Association algorithm to mine the rules that govern enzyme definition and to classify protein sequences

BACKGROUND: The number of sequences compiled in many genome projects is growing exponentially, but most of them have not been characterized experimentally. An automatic annotation scheme must be in an urgent need to reduce the gap between the amount of new sequences produced and reliable functional annotation. This work proposes rules for automatically classifying the fungus genes. The approach involves elucidating the enzyme classifying rule that is hidden in UniProt protein knowledgebase and then applying it for classification. The association algorithm, Apriori, is utilized to mine the relationship between the enzyme class and significant InterPro entries. The candidate rules are evaluated for their classificatory capacity. RESULTS: There were five datasets collected from the Swiss-Prot for establishing the annotation rules. These were treated as the training sets. The TrEMBL entries were treated as the testing set. A correct enzyme classification rate of 70% was obtained for the prokaryote datasets and a similar rate of about 80% was obtained for the eukaryote datasets. The fungus training dataset which lacks an enzyme class description was also used to evaluate the fungus candidate rules. A total of 88 out of 5085 test entries were matched with the fungus rule set. These were otherwise poorly annotated using their functional descriptions. CONCLUSION: The feasibility of using the method presented here to classify enzyme classes based on the enzyme domain rules is evident. The rules may be also employed by the protein annotators in manual annotation or implemented in an automatic annotation flowchart

Charge-Trapping Devices Using Multilayered Dielectrics for Nonvolatile Memory Applications

Charge-trapping devices using multilayered dielectrics were studied for nonvolatile memory applications. The device structure is Al/Y2O3/Ta2O5/SiO2/Si (MYTOS). The MYTOS field effect transistors were fabricated using Ta2O5 as the charge storage layer and Y2O3 as the blocking layer. The electrical characteristics of memory window, program/erase characteristics, and data retention were examined. The memory window is about 1.6 V. Using a pulse voltage of 6 V, a threshold voltage shift of ~1 V can be achieved within 10 ns. The MYTOS transistors can retain a memory window of 0.81 V for 10 years

Evaluation on the Pharmacological Effect of Traditional Chinese Medicine SiJunZiTang on Stress-Induced Peptic Ulcers

Purpose. To explore the effects of SiJunZiTang (SJZT) on central neurotransmitters and the inhibition of HCl hypersecretion, along with the role of the vagus nerve. From this, the effects of SJZT and its constituent ingredients on inhibiting stress-induced peptic ulcers will be determined. Methods. Methods used to determine SJZT's effectiveness included (1) measuring the antipeptic ulcer effects of varying combinations of the constituents of SJZT; (2) evaluations of monoamine (MA) level in the brain; and (3) measuring the effects of longer-term SJZT treatment. Results. Comparing the control and experimental groups where the rats’ vagus nerves were not cut after taking SJZT orally (500 mg/kg and 1000 mg/kg), the volume of enterogastric juice, free HCl and total acidity all reduce dose-dependently. The group administered SJZT at 1000 mg/kg showed significant reductions (P<0.05). For the experimental groups where the vagus nerves were cut, a comparison with the control group suggests that the group receiving SJZT (500 mg/kg) orally for 21 days demonstrated a cure rate of 34.53%. Conclusion. The results display a correlation between the therapeutic effects of SJZT on stress-induced peptic ulcers and central neurotransmitter levels. Further to this, SJZT can inhibit the hypersecretion of HCl in the stomach, thus inhibiting stress-induced peptic ulcers

Charge-Trapping Devices Using Multilayered Dielectrics for Nonvolatile Memory Applications

Charge-trapping devices using multilayered dielectrics were studied for nonvolatile memory applications. The device structure is Al/Y 2 O 3 /Ta 2 O 5 /SiO 2 /Si (MYTOS). The MYTOS field effect transistors were fabricated using Ta 2 O 5 as the charge storage layer and Y 2 O 3 as the blocking layer. The electrical characteristics of memory window, program/erase characteristics, and data retention were examined. The memory window is about 1.6 V. Using a pulse voltage of 6 V, a threshold voltage shift of ∼1 V can be achieved within 10 ns. The MYTOS transistors can retain a memory window of 0.81 V for 10 years

The role of autologous bone graft in surgical treatment of hypertrophic nonunion of midshaft clavicle fractures

