iLoc-lncRNA: predict the subcellular location of lncRNAs by incorporating octamer composition into general PseKNC.

Motivation: Long non-coding RNAs (lncRNAs) are a class of RNA molecules with more than 200 nucleotides. They have important functions in cell development and metabolism, such as genetic markers, genome rearrangements, chromatin modifications, cell cycle regulation, transcription and translation. Their functions are generally closely related to their localization in the cell. Therefore, knowledge about their subcellular locations can provide very useful clues or preliminary insight into their biological functions. Although biochemical experiments could determine the localization of lncRNAs in a cell, they are both time-consuming and expensive. Therefore, it is highly desirable to develop bioinformatics tools for fast and effective identification of their subcellular locations. Results: We developed a sequence-based bioinformatics tool called 'iLoc-lncRNA' to predict the subcellular locations of LncRNAs by incorporating the 8-tuple nucleotide features into the general PseKNC (Pseudo K-tuple Nucleotide Composition) via the binomial distribution approach. Rigorous jackknife tests have shown that the overall accuracy achieved by the new predictor on a stringent benchmark dataset is 86.72%, which is over 20% higher than that by the existing state-of-the-art predictor evaluated on the same tests. Availability and implementation: A user-friendly webserver has been established at http://lin-group.cn/server/iLoc-LncRNA, by which users can easily obtain their desired results. Supplementary information: Supplementary data are available at Bioinformatics online.

Pro54DB: a database for experimentally verified sigma-54 promoters.

Summary: In prokaryotes, the σ54 promoters are unique regulatory elements and have attracted much attention because they are in charge of the transcription of carbon and nitrogen-related genes and participate in numerous ancillary processes and environmental responses. All findings on σ54 promoters are favorable for a better understanding of their regulatory mechanisms in gene transcription and an accurate discovery of genes missed by the wet experimental evidences. In order to provide an up-to-date, interactive and extensible database for σ54 promoter, a free and easy accessed database called Pro54DB (σ54 promoter database) was built to collect information of σ54 promoter. In the current version, it has stored 210 experimental-confirmed σ54 promoters with 297 regulated genes in 43 species manually extracted from 133 publications, which is helpful for researchers in fields of bioinformatics and molecular biology. Availability and Implementation: Pro54DB is freely available on the web at http://lin.uestc.edu.cn/database/pro54db with all major browsers supported. Contacts: greatchen@ncst.edu.cn or hlin@uestc.edu.cn

Exogenous FGF2 reverses depressive-like behaviors and restores the suppressed FGF2-ERK1/2 signaling and the impaired hippocampal neurogenesis induced by neuroinflammation.

Our previous work demonstrated that neuroinflammation evoked by triple repeated central LPS challenges inhibited adult hippocampal neurogenesis that were correlated with the depressive-like behavioral symptoms induced by neuroinflammation. These findings suggest that hippocampal neurogenesis might be one of biological mechanisms underlying depression induced by neuroinflammation and targeting neurogenesis might lead to new therapeutic strategies for the treatment of depression. In this study, we manipulated adult hippocampal neurogenesis using fibroblast growth factor 2 (FGF2), one crucial molecule modulating cell proliferation and survival in central nervous system, and investigate the involvement and the potential therapeutic effects of FGF2 on neuroinflammation-induced depression. Central lipopolysaccharides (LPS) challenges were used as previously to evoke the neuroinflammatory state in the brain of rat. Exogenous FGF2 was infused into lateral ventricle during the neuroinflammatory state. It was found that the protein expression of FGF2 in hippocampus was inhibited by neuroinflammation. The activation of extracellular signal-regulated kinase (ERK), the downstream molecule of FGF2, was also inhibited by neuroinflammation. Exogenous FGF2 infusions prevented the decrease in phosphorylation of ERK1/2 under neuroinflammation state. Exogenous FGF2 reversed depressive-like behaviors and the impaired hippocampal neurogenesis induced by neuroinflammation. These findings provide evidence that the FGF2-ERK1/2 pathway is involved in the pathophysiology of depressive-like behaviors, and manipulating the neurogenesis pathway is a viable therapeutic approach to inflammation-associated depression.

Natural protein sequences are more intrinsically disordered than random sequences.

