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Summary We present a web server, GenCLiP 3, which is an updated version of GenCLiP 2.0 to enhance analysis of human gene functions and regulatory networks, with the following improvements: i) accurate recognition of molecular interactions with polarity and directionality from the entire PubMed database; ii) support for Boolean search to customize multiple-term search and to quickly retrieve function related genes; iii) strengthened association between gene and keyword by a new scoring method; and iv) daily updates following literature release at PubMed FTP. Availability The server is freely available for academic use at: http://ci.smu.edu.cn/genclip3/. Supplementary information Supplementary data are available at Bioinformatics online.

The incidence of prostatic cancer (PCa) has increased significantly, and the measurement of prostate-specific antigen (PSA) is an effective screening tool for its diagnosis. PCa includes a number of specific clinicopathological types, including squamous cell, urothelial, adenoid cystic and small-cell carcinoma, among which small-cell carcinoma of the prostate (SCCP) is extremely rare, accounting for

Long non-coding RNA (lncRNA) plasmacytoma variant translocation 1 (PVT1) has been reported to be overexpressed in prostate cancer cells and associated with tumorigenesis in various types of cancer. However, the biological function of lncRNA PVT1 remains largely unknown. The aim of the present study was to investigate the effect of lncRNA PVT1 expression on the proliferation and migration of prostate cancer cells. Stably transfected prostate cancer cells with downregulated expression of lncRNA PVT1 were constructed by an efficient siRNA fragment, followed by confirmation by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Proliferation was assessed using CCK-8, colony formation and xenograft assays, and cell migration was evaluated using a wound healing assay. The PathScan® Intracellular Signaling Array kit was utilized to explore the underlying molecular mechanisms of lncRNA PVT1 expression in prostate cancer cells. RT-qPCR results confirmed that the lncRNA PVT1 expression level was successfully knocked down in prostate cancer cells. When lncRNA PVT1 expression was downregulated in prostate cancer cells, proliferation and migration were significantly inhibited, compared with the control lncRNA PVT1 group. Furthermore, PVT1 knockdown decreased the phosphorylation of p38 in DU145 cells. Therefore, the present study demonstrated that lncRNA PVT1 downregulation inhibits the proliferation and migration of prostate cancer cells, and is associated with p38 phosphorylation.

To investigate the efficacy and possible action mechanism of Qianlie Beixi Capsules in the treatment of unliquefiable semen.A total of 190 patients with unliquefiable semen were treated with Qianlie Beixi Capsules for 1 or 2 courses (3 weeks per a course). The seminal changes were observed and recorded.Of the 190 patients in the 1-course treatment arm, 99 were cured and 91 failed to respond after the first course. And the effectiveness rate was 52.1%. Of the 122 patients in the 2-course treatment arm, 81 were cured and 41 failed to respond after the second course. And the effectiveness rate was 66.4%. The efficacy of 2-course regimen was obviously better than that of 1-course regiment. In the meantime, sperm density improved in the 2-course treatment arm. Sperm motility improved slightly in the effective subjects of 1-course treatment arm. All the above results had statistically significant differences (P0.05).Qianlie Beixi Capsules is both safe and effective for unliquefiable semen and may shorten the time of seminal liquefaction.

To report our data of patients with clinical stage T(1-3)N(1-2)M(0) renal cell carcinoma (RCC) and explore the biological behavior of this malignancy.A total of 531 patients with no distant metastatic RCC underwent open radical nephrectomy at our institution between 1988 and 2008, among whom 42 patients with histological nodal metastases had successful surgical tumor resection. The clinical data and outcomes of the 42 patients were analyzed.Of those 42 patients, 19.0% had T1, 21.4% had T2, and 59.5% had T3 stage tumors; 42.9% had N1 and 57.1% had N2 stage tumors. Tumor recurred in 30 (71.4%) patients after the surgery, and death occurred in 26 (61.9%) cases at the last follow-up; among the recurrent cases, 83.3% (25/30) had multiple metastases at the initial recurrence. The median cancer-specific survival (CSS) and disease-free survival (DFS) was 23 and 11 months in these cases, respectively. Multivariate analysis demonstrated that Fuhrman grade (P=0.005), N stage (P=0.014) and T stage (P=0.037) were the independent predictors of CSS; Eastern Cooperative Oncology Group (ECOG) performance status (PS) (P=0.002), tumor size (P=0.007), Fuhrman grade (P=0.009) and N stage (P=0.019) were the independent predictors of DFS.Patients with T(1-3)N(1-2)M(0) RCC have poor prognosis. N stage is an independent predictor of both CSS and DFS, suggesting that extended lymph node dissection should be performed when suspicious enlarged nodal disease is found during surgery.