AbstractBackgroundThis study was conducted to evaluate the results of treating hypertrophic nonunion of mid-shaft clavicle fracture with a limited contact dynamic compression plate (LC-DCP) without autologous cancellous bone graft.MethodsFrom 1995 to 2008, 51 cases of hypertrophic nonunion of mid-shaft clavicle fracture were managed with open reduction and internal fixation by LC-DCP without bone graft involvement. Of these 51 cases, 30 had nonunion after failure of initial surgical treatment (Group 1), and 21 had nonunion after failure of conservative treatment (Group 2). Preoperative and postoperative case management were the same for both groups, with the average follow-up period being 20.4 months (range 18–36). Our study evaluated the radiographic results and functional outcomes of these cases according to the quick disability of arm, shoulder, and hand score.ResultsAll 51 cases resulted in uneventful unions. There was no statistically significant difference between the two groups regarding patient demography, cause of injury, preoperative and postoperative functional scores, length of operation, union time, and duration of hospitalization (p>0.05).ConclusionLC-DCP fixation is an effective method for treating hypertrophic nonunion of mid-shaft clavicle fracture. Local bone graft is sufficient to achieve necessary union, and autologous bone graft from other sites of the body appears unnecessary

Evodiamine Induces Transient Receptor Potential Vanilloid-1-Mediated Protective Autophagy in U87-MG Astrocytes

Cerebral ischemia is a leading cause of mortality and morbidity worldwide, which results in cognitive and motor dysfunction, neurodegenerative diseases, and death. Evodiamine (Evo) is extracted from Evodia rutaecarpa Bentham, a plant widely used in Chinese herbal medicine, which possesses variable biological abilities, such as anticancer, anti-inflammation, antiobesity, anti-Alzheimer’s disease, antimetastatic, antianoxic, and antinociceptive functions. But the effect of Evo on ischemic stroke is unclear. Increasing data suggest that activation of autophagy, an adaptive response to environmental stresses, could protect neurons from ischemia-induced cell death. In this study, we found that Evo induced autophagy in U87-MG astrocytes. A scavenger of extracellular calcium and an antagonist of transient receptor potential vanilloid-1 (TRPV-1) decreased the percentage of autophagy accompanied by an increase in apoptosis, suggesting that Evo may induce calcium-mediated protective autophagy resulting from an influx of extracellular calcium. The same phenomena were also confirmed by a small interfering RNA technique to knock down the expression of TRPV1. Finally, Evo-induced c-Jun N-terminal kinases (JNK) activation was reduced by a TRPV1 antagonist, indicating that Evo-induced autophagy may occur through a calcium/c-Jun N-terminal kinase (JNK) pathway. Collectively, Evo induced an influx of extracellular calcium, which led to JNK-mediated protective autophagy, and this provides a new option for ischemic stroke treatment

Estrogen Augments Shear Stress–Induced Signaling and Gene Expression in Osteoblast-like Cells via Estrogen Receptor–Mediated Expression of β1-Integrin

Estrogen and mechanical forces are positive regulators for osteoblast proliferation and bone formation. We investigated the synergistic effect of estrogen and flow-induced shear stress on signal transduction and gene expression in human osetoblast-like MG63 cells and primary osteoblasts (HOBs) using activations of extracellular signal-regulated kinase (ERK) and p38 mitogen-activated protein kinase (MAPK) and expressions of c-fos and cyclooxygenase-2 (I) as readouts. Estrogen (17β-estradiol, 10 nM) and shear stress (12 dyn/cm2) alone induced transient phosphorylations of ERK and p38 MAPK in MG63 cells. Pretreating MG63 cells with 17β-estradiol for 6 hours before shearing augmented these shear-induced MAPK phosphorylations. Western blot and flow cytometric analyses showed that treating MG63 cells with 17β-estradiol for 6 hrs induced their β1-integrin expression. This estrogen-induction of β1-integrin was inhibited by pretreating the cells with a specific antagonist of estrogen receptor ICI 182,780. Both 17β-estradiol and shear stress alone induced c-fos and Cox-2 gene expressions in MG63 cells. Pretreating MG63 cells with 17β-estradiol for 6 hrs augmented the shear-induced c-fos and Cox-2 expressions. The augmented effects of 17β-estradiol on shear-induced MAPK phosphorylations and c-fos and Cox-2 expressions were inhibited by pretreating the cells with ICI 182,780 or transfecting the cells with β1-specific small interfering RNA. Similar results on the augmented effect of estrogen on shear-induced signaling and gene expression were obtained with HOBs. Our findings provide insights into the mechanism by which estrogen augments shear stress responsiveness of signal transduction and gene expression in bone cells via estrogen receptor–mediated increases in β1-integrin expression. © 2010 American Society for Bone and Mineral Research

