used extensively for real-time precise point positioning and ionosphere modeling applications. In this study, we develop a regional model for real-time vertical total electron content (RT-VTEC) and differential code bias (RT-DCB) estimation over Europe using the IGS-RTS satellite orbit and clock products. The developed model has a spatial and temporal resolution of 1°×1° and 15 minutes, respectively. GPS observations from a regional network consisting of 60 IGS and EUREF reference stations are processed in the zero-difference mode using the Bernese-5.2 software package in order to extract the geometry-free linear combination of the smoothed code observations. The spherical harmonic expansion function is used to model the VTEC, the receiver and the satellite DCBs. To validate the proposed model, the RT-VTEC values are computed and compared with the final IGS-global ionospheric map (IGS-GIM) counterparts in three successive days under high solar activity including one of an extreme geomagnetic activity. The real-time satellite DCBs are also estimated and compared with the IGS-GIM counterparts. Moreover, the real-time receiver DCB for six IGS stations are obtained and compared with the IGS-GIM counterparts. The examined stations are located in different latitudes with different receiver types. The findings reveal that the estimated RT-VTEC values show agreement with the IGS-GIM counterparts with root mean-square-errors (RMSEs) values less than 2 TEC units. In addition, RMSEs of both the satellites and receivers DCBs are less than 0.85 ns and 0.65 ns, respectively in comparison with the IGS-GIM.

  9. Positions of Trp codons in the leader peptide-coding region of the at operon influence anti-trap synthesis and trp operon expression in Bacillus licheniformis.

    PubMed

    Levitin, Anastasia; Yanofsky, Charles

    2010-03-01

    Tryptophan, phenylalanine, tyrosine, and several other metabolites are all synthesized from a common precursor, chorismic acid. Since tryptophan is a product of an energetically expensive biosynthetic pathway, bacteria have developed sensing mechanisms to downregulate synthesis of the enzymes of tryptophan formation when synthesis of the amino acid is not needed. In Bacillus subtilis and some other Gram-positive bacteria, trp operon expression is regulated by two proteins, TRAP (the tryptophan-activated RNA binding protein) and AT (the anti-TRAP protein). TRAP is activated by bound tryptophan, and AT synthesis is increased upon accumulation of uncharged tRNA(Trp). Tryptophan-activated TRAP binds to trp operon leader RNA, generating a terminator structure that promotes transcription termination. AT binds to tryptophan-activated TRAP, inhibiting its RNA binding ability. In B. subtilis, AT synthesis is upregulated both transcriptionally and translationally in response to the accumulation of uncharged tRNA(Trp). In this paper, we focus on explaining the differences in organization and regulatory functions of the at operon's leader peptide-coding region, rtpLP, of B. subtilis and Bacillus licheniformis. Our objective was to correlate the greater growth sensitivity of B. licheniformis to tryptophan starvation with the spacing of the three Trp codons in its at operon leader peptide-coding region. Our findings suggest that the Trp codon location in rtpLP of B. licheniformis is designed to allow a mild charged-tRNA(Trp) deficiency to expose the Shine-Dalgarno sequence and start codon for the AT protein, leading to increased AT synthesis. PMID:20061467

  10. MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences

    PubMed Central

    2011-01-01

    Background MicroRNAs are a family of ~22 nt small RNAs that can regulate gene expression at the post-transcriptional level. Identification of these molecules and their targets can aid understanding of regulatory processes. Recently, HTS has become a common identification method but there are two major limitations associated with the technique. Firstly, the method has low efficiency, with typically less than 1 in 10,000 sequences representing miRNA reads and secondly the method preferentially targets highly expressed miRNAs. If sequences are available, computational methods can provide a screening step to investigate the value of an HTS study and aid interpretation of results. However, current methods can only predict miRNAs for short fragments and have usually been trained against small datasets which don't always reflect the diversity of these molecules. Results We have developed a software tool, miRPara, that predicts most probable mature miRNA coding regions from genome scale sequences in a species specific manner. We classified sequences from miRBase into animal, plant and overall categories and used a support vector machine to train three models based on an initial set of 77 parameters related to the physical properties of the pre-miRNA and its miRNAs. By applying parameter filtering we found a subset of ~25 parameters produced higher prediction ability compared to the full set. Our software achieves an accuracy of up to 80% against experimentally verified mature miRNAs, making it one of the most accurate methods available. Conclusions miRPara is an effective tool for locating miRNAs coding regions in genome sequences and can be used as a screening step prior to HTS experiments. It is available at http://www.whiov.ac.cn/bioinformatics/mirpara PMID:21504621

