Simulation study on the disordered state of an Alzheimer's beta amyloid peptide Abeta(12 36) in water consisting of random-structural, beta-structural, and helical clusters

The monomeric Alzheimer's beta amyloid peptide, Abeta, is known to adopt a disordered state in water at room temperature, and a circular dichroism (CD) spectroscopy experiment has provided the secondary-structure contents for the disordered state: 70% random, 25% beta-structural, and 5% helical. We performed an enhanced conformational sampling (multicanonical molecular dynamics simulation) of a 25-residue segment (residues 12-36) of Abeta in explicit water and obtained the conformational ensemble over a wide temperature range. The secondary-structure contents calculated from the conformational ensemble at 300 degrees K reproduced the experimental secondary-structure contents. The constructed free-energy landscape at 300 degrees K was not plain but rugged with five clearly distinguishable clusters, and each cluster had its own characteristic tertiary structure: a helix-structural cluster, two beta-structural clusters, and two random-structural clusters. This indicates that the contribution from the five individual clusters determines the secondary-structure contents experimentally measured. The helical cluster had a similarity with a stable helical structure for monomeric Abeta in 2,2,2-trifluoroethanol (TFE)/water determined by an NMR experiment: The positions of helices in the helical cluster were the same as those in the NMR structure, and the residue-residue contact patterns were also similar with those of the NMR structure. The cluster-cluster separation in the conformational space indicates that free-energy barriers separate the clusters at 300 degrees K. The two beta-structural clusters were characterized by different strand-strand hydrogen-bond (H-bond) patterns, suggesting that the free-energy barrier between the two clusters is due to the H-bond rearrangements.     

Possible immune functions of congerin, a mucosal galectin, in the intestinal lumen of Japanese conger eel

Congerin, a mucosal galectin of the Japanese conger eel, provides chemical fortification through its agglutinating and opsonizing activity. Congerin is produced in the epidermis, and the epithelia of the oral cavity to the esophagus, but not in the stomach or intestine. We hypothesized that congerin secreted from the upper digestive tract can reach and function in the intestinal lumen. We found that congerin possessed marked resistance against digestion by gastric and enteric enzymes of conger eel. It was not degraded until 6h of incubation with stomach extract or intestinal digestion juice. Western blotting demonstrated that congerin essentially remained in the intestinal mucus. The mucus agglutinated rabbit erythrocytes, and the agglutination was hampered by anti-congerin antibody. Furthermore, congerin could bind to some enteric bacteria. These results support the above hypothesis.     

Purification, cloning and characterization of egg lectins from the teleost Tribolodon brandti

Three L-rhamnose-binding egg lectins, TBL1, TBL2 and TBL3, were isolated from the eggs of the Far East dace Tribolodon brandti by a combination of affinity chromatography on L-rhamnose-Sepharose 6B gel and reversed-phase HPLC. L-rhamnose is a common inhibitor of the purified lectins and strongly inhibited the hemagglutinating activity of TBL2 and TBL3, but less weakly that of TBL1. L-arabinose, which has the same hydroxyl group orientation at C2 and C4 as L-rhamnose, and D-galactose showed no inhibitory activity against TBL1 but showed weak inhibitory activity against TBL2 and TBL3. The open reading frames of the cDNAs of TBL1, TBL2 and TBL3 encoded for mature proteins of 207, 189, and 293 amino acid residues, respectively. A BLAST homology search showed that the TBLs have about 40% homology to the carbohydrate recognition domains of rhamnose-binding lectins in salmonid eggs. The tandem repeated domains present in TBL1, TBL2 and TBL3 were two, two and three, respectively. TBL2 was exclusively expressed in ovary, while TBL1 and TBL3 were expressed mainly in ovary and weakly in various tissues including gill, heart, kidney, liver, spleen and testis.     

Mutagenic effects of 8-hydroxy-dGTP in live mammalian cells

The mutagenicity of an oxidized form of dGTP, 8-hydroxy-2'-deoxyguanosine 5'-triphosphate (8-OH-dGTP), was examined using COS-7 cells. 8-OH-dGTP and supF shuttle plasmid DNA were cointroduced by means of cationic liposomes, and the DNAs replicated in the cells were recovered and then transfected into Escherichia coli. 8-OH-dGTP induced A:T-->C:G substitution mutations in the COS-7 cells. This result agrees with previous observations indicating that DNA polymerases misincorporate 8-OH-dGTP opposite A in vitro, and that the oxidized deoxyribonucleotide induces A:T-->C:G transversions in E. coli. These results constitute the first direct evidence to show that 8-OH-dGTP actually induces mutations in living mammalian cells.     

