The high frequency of alternative splicing among the serine/arginine-rich (SR) family of proteins in plants has been linked to important roles in gene regulation during development and in response to ...environmental stress. In this article, we have searched and manually annotated all the SR proteins in the genomes of maize and sorghum. The experimental validation of gene structure by reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed, with few exceptions, that SR genes produced multiple isoforms of transcripts by alternative splicing. Despite sharing high structural similarity and conserved positions of the introns, the profile of alternative splicing diverged significantly between maize and sorghum for the vast majority of SR genes. These include many transcript isoforms discovered by RT-PCR and not represented in extant expressed sequence tag (EST) collection. However, we report the occurrence of various maize and sorghum SR mRNA isoforms that display evolutionary conservation of splicing events with their homologous SR genes in Arabidopsis and moss. Our data also indicate an important role of both 5' and 3' untranslated regions in the regulation of SR gene expression. These observations have potentially important implications for the processes of evolution and adaptation of plants to land.
Helitrons are a family of mobile elements that were discovered in 2001 and are now known to exist in the entire eukaryotic kingdom. Helitrons, particularly those of maize, exhibit an intriguing ...property of capturing gene fragments and placing them into the mobile element. Helitron-captured genes are sometimes transcribed, giving birth to chimeric transcripts that intertwine coding regions of different captured genes. Here, we perused the B73 maize genome for high-quality, putative Helitrons that exhibit plus/minus polymorphisms and contain pieces of more than one captured gene. Selected Helitrons were monitored for expression via in silico EST analysis. Intriguingly, expression validation of selected elements by RT-PCR analysis revealed multiple transcripts not seen in the EST databases. The differing transcripts were generated by alternative selection of splice sites during pre-mRNA processing. Selection of splice sites was not random since different patterns of splicing were observed in the root and shoot tissues. In one case, an exon residing in close proximity but outside of the Helitron was found conjoined with Helitron-derived exons in the mature transcript. Hence, Helitrons have the ability to synthesize new genes not only by placing unrelated exons into common transcripts, but also by transcription readthrough and capture of nearby exons. Thus, Helitrons have a phenomenal ability to "display" new coding regions for possible selection in nature. A highly conservative, minimum estimate of the number of new transcripts expressed by Helitrons is ~11,000 or ~25% of the total number of genes in the maize genome.
The bremsstrahlung tagged photon beam in Hall B at JLab Sober, D.I.; Crannell, Hall; Longhi, Alberto ...
Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
02/2000, Volume:
440, Issue:
2
Journal Article
Peer reviewed
We describe the design and commissioning of the photon tagging beamline installed in experimental Hall B at the Thomas Jefferson National Accelerator Facility (JLab). This system can tag photon ...energies over a range from 20% to 95% of the incident electron energy, and is capable of operation with beam energies up to 6.1
GeV. A single dipole magnet is combined with a hodoscope containing two planar arrays of plastic scintillators to detect energy-degraded electrons from a thin bremsstrahlung radiator. The first layer of 384 partially overlapping small scintillators provides photon energy resolution, while the second layer of 61 larger scintillators provides the timing resolution necessary to form a coincidence with the corresponding nuclear interaction triggered by the tagged photon. The definitions of overlap channels in the first counter plane and of geometric correlation between the two planes are determined using digitized time information from the individual counters. Auxiliary beamline devices are briefly described, and performance results to date under real operating conditions are presented. The entire photon-tagging system has met or exceeded its design goals.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
The CLAS Cherenkov detector Adams, G.; Burkert, V.; Carl, R. ...
Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
06/2001, Volume:
465, Issue:
2
Journal Article
Peer reviewed
The design, construction, and performance of the CLAS Cherenkov threshold gas detector at Jefferson Lab is described. The detector consists of 216 optical modules. Each module consists of three ...adjustable mirrors of lightweight composite construction, a Winston light collecting cone, a 5-in. photomultiplier tube, and specially designed magnetic shielding. Efficiencies and response functions have been measured.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
In an exclusive measurement of the reaction gammad-->K(+)K(-)pn, a narrow peak that can be attributed to an exotic baryon with strangeness S=+1 is seen in the K(+)n invariant mass spectrum. The peak ...is at 1.542+/-0.005 GeV/c(2) with a measured width of 0.021 GeV/c(2) FWHM, which is largely determined by experimental mass resolution. The statistical significance of the peak is (5.2+/-0.6)sigma. The mass and width of the observed peak are consistent with recent reports of a narrow S=+1 baryon by other experimental groups.