  11. Effects of intact versus non-intact families on adolescent head injury rehabilitation.

    PubMed

    Barry, P; Clark, D

    1992-01-01

    Forty-one children, aged 8-18 years, were admitted to a comprehensive in-patient head injury rehabilitation facility over a 5-year period. Over half (59%) came from families with only one biological parent in the home. Data from intact versus non-intact families suggest that the children from the latter were significantly younger and remained as in-patients significantly longer than their counterparts. The severity of injuries and incidence of premorbid psychosocial documentation were equivalent for the two groups. The implications for treatment and future research are discussed. A previous version of this paper was presented at the 97th convention of the American Psychological Association in New Orleans on August 13, 1989. The authors are grateful to Dr Mark Ylvisaker for his comments and suggestions. PMID:1581746

  12. Non-coding RNA derived from the region adjacent to the human HO-1 E2 enhancer selectively regulates HO-1 gene induction by modulating Pol II binding

    PubMed Central

    Maruyama, Atsushi; Mimura, Junsei; Itoh, Ken

    2014-01-01

    Recent studies have disclosed the function of enhancer RNAs (eRNAs), which are long non-coding RNAs transcribed from gene enhancer regions, in transcriptional regulation. However, it remains unclear whether eRNAs are involved in the regulation of human heme oxygenase-1 gene (HO-1) induction. Here, we report that multiple nuclear-enriched eRNAs are transcribed from the regions adjacent to two human HO-1 enhancers (i.e. the distal E2 and proximal E1 enhancers), and some of these eRNAs are induced by the oxidative stress-causing reagent diethyl maleate (DEM). We demonstrated that the expression of one forward direction (5′ to 3′) eRNA transcribed from the human HO-1 E2 enhancer region (named human HO-1enhancer RNA E2-3; hereafter called eRNA E2-3) was induced by DEM in an NRF2-dependent manner in HeLa cells. Conversely, knockdown of BACH1, a repressor of HO-1 transcription, further increased DEM-inducible eRNA E2-3 transcription as well as HO-1 expression. In addition, we showed that knockdown of eRNA E2-3 selectively down-regulated DEM-induced HO-1 expression. Furthermore, eRNA E2-3 knockdown attenuated DEM-induced Pol II binding to the promoter and E2 enhancer regions of HO-1 without affecting NRF2 recruitment to the E2 enhancer. These findings indicate that eRNAE2-3 is functional and is required for HO-1 induction. PMID:25404134

  13. Molecular characterization of severe hemophilia A suggests that about half the mutations are not within the coding regions and splice junctions of the factor VIII gene.

    PubMed Central

    Higuchi, M; Kazazian, H H; Kasch, L; Warren, T C; McGinniss, M J; Phillips, J A; Kasper, C; Janco, R; Antonarakis, S E

