WorldWideScience

Sample records for chord splice joints

  1. Effect of Chord Splice Joints on Force Distribution and Deformations in Trusses with Punched Metal Plate Fasteners

    DEFF Research Database (Denmark)

    Ellegaard, Peter

    2007-01-01

    The span of roof trusses with punched metal plate fasteners (nail plates) makes it often necessary to use splice joints in the top and bottom chords. In the finite element models used for design of the trusses these splice joints are normally assumed to be either rotationally stiff or pinned - th...... of splice joints on section forces and displacements are discussed considering the results from finite element calculations for a fink truss. It seems that the guidelines for treating splice joints as rotationally stiff do not necessarily lead to more realistic truss models....... - their real behaviour is semi-rigid. The influence of splice joints on the distribution of member forces and rotations in the splice joints is investigated in this paper. A finite element program, TrussLab, where the splice joints are given semi-rigid properties is used to analyse the effect of splice joints...... if their deformation has no significant effect upon the distribution of member forces according to Eurocode 5. Two simple guidelines for the design and location of splice joints are given in Eurocode 5 for treating the splice joints as rotationally stiff. The reasonability of these guidelines and the influence...

  2. Structural analysis of Aircraft fuselage splice joint

    Science.gov (United States)

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

    2016-09-01

    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.

  3. Fatigue of hollow section T-joints of circular braces and square chords

    Energy Technology Data Exchange (ETDEWEB)

    Berge, S. [Norwegian Inst. of Technology, Trondheim (Norway); Gandhi, P. [Structural Engineering Research Centre, Madras (India); Lereim, J. [Saga Petroleum A.S., Forus (Norway)

    1995-12-31

    Hollow sections are generally either circular-to-circular (CCHS) or rectangular-to-rectangular (RRHS). Structures with circular braces and rectangular chords (CRHS) may have advantages in certain applications, combining a simple joint geometry for fabrication and relatively small stress concentration factors. Seven different CRHS joints were fatigue tested in constant amplitude axial loading. Stress concentration factors (SCF) were measured experimentally and compared with various parametric formulae. The SCF values for CRHS joints were found to be between those of CCHS and RRHS joints. On the basis of measured SCF values for CRHS joints, the fatigue strength was in good correspondence with current fatigue design codes. Parametric formulae for RRHS joints were in all the cases found to give conservative predictions of SCF. In lack of more rational prediction methods, these formulae in combination with the T curve for tubular joints may be used in fatigue design of CRHS joints.

  4. Assessment of DoD Wounded Warrior Matters -- Joint Base Lewis-McChord

    Science.gov (United States)

    2013-05-31

    Matters - Joint Base Lewis-McChord Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of...NUMBER OF PAGES 104 19a. NAME OF RESPONSIBLE PERSON a. REPORT unclassified b. ABSTRACT unclassified c. THIS PAGE unclassified Standard Form 298...RECOMMENDATION 0 .. 2.: Commander, Madigan Afmy Medical Centercondt, Jct an analysis to determine o’bstacles to access ahd delays encountered and

  5. Implementation Approach for Plug-in Electric Vehicles at Joint Base Lewis McChord. Task 4

    Energy Technology Data Exchange (ETDEWEB)

    Schey, Stephen [Idaho National Lab. (INL), Idaho Falls, ID (United States); Francfort, Jim [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2014-12-01

    This study focused on Joint Base Lewis McChord (JBLM), which is located in Washington State. Task 1 consisted of a survey of the non-tactical fleet of vehicles at JBLM to begin the review of vehicle mission assignments and the types of vehicles in service. In Task 2, daily operational characteristics of select vehicles were identified and vehicle movements were recorded in data loggers in order to characterize the vehicles’ missions. In Task 3, the results of the data analysis and observations were provided. Individual observations of the selected vehicles provided the basis for recommendations related to PEV adoption (i.e., whether a battery electric vehicle or plug-in hybrid electric vehicle [collectively referred to as PEVs] can fulfill the mission requirements0, as well as the basis for recommendations related to placement of PEV charging infrastructure. This report focuses on an implementation plan for the near-term adoption of PEVs into the JBLM fleet.

  6. To optimize splice joint between different PCF-based devices and SMF transmission medium

    Institute of Scientific and Technical Information of China (English)

    Faramarz E. Seraji; S. Farsinezhad

    2009-01-01

    An analysis of splice loss between photonic crystal fibers (PCFs) and conventional single-mode fibers (SMFs) is presented at bending and straight conditions, by using scalar effective index method (SEIM), vectorial effective index method (VEIM), and finite-difference frequency domain (FDFD) methods. It is shown that when there is a slight bending at the vicinity of splice joint, the spot size increases sharply at higher frequencies. On the basis of the obtained results, a mechanism to optimize the splice loss between PCFs and conventional SMFs, both with any geometry, is suggested. The results can be utilized for PCF-based devices to be jointed to SMF as a transmission medium.

  7. FE Studies on Tubular T-joint Reinforced with Reinforced Chord under Axial Force and Impact Loading%轴压下局部加厚T型管节点抗冲击有限元研究

    Institute of Scientific and Technical Information of China (English)

    叶卉; 曲慧; 姜岩

    2016-01-01

    采用有限元软件ABAQUS建立冲击荷载下一端固支一端可轴向移动的T型管节点的有限元分析模型。基于该模型,研究了轴力作用下普通和局部加厚T型管节点在横向冲击荷载下的破坏模态,并对冲击力时程曲线、位移时程曲线、能量耗散等抗冲击性能指标进行了分析。分析结果表明:增加主管的厚度可以显著提高试件的节点抗弯刚度,降低节点区域的损伤;但当主管加厚部分的长度达到一定值,节点抗冲击性能将不再提高,研究结果可为管节点的抗冲击设计和损伤修复提供依据。%A finite element analysis model is established on the base of the finite element software ABAQUS to sim-ulate the dynamic performance of tubular T-joint with/ without reinforced chord under impact loading. One end of the joint model is simulated as fixed support, and the other end is modeled as a sliding support which can only move in the axial direction. Based on the finite element model, the failure modes of T-joint with/ without reinforced by increasing the thickness of the chord on the joint zone are defined, and the impact indexes of the two types of joints, such as time history curve of impact load, time history curve of lateral displacement and energy consump-tion, are investigated. It can be concluded that the flexural stiffness is improved, and the damage of joint zone is reduced after the tubular T-joint is thickened around the joint zone. However, the length of the reinforced joint zone plays the role of a little role in improving the impact performances of tubular T-joint when it exceeds certain value. The analysis results could be served as a reference for the anti-impact design and repair of damaged tubular joint.

  8. Design and Evaluation of joint resistance in SSC Rutherford type cable splices for Torus magnet for the Jefferson Lab 12 GeV Upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Ghoshal, Probir K. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Fair, Ruben J. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Kashy, David H. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Legg, Robert A. [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Rajput-Ghoshal, Renuka [Thomas Jefferson National Accelerator Facility (TJNAF), Newport News, VA (United States); Hampshire, Damian; Tsui, Yeekin; Haden-Gates, Virginia

    2016-06-01

    The Hall B 3.6-T superconducting torus magnet is being designed and built as part of the Jefferson Lab 12-GeV upgrade. The magnet consists of six trapezoidal coils connected in series, with an operating current of 3770 A. The magnet and the joints (or splices) connecting the coils are all conduction cooled by supercritical 4.6-K helium. This paper studies the design and manufacturing process of the splices made between two SSC Rutherford-type cables and discusses the tests performed to evaluate the performance of the splices under varying incident magnetic fields.

  9. A chord recognition method based on joint feature of MFCC and PCP%一种基于MFCC与PCP联合特征的和弦识别方法

    Institute of Scientific and Technical Information of China (English)

    李锵; 秦媛媛

    2015-01-01

    结合乐理理论和信号处理理论,针对传统和弦识别仅考虑音高特性的音级轮廓特征PCP(pitch class profile)造成正确识别率较低的问题,提出一种以反映听觉特性的MFCC(mel frequency cepstral coefficent)与PCP的联合特征和稀疏表示分类器(sparse representation classification,SRC)的和弦识别方法。通过对两特征矢量的叠加构成新的和弦特征,然后利用SRC进行和弦识别。实验结果表明,与传统方法的识别率相比,本方法的识别率大幅提高。%Combined with music and signal process theory, the paper proposes a new chord recognition approach which utilizes the MFCC (Mel Frequency Cepstral Coefficent) reflecting auditory perception properties jointly with the traditional PCP (Pitch Class Profile) as the combined feature and SRC (Sparse Representation classification) to improve the recognition rate. The experimental results show that the recognition rata of the new method is much better in average than that of the traditional methods.

  10. PIC Detector for Piano Chords

    Science.gov (United States)

    Barbancho, Ana M.; Tardón, Lorenzo J.; Barbancho, Isabel

    2010-12-01

    In this paper, a piano chords detector based on parallel interference cancellation (PIC) is presented. The proposed system makes use of the novel idea of modeling a segment of music as a third generation mobile communications signal, specifically, as a CDMA (Code Division Multiple Access) signal. The proposed model considers each piano note as a CDMA user in which the spreading code is replaced by a representative note pattern. The lack of orthogonality between the note patterns will make necessary to design a specific thresholding matrix to decide whether the PIC outputs correspond to the actual notes composing the chord or not. An additional stage that performs an octave test and a fifth test has been included that improves the error rate in the detection of these intervals that are specially difficult to detect. The proposed system attains very good results in both the detection of the notes that compose a chord and the estimation of the polyphony number.

  11. Japanese monkeys perceive sensory consonance of chords.

    Science.gov (United States)

    Izumi, A

    2000-12-01

    Consonance/dissonance affects human perception of chords from early stages of development [e.g., Schellenberg and Trainor, J. Acoust. Soc. Am. 100, 3321-3328 (1996)]. To examine whether consonance has some role in audition of nonhumans, three Japanese monkeys (Macaca fuscata) were trained to discriminate simultaneous two-tone complexes (chords). The task was serial discrimination (AX procedure) with repetitive presentation of background stimuli. Each tone in a chord was comprised of six harmonics, and chords with complex ratios of fundamental frequency (e.g., frequency ratio of 8:15 in major seventh) resulted in dissonance. The chords were transposed for each presentation to make monkeys attend to cues other than the absolute frequency of a component tone. Monkeys were initially trained to detect changes from consonant (octave) to dissonant (major seventh). Following the successful acquisition of the task, transfer tests with novel chords were conducted. In these transfer tests, the performances with detecting changes from consonant to dissonant chords (perfect fifth to major seventh; perfect fourth to major seventh) were better than those with detecting reverse changes. These results suggested that the consonance of chords affected the performances of monkeys.

  12. A Generalization of the Parabolic Chord Property

    Science.gov (United States)

    Mason, John

    2011-01-01

    The well known property of quadratic functions, that the tangents at either end of a chord of a parabola meet in a point aligned vertically with the midpoint of the chord is extended to polynomials of degree d. Given two distinct points on a polynomial of degree d, the Taylor polynomials of degree d - 1 at those points meet in d - 1 points whose…

  13. 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

    2003-01-01

    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).

  14. Partial chord diagrams and matrix models

    DEFF Research Database (Denmark)

    Andersen, Jørgen Ellegaard; Fuji, Hiroyuki; Manabe, Masahide

    spectrum. Furthermore, we consider the boundary length and point spectrum that unifies the last two types of spectra. We introduce matrix models that encode generating functions of partial chord diagrams filtered by each of these spectra. Using these matrix models, we derive partial differential equations......In this article, the enumeration of partial chord diagrams is discussed via matrix model techniques. In addition to the basic data such as the number of backbones and chords, we also consider the Euler characteristic, the backbone spectrum, the boundary point spectrum, and the boundary length...... – obtained independently by cut-and-join arguments in an earlier work – for the corresponding generating functions....

  15. The boundary length and point spectrum enumeration of partial chord diagrams using cut and join recursion

    DEFF Research Database (Denmark)

    Andersen, Jørgen Ellegaard; Fuji, Hiroyuki; Penner, Robert C.

    relation, which combined with an initial condition determines these numbers uniquely. This recursion relation is equivalent to a second order, non-linear, algebraic partial differential equation for the generating function of the numbers of partial chord diagrams filtered by the boundary length and point......We introduce the boundary length and point spectrum, as a joint generalization of the boundary length spectrum and boundary point spectrum in [1]. We establish by cut-and-join methods that the number of partial chord diagrams filtered by the boundary length and point spectrum satisfies a recursion...

  16. PolyChord: nested sampling for cosmology

    CERN Document Server

    Handley, W J; Lasenby, A N

    2015-01-01

    PolyChord is a novel nested sampling algorithm tailored for high dimensional parameter spaces. In addition, it can fully exploit a hierarchy of parameter speeds such as is found in CosmoMC and CAMB. It utilises slice sampling at each iteration to sample within the hard likelihood constraint of nested sampling. It can identify and evolve separate modes of a posterior semi-independently and is parallelised using openMPI. PolyChord is available for download at: http://ccpforge.cse.rl.ac.uk/gf/project/polychord/

  17. Linear chord diagrams on two intervals

    DEFF Research Database (Denmark)

    Andersen, Jørgen Ellegaard; Penner, Robert; Reidys, Christian;

    generating function ${\\bf C}_g(z)=z^{2g}R_g(z)/(1-4z)^{3g-{1\\over 2}}$ for chords attached to a single interval is algebraic, for $g\\geq 1$, where the polynomial $R_g(z)$ with degree at most $g-1$ has integer coefficients and satisfies $R_g(1/4)\

  18. Diffraction method of vocal chord oscillation sensing

    Science.gov (United States)

    Kuzmin, Sergey Y.; Tuchin, Valery V.

    1996-04-01

    A method of small-amplitude biovibrations detection is presented in the paper. The method uses a dependence of properties of speckle-structures formed by focused coherent light field diffraction from rough surfaces on the statistics and movement parameters of the surface. With the help of computer modeling the different components of skin surface vibration were analyzed and their influence on speckles dynamics was studied. Human vocal chord oscillations spectrum was monitored using the developed technique.

  19. The guitar chord-generating algorithm based on complex network

    Science.gov (United States)

    Ren, Tao; Wang, Yi-fan; Du, Dan; Liu, Miao-miao; Siddiqi, Awais

    2016-02-01

    This paper aims to generate chords for popular songs automatically based on complex network. Firstly, according to the characteristics of guitar tablature, six chord networks of popular songs by six pop singers are constructed and the properties of all networks are concluded. By analyzing the diverse chord networks, the accompaniment regulations and features are shown, with which the chords can be generated automatically. Secondly, in terms of the characteristics of popular songs, a two-tiered network containing a verse network and a chorus network is constructed. With this network, the verse and chorus can be composed respectively with the random walk algorithm. Thirdly, the musical motif is considered for generating chords, with which the bad chord progressions can be revised. This method can make the accompaniments sound more melodious. Finally, a popular song is chosen for generating chords and the new generated accompaniment sounds better than those done by the composers.

  20. PolyChord: next-generation nested sampling

    CERN Document Server

    Handley, W J; Lasenby, A N

    2015-01-01

    PolyChord is a novel nested sampling algorithm tailored for high-dimensional parameter spaces. This paper coincides with the release of PolyChord v1.3, and provides an extensive account of the algorithm. PolyChord utilises slice sampling at each iteration to sample within the hard likelihood constraint of nested sampling. It can identify and evolve separate modes of a posterior semi-independently, and is parallelised using openMPI. It is capable of exploiting a hierarchy of parameter speeds such as those present in CosmoMC and CAMB, and is now in use in the CosmoChord and ModeChord codes. PolyChord is available for download at: http://ccpforge.cse.rl.ac.uk/gf/project/polychord/

  1. To speak in chords about sexuality.

    Science.gov (United States)

    Bermant, G

    1995-01-01

    Sexuality emerges from the interdependencies of biology, awareness, and the facts and artifacts of public life. A useful metaphor is that correct accountings of sexuality are not one-finger melodies--they are chords. Unfortunately, the physical vs. mental and nature vs. nurture controversies remain alive, well, and mischievous in regard to the correct understanding of human sexuality. Active political and legal disputes about homosexuality exemplify a continuing reliance on reductionistic models of the causes of conduct. Discourse relying on public misapprehension about biological causality can alter the course of subsequent science and public opinion and thus affect personal experience as well. Both dualistic and reductionistic models are traps and bar progress; the models should not be smuggled into accounts of sexuality.

  2. Stiff, Strong Splice For A Composite Sandwich Structure

    Science.gov (United States)

    Schmaling, D.

    1991-01-01

    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.

  3. Improving audio chord transcription by exploiting harmonic and metric knowledge

    NARCIS (Netherlands)

    de Haas, W.B.; Rodrigues Magalhães, J.P.; Wiering, F.

    2012-01-01

    We present a new system for chord transcription from polyphonic musical audio that uses domain-specific knowledge about tonal harmony and metrical position to improve chord transcription performance. Low-level pulse and spectral features are extracted from an audio source using the Vamp plugin archi

  4. Mild Dissonance Preferred Over Consonance in Single Chord Perception.

    Science.gov (United States)

    Lahdelma, Imre; Eerola, Tuomas

    2016-05-01

    Previous research on harmony perception has mainly been concerned with horizontal aspects of harmony, turning less attention to how listeners perceive psychoacoustic qualities and emotions in single isolated chords. A recent study found mild dissonances to be more preferred than consonances in single chord perception, although the authors did not systematically vary register and consonance in their study; these omissions were explored here. An online empirical experiment was conducted where participants (N = 410) evaluated chords on the dimensions of Valence, Tension, Energy, Consonance, and Preference; 15 different chords were played with piano timbre across two octaves. The results suggest significant differences on all dimensions across chord types, and a strong correlation between perceived dissonance and tension. The register and inversions contributed to the evaluations significantly, nonmusicians distinguishing between triadic inversions similarly to musicians. The mildly dissonant minor ninth, major ninth, and minor seventh chords were rated highest for preference, regardless of musical sophistication. The role of theoretical explanations such as aggregate dyadic consonance, the inverted-U hypothesis, and psychoacoustic roughness, harmonicity, and sharpness will be discussed to account for the preference of mild dissonance over consonance in single chord perception.

  5. Mild Dissonance Preferred Over Consonance in Single Chord Perception

    Science.gov (United States)

    Eerola, Tuomas

    2016-01-01

    Previous research on harmony perception has mainly been concerned with horizontal aspects of harmony, turning less attention to how listeners perceive psychoacoustic qualities and emotions in single isolated chords. A recent study found mild dissonances to be more preferred than consonances in single chord perception, although the authors did not systematically vary register and consonance in their study; these omissions were explored here. An online empirical experiment was conducted where participants (N = 410) evaluated chords on the dimensions of Valence, Tension, Energy, Consonance, and Preference; 15 different chords were played with piano timbre across two octaves. The results suggest significant differences on all dimensions across chord types, and a strong correlation between perceived dissonance and tension. The register and inversions contributed to the evaluations significantly, nonmusicians distinguishing between triadic inversions similarly to musicians. The mildly dissonant minor ninth, major ninth, and minor seventh chords were rated highest for preference, regardless of musical sophistication. The role of theoretical explanations such as aggregate dyadic consonance, the inverted-U hypothesis, and psychoacoustic roughness, harmonicity, and sharpness will be discussed to account for the preference of mild dissonance over consonance in single chord perception. PMID:27433333

  6. Mild Dissonance Preferred Over Consonance in Single Chord Perception

    Directory of Open Access Journals (Sweden)

    Imre Lahdelma

    2016-06-01

    Full Text Available Previous research on harmony perception has mainly been concerned with horizontal aspects of harmony, turning less attention to how listeners perceive psychoacoustic qualities and emotions in single isolated chords. A recent study found mild dissonances to be more preferred than consonances in single chord perception, although the authors did not systematically vary register and consonance in their study; these omissions were explored here. An online empirical experiment was conducted where participants (N = 410 evaluated chords on the dimensions of Valence, Tension, Energy, Consonance, and Preference; 15 different chords were played with piano timbre across two octaves. The results suggest significant differences on all dimensions across chord types, and a strong correlation between perceived dissonance and tension. The register and inversions contributed to the evaluations significantly, nonmusicians distinguishing between triadic inversions similarly to musicians. The mildly dissonant minor ninth, major ninth, and minor seventh chords were rated highest for preference, regardless of musical sophistication. The role of theoretical explanations such as aggregate dyadic consonance, the inverted-U hypothesis, and psychoacoustic roughness, harmonicity, and sharpness will be discussed to account for the preference of mild dissonance over consonance in single chord perception.

  7. Three Layer Hierarchical Model for Chord

    Directory of Open Access Journals (Sweden)

    Waqas A. Imtiaz

    2012-12-01

    Full Text Available Increasing popularity of decentralized Peer-to-Peer (P2P architecture emphasizes on the need to come across an overlay structure that can provide efficient content discovery mechanism, accommodate high churn rate and adapt to failures in the presence of heterogeneity among the peers. Traditional p2p systems incorporate distributed client-server communication, which finds the peer efficiently that store a desires data item, with minimum delay and reduced overhead. However traditional models are not able to solve the problems relating scalability and high churn rates. Hierarchical model were introduced to provide better fault isolation, effective bandwidth utilization, a superior adaptation to the underlying physical network and a reduction of the lookup path length as additional advantages. It is more efficient and easier to manage than traditional p2p networks. This paper discusses a further step in p2p hierarchy via 3-layers hierarchical model with distributed database architecture in different layer, each of which is connected through its root. The peers are divided into three categories according to their physical stability and strength. They are Ultra Super-peer, Super-peer and Ordinary Peer and we assign these peers to first, second and third level of hierarchy respectively. Peers in a group in lower layer have their own local database which hold as associated super-peer in middle layer and access the database among the peers through user queries. In our 3-layer hierarchical model for DHT algorithms, we used an advanced Chord algorithm with optimized finger table which can remove the redundant entry in the finger table in upper layer that influences the system to reduce the lookup latency. Our research work finally resulted that our model really provides faster search since the network lookup latency is decreased by reducing the number of hops. The peers in such network then can contribute with improve functionality and can perform well in

  8. Chord Recognition Based on Temporal Correlation Support Vector Machine

    OpenAIRE

    Zhongyang Rao; Xin Guan; Jianfu Teng

    2016-01-01

    In this paper, we propose a method called temporal correlation support vector machine (TCSVM) for automatic major-minor chord recognition in audio music. We first use robust principal component analysis to separate the singing voice from the music to reduce the influence of the singing voice and consider the temporal correlations of the chord features. Using robust principal component analysis, we expect the low-rank component of the spectrogram matrix to contain the musical accompaniment and...

  9. Mild dissonance preferred over consonance in single chord perception.

    OpenAIRE

    Imre Lahdelma; Tuomas Eerola

    2016-01-01

    Previous research on harmony perception has mainly been concerned with horizontal aspects of harmony, turning less attention to how listeners perceive psychoacoustic qualities and emotions in single isolated chords. A recent study found mild dissonances to be more preferred than consonances in single chord perception, although the authors did not systematically vary register and consonance in their study; these omissions were explored here. An online empirical experiment was conducted where p...

  10. The Influences of Progression Type and Distortion on the Perception of Terminal Power Chords

    Science.gov (United States)

    Juchniewicz, Jay; Silverman, Michael J.

    2013-01-01

    The purpose of this study was to investigate the tonal perception and restoration of thirds within power chords with the instruments and sounds idiosyncratic to the Western rock/pop genre. Four separate chord sequences were performed on electric guitar in four versions; as full chord and power chord versions as well as under both clean-tone and…

  11. Chord Recognition Based on Temporal Correlation Support Vector Machine

    Directory of Open Access Journals (Sweden)

    Zhongyang Rao

    2016-05-01

    Full Text Available In this paper, we propose a method called temporal correlation support vector machine (TCSVM for automatic major-minor chord recognition in audio music. We first use robust principal component analysis to separate the singing voice from the music to reduce the influence of the singing voice and consider the temporal correlations of the chord features. Using robust principal component analysis, we expect the low-rank component of the spectrogram matrix to contain the musical accompaniment and the sparse component to contain the vocal signals. Then, we extract a new logarithmic pitch class profile (LPCP feature called enhanced LPCP from the low-rank part. To exploit the temporal correlation among the LPCP features of chords, we propose an improved support vector machine algorithm called TCSVM. We perform this study using the MIREX’09 (Music Information Retrieval Evaluation eXchange Audio Chord Estimation dataset. Furthermore, we conduct comprehensive experiments using different pitch class profile feature vectors to examine the performance of TCSVM. The results of our method are comparable to the state-of-the-art methods that entered the MIREX in 2013 and 2014 for the MIREX’09 Audio Chord Estimation task dataset.

  12. Consonance perception of complex-tone dyads and chords

    DEFF Research Database (Denmark)

    Rasmussen, Marc; Santurette, Sébastien; MacDonald, Ewen

    2014-01-01

    Sensory consonance and dissonance are perceptual attributes of musical intervals conveying pleasant- ness, tension, and harmony in musical phrases. For complex-tone dyads, corresponding to two musical notes played simultaneously, consonance is known to vary with the ratio in fundamental frequency....... For dyad/chord comparisons, dyads were more consonant in the intervals around the fixed third tone. Overall, chords were not found to be more dissonant than dyads. This suggests that the hypothesis according to which consonance decreases with the amount of interaction between present harmonics, arguing...... (F0) between the two tones in the dyad. While such a relationship is well established for dyads, the subjective consonance of chords containing three or more simultaneous notes, that form the basis of most musical pieces, remains to be explored. The present study aimed at comparing consonance...

  13. SEISMIC PERFORMANCE RESEARCH ON BEAM-COLUMN SPLICE JOINTS OF PREFABRICATED STEEL FRAMED STRUCTURES WITH BRACES%斜撑对装配式钢框架梁柱拼接节点抗震性能影响研究

    Institute of Scientific and Technical Information of China (English)

    张爱林; 惠怡; 刘学春

    2014-01-01

    针对装配式钢框架带柱座梁柱拼接节点连接受力复杂、强度和刚度影响因素多等问题,应用非线性有限元软件ANSYS对带斜撑和无斜撑的两种节点进行数值模拟,研究斜撑对装配式钢框架梁柱节点的滞回性能、极限承载力、延性系数、破坏模式等抗震性能的影响。结果表明:斜撑的设置,可较大幅度地提高节点的刚度和承载力,对于螺栓型连接的梁柱节点,斜撑的设置使其承载力提高3倍多,焊接节点的承载力提高约50%,延性系数提高约70%;且有效地转移了塑性铰,使节点破坏位置位于斜撑之外的桁架梁上,起到保护节点的作用,符合“强节点,弱构件”的设计要求。同时反复荷载作用下的滞回曲线更加饱满,具有更好的抗震性能。%For column-beam splice joint with flange-column of fabricated steel structure ,the mechanical behavior and connection are very complex ,and there are many influencing factors for its strength and rigidity .ANSYS finite element analysis software was used to analyze and simulate the beam-column's joint of the steel framed structure with or without braces .The seism-resisting behavior of the fabricated steel frame beam-column joints including the hysteretic behavior,ultimate bearing capacity, ductility coefficient, failure mode etc.were studied.The results show that for the fabricated steel frame beam-column joints with supports the joint's rigidity and bearing capacity are increased greatly . To bolt connection of beam-column joints with braces , the bearing capacity is improved by more than three times , and to welded joint , it is improved by about 50 percent ,ductility factor is increased by about 70 percent .Through setting braces, the plastic hinge is transferred effectively , and the failure locations are located on the truss beam outside of the brace, which has played an important role in protecting the connection , and accorded

  14. Test results for a subscale (100 kA) SMES splice

    Science.gov (United States)

    Peck, Scott D.; Zeigler, John C.

    1994-07-01

    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.

  15. Learning high-level features for chord recognition using Autoencoder

    Science.gov (United States)

    Phongthongloa, Vilailukkana; Kamonsantiroj, Suwatchai; Pipanmaekaporn, Luepol

    2016-07-01

    Chord transcription is valuable to do by itself. It is known that the manual transcription of chords is very tiresome, time-consuming. It requires, moreover, musical knowledge. Automatic chord recognition has recently attracted a number of researches in the Music Information Retrieval field. It has known that a pitch class profile (PCP) is the commonly signal representation of musical harmonic analysis. However, the PCP may contain additional non-harmonic noise such as harmonic overtones and transient noise. The problem of non-harmonic might be generating the sound energy in term of frequency more than the actual notes of the respective chord. Autoencoder neural network may be trained to learn a mapping from low level feature to one or more higher-level representation. These high-level representations can explain dependencies of the inputs and reduce the effect of non-harmonic noise. Then these improve features are fed into neural network classifier. The proposed high-level musical features show 80.90% of accuracy. The experimental results have shown that the proposed approach can achieve better performance in comparison with other based method.

  16. Analyzing Sound Waves Produced by Musical Notes & Chords.

    Science.gov (United States)

    Cassidy, Michael

    This project description is designed to show how graphing calculators and calculator-based laboratories (CBL) can be used to explore topics in the physics of sound. The activities address topics such as sound waves, musical notes, and chords. Teaching notes, calculator instructions, and blackline masters are included. (MM)

  17. Introduction to cotranscriptional RNA splicing.

    Science.gov (United States)

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

    2014-01-01

    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.

  18. spliceR

    DEFF Research Database (Denmark)

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

    2014-01-01

    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....

  19. Computer-Based Recognition of Perceptual Patterns in Chord Quality Dictation Exercises.

    Science.gov (United States)

    Hofstetter, Fred T.

    1980-01-01

    This experiment measured the achievement of 18 college freshmen music majors in the Graded Units for Interactive Dictation Operations (GUIDO) chord quality program and determined the pattern of student responses to chord quality dictation exercises. (Author/KC)

  20. Guitar Chords Classification Using Uncertainty Measurements of Frequency Bins

    Directory of Open Access Journals (Sweden)

    Jesus Guerrero-Turrubiates

    2015-01-01

    Full Text Available This paper presents a method to perform chord classification from recorded audio. The signal harmonics are obtained by using the Fast Fourier Transform, and timbral information is suppressed by spectral whitening. A multiple fundamental frequency estimation of whitened data is achieved by adding attenuated harmonics by a weighting function. This paper proposes a method that performs feature selection by using a thresholding of the uncertainty of all frequency bins. Those measurements under the threshold are removed from the signal in the frequency domain. This allows a reduction of 95.53% of the signal characteristics, and the other 4.47% of frequency bins are used as enhanced information for the classifier. An Artificial Neural Network was utilized to classify four types of chords: major, minor, major 7th, and minor 7th. Those, played in the twelve musical notes, give a total of 48 different chords. Two reference methods (based on Hidden Markov Models were compared with the method proposed in this paper by having the same database for the evaluation test. In most of the performed tests, the proposed method achieved a reasonably high performance, with an accuracy of 93%.

  1. Optical Fiber Fusion Splicing

    CERN Document Server

    Yablon, Andrew D

    2005-01-01

    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.

  2. Newborn infants' auditory system is sensitive to Western music chord categories.

    Science.gov (United States)

    Virtala, Paula; Huotilainen, Minna; Partanen, Eino; Fellman, Vineta; Tervaniemi, Mari

    2013-01-01

    Neural encoding of abstract rules in the audition of newborn infants has been recently demonstrated in several studies using event-related potentials (ERPs). In the present study the neural encoding of Western music chords was investigated in newborn infants. Using ERPs, we examined whether the categorizations of major vs. minor and consonance vs. dissonance are present at the level of the change-related mismatch response (MMR). Using an oddball paradigm, root minor, dissonant and inverted major chords were presented in a context of consonant root major chords. The chords were transposed to several different frequency levels, so that the deviant chords did not include a physically deviant frequency that could result in an MMR without categorization. The results show that the newborn infants were sensitive to both dissonant and minor chords but not to inverted major chords in the context of consonant root major chords. While the dissonant chords elicited a large positive MMR, the minor chords elicited a negative MMR. This indicates that the two categories were processed differently. The results suggest newborn infants are sensitive to Western music categorizations, which is consistent with the authors' previous studies in adults and school-aged children.

  3. Newborn infants’ auditory system is sensitive to Western music chord categories

    Directory of Open Access Journals (Sweden)

    Paula eVirtala

    2013-08-01

    Full Text Available Neural encoding of abstract rules in the audition of newborn infants has been recently demonstrated in several studies using event-related potentials (ERPs. In the present study the neural encoding of Western music chords was investigated in newborn infants. Using ERPs, we examined whether the categorizations of major versus minor and consonance versus dissonance are present at the level of the change-related mismatch response (MMR. Using an oddball paradigm, root minor, dissonant and inverted major chords were presented in a context of consonant root major chords. The chords were transposed to several different frequency levels, so that the deviant chords did not include a physically deviant frequency that could result in an MMR without categorization. The results show that the newborn infants were sensitive to both dissonant and minor chords but not to inverted major chords in the context of consonant root major chords. While the dissonant chords elicited a large positive MMR, the minor chords elicited a negative MMR. This indicates that the two categories were processed differently. The results suggest newborn infants are sensitive to Western music categorizations, which is consistent with the authors’ previous studies in adults and school-aged children.

  4. Alternative splicing interference by xenobiotics.

    Science.gov (United States)

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

    2012-06-14

    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.

  5. Analysis and Calculation of Axial Stiffness of Tubular X-joints under Compression on Braces

    Institute of Scientific and Technical Information of China (English)

    QIU Guo-zhi; ZHAO Jin-cheng

    2009-01-01

    This paper introduces the influence factors of axial stiffness of tubular X-joints. The analysis model of tubular joints using plate and shell finite element method is also made. Systematic single-parameter analysis of tubular X-joints is performed using Ansys program. The influences of those factors, including ratio of brace diameter to chord diameter (β), ratio of chord diameter to twice chord thickness (γ), ratio of brace wall thickness to that of chord (τ), brace-to-chord intersection angle (θ), and chord stress ratio, ratio of another brace diameter to chord diameter, in-plane and out-of-plane moment of braces, etc., on stiffness of tubular X-joints are analyzed.Two non-dimensional parameters-joint axial stiffness factor ηN and axial force capacity factor ωN are proposed,and the relationship curve of the two factors is determined. Computational formulas of tubular X-joint axial stiffness are obtained by multi-element regression technology. The formulas can be used in design and analysis of steel tubular structures.

  6. Emotional connotations of major and minor musical chords in musically untrained listeners

    DEFF Research Database (Denmark)

    Pallesen, KJ; Brattico, E; Carlson, S

    2003-01-01

    Musically untrained listeners were presented with musical major and minor chords in different octaves and with different timbres, with or without simultaneously presented functional magnetic resonance imaging (fMRI) noise, and were asked to judge the chords according to their emotional connotations...... during the trials, only affected emotional responses to the low pitched chords, which encourages to investigate the neural basis of emotional responses to musical sound elements by means of fMRI...

  7. SpliceDisease database: linking RNA splicing and disease.

    Science.gov (United States)

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

    2012-01-01

    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 http://cmbi.bjmu.edu.cn/sdisease.

  8. ChordPlus:a scalable,decentralized object location and routing algorithm

    Institute of Scientific and Technical Information of China (English)

    柏海寰; 蒋俊杰; 汪为农

    2004-01-01

    Object location is a fundamental problem in distributed system such as grid computing and peer-to-peer environment. Chord is one of the typical scalable object location algorithms for peer-to-peer network. The simplicity, provable correctness and provable performance of Chord make it an attractive option for distributed lookup. However its lookup performance is not satisfying. Based on the decentralized object location mathematical model. This paper proposes ChordPlus, an improved Chord algorithm, by enlarging dimension size of space M (M = 2 in Chord) and utilizing data redundancy technology. ChordPlus is a scalable, fault-tolerant, completely decentralized and self-organizing object location and routing algorithm for overlay network. Results from theoretical analysis and simulation experiments show that increasing the dimension size of space or neighborhood set length can enhance the routing performance of ChordPlus. In a simulation network with 5 000 nodes, the average routing path length of ChordPlus is only as many as half that of Chord algorithm.

  9. spliceR

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...

  10. Introducing Modified Degree 4 Chordal Rings with Two Chord Lengths

    DEFF Research Database (Denmark)

    Pedersen, Jens Myrup

    2007-01-01

    In this paper an analysis of modified degree 4 Chordal Rings with two chord lengths named CHRm is presented and compared to similar topologies: Chordal Rings, N2R and modified N2R. Formulas for approximating diameters and average path lengths are provided and verified, and it is shown...... that the distances in CHRm are significantly smaller than in traditional Chordal Rings and N2R, and also smaller than modified N2R for topologies with up to 1500 nodes. Despite the proposed CHRm being of degree 4, and the modified N2R of degree 3, CHRm may be better suited for the optical level of fiber rings, due...... to its easy mapping onto the ring. It seems to be superior also to the traditional Chordal Rings, but it is not node symmetric....

  11. TaChord:利用拓扑相关路由算法和超级节点的Chord系统%TaChord:a Chord system using topology-aware routing and super peers

    Institute of Scientific and Technical Information of China (English)

    陈东锋; 杨寿保; 彭小燕

    2004-01-01

    由于未考虑实际网络拓扑结构,当前结构化对等网络系统存在高延迟低效率的毛病. 本文提出一种与实际网络拓扑结构相关的路由方法,并开发出一种基于Chord的TaChord系统. 在仿真系统中, 用物理跳数、域间延迟和每个消息占用的带宽来衡量TaChord和其他系统的路由性能. 仿真结果表明,TaChord系统的路由性能有了极大的提高, 如平均物理跳数是Chord的一半,并且不同路由缓存管理策略对TaChord的路由性能能产生重要的影响.%Due to minimum consideration of an actual network topology, the existing peer-to-peer (P2P) overlay networks, such as CAN, Chord, Pastry and Tapestry, will lead to high latency and low efficiency. In TaChord, a topology-aware routing approach in P2P overlays and an improved design in Chord are presented. TaChord and other algorithms are evaluated by physical hops, interdomain-adjusted latency, and aggregate bandwidth used per message. Experimental results demonstrate that TaChord has the drastic improvement in routing performance where average physical hop is half that of chord, and the impact of cache management strategies in the TaChord overlay cannot be neglected.

  12. Measurement of Plasma Ion Temperature and Flow Velocity from Chord-Averaged Emission Line Profile

    Indian Academy of Sciences (India)

    Xu Wei

    2011-03-01

    The distinction between Doppler broadening and Doppler shift has been analysed, the differences between Gaussian fitting and the distribution of chord-integral line shape have also been discussed. Local ion temperature and flow velocity have been derived from the chord-averaged emission line profile by a chosen-point Gaussian fitting technique.

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

    Directory of Open Access Journals (Sweden)

    Byron Yu-Lin Kuo

    2006-04-01

    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 http://www.cisreg.ca.

  14. Black-capped chickadee (Poecile atricapillus) and human (Homo sapiens) chord discrimination.

    Science.gov (United States)

    Hoeschele, Marisa; Cook, Robert G; Guillette, Lauren M; Brooks, Daniel I; Sturdy, Christopher B

    2012-02-01

    Human music perception is related both to musical experience and the physical properties of sound. Examining the processing of music by nonhuman animals has been generally neglected. We tested both black-capped chickadees and humans in a chord discrimination task that replicates and extends prior research with pigeons. We found that chickadees and humans, in common with pigeons, showed similar patterns of discrimination across manipulations of the 3rd and 5th notes of the triadic chords. For all species (chickadee and humans here, pigeons previously), chords with half-step alterations in the 5th note were easier to discriminate than half-step manipulations of the 3rd note, which is likely due to the sensory consonance of these chords. There were differences among species in terms of the fine discrimination of the chords within this larger pattern of results. Further, the ability to relearn the chords when transposed to a new root differed across species. Our results provide new comparative data suggesting some similarities in chord perception that span a wide range of species, from pigeons (nonvocal learners) to songbirds and humans (vocal learners).

