Cloning and expression analysis of two distinct HIF-alpha isoforms – gcHIF-1alpha and gcHIF-4alpha – from the hypoxia-tolerant grass carp,Ctenopharyngodon idellus

Background  

Hypoxia-inducible factors (HIFs) are involved in adaptive and survival responses to hypoxic stress in mammals. In fish, very little is known about the functions of HIFs.     

Age-at-death estimation in an Italian historical sample: A test of the Suchey-Brooks and transition analysis methods

A growing body of research is demonstrating increased accuracy in aging from a relatively new method, transition analysis. Although transition analysis was developed for paleodemographic research, a majority of subsequent studies have been in the forensic arena, with very little work in bioarchaeological contexts. Using the Suchey‐Brooks pubic symphysis phases, scored on a target sample of historic Italians from the island of Sardinia, we compare accuracy of aging between transition analysis combined with a Bayesian approach and the standard Suchey‐Brooks age ranges. Because of the difficulty in identifying a reasonable informative prior for bioarchaeological samples, we also compared results of both an informative prior and a uniform prior for age estimation. Published ages‐of‐transition for the Terry Collection and Balkan genocide victims were used in conjunction with parameters generated from Gompertz hazard models derived from the priors. The ages‐of‐transition and hazard parameters were utilized to calculate the highest posterior density regions, otherwise known as “coverages” or age ranges, for each Suchey‐Brooks phase. Each prior, along with the parameters, were input into cumulative binomial tests. The results indicate that the Bayesian approach outperformed the Suchey‐Brooks technique alone. The Terry Collection surpassed the Balkans as a reasonable sample from which to derive transition analysis parameters. This discrepancy between populations is due to different within phase age‐at‐death distributions that reflect differences in aging between the populations. These results indicate bioarchaeologists should strive to apply a Bayesian analysis when aging historic and archaeological populations by employing an informative prior. Am J Phys Anthropol 149:259–265, 2012. © 2012 Wiley Periodicals, Inc.     

Inhibitory effects of LPA1 on cell motile activities stimulated by hydrogen peroxide and 2,3-dimethoxy-1,4-naphthoquinone in fibroblast 3T3 cells

Reactive oxygen species (ROS) are known to mediate a variety of biological responses, including cell motility. Recently, we indicated that lysophosphatidic acid (LPA) receptor-3 (LPA₃) increased cell motile activity stimulated by hydrogen peroxide. In the present study, we assessed the role of LPA₁ in the cell motile activity mediated by ROS in mouse fibroblast 3T3 cells. 3T3 cells were treated with hydrogen peroxide and 2,3-dimethoxy-1,4-naphthoquinone (DMNQ) at concentrations of 0.1 and 1 μM for 48 h. In cell motility assays with Cell Culture Inserts, the cell motile activities of 3T3 cells treated with hydrogen peroxide and DMNQ were significantly higher than those of untreated cells. 3T3 cells treated with hydrogen peroxide and DMNQ showed elevated expression levels of the Lpar3 gene, but not the Lpar1 and Lpar2 genes. To investigate the effects of LPA₁ on the cell motile activity induced by hydrogen peroxide and DMNQ, Lpar1-overexpressing (3T3-a1) cells were generated from 3T3 cells and treated with hydrogen peroxide and DMNQ. The cell motile activities stimulated by hydrogen peroxide and DMNQ were markedly suppressed in 3T3-a1 cells. These results suggest that LPA signaling via LPA₁ inhibits the cell motile activities stimulated by hydrogen peroxide and DMNQ in 3T3 cells.     

Easy detection of GFP-positive mutants following forward mutations at specific gene locus in cultured human cells

We have generated a new mutation assay system using HT1080 human fibrosarcoma cells, which consists of a combination of tetracycline-operator dependent GFP gene (TetO-EGFP) and tetracycline repressor (TetR) genes, where the expression of GFP gene is under strict control of TetR protein, and the TetR gene is located within the endogenous HPRT gene. In this system, any inactivating mutation at the TetR gene or large deletions including the gene itself results in high expression of GFP gene (>200-fold increase) in the cells, which can be readily scored not only by a flow cytometer but also under a fluorescent microscope. With this new cell line, we show that the spontaneous mutation rate at the TetR locus was 2.8-3.4×10(-6)/cell division, slightly lower than the rate at the endogenous HPRT gene of HT1080 cells, and has a dose response to X rays as a mutagen. We also isolated variant clones with elevated spontaneous mutation rate (i.e., genetically unstable cells) following X irradiation. Spontaneous GFP-positive mutants were predominantly base-change mutations at the TetR gene while those obtained after X irradiation often contained large deletions which spanned up to 6Mb. The results indicate that the bacterial TetR/TetO regulatory units work extremely well as a mutation detection system in human cells, and any part of the human genome may be tested for mutation sensitivity following targeted insertion of the TetR gene in a stably expressing gene.     