    1991-01-01

    Hemophilia A is an X chromosome-linked disorder resulting from deficiency of factor VIII, an important protein in blood coagulation. A large number of disease-producing mutations have been reported in the factor VIII gene. However, a comprehensive analysis of the mutations has been difficult because of the large gene size, its many scattered exons, and the high frequency of de novo mutations. Recently, we have shown that nearly all mutations resulting in mild-to-moderate hemophilia A can be detected by PCR and denaturing gradient gel electrophoresis (DGGE). In this study, we attempted to discover the mutations causing severe hemophilia A by analyzing 47 unselected patients, 30 of whom had severe hemophilia and 17 of whom had mild-to-moderate disease. Using DGGE as a screening method, we analyzed 99% of the coding region, 94% of the splice junctions, the promoter region, and the polyadenylylation site of the gene. We found the mutation in 16 of 17 (94%) patients with mild-to-moderate disease but in only 16 of 30 (53%) patients with severe hemophilia A. Since DGGE after computer analysis appears to detect all mutations in a given fragment, the lower-than-expected yield of mutations in patients with severe disease is likely not due to failure of the detection method; it is probably due to the presence of mutations in DNA sequences outside the regions studied. Such sequences may include locus-controlling regions, other sequences within introns or outside the gene that are important for its expression, or another gene involved in factor VIII expression that is very closely linked to the factor VIII gene. Images PMID:1908096

  14. Development of a novel immunoassay specific for mouse intact proinsulin.

    PubMed

    Imai, Sunao; Takahashi, Tatsuya; Naito, Shoichi; Yamauchi, Akira; Okada, Chihiro; Notsu, Yoshihide; Sakikawa, Ikue; Hatanaka, Michiyoshi; Iwasaki, Takanori; Morita, Atsushi; Fujii, Ikuo; Yamane, Shoji

    2015-09-01

    The blood concentration of intact proinsulin, but not total proinsulin, has been suggested to be a diagnostic marker for type 2 diabetes mellitus (T2DM), but a sensitive assay specific for rodent intact proinsulin is lacking. Here, a novel enzyme-linked immunosorbent assay (ELISA) for mouse intact proinsulin was developed. The developed ELISA detected mouse intact proinsulin with the working range of 8.3 to 2700pg/ml. Cross-reactivity with mouse split-32,33 proinsulin was approximately 100times lower than the reactivity with mouse intact proinsulin, and no cross-reactivity with mouse insulin was detected. The developed ELISA was sufficiently sensitive to detect low levels of intact proinsulin in normal mouse plasma. The measurement by the developed ELISA revealed that intact proinsulin was elevated in the plasma of type 2 diabetic db/db mice as mice aged, and the ratio of intact proinsulin/insulin in plasma was correlated with levels of glycated hemoglobin A1c as seen in T2DM patients. These results suggest that the plasma level of intact proinsulin, but not total proinsulin, is a sensitive marker for pancreatic dysfunction and the ensuring diabetic disease progression of db/db mice. This ELISA could aid nonclinical evaluation of therapeutic interventions in T2DM. PMID:26026387

  15. 33. TURBINE HALL, ORIGINAL TURBO GENERATOR, INTACT CONDENSER Philadelphia ...

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

    33. TURBINE HALL, ORIGINAL TURBO GENERATOR, INTACT CONDENSER - Philadelphia Electric Company, Richmond Power Station, Southeast end of Lewis Street along Delaware River, Philadelphia, Philadelphia County, PA

  16. Teaching basic neurophysiology using intact earthworms.

    PubMed

    Kladt, Nikolay; Hanslik, Ulrike; Heinzel, Hans-Georg

    2010-01-01

    Introductory neurobiology courses face the problem that practical exercises often require expensive equipment, dissections, and a favorable student-instructor ratio. Furthermore, the duration of an experiment might exceed available time or the level of required expertise is too high to successfully complete the experiment. As a result, neurobiological experiments are commonly replaced by models and simulations, or provide only very basic experiments, such as the frog sciatic nerve preparation, which are often time consuming and tedious. Action potential recordings in giant fibers of intact earthworms (Lumbricus terrestris) circumvent many of these problems and result in a nearly 100% success rate. Originally, these experiments were introduced as classroom exercises by Charles Drewes in 1978 using awake, moving earthworms. In 1990, Hans-Georg Heinzel described further experiments using anesthetized earthworms. In this article, we focus on the application of these experiments as teaching tools for basic neurobiology courses. We describe and extend selected experiments, focusing on specific neurobiological principles with experimental protocols optimized for classroom application. Furthermore, we discuss our experience using these experiments in animal physiology and various neurobiology courses at the University of Bonn. PMID:23494516

  17. Nitrite Uptake into Intact Pea Chloroplasts 1

    PubMed Central

    Brunswick, Pamela; Cresswell, Christopher F.

