Cell surface colony-stimulating factor 1 can be cleaved by TNF-alpha converting enzyme or endocytosed in a clathrin-dependent manner

CSF-1 is a hemopoietic growth factor, which plays an essential role in macrophage and osteoclast development. Alternative splice variants of CSF-1 are synthesized as soluble or membrane-anchored molecules, although membrane CSF-1 (mCSF-1) can be cleaved from the cell membrane to become soluble CSF-1. The activities involved in this proteolytic processing, also referred to as ectodomain shedding, remain poorly characterized. In the present study, we examined the properties of the mCSF-1 sheddase in cell-based assays. Shedding of mCSF-1 was up-regulated by phorbol ester treatment and was inhibited by the metalloprotease inhibitors GM6001 and tissue inhibitor of metalloproteases 3. Moreover, the stimulated shedding of mCSF-1 was abrogated in fibroblasts lacking the TNF-alpha converting enzyme (TACE, also known as a disintegrin and metalloprotease 17) and was rescued by expression of wild-type TACE in these cells, strongly suggesting that the stimulated shedding is TACE dependent. Additionally, we observed that mCSF-1 is predominantly localized to intracellular membrane compartments and is efficiently internalized in a clathrin-dependent manner. These results indicate that the local availability of mCSF-1 is actively regulated by ectodomain shedding and endocytosis. This mechanism may have important implications for the development and survival of monocyte lineage cells.     

Both Early and Late Stages of Hepatocarcinogenesis Are Enhanced in Cx32 Dominant Negative Mutant Transgenic Rats with Disrupted Gap Junctional Intercellular Communication

Connexins are a family of transmembrane proteins essential for the gap junctions, which mediate cell-to-cell communication. Several connexins are reported to be tumor suppressors, and we have established transgenic (Tg) rats with a connexin 32 (Cx32) dominant negative mutant showing high sensitivity to early-stage diethylnitrosamine (DEN)-induced liver carcinogenesis. In this study, we carried out two independent experiments using Tg rats to further investigate the roles of disrupted Cx32 in late-stage carcinogenesis (carcinoma induction and metastasis) in the liver. In the first experiment, of 50 weeks’ duration, DEN was administered at 6 weeks of age and at 26 weeks to explore the effects of carcinogen treatments at different stages. The number of hepatocellular carcinomas (HCCs) was significantly increased in Tg compared with non-Tg rats. The second experiment focused on the effects of Cx32 disruption on metastasis by HCCs induced by administration of DEN and N-nitrosomorpholine. Only Tg rats had multiple metastases of HCCs in the lung, and the development and growth of HCCs was dramatically accelerated in Tg compared to non-Tg rats. Thus, normal function of Cx32 may be essential for suppression of both early and late stages of hepatocarcinogenesis.     

Structural and thermodynamic analyses of Escherichia coli RNase HI variant with quintuple thermostabilizing mutations

A combination of five thermostabilizing mutations, Gly23-->Ala, His62-->Pro, Val74-->Leu, Lys95-->Gly, and Asp134-->His, has been shown to additively enhance the thermostability of Escherichia coli RNase HI [Akasako A, Haruki M, Oobatake M & Kanaya S (1995) Biochemistry34, 8115-8122]. In this study, we determined the crystal structure of the protein with these mutations (5H-RNase HI) to analyze the effects of the mutations on the structure in detail. The structures of the mutation sites were almost identical to those of the mutant proteins to which the mutations were individually introduced, except for G23A, for which the structure of the single mutant protein is not available. Moreover, only slight changes in the backbone conformation of the protein were observed, and the interactions of the side chains were almost conserved. These results indicate that these mutations almost independently affect the protein structure, and are consistent with the fact that the thermostabiling effects of the mutations are cumulative. We also determined the protein stability curve describing the temperature dependence of the free energy of unfolding of 5H-RNase HI to elucidate the thermostabilization mechanism. The maximal stability for 5H-RNase HI was as high as that for the cysteine-free variant of Thermus thermophilus RNase HI. In contrast, the heat capacity of unfolding for 5H-RNase H was similar to that for E. coli RNase HI, which is considerably higher than that for T. thermophilus RNase HI. These results suggest that 5H-RNase HI is stabilized, in part, by the thermostabilization mechanism adopted by T. thermophilus RNase HI.     

