Donut-Shaped Fingerprint In Homologous Polypeptide Relationships-A Topological Feature Related To Pathogenic Structural Changes In Conformational Disease

Features of homologous relationship of proteins can provide us a general picture of protein universe, assist protein design and analysis, and further our comprehension of the evolution of organisms. Here we carried Out a Study of the evolution Of protein molecules by investigating homologous relationships among residue segments. The motive was to identify detailed topological features of homologous relationships for short residue segments in the whole protein universe. Based on the data of a large number of non-redundant Proteins, the universe of non-membrane polypeptide was analyzed by considering both residue mutations and structural conservation. By connecting homologous segments with edges, we obtained a homologous relationship network of the whole universe of short residue segments, which we named the graph of polypeptide relationships (GPR). Since the network is extremely complicated for topological transitions, to obtain an in-depth understanding, only subgraphs composed of vital nodes of the GPR were analyzed. Such analysis of vital subgraphs of the GPR revealed a donut-shaped fingerprint. Utilization of this topological feature revealed the switch sites (where the beginning of exposure Of previously hidden "hot spots" of fibril-forming happens, in consequence a further opportunity for protein aggregation is Provided; 188-202) of the conformational conversion of the normal alpha-helix-rich prion protein PrPC to the beta-sheet-rich PrPSc that is thought to be responsible for a group of fatal neurodegenerative diseases, transmissible spongiform encephalopathies. Efforts in analyzing other proteins related to various conformational diseases are also introduced. (C) 2009 Elsevier Ltd. All rights reserved.

Bibliometric analysis of nicotine research in China during the period of 1991 to 2007

With the widespread exposure of people to nicotine through recreational use of tobacco products, research into nicotine has attracted increasing attention. Tobacco smoking is by far the most important cause of lung cancer. As the world's largest producer and consumer of tobacco products, China bears a large proportion of the global burden of smoking-related disease; therefore, information on nicotine publications should be collected to formulate future research policy. In the present study, we investigated nicotine-related research articles published by Chinese authors that were indexed in the Science Citation Index (SCI) from 1991 to 2007. An indicator "citations per publication" (CPP) was used in the study to evaluate the impact of journals, articles, and institutes. The quantity of publications has increased at a quicker pace than the worldwide trend. Article visibility, measured as the frequency of being cited, also increased during the period. However, the overall quality of articles, based on the impact factor of journals publishing those articles, dropped behind the worldwide average level. There has been an increase in international collaboration, mainly with researchers in the USA. The average CPP of international co-authorship articles was higher than that of single country publications. Besides the USA, nicotine research in China will benefit from more collaboration with Taiwan, England, and Germany. Some 110 of 264 articles were published by a single institute, and the top six institutes were compared from various angles. Seventy-two subject categories were covered, and trends (in terms of both quantity and quality) of nicotine research in China were compared with worldwide trends. In addition, analysis of keywords in both nicotine and lung cancer research fields was applied to indicate research interests. Mutual cooperation among multiple disciplines needs further strengthening.

RAPD and AFLP techniques for the analysis of genetic relationships in two genera of Decapoda

RAPD was used fur analysing three (sub-)species of mitten crabs (Eriocheir sinensis, E. japonicus, and E. japonicus hepuensis) and three populations of E. sinensis. The results show that their relationships on DNA level are similar to the classical taxonomic hypotheses (Dai, 1991). No diagnostic RAPD marker could be found, but there were statistically significant genetic differences among these taxa (P < 0.001) or populations (P < 0.001). That is, the intraspecific similarities were larger than the interspecific similarities; the intrasubspecific similarities were larger than the intraspecific similarities; and the intrapopulational similarities were larger than the interpopulational similarities. In AFLP analysis, no significant genetic difference has been found between E. sinensis and E. japonicus, but AFLP markers among four species of Macrobrachium (M. rosenbergii. M. nipponense, M. hainanense, and M. asperulum) were found. The DNA similarities among these four species of Macrobrachium are in accordance with morphological similarities.

