Fluorescent-labeled single-strand ATP aptamer DNA: chemo- and enantio-selectivity in sensing adenosine

One of the intriguing applications of aptamers is sensing molecules. In principle, an aptamer can specifically recognize and bind to a unique ligand, leading to a structural change of an aptamer. By acquiring information for the structural change, the detection of the ligand can be achieved. To design and explore an aptamer molecule to detect adenosine, we have synthesized some ATP aptamer variants labeled with donor and acceptor fluorophores. Although the fluorescent response of the aptamer variants was highly dependent on experimental temperature, we have found one of the variants showing suitable fluorescent response by titration with adenosine. The aptamer variant showed remarkable selectivity for adenosine over the other ribonucleosides. On the other hand, the enantio-specificity of the aptamer variant in the ligand recognition was not enough to selectively detect d-adenosine over l-adenosine.     

Gene interaction in DNA microarray data is decomposed by information geometric measure

MOTIVATION: Given the vast amount of gene expression data, it is essential to develop a simple and reliable method of investigating the fine structure of gene interaction. We show how an information geometric measure achieves this. RESULTS: We introduce an information geometric measure of binary random vectors and show how this measure reveals the fine structure of gene interaction. In particular, we propose an iterative procedure by using this measure (called IPIG). The procedure finds higher-order dependencies which may underlie the interaction between two genes of interest. To demonstrate the method, we investigate the interaction between the two genes of interest in the data from human acute lymphoblastic leukemia cells. The method successfully discovered biologically known findings and also selected other genes as hidden causes that constitute the interaction. AVAILABILITY: Softwares are currently not available but are possibly made available in future at http://www.mns.brain.riken.go.jp/~nakahara/DNA_pub.html where all the related information is also linked.     

Stromal Cells Positively and Negatively Modulate the Growth of Cancer Cells: Stimulation via the PGE2-TNFα-IL-6 Pathway and Inhibition via Secreted GAPDH-E-Cadherin Interaction

Fibroblast-like stromal cells modulate cancer cells through secreted factors and adhesion, but those factors are not fully understood. Here, we have identified critical stromal factors that modulate cancer growth positively and negatively. Using a cell co-culture system, we found that gastric stromal cells secreted IL-6 as a growth and survival factor for gastric cancer cells. Moreover, gastric cancer cells secreted PGE2 and TNFα that stimulated IL-6 secretion by the stromal cells. Furthermore, we found that stromal cells secreted glyceraldehyde 3-phosphate dehydrogenase (GAPDH). Extracellular GAPDH, or its N-terminal domain, inhibited gastric cancer cell growth, a finding confirmed in other cell systems. GAPDH bound to E-cadherin and downregulated the mTOR-p70S6 kinase pathway. These results demonstrate that stromal cells could regulate cancer cell growth through the balance of these secreted factors. We propose that negative regulation of cancer growth using GAPDH could be a new anti-cancer strategy.     

Transfer of phosphatidylcholine between different membranes in Tetrahymena as studied by spin labeling

Transfer of phosphatidylcholine molecules between different membrane fractions of Tetrahymena pyriformis cells grown at 15, 27 and 39.5°C was studied by electron spin resonance (ESR). Microsomes were labeled densely with a phosphatidylcholine spin label and the spin-labeled microsomes were incubated with non-labeled cilia, pellicles or microsomes. The transfer of the phosphatidylcholine spin labels was measured by decrease in the exchange broadening of the electron spin resonance spectrum. In one experiment, the lipid transfer was measured between ³²P-labeled microsomes and non-labeled pellicles by use of their radioactivity. The result was in good agreement with that by ESR. The fluidity of the membrane was estimated using a fatty-acid spin label incorporated into the membranes. Transfer between lipid vesicles was also studied. The results obtained were as follows: (1) The transfer between sonicated vesicles of egg- or dipalmitoyl phosphatidylcholine occurred rapidly in the liquid crystalline phase, with an activation energy of 20 kcal/mol, whereas it hardly occurred in the solid crystalline phase. (2) The transfer rate between microsomal membranes increased with temperature, and an activation energy of the reaction was 17.8 kcal/mol. (3) The transfer from the spin-labeled microsomes to subcellular membranes of the cells grown at 15°C was larger than that to the membranes of the cells grown at 39.5°C. The membrane fluidity was larger for the cells grown at lower temperature. (4) Similar tendency was observed for the transfer between microsomal lipid vesicles prepared from the cells grown at 15°C and at 39.5°C. (5) The transfer from microsomes to various membrane fractions increased in the order, cilia < pellicles < microsomes. The order of increase in the membrane fluidity was cilia < microsomes < pellicles, although the difference between microsomes and pellicles was slight. These results indicate a crucial role of the membrane fluidity in the transfer reaction. (6) Some evidence supported the idea that the lipid transfer between these organelles occurred through the lipid exchange rather than through the fusion.     

