A novel method to produce extensive gastric antral ulcer in rats: pharmacological factors involved in the etiology of antral ulceration.

Gastric antral area is the most susceptible region to gastric ulceration in man. However, only limited information is available on animal models. In the present paper, we have developed an improved method for inducing gastric antral ulcers by the administration of 1.0 M HCl after refeeding for 1 h in rats. On day 4, the severe ulcer was found covering extensively the whole area of the antrum, and penetrated through the muscularis mucosae. The incidence of ulceration was 100% and the mean ulcer index was 37.1 +/- 16.6 mm2. In contrast, none of the erosive lesions were observed in the corpus area. Before 24 h, only slight hyperemia was observed in the antral region, suggesting that some submucosal mechanisms are involved in the ulceration processes other than the direct erosive action of HCl on the mucosal surface. Additional treatment with diethyldithiocarbamate (125 mg x kg(-1), s.c.), superoxide dismutase inhibitor, significantly aggravated this antral ulcer, and the ulcer index was 66.0 +/- 13.6 mm2. Allopurinol (50 mg x kg(-1), p.o.) significantly prevented ulcer formation induced by HCl plus DDC. GSH (150 mg x kg(-1), i.p.) also markedly prevented the ulceration. However, DMSO (0.5%, 5 mL x kg(-1), p.o.) was found not to affect ulcer formation. Famotidine (20 mg x kg(-1), p.o.) almost completely inhibited ulcer formation. From the above results, it was concluded that gastric antral ulcer can be induced by the simple treatment of 1.0 M HCl in refed rats, and the antrum has a different defensive mechanism from that in the corpus area. In addition. oxygen derived radicals, especially superoxide anion and endogenous acid secretion were found to be involved in the etiology of the aggravation of the gastric antral ulcer induced by DDC.     

Cyanidioschyzon merolae ferredoxin: a high resolution crystal structure analysis and its thermal stability

Cyanidioschyzon merolae (Cm) is a single-cell red alga that grows under moderately thermophilic (40-50°C), acidic (pH 1-3) conditions. We purified a Cm ferredoxin (Fd) that was characterized as a plant-type [2Fe-2S] Fd by physicochemical techniques. X-ray crystallography revealed that the overall three-dimensional structure of CmFd was highly similar to, but slightly different from, the [2Fe-2S] Fd from Spinacia oleracea, whose growth temperature is 15-20°C. Therefore, slight structural differences, including non-covalent-bond number and amino acid sequence, may underlie the differential thermostabilities of the plant-type Fds.     

Non-steroidal anti-inflammatory drugs affect the methotrexate transport in IEC-6 cells

Methotrexate (MTX) is used not only for the cancer chemotherapy but also for the treatment of rheumatic disease, often together with non-steroidal anti-inflammatory drugs (NSAIDs). MTX is actively cotransported with H(+) in the small intestine, mediated by a reduced folate carrier (RFC). The coadministration of some NSAIDs with MTX to rats caused a decrease of MTX absorption through the small intestine. This may be due to the uncoupling effect of oxidative phosphorylation of the NSAIDs. The present study investigated whether flufenamic acid, diclofenac and indomethacin, NSAIDs, decreased ATP content of rat-derived intestinal epithelial cell line IEC-6 cells and affected the MTX transport in IEC-6 cells. The MTX uptake in IEC-6 cells was dependent on medium pH and maximum around pH 4.5-5.5. The MTX uptake was composed of a transport inhibited by 4, 4'-diisothiocyanostilbene-2, 2'-disulfonic acid (DIDS) and a non-saturable one. The DIDS-sensitive component in the MTX uptake showed a saturation kinetics (Michaelis-Menten constant (Km): 3.91 +/- 0.52 microM, Maximum velocity (Vmax): 94.66 +/- 6.56 pmol/mg protein/5 min). The cellular ATP content in IEC-6 cells decreased significantly at 30 min after the cells were started to incubate with the NSAIDs (250 microM flufenamic acid, 500 microM diclofenac and 500 microM indomethacin). The MTX uptake in IEC-6 cells in the presence of the NSAIDs decreased with the reduction of cellular ATP content and showed a good correlation with the ATP content (correlation coefficient: 0.982). Thus it seems likely that the ATP content in IEC-6 cells with the NSAIDs decreased due to the uncoupling effect of oxidative phosphorylation of the NSAIDs, resulting in the inhibition of the secondary active transport of MTX in IEC-6 cells. The present results also suggest that IEC-6 cells are useful to evaluate the drug interaction relating to this carrier system.     

