Protein three-dimensional structural databases: Domains, structurally aligned homologues and superfamilies

This paper reports the availability of a database of protein structural domains (DDBASE), an alignment database of homologous proteins (HOMSTRAD) and a database of structurally aligned superfamilies (CAMPASS) on the World Wide Web (WWW). DDBASE contains information on the organization of structural domains and their boundaries; it includes only one representative domain from each of the homologous families. This database has been derived by identifying the presence of structural domains in proteins on the basis of inter-secondary structural distances using the program DIAL [Sowdhamini & Blundell (1995), Protein Sci. 4, 506-520]. The alignment of proteins in superfamilies has been performed on the basis of the structural features and relationships of individual residues using the program COMPARER [Sali & Blundell (1990), J. Mol. Biol. 212, 403-428]. The alignment databases contain information on the conserved structural features in homologous proteins and those belonging to superfamilies. Available data include the sequence alignments in structure-annotated formats and the provision for viewing superposed structures of proteins using a graphical interface. Such information, which is freely accessible on the WWW, should be of value to crystallographers in the comparison of newly determined protein structures with previously identified protein domains or existing families.

Comparison of quantum chemistry calculation methods of nucleic acid base-quartets

Nine base-quartets were calculated by six semi-empirical methods and ab initio Hartree-Fork method using STO-3G basis set. The results showed that PM3 method can be use to calculate base quartets, the results of PM3 calculations are close to the ab initio

4-Benzyl-5-ethyl-2-(2-furylcarbonylmethylsulfanyl) pyrimidin-6(1H)-one

The title compound, C19H18N2O3S, shows favourable activity against HIV-1. The phenyl ring is twisted with respect to the pyrimidine ring by 61.56 (9)degrees. Intermolecular N-H center dot center dot center dot O and C-H center dot center dot center dot O

Cloning,Expression and Sequence Analysis of A Luciferase Gene from the Chinese Firefly Pyrocoelia pygidialis

从一种来自中国日行性萤火虫(云南窗萤)发光器官mRNA中克隆、测序并表达了有功能的荧光素酶.云南窗萤荧光素酶的cDNA序列有1647个碱基,编码548个氨基酸残基.从推测得到的氨基酸序列的比对分析得出:云南窗萤的荧光素酶与来自Lampyris noctiluca,L.turkestanicus和Nyctophila cf.caucasica三种萤火虫的荧光素酶有97.8%的序列一致性.从推测得出的氨基酸序列进行系统发育分析,其结果表明:云南窗萤和Lampyris+Nyctophila聚在一起,与同属的发光强夜行性的萤火虫不形成的单系.云南窗萤荧光素酶在大肠杆菌中表达的条带大约70kDa,并且在有荧光素存在时发出黄绿色荧光.对荧光素酶的结构模拟和分析表明,云南窗萤荧光素酶基因的氨基端和羧基端结构域之间的裂沟处存在这5个多肽环,这正是从其他荧光素酶推测得到的催化荧光反应时的底物结合位点.云南窗萤和窗萤属的其他3种萤火虫的荧光素酶卡目比,有13个不同氨基酸位点,位于模拟分子结构的表面.对于这些多肽环、不刚氨基酸残基和晶体结构的进一步研究有利于解释日行和夜行性萤火虫荧光素酶的差异.

Deconvolution and elastography based on dimensional ultrasound

This paper is in two parts and addresses two of getting more information out of the RF signal from three-dimensional (3D) mechanically-swept medical ultrasound . The first topic is the use of non-blind deconvolution improve the clarity of the data, particularly in the direction to the individual B-scans. The second topic is imaging. We present a robust and efficient approach to estimation and display of axial strain information. deconvolution, we calculate an estimate of the point-spread at each depth in the image using Field II. This is used as of an Expectation Maximisation (EM) framework in which ultrasound scatterer field is modelled as the product of (a) a smooth function and (b) a fine-grain varying function. the E step, a Wiener filter is used to estimate the scatterer based on an assumed piecewise smooth component. In the M , wavelet de-noising is used to estimate the piecewise smooth from the scatterer field. strain imaging, we use a quasi-static approach with efficient based algorithms. Our contributions lie in robust and 3D displacement tracking, point-wise quality-weighted , and a stable display that shows not only strain but an indication of the quality of the data at each point in the . This enables clinicians to see where the strain estimate is and where it is mostly noise. deconvolution, we present in-vivo images and simulations quantitative performance measures. With the blurred 3D taken as OdB, we get an improvement in signal to noise ratio 4.6dB with a Wiener filter alone, 4.36dB with the ForWaRD and S.18dB with our EM algorithm. For strain imaging show images based on 2D and 3D data and describe how full D analysis can be performed in about 20 seconds on a typical . We will also present initial results of our clinical study to explore the applications of our system in our local hospital. © 2008 IEEE.