To study the clinicopathological characteristics of synchronous squamous cell carcinoma (SCC) of the renal pelvis and SCC of the ureter.The clinical data of two cases of synchronous SCC of the renal pelvis and SCC of the ureter were retrospectively reviewed and analyzed. In case 1, a 68-year-old man with hematuria for a month, imaging modalities revealed a right renal pelvis tumor and a right distal ureter tumor. The patient underwent nephroureterectomy and excision of the bladder cuff. Case 2, a 60-year-old man with the complaint of lower abdominal pain and left flank pain for a month, was diagnosed as left distal ureteral stone in another hospital. Ureterolithotomy was performed and a ureteral tumor was found at the lower site of the stone intraoperatively. The pathological report demonstrated SCC, and the patient was transferred to our hospital for further treatment. We found a left renal mass invading the left hemicolon during surgery, and nephroureterectomy was performed with a bladder cuff excision, left hemicolon resection, and also complete lymph node dissection. Neither of patients received adjuvant radiotherapy/chemotherapy.Moderately differentiated SCC was reported in both of renal pelvis and ureter in case 1 and the tumor invaded the subepithelial connective tissue in the renal pelvis and superficial muscle in the ureter. In case 2, moderately differentiated SCC of the left renal pelvis with colon metastasis and poorly differentiated SCC of the ureter was reported with two retroperitoneal lymph node metastases. The two patients died from tumor recurrence and metastasis 5 and 6 months after the surgery, respectively.Synchronous SCC of the renal pelvis and SCC of the ureter are rare and has high likeliness of early recurrence and metastasis, often with poor prognosis.

To separate and identify human testicular embryonal carcinoma proteomics using two-dimensional electrophoresis (2-DE) and mass spectrometry.Immobilized pH gradient two-dimensional polyacrylamide gel electrophoresis was used to separate the total proteins of the samples. After silver staining, PDQuest 7.30 image analysis software was applied to analyze the 2-DE images. Three of the proteins highly expressed in human testicular embryonal carcinoma were identified by matrix-assisted laser adsorption/ionization-time of flight-tandem mass spectrometry (MALDI-TOF-MS/MS).2-DE effectively screened the differentially expressed proteins in the carcinoma tissues. Three proteins highly expressed in the carcinoma were successfully identified.The proteins of human testicular embryonal carcinoma can be effectively separated and analyzed using 2-DE and mass spectrometry. Proteomic analysis offers a new means for further study of this carcinoma.

To analyze the specifically expressed genes in sperms for better understanding of the molecular characteristics of sperms.The hybridization data the genes in the sperms, oocytes and 10 normal tissues were retrieved from the GEO database to identify the genes expressed specifically in sperms and the patterns of their regulation using such bioinformatic tools as GATHER, PANTHER and DAVID.Comparison of the spermatozoal gene expression profiles with those of the normal tissues identified 8998 differentially expressed probes, among which 25 genes were up-regulated by over 200 folds in the sperms. Comparison of the gene expression profiles between the oocytes and normal tissues resulted in the identification of 8981 differentially expressed probes. Of the 1709 up-regulated genes in the sperm with a ratio5, 1218 genes showed similar expressions in the oocytes and the normal tissues, and 129 were up-regulated and 362 down-regulated in the oocytes. The 362 genes up-regulated in the sperms but down-regulated in the oocytes were involved mainly in protein modification and metabolism and nucleic acid metabolism, but very few participated in the intracellular signaling pathways. Numerous transcriptional factors containing the KRAB domain and receptor- independent serine/threonine kinase were specifically overexpressed in sperms, and the a very high proportion of the genes specifically overexpressed in the sperms coincided with the overexpressed genes in the neural stem cells and embryonic stem cells. The genes involved in the glycolysis were down-regulated in the sperms. These findings in the genes specifically expressed in the sperms by data mining using bioinformatic methods may provide better insight into the molecular characteristics of the sperms.

To screen differentially expressed genes in cytochalasin B (CB)-induced denucleated K562 cells by restriction display (RD) technique.The total RNA was isolated and purified from K562 cells before and after CB (10 mug/ml) treatment. The mRNA from both treated and untreated K562 cells were reversely transcribed into cDNA, and the differentially expressed genes were separated using RD technique combined with polyacrylamide gel electrophoresis and sliver staining, followed by cloning, sequencing and homology analysis against GenBank database of these genes.Seven differentially expressed genes were identified in CB-treated cells including aquaporin 1 (AQP1) gene, which was verified to be up-regulated after CB treatment by RT-PCR.AQP1 gene might be in close association with the regulation of denucleation processes and CB-induced proliferation inhibition of K562 cells.