Differential expressed genes in ECV304 Endothelial-like Cells infected with Human Cytomegalovirus

Background: Human cytomegalovirus (HCMV) is a virus which has the potential to alter cellular gene expression through multiple mechanisms.Objective: With the application of DNA microarrays, we could monitor the effects of pathogens on host-cell gene expression programmes in great depth and on a broad scale.Methods: Changes in mRNA expression levels of human endothelial-like ECV304 cells following infection with human cytomegalovirus AD169 strain was analyzed by a microarray system comprising 21073 60-mer oligonucleotide probes which represent 18716 human genes or transcripts.Results: The results from cDNA microarray showed that there were 559 differential expressed genes consisted of 471 upregulated genes and 88 down-regulated genes. Real-time qPCR was performed to validate the expression of 6 selected genes (RPS24, MGC8721, SLC27A3, MST4, TRAF2 and LRRC28), and the results of which were consistent with those from the microarray. Among 237 biology processes, 39 biology processes were found to be related significantly to HCMV-infection. The signal transduction is the most significant biological process with the lowest p value (p=0.005) among all biological process which involved in response to HCMV infection.Conclusion: Several of these gene products might play key roles in virus-induced pathogenesis. These findings may help to elucidate the pathogenic mechanisms of HCMV caused diseases.Keywords: Human cytomegalovirus, microarray, Gene expression profiling; infectomicsAfrican Health Sciences 2013; 13(4): 864 - 87

The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry

Flatfish have the most extreme asymmetric body morphology of vertebrates. During metamorphosis, one eye migrates to the contralateral side of the skull, and this migration is accompanied by extensive craniofacial transformations and simultaneous development of lopsided body pigmentation(1-5). The evolution of this developmental and physiological innovation remains enigmatic. Comparative genomics of two flatfish and transcriptomic analyses during metamorphosis point to a role for thyroid hormone and retinoic acid signaling, as well as phototransduction pathways. We demonstrate that retinoic acid is critical in establishing asymmetric pigmentation and, via cross-talk with thyroid hormones, in modulating eye migration. The unexpected expression of the visual opsins from the phototransduction pathway in the skin translates illumination differences and generates retinoic acid gradients that underlie the generation of asymmetry. Identifying the genetic underpinning of this unique developmental process answers long-standing questions about the evolutionary origin of asymmetry, but it also provides insight into the mechanisms that control body shape in vertebrates.National Natural Science Foundation of China [31130057, 31461163005, 31530078, 31472269, 31472262, 31472273]; State 863 High Technology R&D Project of China [2012AA092203, 2012AA10A408, 2012AA10A403-2]; Education and Research of Guangdong Province [2013B090800017]; Taishan Scholar Climb Project Fund of Shandong of China; Taishan Scholar Project Fund of Shandong of China for Young Scientists; Shanghai Universities First-class Disciplines Project of Fisheries; Program for Professor of Special Appointment (Eastern Scholar) at the Shanghai Institutions of Higher Learning; Shanghai Municipal Science, Special Project on the Integration of Industryinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/publishedVersio

Optical Satellite Image Geo-Positioning with Weak Convergence Geometry

High-resolution optical satellites are widely used in environmental monitoring. With the aim to observe the largest possible coverage, the overlapping areas and intersection angles of respective optical satellite images are usually small. However, the conventional bundle adjustment method leads to erroneous results or even failure under conditions of weak geometric convergence. By transforming the traditional stereo adjustment to a planar adjustment and combining it with linear programming (LP) theory, a new method that can solve the bias compensation parameters of all satellite images is proposed in this paper. With the support of freely available open source digital elevation models (DEMs) and sparse ground control points (GCPs), the method can not only ensure the consistent inner precision of all images, but also the absolute geolocation accuracy of the ground points. Tests of the two data sets covering different landscapes validated the effectiveness and feasibility of the method. The results showed that the geo-positioning performance of the method was better in regions of smaller topographic relief or for satellite images with a larger imaging altitude angle. The best accuracy of image geolocation with weak convergence geometry was as high as to 3.693 m in the horizontal direction and 6.510 m in the vertical direction, which is a level of accuracy equal to that of images with good intersection conditions

Investigation on GNSS Lever Arms and IMU Boresight Misalignment Calibration of Domestic Airborne Wide-field Three CCD Camera

Focusing on the first domestic developed airborne three line CCD camera (GFXJ), it is carried out that the innovative investigation work on GNSS lever arms and IMU boresight misalignment calibration of GFXJ camera. Firstly, a brief introduction is given on the imaging properties of GFXJ camera. Then, the GNSS level arms calibration model and IMU boresight misalignment calibration model are built for GFXJ camera after detailed investigation. Meanwhile, the iterative two-step calibration scheme is put forward for the GNSS level arms and IMU boresight misalignment calibration of GFXJ camera. Finally, multiple sets of flight data are captured under the support of the national Songshan remote sensing comprehensive testfield. Through the block adjustment and calibration experiments of these sets of imaging data, it verifies the correctness and the efficiency of proposed GNSS lever arms calibration model and IMU boresight misalignment calibration model, and also demonstrates the reliability and practicability of the iterative two-step calibration scheme for GFXJ camera. The proposed calibration scheme can significantly enhance the geometric positioning accuracy of GFXJ camera. Using the GNSS level arms and the IMU boresight misalignment calibration values, the uncontrolled positioning accuracy of GFXJ camera can be significantly improved. Aided with several control points for re-block adjustment, the planar positioning accuracy of GFXJ camera can fulfill the accuracy requirements of 1:1000 scale mapping, but there still exists a little gap between its height positioning accuracy and the 1:1000 scale mapping requirements. The camera is still in the calibration flight stage, its geometric performance can be further improved after product approval. Moreover, the GNSS lever arms calibration model, the IMU boresight misalignment calibration model, and the iterative two-step calibration scheme put forward in the paper can be applied to calibration work for other airborne CCD cameras