    1988-01-01

    The relationship between net nitrite uptake and its reduction in intact pea chloroplasts was investigated employing electron transport regulators, uncouplers, and photophosphorylation inhibitors. Observations confirmed the dependence of nitrite uptake on stromal pH and nitrite reduction but also suggested a partial dependance upon PSI phosphorylation. It was also suggested that ammonia stimulates nitrogen assimilation in the dark by association with stromal protons. Inhibition of nitrite uptake by N-ethylmaleimide and dinitrofluorobenzene could not be completely attributed to their inhibition of carbon dioxide fixation. Other protein binding reagents which inhibited photosynthesis showed no effect on nitrite uptake, except for p-chlormercuribenzoate which stimulated nitrite uptake. The results with N-ethylmaleimide and dinitrofluorobenzene tended to support the proposed presence of a protein permeation channel for nitrite uptake in addition to HNO2 penetration. On the basis of a lack of effect by known anion uptake inhibitors, it was concluded that the nitrite uptake mechanism was distinct from that of phosphate and chloride/sulfate transport. PMID:16665917

  18. Teaching Basic Neurophysiology Using Intact Earthworms

    PubMed Central

    Kladt, Nikolay; Hanslik, Ulrike; Heinzel, Hans-Georg

    2010-01-01

    Introductory neurobiology courses face the problem that practical exercises often require expensive equipment, dissections, and a favorable student-instructor ratio. Furthermore, the duration of an experiment might exceed available time or the level of required expertise is too high to successfully complete the experiment. As a result, neurobiological experiments are commonly replaced by models and simulations, or provide only very basic experiments, such as the frog sciatic nerve preparation, which are often time consuming and tedious. Action potential recordings in giant fibers of intact earthworms (Lumbricus terrestris) circumvent many of these problems and result in a nearly 100% success rate. Originally, these experiments were introduced as classroom exercises by Charles Drewes in 1978 using awake, moving earthworms. In 1990, Hans-Georg Heinzel described further experiments using anesthetized earthworms. In this article, we focus on the application of these experiments as teaching tools for basic neurobiology courses. We describe and extend selected experiments, focusing on specific neurobiological principles with experimental protocols optimized for classroom application. Furthermore, we discuss our experience using these experiments in animal physiology and various neurobiology courses at the University of Bonn. PMID:23494516

  19. Vitrification of intact human articular cartilage.

    PubMed

    Jomha, Nadr M; Elliott, Janet A W; Law, Garson K; Maghdoori, Babak; Forbes, J Fraser; Abazari, Alireza; Adesida, Adetola B; Laouar, Leila; Zhou, Xianpei; McGann, Locksley E

    2012-09-01

    Articular cartilage injuries do not heal and large defects result in osteoarthritis with major personal and socioeconomic costs. Osteochondral transplantation is an effective treatment for large joint defects but its use is limited by the inability to store cartilage for long periods of time. Cryopreservation/vitrification is one method to enable banking of this tissue but decades of research have been unable to successfully preserve the tissue while maintaining cartilage on its bone base - a requirement for transplantation. To address this limitation, human knee articular cartilage from total knee arthroplasty patients and deceased donors was exposed to specified concentrations of 4 different cryoprotective agents for mathematically determined periods of time at lowering temperatures. After complete exposure, the cartilage was immersed in liquid nitrogen for up to 3 months. Cell viability was 75.4 ± 12.1% determined by membrane integrity stains and confirmed with a mitochondrial assay and pellet culture documented production of sulfated glycosaminoglycans and collagen II similar to controls. This report documents successful vitrification of intact human articular cartilage on its bone base making it possible to bank this tissue indefinitely. PMID:22698720