Most natural protein sequences have resulted from millions or even billions of years of evolution. How they differ from random sequences is not fully understood. Previous computational and experimental studies of random proteins generated from noncoding regions yielded inclusive results due to species-dependent codon biases and GC contents. Here, we approach this problem by investigating 10,000 sequences randomized at the amino acid level. Using well-established predictors for protein intrinsic disorder, we found that natural sequences have more long disordered regions than random sequences, even when random and natural sequences have the same overall composition of amino acid residues. We also showed that random sequences are as structured as natural sequences according to contents and length distributions of predicted secondary structure, although the structures from random sequences may be in a molten globular-like state, according to molecular dynamics simulations. The bias of natural sequences toward more intrinsic disorder suggests that natural sequences are created and evolved to avoid protein aggregation and increase functional diversity.

IonchanPred 2.0: A Tool to Predict Ion Channels and Their Types.

Ion channels (IC) are ion-permeable protein pores located in the lipid membranes of all cells. Different ion channels have unique functions in different biological processes. Due to the rapid development of high-throughput mass spectrometry, proteomic data are rapidly accumulating and provide us an opportunity to systematically investigate and predict ion channels and their types. In this paper, we constructed a support vector machine (SVM)-based model to quickly predict ion channels and their types. By considering the residue sequence information and their physicochemical properties, a novel feature-extracted method which combined dipeptide composition with the physicochemical correlation between two residues was employed. A feature selection strategy was used to improve the performance of the model. Comparison results of in jackknife cross-validation demonstrated that our method was superior to other methods for predicting ion channels and their types. Based on the model, we built a web server called IonchanPred which can be freely accessed from http://lin.uestc.edu.cn/server/IonchanPredv2.0.

Upregulation of matrix metalloproteinase 14 (MMP14) is associated with poor prognosis in renal clear cell carcinoma-a bioinformatics analysis.

Background: Matrix metalloproteinase 14 (MMP14) has been reported to be upregulated in some types of cancer and to promote cancer cell invasion and metastasis. However, the expression profile and functional role of MMP14 in kidney renal clear cell carcinoma (KIRC) remains unknown. This study investigated the association between MMP14 expression level and prognosis in KIRC. Methods: The messenger RNA (mRNA) expression profile and clinical data (including T stage, N stage, M stage, pathologic stage, gender, race, age, histologic grade, serum calcium, hemoglobin) were obtained from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database. Protein expression was evaluated by immunohistochemistry in the Human Protein Atlas (HPA) database. Correlation analyses between MMP14 and all mRNAs in KIRC were batch calculated, and gene set enrichment analyses (GSEA) were then conducted of Disease Ontology (DO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways using R packages. Multivariate logistic regression analysis was used to explore the prognostic factors of KIRC patients. Results: The gene expression of MMP14 was significantly upregulated in KIRC tissues when compared with the normal tissue (P<0.001). The predictive ability of MMP14 as a variable for predicting tumor and normal outcomes had certain accuracy based on the receiver operating characteristic (ROC) model [area under the curve (AUC) =0.881, confidence interval (CI): 0.844-0.917]. When compared with the normal kidney tissue, the protein expression of MMP14 in KIRC got an increased trend, but due to the limited sample size, the difference is not statistically significant (P>0.05). Survival analysis revealed that MMP14 was significantly associated with overall survival in KIRC (P=0.013). GSEA of DO terms indicated high expression of MMP14 was related to KIRC, and GSEA of KEGG pathways showed that MMP14 and its coexpressed genes were significantly positively correlated with pathways in cancer. Signaling pathway GSEA indicated the upregulation of MMP14 in KIRC may activate cancer pathways. Conclusions: MMP14 may be associated with poor prognosis in KIRC and may be a potential prognostic marker for KIRC.

Inflammation-based different association between anatomical severity of coronary artery disease and lung cancer.