  15. On self-approaching and increasing-chord drawings of 3-connected planar graphs

    Directory of Open Access Journals (Sweden)

    Martin Nöllenburg

    2016-02-01

    Full Text Available An $st$-path in a drawing of a graph is self-approaching if during the traversal of the corresponding curve from $s$ to any point $t'$ on the curve the distance to $t'$ is non-increasing. A path has increasing chords if it is self-approaching in both directions. A drawing is self-approaching (increasing-chord if any pair of vertices is connected by a self-approaching (increasing-chord path.We study self-approaching and increasing-chord drawings of triangulations and 3-connected planar graphs. We show that in the Euclidean plane, triangulations admit increasing-chord drawings, and for planar 3-trees we can ensure planarity. We prove that strongly monotone (and thus increasing-chord drawings of trees and binary cactuses require exponential resolution in the worst case, answering an open question by Kindermann et al. (GD 2014. Moreover, we provide a binary cactus that does not admit a self-approaching drawing. Finally, we show that 3-connected planar graphs admit increasing-chord drawings in the hyperbolic plane and characterize the trees that admit such drawings.

  16. Methods for Characterization of Alternative RNA Splicing.

    Science.gov (United States)

    Harvey, Samuel E; Cheng, Chonghui

    2016-01-01

    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.

  17. Mutual interdependence of splicing and transcription elongation.

    Science.gov (United States)

    Brzyżek, Grzegorz; Świeżewski, Szymon

    2015-01-01

    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.

  18. Strength of tubular welded joints of roof trusses in Shanghai Qizhong Tennis Center

    Institute of Scientific and Technical Information of China (English)

    Lewei TONG; Min GU; Yiyi CHEN; Liying ZHOU; Jiandong SUN; Yangji CHEN; Yingru LIN; Gao LIN

    2008-01-01

    Static strength of multi-planar welded joints with seven brace members and one chord member made of circular hollow sections is investigated in the paper, based on the engineering practice of moveable roof trusses of Shanghai Qizhong Tennis Center. Firstly, comparative experiments were carried out on two model joints with a scale of 1:3. One joint was not reinforced, whereas the other was reinforced with ring stiffeners inside the chord member. Failure mode, stress distribution, plastic-zone development and ultimate load capacity of the joints were investigated, and effects of the ring stiffeners on the joint behavior were observed through the experiments. Secondly, finite element analysis of both the tested model joints was performed. The calculation results are in a good agreement with the experimental results, which indicated that the numerical analysis was quite effective. Finally, the strategy for enhancing strength of the complicated joint is discussed. Parameters study on the constructional details of ring stiffeners was carried out using FE method. The present research shows the multi-planar circular hollow section joint with high ratio of diameter to thickness of the chord and multiple braces is liable to chord plasticity under axial tension and compression on the braces. For the design of the joint, it is suggested that the ring stiffeners are installed insider the chord to meet needs of enough stiffness and strength. Both position and number of the stiffeners should be carefully determined based on the axial forces on the braces and their diameters. The stiffener thickness should not be less than the chord thickness, and the diameter of the hole at the center of the stiffener should not be greater than half of the chord diameter.

  19. Environmental Assessment of the Realignment of Units at McChord Air Force Base, Washington

    Science.gov (United States)

    1989-07-01

    McChord AFB (Department of the Air Force 1986). 3.2.4 Water Resources Clovis Creek and Morey Creek are the primary surface water features at McChord AFB...Morey Creek originates at Spanaway Lake east of the base and merges Swith Clovis Creek at n the eastern portion of the base. Clovis Creek has been...estimated at $166.5 million (Department of the Air Force 1988). 3.2.8 Cultura - Resources In the area within and adjacent to McChord AFB, there is evidence

  20. Replica location mechanism in data grid based on ED-Chord

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A peer-to-peer hierarchical replica location mechanism(PRLM)was designed for data grids to provide better load balancing capability and scalability.Global replica indexes of the PRLM are organized based on even distributed Chord(ED-Chord)structure.The locality can optimize queries on local replica indexes of virtual organizations.ED-Chord protocol collects the node identifiers information using a distributed method and assigns optimal identifiers for new nodes to make them more uniformly distributed in the entire identifier space.Theoretical analysis and simulations show that PRLM provides good performance,scalability and load balancing capability for replica location in data grids.

  1. Human acoustics: From vocal chords to inner ear

    Science.gov (United States)

    Lamar, Michael Drew

    2005-11-01

    Part I covers the vocal chords, more accurately known as the vocal folds (VF). Modeling efforts are split into two areas: the VF tissue and the airflow. There are multiple existing models of the VF, with varying ranges of complexity for both the tissue and the airflow. In our model, the tissue is based on a recent two-mass model of Bogaert's [5], while the airflow is quasi-one-dimensional and is derived from the two-dimensional compressible Navier-Stokes equations. Our model is more accurate than Bernoulli's law (quasi-steady approximation), yet less complex than the full Navier-Stokes system. The model is shown to reproduce important transient behaviour intrinsic in vocal fold motion, such as pressure peaks before and after vocal fold closure. Part II concerns the inner ear, or cochlea. Again the modeling effort is split into two areas: the cochlear tissue and the cochlear fluid. We model the cochlear fluid with the well known two-dimensional box model of the cochlea, derived from the three-dimensional compressible Navier-Stokes equations. The cochlear tissue structure is where the complexity takes place. We start with Neely and Kim's [25] linear active model for the cochlear structure and modify their active gain parameter into a nonlinear nonlocal functional. The nonlinearity forces us to work in the time domain, which is prone to dispersive instabilities if one uses a frequency domain middle ear model. The middle ear's role as a transient absorber is discussed and its time domain formulation is shown to reduce the dispersive instability. We perform simulations on the full system and show that the model recovers many important nonlinear phenomena, such as suppression and difference tones. A spectrogram based on the cochlear response is created and compared with the spectrogram of the input waveform. In both Part I and Part II, the emphasis is on time dependent modeling and numerical implementation.

  2. 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.

  3. Consonance and dissonance of musical chords: neural correlates in auditory cortex of monkeys and humans.

    Science.gov (United States)

    Fishman, Y I; Volkov, I O; Noh, M D; Garell, P C; Bakken, H; Arezzo, J C; Howard, M A; Steinschneider, M

    2001-12-01

    Some musical chords sound pleasant, or consonant, while others sound unpleasant, or dissonant. Helmholtz's psychoacoustic theory of consonance and dissonance attributes the perception of dissonance to the sensation of "beats" and "roughness" caused by interactions in the auditory periphery between adjacent partials of complex tones comprising a musical chord. Conversely, consonance is characterized by the relative absence of beats and roughness. Physiological studies in monkeys suggest that roughness may be represented in primary auditory cortex (A1) by oscillatory neuronal ensemble responses phase-locked to the amplitude-modulated temporal envelope of complex sounds. However, it remains unknown whether phase-locked responses also underlie the representation of dissonance in auditory cortex. In the present study, responses evoked by musical chords with varying degrees of consonance and dissonance were recorded in A1 of awake macaques and evaluated using auditory-evoked potential (AEP), multiunit activity (MUA), and current-source density (CSD) techniques. In parallel studies, intracranial AEPs evoked by the same musical chords were recorded directly from the auditory cortex of two human subjects undergoing surgical evaluation for medically intractable epilepsy. Chords were composed of two simultaneous harmonic complex tones. The magnitude of oscillatory phase-locked activity in A1 of the monkey correlates with the perceived dissonance of the musical chords. Responses evoked by dissonant chords, such as minor and major seconds, display oscillations phase-locked to the predicted difference frequencies, whereas responses evoked by consonant chords, such as octaves and perfect fifths, display little or no phase-locked activity. AEPs recorded in Heschl's gyrus display strikingly similar oscillatory patterns to those observed in monkey A1, with dissonant chords eliciting greater phase-locked activity than consonant chords. In contrast to recordings in Heschl's gyrus

  4. Experience Drives Synchronization: The phase and Amplitude Dynamics of Neural Oscillations to Musical Chords Are Differentially Modulated by Musical Expertise.

    Directory of Open Access Journals (Sweden)

    Karen Johanne Pallesen

    Full Text Available Musical expertise is associated with structural and functional changes in the brain that underlie facilitated auditory perception. We investigated whether the phase locking (PL and amplitude modulations (AM of neuronal oscillations in response to musical chords are correlated with musical expertise and whether they reflect the prototypicality of chords in Western tonal music. To this aim, we recorded magnetoencephalography (MEG while musicians and non-musicians were presented with common prototypical major and minor chords, and with uncommon, non-prototypical dissonant and mistuned chords, while watching a silenced movie. We then analyzed the PL and AM of ongoing oscillations in the theta (4-8 Hz alpha (8-14 Hz, beta- (14-30 Hz and gamma- (30-80 Hz bands to these chords. We found that musical expertise was associated with strengthened PL of ongoing oscillations to chords over a wide frequency range during the first 300 ms from stimulus onset, as opposed to increased alpha-band AM to chords over temporal MEG channels. In musicians, the gamma-band PL was strongest to non-prototypical compared to other chords, while in non-musicians PL was strongest to minor chords. In both musicians and non-musicians the long-latency (> 200 ms gamma-band PL was also sensitive to chord identity, and particularly to the amplitude modulations (beats of the dissonant chord. These findings suggest that musical expertise modulates oscillation PL to musical chords and that the strength of these modulations is dependent on chord prototypicality.

  5. Effects of unexpected chords and of performer's expression on brain responses and electrodermal activity.

    Directory of Open Access Journals (Sweden)

    Stefan Koelsch

    Full Text Available BACKGROUND: There is lack of neuroscientific studies investigating music processing with naturalistic stimuli, and brain responses to real music are, thus, largely unknown. METHODOLOGY/PRINCIPAL FINDINGS: This study investigates event-related brain potentials (ERPs, skin conductance responses (SCRs and heart rate (HR elicited by unexpected chords of piano sonatas as they were originally arranged by composers, and as they were played by professional pianists. From the musical excerpts played by the pianists (with emotional expression, we also created versions without variations in tempo and loudness (without musical expression to investigate effects of musical expression on ERPs and SCRs. Compared to expected chords, unexpected chords elicited an early right anterior negativity (ERAN, reflecting music-syntactic processing and an N5 (reflecting processing of meaning information in the ERPs, as well as clear changes in the SCRs (reflecting that unexpected chords also elicited emotional responses. The ERAN was not influenced by emotional expression, whereas N5 potentials elicited by chords in general (regardless of their chord function differed between the expressive and the non-expressive condition. CONCLUSIONS/SIGNIFICANCE: These results show that the neural mechanisms of music-syntactic processing operate independently of the emotional qualities of a stimulus, justifying the use of stimuli without emotional expression to investigate the cognitive processing of musical structure. Moreover, the data indicate that musical expression affects the neural mechanisms underlying the processing of musical meaning. Our data are the first to reveal influences of musical performance on ERPs and SCRs, and to show physiological responses to unexpected chords in naturalistic music.

  6. ParSplice, Version 1

    Energy Technology Data Exchange (ETDEWEB)

    2017-01-05

    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)

  7. Targeting RNA splicing for disease therapy.

    Science.gov (United States)

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

    2013-01-01

    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.

  8. Methods for Characterization of Alternative RNA Splicing

    Science.gov (United States)

    Harvey, Samuel E.; Cheng, Chonghui

    2016-01-01

    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

  9. Risk of vocal chord dysplasia in relation to smoking, alcohol intake and occupation.

    Science.gov (United States)

    Grasl, M C; Neuwirth-Riedl, K; Vutuc, C; Horak, F; Vorbeck, F; Banyai, M

    1990-03-01

    The significance of tobacco smoking, alcohol consumption and occupation as risk factors for the development of vocal chord dysplasia was evaluated in a case-control study. Twenty-seven male patients with dysplasia of the vocal chords were chosen from the I. ENT-University Clinic in Vienna (1985-1988) and compared with 54 controls. The main results are: The relative risk (RR) of a smoker compared to that of a non-smoker for vocal chord dysplasia is 7.27 (6.81-7.73); the RR adjusted for occupation is 3.58 (2.31-4.84). The most important risk factor, however, is occupational exposure. The relative risk of a blue collar worker compared to that of a white collar worker is 11.04 (10.61-11.46), which is reduced only to 10.02 (10.61-11.46) after stratification according to smoking habits.

  10. Topological recursion for chord diagrams, RNA complexes, and cells in moduli spaces

    CERN Document Server

    Andersen, Jørgen E; Penner, R C; Reidys, Christian M; Sułkowski, Piotr

    2012-01-01

    We introduce and study the Hermitian matrix model with potential V(x)=x^2/2-stx/(1-tx), which enumerates the number of linear chord diagrams of fixed genus with specified numbers of backbones generated by s and chords generated by t. For the one-cut solution, the partition function, correlators and free energies are convergent for small t and all s as a perturbation of the Gaussian potential, which arises for st=0. This perturbation is computed using the formalism of the topological recursion. The corresponding enumeration of chord diagrams gives at once the number of RNA complexes of a given topology as well as the number of cells in Riemann's moduli spaces for bordered surfaces. The free energies are computed here in principle for all genera and explicitly for genera less than four.

  11. Cloud-Hosted Real-time Data Services for the Geosciences (CHORDS)

    Science.gov (United States)

    Daniels, M. D.; Graves, S. J.; Kerkez, B.; Chandrasekar, V.; Vernon, F.; Martin, C. L.; Maskey, M.; Keiser, K.; Dye, M. J.

    2015-12-01

    The Cloud-Hosted Real-time Data Services for the Geosciences (CHORDS) project, funded as part of NSF's EarthCube initiative, addresses the ever-increasing importance of real-time scientific data, particularly in mission critical scenarios, where informed decisions must be made rapidly. Advances in the distribution of real-time data are leading many new transient phenomena in space-time to be observed, however, real-time decision-making is infeasible in many cases as these streaming data are either completely inaccessible or only available to proprietary in-house tools or displays. This lack of accessibility prohibits advanced algorithm and workflow development that could be initiated or enhanced by these data streams. Small research teams do not have resources to develop tools for the broad dissemination of their valuable real-time data and could benefit from an easy to use, scalable, cloud-based solution to facilitate access. CHORDS proposes to make a very diverse suite of real-time data available to the broader geosciences community in order to allow innovative new science in these areas to thrive. This presentation will highlight recently developed CHORDS portal tools and processing systems aimed at addressing some of the gaps in handling real-time data, particularly in the provisioning of data from the "long-tail" scientific community through a simple interface deployed in the cloud. The CHORDS system will connect these real-time streams via standard services from the Open Geospatial Consortium (OGC) and does so in a way that is simple and transparent to the data provider. Broad use of the CHORDS framework will expand the role of real-time data within the geosciences, and enhance the potential of streaming data sources to enable adaptive experimentation and real-time hypothesis testing. Adherence to community data and metadata standards will promote the integration of CHORDS real-time data with existing standards-compliant analysis, visualization and modeling

  12. The effect of conditional probability of chord progression on brain response: an MEG study.

    Directory of Open Access Journals (Sweden)

    Seung-Goo Kim

    Full Text Available BACKGROUND: Recent electrophysiological and neuroimaging studies have explored how and where musical syntax in Western music is processed in the human brain. An inappropriate chord progression elicits an event-related potential (ERP component called an early right anterior negativity (ERAN or simply an early anterior negativity (EAN in an early stage of processing the musical syntax. Though the possible underlying mechanism of the EAN is assumed to be probabilistic learning, the effect of the probability of chord progressions on the EAN response has not been previously explored explicitly. METHODOLOGY/PRINCIPAL FINDINGS: In the present study, the empirical conditional probabilities in a Western music corpus were employed as an approximation of the frequencies in previous exposure of participants. Three types of chord progression were presented to musicians and non-musicians in order to examine the correlation between the probability of chord progression and the neuromagnetic response using magnetoencephalography (MEG. Chord progressions were found to elicit early responses in a negatively correlating fashion with the conditional probability. Observed EANm (as a magnetic counterpart of the EAN component responses were consistent with the previously reported EAN responses in terms of latency and location. The effect of conditional probability interacted with the effect of musical training. In addition, the neural response also correlated with the behavioral measures in the non-musicians. CONCLUSIONS/SIGNIFICANCE: Our study is the first to reveal the correlation between the probability of chord progression and the corresponding neuromagnetic response. The current results suggest that the physiological response is a reflection of the probabilistic representations of the musical syntax. Moreover, the results indicate that the probabilistic representation is related to the musical training as well as the sensitivity of an individual.

  13. Impact of Selected Parameters on the Fatigue Strength of Splices on Multiply Textile Conveyor Belts

    Science.gov (United States)

    Bajda, Mirosław; Błażej, Ryszard; Hardygóra, Monika

    2016-10-01

    Splices are the weakest points in the conveyor belt loop. The strength of these joints, and thus their design as well as the method and quality of splicing, determine the strength of the whole conveyor belt loop. A special zone in a splice exists, where the stresses in the adjacent plies or cables differ considerably from each other. This results in differences in the elongation of these elements and in additional shearing stresses in the rubber layer. The strength of the joints depends on several factors, among others on the parameters of the joined belt, on the connecting layer and the technology of joining, as well as on the materials used to make the joint. The strength of the joint constitutes a criterion for the selection of a belt suitable for the operating conditions, and therefore methods of testing such joints are of great importance. This paper presents the method of testing fatigue strength of splices made on multi-ply textile conveyor belts and the results of these studies.

  14. A method for computing random chord length distributions in geometrical objects.

    Science.gov (United States)

    Borak, T B

    1994-03-01

    A method is described that uses a Monte Carlo approach for computing the distribution of random chord lengths in objects traversed by rays originating uniformly in space (mu-randomness). The resulting distributions converge identically to the analytical solutions for a sphere and satisfy the Cauchy relationship for mean chord lengths in circular cylinders. The method can easily be applied to geometrical shapes that are not convex such as the region between nested cylinders to simulate the sensitive volume of a detector. Comparisons with other computational methods are presented.

  15. 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

    2008-10-01

    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.

  16. Stochastic noise in splicing machinery

    OpenAIRE

    Melamud, Eugene; Moult, John

    2009-01-01

    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...

  17. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs

    Science.gov (United States)

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

    2016-01-01

    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 (http://www.picb.ac.cn/rnomics/circpedia). 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

  18. A Method To Find The Area Of Sector Without The Usage Of Angle Made By The Chord

    OpenAIRE

    Syed Abdul Lateef

    2015-01-01

    ABSTRACT This is the simplest method to find the area of the segment of the circle without the usage of the angle made by the chord and thus the area of sector could be found without the usage of angle made by chord. This is done by relating the area of segment to the area of sector.

  19. A Method To Find The Area Of Sector Without The Usage Of Angle Made By The Chord

    Directory of Open Access Journals (Sweden)

    Syed Abdul Lateef

    2015-02-01

    Full Text Available ABSTRACT This is the simplest method to find the area of the segment of the circle without the usage of the angle made by the chord and thus the area of sector could be found without the usage of angle made by chord. This is done by relating the area of segment to the area of sector.

  20. Neuromagnetic auditory steady state response to chords: effect of frequency ratio.

    Science.gov (United States)

    Otsuka, Asuka; Yumoto, Masato; Kuriki, Shinya; Nakagawa, Seiji

    2013-01-01

    Perceptual degree of consonance or dissonance of a chord is known to be varied as a function of frequency ratio between tones composing the chord. It has been indicated that generation of a sense of dissonance is associated with the auditory steady-state response (ASSR) phase-locked to difference frequencies which are salient in the chords with complex frequency ratios. This study further investigated how the neuromagnetic ASSR would be modulated as a function of the frequency ratio when the acoustic properties of the difference frequency, to which the ASSR was synchronized, was identical in terms of its number, energy and frequency. Neuronal frequency characteristics intrinsic to the ASSR were compensated by utilizing responses to a SAM (Sinusoidally Amplitude Modulated) chirp tone sweeping through the corresponding frequency range. The results showed that ASSR was significantly smaller for the chords with simple frequency ratios than for those with complex frequency ratios. It indicates that the basic neuronal correlates underlying the sensation of consonance/dissonance might be associated with the attenuation rate applied to encode the input information through the afferent auditory pathway. Attentional gating of the thalamo-cortical function might also be one of the factors.

  1. Research and Improvement of Chord Algorithm%Chord算法的研究与改进

    Institute of Scientific and Technical Information of China (English)

    杨艳红

    2014-01-01

    Chord algorithm that is the resource location algorithm of the structured P2P systems is concerned mostly.In this thesis, Ful-Chord algorithm is improved by only storing the same information once time in the finger table. The improved algorithm can reduce storage and maintain information of the system.The class library of PeerSim is used to simulate the improved Chord algorithm and the Sec-Chord algorithm.%Chord算法是结构化P2P系统资源定位算法中最受关注的算法之一。本文在Full- Chord算法的基础上,将指针表中相同项作为一项进行存储,减少了存储冗余并且能够存储整个系统的信息,并利用PeerSim类库仿真了存储冗余减少后的Chord算法。

  2. Integration And Quality Assessment Of Heterogeneous Chord Sequences Using Data Fusion

    NARCIS (Netherlands)

    Koops, Hendrik Vincent; de Haas, W.B.; Bountouridis, D.; Volk, A.

    2016-01-01

    Two heads are better than one, and the many are smarter than the few. Integrating knowledge from multiple sources has shown to increase retrieval and classification accuracy in many domains. The recent explosion of crowd-sourced information, such as on websites hosting chords and tabs for popular so

  3. Effect of Timbre and Register Modifications of Musical Stimuli on Young Children's Identification of Chord Changes.

    Science.gov (United States)

    Costa-Giomi, Eugenia

    1994-01-01

    Reviews research related to children's musical development. Reports on a study of 125 kindergarten and first-grade students on the impact of modification of timbre and register of musical stimuli. Finds that timbre modification helped children recognize chord changes with first graders identifying more changes than did kindergartners. (CFR)

  4. Theory and algorithms for image reconstruction on chords and within regions of interest.

    Science.gov (United States)

    Zou, Yu; Pan, Xiaochuan; Sidky, Emil Y

    2005-11-01

    We introduce a formula for image reconstruction on a chord of a general source trajectory. We subsequently develop three algorithms for exact image reconstruction on a chord from data acquired with the general trajectory. Interestingly, two of the developed algorithms can accommodate data containing transverse truncations. The widely used helical trajectory and other trajectories discussed in literature can be interpreted as special cases of the general trajectory, and the developed theory and algorithms are thus directly applicable to reconstructing images exactly from data acquired with these trajectories. For instance, chords on a helical trajectory are equivalent to the n-PI-line segments. In this situation, the proposed algorithms become the algorithms that we proposed previously for image reconstruction on PI-line segments. We have performed preliminary numerical studies, which include the study on image reconstruction on chords of two-circle trajectory, which is nonsmooth, and on n-PI lines of a helical trajectory, which is smooth. Quantitative results of these studies verify and demonstrate the proposed theory and algorithms.

  5. Stochastic noise in splicing machinery.

    Science.gov (United States)

    Melamud, Eugene; Moult, John

    2009-08-01

    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.

  6. Evolutionary conservation of alternative splicing in chicken

    Science.gov (United States)

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

    2013-01-01

    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

  7. COMMUNICATION: Alternative splicing and genomic stability

    Science.gov (United States)

    Cahill, Kevin

    2004-06-01

    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.

  8. Alcoholism and alternative splicing of candidate genes.

    Science.gov (United States)

    Sasabe, Toshikazu; Ishiura, Shoichi

    2010-04-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Chen Liang

    2011-01-01

    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.

  10. Double-composite rectangular truss bridge and its joint analysis

    Directory of Open Access Journals (Sweden)

    Yongjian Liu

    2015-08-01

    Full Text Available This paper describes a novel composite tubular truss bridge with concrete slab and concrete-filled rectangular chords. With concrete slab plus truss system and joints reinforced with concrete and Perfobond Leiste rib, double composite truss bridge proved to be a fairly suitable solution in negative moment area. Perfobond Leiste shear connector (PBL is widely implemented in the composite structure for its outstanding fatigue resistance. In this pilot bridge, Perfobond Leister ribs (PBR were installed in the truss girder's joints, which played double roles as shear connector and stiffener. An erection method and overall bridge structural analysis were then presented. Typical joints in the pilot bridge were selected to analyze the effect of PBR. Investigation of the effect of PBR in concrete-filled tubular joints was elaborated. Comparison has revealed that concrete-filled tubular joints with PBR have much higher constraint capability than joints without PBR. For rectangular tubular truss, the punching shear force of the concrete filled joint with PBR is approximately 43% larger than that of the joint without PBR. Fatigue performance of the joint installed with PBR was improved, which was found through analysis of the stress concentration factor of joint. The PBR installed in the joints mitigated the stress concentration factor in the chord face. Therefore, the advantages of this new type of bridge are demonstrated, including the convenience of construction using rectangular truss, innovative concept of structural design and better global and local performances.

  11. The RNA Splicing Response to DNA Damage.

    Science.gov (United States)

    Shkreta, Lulzim; Chabot, Benoit

    2015-10-29

    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.

  12. Titin Diversity—Alternative Splicing Gone Wild

    Directory of Open Access Journals (Sweden)

    Wei Guo

    2010-01-01

    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.

  13. Spliced leader RNA trans-splicing discovered in copepods

    Science.gov (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

    2015-12-01

    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.

  14. The preattentive processing of major vs. minor chords in the human brain: An event-related potential study.

    Science.gov (United States)

    Virtala, Paula; Berg, Venla; Kivioja, Maari; Purhonen, Juha; Salmenkivi, Marko; Paavilainen, Petri; Tervaniemi, Mari

    2011-01-10

    Western music has two classifications that are highly familiar to all Western listeners: the dichotomy between the major and minor modalities and consonance vs. dissonance. We aimed at determining whether these classifications already take place at the level of the elicitation of the change-related mismatch negativity (MMN) component of the event-related potential (ERP). To this end, we constructed an oddball-paradigm with root minor, dissonant and inverted major chords in a context of root major chords. These stimuli were composed so that the standard and deviant chords did not include a physically deviant frequency which could cause the MMN. The standard chords were transposed into 12 different keys (=pitch levels) and delivered to the participants while they were watching a silent movie (ignore condition) or detecting softer target sounds (detection condition). In the ignore condition, the MMN was significant for all but inverted major chords. In the detection condition, the MMN was significant for dissonant chords and soft target chords. Our results indicate that the processes underlying MMN are able to make discriminations which are qualitative by nature. Whether the classifications between major and minor modalities and consonance vs. dissonance are innate or based on implicit learning remains a question for the future.

  15. Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants

    Science.gov (United States)

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

    2017-01-01

    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

  16. Construction of Endpoint Constrained Cubic Rational Curve with Chord-Length Parameterization

    Institute of Scientific and Technical Information of China (English)

    LI Pei-pei; ZHANG Xin; ZHANG Ai-wu

    2013-01-01

    This paper discusses the problem that constructing a curve to satisfy the given endpoint constraints and chord-length parameters. Based on the research of Lu, the curve construction method for the entire tangent angles region 0 1(α,α)∈(-π,π) × (-π,π) is given. Firstly, to ensure the weights are always positive, the three characteristics of cubic rational Bezier curve is proved, then the segment construction idea for the other tangent angles are presented in view of the three characteristics. The curve constructed with the new method satisfies the endpoint constraint and chord-length parameters, it’s G1 continuous in every segment curve, and the shapes of the curve are well.

  17. An investigation of the performance of novel chorded keyboards in combination with pointing input devices.

    Science.gov (United States)

    Shi, Wen-Zhou; Wu, Fong-Gong

    2015-01-01

    Rapid advances in computing power have driven the development of smaller and lighter technology products, with novel input devices constantly being produced in response to new user behaviors and usage contexts. The aim of this research was to investigate the feasibility of operating chorded keyboard control modules in concert with pointing devices such as styluses and mice. We compared combinations of two novel chorded keyboards with different pointing devices in hopes of finding a better combination for future electronic products. Twelve participants were recruited for simulation testing, and paired sample t testing was conducted to determine whether input and error rates for the novel keyboards were improved significantly over those of traditional input methods. The most efficient input device combination tested was the combination of a novel cross-shaped key keyboard and a stylus, suggesting the high potential for use of this combination with future mobile IT products.

  18. Results of two multi-chord stellar occultations by dwarf planet (1) Ceres

    CERN Document Server

    Gomes-Júnior, A R; Braga-Ribas, F; Assafin, M; Vieira-Martins, R; Camargo, J I B; Sicardy, B; Timerson, B; George, T; Broughton, J; Blank, T; Benedetti-Rossi, G; Brooks, J; Dantowitz, R F; Dunham, D W; Dunham, J B; Ellington, C K; Emilio, M; Herpich, F R; Jacques, C; Maley, P D; Mehret, L; Mello, A J T; Milone, A C; Pimentel, E; Schoenell, W; Weber, N S

    2015-01-01

    We report the results of two multi-chord stellar occultations by the dwarf planet (1) Ceres that were observed from Brazil on 2010 August 17, and from the USA on 2013 October 25. Four positive detections were obtained for the 2010 occultation, and nine for the 2013 occultation. Elliptical models were adjusted to the observed chords to obtain Ceres' size and shape. Two limb fitting solutions were studied for each event. The first one is a nominal solution with an indeterminate polar aspect angle. The second one was constrained by the pole coordinates as given by Drummond et al. Assuming a Maclaurin spheroid, we determine an equatorial diameter of 972 $\\pm$ 6 km and an apparent oblateness of 0.08 $\\pm$ 0.03 as our best solution. These results are compared to all available size and shape determinations for Ceres made so far, and shall be confirmed by the NASA's Dawn space mission.

  19. Using Different Chord Lengths in Degree Three Chordal Rings and N2R Topologies

    DEFF Research Database (Denmark)

    Pedersen, Jens Myrup; Madsen, Ole Brun; Patel, Ahmed

    2007-01-01

    Degree Three Chordal Rings and N2R Topologies are useful for physial and optical network topologies due to the combination of short distances, regularity and low degrees. In this paper we show how distances in terms of average distances and diameters can be significantly decreased by using chords...... of different lengths. These topologies are slightly less symmetric than the traditional ones, but the distances are virtually the same no matter from which node in a given topology they are measured from....

  20. Alternative Spliced Transcripts as Cancer Markers

    Directory of Open Access Journals (Sweden)

    Otavia L. Caballero

    2001-01-01

    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.

  1. Regulation of splicing factors by alternative splicing and NMD is conserved between kingdoms yet evolutionarily flexible.

    Science.gov (United States)

    Lareau, Liana F; Brenner, Steven E

    2015-04-01

    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.

  2. The low information content of Neurospora splicing signals: implications for RNA splicing and intron origin.

    Science.gov (United States)

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

    2015-05-01

    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.

  3. Perception of musical tension in short chord sequences: the influence of harmonic function, sensory dissonance, horizontal motion, and musical training.

    Science.gov (United States)

    Bigand, E; Parncutt, R; Lerdahl, F

    1996-01-01

    This study investigates the effect of four variables (tonal hierarchies, sensory chordal consonance, horizontal motion, and musical training) on perceived musical tension. Participants were asked to evaluate the tension created by a chord X in sequences of three chords [C major-->X-->C major] in a C major context key. The X chords could be major or minor triads major-minor seventh, or minor seventh chords built on the 12 notes of the chromatic scale. The data were compared with Krumhansl's (1990) harmonic hierarchy and with predictions of Lerdahl's (1988) cognitive theory, Hutchinson and Knopoff's (1978) and Parncutt's (1989) sensory-psychoacoustical theories, and the model of horizontal motion defined in the paper. As a main outcome, it appears that judgments of tension arose from a convergence of several cognitive and psychoacoustics influences, whose relative importance varies, depending on musical training.

  4. Efficient computation of the angularly resolved chord length distributions and lineal path functions in large microstructure datasets

    Science.gov (United States)

    Turner, David M.; Niezgoda, Stephen R.; Kalidindi, Surya R.

    2016-10-01

    Chord length distributions (CLDs) and lineal path functions (LPFs) have been successfully utilized in prior literature as measures of the size and shape distributions of the important microscale constituents in the material system. Typically, these functions are parameterized only by line lengths, and thus calculated and derived independent of the angular orientation of the chord or line segment. We describe in this paper computationally efficient methods for estimating chord length distributions and lineal path functions for 2D (two dimensional) and 3D microstructure images defined on any number of arbitrary chord orientations. These so called fully angularly resolved distributions can be computed for over 1000 orientations on large microstructure images (5003 voxels) in minutes on modest hardware. We present these methods as new tools for characterizing microstructures in a statistically meaningful way.

  5. SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.

    Science.gov (United States)

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

    2015-04-01

    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 https://sourceforge.net/projects/splicingtypes/files/ or http://genome.sdau.edu.cn/research/software/SplicingTypesAnno.html.

  6. Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes.

    Science.gov (United States)

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

    2016-05-12

    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.

  7. Alcoholism and Alternative Splicing of Candidate Genes

    Directory of Open Access Journals (Sweden)

    Toshikazu Sasabe

    2010-03-01

    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.

  8. Spliced

    DEFF Research Database (Denmark)

    Addison, Courtney Page

    2016-01-01

    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...

  9. The Fatigue Behaviour of T- and X-Joints Made of Square Hollow Sections

    NARCIS (Netherlands)

    Van Wingerde, A.M.

    1992-01-01

    This work presents the results of experimental and numerical research on the fatigue behaviour of T- and X-joints between square hollow sections of which the brace is welded to the face of the chord, without any additional stiffeners. The work has been carried out in the framework of the CIDECT prog

  10. Aberrant Splicing in Cancer: Mediators of Malignant Progression through an Imperfect Splice Program Shift.

    Science.gov (United States)

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

    2017-01-01

    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.

  11. 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.

  12. 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

    2006-12-01

    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.

  13. Splicing in Caenorhabditis elegans does not require an AG at the 3' splice acceptor site.

    Science.gov (United States)

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

    1993-01-01

    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

  14. Depolarization-mediated regulation of alternative splicing

    Directory of Open Access Journals (Sweden)

    Alok eSharma

    2011-12-01

    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.

  15. High-Current Bus Splice Resistances and Implications for the Operating Energy of the LHC

    CERN Document Server

    Koratzinos, M; Charifoulline, Z; Dahlerup-Petersen, K; Denz, R; Flora, R H; Pfeffer, H; Scheuerlein, C; Schmidt, R; Siemko, A; Strait, J; Verweij, A

    2010-01-01

    At each interconnection between LHC main magnets a low-resistance solder joint must be made between superconducting cables in order to provide a continuous current path through the superconductor and also to the surrounding copper stabilizer in case the cable quenches [1]. About 10,000 such joints exist in the LHC. An extensive campaign has been undertaken to characterize and map the resistances of these joints. All of the superconducting cable splices were measured at 1.9 K and no splices were found with a resistance larger than 3 nW. Non-invasive measurements of the stabilizer joints were made at 300 K in 5 of the 8 sectors, and at 80 K in 3 sectors. More precise local measurements were made on suspect interconnects that were opened up, and poor joints were repaired. However, it is likely that additional imperfect stabilizer joints still exist in the LHC. A statistical analysis is used to place bounds on the remaining worst-case resistances. This sets limits on the maximum operating energy of the LHC, prior...

  16. Assisted transcriptome reconstruction and splicing orthology

    Directory of Open Access Journals (Sweden)

    Samuel Blanquart

    2016-11-01

    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

  17. THE SIZE, SHAPE, ALBEDO, DENSITY, AND ATMOSPHERIC LIMIT OF TRANSNEPTUNIAN OBJECT (50000) QUAOAR FROM MULTI-CHORD STELLAR OCCULTATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Braga-Ribas, F.; Vieira-Martins, R.; Camargo, J. I. B. [Observatorio Nacional, Rio de Janeiro (Brazil); Sicardy, B.; Lellouch, E.; Lecacheux, J. [Observatoire de Paris, LESIA, F-92195 Meudon (France); Ortiz, J. L.; Morales, N. [Instituto de Astrofisica de Andalucia-CSIC, E-18080 Granada (Spain); Tancredi, G.; Roland, S.; Bruzzone, S. [Observatorio Astronomico Los Molinos, Montevideo U-12400 (Uruguay); Assafin, M. [Observatorio do Valongo/UFRJ, Rio de Janeiro (Brazil); Behrend, R. [Observatoire de Geneve, Sauverny (Switzerland); Vachier, F.; Colas, F. [Observatoire de Paris, IMCCE, F-75014 Paris (France); Maury, A. [San Pedro de Atacama Celestial Explorations, San Pedro de Atacama (Chile); Emilio, M. [Universidade Estadual de Ponta Grossa, Ponta Grossa (Brazil); Amorim, A. [Universidade Federal de Santa Catarina, Florianopolis (Brazil); Unda-Sanzana, E. [Unidad de Astronomia, Universidad de Antofagasta, Antofagasta (Chile); Almeida, L. A., E-mail: ribas@on.br [Instituto Nacional de Pesquisas Espaciais, DAS, Sao Jose dos Campos (Brazil); and others

    2013-08-10

    We present results derived from the first multi-chord stellar occultations by the transneptunian object (50000) Quaoar, observed on 2011 May 4 and 2012 February 17, and from a single-chord occultation observed on 2012 October 15. If the timing of the five chords obtained in 2011 were correct, then Quaoar would possess topographic features (crater or mountain) that would be too large for a body of this mass. An alternative model consists in applying time shifts to some chords to account for possible timing errors. Satisfactory elliptical fits to the chords are then possible, yielding an equivalent radius R{sub equiv} = 555 {+-} 2.5 km and geometric visual albedo p{sub V} = 0.109 {+-} 0.007. Assuming that Quaoar is a Maclaurin spheroid with an indeterminate polar aspect angle, we derive a true oblateness of {epsilon}= 0.087{sup +0.0268}{sub -0.0175}, an equatorial radius of 569{sup +24}{sub -17} km, and a density of 1.99 {+-} 0.46 g cm{sup -3}. The orientation of our preferred solution in the plane of the sky implies that Quaoar's satellite Weywot cannot have an equatorial orbit. Finally, we detect no global atmosphere around Quaoar, considering a pressure upper limit of about 20 nbar for a pure methane atmosphere.

  18. The CHORDS Portal: Lowering the Barrier for Internet Collection, Archival and Distribution of Real-Time Geophysical Observations

    Science.gov (United States)

    Martin, C.; Dye, M. J.; Daniels, M. D.; Keiser, K.; Maskey, M.; Graves, S. J.; Kerkez, B.; Chandrasekar, V.; Vernon, F.

    2015-12-01

    The Cloud-Hosted Real-time Data Services for the Geosciences (CHORDS) project tackles the challenges of collecting and disseminating geophysical observational data in real-time, especially for researchers with limited IT budgets and expertise. The CHORDS Portal is a component that allows research teams to easily configure and operate a cloud-based service which can receive data from dispersed instruments, manage a rolling archive of the observations, and serve these data to any client on the Internet. The research group (user) creates a CHORDS portal simply by running a prepackaged "CHORDS appliance" on Amazon Web Services. The user has complete ownership and management of the portal. Computing expenses are typically very small. RESTful protocols are employed for delivering and fetching data from the portal, which means that any system capable of sending an HTTP GET message is capable of accessing the portal. A simple API is defined, making it straightforward for non-experts to integrate a diverse collection of field instruments. Languages with network access libraries, such as Python, sh, Matlab, R, IDL, Ruby and JavaScript (and most others) can retrieve structured data from the portal with just a few lines of code. The user's private portal provides a browser-based system for configuring, managing and monitoring the health of the integrated real-time system. This talk will highlight the design goals, architecture and agile development of the CHORDS Portal. A running portal, with operational data feeds from across the country, will be presented.

  19. Boundary reconstruction on chords in cone-beam tomography%在锥束CT中基于弦的边缘图像重建

    Institute of Scientific and Technical Information of China (English)

    MarkA.Anastasio; EmilY.Sidky; 邹宇

    2005-01-01

    In this work, we demonstrate that the theory of cone-beam tomography image reconstruction on chords can be modified for use with local tomography problems. Our analysis reveals that discontinuities in the profiles of the object function along chords can be reconstructed readily. By consideration of all possible chords, an image that de-scribes the location of boundaries within an object can be reconstructed. A preliminary numerical study is conducted to validate and demonstrate the reconstruction method.

