Sample records for assemble spliced alignments

  1. Faster exon assembly by sparse spliced alignment

    CERN Document Server

    Tiskin, Alexander


    Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \\emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon chains within a DNA sequence of length $m$ by comparing them to a known related gene sequence of length n, $m = \\Theta(n)$. Gelfand et al.\\ gave an algorithm for spliced alignment running in time O(n^3). Kent et al.\\ considered sparse spliced alignment, where the number of candidate exons is O(n), and proposed an algorithm for this problem running in time O(n^{2.5}). We improve on this result, by proposing an algorithm for sparse spliced alignment running in time O(n^{2.25}). Our approach is based on a new framework of \\emph{quasi-local string comparison}.

  2. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    Energy Technology Data Exchange (ETDEWEB)

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R


    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  3. BBMap: A Fast, Accurate, Splice-Aware Aligner

    Energy Technology Data Exchange (ETDEWEB)

    Bushnell, Brian


    Alignment of reads is one of the primary computational tasks in bioinformatics. Of paramount importance to resequencing, alignment is also crucial to other areas - quality control, scaffolding, string-graph assembly, homology detection, assembly evaluation, error-correction, expression quantification, and even as a tool to evaluate other tools. An optimal aligner would greatly improve virtually any sequencing process, but optimal alignment is prohibitively expensive for gigabases of data. Here, we will present BBMap [1], a fast splice-aware aligner for short and long reads. We will demonstrate that BBMap has superior speed, sensitivity, and specificity to alternative high-throughput aligners bowtie2 [2], bwa [3], smalt, [4] GSNAP [5], and BLASR [6].

  4. SPA: a probabilistic algorithm for spliced alignment.

    Directory of Open Access Journals (Sweden)

    Erik van Nimwegen


    Full Text Available Recent large-scale cDNA sequencing efforts show that elaborate patterns of splice variation are responsible for much of the proteome diversity in higher eukaryotes. To obtain an accurate account of the repertoire of splice variants, and to gain insight into the mechanisms of alternative splicing, it is essential that cDNAs are very accurately mapped to their respective genomes. Currently available algorithms for cDNA-to-genome alignment do not reach the necessary level of accuracy because they use ad hoc scoring models that cannot correctly trade off the likelihoods of various sequencing errors against the probabilities of different gene structures. Here we develop a Bayesian probabilistic approach to cDNA-to-genome alignment. Gene structures are assigned prior probabilities based on the lengths of their introns and exons, and based on the sequences at their splice boundaries. A likelihood model for sequencing errors takes into account the rates at which misincorporation, as well as insertions and deletions of different lengths, occurs during sequencing. The parameters of both the prior and likelihood model can be automatically estimated from a set of cDNAs, thus enabling our method to adapt itself to different organisms and experimental procedures. We implemented our method in a fast cDNA-to-genome alignment program, SPA, and applied it to the FANTOM3 dataset of over 100,000 full-length mouse cDNAs and a dataset of over 20,000 full-length human cDNAs. Comparison with the results of four other mapping programs shows that SPA produces alignments of significantly higher quality. In particular, the quality of the SPA alignments near splice boundaries and SPA's mapping of the 5' and 3' ends of the cDNAs are highly improved, allowing for more accurate identification of transcript starts and ends, and accurate identification of subtle splice variations. Finally, our splice boundary analysis on the human dataset suggests the existence of a novel non

  5. Splign: algorithms for computing spliced alignments with identification of paralogs

    Directory of Open Access Journals (Sweden)

    Tatusova Tatiana


    Full Text Available Abstract Background The computation of accurate alignments of cDNA sequences against a genome is at the foundation of modern genome annotation pipelines. Several factors such as presence of paralogs, small exons, non-consensus splice signals, sequencing errors and polymorphic sites pose recognized difficulties to existing spliced alignment algorithms. Results We describe a set of algorithms behind a tool called Splign for computing cDNA-to-Genome alignments. The algorithms include a high-performance preliminary alignment, a compartment identification based on a formally defined model of adjacent duplicated regions, and a refined sequence alignment. In a series of tests, Splign has produced more accurate results than other tools commonly used to compute spliced alignments, in a reasonable amount of time. Conclusion Splign's ability to deal with various issues complicating the spliced alignment problem makes it a helpful tool in eukaryotic genome annotation processes and alternative splicing studies. Its performance is enough to align the largest currently available pools of cDNA data such as the human EST set on a moderate-sized computing cluster in a matter of hours. The duplications identification (compartmentization algorithm can be used independently in other areas such as the study of pseudogenes. Reviewers This article was reviewed by: Steven Salzberg, Arcady Mushegian and Andrey Mironov (nominated by Mikhail Gelfand.

  6. AGORA: Assembly Guided by Optical Restriction Alignment

    Directory of Open Access Journals (Sweden)

    Lin Henry C


    Full Text Available Abstract Background Genome assembly is difficult due to repeated sequences within the genome, which create ambiguities and cause the final assembly to be broken up into many separate sequences (contigs. Long range linking information, such as mate-pairs or mapping data, is necessary to help assembly software resolve repeats, thereby leading to a more complete reconstruction of genomes. Prior work has used optical maps for validating assemblies and scaffolding contigs, after an initial assembly has been produced. However, optical maps have not previously been used within the genome assembly process. Here, we use optical map information within the popular de Bruijn graph assembly paradigm to eliminate paths in the de Bruijn graph which are not consistent with the optical map and help determine the correct reconstruction of the genome. Results We developed a new algorithm called AGORA: Assembly Guided by Optical Restriction Alignment. AGORA is the first algorithm to use optical map information directly within the de Bruijn graph framework to help produce an accurate assembly of a genome that is consistent with the optical map information provided. Our simulations on bacterial genomes show that AGORA is effective at producing assemblies closely matching the reference sequences. Additionally, we show that noise in the optical map can have a strong impact on the final assembly quality for some complex genomes, and we also measure how various characteristics of the starting de Bruijn graph may impact the quality of the final assembly. Lastly, we show that a proper choice of restriction enzyme for the optical map may substantially improve the quality of the final assembly. Conclusions Our work shows that optical maps can be used effectively to assemble genomes within the de Bruijn graph assembly framework. Our experiments also provide insights into the characteristics of the mapping data that most affect the performance of our algorithm, indicating the

  7. Assembly and alignment of infrared refractive system (United States)

    Yang, Lin; Lin, Jian-chun; Wang, Ya-jing; Chen, Fan-sheng


    Optical systems for scientific instrumentation frequently include lens or mirrors with critical mechanical requirements. Position issues of those components are inextricably bound to the efficiency of the instrument. The position referring to the lens system mainly means spacer and rotation of all elements concerned. Instrument could not be completed without the accuracy assembly even the previous design was top one. The alignment of infrared optical system always is a tough thing due to the IR material being opaque to visible light which hardly effect on the imaging ability of the system. In this paper a large-aperture IR refractive system was described in details and the alignment of this system was presented. The brief work describes the assembly and integration of the camera barrel in lab. First of all, all the mechanical elements must be manufactured with high accuracy requirements to meet alignment tolerances and minimum errors mostly could be ignored. The rotations relative to the optical axis were hardy restricted by the space between barrel and cells. The lens vertex displacements were determined through high accuracy titanium alloy spacer. So the actual shape data of the optical lenses were obtained by coordinate measuring machining (CMM) to calculate the real space between lenses after alignment1 done. All the measured results were critical for instruction of the practical assemble. Based on the properties and tolerances of the system, the camera barrel includes sets of six lenses with their respective supports and cells which are composed of two parts: the flied lens group and the relay lenses group. The first one was aligned by the geometry centering used CMM. And the relay lenses were integrated one by one after centered individually with a classical centering instrument. Then the two separate components were assembled under the monitor of the CMM with micron precision. Three parameters on the opti-mechanical elements which include decenter, tilt and

  8. Alignment Pins for Assembling and Disassembling Structures (United States)

    Campbell, Oliver C.


    Simple, easy-to-use, highly effective tooling has been devised for maintaining alignment of bolt holes in mating structures during assembly and disassembly of the structures. The tooling was originally used during removal of a body flap from the space shuttle Atlantis, in which misalignments during removal of the last few bolts could cause the bolts to bind in their holes. By suitably modifying the dimensions of the tooling components, the basic design of the tooling can readily be adapted to other structures that must be maintained in alignment. The tooling includes tapered, internally threaded alignment pins designed to fit in the bolt holes in one of the mating structures, plus a draw bolt and a cup that are used to install or remove each alignment pin. In preparation for disassembly of two mating structures, external supports are provided to prevent unintended movement of the structures. During disassembly of the structures, as each bolt that joins the structures is removed, an alignment pin is installed in its place. Once all the bolts have been removed and replaced with pins, the pins maintain alignment as the structures are gently pushed or pulled apart on the supports. In assembling the two structures, one reverses the procedure described above: pins are installed in the bolt holes, the structures are pulled or pushed together on the supports, then the pins are removed and replaced with bolts. The figure depicts the tooling and its use. To install an alignment pin in a bolt hole in a structural panel, the tapered end of the pin is inserted from one side of the panel, the cup is placed over the pin on the opposite side of the panel, the draw bolt is inserted through the cup and threaded into the pin, the draw bolt is tightened to pull the pin until the pin is seated firmly in the hole, then the draw bolt and cup are removed, leaving the pin in place. To remove an alignment pin, the cup is placed over the pin on the first-mentioned side of the panel, the draw

  9. Fusion splicing of double-clad specialty fiber using active alignment technology

    Institute of Scientific and Technical Information of China (English)

    Shupeng Yin; Ping Yan; Mali Gong; Jianwei He; Chen Fu


    @@ The fusion splicing of double-clad (DC) specialty fibers based on active alignment is crucial to the investigation of high-power monolithic fiber lasers. Given the wave-guiding characteristic of DC fiber, a light stripper is introduced in an active alignment experiment. We propose a novel method for stripping light that is convenient, highly efficient, and low cost. This method is also effective for low-numerical-aperture beams that escape from the fiber core. A splice loss as low as 0.05 dB is achieved.%The fusion splicing of double-clad (DC) specialty fibers based on active alignment is crucial to the investigation of high-power monolithic fiber lasers. Given the wave-guiding characteristic of DC fiber, a light stripper is introduced in an active alignment experiment. We propose a novel method for stripping light that is convenient, highly efficient, and low cost. This method is also effective for low-numerical-aperture beams that escape from the fiber core. A splice loss as low as 0.05 dB is achieved.

  10. Systematic evaluation of spliced alignment programs for RNA-seq data. (United States)

    Engström, Pär G; Steijger, Tamara; Sipos, Botond; Grant, Gregory R; Kahles, André; Rätsch, Gunnar; Goldman, Nick; Hubbard, Tim J; Harrow, Jennifer; Guigó, Roderic; Bertone, Paul


    High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found major performance differences between methods on numerous benchmarks, including alignment yield, basewise accuracy, mismatch and gap placement, exon junction discovery and suitability of alignments for transcript reconstruction. We observed concordant results on real and simulated RNA-seq data, confirming the relevance of the metrics employed. Future developments in RNA-seq alignment methods would benefit from improved placement of multimapped reads, balanced utilization of existing gene annotation and a reduced false discovery rate for splice junctions.

  11. Nanoplasmonic probes of RNA folding and assembly during pre-mRNA splicing (United States)

    Nguyen, Anh H.; Lee, Jong Uk; Sim, Sang Jun


    RNA splicing plays important roles in transcriptome and proteome diversity. Herein, we describe the use of a nanoplasmonic system that unveils RNA folding and assembly during pre-mRNA splicing wherein the quantification of mRNA splice variants is not taken into account. With a couple of SERS-probes and plasmonic probes binding at the boundary sites of exon-2/intron-2 and intron-2/exon-3 of the pre-mature RNA of the β-globin gene, the splicing process brings the probes into the plasmonic bands. For plasmonic probes, a plasmon shift increase of ~29 nm, corresponding to intron removal and exon-2 and exon-3 connection to form the mRNA molecule, is measured by plasmonic coupling. The increased scattering intensity and surface-enhanced Raman scattering (SERS) fingerprinting reveal the clear dynamics of pre-mRNA splicing. Moreover, a time-resolved experiment of individual RNA molecules exhibited a successful splicing and an inhibited splicing event by 33 μM biflavonoid isoginkgetin, a general inhibitor of RNA splicing. The results suggest that the RNA splicing is successfully monitored with the nanoplasmonic system. Thus, this platform can be useful for studying RNA nanotechnology, biomolecular folding, alternative splicing, and maturation of microRNA.

  12. Assembly of splicing complexes on exon 11 of the human insulin receptor gene does not correlate with splicing efficiency in-vitro

    Directory of Open Access Journals (Sweden)

    Caples Matt


    Full Text Available Abstract Background Incorporation of exon 11 of the insulin receptor gene is both developmentally and hormonally-regulated. Previously, we have shown the presence of enhancer and silencer elements that modulate the incorporation of the small 36-nucleotide exon. In this study, we investigated the role of inherent splice site strength in the alternative splicing decision and whether recognition of the splice sites is the major determinant of exon incorporation. Results We found that mutation of the flanking sub-optimal splice sites to consensus sequences caused the exon to be constitutively spliced in-vivo. These findings are consistent with the exon-definition model for splicing. In-vitro splicing of RNA templates containing exon 11 and portions of the upstream intron recapitulated the regulation seen in-vivo. Unexpectedly, we found that the splice sites are occupied and spliceosomal complex A was assembled on all templates in-vitro irrespective of splicing efficiency. Conclusion These findings demonstrate that the exon-definition model explains alternative splicing of exon 11 in the IR gene in-vivo but not in-vitro. The in-vitro results suggest that the regulation occurs at a later step in spliceosome assembly on this exon.

  13. Alternative pre-mRNA splicing in Drosophila spliceosomal assembly factor RNP-4F during development. (United States)

    Fetherson, Rebecca A; Strock, Stephen B; White, Kristen N; Vaughn, Jack C


    The 5'- and 3'-UTR regions in pre-mRNAs play a variety of roles in controlling eukaryotic gene expression, including translational modulation. Here we report the results of a systematic study of alternative splicing in rnp-4f, which encodes a Drosophila spliceosomal assembly factor. We show that most of the nine introns are constitutively spliced, but several patterns of alternative splicing are observed in two pre-mRNA regions including the 5'-UTR. Intron V is shown to be of recent evolutionary origin and is infrequently spliced, resulting in generation of an in-frame stop codon and a predicted truncated protein lacking a nuclear localization signal, so that alternative splicing regulates its subcellular localization. Intron 0, located in the 5'-UTR, is subject to three different splicing decisions in D. melanogaster. Northern analysis of poly(A+) mRNAs reveals two differently sized rnp-4f mRNA isoforms in this species. A switch in relative isoform abundance occurs during mid-embryo stages, when the larger isoform becomes more abundant. This isoform is shown to represent intron 0 unspliced mRNA, whereas the smaller transcript represents the product of alternative splicing. Comparative genomic analysis predicts that intron 0 is present in diverse Drosophila species. Intron 0 splicing results in loss of an evolutionarily conserved stem-loop constituting a potential cis-regulatory element at the 3'-splice site. A model is proposed for the role of this element both in 5'-UTR alternative splicing decisions and in RNP-4F translational modulation. Preliminary evidences in support of our model are discussed.

  14. Research on uncertainty in measurement assisted alignment in aircraft assembly

    Institute of Scientific and Technical Information of China (English)

    Chen Zhehan; Du Fuzhou; Tang Xiaoqing


    Operations in assembling and joining large size aircraft components are changed to novel digital and flexible ways by digital measurement assisted alignment. Positions and orientations (P&O) of aligned components are critical characters which assure geometrical positions and rela-tionships of those components. Therefore, evaluating the P&O of a component is considered nec-essary and critical for ensuring accuracy in aircraft assembly. Uncertainty of position and orientation (U-P&O), as a part of the evaluating result of P&O, needs to be given for ensuring the integrity and credibility of the result; furthermore, U-P&O is necessary for error tracing and quality evaluating of measurement assisted aircraft assembly. However, current research mainly focuses on the process integration of measurement with assembly, and usually ignores the uncer-tainty of measured result and its influence on quality evaluation. This paper focuses on the expres-sion, analysis, and application of U-P&O in measurement assisted alignment. The geometrical and algebraical connotations of U-P&O are presented. Then, an analytical algorithm for evaluating the multi-dimensional U-P&O is given, and the effect factors and characteristics of U-P&O are dis-cussed. Finally, U-P&O is used to evaluate alignment in aircraft assembly for quality evaluating and improving. Cases are introduced with the methodology.

  15. Aligned and Electrospun Piezoelectric Polymer Fiber Assembly and Scaffold (United States)

    Scott-Carnell, Lisa A. (Inventor); Siochi, Emilie J. (Inventor); Holloway, Nancy M. (Inventor); Leong, Kam W. (Inventor); Kulangara, Karina (Inventor)


    A scaffold assembly and related methods of manufacturing and/or using the scaffold for stem cell culture and tissue engineering applications are disclosed which at least partially mimic a native biological environment by providing biochemical, topographical, mechanical and electrical cues by using an electroactive material. The assembly includes at least one layer of substantially aligned, electrospun polymer fiber having an operative connection for individual voltage application. A method of cell tissue engineering and/or stem cell differentiation uses the assembly seeded with a sample of cells suspended in cell culture media, incubates and applies voltage to one or more layers, and thus produces cells and/or a tissue construct. In another aspect, the invention provides a method of manufacturing the assembly including the steps of providing a first pre-electroded substrate surface; electrospinning a first substantially aligned polymer fiber layer onto the first surface; providing a second pre-electroded substrate surface; electrospinning a second substantially aligned polymer fiber layer onto the second surface; and, retaining together the layered surfaces with a clamp and/or an adhesive compound.

  16. Waferscale assembly of Field-Aligned nanotube Networks (FANs)

    DEFF Research Database (Denmark)

    Dimaki, Maria; Bøggild, Peter


    We demonstrate the integration of nanotube networks on 512 individual devices on a full 4-inch wafer in less than 60 seconds with a roughly 80% yield using dielectrophoresis. We present here investigations of the morphology and electrical resistance of such field aligned networks for different...... frequencies of the electrical field used to attract the nanotubes to the electrodes. Preliminary data of response to visible light irradiation as well as changes in the humidity indicate that the field aligned networks could be used as sensor components that may well integrate with CMOS due to mild assembly...

  17. The Alignment and Assembly for EAST Tokamak Device

    Institute of Scientific and Technical Information of China (English)


    EAST (HT-7U) is a large fusion experimental device. It is a full superconducting tokamak with 1 MA of plasma current, 1000 s of plasma duration, high elongation and triangularity. It mainly consists of superconducting magnets of poloidal and toroidal field (PF& TF),vacuum vessel (VV), thermal radiation shield (TRS) and cryostat vessel (CV). The significant difficulty for assembly of EAST is tight installation tolerances, which are in the order of several tenth of a millimeter. In particular, the alignment of plasma facing components to the magnetic axis of the device is less than ± 0.5 mm.At present, a reasonable assembly process of EAST has been defined, and based on it, the alignment method for EAST, including the survey control network, the location of the main components in different directions, the magnetic axis determination and the accurate positioning of the plasma facing components inside of the vacuum vessel and so on, has been defined by using the sophisticated optical metrology system (SOMS).This paper describes the assembly procedure of EAST and the installation tolerances associated with the main components. Meanwhile, how to establish the assembly survey control network,magnetic axis determination methods, are introduced in detail.

  18. A novel posture alignment system for aircraft wing assembly

    Institute of Scientific and Technical Information of China (English)

    Bin ZHANG; Bao-guo YAO; Ying-lin KE


    A novel 6-degree of freedom (DOF) posture alignment system, based on 3-DOF positioners, is presented for the assembly of aircraft wings. Each positioner is connected with the wing through a rotational and adsorptive half-ball shaped end-effector, and the positioners together with the wing are considered as a 3-PPPS (P denotes a prismatic joint and S denotes a spherical joint) redundantly actuated parallel mechanism. The kinematic model of this system is established and a trajectory planning method is introduced. A complete analysis of inverse dynamics is carried out with the Newton-Euler algorithm, which is used to find the desired actuating torque in the design and path planning phase. Simulation analysis of the displacement and actuating torque of each joint of the positioners based on inverse kinematics and dynamics is conducted, and the results show that the system is feasible for the posture alignment of aircraft wings.

  19. Assembly Test of Elastic Averaging Technique to Improve Mechanical Alignment for Accelerating Structure Assemblies in CLIC

    CERN Document Server

    Huopana, J


    The CLIC (Compact LInear Collider) is being studied at CERN as a potential multi-TeV e+e- collider [1]. The manufacturing and assembly tolerances for the required RF-components are important for the final efficiency and for the operation of CLIC. The proper function of an accelerating structure is very sensitive to errors in shape and location of the accelerating cavity. This causes considerable issues in the field of mechanical design and manufacturing. Currently the design of the accelerating structures is a disk design. Alternatively it is possible to create the accelerating assembly from quadrants, which favour the mass manufacturing. The functional shape inside of the accelerating structure remains the same and a single assembly uses less parts. The alignment of these quadrants has been previously made kinematic by using steel pins or spheres to align the pieces together. This method proved to be a quite tedious and time consuming method of assembly. To limit the number of different error sources, a meth...

  20. Assembling a Correctly Folded and Functional Heptahelical Membrane Protein by Protein Trans-splicing. (United States)

    Mehler, Michaela; Eckert, Carl Elias; Busche, Alena; Kulhei, Jennifer; Michaelis, Jonas; Becker-Baldus, Johanna; Wachtveitl, Josef; Dötsch, Volker; Glaubitz, Clemens


    Protein trans-splicing using split inteins is well established as a useful tool for protein engineering. Here we show, for the first time, that this method can be applied to a membrane protein under native conditions. We provide compelling evidence that the heptahelical proteorhodopsin can be assembled from two separate fragments consisting of helical bundles A and B and C, D, E, F, and G via a splicing site located in the BC loop. The procedure presented here is on the basis of dual expression and ligation in vivo. Global fold, stability, and photodynamics were analyzed in detergent by CD, stationary, as well as time-resolved optical spectroscopy. The fold within lipid bilayers has been probed by high field and dynamic nuclear polarization-enhanced solid-state NMR utilizing a (13)C-labeled retinal cofactor and extensively (13)C-(15)N-labeled protein. Our data show unambiguously that the ligation product is identical to its non-ligated counterpart. Furthermore, our data highlight the effects of BC loop modifications onto the photocycle kinetics of proteorhodopsin. Our data demonstrate that a correctly folded and functionally intact protein can be produced in this artificial way. Our findings are of high relevance for a general understanding of the assembly of membrane proteins for elucidating intramolecular interactions, and they offer the possibility of developing novel labeling schemes for spectroscopic applications.

  1. The precise self-assembly of individual carbon nanotubes using magnetic capturing and fluidic alignment

    Energy Technology Data Exchange (ETDEWEB)

    Shim, Joon S; Rust, Michael J; Do, Jaephil; Ahn, Chong H [Department of Electrical and Computer Engineering, Microsystems and BioMEMS Laboratory, University of Cincinnati, Cincinnati, OH 45221 (United States); Yun, Yeo-Heung; Schulz, Mark J [Department of Mechanical Engineering, University of Cincinnati, 45221 (United States); Shanov, Vesselin, E-mail: chong.ahn@uc.ed [Department of Chemical and Materials Engineering, University of Cincinnati, 45221 (United States)


    A new method for the self-assembly of a carbon nanotube (CNT) using magnetic capturing and fluidic alignment has been developed and characterized in this work. In this new method, the residual iron (Fe) catalyst positioned at one end of the CNT was utilized as a self-assembly driver to attract and position the CNT, while the assembled CNT was aligned by the shear force induced from the fluid flow through the assembly channel. The self-assembly procedures were successfully developed and the electrical properties of the assembled multi-walled carbon nanotube (MWNT) and single-walled carbon nanotube (SWNT) were fully characterized. The new assembly method developed in this work shows its feasibility for the precise self-assembly of parallel CNTs for electronic devices and nanobiosensors.

  2. Systematic evaluation of spliced alignment programs for RNA-seq data


    Engström, Pär G; Steijger, Tamara; Sipos, Botond; Grant, Gregory R; Kahles, André; RGASP Consortium; Rätsch, Gunnar; Goldman, Nick; Hubbard, Tim J.; Harrow, Jennifer; Guigó Serra, Roderic; Bertone, Paul


    High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to a reference genome sequence. To assess the performance of current mapping software, we invited developers of RNA-seq aligners to process four large human and mouse RNA-seq data sets. In total, we compared 26 mapping protocols based on 11 programs and pipelines and found majo...

  3. Testing to evaluate synergistic effects from LOCA environments. Test IX. Simultaneous mode; cables, splice assemblies, and electrical insulation samples

    Energy Technology Data Exchange (ETDEWEB)

    Thome, F.V.


    This test was conducted to complement Test VIII which was a sequential test of cables, cable splices, and insulation samples. In this test, the generic LOCA environments (radiation, temperature, pressure, chemical spray) were simulated and simultaneously applied to the test items. There were no failures of any assemblies and all were able to function at rated current and voltage throughout the entire test. An additional parameter, dissipation factor, was monitored in this test and when used in conjunction with capacitance, provided a better indication of insulation degradation.

  4. Tolerancing, alignment and test of the Transiting Exoplanet Survey Satellite (TESS) optical assembly (United States)

    Primeau, Brian; Balonek, Gregory; MacDonald, Robert; Chrisp, Michael; Chesbrough, Christian; Andre, James; Clark, Kristin


    The Transiting Exoplanet Survey Satellite (TESS) will carry four visible waveband seven-element refractive f/1.4 lenses, each with a 34 degree diagonal field of view. This paper describes the tolerancing, assembly and alignment methods developed during the build of the TESS Risk Reduction Unit optical system. Lens assembly tolerances were derived from a sensitivity analysis using an image quality metric customized for mission performance. The optomechanical design consists of a two-stage lens housing that provides access for active alignment of each lens using a Trioptics OptiCentric measurement system. Thermal stresses and alignment shifts are mitigated by mounting the optics with cast RTV silicone spacers into individually aligned bezels, and custom fixtures were developed to aid in RTV bonding with reduced alignment error. The lens assembly was tested interferometrically over the field of view at room temperature and results were used to successfully predict lens performance and compensator adjustments and detector shim thickness for the -75C operational temperature and pressure.

  5. A Flux-Pinning Mechanism for Segment Assembly and Alignment (United States)

    Gersh-Range, Jessica A.; Arnold, William R.; Peck, Mason A.; Stahl, H. Philip


    Currently, the most compelling astrophysics questions include how planets and the first stars formed and whether there are protostellar disks that contain large organic molecules. Although answering these questions requires space telescopes with apertures of at least 10 meters, such large primaries are challenging to construct by scaling up previous designs; the limited capacity of a launch vehicle bounds the maximum diameter of a monolithic primary, and beyond a certain size, deployable telescopes cannot fit in current launch vehicle fairings. One potential solution is connecting the primary mirror segments edgewise using flux-pinning mechanisms, which are analogous to non-contacting damped springs. In the baseline design, a flux-pinning mechanism consists of a magnet and a superconductor separated by a predetermined gap, with the damping adjusted by placing aluminum near the interface. Since flux pinning is possible only when the superconductor is cooled below a critical temperature, flux-pinning mechanisms are uniquely suited for cryogenic space telescopes. By placing these mechanisms along the edges of the mirror segments, a primary can be built up over time. Since flux pinning requires no mechanical deployments, the assembly process could be robotic or use some other non-contacting scheme. Advantages of this approach include scalability and passive stability.

  6. Self-Assembly of Semiconducting Single-Walled Carbon Nanotubes into Dense, Aligned Rafts

    CERN Document Server

    Wu, Justin; Antaris, Alexander; Choi, Charina L; Xie, Liming; Wu, Yingpeng; Diao, Shuo; Chen, Changxin; Chen, Yongsheng; Dai, Hongjie


    Single-walled carbon nanotubes are promising nanoelectronic materials but face long-standing challenges including production of pure semiconducting SWNTs and integration into ordered structures. Here, highly pure semiconducting single-walled carbon nanotubes are separated from bulk materials and self-assembled into densely aligned rafts driven by depletion attraction forces. Microscopy and spectroscopy revealed a high degree of alignment and a high packing density of ~100 tubes/micron within SWNT rafts. Field-effect transistors made from aligned SWNT rafts afforded short channel (~150 nm long) devices comprised of tens of purely semiconducting SWNTs derived from chemical separation within a < 1 micron channel width, achieving unprecedented high on-currents (up to ~120 microamperes per device) with high on/off ratios. The average on-current was ~ 3-4 microamperes per tube. The results demonstrated densely aligned high quality semiconducting SWNTs for integration into high performance nanoelectronics.

  7. Fully automated hybrid diode laser assembly using high precision active alignment (United States)

    Böttger, Gunnar; Weber, Daniel; Scholz, Friedemann; Schröder, Henning; Schneider-Ramelow, Martin; Lang, Klaus-Dieter


    Fraunhofer IZM, Technische Universität Berlin and eagleyard Photonics present various implementations of current micro-optical assemblies for high quality free space laser beam forming and efficient fiber coupling. The laser modules shown are optimized for fast and automated assembly in small form factor packages via state-of-the-art active alignment machinery, using alignment and joining processes that have been developed and established in various industrial research projects. Operational wavelengths and optical powers ranging from 600 to 1600 nm and from 1 mW to several W respectively are addressed, for application in high-resolution laser spectroscopy, telecom and optical sensors, up to the optical powers needed in industrial and medical laser treatment.

  8. Micro-vision servo control of a multi-axis alignment system for optical fiber assembly (United States)

    Chen, Weihai; Yu, Fei; Qu, Jianliang; Chen, Wenjie; Zhang, Jianbin


    This paper describes a novel optical fiber assembly system featuring a multi-axis alignment function based on micro-vision feedback control. It consists of an active parallel alignment mechanism, a passive compensation mechanism, a micro-gripper and a micro-vision servo control system. The active parallel alignment part is a parallelogram-based design with remote-center-of-motion (RCM) function to achieve precise rotation without fatal lateral motion. The passive mechanism, with five degrees of freedom (5-DOF), is used to implement passive compensation for multi-axis errors. A specially designed 1-DOF micro-gripper mounted onto the active parallel alignment platform is adopted to grasp and rotate the optical fiber. A micro-vision system equipped with two charge-coupled device (CCD) cameras is introduced to observe the small field of view and obtain multi-axis errors for servo feedback control. The two CCD cameras are installed in an orthogonal arrangement—thus the errors can be easily measured via the captured images. Meanwhile, a series of tracking and measurement algorithms based on specific features of the target objects are developed. Details of the force and displacement sensor information acquisition in the assembly experiment are also provided. An experiment demonstrates the validity of the proposed visual algorithm by achieving the task of eliminating errors and inserting an optical fiber to the U-groove accurately.

  9. Thermally Switchable Aligned Nanopores by Magnetic-Field Directed Self-Assembly of Block Copolymers (United States)

    Osuji, Chinedum


    Magnetic fields provide a facile approach to direct the self-assembly of magnetically anisotropic block copolymer nanostructures in a scalable manner. Here we combine such field-based processing with materials design to enable the fabrication of polymer films with highly aligned stimuli-responsive nanopores. Etch removal of a poly(D,L-lactide) (PLA) brush that is the minority component of a liquid crystalline block copolymer is used to produce nanopores of ~ 8 nm diameter. The pores can be reversibly closed and opened while retaining their alignment by appropriate heating and cooling. We present TEM and temperture resolved scattering data during pore closure and re-opening to explore the mechanism and kinetics of pore collapse. NSF DMR-0847534; DMR-1119826.

  10. lncScore: alignment-free identification of long noncoding RNA from assembled novel transcripts (United States)

    Zhao, Jian; Song, Xiaofeng; Wang, Kai


    RNA-Seq based transcriptome assembly has been widely used to identify novel lncRNAs. However, the best-performing transcript reconstruction methods merely identified 21% of full-length protein-coding transcripts from H. sapiens. Those partial-length protein-coding transcripts are more likely to be classified as lncRNAs due to their incomplete CDS, leading to higher false positive rate for lncRNA identification. Furthermore, potential sequencing or assembly error that gain or abolish stop codons also complicates ORF-based prediction of lncRNAs. Therefore, it remains a challenge to identify lncRNAs from the assembled transcripts, particularly the partial-length ones. Here, we present a novel alignment-free tool, lncScore, which uses a logistic regression model with 11 carefully selected features. Compared to other state-of-the-art alignment-free tools (e.g. CPAT, CNCI, and PLEK), lncScore outperforms them on accurately distinguishing lncRNAs from mRNAs, especially partial-length mRNAs in the human and mouse datasets. In addition, lncScore also performed well on transcripts from five other species (Zebrafish, Fly, C. elegans, Rat, and Sheep). To speed up the prediction, multithreading is implemented within lncScore, and it only took 2 minute to classify 64,756 transcripts and 54 seconds to train a new model with 21,000 transcripts with 12 threads, which is much faster than other tools. lncScore is available at PMID:27708423

  11. Assembly of vorticity-aligned hard-sphere colloidal strings in a simple shear flow

    KAUST Repository

    Cheng, X.


    Colloidal suspensions self-assemble into equilibrium structures ranging from face- and body-centered cubic crystals to binary ionic crystals, and even kagome lattices. When driven out of equilibrium by hydrodynamic interactions, even more diverse structures can be accessed. However, mechanisms underlying out-of-equilibrium assembly are much less understood, though such processes are clearly relevant in many natural and industrial systems. Even in the simple case of hard-sphere colloidal particles under shear, there are conflicting predictions about whether particles link up into string-like structures along the shear flow direction. Here, using confocal microscopy, we measure the shear-induced suspension structure. Surprisingly, rather than flow-aligned strings, we observe log-rolling strings of particles normal to the plane of shear. By employing Stokesian dynamics simulations, we address the mechanism leading to this out-of-equilibrium structure and show that it emerges from a delicate balance between hydrodynamic and interparticle interactions. These results demonstrate a method for assembling large-scale particle structures using shear flows.

  12. Fabrication of a Mono-Domain Alignment Ferroelectric Liquid Crystal Device Using a Polar Self-Assembled Monolayer

    Institute of Scientific and Technical Information of China (English)

    ZOU Zhong-Fei; YAO Li-Shuang; TANG Xian-Zhu; JI Xin-Jian; XUAN Li


    A mono-domain ferroelectric liquid crystal device (FLCD) is fabricated using a novel method. The cell used in this method is an asymmetric cell, typically the combination of a polar self-assembled monolayer (SAM) for one substrate and a rubbed polyimide for the other substrate. A defect-free alignment of ferroelectric liquid crystal is fabricated without applying a dc voltage to remove degeneracy in the layer structure. The contact angles of self-assembled monolayer and PI-2942 are measured and the polarity of SAM is higher than the PI alignment. It is found that the polarity of self-assembled monolayer is a key factor in the formation of mono-domain alignment of FLC.

  13. Self-assembled alignment of nanorod by using DNA brush (Conference Presentation) (United States)

    Ijiro, Kuniharu; Nakamura, Satoshi; Mitomo, Hideyuki; Pike, Andrew; Matsuo, Yasutaka; Niikura, Kenichi


    Surface modification with polymer is widely applied to various kinds of applications. Recently, polymer brushes, which is a layer of polymers attached with one end to a surface, have attracted much attention as functionalized surfaces. In particular, ionic polymer brushes provide ultra-low friction or anti-fouling because they act as highly hydrated soft film. Almost ionic polymer brushes have been prepared from synthetic polymers. Few biopolymers have been investigated for polymer brush studies. DNA which is one of ionic biopolymers has unique functions and conformations which synthetic polymers don't have. We found that cationic gold nanorods (30 x 10 nm) were adsorbed to DNA bush (148 bp) prepared on a glass surface in an aqueous solution by observation using extinction spectra. When the cationic charge density of gold nanorods were decreased, nanorods were immobilized perpendicularly to the substrate by binding to DNA elongated. This indicates that self-assembled alignment of gold nanorods can be achieved by using DNA brush. Formed aligned gold nanorods can be used for plasmonic color analysis.

  14. Self-Assembled Epitaxial Au-Oxide Vertically Aligned Nanocomposites for Nanoscale Metamaterials. (United States)

    Li, Leigang; Sun, Liuyang; Gomez-Diaz, Juan Sebastian; Hogan, Nicki L; Lu, Ping; Khatkhatay, Fauzia; Zhang, Wenrui; Jian, Jie; Huang, Jijie; Su, Qing; Fan, Meng; Jacob, Clement; Li, Jin; Zhang, Xinghang; Jia, Quanxi; Sheldon, Matthew; Alù, Andrea; Li, Xiaoqin; Wang, Haiyan


    Metamaterials made of nanoscale inclusions or artificial unit cells exhibit exotic optical properties that do not exist in natural materials. Promising applications, such as super-resolution imaging, cloaking, hyperbolic propagation, and ultrafast phase velocities have been demonstrated based on mostly micrometer-scale metamaterials and few nanoscale metamaterials. To date, most metamaterials are created using costly and tedious fabrication techniques with limited paths toward reliable large-scale fabrication. In this work, we demonstrate the one-step direct growth of self-assembled epitaxial metal-oxide nanocomposites as a drastically different approach to fabricating large-area nanostructured metamaterials. Using pulsed laser deposition, we fabricated nanocomposite films with vertically aligned gold (Au) nanopillars (∼20 nm in diameter) embedded in various oxide matrices with high epitaxial quality. Strong, broad absorption features in the measured absorbance spectrum are clear signatures of plasmon resonances of Au nanopillars. By tuning their densities on selected substrates, anisotropic optical properties are demonstrated via angular dependent and polarization resolved reflectivity measurements and reproduced by full-wave simulations and effective medium theory. Our model predicts exotic properties, such as zero permittivity responses and topological transitions. Our studies suggest that these self-assembled metal-oxide nanostructures provide an exciting new material platform to control and enhance optical response at nanometer scales.

  15. Self-assembly of folic acid: a chiral-aligning medium for enantiodiscrimination of organic molecules in an aqueous environment. (United States)

    Lokesh; Suryaprakash, N


    Weak orienting medium: Self-assembly of alkaline salt of folic acid yielded a weak liquid-crystalline phase in an aqueous environment. This medium has the ability to discriminate enantiomers. The mesophase exists over a broad range and has the physical parameter dependent tunability of degree of alignment (see scheme).

  16. Assembly, Alignment, And Cold Focus Test Methods Utilized On Claes Optics (United States)

    Dawson, Juan C.; Kauer, John F.; Reilly, Charles M.; Steakley, Bruce C.


    The CLAES Telescope and Spectrometer were aligned as separate units. The optical interface between the two units is at the intermediate Lyot stop, where close angular and centering tolerances are required, with control by the use of matched machined tooling. In the alignme-L. of the Spectrometer, all optical components were centered to the chief ray using centering targets to align the optical components. The initial assembly was made at room temperature, and tested at 20K. One key reason for this testing is that the refractive indices for ZnS and ZnSe are not known below 90K, and therefore the exact location of the image plane is not known. The tests at 20K established the location of the image plane. A beam of collimated carbon-dioxide laser power illuminates the cryogenically cooled Spectrometer or the CLAES Instrument along the optical axis. The collimation of the beam is adjustable in small increments; the beam is scanned over the edges of the individual detectors creating edge scans that were used to determine where the image plane is located. Given the offset from exact collimation of the input beam, the corrections required to locate the image at the detector plane are computed. To determine "best focus", the inverse of the slopes of the edge-traces are plotted. Data obtained on both sides of best focus is plotted; the curves look like parabolas with upward arms. The minimum of this curve is defined as the location of the image plane. Shims that compensate for the focus errors are cut to the correct thickness, and installed. In addition to setting focus, the cryogenic tests were used to determine stability of the optics over the specified environment, and blur size measurements were performed at operational temperatures.

  17. Advanced topographic laser altimeter system (ATLAS) receiver telescope assembly (RTA) and transmitter alignment and test (United States)

    Hagopian, John; Bolcar, Matthew; Chambers, John; Crane, Allen; Eegholm, Bente; Evans, Tyler; Hetherington, Samuel; Mentzell, Eric; Thompson, Patrick L.; Ramos-Izquierdo, Luis; Vaughnn, David


    The sole instrument on NASA's ICESat-2 spacecraft shown in Figure 1 will be the Advanced Topographic Laser Altimeter System (ATLAS)1. The ATLAS is a Light Detection and Ranging (LIDAR) instrument; it measures the time of flight of the six transmitted laser beams to the Earth and back to determine altitude for geospatial mapping of global ice. The ATLAS laser beam is split into 6 main beams by a Diffractive Optical Element (DOE) that are reflected off of the earth and imaged by an 800 mm diameter Receiver Telescope Assembly (RTA). The RTA is composed of a 2-mirror telescope and Aft Optics Assembly (AOA) that collects and focuses the light from the 6 probe beams into 6 science fibers. Each fiber optic has a field of view on the earth that subtends 83 micro Radians. The light collected by each fiber is detected by a photomultiplier and timing related to a master clock to determine time of flight and therefore distance. The collection of the light from the 6 laser spots projected to the ground allows for dense cross track sampling to provide for slope measurements of ice fields. NASA LIDAR instruments typically utilize telescopes that are not diffraction limited since they function as a light collector rather than imaging function. The more challenging requirements of the ATLAS instrument require better performance of the telescope at the ¼ wave level to provide for improved sampling and signal to noise. NASA Goddard Space Flight Center (GSFC) contracted the build of the telescope to General Dynamics (GD). GD fabricated and tested the flight and flight spare telescope and then integrated the government supplied AOA for testing of the RTA before and after vibration qualification. The RTA was then delivered to GSFC for independent verification and testing over expected thermal vacuum conditions. The testing at GSFC included a measurement of the RTA wavefront error and encircled energy in several orientations to determine the expected zero gravity figure, encircled

  18. Satellite Alignment: I. Distribution of Substructures and Their Dependence On Assembly History From N-Body Simulations

    CERN Document Server

    Wang, Yang Ocean; Kang, Xi; Dutton, Aaron; Yu, Yu; Macciò, Andrea V


    Observations have shown that the spatial distribution of satellite galaxies is not random, but aligned with the major axes of central galaxies. This alignment is dependent on galaxy properties, such that red satellites are more strongly aligned than blue satellites. Theoretical work done to interpret this phenomena has found that it is due to the non-spherical nature of dark matter halos. However, most studies over-predict the alignment signal under the assumption that the central galaxy shape follows the shape of the host halo. It is also not clear whether the color dependence of alignment is due to an assembly bias or an evolution effect. In this paper we study these problems using a cosmological N-body simulation. Subhalos are used to trace the positions of satellite galaxies. It is found that the shape of dark matter halos are mis-aligned at different radii. If the central galaxy shares the same shape as the inner host halo, then the alignment effect is weaker and agrees with observational data. However, ...

  19. Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis

    Directory of Open Access Journals (Sweden)

    Mount Stephen M


    Full Text Available Abstract Background Recently, genomic sequencing efforts were finished for Oryza sativa (cultivated rice and Arabidopsis thaliana (Arabidopsis. Additionally, these two plant species have extensive cDNA and expressed sequence tag (EST libraries. We employed the Program to Assemble Spliced Alignments (PASA to identify and analyze alternatively spliced isoforms in both species. Results A comprehensive analysis of alternative splicing was performed in rice that started with >1.1 million publicly available spliced ESTs and over 30,000 full length cDNAs in conjunction with the newly enhanced PASA software. A parallel analysis was performed with Arabidopsis to compare and ascertain potential differences between monocots and dicots. Alternative splicing is a widespread phenomenon (observed in greater than 30% of the loci with transcript support and we have described nine alternative splicing variations. While alternative splicing has the potential to create many RNA isoforms from a single locus, the majority of loci generate only two or three isoforms and transcript support indicates that these isoforms are generally not rare events. For the alternate donor (AD and acceptor (AA classes, the distance between the splice sites for the majority of events was found to be less than 50 basepairs (bp. In both species, the most frequent distance between AA is 3 bp, consistent with reports in mammalian systems. Conversely, the most frequent distance between AD is 4 bp in both plant species, as previously observed in mouse. Most alternative splicing variations are localized to the protein coding sequence and are predicted to significantly alter the coding sequence. Conclusion Alternative splicing is widespread in both rice and Arabidopsis and these species share many common features. Interestingly, alternative splicing may play a role beyond creating novel combinations of transcripts that expand the proteome. Many isoforms will presumably have negative

  20. Precisely Assembled Nanofiber Arrays as a Platform to Engineer Aligned Cell Sheets for Biofabrication

    Directory of Open Access Journals (Sweden)

    Vince Beachley


    Full Text Available A hybrid cell sheet engineering approach was developed using ultra-thin nanofiber arrays to host the formation of composite nanofiber/cell sheets. It was found that confluent aligned cell sheets could grow on uniaxially-aligned and crisscrossed nanofiber arrays with extremely low fiber densities. The porosity of the nanofiber sheets was sufficient to allow aligned linear myotube formation from differentiated myoblasts on both sides of the nanofiber sheets, in spite of single-side cell seeding. The nanofiber content of the composite cell sheets is minimized to reduce the hindrance to cell migration, cell-cell contacts, mass transport, as well as the foreign body response or inflammatory response associated with the biomaterial. Even at extremely low densities, the nanofiber component significantly enhanced the stability and mechanical properties of the composite cell sheets. In addition, the aligned nanofiber arrays imparted excellent handling properties to the composite cell sheets, which allowed easy processing into more complex, thick 3D structures of higher hierarchy. Aligned nanofiber array-based composite cell sheet engineering combines several advantages of material-free cell sheet engineering and polymer scaffold-based cell sheet engineering; and it represents a new direction in aligned cell sheet engineering for a multitude of tissue engineering applications.

  1. Alignment of optical system components using an ADM beam through a null assembly (United States)

    Hayden, Joseph E. (Inventor); Olczak, Eugene G. (Inventor)


    A system for testing an optical surface includes a rangefinder configured to emit a light beam and a null assembly located between the rangefinder and the optical surface. The null assembly is configured to receive and to reflect the emitted light beam toward the optical surface. The light beam reflected from the null assembly is further reflected back from the optical surface toward the null assembly as a return light beam. The rangefinder is configured to measure a distance to the optical surface using the return light beam.

  2. Hydrodynamic alignment and assembly of nanofibrils resulting in strong cellulose filaments (United States)

    Håkansson, Karl M. O.; Fall, Andreas B.; Lundell, Fredrik; Yu, Shun; Krywka, Christina; Roth, Stephan V.; Santoro, Gonzalo; Kvick, Mathias; Prahl Wittberg, Lisa; Wågberg, Lars; Söderberg, L. Daniel


    Cellulose nanofibrils can be obtained from trees and have considerable potential as a building block for biobased materials. In order to achieve good properties of these materials, the nanostructure must be controlled. Here we present a process combining hydrodynamic alignment with a dispersion-gel transition that produces homogeneous and smooth filaments from a low-concentration dispersion of cellulose nanofibrils in water. The preferential fibril orientation along the filament direction can be controlled by the process parameters. The specific ultimate strength is considerably higher than previously reported filaments made of cellulose nanofibrils. The strength is even in line with the strongest cellulose pulp fibres extracted from wood with the same degree of fibril alignment. Successful nanoscale alignment before gelation demands a proper separation of the timescales involved. Somewhat surprisingly, the device must not be too small if this is to be achieved.

  3. Charge transport in vertically aligned, self-assembled peptide nanotube junctions (United States)

    Mizrahi, Mordechay; Zakrassov, Alexander; Lerner-Yardeni, Jenny; Ashkenasy, Nurit


    The self-assembly propensity of peptides has been extensively utilized in recent years for the formation of supramolecular nanostructures. In particular, the self-assembly of peptides into fibrils and nanotubes makes them promising building blocks for electronic and electro-optic applications. However, the mechanisms of charge transfer in these wire-like structures, especially in ambient conditions, are not yet fully understood. We describe here a layer-by-layer deposition methodology of short self-assembled cyclic peptide nanotubes, which results in vertically oriented nanotubes on gold substrates. Using this novel deposition methodology, we have fabricated molecular junctions with a conductive atomic force microscopy tip as a second electrode. Studies of the junctions' current-voltage characteristics as a function of the nanotube length revealed an efficient charge transfer in these supramolecular structures, with a low current attenuation constant of 0.1 Å-1, which indicate that electron transfer is dominated by hopping. Moreover, the threshold voltage to field-emission dominated transport was found to increase with peptide length in a manner that depends on the nature of the contact with the electrodes. The flexibility in the design of the peptide monomers and the ability to control their sequential order over the nanotube by means of the layer-by-layer assembly process, which is demonstrated in this work, can be used to engineer the electronic properties of self-assembled peptide nanotubes toward device applications.

  4. Alignment and Use of Self-Assembled Peptide Nanotubes as Dry-Etching Mask

    DEFF Research Database (Denmark)

    Andersen, Karsten Brandt; Castillo, Jaime; Bakmand, Tanya;


    Self-assembled diphenylalanine peptide nanotubes provide a means of achieving nanostructured materials in a very simple and fast way. Recent discoveries have shown that this unique material, in addition to remaining stable under dry conditions, rapidly dissolves in water making it a promising can...

  5. Fabrication of Si3N4 nanowire membranes: free standing disordered nanopapers and aligned nanowire assemblies (United States)

    Liu, Haitao; Fang, Minghao; Huang, Zhaohui; Huang, Juntong; Liu, Yan-gai; Wu, Xiaowen


    Herein, ultralong silicon nitride nanowires were synthesized via a chemical vapor deposition method by using the low-cost quartz and silicon powder as raw materials. Simple processes were used for the fabrication of disordered and ordered nanowire membranes of pure silicon nitride nanowires. The nanowires in the disordered nanopapers are intertwined with each other to form a paper-like structure which exhibit excellent flame retardancy and mechanical properties. Fourier-transform infrared spectroscopy and thermal gravity analysis were employed to characterize the refractory performance of the disordered nanopapers. Highly ordered nanowire membranes were also assembled through a three-phase assembly approach which make the Si3N4 nanowires have potential use in textured ceramics and semiconductor field. Moreover, the surface nanowires can also be modified to be hydrophobic; this characteristic make the as-prepared nanowires have the potential to be assembled by the more effective Langmuir-Blodgett method and also make the disordered nanopapers possess a super-hydrophobic surface.

  6. SAW: a method to identify splicing events from RNA-Seq data based on splicing fingerprints.

    Directory of Open Access Journals (Sweden)

    Kang Ning

    Full Text Available Splicing event identification is one of the most important issues in the comprehensive analysis of transcription profile. Recent development of next-generation sequencing technology has generated an extensive profile of alternative splicing. However, while many of these splicing events are between exons that are relatively close on genome sequences, reads generated by RNA-Seq are not limited to alternative splicing between close exons but occur in virtually all splicing events. In this work, a novel method, SAW, was proposed for the identification of all splicing events based on short reads from RNA-Seq. It was observed that short reads not in known gene models are actually absent words from known gene sequences. An efficient method to filter and cluster these short reads by fingerprint fragments of splicing events without aligning short reads to genome sequences was developed. Additionally, the possible splicing sites were also determined without alignment against genome sequences. A consensus sequence was then generated for each short read cluster, which was then aligned to the genome sequences. Results demonstrated that this method could identify more than 90% of the known splicing events with a very low false discovery rate, as well as accurately identify, a number of novel splicing events between distant exons.

  7. Temperature and chemical bonding-directed self-assembly of cobalt phosphide nanowires in reaction solutions into vertical and horizontal alignments. (United States)

    Zhang, Shuang-Yuan; Ye, Enyi; Liu, Shuhua; Lim, Suo Hon; Tee, Si Yin; Dong, Zhili; Han, Ming-Yong


    The preparation of vertically or horizontally aligned self-assemblies of CoP nanowires is demonstrated for the first time by aging them in the reaction solution for a sufficient time at 20 or 0 °C. This strategy opens up a way for exploring the controlled self-assembly of various highly anisotropic nanostructures into long-range ordered structures with collective properties.

  8. SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data. (United States)

    Sun, Xiaoyong; Zuo, Fenghua; Ru, Yuanbin; Guo, Jiqiang; Yan, Xiaoyan; Sablok, Gaurav


    Alternative splicing plays a key role in the regulation of the central dogma. Four major types of alternative splicing have been classified as intron retention, exon skipping, alternative 5 splice sites or alternative donor sites, and alternative 3 splice sites or alternative acceptor sites. A few algorithms have been developed to detect splice junctions from RNA-Seq reads. However, there are few tools targeting at the major alternative splicing types at the exon/intron level. This type of analysis may reveal subtle, yet important events of alternative splicing, and thus help gain deeper understanding of the mechanism of alternative splicing. This paper describes a user-friendly R package, extracting, annotating and analyzing alternative splicing types for sequence alignment files from RNA-Seq. SplicingTypesAnno can: (1) provide annotation for major alternative splicing at exon/intron level. By comparing the annotation from GTF/GFF file, it identifies the novel alternative splicing sites; (2) offer a convenient two-level analysis: genome-scale annotation for users with high performance computing environment, and gene-scale annotation for users with personal computers; (3) generate a user-friendly web report and additional BED files for IGV visualization. SplicingTypesAnno is a user-friendly R package for extracting, annotating and analyzing alternative splicing types at exon/intron level for sequence alignment files from RNA-Seq. It is publically available at or

  9. HOLLYWOOD: a comparative relational database of alternative splicing. (United States)

    Holste, Dirk; Huo, George; Tung, Vivian; Burge, Christopher B


    RNA splicing is an essential step in gene expression, and is often variable, giving rise to multiple alternatively spliced mRNA and protein isoforms from a single gene locus. The design of effective databases to support experimental and computational investigations of alternative splicing (AS) is a significant challenge. In an effort to integrate accurate exon and splice site annotation with current knowledge about splicing regulatory elements and predicted AS events, and to link information about the splicing of orthologous genes in different species, we have developed the Hollywood system. This database was built upon genomic annotation of splicing patterns of known genes derived from spliced alignment of complementary DNAs (cDNAs) and expressed sequence tags, and links features such as splice site sequence and strength, exonic splicing enhancers and silencers, conserved and non-conserved patterns of splicing, and cDNA library information for inferred alternative exons. Hollywood was implemented as a relational database and currently contains comprehensive information for human and mouse. It is accompanied by a web query tool that allows searches for sets of exons with specific splicing characteristics or splicing regulatory element composition, or gives a graphical or sequence-level summary of splicing patterns for a specific gene. A streamlined graphical representation of gene splicing patterns is provided, and these patterns can alternatively be layered onto existing information in the UCSC Genome Browser. The database is accessible at

  10. Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses.

    Directory of Open Access Journals (Sweden)

    Arthur W Pightling

    Full Text Available The wide availability of whole-genome sequencing (WGS and an abundance of open-source software have made detection of single-nucleotide polymorphisms (SNPs in bacterial genomes an increasingly accessible and effective tool for comparative analyses. Thus, ensuring that real nucleotide differences between genomes (i.e., true SNPs are detected at high rates and that the influences of errors (such as false positive SNPs, ambiguously called sites, and gaps are mitigated is of utmost importance. The choices researchers make regarding the generation and analysis of WGS data can greatly influence the accuracy of short-read sequence alignments and, therefore, the efficacy of such experiments. We studied the effects of some of these choices, including: i depth of sequencing coverage, ii choice of reference-guided short-read sequence assembler, iii choice of reference genome, and iv whether to perform read-quality filtering and trimming, on our ability to detect true SNPs and on the frequencies of errors. We performed benchmarking experiments, during which we assembled simulated and real Listeria monocytogenes strain 08-5578 short-read sequence datasets of varying quality with four commonly used assemblers (BWA, MOSAIK, Novoalign, and SMALT, using reference genomes of varying genetic distances, and with or without read pre-processing (i.e., quality filtering and trimming. We found that assemblies of at least 50-fold coverage provided the most accurate results. In addition, MOSAIK yielded the fewest errors when reads were aligned to a nearly identical reference genome, while using SMALT to align reads against a reference sequence that is ∼0.82% distant from 08-5578 at the nucleotide level resulted in the detection of the greatest numbers of true SNPs and the fewest errors. Finally, we show that whether read pre-processing improves SNP detection depends upon the choice of reference sequence and assembler. In total, this study demonstrates that researchers

  11. The fabrication of single-walled carbon nanotube/polyelectrolyte multilayer composites by layer-by-layer assembly and magnetic field assisted alignment (United States)

    Tian, Ying; Park, Jin Gyu; Cheng, Qunfeng; Liang, Zhiyong; Zhang, Chuck; Wang, Ben


    Single-walled carbon nanotube (SWNT)/polymer composites are widely studied because of their potential for high mechanical performance and multifunctional applications. In order to realize highly ordered multilayer nanostructures, we combined the layer-by-layer (LBL) assembly method with magnetic force-induced alignment to fabricate SWNT/poly(ethylamine) (PEI) multilayer composites. The SWNTs were functionalized with the anionic surfactant sodium dodecylbenzenesulfonate (NaDDBS) to realize negative charge at pH>7, while the PEI is positively charged at pHPEI resin to form multilayer composites on a solid substrate polydimethylsiloxane. Since the fabricated thickness of each SWNT-NaDDBS/PEI bilayer is uniform (~150 nm), the multilayer film thickness can be strictly controlled via the number of deposition cycles. A high magnetic field (8.5 Tesla) was used to align the SWNTs during the LBL process. The resultant LBL composite samples demonstrated high SWNT loading of approximately 50 wt% and uniform distribution of SWNTs in the multilayer structures, which was verified using a quartz crystal microbalance. Good alignment was also realized and observed through using high magnetic fields to align the nanotubes during the LBL deposition process. The results indicate that the LBL/magnetic alignment approach has potential for fabricating nanotube composites with highly ordered nanostructures for multifunctional materials and device applications.

  12. Migration and alignment of spherical particles in sheared viscoelastic suspensions. A quantitative determination of the flow-induced self-assembly kinetics. (United States)

    Pasquino, Rossana; Panariello, Daniele; Grizzuti, Nino


    Flow-Induced Self-Assembly (FISA) is the flow-driven formation of ordered structures in complex fluids. In this paper the effect of shear flow on the microstructure formation of dilute sphere suspensions in a viscoelastic fluid has been studied experimentally by optical microscopy techniques. The system is formed by Polymethylmethacrylate beads suspended in 20 wt.% aqueous solutions of Hydroxypropylcellulose at volume fractions ranging between 0.1% and 1.0%. Experiments show that, under the action of flow, beads migrate from the bulk to the shear walls, there forming strings aligned along the flow direction. Strings grow with time eventually reaching a steady-state final length. The alignment kinetics have been quantified by means of an alignment factor, which is a measure of the average length of the strings. The experimental results indicate that both shear rate and particle concentration are relevant factors in determining the alignment factor kinetics. In particular, it is shown that, upon increasing shear rate, strings grow both faster and longer. As a consequence, the characteristic time of the overall alignment process remains roughly constant. It is also shown that an increase in particle volume fraction determines effects similar to an increase of shear rate.

  13. Propensity of Self-Assembled Leucine-Lysine Diblock Copolymeric α-Helical Peptides To Remain in Parallel and Antiparallel Alignments in Water. (United States)

    Sarkar, Sujit; Pandey, Prithvi Raj; Roy, Sudip


    Molecular dynamics simulation study of α-helical diblock copolypeptides preassembled in parallel and antiparallel alignments in water are presented. The assembled peptide lamellar structures were not disrupted even after performing three-step simulation protocols. Primarily hydrogen bonds between peptide are responsible for the stability. The analysis of the trajectory also suggests that water plays a significant role in favoring self-assembly. We have detected continuous hydrogen bonded network structure, which is further responsible for the stability of the lamellar structures. We have performed a detailed analysis of the hydrogen bonded network structure and its length. Further, free energy calculations revealed that the degree of stability for both lamellae are similar. The present study provides structural insight into the stability of self-assembled structures of block copolypeptides.

  14. Self-Assembly of Chip-Size Components with Cavity Structures: High-Precision Alignment and Direct Bonding without Thermal Compression for Hetero Integration

    Directory of Open Access Journals (Sweden)

    Mitsumasa Koyanagi


    Full Text Available New surface mounting and packaging technologies, using self-assembly with chips having cavity structures, were investigated for three-dimensional (3D and hetero integration of complementary metal-oxide semiconductors (CMOS and microelectromechanical systems (MEMS. By the surface tension of small droplets of 0.5 wt% hydrogen fluoride (HF aqueous solution, the cavity chips, with a side length of 3 mm, were precisely aligned to hydrophilic bonding regions on the surface of plateaus formed on Si substrates. The plateaus have micro-channels to readily evaporate and fully remove the liquid from the cavities. The average alignment accuracy of the chips with a 1 mm square cavity was found to be 0.4 mm. The alignment accuracy depends, not only on the area of the bonding regions on the substrates and the length of chip periphery without the widths of channels in the plateaus, but also the area wetted by the liquid on the bonding regions. The precisely aligned chips were then directly bonded to the substrates at room temperature without thermal compression, resulting in a high shear bonding strength of more than 10 MPa.

