39 research outputs found

    Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops

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    © 2015 Min et al. Background: Protein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms. Results: We carried out the comparative analyses of the functional landscapes of the AS using the consensus assembly of expressed sequence tags and available mRNA sequences in four cereal plants. We identified a total of 8,734 in Oryza sativa subspecies (ssp) japonica, 2,657 in O. sativa ssp indica, 3,971 in Sorghum bicolor, and 10,687 in Zea mays AS genes. Among the identified AS events, intron retention remains to be the dominant type accounting for 23.5 % in S. bicolor, and up to 55.8 % in O. sativa ssp indica. We identified a total of 887 AS genes that were conserved among Z. mays, S. bicolor, and O. sativa ssp japonica; and 248 AS genes were found to be conserved among all four studied species or ssp. Furthermore, we identified 53 AS genes conserved with Brachypodium distachyon. Gene Ontology classification of AS genes revealed functional assignment of these genes in many biological processes with diverse molecular functions. Conclusions: AS is common in cereal plants. The AS genes identified in four cereal crops in this work provide the foundation for further studying the roles of AS in regulation of cereal plant growth and development. The data can be accessed at Plant Alternative Splicing Databas

    Compact CdZnTe-based gamma camera for prostate cancer imaging

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    In this paper, we discuss the design of a compact gamma camera for high-resolution prostate cancer imaging using Cadmium Zinc Telluride (CdZnTe or CZT) radiation detectors. Prostate cancer is a common disease in men. Nowadays, a blood test measuring the level of prostate specific antigen (PSA) is widely used for screening for the disease in males over 50, followed by (ultrasound) imaging-guided biopsy. However, PSA tests have a high false-positive rate and ultrasound-guided biopsy has a high likelihood of missing small cancerous tissues. Commercial methods of nuclear medical imaging, e.g. PET and SPECT, can functionally image the organs, and potentially find cancer tissues at early stages, but their applications in diagnosing prostate cancer has been limited by the smallness of the prostate gland and the long working distance between the organ and the detectors comprising these imaging systems. CZT is a semiconductor material with wide band-gap and relatively high electron mobility, and thus can operate at room temperature without additional cooling. CZT detectors are photon-electron direct-conversion devices, thus offering high energy-resolution in detecting gamma rays, enabling energy-resolved imaging, and reducing the background of Compton-scattering events. In addition, CZT material has high stopping power for gamma rays; for medical imaging, a few-mm-thick CZT material provides adequate detection efficiency for many SPECT radiotracers. Because of these advantages, CZT detectors are becoming popular for several SPECT medical-imaging applications. Most recently, we designed a compact gamma camera using CZT detectors coupled to an application-specific-integrated-circuit (ASIC). This camera functions as a trans-rectal probe to image the prostate gland from a distance of only 1-5 cm, thus offering higher detection efficiency and higher spatial resolution. Hence, it potentially can detect prostate cancers at their early stages. The performance tests of this camera have been completed. The results show better than 6-mm resolution at a distance of 1 cm. Details of the test results are discussed in this paper
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