Optical analysis of dislocation-related physical processes in GaN-based epilayers

In this paper, recent progresses in optical analysis of dislocation-related physical properties in GaN-based epilayers are surveyed with a brief review. The influence of dislocations on both near-band edge emission and yellow luminescence (YL) is examined either in a statistical way as a function of dislocation density or focused on individual dislocation lines with a high spatial resolution. Threading dislocations may introduce non-radiative recombination centers and enhance YL, but their effects are affected by the structural and chemical environment. The minority carrier diffusion length may be dependent on either dislocation density or impurity doping as confirmed by the result of photovoltaic spectra. The in situ optical monitoring of the strain evolution process is employed during GaN heteroepitaxy using an AIN interlayer. A typical transition of strain from compression to tension is observed and its correlation with the reduction and inclination of threading dislocation lines is revealed. (c) 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mode analysis and Q-factor enhancement due to mode coupling in rectangular resonators

Modes in rectangular resonators are analyzed and classified according to symmetry properties, and quality factor (Q-factor) enhancement due to mode coupling is observed. In the analysis, mode numbers p and q are used to denote the number of wave nodes in the direction of two orthogonal sides. The even and odd mode numbers correspond to symmetric and antisymmetric field distribution relative to the midlines of sides, respectively. Thus, the modes in a rectangle resonator can be divided into four classes according to the parity of p and q. Mode coupling between modes of different classes is forbidden; however, anti-crossing mode coupling between the modes in the same class exists and results in new modes due to the combination of the coupled modes. One of the combined modes has very low power loss and high Q-factor based on far-field emission of the analytical field distribution, which agrees well with the numerical results of the finite-difference time-domain (FDTD) simulation. Both the analytical and FDTD results show that the Q-factors of the high Q-factor combined modes are over one order larger than those of the original modes. Furthermore, the general condition required to achieve high-Q modes in the rectangular resonator is given based on the analytical solution.

On-line voltammetric monitoring of dissolved Cu and Ni in the Gulf of Cadiz, south-west Spain

Geochemical processes in estuarine and coastal waters often occur on temporally and spatially small scales, resulting in variability of metal speciation and dissolved concentrations. Thus, surveys, which are aimed to improve our understanding of metal behaviour in such systems, benefit from high-resolution, interactive sampling campaigns. The present paper discusses a high-resolution approach to coastal monitoring, with the application of an automated voltammetric metal analyser for on-line measurements of dissolved trace metals in the Gulf of Cadiz, south-west Spain. This coastal sea receives metal-rich inputs from a metalliferous mining area, mainly via the Huelva estuary. On-line measurements of dissolved Cu, Zn, Ni and Co were carried out on-board ship during an eight-day sampling campaign in the study area in June 1997. A pumping system operated continuously underway and provided sampled water from a depth of ca. 4 m. Total dissolved metal concentrations measured on-line in the Gulf of Cadiz ranged between <5 nM Cu (<3 nM Ni) ca. 50 km off-shore and 60–90 nM Cu (5–13 nM Ni) in the vicinity of the Huelva estuary. The survey revealed steep gradients and strong tidal variability in the dissolved metal plume extending from the Huelva estuary into the Gulf of Cadiz. Further on-line measurements were carried out with the automatic metal monitor from the bank of the Odiel estuary over a full tidal cycle, at dissolved metal concentrations in the μM range. The application confirmed the suitability of the automated metal monitor for coastal sampling, and demonstrated its adaptability to a wide range of environmental conditions in the dynamic waters of estuaries and coastal seas. The near-real time acquisition of dissolved metal concentrations at high resolution enabled an interactive sampling campaign and therefore the close investigation of tidal variability in the development of the Huelva estuary metal plume.

The application of matrix-assisted laser desorption jonization mass spectrometry in enzymes of Agkistrodon blomhoffii Ussurensis venom analysis

The matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF-MS) spectra of four enzymes (PLA, AEase, Fibrolase, L-a.a. oxidase) in Agkistrodon blomhoffii Ussurensis venom, were given and interpreted. The experiment data showed that MALDI-TOF-MS can be used directly in enzyme analysis with high sensitivity and rapidity. In addition, the results were better than those from sodium dodecyl sulfate-polyacrylamide.

Computer-assisted automatic peak recognition and result evaluation for analysis of chlorinated hydrocarbons in environmental samples

A data manipulation method has been developed for automatic peak recognition and result evaluation in the analysis of organic chlorinated hydrocarbons with dual-column gas chromatography. Based on the retention times of two internal standards, pentachlorotoluene and decachlorobiphenyl, the retention times of chlorinated hydrocarbons can be calibrated automatically and accurately. It is very convenient to identify the peaks by comparing the retention times of samples with the calibrated retention times calculated from the relative retention indices of standards. Meanwhile, with a suggested two-step evaluation method the evaluation coefficients and the suitable quantitative results of each component can be automatically achieved for practical samples in an analytical system using two columns with different polarities and two internal standards. (C) 2002 Elsevier Science B.V. All rights reserved.