AmylPepPred: Amyloidogenic Peptide Prediction tool

We present an efficient computational architecture designed using supervised machine learning model to predict amyloid fibril forming protein segments, named AmylPepPred. The proposed prediction model is based on bio-physio-chemical properties of primary sequences and auto-correlation function of their amino acid indices. AmylPepPred provides a user friendly web interface for the researchers to easily observe the fibril forming and non-fibril forming hexmers in a given protein sequence. We expect that this stratagem will be highly encouraging in discovering fibril forming regions in proteins thereby benefit in finding therapeutic agents that specifically aim these sequences for the inhibition and cure of amyloid illnesses.

Availability

AmylPepPred is available freely for academic use at www.zoommicro.in/amylpeppred     

MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis

Background  

Methylthioadenosine, the main by-product of spermidine synthesis, is degraded inBacillus subtilisas adenine and methylthioribose. The latter is an excellent sulfur source and the precursor of quorum-sensing signalling molecules. Nothing was known about methylthioribose recycling in this organism.     

Inducible cytochrome P450 activities in renal glomerular mesangial cells: biochemical basis for antagonistic interactions among nephrocarcinogenic polycyclic aromatic hydrocarbons

BACKGROUND: Benzo(a)pyrene (BaP), anthracene (ANTH) and chrysene (CHRY) are polynuclear aromatic hydrocarbons (PAHs) implicated in renal toxicity and carcinogenesis. These PAHs elicit cell type-specific effects that help predict toxicity outcomes in vitro and in vivo. While BaP and ANTH selectively injure glomerular mesangial cells, and CHRY targets cortico-tubular epithelial cells, binary or ternary mixtures of these hydrocarbons markedly reduce the overall cytotoxic potential of individual hydrocarbons. METHODS: To study the biochemical basis of these antagonistic interactions, renal glomerular mesangial cells were challenged with BaP alone (0.03 - 30 microM) or in the presence of ANTH (3 microM) or CHRY (3 microM) for 24 hr. Total RNA and protein will be harvested for Northern analysis and measurements of aryl hydrocarbon hydroxylase (AHH) and ethoxyresorufin-O-deethylase (EROD) activity, respectively, to evaluate cytochrome P450 mRNA and protein inducibility. Cellular hydrocarbon uptake and metabolic profiles of PAHs were analyzed by high performance liquid chromatography (HPLC). RESULTS: Combined hydrocarbon treatments did not influence the cellular uptake of individual hydrocarbons. ANTH or CHRY strongly repressed BaP-inducible cytochrome P450 mRNA and protein expression, and markedly inhibited oxidative BaP metabolism. CONCLUSION: These findings indicate that antagonistic interactions among nephrocarcinogenic PAHs involve altered expression of cytochrome P450s that modulate bioactivation profiles and nephrotoxic/ nephrocarcinogenic potential.     

Intensive cannibalism and feeding on bregmacerotids in <Emphasis Type="Italic">Champsodon snyderi</Emphasis> (Champsodontidae): evidence for pelagic predation

Analysis of the stomach contents of 1002 specimens of Champsodon snyderi (Champsodontidae) (17.3–91.2mm SL) from Tosa Bay, southern Japan, showed that species to primarily feed on crustaceans and fishes (87.9% by frequency, 37.6% by weight for the former; 17.3% and 60.7% for the latter, respectively), although fishes occurred more often in stomachs of individuals larger than 50mm SL. Champsodon snyderi ingested large prey fishes (60.5–101.0% of predator SL), the maximum weight recorded for a single ingested specimen being 50.9% of the predator weight. Mesopelagic Bregmaceros nectabanus were by far the dominant prey fish, followed by C. snyderi (cannibalism), indicating that C. snyderi leaves the bottom to feed in the pelagic environment during the night.