  20. Detection of Clone Nodes in Wireless Sensor Networks Using RED and Chord Algorithm

    Directory of Open Access Journals (Sweden)

    R. Sindoori

    2015-11-01

    Full Text Available The major issue in WSN is vital information accessed by unauthorized party by clone node. Once a node is captured, the attacker can re-program it and replicate the node in a huge number, thereby easily take over the network process. The detection of node clone attacks in a wireless sensor network is a fundamental problem. Here, the proposed protocols are used to detect clone nodes. The protocols used here are Randomized, Efficient and Distributed (RED protocol, Chord algorithm and distributed hash table (DHT. The first one RED, a new protocol for the detection of clone attacks. And it is used to generate the random number by group leader. The next protocol is chord algorithm for maintaining the neighbor‘s details. The distributed hash table (DHT is a class of a decentralized distributed system that provides a service similar to a hash table and any participating node can efficiently retrieve the neighbor‘s details. The DHT is used to store the member ID, MAC address, preceded ID and successor ID. A witness node is used to verify the random number, member ID, MAC address. The witness node is able to detect the message is send from the authorized party or not by using random key.

  1. Discrete cortical regions associated with the musical beauty of major and minor chords.

    Science.gov (United States)

    Suzuki, Miho; Okamura, Nobuyuki; Kawachi, Yousuke; Tashiro, Manabu; Arao, Hiroshi; Hoshishiba, Takayuki; Gyoba, Jiro; Yanai, Kazuhiko

    2008-06-01

    Previous research has demonstrated that the degree of aesthetic pleasure a person experiences correlates with the activation of reward functions in the brain. However, it is unclear whether different affective qualities and the perceptions of beauty that they evoke correspond to specific areas of brain activation. Major and minor musical keys induce two types of affective qualities--bright/happy and dark/sad--that both evoke aesthetic pleasure. In the present study, we used positron emission tomography to demonstrate that the two musical keys (major and minor) activate distinct brain areas. Minor consonant chords perceived as beautiful strongly activated the right striatum, which has been assumed to play an important role in reward and emotion processing, whereas major consonant chords perceived as beautiful induced significant activity in the left middle temporal gyrus, which is believed to be related to coherent and orderly information processing. These results suggest that major and minor keys, both of which are perceived as beautiful, are processed differently in the brain.

  2. Optimized chord and twist angle distributions of wind turbine blade considering Reynolds number effects

    Energy Technology Data Exchange (ETDEWEB)

    Wang, L.; Tang, X. [Univ. of Central Lancashire. Engineering and Physical Sciences, Preston (United Kingdom); Liu, X. [Univ. of Cumbria. Sustainable Engineering, Workington (United Kingdom)

    2012-07-01

    The aerodynamic performance of a wind turbine depends very much on its blade geometric design, typically based on the blade element momentum (BEM) theory, which divides the blade into several blade elements. In current blade design practices based on Schmitz rotor design theory, the blade geometric parameters including chord and twist angle distributions are determined based on airfoil aerodynamic data at a specific Reynolds number. However, rotating wind turbine blade elements operate at different Reynolds numbers due to variable wind speed and different blade span locations. Therefore, the blade design through Schmitz rotor theory at a specific Reynolds number does not necessarily provide the best power performance under operational conditions. This paper aims to provide an optimal blade design strategy for horizontal-axis wind turbines operating at different Reynolds numbers. A fixed-pitch variable-speed (FPVS) wind turbine with S809 airfoil is chosen as a case study and a Matlab program which considers Reynolds number effects is developed to determine the optimized chord and twist angle distributions of the blade. The performance of the optimized blade is compared with that of the preliminary blade which is designed based on Schmitz rotor design theory at a specific Reynolds number. The results demonstrate that the proposed blade design optimization strategy can improve the power performance of the wind turbine. This approach can be further developed for any practice of horizontal axis wind turbine blade design. (Author)

  3. Regulation of Alternative Splicing in Vivo by Overexpression of Antagonistic Splicing Factors

    Science.gov (United States)

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

    1994-09-01

    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.

  4. Anti-tumor activity of splice-switching oligonucleotides

    OpenAIRE

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

    2010-01-01

    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...

  5. Faster exon assembly by sparse spliced alignment

    CERN Document Server

    Tiskin, Alexander

    2007-01-01

    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}.

  6. Protein splicing and its evolution in eukaryotes

    Directory of Open Access Journals (Sweden)

    Starokadomskyy P. L.

    2010-02-01

    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. HOLLYWOOD: a comparative relational database of alternative splicing.

    Science.gov (United States)

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

    2006-01-01

    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 http://hollywood.mit.edu.

  8. Electric Vehicle Preparedness Task 3: Detailed Assessment of Target Electrification Vehicles at Joint Base Lewis McChord Utilization

    Energy Technology Data Exchange (ETDEWEB)

    Schey, Stephen [Idaho National Lab. (INL), Idaho Falls, ID (United States); Francfort, Jim [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2014-08-01

    Task 2 involved identifying daily operational characteristics of select vehicles and initiating data logging of vehicle movements in order to characterize the vehicle’s mission. Individual observations of these selected vehicles provide the basis for recommendations related to PEV adoption and whether a battery electric vehicle (BEV) or plug-in hybrid electric vehicle (PHEV) (collectively PEVs) can fulfill the mission requirements and provides observations related to placement of PEV charging infrastructure. This report provides the results of the data analysis and observations related to the replacement of current vehicles with PEVs. This fulfills part of the Task 3 requirements. Task 3 also includes an assessment of charging infrastructure required to support this replacement. That is the subject of a separate report.

  9. Alcoholism and Alternative Splicing of Candidate Genes

    OpenAIRE

    Toshikazu Sasabe; Shoichi Ishiura

    2010-01-01

    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. Eddy current quality control of soldered current-carrying busbar splices of superconducting magnets

    CERN Document Server

    Kogan, L; Savary, F; Principe, R; Datskov, V; Rozenfel'd, E; Khudjakov, B

    2015-01-01

    The eddy current technique associated with a U-shaped transducer is studied for the quality control of soldered joints between superconducting busbars ('splices'). Two other quality control techniques, based on X-rays and direct measurement of the electrical resistance, are also studied for comparison. A comparative analysis of the advantages and disadvantages of these three methods in relation to the quality control of soldered superconducting busbar cables enclosed in copper shells is used for benchmarking. The results of inspections with the U-shaped eddy current transducer carried out on several sample joints presenting different types of soldering defects show the potential of this type of nondestructive (ND) quality control technique.

  11. Targeting RNA-splicing for SMA treatment.

    Science.gov (United States)

    Zhou, Jianhua; Zheng, Xuexiu; Shen, Haihong

    2012-03-01

    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. Effect of guide vanes on the performance of a variable chord self-rectifying air turbine

    Science.gov (United States)

    Govardhan, M.; Dhanasekaran, T. S.

    1998-12-01

    Wells turbine is a self rectifying air flow turbine capable of converting pneumatic power of the periodically reversing air stream in Oscillating Water Column into mechanical energy. One of the principal reasons for the low efficiency of the Wells turbine is its lower tangential force compared to its axial force. Guide vanes before and after the rotor suggest a means to improve the tangential force, hence its efficiency. Experimental investigations are carried out on the Wells turbine with a variable chord (VACR) blade rotor fitted with inlet and outlet guide vanes to understand the aerodynamics especially improvement in efficiency and starting characteristics. Numerical simulation has been made to clarify the unsteady characteristics of the turbine with guide vanes. Studies are done at various flow coefficients covering the entire range of flow coefficients over which the turbine is operable. The efficiency, starting characteristics of the Wells turbine has improved when compared with the turbine without guide vanes.

  13. PCNA--a cell proliferation marker in vocal chord cancer. Part I: Premalignant laryngeal lesions.

    Science.gov (United States)

    Pignataro, L D; Broich, G; Lavezzi, A M; Biondo, B; Ottaviani, F

    1995-01-01

    Laryngeal hyperkeratotic lesions can progress to fully developed malignant carcinoma in some cases. These premalignant lesions are proliferative disorders whose potential for further tumour progression is perhaps difficult to assess by mere histology. Immunostaining with PCNA, a protein correlated with cell proliferation, has been used to study tissue behavior in 30 cases of premalignant laryngeal vocal chord lesions treated by epithelial stripping in microlaryngoscopy, 15 of whom had no progression and 15 had recurrence and final development of full malignancy. The results showed a statistically significantly higher PCNA-index in the cases which underwent further tumour progression towards malignancy. PCNA testing may thus be suggested as a marker for tumour progression potential and help in determining clinical treatment choices.

  14. Selection of Twist and Chord Distribution of Horizontal Axis Wind Turbine in Low Wind Conditions

    Science.gov (United States)

    Purusothaman, M.; Valarmathi, T. N.; Praneeth Reddy, S.

    2016-09-01

    India has a vast source of renewable energy sector, in that wind energy contributes a major role. The required source of wind energy in India cannot be able to attain maximum generation due to the operation wind turbine under European atmospheric condition. There is a need to optimize blade profiles which should be suited for low wind condition (India) that leads to increase in coefficient of performance. The present works varying of blade profiles taken in root, mid and tip section of blades are evaluated. According to properties of blade element momentum theory (BEMT) and computational work are developed for getting power curves for varying parameters such as tip speed ratio, lift and drag coefficient and main parameters like chord and twist distribution.

  15. Effect of Guide Vanes on the Performance of a Variable Chord Self—Rectifying Air Turbine

    Institute of Scientific and Technical Information of China (English)

    M.Govardhan; T.S.Dhanasekaran

    1998-01-01

    Wells turbine is a self rectifying air flow turbine capable of converting pneumatic power of the periodically reversing air stream in Oscillating Water Column into mechanical energy,One of the principal reasons for the low effciency of the Wells turbine is its lower tangential force compared to its axial force.Guide vanes before and after the rotor suggest a means to improve the tangential force,hence its efficiency .Experimental investigations are carried out on the Wells turbine with a varible chord (VACR) blade rotor fitted with inlet and outlet guide vanes to understand the aerodynamics especially improvement in efficiency and starting characteristics,Numerical simulaton has been made to clarify the unsteady characteristics of the turbine with guide vanes.Studies are done at various flow coefficients covering the entire range of flow coefficients over which the turbine is operable,The efficiency,Starting characteristics of the Wells turbine has improved when compared with the turbine without guide vanes.

  16. A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection.

    Science.gov (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

    2014-02-10

    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 (http://www.bioinf.uni-leipzig.de/Software/segemehl/).

  17. RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

    Science.gov (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

    2015-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Claudia Tammaro

    2014-07-01

    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.

  19. Vitamin D and alternative splicing of RNA.

    Science.gov (United States)

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

    2015-04-01

    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'.

  20. Differential splicing using whole-transcript microarrays

    Directory of Open Access Journals (Sweden)

    Robinson Mark D

    2009-05-01

    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.

  1. Existence of orthogonal geodesic chords on Riemannian manifolds with concave boundary and homeomorphic to the N-dimensional disk

    CERN Document Server

    Giambo', R; Piccione, P

    2010-01-01

    In this paper we give a proof of the existence of an orthogonal geodesic chord on a Riemannian manifold homeomorphic to a closed disk and with concave boundary. This kind of study is motivated by the link of the multiplicity problem with the famous Seifert conjecture (formulated in 1948) about multiple brake orbits for a class of Hamiltonian systems at a fixed energy level.

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

    Directory of Open Access Journals (Sweden)

    Elela Sherif

    2006-01-01

    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. Splice Resistance Measurements in the LHC Main Superconducting Magnet Circuits by the New Quench Protection System

    CERN Document Server

    Charifoulline, Z; Denz, R; Siemko, A; Steckert, J

    2012-01-01

    The interconnections between the LHC main magnets are made of soldered joints (splices) of two superconducting cables stabilized by a copper bus-bar. After the 2008 LHC incident, caused by a defective interconnection, a new layer of high resolution magnet circuit quench protection (nQPS) has been developed and integrated with the existing systems. It allowed mapping of the resistances of all superconducting splices during the 2009 commissioning campaign. Since April 2010, when the LHC was successfully restarted at 3.5 TeV, every bus bar interconnection is constantly monitored by the nQPS electronics. The acquired data are saved to the LHC Logging Database. The paper will briefly describe the data analysis method and will present the results from the two years of resistance measurements. Although no splice was found with resistance higher than 3.3 n and no significant degradation in time was observed so far, the monitoring of splices will stay active till the end of LHC 4 TeV run. The detected outliers wil...

  4. Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging.

    Science.gov (United States)

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

    2016-04-01

    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.

  5. Nuclearly encoded splicing factors implicated in RNA splicing in higher plant organelles.

    Science.gov (United States)

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

    2010-07-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Daniela Eckert

    2016-01-01

    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.

  7. Splicing variants of porcine synphilin-1

    DEFF Research Database (Denmark)

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

    2015-01-01

    %) 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....

  8. Altered PLP1 splicing causes hypomyelination of early myelinating structures

    DEFF Research Database (Denmark)

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

    2015-01-01

    : 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...

  9. A study of alternative splicing in the pig

    DEFF Research Database (Denmark)

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

    2010-01-01

    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...

  10. Regulation of mammalian pre-mRNA splicing

    Institute of Scientific and Technical Information of China (English)

    HUI JingYi

    2009-01-01

    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.

  11. Regulation of mammalian pre-mRNA splicing

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    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.

  12. Widespread evolutionary conservation of alternatively spliced exons in caenorhabditis

    DEFF Research Database (Denmark)

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

    2007-01-01

    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...

  13. Timber joints under long-term loading

    DEFF Research Database (Denmark)

    Feldborg, T.; Johansen, M.

    This report describes tests and results from stiffness and strength testing of splice joints under long-term loading. During two years of loading the spicimens were exposed to cyclically changing relative humidity. After the loading period the specimens were short-term tested. The connectors were...... integral nail-plates and nailed steel and plywood gussets. The report is intended for designers and researchers in timber engineering....

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

    OpenAIRE

    Bauman, John A; Kole, Ryszard

    2011-01-01

    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...

  15. SPA: a probabilistic algorithm for spliced alignment.

    Directory of Open Access Journals (Sweden)

    Erik van Nimwegen

    2006-04-01

    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

  16. Monte Carlo neutral particle transport through a binary stochastic mixture using chord length sampling

    Science.gov (United States)

    Donovan, Timothy J.

    A Monte Carlo algorithm is developed to estimate the ensemble-averaged behavior of neutral particles within a binary stochastic mixture. A special case stochastic mixture is examined, in which non-overlapping spheres of constant radius are uniformly mixed in a matrix material. Spheres are chosen to represent the stochastic volumes due to their geometric simplicity and because spheres are a common approximation to a large number of applications. The boundaries of the mixture are impenetrable, meaning that spheres in the stochastic mixture cannot be assumed to overlap the mixture boundaries. The algorithm employs a method called Limited Chord Length Sampling (LCLS). While in the matrix material, LCLS uses chord-length sampling to sample the distance to the next stochastic interface. After a surface crossing into a stochastic sphere, transport is treated explicitly until the particle exits or is killed. This capability eliminates the need to explicitly model a representation of the random geometry of the mixture. The algorithm is first proposed and tested against benchmark results for a two dimensional, fixed source model using stand-alone Monte Carlo codes. The algorithm is then implemented and tested in a test version of the Los Alamos M&barbelow;onte C&barbelow;arlo ṉ-p&barbelow;article Code MCNP. This prototype MCNP version has the capability to calculate LCLS results for both fixed source and multiplied source (i.e., eigenvalue) problems. Problems analyzed with MCNP range from simple binary mixtures, designed to test LCLS over a range of optical thicknesses, to a detailed High Temperature Gas Reactor fuel element, which tests the value of LCLS in a current problem of practical significance. Comparisons of LCLS and benchmark results include both accuracy and efficiency comparisons. To ensure conservative efficiency comparisons, the statistical basis for the benchmark technique is derived and a formal method for optimizing the benchmark calculations is developed

  17. 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;

    2007-01-01

    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...

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    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...

  19. 46 CFR 111.60-19 - Cable splices.

    Science.gov (United States)

    2010-10-01

    ... 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...

  20. 30 CFR 75.603 - Temporary splice of trailing cable.

    Science.gov (United States)

    2010-07-01

    ... 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...

  1. Multi-chord fiber-coupled interferometry of supersonic plasma jets and comparisons with synthetic data

    CERN Document Server

    Merritt, Elizabeth C; Gilmore, Mark A; Thoma, Carsten; Loverich, John; Hsu, Scott C

    2012-01-01

    A multi-chord fiber-coupled interferometer [Merritt et al., Rev. Sci. Instrum. 83, 033506 (2012)] is being used to make time-resolved density measurements of supersonic argon plasma jets on the Plasma Liner Experiment [Hsu et al., Bull. Amer. Phys. Soc. 56, 307 (2011)]. The long coherence length of the laser (>10 m) allows signal and reference path lengths to be mismatched by many meters without signal degradation, making for a greatly simplified optical layout. Measured interferometry phase shifts are consistent with a partially ionized plasma in which an initially positive phase shift becomes negative when the ionization fraction drops below a certain threshold. In this case, both free electrons and bound electrons in ions and neutral atoms contribute to the index of refraction. This paper illustrates how the interferometry data, aided by numerical modeling, are used to derive total jet density, jet propagation velocity (~15-50 km/s), jet length (~20-100 cm), and 3D expansion.

  2. Spatial organization of EEG coherence during listening to consonant and dissonant chords.

    Science.gov (United States)

    Passynkova, Natalia; Neubauer, Heinrich; Scheich, Henning

    2007-01-22

    Theories of harmony state that the contribution of both sensory and cognitive components is important for musical consonance perception. The aims of the present study were to analyze (a) functional intra- and inter-hemispheric connectivity associated with listening to consonant and dissonant chords using EEG coherence method; (b) relationships between affective responsiveness, sensory aspects of perceived consonance and associated brain connectivity. We identified two lines of inter-hemispheric connectivity in the theta band; one localized anterior being sensitive to consonance and one localized posterior sensitive to dissonance. Stronger right intra-hemispheric connectivity for consonance than dissonance in the theta band was associated with higher pleasantness ratings. The relationship between sensory aspects of perceived consonance and left intra-hemispheric connectivity found in theta-2 was interpreted as processing of vertical harmony without emotional involvement. The stronger connectivity along the axis "left anterior-right posterior" for dissonance than consonance in the alpha-1 band is discussed as a correlate of novelty processing. By introducing a "auditory object dissociation" hypothesis we suggest to extend the present concept of harmony perception. We believe that "auditory object dissociation" is a component of "sensory dissonance."

  3. A Chord-based resource scheduling approach in drug discovery grid

    Institute of Scientific and Technical Information of China (English)

    Chen Shudong; Zhang Wenju; Zhang Jun; Ma Fanyuan; Shen Jianhua

    2007-01-01

    This paper presents a resource scheduling approach in grid computing environment. Using P2P technology, this novel approach call schedule dynamic grid computing resources efficiently. Grid computing resources in different domains are organized into a structured P2P overlay network. Available resource information is published in type of grid services. Task requests for computational resources are also presented aS grid services. Problem of resources scheduling is translated into services discovery. Different from central scheduling approaches that collect available resources information, this Chord-based approach forwards task requests in the overlay network and discovers satisfied resources for these tasks. Using this approach, the computational resources of a grid system can be scheduled dynamically according to the real-time workload on each peer. Furthermore, the application of this approach is introduced into DDG, a grid system for drug discovery and design, to evaluate the performance. Experimental results show that computational resources of a grid system can be managed efficiently, and the system can hold a perfect load balance state and robustness.

  4. Joint ventures

    DEFF Research Database (Denmark)

    Sørensen, Karsten Engsig

    Afhandlingen analysere de konkurrenceretlige og selskabsretlige regler som er bestemmende for hvordan et joint venture samarbejde er struktureret......Afhandlingen analysere de konkurrenceretlige og selskabsretlige regler som er bestemmende for hvordan et joint venture samarbejde er struktureret...

  5. Joint swelling

    Science.gov (United States)

    ... chap 275. Raftery AT, Lim E, Ostor AJK. Joint disorders. In: Raftery AT, Lim E, Ostor AJK, eds. ... A.M. Editorial team. Related MedlinePlus Health Topics Joint Disorders Browse the Encyclopedia A.D.A.M., Inc. ...

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

    DEFF Research Database (Denmark)

    Honoré, B

    2000-01-01

    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...

  7. 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.

    2006-01-01

    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

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

    Directory of Open Access Journals (Sweden)

    Takahashi Aya

    2009-08-01

    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

  9. Capillary Electrophoresis Analysis of Conventional Splicing Assays

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...

  10. Characterization of trans-splicing in Euglenoids.

    Science.gov (United States)

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

    2000-06-01

    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.

  11. Alternative-splicing-mediated gene expression

    Science.gov (United States)

    Wang, Qianliang; Zhou, Tianshou

    2014-01-01

    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.

  12. Joint ventures

    NARCIS (Netherlands)

    M.N. Hoogendoorn (Martin)

    2009-01-01

    textabstractEen veel voorkomende wijze van samenwerking tussen ondernemingen is het uitvoeren van activiteiten in de vorm van een joint venture. Een joint venture is bijna altijd een afzonderlijke juridische entiteit. De partners in de joint venture voeren gezamenlijk de zeggenschap uit. In internat

  13. Alternative splicing: a pivotal step between eukaryotic transcription and translation.

    Science.gov (United States)

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

    2013-03-01

    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.

  14. Expression and purification of splicing proteins from mammalian cells.

    Science.gov (United States)

    Allemand, Eric; Hastings, Michelle L

    2014-01-01

    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.

  15. Approaches to link RNA secondary structures with splicing regulation

    DEFF Research Database (Denmark)

    Plass, Mireya; Eyras, Eduardo

    2014-01-01

    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...

  16. A chord error conforming tool path B-spline fitting method for NC machining based on energy minimization and LSPIA

    Directory of Open Access Journals (Sweden)

    Shanshan He

    2015-10-01

    Full Text Available Piecewise linear (G01-based tool paths generated by CAM systems lack G1 and G2 continuity. The discontinuity causes vibration and unnecessary hesitation during machining. To ensure efficient high-speed machining, a method to improve the continuity of the tool paths is required, such as B-spline fitting that approximates G01 paths with B-spline curves. Conventional B-spline fitting approaches cannot be directly used for tool path B-spline fitting, because they have shortages such as numerical instability, lack of chord error constraint, and lack of assurance of a usable result. Progressive and Iterative Approximation for Least Squares (LSPIA is an efficient method for data fitting that solves the numerical instability problem. However, it does not consider chord errors and needs more work to ensure ironclad results for commercial applications. In this paper, we use LSPIA method incorporating Energy term (ELSPIA to avoid the numerical instability, and lower chord errors by using stretching energy term. We implement several algorithm improvements, including (1 an improved technique for initial control point determination over Dominant Point Method, (2 an algorithm that updates foot point parameters as needed, (3 analysis of the degrees of freedom of control points to insert new control points only when needed, (4 chord error refinement using a similar ELSPIA method with the above enhancements. The proposed approach can generate a shape-preserving B-spline curve. Experiments with data analysis and machining tests are presented for verification of quality and efficiency. Comparisons with other known solutions are included to evaluate the worthiness of the proposed solution.

  17. SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing.

    Science.gov (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

    2015-07-13

    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: https://github.com/pulyakhina/splicing_analysis_pipeline. The example data can be found at: https://barmsijs.lumc.nl/HG/irina/example_data.tar.gz.

  18. Deregulation of splicing factors and breast cancer development.

    Science.gov (United States)

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

    2015-10-01

    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.

  19. Results from the 2014 November 15th multi-chord stellar occultation by the TNO (229762) 2007 UK$_{126}$

    CERN Document Server

    Benedetti-Rossi, Gustavo; Buie, Marc W; Ortiz, Jose L; Vieira-Martins, Roberto; Keller, John M; Braga-Ribas, Felipe; Camargo, Julio I B; Assafin, Marcelo; Morales, Nicolas; Duffard, Rene; Dias-Oliveira, Alex; Santos-Sanz, Pablo; Desmars, Josselin; Gomes-Junior, Altair R; Leiva, Rodrigo; Bardecker, Jerry; Bean, Jim K Jr; Olsen, Aart M; Ruby, Daniel W; Sumner, Red; Thirouin, Audrey; Gomez-Munoz, Marco A; Gutierrez, Leonel; Wasserman, Larry; Charbonneau, David; Irwin, Jonathan; Levine, Stephen; Skiff, Brian

    2016-01-01

    We present results derived from the first multi-chord stellar occultation by the trans-Neptunian object (229762) 2007 UK$_{126}$, observed on 2014 November 15. The event was observed by the Research and Education Collaborative Occultation Network (RECON) project and International Occultation Timing Association (IOTA) collaborators throughout the United States. Use of two different data analysis methods obtain a satisfactory fit to seven chords, yelding an elliptical fit to the chords with an equatorial radius of $R=338_{-10} ^{+15}$ km and equivalent radius of $R_{eq}=319_{-7} ^{+14}$ km. A circular fit also gives a radius of $R=324_{-23} ^{+30}$ km. Assuming that the object is a Maclaurin spheroid with indeterminate aspect angle, and using two published absolute magnitudes for the body, we derive possible ranges for geometric albedo between $p_{V}=0.159_{-0.013} ^{+0.007}$ and $p_{R}=0.189_{-0.015}^{+0.009}$, and for the body oblateness between $\\epsilon=0.105_{-0.040} ^{+0.050}$ and $\\epsilon=0.118_{-0.048}...

  20. Impact of Spherical Inclusion Mean Chord Length and Radius Distribution on Three-Dimensional Binary Stochastic Medium Particle Transport

    Energy Technology Data Exchange (ETDEWEB)

    Brantley, P S; Martos, J N

    2011-03-02

    We describe a parallel benchmark procedure and numerical results for a three-dimensional binary stochastic medium particle transport benchmark problem. The binary stochastic medium is composed of optically thick spherical inclusions distributed in an optically thin background matrix material. We investigate three sphere mean chord lengths, three distributions for the sphere radii (constant, uniform, and exponential), and six sphere volume fractions ranging from 0.05 to 0.3. For each sampled independent material realization, we solve the associated transport problem using the Mercury Monte Carlo particle transport code. We compare the ensemble-averaged benchmark fiducial tallies of reflection from and transmission through the spatial domain as well as absorption in the spherical inclusion and background matrix materials. For the parameter values investigated, we find a significant dependence of the ensemble-averaged fiducial tallies on both sphere mean chord length and sphere volume fraction, with the most dramatic variation occurring for the transmission through the spatial domain. We find a weaker dependence of most benchmark tally quantities on the distribution describing the sphere radii, provided the sphere mean chord length used is the same in the different distributions. The exponential distribution produces larger differences from the constant distribution than the uniform distribution produces. The transmission through the spatial domain does exhibit a significant variation when an exponential radius distribution is used.

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

    Science.gov (United States)

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

    2014-09-01

    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. 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.

  3. The influence of Argonaute proteins on alternative RNA splicing.

    Science.gov (United States)

    Batsché, Eric; Ameyar-Zazoua, Maya

    2015-01-01

    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.

  4. Axial compression physical testing of traditional and bird beak SHS T-joints

    Institute of Scientific and Technical Information of China (English)

    陈誉; 王江

    2015-01-01

    The static tests of nine traditional and bird beak square hollow structure (SHS) T-joints with differentβ values and connection types under axial compression at brace end were carried out. Experimental test schemes, failure modes of specimens, jack load−vertical displacement curves, jack load−deformation of chord and strain intensity distribution curves of joints were presented. The effects ofβ and connection types on axial compression property of joints were studied. The results show that the ultimate axial compression capacity of common bird beak SHS T-joints and diamond bird beak SHS T-joints is larger than that of traditional SHS T-joint specimens with big values ofβ. The ultimate axial compression capacity of diamond bird beak SHS T-joints is larger than that of common bird beak SHS T-joints. Asβ increases, the increase of the ultimate axial compression capacity of diamond bird beak SHS T-joints over that of common bird beak joints grows. The ultimate axial compression capacity and the initial axial stiffness of all kinds of joints increase asβincreases, and the initial axial stiffness of the diamond bird beak SHS T-joints is the largest. The ductilities of common bird beak and diamond bird beak SHS T-joints increase asβ increases, but the ductility of the traditional SHS T-joints decreases asβ increases.

  5. Determining Points of a Circular Region Reachable by Joints of a Robot Arm.

    Science.gov (United States)

    1982-10-01

    old leading; WoA 0 figure 12. The tInal segment contains sore than one link, Natation is the same as for Figure 10. Proo: Since A does not lie on a...in con taurations Ub and Ilc.) iszt, suppose that A is not the only joint between A and A. on Co so that for sea is Oci<j, LAiAjJ is a chord of C

  6. Resolving deconvolution ambiguity in gene alternative splicing

    Directory of Open Access Journals (Sweden)

    Hubbell Earl

    2009-08-01

    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.

  7. Splicing variants of porcine synphilin-1

    Directory of Open Access Journals (Sweden)

    Knud Larsen

    2015-09-01

    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.

  8. Retrieval of missing spliced leader in dinoflagellates.

    Science.gov (United States)

    Zhang, Huan; Lin, Senjie

    2009-01-01

    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.

  9. 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

    2008-01-01

    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.

  10. The doublesex splicing enhancer components Tra2 and Rbp1 also repress splicing through an intronic silencer.

    Science.gov (United States)

    Qi, Junlin; Su, Shihuang; Mattox, William

    2007-01-01

    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.

  11. Half pint/Puf68 is required for negative regulation of splicing by the SR splicing factor Transformer2.

    Science.gov (United States)

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

    2013-08-01

    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.

  12. 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

    2009-01-01

    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...

  13. A multi-agent system simulating human splice site recognition.

    Science.gov (United States)

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

    1999-06-15

    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.

  14. Splicing modulation therapy in the treatment of genetic diseases

    Directory of Open Access Journals (Sweden)

    Arechavala-Gomeza V

    2014-12-01

    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

  15. Accumulation of GC donor splice signals in mammals

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2008-07-01

    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.

  16. Joint Interdiction

    Science.gov (United States)

    2016-09-09

    exercise of authority by combatant commanders and other joint force commanders (JFCs), and prescribes joint doctrine for operations and training. It...interdiction requirements and dependable, interoperable, and secure communications architecture to exercise control. The JFC exercises C2 through...moving across open desert terrain were more vulnerable to interdiction by coalition airpower than dispersed Serbian forces that benefited from trees

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

    Directory of Open Access Journals (Sweden)

    Jeremy Hull

    2007-06-01

    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.

  18. Pre-mRNA splicing in disease and therapeutics

    OpenAIRE

    Singh, Ravi K; Cooper, Thomas A.

    2012-01-01

    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...

  19. Embracing the complexity of pre-mRNA splicing

    Institute of Scientific and Technical Information of China (English)

    Peter J Shepard; Klemens J Hertel

    2010-01-01

    @@ 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.

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

    Directory of Open Access Journals (Sweden)

    Gene W Yeo

    2007-05-01

    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.

  1. Splice-switching antisense oligonucleotides as therapeutic drugs

    OpenAIRE

    Havens, Mallory A.; Hastings, Michelle L.

    2016-01-01

    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.

    Science.gov (United States)

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

    2016-02-01

    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.

    Science.gov (United States)

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

    2016-03-10

    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. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Thomas Julie

    2010-02-01

    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 http://combi.cs.colostate.edu/as/chlamy. Conclusions The extent of AS in Chlamydomonas that we observed is much

  5. Viral interactions with components of the splicing machinery.

    Science.gov (United States)

    Meyer, F

    2016-01-01

    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.

  6. DNA splice site sequences clustering method for conservativeness analysis

    Institute of Scientific and Technical Information of China (English)

    Quanwei Zhang; Qinke Peng; Tao Xu

    2009-01-01

    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.

  7. Burnup calculation by the method of first-flight collision probabilities using average chords prior to the first collision

    Science.gov (United States)

    Karpushkin, T. Yu.

    2012-12-01

    A technique to calculate the burnup of materials of cells and fuel assemblies using the matrices of first-flight neutron collision probabilities rebuilt at a given burnup step is presented. A method to rebuild and correct first collision probability matrices using average chords prior to the first neutron collision, which are calculated with the help of geometric modules of constructed stochastic neutron trajectories, is described. Results of calculation of the infinite multiplication factor for elementary cells with a modified material composition compared to the reference one as well as calculation of material burnup in the cells and fuel assemblies of a VVER-1000 are presented.

  8. Progressive Damage Analysis of Bonded Composite Joints

    Science.gov (United States)

    Leone, Frank A., Jr.; Girolamo, Donato; Davila, Carlos G.

    2012-01-01

    The present work is related to the development and application of progressive damage modeling techniques to bonded joint technology. The joint designs studied in this work include a conventional composite splice joint and a NASA-patented durable redundant joint. Both designs involve honeycomb sandwich structures with carbon/epoxy facesheets joined using adhesively bonded doublers.Progressive damage modeling allows for the prediction of the initiation and evolution of damage within a structure. For structures that include multiple material systems, such as the joint designs under consideration, the number of potential failure mechanisms that must be accounted for drastically increases the complexity of the analyses. Potential failure mechanisms include fiber fracture, intraply matrix cracking, delamination, core crushing, adhesive failure, and their interactions. The bonded joints were modeled using highly parametric, explicitly solved finite element models, with damage modeling implemented via custom user-written subroutines. Each ply was discretely meshed using three-dimensional solid elements. Layers of cohesive elements were included between each ply to account for the possibility of delaminations and were used to model the adhesive layers forming the joint. Good correlation with experimental results was achieved both in terms of load-displacement history and the predicted failure mechanism(s).

  9. [The cricoarytenoid joint in chronic polyarthritis].

    Science.gov (United States)

    Bolten, W

    1991-01-01

    The cricoarytenoid joints are frequently asymptomatically involved in rheumatoid arthritis with a severe course. At least the symptoms recede into the background compared with the other complaints. Signs of obstructive laryngeal changes are often falsely interpreted. Dangerous respiratory tract obstructions may be initiated by bacterial infections of the larynx and mechanical laryngeal changes or by the acute exacerbation of the arthritis. The clinical diagnosis of CA-arthritis is supplemented by laryngoscopic, radiologic and computertomographic techniques. Simple clinical examination methods only are relevant for routine or screening tests. The differential diagnosis requires consideration of neurogenic, traumatic, infectious or neoplastic and psychosomatic diseases. Corticosteroids and non-steroidal antiinflammatory drugs are of doubtful value in treatment. Physical conservative methods are usually sufficiently effective for prophylaxis and control of symptoms. In an emergency tracheotomy can be life-saving. Arytenoidectomy or mobilisation and lateral fixation of the vocal chord are considered definitive treatment.

  10. Identification of cis-acting elements and splicing factors involved in the regulation of BIM Pre-mRNA splicing.

    Science.gov (United States)

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

    2014-01-01

    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.

  11. 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

    2015-07-01

    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.

  12. 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.

    2010-01-01

    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

  13. A Broad Set of Chromatin Factors Influences Splicing

    Science.gov (United States)

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

    2016-01-01

    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

  14. Quantitative regulation of alternative splicing in evolution and development

    DEFF Research Database (Denmark)

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

    2009-01-01

    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....

  15. 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)

    2008-01-01

    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

  16. Insights into alternative splicing of sarcomeric genes in the heart.

    Science.gov (United States)

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

    2015-04-01

    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.

  17. 30 CFR 18.43 - Explosion-proof splice boxes.

    Science.gov (United States)

    2010-07-01

    ... 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...

  18. Pre-mRNA splicing in disease and therapeutics.

    Science.gov (United States)

    Singh, Ravi K; Cooper, Thomas A

    2012-08-01

    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.

  19. Splice Site Mutations in the ATP7A Gene

    DEFF Research Database (Denmark)

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

    2011-01-01

    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...

  20. [Statistical analysis of DNA sequences nearby splicing sites].

    Science.gov (United States)

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

    2008-01-01

    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.

  1. Comparative Analysis of Splice Site Regions by Information Content

    Institute of Scientific and Technical Information of China (English)

    T. Shashi Rekha; Chanchal K. Mitra

    2006-01-01

    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.

  2. Connecting real-time data to algorithms and databases: EarthCube's Cloud-Hosted Real-time Data Services for the Geosciences (CHORDS)

    Science.gov (United States)

    Daniels, M. D.; Graves, S. J.; Kerkez, B.; Chandrasekar, V.; Vernon, F.; Martin, C. L.; Maskey, M.; Keiser, K.; Dye, M. J.

    2015-12-01

    The Cloud-Hosted Real-time Data Services for the Geosciences (CHORDS) project was funded under the National Science Foundation's EarthCube initiative. CHORDS addresses the ever-increasing importance of real-time scientific data in the geosciences, particularly in mission critical scenarios, where informed decisions must be made rapidly. Access to constant streams of real-time data also allow many new transient phenomena in space-time to be observed, however, much of these streaming data are either completely inaccessible or only available to proprietary in-house tools or displays. Small research teams do not have the resources to develop tools for the broad dissemination of their unique real-time data and require an easy to use, scalable, cloud-based solution to facilitate this access. CHORDS will make these diverse streams of real-time data available to the broader geosciences community. This talk will highlight a recently developed CHORDS portal tools and processing systems which address some of the gaps in handling real-time data, particularly in the provisioning of data from the "long-tail" scientific community through a simple interface that is deployed in the cloud, is scalable and is able to be customized by research teams. A running portal, with operational data feeds from across the nation, will be presented. The processing within the CHORDS system will expose these real-time streams via standard services from the Open Geospatial Consortium (OGC) in a way that is simple and transparent to the data provider, while maximizing the usage of these investments. The ingestion of high velocity, high volume and diverse data has allowed the project to explore a NoSQL database implementation. Broad use of the CHORDS framework by geoscientists will help to facilitate adaptive experimentation, model assimilation and real-time hypothesis testing.

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

    KAUST Repository

    Alshareef, Sahar

    2017-03-27

    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.

  4. A molecular inversion probe assay for detecting alternative splicing

    Directory of Open Access Journals (Sweden)

    Palm Curtis

    2010-12-01

    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

    2006-11-01

    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

    2013-10-01

    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. Noise generated by impingement of turbulent flow on airfoils of varied chord, cylinders, and other flow obstructions

    Science.gov (United States)

    Olsen, W. A.

    1976-01-01

    Noise spectra were measured in three dimensions for several surfaces immersed in turbulent flow from a jet and over a range of flow conditions. The data are free field and were corrected to remove the small contributions of jet noise, atmospheric attenuation and feedback tones. These broadband data were compared with the results of available theories which are only strictly applicable to simple geometries over a limited range of conditions. The available theories proved to be accurate over the range of flow, chord length, thickness, angle of attack, and surface geometries defined by the experiments. These results apply to the noise generated by fixed surfaces in engine passages, the lifting surfaces of aircraft and also to fan noise.

  8. Integration of in situ Imaging and Chord Length Distribution Measurements for Estimation of Particle Size and Shape

    CERN Document Server

    Agimelen, Okpeafoh S; McGinty, John; Tachtatzis, Christos; Dziewierz, Jerzy; Haley, Ian; Sefcik, Jan; Mulholland, Anthony J

    2015-01-01

    Efficient processing of particulate products across various manufacturing steps requires that particles possess desired attributes such as size and shape. Controlling the particle production process to obtain required attributes will be greatly facilitated using robust algorithms providing the size and shape information of the particles from in situ measurements. However, obtaining particle size and shape information in situ during manufacturing has been a big challenge. This is because the problem of estimating particle size and shape (aspect ratio) from signals provided by in-line measuring tools is often ill posed, and therefore it calls for appropriate constraints to be imposed on the problem. One way to constrain uncertainty in estimation of particle size and shape from in-line measurements is to combine data from different measurements such as chord length distribution (CLD) and imaging. This paper presents two different methods for combining imaging and CLD data obtained with in-line tools in order to ...

