Characterization of AP lyase activities of Saccharomyces cerevisiae Ntg1p and Ntg2p: implications for biological function

Saccharomyces cerevisiae possesses two Escherichia coli endonuclease III homologs, NTG1 and NTG2, whose gene products function in the base excision repair pathway and initiate removal of a variety of oxidized pyrimidines from DNA. Although the glycosylase activity of these proteins has been well studied, the in vivo importance of the AP lyase activity has not been determined. Previous genetic studies have suggested that the AP lyase activities of Ntg1p and Ntg2p may be major contributors in the initial processing of abasic sites. We conducted a biochemical characterization of the AP lyase activities of Ntg1p and Ntg2p via a series of kinetic experiments. Such studies were designed to determine if Ntg1p and Ntg2p prefer specific bases located opposite abasic sites and whether these lesions are processed with a catalytic efficiency similar to Apn1p, the major hydrolytic AP endonuclease of yeast. Our results indicate that Ntg1p and Ntg2p are equally effective in processing four types of abasic site-containing substrates. Certain abasic site substrates were processed with greater catalytic efficiency than others, a situation similar to Apn1p processing of such substrates. These biochemical studies strongly support an important biological role for Ntg1p and Ntg2p in the initial processing of abasic sites and maintenance of genomic stability.     

beta-Hydroxybutyrate inhibits myocardial fatty acid oxidation in vivo independent of changes in malonyl-CoA content

This study tested the hypothesis that an acute infusion of beta-hydroxybutyrate inhibits myocardial fatty acid uptake and oxidation in vivo. Anesthetized pigs were untreated (n = 6) or treated with an intravenous infusion of fat emulsion (n = 7) to elevate plasma free fatty acid levels. A third group received fat emulsion plus an intravenous infusion of beta-hydroxybutyrate (25 micromol.kg-1.min-1; n = 7) for 60 min. All animals received a continuous infusion of [3H]palmitate, and myocardial fatty acid oxidation was measured from the cardiac production of 3H2O. Plasma free fatty acid concentrations were elevated in the fat emulsion group (0.77 +/- 0.11 mM) compared with the untreated group (0.15 +/- 0.03 mM), which resulted in greater myocardial free fatty acid oxidation. In contrast, the group receiving beta-hydroxybutyrate in addition to fat emulsion had elevated beta-hydroxybutyrate concentration (0.87 +/- 0.11 vs. 0.04 +/- 0.01 mM), but suppressed fatty acid oxidation (0.053 +/- 0.013 micromol.g-1.min-1) (P < 0.05) compared with the fat emulsion group (0.116 +/- 0.029 micromol.g-1.min-1). There were no differences among the three groups in the tissue content for malonyl-CoA, acetyl-CoA, or free CoA or the activity of acetyl-CoA carboxylase; thus the inhibition of fatty acid oxidation by elevated beta-hydroxybutyrate did not appear to be due to malonyl-CoA inhibition of carnitine palmitoyl transferase-I or to an increase in the acetyl-CoA-to-free CoA ratio. In conclusion, fatty acid uptake and oxidation is blocked by an infusion of beta-hydroxybutyrate; this effect was not due to elevated myocardial malonyl-CoA content.     

The small-subunit ribosomal RNA gene sequences from the hypotrichous ciliates Oxytricha nova and Stylonychia pustulata

We have determined the complete nucleotide sequence of the small- subunit ribosomal RNA genes for the ciliate protozoans Stylonychia pustulata and Oxytricha nova. The sequences are homologous and sufficiently similar that these organisms must be closely related. In a phylogeny inferred from comparisons of several eukaryotic small-subunit ribosomal RNAs, the divergence of the ciliates from the eukaryotic line of descent is seen to coincide with the radiation of the plants, the animals, and the fungi. This radiation is preceded by the divergence of the slime mold, Dictyostelium discoideum.      

Bestimmung von deoxynivalenol mittels LC - MS/MS (Tandem Massenspektrometrie)

A sensitive and selective method using high-performance liquid chromatography in combination with atmospheric pressure chemical ionization tandem mass spetrometry (LC-APCI-MS/MS) has been developed for the determination of Deoxynivalenol (DON) in trace levels. The extract was purified with a MultiSep? column followed by the Vicam? DON immunoaffinity column. Quantification is based on an external standard method using positive Multiple Reaction Monitoring (MRM). The limit of detection was 5 μg/kg with a signal to noise ratio of 3:1.     