Nuclear-translocated Glyceraldehyde-3-phosphate Dehydrogenase Promotes Poly(ADP-ribose) Polymerase-1 Activation during Oxidative/Nitrosative Stress in Stroke

In addition to its role in DNA repair, nuclear poly(ADP-ribose) polymerase-1 (PARP-1) mediates brain damage when it is over-activated by oxidative/nitrosative stress. Nonetheless, it remains unclear how PARP-1 is activated in neuropathological contexts. Here we report that PARP-1 interacts with a pool of glyceradehyde-3-phosphate dehydrogenase (GAPDH) that translocates into the nucleus under oxidative/nitrosative stress both in vitro and in vivo. A well conserved amino acid at the N terminus of GAPDH determines its protein binding with PARP-1. Wild-type (WT) but not mutant GAPDH, that lacks the ability to bind PARP-1, can promote PARP-1 activation. Importantly, disrupting this interaction significantly diminishes PARP-1 overactivation and protects against both brain damage and neurological deficits induced by middle cerebral artery occlusion/reperfusion in a rat stroke model. Together, these findings suggest that nuclear GAPDH is a key regulator of PARP-1 activity, and its signaling underlies the pathology of oxidative/nitrosative stress-induced brain damage including stroke.     

New insights on the roles of BMP signaling in bone-A review of recent mouse genetic studies

It is well known that Bone morphogenetic proteins (BMPs) induce bone formation and that some BMPs, including BMP2 and BMP7, are clinically used in orthopedics. Signaling by BMPs plays an important role in a variety of cell-types in bone such as osteoblasts, chondrocytes, and osteoclasts. It is recently reported using an osteoblast-targeted deletion of BMP signaling that BMP signaling in osteoblasts physiologically induces bone resorption by enhancing osteoclastogenesis via the RANKL-OPG pathway and reduces bone mass. In this review, the physiological function of BMP signaling in bone will be focused, and the current outcomes from mouse genetic studies will be discuss.     

Inflammation provoked by Mycoplasma pneumoniae extract: implications for combination treatment with clarithromycin and dexamethasone

Recently, combination treatment with a macrolide and a steroid for Mycoplasma pneumoniae (Mp) pneumonia has been reported to be effective. Thus, the effect of this combination on a mouse model of lung inflammation associated with Mp extract (the LIMEX mouse) was studied. Interleukin-6 (IL-6) and tumour necrosis factor-α (TNF-α) were induced in Mp extract-treated RAW264.7 cells, and this induction was inhibited by dexamethasone, parthenolide, SB203580 or LY294002. This suggested that Mp extract activates nuclear factor κB-, p38- and PI-3K-linked pro-inflammatory signals. The LIMEX mice were then either treated with or without clarithromycin and/or dexamethasone. Clarithromycin administration enhanced the production of IL-6, TNF-α, macrophage inflammatory protein-1α, monocyte chemotactic protein-1 and RANTES, while their production was perfectly suppressed by the combination of clarithromycin and dexamethasone. IL-17, IL-23, keratinocyte-derived chemokine (KC) and interferon-γ levels were not affected by clarithromycin treatment, but they were significantly suppressed by the combination of dexamethasone and clarithromycin. Collectively, some components of Mp extract provoked an inflammatory reaction in the RAW 264.7 cell line and LIMEX mice. Whereas the lung reaction in LIMEX mice was further exacerbated by clarithromycin treatment, it was resolved by the combinational treatment with clarithromycin and dexamethasone.     

Analysis of outer membrane vesicle protein involved in biofilm formation of Helicobacter pylori

Helicobacter pylori is one of the most common causes of bacterial infection in humans. Infection with H. pylori is closely associated with gastritis and peptic ulcers and is a risk factor for gastric cancer and mucosa-associated lymphoid tissue lymphoma. H. pylori forms biofilms on glass surfaces at the air–liquid interface in in-vitro batch cultures. We previously reported that strain TK1402 showed a strong biofilm-forming ability in vitro. We also suggested the outer membrane vesicles (OMV) produced by strain TK1402 might be related to its biofilm forming ability. In the present study, we analyzed the protein profile of the OMV produced by strain TK1402 and found a unique 22-kDa protein in TK1402 OMV cultured for 2–3 days. In addition, this protein could not be detected in the OMVs produced by other H. pylori strains. These results suggest that the 22-kDa protein is involved in effective biofilm formation by strain TK1402.     

Phosphorus release and sedimentation in three contiguous shallow brackish lakes, as estimated from changes in phosphorus stock and loading from catchment

In situ phosphorus release rates in three contiguous shallow brackish lakes were calculated by considering the amount of water inflow, changes in salinity and phosphorus stock, and loading from phosphorus inflow based on monthly data. The annual amount of sedimental phosphorus relative to that of phosphorus inflow was different for each of the three water bodies: 16% for Lake Shinji, 3% for the Honjo area, and −8% for Lake Nakaumi, as estimated in a 10-year period from January 1993 to December 2002. During the warm season, the quantity of phosphorus released surpassed sedimentation in these three water bodies. The low annual sedimentation ratio in Lake Nakaumi is related to a large seawater backflow resulting in phosphorus removal, in addition to a stable stratified structure promoting phosphorus release from sediment due to oxygen depletion in the lower layer. In Lake Nakaumi, field data shows that if dissolved oxygen at the sediment surface falls below 2.54 mg L⁻¹, phosphorus release from the sediment begins to be accelerated.