  15. Modulating the forces between self-assembling molecules to control the shape of vesicles and the mechanics and alignment of nanofiber networks (United States)

    Greenfield, Megan Ann

    One of the great challenges in supramolecular chemistry is the design of molecules that can self-assemble into functional aggregates with well-defined three-dimensional structures and bulk material properties. Since the self-assembly of nanostructures is greatly influenced by both the nature of the self-assembling components and the environmental conditions in which the components assemble, this work explores how changes in the molecular design and the environment affect the properties of self-assembled structures. We first explore how to control the mechanical properties of self-assembled fibrillar networks by changing environmental conditions. We report here on how changing pH, screening ions, and solution temperature affect the gelation, stiffness, and response to deformation of peptide amphiphile gels. Although the morphology of PA gels formed by charge neutralization and salt-mediated charge screening are similar by electron microscopy, rheological measurements indicate that the calcium-mediated ionic bridges in CaCl2-PA gels form stronger intra- and inter-fiber crosslinks than the hydrogen bonds formed by the protonated carboxylic acid residues in HCl-PA gels. In contrast, the structure of PA gels changes drastically when the PA solution is annealed prior to gel formation. Annealed PA solutions are birefringent and can form viscoelastic strings of aligned nanofibers when manually dragged across a thin film of CaCl2. These aligned arrays of PA nanofibers hold great promise in controlling the orientation of cells in three-dimensions. Separately, we applied the principles of molecular design to create buckled membrane nanostructures that mimic the shape of viruses. When oppositely charged amphiphilic molecules are mixed they can form vesicles with a periodic two-dimensional ionic lattice that opposes the membrane's natural curvature and can result in vesicle buckling. Our results demonstrate that a large +3 to -1 charge imbalance between the cationic and anionic

  16. A short conserved motif in ALYREF directs cap- and EJC-dependent assembly of export complexes on spliced mRNAs. (United States)

    Gromadzka, Agnieszka M; Steckelberg, Anna-Lena; Singh, Kusum K; Hofmann, Kay; Gehring, Niels H


    The export of messenger RNAs (mRNAs) is the final of several nuclear posttranscriptional steps of gene expression. The formation of export-competent mRNPs involves the recruitment of export factors that are assumed to facilitate transport of the mature mRNAs. Using in vitro splicing assays, we show that a core set of export factors, including ALYREF, UAP56 and DDX39, readily associate with the spliced RNAs in an EJC (exon junction complex)- and cap-dependent manner. In order to elucidate how ALYREF and other export adaptors mediate mRNA export, we conducted a computational analysis and discovered four short, conserved, linear motifs present in RNA-binding proteins. We show that mutation in one of the new motifs (WxHD) in an unstructured region of ALYREF reduced RNA binding and abolished the interaction with eIF4A3 and CBP80. Additionally, the mutation impaired proper localization to nuclear speckles and export of a spliced reporter mRNA. Our results reveal important details of the orchestrated recruitment of export factors during the formation of export competent mRNPs.

  17. Embracing the complexity of pre-mRNA splicing

    Institute of Scientific and Technical Information of China (English)

    Peter J Shepard; Klemens J Hertel


    @@ Pre-mRNA splicing is a fundamental process required for the expression of most metazoan genes. It is carried out by the spliceosome, which catalyzes the removal of non-coding intronic sequences to assemble exons into mature mRNAs prior to export and translation.Defects in splicing lead to many human genetic diseases [1], and splicing mutations in a number of genes involved in growth control have been implicated in multiple types of cancer.

  18. The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells. (United States)

    Whisenant, Thomas C; Peralta, Eigen R; Aarreberg, Lauren D; Gao, Nina J; Head, Steven R; Ordoukhanian, Phillip; Williamson, Jamie R; Salomon, Daniel R


    Activation of CD4 T cells is a reaction to challenges such as microbial pathogens, cancer and toxins that defines adaptive immune responses. The roles of T cell receptor crosslinking, intracellular signaling, and transcription factor activation are well described, but the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) has not been considered in depth. We describe a new model expanding and activating primary human CD4 T cells and applied this to characterizing activation-induced assembly of splicing factors centered on U2AF2. We immunoprecipitated U2AF2 to identify what mRNA transcripts were bound as a function of activation by TCR crosslinking and costimulation. In parallel, mass spectrometry revealed the proteins incorporated into the U2AF2-centered RNA/protein interactome. Molecules that retained interaction with the U2AF2 complex after RNAse treatment were designated as "central" interactome members (CIMs). Mass spectrometry also identified a second class of activation-induced proteins, "peripheral" interactome members (PIMs), that bound to the same transcripts but were not in physical association with U2AF2 or its partners. siRNA knockdown of two CIMs and two PIMs caused changes in activation marker expression, cytokine secretion, and gene expression that were unique to each protein and mapped to pathways associated with key aspects of T cell activation. While knocking down the PIM, SYNCRIP, impacts a limited but immunologically important set of U2AF2-bound transcripts, knockdown of U2AF1 significantly impairs assembly of the majority of protein and mRNA components in the activation-induced interactome. These results demonstrated that CIMs and PIMs, either directly or indirectly through RNA, assembled into activation-induced U2AF2 complexes and play roles in post-transcriptional regulation of genes related to cytokine secretion. These data suggest an additional layer of regulation mediated by the activation-induced assembly of RNA

  19. Assisted transcriptome reconstruction and splicing orthology

    Directory of Open Access Journals (Sweden)

    Samuel Blanquart


    Full Text Available Abstract Background Transcriptome reconstruction, defined as the identification of all protein isoforms that may be expressed by a gene, is a notably difficult computational task. With real data, the best methods based on RNA-seq data identify barely 21 % of the expressed transcripts. While waiting for algorithms and sequencing techniques to improve — as has been strongly suggested in the literature — it is important to evaluate assisted transcriptome prediction; this is the question of how alternative transcription in one species performs as a predictor of protein isoforms in another relatively close species. Most evidence-based gene predictors use transcripts from other species to annotate a genome, but the predictive power of procedures that use exclusively transcripts from external species has never been quantified. The cornerstone of such an evaluation is the correct identification of pairs of transcripts with the same splicing patterns, called splicing orthologs. Results We propose a rigorous procedural definition of splicing orthologs, based on the identification of all ortholog pairs of splicing sites in the nucleotide sequences, and alignments at the protein level. Using our definition, we compared 24 382 human transcripts and 17 909 mouse transcripts from the highly curated CCDS database, and identified 11 122 splicing orthologs. In prediction mode, we show that human transcripts can be used to infer over 62 % of mouse protein isoforms. When restricting the predictions to transcripts known eight years ago, the percentage grows to 74 %. Using CCDS timestamped releases, we also analyze the evolution of the number of splicing orthologs over the last decade. Conclusions Alternative splicing is now recognized to play a major role in the protein diversity of eukaryotic organisms, but definitions of spliced isoform orthologs are still approximate. Here we propose a definition adapted to the subtle variations of conserved alternative

  20. Efficient Photocatalytic Degradation of Rhodamine B Dye by Aligned Arrays of Self-Assembled Hydrogen Titanate Nanotubes

    Directory of Open Access Journals (Sweden)

    Sriparna Chatterjee


    Full Text Available We show that an aligned array of hydrothermally grown, multiwalled hydrogen titanate (H2Ti3O7 nanotubes—anchored to both faces of a metallic Ti foil—acts as an efficient photocatalyst. We studied the degradation of rhodamine B dye in the presence of the nanostructured photocatalyst under UV irradiation, by monitoring the optical absorption of the dye. Rhodamine B was chosen as a representative—and particularly harmful—industrial pollutant dye. The inner and outer diameters of the H2Ti3O7 nanotubes were 5 nm and 10 nm, respectively. The nanotube array catalyst is recyclable and structurally stable. Most importantly, it shows comparable or higher photodecomposition rate constant than those of both H2Ti3O7 nanotube powder and P-25 (Degussa. The enhanced photocatalytic performance may be ascribed to the nanotube array having a superhydrophilic surface with a high accessible surface area.

  1. Viral interactions with components of the splicing machinery. (United States)

    Meyer, F


    Eukaryotic genes are often interrupted by stretches of sequence with no protein coding potential or obvious function. After transcription, these interrupting sequences must be removed to give rise to the mature messenger RNA. This fundamental process is called RNA splicing and is achieved by complicated machinery made of protein and RNA that assembles around the RNA to be edited. Viruses also use RNA splicing to maximize their coding potential and economize on genetic space, and use clever strategies to manipulate the splicing machinery to their advantage. This article gives an overview of the splicing process and provides examples of viral strategies that make use of various components of the splicing system to promote their replicative cycle. Representative virus families have been selected to illustrate the interaction with various regulatory proteins and ribonucleoproteins. The unifying theme is fine regulation through protein-protein and protein-RNA interactions with the spliceosome components and associated factors to promote or prevent spliceosome assembly on given splice sites, in addition to a strong influence from cis-regulatory sequences on viral transcripts. Because there is an intimate coupling of splicing with the processes that direct mRNA biogenesis, a description of how these viruses couple the regulation of splicing with the retention or stability of mRNAs is also included. It seems that a unique balance of suppression and activation of splicing and nuclear export works optimally for each family of viruses.

  2. Hydrodynamic alignment and assembly of nano-fibrillated cellulose in the laminar extensional flow: Effects of solidifying agents (United States)

    Mittal, Nitesh; Lundell, Fredrik; Soderberg, Daniel


    There are several fiber production technologies that are based on wet-spinning processes. Many such processes rely on the transformation of a liquid solution into a solid filament. The kinetics of solidification depends largely on the diffusion of the solvents, additives and polymer molecules, which make such systems quite complex and differ from a system to another as a function of the specific chemical, physical and structural features of the used material components. Moreover, tuning the orientation of the polymers in the liquid suspensions makes it further possible to control their structure, which in turn can lead to materials having improved properties. By keeping in mind the facts mentioned above, the aim of the current study is to utilize benefits of a flow focusing approach to align carboxymethylated cellulose nanofibrils (CNF), as a colloidal dispersion, with the help of a laminar elongational flow-field followed by the solidification using different solidifying agents or molecules (with dissimilar diffusion behavior based on their size and charges) to synthesize fibers with enhanced mechanical properties. CNF are charged elongated particles obtained from woods with diameter of 4-10 nm and length of 1-1.5 μm, and they are completely biodegradable.

  3. Assembly, physics, and application of highly electronic-type purified semiconducting carbon nanotubes in aligned array field effect transistors and photovoltaics (United States)

    Arnold, Michael


    Recent advances in (1) achieving highly monodisperse semiconducting carbon nanotubes without problematic metallic nanotubes and (2) depositing these nanotubes into useful, organized arrays and assemblies on substrates have created new opportunities for studying the physics of these one-dimensional conductors and for applying them in electronics and photonics technologies. In this talk, I will present on two topics that are along these lines. In the first, we have pioneered a scalable approach for depositing aligned arrays of ultrahigh purity semiconducting SWCNTs (prepared using polyfluorene-derivatives) called floating evaporative self-assembly (FESA). FESA is exploited to create FETs with exceptionally high combined on-conductance and on-off ratio of 261 μS/ μm and 2 x105, respectively, for a channel length of 240 nm. This is 1400 x greater on-off ratio than SWCNT FETs fabricated by other methods, at comparable on-conductance per width of 250 μS/ μm, and 30-100 x greater on-conductance per width, at comparable on-off ratio of 105-107. In the second, we have discovered how to efficiently harvest photons using semiconducting SWCNTs by driving the dissociation of excitons using donor/acceptor heterojunctions. The flow of energy in SWCNT films occurs across a complex energy landscape, temporally resolved using two-dimensional white light ultrafast spectroscopy. We have demonstrated simple solar cells driven by SWCNT excitons, based on bilayers between C60 and ultrathin (5 nm) films of SWCNTs that achieve a 1% solar power conversion efficiency (7% at the bandgap). High internal quantum efficiency indicates that future blended or multijunction cells exploiting multiple layers will be many times more efficient.

  4. Introduction to cotranscriptional RNA splicing. (United States)

    Merkhofer, Evan C; Hu, Peter; Johnson, Tracy L


    The discovery that many intron-containing genes can be cotranscriptionally spliced has led to an increased understanding of how splicing and transcription are intricately intertwined. Cotranscriptional splicing has been demonstrated in a number of different organisms and has been shown to play roles in coordinating both constitutive and alternative splicing. The nature of cotranscriptional splicing suggests that changes in transcription can dramatically affect splicing, and new evidence suggests that splicing can, in turn, influence transcription. In this chapter, we discuss the mechanisms and consequences of cotranscriptional splicing and introduce some of the tools used to measure this process.

  5. spliceR

    DEFF Research Database (Denmark)

    Vitting-Seerup, Kristoffer; Porse, Bo Torben; Sandelin, Albin;


    RNA-seq data is currently underutilized, in part because it is difficult to predict the functional impact of alternate transcription events. Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternative splicing...... and prediction of coding potential....

  6. A highly order-structured membrane electrode assembly with vertically aligned carbon nanotubes for ultra-low Pt loading PEM fuel cells

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Zhi Qun; Lim, San Hua; Poh, Chee Kok; Lin, Jianyi [Institute of Chemical and Engineering Sciences, 1 Pesek Road, Jurong Island, Singapore 627833 (Singapore); Tang, Zhe; Chua, Daniel [Department of Materials Science and Engineering, National University of Singapore, Singapore 117542 (Singapore); Xia, Zetao [Institute of Materials Research and Engineering, 3 Research Link, Singapore 117602 (Singapore); Luo, Zhiqiang; Shen, Zexiang [Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore (Singapore); Shen, Pei Kang [State Key Laboratory of Optoelectronic Materials and Technologies, and Key Laboratory of Low-carbon Chemistry and Energy Conservation of Guangdong Province, School of Physics and Engineering, Sun Yat-sen University, Guangzhou, 510275 (China); Feng, Yuan Ping [Department of Physics, National University of Singapore, Singapore 117542 (Singapore)


    A simple method was developed to prepare ultra-low Pt loading membrane electrode assembly (MEA) using vertically aligned carbon nanotubes (VACNTs) as highly ordered catalyst support for PEM fuel cells application. In the method, VACNTs were directly grown on the cheap household aluminum foil by plasma enhanced chemical vapor deposition (PECVD), using Fe/Co bimetallic catalyst. By depositing a Pt thin layer on VACNTs/Al and subsequent hot pressing, Pt/VACNTs can be 100% transferred from Al foil onto polymer electrolyte membrane for the fabrication of MEA. The whole transfer process does not need any chemical removal and destroy membrane. The PEM fuel cell with the MEA fabricated using this method showed an excellent performance with ultra-low Pt loading down to 35 {mu}g cm{sup -2} which was comparable to that of the commercial Pt catalyst on carbon powder with 400 {mu}g cm{sup -2}. To the best of our knowledge, for the first time, we identified that it is possible to substantially reduce the Pt loading one order by application of order-structured electrode based on VACNTs as Pt catalysts support, compared with the traditional random electrode at a comparable performance through experimental and mathematical methods. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Thomas Julie


    Full Text Available Abstract Background Genome-wide computational analysis of alternative splicing (AS in several flowering plants has revealed that pre-mRNAs from about 30% of genes undergo AS. Chlamydomonas, a simple unicellular green alga, is part of the lineage that includes land plants. However, it diverged from land plants about one billion years ago. Hence, it serves as a good model system to study alternative splicing in early photosynthetic eukaryotes, to obtain insights into the evolution of this process in plants, and to compare splicing in simple unicellular photosynthetic and non-photosynthetic eukaryotes. We performed a global analysis of alternative splicing in Chlamydomonas reinhardtii using its recently completed genome sequence and all available ESTs and cDNAs. Results Our analysis of AS using BLAT and a modified version of the Sircah tool revealed AS of 498 transcriptional units with 611 events, representing about 3% of the total number of genes. As in land plants, intron retention is the most prevalent form of AS. Retained introns and skipped exons tend to be shorter than their counterparts in constitutively spliced genes. The splice site signals in all types of AS events are weaker than those in constitutively spliced genes. Furthermore, in alternatively spliced genes, the prevalent splice form has a stronger splice site signal than the non-prevalent form. Analysis of constitutively spliced introns revealed an over-abundance of motifs with simple repetitive elements in comparison to introns involved in intron retention. In almost all cases, AS results in a truncated ORF, leading to a coding sequence that is around 50% shorter than the prevalent splice form. Using RT-PCR we verified AS of two genes and show that they produce more isoforms than indicated by EST data. All cDNA/EST alignments and splice graphs are provided in a website at Conclusions The extent of AS in Chlamydomonas that we observed is much

  8. A Broad Set of Chromatin Factors Influences Splicing (United States)

    Allemand, Eric; Myers, Michael P.; Garcia-Bernardo, Jose; Harel-Bellan, Annick; Krainer, Adrian R.; Muchardt, Christian


    Several studies propose an influence of chromatin on pre-mRNA splicing, but it is still unclear how widespread and how direct this phenomenon is. We find here that when assembled in vivo, the U2 snRNP co-purifies with a subset of chromatin-proteins, including histones and remodeling complexes like SWI/SNF. Yet, an unbiased RNAi screen revealed that the outcome of splicing is influenced by a much larger variety of chromatin factors not all associating with the spliceosome. The availability of this broad range of chromatin factors impacting splicing further unveiled their very context specific effect, resulting in either inclusion or skipping, depending on the exon under scrutiny. Finally, a direct assessment of the impact of chromatin on splicing using an in vitro co-transcriptional splicing assay with pre-mRNAs transcribed from a nucleosomal template, demonstrated that chromatin impacts nascent pre-mRNP in their competence for splicing. Altogether, our data show that numerous chromatin factors associated or not with the spliceosome can affect the outcome of splicing, possibly as a function of the local chromatin environment that by default interferes with the efficiency of splicing. PMID:27662573

  9. Optical Fiber Fusion Splicing

    CERN Document Server

    Yablon, Andrew D


    This book is an up-to-date treatment of optical fiber fusion splicing incorporating all the recent innovations in the field. It provides a toolbox of general strategies and specific techniques that the reader can apply when optimizing fusion splices between novel fibers. It specifically addresses considerations important for fusion splicing of contemporary specialty fibers including dispersion compensating fiber, erbium-doped gain fiber, polarization maintaining fiber, and microstructured fiber. Finally, it discusses the future of optical fiber fusion splicing including silica and non-silica based optical fibers as well as the trend toward increasing automation. Whilst serving as a self-contained reference work, abundant citations from the technical literature will enable readers to readily locate primary sources.

  10. Genome-wide assembly and analysis of alternative transcripts in mouse (United States)

    Sharov, Alexei A.; Dudekula, Dawood B.; Ko, Minoru S.H.


    To build a mouse gene index with the most comprehensive coverage of alternative transcription/splicing (ATS), we developed an algorithm and a fully automated computational pipeline for transcript assembly from expressed sequences aligned to the genome. We identified 191,946 genomic loci, which included 27,497 protein-coding genes and 11,906 additional gene candidates (e.g., nonprotein-coding, but multiexon). Comparison of the resulting gene index with TIGR, UniGene, DoTS, and ESTGenes databases revealed that it had a greater number of transcripts, a greater average number of exons and introns with proper splicing sites per gene, and longer ORFs. The 27,497 protein-coding genes had 77,138 transcripts, i.e., 2.8 transcripts per gene on average. Close examination of transcripts led to a combinatorial table of 23 types of ATS units, only nine of which were previously described, i.e., 14 types of alternative splicing, seven types of alternative starts, and two types of alternative termination. The 47%, 18%, and 14% of 20,323 multiexon protein-coding genes with proper splice sites had alternative splicings, alternative starts, and alternative terminations, respectively. The gene index with the comprehensive ATS will provide a useful platform for analyzing the nature and mechanism of ATS, as well as for designing the accurate exon-based DNA microarrays. PMID:15867436

  11. Alternative splicing interference by xenobiotics. (United States)

    Zaharieva, Emanuela; Chipman, J Kevin; Soller, Matthias


    The protein coding sequence of most eukaryotic genes (exons) is interrupted by non-coding parts (introns), which are excised in a process termed splicing. To generate a mature messenger RNA (mRNA) hundreds of combinatorial protein-protein and RNA-protein interactions are required to splice out often very large introns with high fidelity and accuracy. Inherent to splicing is the use of alternative splice sites generating immense proteomic diversity from a limited number of genes. In humans, alternative splicing is a major mode of regulating gene expression, occurs in over 90% of genes and is particularly abundant in the brain. Only recently, it has been recognized that the complexity of the splicing process makes it susceptible to interference by various xenobiotics. These compounds include antineoplastic substances, commonly used drugs and food supplements and cause a spectrum of effects ranging from deleterious inhibition of general splicing to highly specific modifications of alternative splicing affecting only certain genes. Alterations in splicing have been implicated in numerous diseases such as cancer and neurodegeneration. Splicing regulation plays an important role in the execution of programmed cell death. The switch between anti- and pro-apoptotic isoforms by alternative splice site selection and misregulation of a number of splicing factors impacts on cell survival and disease. Here, our current knowledge is summarized on compounds interfering with general and alternative splicing and of the current methodology to study changes in these processes relevant to the field of toxicology and future risk assessments.

  12. Herboxidiene triggers splicing repression and abiotic stress responses in plants

    KAUST Repository

    Alshareef, Sahar


    Background Constitutive and alternative splicing of pre-mRNAs from multiexonic genes controls the diversity of the proteome; these precisely regulated processes also fine-tune responses to cues related to growth, development, and stresses. Small-molecule inhibitors that perturb splicing provide invaluable tools for use as chemical probes to uncover the molecular underpinnings of splicing regulation and as potential anticancer compounds. Results Here, we show that herboxidiene (GEX1A) inhibits both constitutive and alternative splicing. Moreover, GEX1A activates genome-wide transcriptional patterns involved in abiotic stress responses in plants. GEX1A treatment -activated ABA-inducible promoters, and led to stomatal closure. Interestingly, GEX1A and pladienolide B (PB) elicited similar cellular changes, including alterations in the patterns of transcription and splicing, suggesting that these compounds might target the same spliceosome complex in plant cells. Conclusions Our study establishes GEX1A as a potent splicing inhibitor in plants that can be used to probe the assembly, dynamics, and molecular functions of the spliceosome and to study the interplay between splicing stress and abiotic stresses, as well as having potential biotechnological applications.

  13. Designing oligo libraries taking alternative splicing into account (United States)

    Shoshan, Avi; Grebinskiy, Vladimir; Magen, Avner; Scolnicov, Ariel; Fink, Eyal; Lehavi, David; Wasserman, Alon


    We have designed sequences for DNA microarrays and oligo libraries, taking alternative splicing into account. Alternative splicing is a common phenomenon, occurring in more than 25% of the human genes. In many cases, different splice variants have different functions, are expressed in different tissues or may indicate different stages of disease. When designing sequences for DNA microarrays or oligo libraries, it is very important to take into account the sequence information of all the mRNA transcripts. Therefore, when a gene has more than one transcript (as a result of alternative splicing, alternative promoter sites or alternative poly-adenylation sites), it is very important to take all of them into account in the design. We have used the LEADS transcriptome prediction system to cluster and assemble the human sequences in GenBank and design optimal oligonucleotides for all the human genes with a known mRNA sequence based on the LEADS predictions.

  14. SpliceDisease database: linking RNA splicing and disease. (United States)

    Wang, Juan; Zhang, Jie; Li, Kaibo; Zhao, Wei; Cui, Qinghua


    RNA splicing is an important aspect of gene regulation in many organisms. Splicing of RNA is regulated by complicated mechanisms involving numerous RNA-binding proteins and the intricate network of interactions among them. Mutations in cis-acting splicing elements or its regulatory proteins have been shown to be involved in human diseases. Defects in pre-mRNA splicing process have emerged as a common disease-causing mechanism. Therefore, a database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, we manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference Pubmed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. We standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, we give direct links of the entry to the respective position/region in the genome browser. The users can freely browse, search and download the data in SpliceDisease at

  15. spliceR

    DEFF Research Database (Denmark)

    Vitting-Seerup, Kristoffer; Porse, Bo Torben; Sandelin, Albin Gustav;


    BACKGROUND: RNA-seq data is currently underutilized, in part because it is difficult to predict the functional impact of alternate transcription events. Recent software improvements in full-length transcript deconvolution prompted us to develop spliceR, an R package for classification of alternat...

  16. Functional splicing network reveals extensive regulatory potential of the core spliceosomal machinery. (United States)

    Papasaikas, Panagiotis; Tejedor, J Ramón; Vigevani, Luisa; Valcárcel, Juan


    Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the effect of knocking down the components of the splicing machinery on alternative splicing events relevant for cell proliferation and apoptosis and used this information to reconstruct a network of functional interactions. The network accurately captures known physical and functional associations and identifies new ones, revealing remarkable regulatory potential of core spliceosomal components, related to the order and duration of their recruitment during spliceosome assembly. In contrast with standard models of regulation at early steps of splice site recognition, factors involved in catalytic activation of the spliceosome display regulatory properties. The network also sheds light on the antagonism between hnRNP C and U2AF, and on targets of antitumor drugs, and can be widely used to identify mechanisms of splicing regulation.

  17. Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II. (United States)

    Carrillo Oesterreich, Fernando; Herzel, Lydia; Straube, Korinna; Hujer, Katja; Howard, Jonathon; Neugebauer, Karla M


    Protein-coding genes in eukaryotes are transcribed by RNA polymerase II (Pol II) and introns are removed from pre-mRNA by the spliceosome. Understanding the time lag between Pol II progression and splicing could provide mechanistic insights into the regulation of gene expression. Here, we present two single-molecule nascent RNA sequencing methods that directly determine the progress of splicing catalysis as a function of Pol II position. Endogenous genes were analyzed on a global scale in budding yeast. We show that splicing is 50% complete when Pol II is only 45 nt downstream of introns, with the first spliced products observed as introns emerge from Pol II. Perturbations that slow the rate of spliceosome assembly or speed up the rate of transcription caused splicing delays, showing that regulation of both processes determines in vivo splicing profiles. We propose that matched rates streamline the gene expression pathway, while allowing regulation through kinetic competition.

  18. Genome-wide assembly and analysis of alternative transcripts in mouse


    Sharov, Alexei A; Dudekula, Dawood B.; Minoru S.H. Ko


    To build a mouse gene index with the most comprehensive coverage of alternative transcription/splicing (ATS), we developed an algorithm and a fully automated computational pipeline for transcript assembly from expressed sequences aligned to the genome. We identified 191,946 genomic loci, which included 27,497 protein-coding genes and 11,906 additional gene candidates (e.g., nonprotein-coding, but multiexon). Comparison of the resulting gene index with TIGR, UniGene, DoTS, and ESTGenes databas...


    CERN Multimedia

    S. Szillasi


    The CMS detector has been gradually opened and whenever a wheel became exposed the first operation was the removal of the MABs, the sensor structures of the Hardware Barrel Alignment System. By the last days of June all 36 MABs have arrived at the Alignment Lab at the ISR where, as part of the Alignment Upgrade Project, they are refurbished with new Survey target holders. Their electronic checkout is on the way and finally they will be recalibrated. During LS1 the alignment system will be upgraded in order to allow more precise reconstruction of the MB4 chambers in Sector 10 and Sector 4. This requires new sensor components, so called MiniMABs (pictured below), that have already been assembled and calibrated. Image 6: Calibrated MiniMABs are ready for installation For the track-based alignment, the systematic uncertainties of the algorithm are under scrutiny: this study will enable the production of an improved Monte Carlo misalignment scenario and to update alignment position errors eventually, crucial...

  20. Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia.

    Directory of Open Access Journals (Sweden)

    Jing Qin Wu

    Full Text Available BACKGROUND: While hybridization based analysis of the cortical transcriptome has provided important insight into the neuropathology of schizophrenia, it represents a restricted view of disease-associated gene activity based on predetermined probes. By contrast, sequencing technology can provide un-biased analysis of transcription at nucleotide resolution. Here we use this approach to investigate schizophrenia-associated cortical gene expression. METHODOLOGY/PRINCIPAL FINDINGS: The data was generated from 76 bp reads of RNA-Seq, aligned to the reference genome and assembled into transcripts for quantification of exons, splice variants and alternative promoters in postmortem superior temporal gyrus (STG/BA22 from 9 male subjects with schizophrenia and 9 matched non-psychiatric controls. Differentially expressed genes were then subjected to further sequence and functional group analysis. The output, amounting to more than 38 Gb of sequence, revealed significant alteration of gene expression including many previously shown to be associated with schizophrenia. Gene ontology enrichment analysis followed by functional map construction identified three functional clusters highly relevant to schizophrenia including neurotransmission related functions, synaptic vesicle trafficking, and neural development. Significantly, more than 2000 genes displayed schizophrenia-associated alternative promoter usage and more than 1000 genes showed differential splicing (FDR<0.05. Both types of transcriptional isoforms were exemplified by reads aligned to the neurodevelopmentally significant doublecortin-like kinase 1 (DCLK1 gene. CONCLUSIONS: This study provided the first deep and un-biased analysis of schizophrenia-associated transcriptional diversity within the STG, and revealed variants with important implications for the complex pathophysiology of schizophrenia.

  1. Pupil Alignment Measuring Technique and Alignment Reference for Instruments or Optical Systems (United States)

    Hagopian, John G.


    A technique was created to measure the pupil alignment of instruments in situ by measuring calibrated pupil alignment references (PARs) in instruments. The PAR can also be measured using an alignment telescope or an imaging system. PAR allows the verification of the science instrument (SI) pupil alignment at the integrated science instrument module (ISIM) level of assembly at ambient and cryogenic operating temperature. This will allow verification of the ISIM+SI alignment, and provide feedback to realign the SI if necessary.

  2. Biochemical identification of new proteins involved in splicing repression at the Drosophila P-element exonic splicing silencer (United States)

    Horan, Lucas; Yasuhara, Jiro C.; Kohlstaedt, Lori A.; Rio, Donald C.


    Splicing of the Drosophila P-element third intron (IVS3) is repressed in somatic tissues due to the function of an exonic splicing silencer (ESS) complex present on the 5′ exon RNA. To comprehensively characterize the mechanisms of this alternative splicing regulation, we used biochemical fractionation and affinity purification to isolate the silencer complex assembled in vitro and identify the constituent proteins by mass spectrometry. Functional assays using splicing reporter minigenes identified the proteins hrp36 and hrp38 and the cytoplasmic poly(A)-binding protein PABPC1 as novel functional components of the splicing silencer. hrp48, PSI, and PABPC1 have high-affinity RNA-binding sites on the P-element IVS3 5′ exon, whereas hrp36 and hrp38 proteins bind with low affinity to the P-element silencer RNA. RNA pull-down and immobilized protein assays showed that hrp48 protein binding to the silencer RNA can recruit hrp36 and hrp38. These studies identified additional components that function at the P-element ESS and indicated that proteins with low-affinity RNA-binding sites can be recruited in a functional manner through interactions with a protein bound to RNA at a high-affinity binding site. These studies have implications for the role of heterogeneous nuclear ribonucleoproteins (hnRNPs) in the control of alternative splicing at cis-acting regulatory sites. PMID:26545814

  3. Low-temperature self-assembled vertically aligned carbon nanofibers as counter-electrode material for dye-sensitized solar cells (United States)

    Mahpeykar, S. M.; Tabatabaei, M. K.; Ghafoori-fard, H.; Habibiyan, H.; Koohsorkhi, J.


    Low-temperature AC-DC PECVD is employed for direct growth of vertically aligned carbon nanofibers (VACNFs) on ordinary transparent conductive glass as counter-electrode material for dye-sensitized solar cells (DSSCs). To the best of our knowledge, this is the first report on utilization of VACNFs grown directly on ordinary FTO-coated glass as a cost-effective catalyst material in DSSCs. According to the FESEM images, the as-grown arrays are well aligned and dense, and offer uniform coverage on the surface of the substrate. In-plane and out-of-plane conductivity measurements reveal their good electrical conductivity, and Raman spectroscopy suggests a high number of electrocatalytic active sites, favoring charge transport at the electrolyte/electrode interface. Hybrid VACNF/Pt electrodes are also fabricated for performance comparison with Pt and VACNF electrodes. X-ray diffraction results verify the crystallization of Pt in hybrid electrodes and further confirm the vertical alignment of carbon nanofibers. Electrochemical characterization indicates that VACNFs provide both high catalytic and good charge transfer capability, which can be attributed to their high surface area, defect-rich and one-dimensional structure, vertical alignment and low contact resistance. As a result, VACNF cells can achieve a comparable performance (˜5.6%) to that of the reference Pt cells (˜6.5%). Moreover, by combination of the excellent charge transport and catalytic ability of VACNFs and the high conductivity of Pt nanoparticles, hybrid VACNF/Pt cells can deliver a performance superior to that of the Pt cells (˜7.2%), despite having a much smaller amount of Pt loading, which raises hopes for low-cost large-scale production of DSSCs in the future.

  4. Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner

    DEFF Research Database (Denmark)

    Lu, David V; Brown, Randall H; Arumugam, Manimozhiyan;


    MOTIVATION: The most accurate way to determine the intron-exon structures in a genome is to align spliced cDNA sequences to the genome. Thus, cDNA-to-genome alignment programs are a key component of most annotation pipelines. The scoring system used to choose the best alignment is a primary...

  5. Aligned Layers of Silver Nano-Fibers

    Directory of Open Access Journals (Sweden)

    Andrii B. Golovin


    Full Text Available We describe a new dichroic polarizers made by ordering silver nano-fibers to aligned layers. The aligned layers consist of nano-fibers and self-assembled molecular aggregates of lyotropic liquid crystals. Unidirectional alignment of the layers is achieved by means of mechanical shearing. Aligned layers of silver nano-fibers are partially transparent to a linearly polarized electromagnetic radiation. The unidirectional alignment and density of the silver nano-fibers determine degree of polarization of transmitted light. The aligned layers of silver nano-fibers might be used in optics, microwave applications, and organic electronics.

  6. Method of predicting Splice Sites based on signal interactions

    Directory of Open Access Journals (Sweden)

    Deogun Jitender S


    Full Text Available Abstract Background Predicting and proper ranking of canonical splice sites (SSs is a challenging problem in bioinformatics and machine learning communities. Any progress in SSs recognition will lead to better understanding of splicing mechanism. We introduce several new approaches of combining a priori knowledge for improved SS detection. First, we design our new Bayesian SS sensor based on oligonucleotide counting. To further enhance prediction quality, we applied our new de novo motif detection tool MHMMotif to intronic ends and exons. We combine elements found with sensor information using Naive Bayesian Network, as implemented in our new tool SpliceScan. Results According to our tests, the Bayesian sensor outperforms the contemporary Maximum Entropy sensor for 5' SS detection. We report a number of putative Exonic (ESE and Intronic (ISE Splicing Enhancers found by MHMMotif tool. T-test statistics on mouse/rat intronic alignments indicates, that detected elements are on average more conserved as compared to other oligos, which supports our assumption of their functional importance. The tool has been shown to outperform the SpliceView, GeneSplicer, NNSplice, Genio and NetUTR tools for the test set of human genes. SpliceScan outperforms all contemporary ab initio gene structural prediction tools on the set of 5' UTR gene fragments. Conclusion Designed methods have many attractive properties, compared to existing approaches. Bayesian sensor, MHMMotif program and SpliceScan tools are freely available on our web site. Reviewers This article was reviewed by Manyuan Long, Arcady Mushegian and Mikhail Gelfand.

  7. SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.

    Directory of Open Access Journals (Sweden)

    Byron Yu-Lin Kuo


    Full Text Available Serial analysis of gene expression (SAGE not only is a method for profiling the global expression of genes, but also offers the opportunity for the discovery of novel transcripts. SAGE tags are mapped to known transcripts to determine the gene of origin. Tags that map neither to a known transcript nor to the genome were hypothesized to span a splice junction, for which the exon combination or exon(s are unknown. To test this hypothesis, we have developed an algorithm, SAGE2Splice, to efficiently map SAGE tags to potential splice junctions in a genome. The algorithm consists of three search levels. A scoring scheme was designed based on position weight matrices to assess the quality of candidates. Using optimized parameters for SAGE2Splice analysis and two sets of SAGE data, candidate junctions were discovered for 5%-6% of unmapped tags. Candidates were classified into three categories, reflecting the previous annotations of the putative splice junctions. Analysis of predicted tags extracted from EST sequences demonstrated that candidate junctions having the splice junction located closer to the center of the tags are more reliable. Nine of these 12 candidates were validated by RT-PCR and sequencing, and among these, four revealed previously uncharacterized exons. Thus, SAGE2Splice provides a new functionality for the identification of novel transcripts and exons. SAGE2Splice is available online at

  8. Methods for Characterization of Alternative RNA Splicing. (United States)

    Harvey, Samuel E; Cheng, Chonghui


    Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semi-quantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We also describe analysis of alternative splicing using a splicing "minigene" in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest.

  9. Mutual interdependence of splicing and transcription elongation. (United States)

    Brzyżek, Grzegorz; Świeżewski, Szymon


    Transcription and splicing are intrinsically linked, as splicing needs a pre-mRNA substrate to commence. The more nuanced view is that the rate of transcription contributes to splicing regulation. On the other hand there is accumulating evidence that splicing has an active role in controlling transcription elongation by DNA-dependent RNA polymerase II (RNAP II). We briefly review those mechanisms and propose a unifying model where splicing controls transcription elongation to provide an optimal timing for successive rounds of splicing.

  10. Alignment validation

    Energy Technology Data Exchange (ETDEWEB)

    ALICE; ATLAS; CMS; LHCb; Golling, Tobias


    The four experiments, ALICE, ATLAS, CMS and LHCb are currently under constructionat CERN. They will study the products of proton-proton collisions at the Large Hadron Collider. All experiments are equipped with sophisticated tracking systems, unprecedented in size and complexity. Full exploitation of both the inner detector andthe muon system requires an accurate alignment of all detector elements. Alignmentinformation is deduced from dedicated hardware alignment systems and the reconstruction of charged particles. However, the system is degenerate which means the data is insufficient to constrain all alignment degrees of freedom, so the techniques are prone to converging on wrong geometries. This deficiency necessitates validation and monitoring of the alignment. An exhaustive discussion of means to validate is subject to this document, including examples and plans from all four LHC experiments, as well as other high energy experiments.

  11. Binary Mixtures of SH- and CH3-Terminated Self-Assembled Monolayers to Control the Average Spacing Between Aligned Gold Nanoparticles

    Directory of Open Access Journals (Sweden)

    Pavelka Laura


    Full Text Available Abstract This paper presents a method to control the average spacing between organometallic chemical vapor deposition (OMCVD grown gold nanoparticles (Au NPs in a line. Focused ion beam patterned CH3-terminated self-assembled monolayers are refilled systematically with different mixtures of SH- and CH3-terminated silanes. The average spacing between OMCVD Au NPs is demonstrated systematically to decrease by increasing the v/v% ratio of the thiols in the binary silane mixtures with SH- and CH3-terminated groups.

  12. Analysis of a Splice Array Experiment Elucidates Roles of Chromatin Elongation Factor Spt4-5 in Splicing.

    Directory of Open Access Journals (Sweden)


    Full Text Available Splicing is an important process for regulation of gene expression in eukaryotes, and it has important functional links to other steps of gene expression. Two examples of these linkages include Ceg1, a component of the mRNA capping enzyme, and the chromatin elongation factors Spt4-5, both of which have recently been shown to play a role in the normal splicing of several genes in the yeast Saccharomyces cerevisiae. Using a genomic approach to characterize the roles of Spt4-5 in splicing, we used splicing-sensitive DNA microarrays to identify specific sets of genes that are mis-spliced in ceg1, spt4, and spt5 mutants. In the context of a complex, nested, experimental design featuring 22 dye-swap array hybridizations, comprising both biological and technical replicates, we applied five appropriate statistical models for assessing differential expression between wild-type and the mutants. To refine selection of differential expression genes, we then used a robust model-synthesizing approach, Differential Expression via Distance Synthesis, to integrate all five models. The resultant list of differentially expressed genes was then further analyzed with regard to select attributes: we found that highly transcribed genes with long introns were most sensitive to spt mutations. QPCR confirmation of differential expression was established for the limited number of genes evaluated. In this paper, we showcase splicing array technology, as well as powerful, yet general, statistical methodology for assessing differential expression, in the context of a real, complex experimental design. Our results suggest that the Spt4-Spt5 complex may help coordinate splicing with transcription under conditions that present kinetic challenges to spliceosome assembly or function.

  13. Analysis of a splice array experiment elucidates roles of chromatin elongation factor Spt4-5 in splicing.

    Directory of Open Access Journals (Sweden)

    Yuanyuan Xiao


    Full Text Available Splicing is an important process for regulation of gene expression in eukaryotes, and it has important functional links to other steps of gene expression. Two examples of these linkages include Ceg1, a component of the mRNA capping enzyme, and the chromatin elongation factors Spt4-5, both of which have recently been shown to play a role in the normal splicing of several genes in the yeast Saccharomyces cerevisiae. Using a genomic approach to characterize the roles of Spt4-5 in splicing, we used splicing-sensitive DNA microarrays to identify specific sets of genes that are mis-spliced in ceg1, spt4, and spt5 mutants. In the context of a complex, nested, experimental design featuring 22 dye-swap array hybridizations, comprising both biological and technical replicates, we applied five appropriate statistical models for assessing differential expression between wild-type and the mutants. To refine selection of differential expression genes, we then used a robust model-synthesizing approach, Differential Expression via Distance Synthesis, to integrate all five models. The resultant list of differentially expressed genes was then further analyzed with regard to select attributes: we found that highly transcribed genes with long introns were most sensitive to spt mutations. QPCR confirmation of differential expression was established for the limited number of genes evaluated. In this paper, we showcase splicing array technology, as well as powerful, yet general, statistical methodology for assessing differential expression, in the context of a real, complex experimental design. Our results suggest that the Spt4-Spt5 complex may help coordinate splicing with transcription under conditions that present kinetic challenges to spliceosome assembly or function.

  14. Intronic Alus influence alternative splicing.

    Directory of Open Access Journals (Sweden)

    Galit Lev-Maor

    Full Text Available Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA formation within the human transcriptome. Most of the editing sites are located in the primate-specific retrotransposed element called Alu. A large fraction of Alus are found in intronic sequences, implying extensive Alu-Alu dsRNA formation in mRNA precursors. Yet, the effect of these intronic Alus on splicing of the flanking exons is largely unknown. Here, we show that more Alus flank alternatively spliced exons than constitutively spliced ones; this is especially notable for those exons that have changed their mode of splicing from constitutive to alternative during human evolution. This implies that Alu insertions may change the mode of splicing of the flanking exons. Indeed, we demonstrate experimentally that two Alu elements that were inserted into an intron in opposite orientation undergo base-pairing, as evident by RNA editing, and affect the splicing patterns of a downstream exon, shifting it from constitutive to alternative. Our results indicate the importance of intronic Alus in influencing the splicing of flanking exons, further emphasizing the role of Alus in shaping of the human transcriptome.

  15. Beyond Alignment

    DEFF Research Database (Denmark)

    Beyond Alignment: Applying Systems Thinking to Architecting Enterprises is a comprehensive reader about how enterprises can apply systems thinking in their enterprise architecture practice, for business transformation and for strategic execution. The book's contributors find that systems thinking...... is a valuable way of thinking about the viable enterprise and how to architect it....

  16. Dump assembly (United States)

    Goldmann, Louis H.


    A dump assembly having a fixed conduit and a rotatable conduit provided with overlapping plates, respectively, at their adjacent ends. The plates are formed with openings, respectively, normally offset from each other to block flow. The other end of the rotatable conduit is provided with means for securing the open end of a filled container thereto. Rotation of the rotatable conduit raises and inverts the container to empty the contents while concurrently aligning the conduit openings to permit flow of material therethrough.

  17. Alternative Splicing and Expression Profile Analysis of Expressed Sequence Tags in Domestic Pig

    Institute of Scientific and Technical Information of China (English)

    Liang Zhang; Lin Tao; Lin Ye; Ling He; Yuan-Zhong Zhu; Yue-Dong Zhu; Yan Zhou


    Domestic pig (Sus scrofa domestica) is one of the most important mammals to humans. Alternative splicing is a cellular mechanism in eukaryotes that greatly increases the diversity of gene products. Expression sequence tags (ESTs) have been widely used for gene discovery, expression profile analysis, and alternative splicing detection. In this study, a total of 712,905 ESTs extracted from 101 different nonnormalized EST libraries of the domestic pig were analyzed. These EST libraries cover the nervous system, digestive system, immune system, and meat production related tissues from embryo, newborn, and adult pigs, making contributions to the analysis of alternative splicing variants as well as expression profiles in various stages of tissues. A modified approach was designed to cluster and assemble large EST datasets, aiming to detect alternative splicing together with EST abundance of each splicing variant. Much efforts were made to classify alternative splicing into different types and apply different filters to each type to get more reliable results. Finally, a total of 1,223 genes with average 2.8 splicing variants were detected among 16,540 unique genes. The overview of expression profiles would change when we take alternative splicing into account.

  18. Activation and repression functions of an SR splicing regulator depend on exonic versus intronic-binding position. (United States)

    Shen, Manli; Mattox, William


    SR proteins and related factors play widespread roles in alternative pre-mRNA splicing and are known to promote splice site recognition through their Arg-Ser-rich effector domains. However, binding of SR regulators to some targets results in repression of splice sites through a distinct mechanism. Here, we investigate how activated and repressed targets of the Drosophila SR regulator Transformer2 elicit its differing effects on splicing. We find that, like activation, repression affects early steps in the recognition of splice sites and spliceosome assembly. Repositioning of regulatory elements reveals that Tra2 complexes that normally repress splicing from intronic positions activate splicing when located in an exon. Protein tethering experiments demonstrate that this position dependence is an intrinsic property of Tra2 and further show that repression and activation are mediated by separate effector domains of this protein. When other Drosophila SR factors (SF2 and Rbp1) that activate splicing from exonic positions were tethered intronically they failed to either activate or repress splicing. Interestingly, both activities of Tra2 favor the exonic identity of the RNA sequences that encompass its binding sites. This suggests a model in which these two opposite functions act in concert to define both the position and extent of alternatively spliced exons.

  19. ParSplice, Version 1

    Energy Technology Data Exchange (ETDEWEB)


    The ParSplice code implements the Parallel Trajectory Splicing algorithm described in [1]. This method is part of the Accelerated Molecular Dynamics family of techniques developed in Los Alamos National Laboratory over the last 16 years. These methods aim at generating high-quality trajectories of ensembles of atoms in materials. ParSplice uses multiple independent replicas of the system in order to parallelize the generation of such trajectories in the time domain, enabling simulations of systems of modest size over very long timescales. ParSplice includes capabilities to store configurations of the system, to generate and distribute tasks across a large number of processors, and to harvest the results of these tasks to generate long trajectories. ParSplice is a management layer that orchestrate large number of calculations, but it does not perform the actual molecular dynamics itself; this is done by external molecular dynamics engines. [1] Danny Perez, Ekin D Cubuk, Amos Waterland, Efthimios Kaxiras, Arthur F Voter, Long-time dynamics through parallel trajectory splicing, Journal of chemical theory and computation 12, 18 (2015)

  20. Partial Automated Alignment and Integration System (United States)

    Kelley, Gary Wayne (Inventor)


    The present invention is a Partial Automated Alignment and Integration System (PAAIS) used to automate the alignment and integration of space vehicle components. A PAAIS includes ground support apparatuses, a track assembly with a plurality of energy-emitting components and an energy-receiving component containing a plurality of energy-receiving surfaces. Communication components and processors allow communication and feedback through PAAIS.

  1. Targeting RNA splicing for disease therapy. (United States)

    Havens, Mallory A; Duelli, Dominik M; Hastings, Michelle L


    Splicing of pre-messenger RNA into mature messenger RNA is an essential step for the expression of most genes in higher eukaryotes. Defects in this process typically affect cellular function and can have pathological consequences. Many human genetic diseases are caused by mutations that cause splicing defects. Furthermore, a number of diseases are associated with splicing defects that are not attributed to overt mutations. Targeting splicing directly to correct disease-associated aberrant splicing is a logical approach to therapy. Splicing is a favorable intervention point for disease therapeutics, because it is an early step in gene expression and does not alter the genome. Significant advances have been made in the development of approaches to manipulate splicing for therapy. Splicing can be manipulated with a number of tools including antisense oligonucleotides, modified small nuclear RNAs (snRNAs), trans-splicing, and small molecule compounds, all of which have been used to increase specific alternatively spliced isoforms or to correct aberrant gene expression resulting from gene mutations that alter splicing. Here we describe clinically relevant splicing defects in disease states, the current tools used to target and alter splicing, specific mutations and diseases that are being targeted using splice-modulating approaches, and emerging therapeutics.

  2. Methods for Characterization of Alternative RNA Splicing (United States)

    Harvey, Samuel E.; Cheng, Chonghui


    Quantification of alternative splicing to detect the abundance of differentially spliced isoforms of a gene in total RNA can be accomplished via RT-PCR using both quantitative real-time and semi-quantitative PCR methods. These methods require careful PCR primer design to ensure specific detection of particular splice isoforms. We also describe analysis of alternative splicing using a splicing “minigene” in mammalian cell tissue culture to facilitate investigation of the regulation of alternative splicing of a particular exon of interest. PMID:26721495

  3. Extending reference assembly models

    DEFF Research Database (Denmark)

    Church, Deanna M.; Schneider, Valerie A.; Steinberg, Karyn Meltz;


    The human genome reference assembly is crucial for aligning and analyzing sequence data, and for genome annotation, among other roles. However, the models and analysis assumptions that underlie the current assembly need revising to fully represent human sequence diversity. Improved analysis tools...

  4. DIDA: Distributed Indexing Dispatched Alignment.

    Directory of Open Access Journals (Sweden)

    Hamid Mohamadi

    Full Text Available One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through The software is released under the British Columbia Cancer Agency License (BCCA, and is free for academic use.

  5. Splice testing for LHC quadrupole magnets

    CERN Document Server

    Barzi, E; Fehér, S; Kashikhin, V V; Kerby, J S; Lamm, M J; Orris, D; Ray, G; Tartaglia, M; Zlobin, A V


    Electrical splices between NbTi Rutherford type cables need to be made for the LHC IR inner triplet quadrupoles. Splices between magnets as well as internal to the magnets are necessary. Various splice configurations, solders, and fluxes have been considered. Testing of these splices at cryogenic temperatures and at various currents has been completed. The results were satisfactory; Fermilab is capable of making excellent low resistance (<1n Omega ) solder joints for the LHC project. (4 refs).

  6. Stochastic noise in splicing machinery


    Melamud, Eugene; Moult, John


    The number of known alternative human isoforms has been increasing steadily with the amount of available transcription data. To date, over 100 000 isoforms have been detected in EST libraries, and at least 75% of human genes have at least one alternative isoform. In this paper, we propose that most alternative splicing events are the result of noise in the splicing process. We show that the number of isoforms and their abundance can be predicted by a simple stochastic noise model that takes i...

  7. The RRR of the Cu components of the LHC main bus bar splices

    CERN Document Server

    Heck, S; Fessia, P; Principe, R; CERN. Geneva. TE Department


    The different LHC main bus bar splice components (bus bar cable, splice U-piece and wedge and bus bar stabilizer) are subjected to different heat treatments (HTs) during bus bar assembly and splice soldering. The influence of soldering HTs on the RRR of the LHC main bus bar cable strands has been determined. The RRR of several splice U-pieces and wedges dismounted from the LHC has been measured. A correlation between the Vickers hardness and the RRR of the high purity Cu profiles has been established. All U-pieces tested that were produced before 2009 have a RRR>200, while the RRR of all wedges and of U-pieces of 2009 production have a much lower RRR. All tests of LHC main bus bar samples performed so far in the laboratory indicate a RRR of approximately 200 or higher.

  8. The Integrity of ACSR Full Tension Single-Stage Splice Connector at Higher Operation Temperature

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jy-An John [ORNL; Lara-Curzio, Edgar [ORNL; King Jr, Thomas J [ORNL


    Due to increases in power demand and limited investment in new infrastructure, existing overhead power transmission lines often need to operate at temperatures higher than those used for the original design criteria. This has led to the accelerated aging and degradation of splice connectors. It is manifested by the formation of hot-spots that have been revealed by infrared imaging during inspection. The implications of connector aging is two-fold: (1) significant increases in resistivity of the splice connector (i.e., less efficient transmission of electricity) and (2) significant reductions in the connector clamping strength, which could ultimately result in separation of the power transmission line at the joint. Therefore, the splice connector appears to be the weakest link in electric power transmission lines. This report presents a protocol for integrating analytical and experimental approaches to evaluate the integrity of full tension single-stage splice connector assemblies and the associated effective lifetime at high operating temperature.

  9. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs (United States)

    Zhang, Xiao-Ou; Dong, Rui; Zhang, Yang; Zhang, Jia-Lin; Luo, Zheng; Zhang, Jun; Chen, Ling-Ling; Yang, Li


    Circular RNAs (circRNAs) derived from back-spliced exons have been widely identified as being co-expressed with their linear counterparts. A single gene locus can produce multiple circRNAs through alternative back-splice site selection and/or alternative splice site selection; however, a detailed map of alternative back-splicing/splicing in circRNAs is lacking. Here, with the upgraded CIRCexplorer2 pipeline, we systematically annotated different types of alternative back-splicing and alternative splicing events in circRNAs from various cell lines. Compared with their linear cognate RNAs, circRNAs exhibited distinct patterns of alternative back-splicing and alternative splicing. Alternative back-splice site selection was correlated with the competition of putative RNA pairs across introns that bracket alternative back-splice sites. In addition, all four basic types of alternative splicing that have been identified in the (linear) mRNA process were found within circRNAs, and many exons were predominantly spliced in circRNAs. Unexpectedly, thousands of previously unannotated exons were detected in circRNAs from the examined cell lines. Although these novel exons had similar splice site strength, they were much less conserved than known exons in sequences. Finally, both alternative back-splicing and circRNA-predominant alternative splicing were highly diverse among the examined cell lines. All of the identified alternative back-splicing and alternative splicing in circRNAs are available in the CIRCpedia database ( Collectively, the annotation of alternative back-splicing and alternative splicing in circRNAs provides a valuable resource for depicting the complexity of circRNA biogenesis and for studying the potential functions of circRNAs in different cells. PMID:27365365

  10. Stochastic noise in splicing machinery. (United States)

    Melamud, Eugene; Moult, John


    The number of known alternative human isoforms has been increasing steadily with the amount of available transcription data. To date, over 100 000 isoforms have been detected in EST libraries, and at least 75% of human genes have at least one alternative isoform. In this paper, we propose that most alternative splicing events are the result of noise in the splicing process. We show that the number of isoforms and their abundance can be predicted by a simple stochastic noise model that takes into account two factors: the number of introns in a gene and the expression level of a gene. The results strongly support the hypothesis that most alternative splicing is a consequence of stochastic noise in the splicing machinery, and has no functional significance. The results are also consistent with error rates tuned to ensure that an adequate level of functional product is produced and to reduce the toxic effect of accumulation of misfolding proteins. Based on simulation of sampling of virtual cDNA libraries, we estimate that error rates range from 1 to 10% depending on the number of introns and the expression level of a gene.

  11. Evolutionary conservation of alternative splicing in chicken (United States)

    Katyal, S.; Gao, Z.; Liu, R.-Z.; Godbout, R.


    Alternative splicing represents a source of great diversity for regulating protein expression and function. It has been estimated that one-third to two-thirds of mammalian genes are alternatively spliced. With the sequencing of the chicken genome and analysis of transcripts expressed in chicken tissues, we are now in a position to address evolutionary conservation of alternative splicing events in chicken and mammals. Here, we compare chicken and mammalian transcript sequences of 41 alternatively-spliced genes and 50 frequently accessed genes. Our results support a high frequency of splicing events in chicken, similar to that observed in mammals. PMID:17675855

  12. COMMUNICATION: Alternative splicing and genomic stability (United States)

    Cahill, Kevin


    Alternative splicing allows an organism to make different proteins in different cells at different times, all from the same gene. In a cell that uses alternative splicing, the total length of all the exons is much shorter than in a cell that encodes the same set of proteins without alternative splicing. This economical use of exons makes genes more stable during reproduction and development because a genome with a shorter exon length is more resistant to harmful mutations. Genomic stability may be the reason why higher vertebrates splice alternatively. For a broad class of alternatively spliced genes, a formula is given for the increase in their stability.

  13. Alcoholism and alternative splicing of candidate genes. (United States)

    Sasabe, Toshikazu; Ishiura, Shoichi


    Gene expression studies have shown that expression patterns of several genes have changed during the development of alcoholism. Gene expression is regulated not only at the level of transcription but also through alternative splicing of pre-mRNA. In this review, we discuss some of the evidence suggesting that alternative splicing of candidate genes such as DRD2 (encoding dopamine D2 receptor) may form the basis of the mechanisms underlying the pathophysiology of alcoholism. These reports suggest that aberrant expression of splice variants affects alcohol sensitivities, and alcohol consumption also regulates alternative splicing. Thus, investigations of alternative splicing are essential for understanding the molecular events underlying the development of alcoholism.

  14. GC content around splice sites affects splicing through pre-mRNA secondary structures

    Directory of Open Access Journals (Sweden)

    Chen Liang


    Full Text Available Abstract Background Alternative splicing increases protein diversity by generating multiple transcript isoforms from a single gene through different combinations of exons or through different selections of splice sites. It has been reported that RNA secondary structures are involved in alternative splicing. Here we perform a genomic study of RNA secondary structures around splice sites in humans (Homo sapiens, mice (Mus musculus, fruit flies (Drosophila melanogaster, and nematodes (Caenorhabditis elegans to further investigate this phenomenon. Results We observe that GC content around splice sites is closely associated with the splice site usage in multiple species. RNA secondary structure is the possible explanation, because the structural stability difference among alternative splice sites, constitutive splice sites, and skipped splice sites can be explained by the GC content difference. Alternative splice sites tend to be GC-enriched and exhibit more stable RNA secondary structures in all of the considered species. In humans and mice, splice sites of first exons and long exons tend to be GC-enriched and hence form more stable structures, indicating the special role of RNA secondary structures in promoter proximal splicing events and the splicing of long exons. In addition, GC-enriched exon-intron junctions tend to be overrepresented in tissue-specific alternative splice sites, indicating the functional consequence of the GC effect. Compared with regions far from splice sites and decoy splice sites, real splice sites are GC-enriched. We also found that the GC-content effect is much stronger than the nucleotide-order effect to form stable secondary structures. Conclusion All of these results indicate that GC content is related to splice site usage and it may mediate the splicing process through RNA secondary structures.

  15. Single nucleotide polymorphism-based validation of exonic splicing enhancers.

    Directory of Open Access Journals (Sweden)

    William G Fairbrother


    Full Text Available Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a population at any given time. Here, we describe an approach based on this idea called VERIFY (variant elimination reinforces functionality, which can be used to assess the extent of natural selection acting on an oligonucleotide motif or set of motifs predicted to have biological activity. As an application of this approach, we analyzed a set of 238 hexanucleotides previously predicted to have exonic splicing enhancer (ESE activity in human exons using the relative enhancer and silencer classification by unanimous enrichment (RESCUE-ESE method. Aligning the single nucleotide polymorphisms (SNPs from the public human SNP database to the chimpanzee genome allowed inference of the direction of the mutations that created present-day SNPs. Analyzing the set of SNPs that overlap RESCUE-ESE hexamers, we conclude that nearly one-fifth of the mutations that disrupt predicted ESEs have been eliminated by natural selection (odds ratio = 0.82 +/- 0.05. This selection is strongest for the predicted ESEs that are located near splice sites. Our results demonstrate a novel approach for quantifying the extent of natural selection acting on candidate functional motifs and also suggest certain features of mutations/SNPs, such as proximity to the splice site and disruption or alteration of predicted ESEs, that should be useful in identifying variants that might cause a biological phenotype.

  16. The RNA Splicing Response to DNA Damage. (United States)

    Shkreta, Lulzim; Chabot, Benoit


    The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging.

  17. Titin Diversity—Alternative Splicing Gone Wild

    Directory of Open Access Journals (Sweden)

    Wei Guo


    Full Text Available Titin is an extremely large protein found in highest concentrations in heart and skeletal muscle. The single mammalian gene is expressed in multiple isoforms as a result of alternative splicing. Although titin isoform expression is controlled developmentally and in a tissue specific manner, the vast number of potential splicing pathways far exceeds those described in any other alternatively spliced gene. Over 1 million human splice pathways for a single individual can be potentially derived from the PEVK region alone. A new splicing pattern for the human cardiac N2BA isoform type has been found in which the PEVK region includes only the N2B type exons. The alterations in splicing and titin isoform expression in human heart disease provide impetus for future detailed study of the splicing mechanisms for this giant protein.

