Development and implementation of an algorithm for detection of protein complexes in large interaction networks

BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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

ｶｲｺ体液中に存在する細胞増殖抑制ならびに脂肪蓄積促進活性因子に関する研究

ｶｲｺ(Bombyx mori)の幼虫体液中にはｶｲｺ由来培養細胞の増殖を抑制する活性があることを見出した｡また､ｶｲｺ体液によって増殖を阻害された細胞中には脂肪滴の形成が認められた｡本研究ではこれらの細胞増殖抑制および脂肪蓄積促進活性の実体となるｶｲｺ体液因子の解明を行った｡ｶｲｺ体液を出発材料として､細胞増殖抑制活性を指標にﾀﾝﾊﾟｸ質の精製を行った｡6段階の精製過程の後､SDS-ﾎﾟﾘｱｸﾘﾙｱﾐﾄﾞｹﾞﾙ電気泳動において単一ﾊﾞﾝﾄﾞを示す画分を得た｡ｱﾐﾉ酸配列解析の結果､このﾀﾝﾊﾟｸ質はｶｲｺ Niemann-Pick disease type C2(BmNPC2)ﾀﾝﾊﾟｸ質であると同定された｡ﾘｺﾝﾋﾞﾅﾝﾄ BmNPC2 ﾀﾝﾊﾟｸ質は細胞増殖抑制活性を示したことから BmNPC2 ﾀﾝﾊﾟｸ質がｶｲｺ体液中の細胞増殖抑制活性の実体であることが示唆された｡さらに､ﾘｺﾝﾋﾞﾅﾝﾄ BmNPC2 ﾀﾝﾊﾟｸ質をｶｲｺ培養細胞に添加することによって､細胞内ﾄﾘｸﾞﾘｾﾘﾄﾞ量の増大が認められた｡以上の結果は､BmNPC2 ﾀﾝﾊﾟｸ質がｶｲｺにおいて細胞増殖と脂質代謝を制御する体液性因子であることを示唆している｡Silkworm hemolymph induced both the cessation of growth and an increase in neutral lipids storage in the silkworm-derived cell line, BmN4. In this study, we identified a responsible blood factor showing growth-inhibitory and lipid-accumulating activity. We subjected the silkworm hemolymph to successive column chromatographies and measured the growth-inhibitory activity of each fraction. The final purified fraction showed the highest specific activity and a single band of 15kDa protein on SDS-PAGE. The amino acid sequence revealed that the 15kDa protein was Bombyx mori Niemann-Pick disease type C2 (BmNPC2) protein. A recombinant BmNPC2 protein exhibited growth-inhibitory activity comparable with the final purified fraction, indicating that this protein is responsible for the activitiy of silkworm hemolymph. Moreover, the recombinant BmNPC2 protein induced an increase in triglyceride storage in BmN4 cells. These results indicate that BmNPC2 protein regulates both cell growth and lipid metabolism in silkworm

The nucleotide and deduced amino acid sequences of porcine liver proline-β-naphthylamidase swEvidence for the identity with carboxylesterase

AbstractA cDNA clone for porcine liver proline-β-naphthylamidase was isolated and sequenced. The deduced amino acid sequence of 567 residues was highly homologous with those of carboxylesterases (EC 3.1.1.1) previously reported for other species. In addition, proline-β-naphthylamidase purified from porcine liver was shown to have strong activity towards p-nitrophenylacetate, a representative substrate for carboxylesterases. These results suggest that proline-β-naphthylamidase is identical with carboxylesterase

Short communication: epidemiological evidence that simian T-lymphotropic virus type 1 in Macaca fuscata has an alternative transmission route to maternal infection.

Serological inspection of Simian T-lymphotropic Virus Type 1 was conducted for a wild colony of Macaca fuscata, which was captured in the middle Honshu, Japan. The increase of positive rate after the juvenile stage with the positive rate reaching 100% (or 35/35) in youngster and adult stages, was observed. This finding suggests that, in contrast with human T-lymphotropic Virus Type 1, horizontal transmission play an important role in increasing prevalence of STLV-1 with age among M. fuscata

Crystallographic Characterization of Extraterrestrial Materials by Energy-Scanning X-ray Diffraction

We have continued our long-term project using X-ray diffraction to characterize a wide range of extraterrestrial samples. The stationary sample method with polychromatic X-rays is advantageous because the irradiated area of the sample is always same and fixed, meaning that all diffraction spots occur from the same area of the sample, however, unit cell parameters cannot be directly obtained by this method though they are very important for identification of mineral and for determination of crystal structures. In order to obtain the cell parameters even in the case of the sample stationary method, we apply energy scanning of a micro-beam of monochromatic SR at SPring-8

Human Blood Feeding Activity of Female Hybrids between Culex pipiens pipiens and Culex pipiens quinquefasciatus（Diptera: Culicidae）

Human blood feeding activity was examined in females of hybrids between Culex pipiens pipiens and Culex pipiens quinquefasciatus during long photoperiod at 25℃. Blood feeding rates of hybrids were lower than in Culex pipiens quinquefasciatus and Culex pipiens pallens, and higher than in Culex pipiens pipiens, because no females fed on human blood in Culex pipiens pipiens

Eosinophil Hyporesponse of Jirds Induced by Microfilariae of Brugia Pahangi

Male jirds (Meriones unguiculatus) were inoculated sc with 100 infective larvae of Brugia pahangi. After 16 weeks, the animals were reinoculated with a comparable number of organisms. Blood eosinophil responses during the 5 weeks subsequent to this attempt to reinfect were much lower than those of comparable naive animals, while the response to a heterologous infection (Toxocara canis) was comparable to that of controls. Mebendazole was given to infected animals for 2 weeks beginning 5 weeks (prepatent) or 16 weeks (patent) after infection. At comparable intervals after drug administration, the animals were reinoculated with infective larvae and the blood eosinophil response was measured over a 5 week period. The response in the animals treated during the prepatent period was higher than the untreated infected controls. Treatment during the patent period had no demonstrable effect. Jirds made artificially microfilaremic by intravenous inoculation of viable filaria before and after the standard infecting dose had a low eosinophil response to infective larvae

The joint impact on being overweight of self reported behaviours of eating quickly and eating until full : cross sectional survey

Objective To examine whether eating until full or eating quickly or combinations of these eating behaviours are associated with being overweight

Hydrogen Supplementation of Preservation Solution Improves Viability of Osteochondral Grafts

Allogenic osteochondral tissue (OCT) is used for the treatment of large cartilage defects. Typically, OCTs collected during the disease-screening period are preserved at 4°C; however, the gradual reduction in cell viability during cold preservation adversely affects transplantation outcomes. Therefore, improved storage methods that maintain the cell viability of OCTs are needed to increase the availability of high-quality OCTs and improve treatment outcomes. Here, we evaluated whether long-term hydrogen delivery to preservation solution improved the viability of rat OCTs during cold preservation. Hydrogen-supplemented Dulbecco’s Modified Eagles Medium (DMEM) and University of Wisconsin (UW) solution both significantly improved the cell viability of OCTs during preservation at 4°C for 21 days compared to nonsupplemented media. However, the long-term cold preservation of OCTs in DMEM containing hydrogen was associated with the most optimal maintenance of chondrocytes with respect to viability and morphology. Our findings demonstrate that OCTs preserved in DMEM supplemented with hydrogen are a promising material for the repair of large cartilage defects in the clinical setting