  9. Joint purpose?

    DEFF Research Database (Denmark)

    Pristed Nielsen, Helene

    2013-01-01

    Starting from Crenshaw´s point that antiracism often fails to interrogate patriarchy and that feminism often reproduces racist practices (1991: 1252), this paper asks: What are the theoretical reasons for believing that feminism and anti-racism can be regarded as fighting for the joint purpose of...

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

    Directory of Open Access Journals (Sweden)

    Furuichi Teiichi

    2007-04-01

    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

  11. The ultimate strength of doubler plate reinforced Y-joints under compression loading

    Institute of Scientific and Technical Information of China (English)

    FENQ Qi; TAN Jia-hua

    2005-01-01

    It is common practice in the offshore industry to solve the punching shear problem due to compression by using doubler plate. The finite-element method is a useful tool for studying this problem. The aim of this paper is to study the static strength of doubler plate reinforced Y-joints subjected to compression loading. The finite-element method is adopted in numerical parametric studies. The individual influences of the geometric parameters βand τd (doubler plate to chord wall thickness ratio) and ld/d1(dubler plate length to brace diameter ratio) on the ultimate strength are made clear. The results show the size of plate may have important effects on the strength of reinforced joints. It is found that the ultimate strength of Y-joints reinforced with appropriately proportioned doubler plates can be greatly improved nearly up tothree times to un-reinforced Y-joints.

  12. Binding of a candidate splice regulator to a calcitonin-specific splice enhancer regulates calcitonin/CGRP pre-mRNA splicing.

    Science.gov (United States)

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

    2003-01-27

    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.

  13. Designing oligo libraries taking alternative splicing into account

    Science.gov (United States)

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

    2001-06-01

    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. On the use of area-averaged void fraction and local bubble chord length entropies as two-phase flow regime indicators

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez, Leonor; Julia, J.E. [Universitat Jaume I, Departamento de Ingenieria Mecanica y Construccion Campus de Riu Sec, Castellon (Spain); Paranjape, Sidharth; Hibiki, Takashi; Ishii, Mamoru [Purdue University, Nuclear Engineering Department, West Lafayette, IN (United States)

    2010-11-15

    In this work, the use of the area-averaged void fraction and bubble chord length entropies is introduced as flow regime indicators in two-phase flow systems. The entropy provides quantitative information about the disorder in the area-averaged void fraction or bubble chord length distributions. The CPDF (cumulative probability distribution function) of void fractions and bubble chord lengths obtained by means of impedance meters and conductivity probes are used to calculate both entropies. Entropy values for 242 flow conditions in upward two-phase flows in 25.4 and 50.8-mm pipes have been calculated. The measured conditions cover ranges from 0.13 to 5 m/s in the superficial liquid velocity j{sub f} and ranges from 0.01 to 25 m/s in the superficial gas velocity j{sub g}. The physical meaning of both entropies has been interpreted using the visual flow regime map information. The area-averaged void fraction and bubble chord length entropies capability as flow regime indicators have been checked with other statistical parameters and also with different input signals durations. The area-averaged void fraction and the bubble chord length entropies provide better or at least similar results than those obtained with other indicators that include more than one parameter. The entropy is capable to reduce the relevant information of the flow regimes in only one significant and useful parameter. In addition, the entropy computation time is shorter than the majority of the other indicators. The use of one parameter as input also represents faster predictions. (orig.)

  15. 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)

    1998-01-01

    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

  16. The peculiarities of large intron splicing in animals.

    Science.gov (United States)

    Shepard, Samuel; McCreary, Mark; Fedorov, Alexei

    2009-11-16

    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.

  17. Desmin splice variants causing cardiac and skeletal myopathy.

    Science.gov (United States)

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

    2000-11-01

    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.

  18. 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.

  19. 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.

  20. The functional modulation of epigenetic regulators by alternative splicing

    Directory of Open Access Journals (Sweden)

    Martínez-Balbás Marian

    2007-07-01

    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.

  1. 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.

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

    Directory of Open Access Journals (Sweden)

    Zodwa Dlamini

    2015-11-01

    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.

  3. The splicing activator DAZAP1 integrates splicing control into MEK/Erk-regulated cell proliferation and migration

    Science.gov (United States)

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

    2014-01-01

    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.

  4. Biochemical identification of new proteins involved in splicing repression at the Drosophila P-element exonic splicing silencer

    Science.gov (United States)

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

    2015-01-01

    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

  5. Learning the sequence determinants of alternative splicing from millions of random sequences.

    Science.gov (United States)

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

    2015-10-22

    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. Environmental Assessment, Change in C-17 Flight Training Operations at Grant County International Airport, Washington by Joint Base Lewis-McChord

    Science.gov (United States)

    2011-10-01

    No. of Incidents No. of Incidents by Unknown Bird or Bat Bird Species 2010 1 1 -- 2006 13 7 American robin (Turdus migratorius) Song sparrow...urophasianus Threatened Candidate 5 Yellow-billed cuckoo Coccyzus americanus Candidate Candidate 6 Ferruginous hawk Buteo regalis Threatened

  7. Correction of a Cystic Fibrosis Splicing Mutation by Antisense Oligonucleotides.

    Science.gov (United States)

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

    2016-02-01

    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.

  8. Method of predicting Splice Sites based on signal interactions

    Directory of Open Access Journals (Sweden)

    Deogun Jitender S

    2006-04-01

    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.

  9. A polarimeter for JT-60SA: chords layout study with V3FIT for q profile reconstruction

    Science.gov (United States)

    Terranova, David; Boboc, Alexandru; Gil, Christophe; Soare, Sorin; Orsitto, Francesco; Imazawa, Ryota

    2016-10-01

    JT-60SA is the new tokamak device that is being built in Japan under the Broader Approach Satellite Tokamak Programme and the Japanese National Programme [JT-60SA Research Plan, Version 3.3, March 2016, www.jt60sa.org/pdfs/JT-60SA_Res_Plan.pdf] and will operate as a satellite machine for ITER. To provide valuable information for the steady state scenario for ITER and the design of DEMO, a high βN scenario is included in the program, where the real-time control of the q-profile is needed. In this work we present a study of the geometry of the polarimetry chords, derived from a true realistic CAD-driven feasibility study, aiming at an optimization in terms of q-profile reconstruction, using the V3FIT code. Some magnetic and kinetic measurements are considered along with the FIR poloidal polarimeter in order to assess the possibility of estimating q in the core with the required accuracy (around 10%) providing a diagnostic for a continuous measurement useful in high density pulses where MSE measurements would not have adequate time resolution.

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

    Directory of Open Access Journals (Sweden)

    2005-09-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Yuanyuan Xiao

    2005-09-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Tatusova Tatiana

    2008-05-01

    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.

  13. Two new splice variants in porcine PPARGC1A

    Directory of Open Access Journals (Sweden)

    Peelman Luc J

    2008-12-01

    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.

  14. RNA splicing in a new rhabdovirus from Culex mosquitoes.

    Science.gov (United States)

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

    2011-07-01

    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.

  15. Oncogenes and RNA splicing of human tumor viruses.

    Science.gov (United States)

    Ajiro, Masahiko; Zheng, Zhi-Ming

    2014-09-01

    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.

  16. Sec16 alternative splicing dynamically controls COPII transport efficiency.

    Science.gov (United States)

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

    2016-08-05

    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.

  17. Alternative splicing regulates targeting of malate dehydrogenase in Yarrowia lipolytica.

    Science.gov (United States)

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

    2012-06-01

    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.

  18. Genome-wide identification of zero nucleotide recursive splicing in Drosophila.

    Science.gov (United States)

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

    2015-05-21

    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.

  19. Aberrant splicing in maize rough endosperm3 reveals a conserved role for U12 splicing in eukaryotic multicellular development

    Science.gov (United States)

    Barbazuk, W. Brad

    2017-01-01

    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

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

    DEFF Research Database (Denmark)

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

    2005-01-01

    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...

  1. 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.

    2010-01-01

    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

  2. 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;

    2003-01-01

    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....

  3. A combinatorial code for splicing silencing: UAGG and GGGG motifs.

    Directory of Open Access Journals (Sweden)

    Kyoungha Han

    2005-05-01

    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.

  4. Minor class splicing shapes the zebrafish transcriptome during development.

    Science.gov (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

    2014-02-25

    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.

  5. A procedure for identifying homologous alternative splicing events

    Directory of Open Access Journals (Sweden)

    Orozco Modesto

    2007-07-01

    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.

  6. Genome-wide survey of allele-specific splicing in humans

    Directory of Open Access Journals (Sweden)

    Scheffler Konrad

    2008-06-01

    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

  7. Oncogenic Alternative Splicing Switches: Role in Cancer Progression and Prospects for Therapy

    OpenAIRE

    Serena Bonomi; Stefania Gallo; Morena Catillo; Daniela Pignataro; Giuseppe Biamonti; Claudia Ghigna

    2013-01-01

    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 ...

  8. Alt Event Finder: a tool for extracting alternative splicing events from RNA-seq data

    OpenAIRE

    Zhou Ao; Breese Marcus R; Hao Yangyang; Edenberg Howard J; Li Lang; Skaar Todd C; Liu Yunlong

    2012-01-01

    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 ...

  9. Effects of musical experience on different components of MEG responses elicited by sequential piano-tones and chords.

    Science.gov (United States)

    Kuriki, Shinya; Kanda, Satoshi; Hirata, Yoshihiro

    2006-04-12

    Magnetoencephalographic (MEG) studies have revealed enhancement of neural activity of the N1m response of auditory evoked fields in long-term trained musicians, reflecting neuroplastic modification of the representation of the auditory cortex. In contrast, the amplitude of the P2 response of auditory evoked potentials is modified by musical experience, with no alteration of N1. Here, we performed a comprehensive MEG study using stimulation of successive musical-instrument tones to examine how the neural activities of different MEG responses are modified in long-term experienced musicians who commenced musical lessons at ages of approximately 5 years and had continued to practice. The dipole moment of the P2m response occurring at 160-180 ms was significantly enlarged in musicians compared with that in individuals who had not received musical lessons. The enlargement was found for the dipole moment of N1m occurring at 100-120 ms in a restricted condition but not for the moment of P1m at 50-60 ms. Furthermore, the dipole moment of P2m for successive stimuli, normalized by the moment for the first stimulus, was significantly larger for chord tones than single tones and was significantly larger in the musicians than controls. These results suggest that the P2m response is susceptible to be modified by musical training in a period of neural maturation, with a short refractory period of neural activity for the auditory input of composite tones. The P2m activity may be specialized to the processing of multifrequency sounds, such as musical timbre consisting of abundant harmonics.

  10. Application of Generalised sequential crossover of languages to generalised splicing

    CERN Document Server

    Jeganathan, L; Sengupta, Ritabrata

    2009-01-01

    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.

  11. 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

    2002-01-01

    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.

  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

    2004-07-01

    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. Strengthening of defected beam-column joints using CFRP.

    Science.gov (United States)

    Mahmoud, Mohamed H; Afefy, Hamdy M; Kassem, Nesreen M; Fawzy, Tarek M

    2014-01-01

    This paper presents an experimental study for the structural performance of reinforced concrete (RC) exterior beam-column joints rehabilitated using carbon-fiber-reinforced polymer (CFRP). The present experimental program consists of testing 10 half-scale specimens divided into three groups covering three possible defects in addition to an adequately detailed control specimen. The considered defects include the absence of the transverse reinforcement within the joint core, insufficient bond length for the beam main reinforcement and inadequate spliced implanted column on the joint. Three different strengthening schemes were used to rehabilitate the defected beam-column joints including externally bonded CFRP strips and sheets in addition to near surface mounted (NSM) CFRP strips. The failure criteria including ultimate capacity, mode of failure, initial stiffness, ductility and the developed ultimate strain in the reinforcing steel and CFRP were considered and compared for each group for the control and the CFRP-strengthened specimens. The test results showed that the proposed CFRP strengthening configurations represented the best choice for strengthening the first two defects from the viewpoint of the studied failure criteria. On the other hand, the results of the third group showed that strengthening the joint using NSM strip technique enabled the specimen to outperform the structural performance of the control specimen while strengthening the joints using externally bonded CFRP strips and sheets failed to restore the strengthened joints capacity.

  14. Strengthening of defected beam–column joints using CFRP

    Directory of Open Access Journals (Sweden)

    Mohamed H. Mahmoud

    2014-01-01

    Full Text Available This paper presents an experimental study for the structural performance of reinforced concrete (RC exterior beam–column joints rehabilitated using carbon-fiber-reinforced polymer (CFRP. The present experimental program consists of testing 10 half-scale specimens divided into three groups covering three possible defects in addition to an adequately detailed control specimen. The considered defects include the absence of the transverse reinforcement within the joint core, insufficient bond length for the beam main reinforcement and inadequate spliced implanted column on the joint. Three different strengthening schemes were used to rehabilitate the defected beam–column joints including externally bonded CFRP strips and sheets in addition to near surface mounted (NSM CFRP strips. The failure criteria including ultimate capacity, mode of failure, initial stiffness, ductility and the developed ultimate strain in the reinforcing steel and CFRP were considered and compared for each group for the control and the CFRP-strengthened specimens. The test results showed that the proposed CFRP strengthening configurations represented the best choice for strengthening the first two defects from the viewpoint of the studied failure criteria. On the other hand, the results of the third group showed that strengthening the joint using NSM strip technique enabled the specimen to outperform the structural performance of the control specimen while strengthening the joints using externally bonded CFRP strips and sheets failed to restore the strengthened joints capacity.

  15. Strengthening of defected beam–column joints using CFRP

    Science.gov (United States)

    Mahmoud, Mohamed H.; Afefy, Hamdy M.; Kassem, Nesreen M.; Fawzy, Tarek M.

    2013-01-01

    This paper presents an experimental study for the structural performance of reinforced concrete (RC) exterior beam–column joints rehabilitated using carbon-fiber-reinforced polymer (CFRP). The present experimental program consists of testing 10 half-scale specimens divided into three groups covering three possible defects in addition to an adequately detailed control specimen. The considered defects include the absence of the transverse reinforcement within the joint core, insufficient bond length for the beam main reinforcement and inadequate spliced implanted column on the joint. Three different strengthening schemes were used to rehabilitate the defected beam–column joints including externally bonded CFRP strips and sheets in addition to near surface mounted (NSM) CFRP strips. The failure criteria including ultimate capacity, mode of failure, initial stiffness, ductility and the developed ultimate strain in the reinforcing steel and CFRP were considered and compared for each group for the control and the CFRP-strengthened specimens. The test results showed that the proposed CFRP strengthening configurations represented the best choice for strengthening the first two defects from the viewpoint of the studied failure criteria. On the other hand, the results of the third group showed that strengthening the joint using NSM strip technique enabled the specimen to outperform the structural performance of the control specimen while strengthening the joints using externally bonded CFRP strips and sheets failed to restore the strengthened joints capacity. PMID:25685473

  16. Adhesive Characterization and Progressive Damage Analysis of Bonded Composite Joints

    Science.gov (United States)

    Girolamo, Donato; Davila, Carlos G.; Leone, Frank A.; Lin, Shih-Yung

    2014-01-01

    The results of an experimental/numerical campaign aimed to develop progressive damage analysis (PDA) tools for predicting the strength of a composite bonded joint under tensile loads are presented. The PDA is based on continuum damage mechanics (CDM) to account for intralaminar damage, and cohesive laws to account for interlaminar and adhesive damage. The adhesive response is characterized using standard fracture specimens and digital image correlation (DIC). The displacement fields measured by DIC are used to calculate the J-integrals, from which the associated cohesive laws of the structural adhesive can be derived. A finite element model of a sandwich conventional splice joint (CSJ) under tensile loads was developed. The simulations indicate that the model is capable of predicting the interactions of damage modes that lead to the failure of the joint.

  17. 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.

  18. 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.;

    2012-01-01

    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...

  19. 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.

  20. 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;

    2008-01-01

    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...

  1. Reliability of Tubular Joints

    DEFF Research Database (Denmark)

    Sørensen, John Dalsgaard; Thoft-Christensen, Palle

    In this paper the preliminary results obtained by tests on tubular joints are presented. The joints are T-joints and the loading is static. It is the intention in continuation of these tests to perform tests on other types of joints (e.g. Y-joints) and also with dynamic loading. The purpose...... of the test is partly to obtain empirical data for the ultimate load-carrying capacity of tubular T-joints and partly to obtain some experience in performing tests with tubular joints. It is well known that tubular joints are usually designed in offshore engineering on the basis of empirical formulas obtained...

  2. Spacesuit mobility knee joints

    Science.gov (United States)

    Vykukal, H. C. (Inventor)

    1979-01-01

    Pressure suit mobility joints are for use in interconnecting adjacent segments of an hermetically sealed spacesuit in which low torques, low leakage and a high degree of reliability are required. Each of the joints is a special purpose joint characterized by substantially constant volume and low torque characteristics and includes linkages which restrain the joint from longitudinal distension and includes a flexible, substantially impermeable diaphragm of tubular configuration spanning the distance between pivotally supported annuli. The diaphragms of selected joints include rolling convolutions for balancing the joints, while various joints include wedge-shaped sections which enhance the range of motion for the joints.

  3. 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

    2011-06-01

    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

  4. 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.

  5. The Evolutionary Relationship between Alternative Splicing and Gene Duplication

    Science.gov (United States)

    Iñiguez, Luis P.; Hernández, Georgina

    2017-01-01

    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

  6. 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.

  7. 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)

    1997-03-01

    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.

  8. Electromechanical behaviour of REBCO tape lap splices under transverse compressive loading

    CERN Document Server

    Grether, A; Ballarino, A.; Bottura, L.

    2016-01-01

    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.

  9. International joint ventures

    DEFF Research Database (Denmark)

    Sørensen, Karsten Engsig

    2001-01-01

    The article analysis problems connected with corporate joint ventures. Among others the possible conflicts between the joint venture agreement and the statutes of the companies is examined, as well as certain problems connected to the fact that the joint venture partners have created commen control...... over their joint company....

  10. 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: csun1@bsd.uchicago.edu; Southard, Catherine; Di Rienzo, Anna [Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL 60637 (United States)

    2009-03-09

    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.

  11. 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)

    1994-12-01

    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.

  12. SON controls cell-cycle progression by coordinated regulation of RNA splicing.

    Science.gov (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

    2011-04-22

    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.

  13. RNA splicing regulated by RBFOX1 is essential for cardiac function in zebrafish.

    Science.gov (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

    2015-08-15

    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.

  14. 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;

    2010-01-01

    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...

  15. Increased dosage of Dyrk1A alters alternative splicing factor (ASF)-regulated alternative splicing of tau in Down syndrome.

    Science.gov (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

    2008-10-17

    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.

  16. Methods for Using Durable Adhesively Bonded Joints for Sandwich Structures

    Science.gov (United States)

    Smeltzer, Stanley S., III (Inventor); Lundgren, Eric C. (Inventor)

    2016-01-01

    Systems, methods, and apparatus for increasing durability of adhesively bonded joints in a sandwich structure. Such systems, methods, and apparatus includes an first face sheet and an second face sheet as well as an insert structure, the insert structure having a first insert face sheet, a second insert face sheet, and an insert core material. In addition, sandwich core material is arranged between the first face sheet and the second face sheet. A primary bondline may be coupled to the face sheet(s) and the splice. Further, systems, methods, and apparatus of the present disclosure advantageously reduce the load, provide a redundant path, reduce structural fatigue, and/or increase fatigue life.

  17. Strength and stiffness of tubular joints for assessment/design purposes

    Energy Technology Data Exchange (ETDEWEB)

    Dier, A.F.; Lalani, M.

    1995-12-01

    Tubular joints are integral components of offshore structures and, as such, many codes address their design. The strengths predicted by the codes often differ widely due to the adoption of different philosophies during code formulation and to differences in the underlying databases used during curve fitting and calibration exercises. In the assessment of existing structures, a hierarchy of analysis methods, from elastic analysis with improved code checks to nonlinear 3-D pushover analysis, may be employed. To avoid potentially unnecessary and expensive offshore strengthening work, it is important that these assessments are based on best estimates of joint strength (mean or characteristic, depending on application) and joint stiffness behavior. This paper gives the background to and interim results of a major international joint industry project in this area. Based on the most extensive carefully screened database ever assembled, the robustness of present design formulations have been examined, and new formulations have been developed where present codes are found wanting. Other issues, such as chord load, can length and material yield to ultimate strength have also been addressed. For the first time, expressions have been developed for P-{delta} and M-{theta} joint stiffness response, as may be used in advanced analysis including the simulation of joint behavior during pushover analysis. The paper goes on to describe the expected future developments in this field of technology.

  18. Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine.

    Directory of Open Access Journals (Sweden)

    Zhen Sheng

    Full Text Available Berberine has been identified with anti-proliferative effects on various cancer cells. Many researchers have been trying to elucidate the anti-cancer mechanisms of berberine based on differentially expressed genes. However, differentially alternative splicing genes induced by berberine might also contribute to its pharmacological actions and have not been reported yet. Moreover, the potential functional cross-talking between the two sets of genes deserves further exploration. In this study, RNA-seq technology was used to detect the differentially expressed genes and differentially alternative spliced genes in BEL-7402 cancer cells induced by berberine. Functional enrichment analysis indicated that these genes were mainly enriched in the p53 and cell cycle signalling pathway. In addition, it was statistically proven that the two sets of genes were locally co-enriched along chromosomes, closely connected to each other based on protein-protein interaction and functionally similar on Gene Ontology tree. These results suggested that the two sets of genes regulated by berberine might be functionally cross-talked and jointly contribute to its cell cycle arresting effect. It has provided new clues for further researches on the pharmacological mechanisms of berberine as well as the other botanical drugs.

  19. Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine.

    Science.gov (United States)

    Sheng, Zhen; Sun, Yi; Zhu, Ruixin; Jiao, Na; Tang, Kailin; Cao, Zhiwei; Ma, Chao

    2015-01-01

    Berberine has been identified with anti-proliferative effects on various cancer cells. Many researchers have been trying to elucidate the anti-cancer mechanisms of berberine based on differentially expressed genes. However, differentially alternative splicing genes induced by berberine might also contribute to its pharmacological actions and have not been reported yet. Moreover, the potential functional cross-talking between the two sets of genes deserves further exploration. In this study, RNA-seq technology was used to detect the differentially expressed genes and differentially alternative spliced genes in BEL-7402 cancer cells induced by berberine. Functional enrichment analysis indicated that these genes were mainly enriched in the p53 and cell cycle signalling pathway. In addition, it was statistically proven that the two sets of genes were locally co-enriched along chromosomes, closely connected to each other based on protein-protein interaction and functionally similar on Gene Ontology tree. These results suggested that the two sets of genes regulated by berberine might be functionally cross-talked and jointly contribute to its cell cycle arresting effect. It has provided new clues for further researches on the pharmacological mechanisms of berberine as well as the other botanical drugs.

  20. Nanoplasmonic probes of RNA folding and assembly during pre-mRNA splicing

    Science.gov (United States)

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

    2016-02-01

    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.

  1. Estimation of the minimum mRNA splicing error rate in vertebrates.

    Science.gov (United States)

    Skandalis, A

    2016-01-01

    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.

  2. The Role of Canonical and Noncanonical Pre-mRNA Splicing in Plant Stress Responses

    Directory of Open Access Journals (Sweden)

    A. S. Dubrovina

    2013-01-01

    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.

  3. Attenuation of the suppressive activity of cellular splicing factor SRSF3 by Kaposi sarcoma-associated herpesvirus ORF57 protein is required for RNA splicing.

    Science.gov (United States)

    Majerciak, Vladimir; Lu, Mathew; Li, Xiaofan; Zheng, Zhi-Ming

    2014-11-01

    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.

  4. 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

    2012-06-01

    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.

  5. Pentamidine reverses the splicing defects associated with myotonic dystrophy.

    Science.gov (United States)

    Warf, M Bryan; Nakamori, Masayuki; Matthys, Catherine M; Thornton, Charles A; Berglund, J Andrew

    2009-11-03

    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.

  6. A novel splicing mutation in the V2 vasopressin receptor

    DEFF Research Database (Denmark)

    Kamperis, Konstantinos; Siggaard, C; Herlin, Troels;

    2000-01-01

    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...

  7. Minor class splicing shapes the zebrafish transcriptome during development

    DEFF Research Database (Denmark)

    Markmiller, Sebastian; Cloonan, Nicole; Lardelli, Rea M;

    2014-01-01

    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....

  8. Modeling of Human Joint Structures.

    Science.gov (United States)

    1982-09-01

    Radial Lateral " epicondyle Olecranon Radius Ulna Figure 3. Lateral aspect of the right elbow joint. -17- Annular Ligament This strong band encircles... elbow joint, knee joint, human joints, shoulder joint, ankle joint, joint models, hip joint, ligaments. 20. ABSTRACT (Continue on reverse side If...ligaments. -A rather extended discussion of the articulations and anatomical descriptions of the elbow , shoulder, hip, knee and ankle joints are

  9. Characterization and alternative splicing of the complex I 19-kD subunit in Dunaliella salina: expression and mutual correlation of splice variants under diverse stresses.

    Science.gov (United States)

    Cao, Yu; Jin, Nan; Xu, Hui; Liu, Yi; Zhu, Wei Hua; Li, Xin Ran; Qiao, Dai Rong; Cao, Yi

    2010-01-01

    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.

  10. Two-chord interferometry using 3.39 μm He-Ne laser on a flux-coil-generated FRC.

    Science.gov (United States)

    Gota, H; Bolte, N; Deng, B H; Gupta, D; Kiyashko, V; Knapp, K; Mendoza, R; Morehouse, M; Roche, T; Wessel, F

    2010-10-01

    A two-chord λ(IR)∼3.39 μm He-Ne laser interferometer system was developed for a flux-coil-generated field-reversed configuration to estimate the electron density and the total temperature of the field-reversed configuration (FRC) plasma. This two-chord heterodyne interferometer system consists of a single ∼2 mW infrared He-Ne laser, a visible (λ(vis)∼632.8 nm) He-Ne laser for the alignment, a 40 MHz acousto-optic modulator, photodetectors, and quadrature phase detectors. Initial measurement was performed and the measured average electron densities were 2-10×10(19) m(-3) at two different radial positions in the midplane. A time shift in density was observed as the FRC expands radially. The time evolution of the line-averaged density agrees with the density estimated from the in situ internal magnetic probes, based on a rigid-rotor profile model.

  11. Two-chord interferometry using 3.39 {mu}m He-Ne laser on a flux-coil-generated FRC

    Energy Technology Data Exchange (ETDEWEB)

    Gota, H.; Deng, B. H.; Gupta, D.; Kiyashko, V.; Knapp, K.; Mendoza, R.; Morehouse, M. [Tri Alpha Energy, Inc., Rancho Santa Margarita, California 92688 (United States); Bolte, N.; Roche, T.; Wessel, F. [Tri Alpha Energy, Inc., Rancho Santa Margarita, California 92688 (United States); Department of Physics and Astronomy, University of California, Irvine, California 92697 (United States)

    2010-10-15

    A two-chord {lambda}{sub IR}{approx}3.39 {mu}m He-Ne laser interferometer system was developed for a flux-coil-generated field-reversed configuration to estimate the electron density and the total temperature of the field-reversed configuration (FRC) plasma. This two-chord heterodyne interferometer system consists of a single {approx}2 mW infrared He-Ne laser, a visible ({lambda}{sub vis}{approx}632.8 nm) He-Ne laser for the alignment, a 40 MHz acousto-optic modulator, photodetectors, and quadrature phase detectors. Initial measurement was performed and the measured average electron densities were 2-10x10{sup 19} m{sup -3} at two different radial positions in the midplane. A time shift in density was observed as the FRC expands radially. The time evolution of the line-averaged density agrees with the density estimated from the in situ internal magnetic probes, based on a rigid-rotor profile model.

  12. Alternative splicing of the androgen receptor in polycystic ovary syndrome

    OpenAIRE

    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

    2015-01-01

    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...

  13. The role of HMGCR alternative splicing in statin efficacy

    OpenAIRE

    Medina, Marisa Wong; Krauss, Ronald M.

    2009-01-01

    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...

  14. Automatic detection of exonic splicing enhancers (ESEs using SVMs

    Directory of Open Access Journals (Sweden)

    Suhai Sándor

    2008-09-01

    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.

  15. Behind the Scene Role of Conserved Threonine in Intein Splicing

    Science.gov (United States)

    Dearden, Albert; Callahan, Brian; Belfort, Marlene; Nayak, Saroj

    2012-02-01

    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

    2016-03-01

    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

    Science.gov (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

    2001-01-01

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

    Directory of Open Access Journals (Sweden)

    William G Fairbrother

    2004-09-01

    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.

  20. Conserved and species-specific alternative splicing in mammalian genomes

    Directory of Open Access Journals (Sweden)

    Favorov Alexander V

    2007-12-01

    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.

  1. 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.

  2. VEGF Spliced Variants: Possible Role of Anti-Angiogenesis Therapy

    Directory of Open Access Journals (Sweden)

    Caroline Hilmi

    2012-01-01

    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.

  3. Involvement of Alternative Splicing in Barley Seed Germination.

    Science.gov (United States)

    Zhang, Qisen; Zhang, Xiaoqi; Wang, Songbo; Tan, Cong; Zhou, Gaofeng; Li, Chengdao

    2016-01-01

    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.

  4. 和声分析课中等和弦转调的教学思路%The Teaching Ideas on Enharmonic Chord Modulation in Harmony Analysis Course

    Institute of Scientific and Technical Information of China (English)

    刘锦宣

    2012-01-01

    在和声分析课教学中,应强调学生注重用学到的和声理论知识结合个人的音乐实践经验,去认知和解释音乐作品中各种和声手法的运用特点。等和弦转调的教学思路可以从下列几个方面入手:在进行和声分析中,明确等和弦转调的特征与应用条件,根据各种等和弦转调的理论知识要点,结合作品中具体的和声进行特点,确定其应用在音乐作品中的确切位置;从减七和弦等和弦转调的解题口诀的产生原理和依据入手,在实例分析讲述和声逻辑推理中阐述应用口诀的思维过程;让学生牢记属七和弦等和弦转调时等音和弦改写的根音换算关系,对和弦作等音变换时的准确率和完成速度,都将会有很大的提高;详实的阐述增三和弦等和弦转调的调方向及其在应用上的思路拓展,都将对解题中依据该和弦这方面的转调特征去快速寻找和声分析的转调方向与理解其转调的脉络思维过程有所帮助。%In the teaching of harmonic analysis course, the teacher should stress students' the- oretic knowledge combination with their musical practice so as to recognize and in~ terpret the application features of various harmonic methods in musical works. The teaching ideas ofenharmonic chord modulation can be as follows: to define the fea- ture and applying condition of enharmonic chord modulation, and decide its exact location in musical works according to the concrete harmonic progression charac- teristic as well as theory; based on the solution formula principle of the diminished 7th chord of enharmonic chord modulation, to expound the thinking process of ap- plying formula in the course of example analysis and logical inference; to let stu- dents remember the root conversion relationship of enharmonic chord rewriting will be helpful to increase the accuracy and speed in enharmonic exchange, etc.

  5. In vitro splicing of erythropoietin by the Mycobacterium tuberculosis RecA intein without substituting amino acids at the splice junctions.

    Science.gov (United States)

    Gangopadhyay, Jaya Pal; Jiang, Shu-qin; van Berkel, Patrick; Paulus, Henry

    2003-01-20

    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.

  6. Culture - joint fluid

    Science.gov (United States)

    Joint fluid culture ... fungi, or viruses grow. This is called a culture. If these germs are detected, other tests may ... is no special preparation needed for the lab culture. How to prepare for the removal of joint ...

  7. Sacroiliac joint pain - aftercare

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/patientinstructions/000610.htm Sacroiliac joint pain - aftercare To use the sharing features on this page, please enable JavaScript. The sacroiliac joint (SIJ) is a term used to describe the ...

  8. Knee joint replacement - slideshow

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/presentations/100088.htm Knee joint replacement - series—Normal anatomy To use the ... to slide 4 out of 4 Overview The knee is a complex joint. It contains the distal ...

  9. Functional splicing network reveals extensive regulatory potential of the core spliceosomal machinery.

    Science.gov (United States)

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

    2015-01-08

    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.

  10. Splicing factor gene mutations in the myelodysplastic syndromes: impact on disease phenotype and therapeutic applications.

    Science.gov (United States)

    Pellagatti, Andrea; Boultwood, Jacqueline

    2017-01-01

    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.

  11. 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;

    2012-01-01

    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...

  12. Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II.

    Science.gov (United States)

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

    2016-04-01

    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.

  13. 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;

    2008-01-01

    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...

  14. Genome-wide analysis of SRSF10-regulated alternative splicing by deep sequencing of chicken transcriptome

    Directory of Open Access Journals (Sweden)

    Xuexia Zhou

    2014-12-01

    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.

  15. 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

    2003-01-01

    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.

  16. 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

    2005-01-01

    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.

  17. Experimental characterization of resistive joints for use inside ATLAS toroids

    CERN Document Server

    Volpini, G; Pojer, M

    2001-01-01

    The authors have investigated, both experimentally and theoretically, the thermo-electrical behavior of the ATLAS magnets resistive joints. These magnets exploit an Al-clad NbTi Rutherford superconducting cable, and the splices between different sections are performed by TIG-welding the Al matrices of the two cables to be connected. This technique is simple from a construction point of view, and we have shown that its performance is adequate for a safe operation of the magnets. The two main concerns during the design of these joints are the temperature rise due to Joule dissipation and the eddy currents induced under nonstationary conditions. We have devised a reliable model of these joints, that allows estimating their resistances and the induced eddy currents; later we have built and measured several sample joints to give experimental confirmation. The model requires, along with the joint geometry, the knowledge of the Rutherford-matrix interface resistance as well as the RRR of the aluminum matrix. In this...

  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

    Science.gov (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.

    2016-01-01

    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

    2006-02-01

    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

  1. Increased levels of noisy splicing in cancers, but not for oncogene-derived transcripts

    OpenAIRE

    Chen, Lu; Tovar-Corona, Jaime M.; Urrutia, Araxi O.

    2011-01-01

    Recent genome-wide analyses have detected numerous cancer-specific alternative splicing (AS) events. Whether transcripts containing cancer-specific AS events are likely to be translated into functional proteins or simply reflect noisy splicing, thereby determining their clinical relevance, is not known. Here we show that consistent with a noisy-splicing model, cancer-specific AS events generally tend to be rare, containing more premature stop codons and have less identifiable functional domai...

  2. Propionic and Methylmalonic Acidemia: Antisense Therapeutics for Intronic Variations Causing Aberrantly Spliced Messenger RNA

    OpenAIRE

    Rincón, A. ; Aguado, C. ; Desviat, L. R. ; Sánchez-Alcudia, R. ; Ugarte, M. ; Pérez, B. 

    2007-01-01

    We describe the use of antisense morpholino oligonucleotides (AMOs) to restore normal splicing caused by intronic molecular defects identified in methylmalonic acidemia (MMA) and propionic acidemia (PA). The three new point mutations described in deep intronic regions increase the splicing scores of pseudoexons or generate consensus binding motifs for splicing factors, such as SRp40, which favor the intronic inclusions in MUT (r.1957ins76), PCCA (r.1284ins84), or PCCB (r.654ins72) messenger R...

  3. An effective method and its implementation for splicing in terrestrial DMB

    Science.gov (United States)

    Lee, Yonghoon; Lee, Jinhwan; Lee, Gwangsoon; Ahn, Chunghyun; Lee, Soo In; Kim, Nam

    2006-02-01

    The implemented T-DMB Splicing System provides multimedia service without any discontinuity of video and audio when inserting commercial and specific program while transmitting main DMB broadcasting program. And it can be used for inserting local broadcasting program while retransmitting central broadcasting program. This paper introduces Terrestrial Digital Multimedia Broadcasting (T-DMB) splicing method based on Eureka-147 DAB and presents a new architecture of transmission system for T-DMB Splicing.

  4. Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level

    Science.gov (United States)

    Abascal, Federico; Ezkurdia, Iakes; Rodriguez-Rivas, Juan; Rodriguez, Jose Manuel; del Pozo, Angela; Vázquez, Jesús; Valencia, Alfonso; Tress, Michael L.

    2015-01-01

    Alternative splicing of messenger RNA can generate a wide variety of mature RNA transcripts, and these transcripts may produce protein isoforms with diverse cellular functions. While there is much supporting evidence for the expression of alternative transcripts, the same is not true for the alternatively spliced protein products. Large-scale mass spectroscopy experiments have identified evidence of alternative splicing at the protein level, but with conflicting results. Here we carried out a rigorous analysis of the peptide evidence from eight large-scale proteomics experiments to assess the scale of alternative splicing that is detectable by high-resolution mass spectroscopy. We find fewer splice events than would be expected: we identified peptides for almost 64% of human protein coding genes, but detected just 282 splice events. This data suggests that most genes have a single dominant isoform at the protein level. Many of the alternative isoforms that we could identify were only subtly different from the main splice isoform. Very few of the splice events identified at the protein level disrupted functional domains, in stark contrast to the two thirds of splice events annotated in the human genome that would lead to the loss or damage of functional domains. The most striking result was that more than 20% of the splice isoforms we identified were generated by substituting one homologous exon for another. This is significantly more than would be expected from the frequency of these events in the genome. These homologous exon substitution events were remarkably conserved—all the homologous exons we identified evolved over 460 million years ago—and eight of the fourteen tissue-specific splice isoforms we identified were generated from homologous exons. The combination of proteomics evidence, ancient origin and tissue-specific splicing indicates that isoforms generated from homologous exons may have important cellular roles. PMID:26061177

  5. Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level.

    Directory of Open Access Journals (Sweden)

    Federico Abascal

    2015-06-01

    Full Text Available Alternative splicing of messenger RNA can generate a wide variety of mature RNA transcripts, and these transcripts may produce protein isoforms with diverse cellular functions. While there is much supporting evidence for the expression of alternative transcripts, the same is not true for the alternatively spliced protein products. Large-scale mass spectroscopy experiments have identified evidence of alternative splicing at the protein level, but with conflicting results. Here we carried out a rigorous analysis of the peptide evidence from eight large-scale proteomics experiments to assess the scale of alternative splicing that is detectable by high-resolution mass spectroscopy. We find fewer splice events than would be expected: we identified peptides for almost 64% of human protein coding genes, but detected just 282 splice events. This data suggests that most genes have a single dominant isoform at the protein level. Many of the alternative isoforms that we could identify were only subtly different from the main splice isoform. Very few of the splice events identified at the protein level disrupted functional domains, in stark contrast to the two thirds of splice events annotated in the human genome that would lead to the loss or damage of functional domains. The most striking result was that more than 20% of the splice isoforms we identified were generated by substituting one homologous exon for another. This is significantly more than would be expected from the frequency of these events in the genome. These homologous exon substitution events were remarkably conserved--all the homologous exons we identified evolved over 460 million years ago--and eight of the fourteen tissue-specific splice isoforms we identified were generated from homologous exons. The combination of proteomics evidence, ancient origin and tissue-specific splicing indicates that isoforms generated from homologous exons may have important cellular roles.

  6. Identification and characterization of NF1 splicing mutations in Korean patients with neurofibromatosis type 1.

    Science.gov (United States)

    Jang, Mi-Ae; Kim, Young-Eun; Kim, Sun Kyung; Lee, Myoung-Keun; Kim, Jong-Won; Ki, Chang-Seok

    2016-08-01

    Neurofibromatosis type I (NF1) is an autosomal dominant genetic disorder caused by NF1 mutations. Although mutations affecting mRNA splicing are the most common molecular defects in NF1, few studies have analyzed genomic DNA (gDNA)-mRNA correlations in Korean NF1 patients. In this study, we investigated 28 unrelated NF1 patients who showed splicing alterations in reverse transcription-PCR of NF1 mRNA and identified 24 different NF1 splicing mutations, 9 of which were novel. These mutations can be categorized into five groups: exon skipping resulting from mutations at authentic 5' and 3' splice sites (type I, 46%), cryptic exon inclusion caused by deep intronic mutations (type II, 8%), creation of new splice sites causing loss of exonic sequences (type III, 8%), activation of cryptic splice sites due to disruption of authentic splice sites (type IV, 25%) and exonic sequence alterations causing exon skipping (type V, 13%). In total, 42% of all splicing mutations did not involve the conserved AG/GT dinucleotides of the splice sites, making it difficult to identify the correct mutation sites at the gDNA level. These results add to the mutational spectrum of NF1 and further elucidate the gDNA-mRNA correlations of NF1 mutations.