Role of pirenoxine in the effects of catalin on in vitro ultraviolet-induced lens protein turbidity and selenite-induced cataractogenesis in vivo

Purpose: In this study, we investigated the biochemical pharmacology of pirenoxine (PRX) and catalin under in vitro selenite/calcium- and ultraviolet (UV)-induced lens protein turbidity challenges. The systemic effects of catalin were determined using a selenite-induced cataractogenesis rat model. Methods: In vitro cataractogenesis assay systems (including UVB/C photo-oxidation of lens crystallins, calpain-induced proteolysis, and selenite/calcium-induced turbidity of lens crystallin solutions) were used to screen the activity of PRX and catalin eye drop solutions. Turbidity was identified as the optical density measured using spectroscopy at 405 nm. We also determined the in vivo effects of catalin on cataract severity in a selenite-induced cataract rat model. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS–PAGE) was applied to analyze the integrity of crystallin samples. Results: PRX at 1,000 μM significantly delayed UVC-induced turbidity formation compared to controls after 4 h of UVC exposure (p<0.05), but not in groups incubated with PRX concentrations of <1,000 μM. Results were further confirmed by SDS–PAGE. The absolute γ-crystallin turbidity induced by 4 h of UVC exposure was ameliorated in the presence of catalin equivalent to 1~100 μM PRX in a concentration-dependent manner. Samples with catalin-formulated vehicle only (CataV) and those containing PRX equivalent to 100 μM had a similar protective effect after 4 h of UVC exposure compared to the controls (p<0.05). PRX at 0.03, 0.1, and 0.3 μM significantly delayed 10 mM selenite- and calcium-induced turbidity formation compared to controls on days 0~4 (p<0.05). Catalin (equivalent to 32, 80, and 100 μM PRX) had an initial protective effect against selenite-induced lens protein turbidity on day 1 (p<0.05). Subcutaneous pretreatment with catalin (5 mg/kg) also statistically decreased the mean cataract scores in selenite-induced cataract rats on post-induction day 3 compared to the controls (1.3±0.2 versus 2.4±0.4; p<0.05). However, catalin (equivalent to up to 100 μM PRX) did not inhibit calpain-induced proteolysis activated by calcium, and neither did 100 μM PRX. Conclusions: PRX at micromolar levels ameliorated selenite- and calcium-induced lens protein turbidity but required millimolar levels to protect against UVC irradiation. The observed inhibition of UVC-induced turbidity of lens crystallins by catalin at micromolar concentrations may have been a result of the catalin-formulated vehicle. Transient protection by catalin against selenite-induced turbidity of crystallin solutions in vitro was supported by the ameliorated cataract scores in the early stage of cataractogenesis in vivo by subcutaneously administered catalin. PRX could not inhibit calpain-induced proteolysis activated by calcium or catalin itself, and may be detrimental to crystallins under UVB exposure. Further studies on formulation modifications of catalin and recommended doses of PRX to optimize clinical efficacy by cataract type are warranted

Cardiotoxin III Inhibits Proliferation and Migration of Oral Cancer Cells through MAPK and MMP Signaling

Cardiotoxin III (CTXIII), isolated from the snake venom of Formosan cobra Naja naja atra, has previously been found to induce apoptosis in many types of cancer. Early metastasis is typical for the progression of oral cancer. To modulate the cell migration behavior of oral cancer is one of the oral cancer therapies. In this study, the possible modulating effect of CTXIII on oral cancer migration is addressed. In the example of oral squamous carcinoma Ca9-22 cells, the cell viability was decreased by CTXIII treatment in a dose-responsive manner. In wound-healing assay, the cell migration of Ca9-22 cells was attenuated by CTXIII in a dose- and time-responsive manner. After CTXIII treatment, the MMP-2 and MMP-9 protein expressions were downregulated, and the phosphorylation of JNK and p38-MAPK was increased independent of ERK phosphorylation. In conclusion, CTXIII has antiproliferative and -migrating effects on oral cancer cells involving the p38-MAPK and MMP-2/-9 pathways