Multidimensional replica-exchange method for free-energy calculations

We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.Comment: 13 pages, (ReVTeX), 9 figures. J. Chem. Phys. 113 (2000), in pres

Obstacle Effects on Airflow and Containment Dispersion around a Naturally Ventilated Livestock Building

Rosana G. Moreira, Editor-in-Chief; Texas A&M UniversityThis is a Technical Paper from International Commission of Agricultural Engineering (CIGR, Commission Internationale du Genie Rural) E-Journal Volume 5 (2003): G. Zhang, A. Ikeguchi, J. Strom, S. Morsing, H. Takai, P. Ravn, and L. Okushima. Obstacle Effects on Airflow and Containment Dispersion around a Naturally Ventilated Livestock Building. Vol. V. December 2003

In Silico Modeling the Effects of Missense Mutations Causing Snyder-Robinson Syndrome and Rescuing the Effects by Small Molecules Binding

Snyder-Robinson Syndrome (SRS) is an X-linked mental retardation disorder. Three missense mutations (G56S, V132G and I150T) on human spermine synthase (SMS) were reported to cause SRS. SMS is an important enzyme which converts spermindine into spermine, both of which are two polyamines controlling the normal cell growth and development. In vitro experiments showed that the dimer conformation played a crucial role on the SMS function. Our in silico studies including energy calculation, pKa calculation and molecular dynamics (MD) simulation based on the available 3D structure of SMS revealed that these mutations affected SMS function by affecting the dimer affinity, monomer stability or hydrogen bond network. One of the above sites, G56S, is accessible from the water phase, thus it provides the opportunity to rescue the disease-causing effect by binding an appropriate small molecule to the vicinity of the mutation site. Currently we run MD simulation to generate multiple receptor conformations and identified two potent binding pockets. Then two programs, Surflex and Autodock Vina, were applied for structure-based virtual screening (SBVS) and a consensus list of about 200 common compounds selected by both of the programs was created, and these compounds were tested experimentally by our collaborators

Structural analysis of the factors pertaining to attitudes toward and consciousness of organ donation : Comparison between Japanese and Americans

The purpose of this study is to analyze the background factors relating to opinions on organ donation through factorial and structural comparisons between Japanese and Americans. The data were obtained from responses to a questionnaire (371 Japanese and 41 Americans). The main findings are as follows: 1. Most of the factors, ‘a will for organ donation depending on a recipient’, ‘view of remains’, ‘understanding of brain death’ and so on showed significant differences between Japanese and Americans. 2. Japanese had a better understanding of brain death. On the other hand, the ratio of Americans who were willing to donate an organ was higher than that of Japanese. 3. It was revealed that “the approval of organ donation for the third person, not only for one's family” had an impact for having donor card showing the approval for organ donation. Furthermore, as underlying factors generating differences on organ transplant opinions, differences were found among Japanese between “approval of organ transplant” and the attitude assuming that oneself or a member of one's family was the person concerned with organ transplantation. There were also differences between Japanese and Americans on ideas about a view for life and death such as soul existence or view of remains. The argument for transplantation in Japan should consider these structural differences

Nonlinearity of Mechanochemical Motions in Motor Proteins

The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are traditionally analyzed in terms of normal modes and experimental data on thermal fluctuations in such macromolecules is also usually interpreted in terms of the excitation of normal modes. We have chosen two important protein motors - myosin V and kinesin KIF1A - and performed numerical investigations of their conformational relaxation properties within the coarse-grained elastic network approximation. We have found that the linearity assumption is deficient for ligand-induced conformational motions and can even be violated for characteristic thermal fluctuations. The deficiency is particularly pronounced in KIF1A where the normal mode description fails completely in describing functional mechanochemical motions. These results indicate that important assumptions of the theory of protein dynamics may need to be reconsidered. Neither a single normal mode, nor a superposition of such modes yield an approximation of strongly nonlinear dynamics.Comment: 10 pages, 6 figure

Combination of p53AIP1 and survivin expression is a powerful prognostic marker in non-small cell lung cancer

<p>Abstract</p> <p>Background</p> <p>p53AIP1 is a potential mediator of apoptosis depending on p53, which is mutated in many kinds of carcinoma. High survivin expression in non-small cell lung cancer is related with poor prognosis. To investigate the role of these genes in non-small cell lung cancer, we compared the relationship between p53AIP1 or survivin gene expression and the clinicopathological status of lung cancer.</p> <p>Materials and methods</p> <p>Forty-seven samples from non-small cell lung cancer patients were obtained between 1997 and 2003. For quantitative evaluation of RNA expression by PCR, we used Taqman PCR methods.</p> <p>Results</p> <p>Although no correlation between p53AIP1 or survivin gene expression and clinicopathological factors was found, the relationship between survivin gene expression and nodal status was significant (p = 0.03). Overall survival in the p53AIP1-negative group was significantly worse than in the positive group (p = 0.04); however, although survivin expression was not a prognostic factor, the combination of p53AIP1 and survivin was a significant prognostic predictor (p = 0.04). In the multivariate cox proportional hazard model, the combination was an independent predictor of overall survival (p53AIP1 (+) survivin (+), HR 0.21, 95%CI = [0.01–1.66]; p53AIP1 (+) survivin (-), HR 0.01, 95%CI = [0.002–0.28]; p53AIP1 (-) survivin (-), HR 0.01, 95%CI = [0.002–3.1], against p53AIP1 (-) survivin (+), p = 0.03).</p> <p>Conclusion</p> <p>These data suggest that the combination of p53AIP1 and survivin gene expression may be a powerful tool to stratify subgroups with better or worse prognosis from the variable non-small cell lung cancer population.</p