  7. Behavior Of A Confined Tension Lap Splice In High-Strength Reinforced Concrete Beams

    Science.gov (United States)

    Abdel-Kareem, Ahmed H.; Abousafa, Hala; El-Hadidi, Omaia S.

    2015-09-01

    The results of an experimental program conducted on seventeen simply supported concrete beams to study the effect of transverse reinforcement on the behavior of the lap splice of a steel reinforcement in tension zones in high-strength concrete beams are presented. The parameters included in the experimental program were the concrete compressive strength, the lap splice length, the amount of transverse reinforcement provided within the splice region, and the shape of the transverse reinforcement around the spliced bars. The experimental results showed that the displacement ductility increased and the mode of failure changed from a splitting bond failure to a flexural failure when the amount of the transverse reinforcement in the splice region increased, and the compressive strength increased up to 100 MPa. The presence of the transverse reinforcement around the spliced bars had a pronounced effect on increasing the ultimate load, the ultimate deflection, and the displacement ductility. The prediction of maximum steel stresses for spliced bars using the ACI 318-05 building code was compared with the experimental results. The comparison showed that the effect of the transverse reinforcement around spliced bars has to be considered into the design equations for lap splice length in high-strength concrete beams.

  8. Two novel splicing mutations in the SLC45A2 gene cause Oculocutaneous Albinism Type IV by unmasking cryptic splice sites.

    Science.gov (United States)

    Straniero, Letizia; Rimoldi, Valeria; Soldà, Giulia; Mauri, Lucia; Manfredini, Emanuela; Andreucci, Elena; Bargiacchi, Sara; Penco, Silvana; Gesu, Giovanni P; Del Longo, Alessandra; Piozzi, Elena; Asselta, Rosanna; Primignani, Paola

    2015-09-01

    Oculocutaneous albinism (OCA) is characterized by hypopigmentation of the skin, hair and eye, and by ophthalmologic abnormalities caused by a deficiency in melanin biosynthesis. OCA type IV (OCA4) is one of the four commonly recognized forms of albinism, and is determined by mutation in the SLC45A2 gene. Here, we investigated the genetic basis of OCA4 in an Italian child. The mutational screening of the SLC45A2 gene identified two novel potentially pathogenic splicing mutations: a synonymous transition (c.888G>A) involving the last nucleotide of exon 3 and a single-nucleotide insertion (c.1156+2dupT) within the consensus sequence of the donor splice site of intron 5. As computer-assisted analysis for mutant splice-site prediction was not conclusive, we investigated the effects on pre-mRNA splicing of these two variants by using an in vitro minigene approach. Production of mutant transcripts in HeLa cells demonstrated that both mutations cause the almost complete abolishment of the physiologic donor splice site, with the concomitant unmasking of cryptic donor splice sites. To our knowledge, this work represents the first in-depth molecular characterization of splicing defects in a OCA4 patient.

  9. Experimental research on ultimate bearing capacity of grouted-round-steel-tube N-joint

    Institute of Scientific and Technical Information of China (English)

    ZHENG Wen-zhong; LIU Xu-dong; ZHANG Ge-ming; ZHANG Bo-yi

    2007-01-01

    As an important structural member in self-supporting concrete floor during construction, encased steel truss-concrete composite beam has brilliant prospect in outer-jacketing structures for adding stories or mega frame structures. Compared with encased angle truss, encased round steel tube truss can facilitate layout of itself in column and facilitate layout and anchorage of prestressed reinforcement placed horizontally. N-joint is wildly used in encased steel truss. For cave-in failure easily occurs in hollow steel-tube joint, the idea that the chord is grouted to increase cave-in bearing capacity of hollow tube is proposed. Test results of 8 grouted-roundsteel-tube N-joints from the beginning of loading to failure are reported. Mechanical property and failure mode of this kind of truss joint are analyzed, and the formulas of ultimate bearing capacity of the joint corresponding to different failure modes are established. All these can provide basic data for spreading encased steel truss-concrete composite beam.

  10. Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi.

    Science.gov (United States)

    Zafrir, Zohar; Tuller, Tamir

    2015-10-01

    RNA splicing is the central process of intron removal in eukaryotes known to regulate various cellular functions such as growth, development, and response to external signals. The canonical sequences indicating the splicing sites needed for intronic boundary recognition are well known. However, the roles and evolution of the local folding of intronic and exonic sequence features adjacent to splice sites has yet to be thoroughly studied. Here, focusing on four fungi (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, and Candida albicans), we performed for the first time a comprehensive high-resolution study aimed at characterizing the encoding of intronic splicing efficiency in pre-mRNA transcripts and its effect on intron evolution. Our analysis supports the conjecture that pre-mRNA local folding strength at intronic boundaries is under selective pressure, as it significantly affects splicing efficiency. Specifically, we show that in the immediate region of 12-30 nucleotides (nt) surrounding the intronic donor site there is a preference for weak pre-mRNA folding; similarly, in the region of 15-33 nt surrounding the acceptor and branch sites there is a preference for weak pre-mRNA folding. We also show that in most cases there is a preference for strong pre-mRNA folding further away from intronic splice sites. In addition, we demonstrate that these signals are not associated with gene-specific functions, and they correlate with splicing efficiency measurements (r = 0.77, P = 2.98 × 10(-21)) and with expression levels of the corresponding genes (P = 1.24 × 10(-19)). We suggest that pre-mRNA folding strength in the above-mentioned regions has a direct effect on splicing efficiency by improving the recognition of intronic boundaries. These new discoveries are contributory steps toward a broader understanding of splicing regulation and intronic/transcript evolution.

  11. A novel mutation in the β-spectrin gene causes the activation of a cryptic 5'-splice site and the creation of a de novo 3'-splice site.

    Science.gov (United States)

    Salas, Pilar Carrasco; Rosales, José Miguel Lezana; Milla, Carmen Palma; Montiel, Javier López; Siles, Juan López

    2015-01-01

    The analysis of genes involved in hereditary spherocytosis, by next-generation sequencing in two patients with clinical diagnosis of the disease, showed the presence of the c.1795+1G>A mutation in the SPTB gene. cDNA amplification then revealed the occurrence of a consequent aberrant mRNA isoform produced from the activation of a cryptic 5'-splice site and the creation of a newly 3'-splice site. The mechanisms by which these two splice sites are used as a result of the same mutation should be analyzed in depth in further studies.

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

    Directory of Open Access Journals (Sweden)

    Mount Stephen M

    2006-12-01

    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

  13. MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma.

    Science.gov (United States)

    Zhang, Shile; Wei, Jun S; Li, Samuel Q; Badgett, Tom C; Song, Young K; Agarwal, Saurabh; Coarfa, Cristian; Tolman, Catherine; Hurd, Laura; Liao, Hongling; He, Jianbin; Wen, Xinyu; Liu, Zhihui; Thiele, Carol J; Westermann, Frank; Asgharzadeh, Shahab; Seeger, Robert C; Maris, John M; Guidry Auvil, Jamie M; Smith, Malcolm A; Kolaczyk, Eric D; Shohet, Jason; Khan, Javed

    2016-02-28

    The molecular mechanisms underlying the aggressive behavior of MYCN driven neuroblastoma (NBL) is under intense investigation; however, little is known about the impact of this family of transcription factors on the splicing program. Here we used high-throughput RNA sequencing to systematically study the expression of RNA isoforms in stage 4 MYCN-amplified NBL, an aggressive subtype of metastatic NBL. We show that MYCN-amplified NBL tumors display a distinct gene splicing pattern affecting multiple cancer hallmark functions. Six splicing factors displayed unique differential expression patterns in MYCN-amplified tumors and cell lines, and the binding motifs for some of these splicing factors are significantly enriched in differentially-spliced genes. Direct binding of MYCN to promoter regions of the splicing factors PTBP1 and HNRNPA1 detected by ChIP-seq demonstrates that MYCN controls the splicing pattern by direct regulation of the expression of these key splicing factors. Furthermore, high expression of PTBP1 and HNRNPA1 was significantly associated with poor overall survival of stage4 NBL patients (p ≤ 0.05). Knocking down PTBP1, HNRNPA1 and their downstream target PKM2, an isoform of pro-tumor-growth, result in repressed growth of NBL cells. Therefore, our study reveals a novel role of MYCN in controlling global splicing program through regulation of splicing factors in addition to its well-known role in the transcription program. These findings suggest a therapeutically potential to target the key splicing factors or gene isoforms in high-risk NBL with MYCN-amplification.

  14. Performance of Grouted Splice Sleeve Connector under Tensile Load

    Directory of Open Access Journals (Sweden)

    A. Alias

    2016-05-01

    Full Text Available The grouted splice sleeve connector system takes advantage of the bond-slip resistance of the grout and the mechanical gripping of reinforcement bars to provide resistance to tensile force. In this system, grout acts as a load-transferring medium and bonding material between the bars and sleeve. This study adopted the end-to-end rebars connection method to investigate the effect of development length and sleeve diameter on the bonding performance of the sleeve connector. The end-to-end method refers to the condition where reinforcement bars are inserted into the sleeve from both ends and meet at the centre before grout is filled. Eight specimens of grouted splice sleeve connector were tested under tensile load to determine their performance. The sleeve connector was designed using 5 mm thick circular hollow section (CHS steel pipe and consisted of one external and two internal sleeves. The tensile test results show that connectors with a smaller external and internal sleeve diameter appear to provide better bonding performance. Three types of failure were observed in this research, which are bar fracture (outside the sleeve, bar pullout, and internal sleeve pullout. With reference to these failure types, the development length of 200 mm is the optimum value due to its bar fracture type, which indicates that the tensile capacity of the connector is higher than the reinforcement bar. It is found that the performance of the grouted splice sleeve connector is influenced by the development length of the reinforcement bar and the diameter of the sleeve.

  15. Splicing and the evolution of proteins in mammals.

    Directory of Open Access Journals (Sweden)

    Joanna L Parmley

    2007-02-01

    Full Text Available It is often supposed that a protein's rate of evolution and its amino acid content are determined by the function and anatomy of the protein. Here we examine an alternative possibility, namely that the requirement to specify in the unprocessed RNA, in the vicinity of intron-exon boundaries, information necessary for removal of introns (e.g., exonic splice enhancers affects both amino acid usage and rates of protein evolution. We find that the majority of amino acids show skewed usage near intron-exon boundaries, and that differences in the trends for the 2-fold and 4-fold blocks of both arginine and leucine show this to be owing to effects mediated at the nucleotide level. More specifically, there is a robust relationship between the extent to which an amino acid is preferred/avoided near boundaries and its enrichment/paucity in splice enhancers. As might then be expected, the rate of evolution is lowest near intron-exon boundaries, at least in part owing to splice enhancers, such that domains flanking intron-exon junctions evolve on average at under half the rate of exon centres from the same gene. In contrast, the rate of evolution of intronless retrogenes is highest near the domains where intron-exon junctions previously resided. The proportion of sequence near intron-exon boundaries is one of the stronger predictors of a protein's rate of evolution in mammals yet described. We conclude that after intron insertion selection favours modification of amino acid content near intron-exon junctions, so as to enable efficient intron removal, these changes then being subject to strong purifying selection even if nonoptimal for protein function. Thus there exists a strong force operating on protein evolution in mammals that is not explained directly in terms of the biology of the protein.

  16. Classical estrogen receptors and ERα splice variants in the mouse.

    Directory of Open Access Journals (Sweden)

    Debra L Irsik

    Full Text Available Estrogens exert a variety of effects in both reproductive and non-reproductive tissues. With the discovery of ERα splice variants, prior assumptions concerning tissue-specific estrogen signaling need to be re-evaluated. Accordingly, we sought to determine the expression of the classical estrogen receptors and ERα splice variants across reproductive and non-reproductive tissues of male and female mice. Western blotting revealed that the full-length ERα66 was mainly present in female reproductive tissues but was also found in non-reproductive tissues at lower levels. ERα46 was most highly expressed in the heart of both sexes. ERα36 was highly expressed in the kidneys and liver of female mice but not in the kidneys of males. ERβ was most abundant in non-reproductive tissues and in the ovaries. Because the kidney has been reported to be the most estrogenic non-reproductive organ, we sought to elucidate ER renal expression and localization. Immunofluorescence studies revealed ERα66 in the vasculature and the glomerulus. It was also found in the brush border of the proximal tubule and in the cortical collecting duct of female mice. ERα36 was evident in mesangial cells and tubular epithelial cells of both sexes, as well as podocytes of females but not males. ERβ was found primarily in the podocytes in female mice but was also present in the mesangial cells in both sexes. Within the renal cortex, ERα46 and ERα36 were mainly located in the membrane fraction although they were also present in the cytosolic fraction. Given the variability of expression patterns demonstrated herein, identification of the specific estrogen receptors expressed in a tissue is necessary for interpreting estrogenic effects. As this study revealed expression of the ERα splice variants at multiple sites within the kidney, further studies are warranted in order to elucidate the contribution of these receptors to renal estrogen responsiveness.

  17. Static Strength of Concrete-Filled Circular Tubular T-Joints under Axial Loading%圆钢管混凝土T型节点在轴向作用力下静力性能研究

    Institute of Scientific and Technical Information of China (English)

    宋生志; 邵永波

    2011-01-01

    For typical tubular T-joint under axial loading, the failure generally occurs near the weld toe on the chord surface due to the fact that the stiffness of the chord in radial direction is much smaller than that of the brace in axial direction as well as the existence of high stress concentration along the weld toe. The static strength of tubular T-joints can be improved by filling concrete into the chord. Finite element analysis is con ducted to analyze 6 T-joint models under axial compression and tension by using sofware ABAQUS to prove that filling concrete in the chord is effective to improve the static strength. Different failure modes under axial compression and tension between tubular T-joint with circular hollow section and Concrete-Filled Circular Tu bular ( CFCT)T-joint are clarified. Thereafter, parametric investigation for CFCT T-joint, which involves the parameters of chord thickness T, the brace/chord diameter ratio β, the chord diameter/thickness ratio 2γ , the yield strength of the steel tube fy , and the compressive strength of concrete fc , is carried out. From the para metric study , the effect of parameters on the static strength of CFCT T-joints is concluded.%T型圆管节点在支管轴向力作用下,破坏位置一般出现在主管表面的焊趾处.主要是因为主管的径向刚度远小于支管的轴向刚度,并且节点部位存在较大的应力集中.为提高T型管节点的静力强度,可通过在主管中填充混凝土以提高其径向刚度来实现.为了研究主管填充混凝土对T型管节点静力强度的影响,用有限元分析软件(ABAQUS)首先对6个模型分别在支管轴向压力和拉力作用下进行分析,结果发现主管中填充混凝土对节点静力强度的提高是非常有效的.同时得出主管填充混凝土与未填充混凝土节点不同的破坏模态.然后,对圆钢管混凝土T型节点进行参数分析,参数主要包括主管厚度T、支主管管径比β、主管的径厚比2

  18. SEQassembly: A Practical Tools Program for Coding Sequences Splicing

    Science.gov (United States)

    Lee, Hongbin; Yang, Hang; Fu, Lei; Qin, Long; Li, Huili; He, Feng; Wang, Bo; Wu, Xiaoming

    CDS (Coding Sequences) is a portion of mRNA sequences, which are composed by a number of exon sequence segments. The construction of CDS sequence is important for profound genetic analysis such as genotyping. A program in MATLAB environment is presented, which can process batch of samples sequences into code segments under the guide of reference exon models, and splice these code segments of same sample source into CDS according to the exon order in queue file. This program is useful in transcriptional polymorphism detection and gene function study.

  19. Single-Molecule Imaging of RNA Splicing in Live Cells.

    Science.gov (United States)

    Rino, José; Martin, Robert M; Carvalho, Célia; de Jesus, Ana C; Carmo-Fonseca, Maria

    2015-01-01

    Expression of genetic information in eukaryotes involves a series of interconnected processes that ultimately determine the quality and amount of proteins in the cell. Many individual steps in gene expression are kinetically coupled, but tools are lacking to determine how temporal relationships between chemical reactions contribute to the output of the final gene product. Here, we describe a strategy that permits direct measurements of intron dynamics in single pre-mRNA molecules in live cells. This approach reveals that splicing can occur much faster than previously proposed and opens new avenues for studying how kinetic mechanisms impact on RNA biogenesis.

  20. CTCF:from insulators to alternative splicing regulation

    Institute of Scientific and Technical Information of China (English)

    Alberto R Kornblihtt

    2012-01-01

    The zinc-finger DNA-binding protein CTCF has been known for being a constituent of insulators.A recent paper in Nature reports an unforeseen intragenic role for CTCF that links DNA methylation with alternative splicing.By binding to its target DNA site placed within an alternative exon,CTCF creates a roadblock to transcriptional elongation that favors inclusion of the exon into mature mRNA.DNA methylation prevents CTCF binding,which releases pol Ⅱ transient blockage and promotes exon exclusion.

  1. Managing Joint Production Motivation

    DEFF Research Database (Denmark)

    Lindenberg, Siegwart; Foss, Nicolai Juul

    2011-01-01

    We contribute to the microfoundations of organizational performance by proffering the construct of joint production motivation. Under such motivational conditions individuals see themselves as part of a joint endeavor, each with his or her own roles and responsibilities; generate shared represent...... representations of actions and tasks; cognitively coordinate cooperation; and choose their own behaviors in terms of joint goals. Using goal-framing theory, we explain how motivation for joint production can be managed by cognitive/symbolic management and organizational design.......We contribute to the microfoundations of organizational performance by proffering the construct of joint production motivation. Under such motivational conditions individuals see themselves as part of a joint endeavor, each with his or her own roles and responsibilities; generate shared...

  2. Jointly Poisson processes

    CERN Document Server

    Johnson, D H

    2009-01-01

    What constitutes jointly Poisson processes remains an unresolved issue. This report reviews the current state of the theory and indicates how the accepted but unproven model equals that resulting from the small time-interval limit of jointly Bernoulli processes. One intriguing consequence of these models is that jointly Poisson processes can only be positively correlated as measured by the correlation coefficient defined by cumulants of the probability generating functional.

  3. Joint Program Management Handbook

    Science.gov (United States)

    1994-12-01

    the Engieermg and Manufacuring Devopment Phase. Nfilestoae HI- Develommen Annros Devopment approval marks a significant step for any program, but it is...to review concept formulaton. Systems Engilneertn As with service programs, systems engineering in joint program management is an essential tool . I...MANAGEMENT HANDBOOK On=e wd Umawtaiutt As discussed in Chapter 7, systems analysis of relationships is a usef tool for joint program managers. The joint

  4. 30 CFR 75.810 - High-voltage trailing cables; splices.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 1 2010-07-01 2010-07-01 false High-voltage trailing cables; splices. 75.810... SAFETY AND HEALTH MANDATORY SAFETY STANDARDS-UNDERGROUND COAL MINES Underground High-Voltage Distribution § 75.810 High-voltage trailing cables; splices. In the case of high-voltage cables used as...

  5. FOX-2 dependent splicing of ataxin-2 transcript is affected by ataxin-1 overexpression.

    Directory of Open Access Journals (Sweden)

    Franziska Welzel

    Full Text Available Alternative splicing is a fundamental posttranscriptional mechanism for controlling gene expression, and splicing defects have been linked to various human disorders. The splicing factor FOX-2 is part of a main protein interaction hub in a network related to human inherited ataxias, however, its impact remains to be elucidated. Here, we focused on the reported interaction between FOX-2 and ataxin-1, the disease-causing protein in spinocerebellar ataxia type 1. In this line, we further evaluated this interaction by yeast-2-hybrid analyses and co-immunoprecipitation experiments in mammalian cells. Interestingly, we discovered that FOX-2 localization and splicing activity is affected in the presence of nuclear ataxin-1 inclusions. Moreover, we observed that FOX-2 directly interacts with ataxin-2, a protein modulating spinocerebellar ataxia type 1 pathogenesis. Finally, we provide evidence that splicing of pre-mRNA of ataxin-2 depends on FOX-2 activity, since reduction of FOX-2 levels led to increased skipping of exon 18 in ataxin-2 transcripts. Most striking, we observed that ataxin-1 overexpression has an effect on this splicing event as well. Thus, our results demonstrate that FOX-2 is involved in splicing of ataxin-2 transcripts and that this splicing event is altered by overexpression of ataxin-1.

  6. Modulation of alternative splicing with chemical compounds in new therapeutics for human diseases.

    Science.gov (United States)

    Ohe, Kenji; Hagiwara, Masatoshi

    2015-04-17

    Alternative splicing is a critical step where a limited number of human genes generate a complex and diverse proteome. Various diseases, including inherited diseases with abnormalities in the "genome code," have been found to result in an aberrant mis-spliced "transcript code" with correlation to the resulting phenotype. Chemical compound-based and nucleic acid-based strategies are trying to target this mis-spliced "transcript code". We will briefly mention about how to obtain splicing-modifying-compounds by high-throughput screening and overview of what is known about compounds that modify splicing pathways. The main focus will be on RNA-binding protein kinase inhibitors. In the main text, we will refer to diseases where splicing-modifying-compounds have been intensively investigated, with comparison to nucleic acid-based strategies. The information on their involvement in mis-splicing as well as nonsplicing events will be helpful in finding better compounds with less off-target effects for future implications in mis-splicing therapy.

  7. Features of 5'-splice-site efficiency derived from disease-causing mutations and comparative genomics

    DEFF Research Database (Denmark)

    Roca, Xavier; Olson, Andrew J; Rao, Atmakuri R

    2007-01-01

    Many human diseases, including Fanconi anemia, hemophilia B, neurofibromatosis, and phenylketonuria, can be caused by 5'-splice-site (5'ss) mutations that are not predicted to disrupt splicing, according to position weight matrices. By using comparative genomics, we identify pairwise dependencies...

  8. Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize.

    Science.gov (United States)

    Thatcher, Shawn R; Danilevskaya, Olga N; Meng, Xin; Beatty, Mary; Zastrow-Hayes, Gina; Harris, Charlotte; Van Allen, Brandon; Habben, Jeffrey; Li, Bailin

    2016-01-01

    Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.

  9. Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize1[OPEN

    Science.gov (United States)

    Thatcher, Shawn R.; Meng, Xin; Beatty, Mary; Zastrow-Hayes, Gina; Harris, Charlotte; Habben, Jeffrey; Li, Bailin

    2016-01-01

    Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition. PMID:26582726

  10. FULL-GENOME ANALYSIS OF ALTERNATIVE SPLICING IN MOUSE LIVER AFTER HEPATOTOXICANT EXPOSURE

    Science.gov (United States)

    Alternative splicing plays a role in determining gene function and protein diversity. We have employed whole genome exon profiling using Affymetrix Mouse Exon 1.0 ST arrays to understand the significance of alternative splicing on a genome-wide scale in response to multiple toxic...

  11. Assessing the impact of alternative splicing on the diversity and evolution of the proteome in plants

    NARCIS (Netherlands)

    Severing, E.I.

    2011-01-01

    Splicing is one of the key processing steps during the maturation of a gene’s primary transcript into the mRNA molecule used as a template for protein production. Splicing involves the removal of segments called introns and re-joining of the remaining segments called exons. It is by now well e

  12. Autogenous Regulation of Splicing of the Transcript of a Yeast Ribosomal Protein Gene

    Science.gov (United States)

    Dabeva, Mariana D.; Post-Beittenmiller, Martha A.; Warner, Jonathan R.

    1986-08-01

    The gene for a yeast ribosomal protein, RPL32, contains a single intron. The product of this gene appears to participate in feedback control of the splicing of the intron from the transcript. This autogenous regulation of splicing provides a striking analogy to the autogenous regulation of translation of ribosomal proteins in Escherichia coli.

  13. Alternative splicing, a new target to block cellular gene expression by poliovirus 2A protease

    Energy Technology Data Exchange (ETDEWEB)

    Alvarez, Enrique, E-mail: ealvarez@cbm.uam.es [Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera, 1 Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain); Castello, Alfredo; Carrasco, Luis; Izquierdo, Jose M. [Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Nicolas Cabrera, 1 Universidad Autonoma de Madrid, Cantoblanco, 28049 Madrid (Spain)

    2011-10-14

    Highlights: {yields} Novel role for poliovirus 2A protease as splicing modulator. {yields} Poliovirus 2A protease inhibits the alternative splicing of pre-mRNAs. {yields} Poliovirus 2A protease blocks the second catalytic step of splicing. -- Abstract: Viruses have developed multiple strategies to interfere with the gene expression of host cells at different stages to ensure their own survival. Here we report a new role for poliovirus 2A{sup pro} modulating the alternative splicing of pre-mRNAs. Expression of 2A{sup pro} potently inhibits splicing of reporter genes in HeLa cells. Low amounts of 2A{sup pro} abrogate Fas exon 6 skipping, whereas higher levels of protease fully abolish Fas and FGFR2 splicing. In vitro splicing of MINX mRNA using nuclear extracts is also strongly inhibited by 2A{sup pro}, leading to accumulation of the first exon and the lariat product containing the unspliced second exon. These findings reveal that the mechanism of action of 2A{sup pro} on splicing is to selectively block the second catalytic step.

  14. Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells.

    Science.gov (United States)

    Iannone, Camilla; Pohl, Andy; Papasaikas, Panagiotis; Soronellas, Daniel; Vicent, Guillermo P; Beato, Miguel; ValcáRcel, Juan

    2015-03-01

    Splicing of mRNA precursors can occur cotranscriptionally and it has been proposed that chromatin structure influences splice site recognition and regulation. Here we have systematically explored potential links between nucleosome positioning and alternative splicing regulation upon progesterone stimulation of breast cancer cells. We confirm preferential nucleosome positioning in exons and report four distinct profiles of nucleosome density around alternatively spliced exons, with RNA polymerase II accumulation closely following nucleosome positioning. Hormone stimulation induces switches between profile classes, correlating with a subset of alternative splicing changes. Hormone-induced exon inclusion often correlates with higher nucleosome occupancy at the exon or the preceding intronic region and with higher RNA polymerase II accumulation. In contrast, exons skipped upon hormone stimulation display low nucleosome densities even before hormone treatment, suggesting that chromatin structure primes alternative splicing regulation. Skipped exons frequently harbor binding sites for hnRNP AB, a hormone-induced splicing regulator whose knock down prevents some hormone-induced skipping events. Collectively, our results argue that a variety of chromatin architecture mechanisms can influence alternative splicing decisions.

  15. Functional diversity of human protein kinase splice variants marks significant expansion of human kinome

    Directory of Open Access Journals (Sweden)

    Anamika Krishanpal

    2009-12-01

    Full Text Available Abstract Background Protein kinases are involved in diverse spectrum of cellular processes. Availability of draft version of the human genomic data in the year 2001 enabled recognition of repertoire of protein kinases. However, over the years the human genomic data is being refined and the current release of human genomic data has helped us to recognize a larger repertoire of over 900 human protein kinases represented mainly by splice variants. Results Many of these identified protein kinases are alternatively spliced products. Interestingly, some of the human kinase splice variants appear to be significantly diverged in terms of their functional properties as represented by incorporation or absence of one or more domains. Many sets of protein kinase splice variants have substantially different domain organization and in a few sets of splice variants kinase domains belong to different subfamilies of kinases suggesting potential participation in different signal transduction pathways. Conclusions Addition or deletion of a domain between splice variants of multi-domain kinases appears to be a means of generating differences in the functional features of otherwise similar kinases. It is intriguing that marked sequence diversity within the catalytic regions of some of the splice variant kinases result in kinases belonging to different subfamilies. These human kinase splice variants with different functions might contribute to diversity of eukaryotic cellular signaling.

  16. Identification of a novel function of CX-4945 as a splicing regulator.

    Directory of Open Access Journals (Sweden)

    Hyeongki Kim

    Full Text Available Alternative splicing is a nearly ubiquitous versatile process that controls gene expression and creates numerous protein isoforms with different functions from a single gene. The significance of alternative splicing has been confirmed by the increasing number of human diseases that are caused by misregulation of splicing events. Very few compounds, however, have been reported to act as inhibitors of alternative splicing, and their potential clinical use needs to be evaluated. Here, we report that CX-4945, a previously well-characterized inhibitor of casein kinase 2 (CK2 and a molecule currently in clinical trials (Phase II for cancer treatment, regulates splicing in mammalian cells in a CK2-independent manner. Transcriptome-wide analysis using exon array also showed a widespread alteration in alternative splicing of numerous genes. We found that CX-4945 potently inhibits the Cdc2-like kinases (Clks in vitro and in turn, leads to suppression of the phosphorylation of serine/arginine-rich (SR proteins in mammalian cells. Surprisingly, the overall efficacy of CX-4945 on Clks (IC50 = 3-90 nM was stronger than that of TG-003, the strongest inhibitor reported to date. Of the Clks, Clk2 was most strongly inhibited by CX-4945 in an ATP-competitive manner. Our research revealed an unexpected activity of the drug candidate CX-4945 as a potent splicing modulator and also suggested a potential application for therapy of diseases caused by abnormal splicing.

  17. HP1 Is Involved in Regulating the Global Impact of DNA Methylation on Alternative Splicing

    Directory of Open Access Journals (Sweden)

    Ahuvi Yearim

    2015-02-01

    Full Text Available The global impact of DNA methylation on alternative splicing is largely unknown. Using a genome-wide approach in wild-type and methylation-deficient embryonic stem cells, we found that DNA methylation can either enhance or silence exon recognition and affects the splicing of more than 20% of alternative exons. These exons are characterized by distinct genetic and epigenetic signatures. Alternative splicing regulation of a subset of these exons can be explained by heterochromatin protein 1 (HP1, which silences or enhances exon recognition in a position-dependent manner. We constructed an experimental system using site-specific targeting of a methylated/unmethylated gene and demonstrate a direct causal relationship between DNA methylation and alternative splicing. HP1 regulates this gene’s alternative splicing in a methylation-dependent manner by recruiting splicing factors to its methylated form. Our results demonstrate DNA methylation’s significant global influence on mRNA splicing and identify a specific mechanism of splicing regulation mediated by HP1.

  18. Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals.

    NARCIS (Netherlands)

    Parmley, J.L.; Hurst, L.D.

    2007-01-01

    In mammals there is a bias in amino acid usage near splice sites that is explained, in large part, by the high density of exonic splicing enhancers (ESEs) in these regions. Is there a similar bias for the relative use of synonymous codons, and can any such bias be predicted by their abundance in ESE

  19. Strategic performance management evaluation for the Navy's SPLICE local area networks

    OpenAIRE

    Blankenship, David D.

    1985-01-01

    Approved for public release; distribution is unlimited This thesis investigates those aspects of network performance evaluation thought to pertain specifically to strategic performance management evaluation of the Navy's Stock Point Logistics Integrated Communications Environment (SPLICE) local area networks at stock point and inventory control point sites- Background is provided concerning the SPLICE Project, strategic management, computer performance evaluation tools...

  20. Unusual intron conservation near tissue-regulated exons found by splicing microarrays.

    Directory of Open Access Journals (Sweden)

    Charles W Sugnet

    2006-01-01

    Full Text Available Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for about 40% of the 6,216 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif that is strikingly similar to the branchpoint consensus but is located downstream of the 5' splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase genes reveals that each contains a paralogous tissue-regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families.

  1. 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

    2007-01-01

    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.

  2. Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock

    Directory of Open Access Journals (Sweden)

    Reut Shalgi

    2014-06-01

    Full Text Available During heat shock and other proteotoxic stresses, cells regulate multiple steps in gene expression in order to globally repress protein synthesis and selectively upregulate stress response proteins. Splicing of several mRNAs is known to be inhibited during heat stress, often meditated by SRp38, but the extent and specificity of this effect have remained unclear. Here, we examined splicing regulation genome-wide during heat shock in mouse fibroblasts. We observed widespread retention of introns in transcripts from ∼1,700 genes, which were enriched for tRNA synthetase, nuclear pore, and spliceosome functions. Transcripts with retained introns were largely nuclear and untranslated. However, a group of 580+ genes biased for oxidation reduction and protein folding functions continued to be efficiently spliced. Interestingly, these unaffected transcripts are mostly cotranscriptionally spliced under both normal and stress conditions, whereas splicing-inhibited transcripts are mostly spliced posttranscriptionally. Altogether, our data demonstrate widespread repression of splicing in the mammalian heat stress response, disproportionately affecting posttranscriptionally spliced genes.

  3. High-throughput alternative splicing detection using dually constrained correspondence analysis (DCCA).

    Science.gov (United States)

    Baty, Florent; Klingbiel, Dirk; Zappa, Francesco; Brutsche, Martin

    2015-12-01

    Alternative splicing is an important component of tumorigenesis. Recent advent of exon array technology enables the detection of alternative splicing at a genome-wide scale. The analysis of high-throughput alternative splicing is not yet standard and methodological developments are still needed. We propose a novel statistical approach-Dually Constrained Correspondence Analysis-for the detection of splicing changes in exon array data. Using this methodology, we investigated the genome-wide alteration of alternative splicing in patients with non-small cell lung cancer treated by bevacizumab/erlotinib. Splicing candidates reveal a series of genes related to carcinogenesis (SFTPB), cell adhesion (STAB2, PCDH15, HABP2), tumor aggressiveness (ARNTL2), apoptosis, proliferation and differentiation (PDE4D, FLT3, IL1R2), cell invasion (ETV1), as well as tumor growth (OLFM4, FGF14), tumor necrosis (AFF3) or tumor suppression (TUSC3, CSMD1, RHOBTB2, SERPINB5), with indication of known alternative splicing in a majority of genes. DCCA facilitates the identification of putative biologically relevant alternative splicing events in high-throughput exon array data.

  4. Intrasplicing coordinates alternative first exons with alternative splicing in the protein 4.1R gene

    Energy Technology Data Exchange (ETDEWEB)

    Conboy, John G.; Parra, Marilyn K.; Tan, Jeff S.; Mohandas, Narla; Conboy, John G.

    2008-11-07

    In the protein 4.1R gene, alternative first exons splice differentially to alternative 3' splice sites far downstream in exon 2'/2 (E2'/2). We describe a novel intrasplicing mechanism by which exon 1A (E1A) splices exclusively to the distal E2'/2 acceptor via two nested splicing reactions regulated by novel properties of exon 1B (E1B). E1B behaves as an exon in the first step, using its consensus 5' donor to splice to the proximal E2'/2 acceptor. A long region of downstream intron is excised, juxtaposing E1B with E2'/2 to generate a new composite acceptor containing the E1B branchpoint/pyrimidine tract and E2 distal 3' AG-dinucleotide. Next, the upstream E1A splices over E1B to this distal acceptor, excising the remaining intron plus E1B and E2' to form mature E1A/E2 product. We mapped branch points for both intrasplicing reactions and demonstrated that mutation of the E1B 5' splice site or branchpoint abrogates intrasplicing. In the 4.1R gene, intrasplicing ultimately determines N-terminal protein structure and function. More generally, intrasplicing represents a new mechanism whereby alternative promoters can be coordinated with downstream alternative splicing.

  5. Identification of interleukin-26 in the dromedary camel (Camelus dromedarius): Evidence of alternative splicing and isolation of novel splice variants.

    Science.gov (United States)

    Premraj, Avinash; Nautiyal, Binita; Aleyas, Abi G; Rasool, Thaha Jamal

    2015-10-01

    Interleukin-26 (IL-26) is a member of the IL-10 family of cytokines. Though conserved across vertebrates, the IL-26 gene is functionally inactivated in a few mammals like rat, mouse and horse. We report here the identification, isolation and cloning of the cDNA of IL-26 from the dromedary camel. The camel cDNA contains a 516 bp open reading frame encoding a 171 amino acid precursor protein, including a 21 amino acid signal peptide. Sequence analysis revealed high similarity with other mammalian IL-26 homologs and the conservation of IL-10 cytokine family domain structure including key amino acid residues. We also report the identification and cloning of four novel transcript variants produced by alternative splicing at the Exon 3-Exon 4 regions of the gene. Three of the alternative splice variants had premature termination codons and are predicted to code for truncated proteins. The transcript variant 4 (Tv4) having an insertion of an extra 120 bp nucleotides in the ORF was predicted to encode a full length protein product with 40 extra amino acid residues. The mRNA transcripts of all the variants were identified in lymph node, where as fewer variants were observed in other tissues like blood, liver and kidney. The expression of Tv2 and Tv3 were found to be up regulated in mitogen induced camel peripheral blood mononuclear cells. IL-26-Tv2 expression was also induced in camel fibroblast cells infected with Camel pox virus in-vitro. The identification of the transcript variants of IL-26 from the dromedary camel is the first report of alternative splicing for IL-26 in a species in which the gene has not been inactivated.

  6. Verification of predicted alternatively spliced Wnt genes reveals two new splice variants (CTNNB1 and LRP5 and altered Axin-1 expression during tumour progression

    Directory of Open Access Journals (Sweden)

    Reich Jens G

    2006-06-01

    Full Text Available Abstract Background Splicing processes might play a major role in carcinogenesis and tumour progression. The Wnt pathway is of crucial relevance for cancer progression. Therefore we focussed on the Wnt/β-catenin signalling pathway in order to validate the expression of sequences predicted as alternatively spliced by bioinformatic methods. Splice variants of its key molecules were selected, which may be critical components for the understanding of colorectal tumour progression and may have the potential to act as biological markers. For some of the Wnt pathway genes the existence of splice variants was either proposed (e.g. β-Catenin and CTNNB1 or described only in non-colon tissues (e.g. GSK3β or hitherto not published (e.g. LRP5. Results Both splice variants – normal and alternative form – of all selected Wnt pathway components were found to be expressed in cell lines as well as in samples derived from tumour, normal and healthy tissues. All splice positions corresponded totally with the bioinformatical prediction as shown by sequencing. Two hitherto not described alternative splice forms (CTNNB1 and LRP5 were detected. Although the underlying EST data used for the bioinformatic analysis suggested a tumour-specific expression neither a qualitative nor a significant quantitative difference between the expression in tumour and healthy tissues was detected. Axin-1 expression was reduced in later stages and in samples from carcinomas forming distant metastases. Conclusion We were first to describe that splice forms of crucial genes of the Wnt-pathway are expressed in human colorectal tissue. Newly described splicefoms were found for β-Catenin, LRP5, GSK3β, Axin-1 and CtBP1. However, the predicted cancer specificity suggested by the origin of the underlying ESTs was neither qualitatively nor significant quantitatively confirmed. That let us to conclude that EST sequence data can give adequate hints for the existence of alternative splicing

  7. A directed approach for the identification of transcripts harbouring the spliced leader sequence and the effect of trans-splicing knockdown in Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Marina de Moraes Mourao

    2013-09-01

    Full Text Available Schistosomiasis is a major neglected tropical disease caused by trematodes from the genus Schistosoma. Because schistosomes exhibit a complex life cycle and numerous mechanisms for regulating gene expression, it is believed that spliced leader (SL trans-splicing could play an important role in the biology of these parasites. The purpose of this study was to investigate the function of trans-splicing in Schistosoma mansoni through analysis of genes that may be regulated by this mechanism and via silencing SL-containing transcripts through RNA interference. Here, we report our analysis of SL transcript-enriched cDNA libraries from different S. mansoni life stages. Our results show that the trans-splicing mechanism is apparently not associated with specific genes, subcellular localisations or life stages. In cross-species comparisons, even though the sets of genes that are subject to SL trans-splicing regulation appear to differ between organisms, several commonly shared orthologues were observed. Knockdown of trans-spliced transcripts in sporocysts resulted in a systemic reduction of the expression levels of all tested trans-spliced transcripts; however, the only phenotypic effect observed was diminished larval size. Further studies involving the findings from this work will provide new insights into the role of trans-splicing in the biology of S. mansoni and other organisms. All Expressed Sequence Tags generated in this study were submitted to dbEST as five different libraries. The accessions for each library and for the individual sequences are as follows: (i adult worms of mixed sexes (LIBEST_027999: JZ139310 - JZ139779, (ii female adult worms (LIBEST_028000: JZ139780 - JZ140379, (iii male adult worms (LIBEST_028001: JZ140380 - JZ141002, (iv eggs (LIBEST_028002: JZ141003 - JZ141497 and (v schistosomula (LIBEST_028003: JZ141498 - JZ141974.