A genetic algorithm-based protocol for docking ensembles of small ligands using experimental restraints

Summary A genetic algorithm (GA) based method for docking ensembles of small, flexible ligands to receptor proteins using NMR-derived constraints is described. In this method, three translations and rotations of the ligand and the dihedral angles of the ligand are represented by binary strings and evolve under the genetic operators of cross-over, mutation, migration and selection. The fitness function for the selection process includes distance and dihedral restraints and a repulsive van der Waals term. The GA was applied to a three-atom model system as well as to the streptavidin-biotin complex using simulated intermolecular distance restraints. In both systems, the GA was able to obtain low-energy conformations when only a single binding site was simulated. Calculations were also performed using distance restraints from two distinct binding sites. In these simulations, the GA was able to obtain low-energy conformations corresponding to ligand molecules in each of the two sites. The inclusion of additional ligands in the ensemble did not result in an energetic benefit, confirming that only two ligand conformations were necessary to fulfill the distance restraints. This method allows for a direct investigation of the minimum number of ligand orientations necessary to fulfill experimental distance restraints, and simultaneously yields detailed structural information about each site.     

Diagnosis of Partial Body Radiation Exposure in Mice Using Peripheral Blood Gene Expression Profiles

In the event of a terrorist-mediated attack in the United States using radiological or improvised nuclear weapons, it is expected that hundreds of thousands of people could be exposed to life-threatening levels of ionizing radiation. We have recently shown that genome-wide expression analysis of the peripheral blood (PB) can generate gene expression profiles that can predict radiation exposure and distinguish the dose level of exposure following total body irradiation (TBI). However, in the event a radiation-mass casualty scenario, many victims will have heterogeneous exposure due to partial shielding and it is unknown whether PB gene expression profiles would be useful in predicting the status of partially irradiated individuals. Here, we identified gene expression profiles in the PB that were characteristic of anterior hemibody-, posterior hemibody- and single limb-irradiation at 0.5 Gy, 2 Gy and 10 Gy in C57Bl6 mice. These PB signatures predicted the radiation status of partially irradiated mice with a high level of accuracy (range 79–100%) compared to non-irradiated mice. Interestingly, PB signatures of partial body irradiation were poorly predictive of radiation status by site of injury (range 16–43%), suggesting that the PB molecular response to partial body irradiation was anatomic site specific. Importantly, PB gene signatures generated from TBI-treated mice failed completely to predict the radiation status of partially irradiated animals or non-irradiated controls. These data demonstrate that partial body irradiation, even to a single limb, generates a characteristic PB signature of radiation injury and thus may necessitate the use of multiple signatures, both partial body and total body, to accurately assess the status of an individual exposed to radiation.     

Treatment of gastrointestinal and renal adenocarcinomas with interferon-alpha

Treatment of adenocarcinomas with interferon-alpha as a single agent has been disappointing. Recent efforts have focused on the combination of interferon with cytotoxic drugs such as 5-fluorouracil. A number of postulated mechanisms can explain synergistic interactions between 5-fluorouracil and interferon-alpha, including interaction with pyrimidine pathways, and alteration of drug metabolism. Previous studies in colorectal cancer, using 5-fluorouracil and interferon-alpha are reviewed, suggesting that the combination is more active than 5-fluorouracil alone. In renal cell carcinoma, the literature is reviewed, suggesting that daily interferon is the most efficacious schedule; preliminary data suggest that addition of 5-fluorouracil to interferon-alpha can double the expected response rate of 16% achieved by interferon-alpha alone.Supported in part by NCI K08 CA 01306-03 (LM), NCI R01 CA 31080 (HO), and the Lineberger Comprehensive Cancer Center Research Award (LM).     

Copper transfer from Rhus vernicifera laccase.

Tree laccase, a multi-copper oxidase, has been studied as a copper donor in conjunction with the demetalated forms of three blue copper proteins. Copper transfer could be observed under reducing conditions in the absence of air. Only about 10% of the total copper in laccase could be transferred regardless of the amount of acceptor present in solution, hence, the laccase is heterogeneous as isolated. Potential sources of the heterogeneity are considered. After transfer, laccase could be partially resolved into copper-deficient and nearly holoprotein fractions that would not donate copper when recombined with acceptor protein. EPR results in conjunction with thiol titrations indicate that there is no net loss of type 1 copper from laccase but that there is loss of type 2 copper as well as a small amount of type 3 copper. Very little transfer is observed when type 2-depleted laccase is used as the donor. Finally, the implications that these results could have in the elucidation of possibly more physiologically relevant processes are briefly summarized.