  18. Spliced leader RNA trans-splicing discovered in copepods (United States)

    Yang, Feifei; Xu, Donghui; Zhuang, Yunyun; Yi, Xiaoyan; Huang, Yousong; Chen, Hongju; Lin, Senjie; Campbell, David A.; Sturm, Nancy R.; Liu, Guangxing; Zhang, Huan


    Copepods are one of the most abundant metazoans in the marine ecosystem, constituting a critical link in aquatic food webs and contributing significantly to the global carbon budget, yet molecular mechanisms of their gene expression are not well understood. Here we report the detection of spliced leader (SL) trans-splicing in calanoid copepods. We have examined nine species of wild-caught copepods from Jiaozhou Bay, China that represent the major families of the calanoids. All these species contained a common 46-nt SL (CopepodSL). We further determined the size of CopepodSL precursor RNA (slRNA; 108-158 nt) through genomic analysis and 3‧-RACE technique, which was confirmed by RNA blot analysis. Structure modeling showed that the copepod slRNA folded into typical slRNA secondary structures. Using a CopepodSL-based primer set, we selectively enriched and sequenced copepod full-length cDNAs, which led to the characterization of copepod transcripts and the cataloging of the complete set of 79 eukaryotic cytoplasmic ribosomal proteins (cRPs) for a single copepod species. We uncovered the SL trans-splicing in copepod natural populations, and demonstrated that CopepodSL was a sensitive and specific tool for copepod transcriptomic studies at both the individual and population levels and that it would be useful for metatranscriptomic analysis of copepods.

  19. Comparative cross-species alternative splicing in plants. (United States)

    Ner-Gaon, Hadas; Leviatan, Noam; Rubin, Eitan; Fluhr, Robert


    Alternative splicing (AS) can add significantly to genome complexity. Plants are thought to exhibit less AS than animals. An algorithm, based on expressed sequence tag (EST) pairs gapped alignment, was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ESTs to search for AS. EST pairs gapped alignment was first evaluated in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and tomato (Solanum lycopersicum) for which annotated genome sequence is available and was shown to accurately predict splicing events. The method was then applied to 11 plant species that include 17 cultivars for which enough ESTs are available. The results show a large, 3.7-fold difference in AS rates between plant species with Arabidopsis and rice in the lower range and lettuce (Lactuca sativa) and sorghum (Sorghum bicolor) in the upper range. Hence, compared to higher animals, plants show a much greater degree of variety in their AS rates and in some plant species the rates of animal and plant AS are comparable although the distribution of AS types may differ. In eudicots but not monocots, a correlation between genome size and AS rates was detected, implying that in eudicots the mechanisms that lead to larger genomes are a driving force for the evolution of AS.

  20. Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants (United States)

    Bucher, Johan; Lammers, Michiel; Busscher-Lange, Jacqueline; Bonnema, Guusje; Rodenburg, Nicole; Proveniers, Marcel C. G.; Angenent, Gerco C.


    Plants adjust their development and architecture to small variations in ambient temperature. In a time in which temperatures are rising world-wide, the mechanism by which plants are able to sense temperature fluctuations and adapt to it, is becoming of special interest. By performing RNA-sequencing on two Arabidopsis accession and one Brassica species exposed to temperature alterations, we showed that alternative splicing is an important mechanism in ambient temperature sensing and adaptation. We found that amongst the differentially alternatively spliced genes, splicing related genes are enriched, suggesting that the splicing machinery itself is targeted for alternative splicing when temperature changes. Moreover, we showed that many different components of the splicing machinery are targeted for ambient temperature regulated alternative splicing. Mutant analysis of a splicing related gene that was differentially spliced in two of the genotypes showed an altered flowering time response to different temperatures. We propose a two-step mechanism where temperature directly influences alternative splicing of the splicing machinery genes, followed by a second step where the altered splicing machinery affects splicing of downstream genes involved in the adaptation to altered temperatures. PMID:28257507

  1. The influence of magnetic interactions and shape anisotropy on the alignment and assembly of BaFe{sub 12}O{sub 19} and Er{sub 2}O{sub 3} nanoplates

    Energy Technology Data Exchange (ETDEWEB)

    Lisjak, Darja, E-mail:


    Magnetically anisotropic material with useful properties can be obtained when the barium ferrite (BaFe{sub 12}O{sub 19}) plates are aligned in a single plane. We studied the influence of the magnetic forces and the shape anisotropy on the alignment of barium ferrite nanoparticles. Nanoplates with diameters of 10–350 nm and diameter-to-thickness ratios of 3–30 were synthesized hydrothermally and stabilized in 1-butanol with dodecylbenzene sulphonic acid. The nanoplates were then deposited from the suspension on gold-coated substrates and dried with or without an applied magnetic field. In both cases the nanoplates aligned preferentially in the plane of the substrate, as evidenced by the scanning electron microscopy observations. To compare the influence of the magnetic field and the magnetic dipole–dipole interactions with that of the nanoparticle shape anisotropy, the alignment of paramagnetic erbium oxide (Er{sub 2}O{sub 3}) nanoplates was also studied. A lower degree of alignment was obtained with the erbium oxide than with the barium ferrite nanoplates. Barium ferrite films with a minimum orientation of 90% were prepared from the deposits after sintering at 1150 °C for 5 h. A comparable alignment of the erbium oxide films was induced hydrodynamically during the electrophoretic deposition. - Highlights: • Aligned deposits from BaFe{sub 12}O{sub 19} and Er{sub 2}O{sub 3} were prepared. • The magnetic interactions prevail over the shape anisotropy effect. • The alignment of the BaFe{sub 12}O{sub 19} nanoplates was obtained by drying a suspension. • The alignment of Er{sub 2}O{sub 3} nanoplates was obtained only by electrophoretic deposition.

  2. Alternative Spliced Transcripts as Cancer Markers

    Directory of Open Access Journals (Sweden)

    Otavia L. Caballero


    Full Text Available Eukaryotic mRNAs are transcribed as precursors containing their intronic sequences. These are subsequently excised and the exons are spliced together to form mature mRNAs. This process can lead to transcript diversification through the phenomenon of alternative splicing. Alternative splicing can take the form of one or more skipped exons, variable position of intron splicing or intron retention. The effect of alternative splicing in expanding protein repertoire might partially underlie the apparent discrepancy between gene number and the complexity of higher eukaryotes. It is likely that more than 50% form. Many cancer-associated genes, such as CD44 and WT1 are alternatively spliced. Variation of the splicing process occurs during tumor progression and may play a major role in tumorigenesis. Furthermore, alternatively spliced transcripts may be extremely useful as cancer markers, since it appears likely that there may be striking contrasts in usage of alternatively spliced transcript variants between normal and tumor tissue than in alterations in the general levels of gene expression.

  3. Strategies and tools for whole genome alignments

    Energy Technology Data Exchange (ETDEWEB)

    Couronne, Olivier; Poliakov, Alexander; Bray, Nicolas; Ishkhanov,Tigran; Ryaboy, Dmitriy; Rubin, Edward; Pachter, Lior; Dubchak, Inna


    The availability of the assembled mouse genome makespossible, for the first time, an alignment and comparison of two largevertebrate genomes. We have investigated different strategies ofalignment for the subsequent analysis of conservation of genomes that areeffective for different quality assemblies. These strategies were appliedto the comparison of the working draft of the human genome with the MouseGenome Sequencing Consortium assembly, as well as other intermediatemouse assemblies. Our methods are fast and the resulting alignmentsexhibit a high degree of sensitivity, covering more than 90 percent ofknown coding exons in the human genome. We have obtained such coveragewhile preserving specificity. With a view towards the end user, we havedeveloped a suite of tools and websites for automatically aligning, andsubsequently browsing and working with whole genome comparisons. Wedescribe the use of these tools to identify conserved non-coding regionsbetween the human and mouse genomes, some of which have not beenidentified by other methods.

  4. Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible. (United States)

    Lareau, Liana F; Brenner, Steven E


    Ultraconserved elements, unusually long regions of perfect sequence identity, are found in genes encoding numerous RNA-binding proteins including arginine-serine rich (SR) splicing factors. Expression of these genes is regulated via alternative splicing of the ultraconserved regions to yield mRNAs that are degraded by nonsense-mediated mRNA decay (NMD), a process termed unproductive splicing (Lareau et al. 2007; Ni et al. 2007). As all human SR genes are affected by alternative splicing and NMD, one might expect this regulation to have originated in an early SR gene and persisted as duplications expanded the SR family. But in fact, unproductive splicing of most human SR genes arose independently (Lareau et al. 2007). This paradox led us to investigate the origin and proliferation of unproductive splicing in SR genes. We demonstrate that unproductive splicing of the splicing factor SRSF5 (SRp40) is conserved among all animals and even observed in fungi; this is a rare example of alternative splicing conserved between kingdoms, yet its effect is to trigger mRNA degradation. As the gene duplicated, the ancient unproductive splicing was lost in paralogs, and distinct unproductive splicing evolved rapidly and repeatedly to take its place. SR genes have consistently employed unproductive splicing, and while it is exceptionally conserved in some of these genes, turnover in specific events among paralogs shows flexible means to the same regulatory end.

  5. The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin. (United States)

    Collins, Richard A; Stajich, Jason E; Field, Deborah J; Olive, Joan E; DeAbreu, Diane M


    When we expressed a small (0.9 kb) nonprotein-coding transcript derived from the mitochondrial VS plasmid in the nucleus of Neurospora we found that it was efficiently spliced at one or more of eight 5' splice sites and ten 3' splice sites, which are present apparently by chance in the sequence. Further experimental and bioinformatic analyses of other mitochondrial plasmids, random sequences, and natural nuclear genes in Neurospora and other fungi indicate that fungal spliceosomes recognize a wide range of 5' splice site and branchpoint sequences and predict introns to be present at high frequency in random sequence. In contrast, analysis of intronless fungal nuclear genes indicates that branchpoint, 5' splice site and 3' splice site consensus sequences are underrepresented compared with random sequences. This underrepresentation of splicing signals is sufficient to deplete the nuclear genome of splice sites at locations that do not comprise biologically relevant introns. Thus, the splicing machinery can recognize a wide range of splicing signal sequences, but splicing still occurs with great accuracy, not because the splicing machinery distinguishes correct from incorrect introns, but because incorrect introns are substantially depleted from the genome.

  6. Detonator assembly for oil well perforating gun

    Energy Technology Data Exchange (ETDEWEB)

    Regalbuto, J.A.


    A safe/arm detonator assembly for use with an oil well perforating gun assembly has 2 housing members isolated from well-bore fluid which are rotatable from a safe position wherein a detonator and a booster are held out of alignment, to an armed position wherein the detonator and booster are moved into alignment. The detonator assembly is further arranged to be installed in a well perforating gun assembly such that the gun assembly may be transported with the detonator assembly in the safe position, and rotated to the armed position at the well site without disassembling the gun assembly. A safety pin may protrude from one of the housing members across a cavity between the members to cover and protect the booster from accidental detonation when the detonator assembly is in the safe position. The detonator and booster cavities may be held aligned by a detent ball. 16 claims.

  7. Vibrating wire alignment technique

    CERN Document Server

    Xiao-Long, Wang; lei, Wu; Chun-Hua, Li


    Vibrating wire alignment technique is a kind of method which through measuring the spatial distribution of magnetic field to do the alignment and it can achieve very high alignment accuracy. Vibrating wire alignment technique can be applied for magnet fiducialization and accelerator straight section components alignment, it is a necessary supplement for conventional alignment method. This article will systematically expound the international research achievements of vibrating wire alignment technique, including vibrating wire model analysis, system frequency calculation, wire sag calculation and the relation between wire amplitude and magnetic induction intensity. On the basis of model analysis this article will introduce the alignment method which based on magnetic field measurement and the alignment method which based on amplitude and phase measurement. Finally, some basic questions will be discussed and the solutions will be given.

  8. Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes. (United States)

    Sveen, A; Kilpinen, S; Ruusulehto, A; Lothe, R A; Skotheim, R I


    Alternative splicing is a widespread process contributing to structural transcript variation and proteome diversity. In cancer, the splicing process is commonly disrupted, resulting in both functional and non-functional end-products. Cancer-specific splicing events are known to contribute to disease progression; however, the dysregulated splicing patterns found on a genome-wide scale have until recently been less well-studied. In this review, we provide an overview of aberrant RNA splicing and its regulation in cancer. We then focus on the executors of the splicing process. Based on a comprehensive catalog of splicing factor encoding genes and analyses of available gene expression and somatic mutation data, we identify cancer-associated patterns of dysregulation. Splicing factor genes are shown to be significantly differentially expressed between cancer and corresponding normal samples, and to have reduced inter-individual expression variation in cancer. Furthermore, we identify enrichment of predicted cancer-critical genes among the splicing factors. In addition to previously described oncogenic splicing factor genes, we propose 24 novel cancer-critical splicing factors predicted from somatic mutations.

  9. Alcoholism and Alternative Splicing of Candidate Genes

    Directory of Open Access Journals (Sweden)

    Toshikazu Sasabe


    Full Text Available Gene expression studies have shown that expression patterns of several genes have changed during the development of alcoholism. Gene expression is regulated not only at the level of transcription but also through alternative splicing of pre-mRNA. In this review, we discuss some of the evidence suggesting that alternative splicing of candidate genes such as DRD2 (encoding dopamine D2 receptor may form the basis of the mechanisms underlying the pathophysiology of alcoholism. These reports suggest that aberrant expression of splice variants affects alcohol sensitivities, and alcohol consumption also regulates alternative splicing. Thus, investigations of alternative splicing are essential for understanding the molecular events underlying the development of alcoholism.

  10. Alignments between galaxies, satellite systems and haloes (United States)

    Shao, Shi; Cautun, Marius; Frenk, Carlos S.; Gao, Liang; Crain, Robert A.; Schaller, Matthieu; Schaye, Joop; Theuns, Tom


    The spatial distribution of the satellite populations of the Milky Way and Andromeda are puzzling in that they are nearly perpendicular to the discs of their central galaxies. To understand the origin of such configurations we study the alignment of the central galaxy, satellite system and dark matter halo in the largest of the `Evolution and Assembly of GaLaxies and their Environments' (EAGLE) simulation. We find that centrals and their satellite systems tend to be well aligned with their haloes, with a median misalignment angle of 33° in both cases. While the centrals are better aligned with the inner 10 kpc halo, the satellite systems are better aligned with the entire halo indicating that satellites preferentially trace the outer halo. The central-satellite alignment is weak (median misalignment angle of 52°) and we find that around 20 per cent of systems have a misalignment angle larger than 78°, which is the value for the Milky Way. The central-satellite alignment is a consequence of the tendency of both components to align with the dark matter halo. As a consequence, when the central is parallel to the satellite system, it also tends to be parallel to the halo. In contrast, if the central is perpendicular to the satellite system, as in the case of the Milky Way and Andromeda, then the central-halo alignment is much weaker. Dispersion-dominated (spheroidal) centrals have a stronger alignment with both their halo and their satellites than rotation-dominated (disc) centrals. We also found that the halo, the central galaxy and the satellite system tend to be aligned with the surrounding large-scale distribution of matter, with the halo being the better aligned of the three.

  11. iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences

    Directory of Open Access Journals (Sweden)

    Zheng Yi


    Full Text Available Abstract Background Expressed Sequence Tags (ESTs have played significant roles in gene discovery and gene functional analysis, especially for non-model organisms. For organisms with no full genome sequences available, ESTs are normally assembled into longer consensus sequences for further downstream analysis. However current de novo EST assembly programs often generate large number of assembly errors that will negatively affect the downstream analysis. In order to generate more accurate consensus sequences from ESTs, tools are needed to reduce or eliminate errors from de novo assemblies. Results We present iAssembler, a pipeline that can assemble large-scale ESTs into consensus sequences with significantly higher accuracy than current existing assemblers. iAssembler employs MIRA and CAP3 assemblers to generate initial assemblies, followed by identifying and correcting two common types of transcriptome assembly errors: 1 ESTs from different transcripts (mainly alternatively spliced transcripts or paralogs are incorrectly assembled into same contigs; and 2 ESTs from same transcripts fail to be assembled together. iAssembler can be used to assemble ESTs generated using the traditional Sanger method and/or the Roche-454 massive parallel pyrosequencing technology. Conclusion We compared performances of iAssembler and several other de novo EST assembly programs using both Roche-454 and Sanger EST datasets. It demonstrated that iAssembler generated significantly more accurate consensus sequences than other assembly programs.


    CERN Multimedia


    Since June of 2009, the muon alignment group has focused on providing new alignment constants and on finalizing the hardware alignment reconstruction. Alignment constants for DTs and CSCs were provided for CRAFT09 data reprocessing. For DT chambers, the track-based alignment was repeated using CRAFT09 cosmic ray muons and validated using segment extrapolation and split cosmic tools. One difference with respect to the previous alignment is that only five degrees of freedom were aligned, leaving the rotation around the local x-axis to be better determined by the hardware system. Similarly, DT chambers poorly aligned by tracks (due to limited statistics) were aligned by a combination of photogrammetry and hardware-based alignment. For the CSC chambers, the hardware system provided alignment in global z and rotations about local x. Entire muon endcap rings were further corrected in the transverse plane (global x and y) by the track-based alignment. Single chamber track-based alignment suffers from poor statistic...

  13. Spliced

    DEFF Research Database (Denmark)

    Addison, Courtney Page


    Human gene therapy (HGT) aims to cure disease by inserting or editing the DNA of patients with genetic conditions. Since foundational genetic techniques came into use in the 1970s, the field has developed to the point that now three therapies have market approval, and over 1800 clinical trials have...... been initiated. In this article I present a brief history of HGT, showing how the ethical and practical viability of the field was achieved by key scientific and regulatory actors. These parties carefully articulated gene therapy’s scope, limiting it to therapeutic interventions on somatic cells......, and cultivated alliances and divisions that bolstered the field’s legitimacy. At times these measures faltered, and then practitioners and sometimes patients would invoke an ethical imperative, posing gene therapy as the best solution to life and death problems. I suggest that we consider how boundary...


    CERN Multimedia

    G. Gomez and J. Pivarski


    Alignment efforts in the first few months of 2011 have shifted away from providing alignment constants (now a well established procedure) and focussed on some critical remaining issues. The single most important task left was to understand the systematic differences observed between the track-based (TB) and hardware-based (HW) barrel alignments: a systematic difference in r-φ and in z, which grew as a function of z, and which amounted to ~4-5 mm differences going from one end of the barrel to the other. This difference is now understood to be caused by the tracker alignment. The systematic differences disappear when the track-based barrel alignment is performed using the new “twist-free” tracker alignment. This removes the largest remaining source of systematic uncertainty. Since the barrel alignment is based on hardware, it does not suffer from the tracker twist. However, untwisting the tracker causes endcap disks (which are aligned ...

  15. Microbial and Natural Metabolites That Inhibit Splicing: A Powerful Alternative for Cancer Treatment

    Directory of Open Access Journals (Sweden)

    Nancy Martínez-Montiel


    Full Text Available In eukaryotes, genes are frequently interrupted with noncoding sequences named introns. Alternative splicing is a nuclear mechanism by which these introns are removed and flanking coding regions named exons are joined together to generate a message that will be translated in the cytoplasm. This mechanism is catalyzed by a complex machinery known as the spliceosome, which is conformed by more than 300 proteins and ribonucleoproteins that activate and regulate the precision of gene expression when assembled. It has been proposed that several genetic diseases are related to defects in the splicing process, including cancer. For this reason, natural products that show the ability to regulate splicing have attracted enormous attention due to its potential use for cancer treatment. Some microbial metabolites have shown the ability to inhibit gene splicing and the molecular mechanism responsible for this inhibition is being studied for future applications. Here, we summarize the main types of natural products that have been characterized as splicing inhibitors, the recent advances regarding molecular and cellular effects related to these molecules, and the applications reported so far in cancer therapeutics.

  16. Microbial and Natural Metabolites That Inhibit Splicing: A Powerful Alternative for Cancer Treatment (United States)

    Rosas-Murrieta, Nora Hilda; Martínez-Montiel, Mónica; Gaspariano-Cholula, Mayra Patricia


    In eukaryotes, genes are frequently interrupted with noncoding sequences named introns. Alternative splicing is a nuclear mechanism by which these introns are removed and flanking coding regions named exons are joined together to generate a message that will be translated in the cytoplasm. This mechanism is catalyzed by a complex machinery known as the spliceosome, which is conformed by more than 300 proteins and ribonucleoproteins that activate and regulate the precision of gene expression when assembled. It has been proposed that several genetic diseases are related to defects in the splicing process, including cancer. For this reason, natural products that show the ability to regulate splicing have attracted enormous attention due to its potential use for cancer treatment. Some microbial metabolites have shown the ability to inhibit gene splicing and the molecular mechanism responsible for this inhibition is being studied for future applications. Here, we summarize the main types of natural products that have been characterized as splicing inhibitors, the recent advances regarding molecular and cellular effects related to these molecules, and the applications reported so far in cancer therapeutics. PMID:27610372

  17. Aberrant Splicing in Cancer: Mediators of Malignant Progression through an Imperfect Splice Program Shift. (United States)

    Luz, Felipe Andrés Cordero; Brígido, Paula Cristina; Moraes, Alberto Silva; Silva, Marcelo José Barbosa


    Although the efforts to understand the genetic basis of cancer allowed advances in diagnosis and therapy, little is known about other molecular bases. Splicing is a key event in gene expression, controlling the excision of introns decoded inside genes and being responsible for 80% of the proteome amplification through events of alternative splicing. Growing data from the last decade point to deregulation of splicing events as crucial in carcinogenesis and tumor progression. Several alterations in splicing events were observed in cancer, caused by either missexpression of or detrimental mutations in some splicing factors, and appear to be critical in carcinogenesis and key events during tumor progression. Notwithstanding, it is difficult to determine whether it is a cause or consequence of cancer and/or tumorigenesis. Most reviews focus on the generated isoforms of deregulated splicing pattern, while others mainly summarize deregulated splicing factors observed in cancer. In this review, events associated with carcinogenesis and tumor progression mainly, and epithelial-to-mesenchymal transition, which is also implicated in alternative splicing regulation, will be progressively discussed in the light of a new perspective, suggesting that splicing deregulation mediates cell reprogramming in tumor progression by an imperfect shift of the splice program.

  18. Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns

    Directory of Open Access Journals (Sweden)

    Rogozin Igor B


    Full Text Available Abstract Background The signals that determine the specificity and efficiency of splicing are multiple and complex, and are not fully understood. Among other factors, the relative contributions of different mechanisms appear to depend on intron size inasmuch as long introns might hinder the activity of the spliceosome through interference with the proper positioning of the intron-exon junctions. Indeed, it has been shown that the information content of splice sites positively correlates with intron length in the nematode, Drosophila, and fungi. We explored the connections between the length of vertebrate introns, the strength of splice sites, exonic splicing signals, and evolution of flanking exons. Results A compensatory relationship is shown to exist between different types of signals, namely, the splice sites and the exonic splicing enhancers (ESEs. In the range of relatively short introns (approximately, Conclusion Several weak but statistically significant correlations were observed between vertebrate intron length, splice site strength, and potential exonic splicing signals. Taken together, these findings attest to a compensatory relationship between splice sites and exonic splicing signals, depending on intron length.

  19. Splicing in Caenorhabditis elegans does not require an AG at the 3' splice acceptor site. (United States)

    Aroian, R V; Levy, A D; Koga, M; Ohshima, Y; Kramer, J M; Sternberg, P W


    The dinucleotide AG, found at the 3' end of virtually all eukaryotic pre-mRNA introns, is thought to be essential for splicing. Reduction-of-function mutations in two Caenorhabditis elegans genes, the receptor tyrosine kinase gene let-23 and the collagen gene dpy-10, both alter the AG at the end of a short (ca. 50-nucleotide) intron to AA. The in vivo effects of these mutations were studied by sequencing polymerase chain reaction-amplified reverse-transcribed RNA isolated from the two mutants. As expected, we find transcripts that splice to a cryptic AG, skip an exon, and retain an unspliced intron. However, we also find significant levels of splicing at the mutated 3' splice site (AA) and at nearby non-AG dinucleotides. Our results indicate that for short C. elegans introns an AG is not required for splicing at either the correct 3' splice site or incorrect sites. Analysis of a splice site mutant involving a longer, 316-nucleotide C. elegans intron indicates that an AG is also not required there for splicing. We hypothesize that elements besides the invariant AG, e.g., an A-U-rich region, a UUUC motif, and/or a potential branch point sequence, are directing the selection of the 3' splice site and that in wild-type genes these elements cooperate so that proper splicing occurs. Images PMID:8417357

  20. Alignment of the NOMAD-STAR detector

    CERN Document Server

    Cervera-Villanueva, A


    This note describes the alignment of the NOMAD-STAR detector. This is the B/sub 4/C-silicon target installed in the NOMAD spectrometer in 1997. NOMAD-STAR is composed of modules of 12 silicon detectors each giving a total length of 72 cm. Ten of these modules (called ladders) are assembled to form a layer. There are five layers interleaved with passive boron carbide plates. The total surface of silicon is 1.14 m /sup 2/. Energetic muons from the flat-top of the CERN SPS cycle provide the necessary information to perform a very precise software alignment. This alignment is needed to ensure that the impact parameter measurement needed for the identification of taus in a detector like NOMAD-STAR will not be limited by the error in the alignment. (15 refs).

  1. Depolarization-mediated regulation of alternative splicing

    Directory of Open Access Journals (Sweden)

    Alok eSharma


    Full Text Available Alternative splicing in eukaryotes plays an important role in regulating gene expression by selectively including alternative exons. A wealth of information has been accumulated that explains how alternative exons are selected in a developmental stage- or tissue-specific fashion. However, our knowledge of how cells respond to environmental changes to alter alternative splicing is very limited. For example, although a number of alternative exons have been shown to be regulated by calcium level alterations, the underlying mechanisms are not well understood. As calcium signaling in neurons plays a crucial role in essential neuronal functions such as learning and memory formation, it is important to understand how this process is regulated at every level in gene expression. The significance of the dynamic control of alternative splicing in response to changes of calcium levels has been largely unappreciated. In this communication, we will summarize the recent advances in calcium signaling-mediated alternative splicing that have provided some insights into the important regulatory mechanisms. In addition to describing the cis-acting RNA elements on the pre-mRNA molecules that respond to changes of intracellular calcium levels, we will summarize how splicing regulators change and affect alternative splicing in this process. We will also discuss a novel mode of calcium-mediated splicing regulation at the level of chromatin structure and transcription.

  2. Regulation of Alternative Splicing in Vivo by Overexpression of Antagonistic Splicing Factors (United States)

    Caceres, Javier F.; Stamm, Stefan; Helfman, David M.; Krainer, Adrian R.


    The opposing effects of SF2/ASF and heterogeneous nuclear ribonucleoprotein (hnRNP) A1 influence alternative splicing in vitro. SF2/ASF or hnRNP A1 complementary DNAs were transiently overexpressed in HeLa cells, and the effect on alternative splicing of several cotransfected reporter genes was measured. Increased expression of SF2/ASF activated proximal 5' splice sites, promoted inclusion of a neuron-specific exon, and prevented abnormal exon skipping. Increased expression of hnRNP A1 activated distal 5' splice sites. Therefore, variations in the intracellular levels of antagonistic splicing factors influence different modes of alternative splicing in vivo and may be a natural mechanism for tissue-specific or developmental regulation of gene expression.


    CERN Multimedia



    The main developments in muon alignment since March 2010 have been the production, approval and deployment of alignment constants for the ICHEP data reprocessing. In the barrel, a new geometry, combining information from both hardware and track-based alignment systems, has been developed for the first time. The hardware alignment provides an initial DT geometry, which is then anchored as a rigid solid, using the link alignment system, to a reference frame common to the tracker. The “GlobalPositionRecords” for both the Tracker and Muon systems are being used for the first time, and the initial tracker-muon relative positioning, based on the link alignment, yields good results within the photogrammetry uncertainties of the Tracker and alignment ring positions. For the first time, the optical and track-based alignments show good agreement between them; the optical alignment being refined by the track-based alignment. The resulting geometry is the most complete to date, aligning all 250 DTs, ...


    CERN Multimedia

    Z. Szillasi and G. Gomez.


    When CMS is opened up, major components of the Link and Barrel Alignment systems will be removed. This operation, besides allowing for maintenance of the detector underneath, is needed for making interventions that will reinforce the alignment measurements and make the operation of the alignment system more reliable. For that purpose and also for their general maintenance and recalibration, the alignment components will be transferred to the Alignment Lab situated in the ISR area. For the track-based alignment, attention is focused on the determination of systematic uncertainties, which have become dominant, since now there is a large statistics of muon tracks. This will allow for an improved Monte Carlo misalignment scenario and updated alignment position errors, crucial for high-momentum muon analysis such as Z′ searches.

  5. Anti-tumor activity of splice-switching oligonucleotides


    Bauman, John A; Li, Shyh-Dar; Yang, Angela; Huang, Leaf; Kole, Ryszard


    Alternative splicing has emerged as an important target for molecular therapies. Splice-switching oligonucleotides (SSOs) modulate alternative splicing by hybridizing to pre-mRNA sequences involved in splicing and blocking access to the transcript by splicing factors. Recently, the efficacy of SSOs has been established in various animal disease models; however, the application of SSOs against cancer targets has been hindered by poor in vivo delivery of antisense therapeutics to tumor cells. T...

  6. Protein splicing and its evolution in eukaryotes

    Directory of Open Access Journals (Sweden)

    Starokadomskyy P. L.


    Full Text Available Inteins, or protein introns, are parts of protein sequences that are post-translationally excised, their flanking regions (exteins being spliced together. This process was called protein splicing. Originally inteins were found in prokaryotic or unicellular eukaryotic organisms. But the general principles of post-translation protein rearrangement are evolving yielding different post-translation modification of proteins in multicellular organisms. For clarity, these non-intein mediated events call either protein rearrangements or protein editing. The most intriguing example of protein editing is proteasome-mediated splicing of antigens in vertebrates that may play important role in antigen presentation. Other examples of protein rearrangements are maturation of Hg-proteins (critical receptors in embryogenesis as well as maturation of several metabolic enzymes. Despite a lack of experimental data we try to analyze some intriguing examples of protein splicing evolution.

  7. Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array

    Directory of Open Access Journals (Sweden)

    Sugnet Charles


    Full Text Available Abstract Background Alternative splicing is a mechanism for increasing protein diversity by excluding or including exons during post-transcriptional processing. Alternatively spliced proteins are particularly relevant in oncology since they may contribute to the etiology of cancer, provide selective drug targets, or serve as a marker set for cancer diagnosis. While conventional identification of splice variants generally targets individual genes, we present here a new exon-centric array (GeneChip Human Exon 1.0 ST that allows genome-wide identification of differential splice variation, and concurrently provides a flexible and inclusive analysis of gene expression. Results We analyzed 20 paired tumor-normal colon cancer samples using a microarray designed to detect over one million putative exons that can be virtually assembled into potential gene-level transcripts according to various levels of prior supporting evidence. Analysis of high confidence (empirically supported transcripts identified 160 differentially expressed genes, with 42 genes occupying a network impacting cell proliferation and another twenty nine genes with unknown functions. A more speculative analysis, including transcripts based solely on computational prediction, produced another 160 differentially expressed genes, three-fourths of which have no previous annotation. We also present a comparison of gene signal estimations from the Exon 1.0 ST and the U133 Plus 2.0 arrays. Novel splicing events were predicted by experimental algorithms that compare the relative contribution of each exon to the cognate transcript intensity in each tissue. The resulting candidate splice variants were validated with RT-PCR. We found nine genes that were differentially spliced between colon tumors and normal colon tissues, several of which have not been previously implicated in cancer. Top scoring candidates from our analysis were also found to substantially overlap with EST-based bioinformatic

  8. Structural insights into RNA recognition by the alternative-splicing regulator muscleblind-like MBNL1

    Energy Technology Data Exchange (ETDEWEB)

    Teplova, Marianna; Patel, Dinshaw J. (MSKCC)


    Muscleblind-like (MBNL) proteins, regulators of developmentally programmed alternative splicing, harbor tandem CCCH zinc-finger (ZnF) domains that target pre-mRNAs containing YGCU(U/G)Y sequence elements (where Y is a pyrimidine). In myotonic dystrophy, reduced levels of MBNL proteins lead to aberrant alternative splicing of a subset of pre-mRNAs. The crystal structure of MBNL1 ZnF3/4 bound to r(CGCUGU) establishes that both ZnF3 and ZnF4 target GC steps, with site-specific recognition mediated by a network of hydrogen bonds formed primarily with main chain groups of the protein. The relative alignment of ZnF3 and ZnF4 domains is dictated by the topology of the interdomain linker, with a resulting antiparallel orientation of bound GC elements, supportive of a chain-reversal loop trajectory for MBNL1-bound pre-mRNA targets. We anticipate that MBNL1-mediated targeting of looped RNA segments proximal to splice-site junctions could contribute to pre-mRNA alternative-splicing regulation.

  9. Alcoholism and Alternative Splicing of Candidate Genes


    Toshikazu Sasabe; Shoichi Ishiura


    Gene expression studies have shown that expression patterns of several genes have changed during the development of alcoholism. Gene expression is regulated not only at the level of transcription but also through alternative splicing of pre-mRNA. In this review, we discuss some of the evidence suggesting that alternative splicing of candidate genes such as DRD2 (encoding dopamine D2 receptor) may form the basis of the mechanisms underlying the pathophysiology of alcoholism. These reports sugg...

  10. [The role of RNA splicing in the pathogenesis of spinal muscular atrophy and development of its therapeutics]. (United States)

    Sahashi, Kentaro; Sobue, Gen


    Loss-of-function mutations in SMN1 cause spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. Degeneration of alpha-motor neurons that results in progressive paralysis is a pathological hallmark of SMA. Recently, peripheral-tissue involvement has also been reported in SMA. Patients have low levels of functional SMN which is attributed to alternative splicing in SMN2, a gene closely-related to SMN1. This decrease in the expression of SMN, a ubiquitously expressed protein involved in promoting snRNP assembly required for splicing, is responsible for SMA. However, the mechanism through which decrease in SMN levels causes SMA remains unclear. Currently, no curative treatment is available for SMA, but SMN restoration is thought to be necessary and sufficient for cure. Antisense oligonucleotides (ASOs) can be designed to specifically alter splicing patterns of target pre-mRNAs. We identified an ASO that redirects SMN2 splicing and is currently in clinical trials for use as RNA-targeting therapeutics. Further, we have also reported a novel application of splicing-modulating ASOs--creation of animal phenocopy models of diseases by inducing mis-splicing. Exploring the relationship between the spatial and temporal effects of therapeutic and pathogenic ASOs yields relevant insights into the roles of SMN in SMA pathogenesis and into its normal physiological functions. This knowledge, in turn, contributes to the ongoing development of targeted therapeutics.

  11. Targeting RNA-splicing for SMA treatment. (United States)

    Zhou, Jianhua; Zheng, Xuexiu; Shen, Haihong


    The central dogma of DNA-RNA-protein was established more than 40 years ago. However, important biological processes have been identified since the central dogma was developed. For example, methylation is important in the regulation of transcription. In contrast, proteins, are more complex due to modifications such as phosphorylation, glycosylation, ubiquitination, or cleavage. RNA is the mediator between DNA and protein, but it can also be modulated at several levels. Among the most profound discoveries of RNA regulation is RNA splicing. It has been estimated that 80% of pre-mRNA undergo alternative splicing, which exponentially increases biological information flow in cellular processes. However, an increased number of regulated steps inevitably accompanies an increased number of errors. Abnormal splicing is often found in cells, resulting in protein dysfunction that causes disease. Splicing of the survival motor neuron (SMN) gene has been extensively studied during the last two decades. Accumulating knowledge on SMN splicing has led to speculation and search for spinal muscular atrophy (SMA) treatment by stimulating the inclusion of exon 7 into SMN mRNA. This mini-review summaries the latest progress on SMN splicing research as a potential treatment for SMA disease.

  12. Antisense oligonucleotide-induced alternative splicing of the APOB mRNA generates a novel isoform of APOB

    Directory of Open Access Journals (Sweden)

    Chew Shern L


    Full Text Available Abstract Background Apolipoprotein B (APOB is an integral part of the LDL, VLDL, IDL, Lp(a and chylomicron lipoprotein particles. The APOB pre-mRNA consists of 29 constitutively-spliced exons. APOB exists as two natural isoforms: the full-length APOB100 isoform, assembled into LDL, VLDL, IDL and Lp(a and secreted by the liver in humans; and the C-terminally truncated APOB48, assembled into chylomicrons and secreted by the intestine in humans. Down-regulation of APOB100 is a potential therapy to lower circulating LDL and cholesterol levels. Results We investigated the ability of 2'O-methyl RNA antisense oligonucleotides (ASOs to induce the skipping of exon 27 in endogenous APOB mRNA in HepG2 cells. These ASOs are directed towards the 5' and 3' splice-sites of exon 27, the branch-point sequence (BPS of intron 26–27 and several predicted exonic splicing enhancers within exon 27. ASOs targeting either the 5' or 3' splice-site, in combination with the BPS, are the most effective. The splicing of other alternatively spliced genes are not influenced by these ASOs, suggesting that the effects seen are not due to non-specific changes in alternative splicing. The skip 27 mRNA is translated into a truncated isoform, APOB87SKIP27. Conclusion The induction of APOB87SKIP27 expression in vivo should lead to decreased LDL and cholesterol levels, by analogy to patients with hypobetalipoproteinemia. As intestinal APOB mRNA editing and APOB48 expression rely on sequences within exon 26, exon 27 skipping should not affect APOB48 expression unlike other methods of down-regulating APOB100 expression which also down-regulate APOB48.

  13. Ontology alignment with OLA


    Euzenat, Jérôme; Loup, David; Touzani, Mohamed; Valtchev, Petko


    euzenat2004d; International audience; Using ontologies is the standard way to achieve interoperability of heterogeneous systems within the Semantic web. However, as the ontologies underlying two systems are not necessarily compatible, they may in turn need to be aligned. Similarity-based approaches to alignment seems to be both powerful and flexible enough to match the expressive power of languages like OWL. We present an alignment tool that follows the similarity-based paradigm, called OLA. ...


    CERN Multimedia



    Most of the work in muon alignment since December 2009 has focused on the geometry reconstruction from the optical systems and improvements in the internal alignment of the DT chambers. The barrel optical alignment system has progressively evolved from reconstruction of single active planes to super-planes (December 09) to a new, full barrel reconstruction. Initial validation studies comparing this full barrel alignment at 0T with photogrammetry provide promising results. In addition, the method has been applied to CRAFT09 data, and the resulting alignment at 3.8T yields residuals from tracks (extrapolated from the tracker) which look smooth, suggesting a good internal barrel alignment with a small overall offset with respect to the tracker. This is a significant improvement, which should allow the optical system to provide a start-up alignment for 2010. The end-cap optical alignment has made considerable progress in the analysis of transfer line data. The next set of alignment constants for CSCs will there...

  15. Results from Tests of the Muon Endcap Alignment System in the H8 Beam Line 2002

    CERN Document Server

    Amelung, C; Cerutti, F; Handrich, K; Hashemi, K S; Mair, K; Palestini, S; Rothberg, J E; Schricker, A; Trigger, I


    The ATLAS muon spectrometer endcap test setup assembled in the H8 beam line at CERN in 2002 consisted of six alignment bars and six MDT chambers, representing part of one octant of the endcap. These elements were equipped with a full set of alignment sensors, which were used to obtain a first appraisal of the performance of the alignment system.

  16. Alignments between galaxies, satellite systems and haloes

    CERN Document Server

    Shao, Shi; Frenk, Carlos S; Gao, Liang; Crain, Robert A; Schaller, Matthieu; Schaye, Joop; Theuns, Tom


    The spatial distribution of the satellite populations of the Milky Way and Andromeda are puzzling in that they are nearly perpendicular to the disks of their central galaxies. To understand the origin of such configurations we study the alignment of the central galaxy, satellite system and dark matter halo in the largest of the "Evolution and Assembly of GaLaxies and their Environments" (EAGLE) simulation. We find that centrals and their satellite systems tend to be well aligned with their haloes, with a median misalignment angle of $33^{\\circ}$ in both cases. While the centrals are better aligned with the inner $10$ kpc halo, the satellite systems are better aligned with the entire halo indicating that satellites preferentially trace the outer halo. The central - satellite alignment is weak (median misalignment angle of $52^{\\circ}$) and we find that around $20\\%$ of systems have a misalignment angle larger than $78^{\\circ}$, which is the value for the Milky Way. The central - satellite alignment is a conseq...

  17. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. (United States)

    Hoffmann, Steve; Otto, Christian; Doose, Gero; Tanzer, Andrea; Langenberger, David; Christ, Sabina; Kunz, Manfred; Holdt, Lesca M; Teupser, Daniel; Hackermüller, Jörg; Stadler, Peter F


    Numerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization or trans-splicing are often neglected. We introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, our approach accommodates multi-junction structures. Our method compares favorably with competing tools for conventionally spliced mRNAs and, with a gain of up to 40% of recall, systematically outperforms them on reads with multiple splits, trans-splicing and circular products. The algorithm is integrated into our mapping tool segemehl (

  18. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. (United States)

    Xiong, Hui Y; Alipanahi, Babak; Lee, Leo J; Bretschneider, Hannes; Merico, Daniele; Yuen, Ryan K C; Hua, Yimin; Gueroussov, Serge; Najafabadi, Hamed S; Hughes, Timothy R; Morris, Quaid; Barash, Yoseph; Krainer, Adrian R; Jojic, Nebojsa; Scherer, Stephen W; Blencowe, Benjamin J; Frey, Brendan J


    To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affect RNA splicing, whose alteration contributes to many diseases. Analysis of more than 650,000 intronic and exonic variants revealed widespread patterns of mutation-driven aberrant splicing. Intronic disease mutations that are more than 30 nucleotides from any splice site alter splicing nine times as often as common variants, and missense exonic disease mutations that have the least impact on protein function are five times as likely as others to alter splicing. We detected tens of thousands of disease-causing mutations, including those involved in cancers and spinal muscular atrophy. Examination of intronic and exonic variants found using whole-genome sequencing of individuals with autism revealed misspliced genes with neurodevelopmental phenotypes. Our approach provides evidence for causal variants and should enable new discoveries in precision medicine.

  19. BRCA1 Exon 11, a CERES (Composite Regulatory Element of Splicing Element Involved in Splice Regulation

    Directory of Open Access Journals (Sweden)

    Claudia Tammaro


    Full Text Available Unclassified variants (UV of BRCA1 can affect normal pre-mRNA splicing. Here, we investigate the UV c.693G>A, a “silent” change in BRCA1 exon 11, which we have found induces aberrant splicing in patient carriers and in vitro. Using a minigene assay, we show that the UV c.693G>A has a strong effect on the splicing isoform ratio of BRCA1. Systematic site-directed mutagenesis of the area surrounding the nucleotide position c.693G>A induced variable changes in the level of exon 11 inclusion/exclusion in the mRNA, pointing to the presence of a complex regulatory element with overlapping enhancer and silencer functions. Accordingly, protein binding analysis in the region detected several splicing regulatory factors involved, including SRSF1, SRSF6 and SRSF9, suggesting that this sequence represents a composite regulatory element of splicing (CERES.

  20. Vitamin D and alternative splicing of RNA. (United States)

    Zhou, Rui; Chun, Rene F; Lisse, Thomas S; Garcia, Alejandro J; Xu, Jianzhong; Adams, John S; Hewison, Martin


    The active form of vitamin D (1α,25-dihydroxyvitamin D, 1,25(OH)2D) exerts its genomic effects via binding to a nuclear high-affinity vitamin D receptor (VDR). Recent deep sequencing analysis of VDR binding locations across the complete genome has significantly expanded our understanding of the actions of vitamin D and VDR on gene transcription. However, these studies have also promoted appreciation of the extra-transcriptional impact of vitamin D on gene expression. It is now clear that vitamin D interacts with the epigenome via effects on DNA methylation, histone acetylation, and microRNA generation to maintain normal biological functions. There is also increasing evidence that vitamin D can influence pre-mRNA constitutive splicing and alternative splicing, although the mechanism for this remains unclear. Pre-mRNA splicing has long been thought to be a post-transcription RNA processing event, but current data indicate that this occurs co-transcriptionally. Several steroid hormones have been recognized to coordinately control gene transcription and pre-mRNA splicing through the recruitment of nuclear receptor co-regulators that can both control gene transcription and splicing. The current review will discuss this concept with specific reference to vitamin D, and the potential role of heterogeneous nuclear ribonucleoprotein C (hnRNPC), a nuclear factor with an established function in RNA splicing. hnRNPC, has been shown to be involved in the VDR transcriptional complex as a vitamin D-response element-binding protein (VDRE-BP), and may act as a coupling factor linking VDR-directed gene transcription with RNA splicing. In this way hnRNPC may provide an additional mechanism for the fine-tuning of vitamin D-regulated target gene expression. This article is part of a Special Issue entitled '17th Vitamin D Workshop'.

  1. Differential splicing using whole-transcript microarrays

    Directory of Open Access Journals (Sweden)

    Robinson Mark D


    Full Text Available Abstract Background The latest generation of Affymetrix microarrays are designed to interrogate expression over the entire length of every locus, thus giving the opportunity to study alternative splicing genome-wide. The Exon 1.0 ST (sense target platform, with versions for Human, Mouse and Rat, is designed primarily to probe every known or predicted exon. The smaller Gene 1.0 ST array is designed as an expression microarray but still interrogates expression with probes along the full length of each well-characterized transcript. We explore the possibility of using the Gene 1.0 ST platform to identify differential splicing events. Results We propose a strategy to score differential splicing by using the auxiliary information from fitting the statistical model, RMA (robust multichip analysis. RMA partitions the probe-level data into probe effects and expression levels, operating robustly so that if a small number of probes behave differently than the rest, they are downweighted in the fitting step. We argue that adjacent poorly fitting probes for a given sample can be evidence of differential splicing and have designed a statistic to search for this behaviour. Using a public tissue panel dataset, we show many examples of tissue-specific alternative splicing. Furthermore, we show that evidence for putative alternative splicing has a strong correspondence between the Gene 1.0 ST and Exon 1.0 ST platforms. Conclusion We propose a new approach, FIRMAGene, to search for differentially spliced genes using the Gene 1.0 ST platform. Such an analysis complements the search for differential expression. We validate the method by illustrating several known examples and we note some of the challenges in interpreting the probe-level data. Software implementing our methods is freely available as an R package.

  2. Modulation of 5' splice site selection using tailed oligonucleotides carrying splicing signals

    Directory of Open Access Journals (Sweden)

    Elela Sherif


    Full Text Available Abstract Background We previously described the use of tailed oligonucleotides as a means of reprogramming alternative pre-mRNA splicing in vitro and in vivo. The tailed oligonucleotides that were used interfere with splicing because they contain a portion complementary to sequences immediately upstream of the target 5' splice site combined with a non-hybridizing 5' tail carrying binding sites for the hnRNP A1/A2 proteins. In the present study, we have tested the inhibitory activity of RNA oligonucleotides carrying different tail structures. Results We show that an oligonucleotide with a 5' tail containing the human β-globin branch site sequence inhibits the use of the 5' splice site of Bcl-xL, albeit less efficiently than a tail containing binding sites for the hnRNP A1/A2 proteins. A branch site-containing tail positioned at the 3' end of the oligonucleotide also elicited splicing inhibition but not as efficiently as a 5' tail. The interfering activity of a 3' tail was improved by adding a 5' splice site sequence next to the branch site sequence. A 3' tail carrying a Y-shaped branch structure promoted similar splicing interference. The inclusion of branch site or 5' splice site sequences in the Y-shaped 3' tail further improved splicing inhibition. Conclusion Our in vitro results indicate that a variety of tail architectures can be used to elicit splicing interference at low nanomolar concentrations, thereby broadening the scope and the potential impact of this antisense technology.

  3. Human 5–HT4 and 5–HT7 Receptor Splice Variants: Are they Important?


    Coupar, Ian M; Desmond, Paul V; Irving, Helen R.


    G-protein-coupled receptors (GPCRs), which are encoded by >300 genes in the human genome, are by far the largest class of targets for modern drugs. These macromolecules display inherent adaptability of function, which is partly due to the production of different forms of the receptor protein. These are commonly called ‘isoforms’ or ‘splice variants’ denoting the molecular process of their production/assembly. Not all GPCRs are expressed as splice variants, but certain subclasses of 5–HT recep...


    CERN Multimedia



    The Muon Alignment work now focuses on producing a new track-based alignment with higher track statistics, making systematic studies between the results of the hardware and track-based alignment methods and aligning the barrel using standalone muon tracks. Currently, the muon track reconstruction software uses a hardware-based alignment in the barrel (DT) and a track-based alignment in the endcaps (CSC). An important task is to assess the muon momentum resolution that can be achieved using the current muon alignment, especially for highly energetic muons. For this purpose, cosmic ray muons are used, since the rate of high-energy muons from collisions is very low and the event statistics are still limited. Cosmics have the advantage of higher statistics in the pT region above 100 GeV/c, but they have the disadvantage of having a mostly vertical topology, resulting in a very few global endcap muons. Only the barrel alignment has therefore been tested so far. Cosmic muons traversing CMS from top to bottom are s...


    CERN Multimedia

    Gervasio Gomez

    The main progress of the muon alignment group since March has been in the refinement of both the track-based alignment for the DTs and the hardware-based alignment for the CSCs. For DT track-based alignment, there has been significant improvement in the internal alignment of the superlayers inside the DTs. In particular, the distance between superlayers is now corrected, eliminating the residual dependence on track impact angles, and good agreement is found between survey and track-based corrections. The new internal geometry has been approved to be included in the forthcoming reprocessing of CRAFT samples. The alignment of DTs with respect to the tracker using global tracks has also improved significantly, since the algorithms use the latest B-field mapping, better run selection criteria, optimized momentum cuts, and an alignment is now obtained for all six degrees of freedom (three spatial coordinates and three rotations) of the aligned DTs. This work is ongoing and at a stage where we are trying to unders...


    CERN Multimedia

    G. Gomez

    Since December, the muon alignment community has focused on analyzing the data recorded so far in order to produce new DT and CSC Alignment Records for the second reprocessing of CRAFT data. Two independent algorithms were developed which align the DT chambers using global tracks, thus providing, for the first time, a relative alignment of the barrel with respect to the tracker. These results are an important ingredient for the second CRAFT reprocessing and allow, for example, a more detailed study of any possible mis-modelling of the magnetic field in the muon spectrometer. Both algorithms are constructed in such a way that the resulting alignment constants are not affected, to first order, by any such mis-modelling. The CSC chambers have not yet been included in this global track-based alignment due to a lack of statistics, since only a few cosmics go through the tracker and the CSCs. A strategy exists to align the CSCs using the barrel as a reference until collision tracks become available. Aligning the ...

  7. Mapping Quantitative Trait Loci (QTL in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL

    Directory of Open Access Journals (Sweden)

    Thomson Peter C


    Full Text Available Abstract An (Awassi × Merino × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1 and 3.5 (cohort 2 years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3, 15 significant (LOD ≥ 2, and 11 suggestive QTL (1.7 ≤ LOD P P A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

  8. SPEAR3 Construction Alignment

    Energy Technology Data Exchange (ETDEWEB)

    LeCocq, Catherine; Banuelos, Cristobal; Fuss, Brian; Gaudreault, Francis; Gaydosh, Michael; Griffin, Levirt; Imfeld, Hans; McDougal, John; Perry, Michael; Rogers,; /SLAC


    An ambitious seven month shutdown of the existing SPEAR2 synchrotron radiation facility was successfully completed in March 2004 when the first synchrotron light was observed in the new SPEAR3 ring, SPEAR3 completely replaced SPEAR2 with new components aligned on a new highly-flat concrete floor. Devices such as magnets and vacuum chambers had to be fiducialized and later aligned on girder rafts that were then placed into the ring over pre-aligned support plates. Key to the success of aligning this new ring was to ensure that the new beam orbit matched the old SPEAR2 orbit so that existing experimental beamlines would not have to be reoriented. In this presentation a pictorial summary of the Alignment Engineering Group's surveying tasks for the construction of the SPEAR3 ring is provided. Details on the networking and analysis of various surveys throughout the project can be found in the accompanying paper.


    CERN Multimedia

    G. Gomez


    A new set of muon alignment constants was approved in August. The relative position between muon chambers is essentially unchanged, indicating good detector stability. The main changes concern the global positioning of the barrel and of the endcap rings to match the new Tracker geometry. Detailed studies of the differences between track-based and optical alignment of DTs have proven to be a valuable tool for constraining Tracker alignment weak modes, and this information is now being used as part of the alignment procedure. In addition to the “split-cosmic” analysis used to investigate the muon momentum resolution at high momentum, a new procedure based on reconstructing the invariant mass of di-muons from boosted Zs is under development. Both procedures show an improvement in the momentum precision of Global Muons with respect to Tracker-only Muons. Recent developments in track-based alignment include a better treatment of the tails of residual distributions and accounting for correla...

  10. Physics of Grain Alignment

    CERN Document Server

    Lazarian, A


    Aligned grains provide one of the easiest ways to study magnetic fields in diffuse gas and molecular clouds. How reliable our conclusions about the inferred magnetic field depends critically on our understanding of the physics of grain alignment. Although grain alignment is a problem of half a century standing recent progress achieved in the field makes us believe that we are approaching the solution of this mystery. I review basic physical processes involved in grain alignment and show why mechanisms that were favored for decades do not look so promising right now. I also discuss why the radiative torque mechanism ignored for more than 20 years looks right now the most powerful means of grain alignment.

  11. Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence

    Directory of Open Access Journals (Sweden)

    Kim Dong Seon


    Full Text Available Abstract Background Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to protein products. Here, we analyzed annotated human protein-coding exons and identified human-specific splice sites that arose after the human-chimpanzee divergence. Results We analyzed multiple alignments of the annotated human protein-coding exons and their respective orthologous mammalian genome sequences to identify 85 novel splice sites (50 splice acceptors and 35 donors in the human genome. The novel protein-coding exons, which are expressed either constitutively or alternatively, produce novel protein isoforms by insertion, deletion, or frameshift. We found three cases in which the human-specific isoform conferred novel molecular function in the human cells: the human-specific IMUP protein isoform induces apoptosis of the trophoblast and is implicated in pre-eclampsia; the intronization of a part of SMOX gene exon produces inactive spermine oxidase; the human-specific NUB1 isoform shows reduced interaction with ubiquitin-like proteins, possibly affecting ubiquitin pathways. Conclusions Although the generation of novel protein isoforms does not equate to adaptive evolution, we propose that these cases are useful candidates for a molecular functional study to identify proteomic changes that might bring about novel phenotypes during human evolution.

  12. Discovery of Novel Splice Variants and Regulatory Mechanisms for Microsomal Triglyceride Transfer Protein in Human Tissues (United States)

    Suzuki, Takashi; Swift, Larry L.


    Microsomal triglyceride transfer protein (MTP) is a unique lipid transfer protein essential for the assembly of triglyceride-rich lipoproteins by the liver and intestine. Previous studies in mice identified a splice variant of MTP with an alternate first exon. Splice variants of human MTP have not been reported. Using PCR approaches we have identified two splice variants in human tissues, which we have named MTP-B and MTP-C. MTP-B has a unique first exon (Ex1B) located 10.5 kb upstream of the first exon (Ex1A) for canonical MTP (MTP-A); MTP-C contains both first exons for MTP-A and MTP-B. MTP-B was found in a number of tissues, whereas MTP-C was prominent in brain and testis. MTP-B does not encode a protein; MTP-C encodes the same protein encoded by MTP-A, although MTP-C translation is strongly inhibited by regulatory elements within its 5′-UTR. Using luciferase assays, we demonstrate that the promoter region upstream of exon 1B is quite adequate to drive expression of MTP. We conclude that alternate splicing plays a key role in regulating cellular MTP levels by introducing distinct promoter regions and unique 5′-UTRs, which contain elements that alter translation efficiency, enabling the cell to optimize MTP activity. PMID:27256115

  13. Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging. (United States)

    Rodríguez, Sofía A; Grochová, Diana; McKenna, Tomás; Borate, Bhavesh; Trivedi, Niraj S; Erdos, Michael R; Eriksson, Maria


    Alternative splicing (AS) is a key regulatory mechanism for the development of different tissues; however, not much is known about changes to alternative splicing during aging. Splicing events may become more frequent and widespread genome-wide as tissues age and the splicing machinery stringency decreases. Using skin, skeletal muscle, bone, thymus, and white adipose tissue from wild-type C57BL6/J male mice (4 and 18 months old), we examined the effect of age on splicing by AS analysis of the differential exon usage of the genome. The results identified a considerable number of AS genes in skeletal muscle, thymus, bone, and white adipose tissue between the different age groups (ranging from 27 to 246 AS genes corresponding to 0.3-3.2% of the total number of genes analyzed). For skin, skeletal muscle, and bone, we included a later age group (28 months old) that showed that the number of alternatively spliced genes increased with age in all three tissues (P aging disease Hutchinson-Gilford progeria syndrome was performed. The results show that expression of the mutant protein, progerin, is associated with an impaired developmental splicing. As progerin accumulates, the number of genes with AS increases compared to in wild-type skin. Our results indicate the existence of a mechanism for increased AS during aging in several tissues, emphasizing that AS has a more important role in the aging process than previously known.

  14. Nuclearly encoded splicing factors implicated in RNA splicing in higher plant organelles. (United States)

    de Longevialle, Andéol Falcon; Small, Ian D; Lurin, Claire


    Plant organelles arose from two independent endosymbiosis events. Throughout evolutionary history, tight control of chloroplasts and mitochondria has been gained by the nucleus, which regulates most steps of organelle genome expression and metabolism. In particular, RNA maturation, including RNA splicing, is highly dependent on nuclearly encoded splicing factors. Most introns in organelles are group II introns, whose catalytic mechanism closely resembles that of the nuclear spliceosome. Plant group II introns have lost the ability to self-splice in vivo and require nuclearly encoded proteins as cofactors. Since the first splicing factor was identified in chloroplasts more than 10 years ago, many other proteins have been shown to be involved in splicing of one or more introns in chloroplasts or mitochondria. These new proteins belong to a variety of different families of RNA binding proteins and provide new insights into ribonucleo-protein complexes and RNA splicing machineries in organelles. In this review, we describe how splicing factors, encoded by the nucleus and targeted to the organelles, take part in post-transcriptional steps in higher plant organelle gene expression. We go on to discuss the potential for these factors to regulate organelle gene expression.

  15. Prp4 Kinase Grants the License to Splice: Control of Weak Splice Sites during Spliceosome Activation.

    Directory of Open Access Journals (Sweden)

    Daniela Eckert


    Full Text Available The genome of the fission yeast Schizosaccharomyces pombe encodes 17 kinases that are essential for cell growth. These include the cell-cycle regulator Cdc2, as well as several kinases that coordinate cell growth, polarity, and morphogenesis during the cell cycle. In this study, we further characterized another of these essential kinases, Prp4, and showed that the splicing of many introns is dependent on Prp4 kinase activity. For detailed characterization, we chose the genes res1 and ppk8, each of which contains one intron of typical size and position. Splicing of the res1 intron was dependent on Prp4 kinase activity, whereas splicing of the ppk8 intron was not. Extensive mutational analyses of the 5' splice site of both genes revealed that proper transient interaction with the 5' end of snRNA U1 governs the dependence of splicing on Prp4 kinase activity. Proper transient interaction between the branch sequence and snRNA U2 was also important. Therefore, the Prp4 kinase is required for recognition and efficient splicing of introns displaying weak exon1/5' splice sites and weak branch sequences.

  16. Nearly complete rRNA genes assembled from across the metazoan animals: effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction. (United States)

    Mallatt, Jon; Craig, Catherine Waggoner; Yoder, Matthew J


    This study (1) uses nearly complete rRNA-gene sequences from across Metazoa (197 taxa) to reconstruct animal phylogeny; (2) presents a highly annotated, manual alignment of these sequences with special reference to rRNA features including paired sites ( and (3) tests, after eliminating as few disruptive, rogue sequences as possible, if a likelihood framework can recover the main metazoan clades. We found that systematic elimination of approximately 6% of the sequences, including the divergent or unstably placed sequences of cephalopods, arrowworm, symphylan and pauropod myriapods, and of myzostomid and nemertodermatid worms, led to a tree that supported Ecdysozoa, Lophotrochozoa, Protostomia, and Bilateria. Deuterostomia, however, was never recovered, because the rRNA of urochordates goes (nonsignificantly) near the base of the Bilateria. Counterintuitively, when we modeled the evolution of the paired sites, phylogenetic resolution was not increased over traditional tree-building models that assume all sites in rRNA evolve independently. The rRNA genes of non-bilaterians contain a higher % AT than do those of most bilaterians. The rRNA genes of Acoela and Myzostomida were found to be secondarily shortened, AT-enriched, and highly modified, throwing some doubt on the location of these worms at the base of Bilateria in the rRNA tree--especially myzostomids, which other evidence suggests are annelids instead. Other findings are marsupial-with-placental mammals, arrowworms in Ecdysozoa (well supported here but contradicted by morphology), and Placozoa as sister to Cnidaria. Finally, despite the difficulties, the rRNA-gene trees are in strong concordance with trees derived from multiple protein-coding genes in supporting the new animal phylogeny.