  8. Sororin pre-mRNA splicing is required for proper sister chromatid cohesion in human cells.

    Science.gov (United States)

    Watrin, Erwan; Demidova, Maria; Watrin, Tanguy; Hu, Zheng; Prigent, Claude

    2014-09-01

    Sister chromatid cohesion, which depends on cohesin, is essential for the faithful segregation of replicated chromosomes. Here, we report that splicing complex Prp19 is essential for cohesion in both G2 and mitosis, and consequently for the proper progression of the cell through mitosis. Inactivation of splicing factors SF3a120 and U2AF65 induces similar cohesion defects to Prp19 complex inactivation. Our data indicate that these splicing factors are all required for the accumulation of cohesion factor Sororin, by facilitating the proper splicing of its pre-mRNA. Finally, we show that ectopic expression of Sororin corrects defective cohesion caused by Prp19 complex inactivation. We propose that the Prp19 complex and the splicing machinery contribute to the establishment of cohesion by promoting Sororin accumulation during S phase, and are, therefore, essential to the maintenance of genome stability.

  9. Oncogenic Alternative Splicing Switches: Role in Cancer Progression and Prospects for Therapy

    Directory of Open Access Journals (Sweden)

    Serena Bonomi

    2013-01-01

    Full Text Available 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 might provide a better understanding of the malignant transformation and identify novel pathways that are uniquely relevant to tumorigenesis. Understanding the molecular underpinnings of cancer-associated alternative splicing isoforms will not only help to explain many fundamental hallmarks of cancer, but will also offer unprecedented opportunities to improve the efficacy of anti-cancer treatments.

  10. Genetic variations and alternative splicing. The Glioma associated oncogene 1, GLI1.

    Directory of Open Access Journals (Sweden)

    Peter eZaphiropoulos

    2012-07-01

    Full Text Available Alternative splicing is a post-transcriptional regulatory process that is attaining stronger recognition as a modulator of gene expression. Alternative splicing occurs when the primary RNA transcript is differentially processed into more than one mature RNAs. This is the result of a variable definition/inclusion of the exons, the sequences that are excised from the primary RNA to form the mature RNAs. Consequently, RNA expression can generate a collection of differentially spliced RNAs, which may distinctly influence subsequent biological events, such as protein synthesis or other biomolecular interactions. Still the mechanisms that control exon definition and exon inclusion are not fully clarified. This mini-review highlights advances in this field as well as the impact of single nucleotide polymorphisms in affecting splicing decisions. The Glioma associated oncogene 1, GLI1, is taken as an example in addressing the role of nucleotide substitutions for splicing regulation.

  11. Experimental approaches to studying the nature and impact of splicing variation in zebrafish.

    Science.gov (United States)

    Keightley, M C; Markmiller, S; Love, C G; Rasko, J E J; Lieschke, G J; Heath, J K

    2016-01-01

    From a fixed number of genes carried in all cells, organisms create considerable diversity in cellular phenotype through differential regulation of gene expression. One prevalent source of transcriptome diversity is alternative pre-mRNA splicing, which is manifested in many different forms. Zebrafish models of splicing dysfunction due to mutated spliceosome components provide opportunity to link biochemical analyses of spliceosome structure and function with whole organism phenotypic outcomes. Drawing from experience with two zebrafish mutants: cephalophŏnus (a prpf8 mutant, isolated for defects in granulopoiesis) and caliban (a rnpc3 mutant, isolated for defects in digestive organ development), we describe the use of glycerol gradient sedimentation and native gel electrophoresis to resolve components of aberrant splicing complexes. We also describe how RNAseq can be employed to examine relatively rare alternative splicing events including intron retention. Such experimental approaches in zebrafish can promote understanding of how splicing variation and dysfunction contribute to phenotypic diversity and disease pathogenesis.

  12. On the path to genetic novelties: insights from programmed DNA elimination and RNA splicing.

    Science.gov (United States)

    Catania, Francesco; Schmitz, Jürgen

    2015-01-01

    Understanding how genetic novelties arise is a central goal of evolutionary biology. To this end, programmed DNA elimination and RNA splicing deserve special consideration. While programmed DNA elimination reshapes genomes by eliminating chromatin during organismal development, RNA splicing rearranges genetic messages by removing intronic regions during transcription. Small RNAs help to mediate this class of sequence reorganization, which is not error-free. It is this imperfection that makes programmed DNA elimination and RNA splicing excellent candidates for generating evolutionary novelties. Leveraging a number of these two processes' mechanistic and evolutionary properties, which have been uncovered over the past years, we present recently proposed models and empirical evidence for how splicing can shape the structure of protein-coding genes in eukaryotes. We also chronicle a number of intriguing similarities between the processes of programmed DNA elimination and RNA splicing, and highlight the role that the variation in the population-genetic environment may play in shaping their target sequences.

  13. The splicing factor SRSF6 is amplified and is an oncoprotein in lung and colon cancers

    DEFF Research Database (Denmark)

    Cohen-Eliav, Michal; Golan-Gerstl, Regina; Siegfried, Zahava;

    2013-01-01

    An increasing body of evidence connects alterations in the process of alternative splicing with cancer development and progression. However, a direct role of splicing factors as drivers of cancer development is mostly unknown. We analyzed the gene copy number of several splicing factors in colon...... and lung tumors and found that the gene encoding for the splicing factor SRSF6 is amplified and overexpressed in these cancers. Moreover, overexpression of SRSF6 in immortal lung epithelial cells enhanced proliferation, protected them from chemotherapy-induced cell death and converted them...... to be tumorigenic in mice. In contrast, knockdown of SRSF6 in lung and colon cancer cell lines inhibited their tumorigenic abilities. SRSF6 up- or down regulation altered the splicing of several tumor suppressors and oncogenes to generate the oncogenic isoforms and reduce the tumor suppressive isoforms. Our data...

  14. On splice site prediction using weight array models: a comparison of smoothing techniques

    Science.gov (United States)

    Taher, Leila; Meinicke, Peter; Morgenstern, Burkhard

    2007-11-01

    In most eukaryotic genes, protein-coding exons are separated by non-coding introns which are removed from the primary transcript by a process called "splicing". The positions where introns are cut and exons are spliced together are called "splice sites". Thus, computational prediction of splice sites is crucial for gene finding in eukaryotes. Weight array models are a powerful probabilistic approach to splice site detection. Parameters for these models are usually derived from m-tuple frequencies in trusted training data and subsequently smoothed to avoid zero probabilities. In this study we compare three different ways of parameter estimation for m-tuple frequencies, namely (a) non-smoothed probability estimation, (b) standard pseudo counts and (c) a Gaussian smoothing procedure that we recently developed.

  15. Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants.

    Science.gov (United States)

    Yoshida, Masa-aki; Yura, Kei; Ogura, Atsushi

    2014-03-05

    Previous studies have reported that the developmental processes of vertebrate eyes are controlled by four Pax-6 splicing variants, each modulating different downstream genes, whereas those of insect eyes are controlled by duplicated Pax-6 genes. Cephalopods belong to the Protostomes but possess a camera-type eye similar to those in vertebrates. We examined Pax-6 variations in the squid and found five types of Pax-6 splicing variants but no duplication of the Pax-6 gene. In the five splicing variants, the splicing patterns were produced by the combination of two additional exons to the ortholog and one jettisoned exon containing most of the Homeobox domain (HD). These five variants show spatio-temporal patterns of gene expression during development in the squid. Our study suggests that cephalopods acquired Pax-6 splicing variants independent of those in vertebrates and that these variants were similarly utilized in the development of the squid eye.

  16. Diagnosis of trypanosomatid infections: targeting the spliced leader RNA.

    Science.gov (United States)

    González-Andrade, Pablo; Camara, Mamady; Ilboudo, Hamidou; Bucheton, Bruno; Jamonneau, Vincent; Deborggraeve, Stijn

    2014-07-01

    Trypanosomatids transcribe their genes in large polycistronic clusters that are further processed into mature mRNA molecules by trans-splicing. During this maturation process, a conserved spliced leader RNA (SL-RNA) sequence of 39 bp is physically linked to the 5' end of the pre-mRNA molecules. Trypanosomatid infections cause a series of devastating diseases in man (sleeping sickness, leishmaniasis, Chagas disease) and animals (nagana, surra, dourine). Here, we investigated the SL-RNA molecule for its diagnostic potential using reverse transcription followed by real-time PCR. As a model, we used Trypanosoma brucei gambiense, which causes sleeping sickness in west and central Africa. We showed that the copy number of the SL-RNA molecule in one single parasitic cell is at least 8600. We observed a lower detection limit of the SL-RNA assay in spiked blood samples of 100 trypanosomes per milliliter of blood. We also proved that we can detect the trypanosome's SL-RNA in the blood of sleeping sickness patients with a sensitivity of 92% (95% CI, 78%-97%) and a specificity of 96% (95% CI, 86%-99%). The SL-RNA is thus an attractive new molecular target for next-generation diagnostics in diseases caused by trypanosomatids.

  17. Comparative cross-species alternative splicing in plants.

    Science.gov (United States)

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

    2007-07-01

    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.

  18. Coding potential of the products of alternative splicing in human.

    KAUST Repository

    Leoni, Guido

    2011-01-20

    BACKGROUND: Analysis of the human genome has revealed that as much as an order of magnitude more of the genomic sequence is transcribed than accounted for by the predicted and characterized genes. A number of these transcripts are alternatively spliced forms of known protein coding genes; however, it is becoming clear that many of them do not necessarily correspond to a functional protein. RESULTS: In this study we analyze alternative splicing isoforms of human gene products that are unambiguously identified by mass spectrometry and compare their properties with those of isoforms of the same genes for which no peptide was found in publicly available mass spectrometry datasets. We analyze them in detail for the presence of uninterrupted functional domains, active sites as well as the plausibility of their predicted structure. We report how well each of these strategies and their combination can correctly identify translated isoforms and derive a lower limit for their specificity, that is, their ability to correctly identify non-translated products. CONCLUSIONS: The most effective strategy for correctly identifying translated products relies on the conservation of active sites, but it can only be applied to a small fraction of isoforms, while a reasonably high coverage, sensitivity and specificity can be achieved by analyzing the presence of non-truncated functional domains. Combining the latter with an assessment of the plausibility of the modeled structure of the isoform increases both coverage and specificity with a moderate cost in terms of sensitivity.

  19. Correlated Evolution of Nucleotide Positions within Splice Sites in Mammals.

    Science.gov (United States)

    Denisov, Stepan; Bazykin, Georgii; Favorov, Alexander; Mironov, Andrey; Gelfand, Mikhail

    2015-01-01

    Splice sites (SSs)--short nucleotide sequences flanking introns--are under selection for spliceosome binding, and adhere to consensus sequences. However, non-consensus nucleotides, many of which probably reduce SS performance, are frequent. Little is known about the mechanisms maintaining such apparently suboptimal SSs. Here, we study the correlations between strengths of nucleotides occupying different positions of the same SS. Such correlations may arise due to epistatic interactions between positions (i.e., a situation when the fitness effect of a nucleotide in one position depends on the nucleotide in another position), their evolutionary history, or to other reasons. Within both the intronic and the exonic parts of donor SSs, nucleotides that increase (decrease) SS strength tend to co-occur with other nucleotides increasing (respectively, decreasing) it, consistent with positive epistasis. Between the intronic and exonic parts of donor SSs, the correlations of nucleotide strengths tend to be negative, consistent with negative epistasis. In the course of evolution, substitutions at a donor SS tend to decrease the strength of its exonic part, and either increase or do not change the strength of its intronic part. In acceptor SSs, the situation is more complicated; the correlations between adjacent positions appear to be driven mainly by avoidance of the AG dinucleotide which may cause aberrant splicing. In summary, both the content and the evolution of SSs is shaped by a complex network of interdependences between adjacent nucleotides that respond to a range of sometimes conflicting selective constraints.

  20. Molecular heterogeneity and alternative splicing of human lactoperoxidase.

    Science.gov (United States)

    Fragoso, Miryam A; Torbati, Aliza; Fregien, Nevis; Conner, Gregory E

    2009-02-01

    Human lactoperoxidase (LPO) exists as two distinct molecules independent of glycosylation. The N-terminus of one form is blocked and has not been identified while the other is proteolytically processed at the N-terminus similar to myeloperoxidase. Our analysis identified alternatively spliced human LPO mRNAs that may explain the observed molecular heterogeneity of LPO. Two mRNAs omit propeptide encoding exons while retaining the 5' exon encoding the secretion signal, consistent with the heterogeneity and suggesting a possible functional role for the propeptide. Two LPO forms were expressed using baculovirus and both showed similar enzyme activity. LC/MS/MS analysis of trypsin digested, partially purified, salivary LPO confirmed the larger unprocessed LPO is present in saliva. To compare variant expression patterns, antisera were raised against purified recombinant (rhLPO) as well as against an antigenic peptide sequence within the exons encoding the propeptide region. Immunohistochemistry demonstrated proLPO was differently localized within gland cells compared to other forms of LPO. The data suggested splice variants may contribute to LPO molecular heterogeneity and its regulation by intracellular compartmental localization.

  1. Cancer-Associated Perturbations in Alternative Pre-messenger RNA Splicing.

    Science.gov (United States)

    Shkreta, Lulzim; Bell, Brendan; Revil, Timothée; Venables, Julian P; Prinos, Panagiotis; Elela, Sherif Abou; Chabot, Benoit

    2013-01-01

    For most of our 25,000 genes, the removal of introns by pre-messenger RNA (pre-mRNA) splicing represents an essential step toward the production of functional messenger RNAs (mRNAs). Alternative splicing of a single pre-mRNA results in the production of different mRNAs. Although complex organisms use alternative splicing to expand protein function and phenotypic diversity, patterns of alternative splicing are often altered in cancer cells. Alternative splicing contributes to tumorigenesis by producing splice isoforms that can stimulate cell proliferation and cell migration or induce resistance to apoptosis and anticancer agents. Cancer-specific changes in splicing profiles can occur through mutations that are affecting splice sites and splicing control elements, and also by alterations in the expression of proteins that control splicing decisions. Recent progress in global approaches that interrogate splicing diversity should help to obtain specific splicing signatures for cancer types. The development of innovative approaches for annotating and reprogramming splicing events will more fully establish the essential contribution of alternative splicing to the biology of cancer and will hopefully provide novel targets and anticancer strategies. Metazoan genes are usually made up of several exons interrupted by introns. The introns are removed from the pre-mRNA by RNA splicing. In conjunction with other maturation steps, such as capping and polyadenylation, the spliced mRNA is then transported to the cytoplasm to be translated into a functional protein. The basic mechanism of splicing requires accurate recognition of each extremity of each intron by the spliceosome. Introns are identified by the binding of U1 snRNP to the 5' splice site and the U2AF65/U2AF35 complex to the 3' splice site. Following these interactions, other proteins and snRNPs are recruited to generate the complete spliceosomal complex needed to excise the intron. While many introns are constitutively

  2. Alternative pre-mRNA splicing in Drosophila spliceosomal assembly factor RNP-4F during development.

    Science.gov (United States)

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

    2006-04-26

    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.

  3. The emergence of alternative 3' and 5' splice site exons from constitutive exons.

    Directory of Open Access Journals (Sweden)

    Eli Koren

    2007-05-01

    Full Text Available Alternative 3' and 5' splice site (ss events constitute a significant part of all alternative splicing events. These events were also found to be related to several aberrant splicing diseases. However, only few of the characteristics that distinguish these events from alternative cassette exons are known currently. In this study, we compared the characteristics of constitutive exons, alternative cassette exons, and alternative 3'ss and 5'ss exons. The results revealed that alternative 3'ss and 5'ss exons are an intermediate state between constitutive and alternative cassette exons, where the constitutive side resembles constitutive exons, and the alternative side resembles alternative cassette exons. The results also show that alternative 3'ss and 5'ss exons exhibit low levels of symmetry (frame-preserving, similar to constitutive exons, whereas the sequence between the two alternative splice sites shows high symmetry levels, similar to alternative cassette exons. In addition, flanking intronic conservation analysis revealed that exons whose alternative splice sites are at least nine nucleotides apart show a high conservation level, indicating intronic participation in the regulation of their splicing, whereas exons whose alternative splice sites are fewer than nine nucleotides apart show a low conservation level. Further examination of these exons, spanning seven vertebrate species, suggests an evolutionary model in which the alternative state is a derivative of an ancestral constitutive exon, where a mutation inside the exon or along the flanking intron resulted in the creation of a new splice site that competes with the original one, leading to alternative splice site selection. This model was validated experimentally on four exons, showing that they indeed originated from constitutive exons that acquired a new competing splice site during evolution.

  4. Mechanics of Sheeting Joints

    Science.gov (United States)

    Martel, S. J.

    2015-12-01

    Physical breakdown of rock across a broad scale spectrum involves fracturing. In many areas large fractures develop near the topographic surface, with sheeting joints being among the most impressive. Sheeting joints share many geometric, textural, and kinematic features with other joints (opening-mode fractures) but differ in that they are (a) discernibly curved, (b) open near the topographic surface, and (c) form subparallel to the topographic surface. Where sheeting joints are geologically young, the surface-parallel compressive stresses are typically several MPa or greater. Sheeting joints are best developed beneath domes, ridges, and saddles; they also are reported, albeit rarely, beneath valleys or bowls. A mechanism that accounts for all these associations has been sought for more than a century: neither erosion of overburden nor high lateral compressive stresses alone suffices. Sheeting joints are not accounted for by Mohr-Coulomb shear failure criteria. Principles of linear elastic fracture mechanics, together with the mechanical effect of a curved topographic surface, do provide a basis for understanding sheeting joint growth and the pattern sheeting joints form. Compressive stresses parallel to a singly or doubly convex topographic surface induce a tensile stress perpendicular to the surface at shallow depths; in some cases this alone could overcome the weight of overburden to open sheeting joints. If regional horizontal compressive stresses, augmented by thermal stresses, are an order of magnitude or so greater than a characteristic vertical stress that scales with topographic amplitude, then topographic stress perturbations can cause sheeting joints to open near the top of a ridge. This topographic effect can be augmented by pressure within sheeting joints arising from water, ice, or salt. Water pressure could be particularly important in helping drive sheeting joints downslope beneath valleys. Once sheeting joints have formed, the rock sheets between

  5. Probabilistic Assessment of Degree of Bending in Tubular X-Joints of Offshore Structures Subjected to Bending Loads

    Directory of Open Access Journals (Sweden)

    Hamid Ahmadi

    2015-01-01

    Full Text Available Fatigue life of tubular joints in offshore structures is significantly influenced by the degree of bending (DoB. The DoB exhibits considerable scatter calling for greater emphasis in accurate determination of its governing probability distribution which is a key input for the fatigue reliability analysis of a tubular joint. Although the tubular X-joints are commonly found in offshore jacket structures, as far as the authors are aware, no comprehensive research has been carried out on the probability distribution of the DoB in tubular X-joints. In the present paper, results of parametric equations available for the calculation of the DoB have been used to develop probability distribution models for the DoB in the chord member of tubular X-joints subjected to four types of bending loads. Based on a parametric study, a set of samples was prepared and density histograms were generated for these samples using Freedman-Diaconis method. Twelve different probability density functions (PDFs were fitted to these histograms. In each case, Kolmogorov-Smirnov test was used to evaluate the goodness of fit. Finally, after substituting the values of estimated parameters for each distribution, a set of fully defined PDFs have been proposed for the DoB in tubular X-joints subjected to bending loads.

  6. MR diagnosis of temporomandibular joint. A study of joint effusion

    Energy Technology Data Exchange (ETDEWEB)

    Kaneda, Takashi; Yamashiro, Mitsuaki; Ozawa, Kaoru; Suzuki, Hiromi; Okada, Hiroyuki; Yamamoto, Hirotsugu [Nihon Univ., Matsudo, Chiba (Japan). School of Dentistry

    1998-03-01

    The purposes of this study were to evaluate the relationship between correlation of MR joint effusion of the temporomandibular joint and disk position, to evaluate the relationship between joint effusion and aging, and to assess the frequency of MR joint effusion of bilateral temporomandibular joints. The temporomandibular joints of 192 patients with clinical symptoms of temporomandibular joint disorders were imaged bilaterally using high field, surface-coil MR imaging. Oblique sagittal and coronal proton density-weighted and T2-weighted images were obtained. Imaging findings of joint effusion were correlated with disk position, aging, and bilateral temporomandibular joints. MR showed effusion in 4% of the joints with normal superior disk position, 36% of the joints with disk displacement with reduction, and 45% of the joints with disk displacement without reduction. There were significant differences in the incidence of joint effusion between normal disk position and anterior disk displacement with or without reduction. Younger patients less than 40 years were significant higher the incidence of joint effusion than those of older patients. A significant association was seen between joint effusion and aging. MR showed effusion in 17% of the unilateral temporomandibular joint, 24% of the bilateral temporomandibular joints. There was no significant difference between unilateral and bilateral case. These results indicated that joint effusion using MR imaging was associated with varied temporomandibular joint pathologic states. (author)

  7. Acromioclavicular Joint Separations

    Science.gov (United States)

    2013-01-01

    Published online: 16 December 2012 # Springer Science+Business Media New York 2012 Abstract Acromioclavicular (AC) joint separations are common...injuries. The sports most likely to cause AC joint dislocations are football, soccer , hockey, rugby, and skiing, among others [9, 28, 29]. The major cause

  8. Jointness for the Rest of Us: Reforming Joint Professional Development

    Science.gov (United States)

    2016-06-10

    service members for joint employment . Similar to their enlisted counterparts, the training, education and professional development of DOD civilian...the U.S. Armed forces sought by Congressional legislators and Defense leaders is not possible as long as joint education and training are limited to a...SUBJECT TERMS joint training, joint education , Goldwater Nichols Act, jointness, joint development reform analytics 16. SECURITY CLASSIFICATION OF

  9. Chord protocol and algorithm in distributed programming language%基于分布式编程语言的Chord协议和算法

    Institute of Scientific and Technical Information of China (English)

    彭成章; 蒋泽军; 蔡小斌; 张志珂

    2013-01-01

    The Peer-to-Peer (P2P) Distributed Hash Table (DHT) protocol is concise,and can be understood easily,but implementing and deploying a component like Chord with all functions in practice is very difficult and complicated because of the mismatch between popular imperative language and distributed architecture.To resolve these problems,a P2P DHT protocol based on Bloom system was proposed.Firstly,the distributed logic programming language's key elements of Bloom system were expounded.Secondly,a minimal distributed system was designed.Thirdly,a Chord prototype system was implemented through defining persistent,transient,asynchronous communicating and periodic collections and designing several algorithms for finger table maintaining,successor listing,stabilization preseving and so on.The experimental results show that the prototype system can finish full functions of Chord,and compared to traditional languages,60% of the code lines can be saved.The analysis indicates such a high degree of uniformity between final code of the algorithm and the DHT protocol specification makes it more readable and reusable,and helpful for further understanding the specific protocol and relative applications.%P2P分布式哈希表(DHT)协议本身简洁并且易于理解,但是命令式语言与分布式架构的不匹配使得实现和部署一个拥有全部功能的类似Chord的组件相当困难和复杂.针对这些问题,提出一种基于Bloom系统来设计P2P分布式哈希表协议的方法.首先,阐述了Bloom系统的分布式逻辑编程语言要素;其次,设计了一个最小分布式系统;再次,通过定义永久、暂时、异步通信和周期集合,设计了指表维护算法、后继列表算法以及维持稳定算法等,实现一个Chord原型系统.实验结果证明,原型系统能完成Chord所有功能,并且与传统语言相比,代码量减少60%.分析表明最终的算法代码和分布式哈希表协议规范高度一致,不仅增强了代码的

  10. An alternative splicing switch shapes neurexin repertoires in principal neurons versus interneurons in the mouse hippocampus

    Science.gov (United States)

    Nguyen, Thi-Minh; Schreiner, Dietmar; Xiao, Le; Traunmüller, Lisa; Bornmann, Caroline; Scheiffele, Peter

    2016-01-01

    The unique anatomical and functional features of principal and interneuron populations are critical for the appropriate function of neuronal circuits. Cell type-specific properties are encoded by selective gene expression programs that shape molecular repertoires and synaptic protein complexes. However, the nature of such programs, particularly for post-transcriptional regulation at the level of alternative splicing is only beginning to emerge. We here demonstrate that transcripts encoding the synaptic adhesion molecules neurexin-1,2,3 are commonly expressed in principal cells and interneurons of the mouse hippocampus but undergo highly differential, cell type-specific alternative splicing. Principal cell-specific neurexin splice isoforms depend on the RNA-binding protein Slm2. By contrast, most parvalbumin-positive (PV+) interneurons lack Slm2, express a different neurexin splice isoform and co-express the corresponding splice isoform-specific neurexin ligand Cbln4. Conditional ablation of Nrxn alternative splice insertions selectively in PV+ cells results in elevated hippocampal network activity and impairment in a learning task. Thus, PV-cell-specific alternative splicing of neurexins is critical for neuronal circuit function DOI: http://dx.doi.org/10.7554/eLife.22757.001 PMID:27960072

  11. The evolutionary fate of alternatively spliced homologous exons after gene duplication.

    Science.gov (United States)

    Abascal, Federico; Tress, Michael L; Valencia, Alfonso

    2015-04-29

    Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly understood. Here, we have carried out a study of the evolution of alternatively spliced exons after gene duplication to better understand the interaction between the two processes. We created a manually curated set of 97 human genes with mutually exclusively spliced homologous exons and analyzed the evolution of these exons across five distantly related vertebrates (lamprey, spotted gar, zebrafish, fugu, and coelacanth). Most of these exons had an ancient origin (more than 400 Ma). We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication. We observed 11 events in which gene duplication was accompanied by splice isoform separation, that is, each paralog specifically conserved just one distinct ancestral homologous exon. At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes. That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene.

  12. RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure.

    Science.gov (United States)

    Gao, Chen; Ren, Shuxun; Lee, Jae-Hyung; Qiu, Jinsong; Chapski, Douglas J; Rau, Christoph D; Zhou, Yu; Abdellatif, Maha; Nakano, Astushi; Vondriska, Thomas M; Xiao, Xinshu; Fu, Xiang-Dong; Chen, Jau-Nian; Wang, Yibin

    2016-01-01

    RNA splicing is a major contributor to total transcriptome complexity; however, the functional role and regulation of splicing in heart failure remain poorly understood. Here, we used a total transcriptome profiling and bioinformatic analysis approach and identified a muscle-specific isoform of an RNA splicing regulator, RBFox1 (also known as A2BP1), as a prominent regulator of alternative RNA splicing during heart failure. Evaluation of developing murine and zebrafish hearts revealed that RBFox1 is induced during postnatal cardiac maturation. However, we found that RBFox1 is markedly diminished in failing human and mouse hearts. In a mouse model, RBFox1 deficiency in the heart promoted pressure overload-induced heart failure. We determined that RBFox1 is a potent regulator of RNA splicing and is required for a conserved splicing process of transcription factor MEF2 family members that yields different MEF2 isoforms with differential effects on cardiac hypertrophic gene expression. Finally, induction of RBFox1 expression in murine pressure overload models substantially attenuated cardiac hypertrophy and pathological manifestations. Together, this study identifies regulation of RNA splicing by RBFox1 as an important player in transcriptome reprogramming during heart failure that influence pathogenesis of the disease.

  13. Modification of Alternative Splicing of Bcl-x Pre-mRNA in Bladder Cancer Cells

    Institute of Scientific and Technical Information of China (English)

    ZHU Zhaohui; XING Shi'an; CHENG Ping; ZENG Fuqing; LU Gongcheng

    2006-01-01

    To modify the splicing pattern of Bcl-x and compare the effect of this approach with that of the antisense gene therapy in BIU-87 cell line of bladder cancer, by using 5'-Bcl-x AS to target downstream alternative 5'-Bcl-x splice site to shift splicing from Bcl-xL to Bcl-xS and 3'-Bcl-x AS antisense to the 3'-splice site of exon Ⅲ in Bcl-x pre- mRNA to down regulation of Bcl-xL expression,the inhibitory effects on cancer cells by modification of alternative splicing and antisense gene therapy were observed and compared by microscopy, MTT Assay, RT-PCR, FACS, Westhern bloting and clone formation. The growth of cells BIU-87 was inhibited in a dose- and time-dependent manner. Its inhibitory effect began 12 h after the exposure, reaching a maximum value after 72h. The number of cells decreased in S phase and the number increased in G1 phase. The ability to form foci was reduced and the antisense gene therapy was approximately half as efficient as modification of alternative splicing in inducing apoptosis. It is concluded that modification of splicing pattern of Bcl-x pre-mRNA in bladder cancer cell BIU-87 is better than antisense gene therapy in terms of tumor inhibition.

  14. Spatio-temporal regulations and functions of neuronal alternative RNA splicing in developing and adult brains.

    Science.gov (United States)

    Iijima, Takatoshi; Hidaka, Chiharu; Iijima, Yoko

    2016-08-01

    Alternative pre-mRNA splicing is a fundamental mechanism that generates molecular diversity from a single gene. In the central nervous system (CNS), key neural developmental steps are thought to be controlled by alternative splicing decisions, including the molecular diversity underlying synaptic wiring, plasticity, and remodeling. Significant progress has been made in understanding the molecular mechanisms and functions of alternative pre-mRNA splicing in neurons through studies in invertebrate systems; however, recent studies have begun to uncover the potential role of neuronal alternative splicing in the mammalian CNS. This article provides an overview of recent findings regarding the regulation and function of neuronal alternative splicing. In particular, we focus on the spatio-temporal regulation of neurexin, a synaptic adhesion molecule, by neuronal cell type-specific factors and neuronal activity, which are thought to be especially important for characterizing neural development and function within the mammalian CNS. Notably, there is increasing evidence that implicates the dysregulation of neuronal splicing events in several neurological disorders. Therefore, understanding the detailed mechanisms of neuronal alternative splicing in the mammalian CNS may provide plausible treatment strategies for these diseases.

  15. Evolutionary constraint helps unmask a splicing regulatory region in BRCA1 exon 11.

    Directory of Open Access Journals (Sweden)

    Michela Raponi

    Full Text Available BACKGROUND: Alternative splicing across exon 11 produces several BRCA1 isoforms. Their proportion varies during the cell cycle, between tissues and in cancer suggesting functional importance of BRCA1 splicing regulation around this exon. Although the regulatory elements driving exon 11 splicing have never been identified, a selective constraint against synonymous substitutions (silent nucleotide variations that do not alter the amino acid residue sequence in a critical region of BRCA1 exon 11 has been reported to be associated with the necessity to maintain regulatory sequences. METHODOLOGY/PRINCIPAL FINDINGS: Here we have designed a specific minigene to investigate the possibility that this bias in synonymous codon usage reflects the need to preserve the BRCA1 alternative splicing program. We report that in-frame deletions and translationally silent nucleotide substitutions in the critical region affect splicing regulation of BRCA1 exon 11. CONCLUSIONS/SIGNIFICANCE: Using a hybrid minigene approach, we have experimentally validated the hypothesis that the need to maintain correct alternative splicing is a selective pressure against translationally silent sequence variations in the critical region of BRCA1 exon 11. Identification of the trans-acting factors involved in regulating exon 11 alternative splicing will be important in understanding BRCA1-associated tumorigenesis.

  16. Misregulation of Alternative Splicing in a Mouse Model of Rett Syndrome.

    Directory of Open Access Journals (Sweden)

    Ronghui Li

    2016-06-01

    Full Text Available Mutations in the human MECP2 gene cause Rett syndrome (RTT, a severe neurodevelopmental disorder that predominantly affects girls. Despite decades of work, the molecular function of MeCP2 is not fully understood. Here we report a systematic identification of MeCP2-interacting proteins in the mouse brain. In addition to transcription regulators, we found that MeCP2 physically interacts with several modulators of RNA splicing, including LEDGF and DHX9. These interactions are disrupted by RTT causing mutations, suggesting that they may play a role in RTT pathogenesis. Consistent with the idea, deep RNA sequencing revealed misregulation of hundreds of splicing events in the cortex of Mecp2 knockout mice. To reveal the functional consequence of altered RNA splicing due to the loss of MeCP2, we focused on the regulation of the splicing of the flip/flop exon of Gria2 and other AMPAR genes. We found a significant splicing shift in the flip/flop exon toward the flop inclusion, leading to a faster decay in the AMPAR gated current and altered synaptic transmission. In summary, our study identified direct physical interaction between MeCP2 and splicing factors, a novel MeCP2 target gene, and established functional connection between a specific RNA splicing change and synaptic phenotypes in RTT mice. These results not only help our understanding of the molecular function of MeCP2, but also reveal potential drug targets for future therapies.

  17. Tissue-specific genetic control of splicing: implications for the study of complex traits.

    Directory of Open Access Journals (Sweden)

    Erin L Heinzen

    2008-12-01

    Full Text Available Numerous genome-wide screens for polymorphisms that influence gene expression have provided key insights into the genetic control of transcription. Despite this work, the relevance of specific polymorphisms to in vivo expression and splicing remains unclear. We carried out the first genome-wide screen, to our knowledge, for SNPs that associate with alternative splicing and gene expression in human primary cells, evaluating 93 autopsy-collected cortical brain tissue samples with no defined neuropsychiatric condition and 80 peripheral blood mononucleated cell samples collected from living healthy donors. We identified 23 high confidence associations with total expression and 80 with alternative splicing as reflected by expression levels of specific exons. Fewer than 50% of the implicated SNPs however show effects in both tissue types, reflecting strong evidence for distinct genetic control of splicing and expression in the two tissue types. The data generated here also suggest the possibility that splicing effects may be responsible for up to 13 out of 84 reported genome-wide significant associations with human traits. These results emphasize the importance of establishing a database of polymorphisms affecting splicing and expression in primary tissue types and suggest that splicing effects may be of more phenotypic significance than overall gene expression changes.

  18. Alternative splicing of the maize Ac transposase transcript in transgenic sugar beet (Beta vulgaris L.).

    Science.gov (United States)

    Lisson, Ralph; Hellert, Jan; Ringleb, Malte; Machens, Fabian; Kraus, Josef; Hehl, Reinhard

    2010-09-01

    The maize Activator/Dissociation (Ac/Ds) transposable element system was introduced into sugar beet. The autonomous Ac and non-autonomous Ds element excise from the T-DNA vector and integrate at novel positions in the sugar beet genome. Ac and Ds excisions generate footprints in the donor T-DNA that support the hairpin model for transposon excision. Two complete integration events into genomic sugar beet DNA were obtained by IPCR. Integration of Ac leads to an eight bp duplication, while integration of Ds in a homologue of a sugar beet flowering locus gene did not induce a duplication. The molecular structure of the target site indicates Ds integration into a double strand break. Analyses of transposase transcription using RT-PCR revealed low amounts of alternatively spliced mRNAs. The fourth intron of the transposase was found to be partially misspliced. Four different splice products were identified. In addition, the second and third exon were found to harbour two and three novel introns, respectively. These utilize each the same splice donor but several alternative splice acceptor sites. Using the SplicePredictor online tool, one of the two introns within exon two is predicted to be efficiently spliced in maize. Most interestingly, splicing of this intron together with the four major introns of Ac would generate a transposase that lacks the DNA binding domain and two of its three nuclear localization signals, but still harbours the dimerization domain.

  19. Unfolding the mystery of alternative splicing through a unique method of in vivo selection.

    Science.gov (United States)

    Singh, Ravindra N

    2007-05-01

    Alternative splicing of pre-messenger RNA (pre-mRNA) is a fundamental mechanism of gene regulation in higher eukaryotes. In addition to creating protein diversity, alternative splicing provides the safest mode of gene evolution. Of late, more and more forms of alternatively spliced transcripts (mRNAs) are being discovered for key genes. Some of the alternatively spliced transcripts are also associated with major human diseases. This has created a sense of urgency to find the methods by which regulation of alternative splicing of specific exons could be best understood. Here I review a powerful in vivo selection method that uses a combinatorial library of partially random sequences. Several advantages of this method include in vivo analysis of large sequences, identification of unique sequence motifs, determination of relative strength of splice sites and identification of long-distance interactions including role of RNA structures. This unique method could be applied to identify tissue-specific cis-elements. Similarly, the method is suitable to find cis-elements that become active in response to specific treatments of cells. Considering this unbiased method uses in vivo conditions, it has potential to identify critical regulatory elements as therapeutic targets for a growing number of splicing-associated diseases.

  20. A competitive regulatory mechanism discriminates between juxtaposed splice sites and pri-miRNA structures.

    Science.gov (United States)

    Mattioli, Chiara; Pianigiani, Giulia; Pagani, Franco

    2013-10-01

    We have explored the functional relationships between spliceosome and Microprocessor complex activities in a novel class of microRNAs (miRNAs), named Splice site Overlapping (SO) miRNAs, whose pri-miRNA hairpins overlap splice sites. We focused on the evolutionarily conserved SO miR-34b, and we identified two indispensable elements for recognition of its 3' splice site: a branch point located in the hairpin and a downstream purine-rich exonic splicing enhancer. In minigene systems, splicing inhibition owing to exonic splicing enhancer deletion or AG 3'ss mutation increases miR-34b levels. Moreover, small interfering-mediated silencing of Drosha and/or DGCR8 improves splicing efficiency and abolishes miR-34b production. Thus, the processing of this 3' SO miRNA is regulated in an antagonistic manner by the Microprocessor and the spliceosome owing to competition between these two machineries for the nascent transcript. We propose that this novel mechanism is commonly used to regulate the relative amount of SO miRNA and messenger RNA produced from primary transcripts.

  1. Compensatory signals associated with the activation of human GC 5' splice sites.

    Science.gov (United States)

    Kralovicova, Jana; Hwang, Gyulin; Asplund, A Charlotta; Churbanov, Alexander; Smith, C I Edvard; Vorechovsky, Igor

    2011-09-01

    GC 5' splice sites (5'ss) are present in ∼1% of human introns, but factors promoting their efficient selection are poorly understood. Here, we describe a case of X-linked agammaglobulinemia resulting from a GC 5'ss activated by a mutation in BTK intron 3. This GC 5'ss was intrinsically weak, yet it was selected in >90% primary transcripts in the presence of a strong and intact natural GT counterpart. We show that efficient selection of this GC 5'ss required a high density of GAA/CAA-containing splicing enhancers in the exonized segment and was promoted by SR proteins 9G8, Tra2β and SC35. The GC 5'ss was efficiently inhibited by splice-switching oligonucleotides targeting either the GC 5'ss itself or the enhancer. Comprehensive analysis of natural GC-AG introns and previously reported pathogenic GC 5'ss showed that their efficient activation was facilitated by higher densities of splicing enhancers and lower densities of silencers than their GT 5'ss equivalents. Removal of the GC-AG introns was promoted to a minor extent by the splice-site strength of adjacent exons and inhibited by flanking Alu repeats, with the first downstream Alus located on average at a longer distance from the GC 5'ss than other transposable elements. These results provide new insights into the splicing code that governs selection of noncanonical splice sites.

  2. Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors.