  20. The Near Naked Hairless (HrN) Mutation Disrupts Hair Formation but is not Due to a Mutation in the Hairless Coding Region

    SciTech Connect

    Liu, Yutao; Das, Suchita; Olszewski, Robert Edward; Culiat, Cymbeline T; Carpenter, D A; Sundberg, John P; Soteropoulos, Patricia; Liu, Xiaochen; Doktycz, Mitchel John; Michaud III, Edward J; Voy, Brynn H

    2007-01-01

    Near naked hairless (HrN) is a semi-dominant mutation that arose spontaneously and was suggested by allelism testing to be an allele of mouse Hairless (Hr). HrN mice differ from other Hr mutants in that hair loss appears as the postnatal coat begins to emerge, as opposed to failure to initiate the first postnatal hair cycle, and that the mutation displays semi-dominant inheritance. We sequenced the Hr cDNA in HrN/HrN mice and characterized the pathological and molecular phenotypes to identify the basis for hair loss in this model. HrN/HrN mice exhibit dystrophic hairs that are unable to consistently emerge from the hair follicle, while HrN/+ mice display a sparse coat of hair and a milder degree of follicular dystrophy than their homozygous littermates. DNA microarray analysis of cutaneous gene expression demonstrates that numerous genes are downregulated in HrN/HrN mice, primarily genes important for hair structure. By contrast, Hr expression is significantly increased. Sequencing the Hr coding region, intron-exon boundaries, 5'- and 3'- UTR and immediate upstream region did not reveal the underlying mutation. Therefore HrN does not appear to be an allele of Hr but may result from a mutation in a closely linked gene or from a regulatory mutation in Hr.

  1. SHAPE Analysis of the RNA Secondary Structure of the Mouse Hepatitis Virus 5′ Untranslated Region and N-Terminal Nsp1 Coding Sequences

    PubMed Central

    Yang, Dong; Liu, Pinghua; Wudeck, Elyse V.; Giedroc, David P.; Leibowitz, Julian L.

    2014-01-01

    SHAPE technology was used to analyze RNA secondary structure of the 5′ most 474 nts of the MHV-A59 genome encompassing the minimal 5′ cis-acting region required for defective interfering RNA replication. The structures generated were in agreement with previous characterizations of SL1 through SL4 and two recently predicted secondary structure elements, S5 and SL5A. SHAPE provided biochemical support for four additional stem-loops not previously functionally investigated in MHV. Secondary structure predictions for 5′ regions of MHV-A59, BCoV and SARS-CoV were similar despite high sequence divergence. The pattern of SHAPE reactivity of in virio genomic RNA, ex virio genomic RNA, and in vitro synthesized RNA were similar, suggesting that binding of N protein or other proteins to virion RNA fails to protect the RNA from reaction with lipid permeable SHAPE reagent. Reverse genetic experiments suggested that SL5C and SL6 within the nsp1 coding sequence are not required for viral replication. PMID:25462342

  2. Detection of genetic diversity and selection at the coding region of the melanocortin receptor 1 (MC1R) gene in Tibetan pigs and Landrace pigs.

    PubMed

    Liu, Rui; Jin, Long; Long, Keren; Chai, Jie; Ma, Jideng; Tang, Qianzi; Tian, Shilin; Hu, Yaodong; Lin, Ling; Wang, Xun; Jiang, Anan; Li, Xuewei; Li, Mingzhou