  17. Splicing variants of porcine synphilin-1

    DEFF Research Database (Denmark)

    Larsen, Knud Erik; Madsen, Lone Bruhn; Farajzadeh, Leila;


    %) and to mouse (84%) synphilin-1. Three shorter transcript variants of the synphilin-1 gene were identified, all lacking one or more exons. SNCAIP transcripts were detected in most examined organs and tissues and the highest expression was found in brain tissues and lung. Conserved splicing variants and a novel......RNA was investigated by RNAseq. The presented work reports the molecular cloning and characterization of the porcine (Sus scrofa) synphilin-1 cDNA (SNCAIP) and three splice variants hereof. The porcine SNCAIP cDNA codes for a protein (synphilin-1) of 919 amino acids which shows a high similarity to human (90...... splice form of synhilin-1 were found in this study. All synphilin-1 isoforms encoded by the identified transcript variants lack functional domains important for protein degradation....

  18. Altered PLP1 splicing causes hypomyelination of early myelinating structures

    DEFF Research Database (Denmark)

    Kevelam, Sietske H; Taube, Jennifer R; van Spaendonk, Rosalina M L


    : All patients had unusual hemizygous mutations of PLP1 located in exon 3B (one deletion, one missense and two silent), which is spliced out in isoform DM20, or in intron 3 (five mutations). The deletion led to truncation of PLP1, but not DM20. Four mutations were predicted to affect PLP1/DM20...... for causal mutations. In silico analysis of effects of the mutations on splicing and RNA folding was performed. In vitro gene splicing was examined in RNA from patients' fibroblasts and an immortalized immature oligodendrocyte cell line after transfection with mutant minigene splicing constructs. RESULTS...... alternative splicing by creating exonic splicing silencer motifs or new splice donor sites or by affecting the local RNA structure of the PLP1 splice donor site. Four deep intronic mutations were predicted to destabilize a long-distance interaction structure in the secondary PLP1 RNA fragment involved...

  19. A study of alternative splicing in the pig

    DEFF Research Database (Denmark)

    Hillig, Ann-Britt Nygaard; Cirera Salicio, Susanna; Gilchrist, Michael J.;


    BACKGROUND: Since at least half of the genes in mammalian genomes are subjected to alternative splicing, alternative pre-mRNA splicing plays an important contribution to the complexity of the mammalian proteome. Expressed sequence tags (ESTs) provide evidence of a great number of possible...... and mouse, we find putative splice variants in about 30% of the contigs with more than 50 ESTs. Based on the criteria that a minimum of two EST sequences confirmed each splice event, a list of 100 genes with the most distinct tissue-specific alternative splice events was generated from the list...... of candidates. To confirm the tissue specificity of the splice events, 10 genes with functional annotation were randomly selected from which 16 individual splice events were chosen for experimental verification by quantitative PCR (qPCR). Six genes were shown to have tissue specific alternatively spliced...

  20. Regulation of mammalian pre-mRNA splicing

    Institute of Scientific and Technical Information of China (English)

    HUI JingYi


    In eukaryotes, most protein-coding genes contain introns which are removed by precursor messenger RNA (pre-mRNA) splicing. Alternative splicing is a process by which multiple messenger RNAs (mRNAs) are generated from a single pre-mRNA, resulting in functionally distinct proteins. Recent genome-wide analyses of alternative splicing indicated that in higher eukaryotes alternative splicing is an important mechanism that generates proteomic complexity and regulates gene expression. Mis-regulation of splicing causes a wide range of human diseases. This review describes the current understanding of pre-mRNA splicing and the mechanisms that regulate mammalian pre-mRNA splicing. It also discusses emerging directions in the field of alternative splicing.

  1. Regulation of mammalian pre-mRNA splicing

    Institute of Scientific and Technical Information of China (English)


    In eukaryotes,most protein-coding genes contain introns which are removed by precursor messenger RNA(pre-mRNA) splicing.Alternative splicing is a process by which multiple messenger RNAs(mRNAs) are generated from a single pre-mRNA,resulting in functionally distinct proteins.Recent genome-wide analyses of alternative splicing indicated that in higher eukaryotes alternative splicing is an important mechanism that generates proteomic complexity and regulates gene expression.Mis-regulation of splicing causes a wide range of human diseases.This review describes the current understanding of pre-mRNA splicing and the mechanisms that regulate mammalian pre-mRNA splicing.It also discusses emerging directions in the field of alternative splicing.

  2. Widespread evolutionary conservation of alternatively spliced exons in caenorhabditis

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob L; Penny, David


    Alternative splicing (AS) contributes to increased transcriptome and proteome diversity in various eukaryotic lineages. Previous studies showed low levels of conservation of alternatively spliced (cassette) exons within mammals and within dipterans. We report a strikingly different pattern...

  3. Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL. (United States)

    Cavanagh, Colin R; Jonas, Elisabeth; Hobbs, Matthew; Thomson, Peter C; Tammen, Imke; Raadsma, Herman W


    An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.

  4. Galaxy alignments: An overview

    CERN Document Server

    Joachimi, Benjamin; Kitching, Thomas D; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Hoekstra, Henk; Kiessling, Alina; Kirk, Donnacha; Rassat, Anais


    The alignments between galaxies, their underlying matter structures, and the cosmic web constitute vital ingredients for a comprehensive understanding of gravity, the nature of matter, and structure formation in the Universe. We provide an overview on the state of the art in the study of these alignment processes and their observational signatures, aimed at a non-specialist audience. The development of the field over the past one hundred years is briefly reviewed. We also discuss the impact of galaxy alignments on measurements of weak gravitational lensing, and discuss avenues for making theoretical and observational progress over the coming decade.

  5. Discriminative Shape Alignment

    DEFF Research Database (Denmark)

    Loog, M.; de Bruijne, M.


    The alignment of shape data to a common mean before its subsequent processing is an ubiquitous step within the area shape analysis. Current approaches to shape analysis or, as more specifically considered in this work, shape classification perform the alignment in a fully unsupervised way......, not taking into account that eventually the shapes are to be assigned to two or more different classes. This work introduces a discriminative variation to well-known Procrustes alignment and demonstrates its benefit over this classical method in shape classification tasks. The focus is on two......-dimensional shapes from a two-class recognition problem....

  6. Modulation of RNA splicing as a potential treatment for cancer


    Bauman, John A; Kole, Ryszard


    Close to 90% of human genes are transcribed into pre-mRNA that undergoes alternative splicing, producing multiple mRNAs and proteins from single genes. This process is largely responsible for human proteome diversity, and about half of genetic disease-causing mutations affect splicing. Splice-switching oligonucleotides (SSOs) comprise an emerging class of antisense therapeutics that modify gene expression by directing pre-mRNA splice site usage. Bauman et al. investigated an SSO that upregula...

  7. Kaposi's sarcoma-associated herpesvirus ORF57 functions as a viral splicing factor and promotes expression of intron-containing viral lytic genes in spliceosome-mediated RNA splicing. (United States)

    Majerciak, Vladimir; Yamanegi, Koji; Allemand, Eric; Kruhlak, Michael; Krainer, Adrian R; Zheng, Zhi-Ming


    Kaposi's sarcoma-associated herpesvirus (KSHV) ORF57 facilitates the expression of both intronless viral ORF59 genes and intron-containing viral K8 and K8.1 genes (V. Majerciak, N. Pripuzova, J. P. McCoy, S. J. Gao, and Z. M. Zheng, J. Virol. 81:1062-1071, 2007). In this study, we showed that disruption of ORF57 in a KSHV genome led to increased accumulation of ORF50 and K8 pre-mRNAs and reduced expression of ORF50 and K-bZIP proteins but had no effect on latency-associated nuclear antigen (LANA). Cotransfection of ORF57 and K8beta cDNA, which retains a suboptimal intron of K8 pre-mRNA due to alternative splicing, promoted RNA splicing of K8beta and production of K8alpha (K-bZIP). Although Epstein-Barr virus EB2, a closely related homolog of ORF57, had a similar activity in the cotransfection assays, herpes simplex virus type 1 ICP27 was inactive. This enhancement of RNA splicing by ORF57 correlates with the intact N-terminal nuclear localization signal motifs of ORF57 and takes place in the absence of other viral proteins. In activated KSHV-infected B cells, KSHV ORF57 partially colocalizes with splicing factors in nuclear speckles and assembles into spliceosomal complexes in association with low-abundance viral ORF50 and K8 pre-mRNAs and essential splicing components. The association of ORF57 with snRNAs occurs by ORF57-Sm protein interaction. We also found that ORF57 binds K8beta pre-mRNAs in vitro in the presence of nuclear extracts. Collectively our data indicate that KSHV ORF57 functions as a novel splicing factor in the spliceosome-mediated splicing of viral RNA transcripts.

  8. Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob Lewin; Penny, David;


    Alternative splicing has been reported in various eukaryotic groups including plants, apicomplexans, diatoms, amoebae, animals and fungi. However, whether widespread alternative splicing has evolved independently in the different eukaryotic groups or was inherited from their last common ancestor...

  9. The implications of alternative splicing in the ENCODE protein complement

    DEFF Research Database (Denmark)

    Tress, Michael L.; Martelli, Pier Luigi; Frankish, Adam;


    Alternative premessenger RNA splicing enables genes to generate more than one gene product. Splicing events that occur within protein coding regions have the potential to alter the biological function of the expressed protein and even to create new protein functions. Alternative splicing has been...

  10. 46 CFR 111.60-19 - Cable splices. (United States)


    ... with section 25.11 of IEEE 45-2002 (incorporated by reference; see 46 CFR 110.10-1). ... 46 Shipping 4 2010-10-01 2010-10-01 false Cable splices. 111.60-19 Section 111.60-19 Shipping... REQUIREMENTS Wiring Materials and Methods § 111.60-19 Cable splices. (a) A cable must not be spliced in...

  11. 30 CFR 75.603 - Temporary splice of trailing cable. (United States)


    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Temporary splice of trailing cable. 75.603... SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Trailing Cables § 75.603 Temporary splice of trailing cable. One temporary splice may be made in any trailing cable. Such trailing cable...

  12. Integrated magnetic transformer assembly

    DEFF Research Database (Denmark)


    The present invention relates to an integrated magnetics transformer assembly comprising a first magnetically permeable core forming a first substantially closed magnetic flux path and a second magnetically permeable core forming a second substantially closed magnetic flux path. A first input...... inductor winding is wound around a first predetermined segment of the first magnetically permeable core and a second input inductor winding is wound around a first predetermined segment of the second magnetically permeable core. The integrated magnetics transformer assembly further comprises a first output......-winding of the first output inductor winding and the first half-winding of the second output inductor winding are configured to produce aligned, i.e. in the same direction, magnetic fluxes through the first substantially closed magnetic flux path. The integrated magnetics transformer assembly is well- suited for use...


    CERN Multimedia


    Since September, the muon alignment system shifted from a mode of hardware installation and commissioning to operation and data taking. All three optical subsystems (Barrel, Endcap and Link alignment) have recorded data before, during and after CRAFT, at different magnetic fields and during ramps of the magnet. This first data taking experience has several interesting goals: •    study detector deformations and movements under the influence of the huge magnetic forces; •    study the stability of detector structures and of the alignment system over long periods, •    study geometry reproducibility at equal fields (specially at 0T and 3.8T); •    reconstruct B=0T geometry and compare to nominal/survey geometries; •    reconstruct B=3.8T geometry and provide DT and CSC alignment records for CMSSW. However, the main goal is to recons...


    CERN Multimedia

    G. Gomez


      A new muon alignment has been produced for 2012 A+B data reconstruction. It uses the latest Tracker alignment and single-muon data samples to align both DTs and CSCs. Physics validation has been performed and shows a modest improvement in stand-alone muon momentum resolution in the barrel, where the alignment is essentially unchanged from the previous version. The reference-target track-based algorithm using only collision muons is employed for the first time to align the CSCs, and a substantial improvement in resolution is observed in the endcap and overlap regions for stand-alone muons. This new alignment is undergoing the approval process and is expected to be deployed as part of a new global tag in the beginning of December. The pT dependence of the φ-bias in curvature observed in Monte Carlo was traced to a relative vertical misalignment between the Tracker and barrel muon systems. Moving the barrel as a whole to match the Tracker cures this pT dependence, leaving only the &phi...

  15. Incremental Alignment Manifold Learning

    Institute of Scientific and Technical Information of China (English)

    Zhi Han; De-Yu Meng; Zong-Sen Xu; Nan-Nan Gu


    A new manifold learning method, called incremental alignment method (IAM), is proposed for nonlinear dimensionality reduction of high dimensional data with intrinsic low dimensionality. The main idea is to incrementally align low-dimensional coordinates of input data patch-by-patch to iteratively generate the representation of the entire dataset. The method consists of two major steps, the incremental step and the alignment step. The incremental step incrementally searches neighborhood patch to be aligned in the next step, and the alignment step iteratively aligns the low-dimensional coordinates of the neighborhood patch searched to generate the embeddings of the entire dataset. Compared with the existing manifold learning methods, the proposed method dominates in several aspects: high efficiency, easy out-of-sample extension, well metric-preserving, and averting of the local minima issue. All these properties are supported by a series of experiments performed on the synthetic and real-life datasets. In addition, the computational complexity of the proposed method is analyzed, and its efficiency is theoretically argued and experimentally demonstrated.

  16. Novel splice site mutation in keratin 1 underlies mild epidermolytic palmoplantar keratoderma in three kindreds. (United States)

    Hatsell, S J; Eady, R A; Wennerstrand, L; Dopping-Hepenstal, P; Leigh, I M; Munro, C; Kelsell, D P


    We report a novel mutation in the exon 6 splice donor site of keratin 1 (G4134A) that segregates with a palmoplantar keratoderma in three kindreds. The nucleotide substitution leads to the utilization of a novel in-frame splice site 54 bases downstream of the mutation with the subsequent insertion of 18 amino acids into the 2B rod domain. This mutation appears to have a milder effect than previously described mutations in the helix initiation and termination sequence on the function of the rod domain, with regard to filament assembly and stability. Affected individuals displayed only mild focal epidermolysis in the spinous layer of palmoplantar epidermis, in comparison with cases of bullous congenital ichthyosiform erythroderma also due to keratin 1 mutations, which show widespread and severe epidermolysis. This study describes a novel mutation in KRT1 that results in a phenotype distinct from classical bullous congenital ichthyosiform erythroderma.

  17. The hnRNP 2H9 gene, which is involved in the splicing reaction, is a multiply spliced gene

    DEFF Research Database (Denmark)

    Honoré, B


    The hnRNP 2H9 gene products are involved in the splicing process and participate in early heat shock-induced splicing arrest. By combining low/high stringency hybridisation, database search, Northern and Western blotting it is shown that the gene is alternatively spliced into at least six transcr...

  18. Auxiliary splice factor U2AF26 and transcription factor Gfi1 cooperate directly in regulating CD45 alternative splicing.

    NARCIS (Netherlands)

    Heyd, F.; Dam, G.B. ten; Moroy, T.


    By alternative splicing, different isoforms of the transmembrane tyrosine phosphatase CD45 are generated that either enhance or limit T cell receptor signaling. We report here that CD45 alternative splicing is regulated by cooperative action of the splice factor U2AF26 and the transcription factor G

  19. Effect of exonic splicing regulation on synonymous codon usage in alternatively spliced exons of Dscam

    Directory of Open Access Journals (Sweden)

    Takahashi Aya


    Full Text Available Abstract Background Synonymous codon usage is typically biased towards translationally superior codons in many organisms. In Drosophila, genomic data indicates that translationally optimal codons and splice optimal codons are mostly mutually exclusive, and adaptation to translational efficiency is reduced in the intron-exon boundary regions where potential exonic splicing enhancers (ESEs reside. In contrast to genomic scale analyses on large datasets, a refined study on a well-controlled set of samples can be effective in demonstrating the effects of particular splice-related factors. Down syndrome cell adhesion molecule (Dscam has the largest number of alternatively spliced exons (ASEs known to date, and the splicing frequency of each ASE is accessible from the relative abundance of the transcript. Thus, these ASEs comprise a unique model system for studying the effect of splicing regulation on synonymous codon usage. Results Codon Bias Indices (CBI in the 3' boundary regions were reduced compared to the rest of the exonic regions among 48 and 33 ASEs of exon 6 and 9 clusters, respectively. These regional differences in CBI were affected by splicing frequency and distance from adjacent exons. Synonymous divergence levels between the 3' boundary region and the remaining exonic region of exon 6 ASEs were similar. Additionally, another sensitive comparison of paralogous exonic regions in recently retrotransposed processed genes and their parental genes revealed that, in the former, the differences in CBI between what were formerly the central regions and the boundary regions gradually became smaller over time. Conclusion Analyses of the multiple ASEs of Dscam allowed direct tests of the effect of splice-related factors on synonymous codon usage and provided clear evidence that synonymous codon usage bias is restricted by exonic splicing signals near the intron-exon boundary. A similar synonymous divergence level between the different exonic

  20. Specific genomic cues regulate Cajal body assembly. (United States)

    Sawyer, Iain A; Hager, Gordon L; Dundr, Miroslav


    The assembly of specialized sub-nuclear microenvironments known as nuclear bodies (NBs) is important for promoting efficient nuclear function. In particular, the Cajal body (CB), a prominent NB that facilitates spliceosomal snRNP biogenesis, assembles in response to genomic cues. Here, we detail the factors that regulate CB assembly and structural maintenance. These include the importance of transcription at nucleating gene loci, the grouping of these genes on human chromosomes 1, 6 and 17, as well as cell cycle and biochemical regulation of CB protein function. We also speculate on the correlation between CB formation and RNA splicing levels in neurons and cancer. The timing and location of these specific molecular events is critical to CB assembly and its contribution to genome function. However, further work is required to explore the emerging biophysical characteristics of CB assembly and the impact upon subsequent genome reorganization.

  1. Capillary Electrophoresis Analysis of Conventional Splicing Assays

    DEFF Research Database (Denmark)

    de Garibay, Gorka Ruiz; Acedo, Alberto; García-Casado, Zaida;


    of these assays is often challenging. Here, we explore this issue by conducting splicing assays in 31 BRCA2 genetic variants. All variants were assessed by RT-PCR followed by capillary electrophoresis and direct sequencing. If assays did not produce clear-cut outputs (Class-2 or Class-5 according to analytical...

  2. Characterization of trans-splicing in Euglenoids. (United States)

    Frantz, C; Ebel, C; Paulus, F; Imbault, P


    We have looked for trans-splicing of nuclear mRNAs in several Euglenoid species. In Cyclidiopsis acus, Phacus curvicauda, Rhabdomonas costata and Menoidium pellucidum we showed that several premRNAs chosen at random are matured by a transsplicing process: we identified SL-RNA genes whose 5' ends (SLs for spliced leader-sequences) were transferred to the 5' extremities of mRNAs. The SL-RNA genes are located on repeated DNA fragments which also encode 5S rRNA in P. curvicauda and C. acus. The potential secondary structures of SL-RNAs are compared to those previously characterized in two other Euglenoids: Euglena gracilis and Entosiphon sulcatum. In another Euglenoid species, Distigma proteus, since none of the mRNAs examined were trans-spliced, it is possible that trans-splicing does not occur. Phylogeny based on 5S rRNA sequences suggests that the species which have, or have had, chloroplasts (E. gracilis, P. curvicauda, C. acus) diverged early from the others.

  3. Alternative-splicing-mediated gene expression (United States)

    Wang, Qianliang; Zhou, Tianshou


    Alternative splicing (AS) is a fundamental process during gene expression and has been found to be ubiquitous in eukaryotes. However, how AS impacts gene expression levels both quantitatively and qualitatively remains to be fully explored. Here, we analyze two common models of gene expression, each incorporating a simple splice mechanism that a pre-mRNA is spliced into two mature mRNA isoforms in a probabilistic manner. In the constitutive expression case, we show that the steady-state molecular numbers of two mature mRNA isoforms follow mutually independent Poisson distributions. In the bursting expression case, we demonstrate that the tail decay of the steady-state distribution for both mature mRNA isoforms that in general are not mutually independent can be characterized by the product of mean burst size and splicing probability. In both cases, we find that AS can efficiently modulate both the variability (measured by variance) and the noise level of the total mature mRNA, and in particular, the latter is always lower than the noise level of the pre-mRNA, implying that AS always reduces the noise. These results altogether reveal that AS is a mechanism of efficiently controlling the gene expression noise.

  4. Curriculum Alignment Research Suggests that Alignment Can Improve Student Achievement (United States)

    Squires, David


    Curriculum alignment research has developed showing the relationship among three alignment categories: the taught curriculum, the tested curriculum and the written curriculum. Each pair (for example, the taught and the written curriculum) shows a positive impact for aligning those results. Following this, alignment results from the Third…

  5. Alternative splicing: a pivotal step between eukaryotic transcription and translation. (United States)

    Kornblihtt, Alberto R; Schor, Ignacio E; Alló, Mariano; Dujardin, Gwendal; Petrillo, Ezequiel; Muñoz, Manuel J


    Alternative splicing was discovered simultaneously with splicing over three decades ago. Since then, an enormous body of evidence has demonstrated the prevalence of alternative splicing in multicellular eukaryotes, its key roles in determining tissue- and species-specific differentiation patterns, the multiple post- and co-transcriptional regulatory mechanisms that control it, and its causal role in hereditary disease and cancer. The emerging evidence places alternative splicing in a central position in the flow of eukaryotic genetic information, between transcription and translation, in that it can respond not only to various signalling pathways that target the splicing machinery but also to transcription factors and chromatin structure.

  6. Expression and purification of splicing proteins from mammalian cells. (United States)

    Allemand, Eric; Hastings, Michelle L


    Pre-mRNA splicing is a complex process that is carried out by a large ribonucleoprotein enzyme, termed the spliceosome, which comprises up to 200 proteins. Despite this complexity, the role of individual spliceosomal proteins in the splicing reaction has been successfully investigated using cell-free assays. In many cases, the splicing factor of interest must be expressed and purified in order to study its function in vitro. Posttranslational modifications such as phosphorylation, methylation, acetylation, and ubiquitination of splicing factors are important for activity. Thus, their purification from mammalian cells presents numerous advantages. Here, we describe a method for expression and purification of splicing proteins from mammalian cells.

  7. Approaches to link RNA secondary structures with splicing regulation

    DEFF Research Database (Denmark)

    Plass, Mireya; Eyras, Eduardo


    by facilitating or hindering the interaction with factors and small nuclear ribonucleoproteins (snRNPs) that regulate splicing. Moreover, the secondary structure could play a fundamental role in the splicing of yeast species, which lack many of the regulatory splicing factors present in metazoans. This chapter......In higher eukaryotes, alternative splicing is usually regulated by protein factors, which bind to the pre-mRNA and affect the recognition of splicing signals. There is recent evidence that the secondary structure of the pre-mRNA may also play an important role in this process, either...

  8. Discovery of a Splicing Regulator Required for Cell Cycle Progression

    Energy Technology Data Exchange (ETDEWEB)

    Suvorova, Elena S.; Croken, Matthew; Kratzer, Stella; Ting, Li-Min; Conde de Felipe, Magnolia; Balu, Bharath; Markillie, Lye Meng; Weiss, Louis M.; Kim, Kami; White, Michael W.


    In the G1 phase of the cell division cycle, eukaryotic cells prepare many of the resources necessary for a new round of growth including renewal of the transcriptional and protein synthetic capacities and building the machinery for chromosome replication. The function of G1 has an early evolutionary origin and is preserved in single and multicellular organisms, although the regulatory mechanisms conducting G1 specific functions are only understood in a few model eukaryotes. Here we describe a new G1 mutant from an ancient family of apicomplexan protozoans. Toxoplasma gondii temperature-sensitive mutant 12-109C6 conditionally arrests in the G1 phase due to a single point mutation in a novel protein containing a single RNA-recognition-motif (TgRRM1). The resulting tyrosine to asparagine amino acid change in TgRRM1 causes severe temperature instability that generates an effective null phenotype for this protein when the mutant is shifted to the restrictive temperature. Orthologs of TgRRM1 are widely conserved in diverse eukaryote lineages, and the human counterpart (RBM42) can functionally replace the missing Toxoplasma factor. Transcriptome studies demonstrate that gene expression is downregulated in the mutant at the restrictive temperature due to a severe defect in splicing that affects both cell cycle and constitutively expressed mRNAs. The interaction of TgRRM1 with factors of the tri-SNP complex (U4/U6 & U5 snRNPs) indicate this factor may be required to assemble an active spliceosome. Thus, the TgRRM1 family of proteins is an unrecognized and evolutionarily conserved class of splicing regulators. This study demonstrates investigations into diverse unicellular eukaryotes, like the Apicomplexa, have the potential to yield new insights into important mechanisms conserved across modern eukaryotic kingdoms.

  9. MaxAlign: maximizing usable data in an alignment

    DEFF Research Database (Denmark)

    Oliveira, Rodrigo Gouveia; Sackett, Peter Wad; Pedersen, Anders Gorm


    BACKGROUND: The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discarded entirely from the alignment. RESULTS: MaxAlign is a program that optimizes...... the alignment prior to such analyses. Specifically, it maximizes the number of nucleotide (or amino acid) symbols that are present in gap-free columns - the alignment area - by selecting the optimal subset of sequences to exclude from the alignment. MaxAlign can be used prior to phylogenetic and bioinformatical...... analyses as well as in other situations where this form of alignment improvement is useful. In this work we test MaxAlign's performance in these tasks and compare the accuracy of phylogenetic estimates including and excluding gapped columns from the analysis, with and without processing with MaxAlign...

  10. SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing. (United States)

    Pulyakhina, Irina; Gazzoli, Isabella; 't Hoen, Peter A C; Verwey, Nisha; den Dunnen, Johan T; den Dunnen, Johan; Aartsma-Rus, Annemieke; Laros, Jeroen F J


    Alternative splicing is a powerful mechanism present in eukaryotic cells to obtain a wide range of transcripts and protein isoforms from a relatively small number of genes. The mechanisms regulating (alternative) splicing and the paradigm of consecutive splicing have recently been challenged, especially for genes with a large number of introns. RNA-Seq, a powerful technology using deep sequencing in order to determine transcript structure and expression levels, is usually performed on mature mRNA, therefore not allowing detailed analysis of splicing progression. Sequencing pre-mRNA at different stages of splicing potentially provides insight into mRNA maturation. Although the number of tools that analyze total and cytoplasmic RNA in order to elucidate the transcriptome composition is rapidly growing, there are no tools specifically designed for the analysis of nuclear RNA (which contains mixtures of pre- and mature mRNA). We developed dedicated algorithms to investigate the splicing process. In this paper, we present a new classification of RNA-Seq reads based on three major stages of splicing: pre-, intermediate- and post-splicing. Applying this novel classification we demonstrate the possibility to analyze the order of splicing. Furthermore, we uncover the potential to investigate the multi-step nature of splicing, assessing various types of recursive splicing events. We provide the data that gives biological insight into the order of splicing, show that non-sequential splicing of certain introns is reproducible and coinciding in multiple cell lines. We validated our observations with independent experimental technologies and showed the reliability of our method. The pipeline, named SplicePie, is freely available at: The example data can be found at:

  11. Deregulation of splicing factors and breast cancer development. (United States)

    Silipo, Marco; Gautrey, Hannah; Tyson-Capper, Alison


    It is well known that many genes implicated in the development and progression of breast cancer undergo aberrant alternative splicing events to produce proteins with pro-cancer properties. These changes in alternative splicing can arise from mutations or single-nucleotide polymorphisms (SNPs) within the DNA sequences of cancer-related genes, which can strongly affect the activity of splicing factors and influence the splice site choice. However, it is important to note that absence of mutations is not sufficient to prevent misleading choices in splice site selection. There is now increasing evidence to demonstrate that the expression profile of ten splicing factors (including SRs and hnRNPs) and eight RNA-binding proteins changes in breast cancer cells compared with normal cells. These modifications strongly influence the alternative splicing pattern of many cancer-related genes despite the absence of any detrimental mutations within their DNA sequences. Thus, a comprehensive assessment of the splicing factor status in breast cancer is important to provide insights into the mechanisms that lead to breast cancer development and metastasis. Whilst most studies focus on mutations that affect alternative splicing in cancer-related genes, this review focuses on splicing factors and RNA-binding proteins that are themselves deregulated in breast cancer and implicated in cancer-related alternative splicing events.

  12. Study and Development of a Laser Based Alignment System

    CERN Multimedia

    Stern, G


    CLIC (Compact Linear Collider) has tight requirements regarding pre-alignment of beam related components: 10 µm accuracy over a sliding window of 200 m along the 20 km of linac. To perform such an alignment, a new system is proposed combining laser beam as straight line reference and camera/shutter assemblies as sensors. The poster describes the alignment system and shows results regarding laser pointing stability with respect to time, shutter type, distance and environment. These results give a frame for future building and calibrating of sensors.

  13. Alignment of the Fibrin Network Within an Autologous Plasma Clot. (United States)

    Gessmann, Jan; Seybold, Dominik; Peter, Elvira; Schildhauer, Thomas Armin; Köller, Manfred


    Autologous plasma clots with longitudinally aligned fibrin fibers could serve as a scaffold for longitudinal axonal regrowth in cases of traumatic peripheral nerve injuries. Three different techniques for assembling longitudinally oriented fibrin fibers during the fibrin polymerization process were investigated as follows: fiber alignment was induced by the application of either a magnetic field or-as a novel approach-electric field or by the induction of orientated flow. Fiber alignment was characterized by scanning electron microscopy analysis followed by image processing using fast Fourier transformation (FFT). Besides FFT output images, area xmin to xmax, as well as full width at half maximum (FWHM) of the FFT graph plot peaks, was calculated to determine the relative degree of fiber alignment. In addition, fluorescently labeled human fibrinogen and mesenchymal stem cells (MSCs) were used to visualize fibrin and cell orientation in aligned and nonaligned plasma clots. Varying degrees of fiber alignment were achieved by the three different methods, with the electric field application producing the highest degree of fiber alignment. The embedded MSCs showed a longitudinal orientation in the electric field-aligned plasma clots. The key feature of this study is the ability to produce autologous plasma clots with aligned fibrin fibers using physical techniques. This orientated internal structure of an autologous biomaterial is promising for distinct therapeutic applications, such as a guiding structure for cell migration and growth dynamics.


    CERN Multimedia

    M. Dallavalle


    A new Muon misalignment scenario for 2011 (7 TeV) Monte Carlo re-processing was re-leased. The scenario is based on running of standard track-based reference-target algorithm (exactly as in data) using single-muon simulated sample (with the transverse-momentum spectrum matching data). It used statistics similar to what was used for alignment with 2011 data, starting from an initially misaligned Muon geometry from uncertainties of hardware measurements and using the latest Tracker misalignment geometry. Validation of the scenario (with muons from Z decay and high-pT simulated muons) shows that it describes data well. The study of systematic uncertainties (dominant by now due to huge amount of data collected by CMS and used for muon alignment) is finalised. Realistic alignment position errors are being obtained from the estimated uncertainties and are expected to improve the muon reconstruction performance. Concerning the Hardware Alignment System, the upgrade of the Barrel Alignment is in progress. By now, d...


    CERN Multimedia

    G. Gomez


    For the last three months, the Muon Alignment group has focussed on providing a new, improved set of alignment constants for the end-of-year data reprocessing. These constants were delivered on time and approved by the CMS physics validation team on November 17. The new alignment incorporates several improvements over the previous one from March for nearly all sub-systems. Motivated by the loss of information from a hardware failure in May (an entire MAB was lost), the optical barrel alignment has moved from a modular, super-plane reconstruction, to a full, single loop calculation of the entire geometry for all DTs in stations 1, 2 and 3. This makes better use of the system redundancy, mitigating the effect of the information loss. Station 4 is factorised and added afterwards to make the system smaller (and therefore faster to run), and also because the MAB calibration at the MB4 zone is less precise. This new alignment procedure was tested at 0 T against photogrammetry resulting in precisions of the order...


    CERN Multimedia

    Gervasio Gomez


      The new alignment for the DT chambers has been successfully used in physics analysis starting with the 52X Global Tag. The remaining main areas of development over the next few months will be preparing a new track-based CSC alignment and producing realistic APEs (alignment position errors) and MC misalignment scenarios to match the latest muon alignment constants. Work on these items has been delayed from the intended timeline, mostly due to a large involvement of the muon alignment man-power in physics analyses over the first half of this year. As CMS keeps probing higher and higher energies, special attention must be paid to the reconstruction of very-high-energy muons. Recent muon POG reports from mid-June show a φ-dependence in curvature bias in Monte Carlo samples. This bias is observed already at the tracker level, where it is constant with muon pT, while it grows with pT as muon chamber information is added to the tracks. Similar studies show a much smaller effect in data, at le...

  17. Ergodic Secret Alignment

    CERN Document Server

    Bassily, Raef


    In this paper, we introduce two new achievable schemes for the fading multiple access wiretap channel (MAC-WT). In the model that we consider, we assume that perfect knowledge of the state of all channels is available at all the nodes in a causal fashion. Our schemes use this knowledge together with the time varying nature of the channel model to align the interference from different users at the eavesdropper perfectly in a one-dimensional space while creating a higher dimensionality space for the interfering signals at the legitimate receiver hence allowing for better chance of recovery. While we achieve this alignment through signal scaling at the transmitters in our first scheme (scaling based alignment (SBA)), we let nature provide this alignment through the ergodicity of the channel coefficients in the second scheme (ergodic secret alignment (ESA)). For each scheme, we obtain the resulting achievable secrecy rate region. We show that the secrecy rates achieved by both schemes scale with SNR as 1/2log(SNR...

  18. Magnetically aligned polymer-nanowire composites for solar energy harvesting (United States)

    Majewski, Pawel; Pelligra, Candice; Osuji, Chinedum


    We present a solution-based approach of producing aligned arrays of ZnO nanowire-polythiophene composites for photovoltaic applications. We employ a two-step hierarchical self-assembly to maximize the efficiency of electron and hole transport in the system. First, we coat the wires with the polymer utilizing nanowire surface-directed crystallization and alignment of the polymer backbones along the long axes of the wires, then we employ magnetic fields to direct the assembly of the composites into the ordered arrays. We present quantitative SAXS data taken in-situ during the alignment process addressing the influence of paramagnetic doping level of ZnO and the magnetic field strength on the quality of the alignment. We compare the electrical conductivity of the aligned arrays of the composites to non-aligned ones and discuss the possible degree of conductivity enhancement upon the alignment in this and in analogous systems. This work is funded by the NSF under DMR-0847534 and DMR-0934520

  19. Tablet—next generation sequence assembly visualization


    Milne, Iain; Bayer, Micha; Cardle, Linda; Shaw, Paul; Stephen, Gordon; Wright, Frank; Marshall, David


    Summary: Tablet is a lightweight, high-performance graphical viewer for next-generation sequence assemblies and alignments. Supporting a range of input assembly formats, Tablet provides high-quality visualizations showing data in packed or stacked views, allowing instant access and navigation to any region of interest, and whole contig overviews and data summaries. Tablet is both multi-core aware and memory efficient, allowing it to handle assemblies containing millions of reads, even on a 32...

  20. RF/Optical Demonstration: Focal Plane Assembly (United States)

    Hoppe, D. J.; Chung, S.; Kovalik, J.; Gama, E.; Fernandez, M. M.


    In this article, we describe the second-generation focal plane optical assembly employed in the RF/optical demonstration at DSS-13. This assembly receives reflected light from the two mirror segments mounted on the RF primary. The focal plane assembly contains a fast steering mirror (FSM) to stabilize the focal plane spot, a pupil camera to aid in aligning the two segments, and several additional cameras for receiving the optical signal prior to as well as after the FSM loop.

  1. Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome. (United States)

    Zuo, Yongchun; Zhang, Pengfei; Liu, Li; Li, Tao; Peng, Yong; Li, Guangpeng; Li, Qianzhong


    More and more reported results of nucleosome positioning and histone modifications showed that DNA structure play a well-established role in splicing. In this study, a set of DNA geometric flexibility parameters originated from molecular dynamics (MD) simulations were introduced to discuss the structure organization around splice sites at the DNA level. The obtained profiles of specific flexibility/stiffness around splice sites indicated that the DNA physical-geometry deformation could be used as an alternative way to describe the splicing junction region. In combination with structural flexibility as discriminatory parameter, we developed a hybrid computational model for predicting potential splicing sites. And the better prediction performance was achieved when the benchmark dataset evaluated. Our results showed that the mechanical deformability character of a splice junction is closely correlated with both the splice site strength and structural information in its flanking sequences.

  2. Strategic Alignment of Business Intelligence


    Cederberg, Niclas


    This thesis is about the concept of strategic alignment of business intelligence. It is based on a theoretical foundation that is used to define and explain business intelligence, data warehousing and strategic alignment. By combining a number of different methods for strategic alignment a framework for alignment of business intelligence is suggested. This framework addresses all different aspects of business intelligence identified as relevant for strategic alignment of business intelligence...

  3. Orientation and Alignment Echoes

    CERN Document Server

    Karras, G; Billard, F; Lavorel, B; Hartmann, J -M; Faucher, O; Gershnabel, E; Prior, Y; Averbukh, I Sh


    We present what is probably the simplest classical system featuring the echo phenomenon - a collection of randomly oriented free rotors with dispersed rotational velocities. Following excitation by a pair of time-delayed impulsive kicks, the mean orientation/alignment of the ensemble exhibits multiple echoes and fractional echoes. We elucidate the mechanism of the echo formation by kick-induced filamentation of phase space, and provide the first experimental demonstration of classical alignment echoes in a thermal gas of CO_2 molecules excited by a pair of femtosecond laser pulses.

  4. Group Based Interference Alignment

    CERN Document Server

    Ma, Yanjun; Chen, Rui; Yao, Junliang


    in $K$-user single-input single-output (SISO) frequency selective fading interference channels, it is shown that the achievable multiplexing gain is almost surely $K/2$ by using interference alignment (IA). However when the signaling dimensions is limited, allocating all the resource to all the users simultaneously is not optimal. According to this problem, a group based interference alignment (GIA) scheme is proposed and a search algorithm is designed to get the group patterns and the resource allocation among them. Analysis results show that our proposed scheme achieves a higher multiplexing gain when the resource is limited.

  5. PILOT optical alignment (United States)

    Longval, Y.; Mot, B.; Ade, P.; André, Y.; Aumont, J.; Baustista, L.; Bernard, J.-Ph.; Bray, N.; de Bernardis, P.; Boulade, O.; Bousquet, F.; Bouzit, M.; Buttice, V.; Caillat, A.; Charra, M.; Chaigneau, M.; Crane, B.; Crussaire, J.-P.; Douchin, F.; Doumayrou, E.; Dubois, J.-P.; Engel, C.; Etcheto, P.; Gélot, P.; Griffin, M.; Foenard, G.; Grabarnik, S.; Hargrave, P..; Hughes, A.; Laureijs, R.; Lepennec, Y.; Leriche, B.; Maestre, S.; Maffei, B.; Martignac, J.; Marty, C.; Marty, W.; Masi, S.; Mirc, F.; Misawa, R.; Montel, J.; Montier, L.; Narbonne, J.; Nicot, J.-M.; Pajot, F.; Parot, G.; Pérot, E.; Pimentao, J.; Pisano, G.; Ponthieu, N.; Ristorcelli, I.; Rodriguez, L.; Roudil, G.; Salatino, M.; Savini, G.; Simonella, O.; Saccoccio, M.; Tapie, P.; Tauber, J.; Torre, J.-P.; Tucker, C.


    PILOT is a balloon-borne astronomy experiment designed to study the polarization of dust emission in the diffuse interstellar medium in our Galaxy at wavelengths 240 μm with an angular resolution about two arcminutes. Pilot optics is composed an off-axis Gregorian type telescope and a refractive re-imager system. All optical elements, except the primary mirror, are in a cryostat cooled to 3K. We combined the optical, 3D dimensional measurement methods and thermo-elastic modeling to perform the optical alignment. The talk describes the system analysis, the alignment procedure, and finally the performances obtained during the first flight in September 2015.

  6. Comparative Cross-Species Alternative Splicing in Plants1[W][OA (United States)

    Ner-Gaon, Hadas; Leviatan, Noam; Rubin, Eitan; Fluhr, Robert


    Alternative splicing (AS) can add significantly to genome complexity. Plants are thought to exhibit less AS than animals. An algorithm, based on expressed sequence tag (EST) pairs gapped alignment, was developed that takes advantage of the relatively small intron and exon size in plants and directly compares pairs of ESTs to search for AS. EST pairs gapped alignment was first evaluated in Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and tomato (Solanum lycopersicum) for which annotated genome sequence is available and was shown to accurately predict splicing events. The method was then applied to 11 plant species that include 17 cultivars for which enough ESTs are available. The results show a large, 3.7-fold difference in AS rates between plant species with Arabidopsis and rice in the lower range and lettuce (Lactuca sativa) and sorghum (Sorghum bicolor) in the upper range. Hence, compared to higher animals, plants show a much greater degree of variety in their AS rates and in some plant species the rates of animal and plant AS are comparable although the distribution of AS types may differ. In eudicots but not monocots, a correlation between genome size and AS rates was detected, implying that in eudicots the mechanisms that lead to larger genomes are a driving force for the evolution of AS. PMID:17496110

  7. Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates.

    Directory of Open Access Journals (Sweden)

    Manuel Irimia

    Full Text Available Alternative splicing is tightly regulated in a spatio-temporal and quantitative manner. This regulation is achieved by a complex interplay between spliceosomal (trans factors that bind to different sequence (cis elements. cis-elements reside in both introns and exons and may either enhance or silence splicing. Differential combinations of cis-elements allows for a huge diversity of overall splicing signals, together comprising a complex 'splicing code'. Many cis-elements have been identified, and their effects on exon inclusion levels demonstrated in reporter systems. However, the impact of interspecific differences in these elements on the evolution of alternative splicing levels has not yet been investigated at genomic level. Here we study the effect of interspecific differences in predicted exonic splicing regulators (ESRs on exon inclusion levels in human and chimpanzee. For this purpose, we compiled and studied comprehensive datasets of predicted ESRs, identified by several computational and experimental approaches, as well as microarray data for changes in alternative splicing levels between human and chimpanzee. Surprisingly, we found no association between changes in predicted ESRs and changes in alternative splicing levels. This observation holds across different ESR exon positions, exon lengths, and 5' splice site strengths. We suggest that this lack of association is mainly due to the great importance of context for ESR functionality: many ESR-like motifs in primates may have little or no effect on splicing, and thus interspecific changes at short-time scales may primarily occur in these effectively neutral ESRs. These results underscore the difficulties of using current computational ESR prediction algorithms to identify truly functionally important motifs, and provide a cautionary tale for studies of the effect of SNPs on splicing in human disease.

  8. The influence of Argonaute proteins on alternative RNA splicing. (United States)

    Batsché, Eric; Ameyar-Zazoua, Maya


    Alternative splicing of precursor RNAs is an important process in multicellular species because it impacts several aspects of gene expression: from the increase of protein repertoire to the level of expression. A large body of evidences demonstrates that factors regulating chromatin and transcription impact the outcomes of alternative splicing. Argonaute (AGO) proteins were known to play key roles in the regulation of gene expression at the post-transcriptional level. More recently, their role in the nucleus of human somatic cells has emerged. Here, we will discuss some of the nuclear functions of AGO, with special emphasis on alternative splicing. The AGO-mediated modulation of alternative splicing is based on several properties of these proteins: their binding to transcripts on chromatin and their interactions with many proteins, especially histone tail-modifying enzymes, HP1γ and splicing factors. AGO proteins may favor a decrease in the RNA-polymerase II kinetics at actively transcribed genes leading to the modulation of alternative splicing decisions. They could also influence alternative splicing through their interaction with core components of the splicing machinery and several splicing factors. We will discuss the modes of AGO recruitment on chromatin at active genes. We suggest that long intragenic antisense transcripts (lincRNA) might be an important feature of genes containing splicing events regulated by AGO.

  9. Aligning Theory with Practice (United States)

    Kurz, Terri L.; Batarelo, Ivana


    This article describes a structure to help preservice teachers get invaluable field experience by aligning theory with practice supported by the integration of elementary school children into their university mathematics methodology course. This course structure allowed preservice teachers to learn about teaching mathematics in a nonthreatening…


    CERN Multimedia

    G. Gomez and Y. Pakhotin


      A new track-based alignment for the DT chambers is ready for deployment: an offline tag has already been produced which will become part of the 52X Global Tag. This alignment was validated within the muon alignment group both at low and high momentum using a W/Z skim sample. It shows an improved mass resolution for pairs of stand-alone muons, improved curvature resolution at high momentum, and improved DT segment extrapolation residuals. The validation workflow for high-momentum muons used to depend solely on the “split cosmics” method, looking at the curvature difference between muon tracks reconstructed in the upper or lower half of CMS. The validation has now been extended to include energetic muons decaying from heavily boosted Zs: the di-muon invariant mass for global and stand-alone muons is reconstructed, and the invariant mass resolution is compared for different alignments. The main areas of development over the next few months will be preparing a new track-based C...

  11. Alignment of concerns

    DEFF Research Database (Denmark)

    Andersen, Tariq Osman; Bansler, Jørgen P.; Kensing, Finn;


    The emergence of patient-centered eHealth systems introduces new challenges, where patients come to play an increasingly important role. Realizing the promises requires an in-depth understanding of not only the technology, but also the needs of both clinicians and patients. However, insights from...... as a design rationale for successful eHealth, termed 'alignment of concerns'....

  12. Aligning Mental Representations

    DEFF Research Database (Denmark)

    Kano Glückstad, Fumiko


    This work introduces a framework that implements asymmetric communication theory proposed by Sperber and Wilson [1]. The framework applies a generalization model known as the Bayesian model of generalization (BMG) [2] for aligning knowledge possessed by two communicating parties. The work focuses...

  13. Muscleblind-like 1 activates insulin receptor exon 11 inclusion by enhancing U2AF65 binding and splicing of the upstream intron. (United States)

    Echeverria, Gloria V; Cooper, Thomas A


    Alternative splicing regulates developmentally and tissue-specific gene expression programs, disruption of which have been implicated in numerous diseases. Muscleblind-like 1 (MBNL1) regulates splicing transitions, which are disrupted on loss of MBNL1 function in myotonic dystrophy type 1 (DM1). One such event is MBNL1-mediated activation of insulin receptor exon 11 inclusion, which requires an intronic enhancer element downstream of exon 11. The mechanism of MBNL1-mediated activation of exon inclusion is unknown. We developed an in vitro splicing assay, which robustly recapitulates MBNL1-mediated splicing activation of insulin receptor exon 11 and found that MBNL1 activates removal of the intron upstream of exon 11 upon binding its functional response element in the downstream intron. MBNL1 enhances early spliceosome assembly as evidenced by enhanced complex A formation and binding of U2 small nuclear ribonucleoprotein auxiliary factor 65 kDa subunit (U2AF65) on the upstream intron. We demonstrated that neither the 5' splice site nor exon 11 sequences are required for MBNL1-activated U2AF65 binding. Interestingly, the 5' splice site is required for MBNL1-mediated activation of upstream intron removal, although MBNL1 has no effect on U1 snRNA recruitment. These results suggest that MBNL1 directly activates binding of U2AF65 to enhance upstream intron removal to ultimately activate alternative exon inclusion.

  14. Evryscope Robotilter automated camera / ccd alignment system (United States)

    Ratzloff, Jeff K.; Law, Nicholas M.; Fors, Octavi; Ser, Daniel d.; Corbett, Henry T.


    We have deployed a new class of telescope, the Evryscope, which opens a new parameter space in optical astronomy - the ability to detect short time scale events across the entire sky simultaneously. The system is a gigapixel-scale array camera with an 8000 sq. deg. field of view, 13 arcsec per pixel sampling, and the ability to detect objects brighter than g = 16 in each 2-minute exposure. The Evryscope is designed to find transiting exoplanets around exotic stars, as well as detect nearby supernovae and provide continuous records of distant relativistic explosions like gamma-ray-bursts. The Evryscope uses commercially available CCDs and optics; the machine and assembly tolerances inherent in the mass production of these parts introduce problematic variations in the lens / CCD alignment which degrades image quality. We have built an automated alignment system (Robotilters) to solve this challenge. In this paper we describe the Robotilter system, mechanical and software design, image quality improvement, and current status.

  15. The surveyors' quest for perfect alignment

    CERN Multimedia


    Photogrammetry of a CMS endcap and part of the hadronic calorimeter.The structure was covered with targets photographed by digital cameras. Perfect alignment.... Although CERN's surveyors do not claim to achieve it, they are constantly striving for it and deploy all necessary means to come as close as they can. In their highly specialised field of large-scale metrology, the solution lies in geodesy and photogrammetry, both of which are based on increasingly sophisticated instruments and systems. In civil engineering, these techniques are used for non-destructive inspection of bridges, dams and other structures, while industrial applications include dimensional verification and deformation measurement in large mechanical assemblies. The same techniques also come into play for the metrology of research tools such as large telescopes and of course, particle accelerators. Particle physics laboratories are especially demanding customers, and CERN has often asked for the impossible. As a result, the alignment metro...

  16. Resolving deconvolution ambiguity in gene alternative splicing

    Directory of Open Access Journals (Sweden)

    Hubbell Earl


    Full Text Available Abstract Background For many gene structures it is impossible to resolve intensity data uniquely to establish abundances of splice variants. This was empirically noted by Wang et al. in which it was called a "degeneracy problem". The ambiguity results from an ill-posed problem where additional information is needed in order to obtain an unique answer in splice variant deconvolution. Results In this paper, we analyze the situations under which the problem occurs and perform a rigorous mathematical study which gives necessary and sufficient conditions on how many and what type of constraints are needed to resolve all ambiguity. This analysis is generally applicable to matrix models of splice variants. We explore the proposal that probe sequence information may provide sufficient additional constraints to resolve real-world instances. However, probe behavior cannot be predicted with sufficient accuracy by any existing probe sequence model, and so we present a Bayesian framework for estimating variant abundances by incorporating the prediction uncertainty from the micro-model of probe responsiveness into the macro-model of probe intensities. Conclusion The matrix analysis of constraints provides a tool for detecting real-world instances in which additional constraints may be necessary to resolve splice variants. While purely mathematical constraints can be stated without error, real-world constraints may themselves be poorly resolved. Our Bayesian framework provides a generic solution to the problem of uniquely estimating transcript abundances given additional constraints that themselves may be uncertain, such as regression fit to probe sequence models. We demonstrate the efficacy of it by extensive simulations as well as various biological data.

  17. Splicing variants of porcine synphilin-1

    Directory of Open Access Journals (Sweden)

    Knud Larsen


    Full Text Available Parkinson's disease (PD, idiopathic and familial, is characterized by degradation of dopaminergic neurons and the presence of Lewy bodies (LB in the substantia nigra. LBs contain aggregated proteins of which α-synuclein is the major component. The protein synphilin-1 interacts and colocalizes with α-synuclein in LBs. The aim of this study was to isolate and characterize porcine synphilin-1 and isoforms hereof with the future perspective to use the pig as a model for Parkinson's disease. The porcine SNCAIP cDNA was cloned by reverse transcriptase PCR. The spatial expression of SNCAIP mRNA was investigated by RNAseq. The presented work reports the molecular cloning and characterization of the porcine (Sus scrofa synphilin-1 cDNA (SNCAIP and three splice variants hereof. The porcine SNCAIP cDNA codes for a protein (synphilin-1 of 919 amino acids which shows a high similarity to human (90% and to mouse (84% synphilin-1. Three shorter transcript variants of the synphilin-1 gene were identified, all lacking one or more exons. SNCAIP transcripts were detected in most examined organs and tissues and the highest expression was found in brain tissues and lung. Conserved splicing variants and a novel splice form of synhilin-1 were found in this study. All synphilin-1 isoforms encoded by the identified transcript variants lack functional domains important for protein degradation.

  18. Retrieval of missing spliced leader in dinoflagellates. (United States)

    Zhang, Huan; Lin, Senjie


    Spliced leader (SL) trans-splicing has recently been shown to be a common mRNA processing mechanism in dinoflagellates, in which a short (22-nt) sequence, DCCGUAGCCAUUUUGGCUCAAG (D = U, A, or G), is transplanted from the 5'-end of a small non-coding RNA (SL RNA) to the 5' end of mRNA molecules. The widespread existence of the mechanism in dinoflagellates has been demonstrated by detection of this SL (DinoSL) in a wide phylogenetic range of dinoflagellates. Furthermore, the presence of DinoSL in the transcripts of highly diverse groups of nuclear-encoded genes has led us to postulate that SL trans-splicing is universal in dinoflagellate nuclear genome. However, some observations inconsistent to this postulation have been reported, exemplified by a recent article reporting apparent absence of DinoSL in the transcripts of some nuclear-encoded genes in Amphidinium carterae. Absence of SL in these gene transcripts would have important implication on gene regulation in dinoflagellates and utility of DinoSL as a universal dinoflagellate-specific primer to study dinoflagellate transcriptomics. In this study, we re-examined transcripts of these genes and found that all of them actually contained DinoSL. Therefore, results to date are consistent to our initial postulation that DinoSL occurs in all dinoflagellate nuclear-encoded mRNAs.

  19. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria


    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at:

  20. A new method for splice site prediction based on the sequence patterns of splicing signals and regulatory elements

    Institute of Scientific and Technical Information of China (English)

    SUN ZongXiao; SANG LingJie; JU LiNing; ZHU HuaiQiu


    It is of significance for splice site prediction to develop novel algorithms that combine the sequence patterns of regulatory elements such as enhancers and silencers with the patterns of splicing signals. In this paper, a statistical model of splicing signals was built based on the entropy density profile (EDP) method, weight array method (WAM) and κ test; moreover, the model of splicing regulatory elements was developed by an unsupervised self-learning method to detect motifs associated with regulatory elements. With two models incorporated, a multi-level support vector machine (SVM) system was de-vised to perform ab initio prediction for splice sites originating from DNA sequence in eukaryotic ge-home. Results of large scale tests on human genomic splice sites show that the new method achieves a comparative high performance in splice site prediction. The method is demonstrated to be with at least the same level of performance and usually better performance than the existing SpliceScan method based on modeling regulatory elements, and shown to have higher accuracies than the traditional methods with modeling splicing signals such as the GeneSplicer. In particular, the method has evident advantage over splice site prediction for the genes with lower GC content.

  1. The doublesex splicing enhancer components Tra2 and Rbp1 also repress splicing through an intronic silencer. (United States)

    Qi, Junlin; Su, Shihuang; Mattox, William


    The activation of sex-specific alternative splice sites in the Drosophila melanogaster doublesex and fruitless pre-mRNAs has been well studied and depends on the serine-arginine-rich (SR) splicing factors Tra, Tra2, and Rbp1. Little is known, however, about how SR factors negatively regulate splice sites in other RNAs. Here we examine how Tra2 blocks splicing of the M1 intron from its own transcript. We identify an intronic splicing silencer (ISS) adjacent to the M1 branch point that is sufficient to confer Tra2-dependent repression on another RNA. The ISS was found to function independently of its position within the intron, arguing against the idea that bound repressors function by simply interfering with branch point accessibility to general splicing factors. Conserved subelements of the silencer include five short repeated sequences that are required for Tra2 binding but differ from repeated binding sites found in Tra2-dependent splicing enhancers. The ISS also contains a consensus binding site for Rbp1, and this protein was found to facilitate repression of M1 splicing both in vitro and in Drosophila larvae. In contrast to the cooperative binding of SR proteins observed on the doublesex splicing enhancer, we found that Rbp1 and Tra2 bind to the ISS independently through distinct sequences. Our results suggest that functionally synergistic interactions of these SR factors can cause either splicing activation or repression.

  2. Half pint/Puf68 is required for negative regulation of splicing by the SR splicing factor Transformer2. (United States)

    Wang, Shanzhi; Wagner, Eric J; Mattox, William


    The SR family of proteins plays important regulatory roles in the control of alternative splicing in a wide range of organisms. These factors affect splicing through both positive and negative controls of splice site recognition by pre-spliceosomal factors. Recent studies indicate that the Drosophila SR factor Transformer 2 (Tra2) activates and represses splicing through distinct and separable effector regions of the protein. While the interactions of its Arg-Ser-rich activator region have been well studied, cofactors involved in splicing repression have yet to be found. Here we use a luciferase-based splicing reporter assay to screen for novel proteins necessary for Tra2-dependent repression of splicing. This approach identified Half pint, also known as Puf68, as a co-repressor required for Tra2-mediated autoregulation of the M1 intron. In vivo, Half pint is required for Tra2-dependent repression of M1 splicing but is not necessary for Tra2-dependent activation of doublesex splicing. Further experiments indicate that the effect of Hfp is sequence-specific and that it associates with these target transcripts in cells. Importantly, known M1 splicing regulatory elements are sufficient to sensitize a heterologous intron to Hfp regulation. Two alternative proteins deriving from Hfp transcripts, Hfp68, and Hfp58, were found to be expressed in vivo but differed dramatically in their effect on M1 splicing. Comparison of the cellular localization of these forms in S2 cells revealed that Hfp68 is predominantly localized to the nucleus while Hfp58 is distributed across both the nucleus and cytoplasm. This accords with their observed effects on splicing and suggests that differential compartmentalization may contribute to the specificity of these isoforms. Together, these studies reveal a function for Half pint in splicing repression and demonstrate it to be specifically required for Tra2-dependent intron inclusion.

  3. Regulation of FT splicing by an endogenous cue in temperate grasses. (United States)

    Qin, Zhengrui; Wu, Jiajie; Geng, Shuaifeng; Feng, Nan; Chen, Fengjuan; Kong, Xingchen; Song, Gaoyuan; Chen, Kai; Li, Aili; Mao, Long; Wu, Liang


    Appropriate flowering timing is crucial for plant reproductive success. The florigen, FLOWERING LOCUS T (FT), interacts with 14-3-3 proteins and the bZIP transcription factor FD, functioning at core nodes in multiple flowering pathways. There are two FT homologues, FT1 and FT2, in Brachypodium distachyon. Here we show that FT2 undergoes age-dependent alternative splicing (AS), resulting in two splice variants (FT2α and FT2β). The FT2β-encoded protein cannot interact with FD or 14-3-3s but is able to form heterodimers with FT2α and FT1, thereby interfering with the florigen-mediated assembly of the flowering initiation complex. Notably, transgenic plants overproducing FT2β exhibit delayed flowering, while transgenic plants in which FT2β is silenced by an artificial microRNA display accelerated flowering, demonstrating a dominant-negative role of FT2β in flowering induction. Furthermore, we show that the AS splicing of FT2 is conserved in important cereal crops, such as barley and wheat. Collectively, these findings reveal a novel posttranscriptional mode of FT regulation in temperate grasses.

  4. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal


    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  5. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal


    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  6. Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob Lewin; Roy, Scott William


    Alternative splicing is tightly regulated in a spatio-temporal and quantitative manner. This regulation is achieved by a complex interplay between spliceosomal (trans) factors that bind to different sequence (cis) elements. cis-elements reside in both introns and exons and may either enhance...... of interspecific differences in these elements on the evolution of alternative splicing levels has not yet been investigated at genomic level. Here we study the effect of interspecific differences in predicted exonic splicing regulators (ESRs) on exon inclusion levels in human and chimpanzee. For this purpose, we...... and changes in alternative splicing levels. This observation holds across different ESR exon positions, exon lengths, and 5' splice site strengths. We suggest that this lack of association is mainly due to the great importance of context for ESR functionality: many ESR-like motifs in primates may have little...

  7. A multi-agent system simulating human splice site recognition. (United States)

    Vignal, L; Lisacek, F; Quinqueton, J; d'Aubenton-Carafa, Y; Thermes, C


    The present paper describes a method detecting splice sites automatically on the basis of sequence data and models of site/signal recognition supported by experimental evidences. The method is designed to simulate splicing and while doing so, track prediction failures, missing information and possibly test correcting hypotheses. Correlations between nucleotides in the splice site regions and the various elements of the acceptor region are evaluated and combined to assess compensating interactions between elements of the splicing machinery. A scanning model of the acceptor region and a model of interaction between the splicing complexes (exon definition model) are also incorporated in the detection process. Subsets of sites presenting deficiencies of several splice site elements could be identified. Further examination of these sites helps to determine lacking elements and refine models.