An efficient grid layout algorithm for biological networks utilizing various biological attributes

Background  

Clearly visualized biopathways provide a great help in understanding biological systems. However, manual drawing of large-scale biopathways is time consuming. We proposed a grid layout algorithm that can handle gene-regulatory networks and signal transduction pathways by considering edge-edge crossing, node-edge crossing, distance measure between nodes, and subcellular localization information from Gene Ontology. Consequently, the layout algorithm succeeded in drastically reducing these crossings in the apoptosis model. However, for larger-scale networks, we encountered three problems: (i) the initial layout is often very far from any local optimum because nodes are initially placed at random, (ii) from a biological viewpoint, human layouts still exceed automatic layouts in understanding because except subcellular localization, it does not fully utilize biological information of pathways, and (iii) it employs a local search strategy in which the neighborhood is obtained by moving one node at each step, and automatic layouts suggest that simultaneous movements of multiple nodes are necessary for better layouts, while such extension may face worsening the time complexity.     

Changes in the distribution of grassland in the twentieth century in the Chugoku region of western Japan

Many plant and animal species that inhabit grassland in Japan are endangered because of habitat loss over the last century. Here, we mapped the historical distribution of grassland in the Chugoku region of western Japan using old editions of topographic maps (scale 1:50,000) and compared the historical distributions of grassland with the current distribution using digitized vegetation maps (scales 1:25,000 and 1:50,000). The area of grassland in the 1900s and 1950s was estimated to be 4602 km² (14.8% of the total area analyzed) and 3007 km² (9.5%), respectively. The current grassland area was estimated to be 217 km² (0.7%). Our results indicate that the area of grassland in the Chugoku region began to decrease during the first half of the twentieth century and sharply decreased during the second half of the twentieth century. Additionally, we evaluated the contribution of natural parks to the long-term conservation of grassland. The area of grassland maintained over a century was estimated to be 36.0 km², of which 23.4 km² was located in natural parks. Most of the area of grassland maintained over a century was located in Akiyoshidai Quasi-National Park (10.1 km²) and Daisen-Oki National Park (6.1 km²). Our results show that natural parks play an important role in the long-term conservation of grassland.

     

Efficient generation of antigen-specific cellular immunity by vaccination with poly(gamma-glutamic acid) nanoparticles entrapping endoplasmic reticulum-targeted peptides

Because antigen-specific cytotoxic T-lymphocytes (CTLs) are major effector cells in tumor immunity, more efficient delivery of tumor-associated antigens to the major histocompatibility complex class I-presentation pathway in antigen-presenting cells (APCs) will substantially contribute to establish more effective cancer immunotherapy. Herein, we demonstrated that a combinational approach based on the antigen-delivery system using poly(gamma-glutamic acid) nanoparticles (gamma-PGA NPs) and an endoplasmic reticulum (ER)-transport system containing an ER-insertion signal sequence (Eriss) significantly enhanced the ability of a peptide vaccine to induce cellular immune responses, including CTL activity. Immunization with gamma-PGA NPs entrapping Eriss-conjugated antigenic peptides markedly amplified and activated CTLs and interferon-gamma-secreting cells specific for the antigen, whereas no cellular immune responses were detected following vaccination with only one of the systems alone. Our data provide evidence that efficient delivery of antigenic peptides into APCs, as well as active ER-translocation of antigenic peptides in APCs should be considered in the development of peptide-based cancer immunotherapy.     

Reactive oxygen species generation through NADH oxidation by 6-formylpterin derivatives in the dark

6-formylpterin (6FP) has been reported to produce reactive oxygen species (ROS) such as *O2- and H2O2 from O2 in the presence of NADH under light condition. In the present study, we prepared a variety of 6FP derivatives and found that 2-(N,N-dimethylaminomethyleneamino)-6-formyl-3-pivaloylpteridin-4-one and 2-(N,N-dimethylaminomethyleneamino)-6-formyl-3-methylpteridin-4-one, in which the 2-amino groups are modified by a dimethylaminomethylene group and the 3-positions by pivaloyl and methyl groups and 2-amino-6-formyl-3-methylpteridin-4-one in which the amino group at the 2-position is free and the 3-position is modified by a methyl group generated H2O2 from O2 on oxidation of NADH to NAD+ in the dark. However, 6FP and 2-(N,N-dimethylaminomethyleneamino)-6-formylpteridin-4-one, in which the 3-position is free did not yield H2O2. These results indicate that modification of the 3-position is essential to make the activities of 6FP available in the dark and would be suggestive for designing pharmaceutical compounds that generate appropriate and controllable amounts of ROS in vivo.