    2016-01-10

    Domestication and subsequent selective pressures have produced a large variety of pig coat colors in different regions and breeds. The melanocortin 1 receptor (MC1R) gene plays a crucial role in determining coat color of mammals. Here, we investigated genetic diversity and selection at the coding region of the porcine melanocortin receptor 1 (MC1R) in Tibetan pigs and Landrace pigs. By contrast, genetic variability was much lower in Landrace pigs than in Tibetan pigs. Meanwhile, haplotype analysis showed that Tibetan pigs possessed shared haplotypes, suggesting a possibility of recent introgression event by way of crossbreeding with neighboring domestic pigs or shared ancestral polymorphism. Additionally, we detected positive selection at the MC1R in both Tibetan pigs and Landrace pigs through the dN/dS analysis. These findings suggested that novel phenotypic change (dark coat color) caused by novel mutations may help Tibetan pigs against intensive solar ultraviolet (UV) radiation and camouflage in wild environment, whereas white coat color in Landrace were intentionally selected by human after domestication. Furthermore, both the phylogenetic analysis and the network analysis provided clues that MC1R in Asian and European wild boars may have initially experienced different selective pressures, and MC1R alleles diversified in modern domesticated pigs. PMID:26431999

  3. The non-coding B2 RNA binds to the DNA cleft and active-site region of RNA polymerase II.

    PubMed

    Ponicsan, Steven L; Houel, Stephane; Old, William M; Ahn, Natalie G; Goodrich, James A; Kugel, Jennifer F

    2013-10-01

    The B2 family of short interspersed elements is transcribed into non-coding RNA by RNA polymerase III. The ~180-nt B2 RNA has been shown to potently repress mRNA transcription by binding tightly to RNA polymerase II (Pol II) and assembling with it into complexes on promoter DNA, where it keeps the polymerase from properly engaging the promoter DNA. Mammalian Pol II is an ~500-kDa complex that contains 12 different protein subunits, providing many possible surfaces for interaction with B2 RNA. We found that the carboxy-terminal domain of the largest Pol II subunit was not required for B2 RNA to bind Pol II and repress transcription in vitro. To identify the surface on Pol II to which the minimal functional region of B2 RNA binds, we coupled multi-step affinity purification, reversible formaldehyde cross-linking, peptide sequencing by mass spectrometry, and analysis of peptide enrichment. The Pol II peptides most highly recovered after cross-linking to B2 RNA mapped to the DNA binding cleft and active-site region of Pol II. These studies determine the location of a defined nucleic acid binding site on a large, native, multi-subunit complex and provide insight into the mechanism of transcriptional repression by B2 RNA. PMID:23416138

  4. Mutation spectra of the surface-protein-coding region of the HBV genome in HBV-vaccinated and non-vaccinated individuals in Hungary.

    PubMed

    Szomor, Katalin N; Dencs, Agnes; Garai, Eszter; Rusvai, Erzsébet; Berencsi, György; Takács, Mária

    2008-01-01

    Hepatitis B virus (HBV) infection has a major effect on health care systems, with about one-third of the world's population currently infected with the virus. There is an effective vaccine against HBV, which contains a recombinant "surface antigen" produced in an expression vector. Vaccination has proved to be successful in Hungary: the number of acute HBV cases has decreased in the past 10 years. Although an increasing number of publications report on "vaccine-escape" HBV variants which can infect HBV-vaccinated individuals, such mutant HBV strains have not yet been detected in Hungary. We therefore surveyed two risk groups for vaccine-escape or immunoglobulin-escape HBV mutations in Hungary: 28 actively and/or passively HBV-immunized children of HBV carrier mothers who proved to be HBsAg and/or anti-HBc positive and 40 symptomless HBV carrier pregnant women (presumably carrying genotype B or C). We focused on the coding sequences of the "a" immundominant region of the surface protein. We could not detect the G145R amino acid substitution associated with vaccine escape mutant virus. However, we could map other mutations potentially affecting the immunodominant "a" region of the HBV surface protein. PMID:18813870

  5. H3.3 demarcates GC-rich coding and subtelomeric regions and serves as potential memory mark for virulence gene expression in Plasmodium falciparum.