BACKGROUND: Coronary artery disease (CAD) is associated with cancer. The role of inflammation in the association of CAD with cancer remains unclear. The study investigated whether inflammation could impact the relationship between CAD and lung cancer. METHODS: The study involved 96 newly diagnosed lung cancer patients without receiving anti-cancer therapy and 288 matched non-cancer patients. All the patients underwent coronary angiography and were free from previous percutaneous coronary intervention or coronary artery bypass grafting. SYNTAX score (SXscore) were used to assess severity of CAD. High SXscore (SXhigh) grade was defined as SXscore > 16 (highest quartile). Neutrophil-to-lymphocyte ratio (NLR) served as an inflammatory biomarker. NLR-high grade referred to NLR > 2.221 (median). RESULTS: Among 384 study patients, 380 patients (98.96%) had NLR value (median: 2.221, interquartile range: 1.637-3.040). Compared to non-cancer patients, lung cancer patients had higher rate of SXhigh among total study patients (P = 0.014) and among patients with NLR-high (P = 0.006), but had not significantly higher rate of SXhigh among patients with NLR-low (P = 0.839). Multivariate logistic regression analysis showed that SXhigh was associated with lung cancer [odds ratio (OR) = 1.834, 95% CI: 1.063-3.162, P = 0.029]. Subgroup analysis showed that SXhigh was associated with lung cancer among patients with NLR-high (OR = 2.801, 95% CI: 1.355-5.794, P = 0.005), however, the association between SXhigh and lung cancer was not significant among patients with NLR-low (OR = 0.897, 95% CI: 0.346-2.232, P = 0.823). CONCLUSIONS: Inflammation could lead different association between anatomical severity of CAD and lung cancer. Severity of CAD was significantly associated with increased risk of lung cancer among patients with high inflammation rather than among patients with low inflammation.

Feasibility of laparoscopic extraperitoneal pelvic lymphadenectomy in gynecologic malignancies.

OBJECTIVE: The aim of this study is to evaluate the feasibility of laparoscopic extraperitoneal pelvic lymphadenectomy (LEPL) in gynecologic malignancies. METHODS: Twenty-nine women with cervical, ovarian or endometrial cancer underwent laparoscopic extraperitoneal pelvic lymphadenectomy between July 2008 and December 2010. The operating time, nodal yield, blood loss and complications were recorded. RESULTS: The number of patients with cervical, ovarian and endometrial carcinoma was 14, 3 and 12, respectively. The median age of patients was 48.9±12.6 years. The median body mass index was 25.6±4.8. Conversion to the transperitoneal laparoscopic approach was necessary in 6 patients for peritoneal tears causing CO(2) gas leakage. Among the remaining 23 patients, the median operating time for laparoscopic extraperitoneal pelvic lymphadenectomy was 69 min (range 50-126 min), and the median estimated blood loss was 20 ml (range 5-105 ml). The median total number of resected nodes was 26 (range 14-42), and complications related to the procedure were rare. CONCLUSIONS: Laparoscopic extraperitoneal pelvic lymphadenectomy is a feasible and safe procedure. It can be used in gynecologic malignancies.

A study on the mechanism of 5-aminolevulinic acid photodynamic therapy in vitro and in vivo in cervical cancer.

5-Aminolevulinic acid-mediated photodynamic therapy (ALA-PDT) is a new ablation treatment for tumors, while its function mechanism in cervical cancer has not been elucidated. In this study, we investigated the effects of ALA-PDT on the cervical cancer cell line Me180, to search for optimal parameters of PDT. ALA-PDT on proliferation of Me180 was examined by MTT assay to find the optimal function parameters of ALA-PDT. Apoptosis was observed by using AnnexinV-FITC/PI double staining, Hoechst 33342 staining and May-Grünwald-Farbstoff Giemsa staining. Furthermore, we established a tumor model and 6 mice of each group underwent measurement of the tumor size on days 3, 7, 14, and 21 after treatment. The mRNA expression of survivin, bcl-2, p53, bax and bad in Me180 cells were detected by real-time fluorescence reverse transcription-polymerase chain reaction (RT-PCR) in vitro and in vivo. Finally, we compared the effects between topical and intravenous administration. Based on the above studies, we found ALA-PDT induced apoptosis and G0-G1 phase arrest of Me180 cells. The tumor volume of the topical administration and PDT group was the smallest at 7-14 days post-PDT. H&E staining showed remarkable subcutaneous necrosis in the PDT groups. The mRNA expression of survivin and bcl-2 in Me180 cells were suppressed post-PDT. Topical administration of PDT is recommended in treating cervical cancer so as to minimize the side-effects and inconvenience of phototoxic reaction brought by PDT. Our data may contribute to making the mechanism of PDT on cervical cancer clearer and give some useful suggestions for clinical application.