    Directory of Open Access Journals (Sweden)

    Nathan Salomonis

    2009-11-01

    Full Text Available The role of alternative splicing in self-renewal, pluripotency and tissue lineage specification of human embryonic stem cells (hESCs is largely unknown. To better define these regulatory cues, we modified the H9 hESC line to allow selection of pluripotent hESCs by neomycin resistance and cardiac progenitors by puromycin resistance. Exon-level microarray expression data from undifferentiated hESCs and cardiac and neural precursors were used to identify splice isoforms with cardiac-restricted or common cardiac/neural differentiation expression patterns. Splice events for these groups corresponded to the pathways of cytoskeletal remodeling, RNA splicing, muscle specification, and cell cycle checkpoint control as well as genes with serine/threonine kinase and helicase activity. Using a new program named AltAnalyze (http://www.AltAnalyze.org, we identified novel changes in protein domain and microRNA binding site architecture that were predicted to affect protein function and expression. These included an enrichment of splice isoforms that oppose cell-cycle arrest in hESCs and that promote calcium signaling and cardiac development in cardiac precursors. By combining genome-wide predictions of alternative splicing with new functional annotations, our data suggest potential mechanisms that may influence lineage commitment and hESC maintenance at the level of specific splice isoforms and microRNA regulation.

  3. Resistance of LHC main bus bar splices at room temperature and at 77.4 K

    CERN Document Server

    Heck, S; Scheuerlein, Chr; CERN. Geneva. TE Department

    2009-01-01

    As part of the quality control the resistance of newly produced LHC main bus bar splices is now routinely measured at room temperature (RT) in order to conclude on the electrical continuity of the bus bar stabiliser across the splice under operating conditions. In this note we present splice resistance measurements that have been performed at RT and in liquid nitrogen (LN) in the CERN Cryolab with “ideal” splices (represented by continuous dipole and quadrupole bus bars), and with dipole and quadrupole splices with different defects, which cause an additional RT splice resistance of up to 60 µΩ. The RT resistance (RRT) results obtained with the Cryolab set-up are compared to the calculated resistance values and with the so-called R-8 and R-16 resistance results, as they are measured in the LHC tunnel with a Digital Low Resistance Ohmmeter with a voltage tap distance of 8 cm or 16 cm. The RT to LN resistance ratio has been determined for all splices in order to study the influence of the resistance of th...

  4. TBX3 regulates splicing in vivo: a novel molecular mechanism for Ulnar-mammary syndrome.

    Directory of Open Access Journals (Sweden)

    Pavan Kumar P

    2014-03-01

    Full Text Available TBX3 is a member of the T-box family of transcription factors with critical roles in development, oncogenesis, cell fate, and tissue homeostasis. TBX3 mutations in humans cause complex congenital malformations and Ulnar-mammary syndrome. Previous investigations into TBX3 function focused on its activity as a transcriptional repressor. We used an unbiased proteomic approach to identify TBX3 interacting proteins in vivo and discovered that TBX3 interacts with multiple mRNA splicing factors and RNA metabolic proteins. We discovered that TBX3 regulates alternative splicing in vivo and can promote or inhibit splicing depending on context and transcript. TBX3 associates with alternatively spliced mRNAs and binds RNA directly. TBX3 binds RNAs containing TBX binding motifs, and these motifs are required for regulation of splicing. Our study reveals that TBX3 mutations seen in humans with UMS disrupt its splicing regulatory function. The pleiotropic effects of TBX3 mutations in humans and mice likely result from disrupting at least two molecular functions of this protein: transcriptional regulation and pre-mRNA splicing.

  5. Results from a triple chord stellar occultation and far-infrared photometry of the trans-Neptunian object (229762) 2007 UK126

    Science.gov (United States)

    Schindler, K.; Wolf, J.; Bardecker, J.; Olsen, A.; Müller, T.; Kiss, C.; Ortiz, J. L.; Braga-Ribas, F.; Camargo, J. I. B.; Herald, D.; Krabbe, A.

    2017-03-01

    Context. A stellar occultation by a trans-Neptunian object (TNO) provides an opportunity to probe the size and shape of these distant solar system bodies. In the past seven years, several occultations by TNOs have been observed, but mostly from a single location. Only very few TNOs have been sampled simultaneously from multiple locations. Sufficient data that enable a robust estimation of shadow size through an ellipse fit could only be obtained for two objects. Aims: We present the first observation of an occultation by the TNO 2007 UK126 on 15 November 2014, measured by three observers, one nearly on and two almost symmetrical to the shadow's centerline. This is the first multi-chord dataset obtained for a so-called detached object, a TNO subgroup with perihelion distances so large that the giant planets have likely not perturbed their orbits. We also revisit Herschel/PACS far-infrared data, applying a new reduction method to improve the accuracy of the measured fluxes. Combining both datasets allows us to comprehensively characterize 2007 UK126. Methods: We use error-in-variable regression to solve the non-linear problem of propagating timing errors into uncertainties of the ellipse parameters. Based on the shadow's size and a previously reported rotation period, we expect a shape of a Maclaurin spheroid and derive a geometrically plausible size range. To refine our size estimate of 2007 UK126, we model its thermal emission using a thermophysical model code. We conduct a parametric study to predict far-infrared fluxes and compare them to the Herschel/PACS measurements. Results: The favorable geometry of our occultation chords, combined with minimal dead-time imaging, and precise GPS time measurements, allow for an accurate estimation of the shadow size (best-fitting ellipse with axes 645.80 ± 5.68 km × 597.81 ± 12.74 km) and the visual geometric albedo (pV = 15.0 ± 1.6%). By combining our analyses of the occultation and the far-infrared data, we can

  6. Fabrication and Testing of Durable Redundant and Fluted-Core Joints for Composite Sandwich Structures

    Science.gov (United States)

    Lin, Shih-Yung; Splinter, Scott C.; Tarkenton, Chris; Paddock, David A.; Smeltzer, Stanley S.; Ghose, Sayata; Guzman, Juan C.; Stukus, Donald J.; McCarville, Douglas A.

    2013-01-01

    The development of durable bonded joint technology for assembling composite structures is an essential component of future space technologies. While NASA is working toward providing an entirely new capability for human space exploration beyond low Earth orbit, the objective of this project is to design, fabricate, analyze, and test a NASA patented durable redundant joint (DRJ) and a NASA/Boeing co-designed fluted-core joint (FCJ). The potential applications include a wide range of sandwich structures for NASA's future launch vehicles. Three types of joints were studied -- splice joint (SJ, as baseline), DRJ, and FCJ. Tests included tension, after-impact tension, and compression. Teflon strips were used at the joint area to increase failure strength by shifting stress concentration to a less sensitive area. Test results were compared to those of pristine coupons fabricated utilizing the same methods. Tensile test results indicated that the DRJ design was stiffer, stronger, and more impact resistant than other designs. The drawbacks of the DRJ design were extra mass and complex fabrication processes. The FCJ was lighter than the DRJ but less impact resistant. With barely visible but detectable impact damages, all three joints showed no sign of tensile strength reduction. No compression test was conducted on any impact-damaged sample due to limited scope and resource. Failure modes and damage propagation were also studied to support progressive damage modeling of the SJ and the DRJ.

  7. A method of predicting changes in human gene splicing induced by genetic variants in context of cis-acting elements

    Directory of Open Access Journals (Sweden)

    Hicks Chindo

    2010-01-01

    Full Text Available Abstract Background Polymorphic variants and mutations disrupting canonical splicing isoforms are among the leading causes of human hereditary disorders. While there is a substantial evidence of aberrant splicing causing Mendelian diseases, the implication of such events in multi-genic disorders is yet to be well understood. We have developed a new tool (SpliceScan II for predicting the effects of genetic variants on splicing and cis-regulatory elements. The novel Bayesian non-canonical 5'GC splice site (SS sensor used in our tool allows inference on non-canonical exons. Results Our tool performed favorably when compared with the existing methods in the context of genes linked to the Autism Spectrum Disorder (ASD. SpliceScan II was able to predict more aberrant splicing isoforms triggered by the mutations, as documented in DBASS5 and DBASS3 aberrant splicing databases, than other existing methods. Detrimental effects behind some of the polymorphic variations previously associated with Alzheimer's and breast cancer could be explained by changes in predicted splicing patterns. Conclusions We have developed SpliceScan II, an effective and sensitive tool for predicting the detrimental effects of genomic variants on splicing leading to Mendelian and complex hereditary disorders. The method could potentially be used to screen resequenced patient DNA to identify de novo mutations and polymorphic variants that could contribute to a genetic disorder.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bushnell, Brian

    2014-03-17

    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].

  9. RNA的可变剪接%Alternative RNA Splicing

    Institute of Scientific and Technical Information of China (English)

    邱莫寒; 俞宁

    2010-01-01

    在高等真核生物基因组中存在大量的割裂基因,而这些割裂基因的mRNA却是非割裂结构,在这个转化过程中去除内含子的过程就成为RNA的剪接或剪接RNA(RNA splicing).RNA剪接特别是可变剪接是真核基因表达调控研究的重要内容之一.介绍了RNA可变剪接的特点、功能与调控、可变剪接基因以及剪接形式的识别,并对可变剪接的应用进行了举例.

  10. Fine-scale variation and genetic determinants of alternative splicing across individuals.

    Directory of Open Access Journals (Sweden)

    Jasmin Coulombe-Huntington

    2009-12-01

    Full Text Available Recently, thanks to the increasing throughput of new technologies, we have begun to explore the full extent of alternative pre-mRNA splicing (AS in the human transcriptome. This is unveiling a vast layer of complexity in isoform-level expression differences between individuals. We used previously published splicing sensitive microarray data from lymphoblastoid cell lines to conduct an in-depth analysis on splicing efficiency of known and predicted exons. By combining publicly available AS annotation with a novel algorithm designed to search for AS, we show that many real AS events can be detected within the usually unexploited, speculative majority of the array and at significance levels much below standard multiple-testing thresholds, demonstrating that the extent of cis-regulated differential splicing between individuals is potentially far greater than previously reported. Specifically, many genes show subtle but significant genetically controlled differences in splice-site usage. PCR validation shows that 42 out of 58 (72% candidate gene regions undergo detectable AS, amounting to the largest scale validation of isoform eQTLs to date. Targeted sequencing revealed a likely causative SNP in most validated cases. In all 17 incidences where a SNP affected a splice-site region, in silico splice-site strength modeling correctly predicted the direction of the micro-array and PCR results. In 13 other cases, we identified likely causative SNPs disrupting predicted splicing enhancers. Using Fst and REHH analysis, we uncovered significant evidence that 2 putative causative SNPs have undergone recent positive selection. We verified the effect of five SNPs using in vivo minigene assays. This study shows that splicing differences between individuals, including quantitative differences in isoform ratios, are frequent in human populations and that causative SNPs can be identified using in silico predictions. Several cases affected disease-relevant genes and

  11. PTBP1-dependent regulation of USP5 alternative RNA splicing plays a role in glioblastoma tumorigenesis.

    Science.gov (United States)

    Izaguirre, Daisy I; Zhu, Wen; Hai, Tao; Cheung, Hannah C; Krahe, Ralf; Cote, Gilbert J

    2012-11-01

    Aberrant RNA splicing is thought to play a key role in tumorigenesis. The assessment of its specific contributions is limited by the complexity of information derived from genome-wide array-based approaches. We describe how performing splicing factor-specific comparisons using both tumor and cell line data sets may more readily identify physiologically relevant tumor-specific splicing events. Affymetrix exon array data derived from glioblastoma (GBM) tumor samples with defined polypyrimidine tract-binding protein 1 (PTBP1) levels were compared with data from U251 GBM cells with and without PTBP1 knockdown. This comparison yielded overlapping gene sets that comprised only a minor fraction of each data set. The identification of a novel GBM-specific splicing event involving the USP5 gene led us to further examine its role in tumorigenesis. In GBM, USP5 generates a shorter isoform 2 through recognition of a 5' splice site within exon 15. Production of the USP5 isoform 2 was strongly correlated with PTBP1 expression in GBM tumor samples and cell lines. Splicing regulation was consistent with the presence of an intronic PTBP1 binding site and could be modulated through antisense targeting of the isoform 2 splice site to force expression of isoform 1 in GBM cells. The forced expression of USP5 isoform 1 in two GBM cell lines inhibited cell growth and migration, implying an important role for USP5 splicing in gliomagenesis. These results support a role for aberrant RNA splicing in tumorigenesis and suggest that changes in relatively few genes may be sufficient to drive the process.

  12. Copy number variations in alternative splicing gene networks impact lifespan.

    Directory of Open Access Journals (Sweden)

    Joseph T Glessner

    Full Text Available Longevity has a strong genetic component evidenced by family-based studies. Lipoprotein metabolism, FOXO proteins, and insulin/IGF-1 signaling pathways in model systems have shown polygenic variations predisposing to shorter lifespan. To test the hypothesis that rare variants could influence lifespan, we compared the rates of CNVs in healthy children (0-18 years of age with individuals 67 years or older. CNVs at a significantly higher frequency in the pediatric cohort were considered risk variants impacting lifespan, while those enriched in the geriatric cohort were considered longevity protective variants. We performed a whole-genome CNV analysis on 7,313 children and 2,701 adults of European ancestry genotyped with 302,108 SNP probes. Positive findings were evaluated in an independent cohort of 2,079 pediatric and 4,692 geriatric subjects. We detected 8 deletions and 10 duplications that were enriched in the pediatric group (P=3.33×10(-8-1.6×10(-2 unadjusted, while only one duplication was enriched in the geriatric cohort (P=6.3×10(-4. Population stratification correction resulted in 5 deletions and 3 duplications remaining significant (P=5.16×10(-5-4.26×10(-2 in the replication cohort. Three deletions and four duplications were significant combined (combined P=3.7×10(-4-3.9×10(-2. All associated loci were experimentally validated using qPCR. Evaluation of these genes for pathway enrichment demonstrated ~50% are involved in alternative splicing (P=0.0077 Benjamini and Hochberg corrected. We conclude that genetic variations disrupting RNA splicing could have long-term biological effects impacting lifespan.

  13. 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.

    2013-02-01

    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.

  14. Informational structure of genetic sequences and nature of gene splicing

    Science.gov (United States)

    Trifonov, E. N.

    1991-10-01

    Only about 1/20 of DNA of higher organisms codes for proteins, by means of classical triplet code. The rest of DNA sequences is largely silent, with unclear functions, if any. The triplet code is not the only code (message) carried by the sequences. There are three levels of molecular communication, where the same sequence ``talks'' to various bimolecules, while having, respectively, three different appearances: DNA, RNA and protein. Since the molecular structures and, hence, sequence specific preferences of these are substantially different, the original DNA sequence has to carry simultaneously three types of sequence patterns (codes, messages), thus, being a composite structure in which one had the same letter (nucleotide) is frequently involved in several overlapping codes of different nature. This multiplicity and overlapping of the codes is a unique feature of the Gnomic, language of genetic sequences. The coexisting codes have to be degenerate in various degrees to allow an optimal and concerted performance of all the encoded functions. There is an obvious conflict between the best possible performance of a given function and necessity to compromise the quality of a given sequence pattern in favor of other patterns. It appears that the major role of various changes in the sequences on their ``ontogenetic'' way from DNA to RNA to protein, like RNA editing and splicing, or protein post-translational modifications is to resolve such conflicts. New data are presented strongly indicating that the gene splicing is such a device to resolve the conflict between the code of DNA folding in chromatin and the triplet code for protein synthesis.

  15. Characterization, phylogeny, alternative splicing and expression of Sox30 gene

    Directory of Open Access Journals (Sweden)

    Huang Baofeng

    2010-12-01

    Full Text Available Abstract Background Members of the Sox gene family isolated from both vertebrates and invertebrates have been proved to participate in a wide variety of developmental processes, including sex determination and differentiation. Among these members, Sox30 had been considered to exist only in mammals since its discovery, and its exact function remains unclear. Results Sox30 cDNA was cloned from the Nile tilapia by RT-PCR and RACE. Screening of available genome and EST databases and phylogenetic analysis showed that Sox30 also exists in non-mammalian vertebrates and invertebrates, which was further supported by synteny analyses. Tissue expression in human, mouse and tilapia suggested that Sox30 was probably a gonad-specific gene, which was also supported by the fact that Sox30 EST sequences were obtained from gonads of the animal species. In addition, four alternatively spliced isoforms were isolated from tilapia gonad. Their temporal and spatial expression patterns during normal and sex reversed gonadal development were investigated by RT-PCR and in situ hybridization. Our data suggest that expressions of Sox30 isoforms are related to stage and phenotypic-sex, observed in the germ cells of male gonad and in somatic cells of the female gonad. Conclusions Sox30 is not a gene only existed in mammals, but exists widely throughout the animal kingdom as supported by our bioinformatic, phylogenetic and syntenic analyses. It is very likely that Sox30 is expressed exclusively in gonads. Expression analyses revealed that Sox30 may be involved in female and male gonadal development at different stages by alternative splicing.

  16. Total ankle joint replacement.

    Science.gov (United States)

    2016-02-01

    Ankle arthritis results in a stiff and painful ankle and can be a major cause of disability. For people with end-stage ankle arthritis, arthrodesis (ankle fusion) is effective at reducing pain in the shorter term, but results in a fixed joint, and over time the loss of mobility places stress on other joints in the foot that may lead to arthritis, pain and dysfunction. Another option is to perform a total ankle joint replacement, with the aim of giving the patient a mobile and pain-free ankle. In this article we review the efficacy of this procedure, including how it compares to ankle arthrodesis, and consider the indications and complications.

  17. Joint Robotics Program

    Science.gov (United States)

    2008-04-23

    Åèìáëáíáçå= oÉëÉ~êÅÜ=póãéçëáìã= JOINT ROBOTICS PROGRAM Published: 23 April 2008 by Joel Brown and Paul Varian 5th Annual Acquisition Research...3. DATES COVERED 00-00-2008 to 00-00-2008 4. TITLE AND SUBTITLE Joint Robotics Program 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM...ëóåÉêÖó=Ñçê=áåÑçêãÉÇ=ÅÜ~åÖÉ=======- 464 - = = Joint Robotics Program Presenter: Joel Brown, Defense Acquisition University Author: Paul Varian

  18. Joints in steel buildings

    Directory of Open Access Journals (Sweden)

    Gabriel F. Valencia Clement

    2010-04-01

    Full Text Available Masonry and steel components used in constructing buildings are in a constant state of motion. Volumetric changes are produced by temperature variation and deformation resulting from static or dynamic loading and in some materials, such as masonry, due to moisture content. This article addresses means of determining when expansion and seismic joints are required and how to proportion and design appropriate joints, specifically in steel buildings. It does not cover the study of expansion joints in concrete structures, in masonry construction or in non-structural (architectural elements.

  19. Salt-Dependent Conditional Protein Splicing of an Intein from Halobacterium salinarum.

    Science.gov (United States)

    Reitter, Julie N; Cousin, Christopher E; Nicastri, Michael C; Jaramillo, Mario V; Mills, Kenneth V

    2016-03-01

    An intein from Halobacterium salinarum can be isolated as an unspliced precursor protein with exogenous exteins after Escherichia coli overexpression. The intein promotes protein splicing and uncoupled N-terminal cleavage in vitro, conditional on incubation with NaCl or KCl at concentrations of >1.5 M. The protein splicing reaction also is conditional on reduction of a disulfide bond between two active site cysteines. Conditional protein splicing under these relatively mild conditions may lead to advances in intein-based biotechnology applications and hints at the possibility that this H. salinarum intein could serve as a switch to control extein activity under physiologically relevant conditions.

  20. Splicing mosaic of the myophosphorylase gene due to a silent mutation in McArdle disease.

    Science.gov (United States)

    Fernandez-Cadenas, I; Andreu, A L; Gamez, J; Gonzalo, R; Martín, M A; Rubio, J C; Arenas, J

    2003-11-25

    The authors report the molecular findings in a patient with McArdle disease who harbored a silent polymorphism (K608K) in the myophosphorylase gene. cDNA studies demonstrated that this polymorphism leads to a severe mosaic alteration in mRNA splicing, including exon skipping, activation of cryptic splice-sites, and exon-intron reorganizations. These findings suggest that, in patients with McArdle disease in whom no pathogenic mutation has been found, any a priori silent polymorphism should be re-evaluated as a putative splicing mutation.

  1. Splicing factor 1 modulates dietary restriction and TORC1 pathway longevity in C. elegans

    DEFF Research Database (Denmark)

    Heintz, Caroline; Doktor, Thomas K; Lanjuin, Anne;

    2017-01-01

    via splicing factor 1 (SFA-1; the C. elegans homologue of SF1, also known as branchpoint binding protein, BBP). We show that SFA-1 is specifically required for lifespan extension by dietary restriction and by modulation of the TORC1 pathway components AMPK, RAGA-1 and RSKS-1/S6 kinase. We also...... homeostasis is a biomarker and predictor of life expectancy in Caenorhabditis elegans. Using transcriptomics and in-depth splicing analysis in young and old animals fed ad libitum or subjected to dietary restriction, we find defects in global pre-mRNA splicing with age that are reduced by dietary restriction...

  2. 环口板加强型T型圆钢管节点滞回性能研究%Study on Hysteretic Behaviour of Circular Tubular T-joints with Collar Plate Reinforcement

    Institute of Scientific and Technical Information of China (English)

    蔡艳青; 邵永波

    2011-01-01

    为了研究环口板加固对T型圆钢管节点滞回性能的影响,运用有限元方法对环口板加固T型圆钢管节点进行了滞回性能的参数分析.参数包括支管直径与主管直径比β,主管直径与2倍主管壁厚的比γ,环口板厚度与主管管壁厚之比γc,和环口板长度与支管直径之比lc/d1.有限元分析结果表明:环口板加固T型圆钢管节点的滞回性能相对于未加固节点得到了很大的改善.参数β和γ对节点的滞回性能有显著影响.为了改善节点的滞回性能,建议环口板的厚度不宜超过主管厚度的1.5倍,环口板的长度不宜超过支管直径的2倍.%To study the hysteretic performance of circular tubular T-joints with collar plate reinforcement, a parametric analysis is conducted by using the finite element method. The parameters include; the brace-to-chord diameter ratio β, chord radius to twice chord wall thickness ratio y, collar-plate to chord wall thickness ratio tc , and collar-plate length to brace diameter ratio lc/dl. It is found that the hysteretic behaviour of collar plate reinforced T-joints has been greatly improved compared to that of the un-reinforced T-joints. In addition, the parameters y and ^8 have significant effect on the hysteretic behaviour. It can be suggested that the thickness of collar plate should not exceed 1. 5 times of the chord thickness, and the length of collar plate also should not exceed 2 times of the brace diameter for improving the hysteretic performance efficiently.

  3. Overlapping cis sites used for splicing of HIV-1 env/nef and rev mRNAs.

    Science.gov (United States)

    Swanson, A K; Stoltzfus, C M

    1998-12-18

    Alternative splicing is used to generate more than 30 human immunodeficiency virus type 1 (HIV-1) spliced and unspliced mRNAs from a single primary transcript. The abundance of HIV-1 mRNAs is determined by the efficiencies with which its different 5' and 3' splice sites are used. Three splice sites (A4c, A4a, and A4b) are upstream of the rev initiator AUG. RNAs spliced at A4c, A4a, and A4b are used as mRNAs for Rev. Another 3' splice site (A5) is immediately downstream of the rev initiator. RNAs spliced at A5 are used as mRNAs for Env and Nef. In this report, primer extension analysis of splicing intermediates was used to show that there are eight branch points in this region, all of which map to adenosine residues. In addition, cis elements recognized by the cellular splicing machinery overlap; the two most 3' branch points overlap with the AG dinucleotides at rev 3' splice sites A4a and A4b. Competition of the overlapping cis sites for different splicing factors may play a role in maintaining the appropriate balance of mRNAs in HIV-1-infected cells. In support of this possibility, mutations at rev 3' splice site A4b AG dinucleotide dramatically increased splicing of the env/nef 3' splice site A5. This correlated with increased usage of the four most 3' branch points, which include those within the rev 3' splice site AG dinucleotides. Consistent with these results, analysis of a mutant in which three of the four env/nef branch points were inactivated indicated that use of splice site A5 was inhibited and splicing was shifted predominantly to the most 5' rev 3' splice site A4c with preferential use of the two most 5' branch points. Our results suggest that spliceosomes formed at rev A4a-4b, rev A4c, and env/nef A5 3' splice sites each recognize different subsets of the eight branch point sequences.

  4. Results from a triple chord stellar occultation and far-infrared photometry of the trans-Neptunian object (229762) 2007 UK126

    CERN Document Server

    Schindler, Karsten; Bardecker, Jerry; Olsen, Aart; Müller, Thomas; Kiss, Csaba; Ortiz, Jose-Luis; Braga-Ribas, Felipe; de Camargo, Julio Ignacio Bueno; Herald, Dave; Krabbe, Alfred

    2016-01-01

    A stellar occultation by a trans-Neptunian object (TNO) provides an opportunity to probe its size and shape. Very few occultations by TNOs have been sampled simultaneously from multiple locations, while a robust estimation of shadow size has been possible for only two objects. We present the first observation of an occultation by the TNO 2007 UK126 on 15 November 2014, measured by three observers, one nearly on and two almost symmetrical to the shadow's centerline. This is the first multi-chord dataset obtained for a so-called detached object, a TNO subgroup with perihelion distances so large that the giant planets have likely not perturbed their orbits. We revisit Herschel/PACS far-infrared data, applying a new reduction method to improve the accuracy of the measured fluxes. Combining both datasets allows us to comprehensively characterize 2007 UK126. We use error-in-variable regression to solve the non-linear problem of propagating timing errors into uncertainties of the ellipse parameters. Based on the sha...

  5. 平行弦钢桁架过街人行天桥设计%The Design of a Parallel Chord Steel Truss Pedestrian Bridge

    Institute of Scientific and Technical Information of China (English)

    董震

    2016-01-01

    分析北京某平行弦桁架人行过街天桥设计,该天桥主体结构由上部两榀钢桁架和下部混凝土柱组成,总长52.5m,单跨最大跨径30m。设计考虑竖向地震、温度效应等荷载作用,并计算结构竖向第一振动频率,避免人群行走时桥身产生共振。设计方法和结构选型可供技术人员作同类设计参考。%The paper describes the design of a parallel chord steel truss pedestrian bridge in Beijing. The main structure of the bridge is composed of above two steel trusses and concrete columns bottom. The most span of the bridge is 30m, and the whole length is 50m. The structure calculation includes of the vertical earthquake, temperature effect and the first natural frequency of vertical vibration for avoiding the resonance of the bridge caused by human walking. The design method and selection of the structure provide reference for similar design.

  6. P2P网络中Chord搜索算法的改进研究%Improvement of Chord search algorithm research in P2P network

    Institute of Scientific and Technical Information of China (English)

    CAO Lei; ZHANG Yu-mei; WU Xiao-jun; YIN Jia-le; GUO Hai-liang; WANG Ting

    2014-01-01

    为解决P2P网络中Chord算法众多节点性能不一、节点频繁离开和加入制约系统性能的问题,提出了基于信息相关度的分组改进算法。该算法通过引入节点信息相关度的概念,对原Chord进行信息相关度的一个分组调整。从每个组选出两个超级节点组成超级组,同时为每个节点增加了逆时针路由,在两个超级节点顺逆两个方向上选择出最短路径进行查找。实验表明,改进后的算法使得系统的性能和适应性都得到了加强,提高了Chord在对等网中的查找效率。%In P2P network, performances of many nodes in Chord algorithm are inconsonant. The problem that nodes leave and join frequently will restrict the performance of system seriously.Therefore,this paper presented grouping improved algorithm based on related d

  7. Joint Quantum Institute

    Data.gov (United States)

    Federal Laboratory Consortium — The Joint Quantum Institute (JQI) is pursuing that goal through the work of leading quantum scientists from the Department of Physics of the University of Maryland...

  8. Healthy Joints Matter

    Science.gov (United States)

    ... my joints more healthy? Definitions What can go wrong? Although you might think arthritis affects only older ... Discovery Into Health ® Home | Health Information | Research | Funding | News & Events | About Us | Portal en español | Asian-Language ...

  9. Improved orthopedic arm joint

    Science.gov (United States)

    Dane, D. H.

    1971-01-01

    Joint permits smooth and easy movement of disabled arm and is smaller, lighter and less expensive than previous models. Device is interchangeable and may be used on either arm at the shoulder or at the elbow.

  10. T形、Y形带内置环肋圆钢管相贯节点承载力计算方法%Calculation method for bearing capacities of internal ring-stiffened tubular T-and Y-joints

    Institute of Scientific and Technical Information of China (English)

    王帆; 陈志进; 刘丁丁; 罗敏; 宁晨; 蓝小艺

    2014-01-01

    为了得到T形、Y形带内置环肋圆钢管相贯节点的承载力计算公式,对528个节点进行参数化分析.结果表明:T形、Y形节点的环肋设置在冠点时,对节点承载力提高率的贡献最小,而设置在距冠点到鞍点距离的0.7~0.8倍时,贡献最大;支管受压时,T形带肋节点承载力提高值随环肋厚度和宽度的增大而增大,但受支主管直径比和主管径厚比的影响较小;T形、Y形带肋节点承载力提高值之比受支主管直径比和环肋厚度、宽度的影响较小,而随支主管夹角的增大呈近似线性增加;考虑主管应力比以及支管拉力的影响时,可沿用现行规范中无肋节点的相关参数.结合现行规范,提出了T形和Y形节点的承载力计算公式,适用性检验结果证明了所提公式的可靠性.%In order to obtain calculation equations for the bearing capacities of internal ring-stiffened tubular T-and Y-joints,parametric analysis for 528 tubular joints is carried out.The results show that for T-and Y-joints,the smallest increase in joints’ bearing capacity occurs when the stiffeners are lo-cated on the crown,while the increases are highest when the stiffeners are located 0.7 to 0.8 times of the distance between the crown and the saddle from the crown.When the brace is under compres-sion,the ring-stiffened T-joints’ bearing capacity increases with the increase of the thickness and the width of the ring-stiffeners,and the effects of the ratio of brace diameter to chord diameter and the ratio of chord diameter to chord thickness are insignificant.The ratio of the increase of the bearing capacity of T-joints to that of Y-joints linearly increases with the increase of the angle between the brace and the chord,and the ratio of brace diameter to chord diameter, as well as the thickness and the width of ring-stiffeners are less effective.The related parameters of the unstiffened joints in exist-ing codes can be

  11. Concrete Pavement Joint Deterioration

    OpenAIRE

    2016-01-01

    Concrete pavements are an important part of our national infrastructure. In recent years the relatively small number of reported joints deteriorating prematurely in concrete pavements around Indiana has increased. Changes over the past 45 years in INDOT specification, pavement materials, designs and construction practices, and current de-icing materials were examined and related to the durability of concrete at the joints of existing pavements. A survey of concrete pavements across the state ...

  12. High pressure ceramic joint

    Science.gov (United States)

    Ward, Michael E.; Harkins, Bruce D.

    1993-01-01

    Many recuperators have components which react to corrosive gases and are used in applications where the donor fluid includes highly corrosive gases. These recuperators have suffered reduced life, increased service or maintenance, and resulted in increased cost. The present joint when used with recuperators increases the use of ceramic components which do not react to highly corrosive gases. Thus, the present joint used with the present recuperator increases the life, reduces the service and maintenance, and reduces the increased cost associated with corrosive action of components used to manufacture recuperators. The present joint is comprised of a first ceramic member, a second ceramic member, a mechanical locking device having a groove defined in one of the first ceramic member and the second ceramic member. The joint and the mechanical locking device is further comprised of a refractory material disposed in the groove and contacting the first ceramic member and the second ceramic member. The present joint mechanically provides a high strength load bearing joint having good thermal cycling characteristics, good resistance to a corrosive environment and good steady state strength at elevated temperatures.

  13. Posttranscriptional Regulation of Splicing Factor SRSF1 and Its Role in Cancer Cell Biology

    Directory of Open Access Journals (Sweden)

    Vânia Gonçalves

    2015-01-01

    Full Text Available Over the past decade, alternative splicing has been progressively recognized as a major mechanism regulating gene expression patterns in different tissues and disease states through the generation of multiple mRNAs from the same gene transcript. This process requires the joining of selected exons or usage of different pairs of splice sites and is regulated by gene-specific combinations of RNA-binding proteins. One archetypical splicing regulator is SRSF1, for which we review the molecular mechanisms and posttranscriptional modifications involved in its life cycle. These include alternative splicing of SRSF1 itself, regulatory protein phosphorylation events, and the role of nuclear versus cytoplasmic SRSF1 localization. In addition, we resume current knowledge on deregulated SRSF1 expression in tumors and describe SRSF1-regulated alternative transcripts with functional consequences for cancer cell biology at different stages of tumor development.

  14. Clinical Significance of HER-2 Splice Variants in Breast Cancer Progression and Drug Resistance

    Directory of Open Access Journals (Sweden)

    Claire Jackson

    2013-01-01

    Full Text Available Overexpression of human epidermal growth factor receptor (HER-2 occurs in 20–30% of breast cancers and confers survival and proliferative advantages on the tumour cells making HER-2 an ideal therapeutic target for drugs like Herceptin. Continued delineation of tumour biology has identified splice variants of HER-2, with contrasting roles in tumour cell biology. For example, the splice variant 16HER-2 (results from exon 16 skipping increases transformation of cancer cells and is associated with treatment resistance; conversely, Herstatin (results from intron 8 retention and p100 (results from intron 15 retention inhibit tumour cell proliferation. This review focuses on the potential clinical implications of the expression and coexistence of HER-2 splice variants in cancer cells in relation to breast cancer progression and drug resistance. “Individualised” strategies currently guide breast cancer management; in accordance, HER-2 splice variants may prove valuable as future prognostic and predictive factors, as well as potential therapeutic targets.

  15. Coupling and Coordination in Gene Expression Processes with Pre-mRNA Splicing

    Directory of Open Access Journals (Sweden)

    Kewu Pan

    2015-03-01

    Full Text Available A processing is a tightly regulated and highly complex pathway which includes transcription, splicing, editing, transportation, translation and degradation. It has been well-documented that splicing of RNA polymerase II medicated nascent transcripts occurs co-transcriptionally and is functionally coupled to other RNA processing. Recently, increasing experimental evidence indicated that pre-mRNA splicing influences RNA degradation and vice versa. In this review, we summarized the recent findings demonstrating the coupling of these two processes. In addition, we highlighted the importance of splicing in the production of intronic miRNA and circular RNAs, and hence the discovery of the novel mechanisms in the regulation of gene expression.

  16. DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation

    DEFF Research Database (Denmark)

    Close, Pierre; East, Philip; Dirac-Svejstrup, A Barbara;

    2012-01-01

    Alternative messenger RNA splicing is the main reason that vast mammalian proteomic complexity can be achieved with a limited number of genes. Splicing is physically and functionally coupled to transcription, and is greatly affected by the rate of transcript elongation. As the nascent pre...... and help to integrate transcript elongation with mRNA splicing remain unclear. Here we characterize the human interactome of chromatin-associated mRNP particles. This led us to identify deleted in breast cancer 1 (DBC1) and ZNF326 (which we call ZNF-protein interacting with nuclear mRNPs and DBC1 (ZIRD......)) as subunits of a novel protein complex--named DBIRD--that binds directly to RNAPII. DBIRD regulates alternative splicing of a large set of exons embedded in (A + T)-rich DNA, and is present at the affected exons. RNA-interference-mediated DBIRD depletion results in region-specific decreases in transcript...

  17. Alternative RNA splicing of KSHV ORF57 produces two different RNA isoforms.

    Science.gov (United States)

    Majerciak, Vladimir; Zheng, Zhi-Ming

    2016-01-15

    In lytically infected B cells Kaposi sarcoma-associated herpesvirus (KSHV) ORF57 gene encodes two RNA isoforms by alternative splicing of its pre-mRNA, which contains a small, constitutive intron in its 5' half and a large, suboptimal intron in its 3's half. The RNA1 isoform encodes full-length ORF57 and is a major isoform derived from splicing of the constitutive small intron, but retaining the suboptimal large intron as the coding region. A small fraction (splicing to produce a smaller non-coding RNA2 due to lack of a translational termination codon. Both RNAs are cleaved and polyadenylated at the same cleavage site CS83636. The insertion of ORF57 RNA1 into a restriction cutting site in certain mammalian expression vectors activates splicing of the subopitmal intron and produces a truncated ORF57 protein.

  18. High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae

    DEFF Research Database (Denmark)

    Rukov, Jakob Lewin; Irimia, Manuel; Mørk, Søren;

    2007-01-01

    Alternative splicing (AS) is an important contributor to proteome diversity and is regarded as an explanatory factor for the relatively low number of human genes compared with less complex animals. To assess the evolutionary conservation of AS and its developmental regulation, we have investigated...... the qualitative and quantitative expression of 21 orthologous alternative splice events through the development of 2 nematode species separated by 85-110 Myr of evolutionary time. We demonstrate that most of these alternative splice events present in Caenorhabditis elegans are conserved in Caenorhabditis briggsae...... mechanisms controlling AS are to a large extent conserved during the evolution of Caenorhabditis. This strong conservation indicates that both major and minor splice forms have important functional roles and that the relative quantities in which they are expressed are crucial. Our results therefore suggest...

  19. Analysis and prediction of gene splice sites in four Aspergillus genomes

    DEFF Research Database (Denmark)

    Wang, Kai; Ussery, David; Brunak, Søren

    2009-01-01

    , splice site prediction program called NetAspGene, for the genus Aspergillus. Gene sequences from Aspergillus fumigatus, the most common mould pathogen, were used to build and test our model. Compared to many animals and plants, Aspergillus contains smaller introns; thus we have applied a larger window...... better splice site prediction than other available tools. NetAspGene will be very helpful for the study in Aspergillus splice sites and especially in alternative splicing. A webpage for NetAspGene is publicly available at http://www.cbs.dtu.dk/services/NetAspGene....... size on single local networks for training, to cover both donor and acceptor site information. We have applied NetAspGene to other Aspergilli, including Aspergillus nidulans, Aspergillus oryzae, and Aspergillus niger. Evaluation with independent data sets reveal that NetAspGene performs substantially...

  20. Corticotropin (ACTH) regulates alternative RNA splicing in Y1 mouse adrenocortical tumor cells.

    Science.gov (United States)

    Schimmer, Bernard P; Cordova, Martha

    2015-06-15

    The stimulatory effect of ACTH on gene expression is well documented and is thought to be a major mechanism by which ACTH maintains the functional and structural integrity of the gland. Previously, we showed that ACTH regulates the accumulation of over 1200 transcripts in Y1 adrenal cells, including a cluster with functions in alternative splicing of RNA. On this basis, we postulated that some of the effects of ACTH on the transcription landscape of Y1 cells are mediated by alternative splicing. In this study, we demonstrate that ACTH regulates the alternative splicing of four transcripts - Gnas, Cd151, Dab2 and Tia1. Inasmuch as alternative splicing potentially affects transcripts from more than two-thirds of the mouse genome, we suggest that these findings are representative of a genome-wide effect of ACTH that impacts on the mRNA and protein composition of the adrenal cortex.

  1. The RNA splicing factor ASF/SF2 inhibits human topoisomerase I mediated DNA relaxation

    DEFF Research Database (Denmark)

    Andersen, Félicie Faucon; Tange, Thomas Ø.; Sinnathamby, Thayaline;

    2002-01-01

    Human topoisomerase I interacts with and phosphorylates the SR-family of RNA splicing factors, including ASF/SF2, and has been suggested to play an important role in the regulation of RNA splicing. Here we present evidence to support the theory that the regulation can go the other way around...... with the SR-proteins controlling topoisomerase I DNA activity. We demonstrate that the splicing factor ASF/SF2 inhibits relaxation by interfering with the DNA cleavage and/or DNA binding steps of human topoisomerase I catalysis. The inhibition of relaxation correlated with the ability of various deletion...... extract reduced the inhibition of relaxation activity. Taken together with the previously published studies of the topoisomerase I kinase activity, these observations suggest that topoisomerase I activity is shifted from relaxation to kinasing by specific interaction with SR-splicing factors....

  2. 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

    2010-01-01

    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.

