EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data

<p>Abstract</p> <p>Background</p> <p>ESTs and full-length cDNAs represent an invaluable source of evidence for inferring reliable gene structures and discovering potential alternative splicing events. In newly sequenced genomes, these tasks may not be practicable owing to the lack of appropriate training sets. However, when expression data are available, they can be used to build EST clusters related to specific genomic transcribed <it>loci</it>. Common strategies recently employed to this end are based on sequence similarity between transcripts and can lead, in specific conditions, to inconsistent and erroneous clustering. In order to improve the cluster building and facilitate all downstream annotation analyses, we developed a simple genome-based methodology to generate gene-oriented clusters of ESTs when a genomic sequence and a pool of related expressed sequences are provided. Our procedure has been implemented in the software EasyCluster and takes into account the spliced nature of ESTs after an <it>ad hoc </it>genomic mapping.</p> <p>Methods</p> <p>EasyCluster uses the well-known GMAP program in order to perform a very quick EST-to-genome mapping in addition to the detection of reliable splice sites. Given a genomic sequence and a pool of ESTs/FL-cDNAs, EasyCluster starts building genomic and EST local databases and runs GMAP. Subsequently, it parses results creating an initial collection of pseudo-clusters by grouping ESTs according to the overlap of their genomic coordinates on the same strand. In the final step, EasyCluster refines the clustering by again running GMAP on each pseudo-cluster and groups together ESTs sharing at least one splice site.</p> <p>Results</p> <p>The higher accuracy of EasyCluster with respect to other clustering tools has been verified by means of a manually cured benchmark of human EST clusters. Additional datasets including the Unigene cluster Hs.122986 and ESTs related to the human <it>HOXA </it>gene family have also been used to demonstrate the better clustering capability of EasyCluster over current genome-based web service tools such as ASmodeler and BIPASS. EasyCluster has also been used to provide a first compilation of gene-oriented clusters in the <it>Ricinus communis </it>oilseed plant for which no Unigene clusters are yet available, as well as an evaluation of the alternative splicing in this plant species.</p

Attenuation of Salt-Induced Cardiac Remodeling and Diastolic Dysfunction by the GPER Agonist G-1 in Female mRen2.Lewis Rats

The G protein-coupled estrogen receptor (GPER) is expressed in various tissues including the heart. Since the mRen2.Lewis strain exhibits salt-dependent hypertension and early diastolic dysfunction, we assessed the effects of the GPER agonist (G-1, 40 nmol/kg/hr for 14 days) or vehicle (VEH, DMSO/EtOH) on cardiac function and structure.Intact female mRen2.Lewis rats were fed a normal salt (0.5% sodium; NS) diet or a high salt (4% sodium; HS) diet for 10 weeks beginning at 5 weeks of age.Prolonged intake of HS in mRen2.Lewis females resulted in significantly increased blood pressure, mildly reduced systolic function, and left ventricular (LV) diastolic compliance (as signified by a reduced E deceleration time and E deceleration slope), increased relative wall thickness, myocyte size, and mid-myocardial interstitial and perivascular fibrosis. G-1 administration attenuated wall thickness and myocyte hypertrophy, with nominal effects on blood pressure, LV systolic function, LV compliance and cardiac fibrosis in the HS group. G-1 treatment significantly increased LV lusitropy [early mitral annular descent (e')] independent of prevailing salt, and improved the e'/a' ratio in HS versus NS rats (P<0.05) as determined by tissue Doppler.Activation of GPER improved myocardial relaxation in the hypertensive female mRen2.Lewis rat and reduced cardiac myocyte hypertrophy and wall thickness in those rats fed a high salt diet. Moreover, these advantageous effects of the GPER agonist on ventricular lusitropy and remodeling do not appear to be associated with overt changes in blood pressure

Induction of Programmed Cell Death in Human Alveolar Epithelial Cells Infected with Influenza Virus

Introduction: Avian influenza viruses are considered as a serious threat to human and animal health. An increase in expression of proinflammatory cytokines and type I IFN genes, as well as host cell death responses contribute to the pathogenesis of influenza infection. Hence, this study aimed to evaluate the growth dynamics of subacute avian influenza virus in human respiratory alveolar epithelium cells (A549).\ud Methods: The A549 cell cultures were infected at MOIs 0.1 and 2.0 viral doses in the presence and absence of trypsin. The virus growth kinetics were elucidated by the plaque assay and the cell viability was determined by MTT at various times after the infection. The induction quality of programmed cell death as well as the signal transduction pathway of death were assessed by genomic DNA fragmentation and western blotting respectively.\ud Results: The study findings indicated that although the H9N2 virus replication did produce a marked cytopathic effect on the alveolar cells, which led to a reduction in the cell viability, the viral titers were increased in the infected cells. The virus replication of in these cells indicated repression of host defense mechanism as well as activation of cell death. The induction of apoptosis in A549 cells was correlated with the increased virus titers as well as virus replication (p< 0.05).\ud Conclusion: H9N2 avian influenza virus were demonstrated to induce apoptosis in human alveolar epithelial cells via the intrinsic pathway in a dose-dependent manner. \ud \u

Effects of Defining Realistic Compositions of the Ocular Melanoma on Proton Therapy

Background: Recent studies in eye plaque brachytherapy have shown a considerable difference between the dosimetric results using water phantom and a model of human eye containing realistic materials. In spite of this fact, there is a lack of simulation studies based on such a model in proton therapy literatures. In the presented work, the effect of utilizing an eye model with ocular media on proton therapy is investigated using the MCNPX Monte Carlo Code. Methods: Two different eye models are proposed to study the effect of defining realistic materials on dose deposition due to utilizing pencil beam scanning (PBS) method for proton therapy of ocular melanoma. The first model is filled with water, and the second one contains the realistic materials of tumor and vitreous. Spread out Bragg peaks (SOBP) are created to cover a typical tumor volume. Moreover, isodose curves are figured in order to evaluate planar variations of absorbed dose in two models. Results: The results show that the maximum delivered dose in ocular media is approximately 12-32% more than in water phantom. Also it is found that using the optimized weighted beams in water phantom leads to disturbance of uniformity of SOBP in ocular media. Conclusion: Similar to the results reported in eye brachytherapy published papers, considering the ocular media in simulation studies leads to a more realistic assessment of sufficiency of the designed proton beam in tissue. This effect is of special importance in creating SOBP, as well as in delivered dose in the tumor boundaries in proton pencil beam scanning method