[Effects of 5-aminolevulinic acid photodynamic therapy on cervical cancer: in vivo experiment with nude mice].

OBJECTIVE: To study the effects of 5-aminolevulinic acid photodynamic therapy (ALA-PDT) on human cervical cancer, and to identify the best administration regimen with the least phototoxic reaction. METHODS: Seventy-two BALB/c nude mice underwent subcutaneous injection of human cervical cancer cells of the line Me180 so as to establish animal models, and then randomly divided into 6 equal groups: pure topical administration group (undergoing injection of ALA 60 mg/kg around the tumor), pure intravenous administration group (undergoing injection of ALA 250 mg/kg into the caudal vein), topical administration and PDT group (undergoing injection of ALA 60 mg/kg around the tumor and radiotherapy of 630 nm He-Ne laser 6 h after the drug administration), intravenous administration and PDT group (undergoing injection of ALA 250 mg/kg into the caudal vein and radiotherapy of 630 nm He-Ne laser 6 h after the drug administration), and control group (undergoing none of the treatment). 24 h later 6 mice from each group were killed with their tumors taken out. On the days 3, 7, 14, and 21 after treatment the remaining mice underwent measurement of the tumor size. HE staining and pathological examination were performed. Immunohistochemical study was conducted to detect the protein expression of the apoptosis-inhibiting genes of survivin and vascular endothelial growth factor (VEGF). RT-PCR was used to detect the mRNA expression of the apoptosis-inhibiting gene of Bcl-2 and apoptosis-promoting genes of P53, Bax, and Bad. RESULTS: The tumor volumes after treatment of the pure topical administration and pure caudal vein administration groups were (0.09 +/- 0. 02) cm3 and (0.14 +/- 0.04) cm3 respectively, both significantly smaller than that of the control group [(0.67 +/- 0.06) cm3, both P < 0.01]. The tumor volume of the pure topical administration group 7-14 days after treatment was the smallest. HE staining showed remarkable subcutaneous necrosis in the 2 PDT groups. Immunohistochemistry showed remarkable down-regulation of protein expression of survivin and VEGF in the PDT groups. RT-PCR showed that the mRNA expression levels of survivin and Bcl-2 were both significantly lower than that of the control group (both P < 0.01), and the mRNA expression levels of P53, Bax, and Bad were higher than those of the control group, however, not significantly (all P > 0.05). CONCLUSION: ALA-PDT is effective in treatment of cervical cancer. Topical ALA administration + PDT is recommended in treating cervical cancer so as to minimize the side-effects and inconvenience of phototoxic reaction brought by PDT.

Blocking p38 Signaling Reduces the Activation of Pro-inflammatory Cytokines and the Phosphorylation of p38 in the Habenula and Reverses Depressive-Like Behaviors Induced by Neuroinflammation.

Increasing evidence has demonstrated that neuroinflammation contributes to the development of depressive-like behaviors, in both animal models and human patients; however, the brain areas and signaling pathways involved are still elusive. Recent studies have suggested novel roles of the habenula in the onset of depression and other psychiatric disorders; however, there is no evidence for whether the habenula has a function in neuroinflammation-induced depression. Using an animal model of depression, which is induced by the repeated central administration of lipopolysaccharide (LPS), we examined whether cytokine expression and p38 signal activation in the habenula were involved in the depressive-like behaviors. Body weight, saccharin preference test, and tail suspension test were used to measure depressive-like behaviors. Immunohistochemistry, quantitative-polymerase chain reaction (q-PCR), and western blot were used to measure the expression of tumor necrosis factor-α (TNF-α), interleukin-10 (IL-10), and the phosphorylation of p38 in the habenula. The results showed that central LPS administration induced depressive-like behaviors, characterized by anhedonia in the saccharin preference test and increased immobility in the tail suspension test. Central LPS administration also significantly increased the p-p38 level in microglial cells and increased TNF-α expression in the habenula. Treatment with fluoxetine, a widely prescribed antidepressant, or SB203580, a p38-specific inhibitor, reversed the depressive-like behaviors, normalized the alterations in p-p38 and TNF-α levels and increased the levels of the anti-inflammatory cytokine IL-10 in the habenula. The present findings suggest that the habenula is involved in the pathophysiology of behavioral depression induced by neuroinflammation, and the p38 pathway may serve as a novel mechanism-based target for the treatment of inflammation-related depression.