A Caenorhabditis elegans TGF-beta, DBL-1, controls the expression of LON-1, a PR-related protein, that regulates polyploidization and body length

Using cDNA-based array analysis combined with double-stranded RNA interference (dsRNAi), we have identified yk298h6 as a target gene of Caenorhabditis elegans TGF-beta signaling. Worms overexpressing dbl-1, a TGF-beta ligand, are 16% longer than wild type. Array analysis shows yk298h6 to be one of several genes suppressed in such worms. Disruption of yk298h6 function by dsRNAi also resulted in long worms, suggesting that it is a negative regulator of body length. yk298h6 was then mapped to, and shown to be identical to, lon-1, a known gene that affects body length. lon-1 encodes a 312 amino acid protein with a motif sequence that is conserved from plants to humans. Expression studies confirm that LON-1 is repressed by DBL-1, suggesting that LON-1 is a novel downstream component of the C.elegans TGF-beta growth regulation pathway. Consistent with this, LON-1 is expressed mainly in the larval and adult hypodermis and has dose-dependent effects on body length associated with changes in hypodermal ploidy, but not hypodermal cell proliferation.     

Lung burden of green nickel oxide aerosol and histopathological findings in rats after continuous inhalation

There are few inhalation studies of nickel carcinogenesis. In this study, Wistar male rats were exposed to green nickel oxide (NiO(G)) aerosols (mass median aerodynamic diameter, 0.6 μm) for 7 h/d, 5 d/wk for up to 12 mo. The average exposure concentration was controlled at 0.3 and 1.2 mg/m³ during the exposure. For histopathological examination and measurement of the nickel concentration in rat organs, the rats were sacrificed at 3, 6, and 12 mo of exposure and 8 mo clearance period following 12 mo of exposure. The nickel content in rat lungs that was observed up to 2.6 mg after 12 mo exposure, was proportional to the exposure concentration during the exposure. The clearance of the nickel from the lungs was very slow and the biological half time was determined 7.7 mo. Although the rats were exposed continuously to NiO(G), for 12 mo and kept for 8 mo clearance period, there were no malignant tumors in any of the exposed animals.     

Structural basis of sugar-recognizing ubiquitin ligase

SCF(Fbs1) is a ubiquitin ligase that functions in the endoplasmic reticulum (ER)-associated degradation pathway. Fbs1/Fbx2, a member of the F-box proteins, recognizes high-mannose oligosaccharides. Efficient binding to an N-glycan requires di-N-acetylchitobiose (chitobiose). Here we report the crystal structures of the sugar-binding domain (SBD) of Fbs1 alone and in complex with chitobiose. The SBD is composed of a ten-stranded antiparallel beta-sandwich. The structure of the SBD-chitobiose complex includes hydrogen bonds between Fbs1 and chitobiose and insertion of the methyl group of chitobiose into a small hydrophobic pocket of Fbs1. Moreover, NMR spectroscopy has demonstrated that the amino acid residues adjoining the chitobiose-binding site interact with the outer branches of the carbohydrate moiety. Considering that the innermost chitobiose moieties in N-glycans are usually involved in intramolecular interactions with the polypeptide moieties, we propose that Fbs1 interacts with the chitobiose in unfolded N-glycoprotein, pointing the protein moiety toward E2 for ubiquitination.     

BioPAX support in CellDesigner

MOTIVATION: BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format. AVAILABILITY: The plug-in is freely available and can be downloaded at ftp://ftp.pantherdb.org/CellDesigner/plugins/BioPAX/ CONTACT: huaiyumi@usc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.