  8. Splicing modulation therapy in the treatment of genetic diseases

    Directory of Open Access Journals (Sweden)

    Arechavala-Gomeza V


    Full Text Available Virginia Arechavala-Gomeza,1 Bernard Khoo,2 Annemieke Aartsma-Rus3 1Neuromuscular Disorders Group, BioCruces Health Research Institute, Barakaldo, Bizkaia, Spain; 2Endocrinology, Division of Medicine, University College London, London, UK; 3Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands All authors contributed equally to this manuscript Abstract: Antisense-mediated splicing modulation is a tool that can be exploited in several ways to provide a potential therapy for rare genetic diseases. This approach is currently being tested in clinical trials for Duchenne muscular dystrophy and spinal muscular atrophy. The present review outlines the versatility of the approach to correct cryptic splicing, modulate alternative splicing, restore the open reading frame, and induce protein knockdown, providing examples of each. Finally, we outline a possible path forward toward the clinical application of this approach for a wide variety of inherited rare diseases. Keywords: splicing, therapy, antisense oligonucleotides, cryptic splicing, alternative splicing

  9. Accumulation of GC donor splice signals in mammals

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V


    Full Text Available Abstract The GT dinucleotide in the first two intron positions is the most conserved element of the U2 donor splice signals. However, in a small fraction of donor sites, GT is replaced by GC. A substantial enrichment of GC in donor sites of alternatively spliced genes has been observed previously in human, nematode and Arabidopsis, suggesting that GC signals are important for regulation of alternative splicing. We used parsimony analysis to reconstruct evolution of donor splice sites and inferred 298 GT > GC conversion events compared to 40 GC > GT conversion events in primate and rodent genomes. Thus, there was substantive accumulation of GC donor splice sites during the evolution of mammals. Accumulation of GC sites might have been driven by selection for alternative splicing. Reviewers This article was reviewed by Jerzy Jurka and Anton Nekrutenko. For the full reviews, please go to the Reviewers' Reports section.

  10. In-plane laser forming for high precision alignment

    NARCIS (Netherlands)

    Folkersma, Ger; Römer, Gert-Willem; Brouwer, Dannis; Huis in 't Veld, Bert


    Laser microforming is extensively used to align components with submicrometer accuracy, often after assembly. While laser-bending sheet metal is the most common laser-forming mechanism, the in-plane upsetting mechanism is preferred when a high actuator stiffness is required. A three-bridge planar ac

  11. Alignment Between Genetic and Physical Maps of Gibberella zeae (United States)

    We previously published a genetic map of Gibberella zeae (Fusarium graminearum) based on a cross between Kansas strain Z-3639 (lineage 7) and Japanese strain R-5470 (lineage 6). In this study, that genetic map was aligned with the third assembly of the genomic sequence of G. zeae strain PH-1 (linea...

  12. MUSE alignment onto VLT (United States)

    Laurent, Florence; Renault, Edgard; Boudon, Didier; Caillier, Patrick; Daguisé, Eric; Dupuy, Christophe; Jarno, Aurélien; Lizon, Jean-Louis; Migniau, Jean-Emmanuel; Nicklas, Harald; Piqueras, Laure


    MUSE (Multi Unit Spectroscopic Explorer) is a second generation Very Large Telescope (VLT) integral field spectrograph developed for the European Southern Observatory (ESO). It combines a 1' x 1' field of view sampled at 0.2 arcsec for its Wide Field Mode (WFM) and a 7.5"x7.5" field of view for its Narrow Field Mode (NFM). Both modes will operate with the improved spatial resolution provided by GALACSI (Ground Atmospheric Layer Adaptive Optics for Spectroscopic Imaging), that will use the VLT deformable secondary mirror and 4 Laser Guide Stars (LGS) foreseen in 2015. MUSE operates in the visible wavelength range (0.465-0.93 μm). A consortium of seven institutes is currently commissioning MUSE in the Very Large Telescope for the Preliminary Acceptance in Chile, scheduled for September, 2014. MUSE is composed of several subsystems which are under the responsibility of each institute. The Fore Optics derotates and anamorphoses the image at the focal plane. A Splitting and Relay Optics feed the 24 identical Integral Field Units (IFU), that are mounted within a large monolithic structure. Each IFU incorporates an image slicer, a fully refractive spectrograph with VPH-grating and a detector system connected to a global vacuum and cryogenic system. During 2012 and 2013, all MUSE subsystems were integrated, aligned and tested to the P.I. institute at Lyon. After successful PAE in September 2013, MUSE instrument was shipped to the Very Large Telescope in Chile where that was aligned and tested in ESO integration hall at Paranal. After, MUSE was directly transported, fully aligned and without any optomechanical dismounting, onto VLT telescope where the first light was overcame the 7th of February, 2014. This paper describes the alignment procedure of the whole MUSE instrument with respect to the Very Large Telescope (VLT). It describes how 6 tons could be move with accuracy better than 0.025mm and less than 0.25 arcmin in order to reach alignment requirements. The success

  13. Fiducialisation and initial alignment of CLIC component with micrometric accuracy

    CERN Document Server

    Mainaud Durand, Helene; Buzio, Marco; Caiazza, Domenico; Catalan Lasheras, Nuria; Cherif, Ahmed; Doytchinov, Iordan Petrov; Fuchs, Jean-Frederic; Gaddi, Andrea; Galindo Munoz, Natalia; Gayde, Jean-Christophe; Kamugasa, Solomon William; Modena, Michele; Novotny, Peter; Sanz, Claude; Severino, Giordana; Russenschuck, Stephan; Tshilumba, David; Vlachakis, Vasileios; Wendt, Manfred; Zorzetti, Silvia; CERN. Geneva. ATS Department


    We propose a new solution to fiducialise the three major components of the CLIC collider: quadrupoles, beam-position monitors (BPM), and accelerating structures (AS). This solution is based on the use of a copper-beryllium (CuBe) wire to locate the reference position, i.e. the symmetry axes of the components (their magnetic, respectively electromagnetic centre axis), and to determine their position in the common support assembly defining a local coordinate system, with respect to the fiducials. These alignment targets will be used later to align the support assembly in the tunnel. With such a method, several accelerator components of different types, supported by a dedicated adjustment system, can be simultaneously fiducialised and pre-aligned using the same wire, enabling a micrometric accuracy with help of a 3D coordinate measurement machine (CMM). Alternative solutions based on frequency scanning interferometry (FSI) and micro-triangulation are also under development, to perform such fiducialisation and in...

  14. Identification of common genetic variation that modulates alternative splicing.

    Directory of Open Access Journals (Sweden)

    Jeremy Hull


    Full Text Available Alternative splicing of genes is an efficient means of generating variation in protein function. Several disease states have been associated with rare genetic variants that affect splicing patterns. Conversely, splicing efficiency of some genes is known to vary between individuals without apparent ill effects. What is not clear is whether commonly observed phenotypic variation in splicing patterns, and hence potential variation in protein function, is to a significant extent determined by naturally occurring DNA sequence variation and in particular by single nucleotide polymorphisms (SNPs. In this study, we surveyed the splicing patterns of 250 exons in 22 individuals who had been previously genotyped by the International HapMap Project. We identified 70 simple cassette exon alternative splicing events in our experimental system; for six of these, we detected consistent differences in splicing pattern between individuals, with a highly significant association between splice phenotype and neighbouring SNPs. Remarkably, for five out of six of these events, the strongest correlation was found with the SNP closest to the intron-exon boundary, although the distance between these SNPs and the intron-exon boundary ranged from 2 bp to greater than 1,000 bp. Two of these SNPs were further investigated using a minigene splicing system, and in each case the SNPs were found to exert cis-acting effects on exon splicing efficiency in vitro. The functional consequences of these SNPs could not be predicted using bioinformatic algorithms. Our findings suggest that phenotypic variation in splicing patterns is determined by the presence of SNPs within flanking introns or exons. Effects on splicing may represent an important mechanism by which SNPs influence gene function.

  15. Pre-mRNA splicing in disease and therapeutics


    Singh, Ravi K; Cooper, Thomas A.


    In metazoans, alternative splicing of genes is essential for regulating gene expression and contributing to functional complexity. Computational predictions, comparative genomics, and transcriptome profiling of normal and diseased tissues indicate an unexpectedly high fraction of diseases are caused by mutations that alter splicing. Mutations in cis elements cause mis-splicing of genes that alter gene function and contribute to disease pathology. Mutations of core spliceosomal factors are ass...

  16. Discovery and analysis of evolutionarily conserved intronic splicing regulatory elements.

    Directory of Open Access Journals (Sweden)

    Gene W Yeo


    Full Text Available Knowledge of the functional cis-regulatory elements that regulate constitutive and alternative pre-mRNA splicing is fundamental for biology and medicine. Here we undertook a genome-wide comparative genomics approach using available mammalian genomes to identify conserved intronic splicing regulatory elements (ISREs. Our approach yielded 314 ISREs, and insertions of ~70 ISREs between competing splice sites demonstrated that 84% of ISREs altered 5' and 94% altered 3' splice site choice in human cells. Consistent with our experiments, comparisons of ISREs to known splicing regulatory elements revealed that 40%-45% of ISREs might have dual roles as exonic splicing silencers. Supporting a role for ISREs in alternative splicing, we found that 30%-50% of ISREs were enriched near alternatively spliced (AS exons, and included almost all known binding sites of tissue-specific alternative splicing factors. Further, we observed that genes harboring ISRE-proximal exons have biases for tissue expression and molecular functions that are ISRE-specific. Finally, we discovered that for Nova1, neuronal PTB, hnRNP C, and FOX1, the most frequently occurring ISRE proximal to an alternative conserved exon in the splicing factor strongly resembled its own known RNA binding site, suggesting a novel application of ISRE density and the propensity for splicing factors to auto-regulate to associate RNA binding sites to splicing factors. Our results demonstrate that ISREs are crucial building blocks in understanding general and tissue-specific AS regulation and the biological pathways and functions regulated by these AS events.

  17. Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment

    Directory of Open Access Journals (Sweden)

    Daniels Noah M


    Full Text Available Abstract Background The quality of multiple protein structure alignments are usually computed and assessed based on geometric functions of the coordinates of the backbone atoms from the protein chains. These purely geometric methods do not utilize directly protein sequence similarity, and in fact, determining the proper way to incorporate sequence similarity measures into the construction and assessment of protein multiple structure alignments has proved surprisingly difficult. Results We present Formatt, a multiple structure alignment based on the Matt purely geometric multiple structure alignment program, that also takes into account sequence similarity when constructing alignments. We show that Formatt outperforms Matt and other popular structure alignment programs on the popular HOMSTRAD benchmark. For the SABMark twilight zone benchmark set that captures more remote homology, Formatt and Matt outperform other programs; depending on choice of embedded sequence aligner, Formatt produces either better sequence and structural alignments with a smaller core size than Matt, or similarly sized alignments with better sequence similarity, for a small cost in average RMSD. Conclusions Considering sequence information as well as purely geometric information seems to improve quality of multiple structure alignments, though defining what constitutes the best alignment when sequence and structural measures would suggest different alignments remains a difficult open question.

  18. Spatially confined assembly of nanoparticles. (United States)

    Jiang, Lin; Chen, Xiaodong; Lu, Nan; Chi, Lifeng


    The ability to assemble NPs into ordered structures that are expected to yield collective physical or chemical properties has afforded new and exciting opportunities in the field of nanotechnology. Among the various configurations of nanoparticle assemblies, two-dimensional (2D) NP patterns and one-dimensional (1D) NP arrays on surfaces are regarded as the ideal assembly configurations for many technological devices, for example, solar cells, magnetic memory, switching devices, and sensing devices, due to their unique transport phenomena and the cooperative properties of NPs in assemblies. To realize the potential applications of NP assemblies, especially in nanodevice-related applications, certain key issues must still be resolved, for example, ordering and alignment, manipulating and positioning in nanodevices, and multicomponent or hierarchical structures of NP assemblies for device integration. Additionally, the assembly of NPs with high precision and high levels of integration and uniformity for devices with scaled-down dimensions has become a key and challenging issue. Two-dimensional NP patterns and 1D NP arrays are obtained using traditional lithography techniques (top-down strategies) or interfacial assembly techniques (bottom-up strategies). However, a formidable challenge that persists is the controllable assembly of NPs in desired locations over large areas with high precision and high levels of integration. The difficulty of this assembly is due to the low efficiency of small features over large areas in lithography techniques or the inevitable structural defects that occur during the assembly process. The combination of self-assembly strategies with existing nanofabrication techniques could potentially provide effective and distinctive solutions for fabricating NPs with precise position control and high resolution. Furthermore, the synergistic combination of spatially mediated interactions between nanoparticles and prestructures on surfaces may play

  19. Aligning component upgrades

    Directory of Open Access Journals (Sweden)

    Roberto Di Cosmo


    Full Text Available Modern software systems, like GNU/Linux distributions or Eclipse-based development environment, are often deployed by selecting components out of large component repositories. Maintaining such software systems by performing component upgrades is a complex task, and the users need to have an expressive preferences language at their disposal to specify the kind of upgrades they are interested in. Recent research has shown that it is possible to develop solvers that handle preferences expressed as a combination of a few basic criteria used in the MISC competition, ranging from the number of new components to the freshness of the final configuration. In this work we introduce a set of new criteria that allow the users to specify their preferences for solutions with components aligned to the same upstream sources, provide an efficient encoding and report on the experimental results that prove that optimising these alignment criteria is a tractable problem in practice.

  20. Inflation by alignment

    Energy Technology Data Exchange (ETDEWEB)

    Burgess, C.P. [PH -TH Division, CERN,CH-1211, Genève 23 (Switzerland); Department of Physics & Astronomy, McMaster University,1280 Main Street West, Hamilton ON (Canada); Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo ON (Canada); Roest, Diederik [Van Swinderen Institute for Particle Physics and Gravity, University of Groningen,Nijenborgh 4, 9747 AG Groningen (Netherlands)


    Pseudo-Goldstone bosons (pGBs) can provide technically natural inflatons, as has been comparatively well-explored in the simplest axion examples. Although inflationary success requires trans-Planckian decay constants, f≳M{sub p}, several mechanisms have been proposed to obtain this, relying on (mis-)alignments between potential and kinetic energies in multiple-field models. We extend these mechanisms to a broader class of inflationary models, including in particular the exponential potentials that arise for pGB potentials based on noncompact groups (and so which might apply to moduli in an extra-dimensional setting). The resulting potentials provide natural large-field inflationary models and can predict a larger primordial tensor signal than is true for simpler single-field versions of these models. In so doing we provide a unified treatment of several alignment mechanisms, showing how each emerges as a limit of the more general setup.

  1. Splice-switching antisense oligonucleotides as therapeutic drugs


    Havens, Mallory A.; Hastings, Michelle L.


    Splice-switching oligonucleotides (SSOs) are short, synthetic, antisense, modified nucleic acids that base-pair with a pre-mRNA and disrupt the normal splicing repertoire of the transcript by blocking the RNA–RNA base-pairing or protein–RNA binding interactions that occur between components of the splicing machinery and the pre-mRNA. Splicing of pre-mRNA is required for the proper expression of the vast majority of protein-coding genes, and thus, targeting the process offers a means to manipu...

  2. RNA Splicing: Regulation and Dysregulation in the Heart. (United States)

    van den Hoogenhof, Maarten M G; Pinto, Yigal M; Creemers, Esther E


    RNA splicing represents a post-transcriptional mechanism to generate multiple functional RNAs or proteins from a single transcript. The evolution of RNA splicing is a prime example of the Darwinian function follows form concept. A mutation that leads to a new mRNA (form) that encodes for a new functional protein (function) is likely to be retained, and this way, the genome has gradually evolved to encode for genes with multiple isoforms, thereby creating an enormously diverse transcriptome. Advances in technologies to characterize RNA populations have led to a better understanding of RNA processing in health and disease. In the heart, alternative splicing is increasingly being recognized as an important layer of post-transcriptional gene regulation. Moreover, the recent identification of several cardiac splice factors, such as RNA-binding motif protein 20 and SF3B1, not only provided important insight into the mechanisms underlying alternative splicing but also revealed how these splicing factors impact functional properties of the heart. Here, we review our current knowledge of alternative splicing in the heart, with a particular focus on the major and minor spliceosome, the factors controlling RNA splicing, and the role of alternative splicing in cardiac development and disease.

  3. Evolutionary Insights into RNA trans-Splicing in Vertebrates. (United States)

    Lei, Quan; Li, Cong; Zuo, Zhixiang; Huang, Chunhua; Cheng, Hanhua; Zhou, Rongjia


    Pre-RNA splicing is an essential step in generating mature mRNA. RNA trans-splicing combines two separate pre-mRNA molecules to form a chimeric non-co-linear RNA, which may exert a function distinct from its original molecules. Trans-spliced RNAs may encode novel proteins or serve as noncoding or regulatory RNAs. These novel RNAs not only increase the complexity of the proteome but also provide new regulatory mechanisms for gene expression. An increasing amount of evidence indicates that trans-splicing occurs frequently in both physiological and pathological processes. In addition, mRNA reprogramming based on trans-splicing has been successfully applied in RNA-based therapies for human genetic diseases. Nevertheless, clarifying the extent and evolution of trans-splicing in vertebrates and developing detection methods for trans-splicing remain challenging. In this review, we summarize previous research, highlight recent advances in trans-splicing, and discuss possible splicing mechanisms and functions from an evolutionary viewpoint.

  4. DNA splice site sequences clustering method for conservativeness analysis

    Institute of Scientific and Technical Information of China (English)

    Quanwei Zhang; Qinke Peng; Tao Xu


    DNA sequences that are near to splice sites have remarkable conservativeness,and many researchers have contributed to the prediction of splice site.In order to mine the underlying biological knowledge,we analyze the conservativeness of DNA splice site adjacent sequences by clustering.Firstly,we propose a kind of DNA splice site sequences clustering method which is based on DBSCAN,and use four kinds of dissimilarity calculating methods.Then,we analyze the conservative feature of the clustering results and the experimental data set.

  5. Alignment of concerns

    DEFF Research Database (Denmark)

    Andersen, Tariq Osman; Bansler, Jørgen P.; Kensing, Finn;

    E-health promises to enable and support active patient participation in chronic care. However, these fairly recent innovations are complicated matters and emphasize significant challenges, such as patients’ and clinicians’ different ways of conceptualizing disease and illness. Informed by insight...... from medical phenomenology and our own empirical work in telemonitoring and medical care of heart patients, we propose a design rationale for e-health systems conceptualized as the ‘alignment of concerns’....

  6. Nuclear reactor alignment plate configuration

    Energy Technology Data Exchange (ETDEWEB)

    Altman, David A; Forsyth, David R; Smith, Richard E; Singleton, Norman R


    An alignment plate that is attached to a core barrel of a pressurized water reactor and fits within slots within a top plate of a lower core shroud and upper core plate to maintain lateral alignment of the reactor internals. The alignment plate is connected to the core barrel through two vertically-spaced dowel pins that extend from the outside surface of the core barrel through a reinforcement pad and into corresponding holes in the alignment plate. Additionally, threaded fasteners are inserted around the perimeter of the reinforcement pad and into the alignment plate to further secure the alignment plate to the core barrel. A fillet weld also is deposited around the perimeter of the reinforcement pad. To accomodate thermal growth between the alignment plate and the core barrel, a gap is left above, below and at both sides of one of the dowel pins in the alignment plate holes through with the dowel pins pass.

  7. Orbit IMU alignment: Error analysis (United States)

    Corson, R. W.


    A comprehensive accuracy analysis of orbit inertial measurement unit (IMU) alignments using the shuttle star trackers was completed and the results are presented. Monte Carlo techniques were used in a computer simulation of the IMU alignment hardware and software systems to: (1) determine the expected Space Transportation System 1 Flight (STS-1) manual mode IMU alignment accuracy; (2) investigate the accuracy of alignments in later shuttle flights when the automatic mode of star acquisition may be used; and (3) verify that an analytical model previously used for estimating the alignment error is a valid model. The analysis results do not differ significantly from expectations. The standard deviation in the IMU alignment error for STS-1 alignments was determined to the 68 arc seconds per axis. This corresponds to a 99.7% probability that the magnitude of the total alignment error is less than 258 arc seconds.

  8. Alignment and Load Transfer in Carbon Nanotube and Dicyclopentadiene Composites (United States)

    Severino, Joseph Vincent

    Individual carbon nanotubes (CNTs) are the strongest materials available but their macroscopic assemblies are weak. This work establishes a new thermosetting dicyclopentadiene (DCPD) and CNT composite that increases the strength of CNT assemblies. These high volume fraction and void free structures constitute advanced materials that could one day replace traditional composite systems. To further the understanding of physical interactions between polymer and CNTs, a novel "capstan" load transfer mechanism is also introduced. Self-supporting assemblies of interconnected carbon nanotubes were stretched, twisted and compressed to fashion composites by the infusion and polymerization of low viscosity DCPD based monomeric resins. The properties of the CNTs, polymer and composite were characterized with thermal gravimetric analysis (TGA), dynamic mechanical analysis (DMA) and Raman spectroscopy. The microstructure was analyzed by wide angle X-ray scattering (WAXS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Sheets were drawn at 15 m/min from a growth furnace to impart alignment then stretched to further modify alignment. The mechanical properties were determined in five orientations with respect to the growth direction. The strength was nearly three times higher along this growth direction than it was perpendicular, and modulus was nearly six times higher. Transverse stretching achieved 1.5 times the elongation but alignment was inferior due to CNT kinking that prevented alignment and consolidation. Composites yarns and sheets were investigated for the mechanical properties, microstructure and load transfer. The DCPD resin was found to wet the CNTs and lubricated deformation. This reduced loads during processing, and curing solidified the aligned and consolidated structure. The stretched and twisted composite yarns increased the failure stress 51%. In aligned composite sheet, the failure stress increased 200%. The increased stresses

  9. Seeking the perfect alignment

    CERN Multimedia


    The first full-scale tests of the ATLAS Muon Spectrometer are about to begin in Prévessin. The set-up includes several layers of Monitored Drift Tubes Chambers (MDTs) and will allow tests of the performance of the detectors and of their highly accurate alignment system.   Monitored Drift Chambers in Building 887 in Prévessin, where they are just about to be tested. Muon chambers are keeping the ATLAS Muon Spectrometer team quite busy this summer. Now that most people go on holiday, the beam and alignment tests for these chambers are just starting. These chambers will measure with high accuracy the momentum of high-energy muons, and this implies very demanding requirements for their alignment. The MDT chambers consist of drift tubes, which are gas-filled metal tubes, 3 cm in diameter, with wires running down their axes. With high voltage between the wire and the tube wall, the ionisation due to traversing muons is detected as electrical pulses. With careful timing of the pulses, the position of the muon t...

  10. RECAT - Redundant Channel Alignment Technique (United States)


    distribution unlimited 13. SUPPLEMENTARY NOTES NUWC2015 14. ABSTRACT A problem in the analog-to- digital , (A/D), conversion of broadband tape recorded...Alignment Technique, is used to align data taken on one pass with data from any other pass. The accuracy of this alignment is a function of the digital ...Redundant Channel Alignment Technique; analog-to- digital ; A/D; Broadband Bearing Time Processing 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF

  11. Method for alignment of microwires

    Energy Technology Data Exchange (ETDEWEB)

    Beardslee, Joseph A.; Lewis, Nathan S.; Sadtler, Bryce


    A method of aligning microwires includes modifying the microwires so they are more responsive to a magnetic field. The method also includes using a magnetic field so as to magnetically align the microwires. The method can further include capturing the microwires in a solid support structure that retains the longitudinal alignment of the microwires when the magnetic field is not applied to the microwires.

  12. Identification of cis-acting elements and splicing factors involved in the regulation of BIM Pre-mRNA splicing. (United States)

    Juan, Wen Chun; Roca, Xavier; Ong, S Tiong


    Aberrant changes in the expression of the pro-apoptotic protein, BCL-2-like 11 (BIM), can result in either impaired or excessive apoptosis, which can contribute to tumorigenesis and degenerative disorders, respectively. Altering BIM pre-mRNA splicing is an attractive approach to modulate apoptosis because BIM activity is partly determined by the alternative splicing of exons 3 or 4, whereby exon 3-containing transcripts are not apoptotic. Here we identified several cis-acting elements and splicing factors involved in BIM alternative splicing, as a step to better understand the regulation of BIM expression. We analyzed a recently discovered 2,903-bp deletion polymorphism within BIM intron 2 that biased splicing towards exon 3, and which also impaired BIM-dependent apoptosis. We found that this region harbors multiple redundant cis-acting elements that repress exon 3 inclusion. Furthermore, we have isolated a 23-nt intronic splicing silencer at the 3' end of the deletion that is important for excluding exon 3. We also show that PTBP1 and hnRNP C repress exon 3 inclusion, and that downregulation of PTBP1 inhibited BIM-mediated apoptosis. Collectively, these findings start building our understanding of the cis-acting elements and splicing factors that regulate BIM alternative splicing, and also suggest potential approaches to alter BIM splicing for therapeutic purposes.

  13. Pre-mRNA Splicing in Plants: In Vivo Functions of RNA-Binding Proteins Implicated in the Splicing Process

    Directory of Open Access Journals (Sweden)

    Katja Meyer


    Full Text Available Alternative pre-messenger RNA splicing in higher plants emerges as an important layer of regulation upon exposure to exogenous and endogenous cues. Accordingly, mutants defective in RNA-binding proteins predicted to function in the splicing process show severe phenotypic alterations. Among those are developmental defects, impaired responses to pathogen threat or abiotic stress factors, and misregulation of the circadian timing system. A suite of splicing factors has been identified in the model plant Arabidopsis thaliana. Here we summarize recent insights on how defects in these splicing factors impair plant performance.

  14. SOAP2: an improved ultrafast tool for short read alignment

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Yu, Chang; Li, Yingrui


    SUMMARY: SOAP2 is a significantly improved version of the short oligonucleotide alignment program that both reduces computer memory usage and increases alignment speed at an unprecedented rate. We used a Burrows Wheeler Transformation (BWT) compression index to substitute the seed strategy...... for indexing the reference sequence in the main memory. We tested it on the whole human genome and found that this new algorithm reduced memory usage from 14.7 to 5.4 GB and improved alignment speed by 20-30 times. SOAP2 is compatible with both single- and paired-end reads. Additionally, this tool now supports...... multiple text and compressed file formats. A consensus builder has also been developed for consensus assembly and SNP detection from alignment of short reads on a reference genome. AVAILABILITY:

  15. Small-molecule inhibition of HIV pre-mRNA splicing as a novel antiretroviral therapy to overcome drug resistance.

    Directory of Open Access Journals (Sweden)

    Nadia Bakkour


    Full Text Available The development of multidrug-resistant viruses compromises antiretroviral therapy efficacy and limits therapeutic options. Therefore, it is an ongoing task to identify new targets for antiretroviral therapy and to develop new drugs. Here, we show that an indole derivative (IDC16 that interferes with exonic splicing enhancer activity of the SR protein splicing factor SF2/ASF suppresses the production of key viral proteins, thereby compromising subsequent synthesis of full-length HIV-1 pre-mRNA and assembly of infectious particles. IDC16 inhibits replication of macrophage- and T cell-tropic laboratory strains, clinical isolates, and strains with high-level resistance to inhibitors of viral protease and reverse transcriptase. Importantly, drug treatment of primary blood cells did not alter splicing profiles of endogenous genes involved in cell cycle transition and apoptosis. Thus, human splicing factors represent novel and promising drug targets for the development of antiretroviral therapies, particularly for the inhibition of multidrug-resistant viruses.

  16. The conserved splicing factor SUA controls alternative splicing of the developmental regulator ABI3 in Arabidopsis.

    NARCIS (Netherlands)

    Sugliani, M.; Brambilla, V.; Clerkx, E.J.M.; Koornneef, M.; Soppe, W.J.J.


    ABSCISIC ACID INSENSITIVE3 (ABI3) is a major regulator of seed maturation in Arabidopsis thaliana. We detected two ABI3 transcripts, ABI3- and ABI3-ß, which encode full-length and truncated proteins, respectively. Alternative splicing of ABI3 is developmentally regulated, and the ABI3-ß transcript a

  17. Semiautomated improvement of RNA alignments

    DEFF Research Database (Denmark)

    Andersen, Ebbe Sloth; Lind-Thomsen, Allan; Knudsen, Bjarne


    We have developed a semiautomated RNA sequence editor (SARSE) that integrates tools for analyzing RNA alignments. The editor highlights different properties of the alignment by color, and its integrated analysis tools prevent the introduction of errors when doing alignment editing. SARSE readily...... connects to external tools to provide a flexible semiautomatic editing environment. A new method, Pcluster, is introduced for dividing the sequences of an RNA alignment into subgroups with secondary structure differences. Pcluster was used to evaluate 574 seed alignments obtained from the Rfam database...... and we identified 71 alignments with significant prediction of inconsistent base pairs and 102 alignments with significant prediction of novel base pairs. Four RNA families were used to illustrate how SARSE can be used to manually or automatically correct the inconsistent base pairs detected by Pcluster...

  18. ATLAS Inner Detector Alignment

    CERN Document Server

    Bocci, A


    The ATLAS experiment is a multi-purpose particle detector that will study high-energy particle collisions produced by the Large Hadron Collider at CERN. In order to achieve its physics goals, the ATLAS tracking requires that the positions of the silicon detector elements have to be known to a precision better than 10 μm. Several track-based alignment algorithms have been developed for the Inner Detector. An extensive validation has been performed with simulated events and real data coming from the ATLAS. Results from such validation are reported in this paper.

  19. CELT optics Alignment Procedure (United States)

    Mast, Terry S.; Nelson, Jerry E.; Chanan, Gary A.; Noethe, Lothar


    The California Extremely Large Telescope (CELT) is a project to build a 30-meter diameter telescope for research in astronomy at visible and infrared wavelengths. The current optical design calls for a primary, secondary, and tertiary mirror with Ritchey-Chretién foci at two Nasmyth platforms. The primary mirror is a mosaic of 1080 actively-stabilized hexagonal segments. This paper summarizes a CELT report that describes a step-by-step procedure for aligning the many degrees of freedom of the CELT optics.

  20. TSGC and JSC Alignment (United States)

    Sanchez, Humberto


    NASA and the SGCs are, by design, intended to work closely together and have synergistic Vision, Mission, and Goals. The TSGC affiliates and JSC have been working together, but not always in a concise, coordinated, nor strategic manner. Today we have a couple of simple ideas to present about how TSGC and JSC have started to work together in a more concise, coordinated, and strategic manner, and how JSC and non-TSG Jurisdiction members have started to collaborate: Idea I: TSGC and JSC Technical Alignment Idea II: Concept of Clusters.

  1. A comprehensive evaluation of alignment algorithms in the context of RNA-seq. (United States)

    Lindner, Robert; Friedel, Caroline C


    Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete.

  2. A comprehensive evaluation of alignment algorithms in the context of RNA-seq.

    Directory of Open Access Journals (Sweden)

    Robert Lindner

    Full Text Available Transcriptome sequencing (RNA-Seq overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete.

  3. Quantitative regulation of alternative splicing in evolution and development

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob L; Roy, Scott W;


    Alternative splicing (AS) is a widespread mechanism with an important role in increasing transcriptome and proteome diversity by generating multiple different products from the same gene. Evolutionary studies of AS have focused primarily on the conservation of alternatively spliced sequences...... layer in complex gene regulatory networks and in the emergence of genetic novelties....

  4. Tissue-specific splicing factor gene expression signatures

    NARCIS (Netherlands)

    A.R. Grosso; A.Q. Gomes (Anita); N.L. Barbosa-Morais (Nuno); S. Caldeira (Sandra); N.P. Thorne (Natalie); G. Grech (Godfrey); M.M. von Lindern (Marieke); M. Carmo-Fonseca (Maria)


    textabstractThe alternative splicing code that controls and coordinates the transcriptome in complex multicellular organisms remains poorly understood. It has long been argued that regulation of alternative splicing relies on combinatorial interactions between multiple proteins, and that tissue-spec

  5. Insights into alternative splicing of sarcomeric genes in the heart. (United States)

    Weeland, Cornelis J; van den Hoogenhof, Maarten M; Beqqali, Abdelaziz; Creemers, Esther E


    Driven by rapidly evolving technologies in next-generation sequencing, alternative splicing has emerged as a crucial layer in gene expression, greatly expanding protein diversity and governing complex biological processes in the cardiomyocyte. At the core of cardiac contraction, the physical properties of the sarcomere are carefully orchestrated through alternative splicing to fit the varying demands on the heart. By the recent discovery of RBM20 and RBM24, two major heart and skeletal muscle-restricted splicing factors, it became evident that alternative splicing events in the heart occur in regulated networks rather than in isolated events. Analysis of knockout mice of these splice factors has shed light on the importance of these fundamental processes in the heart. In this review, we discuss recent advances in our understanding of the role and regulation of alternative splicing in the developing and diseased heart, specifically within the sarcomere. Through various examples (titin, myomesin, troponin T, tropomyosin and LDB3) we illustrate how alternative splicing regulates the functional properties of the sarcomere. Finally, we evaluate opportunities and obstacles to modulate alternative splicing in therapeutic approaches for cardiac disease.

  6. 30 CFR 18.43 - Explosion-proof splice boxes. (United States)


    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false Explosion-proof splice boxes. 18.43 Section 18.43 Mineral Resources MINE SAFETY AND HEALTH ADMINISTRATION, DEPARTMENT OF LABOR TESTING, EVALUATION... Design Requirements § 18.43 Explosion-proof splice boxes. Internal connections shall be rigidly held...

  7. Pre-mRNA splicing in disease and therapeutics. (United States)

    Singh, Ravi K; Cooper, Thomas A


    In metazoans, alternative splicing of genes is essential for regulating gene expression and contributing to functional complexity. Computational predictions, comparative genomics, and transcriptome profiling of normal and diseased tissues indicate that an unexpectedly high fraction of diseases are caused by mutations that alter splicing. Mutations in cis elements cause missplicing of genes that alter gene function and contribute to disease pathology. Mutations of core spliceosomal factors are associated with hematolymphoid neoplasias, retinitis pigmentosa, and microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1). Mutations in the trans regulatory factors that control alternative splicing are associated with autism spectrum disorder, amyotrophic lateral sclerosis (ALS), and various cancers. In addition to discussing the disorders caused by these mutations, this review summarizes therapeutic approaches that have emerged to correct splicing of individual genes or target the splicing machinery.

  8. Splice Site Mutations in the ATP7A Gene

    DEFF Research Database (Denmark)

    Skjørringe, Tina; Tümer, Zeynep; Møller, Lisbeth Birk


    Menkes disease (MD) is caused by mutations in the ATP7A gene. We describe 33 novel splice site mutations detected in patients with MD or the milder phenotypic form, Occipital Horn Syndrome. We review these 33 mutations together with 28 previously published splice site mutations. We investigate 12...... mutations for their effect on the mRNA transcript in vivo. Transcriptional data from another 16 mutations were collected from the literature. The theoretical consequences of splice site mutations, predicted with the bioinformatics tool Human Splice Finder, were investigated and evaluated in relation...... to in vivo results. Ninety-six percent of the mutations identified in 45 patients with classical MD were predicted to have a significant effect on splicing, which concurs with the absence of any detectable wild-type transcript in all 19 patients investigated in vivo. Sixty-seven percent of the mutations...

  9. [Statistical analysis of DNA sequences nearby splicing sites]. (United States)

    Korzinov, O M; Astakhova, T V; Vlasov, P K; Roĭtberg, M A


    Recognition of coding regions within eukaryotic genomes is one of oldest but yet not solved problems of bioinformatics. New high-accuracy methods of splicing sites recognition are needed to solve this problem. A question of current interest is to identify specific features of nucleotide sequences nearby splicing sites and recognize sites in sequence context. We performed a statistical analysis of human genes fragment database and revealed some characteristics of nucleotide sequences in splicing sites neighborhood. Frequencies of all nucleotides and dinucleotides in splicing sites environment were computed and nucleotides and dinucleotides with extremely high\\low occurrences were identified. Statistical information obtained in this work can be used in further development of the methods of splicing sites annotation and exon-intron structure recognition.

  10. Comparative Analysis of Splice Site Regions by Information Content

    Institute of Scientific and Technical Information of China (English)

    T. Shashi Rekha; Chanchal K. Mitra


    We have applied concepts from information theory for a comparative analysis of donor (gt) and acceptor (ag) splice site regions in the genes of five different organisms by calculating their mutual information content (relative entropy) over a selected block of nucleotides. A similar pattern that the information content decreases as the block size increases was observed for both regions in all the organisms studied. This result suggests that the information required for splicing might be contained in the consensus of ~6-8 nt at both regions. We assume from our study that even though the nucleotides are showing some degrees of conservation in the flanking regions of the splice sites, certain level of variability is still tolerated,which leads the splicing process to occur normally even if the extent of base pairing is not fully satisfied. We also suggest that this variability can be compensated by recognizing different splice sites with different spliceosomal factors.

  11. Using Sorting by Reversal: Breakpoint Graph for Gene Assembly in Ciliates (United States)

    Brijder, Robert; Jan Hoogeboom, Hendrik


    The theory of gene assembly in ciliates has much in common with the theory of sorting by reversal. Both model processes that are based on splicing, and have a fixed begin and end product. The main difference is the type of splicing operations used to obtain the end product from the begin product. In this overview paper we show that the concept of breakpoint graph, known from the theory of sorting by reversal, has many uses in the theory of gene assembly. Our aim is to present the material in an intuitive and informal manner to allow for an efficient introduction into the subject.

  12. Structural analysis of Aircraft fuselage splice joint (United States)

    Udaya Prakash, R.; Kumar, G. Raj; Vijayanandh, R.; Senthil Kumar, M.; Ramganesh, T.


    In Aviation sector, composite materials and its application to each component are one of the prime factors of consideration due to the high strength to weight ratio, design flexibility and non-corrosive so that the composite materials are widely used in the low weight constructions and also it can be treated as a suitable alternative to metals. The objective of this paper is to estimate and compare the suitability of a composite skin joint in an aircraft fuselage with different joints by simulating the displacement, normal stress, vonmises stress and shear stress with the help of numerical solution methods. The reference Z-stringer component of this paper is modeled by CATIA and numerical simulation is carried out by ANSYS has been used for splice joint presents in the aircraft fuselage with three combinations of joints such as riveted joint, bonded joint and hybrid joint. Nowadays the stringers are using to avoid buckling of fuselage skin, it has joined together by rivets and they are connected end to end by splice joint. Design and static analysis of three-dimensional models of joints such as bonded, riveted and hybrid are carried out and results are compared.

  13. All about alignment

    CERN Multimedia


    The ALICE absorbers, iron wall and superstructure have been installed with great precision. The ALICE front absorber, positioned in the centre of the detector, has been installed and aligned. Weighing more than 400 tonnes, the ALICE absorbers and the surrounding support structures have been installed and aligned with a precision of 1-2 mm, hardly an easy task but a very important one. The ALICE absorbers are made of three parts: the front absorber, a 35-tonne cone-shaped structure, and two small-angle absorbers, long straight cylinder sections weighing 18 and 40 tonnes. The three pieces lined up have a total length of about 17 m. In addition to these, ALICE technicians have installed a 300-tonne iron filter wall made of blocks that fit together like large Lego pieces and a surrounding metal support structure to hold the tracking and trigger chambers. The absorbers house the vacuum chamber and are also the reference surface for the positioning of the tracking and trigger chambers. For this reason, the ab...

  14. Testing the tidal alignment model of galaxy intrinsic alignment

    CERN Document Server

    Blazek, Jonathan; Seljak, Uros


    Weak gravitational lensing has become a powerful probe of large-scale structure and cosmological parameters. Precision weak lensing measurements require an understanding of the intrinsic alignment of galaxy ellipticities, which can in turn inform models of galaxy formation. It is hypothesized that elliptical galaxies align with the background tidal field and that this alignment mechanism dominates the correlation between ellipticities on cosmological scales (in the absence of lensing). We use recent large-scale structure measurements from the Sloan Digital Sky Survey to test this picture with several statistics: (1) the correlation between ellipticity and galaxy overdensity, w_{g+}; (2) the intrinsic alignment auto-correlation functions; (3) the correlation functions of curl-free, E, and divergence-free, B, modes (the latter of which is zero in the linear tidal alignment theory); (4) the alignment correlation function, w_g(r_p,theta), a recently developed statistic that generalizes the galaxy correlation func...

  15. Overcoming low-alignment signal contrast induced alignment failure by alignment signal enhancement (United States)

    Lee, Byeong Soo; Kim, Young Ha; Hwang, Hyunwoo; Lee, Jeongjin; Kong, Jeong Heung; Kang, Young Seog; Paarhuis, Bart; Kok, Haico; de Graaf, Roelof; Weichselbaum, Stefan; Droste, Richard; Mason, Christopher; Aarts, Igor; de Boeij, Wim P.


    Overlay is one of the key factors which enables optical lithography extension to 1X node DRAM manufacturing. It is natural that accurate wafer alignment is a prerequisite for good device overlay. However, alignment failures or misalignments are commonly observed in a fab. There are many factors which could induce alignment problems. Low alignment signal contrast is one of the main issues. Alignment signal contrast can be degraded by opaque stack materials or by alignment mark degradation due to processes like CMP. This issue can be compounded by mark sub-segmentation from design rules in combination with double or quadruple spacer process. Alignment signal contrast can be improved by applying new material or process optimization, which sometimes lead to the addition of another process-step with higher costs. If we can amplify the signal components containing the position information and reduce other unwanted signal and background contributions then we can improve alignment performance without process change. In this paper we use ASML's new alignment sensor (as was introduced and released on the NXT:1980Di) and sample wafers with special stacks which can induce poor alignment signal to demonstrate alignment and overlay improvement.

  16. Pareto optimal pairwise sequence alignment. (United States)

    DeRonne, Kevin W; Karypis, George


    Sequence alignment using evolutionary profiles is a commonly employed tool when investigating a protein. Many profile-profile scoring functions have been developed for use in such alignments, but there has not yet been a comprehensive study of Pareto optimal pairwise alignments for combining multiple such functions. We show that the problem of generating Pareto optimal pairwise alignments has an optimal substructure property, and develop an efficient algorithm for generating Pareto optimal frontiers of pairwise alignments. All possible sets of two, three, and four profile scoring functions are used from a pool of 11 functions and applied to 588 pairs of proteins in the ce_ref data set. The performance of the best objective combinations on ce_ref is also evaluated on an independent set of 913 protein pairs extracted from the BAliBASE RV11 data set. Our dynamic-programming-based heuristic approach produces approximated Pareto optimal frontiers of pairwise alignments that contain comparable alignments to those on the exact frontier, but on average in less than 1/58th the time in the case of four objectives. Our results show that the Pareto frontiers contain alignments whose quality is better than the alignments obtained by single objectives. However, the task of identifying a single high-quality alignment among those in the Pareto frontier remains challenging.

  17. A quantitative, high-throughput reverse genetic screen reveals novel connections between Pre-mRNA splicing and 5' and 3' end transcript determinants.

    Directory of Open Access Journals (Sweden)

    Laura-Oana Albulescu

    Full Text Available Here we present the development and implementation of a genome-wide reverse genetic screen in the budding yeast, Saccharomyces cerevisiae, that couples high-throughput strain growth, robotic RNA isolation and cDNA synthesis, and quantitative PCR to allow for a robust determination of the level of nearly any cellular RNA in the background of ~5,500 different mutants. As an initial test of this approach, we sought to identify the full complement of factors that impact pre-mRNA splicing. Increasing lines of evidence suggest a relationship between pre-mRNA splicing and other cellular pathways including chromatin remodeling, transcription, and 3' end processing, yet in many cases the specific proteins responsible for functionally connecting these pathways remain unclear. Moreover, it is unclear whether all pathways that are coupled to splicing have been identified. As expected, our approach sensitively detects pre-mRNA accumulation in the vast majority of strains containing mutations in known splicing factors. Remarkably, however, several additional candidates were found to cause increases in pre-mRNA levels similar to that seen for canonical splicing mutants, none of which had previously been implicated in the splicing pathway. Instead, several of these factors have been previously implicated to play roles in chromatin remodeling, 3' end processing, and other novel categories. Further analysis of these factors using splicing-sensitive microarrays confirms that deletion of Bdf1, a factor that links transcription initiation and chromatin remodeling, leads to a global splicing defect, providing evidence for a novel connection between pre-mRNA splicing and this component of the SWR1 complex. By contrast, mutations in 3' end processing factors such as Cft2 and Yth1 also result in pre-mRNA splicing defects, although only for a subset of transcripts, suggesting that spliceosome assembly in S. cerevisiae may more closely resemble mammalian models of exon

  18. Deciphering Transcriptome and Complex Alternative Splicing Transcripts in Mammary Gland Tissues from Cows Naturally Infected with Staphylococcus aureus Mastitis (United States)

    Jiang, Qiang; Yang, Chun Hong; Zhang, Yan; Sun, Yan; Li, Rong Ling; Wang, Chang Fa; Zhong, Ji Feng; Huang, Jin Ming


    Alternative splicing (AS) contributes to the complexity of the mammalian proteome and plays an important role in diseases, including infectious diseases. The differential AS patterns of these transcript sequences between the healthy (HS3A) and mastitic (HS8A) cows naturally infected by Staphylococcus aureus were compared to understand the molecular mechanisms underlying mastitis resistance and susceptibility. In this study, using the Illumina paired-end RNA sequencing method, 1352 differentially expressed genes (DEGs) with higher than twofold changes were found in the HS3A and HS8A mammary gland tissues. Gene ontology and KEGG pathway analyses revealed that the cytokine–cytokine receptor interaction pathway is the most significantly enriched pathway. Approximately 16k annotated unigenes were respectively identified in two libraries, based on the bovine Bos taurus UMD3.1 sequence assembly and search. A total of 52.62% and 51.24% annotated unigenes were alternatively spliced in term of exon skipping, intron retention, alternative 5′ splicing and alternative 3ʹ splicing. Additionally, 1,317 AS unigenes were HS3A-specific, whereas 1,093 AS unigenes were HS8A-specific. Some immune-related genes, such as ITGB6, MYD88, ADA, ACKR1, and TNFRSF1B, and their potential relationships with mastitis were highlighted. From Chromosome 2, 4, 6, 7, 10, 13, 14, 17, and 20, 3.66% (HS3A) and 5.4% (HS8A) novel transcripts, which harbor known quantitative trait locus associated with clinical mastitis, were identified. Many DEGs in the healthy and mastitic mammary glands are involved in immune, defense, and inflammation responses. These DEGs, which exhibit diverse and specific splicing patterns and events, can endow dairy cattle with the potential complex genetic resistance against mastitis. PMID:27459697

  19. AXAF Alignment Test System Autocollimating Flat Error Correction (United States)

    Lewis, Timothy S.


    The alignment test system for the advanced x ray astrophysics facility (AXAF) high-resolution mirror assembly (HRMA) determines the misalignment of the HRMA by measuring the displacement of a beam of light reflected by the HRMA mirrors and an autocollimating flat (ACF). This report shows how to calibrate the system to compensate for errors introduced by the ACF, using measurements taken with the ACF in different positions. It also shows what information can be obtained from alignment test data regarding errors in the shapes of the HRMA mirrors. Simulated results based on measured ACF surface data are presented.

  20. Onorbit IMU alignment error budget (United States)

    Corson, R. W.


    The Star Tracker, Crew Optical Alignment Sight (COAS), and Inertial Measurement Unit (IMU) from a complex navigation system with a multitude of error sources were combined. A complete list of the system errors is presented. The errors were combined in a rational way to yield an estimate of the IMU alignment accuracy for STS-1. The expected standard deviation in the IMU alignment error for STS-1 type alignments was determined to be 72 arc seconds per axis for star tracker alignments and 188 arc seconds per axis for COAS alignments. These estimates are based on current knowledge of the star tracker, COAS, IMU, and navigation base error specifications, and were partially verified by preliminary Monte Carlo analysis.

  1. Lunar Alignments - Identification and Analysis (United States)

    González-García, A. César

    Lunar alignments are difficult to establish given the apparent lack of written accounts clearly pointing toward lunar alignments for individual temples. While some individual cases are reviewed and highlighted, the weight of the proof must fall on statistical sampling. Some definitions for the lunar alignments are provided in order to clarify the targets, and thus, some new tools are provided to try to test the lunar hypothesis in several cases, especially in megalithic astronomy.

  2. GraphAlignment: Bayesian pairwise alignment of biological networks

    Directory of Open Access Journals (Sweden)

    Kolář Michal


    Full Text Available Abstract Background With increased experimental availability and accuracy of bio-molecular networks, tools for their comparative and evolutionary analysis are needed. A key component for such studies is the alignment of networks. Results We introduce the Bioconductor package GraphAlignment for pairwise alignment of bio-molecular networks. The alignment incorporates information both from network vertices and network edges and is based on an explicit evolutionary model, allowing inference of all scoring parameters directly from empirical data. We compare the performance of our algorithm to an alternative algorithm, Græmlin 2.0. On simulated data, GraphAlignment outperforms Græmlin 2.0 in several benchmarks except for computational complexity. When there is little or no noise in the data, GraphAlignment is slower than Græmlin 2.0. It is faster than Græmlin 2.0 when processing noisy data containing spurious vertex associations. Its typical case complexity grows approximately as O(N2.6. On empirical bacterial protein-protein interaction networks (PIN and gene co-expression networks, GraphAlignment outperforms Græmlin 2.0 with respect to coverage and specificity, albeit by a small margin. On large eukaryotic PIN, Græmlin 2.0 outperforms GraphAlignment. Conclusions The GraphAlignment algorithm is robust to spurious vertex associations, correctly resolves paralogs, and shows very good performance in identification of homologous vertices defined by high vertex and/or interaction similarity. The simplicity and generality of GraphAlignment edge scoring makes the algorithm an appropriate choice for global alignment of networks.

  3. Functional analysis of alternative splicing of the FLOWERING LOCUS T orthologous gene in Chrysanthemum morifolium (United States)

    Mao, Yachao; Sun, Jing; Cao, Peipei; Zhang, Rong; Fu, Qike; Chen, Sumei; Chen, Fadi; Jiang, Jiafu


    As the junction of floral development pathways, the FLOWERING LOCUS T (FT) protein called ‘florigen’ plays an important role in the process of plant flowering through signal integration. We isolated four transcripts encoding different isoforms of a FT orthologous gene CmFTL1, from Chrysanthemum morifolium cultivar ‘Jimba’. Sequence alignments suggested that the four transcripts are related to the intron 1. Expression analysis showed that four alternative splicing (AS) forms of CmFTL1 varied depending on the developmental stage of the flower. The functional complement experiment using an Arabidopsis mutant ft-10 revealed that the archetypal and AS forms of CmFTL1 had the function of complementing late flower phenotype in different levels. In addition, transgenic confirmation at transcript level showed CmFTL1 and CmFTL1ast coexist in the same tissue type at the same developmental stage, indicating a post-transcriptional modification of CmFTL1 in Arabidopsis. Moreover, ectopic expression of different AS forms in chrysanthemum resulted in the development of multiple altered phenotypes, varying degrees of early flowering. We found that an alternative splicing form (CmFTL1-astE134) without the exon 2 lacked the ability causing the earlier flower phenotype. The evidence in this study indicates that complex alternative processing of CmFTL1 transcripts in C. morifolium may be associated with flowering regulation and hold some potential for biotechnical engineering to create early-flowering phenotypes in ornamental cultivars. PMID:27917290

  4. A molecular inversion probe assay for detecting alternative splicing

    Directory of Open Access Journals (Sweden)

    Palm Curtis


    Full Text Available Absract Background A sensitive, high-throughput method for monitoring pre-mRNA splicing on a genomic scale is needed to understand the spectrum of alternatively spliced mRNA in human cells. Results We adapted Molecular Inversion Probes (MIPs, a padlock-probe based technology, for the multiplexed capture and quantitation of individual splice events in human tissues. Individual MIP capture probes can be quantified using either DNA microarrays or high-throughput sequencing, which permits independent assessment of each spliced junction. Using our methodology we successfully identified 100% of our positive controls and showed that there is a strong correlation between the data from our alternative splicing MIP (asMIP assay and quantitative PCR. Conclusion The asMIP assay provides a sensitive, accurate and multiplexed means for measuring pre-mRNA splicing. Fully optimized, we estimate that the assay could accommodate a throughput of greater than 20,000 splice junctions in a single reaction. This would represent a significant improvement over existing technologies.

  5. Inference of splicing regulatory activities by sequence neighborhood analysis.

    Directory of Open Access Journals (Sweden)

    Michael B Stadler


    Full Text Available Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI that predicts sequences with activity in regulating a biochemical process based on the local density of known sites in sequence space. Applied to the problem of RNA splicing regulation, NI was used to predict hundreds of new exonic splicing enhancer (ESE and silencer (ESS hexanucleotides from known human ESEs and ESSs. These predictions were supported by cross-validation analysis, by analysis of published splicing regulatory activity data, by sequence-conservation analysis, and by measurement of the splicing regulatory activity of 24 novel predicted ESEs, ESSs, and neutral sequences using an in vivo splicing reporter assay. These results demonstrate the ability of NI to accurately predict splicing regulatory activity and show that the scope of exonic splicing regulatory elements is substantially larger than previously anticipated. Analysis of orthologous exons in four mammals showed that the NI score of ESEs, a measure of function, is much more highly conserved above background than ESE primary sequence. This observation indicates a high degree of selection for ESE activity in mammalian exons, with surprisingly frequent interchangeability between ESE sequences.

  6. Global Splicing Pattern Reversion during Somatic Cell Reprogramming

    Directory of Open Access Journals (Sweden)

    Sho Ohta


    Full Text Available Alternative splicing generates multiple transcripts from a single gene, and cell-type-specific splicing profiles are important for the properties and functions of the cells. Recently, somatic cells have been shown to undergo dedifferentiation after the forced expression of transcription factors. However, it remains unclear whether somatic cell splicing is reorganized during reprogramming. Here, by combining deep sequencing with high-throughput absolute qRT-PCR, we show that somatic splicing profiles revert to pluripotent ones during reprogramming. Remarkably, the splicing pattern in pluripotent stem cells resembles that in testes, and the regulatory regions have specific characteristics in length and sequence. Furthermore, our siRNA screen has identified RNA-binding proteins that regulate splicing events in iPSCs. We have then demonstrated that two of the RNA-binding proteins, U2af1 and Srsf3, play a role in somatic cell reprogramming. Our results indicate that the drastic alteration in splicing represents part of the molecular network involved in the reprogramming process.

  7. A synonymous polymorphic variation in ACADM exon 11 affects splicing efficiency and may affect fatty acid oxidation

    DEFF Research Database (Denmark)

    Bruun, Gitte Hoffmann; Doktor, Thomas Koed; Andresen, Brage Storstein


    beta-oxidation of medium-chain fatty acids. We examined the functional basis for this association and identified linkage between rs211718 and the intragenic synonymous polymorphic variant c.1161A>G in ACADM exon 11 (rs1061337). Employing minigene studies we show that the c.1161A allele is associated...... proteins SRSF1 and hnRNP A1. Using publicly available pre-aligned RNA-seq data, we find that the ACADM c.1161G allele is expressed at significantly higher levels than the c.1161A allele across different tissues. This supports that c.1161A>G is a functional SNP, which leads to higher MCAD expression......, perhaps due to improved splicing. This study is a proof of principle that synonymous SNPs are not neutral. By changing the binding sites for splicing regulatory proteins they can have significant effects on pre-mRNA splicing and thus protein function. In addition, this study shows that for a sequence...

  8. Pyro-Align: Sample-Align based Multiple Alignment system for Pyrosequencing Reads of Large Number

    CERN Document Server

    Saeed, Fahad


    Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment of pyrosequenceing reads is complex mainly because of 2 factors. One being the huge number of reads, making the use of traditional heuristics,that scale very poorly for large number, unsuitable. The second reason is that the alignment cannot be performed arbitrarily, because the position of the reads with respect to the original genome is important and has to be taken into account.In this report we present a short description of the multiple alignment system for pyrosequencing reads.

  9. Capillary Self-Alignment of Microchips on Soft Substrates

    Directory of Open Access Journals (Sweden)

    Bo Chang


    Full Text Available Soft micro devices and stretchable electronics have attracted great interest for their potential applications in sensory skins and wearable bio-integrated devices. One of the most important steps in building printed circuits is the alignment of assembled micro objects. Previously, the capillary self-alignment of microchips driven by surface tension effects has been shown to be able to achieve high-throughput and high-precision in the integration of micro parts on rigid hydrophilic/superhydrophobic patterned surfaces. In this paper, the self-alignment of microchips on a patterned soft and stretchable substrate, which consists of hydrophilic pads surrounded by a superhydrophobic polydimethylsiloxane (PDMS background, is demonstrated for the first time. A simple process has been developed for making superhydrophobic soft surface by replicating nanostructures of black silicon onto a PDMS surface. Different kinds of PDMS have been investigated, and the parameters for fabricating superhydrophobic PDMS have been optimized. A self-alignment strategy has been proposed that can result in reliable self-alignment on a soft PDMS substrate. Our results show that capillary self-alignment has great potential for building soft printed circuits.

  10. Mask alignment system for semiconductor processing

    Energy Technology Data Exchange (ETDEWEB)

    Webb, Aaron P.; Carlson, Charles T.; Weaver, William T.; Grant, Christopher N.


    A mask alignment system for providing precise and repeatable alignment between ion implantation masks and workpieces. The system includes a mask frame having a plurality of ion implantation masks loosely connected thereto. The mask frame is provided with a plurality of frame alignment cavities, and each mask is provided with a plurality of mask alignment cavities. The system further includes a platen for holding workpieces. The platen may be provided with a plurality of mask alignment pins and frame alignment pins configured to engage the mask alignment cavities and frame alignment cavities, respectively. The mask frame can be lowered onto the platen, with the frame alignment cavities moving into registration with the frame alignment pins to provide rough alignment between the masks and workpieces. The mask alignment cavities are then moved into registration with the mask alignment pins, thereby shifting each individual mask into precise alignment with a respective workpiece.

  11. Alternative splicing variations in mouse CAPS2: differential expression and functional properties of splicing variants

    Directory of Open Access Journals (Sweden)

    Furuichi Teiichi


    Full Text Available Abstract Background Ca2+-dependent activator protein 2 (CAPS2/CADPS2 is a secretory vesicle-associated protein involved in the release of neurotrophin. We recently reported that an aberrant, alternatively spliced CAPS2 mRNA that lacks exon 3 (CAPS2Δexon3 is detected in some patients with autism. Splicing variations in mouse CAPS2 and their expression and functions remain unclear. Results In this study, we defined 31 exons in the mouse CAPS2 gene and identified six alternative splicing variants, CAPS2a-f. CAPS2a is an isoform lacking exons 22 and 25, which encode part of the Munc13-1-homologous domain (MHD. CAPS2b lacks exon 25. CAPS2c lacks exons 11 and 22. CAPS2d, 2e, and 2f have C-terminal deletions from exon 14, exon 12, and exon 5, respectively. On the other hand, a mouse counterpart of CAPS2Δexon3 was not detected in the mouse tissues tested. CAPS2b was expressed exclusively in the brain, and the other isoforms were highly expressed in the brain, but also in some non-neural tissues. In the brain, all isoforms showed predominant expression patterns in the cerebellum. In the developing cerebellum, CAPS2b showed an up-regulated expression pattern, whereas the other isoforms exhibited transiently peaked expression patterns. CAPS2 proteins were mostly recovered in soluble fractions, but some were present in membrane fractions, except for CAPS2c and 2f, both of which lack the PH domain, suggesting that the PH domain is important for membrane association. In contrast to CAPS2a and 2b, CAPS2c showed slightly decreased BDNF-releasing activity, which is likely due to the C-terminal truncation of the PH domain in CAPS2c. Conclusion This study indicates that, in mouse, there are six splicing variants of CAPS2 (CAPS2a-f, and that these are subdivided into two groups: a long form containing the C-terminal MHD and a short form lacking the C-terminal MHD. These results demonstrate that the splicing variations correlate with their expression patterns and

  12. Comparing de novo assemblers for 454 transcriptome data

    Directory of Open Access Journals (Sweden)

    Blaxter Mark L


    Full Text Available Abstract Background Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Results Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects, which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Conclusions Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies

  13. CATO: The Clone Alignment Tool.

    Directory of Open Access Journals (Sweden)

    Peter V Henstock

    Full Text Available High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1 a top-level summary of the top candidate sequences aligned to each reference sequence, 2 a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3 a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow.

  14. CATO: The Clone Alignment Tool. (United States)

    Henstock, Peter V; LaPan, Peter


    High-throughput cloning efforts produce large numbers of sequences that need to be aligned, edited, compared with reference sequences, and organized as files and selected clones. Different pieces of software are typically required to perform each of these tasks. We have designed a single piece of software, CATO, the Clone Alignment Tool, that allows a user to align, evaluate, edit, and select clone sequences based on comparisons to reference sequences. The input and output are designed to be compatible with standard data formats, and thus suitable for integration into a clone processing pipeline. CATO provides both sequence alignment and visualizations to facilitate the analysis of cloning experiments. The alignment algorithm matches each of the relevant candidate sequences against each reference sequence. The visualization portion displays three levels of matching: 1) a top-level summary of the top candidate sequences aligned to each reference sequence, 2) a focused alignment view with the nucleotides of matched sequences displayed against one reference sequence, and 3) a pair-wise alignment of a single reference and candidate sequence pair. Users can select the minimum matching criteria for valid clones, edit or swap reference sequences, and export the results to a summary file as part of the high-throughput cloning workflow.