HBPred: a tool to identify growth hormone-binding proteins.

Hormone-binding protein (HBP) is a kind of soluble carrier protein and can selectively and non-covalently interact with hormone. HBP plays an important role in life growth, but its function is still unclear. Correct recognition of HBPs is the first step to further study their function and understand their biological process. However, it is difficult to correctly recognize HBPs from more and more proteins through traditional biochemical experiments because of high experimental cost and long experimental period. To overcome these disadvantages, we designed a computational method for identifying HBPs accurately in the study. At first, we collected HBP data from UniProt to establish a high-quality benchmark dataset. Based on the dataset, the dipeptide composition was extracted from HBP residue sequences. In order to find out the optimal features to provide key clues for HBP identification, the analysis of various (ANOVA) was performed for feature ranking. The optimal features were selected through the incremental feature selection strategy. Subsequently, the features were inputted into support vector machine (SVM) for prediction model construction. Jackknife cross-validation results showed that 88.6% HBPs and 81.3% non-HBPs were correctly recognized, suggesting that our proposed model was powerful. This study provides a new strategy to identify HBPs. Moreover, based on the proposed model, we established a webserver called HBPred, which could be freely accessed at http://lin-group.cn/server/HBPred.

The shape effect of magnetic mesoporous silica nanoparticles on endocytosis, biocompatibility and biodistribution.

Although the aspect ratio (AR) play a crucial role in determining biological effects of homogeneous nanomaterials, studies available concerning how the shape contributes to biological effect of heterogeneous nanomaterials is limited. To systematically clarify the shape influence on the endocytosis, biocompatibility and biodistribution of magnetic mesoporous silica nanoparticles (M-MSNPs), three FITC-labeled M-MSNPs with different aspect ratio (AR=1, 2, and 4) were specifically designed and constructed through altering the ratios of CTAB/TEOS in a modified so-gel method. We have demonstrated that long-rod M-MSNP2 possessed higher intracellular internalization amount than the short-rod M-MSNP1 and the sphere-like M-MSNP0 in both cancer cells and normal cells due to the difference in the endocytosis pathways. However, there are no significant shape effects on biocompatibility including cytotoxicity and hemolytic rate. Moreover, biodistribution in HepG2 tumor-bearing mice showed that M-MSNPs administrated intravenously were mainly presented in reticuloendothelial system (RES) organs including liver, spleen and kidney. In particular, sphere-like M-MSNP0 were easily trapped in the liver, while long-rod M-MSP2 exhibited more retention in the spleen. It is worth noting that rod-like M-MSNPs are preferentially accumulated in tumor sites than sphere-like M-MSNPs, indicating an improved drug delivery efficacy in cancer therapy. Our findings may provide useful data for deeply understanding the interaction between the different shapes and biological behavior of M-MSNPs, which is expected to give rise to a new generation of heterogeneous M-MSNPs with significantly enhanced efficacy and safety for the cancer theranostics. STATEMENT OF SIGNIFICANCE: In this work, we systematically clarified the shape influence on the endocytosis, biocompatibility and biodistribution of homogeneous nanomaterials. We have demonstrated that rod-like magnetic mesoporous silica nanoparticles (M-MSNPs) were capable of higher intracellular internalization and tumor accumulation than sphere-like M-MSNPs, which was expected to give rise to a new generation of heterogeneous M-MSNPs with significantly enhanced efficacy and safety for the cancer theranostics.

Prediction of phosphothreonine sites in human proteins by fusing different features.