  3. Differential gene expression and alternative splicing between diploid and tetraploid watermelon lines

    Science.gov (United States)

    Synthetic tetraploid plants have been used for production of seedless triploid watermelon lines being pollinated with diploid plants. When compared to their diploid or triploid counterparts, the tetraploid exhibit wide phenotypic differences. Though many factors, including alternative splicing (AS),...

  4. Poliovirus 2A protease triggers a selective nucleo-cytoplasmic redistribution of splicing factors to regulate alternative pre-mRNA splicing.

    Directory of Open Access Journals (Sweden)

    Enrique Álvarez

    Full Text Available Poliovirus protease 2A (2A(pro obstructs host gene expression by reprogramming transcriptional and post-transcriptional regulatory events during infection. Here we demonstrate that expression of 2A(pro induces a selective nucleo-cytoplasm translocation of several important RNA binding proteins and splicing factors. Subcellular fractionation studies, together with immunofluorescence microscopy revealed an asymmetric distribution of HuR and TIA1/TIAR in 2A(pro expressing cells, which modulates splicing of the human Fas exon 6. Consistent with this result, knockdown of HuR or overexpression of TIA1/TIAR, leads to Fas exon 6 inclusion in 2A(pro-expressing cells. Therefore, poliovirus 2A(pro can target alternative pre-mRNA splicing by regulating protein shuttling between the nucleus and the cytoplasm.

  5. Proximal Tibiofibular Joint: An overview

    Directory of Open Access Journals (Sweden)

    Tze Wang Chan

    2016-06-01

    Full Text Available Proximal tibiofibular joint is a frequently neglected joint which can be a source of lateral knee pain. Open surgery is the current mainstay of surgical management of proximal tibiofibular joint disorders. The proximal tibiofibular arthroscopy allows access to the joint and adjacent important ligamentous structures. This forms the basis of further development of arthroscopic procedures for a variety of pathologies.

  6. Skipping of exons by premature termination of transcription and alternative splicing within intron-5 of the sheep SCF gene: a novel splice variant.

    Directory of Open Access Journals (Sweden)

    Siva Arumugam Saravanaperumal

    Full Text Available Stem cell factor (SCF is a growth factor, essential for haemopoiesis, mast cell development and melanogenesis. In the hematopoietic microenvironment (HM, SCF is produced either as a membrane-bound (- or soluble (+ forms. Skin expression of SCF stimulates melanocyte migration, proliferation, differentiation, and survival. We report for the first time, a novel mRNA splice variant of SCF from the skin of white merino sheep via cloning and sequencing. Reverse transcriptase (RT-PCR and molecular prediction revealed two different cDNA products of SCF. Full-length cDNA libraries were enriched by the method of rapid amplification of cDNA ends (RACE-PCR. Nucleotide sequencing and molecular prediction revealed that the primary 1519 base pair (bp cDNA encodes a precursor protein of 274 amino acids (aa, commonly known as 'soluble' isoform. In contrast, the shorter (835 and/or 725 bp cDNA was found to be a 'novel' mRNA splice variant. It contains an open reading frame (ORF corresponding to a truncated protein of 181 aa (vs 245 aa with an unique C-terminus lacking the primary proteolytic segment (28 aa right after the D(175G site which is necessary to produce 'soluble' form of SCF. This alternative splice (AS variant was explained by the complete nucleotide sequencing of splice junction covering exon 5-intron (5-exon 6 (948 bp with a premature termination codon (PTC whereby exons 6 to 9/10 are skipped (Cassette Exon, CE 6-9/10. We also demonstrated that the Northern blot analysis at transcript level is mediated via an intron-5 splicing event. Our data refine the structure of SCF gene; clarify the presence (+ and/or absence (- of primary proteolytic-cleavage site specific SCF splice variants. This work provides a basis for understanding the functional role and regulation of SCF in hair follicle melanogenesis in sheep beyond what was known in mice, humans and other mammals.

  7. Retrospective study of patients treated for a carcinoma of the vocal chords by exclusive irradiation; Etude retrospective de patients traites pour un carcinome des cordes vocales par irradiation exclusive

    Energy Technology Data Exchange (ETDEWEB)

    Servagi Vernat, S.; Bontemps, P.; Bosset, J.F. [Service de Radiotherapie-oncologie, 25 - Besancon (France); Pozet, A.; Mercier, M. [Laboratoire de Biostatistique, 25 -Besancon (France)

    2007-11-15

    The objectives of this study are to evaluate the tumor local control, the survival, the acute and delayed toxicity after exclusive radiotherapy for a vocal chords carcinoma. This study confirms the literature data. At distance, it appears that the rate of second cancer is the vital element. Also, it would be interesting to make a prospective analysis of the voice quality before and after radiotherapy. (N.C.)

  8. Alternative Splicing: A Potential Source of Functional Innovation in the Eukaryotic Genome

    OpenAIRE

    Lu Chen; Tovar-Corona, Jaime M.; Urrutia, Araxi O.

    2012-01-01

    Alternative splicing (AS) is a common posttranscriptional process in eukaryotic organisms, by which multiple distinct functional transcripts are produced from a single gene. The release of the human genome draft revealed a much smaller number of genes than anticipated. Because of its potential role in expanding protein diversity, interest in alternative splicing has been increasing over the last decade. Although recent studies have shown that 94% human multiexon genes undergo AS, evolution of...

  9. Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity

    OpenAIRE

    Chen, Lu; Bush, Stephen J; Tovar-Corona, Jaime M.; Castillo-Morales, Atahualpa; Urrutia, Araxi O.

    2014-01-01

    What at the genomic level underlies organism complexity? Although several genomic features have been associated with organism complexity, in the case of alternative splicing, which has long been proposed to explain the variation in complexity, no such link has been established. Here, we analyzed over 39 million expressed sequence tags available for 47 eukaryotic species with fully sequenced genomes to obtain a comparable index of alternative splicing estimates, which corrects for the distorti...

  10. Impairment of pre-mRNA splicing in liver disease: Mechanisms and consequences

    Institute of Scientific and Technical Information of China (English)

    Carmen; Berasain; Saioa; Gońi; Josefa; Castillo; Maria; Ujue; Latasa; Jesús; Prieto; Matias; A; Avila

    2010-01-01

    Pre-mRNA splicing is an essential step in the process of gene expression in eukaryotes and consists of the removal ofintrons and the linking of exons to generate mature mRNAs. This is a highly regulated mechanism that allows the alternative usage of exons, the retention ofintronic sequences and the generation of exonic sequences of variable length. Most human genes undergo splicing events, and disruptions of this process have been associated with a variety of diseases, including cancer. Hepatocellular carci...

  11. Quantification of co-transcriptional splicing from RNA-Seq data.

    Science.gov (United States)

    Herzel, Lydia; Neugebauer, Karla M

    2015-09-01

    During gene expression, protein-coding transcripts are shaped by multiple processing events: 5' end capping, pre-mRNA splicing, RNA editing, and 3' end cleavage and polyadenylation. These events are required to produce mature mRNA, which can be subsequently translated. Nearly all of these RNA processing steps occur during transcription, while the nascent RNA is still attached to the DNA template by RNA polymerase II (i.e. co-transcriptionally). Polyadenylation occurs after 3' end cleavage or post-transcriptionally. Pre-mRNA splicing - the removal of introns and ligation of exons - can be initiated and concluded co-transcriptionally, although this is not strictly required. Recently, a number of studies using global methods have shown that the majority of splicing is co-transcriptional, yet not all published studies agree in their conclusions. Short read sequencing of RNA (RNA-Seq) is the prevailing approach to measuring splicing levels in nascent RNA, mRNA or total RNA. Here, we compare four different strategies for analyzing and quantifying co-transcriptional splicing. To do so, we reanalyze two nascent RNA-Seq datasets of the same species, but different cell type and RNA isolation procedure. Average co-transcriptional splicing values calculated on a per intron basis are similar, independent of the strategy used. We emphasize the technical requirements for identifying co-transcriptional splicing events with high confidence, e.g. how to calculate co-transcriptional splicing from nascent RNA- versus mRNA-Seq data, the number of biological replicates needed, depletion of polyA+RNA, and appropriate normalization. Finally, we present guidelines for planning a nascent RNA-Seq experiment.

  12. Expression of thyroid stimulating hormone β splice variant in thyroid of mouse with autoimmune thyroiditis

    Institute of Scientific and Technical Information of China (English)

    袁继红

    2014-01-01

    Objective To investigate the expression of marrowderived thyroid stimulating hormoneβ(TSHβ)splice variant in thyroid of mouse with autoimmune thyroiditis induced by thyroglobulin(Tg)immunization,and to analyze whether TSHβsplice variant participated in the pathological process of autoimmune thyroiditis.Methods Using random number table,forty-eight mice(24 females and 24 males)of 7 to 8 weeks old with body mass 20 to25 g were randomly divided into 4 groups(12 females

  13. Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray.

    Directory of Open Access Journals (Sweden)

    Noam Leviatan

    Full Text Available Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Alternative splicing is often regulated in a tissue-specific and stress-responsive manner. Cold stress, which adversely affects plant growth and development, regulates the transcription and splicing of plant splicing factors. This can affect the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions. A novel algorithm was used for detection of statistically relevant changes in intron expression within a transcript between control and cold growth conditions. A reverse transcription polymerase chain reaction (RT-PCR analysis of a number of randomly selected genes confirmed the changes in splicing patterns under cold stress predicted by tiling array. Our analysis revealed new types of cold responsive genes. While their expression level remains relatively unchanged under cold stress their splicing pattern shows detectable changes in the relative abundance of isoforms. The majority of cold regulated alternative splicing introduced a premature termination codon (PTC into the transcripts creating potential targets for degradation by the nonsense mediated mRNA decay (NMD process. A number of these genes were analyzed in NMD-defective mutants by RT-PCR and shown to evade NMD. This may result in new and truncated proteins with altered functions or dominant negative effects. The results indicate that cold affects both quantitative and qualitative aspects of gene expression.

  14. Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray.

    Science.gov (United States)

    Leviatan, Noam; Alkan, Noam; Leshkowitz, Dena; Fluhr, Robert

    2013-01-01

    Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Alternative splicing is often regulated in a tissue-specific and stress-responsive manner. Cold stress, which adversely affects plant growth and development, regulates the transcription and splicing of plant splicing factors. This can affect the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix Arabidopsis tiling arrays to survey the transcriptome under cold treatment conditions. A novel algorithm was used for detection of statistically relevant changes in intron expression within a transcript between control and cold growth conditions. A reverse transcription polymerase chain reaction (RT-PCR) analysis of a number of randomly selected genes confirmed the changes in splicing patterns under cold stress predicted by tiling array. Our analysis revealed new types of cold responsive genes. While their expression level remains relatively unchanged under cold stress their splicing pattern shows detectable changes in the relative abundance of isoforms. The majority of cold regulated alternative splicing introduced a premature termination codon (PTC) into the transcripts creating potential targets for degradation by the nonsense mediated mRNA decay (NMD) process. A number of these genes were analyzed in NMD-defective mutants by RT-PCR and shown to evade NMD. This may result in new and truncated proteins with altered functions or dominant negative effects. The results indicate that cold affects both quantitative and qualitative aspects of gene expression.

  15. Splicosomal and serine and arginine-rich splicing factors as targets for TGF-β

    Directory of Open Access Journals (Sweden)

    Hallgren Oskar

    2012-04-01

    Full Text Available Abstract Background Transforming growth factor-β1 (TGF-β1 is a potent regulator of cell growth and differentiation. TGF-β1 has been shown to be a key player in tissue remodeling processes in a number of disease states by inducing expression of extracellular matrix proteins. In this study a quantitative proteomic analysis was undertaken to investigate if TGF-β1 contributes to tissue remodeling by mediating mRNA splicing and production of alternative isoforms of proteins. Methodology/Principal findings The expression of proteins involved in mRNA splicing from TGF-β1-stimulated lung fibroblasts was compared to non-stimulated cells by employing isotope coded affinity tag (ICATTM reagent labeling and tandem mass spectrometry. A total of 1733 proteins were identified and quantified with a relative standard deviation of 11% +/− 8 from enriched nuclear fractions. Seventy-six of these proteins were associated with mRNA splicing, including 22 proteins involved in splice site selection. In addition, TGF-β1 was observed to alter the relative expression of splicing proteins that may be important for alternative splicing of fibronectin. Specifically, TGF-β1 significantly induced expression of SRp20, and reduced the expression of SRp30C, which has been suggested to be a prerequisite for generation of alternatively spliced fibronectin. The induction of SRp20 was further confirmed by western blot and immunofluorescence. Conclusions The results show that TGF-β1 induces the expression of proteins involved in mRNA splicing and RNA processing in human lung fibroblasts. This may have an impact on the production of alternative isoforms of matrix proteins and can therefore be an important factor in tissue remodeling and disease progression.

  16. 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

    2007-12-10

    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.

  17. Assessment of orthologous splicing isoforms in human and mouse orthologous genes

    Directory of Open Access Journals (Sweden)

    Horner David S

    2010-10-01

    Full Text Available Abstract Background Recent discoveries have highlighted the fact that alternative splicing and alternative transcripts are the rule, rather than the exception, in metazoan genes. Since multiple transcript and protein variants expressed by the same gene are, by definition, structurally distinct and need not to be functionally equivalent, the concept of gene orthology should be extended to the transcript level in order to describe evolutionary relationships between structurally similar transcript variants. In other words, the identification of true orthology relationships between gene products now should progress beyond primary sequence and "splicing orthology", consisting in ancestrally shared exon-intron structures, is required to define orthologous isoforms at transcript level. Results As a starting step in this direction, in this work we performed a large scale human- mouse gene comparison with a twofold goal: first, to assess if and to which extent traditional gene annotations such as RefSeq capture genuine splicing orthology; second, to provide a more detailed annotation and quantification of true human-mouse orthologous transcripts defined as transcripts of orthologous genes exhibiting the same splicing patterns. Conclusions We observed an identical exon/intron structure for 32% of human and mouse orthologous genes. This figure increases to 87% using less stringent criteria for gene structure similarity, thus implying that for about 13% of the human RefSeq annotated genes (and about 25% of the corresponding transcripts we could not identify any mouse transcript showing sufficient similarity to be confidently assigned as a splicing ortholog. Our data suggest that current gene and transcript data may still be rather incomplete - with several splicing variants still unknown. The observation that alternative splicing produces large numbers of alternative transcripts and proteins, some of them conserved across species and others truly species

  18. Splicing-Sensitive DNA-Microarrays: Peculiarities and Application in Biomedical Research (Review)

    OpenAIRE

    2015-01-01

    Alternative splicing (АS) provides a variety of protein and mature mRNA isoforms encoded by a single gene, and is the essential component of cell and tissue differentiation and functioning. DNA-microarrays are highly productive transcriptome research technique both at the level of total gene expression assessment and alternatively spliced mRNA isoforms exploration. The study of AS patterns requires thorough probe design to achieve appropriate accuracy of the analysis. There are tw...

  19. Splicing-Sensitive DNA-Microarrays: Peculiarities and Applicationin Biomedical Research (Review)

    OpenAIRE

    2015-01-01

    Alternative splicing (АS) provides a variety of protein and mature mRNA isoforms encoded by a single gene, and is the essential component of cell and tissue differentiation and functioning. DNA-microarrays are highly productive transcriptome research technique both at the level of total gene expression assessment and alternatively spliced mRNA isoforms exploration. The study of AS patterns requires thorough probe design to achieve appropriate accuracy of the analysis. There are two types ...

  20. α-MSH regulates intergenic splicing of MC1R and TUBB3 in human melanocytes

    OpenAIRE

    Dalziel, Martin; Kolesnichenko, Marina; das Neves, Ricardo Pires; Iborra, Francisco; Goding, Colin; Furger, André

    2010-01-01

    Alternative splicing enables higher eukaryotes to increase their repertoire of proteins derived from a restricted number of genes. However, the possibility that functional diversity may also be augmented by splicing between adjacent genes has been largely neglected. Here, we show that the human melanocortin 1 receptor (MC1R) gene, a critical component of the facultative skin pigmentation system, has a highly complex and inefficient poly(A) site which is instrumental in allowing intergenic spl...

  1. Protein trans-splicing of an atypical split intein showing structural flexibility and cross-reactivity.

    Directory of Open Access Journals (Sweden)

    Huiling Song

    Full Text Available Inteins catalyze a protein splicing reaction to excise the intein from a precursor protein and join the flanking sequences (exteins with a peptide bond. In a split intein, the intein fragments (I(N and I(C can reassemble non-covalently to catalyze a trans-splicing reaction that joins the exteins from separate polypeptides. An atypical split intein having a very small I(N and a large I(C is particularly useful for joining synthetic peptides with recombinant proteins, which can be a generally useful method of introducing site-specific chemical labeling or modifications into proteins. However, a large I(C derived from an Ssp DnaX intein was found recently to undergo spontaneous C-cleavage, which raised questions regarding its structure-function and ability to trans-splice. Here, we show that this I(C could undergo trans-splicing in the presence of I(N, and the trans-splicing activity completely suppressed the C-cleavage activity. We also found that this I(C could trans-splice with small I(N sequences derived from two other inteins, showing a cross-reactivity of this atypical split intein. Furthermore, we found that this I(C could trans-splice even when the I(N sequence was embedded in a nearly complete intein sequence, suggesting that the small I(N could project out of the central pocket of the intein to become accessible to the I(C. Overall, these findings uncovered a new atypical split intein that can be valuable for peptide-protein trans-splicing, and they also revealed an interesting structural flexibility and cross-reactivity at the active site of this intein.

  2. Delivering Antisense Morpholino Oligonucleotides to Target Telomerase Splice Variants in Human Embryonic Stem Cells.

    Science.gov (United States)

    Radan, Lida; Hughes, Chris S; Teichroeb, Jonathan H; Postovit, Lynne-Marie; Betts, Dean H

    2016-01-01

    Morpholino oligonucleotides (MO) are an innovative tool that provides a means for examining and modifying gene expression outcomes by antisense interaction with targeted RNA transcripts. The site-specific nature of their binding facilitates focused modulation to alter splice variant expression patterns. Here we describe the steric-blocking of human telomerase reverse transcriptase (hTERT) Δα and Δβ splice variants using MO to examine cellular outcomes related to pluripotency and differentiation in human embryonic stem cells.

  3. Activation and repression functions of an SR splicing regulator depend on exonic versus intronic-binding position.

    Science.gov (United States)

    Shen, Manli; Mattox, William

    2012-01-01

    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.

  4. [Biomechanics of the ankle joint].

    Science.gov (United States)

    Zwipp, H

    1989-03-01

    According to Fick, the tree-dimensional patterns of foot motion are best characterized as jawlike movement. Anatomically and biomechanically, this process represents conjoined, synchronous motion within the three mobile segments of the hindfoot: the ankle joint, the posterior subtalar joint, and the anterior subtalar joint. Foot kinematics can be described more completely if the anterior subtalar joint is defined not only as the talocalcaneal navicular joint, but as including the calcaneocuboid joint, thus representing the transverse joint of the tarsus, i.e., the Chopart joint. The axes of these three joints can be defined precisely. In some parts they represent a screwlike motion, clockwise or counter-clockwise, around the central ligamentous structures (fibulotibial ligament, talocalcaneal interosseous ligament, bifurcate ligament). The individual anatomy and structure of these ligaments provide variations in the degree and direction of foot motion. A precise knowledge of foot kinematics is important in surgical ligament and joint reconstruction and in selective foot arthrodeses.

  5. Half Pint/Puf68 is required for negative regulation of splicing by the SR factor Transformer2

    Science.gov (United States)

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

    2013-01-01

    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. PMID:23880637

  6. A 22-nucleotide spliced leader sequence in the human parasitic nematode Brugia malayi is identical to the trans-spliced leader exon in Caenorhabditis elegans.

    OpenAIRE

    Takacs, A M; Denker, J A; Perrine, K G; Maroney, P A; Nilsen, T W

    1988-01-01

    The mRNAs encoding a 63-kDa antigen in the human parasitic nematode Brugia Malayi contain a spliced leader sequence of 22 nucleotides (nt) that is identical to the trans-spliced leader found on certain actin mRNAs in the distantly related nematode Caenorhabditis elegans. The 22-nt sequence does not appear to be encoded near the 63-kDa genes but is present in multiple copies in several locations within the parasite genome, including the 5S rRNA gene repeat. The 5S-linked copies of the 22-nt se...

  7. Correct splicing despite mutation of the invariant first nucleotide of a 5[prime] splice site: A possible basis for disparate clinical phenotypes in siblings with adenosine deaminase deficiency

    Energy Technology Data Exchange (ETDEWEB)

    Arredondo-Vega, F.X.; Santisteban, I.; Kelly, S.; Hershfield, M.S. (Duke Univ. Medical Center, Durham, NC (United States)); Umetsu, D.T. (Stanford Univ., CA (United States)); Schlossman, C.M.

    1994-05-01

    Adenosine deaminase (ADA) deficiency usually causes severe combined immune deficiency in infancy. Milder phenotypes also occur and are associated with less severely impaired deoxyadenosine (dAdo) catabolism. The authors have characterized the mutations responsible for ADA deficiency in siblings with disparity in clinical phenotype. Erythrocyte dAdo nucleotide pool size, which reflects total residual ADA activity, was lower in the older, more mildly affected sib (RG) than in her younger, more severely affected sister (EG). Cultured T cells, fibroblasts, and B lymphoblasts of RG had detectable residual ADA activity, while cells of EG did not. ADA mRNA was undetectable by northern analysis in cells of both patients. Both sibs were found to be compound heterozygotes for the following novel splicing defects: (1) a G[sup +1][yields]A substitution at the 5' splice site of IVS 2 and (2) a complex 17-bp rearrangement of the 3' splice site of IVS 8, which inserted a run of seven purines into the polypyrimidine tract and altered the reading frame of exon 9. PCR-amplified ADA cDNA clones with premature translation stop codons arising from aberrant pre-mRNA splicing were identified, which were consistent with these mutations. However, some cDNA clones from T cells of both patients and from fibroblasts and Epstein-Barr virus (EBV)-transformed B cells of RG, were normally spliced at both the exon 2/3 and exon 8/9 junctions. A normal coding sequence was documented for clones from both sibs. The normal cDNA clones did not appear to arise from either contamination or PCR artifact, and mosaicism seems unlikely to have been involved. These findings suggest (1) that a low level of normal pre-mRNA splicing may occur despite mutation of the invariant first nucleotide of the 5' splice sequence and (2) that differences in efficiency of such splicing may account for the difference in residual ADA activity, immune dysfunction, and clinical severity in these siblings. 66 refs

  8. Bipartite functions of the CREB co-activators selectively direct alternative splicing or transcriptional activation.

    Science.gov (United States)

    Amelio, Antonio L; Caputi, Massimo; Conkright, Michael D

    2009-09-16

    The CREB regulated transcription co-activators (CRTCs) regulate many biological processes by integrating and converting environmental inputs into transcriptional responses. Although the mechanisms by which CRTCs sense cellular signals are characterized, little is known regarding how CRTCs contribute to the regulation of cAMP inducible genes. Here we show that these dynamic regulators, unlike other co-activators, independently direct either pre-mRNA splice-site selection or transcriptional activation depending on the cell type or promoter context. Moreover, in other scenarios, the CRTC co-activators coordinately regulate transcription and splicing. Mutational analyses showed that CRTCs possess distinct functional domains responsible for regulating either pre-mRNA splicing or transcriptional activation. Interestingly, the CRTC1-MAML2 oncoprotein lacks the splicing domain and is incapable of altering splice-site selection despite robustly activating transcription. The differential usage of these distinct domains allows CRTCs to selectively mediate multiple facets of gene regulation, indicating that co-activators are not solely restricted to coordinating alternative splicing with increase in transcriptional activity.

  9. Development and media regulate alternative splicing of a methyltransferase pre-mRNA in Monascus pilosus.

    Science.gov (United States)

    Zhang, Ming-Yong; Miyake, Tsuyoshi

    2009-05-27

    Two alternatively spliced mRNAs (d- and l-MpLaeA) of a methyltransferase gene (MpLaeA) were identified from Monascus pilosus IFO4520 and its mutant MK-1. Alternative splicing of the MpLaeA pre-mRNA occurred in the 5'-untranslated region (5'-UTR). The alternative splicing patterns of MpLaeA were regulated by the fungal growth stage and the principal nutrients: that is, the short l-MpLaeA mRNA was a constitutive transcript at all growth stages and different carbon or nitrogen sources, but the glutamate and NaNO(3) as main nitrogen source could up-regulate the long d-MpLaeA mRNA form. The long spliced 5'-UTR of d-MpLaeA blocked GFP expression in Escherichia coli , suggesting that d-MpLaeA mRNA was an ineffective spliced mRNA. Down-regulation of MpLaeA by transgenic antisense d-MpLaeA cDNA resulted in decreasing synthesis of monacolin K in M. pilosus. This suggested that the alternative splicing of MpLaeA mRNA might regulate the synthesis of monacolin K.

  10. Functional genomics identifies a requirement of pre-mRNA splicing factors for sister chromatid cohesion.

    Science.gov (United States)

    Sundaramoorthy, Sriramkumar; Vázquez-Novelle, María Dolores; Lekomtsev, Sergey; Howell, Michael; Petronczki, Mark

    2014-11-18

    Sister chromatid cohesion mediated by the cohesin complex is essential for chromosome segregation during cell division. Using functional genomic screening, we identify a set of 26 pre-mRNA splicing factors that are required for sister chromatid cohesion in human cells. Loss of spliceosome subunits increases the dissociation rate of cohesin from chromatin and abrogates cohesion after DNA replication, ultimately causing mitotic catastrophe. Depletion of splicing factors causes defective processing of the pre-mRNA encoding sororin, a factor required for the stable association of cohesin with chromatin, and an associated reduction of sororin protein level. Expression of an intronless version of sororin and depletion of the cohesin release protein WAPL suppress the cohesion defect in cells lacking splicing factors. We propose that spliceosome components contribute to sister chromatid cohesion and mitotic chromosome segregation through splicing of sororin pre-mRNA. Our results highlight the loss of cohesion as an early cellular consequence of compromised splicing. This may have clinical implications because SF3B1, a splicing factor that we identify to be essential for cohesion, is recurrently mutated in chronic lymphocytic leukaemia.

  11. Suppression of 5' splice-sites through multiple exonic motifs by hnRNP L.

    Science.gov (United States)

    Loh, Tiing Jen; Choi, Namjeong; Moon, Heegyum; Jang, Ha Na; Liu, Yongchao; Zhou, Jianhua; Zheng, Xuexiu; Shen, Haihong

    2017-03-01

    Selection of 5' splice-sites (5'SS) in alternative splicing plays an important role in gene regulation. Although regulatory mechanisms of heterogeneous nuclear ribonucleoprotein L (hnRNP L), a well-known splicing regulatory protein, have been studied in a substantial level, its role in 5'SS selection is not thoroughly defined. By using a KLF6 pre-mRNA alternative splicing model, we demonstrate in this report that hnRNP L inhibits proximal 5'SS but promotes two consecutive distal 5'SS splicing, antagonizing SRSF1 roles in KLF6 pre-mRNA splicing. In addition, three consecutive CA-rich sequences in a CA cassette immediately upstream of the proximal 5'SS are all required for hnRNP L functions. Importantly, the CA-cassette locations on the proximal exon do not affect hnRNP L roles. We further show that the proximal 5'SS but not the two distal 5'SSs are essential for hnRNP L activities. Notably, in a Bcl-x pre-mRNA model that contains two alternative 5'SS but includes CA-rich elements at distal exon, we demonstrate that hnRNP L also suppresses nearby 5'SS activation. Taken together, we conclude that hnRNP L suppresses 5'SS selection through multiple exonic motifs.

  12. Electrical Resistance of the Solder Connections for the Consolidation of the LHC Main Interconnection Splices

    CERN Document Server

    Lutum, R; Scheuerlein, C

    2013-01-01

    For the consolidation of the LHC 13 kA main interconnection splices, shunts will be soldered onto each of the 10170 splices. The solder alloy selected for this purpose is Sn60Pb40. In this context the electrical resistance of shunt to busbar lap splices has been measured in the temperature range from RT to 20 K. A cryocooler set-up has been adapted such that a test current of 150 A could be injected for accurate resistance measurements in the low nΩ range. To study the influence of the solder bulk resistivity on the overall splice resistance, connections produced with Sn96Ag4 and Sn77.2In20Ag2.8 have been studied as well. The influence of the Sn60Pb40 solder resistance is negligible when measuring the splice resistance in a longitudinal configuration over a length of 6 cm. In a transverse measurement configuration the splice resistance is significantly influenced by the solder. The connections prepared with Sn77.2In20Ag2.8 show significantly higher resistance values, as expected from the relatively high sol...

  13. Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms

    Directory of Open Access Journals (Sweden)

    Haifeng eWang

    2014-02-01

    Full Text Available Alternative splicing (AS is a process in eukaryotic gene expression, in which the primary transcript of a multi-exon gene is spliced into two or more different mature transcripts, thereby increasing proteome diversity. AS is often regulated differentially between different tissues or developmental stages. Recent studies suggested that up to 60% of intron-containing genes in Arabidopsis thaliana undergo AS. Yet little is known about this complicated and important process during floral development. To investigate the preferential expression of different isoforms of individual alternatively spliced genes, we used high throughput RNA-Seq technology to explore the transcriptomes of three floral development stages of Arabidopsis thaliana and obtained information of various alternative splicing events. We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants. This is less frequent than the previously reported 40%~60% for multiple organs and stages of A. thaliana, indicating that many genes expressed in floral development function with a single predominant isoform. On the other hand, 1,716 isoforms were differentially expressed between the three stages, suggesting that AS might still play important roles in stage transition during floral development. Moreover, 337 novel transcribed regions were identified and most of them have a single exon. In addition, our analyses provide a comprehensive survey of alternative splicing in floral development and facilitate further genomic and genetic studies.

  14. Computational Analysis of an Evolutionarily Conserved VertebrateMuscle Alternative Splicing Program

    Energy Technology Data Exchange (ETDEWEB)

    Das, Debopriya; Clark, Tyson A.; Schweitzer, Anthony; Marr,Henry; Yamamoto, Miki L.; Parra, Marilyn K.; Arribere, Josh; Minovitsky,Simon; Dubchak, Inna; Blume, John E.; Conboy, John G.

    2006-06-15

    A novel exon microarray format that probes gene expression with single exon resolution was employed to elucidate critical features of a vertebrate muscle alternative splicing program. A dataset of 56 microarray-defined, muscle-enriched exons and their flanking introns were examined computationally in order to investigate coordination of the muscle splicing program. Candidate intron regulatory motifs were required to meet several stringent criteria: significant over-representation near muscle-enriched exons, correlation with muscle expression, and phylogenetic conservation among genomes of several vertebrate orders. Three classes of regulatory motifs were identified in the proximal downstream intron, within 200nt of the target exons: UGCAUG, a specific binding site for Fox-1 related splicing factors; ACUAAC, a novel branchpoint-like element; and UG-/UGC-rich elements characteristic of binding sites for CELF splicing factors. UGCAUG was remarkably enriched, being present in nearly one-half of all cases. These studies suggest that Fox and CELF splicing factors play a major role in enforcing the muscle-specific alternative splicing program, facilitating expression of a set of unique isoforms of cytoskeletal proteins that are critical to muscle cell differentiation. Supplementary materials: There are four supplementary tables and one supplementary figure. The tables provide additional detailed information concerning the muscle-enriched datasets, and about over-represented oligonucleotide sequences in the flanking introns. The supplementary figure shows RT-PCR data confirming the muscle-enriched expression of exons predicted from the microarray analysis.

  15. Splicing analysis of 14 BRCA1 missense variants classifies nine variants as pathogenic

    DEFF Research Database (Denmark)

    Ahlborn, Lise B; Dandanell, Mette; Steffensen, Ane Y;

    2015-01-01

    needed to classify whether these uncertain variants are pathogenic or benign. In this study, we investigated 14 BRCA1 variants by in silico splicing analysis and mini-gene splicing assay. All 14 alterations were missense variants located within the BRCT domain of BRCA1 and had previously been examined...... by functional analysis at the protein level. Results from a validated mini-gene splicing assay indicated that nine BRCA1 variants resulted in splicing aberrations leading to truncated transcripts and thus can be considered pathogenic (c.4987A>T/p.Met1663Leu, c.4988T>A/p.Met1663Lys, c.5072C>T/p.Thr1691Ile, c...... to have no or an uncertain effect on the protein level, whereas one variant (c.5072C>T/p.Thr1691Ile) were shown to have a strong effect on the protein level as well. In conclusion, our study emphasizes that in silico splicing prediction and mini-gene splicing analysis are important for the classification...

  16. New discoveries of old SON: a link between RNA splicing and cancer.

    Science.gov (United States)

    Hickey, Christopher J; Kim, Jung-Hyun; Ahn, Eun-Young Erin

    2014-02-01

    The SON protein is a ubiquitously expressed DNA- and RNA-binding protein primarily localized to nuclear speckles. Although several early studies implicated SON in DNA-binding, tumorigenesis and apoptosis, functional significance of this protein had not been recognized until recent studies discovered SON as a novel RNA splicing co-factor. During constitutive RNA splicing, SON ensures efficient intron removal from the transcripts containing suboptimal splice sites. Importantly, SON-mediated splicing is required for proper processing of selective transcripts related to cell cycle, microtubules, centrosome maintenance, and genome stability. Moreover, SON regulates alternative splicing of RNAs from the genes involved in apoptosis and epigenetic modification. In addition to the role in RNA splicing, SON has an ability to suppress transcriptional activation at certain promoter/enhancer DNA sequences. Considering the multiple SON target genes which are directly involved in cell proliferation, genome stability and chromatin modifications, SON is an emerging player in gene regulation during cancer development and progression. Here, we summarize available information from several early studies on SON, and highlight recent discoveries describing molecular mechanisms of SON-mediated gene regulation. We propose that our future effort on better understanding of diverse SON functions would reveal novel targets for cancer therapy.

  17. A novel splicing mutation alters DSPP transcription and leads to dentinogenesis imperfecta type II.

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    Full Text Available Dentinogenesis imperfecta (DGI type II is an autosomal dominant disease characterized by a serious disorders in teeth. Mutations of dentin sialophosphoprotein (DSPP gene were revealed to be the causation of DGI type II (DGI-II. In this study, we identified a novel mutation (NG_011595.1:g.8662T>C, c.135+2T>C lying in the splice donor site of intron 3 of DSPP gene in a Chinese Han DGI-II pedigree. It was found in all affected subjects but not in unaffected ones or other unrelated healthy controls. The function of the mutant DSPP gene, which was predicted online and subsequently confirmed by in vitro splicing analysis, was the loss of splicing of intron 3, leading to the extended length of DSPP mRNA. For the first time, the functional non-splicing of intron was revealed in a novel DSPP mutation and was considered as the causation of DGI-II. It was also indicated that splicing was of key importance to the function of DSPP and this splice donor site might be a sensitive mutation hot spot. Our findings combined with other reports would facilitate the genetic diagnosis of DGI-II, shed light on its gene therapy and help to finally conquer human diseases.

  18. A novel splicing mutation alters DSPP transcription and leads to dentinogenesis imperfecta type II.

    Science.gov (United States)

    Zhang, Jun; Wang, Jiucun; Ma, Yanyun; Du, Wenqi; Zhao, Siyang; Zhang, Zuowei; Zhang, Xiaojiao; Liu, Yue; Xiao, Huasheng; Wang, Hongyan; Jin, Li; Liu, Jie

    2011-01-01

    Dentinogenesis imperfecta (DGI) type II is an autosomal dominant disease characterized by a serious disorders in teeth. Mutations of dentin sialophosphoprotein (DSPP) gene were revealed to be the causation of DGI type II (DGI-II). In this study, we identified a novel mutation (NG_011595.1:g.8662T>C, c.135+2T>C) lying in the splice donor site of intron 3 of DSPP gene in a Chinese Han DGI-II pedigree. It was found in all affected subjects but not in unaffected ones or other unrelated healthy controls. The function of the mutant DSPP gene, which was predicted online and subsequently confirmed by in vitro splicing analysis, was the loss of splicing of intron 3, leading to the extended length of DSPP mRNA. For the first time, the functional non-splicing of intron was revealed in a novel DSPP mutation and was considered as the causation of DGI-II. It was also indicated that splicing was of key importance to the function of DSPP and this splice donor site might be a sensitive mutation hot spot. Our findings combined with other reports would facilitate the genetic diagnosis of DGI-II, shed light on its gene therapy and help to finally conquer human diseases.

  19. The evolutionary landscape of intergenic trans-splicing events in insects.

    Science.gov (United States)

    Kong, Yimeng; Zhou, Hongxia; Yu, Yao; Chen, Longxian; Hao, Pei; Li, Xuan

    2015-11-02

    To explore the landscape of intergenic trans-splicing events and characterize their functions and evolutionary dynamics, we conduct a mega-data study of a phylogeny containing eight species across five orders of class Insecta, a model system spanning 400 million years of evolution. A total of 1,627 trans-splicing events involving 2,199 genes are identified, accounting for 1.58% of the total genes. Homology analysis reveals that mod(mdg4)-like trans-splicing is the only conserved event that is consistently observed in multiple species across two orders, which represents a unique case of functional diversification involving trans-splicing. Thus, evolutionarily its potential for generating proteins with novel function is not broadly utilized by insects. Furthermore, 146 non-mod trans-spliced transcripts are found to resemble canonical genes from different species. Trans-splicing preserving the function of 'breakup' genes may serve as a general mechanism for relaxing the constraints on gene structure, with profound implications for the evolution of genes and genomes.

  20. Benzo[a]pyrene treatment leads to changes in nuclear protein expression and alternative splicing

    Energy Technology Data Exchange (ETDEWEB)

    Yan Chunlan; Wu Wei [Department of Toxicology, Zhejiang University School of Public Health, 388 Yu-Hang-Tang Road, Hangzhou, Zhejiang 310058 (China); Li Haiyan [Department of Toxicology, Zhejiang University School of Public Health, 388 Yu-Hang-Tang Road, Hangzhou, Zhejiang 310058 (China); Huzhou Maternity and Child Care Hospital, Huzhou, Zhejiang 313000 (China); Zhang Guanglin [Department of Toxicology, Zhejiang University School of Public Health, 388 Yu-Hang-Tang Road, Hangzhou, Zhejiang 310058 (China); Duerksen-Hughes, Penelope J. [Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92354 (United States); Zhu Xinqiang, E-mail: zhuxq@zju.edu.cn [Department of Toxicology, Zhejiang University School of Public Health, 388 Yu-Hang-Tang Road, Hangzhou, Zhejiang 310058 (China); Yang Jun, E-mail: gastate@zju.edu.cn [Department of Toxicology, Zhejiang University School of Public Health, 388 Yu-Hang-Tang Road, Hangzhou, Zhejiang 310058 (China); Zhejiang-California International Nanosystems Institute, Hangzhou, Zhejiang 310029 (China)

    2010-04-01

    Benzo[a]pyrene (BaP) is a potent pro-carcinogen generated from the combustion of fossil fuel and cigarette smoke. Previously, using a proteomic approach, we have shown that BaP can induce changes in the expression of many cellular proteins, including transcription regulators. In the present study, using a similar approach, we examined the nuclear protein response to BaP in HeLa cells and found that BaP treatment caused expression changes in many nuclear proteins. Twenty-four of these proteins were successfully identified, several of which are involved in the alternative splicing of mRNA, DNA replication, recombination, and repair. The changed expression levels were further confirmed by immunoblot analysis using specific antibodies for two proteins, Lamin A and mitotic checkpoint protein Bub3. The nuclear localization of these two proteins was also confirmed by confocal microscopy. To determine whether alternative splicing was activated following BaP treatment, we examined Fas and CD44, two genes previously shown to be targets of alternative splicing in respond to DNA damage. While no significant activation of alternative splicing was observed for Fas, CD44 splicing variants were found after BaP treatment. Together, these data show that DNA damage induces dramatic changes in nuclear protein expression, and that alternative splicing might be involved in the cellular response to DNA damage.