  15. RNA Structural Alignments, Part I

    DEFF Research Database (Denmark)

    Havgaard, Jakob Hull; Gorodkin, Jan


    Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and alig...... the methods based on the Sankoff algorithm. All the practical implementations of the algorithm use heuristics to make them run in reasonable time and memory. These heuristics are also described in this chapter.......Simultaneous alignment and secondary structure prediction of RNA sequences is often referred to as "RNA structural alignment." A class of the methods for structural alignment is based on the principles proposed by Sankoff more than 25 years ago. The Sankoff algorithm simultaneously folds and aligns...... two or more sequences. The advantage of this algorithm over those that separate the folding and alignment steps is that it makes better predictions. The disadvantage is that it is slower and requires more computer memory to run. The amount of computational resources needed to run the Sankoff algorithm...

  16. Lexical alignment in triadic communication. (United States)

    Foltz, Anouschka; Gaspers, Judith; Thiele, Kristina; Stenneken, Prisca; Cimiano, Philipp


    Lexical alignment refers to the adoption of one's interlocutor's lexical items. Accounts of the mechanisms underlying such lexical alignment differ (among other aspects) in the role assigned to addressee-centered behavior. In this study, we used a triadic communicative situation to test which factors may modulate the extent to which participants' lexical alignment reflects addressee-centered behavior. Pairs of naïve participants played a picture matching game and received information about the order in which pictures were to be matched from a voice over headphones. On critical trials, participants did or did not hear a name for the picture to be matched next over headphones. Importantly, when the voice over headphones provided a name, it did not match the name that the interlocutor had previously used to describe the object. Participants overwhelmingly used the word that the voice over headphones provided. This result points to non-addressee-centered behavior and is discussed in terms of disrupting alignment with the interlocutor as well as in terms of establishing alignment with the voice over headphones. In addition, the type of picture (line drawing vs. tangram shape) independently modulated lexical alignment, such that participants showed more lexical alignment to their interlocutor for (more ambiguous) tangram shapes compared to line drawings. Overall, the results point to a rather large role for non-addressee-centered behavior during lexical alignment.

  17. Vacuum Alignment with more Flavors

    DEFF Research Database (Denmark)

    Ryttov, Thomas


    We study the alignment of the vacuum in gauge theories with $N_f$ Dirac fermions transforming according to a complex representation of the gauge group. The alignment of the vacuum is produced by adding a small mass perturbation to the theory. We study in detail the $N_f=2,3$ and $4$ case. For $N...

  18. Anisotropic hypersonic phonon propagation in films of aligned ellipsoids. (United States)

    Beltramo, Peter J; Schneider, Dirk; Fytas, George; Furst, Eric M


    A material with anisotropic elastic mechanical properties and a direction-dependent hypersonic band gap is fabricated using ac electric field-directed convective self-assembly of colloidal ellipsoids. The frequency of the gap, which is detected in the direction perpendicular to particle alignment and entirely absent parallel to alignment, and the effective sound velocities can be tuned by the particle aspect ratio. We hypothesize that the band gap originates from the primary eigenmode peak, the m-splitted (s,1,2) mode, of the particle resonating with the effective medium. These results reveal the potential for powerful control of the hypersonic phononic band diagram by combining anisotropic particles and self-assembly.

  19. Null Lens Assembly for X-Ray Mirror Segments (United States)

    Robinson, David W.


    A document discusses a null lens assembly that allows laser interferometry of 60 deg. slumped glass mirror segments used in x-ray mirrors. The assembly consists of four lenses in precise alignment to each other, with incorporated piezoelectric nanometer stepping actuators to position the lenses in six degrees of freedom for positioning relative to each other.

  20. The CMS Silicon Tracker Alignment

    CERN Document Server

    Castello, R


    The alignment of the Strip and Pixel Tracker of the Compact Muon Solenoid experiment, with its large number of independent silicon sensors and its excellent spatial resolution, is a complex and challenging task. Besides high precision mounting, survey measurements and the Laser Alignment System, track-based alignment is needed to reach the envisaged precision.\\\\ Three different algorithms for track-based alignment were successfully tested on a sample of cosmic-ray data collected at the Tracker Integration Facility, where 15\\% of the Tracker was tested. These results, together with those coming from the CMS global run, will provide the basis for the full-scale alignment of the Tracker, which will be carried out with the first \\emph{p-p} collisions.

  1. Alignment of flexible protein structures. (United States)

    Shatsky, M; Fligelman, Z Y; Nussinov, R; Wolfson, H J


    We present two algorithms which align flexible protein structures. Both apply efficient structural pattern detection and graph theoretic techniques. The FlexProt algorithm simultaneously detects the hinge regions and aligns the rigid subparts of the molecules. It does it by efficiently detecting maximal congruent rigid fragments in both molecules and calculating their optimal arrangement which does not violate the protein sequence order. The FlexMol algorithm is sequence order independent, yet requires as input the hypothesized hinge positions. Due its sequence order independence it can also be applied to protein-protein interface matching and drug molecule alignment. It aligns the rigid parts of the molecule using the Geometric Hashing method and calculates optimal connectivity among these parts by graph-theoretic techniques. Both algorithms are highly efficient even compared with rigid structure alignment algorithms. Typical running times on a standard desktop PC (400 MHz) are about 7 seconds for FlexProt and about 1 minute for FlexMol.

  2. Alignments in the nobelium isotopes

    Institute of Scientific and Technical Information of China (English)

    ZHENG Shi-Zie; XU Fu-Rong; YUAN Cen-Xi; QI Chong


    Total-Routhian-Surface calculations have been performed to investigate the deformation and align-ment properties of the No isotopes. It is found that normal deformed and superdeformed states in these nuclei can coexist at low excitation energies. In neutron-deficient No isotopes, the superdeformed shapes can even become the ground states. Moreover, we plotted the kinematic moments of inertia of the No isotopes, which follow very nicely available experimental data. It is noted that, as the rotational frequency increases, align-ments develop at hω=0.2-0.3 MeV. Our calculations show that the occupation of the vj orbital plays an important role in the alignments of the No isotopes.

  3. Downlink Interference Alignment

    CERN Document Server

    Suh, Changho; Tse, David


    We develop an interference alignment (IA) technique for a downlink cellular system. In the uplink, IA schemes need channel-state-information exchange across base-stations of different cells, but our downlink IA technique requires feedback only within a cell. As a result, the proposed scheme can be implemented with a few changes to an existing cellular system where the feedback mechanism (within a cell) is already being considered for supporting multi-user MIMO. Not only is our proposed scheme implementable with little effort, it can in fact provide substantial gain especially when interference from a dominant interferer (base-station) is significantly stronger than the remaining interference: it is shown that in the two-isolated cell layout, our scheme provides four-fold gain in throughput performance over a standard multi-user MIMO technique. We show through simulations that our technique provides respectable gain under more realistic scenarios: it gives approximately 55% and 20% gain for a linear cell layou...

  4. Interference Alignment for Secrecy

    CERN Document Server

    Koyluoglu, Onur Ozan; Lai, Lifeng; Poor, H Vincent


    This paper studies the frequency/time selective $K$-user Gaussian interference channel with secrecy constraints. Two distinct models, namely the interference channel with confidential messages and the one with an external eavesdropper, are analyzed. The key difference between the two models is the lack of channel state information (CSI) about the external eavesdropper. Using interference alignment along with secrecy pre-coding, it is shown that each user can achieve non-zero secure Degrees of Freedom (DoF) for both cases. More precisely, the proposed coding scheme achieves $\\frac{K-2}{2K-2}$ secure DoF {\\em with probability one} per user in the confidential messages model. For the external eavesdropper scenario, on the other hand, it is shown that each user can achieve $\\frac{K-2}{2K}$ secure DoF {\\em in the ergodic setting}. Remarkably, these results establish the {\\em positive impact} of interference on the secrecy capacity region of wireless networks.

  5. Space Mirror Alignment System (United States)

    Jau, Bruno M.; McKinney, Colin; Smythe, Robert F.; Palmer, Dean L.


    An optical alignment mirror mechanism (AMM) has been developed with angular positioning accuracy of +/-0.2 arcsec. This requires the mirror s linear positioning actuators to have positioning resolutions of +/-112 nm to enable the mirror to meet the angular tip/tilt accuracy requirement. Demonstrated capabilities are 0.1 arc-sec angular mirror positioning accuracy, which translates into linear positioning resolutions at the actuator of 50 nm. The mechanism consists of a structure with sets of cross-directional flexures that enable the mirror s tip and tilt motion, a mirror with its kinematic mount, and two linear actuators. An actuator comprises a brushless DC motor, a linear ball screw, and a piezoelectric brake that holds the mirror s position while the unit is unpowered. An interferometric linear position sensor senses the actuator s position. The AMMs were developed for an Astrometric Beam Combiner (ABC) optical bench, which is part of an interferometer development. Custom electronics were also developed to accommodate the presence of multiple AMMs within the ABC and provide a compact, all-in-one solution to power and control the AMMs.

  6. RNA-sequencing of a mouse-model of spinal muscular atrophy reveals tissue-wide changes in splicing of U12-dependent introns

    DEFF Research Database (Denmark)

    Doktor, Thomas Koed; Hua, Yimin; Andersen, Henriette Skovgaard;


    Spinal Muscular Atrophy (SMA) is a neuromuscular disorder caused by insufficient levels of the Survival of Motor Neuron (SMN) protein. SMN is expressed ubiquitously and functions in RNA processing pathways that include trafficking of mRNA and assembly of snRNP complexes. Importantly, SMA severity...... is correlated with decreased snRNP assembly activity. In particular, the minor spliceosomal snRNPs are affected, and some U12-dependent introns have been reported to be aberrantly spliced in patient cells and animal models. SMA is characterized by loss of motor neurons, but the underlying mechanism is largely...... unknown. It is likely that aberrant splicing of genes expressed in motor neurons is involved in SMA pathogenesis, but increasing evidence indicates that pathologies also exist in other tissues. We present here a comprehensive RNA-seq study that covers multiple tissues in an SMA mouse model. We show...

  7. High-throughput sequence alignment using Graphics Processing Units

    Directory of Open Access Journals (Sweden)

    Trapnell Cole


    Full Text Available Abstract Background The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies. Results This paper describes MUMmerGPU, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity Graphics Processing Units (GPUs in common workstations. MUMmerGPU uses the new Compute Unified Device Architecture (CUDA from nVidia to align multiple query sequences against a single reference sequence stored as a suffix tree. By processing the queries in parallel on the highly parallel graphics card, MUMmerGPU achieves more than a 10-fold speedup over a serial CPU version of the sequence alignment kernel, and outperforms the exact alignment component of MUMmer on a high end CPU by 3.5-fold in total application time when aligning reads from recent sequencing projects using Solexa/Illumina, 454, and Sanger sequencing technologies. Conclusion MUMmerGPU is a low cost, ultra-fast sequence alignment program designed to handle the increasing volume of data produced by new, high-throughput sequencing technologies. MUMmerGPU demonstrates that even memory-intensive applications can run significantly faster on the relatively low-cost GPU than on the CPU.

  8. Magnetic alignment and the Poisson alignment reference system (United States)

    Griffith, L. V.; Schenz, R. F.; Sommargren, G. E.


    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This article begins with a review of the motivation for developing an alignment system that will assure better than 100-μm accuracy in the alignment of the magnetic axis throughout an FEL. The 100-μm accuracy is an error circle about an ideal axis for 300 m or more. The article describes techniques for identifying the magnetic axes of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development of a straight-line reference based on the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. The Poisson alignment reference system should be accurate to 25 μm over 300 m, which is believed to be a factor-of-4 improvement over earlier techniques. An error budget shows that only 25% of the total budgeted tolerance is used for the alignment reference system, so the remaining tolerances should fall within the allowable range for FEL alignment.

  9. Binding of a candidate splice regulator to a calcitonin-specific splice enhancer regulates calcitonin/CGRP pre-mRNA splicing. (United States)

    Coleman, Timothy P; Tran, Quincy; Roesser, James R


    The calcitonin/calcitonin gene-related peptide (CGRP) pre-mRNA is alternatively processed in a tissue-specific manner leading to the production of calcitonin mRNA in thyroid C cells and CGRP mRNA in neurons. A candidate calcitonin/CGRP splice regulator (CSR) isolated from rat brain was shown to inhibit calcitonin-specific splicing in vitro. CSR specifically binds to two regions in the calcitonin-specific exon 4 RNA previously demonstrated to function as a bipartate exonic splice enhancer (ESE). The two regions, A and B element, are necessary for inclusion of exon 4 into calcitonin mRNA. A novel RNA footprinting method based on the UV cross-linking assay was used to define the site of interaction between CSR and B element RNA. Base changes at the CSR binding site prevented CSR binding to B element RNA and CSR was unable to inhibit in vitro splicing of pre-mRNAs containing the mutated CSR binding site. When expressed in cells that normally produce predominantly CGRP mRNA, a calcitonin/CGRP gene containing the mutated CSR binding site expressed predominantly calcitonin mRNA. These observations demonstrate that CSR binding to the calcitonin-specific ESE regulates calcitonin/CGRP pre-mRNA splicing.

  10. Sabot assembly

    Energy Technology Data Exchange (ETDEWEB)

    Bzorgi, Fariborz


    A sabot assembly includes a projectile and a housing dimensioned and configured for receiving the projectile. An air pressure cavity having a cavity diameter is disposed between a front end and a rear end of the housing. Air intake nozzles are in fluid communication with the air pressure cavity and each has a nozzle diameter less than the cavity diameter. In operation, air flows through the plurality of air intake nozzles and into the air pressure cavity upon firing of the projectile from a gun barrel to pressurize the air pressure cavity for assisting in separation of the housing from the projectile upon the sabot assembly exiting the gun barrel.

  11. Alternative splicing of follicle-stimulating hormone receptor pre-mRNA: cloning and characterization of two alternatively spliced mRNA transcripts

    NARCIS (Netherlands)

    R. Kraaij (Robert); M. Verhoef-Post (Miriam); J.A. Grootegoed (Anton); A.P.N. Themmen (Axel)


    textabstractGlycoprotein hormone receptors contain a large extracellular domain that is encoded by multiple exons, facilitating the possibility of expressing alternatively spliced transcripts. We have cloned two new splice variants of the rat follicle-stimulating hormon

  12. Alternative splice variants in TIM barrel proteins from human genome correlate with the structural and evolutionary modularity of this versatile protein fold. (United States)

    Ochoa-Leyva, Adrián; Montero-Morán, Gabriela; Saab-Rincón, Gloria; Brieba, Luis G; Soberón, Xavier


    After the surprisingly low number of genes identified in the human genome, alternative splicing emerged as a major mechanism to generate protein diversity in higher eukaryotes. However, it is still not known if its prevalence along the genome evolution has contributed to the overall functional protein diversity or if it simply reflects splicing noise. The (βα)8 barrel or TIM barrel is one of the most frequent, versatile, and ancient fold encountered among enzymes. Here, we analyze the structural modifications present in TIM barrel proteins from the human genome product of alternative splicing events. We found that 87% of all splicing events involved deletions; most of these events resulted in protein fragments that corresponded to the (βα)2, (βα)4, (βα)5, (βα)6, and (βα)7 subdomains of TIM barrels. Because approximately 7% of all the splicing events involved internal β-strand substitutions, we decided, based on the genomic data, to design β-strand and α-helix substitutions in a well-studied TIM barrel enzyme. The biochemical characterization of one of the chimeric variants suggests that some of the splice variants in the human genome with β-strand substitutions may be evolving novel functions via either the oligomeric state or substrate specificity. We provide results of how the splice variants represent subdomains that correlate with the independently folding and evolving structural units previously reported. This work is the first to observe a link between the structural features of the barrel and a recurrent genetic mechanism. Our results suggest that it is reasonable to expect that a sizeable fraction of splice variants found in the human genome represent structurally viable functional proteins. Our data provide additional support for the hypothesis of the origin of the TIM barrel fold through the assembly of smaller subdomains. We suggest a model of how nature explores new proteins through alternative splicing as a mechanism to diversify the

  13. The peculiarities of large intron splicing in animals. (United States)

    Shepard, Samuel; McCreary, Mark; Fedorov, Alexei


    In mammals a considerable 92% of genes contain introns, with hundreds and hundreds of these introns reaching the incredible size of over 50,000 nucleotides. These "large introns" must be spliced out of the pre-mRNA in a timely fashion, which involves bringing together distant 5' and 3' acceptor and donor splice sites. In invertebrates, especially Drosophila, it has been shown that larger introns can be spliced efficiently through a process known as recursive splicing-a consecutive splicing from the 5'-end at a series of combined donor-acceptor splice sites called RP-sites. Using a computational analysis of the genomic sequences, we show that vertebrates lack the proper enrichment of RP-sites in their large introns, and, therefore, require some other method to aid splicing. We analyzed over 15,000 non-redundant, large introns from six mammals, 1,600 from chicken and zebrafish, and 560 non-redundant large introns from five invertebrates. Our bioinformatic investigation demonstrates that, unlike the studied invertebrates, the studied vertebrate genomes contain consistently abundant amounts of direct and complementary strand interspersed repetitive elements (mainly SINEs and LINEs) that may form stems with each other in large introns. This examination showed that predicted stems are indeed abundant and stable in the large introns of mammals. We hypothesize that such stems with long loops within large introns allow intron splice sites to find each other more quickly by folding the intronic RNA upon itself at smaller intervals and, thus, reducing the distance between donor and acceptor sites.

  14. Co-transcriptional splicing in two yeasts


    Herzel, Lydia


    Cellular function and physiology are largely established through regulated gene expression. The first step in gene expression, transcription of the genomic DNA into RNA, is a process that is highly aligned at the levels of initiation, elongation and termination. In eukaryotes, protein-coding genes are exclusively transcribed by RNA polymerase II (Pol II). Upon transcription of the first 15-20 nucleotides (nt), the emerging nascent RNA 5’ end is modified with a 7-methylguanosyl cap. This is on...

  15. Desmin splice variants causing cardiac and skeletal myopathy. (United States)

    Park, K Y; Dalakas, M C; Goebel, H H; Ferrans, V J; Semino-Mora, C; Litvak, S; Takeda, K; Goldfarb, L G


    Desmin myopathy is a hereditary or sporadic cardiac and skeletal myopathy characterised by intracytoplasmic accumulation of desmin reactive deposits in muscle cells. We have characterised novel splice site mutations in the gene desmin resulting in deletion of the entire exon 3 during the pre-mRNA splicing. Sequencing of cDNA and genomic DNA identified a heterozygous de novo A to G change at the +3 position of the splice donor site of intron 3 (IVS3+3A-->G) in a patient with sporadic skeletal and cardiac myopathy. A G to A transition at the highly conserved -1 nucleotide position of intron 2 affecting the splice acceptor site (IVS2-1G-->A) was found in an unrelated patient with a similar phenotype. Expression of genomic DNA fragments carrying the IVS3+3A-->G and IVS2-1G-->A mutations confirmed that these mutations cause exon 3 deletion. Aberrant splicing leads to an in frame deletion of 32 complete codons and is predicted to result in mutant desmin lacking 32 amino acids from the 1B segment of the alpha helical rod. Functional analysis of the mutant desmin in SW13 (vim-) cells showed aggregation of abnormal coarse clumps of desmin positive material dispersed throughout the cytoplasm. This is the first report on the pathogenic potentials of splice site mutations in the desmin gene.

  16. Width of gene expression profile drives alternative splicing.

    Directory of Open Access Journals (Sweden)

    Daniel Wegmann

    Full Text Available Alternative splicing generates an enormous amount of functional and proteomic diversity in metazoan organisms. This process is probably central to the macromolecular and cellular complexity of higher eukaryotes. While most studies have focused on the molecular mechanism triggering and controlling alternative splicing, as well as on its incidence in different species, its maintenance and evolution within populations has been little investigated. Here, we propose to address these questions by comparing the structural characteristics as well as the functional and transcriptional profiles of genes with monomorphic or polymorphic splicing, referred to as MS and PS genes, respectively. We find that MS and PS genes differ particularly in the number of tissues and cell types where they are expressed.We find a striking deficit of PS genes on the sex chromosomes, particularly on the Y chromosome where it is shown not to be due to the observed lower breadth of expression of genes on that chromosome. The development of a simple model of evolution of cis-regulated alternative splicing leads to predictions in agreement with these observations. It further predicts the conditions for the emergence and the maintenance of cis-regulated alternative splicing, which are both favored by the tissue specific expression of splicing variants. We finally propose that the width of the gene expression profile is an essential factor for the acquisition of new transcript isoforms that could later be maintained by a new form of balancing selection.

  17. Splice site mutations in the ATP7A gene.

    Directory of Open Access Journals (Sweden)

    Tina Skjørringe

    Full Text Available Menkes disease (MD is caused by mutations in the ATP7A gene. We describe 33 novel splice site mutations detected in patients with MD or the milder phenotypic form, Occipital Horn Syndrome. We review these 33 mutations together with 28 previously published splice site mutations. We investigate 12 mutations for their effect on the mRNA transcript in vivo. Transcriptional data from another 16 mutations were collected from the literature. The theoretical consequences of splice site mutations, predicted with the bioinformatics tool Human Splice Finder, were investigated and evaluated in relation to in vivo results. Ninety-six percent of the mutations identified in 45 patients with classical MD were predicted to have a significant effect on splicing, which concurs with the absence of any detectable wild-type transcript in all 19 patients investigated in vivo. Sixty-seven percent of the mutations identified in 12 patients with milder phenotypes were predicted to have no significant effect on splicing, which concurs with the presence of wild-type transcript in 7 out of 9 patients investigated in vivo. Both the in silico predictions and the in vivo results support the hypothesis previously suggested by us and others, that the presence of some wild-type transcript is correlated to a milder phenotype.

  18. The functional modulation of epigenetic regulators by alternative splicing

    Directory of Open Access Journals (Sweden)

    Martínez-Balbás Marian


    Full Text Available Abstract Background Epigenetic regulators (histone acetyltransferases, methyltransferases, chromatin-remodelling enzymes, etc play a fundamental role in the control of gene expression by modifying the local state of chromatin. However, due to their recent discovery, little is yet known about their own regulation. This paper addresses this point, focusing on alternative splicing regulation, a mechanism already known to play an important role in other protein families, e.g. transcription factors, membrane receptors, etc. Results To this end, we compiled the data available on the presence/absence of alternative splicing for a set of 160 different epigenetic regulators, taking advantage of the relatively large amount of unexplored data on alternative splicing available in public databases. We found that 49 % (70 % in human of these genes express more than one transcript. We then studied their alternative splicing patterns, focusing on those changes affecting the enzyme's domain composition. In general, we found that these sequence changes correspond to different mechanisms, either repressing the enzyme's function (e.g. by creating dominant-negative inhibitors of the functional isoform or creating isoforms with new functions. Conclusion We conclude that alternative splicing of epigenetic regulators can be an important tool for the function modulation of these enzymes. Considering that the latter control the transcriptional state of large sets of genes, we propose that epigenetic regulation of gene expression is itself strongly regulated by alternative splicing.

  19. RNA splicing is responsive to MBNL1 dose.

    Directory of Open Access Journals (Sweden)

    Sonali P Jog

    Full Text Available Myotonic dystrophy (DM1 is a highly variable, multi-system disorder resulting from the expansion of an untranslated CTG tract in DMPK. In DM1 expanded CUG repeat RNAs form hairpin secondary structures that bind and aberrantly sequester the RNA splice regulator, MBNL1. RNA splice defects resulting as a consequence of MBNL1 depletion have been shown to play a key role in the development of DM1 pathology. In patient populations, both the number and severity of DM1 symptoms increase broadly as a function of CTG tract length. However significant variability in the DM1 phenotype is observed in patients encoding similar CTG repeat numbers. Here we demonstrate that a gradual decrease in MBNL1 levels results both in the expansion of the repertoire of splice defects and an increase in the severity of the splice alterations. Thus, MBNL1 loss does not have an all or none outcome but rather shows a graded effect on the number and severity of the ensuing splice defects. Our results suggest that once a critical threshold is reached, relatively small dose variations of free MBNL1 levels, which may reflect modest changes in the size of the CUG tract or the extent of hairpin secondary structure formation, can significantly alter the number and severity of splice abnormalities and thus contribute to the phenotype variability observed in DM1 patients.

  20. Abnormalities in Alternative Splicing of Apoptotic Genes and Cardiovascular Diseases

    Directory of Open Access Journals (Sweden)

    Zodwa Dlamini


    Full Text Available Apoptosis is required for normal heart development in the embryo, but has also been shown to be an important factor in the occurrence of heart disease. Alternative splicing of apoptotic genes is currently emerging as a diagnostic and therapeutic target for heart disease. This review addresses the involvement of abnormalities in alternative splicing of apoptotic genes in cardiac disorders including cardiomyopathy, myocardial ischemia and heart failure. Many pro-apoptotic members of the Bcl-2 family have alternatively spliced isoforms that lack important active domains. These isoforms can play a negative regulatory role by binding to and inhibiting the pro-apoptotic forms. Alternative splicing is observed to be increased in various cardiovascular diseases with the level of alternate transcripts increasing elevated in diseased hearts compared to healthy subjects. In many cases these isoforms appear to be the underlying cause of the disease, while in others they may be induced in response to cardiovascular pathologies. Regardless of this, the detection of alternate splicing events in the heart can serve as useful diagnostic or prognostic tools, while those splicing events that seem to play a causative role in cardiovascular disease make attractive future drug targets.

  1. Aligning for Innovation - Alignment Strategy to Drive Innovation (United States)

    Johnson, Hurel; Teltschik, David; Bussey, Horace, Jr.; Moy, James


    With the sudden need for innovation that will help the country achieve its long-term space exploration objectives, the question of whether NASA is aligned effectively to drive the innovation that it so desperately needs to take space exploration to the next level should be entertained. Authors such as Robert Kaplan and David North have noted that companies that use a formal system for implementing strategy consistently outperform their peers. They have outlined a six-stage management systems model for implementing strategy, which includes the aligning of the organization towards its objectives. This involves the alignment of the organization from the top down. This presentation will explore the impacts of existing U.S. industrial policy on technological innovation; assess the current NASA organizational alignment and its impacts on driving technological innovation; and finally suggest an alternative approach that may drive the innovation needed to take the world to the next level of space exploration, with NASA truly leading the way.

  2. Magnetic axis alignment and the Poisson alignment reference system (United States)

    Griffith, Lee V.; Schenz, Richard F.; Sommargren, Gary E.


    Three distinct metrological operations are necessary to align a free-electron laser (FEL): the magnetic axis must be located, a straight line reference (SLR) must be generated, and the magnetic axis must be related to the SLR. This paper begins with a review of the motivation for developing an alignment system that will assure better than 100 micrometer accuracy in the alignment of the magnetic axis throughout an FEL. The paper describes techniques for identifying the magnetic axis of solenoids, quadrupoles, and wiggler poles. Propagation of a laser beam is described to the extent of revealing sources of nonlinearity in the beam. Development and use of the Poisson line, a diffraction effect, is described in detail. Spheres in a large-diameter laser beam create Poisson lines and thus provide a necessary mechanism for gauging between the magnetic axis and the SLR. Procedures for installing FEL components and calibrating alignment fiducials to the magnetic axes of the components are also described. An error budget shows that the Poisson alignment reference system will make it possible to meet the alignment tolerances for an FEL.

  3. A factor related to pseudouridine synthases is required for chloroplast group II intron trans-splicing in Chlamydomonas reinhardtii. (United States)

    Perron, K; Goldschmidt-Clermont, M; Rochaix, J D


    In Chlamydomonas reinhardtii, the psaA mRNA is assembled by a process involving two steps of trans-splicing that remove two group II introns and give rise to the mature mRNA. The products of at least 14 nuclear genes and one chloroplast gene (tscA) are necessary for this process. We have cloned Maa2, one of the nuclear genes involved in trans-splicing of the second intron. Maa2 encodes a protein with similarity to conserved domains of pseudouridine synthases, but mutagenesis of putative catalytic residues showed that this activity may not be required for trans-splicing of psaA RNA. Although it is not clear whether the pseudouridine synthase activity has been maintained in Maa2, it is possible that this enzyme was recruited during evolution as an RNA chaperone for folding or stabilizing the psaA intron. The Maa2 protein appears to be associated through ionic interactions with a low density membrane system in the chloroplast that also contains RNA-binding proteins involved in translation.

  4. The splicing activator DAZAP1 integrates splicing control into MEK/Erk-regulated cell proliferation and migration (United States)

    Choudhury, Rajarshi; Roy, Sreerupa Ghose; Tsai, Yihsuan S.; Tripathy, Ashutosh; Graves, Lee M.; Wang, Zefeng


    Alternative splicing of pre-messenger RNA (mRNA) is a critical stage of gene regulation in response to environmental stimuli. Here we show that DAZAP1, an RNA-binding protein involved in mammalian development and spermatogenesis, promotes inclusion of weak exons through specific recognition of diverse cis-elements. The carboxy-terminal proline-rich domain of DAZAP1 interacts with and neutralizes general splicing inhibitors, and is sufficient to activate splicing when recruited to pre-mRNA. This domain is phosphorylated by the MEK/Erk (extracellular signal-regulated protein kinase) pathway and this modification is essential for the splicing regulatory activity and the nuclear/cytoplasmic translocation of DAZAP1. Using mRNA-seq, we identify endogenous splicing events regulated by DAZAP1, many of which are involved in maintaining cell growth. Knockdown or over-expression of DAZAP1 causes a cell proliferation defect. Taken together, these studies reveal a molecular mechanism that integrates splicing control into MEK/Erk-regulated cell proliferation.

  5. Learning the sequence determinants of alternative splicing from millions of random sequences. (United States)

    Rosenberg, Alexander B; Patwardhan, Rupali P; Shendure, Jay; Seelig, Georg


    Most human transcripts are alternatively spliced, and many disease-causing mutations affect RNA splicing. Toward better modeling the sequence determinants of alternative splicing, we measured the splicing patterns of over two million (M) synthetic mini-genes, which include degenerate subsequences totaling over 100 M bases of variation. The massive size of these training data allowed us to improve upon current models of splicing, as well as to gain new mechanistic insights. Our results show that the vast majority of hexamer sequence motifs measurably influence splice site selection when positioned within alternative exons, with multiple motifs acting additively rather than cooperatively. Intriguingly, motifs that enhance (suppress) exon inclusion in alternative 5' splicing also enhance (suppress) exon inclusion in alternative 3' or cassette exon splicing, suggesting a universal mechanism for alternative exon recognition. Finally, our empirically trained models are highly predictive of the effects of naturally occurring variants on alternative splicing in vivo.

  6. Pupil Alignment Considerations for Large, Deployable Space Telescopes (United States)

    Bos, Brent J.; Ohl, Raymond G.; Kubalak, Daivd A.


    For many optical systems the properties and alignment of the internal apertures and pupils are not critical or controlled with high precision during optical system design, fabrication or assembly. In wide angle imaging systems, for instance, the entrance pupil position and orientation is typically unconstrained and varies over the system s field of view in order to optimize image quality. Aperture tolerances usually do not receive the same amount of scrutiny as optical surface aberrations or throughput characteristics because performance degradation is typically graceful with misalignment, generally only causing a slight reduction in system sensitivity due to vignetting. But for a large deployable space-based observatory like the James Webb Space Telescope (JWST), we have found that pupil alignment is a key parameter. For in addition to vignetting, JWST pupil errors cause uncertainty in the wavefront sensing process that is used to construct the observatory on-orbit. Furthermore they also open stray light paths that degrade the science return from some of the telescope s instrument channels. In response to these consequences, we have developed several pupil measurement techniques for the cryogenic vacuum test where JWST science instrument pupil alignment is verified. These approaches use pupil alignment references within the JWST science instruments; pupil imaging lenses in three science instrument channels; and unique pupil characterization features in the optical test equipment. This will allow us to verify and crosscheck the lateral pupil alignment of the JWST science instruments to approximately 1-2% of their pupil diameters.

  7. RF Jitter Modulation Alignment Sensing (United States)

    Ortega, L. F.; Fulda, P.; Diaz-Ortiz, M.; Perez Sanchez, G.; Ciani, G.; Voss, D.; Mueller, G.; Tanner, D. B.


    We will present the numerical and experimental results of a new alignment sensing scheme which can reduce the complexity of alignment sensing systems currently used, while maintaining the same shot noise limited sensitivity. This scheme relies on the ability of electro-optic beam deflectors to create angular modulation sidebands in radio frequency, and needs only a single-element photodiode and IQ demodulation to generate error signals for tilt and translation degrees of freedom in one dimension. It distances itself from current techniques by eliminating the need for beam centering servo systems, quadrant photodetectors and Gouy phase telescopes. RF Jitter alignment sensing can be used to reduce the complexity in the alignment systems of many laser optical experiments, including LIGO and the ALPS experiment.

  8. SmD1 Modulates the miRNA Pathway Independently of Its Pre-mRNA Splicing Function.

    Directory of Open Access Journals (Sweden)

    Xiao-Peng Xiong


    Full Text Available microRNAs (miRNAs are a class of endogenous regulatory RNAs that play a key role in myriad biological processes. Upon transcription, primary miRNA transcripts are sequentially processed by Drosha and Dicer ribonucleases into ~22-24 nt miRNAs. Subsequently, miRNAs are incorporated into the RNA-induced silencing complexes (RISCs that contain Argonaute (AGO family proteins and guide RISC to target RNAs via complementary base pairing, leading to post-transcriptional gene silencing by a combination of translation inhibition and mRNA destabilization. Select pre-mRNA splicing factors have been implicated in small RNA-mediated gene silencing pathways in fission yeast, worms, flies and mammals, but the underlying molecular mechanisms are not well understood. Here, we show that SmD1, a core component of the Drosophila small nuclear ribonucleoprotein particle (snRNP implicated in splicing, is required for miRNA biogenesis and function. SmD1 interacts with both the microprocessor component Pasha and pri-miRNAs, and is indispensable for optimal miRNA biogenesis. Depletion of SmD1 impairs the assembly and function of the miRISC without significantly affecting the expression of major canonical miRNA pathway components. Moreover, SmD1 physically and functionally associates with components of the miRISC, including AGO1 and GW182. Notably, miRNA defects resulting from SmD1 silencing can be uncoupled from defects in pre-mRNA splicing, and the miRNA and splicing machineries are physically and functionally distinct entities. Finally, photoactivatable-ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP analysis identifies numerous SmD1-binding events across the transcriptome and reveals direct SmD1-miRNA interactions. Our study suggests that SmD1 plays a direct role in miRNA-mediated gene silencing independently of its pre-mRNA splicing activity and indicates that the dual roles of splicing factors in post-transcriptional gene regulation may be

  9. Alignment of in-vessel components by metrology defined adaptive machining

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, David [ITER Organization, Route de Vinon sur Verdon, CS90 046, St Paul-lez-Durance (France); Bernard, Nathanaël [G2Métric, Launaguet 31140 (France); Mariani, Antony [Spatial Alignment Ltd., Witney (United Kingdom)


    Highlights: • Advanced metrology techniques developed for large volume high density in-vessel surveys. • Virtual alignment process employed to optimize the alignment of 440 blanket modules. • Auto-geometry construct, from survey data, using CAD proximity detection and orientation logic. • HMI developed to relocate blanket modules if customization limits on interfaces are exceeded. • Data export format derived for Catia parametric models, defining customization requirements. - Abstract: The assembly of ITER will involve the precise and accurate alignment of a large number of components and assemblies in areas where access will often be severely constrained and where process efficiency will be critical. One such area is the inside of the vacuum vessel where several thousand components shall be custom machined to provide the alignment references for in-vessel systems. The paper gives an overview of the process that will be employed; to survey the interfaces for approximately 3500 components then define and execute the customization process.

  10. Magnetic fields in long-range alignment of functional hybrid soft materials (United States)

    Majewski, Pawel; Gopinadhan, Manesh; Pelligra, Candice; Zhang, Shanju; Pfefferle, Lisa; Osuji, Chinedum


    We present a magnetic field-based method to impose long range order in self-assembled soft materials including polymer-nanowire composites, block copolymers and surfactant mesophases. We discuss the broad utility of this approach, indicating its advantages and limitations. Our method yields highly anisotropic materials with quality of alignment in many cases comparable to that of single crystals as assessed by X-ray scattering techniques. We take advantage of the high fidelity of alignment to systematically explore and characterize the anisotropic properties of these materials. We present a perspective for improving electron and hole transport, as well as exciton utilization in magnetically doped ZnO nanowire-polythiophene composites for photovoltaic applications by global alignment of the nanowires. For block copolymers, we focus on enhancing Li-ion transport in membranes with self-assembled cylindrical and lamellar morphology by alignment of the Li-conducting PEO domains.

  11. Splice Isoforms of Phosducin-like Protein Control the Expression of Heterotrimeric G Proteins* (United States)

    Gao, Xueli; Sinha, Satyabrata; Belcastro, Marycharmain; Woodard, Catherine; Ramamurthy, Visvanathan; Stoilov, Peter; Sokolov, Maxim


    Heterotrimeric G proteins play an essential role in cellular signaling; however, the mechanism regulating their synthesis and assembly remains poorly understood. A line of evidence indicates that the posttranslational processing of G protein β subunits begins inside the protein-folding chamber of the chaperonin containing t-complex protein 1. This process is facilitated by the ubiquitously expressed phosducin-like protein (PhLP), which is thought to act as a CCT co-factor. Here we demonstrate that alternative splicing of the PhLP gene gives rise to a transcript encoding a truncated, short protein (PhLPs) that is broadly expressed in human tissues but absent in mice. Seeking to elucidate the function of PhLPs, we expressed this protein in the rod photoreceptors of mice and found that this manipulation caused a dramatic translational and posttranslational suppression of rod heterotrimeric G proteins. The investigation of the underlying mechanism revealed that PhLPs disrupts the folding of Gβ and the assembly of Gβ and Gγ subunits, events normally assisted by PhLP, by forming a stable and apparently inactive tertiary complex with CCT preloaded with nascent Gβ. As a result, the cellular levels of Gβ and Gγ, which depends on Gβ for stability, decline. In addition, PhLPs evokes a profound and rather specific down-regulation of the Gα transcript, leading to a complete disappearance of the protein. This study provides the first evidence of a generic mechanism, whereby the splicing of the PhLP gene could potentially and efficiently regulate the cellular levels of heterotrimeric G proteins. PMID:23888055

  12. Correction of a Cystic Fibrosis Splicing Mutation by Antisense Oligonucleotides. (United States)

    Igreja, Susana; Clarke, Luka A; Botelho, Hugo M; Marques, Luís; Amaral, Margarida D


    Cystic fibrosis (CF), the most common life-threatening genetic disease in Caucasians, is caused by ∼2,000 different mutations in the CF transmembrane conductance regulator (CFTR) gene. A significant fraction of these (∼13%) affect pre-mRNA splicing for which novel therapies have been somewhat neglected. We have previously described the effect of the CFTR splicing mutation c.2657+5G>A in IVS16, showing that it originates transcripts lacking exon 16 as well as wild-type transcripts. Here, we tested an RNA-based antisense oligonucleotide (AON) strategy to correct the aberrant splicing caused by this mutation. Two AONs (AON1/2) complementary to the pre-mRNA IVS16 mutant region were designed and their effect on splicing was assessed at the RNA and protein levels, on intracellular protein localization and function. To this end, we used the 2657+5G>A mutant CFTR minigene stably expressed in HEK293 Flp-In cells that express a single copy of the transgene. RNA data from AON1-treated mutant cells show that exon 16 inclusion was almost completely restored (to 95%), also resulting in increased levels of correctly localized CFTR protein at the plasma membrane (PM) and with increased function. A novel two-color CFTR splicing reporter minigene developed here allowed the quantitative monitoring of splicing by automated microscopy localization of CFTR at the PM. The AON strategy is thus a promising therapeutic approach for the specific correction of alternative splicing.

  13. General Assembly

    CERN Multimedia

    Staff Association


    5th April, 2016 – Ordinary General Assembly of the Staff Association! In the first semester of each year, the Staff Association (SA) invites its members to attend and participate in the Ordinary General Assembly (OGA). This year the OGA will be held on Tuesday, April 5th 2016 from 11:00 to 12:00 in BE Auditorium, Meyrin (6-2-024). During the Ordinary General Assembly, the activity and financial reports of the SA are presented and submitted for approval to the members. This is the occasion to get a global view on the activities of the SA, its financial management, and an opportunity to express one’s opinion, including taking part in the votes. Other points are listed on the agenda, as proposed by the Staff Council. Who can vote? Only “ordinary” members (MPE) of the SA can vote. Associated members (MPA) of the SA and/or affiliated pensioners have a right to vote on those topics that are of direct interest to them. Who can give his/her opinion? The Ordinary General Asse...

  14. Self-fabrication of 3D Patterns on Aligned Carbon Nanotubes Films

    Institute of Scientific and Technical Information of China (English)


    Because of its outstanding performance, an aligned nanotube film with micropatterns has been a research focus in the field of nano-science and technology. Although quite a number of researchers have been successful in constructing such patterns, the precondition for the success, until recently, is to obtain the patterned substrates in advance.A research group at the CAS Institute of Chemistry (ICCAS) has succeeded in self-assembly of threedimensional (3-D) micropatterns on aligned carbon nanotube films.

  15. Molecular alignment enhancement phenomenon of polymer formed from a liquid crystal monomer in a liquid crystal solvent (United States)

    Fujikake, Hideo; Murashige, Takeshi; Sato, Hiroto; Kawakita, Masahiro; Kikuchi, Hiroshi


    We report an abnormal alignment enhancement phenomenon of polymer molecules. The alignment order of a rigid-skeleton polymer made from a liquid crystalline monomer in a low-molecular-weight liquid crystal solvent was drastically enhanced with increasing temperature, even though the alignment order of the solution of the liquid crystal and monomer decreased. From polymer molecular alignment observations using polarizing Raman scattering microscopy, it was found that the polymer alignment order was three times greater than that of the original aligned monomer and polymer. This super alignment technique of polymer using a molecular-scaled self-assembly mechanism is applicable to the formation of electrically and/or optically functional nanopolymer wires.

  16. Sensing Characteristics of A Precision Aligner Using Moire Gratings for Precision Alignment System

    Institute of Scientific and Technical Information of China (English)

    ZHOU Lizhong; Hideo Furuhashi; Yoshiyuki Uchida


    Sensing characteristics of a precision aligner using moire gratings for precision alignment sysem has been investigated. A differential moire alignment system and a modified alignment system were used. The influence of the setting accuracy of the gap length and inclination of gratings on the alignment accuracy has been studied experimentally and theoretically. Setting accuracy of the gap length less than 2.5μm is required in modified moire alignment. There is no influence of the gap length on the alignment accuracy in the differential alignment system. The inclination affects alignment accuracies in both differential and modified moire alignment systems.

  17. Templating of self-alignment patterns of anisotropic gold nanoparticles on ordered SWNT macrostructures. (United States)

    Dan, Budhadipta; Wingfield, Tyler B; Evans, Julian S; Mirri, Francesca; Pint, Cary L; Pasquali, Matteo; Smalyukh, Ivan I


    We report a simple and versatile technique for oriented assembly of gold nanorods on aligned single-walled carbon nanotube (SWNT) macrostructures, such as thin nanotube films and nanotube fibers. The deposition and assembly is accomplished via drop drying of dilute gold nanorod suspensions on SWNT macrostructures under ambient conditions. Guided by anisotropic interactions, gold nanorods, and polygonal platelets spontaneously align with SWNTs, resulting in macroscopic arrays of locally ordered nanorods supported on aligned SWNT substrates. SEM reveals that the scalar order parameter of rods relative to the local average SWNT alignment is 0.7 for rods on SWNT films and 0.9 for rods on SWNT fibers. This self-alignment is enabled by anisotropic gold nanoparticle-SWNT interactions and is observed for a wide range of nanoparticles, including nanorods with aspect ratios ranging from 2-35, thin gold triangular and other polygonal platelets. The plasmonic properties of aligned gold nanorods together with superior electronic, chemical and mechanical properties of SWNTs make these hybrid nanocomposites valuable for the design of self-assembled multifunctional optoelectronic materials and optical metamaterials.

  18. Two new splice variants in porcine PPARGC1A

    Directory of Open Access Journals (Sweden)

    Peelman Luc J


    Full Text Available Abstract Background Peroxisome proliferator-activated receptor γ coactivator 1α (PPARGC1A is a coactivator with a vital and central role in fat and energy metabolism. It is considered to be a candidate gene for meat quality in pigs and is involved in the development of obesity and diabetes in humans. How its many functions are regulated, is however still largely unclear. Therefore a transcription profile of PPARGC1A in 32 tissues and 4 embryonic developmental stages in the pig was constructed by screening its cDNA for possible splice variants with exon-spanning primers. Findings This led to the discovery of 2 new splice variants in the pig, which were subsequently also detected in human tissues. In these variants, exon 8 was either completely or partly (the last 66 bp were conserved spliced out, potentially coding for a much shorter protein of respectively 337 and 359 amino acids (aa, of which the first 291 aa would be the same compared to the complete protein (796 aa. Conclusion Considering the functional domains of the PPARGC1A protein, it is very likely these splice variants considerably affect the function of the protein and alternative splicing could be one of the mechanisms by which the diverse functions of PPARGC1A are regulated.

  19. RNA splicing in a new rhabdovirus from Culex mosquitoes. (United States)

    Kuwata, Ryusei; Isawa, Haruhiko; Hoshino, Keita; Tsuda, Yoshio; Yanase, Tohru; Sasaki, Toshinori; Kobayashi, Mutsuo; Sawabe, Kyoko


    Among members of the order Mononegavirales, RNA splicing events have been found only in the family Bornaviridae. Here, we report that a new rhabdovirus isolated from the mosquito Culex tritaeniorhynchus replicates in the nuclei of infected cells and requires RNA splicing for viral mRNA maturation. The virus, designated Culex tritaeniorhynchus rhabdovirus (CTRV), shares a similar genome organization with other rhabdoviruses, except for the presence of a putative intron in the coding region for the L protein. Molecular phylogenetic studies indicated that CTRV belongs to the family Rhabdoviridae, but it is yet to be assigned a genus. Electron microscopic analysis revealed that the CTRV virion is extremely elongated, unlike virions of rhabdoviruses, which are generally bullet shaped. Northern hybridization confirmed that a large transcript (approximately 6,500 nucleotides [nt]) from the CTRV L gene was present in the infected cells. Strand-specific reverse transcription-PCR (RT-PCR) analyses identified the intron-exon boundaries and the 76-nt intron sequence, which contains the typical motif for eukaryotic spliceosomal intron-splice donor/acceptor sites (GU-AG), a predicted branch point, and a polypyrimidine tract. In situ hybridization exhibited that viral RNAs are primarily localized in the nucleus of infected cells, indicating that CTRV replicates in the nucleus and is allowed to utilize the host's nuclear splicing machinery. This is the first report of RNA splicing among the members of the family Rhabdoviridae.

  20. Oncogenes and RNA splicing of human tumor viruses. (United States)

    Ajiro, Masahiko; Zheng, Zhi-Ming


    Approximately 10.8% of human cancers are associated with infection by an oncogenic virus. These viruses include human papillomavirus (HPV), Epstein-Barr virus (EBV), Merkel cell polyomavirus (MCV), human T-cell leukemia virus 1 (HTLV-1), Kaposi's sarcoma-associated herpesvirus (KSHV), hepatitis C virus (HCV) and hepatitis B virus (HBV). These oncogenic viruses, with the exception of HCV, require the host RNA splicing machinery in order to exercise their oncogenic activities, a strategy that allows the viruses to efficiently export and stabilize viral RNA and to produce spliced RNA isoforms from a bicistronic or polycistronic RNA transcript for efficient protein translation. Infection with a tumor virus affects the expression of host genes, including host RNA splicing factors, which play a key role in regulating viral RNA splicing of oncogene transcripts. A current prospective focus is to explore how alternative RNA splicing and the expression of viral oncogenes take place in a cell- or tissue-specific manner in virus-induced human carcinogenesis.

  1. Sec16 alternative splicing dynamically controls COPII transport efficiency. (United States)

    Wilhelmi, Ilka; Kanski, Regina; Neumann, Alexander; Herdt, Olga; Hoff, Florian; Jacob, Ralf; Preußner, Marco; Heyd, Florian


    The transport of secretory proteins from the endoplasmic reticulum (ER) to the Golgi depends on COPII-coated vesicles. While the basic principles of the COPII machinery have been identified, it remains largely unknown how COPII transport is regulated to accommodate tissue- or activation-specific differences in cargo load and identity. Here we show that activation-induced alternative splicing of Sec16 controls adaptation of COPII transport to increased secretory cargo upon T-cell activation. Using splice-site blocking morpholinos and CRISPR/Cas9-mediated genome engineering, we show that the number of ER exit sites, COPII dynamics and transport efficiency depend on Sec16 alternative splicing. As the mechanistic basis, we suggest the C-terminal Sec16 domain to be a splicing-controlled protein interaction platform, with individual isoforms showing differential abilities to recruit COPII components. Our work connects the COPII pathway with alternative splicing, adding a new regulatory layer to protein secretion and its adaptation to changing cellular environments.

  2. Alternative splicing regulates targeting of malate dehydrogenase in Yarrowia lipolytica. (United States)

    Kabran, Philomène; Rossignol, Tristan; Gaillardin, Claude; Nicaud, Jean-Marc; Neuvéglise, Cécile


    Alternative pre-mRNA splicing is a major mechanism contributing to the proteome complexity of most eukaryotes, especially mammals. In less complex organisms, such as yeasts, the numbers of genes that contain introns are low and cases of alternative splicing (AS) with functional implications are rare. We report the first case of AS with functional consequences in the yeast Yarrowia lipolytica. The splicing pattern was found to govern the cellular localization of malate dehydrogenase, an enzyme of the central carbon metabolism. This ubiquitous enzyme is involved in the tricarboxylic acid cycle in mitochondria and in the glyoxylate cycle, which takes place in peroxisomes and the cytosol. In Saccharomyces cerevisiae, three genes encode three compartment-specific enzymes. In contrast, only two genes exist in Y. lipolytica. One gene (YlMDH1, YALI0D16753g) encodes a predicted mitochondrial protein, whereas the second gene (YlMDH2, YALI0E14190g) generates the cytosolic and peroxisomal forms through the alternative use of two 3'-splice sites in the second intron. Both splicing variants were detected in cDNA libraries obtained from cells grown under different conditions. Mutants expressing the individual YlMdh2p isoforms tagged with fluorescent proteins confirmed that they localized to either the cytosolic or the peroxisomal compartment.

  3. Genome-wide identification of zero nucleotide recursive splicing in Drosophila. (United States)

    Duff, Michael O; Olson, Sara; Wei, Xintao; Garrett, Sandra C; Osman, Ahmad; Bolisetty, Mohan; Plocik, Alex; Celniker, Susan E; Graveley, Brenton R


    Recursive splicing is a process in which large introns are removed in multiple steps by re-splicing at ratchet points--5' splice sites recreated after splicing. Recursive splicing was first identified in the Drosophila Ultrabithorax (Ubx) gene and only three additional Drosophila genes have since been experimentally shown to undergo recursive splicing. Here we identify 197 zero nucleotide exon ratchet points in 130 introns of 115 Drosophila genes from total RNA sequencing data generated from developmental time points, dissected tissues and cultured cells. The sequential nature of recursive splicing was confirmed by identification of lariat introns generated by splicing to and from the ratchet points. We also show that recursive splicing is a constitutive process, that depletion of U2AF inhibits recursive splicing, and that the sequence and function of ratchet points are evolutionarily conserved in Drosophila. Finally, we identify four recursively spliced human genes, one of which is also recursively spliced in Drosophila. Together, these results indicate that recursive splicing is commonly used in Drosophila, occurs in humans, and provides insight into the mechanisms by which some large introns are removed.

  4. Cinnamate-functionalized hyperbranched polymer as liquid crystal photo-alignment layer

    Institute of Scientific and Technical Information of China (English)

    Bin Jun Shen; Zheng Xie; Ya Ning He; Yan Qing Lian


    In this work, 4-methoxylcirmamoyl chloride was reacted with a commercial hyperbranched polymer (Boltom~TM H30) to prepare a hyperbranched photosensitive polymer (H30-Ci). The polymer was characterized by UV absorption spectrum and 1H-NMR spectrum. After processed by Linearly Polarized Polymerization (LPP) method, the spin-coated films of H30-Ci were used as photo-alignment layers to assemble liquid crystal (LC) cells containing nematic liquid crystal (5CB). The observation by polarized microscope showed that the H30-Ci blended with a linear polymer (BP-AN-Ci) photo-alignment layers could align LC molecules in a very uniform way.

  5. Magnetic field alignment of randomly oriented, high aspect ratio silicon microwires into vertically oriented arrays. (United States)

    Beardslee, Joseph A; Sadtler, Bryce; Lewis, Nathan S


    External magnetic fields have been used to vertically align ensembles of silicon microwires coated with ferromagnetic nickel films. X-ray diffraction and image analysis techniques were used to quantify the degree of vertical orientation of the microwires. The degree of vertical alignment and the minimum field strength required for alignment were evaluated as a function of the wire length, coating thickness, magnetic history, and substrate surface properties. Nearly 100% of 100 μm long, 2 μm diameter, Si microwires that had been coated with 300 nm of Ni could be vertically aligned by a 300 G magnetic field. For wires ranging from 40 to 60 μm in length, as the length of the wire increased, a higher degree of alignment was observed at lower field strengths, consistent with an increase in the available magnetic torque. Microwires that had been exposed to a magnetic sweep up to 300 G remained magnetized and, therefore, aligned more readily during subsequent magnetic field alignment sweeps. Alignment of the Ni-coated Si microwires occurred at lower field strengths on hydrophilic Si substrates than on hydrophobic Si substrates. The magnetic field alignment approach provides a pathway for the directed assembly of solution-grown semiconductor wires into vertical arrays, with potential applications in solar cells as well as in other electronic devices that utilize nano- and microscale components as active elements.

  6. Modification and alignment of beam line of 10 MeV RF electron beam accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Barnwal, R; Ghodke, S R; Bhattacharjee, D; Kumar, M; Jayaprakash, D; Chindarkar, A R; Mishra, R L; Kumar, M; P, Dixit K; S, Acharya; Barje, S R; Lawangare, N K; C, Saroj P; Nimje, V T; Chandan, S; Tillu, A R; V, Sharma; Chavan, R B [Accelerator and Pulse Power Division, BARC, Mumbai, India-400085 (India); Dolas, S [Centre for Design and Manufacturing, BARC, Mumbai, India-400085 (India); Kulkarni, S Y [SAMEER, IIT Powai campus, Mumbai, India-400076 (India)], E-mail: (and others)


    A 10 MeV, 10 kW RF industrial Electron linac designed and developed at BARC is installed at the Electron Beam Center Kharghar, Navi Mumbai. The entire RF accelerator assembly consists of Electron gun, RF source, RF linac structure, Beam diagnostic chamber, Drift tube, Scanning magnet, Beam sensing aperture, Scan horn, and is spread over two floors at EBC. The paper discusses in detail about the alignment procedure adopted for the equipments of 10 MeV RF beamline. The complete electron beamline will be maintained under ultra high vacuum of the order of 10-7 torr. The paper discusses about the present problem of alignment, measurement technique of alignment, reason for misalignment, possible ways to solve the problem, equipment used for alignment, supports and arrestors, verification of alignment under vacuum.

  7. Modification & alignment of beam line of 10 MeV RF electron beam accelerator (United States)

    Barnwal, R.; Ghodke, S. R.; Bhattacharjee, D.; Kumar, M.; Jayaprakash, D.; Chindarkar, A. R.; Mishra, R. L.; Dolas, S.; Kulkarni, S. Y.; Kumar, M.; P, Dixit K.; S, Acharya; Barje, S. R.; Lawangare, N. K.; C, Saroj P.; Nimje, V. T.; Chandan, S.; Tillu, A. R.; V, Sharma; Chavan, R. B.; V, Yadav; P, Roychowdhury; Mittal, K. C.; Chakravarthy, D. P.; Ray, A. K.


    A 10 MeV, 10 kW RF industrial Electron linac designed and developed at BARC is installed at the Electron Beam Center Kharghar, Navi Mumbai. The entire RF accelerator assembly consists of Electron gun, RF source, RF linac structure, Beam diagnostic chamber, Drift tube, Scanning magnet, Beam sensing aperture, Scan horn, and is spread over two floors at EBC. The paper discusses in detail about the alignment procedure adopted for the equipments of 10 MeV RF beamline. The complete electron beamline will be maintained under ultra high vacuum of the order of 10-7 torr. The paper discusses about the present problem of alignment, measurement technique of alignment, reason for misalignment, possible ways to solve the problem, equipment used for alignment, supports & arrestors, verification of alignment under vacuum

  8. Versatile alignment layer method for new types of liquid crystal photonic devices

    Energy Technology Data Exchange (ETDEWEB)

    Finnemeyer, V.; Bryant, D.; Lu, L.; Bos, P. [Liquid Crystal Institute, Kent State University, Kent, Ohio 44242 (United States); Reich, R.; Clark, H.; Berry, S.; Bozler, C. [MIT Lincoln Laboratory, 244 Wood St., Lexington, Massachusetts 02420 (United States); Yaroshchuk, O. [Institute of Physics, NAS of Ukraine, 44 Prospect Nauky, Kyiv 03680 (Ukraine)


    Liquid crystal photonic devices are becoming increasingly popular. These devices often present a challenge when it comes to creating a robust alignment layer in pre-assembled cells. In this paper, we describe a method of infusing a dye into a microcavity to produce an effective photo-definable alignment layer. However, previous research on such alignment layers has shown that they have limited stability, particularly against subsequent light exposure. As such, we further describe a method of utilizing a pre-polymer, infused into the microcavity along with the liquid crystal, to provide photostability. We demonstrate that the polymer layer, formed under ultraviolet irradiation of liquid crystal cells, has been effectively localized to a thin region near the substrate surface and provides a significant improvement in the photostability of the liquid crystal alignment. This versatile alignment layer method, capable of being utilized in devices from the described microcavities to displays, offers significant promise for new photonics applications.

  9. Assembling consumption

    DEFF Research Database (Denmark)

    Assembling Consumption marks a definitive step in the institutionalisation of qualitative business research. By gathering leading scholars and educators who study markets, marketing and consumption through the lenses of philosophy, sociology and anthropology, this book clarifies and applies...... the investigative tools offered by assemblage theory, actor-network theory and non-representational theory. Clear theoretical explanation and methodological innovation, alongside empirical applications of these emerging frameworks will offer readers new and refreshing perspectives on consumer culture and market...... societies. This is an essential reading for both seasoned scholars and advanced students of markets, economies and social forms of consumption....

  10. General Alignment Concept of the CMS experiment

    CERN Document Server

    Lampen, T


    Efficient and accurate track reconstruction requires proper alignment of the tracking devices used. Here we describe the general alignment strategy envisaged for the CMS experiment. The hardware alignment devices of CMS are presented as well as the different track based alignment approaches.

  11. Photosensitive Polymers for Liquid Crystal Alignment (United States)

    Mahilny, U. V.; Stankevich, A. I.; Trofimova, A. V.; Muravsky, A. A.; Murauski, A. A.

    The peculiarities of alignment of liquid crystal (LC) materials by the layers of photocrosslinkable polymers with side benzaldehyde groups are considered. The investigation of mechanism of photostimulated alignment by rubbed benzaldehyde layer is performed. The methods of creation of multidomain aligning layers on the basis of photostimulated rubbing alignment are described.

  12. Aberrant splicing in maize rough endosperm3 reveals a conserved role for U12 splicing in eukaryotic multicellular development (United States)

    Barbazuk, W. Brad


    RNA splicing of U12-type introns functions in human cell differentiation, but it is not known whether this class of introns has a similar role in plants. The maize ROUGH ENDOSPERM3 (RGH3) protein is orthologous to the human splicing factor, ZRSR2. ZRSR2 mutations are associated with myelodysplastic syndrome (MDS) and cause U12 splicing defects. Maize rgh3 mutants have aberrant endosperm cell differentiation and proliferation. We found that most U12-type introns are retained or misspliced in rgh3. Genes affected in rgh3 and ZRSR2 mutants identify cell cycle and protein glycosylation as common pathways disrupted. Transcripts with retained U12-type introns can be found in polysomes, suggesting that splicing efficiency can alter protein isoforms. The rgh3 mutant protein disrupts colocalization with a known ZRSR2-interacting protein, U2AF2. These results indicate conserved function for RGH3/ZRSR2 in U12 splicing and a deeply conserved role for the minor spliceosome to promote cell differentiation from stem cells to terminal fates. PMID:28242684

  13. Alternative splice variants of the human PD-1 gene

    DEFF Research Database (Denmark)

    Nielsen, Christian; Ohm-Laursen, Line; Barington, Torben;


    PD-1 is an immunoregulatory receptor expressed on the surface of activated T cells, B cells, and monocytes. We describe four alternatively spliced PD-1 mRNA transcripts (PD-1Deltaex2, PD-1Deltaex3, PD-1Deltaex2,3, and PD-1Deltaex2,3,4) in addition to the full length isoform. PD-1Deltaex2 and PD-1......Deltaex3 are generated by alternative splicing where exon 2 (extracellular IgV-like domain) and exon 3 (transmembrane domain) respectively are spliced out. PD-1Deltaex3 is therefore likely to encode a soluble form of PD-1. PD-1Deltaex2,3 lacks exon 2 and 3. These three variants have unaffected open...