Phosphorylation is one of the most important protein post-translation modifications. With the rapid development of high-throughput mass spectrometry, phosphorylation site data is rapidly accumulating, which provides us an opportunity to systematically investigate and predict phosphorylation in proteins. The phosphorylation of threonine is the addition of a phosphoryl group to its polar side chains group. In this work, we statistically analyzed the distribution of the different properties including position conservation, secondary structure, accessibility and some other physicochemical properties of the residues surrounding the phosphothreonine site and non-phosphothreonine site. We found that the distributions of those features are non-symmetrical. Based on the distribution of properties, we developed a new model by using optimal window size strategy and feature selection technique. The cross-validated results show that the area under receiver operating characteristic curve reaches to 0.847, suggesting that our model may play a complementary role to other existing methods for predicting phosphothreonine site in proteins.

An intramedullary nail with multifunctional interlocking for all types of fracture in both femurs.

OBJECTIVE: A femoral compound interlocking intramedullary nail (FCIIN) was designed to treat all types of fractures between the trochanter and epicondyle of both femurs. It could substitute for femoral interlocking intramedullary nails (FIIN) at five points. METHODS: According to the morphological characteristics of the femoral medullary canal, the nail is designed to accommodate a 1250 mm radius of radian and a 135° neck-shaft angle. Three interlocking holes of 6.5 mm diameter are located at the proximal end of the FCIIN, making crossing of the screws possible. The hole is designed to be vertical (90°) or oblique (45° upper or lower). At the tip of the proximal interlocking screws, whose root diameter gradually increases from 3.5 mm to 6.5 mm, a self-tapping cancellous screw is placed. There are two types of distal interlocking screws. One is a fine thread and the other a bolt screw. Two interlocking holes and a recess 4.5 mm in diameter are located at the distal end of the FCIIN. Under biomechanical destructive testing, the proximal interlocking screw device has satisfactory strength and reasonable structure. A total of 47 patients (31 males and 16 females, with an average age of 39.83 years) with femoral fractures were assessed in this study. Fourteen cases were diagnosed as intertrochanteric, 7 as subtrochanteric, 18 as femoral shaft, and 8 as supracondylar fractures. All 47 patients were treated with the FCIIN. RESULTS: Of the 47 patients, anatomic reduction was achieved in 34, good reduction in 11, and forced line reduction in 2 cases. Reduction was excellent or good in 95.87% of the fractures. The removal time of the FCIIN was 12 to 21 months (average, 16.9 months). One patient with an intertrochanteric fracture who had a fixation failure combined with non-union achieved healing with an external fixator at 18 months. Failure to insert the distal interlocking screws occurred in 5 patients but did not affect bone healing. CONCLUSION: The FCIIN is a useful device in the treatment of a variety of femoral fractures.

[Apoptosis-inducing effect of 5-aminolevulinic acid-mediated photodynamic therapy (5-ALA-PDT) on cervical cancer cell lines].

BACKGROUND & OBJECTIVE: 5-Aminolevulinic acid-mediated photodynamic therapy (ALA-PDT) is a new ablation treatment for tumors, while its function mechanism in cervical cancer is unclear. This study was to investigate the effects of ALA-PDT on cervical cancer cell lines. METHODS: The effects of ALA-PDT on proliferation of 8 human cervical cancer cell lines were examined by MTT assay to find out the optimal function parameters of ALA-PDT and the most sensitive cell line. The effect of ALA-PDT on apoptosis of cervical cancer cell line Me180 was investigated by using Annexin V-FITC/PI double staining, Hoechst 33342 staining and May-Grunwald-Farbstoff Giemsa staining. Cell cycle of Me180 cells was observed by flow cytometry with PI staining. The effect of ALA-PDT on the expression of survivin in Me180 cells was detected by Western blot and real-time fluorescence reverse transcription-polymerase chain reaction (RT-PCR). RESULTS: Among the 8 cell lines, Me180 cell line was most sensitive to ALA-PDT; 2 mmol/L ALA, 10 J/cm(2) light dose and 3-hour treatment were the optimal function parameters of ALA-PDT, and the 50% inhibition concentration (IC(50)) of ALA-PDT under this situation for Me180 cells was 7.28x10(-4) mmol/L. ALA-PDT induced apoptosis and G0/G1 phase arrest of Me180 cells, and suppressed the mRNA and protein expression of survivin in Me180 cells. CONCLUSION: ALA-PDT can inhibit the proliferation and induce apoptosis of cervical cancer cell line Me180 in vitro, which may relate with the suppression of survivin expression.