    PubMed

    Fraschka, Sabine Anne-Kristin; Henderson, Rob Wilhelmus Maria; Bártfai, Richárd

    2016-01-01

    Histones, by packaging and organizing the DNA into chromatin, serve as essential building blocks for eukaryotic life. The basic structure of the chromatin is established by four canonical histones (H2A, H2B, H3 and H4), while histone variants are more commonly utilized to alter the properties of specific chromatin domains. H3.3, a variant of histone H3, was found to have diverse localization patterns and functions across species but has been rather poorly studied in protists. Here we present the first genome-wide analysis of H3.3 in the malaria-causing, apicomplexan parasite, P. falciparum, which revealed a complex occupancy profile consisting of conserved and parasite-specific features. In contrast to other histone variants, PfH3.3 primarily demarcates euchromatic coding and subtelomeric repetitive sequences. Stable occupancy of PfH3.3 in these regions is largely uncoupled from the transcriptional activity and appears to be primarily dependent on the GC-content of the underlying DNA. Importantly, PfH3.3 specifically marks the promoter region of an active and poised, but not inactive antigenic variation (var) gene, thereby potentially contributing to immune evasion. Collectively, our data suggest that PfH3.3, together with other histone variants, indexes the P. falciparum genome to functionally distinct domains and contribute to a key survival strategy of this deadly pathogen. PMID:27555062

  6. H3.3 demarcates GC-rich coding and subtelomeric regions and serves as potential memory mark for virulence gene expression in Plasmodium falciparum

    PubMed Central

    Fraschka, Sabine Anne-Kristin; Henderson, Rob Wilhelmus Maria; Bártfai, Richárd

    2016-01-01

    Histones, by packaging and organizing the DNA into chromatin, serve as essential building blocks for eukaryotic life. The basic structure of the chromatin is established by four canonical histones (H2A, H2B, H3 and H4), while histone variants are more commonly utilized to alter the properties of specific chromatin domains. H3.3, a variant of histone H3, was found to have diverse localization patterns and functions across species but has been rather poorly studied in protists. Here we present the first genome-wide analysis of H3.3 in the malaria-causing, apicomplexan parasite, P. falciparum, which revealed a complex occupancy profile consisting of conserved and parasite-specific features. In contrast to other histone variants, PfH3.3 primarily demarcates euchromatic coding and subtelomeric repetitive sequences. Stable occupancy of PfH3.3 in these regions is largely uncoupled from the transcriptional activity and appears to be primarily dependent on the GC-content of the underlying DNA. Importantly, PfH3.3 specifically marks the promoter region of an active and poised, but not inactive antigenic variation (var) gene, thereby potentially contributing to immune evasion. Collectively, our data suggest that PfH3.3, together with other histone variants, indexes the P. falciparum genome to functionally distinct domains and contribute to a key survival strategy of this deadly pathogen. PMID:27555062

  7. Reverse genetic manipulation of the overlapping coding regions for structural proteins of the type II porcine reproductive and respiratory syndrome virus.

    PubMed

    Yu, Dandan; Lv, Jian; Sun, Zhi; Zheng, Haihong; Lu, Jiaqi; Yuan, Shishan

    2009-01-01

    The overlapping genomic regions coding for structural proteins of porcine reproductive and respiratory syndrome virus (PRRSV) poses problems for molecular dissection of the virus replication process. We constructed five mutant full-length cDNA clones with the overlapping regions unwound and 1 to 3 restriction sites inserted between two adjacent ORFs (ORF1/2, ORF4/5, ORF5/6, ORF 6/7 and ORF7/3' UTR), which generated the recombinant viruses. Our findings demonstrated that 1) the overlapping structural protein ORFs can be physically separated, and is dispensable for virus viability; 2) such ORF separations did not interrupt the subgenomic RNA synthesis; 3) the plaque morphology, growth kinetics, and antigenicity of these mutant viruses were virtually indistinguishable from those of the parental virus in cultured cells; and 4) these mutant viruses remained genetic stable in vitro. This study lays a foundation for further molecular dissection of PRRSV replication process, and development of genetically tagged vaccines against PRRS. PMID:18977502

