OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures

The large number of experimentally determined protein 3D structures is a rich resource for studying protein function and evolution, and protein structure comparison (PSC) is a key method for such studies. When comparing two protein structures, almost all currently available PSC servers report a single and sequential (i.e. topological) alignment, whereas the existence of good alternative alignments, including those involving permutations (i.e. non-sequential or non-topological alignments), is well known. We have recently developed a novel PSC method that can detect alternative alignments of statistical significance (alignment similarity P-value <10(−5)), including structural permutations at all levels of complexity. OPAAS, the server of this PSC method freely accessible at our website (), provides an easy-to-read hierarchical layout of output to display detailed information on all of the significant alternative alignments detected. Because these alternative alignments can offer a more complete picture on the structural, evolutionary and functional relationship between two proteins, OPAAS can be used in structural bioinformatics research to gain additional insight that is not readily provided by existing PSC servers

Synthesis of SnO 2

Zinc oxides deposited on Tin dioxide nanowires have been successfully synthesized by atomic layer deposition (ALD). The diameter of SnO2-ZnO core-shell nanowires is 100 nm by ALD 200 cycles. The result of electricity measurements shows that the resistance of SnO2-ZnO core-shell nanowires (ALD: 200 cycles) is 925 Ω, which is much lower than pure SnO2 nanowires (3.6 × 106 Ω). The result of UV light test shows that the recovery time of SnO2-ZnO core-shell nanowires (ALD: 200 cycles) is 328 seconds, which is lower than pure SnO2 nanowires (938 seconds). These results demonstrated that the SnO2-ZnO core-shell nanowires have potential application as UV photodetectors with high photon-sensing properties

The VNTR 2 repeat in MAOA and delinquent behavior in adolescence and young adulthood: associations and MAOA promoter activity

Genetic studies of delinquent and criminal behavior are rare in spite of the wide recognition that individuals may differ in their propensity for delinquency and criminality. Using 2524 participants in Add Health in the United States, the present study demonstrates a link between the rare 2 repeat of the 30-bp VNTR in the MAOA gene and much higher levels of self-reported serious and violent delinquency. The evidence is based on a statistical association analysis and a functional analysis of MAOA promoter activity using two human brain-derived cell lines: neuroblastoma SH-SY5Y and human glioblastoma 1242-MG. The association analysis shows that men with a 2R report a level of serious delinquency and violent delinquency in adolescence and young adulthood that were about twice (CI: (0.21, 3.24), P = 0.025; and CI: (0.37, 2.5), P = 0.008 for serious and violent delinquency, respectively) as high as those for participants with the other variants. The results for women are similar, but weaker. In the functional analysis, the 2 repeat exhibits much lower levels of promoter activity than the 3 or 4 repeat

Efficient Prodrug Activator Gene Therapy by Retroviral Replicating Vectors Prolongs Survival in an Immune-Competent Intracerebral Glioma Model.

Prodrug activator gene therapy mediated by murine leukemia virus (MLV)-based retroviral replicating vectors (RRV) was previously shown to be highly effective in killing glioma cells both in culture and in vivo. To avoid receptor interference and enable dual vector co-infection with MLV-RRV, we have developed another RRV based on gibbon ape leukemia virus (GALV) that also shows robust replicative spread in a wide variety of tumor cells. We evaluated the potential of GALV-based RRV as a cancer therapeutic agent by incorporating yeast cytosine deaminase (CD) and E. coli nitroreductase (NTR) prodrug activator genes into the vector. The expression of CD and NTR genes from GALV-RRV achieved highly efficient delivery of these prodrug activator genes to RG-2 glioma cells, resulting in enhanced cytotoxicity after administering their respective prodrugs 5-fluorocytosine and CB1954 in vitro. In an immune-competent intracerebral RG-2 glioma model, GALV-mediated CD and NTR gene therapy both significantly suppressed tumor growth with CB1954 administration after a single injection of vector supernatant. However, NTR showed greater potency than CD, with control animals receiving GALV-NTR vector alone (i.e., without CB1954 prodrug) showing extensive tumor growth with a median survival time of 17.5 days, while animals receiving GALV-NTR and CB1954 showed significantly prolonged survival with a median survival time of 30 days. In conclusion, GALV-RRV enabled high-efficiency gene transfer and persistent expression of NTR, resulting in efficient cell killing, suppression of tumor growth, and prolonged survival upon CB1954 administration. This validates the use of therapeutic strategies employing this prodrug activator gene to arm GALV-RRV, and opens the door to the possibility of future combination gene therapy with CD-armed MLV-RRV, as the latter vector is currently being evaluated in clinical trials

Partially incoherent optical vortices in self-focusing nonlinear media

We observe stable propagation of spatially localized single- and double-charge optical vortices in a self-focusing nonlinear medium. The vortices are created by self-trapping of partially incoherent light carrying a phase dislocation, and they are stabilized when the spatial incoherence of light exceeds a certain threshold. We confirm the vortex stabilization effect by numerical simulations and also show that the similar mechanism of stabilization applies to higher-order vortices.Comment: 4 pages and 6 figures (including 3 experimental figures

Cellular prostatic acid phosphatase (cPAcP) serves as a useful biomarker of histone deacetylase (HDAC) inhibitors in prostate cancer cell growth suppression.