ECOLOGY AND BEHAVIOR OF WILD BLACK-CRESTED GIBBONS (HYLOBATES-CONCOLOR) IN CHINA WITH A RECONSIDERATION OF EVIDENCE FOR POLYGYNY

The black-crested gibbon, Hylobates concolor, is one of the few species of gibbons that has not yet been the subject of a long term field study. Field observations in the Ai Lao and Wu Liang Mountains of Yunnan Province, China indicate that in this area the habitat and ecology of this species differ markedly from those of other gibbons that have been studied to date. These differences are correlated with some behavioral differences. In particular, these gibbons apparently have greater day ranges than other gibbons. It has also been suggested that this species lives in polygynous groups. To demonstrate this requires observation of groups with two or more females with young. Our own observations and those from other recent studies suggest that there are alternative explanations consistent with available data.

Deposition of c-axis orientation aluminum nitride films on flexible polymer substrates by reactive direct-current magnetron sputtering

Aluminum nitride (AlN) piezoelectric thin films with c-axis crystal orientation on polymer substrates can potentially be used for development of flexible electronics and lab-on-chip systems. In this study, we investigated the effects of deposition parameters on the crystal structure of AlN thin films on polymer substrates deposited by reactive direct-current magnetron sputtering. The results show that low sputtering pressure as well as optimized N 2/Ar flow ratio and sputtering power is beneficial for AlN (002) orientation and can produce a highly (002) oriented columnar structure on polymer substrates. High sputtering power and low N 2/Ar flow ratio increase the deposition rate. In addition, the thickness of Al underlayer also has a strong influence on the film crystallography. The optimal deposition parameters in our experiments are: deposition pressure 0.38 Pa, N 2/Ar flow ratio 2:3, sputtering power 414 W, and thickness of Al underlayer less than 100 nm. © 2012 Elsevier B.V. All rights reserved.

The parameter space of graphene chemical vapor deposition on polycrystalline Cu

A systematic study of the parameter space of graphene chemical vapor deposition (CVD) on polycrystalline Cu foils is presented, aiming at a more fundamental process rationale in particular regarding the choice of carbon precursor and mitigation of Cu sublimation. CH 4 as precursor requires H 2 dilution and temperatures ≥1000 °C to keep the Cu surface reduced and yield a high-quality, complete monolayer graphene coverage. The H 2 atmosphere etches as-grown graphene; hence, maintaining a balanced CH 4/H 2 ratio is critical. Such balance is more easily achieved at low-pressure conditions, at which however Cu sublimation reaches deleterious levels. In contrast, C 6H 6 as precursor requires no reactive diluent and consistently gives similar graphene quality at 100-150 °C lower temperatures. The lower process temperature and more robust processing conditions allow the problem of Cu sublimation to be effectively addressed. Graphene formation is not inherently self-limited to a monolayer for any of the precursors. Rather, the higher the supplied carbon chemical potential, the higher the likelihood of film inhomogeneity and primary and secondary multilayer graphene nucleation. For the latter, domain boundaries of the inherently polycrystalline CVD graphene offer pathways for a continued carbon supply to the catalyst. Graphene formation is significantly affected by the Cu crystallography; i.e., the evolution of microstructure and texture of the catalyst template form an integral part of the CVD process. © 2012 American Chemical Society.

光滑侧链藻——中国淡水硅藻新记录

2004~2006年,对武汉东湖的底栖藻类进行了生态学调查研究。在对底栖硅藻的定性和定量研究中,发现了一种中心纲种类为中国新记录,它具有一些海洋角盘藻科种类的特征,如眼纹斑(Ocellus)等。经鉴定为光滑侧链藻Pleurosira laevis(Ehrenberg) Compere。参考Compere 1982年的研究,我们同意他的看法,即以前在我国台湾发现的台湾多变筒藻Proteucylindrus taiwanensis Li et Chiang和广东发现的Cerataulus laevis var

饲料淀粉水平对南方鲇幼鱼摄食后肝指数的影响

以白鱼粉、玉米油、玉米淀粉分别作为蛋白质、脂肪和碳水化合物原料,配制等蛋白质(含量40%)、等脂肪(含量10%)和不同碳水化合物梯度的3组饲料,饲料碳水化合物水平分别设计为0%,15%,30%.以南方鲇(Silurus meridionalisChen)幼鱼为实验对象,经各组饲料驯养8周后,实验鱼用不同饲料等日粮投喂,研究不同饲料碳水化合物水平下餐后肝脏的变化.实验结果表明:0%碳水化合物饲料组肝指数(HSI)在摄食过程中无显著变化;15%碳水化合物饲料组肝指数在摄食后3～6h无显著变化,12h的肝指数显