The effects of preoperative chemotherapy on isolated tumour cells in the blood and bone marrow of gastric cancer patients

Recent studies in breast cancer suggest that monitoring the isolated tumour cells (ITC) may be used as a surrogate marker to evaluate the efficacy of systemic chemotherapy. In the present study, we have investigated the effects of preoperative chemotherapy on ITC in the blood and bone marrow of patients with potentially resectable gastric cancer. After sorting out the CD45-positive cells, the presence of ITC defined as cytokeratin-positive cells was examined before and after preoperative chemotherapy. The patients received two courses of preoperative chemotherapy with cisplatin (100 mg m−2, day 1) and 5-fluorouracil (1000 mg m−2, days 1–5), administered every 28 days. Fourteen of 32 (44%) patients initially diagnosed with ITC in blood and/or bone marrow were found to be negative (responders) after preoperative chemotherapy (P<0.01). The incidence of ITC in bone marrow was also significantly (P<0.01) reduced from 97 (31 of 32) to 53% (17 of 32). The difference between patients positive for ITC in the blood before (n=7, 22%) and after (n=5, 16%) chemotherapy was statistically insignificant. The overall 3-year survival rates were 32 and 49% in the responders and non-responders, respectively (P=0.683). These data indicate that preoperative chemotherapy can reduce the incidence of ITC in patients with gastric cancer

Expression of p53, inducible nitric oxide synthase and vascular endothelial growth factor in gastric precancerous and cancerous lesions: correlation with clinical features

BACKGROUND: The growth and metastasis of tumors depend on the development of an adequate blood supply via angiogenesis. Recent studies indicate that the inducible nitric oxide synthase (iNOS), vascular endothelial growth factor (VEGF) and the tumor suppressor p53 are fundamental play-markers of the angiogenic process. Overexpression of iNOS and VEGF has been shown to induce angiogenesis in tumors. P53 suppresses angiogenesis by down-regulating VEGF and iNOS. The correlation of expression of p53, VEGF and iNOS and clinical features in gastric carcinogenesis, however, has not been well characterized. METHODS: The expression of p53, iNOS and VEGF in gastric precancerous and cancerous lesions and its relation with the clinical features was determined with immunohistochemistry (avidin-biotin-peroxidase complex method) on 55 randomly selected GC patients and 60 symptom-free subjects from the mass survey in the high-incidence area for GC in Henan, northern China. RESULTS: The positive immunostainig rates for p53, iNOS and VEGF in gastric carcinomas were 51%, 44% and 51%, respectively, and correlated well with TNM stages, but did not show significant difference among the groups with different degrees of gastric wall invasion depth by GC. A positive immunostaining reaction for the iNOS protein was significantly correlated with lymph node metastasis (p = 0.019; Spearman correlation coefficient). P53 protein accumulation was higher in the poorly-differentiated gastric carcinoma than in well-differentiated one. In gastric biopsies, no positive immunosatining was observed for p53, iNOS and VEGF in the histologically normal tissue and chronic superficial gastritis (CSG). However, p53, iNOS and VEGF positive immunostaining was observed in the tissues with different severities of lesions of chronic atrophic gastritis (CAG), intestinal metaplasia (IM) and dysplasia (DYS), and the positive rates increased with the lesion progression from CAG to IM to DYS. A high coincidental positive and negative immunostaining rate for p53, iNOS and VEGF was observed both in biopsy samples with CAG, IM and DYS from the symptom-free subjects and in gastric cancer tissue from the GC patients. CONCLUSIONS: The present results indicated that p53 protein accumulation and increased expression of iNOS and VEGF might be responsible for gastric carcinogenesis and tumor aggressiveness of gastric cancer

Small RNA interference-mediated gene silencing of heparanase abolishes the invasion, metastasis and angiogenesis of gastric cancer cells

<p>Abstract</p> <p>Background</p> <p>Heparanase facilitates the invasion and metastasis of cancer cells, and is over-expressed in many kinds of malignancies. Our studies indicated that heparanase was frequently expressed in advanced gastric cancers. The aim of this study is to determine whether silencing of heparanase expression can abolish the malignant characteristics of gastric cancer cells.</p> <p>Methods</p> <p>Three heparanase-specific small interfering RNA (siRNAs) were designed, synthesized, and transfected into cultured gastric cancer cell line SGC-7901. Heparanase expression was measured by RT-PCR, real-time quantitative PCR and Western blot. Cell proliferation was detected by MTT colorimetry and colony formation assay. The <it>in vitro </it>invasion and metastasis of cancer cells were measured by cell adhesion assay, scratch assay and matrigel invasion assay. The angiogenesis capabilities of cancer cells were measured by tube formation of endothelial cells.</p> <p>Results</p> <p>Transfection of siRNA against 1496-1514 bp of encoding regions resulted in reduced expression of heparanase, which started at 24 hrs and lasted for 120 hrs post-transfection. The siRNA-mediated silencing of heparanase suppressed the cellular proliferation of SGC-7901 cells. In addition, the <it>in vitro </it>invasion and metastasis of cancer cells were attenuated after knock-down of heparanase. Moreover, transfection of heparanase-specific siRNA attenuated the <it>in vitro </it>angiogenesis of cancer cells in a dose-dependent manner.</p> <p>Conclusions</p> <p>These results demonstrated that gene silencing of heparanase can efficiently abolish the proliferation, invasion, metastasis and angiogenesis of human gastric cancer cells <it>in vitro</it>, suggesting that heparanase-specific siRNA is of potential values as a novel therapeutic agent for human gastric cancer.</p