The production of chaetoglobosins, sterigmatocystin, O-methylsterigmatocystin, and chaetocin by Chaetomium spp. and related fungi.

Production of mycotoxins by Chaetomium spp. and related fungi on rice culture was examined by a combination of cytotoxicity tests using HeLa cells and thin-layer chromatography. Three species, C. mollipilium, C. rectum, and C. subaffine, as well as C. cochliodes and C. globosum, were proved to produce chaetoglobosins. From cultures of four strains of Chaetomium sp., assigned to C. thielavioideum, and one strain of Farrowia sp., chaetocin, sterigmatocystin, and O-methylsterigmatocystin were isolated. Morphological characteristics of the producers of sterigmatocystins are described.     

Secretion of L-glutamate from osteoclasts through transcytosis

Osteoclasts are involved in the catabolism of the bone matrix and eliminate the resulting degradation products through transcytosis, but the molecular mechanism and regulation of transcytosis remain poorly understood. Upon differentiation, osteoclasts express vesicular glutamate transporter 1 (VGLUT1), which is essential for vesicular storage and subsequent exocytosis of glutamate in neurons. VGLUT1 is localized in transcytotic vesicles and accumulates L-glutamate. Osteoclasts secrete L-glutamate and the bone degradation products upon stimulation with KCl or ATP in a Ca2+-dependent manner. KCl- and ATP-dependent secretion of L-glutamate was absent in osteoclasts prepared from VGLUT1-/- knockout mice. Osteoclasts express mGluR8, a class III metabotropic glutamate receptor. Its stimulation by a specific agonist inhibits secretion of L-glutamate and bone degradation products, whereas its suppression by a specific antagonist stimulates bone resorption. Finally, it was found that VGLUT1-/- mice develop osteoporosis. Thus, in bone-resorbing osteoclasts, L-glutamate and bone degradation products are secreted through transcytosis and the released L-glutamate is involved in autoregulation of transcytosis. Glutamate signaling may play an important role in the bone homeostasis.     

Requirement of left-handed glycine residue for high stability of the Tk-subtilisin propeptide as revealed by mutational and crystallographic analyses

Tk-subtilisin [the mature domain of Pro-Tk-subtilisin in active form (Gly70-Gly398)] from the hyperthermophilic archaeon Thermococcus kodakaraensis is matured from Pro-Tk-subtilisin [a subtilisin homologue from T. kodakaraensis in pro form (Gly1-Gly398)] upon autoprocessing and degradation of propeptide. Pro-Tk-subtilisin is characterized by extremely slow maturation at mild temperatures, but this maturation rate is greatly increased by a single Gly56 → Ser mutation in the propeptide region. To analyze the role of Gly56, which assumes a left-handed conformation, Pro-Tk-subtilisin variants with complete amino acid substitutions at Gly56 were constructed. A comparison of their halo-forming activities suggests that all variants, except for Pro-G56W [Pro-G56X, Pro-Tk-subtilisin with Gly56 → X mutation (X = any amino acid)], mature faster than WT. Pro-G56W and Pro-G56E with the lowest and highest maturation rates, respectively, among 19 variants, as well as WT and Pro-G56S, were overproduced, purified, and characterized. SDS-PAGE analyses and Tk-subtilisin activity assay indicated that their maturation rates increased in the order WT ≤ Pro-G56W < Pro-G56S < Pro-G56E. The propeptides of these variants were also overproduced, purified, and characterized. The stability and inhibitory potency of these propeptides decreased in the order Tk-propeptide [propeptide of Tk-subtilisin (Gly1-Leu69)] ≥ G56W-propeptide > G56S-propeptide > G56E-propeptide, indicating that they are inversely correlated with the maturation rates of Pro7-Tk-subtilisin and its derivatives. The crystal structures of these propeptides determined in complex with S324A-subtilisin indicate that the conformation of the propeptide is altered by the mutation, such that nonglycine residues at position 56 assume a right-handed conformation and hydrophobic interactions at the core region decrease. These results indicate that Gly56 is required in stabilizing the propeptide fold. Stabilization of this fold leads to strong binding of Tk-propeptide to Tk-subtilisin, high resistance of Tk-propeptide to proteolytic degradation, and slow maturation of Pro-Tk-subtilisin.     