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CMK, CTK, FMFMET, IJS, NUK, PNG, UM
The CEBAF large acceptance spectrometer (CLAS) Mecking, B.A.; Adams, G.; Anciant, E. ...
Nuclear instruments & methods in physics research. Section A, Accelerators, spectrometers, detectors and associated equipment,
05/2003, Volume:
503, Issue:
3
Journal Article, Conference Proceeding
Peer reviewed
Open access
The CEBAF large acceptance spectrometer (CLAS) is used to study photo- and electro-induced nuclear and hadronic reactions by providing efficient detection of neutral and charged particles over a good ...fraction of the full solid angle. A collaboration of about 30 institutions has designed, assembled, and commissioned CLAS in Hall B at the Thomas Jefferson National Accelerator Facility. The CLAS detector is based on a novel six-coil toroidal magnet which provides a largely azimuthal field distribution. Trajectory reconstruction using drift chambers results in a momentum resolution of 0.5% at forward angles. Cherenkov counters, time-of-flight scintillators, and electromagnetic calorimeters provide good particle identification. Fast triggering and high data-acquisition rates allow operation at a luminosity of
10
34
nucleon
cm
−2
s
−1
. These capabilities are being used in a broad experimental program to study the structure and interactions of mesons, nucleons, and nuclei using polarized and unpolarized electron and photon beams and targets. This paper is a comprehensive and general description of the design, construction and performance of CLAS.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, SAZU, SBCE, SBJE, UL, UM, UPCLJ, UPUK
The propensity to capture and mobilize gene fragments by the highly abundant Helitron family of transposable elements likely impacts the evolution of genes in Zea mays. These elements provide a ...substrate for natural selection by giving birth to chimeric transcripts by intertwining exons of disparate genes. They also capture flanking exons by read-through transcription. Here, we describe the expression of selected Helitrons in different maize inbred lines. We recently reported that these Helitrons produce multiple isoforms of transcripts in inbred B73 via alternative splicing. Despite sharing high degrees of sequence similarity, the splicing profile of Helitrons differed among various maize inbred lines. The comparison of Helitron sequences identified unique polymorphisms in inbred B73, which potentially give rise to the alternatively spliced sites utilized by transcript isoforms. Some alterations in splicing, however, do not have obvious explanations. These observations not only add another level to the creation of transcript diversity by Helitrons among inbred lines but also provide novel insights into the cis-acting elements governing splice-site selection during pre-mRNA processing.
The longitudinal target-spin asymmetry AUL for the exclusive electroproduction of high-energy photons was measured for the first time in ep-->e;'pgamma. The data have been accumulated at JLab with ...the CLAS spectrometer using 5.7 GeV electrons and a longitudinally polarized NH3 target. A significant azimuthal angular dependence was observed, resulting from the interference of the deeply virtual Compton scattering and Bethe-Heitler processes. The amplitude of the sinvarphi moment is 0.252+/-0.042stat+/-0.020sys. Theoretical calculations are in good agreement with the magnitude and the kinematic dependence of the target-spin asymmetry, which is sensitive to the generalized parton distributions H and H.
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The reaction gamma p-->pi(+)K(-)K(+)n was studied at Jefferson Laboratory using a tagged photon beam with an energy range of 3-5.47 GeV. A narrow baryon state with strangeness S=+1 and mass ...M=1555+/-10 MeV/c(2) was observed in the nK(+) invariant mass spectrum. The peak's width is consistent with the CLAS resolution (FWHM=26 MeV/c(2)), and its statistical significance is (7.8+/-1.0)sigma. A baryon with positive strangeness has exotic structure and cannot be described in the framework of the naive constituent quark model. The mass of the observed state is consistent with the mass predicted by the chiral soliton model for the Theta(+) baryon. In addition, the pK(+) invariant mass distribution was analyzed in the reaction gamma p-->K(-)K(+)p with high statistics in search of doubly charged exotic baryon states. No resonance structures were found in this spectrum.
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CMK, CTK, FMFMET, IJS, NUK, PNG, UM
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