Sensitivity Analysis Based on Markovian Integration by Parts Formula

Sensitivity analysis is widely applied in financial risk management and engineering; it describes the variations brought by the changes of parameters. Since the integration by parts technique for Markov chains is well developed in recent years, in this paper we apply it for computation of sensitivity and show the closed-form expressions for two commonly-used time-continuous Markovian models. By comparison, we conclude that our approach outperforms the existing technique of computing sensitivity on Markovian models

A Back Projection Algorithm for Linear Array Imageries Based on the Constraints of Object-space Relation

Back projection is the key technology for rectification of linear array CCD imageries. On the basis of analyzing the imaging mode and characteristics of linear whiskbroom image, a back projection algorithm based on the constraints of object-space relation was proposed, aiming at the inefficiency of conventional image-based sequential or iterative search methods. The best scan-line of the adjacent point was used as a priori value, to estimate the number of the scan-lines between the adjacent point and the current point, thus locating the initial best scan-line. Then, a search window was constructed by the center of the initial best scan-line, and an accurate searching was implemented. At last, according to the orientation elements of the best scan-line, the coordinates back projection was carried out. The feasibility, accuracy and efficiency of the proposed method were verified by the experimental results of the airborne linear array whiskbroom simulated image data and the pushbroom real image data

PTBP1 promotes hepatocellular carcinoma progression by regulating the skipping of exon 9 in NUMB pre-mRNA

Aberrant alternative splicing is one of the important causes of cancer. Polypyrimidine tract binding protein 1 (PTBP1) has been found to be involved in splicing regulation in a variety of tumors. Here, we observed significant up-regulation of PTBP1 in primary hepatocellular carcinoma (HCC) tissues. High levels of PTBP1 expression were associated with poor prognosis and increased metastatic potential in HCC. In vitro studies demonstrated that elevated PTBP1 promoted both migration and invasion by HCC cells. In contrast, knockdown of PTBP1 significantly inhibited the migration and invasion of HCC cells in vitro. Further, up-regulation of PTBP1 markedly accumulated the expression of oncogenic isoform of NUMB, NUMB-PRRL. We observed two isoforms of NUMB, NUMB-PRRL and NUMB-PRRS exhibit opposite function in HCC cells, which partially explain PTBP1 plays the tumor promoting roles in a NUMB splicing-dependent manner. In summary, our study indicates that PTBP1 may serve as an oncogene in HCC patients by regulating the alternative splicing of NUMB exon 9 and could potentially serve as a prognostic indicator

Original Article Expression and clinical significance of cancer-testis genes in clear cell renal cell carcinoma

Abstract: Cancer-testis (CT) antigens, which are encoded by CT genes, have been recognized as a group of highly attractive targets for cancer immunotherapy. However, the expression and clinical relevance of CT genes in clear cell renal cell carcinoma (ccRCC) remains largely unknown. The present study aims to analyze the expression profile of 6 individual CT genes including MAGE-A1, MAGE-A3, MAGE-A12, cTAGE-1, cTAGE-2, and NY-ESO-1 in ccRCC and further investigate their possible correlations with clinicopathologic characteristics. The mRNA expressions of these CT genes were detected using reverse transcriptase-polymerase chain reaction (RT-PCR) in 105 ccRCC tissue samples (T 1-2 in 70 samples, T 3-4 in 35 samples; G 1-2 in 65 samples, G 3-4 in 40 samples) as well as the paired adjacent normal tissues. The most frequently expressed CT gene was MAGE-A3 (27.6%), followed by MAGE-A12 (23.8%), NY-ESO-1 (21%), MAGE-A1 (20%), cTAGE-1 (17.1%), and cTAGE-2 (14.3%). In contrast, no expression of CT genes was detected in the paired adjacent normal tissues. Furthermore, the MAGE-A3 protein expression was determined by Western blot and immunohistochemistry. MAGE-A3 protein was expressed in 21.9% ccRCC samples with a cytoplasmic staining pattern. No MAGE-A3 protein expression was found in the paired adjacent normal tissues. There was a significant correlation between MAGE-A3 expression at both mRNA (P =0.045) and protein (P = 0.03) levels with advanced stages of the disease. Taken together, CT genes may serve as promising targets of specific immunotherapy for ccRCC and particularly, MAGE-A3 may serve as a potential prognostic marker for ccRCC patients