After complete sequencing of a number of genomes the focus has now turned to proteomics. Advanced proteomics technologies such as two-hybrid assay, mass spectrometry etc. are producing huge data sets ...of protein-protein interactions which can be portrayed as networks, and one of the burning issues is to find protein complexes in such networks. The enormous size of protein-protein interaction (PPI) networks warrants development of efficient computational methods for extraction of significant complexes.
This paper presents an algorithm for detection of protein complexes in large interaction networks. In a PPI network, a node represents a protein and an edge represents an interaction. The input to the algorithm is the associated matrix of an interaction network and the outputs are protein complexes. The complexes are determined by way of finding clusters, i. e. the densely connected regions in the network. We also show and analyze some protein complexes generated by the proposed algorithm from typical PPI networks of Escherichia coli and Saccharomyces cerevisiae. A comparison between a PPI and a random network is also performed in the context of the proposed algorithm.
The proposed algorithm makes it possible to detect clusters of proteins in PPI networks which mostly represent molecular biological functional units. Therefore, protein complexes determined solely based on interaction data can help us to predict the functions of proteins, and they are also useful to understand and explain certain biological processes.
Little is known about mechanisms for the perception of gibberellin (GA), a phytohormone, by plants. A GA-binding protein (GBP) with receptor-like characteristics was partially purified from azuki ...bean (Azukia angularis) seedlings. Gibberellins that caused much elongation of azuki epicotyl sections showed strong binding affinity for the GBP, and their biosynthetic precursors and inactive metabolites had weak affinity for it. The apparentKdvalue for GA4was calculated to be 7 × 10−10M from Scatchard plots. The molecular weight of the GBP in the native state was estimated to be 25,000 by high-performance liquid chromatography with a gel-permeation column. The GBP may be one of the receptor candidates for GAs.
Regarding innovation measurement utilizing patent information, a number of researchers are making great efforts to measure a "patent value (patent quality)." For patent valuation, patent ...classification and citation are often utilized as patent information. Also, biotechnological field is attracting attention from the viewpoint of application to environmental or medical study, and considerable researches on patent valuation are ongoing in this technical field. However, it is not enough recognized that researchers cannot be too careful when they deal with classification information in the biotech field because patent classification structure in this field is not well-established. And also, it is not known enough that citation patterns of both academic papers and patent documents are so complicated that the patterns cannot be easily generalized. In this article, the issues above were verified from a position based on working experiences of biotech patent examiner at Japan Patent Office, and considerations and implications were given on what patent valuation should be.
Information concerning DNA and amino acid sequences is increasing explosively year by year with development of analytical methods using whole genome sequences from lots of species including human. As ...for patent applications, enormous sequence data are stored into patent database, and it would be necessary to establish effective way to store the sequence data and well-utilization for sequence search. In this paper, four issues concerning sequences in patent applications were picked up and discussed. 1. Registration of short sequences, 2. Registration of long sequences and huge number of sequence, 3. Redundant sequence database, 4. Sequence data submission standards (XML). Finally, credibility of sequence data in patent applications is also discussed.
Little is known about mechanisms for the perception of gibberellin (GA), a phytohormone, by plants. A GA-binding protein (GBP) with receptor-like characteristics was partially purified from azuki ...bean (Azukia angularis) seedlings. Gibberellins that caused much elongation of azuki epicotyl sections showed strong binding affinity for the GBP, and their biosynthetic precursors and inactive metabolites had weak affinity for it. The apparent Kd value for GA4 was calculated to be 7 x 10(-10) M from Scatchard plots. The molecular weight of the GBP in the native state was estimated to be 25,000 by high-performance liquid chromatography with a gel-permeation column. The GBP may be one of the receptor candidates for GAs.
It is very important for the control of particulate emissions in diesel engines to reduce oil consumption. In order to control oil consumption in diesel engines, the mechanism by which sliding ...surface profiles of piston top rings are changed during endurance testing and the effect of the profiles on oil consumption were determined. The results obtained indicate that oil consumption depends largely upon the ratio of barrel face drop (e) to effective sliding surface width(B) of top ring profiles after endurance testing. The results also indicate that when the e/B is less than 6 /1000, oil consumption increases greatly. A technique is proposed for reducing oil consumption by controlling the e/B ratio through optimizing the top ring design.
The degradation of magnetic tunnel junctions (MTJs) with AlO
x
barrier was experimentally investigated. Constant voltage stress (CVS) measurement was carried out to monitor the time evolution of the ...conductance and tunneling magnetoresistance (TMR) of MTJs. The gradual increase of the stress-induced leakage current (SILC) was observed prior to the breakdown, following a power law function of stress time with an exponent of about 0.2-0.4, which is similar to the case of the ultrathin gate oxide films in MOSFETs. The measured TMR for SILC suggests that the spin-dependent current component would be involved in the early stage of degradation, while spin-independent conduction becomes dominant before the breakdown resulting in a decrease of TMR.
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