  14. Global Genetic Robustness of the Alternative Splicing Machinery in Caenorhabditis elegans

    NARCIS (Netherlands)

    Li, Yang; Breitling, Rainer; Snoek, L. Basten; van der Velde, K. Joeri; Swertz, Morris A.; Riksen, Joost; Jansen, Ritsert C.; Kammenga, Jan E.; Borevitz, J.


    Alternative splicing is considered a major mechanism for creating multicellular diversity from a limited repertoire of genes. Here, we performed the first study of genetic variation controlling alternative splicing patterns by comprehensively identifying quantitative trait loci affecting the differe

  15. Cloning, expression and alternative splicing of the novel isoform of hTCP11 gene

    DEFF Research Database (Denmark)

    Ma, Yong-xin; Zhang, Si-zhong; Wu, Qia-qing;


    To identify a novel isoform of hTCP11 gene and investigate its expression and alternative splicing.......To identify a novel isoform of hTCP11 gene and investigate its expression and alternative splicing....

  16. Alignment method for parabolic trough solar concentrators (United States)

    Diver, Richard B.


    A Theoretical Overlay Photographic (TOP) alignment method uses the overlay of a theoretical projected image of a perfectly aligned concentrator on a photographic image of the concentrator to align the mirror facets of a parabolic trough solar concentrator. The alignment method is practical and straightforward, and inherently aligns the mirror facets to the receiver. When integrated with clinometer measurements for which gravity and mechanical drag effects have been accounted for and which are made in a manner and location consistent with the alignment method, all of the mirrors on a common drive can be aligned and optimized for any concentrator orientation.

  17. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan


    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  18. Laser shaft alignment measurement model (United States)

    Mo, Chang-tao; Chen, Changzheng; Hou, Xiang-lin; Zhang, Guoyu


    Laser beam's track which is on photosensitive surface of the a receiver will be closed curve, when driving shaft and the driven shaft rotate with same angular velocity and rotation direction. The coordinate of arbitrary point which is on the curve is decided by the relative position of two shafts. Basing on the viewpoint, a mathematic model of laser alignment is set up. By using a data acquisition system and a data processing model of laser alignment meter with single laser beam and a detector, and basing on the installation parameter of computer, the state parameter between two shafts can be obtained by more complicated calculation and correction. The correcting data of the four under chassis of the adjusted apparatus moving on the level and the vertical plane can be calculated. This will instruct us to move the apparatus to align the shafts.

  19. General Assembly

    CERN Multimedia

    Staff Association


    Mardi 5 mai à 11 h 00 Salle 13-2-005 Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : 1- Adoption de l’ordre du jour. 2- Approbation du procès-verbal de l’Assemblée générale ordinaire du 22 mai 2014. 3- Présentation et approbation du rapport d’activités 2014. 4- Présentation et approbation du rapport financier 2014. 5- Présentation et approbation du rapport des vérificateurs aux comptes pour 2014. 6- Programme 2015. 7- Présentation et approbation du projet de budget 2015 et taux de cotisation pour 2015. 8- Pas de modifications aux Statuts de l'Association du personnel proposée. 9- Élections des membres de la Commission é...

  20. General Assembly

    CERN Multimedia

    Staff Association


    Mardi 5 avril à 11 h 00 BE Auditorium Meyrin (6-2-024) Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : Adoption de l’ordre du jour. Approbation du procès-verbal de l’Assemblée générale ordinaire du 5 mai 2015. Présentation et approbation du rapport d’activités 2015. Présentation et approbation du rapport financier 2015. Présentation et approbation du rapport des vérificateurs aux comptes pour 2015. Programme de travail 2016. Présentation et approbation du projet de budget 2016 Approbation du taux de cotisation pour 2017. Modifications aux Statuts de l'Association du personnel proposée. Élections des membres de la Commissio...

  1. General assembly

    CERN Multimedia

    Staff Association


    Mardi 5 mai à 11 h 00 Salle 13-2-005 Conformément aux statuts de l’Association du personnel, une Assemblée générale ordinaire est organisée une fois par année (article IV.2.1). Projet d’ordre du jour : Adoption de l’ordre du jour. Approbation du procès-verbal de l’Assemblée générale ordinaire du 22 mai 2014. Présentation et approbation du rapport d’activités 2014. Présentation et approbation du rapport financier 2014. Présentation et approbation du rapport des vérificateurs aux comptes pour 2014. Programme 2015. Présentation et approbation du projet de budget 2015 et taux de cotisation pour 2015. Pas de modifications aux Statuts de l'Association du personnel proposée. Élections des membres de la Commission électorale. &am...

  2. A combinatorial code for splicing silencing: UAGG and GGGG motifs.

    Directory of Open Access Journals (Sweden)

    Kyoungha Han


    Full Text Available Alternative pre-mRNA splicing is widely used to regulate gene expression by tuning the levels of tissue-specific mRNA isoforms. Few regulatory mechanisms are understood at the level of combinatorial control despite numerous sequences, distinct from splice sites, that have been shown to play roles in splicing enhancement or silencing. Here we use molecular approaches to identify a ternary combination of exonic UAGG and 5'-splice-site-proximal GGGG motifs that functions cooperatively to silence the brain-region-specific CI cassette exon (exon 19 of the glutamate NMDA R1 receptor (GRIN1 transcript. Disruption of three components of the motif pattern converted the CI cassette into a constitutive exon, while predominant skipping was conferred when the same components were introduced, de novo, into a heterologous constitutive exon. Predominant exon silencing was directed by the motif pattern in the presence of six competing exonic splicing enhancers, and this effect was retained after systematically repositioning the two exonic UAGGs within the CI cassette. In this system, hnRNP A1 was shown to mediate silencing while hnRNP H antagonized silencing. Genome-wide computational analysis combined with RT-PCR testing showed that a class of skipped human and mouse exons can be identified by searches that preserve the sequence and spatial configuration of the UAGG and GGGG motifs. This analysis suggests that the multi-component silencing code may play an important role in the tissue-specific regulation of the CI cassette exon, and that it may serve more generally as a molecular language to allow for intricate adjustments and the coordination of splicing patterns from different genes.

  3. Minor class splicing shapes the zebrafish transcriptome during development. (United States)

    Markmiller, Sebastian; Cloonan, Nicole; Lardelli, Rea M; Doggett, Karen; Keightley, Maria-Cristina; Boglev, Yeliz; Trotter, Andrew J; Ng, Annie Y; Wilkins, Simon J; Verkade, Heather; Ober, Elke A; Field, Holly A; Grimmond, Sean M; Lieschke, Graham J; Stainier, Didier Y R; Heath, Joan K


    Minor class or U12-type splicing is a highly conserved process required to remove a minute fraction of introns from human pre-mRNAs. Defects in this splicing pathway have recently been linked to human disease, including a severe developmental disorder encompassing brain and skeletal abnormalities known as Taybi-Linder syndrome or microcephalic osteodysplastic primordial dwarfism 1, and a hereditary intestinal polyposis condition, Peutz-Jeghers syndrome. Although a key mechanism for regulating gene expression, the impact of impaired U12-type splicing on the transcriptome is unknown. Here, we describe a unique zebrafish mutant, caliban (clbn), with arrested development of the digestive organs caused by an ethylnitrosourea-induced recessive lethal point mutation in the rnpc3 [RNA-binding region (RNP1, RRM) containing 3] gene. rnpc3 encodes the zebrafish ortholog of human RNPC3, also known as the U11/U12 di-snRNP 65-kDa protein, a unique component of the U12-type spliceosome. The biochemical impact of the mutation in clbn is the formation of aberrant U11- and U12-containing small nuclear ribonucleoproteins that impair the efficiency of U12-type splicing. Using RNA sequencing and microarrays, we show that multiple genes involved in various steps of mRNA processing, including transcription, splicing, and nuclear export are disrupted in clbn, either through intron retention or differential gene expression. Thus, clbn provides a useful and specific model of aberrant U12-type splicing in vivo. Analysis of its transcriptome reveals efficient mRNA processing as a critical process for the growth and proliferation of cells during vertebrate development.

  4. A procedure for identifying homologous alternative splicing events

    Directory of Open Access Journals (Sweden)

    Orozco Modesto


    Full Text Available Abstract Background The study of the functional role of alternative splice isoforms of a gene is a very active area of research in biology. The difficulty of the experimental approach (in particular, in its high-throughput version leaves ample room for the development of bioinformatics tools that can provide a useful first picture of the problem. Among the possible approaches, one of the simplest is to follow classical protein function annotation protocols and annotate target alternative splice events with the information available from conserved events in other species. However, the application of this protocol requires a procedure capable of recognising such events. Here we present a simple but accurate method developed for this purpose. Results We have developed a method for identifying homologous, or equivalent, alternative splicing events, based on the combined use of neural networks and sequence searches. The procedure comprises four steps: (i BLAST search for homologues of the two isoforms defining the target alternative splicing event; (ii construction of all possible candidate events; (iii scoring of the latter with a series of neural networks; and (iv filtering of the results. When tested in a set of 473 manually annotated pairs of homologous events, our method showed a good performance, with an accuracy of 0.99, a precision of 0.98 and a sensitivity of 0.93. When no candidates were available, the specificity of our method varied between 0.81 and 0.91. Conclusion The method described in this article allows the identification of homologous alternative splicing events, with a good success rate, indicating that such method could be used for the development of functional annotation of alternative splice isoforms.

  5. Genome-wide survey of allele-specific splicing in humans

    Directory of Open Access Journals (Sweden)

    Scheffler Konrad


    Full Text Available Abstract Background Accurate mRNA splicing depends on multiple regulatory signals encoded in the transcribed RNA sequence. Many examples of mutations within human splice regulatory regions that alter splicing qualitatively or quantitatively have been reported and allelic differences in mRNA splicing are likely to be a common and important source of phenotypic diversity at the molecular level, in addition to their contribution to genetic disease susceptibility. However, because the effect of a mutation on the efficiency of mRNA splicing is often difficult to predict, many mutations that cause disease through an effect on splicing are likely to remain undiscovered. Results We have combined a genome-wide scan for sequence polymorphisms likely to affect mRNA splicing with analysis of publicly available Expressed Sequence Tag (EST and exon array data. The genome-wide scan uses published tools and identified 30,977 SNPs located within donor and acceptor splice sites, branch points and exonic splicing enhancer elements. For 1,185 candidate splicing polymorphisms the difference in splicing between alternative alleles was corroborated by publicly available exon array data from 166 lymphoblastoid cell lines. We developed a novel probabilistic method to infer allele-specific splicing from EST data. The method uses SNPs and alternative mRNA isoforms mapped to EST sequences and models both regulated alternative splicing as well as allele-specific splicing. We have also estimated heritability of splicing and report that a greater proportion of genes show evidence of splicing heritability than show heritability of overall gene expression level. Our results provide an extensive resource that can be used to assess the possible effect on splicing of human polymorphisms in putative splice-regulatory sites. Conclusion We report a set of genes showing evidence of allele-specific splicing from an integrated analysis of genomic polymorphisms, EST data and exon array

  6. Photonic hybrid assembly through flexible waveguides (United States)

    Wörhoff, K.; Prak, A.; Postma, F.; Leinse, A.; Wu, K.; Peters, T. J.; Tichem, M.; Amaning-Appiah, B.; Renukappa, V.; Vollrath, G.; Balcells-Ventura, J.; Uhlig, P.; Seyfried, M.; Rose, D.; Santos, R.; Leijtens, X. J. M.; Flintham, B.; Wale, M.; Robbins, D.


    Fully automated, high precision, cost-effective assembly technology for photonic packages remains one of the main challenges in photonic component manufacturing. Next to the cost aspect the most demanding assembly task for multiport photonic integrated circuits (PICs) is the high-precision (±0.1 μm) alignment and fixing required for optical I/O in InP PICs, even with waveguide spot size conversion. In a European research initiative - PHASTFlex - we develop and investigate an innovative, novel assembly concept, in which the waveguides in a matching TriPleX interposer PIC are released during fabrication to make them movable. After assembly of both chips by flip-chip bonding on a common carrier, TriPleX based actuators and clamping functions position and fix the flexible waveguides with the required accuracy.

  7. Passive micro-assembly of modular, hot embossed, polymer microfluidic devices using exact constraint design (United States)

    You, Byoung Hee; Chen, Pin-Chuan; Park, Daniel S.; Park, Sunggook; Nikitopoulos, Dimitris E.; Soper, Steven A.; Murphy, Michael C.


    Low-cost microfluidic platforms have the potential to change accepted practices in many fields, including biology and medicine, in the near future. Micro-assembly of molded polymer microfluidic devices is one approach to cost-effective mass production of modular, microfluidic instruments. Polymer, passive alignment structures were used to precisely assemble molded polymer components to prevent infinitesimal motions and minimize the misalignment between assembled components and devices. The motion and constraint of the assemblies were analyzed using screw theory to identify combinations of passive alignment structures that would provide exact constraint of all degrees of freedom of the two mating parts without over-constraint. One option identified by kinematic analysis was a set of three v-groove and hemisphere-tipped pin joints, which are well known from precision engineering and suitable for microfabrication. To validate the passive alignment scheme, brass mold inserts containing alignment structures were micro-milled and used to hot emboss components in polycarbonate (PC). Dimensional and location variations of prototype alignment structures were measured to quantify the difference between the as-designed and actual dimensions and the locations of the alignment structures. The dimensional variation was 0.2-3% less than the designed dimensions and the location variation was 0.7% less. The alignment accuracy of an assembly was characterized by measuring the mismatch and vertical variation between molded alignment standards embossed on each pair of mating plates. With molded, polymer alignment structures the mean mismatch and mean vertical variation were as low as 13 ± 3 µm in the lateral plane along the x- and y-axes and -6 ± 15 µm with respect to the nominal value of 107 µm. This micro-assembly technology is applicable to the integration of all microsystems including the interconnection of microfluidic devices, the assembly of hybrid microsystems and the

  8. Oncogenic Alternative Splicing Switches: Role in Cancer Progression and Prospects for Therapy


    Serena Bonomi; Stefania Gallo; Morena Catillo; Daniela Pignataro; Giuseppe Biamonti; Claudia Ghigna


    Alterations in the abundance or activities of alternative splicing regulators generate alternatively spliced variants that contribute to multiple aspects of tumor establishment, progression and resistance to therapeutic treatments. Notably, many cancer-associated genes are regulated through alternative splicing suggesting a significant role of this post-transcriptional regulatory mechanism in the production of oncogenes and tumor suppressors. Thus, the study of alternative splicing in cancer ...

  9. Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data


    Zhou Ao; Breese Marcus R; Hao Yangyang; Edenberg Howard J; Li Lang; Skaar Todd C; Liu Yunlong


    Abstract Background Alternative splicing increases proteome diversity by expressing multiple gene isoforms that often differ in function. Identifying alternative splicing events from RNA-seq experiments is important for understanding the diversity of transcripts and for investigating the regulation of splicing. Results We developed Alt Event Finder, a tool for identifying novel splicing events by using transcript annotation derived from genome-guided construction tools, such as Cufflinks and ...

  10. The alignment-distribution graph (United States)

    Chatterjee, Siddhartha; Gilbert, John R.; Schreiber, Robert


    Implementing a data-parallel language such as Fortran 90 on a distributed-memory parallel computer requires distributing aggregate data objects (such as arrays) among the memory modules attached to the processors. The mapping of objects to the machine determines the amount of residual communication needed to bring operands of parallel operations into alignment with each other. We present a program representation called the alignment distribution graph that makes these communication requirements explicit. We describe the details of the representation, show how to model communication cost in this framework, and outline several algorithms for determining object mappings that approximately minimize residual communication.

  11. XUV ionization of aligned molecules

    Energy Technology Data Exchange (ETDEWEB)

    Kelkensberg, F.; Siu, W.; Gademann, G. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Rouzee, A.; Vrakking, M. J. J. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Max-Born-Institut, Max-Born Strasse 2A, D-12489 Berlin (Germany); Johnsson, P. [FOM Institute AMOLF, Science Park 104, NL-1098 XG Amsterdam (Netherlands); Department of Physics, Lund University, Post Office Box 118, SE-221 00 Lund (Sweden); Lucchini, M. [Department of Physics, Politecnico di Milano, Istituto di Fotonica e Nanotecnologie CNR-IFN, Piazza Leonardo da Vinci 32, 20133 Milano (Italy); Lucchese, R. R. [Department of Chemistry, Texas A and M University, College Station, Texas 77843-3255 (United States)


    New extreme-ultraviolet (XUV) light sources such as high-order-harmonic generation (HHG) and free-electron lasers (FELs), combined with laser-induced alignment techniques, enable novel methods for making molecular movies based on measuring molecular frame photoelectron angular distributions. Experiments are presented where CO{sub 2} molecules were impulsively aligned using a near-infrared laser and ionized using femtosecond XUV pulses obtained by HHG. Measured electron angular distributions reveal contributions from four orbitals and the onset of the influence of the molecular structure.

  12. Controlled Synthesis and Functionalization of Vertically-Aligned Carbon Nanotubes for Multifunctional Applications (United States)


    cluster and hollow microfibers by multicomponent self-assembling of citrate stabilized gold nanoparticles with temperature-responsive amphiphilic...assembling of citrate stabilized gold nanoparticles with temperature-responsive amphiphilic dendrimers" J. Mater. Chem. 22, 13365-13373, 2012. 35. D. Yu...AFRL-OSR-VA-TR-2015-0108 CONTROLLED SYNTHESIS AND FUNCTIONALIZATION OF VERTICALLY-ALIGNED CARBON NANOTUBES FOR MULTIFUNCTIONAL APPLICATIONS LIMING

  13. Application of Generalised sequential crossover of languages to generalised splicing

    CERN Document Server

    Jeganathan, L; Sengupta, Ritabrata


    This paper outlines an application of iterated version of generalised sequential crossover of two languages (which in some sense, an abstraction of the crossover of chromosomes in living organisms) in studying some classes of the newly proposed generalised splicing ($GS$) over two languages. It is proved that, for $X,Y \\in \\{FIN, REG, LIN, CF, CS, RE \\}, \\sg \\in FIN$, the subclass of generalized splicing languages namely $GS(X,Y,\\sg)$, (which is a subclass of the class $GS(X,Y,FIN)$) is always regular.

  14. Splicing growth of zeolite 4A in hydrothermal system

    Institute of Scientific and Technical Information of China (English)

    李酽; 汪信; 杨绪杰; 张术根


    The morphology evolution of zeolite 4A in hydrothermal system was studied via XRD, TEM and electron diffractometry. A phenomenon of aggregation of nano-crystals of zeolite 4A exists in the crystallization process, and microcrystals are derived from nano-crystal aggregating directly. The splicing growth model of zeolite 4A is described as: 1)an induction period which exists at the beginning of crystallization, 2)followed by many nano-meter crystals initiating immediately, and 3)the nanocrystals congregated as slices and spliced with each other to form a larger crystal.

  15. Interplay between DMD point mutations and splicing signals in Dystrophinopathy phenotypes.

    Directory of Open Access Journals (Sweden)

    Jonàs Juan-Mateu

    Full Text Available DMD nonsense and frameshift mutations lead to severe Duchenne muscular dystrophy while in-frame mutations lead to milder Becker muscular dystrophy. Exceptions are found in 10% of cases and the production of alternatively spliced transcripts is considered a key modifier of disease severity. Several exonic mutations have been shown to induce exon-skipping, while splice site mutations result in exon-skipping or activation of cryptic splice sites. However, factors determining the splicing pathway are still unclear. Point mutations provide valuable information regarding the regulation of pre-mRNA splicing and elements defining exon identity in the DMD gene. Here we provide a comprehensive analysis of 98 point mutations related to clinical phenotype and their effect on muscle mRNA and dystrophin expression. Aberrant splicing was found in 27 mutations due to alteration of splice sites or splicing regulatory elements. Bioinformatics analysis was performed to test the ability of the available algorithms to predict consequences on mRNA and to investigate the major factors that determine the splicing pathway in mutations affecting splicing signals. Our findings suggest that the splicing pathway is highly dependent on the interplay between splice site strength and density of regulatory elements.

  16. A cryptic BAP1 splice mutation in a family with uveal and cutaneous melanoma, and paraganglioma

    DEFF Research Database (Denmark)

    Wadt, K.; Choi, J.; Chung, J.Y.;


    as paraganglioma, breast cancer, and suspected mesothelioma cases in the family. Bioinformatic analysis and splicing assays demonstrated that this mutation creates a strong cryptic splice donor, resulting in aberrant splicing and a truncating frameshift of the BAP1 transcript. Somatic loss of the wild-type allele...

  17. Pre-mRNA splicing is a determinant of nucleosome organization.

    Directory of Open Access Journals (Sweden)

    Hadas Keren-Shaul

    Full Text Available Chromatin organization affects alternative splicing and previous studies have shown that exons have increased nucleosome occupancy compared with their flanking introns. To determine whether alternative splicing affects chromatin organization we developed a system in which the alternative splicing pattern switched from inclusion to skipping as a function of time. Changes in nucleosome occupancy were correlated with the change in the splicing pattern. Surprisingly, strengthening of the 5' splice site or strengthening the base pairing of U1 snRNA with an internal exon abrogated the skipping of the internal exons and also affected chromatin organization. Over-expression of splicing regulatory proteins also affected the splicing pattern and changed nucleosome occupancy. A specific splicing inhibitor was used to show that splicing impacts nucleosome organization endogenously. The effect of splicing on the chromatin required a functional U1 snRNA base pairing with the 5' splice site, but U1 pairing was not essential for U1 snRNA enhancement of transcription. Overall, these results suggest that splicing can affect chromatin organization.

  18. A 5' splice site enhances the recruitment of basal transcription initiation factors in vivo

    DEFF Research Database (Denmark)

    Damgaard, Christian Kroun; Kahns, Søren; Lykke-Andersen, Søren;


    Transcription and pre-mRNA splicing are interdependent events. Although mechanisms governing the effects of transcription on splicing are becoming increasingly clear, the means by which splicing affects transcription remain elusive. Using cell lines stably expressing HIV-1 or β-globin mRNAs, harb...

  19. Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology

    Directory of Open Access Journals (Sweden)

    Hammesfahr Björn


    Full Text Available Abstract Background Alternative splicing of pre-mature RNA is an important process eukaryotes utilize to increase their repertoire of different protein products. Several types of different alternative splice forms exist including exon skipping, differential splicing of exons at their 3'- or 5'-end, intron retention, and mutually exclusive splicing. The latter term is used for clusters of internal exons that are spliced in a mutually exclusive manner. Results We have implemented an extension to the WebScipio software to search for mutually exclusive exons. Here, the search is based on the precondition that mutually exclusive exons encode regions of the same structural part of the protein product. This precondition provides restrictions to the search for candidate exons concerning their length, splice site conservation and reading frame preservation, and overall homology. Mutually exclusive exons that are not homologous and not of about the same length will not be found. Using the new algorithm, mutually exclusive exons in several example genes, a dynein heavy chain, a muscle myosin heavy chain, and Dscam were correctly identified. In addition, the algorithm was applied to the whole Drosophila melanogaster X chromosome and the results were compared to the Flybase annotation and an ab initio prediction. Clusters of mutually exclusive exons might be subsequent to each other and might encode dozens of exons. Conclusions This is the first implementation of an automatic search for mutually exclusive exons in eukaryotes. Exons are predicted and reconstructed in the same run providing the complete gene structure for the protein query of interest. WebScipio offers high quality gene structure figures with the clusters of mutually exclusive exons colour-coded, and several analysis tools for further manual inspection. The genome scale analysis of all genes of the Drosophila melanogaster X chromosome showed that WebScipio is able to find all but two of the 28

  20. The Rigors of Aligning Performance (United States)


    organization must consider and work closely with its many stakeholders so as to guarantee satisfaction ; this idea is especially important as there is no...define success. Methodology includes a literature review, employee and customer surveys and a Strength, Weaknesses, Opportunities, Threats...bearing in mind customer perceptions. Recommendations include employee training centered on goal alignment, which is vital to highlight the

  1. Aligning Assessments for COSMA Accreditation (United States)

    Laird, Curt; Johnson, Dennis A.; Alderman, Heather


    Many higher education sport management programs are currently in the process of seeking accreditation from the Commission on Sport Management Accreditation (COSMA). This article provides a best-practice method for aligning student learning outcomes with a sport management program's mission and goals. Formative and summative assessment procedures…

  2. Aligned natural inflation with modulations

    Directory of Open Access Journals (Sweden)

    Kiwoon Choi


    Full Text Available The weak gravity conjecture applied for the aligned natural inflation indicates that generically there can be a modulation of the inflaton potential, with a period determined by sub-Planckian axion scale. We study the oscillations in the primordial power spectrum induced by such modulation, and discuss the resulting observational constraints on the model.

  3. Progressive multiple sequence alignments from triplets

    Directory of Open Access Journals (Sweden)

    Stadler Peter F


    Full Text Available Abstract Background The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments and hence form an unavoidable source of errors. Research Here we present a modified variant of progressive sequence alignments that addresses both issues. Instead of pairwise alignments we use exact dynamic programming to align sequence or profile triples. This avoids a large fractions of the ambiguities arising in pairwise alignments. In the subsequent aggregation steps we follow the logic of the Neighbor-Net algorithm, which constructs a phylogenetic network by step-wisely replacing triples by pairs instead of combining pairs to singletons. To this end the three-way alignments are subdivided into two partial alignments, at which stage all-gap columns are naturally removed. This alleviates the "once a gap, always a gap" problem of progressive alignment procedures. Conclusion The three-way Neighbor-Net based alignment program aln3nn is shown to compare favorably on both protein sequences and nucleic acids sequences to other progressive alignment tools. In the latter case one easily can include scoring terms that consider secondary structure features. Overall, the quality of resulting alignments in general exceeds that of clustalw or other multiple alignments tools even though our software does not included heuristics for context dependent (mismatch scores.

  4. Stiff, Strong Splice For A Composite Sandwich Structure (United States)

    Schmaling, D.


    New type of splice for composite sandwich structure reduces peak shear stress in structure. Layers of alternating fiber orientation interposed between thin ears in adhesive joint. Developed for structural joint in spar of helicopter rotor blade, increases precision of control over thickness of adhesive at joint. Joint easy to make, requires no additional pieces, and adds little weight.

  5. Mouse tissues express multiple splice variants of prominin-1.

    Directory of Open Access Journals (Sweden)

    Kristel Kemper

    Full Text Available Prominin-1, a heavily glycosylated pentaspan membrane protein, is mainly known for its function as a marker for (cancer stem cells, although it can also be detected on differentiated cells. Mouse prominin-1 expression is heavily regulated by splicing in eight different variants. The function or the expression pattern of prominin-1 and its splice variants (SVs is thus far unknown. In this study, we analyzed the expression of the prominin-1 splice variants on mRNA level in several mouse tissues and found a broad tissue expression of the majority of SVs, but a specific set of SVs had a much more restricted expression profile. For instance, the testis expressed only SV3 and SV7. Moreover, SV8 was solely detected in the eye. Intriguingly, prominin-1 knockout mice do not suffer from gross abnormalities, but do show signs of blindness, which suggest that SV8 has a specific function in this tissue. In addition, databases searches for putative promoter regions in the mouse prominin-1 gene revealed three potential promoter regions that could be linked to specific SVs. Interestingly, for both SV7 and SV8, a specific potential promoter region could be identified. To conclude, the majority of mouse prominin-1 splice variants are widely expressed in mouse tissues. However, specific expression of a few variants, likely driven by specific promoters, suggests distinct regulation and a potential important function for these variants in certain tissues.

  6. The Evolutionary Relationship between Alternative Splicing and Gene Duplication (United States)

    Iñiguez, Luis P.; Hernández, Georgina


    The protein diversity that exists today has resulted from various evolutionary processes. It is well known that gene duplication (GD) along with the accumulation of mutations are responsible, among other factors, for an increase in the number of different proteins. The gene structure in eukaryotes requires the removal of non-coding sequences, introns, to produce mature mRNAs. This process, known as cis-splicing, referred to here as splicing, is regulated by several factors which can lead to numerous splicing arrangements, commonly designated as alternative splicing (AS). AS, producing several transcripts isoforms form a single gene, also increases the protein diversity. However, the evolution and manner for increasing protein variation differs between AS and GD. An important question is how are patterns of AS affected after a GD event. Here, we review the current knowledge of AS and GD, focusing on their evolutionary relationship. These two processes are now considered the main contributors to the increasing protein diversity and therefore their relationship is a relevant, yet understudied, area of evolutionary study. PMID:28261262

  7. A novel CDX2 isoform regulates alternative splicing.

    Directory of Open Access Journals (Sweden)

    Matthew E Witek

    Full Text Available Gene expression is a dynamic and coordinated process coupling transcription with pre-mRNA processing. This regulation enables tissue-specific transcription factors to induce expression of specific transcripts that are subsequently amplified by alternative splicing allowing for increased proteome complexity and functional diversity. The intestine-specific transcription factor CDX2 regulates development and maintenance of the intestinal epithelium by inducing expression of genes characteristic of the mature enterocyte phenotype. Here, sequence analysis of CDX2 mRNA from colonic mucosa-derived tissues revealed an alternatively spliced transcript (CDX2/AS that encodes a protein with a truncated homeodomain and a novel carboxy-terminal domain enriched in serine and arginine residues (RS domain. CDX2 and CDX2/AS exhibited distinct nuclear expression patterns with minimal areas of co-localization. CDX2/AS did not activate the CDX2-dependent promoter of guanylyl cyclase C nor inhibit transcriptional activity of CDX2. Unlike CDX2, CDX2/AS co-localized with the putative splicing factors ASF/SF2 and SC35. CDX2/AS altered splicing patterns of CD44v5 and Tra2-β1 minigenes in Lovo colon cancer cells independent of CDX2 expression. These data demonstrate unique dual functions of the CDX2 gene enabling it to regulate gene expression through both transcription (CDX2 and pre-mRNA processing (CDX2/AS.

  8. Nonsense mutations and altered splice-site selection

    Energy Technology Data Exchange (ETDEWEB)

    Dietz, H.C. [Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)


    The invited editorial by Maquat, regarding defects in RNA splicing and the consequence of shortened translational reading frames, provided a balanced and comprehensive review of the topic. We believe, however, that our work describing the nonsense codon-mediated skipping of fibrillin-1 exon 51 was interpreted in a manner that is not fully supported by our data. 6 refs.

  9. Influence of intron length on interaction characters between post-spliced intron and its CDS in ribosomal protein genes (United States)

    Zhao, Xiaoqing; Li, Hong; Bao, Tonglaga; Ying, Zhiqiang


    Many experiment evidences showed that sequence structures of introns and intron loss/gain can influence gene expression, but current mechanisms did not refer to the functions of post-spliced introns directly. We propose that postspliced introns play their functions in gene expression by interacting with their mRNA sequences and the interaction is characterized by the matched segments between introns and their CDS. In this study, we investigated the interaction characters with length series by improved Smith-Waterman local alignment software for the ribosomal protein genes in C. elegans and D. melanogaster. Our results showed that RF values of five intron groups are significantly high in the central non-conserved region and very low in 5'-end and 3'-end splicing region. It is interesting that the number of the optimal matched regions gradually increases with intron length. Distributions of the optimal matched regions are different for five intron groups. Our study revealed that there are more interaction regions between longer introns and their CDS than shorter, and it provides a positive pattern for regulating the gene expression.

  10. Electromechanical behaviour of REBCO tape lap splices under transverse compressive loading

    CERN Document Server

    Grether, A; Ballarino, A.; Bottura, L.


    We have studied the influence of transverse compressive stress on the resistance and critical current (Ic) of soldered REBCO tape lap splices. Internal contact resistances dominate the overall REBCO lap splice resistances. Application of transverse compressive stress up to 250 MPa during the resistance measurements does not alter the resistance and Ic of the soldered REBCO splices that were studied. The resistance of unsoldered REBCO tape lap splices depends strongly on the contact pressure. At a transverse compressive stress of 100 MPa to which Roebel cables are typically exposed in high field magnets, the crossover splice contact resistance is comparable to the internal tape resistances.

  11. Spliced leader-based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates. (United States)

    Lin, Senjie; Zhang, Huan; Zhuang, Yunyun; Tran, Bao; Gill, John


    Environmental transcriptomics (metatranscriptomics) for a specific lineage of eukaryotic microbes (e.g., Dinoflagellata) would be instrumental for unraveling the genetic mechanisms by which these microbes respond to the natural environment, but it has not been exploited because of technical difficulties. Using the recently discovered dinoflagellate mRNA-specific spliced leader as a selective primer, we constructed cDNA libraries (e-cDNAs) from one marine and two freshwater plankton assemblages. Small-scale sequencing of the e-cDNAs revealed functionally diverse transcriptomes proven to be of dinoflagellate origin. A set of dinoflagellate common genes and transcripts of dominant dinoflagellate species were identified. Further analyses of the dataset prompted us to delve into the existing, largely unannotated dinoflagellate EST datasets (DinoEST). Consequently, all four nucleosome core histones, two histone modification proteins, and a nucleosome assembly protein were detected, clearly indicating the presence of nucleosome-like machinery long thought not to exist in dinoflagellates. The isolation of rhodopsin from taxonomically and ecotypically diverse dinoflagellates and its structural similarity and phylogenetic affinity to xanthorhodopsin suggest a common genetic potential in dinoflagellates to use solar energy nonphotosynthetically. Furthermore, we found 55 cytoplasmic ribosomal proteins (RPs) from the e-cDNAs and 24 more from DinoEST, showing that the dinoflagellate phylum possesses all 79 eukaryotic RPs. Our results suggest that a sophisticated eukaryotic molecular machine operates in dinoflagellates that likely encodes many more unsuspected physiological capabilities and, meanwhile, demonstrate that unique spliced leaders are useful for profiling lineage-specific microbial transcriptomes in situ.

  12. Combined Cell Culture-Biosensing Platform Using Vertically Aligned Patterned Peptide Nanofibers for Cellular Studies

    DEFF Research Database (Denmark)

    Taskin, Mehmet B.; Sasso, Luigi; Dimaki, Maria


    This Article presents the development of a combined cell culture–biosensing platform using vertically aligned self-assembled peptide nanofibers. Peptide nanofibers were patterned on a microchip containing gold microelectrodes to provide the cells with a 3D environment enabling them to grow...

  13. Coupling of a single quantum emitter to end-to-end aligned silver nanowires

    DEFF Research Database (Denmark)

    Kumar, Shailesh; Huck, Alexander; Chen, Yuntian;


    observe an enhancement of the NV-centers' decay rate in both cases as a result of the coupling to the plasmons. The devices are nano-assembled with a scanning probe technique. Through simulations, we show that end-to-end aligned silver nanowires can be used as a controllable splitter for emission from...

  14. Characterization of a novel splicing variant in the RAPTOR gene

    Energy Technology Data Exchange (ETDEWEB)

    Sun Chang [Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637 (United States)], E-mail:; Southard, Catherine; Di Rienzo, Anna [Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637 (United States)


    The mammalian target of rapamycin (mTOR) plays an essential role in the regulation of cell growth, proliferation and apoptosis. Raptor, the regulatory associated protein of mTOR, is an important member in this signaling pathway. In the present report, we identified and characterized a novel splicing variant of this gene, RAPTOR{sub v}2, in which exons 14-17, 474 bp in total, are omitted from the mRNA. This deletion does not change the open reading frame, but causes a nearly complete absence of HEAT repeats, which were shown to be involved in the binding of mTOR substrates. Real time PCR performed on 48 different human tissues demonstrated the ubiquitous presence of this splice variant. Quantification of mRNA levels in lymphoblastoid cell lines (LCL) from 56 unrelated HapMap individuals revealed that the expression of this splicing form is quite variable. One synonymous SNP, rs2289759 in exon 14, was predicted by ESEfinder to cause a significant gain/loss of SRp55 and/or SF2/ASF binding sites, and thus potentially influence splicing. This prediction was confirmed by linear regression analysis between the ratio of RAPTOR{sub v}2 to total RAPTOR mRNA levels and the SNP genotype in the above 56 individuals (r = 0.281 and P = 0.036). Moreover, the functional evaluation indicated that this splicing isoform is expected to retain the ability to bind mTOR, but is unlikely to bind mTOR substrates, hence affecting signal transduction and further cell proliferation.

  15. NMR studies of two spliced leader RNAs using isotope labeling

    Energy Technology Data Exchange (ETDEWEB)

    Lapham, J.; Crothers, D.M. [Yale Univ., New Haven, CT (United States)


    Spliced leader RNAs are a class of RNA molecules (<200 nts) involved in the trans splicing of messenger RNA found in trypanosomes, nematodes, and other lower eukaryotes. The spliced leader RNA from the trypanosome Leptomonas Collosoma exists in two alternate structural forms with similar thermal stabilities. The 54 nucleotides on the 5{prime} end of the SL molecule is structurally independent from the 3{prime} half of the RNA, and displays the two structural forms. Furthermore, the favored of the two structures was shown to contain anomalous nuclease sensitivity and thermal stability features, which suggests that there may be tertiary interactions between the splice site and other nucleotides in the 5{prime} end. Multidimensional NMR studies are underway to elucidate the structural elements present in the SL RNAs that give rise to their physical properties. Two spliced leader sequences have been studied. The first, the 54 nucleotides on the 5{prime} end of the L. Collosoma sequence, was selected because of earlier studies in our laboratory. The second sequence is the 5{prime} end of the trypanosome Crithidia Fasciculata, which was chosen because of its greater sequence homology to other SL sequences. Given the complexity of the NMR spectra for RNA molecules of this size, we have incorporated {sup 15}N/{sup 13}C-labeled nucleotides into the RNA. One of the techniques we have developed to simplify the spectra of these RNA molecules is isotope labeling of specific regions of the RNA. This has been especially helpful in assigning the secondary structure of molecules that may be able to adopt multiple conformations. Using this technique one can examine a part of the molecule without spectral interference from the unlabeled portion. We hope this approach will promote an avenue for studying the structure of larger RNAs in their native surroundings.

  16. Design and Test of Object Aligning Grippers for Industrial Applications

    DEFF Research Database (Denmark)

    Ellekilde, Lars-Peter; Petersen, Henrik Gordon


    In this paper we will present a new concept for gripping objects in industrial applications. We assume that a priori, the object pose is only known with a relative low accuracy. Despite this, our method can lead to high accuracy gripping suitable for e.g. industrial assembly. Our concept...... is to augment a simple parallel gripper by mounting a set of object speci?c jaws. Given the right shapes these jaws enable the gripper to automatically align the object, and thereby compensate for errors in the original object pose estimation. We will introduce a couple of automatic and semi-automatic design...

  17. SON controls cell-cycle progression by coordinated regulation of RNA splicing. (United States)

    Ahn, Eun-Young; DeKelver, Russell C; Lo, Miao-Chia; Nguyen, Tuyet Ann; Matsuura, Shinobu; Boyapati, Anita; Pandit, Shatakshi; Fu, Xiang-Dong; Zhang, Dong-Er


    It has been suspected that cell-cycle progression might be functionally coupled with RNA processing. However, little is known about the role of the precise splicing control in cell-cycle progression. Here, we report that SON, a large Ser/Arg (SR)-related protein, is a splicing cofactor contributing to efficient splicing of cell-cycle regulators. Downregulation of SON leads to severe impairment of spindle pole separation, microtubule dynamics, and genome integrity. These molecular defects result from inadequate RNA splicing of a specific set of cell-cycle-related genes that possess weak splice sites. Furthermore, we show that SON facilitates the interaction of SR proteins with RNA polymerase II and other key spliceosome components, suggesting its function in efficient cotranscriptional RNA processing. These results reveal a mechanism for controlling cell-cycle progression through SON-dependent constitutive splicing at suboptimal splice sites, with strong implications for its role in cancer and other human diseases.

  18. RNA splicing regulated by RBFOX1 is essential for cardiac function in zebrafish. (United States)

    Frese, Karen S; Meder, Benjamin; Keller, Andreas; Just, Steffen; Haas, Jan; Vogel, Britta; Fischer, Simon; Backes, Christina; Matzas, Mark; Köhler, Doreen; Benes, Vladimir; Katus, Hugo A; Rottbauer, Wolfgang


    Alternative splicing is one of the major mechanisms through which the proteomic and functional diversity of eukaryotes is achieved. However, the complex nature of the splicing machinery, its associated splicing regulators and the functional implications of alternatively spliced transcripts are only poorly understood. Here, we investigated the functional role of the splicing regulator rbfox1 in vivo using the zebrafish as a model system. We found that loss of rbfox1 led to progressive cardiac contractile dysfunction and heart failure. By using deep-transcriptome sequencing and quantitative real-time PCR, we show that depletion of rbfox1 in zebrafish results in an altered isoform expression of several crucial target genes, such as actn3a and hug. This study underlines that tightly regulated splicing is necessary for unconstrained cardiac function and renders the splicing regulator rbfox1 an interesting target for investigation in human heart failure and cardiomyopathy.

  19. Investigation of tissue-specific human orthologous alternative splice events in pig

    DEFF Research Database (Denmark)

    Hillig, Ann-Britt Nygaard; Jørgensen, Claus Bøttcher; Salicio, Susanna Cirera;


    Alternative splicing of pre-mRNA can contribute to differences between tissues or cells either by regulating gene expression or creating proteins with various functions encoded by one gene. The number of investigated alternative splice events in pig has so far been limited. In this study we have...... investigated alternative splice events detected in humans, in orthologous pig genes. A total of 17 genes with predicted exon skipping events were selected for further studies. The splice events for the selected genes were experimentally verified using real-time quantitative PCR analysis (qPCR) with splice......-specific primers in 19 different tissues. The same splice variants as reported in humans were detected in 15 orthologous pig genes, however, the expression pattern predicted in the in silico analyses was only experimentally verified in a few cases. The results support the findings that splice events resulting...

  20. Test results for a subscale (100 kA) SMES splice (United States)

    Peck, Scott D.; Zeigler, John C.


    The design for the 20 MW-hr SMES-ETM for the Bechtel concept calls for two splices per turn of conductor, and over 100 turns. The design value of resistance for the splices is on the order of 10(exp -11) ohms (0.4 W/splice at 200 kA), which is an order of magnitude less than the state of the art for high current devices. The splice design utilizes a superconducting braid wrapped around lapped subcables for an extremely low resistance joint. A history of the manufacturing development for the splice is presented. The performance of a sub-scale version of the splice joint has been measured at Texas Accelerator Center. Values of splice resistance at 1.8 K and background fields up to 5 T are reported. Performance of a 100 kA conductor is also reported.

  1. Increased dosage of Dyrk1A alters alternative splicing factor (ASF)-regulated alternative splicing of tau in Down syndrome. (United States)

    Shi, Jianhua; Zhang, Tianyi; Zhou, Chunlei; Chohan, Muhammad Omar; Gu, Xiaosong; Wegiel, Jerzy; Zhou, Jianhua; Hwang, Yu-Wen; Iqbal, Khalid; Grundke-Iqbal, Inge; Gong, Cheng-Xin; Liu, Fei


    Two groups of tau, 3R- and 4R-tau, are generated by alternative splicing of tau exon 10. Normal adult human brain expresses equal levels of them. Disruption of the physiological balance is a common feature of several tauopathies. Very early in their life, individuals with Down syndrome (DS) develop Alzheimer-type tau pathology, the molecular basis for which is not fully understood. Here, we demonstrate that Dyrk1A, a kinase encoded by a gene in the DS critical region, phosphorylates alternative splicing factor (ASF) at Ser-227, Ser-234, and Ser-238, driving it into nuclear speckles and preventing it from facilitating tau exon 10 inclusion. The increased dosage of Dyrk1A in DS brain due to trisomy of chromosome 21 correlates to an increase in 3R-tau level, which on abnormal hyperphosphorylation and aggregation of tau results in neurofibrillary degeneration. Imbalance of 3R- and 4R-tau in DS brain by Dyrk1A-induced dysregulation of alternative splicing factor-mediated alternative splicing of tau exon 10 represents a novel mechanism of neurofibrillary degeneration and may help explain early onset tauopathy in individuals with DS.

  2. Precise Alignment and Permanent Mounting of Thin and Lightweight X-ray Segments (United States)

    Biskach, Michael P.; Chan, Kai-Wing; Hong, Melinda N.; Mazzarella, James R.; McClelland, Ryan S.; Norman, Michael J.; Saha, Timo T.; Zhang, William W.


    To provide observations to support current research efforts in high energy astrophysics. future X-ray telescope designs must provide matching or better angular resolution while significantly increasing the total collecting area. In such a design the permanent mounting of thin and lightweight segments is critical to the overall performance of the complete X-ray optic assembly. The thin and lightweight segments used in the assemhly of the modules are desigued to maintain and/or exceed the resolution of existing X-ray telescopes while providing a substantial increase in collecting area. Such thin and delicate X-ray segments are easily distorted and yet must be aligned to the arcsecond level and retain accurate alignment for many years. The Next Generation X-ray Optic (NGXO) group at NASA Goddard Space Flight Center has designed, assembled. and implemented new hardware and procedures mth the short term goal of aligning three pairs of X-ray segments in a technology demonstration module while maintaining 10 arcsec alignment through environmental testing as part of the eventual design and construction of a full sized module capable of housing hundreds of X-ray segments. The recent attempts at multiple segment pair alignment and permanent mounting is described along with an overview of the procedure used. A look into what the next year mll bring for the alignment and permanent segment mounting effort illustrates some of the challenges left to overcome before an attempt to populate a full sized module can begin.

  3. Shape-induced separation of nanospheres and aligned nanorods. (United States)

    Ahmad, I; Zandvliet, H J W; Kooij, E S


    We studied the phase separation and spatial arrangement of gold nanorods and nanospheres after evaporative self-assembly from aqueous suspension. Depending on the position relative to the contact line of the drying droplet, spheres and rods separate into various liquid-crystalline phases. Nanorods exhibit a strong preference for side-by-side alignment, giving rise to smectic phases; spheres in solution are forced out of these regions and form close-packed arrays. We discuss this self-separation into nanorod- and sphere-rich phases in terms of various interactions, including electrostatic, van der Waals, and deplection interactions forces. The experimental results are compared to quantitative calculations of the colloidal interaction energies. We also describe and discuss the role of the surfactant on the different crystal facets of the nanorods on the assembly process.

  4. Aligning seminars with Bologna requirements

    DEFF Research Database (Denmark)

    Lueg, Klarissa; Lueg, Rainer; Lauridsen, Ole


    Changes in public policy, such as the Bologna Process, require students to be equipped with multifunctional competencies to master relevant tasks in unfamiliar situations. Achieving this goal might imply a change in many curricula toward deeper learning. As a didactical means to achieve deep...... learning results, the authors suggest reciprocal peer tutoring (RPT); as a conceptual framework the authors suggest the SOLO (Structure of Observed Learning Outcomes) taxonomy and constructive alignment as suggested by Biggs and Tang. Our study presents results from the introduction of RPT in a large...... course. The authors find that RPT produces satisfying learning outcomes, active students, and ideal constructive alignments of the seminar content with the exam, the intended learning outcomes, and the requirements of the Bologna Process. Our data, which comprise surveys and evaluations from both faculty...

  5. Prism Window for Optical Alignment (United States)

    Tang, Hong


    A prism window has been devised for use, with an autocollimator, in aligning optical components that are (1) required to be oriented parallel to each other and/or at a specified angle of incidence with respect to a common optical path and (2) mounted at different positions along the common optical path. The prism window can also be used to align a single optical component at a specified angle of incidence. Prism windows could be generally useful for orienting optical components in manufacture of optical instruments. "Prism window" denotes an application-specific unit comprising two beam-splitter windows that are bonded together at an angle chosen to obtain the specified angle of incidence.

  6. Shuttle onboard IMU alignment methods (United States)

    Henderson, D. M.


    The current approach to the shuttle IMU alignment is based solely on the Apollo Deterministic Method. This method is simple, fast, reliable and provides an accurate estimate for the present cluster to mean of 1,950 transformation matrix. If four or more star sightings are available, the application of least squares analysis can be utilized. The least squares method offers the next level of sophistication to the IMU alignment solution. The least squares method studied shows that a more accurate estimate for the misalignment angles is computed, and the IMU drift rates are a free by-product of the analysis. Core storage requirements are considerably more; estimated 20 to 30 times the core required for the Apollo Deterministic Method. The least squares method offers an intermediate solution utilizing as much data that is available without a complete statistical analysis as in Kalman filtering.

  7. Aligned mesoporous architectures and devices.

    Energy Technology Data Exchange (ETDEWEB)

    Brinker, C. Jeffrey; Lu, Yunfeng (University of California Los Angeles, Los Angeles, CA)


    This is the final report for the Presidential Early Career Award for Science and Engineering - PECASE (LDRD projects 93369 and 118841) awarded to Professor Yunfeng Lu (Tulane University and University of California-Los Angeles). During the last decade, mesoporous materials with tunable periodic pores have been synthesized using surfactant liquid crystalline as templates, opening a new avenue for a wide spectrum of applications. However, the applications are somewhat limited by the unfavorabe pore orientation of these materials. Although substantial effort has been devoted to align the pore channels, fabrication of mesoporous materials with perpendicular pore channels remains challenging. This project focused on fabrication of mesoporous materials with perpendicularly aligned pore channels. We demonstrated structures for use in water purification, separation, sensors, templated synthesis, microelectronics, optics, controlled release, and highly selective catalysts.

  8. The Cluster Substructure - Alignment Connection


    Plionis, Manolis


    Using the APM cluster data we investigate whether the dynamical status of clusters is related to the large-scale structure of the Universe. We find that cluster substructure is strongly correlated with the tendency of clusters to be aligned with their nearest neighbour and in general with the nearby clusters that belong to the same supercluster. Furthermore, dynamically young clusters are more clustered than the overall cluster population. These are strong indications that cluster develop in ...

  9. NoFold: RNA structure clustering without folding or alignment. (United States)

    Middleton, Sarah A; Kim, Junhyong


    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures.

  10. Grain alignment in starless cores

    Energy Technology Data Exchange (ETDEWEB)

    Jones, T. J.; Bagley, M. [Minnesota Institute for Astrophysics, University of Minnesota, Minneapolis, MN 55455 (United States); Krejny, M. [Cree Inc., 4600 Silicon Dr., Durham, NC (United States); Andersson, B.-G. [SOFIA Science Center, USRA, Moffett Field, CA (United States); Bastien, P., E-mail: [Centre de recherche en astrophysique du Québec and Départment de Physique, Université de Montréal, Montréal (Canada)


    We present near-IR polarimetry data of background stars shining through a selection of starless cores taken in the K band, probing visual extinctions up to A{sub V}∼48. We find that P{sub K}/τ{sub K} continues to decline with increasing A{sub V} with a power law slope of roughly −0.5. Examination of published submillimeter (submm) polarimetry of starless cores suggests that by A{sub V}≳20 the slope for P versus τ becomes ∼−1, indicating no grain alignment at greater optical depths. Combining these two data sets, we find good evidence that, in the absence of a central illuminating source, the dust grains in dense molecular cloud cores with no internal radiation source cease to become aligned with the local magnetic field at optical depths greater than A{sub V}∼20. A simple model relating the alignment efficiency to the optical depth into the cloud reproduces the observations well.

  11. AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data

    KAUST Repository

    Zhang, Runxuan


    Background Alternative splicing is the major post-transcriptional mechanism by which gene expression is regulated and affects a wide range of processes and responses in most eukaryotic organisms. RNA-sequencing (RNA-seq) can generate genome-wide quantification of individual transcript isoforms to identify changes in expression and alternative splicing. RNA-seq is an essential modern tool but its ability to accurately quantify transcript isoforms depends on the diversity, completeness and quality of the transcript information. Results We have developed a new Reference Transcript Dataset for Arabidopsis (AtRTD2) for RNA-seq analysis containing over 82k non-redundant transcripts, whereby 74,194 transcripts originate from 27,667 protein-coding genes. A total of 13,524 protein-coding genes have at least one alternatively spliced transcript in AtRTD2 such that about 60% of the 22,453 protein-coding, intron-containing genes in Arabidopsis undergo alternative splicing. More than 600 putative U12 introns were identified in more than 2,000 transcripts. AtRTD2 was generated from transcript assemblies of ca. 8.5 billion pairs of reads from 285 RNA-seq data sets obtained from 129 RNA-seq libraries and merged along with the previous version, AtRTD, and Araport11 transcript assemblies. AtRTD2 increases the diversity of transcripts and through application of stringent filters represents the most extensive and accurate transcript collection for Arabidopsis to date. We have demonstrated a generally good correlation of alternative splicing ratios from RNA-seq data analysed by Salmon and experimental data from high resolution RT-PCR. However, we have observed inaccurate quantification of transcript isoforms for genes with multiple transcripts which have variation in the lengths of their UTRs. This variation is not effectively corrected in RNA-seq analysis programmes and will therefore impact RNA-seq analyses generally. To address this, we have tested different genome

  12. Cactus: Algorithms for genome multiple sequence alignment


    Paten, Benedict; Earl, Dent; Nguyen, Ngan; Diekhans, Mark; Zerbino, Daniel; Haussler, David


    Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms...

  13. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    NARCIS (Netherlands)

    Hasan, L.


    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of pr

  14. Physician-Hospital Alignment in Orthopedic Surgery. (United States)

    Bushnell, Brandon D


    The concept of "alignment" between physicians and hospitals is a popular buzzword in the age of health care reform. Despite their often tumultuous histories, physicians and hospitals find themselves under increasing pressures to work together toward common goals. However, effective alignment is more than just simple cooperation between parties. The process of achieving alignment does not have simple, universal steps. Alignment will differ based on individual situational factors and the type of specialty involved. Ultimately, however, there are principles that underlie the concept of alignment and should be a part of any physician-hospital alignment efforts. In orthopedic surgery, alignment involves the clinical, administrative, financial, and even personal aspects of a surgeon's practice. It must be based on the principles of financial interest, clinical authority, administrative participation, transparency, focus on the patient, and mutual necessity. Alignment can take on various forms as well, with popular models consisting of shared governance and comanagement, gainsharing, bundled payments, accountable care organizations, and other methods. As regulatory and financial pressures continue to motivate physicians and hospitals to develop alignment relationships, new and innovative methods of alignment will also appear. Existing models will mature and evolve, with individual variability based on local factors. However, certain trends seem to be appearing as time progresses and alignment relationships deepen, including regional and national collaboration, population management, and changes in the legal system. This article explores the history, principles, and specific methods of physician-hospital alignment and its critical importance for the future of health care delivery.

  15. An Overview of Multiple Sequence Alignment Systems

    CERN Document Server

    Saeed, Fahad


    An overview of current multiple alignment systems to date are described.The useful algorithms, the procedures adopted and their limitations are presented.We also present the quality of the alignments obtained and in which cases(kind of alignments, kind of sequences etc) the particular systems are useful.

  16. A cross-species alignment tool (CAT)

    DEFF Research Database (Denmark)

    Li, Heng; Guan, Liang; Liu, Tao;


    sensitive methods which are usually applied in aligning inter-species sequences. RESULTS: Here we present a new algorithm called CAT (for Cross-species Alignment Tool). It is designed to align mRNA sequences to mammalian-sized genomes. CAT is implemented using C scripts and is freely available on the web...

  17. Inferring comprehensible business/ICT alignment rules

    NARCIS (Netherlands)

    Cumps, B.; Martens, D.; De Backer, M.; Haesen, R.; Viaene, S.; Dedene, G.; Baesens, B.; Snoeck, M.


    We inferred business rules for business/ICT alignment by applying a novel rule induction algorithm on a data set containing rich alignment information polled from 641 organisations in 7 European countries. The alignment rule set was created using AntMiner+, a rule induction technique with a reputati

  18. Shift dynamics of capillary self-alignment

    NARCIS (Netherlands)

    Arutinov, G.; Mastrangeli, M.; Smits, E.C.P.; Heck, G.V.; Schoo, H.F.M.; Toonder, J.J.M. den; Dietzel, A.H.


    This paper describes the dynamics of capillary self-alignment of components with initial shift offsets from matching receptor sites. The analysis of the full uniaxial self-alignment dynamics of foil-based mesoscopic dies from pre-alignment to final settling evidenced three distinct, sequential regim

  19. Alignment of lower-limb prostheses. (United States)

    Zahedi, M S; Spence, W D; Solomonidis, S E; Paul, J P


    Alignment of a prosthesis is defined as the position of the socket relative to the other prosthetic components of the limb. During dynamic alignment the prosthetist, using subjective judgment and feedback from the patient, aims to achieve the most suitable limb geometry for best function and comfort. Until recently it was generally believed that a patient could only be satisfied with a unique "optimum alignment." The purpose of this systematic study of lower-limb alignment parameters was to gain an understanding of the factors that make a limb configuration or optimum alignment, acceptable to the patient, and to obtain a measure of the variation of this alignment that would be acceptable to the amputee. In this paper, the acceptable range of alignments for 10 below- and 10 above-knee amputees are established. Three prosthetists were involved in the majority of the 183 below-knee and 100 above-knee fittings, although several other prosthetists were also involved. The effects of each different prosthetist on the established range of alignment for each patient are reported to be significant. It is now established that an amputee can tolerate several alignments ranging in some parameters by as much as 148 mm in shifts and 17 degrees in tilts. This paper describes the method of defining and measuring the alignment of lower-limb prostheses. It presents quantitatively established values for bench alignment position and the range of adjustment required for incorporation into the design of new alignment units.

  20. Aligning Projection Images from Binary Volumes

    NARCIS (Netherlands)

    Bleichrodt, F.; Beenhouwer, J. de; Sijbers, J.; Batenburg, K.J.


    In tomography, slight differences between the geometry of the scanner hardware and the geometric model used in the reconstruction lead to alignment artifacts. To exploit high-resolution detectors used in many applications of tomography, alignment of the projection data is essential. Markerless align

  1. Vertically aligned nanostructure scanning probe microscope tips (United States)

    Guillorn, Michael A.; Ilic, Bojan; Melechko, Anatoli V.; Merkulov, Vladimir I.; Lowndes, Douglas H.; Simpson, Michael L.


    Methods and apparatus are described for cantilever structures that include a vertically aligned nanostructure, especially vertically aligned carbon nanofiber scanning probe microscope tips. An apparatus includes a cantilever structure including a substrate including a cantilever body, that optionally includes a doped layer, and a vertically aligned nanostructure coupled to the cantilever body.

  2. Strategic Alignment and New Product Development

    DEFF Research Database (Denmark)

    Acur, Nuran; Kandemir, Destan; Boer, Harry


    Strategic alignment is widely accepted as a prerequisite for a firm’s success, but insight into the role of alignment in, and its impact on, the new product evelopment (NPD) process and its performance is less well developed. Most publications on this topic either focus on one form of alignment o...

  3. Alignment of Nanoscale Single-Walled Carb on Nanotub es Strands

    Institute of Scientific and Technical Information of China (English)

    Danna Yang; Lin Wang; Xiaoxian Zhang; Dongwei Wang; Zhiqiang Shen; Sai Li


    Depositing single-walled carbon nanotubes (SWNTs) with controllable density, pattern and ori-entation on electrodes presents a challenge in today’s research. Here, we report a novel solvent evaporation method to align SWNTs in patterns having nanoscale width and micronscale length. SWNTs suspension has been introduced dropwise onto photoresist resin microchannels; and the capillary force can stretch and align SWNTs into strands with nanoscale width in the microchannels. Then these narrow and long aligned SWNTs patterns were successfully transferred to a pair of gold electrodes with different gaps to fabricate carbon nan-otube field-effect transistor (CNTFET). Moreover, the electrical performance of the CNTFET show that the SWNTs strands can bridge different gaps and fabricate good electrical performance CNTFET with ON/OFF ratio around 106. This result suggests a promising and simple strategy for assembling well-aligned SWNTs into CNTFET device with good electrical performance.

  4. Recent Advances in Directed Assembly of Nanowires or Nanotub es

    Institute of Scientific and Technical Information of China (English)

    Mei Liu; Zhizheng Wu; Woon Ming Lau; Jun Yang


    Nanowires and nanotubes of diverse material compositions, properties and/or functions have been produced or fabricated through various bottom-up or top-down approaches. These nanowires or nanotubes have also been utilized as potential building blocks for functional nanodevices. The key for the integration of those nanowire or nanotube based devices is to assemble these one dimensional nanomaterials to specific locations using techniques that are highly controllable and scalable. Ideally such techniques should enable assembly of highly uniform nanowire/nanotube arrays with precise control of density, location, dimension or even ma-terial types of nanowires/nanotubes. Numerous assembly techniques are being developed that can quickly align and assemble large quantities of one type or multiple types of nanowires through parallel processes, in-cluding flow-assisted alignment, Langmuir-Blodgett assembly, bubble-blown technique, electric/magnetic- field directed assembly, contact/roll printing, knocking-down, etc.. With these assembling techniques, applications of nanowire/nanotube based devices such as flexible electronics and sensors have been demonstrated. This paper delivers an overall review of directed nanowire/nanotube assembling approaches and analyzes advantages and limitations of each method. The future research directions have also been discussed.