  8. Molecular characterization of severe hemophilia A suggests that about half the mutations are not within the coding regions and splice junctions of the factor VIII gene

    SciTech Connect

    Higuchi, Miyoko; Kazazian, H.H. Jr.; Kasch, L.; Warren, T.C.; McGinniss, M.J.; Antonarakis, S.E. ); Phillips, J.A. III; Janco, R. ); Kasper, C. )

    1991-08-15

    Hemophilia A is an X chromosome-linked disorder resulting from deficiency of factor VIII, an important protein in blood coagulation. A large number of disease-producing mutations have been reported in the factor VIII gene. However, a comprehensive analysis of the mutations has been difficult because of the larger gene size, its many scattered exons, and the high frequency of de novo mutations. Recently, the authors have shown that nearly all mutations resulting in mild-to-moderate hemophilia A can be detected by PCR and denaturing gradient gel electrophoresis (DGGE). In this study, they attempted to discover the mutations causing severe hemophilia A by analyzing 47 unselected patients, 30 of whom had severe hemophilia and 17 of whom had mild-to-moderate disease. Using DGGE as a screening method, they analyzed 99% of the coding region, 94% of the splice junctions, the promoter region, and the polyadenylylation site of the gene. They found the mutation in 16 of 17 (94%) patients with mild-to-moderate disease but in only 16 of 30 (53%) patients with severe hemophilia A.

  9. Positive Youth Development, Life Satisfaction, and Problem Behaviors of Adolescents in Intact and Non-Intact Families in Hong Kong

    PubMed Central

    Shek, Daniel T. L.; Leung, Hildie

    2013-01-01

    This study investigated whether Chinese adolescents living in intact and non-intact families differed in their positive development, life satisfaction, and risk behavior. A total of 3,328 Secondary 1 students responded to measures of positive youth development (such as resilience and psychosocial competencies), life satisfaction, and risk behavior (substance abuse, delinquency, Internet addiction, consumption of pornographic materials, self-harm, and behavioral intention to engage in problem behavior). Findings revealed that adolescents growing up in intact families reported higher levels of positive developmental outcomes and life satisfaction as compared with adolescents from non-intact families. Adolescents in non-intact families also reported higher levels of risk behaviors than those growing up in intact families. PMID:24400264

  10. Characterization of Multiple Regions Involved in Replication and Mobilization of Plasmid pNZ4000 Coding for Exopolysaccharide Production in Lactococcus lactis

    PubMed Central

    van Kranenburg, Richard; de Vos, Willem M.

    1998-01-01

    We characterized the regions involved in replication and mobilization of the 40-kb plasmid pNZ4000, encoding exopolysaccharide (EPS) production in Lactococcus lactis NIZO B40. The plasmid contains four highly conserved replication regions with homologous rep genes (repB1, repB2, repB3, and repB4) that belong to the lactococcal theta replicon family. Subcloning of each replicon individually showed that all are functional and compatible in L. lactis. Plasmid pNZ4000 and genetically labeled derivatives could be transferred to different L. lactis strains by conjugation, and pNZ4000 was shown to be a mobilization plasmid. Two regions involved in mobilization were identified near two of the replicons; both included an oriT sequence rich in inverted repeats. Conjugative mobilization of the nonmobilizable plasmid pNZ124 was promoted by either one of these oriT sequences, demonstrating their functionality. One oriT sequence was followed by a mobA gene, coding for a trans-acting protein, which increased the frequency of conjugative transfer 100-fold. The predicted MobA protein and the oriT sequences show protein and nucleotide similarity, respectively, with the relaxase and with the inverted repeat and nic site of the oriT from the Escherichia coli plasmid R64. The presence on pNZ4000 of four functional replicons, two oriT sequences, and several insertion sequence-like elements strongly suggests that this EPS plasmid is a naturally occurring cointegrate. PMID:9765557