BACKGROUND: Prostate cancer (PCa) is the most commonly diagnosed solid tumor and the second leading cancer death in the United States, and also one of the major cancer-related deaths in Chinese. Androgen deprivation therapy (ADT) is the first line treatment for metastatic PCa. PCa ultimately relapses with subsequent ADT treatment failure and becomes castrate-resistant (CR). It is important to develop effective therapies with a surrogate marker towards CR PCa. METHOD: Histone deacetylase (HDAC) inhibitors were examined to determine their effects in androgen receptor (AR)/cellular prostatic acid phosphatase (cPAcP)-positive PCa cells, including LNCaP C-33, C-81, C4-2 and C4-2B and MDA PCa2b androgen-sensitive and androgen-independent cells, and AR/cPAcP-negative PCa cells, including PC-3 and DU 145 cells. Cell growth was determined by cell number counting. Western blot analyses were carried out to determine AR, cPAcP and PSA protein levels. RESULTS: cPAcP protein level was increased by HDAC inhibitor treatment. Valproic acid, a HDAC inhibitor, suppressed the growth of AR/cPAcP-positive PCa cells by over 50% in steroid-reduced conditions, higher than on AR/cPAcP-negative PCa cells. Further, HDAC inhibitor pretreatments increased androgen responsiveness as demonstrated by PSA protein level quantitation. CONCLUSION: Our results clearly demonstrate that HDAC inhibitors can induce cPAcP protein level, increase androgen responsiveness, and exhibit higher inhibitory activities on AR/cPAcP-positive PCa cells than on AR/cPAcP-negative PCa cells. Upon HDAC inhibitor pretreatment, PSA level was greatly elevated by androgens. This data indicates the potential clinical importance of cPAcP serving as a useful biomarker in the identification of PCa patient sub-population suitable for HDAC inhibitor treatment

Discrete States in Light-Like Linear Dilaton Background

We study the spectrum of bosonic strings in the light-like linear dilaton background and find discrete states. These are physical states which exist only at specific values of momentum. All except one discrete states generate spacetime symmetries. The exceptional discrete state corresponds to constraints which are deformations of conservation laws. The constraints resemble those arising from symmetries, and are equally powerful, suggesting that our notion of symmetry should be generalized.Comment: Latex, 21 pages, minor change

Void Structures in Regularly Patterned ZnO Nanorods Grown with the Hydrothermal Method

The void structures and related optical properties after thermal annealing with ambient oxygen in regularly patterned ZnO nanrorod (NR) arrays grown with the hydrothermal method are studied. In increasing the thermal annealing temperature, void distribution starts from the bottom and extends to the top of an NR in the vertical (c-axis) growth region. When the annealing temperature is higher than 400°C, void distribution spreads into the lateral (m-axis) growth region. Photoluminescence measurement shows that the ZnO band-edge emission, in contrast to defect emission in the yellow-red range, is the strongest under the n-ZnO NR process conditions of 0.003 M in Ga-doping concentration and 300°C in thermal annealing temperature with ambient oxygen. Energy dispersive X-ray spectroscopy data indicate that the concentration of hydroxyl groups in the vertical growth region is significantly higher than that in the lateral growth region. During thermal annealing, hydroxyl groups are desorbed from the NR leaving anion vacancies for reacting with cation vacancies to form voids

Características clínicas e de neuroimagem molecular de pacientes brasileiros com doença de Parkinson e mutações nos genes PARK2 ou PARK8

OBJECTIVE: To describe clinical and neuroimaging (SPECT) characteristics of Brazilian patients with Parkinson's disease (PD) and mutations in PARK2 or PARK8 genes. METHOD: A total of 119 patients meeting clinical criteria for PD were evaluated. RESULTS: Of all patients studied, 13 had mutations in either PARK2 (n=9) or PARK8 genes (n=4). No statistically significant differences in clinical characteristics in both groups were seen. SPECT with [99mTc] TRODAT-1 showed significant differences between patient and control and the most remarkable difference was between PARK2 and control. CONCLUSION: The study found a frequency of mutation of 10.1% and it was most commonly seen in women. These patients had long disease course and high rates of dyskinesia after L-DOPA use. PARK8 patients did not have a relevant family history of PD.OBJETIVO: Descrever as características clínicas e de neuroimagem (SPECT) de pacientes brasileiros com doença de Parkinson e mutações PARK2 e PARK8. MÉTODO: Foram avaliados 119 pacientes com critérios clínicos para a doença de Parkinson. RESULTADO: Entre os pacientes avaliados foram encontrados 13 pacientes com mutação nos genes PARK2 (n=9) ou PARK8 (n=4). Não houve diferença significativa na avaliação das características clínicas entre os dois grupos. Os resultados de SPECT mostraram diferenças significativas quanto ao potencial de ligação do [99mTc] TRODAT-1 SPECT entre pacientes vs. controle, sendo a diferença mais pronunciada entre PARK2 e controle. CONCLUSÃO: A freqüência de mutação encontrada foi 10,1%, sendo mais comum em mulheres. Estes pacientes apresentavam longo tempo de doença e alta prevalência de discinesias associadas ao uso da levodopa. Nossos pacientes com PARK8 não apresentaram uma história familiar relevante de doença de Parkinson.Hospital Israelita Albert Einstein Instituto Israelita de Ensino e PesquisaUniversidade Federal de São Paulo (UNIFESP) Escola Paulista de Medicina Division of Movement DisordersUNIFESP-EPM Laboratório Interdisciplinar de Neurociências ClínicasUNIFESP, EPM, Division of Movement DisordersUNIFESP, EPM Laboratório Interdisciplinar de Neurociências ClínicasSciEL