Isolation and identification ofNeosartorya species from house dust as hazardous indoor pollutants

Isolation of ascomycetous microfungi from 58 house dust samples from detached and apartment dwellings around Kobe City revealed that species ofTalaromyces, Eurotium andNeosartorya were common ascomycetous propagules in the house dust.Neosartorya species accounted for 8.3% of the total identified isolates, of whichN. pseudofischeri was the main constituent, indicating that it may be a common potential fungal pathogen in the dwelling environment. Based on the specimens collected,N. pseudofischeri is described and illustrated as new to Japan.     

Purification and characterization of aβ-galactosidase fromTreponema phagedenis (Reiter strain)

A β-galactosidase was highly purified from a cellular extract ofTreponema phagedenis (Reiter strain) by ammonium sulfate precipitation and successive chromatography on Sepharose 6B and DEAE-Sephadex. The purified enzyme was homogeneous in SDS-polyacrylamide gel electrophoresis. The molecular weight estimated was 580,000. The optimal pH, ionic strength, and temperature were 6.5, 0.1, and 50°C, respecitvely. The enzyme was stable only at around pH 6.5 and at temperatures lower than 35°C. The enzyme was irreversibly inhibited byp-chloromercuribenzoate and divalent cations such as Hg²⁺, Cu²⁺, Zn²⁺, Cd²⁺, and Pb²⁺. The Km values forp-nitrophenyl-β-D-galactopyranoside,o-nitrophenyl-β-D-galactopyranoside, and lactose were 0.29, 0.36, and 5.4 mM, respectively.     

Lack of bone resorption in osteosclerotic (oc/oc) mice is due to a defect in osteoclast progenitors rather than the local microenvironment provided by osteoblastic cells.

In a co-culture system of mouse spleen cells and osteoblastic cells, we have demonstrated that a suitable microenvironment must be provided by osteoblastic cells in order for osteoclast-like multinucleated cell (MNC) formation. Using this co-culture system, we examined the pathogenetic mechanism underlying the lack of bone resorption in osteosclerotic oc/oc mice. Numerous tartrate-resistant acid phosphatase (TRAP, an osteoclast marker enzyme)-positive MNCs were formed in response to 1 alpha,25-dihydroxyvitamin D3 [1 alpha,25(OH)2D3] both in co-cultures of oc/oc spleen cells and normal osteoblastic cells and in those of normal spleen cells and oc/oc osteoblastic cells. TRAP-positive MNCs derived from normal spleen cells tended to spread out on culture dishes, whereas those from oc/oc spleen cells remained as small, compact MNCs. When TRAP-positive MNCs enriched from co-cultures of normal spleen cells and oc/oc osteoblastic cells were cultured on dentine slices, they formed numerous resorption pits with ruffled borders and clear zones. In contrast, none of the TRAP-positive MNCs derived from oc/oc spleen cells formed either ruffled borders or resorption pits. These results indicate that the lack of bone resorption in oc/oc mice is due to a defect in osteoclast progenitors rather than the local microenvironment provided by osteoblastic cells.