  5. Finishing of the cold mass assembly

    CERN Multimedia

    Maximilien Brice


    Photo 1 The connection-side end of the active part assembly. This view shows the electrical connections between the poles and the curved bus ended with flanges for the connection with the protection diode. Photo 2 The connection-side end of the active part assembly. This view shows the electrical connections between the poles, the auxiliary bus bars and the instrumentation wires. Photo 3 Lyre-side end of the active part assembly. One can see the mechanical support of the corretor magnets that are to be installed around the cold bore tubes. Photo 4 General view of the finishing station showing the special supporting structures (blue and yellow structures) needed for the geometric measurements and for the alignment operations. Around the magnet, there are datum points (on the tripodes) needed to build up the coordinates system for the measurements.

  6. Finishing of the cold mass assembly

    CERN Multimedia

    Maximilien Brice


    Photo 1 Zoom of the lyre-side end of the active part assembly. The extremity of the shrinking cylinder has been bevelled in view of welding the end cover. Photo 2 General view of the finishing station showing the special supporting structures (blue and yellow structures) needed for the geometric measurements and for the alignment operations. Photo 3 Zoom of the lyre-side end of the active part assembly. One can also see the auxiliary bus bars needed to power the corrector magnets that are installed in the dipole cold mass assembly. Photo 4 Technicians are putting in order the instrumentation wires. The prototype magnets were equipped with numerous sensors to monitor key parameters during the performance tests at cold conditions.

  7. Estimation of the minimum mRNA splicing error rate in vertebrates. (United States)

    Skandalis, A


    The majority of protein coding genes in vertebrates contain several introns that are removed by the mRNA splicing machinery. Errors during splicing can generate aberrant transcripts and degrade the transmission of genetic information thus contributing to genomic instability and disease. However, estimating the error rate of constitutive splicing is complicated by the process of alternative splicing which can generate multiple alternative transcripts per locus and is particularly active in humans. In order to estimate the error frequency of constitutive mRNA splicing and avoid bias by alternative splicing we have characterized the frequency of splice variants at three loci, HPRT, POLB, and TRPV1 in multiple tissues of six vertebrate species. Our analysis revealed that the frequency of splice variants varied widely among loci, tissues, and species. However, the lowest observed frequency is quite constant among loci and approximately 0.1% aberrant transcripts per intron. Arguably this reflects the "irreducible" error rate of splicing, which consists primarily of the combination of replication errors by RNA polymerase II in splice consensus sequences and spliceosome errors in correctly pairing exons.

  8. The Role of Canonical and Noncanonical Pre-mRNA Splicing in Plant Stress Responses

    Directory of Open Access Journals (Sweden)

    A. S. Dubrovina


    Full Text Available Plants are sessile organisms capable of adapting to various environmental constraints, such as high or low temperatures, drought, soil salinity, or pathogen attack. To survive the unfavorable conditions, plants actively employ pre-mRNA splicing as a mechanism to regulate expression of stress-responsive genes and reprogram intracellular regulatory networks. There is a growing evidence that various stresses strongly affect the frequency and diversity of alternative splicing events in the stress-responsive genes and lead to an increased accumulation of mRNAs containing premature stop codons, which in turn have an impact on plant stress response. A number of studies revealed that some mRNAs involved in plant stress response are spliced counter to the traditional conception of alternative splicing. Such noncanonical mRNA splicing events include trans-splicing, intraexonic deletions, or variations affecting multiple exons and often require short direct repeats to occur. The noncanonical alternative splicing, along with common splicing events, targets the spliced transcripts to degradation through nonsense-mediated mRNA decay or leads to translation of truncated proteins. Investigation of the diversity, biological consequences, and mechanisms of the canonical and noncanonical alternative splicing events will help one to identify those transcripts which are promising for using in genetic engineering and selection of stress-tolerant plants.

  9. Attenuation of the suppressive activity of cellular splicing factor SRSF3 by Kaposi sarcoma-associated herpesvirus ORF57 protein is required for RNA splicing. (United States)

    Majerciak, Vladimir; Lu, Mathew; Li, Xiaofan; Zheng, Zhi-Ming


    Kaposi sarcoma-associated herpesvirus (KSHV) ORF57 is a multifunctional post-transcriptional regulator essential for viral gene expression during KSHV lytic infection. ORF57 requires interactions with various cellular proteins for its function. Here, we identified serine/arginine-rich splicing factor 3 (SRSF3, formerly known as SRp20) as a cellular cofactor involved in ORF57-mediated splicing of KSHV K8β RNA. In the absence of ORF57, SRSF3 binds to a suboptimal K8β intron and inhibits K8β splicing. Knockdown of SRSF3 promotes K8β splicing, mimicking the effect of ORF57. The N-terminal half of ORF57 binds to the RNA recognition motif of SRSF3, which prevents SRSF3 from associating with the K8β intron RNA and therefore attenuates the suppressive effect of SRSF3 on K8β splicing. ORF57 also promotes splicing of heterologous non-KSHV transcripts that are negatively regulated by SRSF3, indicating that the effect of ORF57 on SRSF3 activity is independent of RNA target. SPEN proteins, previously identified as ORF57-interacting partners, suppress ORF57 splicing activity by displacing ORF57 from SRSF3-RNA complexes. In summary, we have identified modulation of SRSF3 activity as the molecular mechanism by which ORF57 promotes RNA splicing.

  10. Footprints of a trypanosomatid RNA world: pre-small subunit rRNA processing by spliced leader addition trans-splicing

    Directory of Open Access Journals (Sweden)

    Mario Gustavo Mayer


    Full Text Available The addition of a capped mini-exon [spliced leader (SL] through trans-splicing is essential for the maturation of RNA polymerase (pol II-transcribed polycistronic pre-mRNAs in all members of the Trypanosomatidae family. This process is an inter-molecular splicing reaction that follows the same basic rules of cis-splicing reactions. In this study, we demonstrated that mini-exons were added to precursor ribosomal RNA (pre-rRNA are transcribed by RNA pol I, including the 5' external transcribed spacer (ETS region. Additionally, we detected the SL-5'ETS molecule using three distinct methods and located the acceptor site between two known 5'ETS rRNA processing sites (A' and A1 in four different trypanosomatids. Moreover, we detected a polyadenylated 5'ETS upstream of the trans-splicing acceptor site, which also occurs in pre-mRNA trans-splicing. After treatment with an indirect trans-splicing inhibitor (sinefungin, we observed SL-5'ETS decay. However, treatment with 5-fluorouracil (a precursor of RNA synthesis that inhibits the degradation of pre-rRNA led to the accumulation of SL-5'ETS, suggesting that the molecule may play a role in rRNA degradation. The detection of trans-splicing in these molecules may indicate broad RNA-joining properties, regardless of the polymerase used for transcription.

  11. Aligning molecules with intense nonresonant laser fields

    DEFF Research Database (Denmark)

    Larsen, J.J.; Safvan, C.P.; Sakai, H.;


    Molecules in a seeded supersonic beam are aligned by the interaction between an intense nonresonant linearly polarized laser field and the molecular polarizability. We demonstrate the general applicability of the scheme by aligning I2, ICl, CS2, CH3I, and C6H5I molecules. The alignment is probed...... by mass selective two dimensional imaging of the photofragment ions produced by femtosecond laser pulses. Calculations on the degree of alignment of I2 are in good agreement with the experiments. We discuss some future applications of laser aligned molecules....

  12. Subsonic Mechanical Alignment of Irregular Grains

    CERN Document Server

    Lazarian, Alex


    We show that grains can be efficiently aligned by interacting with a subsonic gaseous flow. The alignment arises from grains having irregularities that scatter atoms with different efficiency in the right and left directions. The grains tend to align with long axes perpendicular to magnetic field, which corresponds to Davis-Greenstein predictions, but does not involve magnetic field. For rather conservative factors characterizing the grain helicity and scattering efficiency of impinging atoms, the alignment of helical grains is much more efficient than the Gold-type alignment processes.

  13. Self-assembly micro optical filter (United States)

    Zhang, Ping (Cerina); Le, Kevin; Malalur-Nagaraja-Rao, Smitha; Hsu, Lun-Chen; Chiao, J.-C.


    Optical communication and sensor industry face critical challenges in manufacturing for system integration. Due to the assembly complexity and integration platform variety, micro optical components require costly alignment and assembly procedures, in which many required manual efforts. Consequently, self-assembly device architectures have become a great interest and could provide major advantages over the conventional optical devices. In this paper, we discussed a self-assembly integration platform for micro optical components. To demonstrate the adaptability and flexibility of the proposed optical device architectures, we chose a commercially available MEMS fabrication foundry service - MUMPs (Multi-User MEMS Process). In this work, polysilicon layers of MUMPS are used as the 3-D structural material for construction of micro component framework and actuators. However, because the polysilicon has high absorption in the visible and near infrared wavelength ranges, it is not suitable for optical interaction. To demonstrate the required optical performance, hybrid integration of materials was proposed and implemented. Organic compound materials were applied on the silicon-based framework to form the required optical interfaces. Organic compounds provide good optical transparency, flexibility to form filters or lens and inexpensive manufacturing procedures. In this paper, we have demonstrated a micro optical filter integrated with self-assembly structures. We will discuss the self-assembly mechanism, optical filter designs, fabrication issues and results.

  14. NIF Target Assembly Metrology Methodology and Results

    Energy Technology Data Exchange (ETDEWEB)

    Alger, E. T. [General Atomics, San Diego, CA (United States); Kroll, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Dzenitis, E. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Montesanti, R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hughes, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Swisher, M. [IAP, Livermore, CA (United States); Taylor, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Segraves, K. [IAP, Livermore, CA (United States); Lord, D. M. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Reynolds, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Castro, C. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Edwards, G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)


    During our inertial confinement fusion (ICF) experiments at the National Ignition Facility (NIF) we require cryogenic targets at the 1-cm scale to be fabricated, assembled, and metrologized to micron-level tolerances. During assembly of these ICF targets, there are physical dimensmetrology is completed using optical coordinate measurement machines that provide repeatable measurements with micron precision, while also allowing in-process data collection for absolute accuracy in assembly. To date, 51 targets have been assembled and metrologized, and 34 targets have been successfully fielded on NIF relying on these metrology data. In the near future, ignition experiments on NIF will require tighter tolerances and more demanding target assembly and metrology capability. Metrology methods, calculations, and uncertainty estimates will be discussed. Target diagnostic port alignment, target position, and capsule location results will be reviewed for the 2009 Energetics Campaign. The information is presented via control charts showing the effect of process improvements that were made during target production. Certain parameters, including capsule position, met the 2009 campaign specifications but will have much tighter requirements in the future. Finally, in order to meet these new requirements assembly process changes and metrology capability upgrades will be necessary.

  15. Pentamidine reverses the splicing defects associated with myotonic dystrophy. (United States)

    Warf, M Bryan; Nakamori, Masayuki; Matthys, Catherine M; Thornton, Charles A; Berglund, J Andrew


    Myotonic dystrophy (DM) is a genetic disorder caused by the expression (as RNA) of expanded CTG or CCTG repeats. The alternative splicing factor MBNL1 is sequestered to the expanded RNA repeats, resulting in missplicing of a subset of pre-mRNAs linked to symptoms found in DM patients. Current data suggest that if MBNL1 is released from sequestration, disease symptoms may be alleviated. We identified the small molecules pentamidine and neomycin B as compounds that disrupt MBNL1 binding to CUG repeats in vitro. We show in cell culture that pentamidine was able to reverse the missplicing of 2 pre-mRNAs affected in DM, whereas neomycin B had no effect. Pentamidine also significantly reduced the formation of ribonuclear foci in tissue culture cells, releasing MBNL1 from the foci in the treated cells. Furthermore, pentamidine partially rescued splicing defects of 2 pre-mRNAs in mice expressing expanded CUG repeats.

  16. A novel splicing mutation in the V2 vasopressin receptor

    DEFF Research Database (Denmark)

    Kamperis, Konstantinos; Siggaard, C; Herlin, Troels;


    of the gene in both the affected male (hemizygous) and his mother (heterozygous). This mutation is likely to cause aberrant splicing of the terminal intron of the gene, leading to a non-functional AVP receptor. The clinical studies were consistent with such a hypothesis, as the affected subject had a severe......In order to elucidate the molecular basis and the clinical characteristics of X-linked recessive nephrogenic diabetes insipidus (CNDI) in a kindred of Danish descent, we performed direct sequencing of the arginine vasopressin receptor 2 (AVPR2) gene in five members of the family, as well...... as clinical investigations comprising a fluid deprivation test and a 1-deamino-8-D-arginine-vasopressin (dDAVP) infusion test in the study subject and his mother. We found a highly unusual, novel, de novo 1447A-->C point mutation (gDNA), involving the invariable splice acceptor of the second intron...

  17. Minor class splicing shapes the zebrafish transcriptome during development

    DEFF Research Database (Denmark)

    Markmiller, Sebastian; Cloonan, Nicole; Lardelli, Rea M;


    Minor class or U12-type splicing is a highly conserved process required to remove a minute fraction of introns from human pre-mRNAs. Defects in this splicing pathway have recently been linked to human disease, including a severe developmental disorder encompassing brain and skeletal abnormalities...... describe a unique zebrafish mutant, caliban (clbn), with arrested development of the digestive organs caused by an ethylnitrosourea-induced recessive lethal point mutation in the rnpc3 [RNA-binding region (RNP1, RRM) containing 3] gene. rnpc3 encodes the zebrafish ortholog of human RNPC3, also known....... Analysis of its transcriptome reveals efficient mRNA processing as a critical process for the growth and proliferation of cells during vertebrate development....

  18. Self-transport and self-alignment of microchips using microscopic rain (United States)

    Chang, Bo; Shah, Ali; Zhou, Quan; Ras, Robin H. A.; Hjort, Klas


    Alignment of microchips with receptors is an important process step in the construction of integrated micro- and nanosystems for emerging technologies, and facilitating alignment by spontaneous self-assembly processes is highly desired. Previously, capillary self-alignment of microchips driven by surface tension effects on patterned surfaces has been reported, where it was essential for microchips to have sufficient overlap with receptor sites. Here we demonstrate for the first time capillary self-transport and self-alignment of microchips, where microchips are initially placed outside the corresponding receptor sites and can be self-transported by capillary force to the receptor sites followed by self-alignment. The surface consists of hydrophilic silicon receptor sites surrounded by superhydrophobic black silicon. Rain-induced microscopic droplets are used to form the meniscus for the self-transport and self-alignment. The boundary conditions for the self-transport have been explored by modeling and confirmed experimentally. The maximum permitted gap between a microchip and a receptor site is determined by the volume of the liquid and by the wetting contrast between receptor site and substrate. Microscopic rain applied on hydrophilic-superhydrophobic patterned surfaces greatly improves the capability, reliability and error-tolerance of the process, avoiding the need for accurate initial placement of microchips, and thereby greatly simplifying the alignment process.

  19. Self-transport and self-alignment of microchips using microscopic rain. (United States)

    Chang, Bo; Shah, Ali; Zhou, Quan; Ras, Robin H A; Hjort, Klas


    Alignment of microchips with receptors is an important process step in the construction of integrated micro- and nanosystems for emerging technologies, and facilitating alignment by spontaneous self-assembly processes is highly desired. Previously, capillary self-alignment of microchips driven by surface tension effects on patterned surfaces has been reported, where it was essential for microchips to have sufficient overlap with receptor sites. Here we demonstrate for the first time capillary self-transport and self-alignment of microchips, where microchips are initially placed outside the corresponding receptor sites and can be self-transported by capillary force to the receptor sites followed by self-alignment. The surface consists of hydrophilic silicon receptor sites surrounded by superhydrophobic black silicon. Rain-induced microscopic droplets are used to form the meniscus for the self-transport and self-alignment. The boundary conditions for the self-transport have been explored by modeling and confirmed experimentally. The maximum permitted gap between a microchip and a receptor site is determined by the volume of the liquid and by the wetting contrast between receptor site and substrate. Microscopic rain applied on hydrophilic-superhydrophobic patterned surfaces greatly improves the capability, reliability and error-tolerance of the process, avoiding the need for accurate initial placement of microchips, and thereby greatly simplifying the alignment process.

  20. Vision Servo Motion Control and Error Analysis of a Coplanar XXY Stage for Image Alignment Motion

    Directory of Open Access Journals (Sweden)

    Hau-Wei Lee


    Full Text Available In recent years, as there is demand for smart mobile phones with touch panels, the alignment/compensation system of alignment stage with vision servo control has also increased. Due to the fact that the traditional stacked-type XYθ stage has cumulative errors of assembly and it is heavy, it has been gradually replaced by the coplanar stage characterized by three actuators on the same plane with three degrees of freedom. The simplest image alignment mode uses two cameras as the equipments for feedback control, and the work piece is placed on the working stage. The work piece is usually engraved/marked. After the cameras capture images and when the position of the mark in the camera is obtained by image processing, the mark can be moved to the designated position in the camera by moving the stage and using alignment algorithm. This study used a coplanar XXY stage with 1 μm positioning resolution. Due to the fact that the resolution of the camera is about 3.75 μm per pixel, thus a subpixel technology is used, and the linear and angular alignment repeatability of the alignment system can achieve 1 μm and 5 arcsec, respectively. The visual servo motion control for alignment motion is completed within 1 second using the coplanar XXY stage.

  1. Self-aligning and compressed autosophy video databases (United States)

    Holtz, Klaus E.


    Autosophy, an emerging new science, explains `self-assembling structures,' such as crystals or living trees, in mathematical terms. This research provides a new mathematical theory of `learning' and a new `information theory' which permits the growing of self-assembling data network in a computer memory similar to the growing of `data crystals' or `data trees' without data processing or programming. Autosophy databases are educated very much like a human child to organize their own internal data storage. Input patterns, such as written questions or images, are converted to points in a mathematical omni dimensional hyperspace. The input patterns are then associated with output patterns, such as written answers or images. Omni dimensional information storage will result in enormous data compression because each pattern fragment is only stored once. Pattern recognition in the text or image files is greatly simplified by the peculiar omni dimensional storage method. Video databases will absorb input images from a TV camera and associate them with textual information. The `black box' operations are totally self-aligning where the input data will determine their own hyperspace storage locations. Self-aligning autosophy databases may lead to a new generation of brain-like devices.

  2. Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing. (United States)

    Wu, Dong-Dong; Ye, Ling-Qun; Li, Yan; Sun, Yan-Bo; Shao, Yi; Chen, Chunyan; Zhu, Zhu; Zhong, Li; Wang, Lu; Irwin, David M; Zhang, Yong E; Zhang, Ya-Ping


    Next-generation RNA sequencing has been successfully used for identification of transcript assembly, evaluation of gene expression levels, and detection of post-transcriptional modifications. Despite these large-scale studies, additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome. Here, we provide a total of 6.5 billion RNA-seq reads from different subregions of the human brain. A significant correlation was observed between the levels of alternative splicing and RNA editing, which might be explained by a competition between the molecular machineries responsible for the splicing and editing of RNA. Young human protein-coding genes demonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans. We also found that a significantly greater number of young human protein-coding genes are expressed in the putamen, a tissue that was also observed to have the highest level of RNA-editing activity. The putamen, which previously received little attention, plays an important role in cognitive ability, and our data suggest a potential contribution of the putamen to human evolution.

  3. Characterization and alternative splicing of the complex I 19-kD subunit in Dunaliella salina: expression and mutual correlation of splice variants under diverse stresses. (United States)

    Cao, Yu; Jin, Nan; Xu, Hui; Liu, Yi; Zhu, Wei Hua; Li, Xin Ran; Qiao, Dai Rong; Cao, Yi


    Complex I is the first enzyme in the mitochondrial respiratory chain. It extracts energy from NADH, which is produced by the oxidation of sugars and fats, and traps the energy by virtue of a potential difference or voltage across the mitochondrial inner membrane. Herein, the genomic sequence and four splice variants encoding the complex I 19-kD subunit were isolated from Dunaliella salina. There were four transcripts coding for the complex I 19-kD subunit due to alternative splicing in algae, and the four transcripts were translated to two protein isoforms with varying C-terminals. We report the splicing pattern in the 3'-region of the D. salina 19-kD subunit, in which three of the exons (5, 6, and 7) could be alternatively spliced. Moreover, we found that four alternatively spliced variants were subject to coordinated transcription in response to different stresses by real-time quantitative PCR.

  4. Galaxy alignments: Theory, modelling and simulations

    CERN Document Server

    Kiessling, Alina; Joachimi, Benjamin; Kirk, Donnacha; Kitching, Thomas D; Leonard, Adrienne; Mandelbaum, Rachel; Schäfer, Björn Malte; Sifón, Cristóbal; Brown, Michael L; Rassat, Anais


    The shapes of galaxies are not randomly oriented on the sky. During the galaxy formation and evolution process, environment has a strong influence, as tidal gravitational fields in large-scale structure tend to align the shapes and angular momenta of nearby galaxies. Additionally, events such as galaxy mergers affect the relative alignments of galaxies throughout their history. These "intrinsic galaxy alignments" are known to exist, but are still poorly understood. This review will offer a pedagogical introduction to the current theories that describe intrinsic galaxy alignments, including the apparent difference in intrinsic alignment between early- and late-type galaxies and the latest efforts to model them analytically. It will then describe the ongoing efforts to simulate intrinsic alignments using both $N$-body and hydrodynamic simulations. Due to the relative youth of this field, there is still much to be done to understand intrinsic galaxy alignments and this review summarises the current state of the ...

  5. Alignment method for solar collector arrays (United States)

    Driver, Jr., Richard B


    The present invention is directed to an improved method for establishing camera fixture location for aligning mirrors on a solar collector array (SCA) comprising multiple mirror modules. The method aligns the mirrors on a module by comparing the location of the receiver image in photographs with the predicted theoretical receiver image location. To accurately align an entire SCA, a common reference is used for all of the individual module images within the SCA. The improved method can use relative pixel location information in digital photographs along with alignment fixture inclinometer data to calculate relative locations of the fixture between modules. The absolute locations are determined by minimizing alignment asymmetry for the SCA. The method inherently aligns all of the mirrors in an SCA to the receiver, even with receiver position and module-to-module alignment errors.

  6. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm (United States)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra


    In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a time gain of (70-90)% for highly similar nucleotide sequences (> 80% similarity), and (54-70)% for sequences having (30-80)% similarity. For other sequences, it terminates with an approximate score. For protein sequences, the average time gain is between (25-40)%. Compared to three heuristic global alignment methods, the quality of alignment is improved by about 23%-53%. FOGSAA is, in general, suitable for aligning any two sequences defined over a finite alphabet set, where the quality of the global alignment is of supreme importance.

  7. Alternative splicing of the androgen receptor in polycystic ovary syndrome


    Wang, Fangfang; Pan, Jiexue; Liu, Ye; Meng, Qing; Lv, Pingping; Qu, Fan; Ding, Guo-Lian; Klausen, Christian; Leung, Peter C. K.; Chan, Hsiao Chang; Yao, Weimiao; Zhou, Cai-Yun; Shi, Biwei; ZHANG, JUNYU; Sheng, Jianzhong


    Excess androgens and abnormal follicle development, largely due to ovarian granulosa cell (GC) dysfunction, characterize polycystic ovary syndrome (PCOS), a common endocrinopathy of women predisposing to infertility. Thus, it is important to understand GC dysfunction. The androgen receptor (AR) is widely believed to be an essential regulator of GC biology. High expression of AR in GCs is primarily considered to associate with PCOS. However, we show that AR alternative splice variants in GCs d...

  8. The role of HMGCR alternative splicing in statin efficacy


    Medina, Marisa Wong; Krauss, Ronald M.


    Statins, or 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) inhibitors, are widely prescribed to lower plasma cholesterol levels and reduce cardiovascular disease (CVD) risk. Despite the well documented efficacy of statins, there is large inter-individual variation in response. Using a panel of immortalized lymphocyte cell lines incubated with simvastatin, we recently found that the magnitude of expression of an alternatively spliced HMGCR transcript lacking exon 13 was inversely corr...

  9. Automatic detection of exonic splicing enhancers (ESEs using SVMs

    Directory of Open Access Journals (Sweden)

    Suhai Sándor


    Full Text Available Abstract Background Exonic splicing enhancers (ESEs activate nearby splice sites and promote the inclusion (vs. exclusion of exons in which they reside, while being a binding site for SR proteins. To study the impact of ESEs on alternative splicing it would be useful to have a possibility to detect them in exons. Identifying SR protein-binding sites in human DNA sequences by machine learning techniques is a formidable task, since the exon sequences are also constrained by their functional role in coding for proteins. Results The choice of training examples needed for machine learning approaches is difficult since there are only few exact locations of human ESEs described in the literature which could be considered as positive examples. Additionally, it is unclear which sequences are suitable as negative examples. Therefore, we developed a motif-oriented data-extraction method that extracts exon sequences around experimentally or theoretically determined ESE patterns. Positive examples are restricted by heuristics based on known properties of ESEs, e.g. location in the vicinity of a splice site, whereas negative examples are taken in the same way from the middle of long exons. We show that a suitably chosen SVM using optimized sequence kernels (e.g., combined oligo kernel can extract meaningful properties from these training examples. Once the classifier is trained, every potential ESE sequence can be passed to the SVM for verification. Using SVMs with the combined oligo kernel yields a high accuracy of about 90 percent and well interpretable parameters. Conclusion The motif-oriented data-extraction method seems to produce consistent training and test data leading to good classification rates and thus allows verification of potential ESE motifs. The best results were obtained using an SVM with the combined oligo kernel, while oligo kernels with oligomers of a certain length could be used to extract relevant features.

  10. Probe tip heating assembly (United States)

    Schmitz, Roger William; Oh, Yunje


    A heating assembly configured for use in mechanical testing at a scale of microns or less. The heating assembly includes a probe tip assembly configured for coupling with a transducer of the mechanical testing system. The probe tip assembly includes a probe tip heater system having a heating element, a probe tip coupled with the probe tip heater system, and a heater socket assembly. The heater socket assembly, in one example, includes a yoke and a heater interface that form a socket within the heater socket assembly. The probe tip heater system, coupled with the probe tip, is slidably received and clamped within the socket.

  11. Direct Nanorod Assembly Using Block Copolymer-Based Supramolecules (United States)

    Thorkelsson, Kari; Mastroianni, Alexander; Ercius, Peter; Xu, Ting


    One-dimensional nanomaterials with high aspect ratios, such as nanorods, exhibit unique and useful anisotropic optical, magnetic, and electrical properties. The collective properties of 1-D nanomaterials depend on their spatial arrangements, interparticle ordering, and macroscopic alignment. Developing routes to control their organization with high precision is critical to generate functional materials. We have investigated the co-assemblies of nanorods and block copolymer (BCP)-based supramolecules that self-assemble into spherical, lamellar and cylindrical morphologies. By varying energetic contributions from the rod-rod interactions and the deformation of the supramolecule, a wide library of nanorod assemblies including highly aligned arrays, continuous networks, and clusters can be readily accessed. Since macroscopic alignment of BCP microdomains can be obtained by application of external fields, present studies open up a new route to manipulate macroscopic alignments of nanorods. Fundamentally, these studies have demonstrated that in these blends, the energetic contributions from the polymer chain deformation and rod-rod interactions are comparable and can be tailored to disperse nanorods with control over inter-rod ordering and their relative alignment.

  12. Aligned interactions in cosmic rays

    Energy Technology Data Exchange (ETDEWEB)

    Kempa, J., E-mail: [Warsaw University of Technology Branch Plock (Poland)


    The first clean Centauro was found in cosmic rays years many ago at Mt Chacaltaya experiment. Since that time, many people have tried to find this type of interaction, both in cosmic rays and at accelerators. But no one has found a clean cases of this type of interaction.It happened finally in the last exposure of emulsion at Mt Chacaltaya where the second clean Centauro has been found. The experimental data for both the Centauros and STRANA will be presented and discussed in this paper. We also present our comments to the intriguing question of the existence of a type of nuclear interactions at high energy with alignment.


    Smith, W.Q.


    An apparatus is presented for remotely determining the alignment of a centrifuge. The centrifage shaft is provided with a shoulder, upon which two followers ride, one for detecting radial movements, and one upon the shoulder face for determining the axial motion. The followers are attached to separate liquid filled bellows, and a tube connects each bellows to its respective indicating gage at a remote location. Vibrations produced by misalignment of the centrifuge shaft are transmitted to the bellows, and tbence through the tubing to the indicator gage. This apparatus is particularly useful for operation in a hot cell where the materials handled are dangerous to the operating personnel.

  14. T-IDBA: A de novo Iterative de Bruijn Graph Assembler for Transcriptome (United States)

    Peng, Yu; Leung, Henry C. M.; Yiu, S. M.; Chin, Francis Y. L.

    RNA-seq data produced by next-generation sequencing technology is a useful tool for analyzing transcriptomes. However, existing de novo transcriptome assemblers do not fully utilize the properties of transcriptomes and may result in short contigs because of the splicing nature (shared exons) of the genes. We propose the T-IDBA algorithm to reconstruct expressed isoforms without reference genome. By using pair-end information to solve the problem of long repeats in different genes and branching in the same gene due to alternative splicing, the graph can be decomposed into small components, each corresponds to a gene. The most possible isoforms with sufficient support from the pair-end reads will be found heuristically. In practice, our de novo transcriptome assembler, T-IDBA, outperforms Abyss substantially in terms of sensitivity and precision for both simulated and real data. T-IDBA is available at

  15. Behind the Scene Role of Conserved Threonine in Intein Splicing (United States)

    Dearden, Albert; Callahan, Brian; Belfort, Marlene; Nayak, Saroj


    Protein splicing is an autocatalytic process where an ``intein'' self-cleaves from a precursor protein and catalyzes ligation of the flanking fragments. Inteins occur in all domains of life and have myriad uses in biotechnology. While reaction steps of intein splicing are known, mechanistic details remain incomplete. Here, we investigate the possible role of a highly conserved active-site Threonine residue in bringing about the initial step of splicing: peptide bond rearrangement at a conserved Glycine-Cysteine motif. We report that although not part of the active transition state in this reaction, Threonine plays an important role in reducing the energy barrier through charge screening of active residues in the transition state. Interestingly, Threonine-Glycine hydrogen bonding makes sulfur of the attacking Cysteine less nucleophilic, thereby minimizing Coulomb repulsion in the transition state. These non-intuitive results are obtained through a combination of crystal structure, quantum mechanical simulations, and mutagenesis data. Our results further predict that the sluggish reaction rates observed with intein mutants harboring Threonine-Alanine substitutions can be accelerated in the presence of non-aqueous solvents.

  16. Alternative Splicing of G9a Regulates Neuronal Differentiation

    Directory of Open Access Journals (Sweden)

    Ana Fiszbein


    Full Text Available Chromatin modifications are critical for the establishment and maintenance of differentiation programs. G9a, the enzyme responsible for histone H3 lysine 9 dimethylation in mammalian euchromatin, exists as two isoforms with differential inclusion of exon 10 (E10 through alternative splicing. We find that the G9a methyltransferase is required for differentiation of the mouse neuronal cell line N2a and that E10 inclusion increases during neuronal differentiation of cultured cells, as well as in the developing mouse brain. Although E10 inclusion greatly stimulates overall H3K9me2 levels, it does not affect G9a catalytic activity. Instead, E10 increases G9a nuclear localization. We show that the G9a E10+ isoform is necessary for neuron differentiation and regulates the alternative splicing pattern of its own pre-mRNA, enhancing E10 inclusion. Overall, our findings indicate that by regulating its own alternative splicing, G9a promotes neuron differentiation and creates a positive feedback loop that reinforces cellular commitment to differentiation.

  17. Detection of Splice Sites Using Support Vector Machine (United States)

    Varadwaj, Pritish; Purohit, Neetesh; Arora, Bhumika

    Automatic identification and annotation of exon and intron region of gene, from DNA sequences has been an important research area in field of computational biology. Several approaches viz. Hidden Markov Model (HMM), Artificial Intelligence (AI) based machine learning and Digital Signal Processing (DSP) techniques have extensively and independently been used by various researchers to cater this challenging task. In this work, we propose a Support Vector Machine based kernel learning approach for detection of splice sites (the exon-intron boundary) in a gene. Electron-Ion Interaction Potential (EIIP) values of nucleotides have been used for mapping character sequences to corresponding numeric sequences. Radial Basis Function (RBF) SVM kernel is trained using EIIP numeric sequences. Furthermore this was tested on test gene dataset for detection of splice site by window (of 12 residues) shifting. Optimum values of window size, various important parameters of SVM kernel have been optimized for a better accuracy. Receiver Operating Characteristic (ROC) curves have been utilized for displaying the sensitivity rate of the classifier and results showed 94.82% accuracy for splice site detection on test dataset.

  18. Effect of Splice Marking on Fabric Roll Planning

    Institute of Scientific and Technical Information of China (English)

    吴秀芬; 许赐亮; 陈建中


    Minimising the fabric loss during spreading can reduce the total production costs of garment manufacturing.Although marker planning is a major determinant of material utilisation, considerable savings on materials also will be made from the area of spreading loss. In the spreading process, it is general to have variance on the fabric yardage between each fabric roll, and the number of splice markings on each cutting lay is also varied. This paper aim to study how the fabric roll planning and the number of splice marks of a cutting lay will affect the material usage in the spreading process. By using a genetic algorithm approach, the amount of fabric to be saved by optimising the fabric roll sequence was derived by comparing the best arrangement and the worst arrangement of the fabric roll sequences of a cutting lay.The result of the study showed that both fabric roll planning and the number of splice marking have effect on the fabric loss. The findings could help the apparel manufacturer to reduce the fabric loss by improving the roll planning in fabric spreading.

  19. Conserved and species-specific alternative splicing in mammalian genomes

    Directory of Open Access Journals (Sweden)

    Favorov Alexander V


    Full Text Available Abstract Background Alternative splicing has been shown to be one of the major evolutionary mechanisms for protein diversification and proteome expansion, since a considerable fraction of alternative splicing events appears to be species- or lineage-specific. However, most studies were restricted to the analysis of cassette exons in pairs of genomes and did not analyze functionality of the alternative variants. Results We analyzed conservation of human alternative splice sites and cassette exons in the mouse and dog genomes. Alternative exons, especially minor-isofom ones, were shown to be less conserved than constitutive exons. Frame-shifting alternatives in the protein-coding regions are less conserved than frame-preserving ones. Similarly, the conservation of alternative sites is highest for evenly used alternatives, and higher when the distance between the sites is divisible by three. The rate of alternative-exon and site loss in mouse is slightly higher than in dog, consistent with faster evolution of the former. The evolutionary dynamics of alternative sites was shown to be consistent with the model of random activation of cryptic sites. Conclusion Consistent with other studies, our results show that minor cassette exons are less conserved than major-alternative and constitutive exons. However, our study provides evidence that this is caused not only by exon birth, but also lineage-specific loss of alternative exons and sites, and it depends on exon functionality.

  20. An Engineered Split Intein for Photoactivated Protein Trans-Splicing.

    Directory of Open Access Journals (Sweden)

    Stanley Wong

    Full Text Available Protein splicing is mediated by inteins that auto-catalytically join two separated protein fragments with a peptide bond. Here we engineered a genetically encoded synthetic photoactivatable intein (named LOVInC, by using the light-sensitive LOV2 domain from Avena sativa as a switch to modulate the splicing activity of the split DnaE intein from Nostoc punctiforme. Periodic blue light illumination of LOVInC induced protein splicing activity in mammalian cells. To demonstrate the broad applicability of LOVInC, synthetic protein systems were engineered for the light-induced reassembly of several target proteins such as fluorescent protein markers, a dominant positive mutant of RhoA, caspase-7, and the genetically encoded Ca2+ indicator GCaMP2. Spatial precision of LOVInC was demonstrated by targeting activity to specific mammalian cells. Thus, LOVInC can serve as a general platform for engineering light-based control for modulating the activity of many different proteins.

  1. VEGF Spliced Variants: Possible Role of Anti-Angiogenesis Therapy

    Directory of Open Access Journals (Sweden)

    Caroline Hilmi


    Full Text Available Angiogenesis has been targeted in retinopathies, psoriasis, and a variety of cancers (colon, breast, lung, and kidney. Among these tumour types, clear cell renal cell carcinomas (RCCs are the most vascularized tumours due to mutations of the von Hippel Lindau gene resulting in HIF-1 alpha stabilisation and overexpression of Vascular Endothelial Growth Factor (VEGF. Surgical nephrectomy remains the most efficient curative treatment for patients with noninvasive disease, while VEGF targeting has resulted in varying degrees of success for treating metastatic disease. VEGF pre-mRNA undergoes alternative splicing generating pro-angiogenic isoforms. However, the recent identification of novel splice variants of VEGF with anti-angiogenic properties has provided some insight for the lack of current treatment efficacy. Here we discuss an explanation for the relapse to anti-angiogenesis treatment as being due to either an initial or acquired resistance to the therapy. We also discuss targeting angiogenesis via SR (serine/arginine-rich proteins implicated in VEGF splicing.

  2. Involvement of Alternative Splicing in Barley Seed Germination. (United States)

    Zhang, Qisen; Zhang, Xiaoqi; Wang, Songbo; Tan, Cong; Zhou, Gaofeng; Li, Chengdao


    Seed germination activates many new biological processes including DNA, membrane and mitochondrial repairs and requires active protein synthesis and sufficient energy supply. Alternative splicing (AS) regulates many cellular processes including cell differentiation and environmental adaptations. However, limited information is available on the regulation of seed germination at post-transcriptional levels. We have conducted RNA-sequencing experiments to dissect AS events in barley seed germination. We identified between 552 and 669 common AS transcripts in germinating barley embryos from four barley varieties (Hordeum vulgare L. Bass, Baudin, Harrington and Stirling). Alternative 3' splicing (34%-45%), intron retention (32%-34%) and alternative 5' splicing (16%-21%) were three major AS events in germinating embryos. The AS transcripts were predominantly mapped onto ribosome, RNA transport machineries, spliceosome, plant hormone signal transduction, glycolysis, sugar and carbon metabolism pathways. Transcripts of these genes were also very abundant in the early stage of seed germination. Correlation analysis of gene expression showed that AS hormone responsive transcripts could also be co-expressed with genes responsible for protein biosynthesis and sugar metabolisms. Our RNA-sequencing data revealed that AS could play important roles in barley seed germination.

  3. In vitro splicing of erythropoietin by the Mycobacterium tuberculosis RecA intein without substituting amino acids at the splice junctions. (United States)

    Gangopadhyay, Jaya Pal; Jiang, Shu-qin; van Berkel, Patrick; Paulus, Henry


    Protein splicing is a self-catalyzed process involving the excision of an intervening polypeptide sequence, the intein, and joining of the flanking polypeptide sequences, the extein, by a peptide bond. We have studied the in vitro splicing of erythropoietin (EPO) using a truncated form of the Mycobacterium tuberculosis RecA mini-intein in which the homing endonuclease domain was replaced with a hexahistidine sequence (His-tag). The intein was inserted adjacent to cysteine residues to assure that the spliced product had the natural amino acid sequence. When expressed in Escherichia coli, intein-containing EPO was found entirely as inclusion bodies but could be refolded in soluble form in the presence of 0.5 M arginine. Protein splicing of the refolded protein could be induced with a reducing agent such as DTT or tris(2-carboxyethyl)phosphine and led to the formation of EPO and mini-intein along with some cleavage products. Protein splicing mediated by the RecA intein requires the presence of a cysteine residue adjacent to the intein insertion site. We compared the efficiencies of protein splicing adjacent to three of the four cysteine residues of EPO (Cys29, Cys33 and Cys161) and found that insertion of intein adjacent to Cys29 allowed far more efficient protein splicing than insertion adjacent to Cys33 or Cys161. For ease of purification, our experiments involved a His-tagged EPO fusion protein and a His-tagged intein and the spliced products (25 kDa EPO and 24 kDa mini-intein) were identified by Western blotting using anti-EPO and anti-His-tag antibodies and by mass spectroscopy. The optimal splicing yield at Cys29 (40%) occurred at pH 7.0 after refolding at 4 degrees C and splicing for 18 h at 25 degrees C in the presence of 1 mM DTT.

  4. Newnes electronics assembly handbook

    CERN Document Server

    Brindley, Keith


    Newnes Electronics Assembly Handbook: Techniques, Standards and Quality Assurance focuses on the aspects of electronic assembling. The handbook first looks at the printed circuit board (PCB). Base materials, basic mechanical properties, cleaning of assemblies, design, and PCB manufacturing processes are then explained. The text also discusses surface mounted assemblies and packaging of electromechanical assemblies, as well as the soldering process. Requirements for the soldering process; solderability and protective coatings; cleaning of PCBs; and mass solder/component reflow soldering are des

  5. Multispectral Thermal Imager Optical Assembly Performance and Intergration of the Flight Focal Plane Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Blake, Dick; Byrd, Don; Christensen, Wynn; Henson, Tammy; Krumel, Les; Rappoport, William; Shen, Gon-Yen


    The Multispectral Thermal Imager Optical Assembly (OA) has been fabricated, assembled, successfully performance tested, and integrated into the flight payload structure with the flight Focal Plane Assembly (FPA) integrated and aligned to it. This represents a major milestone achieved towards completion of this earth observing E-O imaging sensor that is to be operated in low earth orbit. The OA consists of an off-axis three mirror anastigmatic (TMA) telescope with a 36 cm unobscured clear aperture, a wide-field-of-view (WFOV) of 1.82° along the direction of spacecraft motion and 1.38° across the direction of spacecraft motion. It also contains a comprehensive on-board radiometric calibration system. The OA is part of a multispectral pushbroom imaging sensor which employs a single mechanically cooled focal plane with 15 spectral bands covering a wavelength range from 0.45 to 10.7 µm. The OA achieves near diffraction-limited performance from visible to the long-wave infrared (LWIR) wavelengths. The two major design drivers for the OA are 80% enpixeled energy in the visible bands and radiometric stability. Enpixeled energy in the visible bands also drove the alignment of the FPA detectors to the OA image plane to a requirement of less than ± 20 µm over the entire visible detector field of view (FOV). Radiometric stability requirements mandated a cold Lyot stop for stray light rejection and thermal background reduction. The Lyot stop is part of the FPA assembly and acts as the aperture stop for the imaging system. The alignment of the Lyot stop to the OA drove the centering and to some extent the tilt alignment requirements of the FPA to the OA.

  6. Exon definition complexes contain the tri-snRNP and can be directly converted into B-like precatalytic splicing complexes. (United States)

    Schneider, Marc; Will, Cindy L; Anokhina, Maria; Tazi, Jamal; Urlaub, Henning; Lührmann, Reinhard


    The first step in splicing of pre-mRNAs with long introns is exon definition, where U1 and U2 snRNPs bind at opposite ends of an exon. After exon definition, these snRNPs must form a complex across the upstream intron to allow splicing catalysis. Exon definition and conversion of cross-exon to cross-intron spliceosomal complexes are poorly understood. Here we demonstrate that, in addition to U1 and U2 snRNPs, cross-exon complexes contain U4, U5, and U6 (which form the tri-snRNP). Tri-snRNP docking involves the formation of U2/U6 helix II. This interaction is stabilized by a 5' splice site (SS)-containing oligonucleotide, which can bind the tri-snRNP and convert the cross-exon complex into a cross-intron, B-like complex. Our data suggest that the switch from cross-exon to cross-intron complexes can occur directly when an exon-bound tri-snRNP interacts with an upstream 5'SS, without prior formation of a cross-intron A complex, revealing an alternative spliceosome assembly pathway.

  7. Conveniently assembled multiple-electrode-pair CO2 laser (United States)

    Ye, Lihua; Li, Xiangyen; He, Anzhi


    A conveniently assembled multiple-electrode-pair (MEP) transversely excited amplify (TEA) CO2 laser is introduced in this paper. The laser is described from the view of device configuration, power supply, control circuit, and etc. The laser output is variable from single pulse to double pulse and multiple pulse with different assembly. We adopt a new alignment method for cavity. The pulse time interval given by control system is continuously adjustable from 0 to 150 microseconds. Experiments prove that the pulse series property is stable and that the pulse parameters are perfect. The conveniently assembled laser lay a foundation for the industry application of multiple-electrode-pair CO2 laser.

  8. Velocity-aligned Doppler spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Z.; Koplitz, B.; Wittig, C.


    The technique of velocity-aligned Doppler spectrosocopy (VADS) is presented and discussed. For photolysis/probe experiments with pulsed initiation, VADS can yield Doppler profiles for nascent photofragments that allow detailed center-of-mass (c.m.) kinetic energy distributions to be extracted. When compared with traditional forms of Doppler spectroscopy, the improvement in kinetic energy resolution is dramatic. Changes in the measured profiles are a consequence of spatial discrimination (i.e., focused and overlapping photolysis and probe beams) and delayed observation. These factors result in the selective detection of species whose velocities are aligned with the wave vector of the probe radiation k/sub pr/, thus revealing the speed distribution along k/sub pr/ rather than the distribution of nascent velocity components projected upon this direction. Mathematical details of the procedure used to model VADS are given, and experimental illustrations for HI, H/sub 2/S, and NH/sub 3/ photodissociation are presented. In these examples, pulsed photodissociation produces H atoms that are detected by sequential two-photon, two-frequency ionization via Lyman-..cap alpha.. with a pulsed laser (121.6+364.7 nm), and measuring the Lyman-..cap alpha.. Doppler profile as a function of probe delay reveals both internal and c.m. kinetic energy distributions for the photofragments. Strengths and weaknesses of VADS as a tool for investigating photofragmentation phenomena are also discussed.

  9. Splicing factor gene mutations in the myelodysplastic syndromes: impact on disease phenotype and therapeutic applications. (United States)

    Pellagatti, Andrea; Boultwood, Jacqueline


    Splicing factor gene mutations are the most frequent mutations found in patients with the myeloid malignancy myelodysplastic syndrome (MDS), suggesting that spliceosomal dysfunction plays a major role in disease pathogenesis. The aberrantly spliced target genes and deregulated cellular pathways associated with the commonly mutated splicing factor genes in MDS (SF3B1, SRSF2 and U2AF1) are being identified, illuminating the molecular mechanisms underlying MDS. Emerging data from mouse modeling studies indicate that the presence of splicing factor gene mutations can lead to bone marrow hematopoietic stem/myeloid progenitor cell expansion, impaired hematopoiesis and dysplastic differentiation that are hallmarks of MDS. Importantly, recent evidence suggests that spliceosome inhibitors and splicing modulators may have therapeutic value in the treatment of splicing factor mutant myeloid malignancies.

  10. Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

    DEFF Research Database (Denmark)

    Weischenfeldt, Joachim Lütken; Waage, Johannes Eichler; Tian, Geng;


    a bioinformatic pipeline that maps RNA-seq data to a combinatorial exon database, predicts NMD-susceptibility for mRNA isoforms and calculates the distribution of major splice isoform classes. We present a catalog of NMD-regulated alternative splicing events, showing that isoforms of 30% of all expressed genes......ABSTRACT: BACKGROUND: Nonsense-mediated mRNA decay (NMD) affects the outcome of alternative splicing by degrading mRNA isoforms with premature termination codons. Splicing regulators constitute important NMD targets; however, the extent to which loss of NMD causes extensive deregulation...... of alternative splicing has not previously been assayed in a global, unbiased manner. Here, we combine mouse genetics and RNA-seq to provide the first in vivo analysis of the global impact of NMD on splicing patterns in two primary mouse tissues ablated for the NMD factor UPF2. RESULTS: We developed...

  11. Alternative splicing in colon, bladder, and prostate cancer identified by exon-array analysis

    DEFF Research Database (Denmark)

    Thorsen, Kasper; Sørensen, Karina D.; Brems-Eskildsen, Anne Sofie;


    Alternative splicing enhances proteome diversity and modulates cancer-associated proteins. To identify tissue- and tumor-specific alternative splicing, we used the GeneChip Human Exon 1.0 ST Array to measure whole-genome exon expression in 102 normal and cancer tissue samples of different stages......, and 18 candidate tumor-specific splicing alterations in colon, bladder, and prostate, respectively, were selected for RT-PCR validation on an independent set of 81 normal and tumor tissue samples. In total, seven genes with tumor-specific splice variants were identified (ACTN1, CALD1, COL6A3, LRRFIP2...... from colon, urinary bladder, and prostate. We identified 2069 candidate alternative splicing events between normal tissue samples from colon, bladder, and prostate and selected 15 splicing events for RT-PCR validation, 10 of which were successfully validated by RT-PCR and sequencing. Furthermore 23, 19...

  12. Genome-wide analysis of SRSF10-regulated alternative splicing by deep sequencing of chicken transcriptome

    Directory of Open Access Journals (Sweden)

    Xuexia Zhou


    Full Text Available Splicing factor SRSF10 is known to function as a sequence-specific splicing activator that is capable of regulating alternative splicing both in vitro and in vivo. We recently used an RNA-seq approach coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. We found that SRSF10 promoted both exon inclusion and exclusion. Functionally, many of the SRSF10-verified alternative exons are linked to pathways of response to external stimulus. Here we describe in detail the experimental design, bioinformatics analysis and GO/pathway enrichment analysis of SRSF10-regulated genes to correspond with our data in the Gene Expression Omnibus with accession number GSE53354. Our data thus provide a resource for studying regulation of alternative splicing in vivo that underlines biological functions of splicing regulatory proteins in cells.

  13. Splicing-site recognition of rice (Oryza sativa L.)DNA sequences by support vector machines

    Institute of Scientific and Technical Information of China (English)

    彭司华; 樊龙江; 彭小宁; 庄树林; 杜维; 陈良标


    Motivation: It was found that high accuracy splicing-site recognition of rice (Oryza sativa L.) DNA sequence is especially difficult. We described a new method for the splicing-site recognition of rice DNA sequences. Method: Based on the intron in eukaryotic organisms conforming to the principle of GT-AG, we used support vector machines (SVM) to predict the splicing sites. By machine learning, we built a model and used it to test the effect of the test data set of true and pseudo splicing sites. Results: The prediction accuracy we obtained was 87.53% at the true 5' end splicing site and 87.37% at the true 3' end splicing sites. The results suggested that the SVM approach could achieve higher accuracy than the previous approaches.

  14. Inducible Expression and Splicing of Candida Group Ⅰ Ribozyme in E.coli

    Institute of Scientific and Technical Information of China (English)

    SHANG Yuan; WANG Chen; ZHANG Yi


    The Ca. LSU intron flanking a 129 bp exon upstream and a 100 bp exon downstream was inserted into the lacZ gene on pRS426 to transform E. coli. Northern blot analysis and RT-PCR showed that splicing of Ca. LSU in E.coli is efficient upon inducible expression of the precursor RNA. In contrast, co-transcriptional self-splicing of the intron in vitro is much less active. Therefore, this E. coli splicing system can be used as a better model to investigate the effect of the ribozyme inhibitors on Ca. LSU splicing in living cell. We examined the effects of neomycin sulfate and pentamidine on Ca. LSU splicing in E. coli, and found that these drugs does-dependently inhibit the intron splicing.However, heomycin is more potent than pentamidine in this action.

  15. Microscale fibre alignment by a three-dimensional sessile drop on a wettable pad (United States)

    Reznik, S. N.; Salalha, W.; Yarin, A. L.; Zussman, E.

    Fluidic assembly provides solutions for assembling particles with sizes from nano- metres to centimetres. Fluidic techniques based on patterned shapes of monolayers and capillary forces are widely used to assemble microfabrication devices. Usually, for self-assembly, the precondition is that the components must be mobile in a fluidic environment. In the present work, a shape-directed fluidic self-assembly of rod-like microstructures, such as an optical fibre on a wettable pad is demonstrated experimentally with submicrometre positioning precision. A model of the process is proposed, which accounts for the following two stages of the orientation of a fibre submerged in a sessile drop: (i) the drop melting and spreading over a wettable pad; (ii) fibre reorientation related to the surface-tension-driven shrinkage of the drop surface area. At the end of stage (ii), the fibre is oriented along the pad. The experi- mental results for the optical-fibre assembly by a solder joint have been compared to the modelling results, and a reasonable agreement has been found. The major outcome of the experiments and modelling is that surface tension forces on the fibre piercing a drop align the fibre rather than the flow owing to the spreading of the drop over the horizontal pad, i.e. stage (ii) mostly contributes to the alignment.

  16. Multiple sequence alignment accuracy and phylogenetic inference. (United States)

    Ogden, T Heath; Rosenberg, Michael S


    Phylogenies are often thought to be more dependent upon the specifics of the sequence alignment rather than on the method of reconstruction. Simulation of sequences containing insertion and deletion events was performed in order to determine the role that alignment accuracy plays during phylogenetic inference. Data sets were simulated for pectinate, balanced, and random tree shapes under different conditions (ultrametric equal branch length, ultrametric random branch length, nonultrametric random branch length). Comparisons between hypothesized alignments and true alignments enabled determination of two measures of alignment accuracy, that of the total data set and that of individual branches. In general, our results indicate that as alignment error increases, topological accuracy decreases. This trend was much more pronounced for data sets derived from more pectinate topologies. In contrast, for balanced, ultrametric, equal branch length tree shapes, alignment inaccuracy had little average effect on tree reconstruction. These conclusions are based on average trends of many analyses under different conditions, and any one specific analysis, independent of the alignment accuracy, may recover very accurate or inaccurate topologies. Maximum likelihood and Bayesian, in general, outperformed neighbor joining and maximum parsimony in terms of tree reconstruction accuracy. Results also indicated that as the length of the branch and of the neighboring branches increase, alignment accuracy decreases, and the length of the neighboring branches is the major factor in topological accuracy. Thus, multiple-sequence alignment can be an important factor in downstream effects on topological reconstruction.

  17. Galaxy alignment on large and small scales (United States)

    Kang, X.; Lin, W. P.; Dong, X.; Wang, Y. O.; Dutton, A.; Macciò, A.


    Galaxies are not randomly distributed across the universe but showing different kinds of alignment on different scales. On small scales satellite galaxies have a tendency to distribute along the major axis of the central galaxy, with dependence on galaxy properties that both red satellites and centrals have stronger alignment than their blue counterparts. On large scales, it is found that the major axes of Luminous Red Galaxies (LRGs) have correlation up to 30Mpc/h. Using hydro-dynamical simulation with star formation, we investigate the origin of galaxy alignment on different scales. It is found that most red satellite galaxies stay in the inner region of dark matter halo inside which the shape of central galaxy is well aligned with the dark matter distribution. Red centrals have stronger alignment than blue ones as they live in massive haloes and the central galaxy-halo alignment increases with halo mass. On large scales, the alignment of LRGs is also from the galaxy-halo shape correlation, but with some extent of mis-alignment. The massive haloes have stronger alignment than haloes in filament which connect massive haloes. This is contrary to the naive expectation that cosmic filament is the cause of halo alignment.

  18. Sequence Analysis of In Vivo-Expressed HIV-1 Spliced RNAs Reveals the Usage of New and Unusual Splice Sites by Viruses of Different Subtypes (United States)

    Vega, Yolanda; Delgado, Elena; de la Barrera, Jorge; Carrera, Cristina; Zaballos, Ángel; Cuesta, Isabel; Mariño, Ana; Ocampo, Antonio; Miralles, Celia; Pérez-Castro, Sonia; Álvarez, Hortensia; López-Miragaya, Isabel; García-Bodas, Elena; Díez-Fuertes, Francisco; Thomson, Michael M.


    HIV-1 RNAs are generated through a complex splicing mechanism, resulting in a great diversity of transcripts, which are classified in three major categories: unspliced, singly spliced (SS), and doubly spliced (DS). Knowledge on HIV-1 RNA splicing in vivo and by non-subtype B viruses is scarce. Here we analyze HIV-1 RNA splice site usage in CD4+CD25+ lymphocytes from HIV-1-infected individuals through pyrosequencing. HIV-1 DS and SS RNAs were amplified by RT-PCR in 19 and 12 samples, respectively. 13,108 sequences from HIV-1 spliced RNAs, derived from viruses of five subtypes (A, B, C, F, G), were identified. In four samples, three of non-B subtypes, five 3’ splice sites (3’ss) mapping to unreported positions in the HIV-1 genome were identified. Two, designated A4i and A4j, were used in 22% and 25% of rev RNAs in two viruses of subtypes B and A, respectively. Given their close proximity (one or two nucleotides) to A4c and A4d, respectively, they could be viewed as variants of these sites. Three 3’ss, designated A7g, A7h, and A7i, located 20, 32, and 18 nucleotides downstream of A7, respectively, were identified in a subtype C (A7g, A7h) and a subtype G (A7i) viruses, each in around 2% of nef RNAs. The new splice sites or variants of splice sites were associated with the usual sequence features of 3’ss. Usage of unusual 3’ss A4d, A4e, A5a, A7a, and A7b was also detected. A4f, previously identified in two subtype C viruses, was preferentially used by rev RNAs of a subtype C virus. These results highlight the great diversity of in vivo splice site usage by HIV-1 RNAs. The fact that four of five newly identified splice sites or variants of splice sites were detected in non-subtype B viruses allows anticipating an even greater diversity of HIV-1 splice site usage than currently known. PMID:27355361

  19. Sequence Analysis of In Vivo-Expressed HIV-1 Spliced RNAs Reveals the Usage of New and Unusual Splice Sites by Viruses of Different Subtypes.

    Directory of Open Access Journals (Sweden)

    Yolanda Vega

    Full Text Available HIV-1 RNAs are generated through a complex splicing mechanism, resulting in a great diversity of transcripts, which are classified in three major categories: unspliced, singly spliced (SS, and doubly spliced (DS. Knowledge on HIV-1 RNA splicing in vivo and by non-subtype B viruses is scarce. Here we analyze HIV-1 RNA splice site usage in CD4+CD25+ lymphocytes from HIV-1-infected individuals through pyrosequencing. HIV-1 DS and SS RNAs were amplified by RT-PCR in 19 and 12 samples, respectively. 13,108 sequences from HIV-1 spliced RNAs, derived from viruses of five subtypes (A, B, C, F, G, were identified. In four samples, three of non-B subtypes, five 3' splice sites (3'ss mapping to unreported positions in the HIV-1 genome were identified. Two, designated A4i and A4j, were used in 22% and 25% of rev RNAs in two viruses of subtypes B and A, respectively. Given their close proximity (one or two nucleotides to A4c and A4d, respectively, they could be viewed as variants of these sites. Three 3'ss, designated A7g, A7h, and A7i, located 20, 32, and 18 nucleotides downstream of A7, respectively, were identified in a subtype C (A7g, A7h and a subtype G (A7i viruses, each in around 2% of nef RNAs. The new splice sites or variants of splice sites were associated with the usual sequence features of 3'ss. Usage of unusual 3'ss A4d, A4e, A5a, A7a, and A7b was also detected. A4f, previously identified in two subtype C viruses, was preferentially used by rev RNAs of a subtype C virus. These results highlight the great diversity of in vivo splice site usage by HIV-1 RNAs. The fact that four of five newly identified splice sites or variants of splice sites were detected in non-subtype B viruses allows anticipating an even greater diversity of HIV-1 splice site usage than currently known.

  20. A suboptimal 5' splice site downstream of HIV-1 splice site A1 is required for unspliced viral mRNA accumulation and efficient virus replication

    Directory of Open Access Journals (Sweden)

    Stoltzfus C Martin


    Full Text Available Abstract Background Inefficient alternative splicing of the human immunodeficiency virus type 1(HIV-1 primary RNA transcript results in greater than half of all viral mRNA remaining unspliced. Regulation of HIV-1 alternative splicing occurs through the presence of suboptimal viral 5' and 3' splice sites (5' and 3'ss, which are positively regulated by exonic splicing enhancers (ESE and negatively regulated by exonic splicing silencers (ESS and intronic splicing silencers (ISS. We previously showed that splicing at HIV-1 3'ss A2 is repressed by ESSV and enhanced by the downstream 5'ss D3 signal. Disruption of ESSV results in increased vpr mRNA accumulation and exon 3 inclusion, decreased accumulation of unspliced viral mRNA, and decreased virus production. Results Here we show that optimization of the 5'ss D2 signal results in increased splicing at the upstream 3'ss A1, increased inclusion of exon 2 into viral mRNA, decreased accumulation of unspliced viral mRNA, and decreased virus production. Virus production from the 5'ss D2 and ESSV mutants was rescued by transient expression of HIV-1 Gag and Pol. We further show that the increased inclusion of either exon 2 or 3 does not significantly affect the stability of viral mRNA but does result in an increase and decrease, respectively, in HIV-1 mRNA levels. The changes in viral mRNA levels directly correlate with changes in tat mRNA levels observed upon increased inclusion of exon 2 or 3. Conclusion These results demonstrate that splicing at HIV-1 3'ss A1 is regulated by the strength of the downstream 5'ss signal and that suboptimal splicing at 3'ss A1 is necessary for virus replication. Furthermore, the replication defective phenotype resulting from increased splicing at 3'ss A1 is similar to the phenotype observed upon increased splicing at 3'ss A2. Further examination of the role of 5'ss D2 and D3 in the alternative splicing of 3'ss A1 and A2, respectively, is necessary to delineate a role for non