Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals.

We propose a framework for modeling sequence motifs based on the maximum entropy principle (MEP). We recommend approximating short sequence motif distributions with the maximum entropy distribution (MED) consistent with low-order marginal constraints estimated from available data, which may include dependencies between nonadjacent as well as adjacent positions. Many maximum entropy models (MEMs) are specified by simply changing the set of constraints. Such models can be utilized to discriminate between signals and decoys. Classification performance using different MEMs gives insight into the relative importance of dependencies between different positions. We apply our framework to large datasets of RNA splicing signals. Our best models out-perform previous probabilistic models in the discrimination of human 5' (donor) and 3' (acceptor) splice sites from decoys. Finally, we discuss mechanistically motivated ways of comparing models.     

Transient and long-term differential modulations of branched-chain α-keto acid decarboxylase activity in hypophysectomized rats

Hypophysectomy caused a marked but transient increase in branched-chain α-keto acid decarboxylase activities in rat liver mitochondria, peaking at about nine days post-surgery. The magnitude of increase is different for each of the three branched-chain α-keto acids. The activities then fall to a new steady state in three weeks with α-ketoisovalerate decarboxylase activity within the normal range, α-keto-β-methylvalerate decarboxylase activity at twice normal, and α-ketoisocaproate decarboxylase activity decreased to a level too low for accurate measurements.     

Plasminogen activator and MIF-like activities in Kirsten virus transformed mouse NIH culture fluids.

Kirsten virus transformed mouse NIH cells produce both a macrophage migration inhibition activity for guinea pig and mouse peritoneal exudate cells and a plasminogen activator. The migration inhibition factor activity exhibited thermal stability up to 80°C while the plasminogen activator was inactivated after 15 minutes at 70°C. Separation of these activities was achieved by absorption of the migration inhibition activity on agarose-fucosamine or high speed centrifugation.     

Photon correlation spectroscopy of human IgG

The translational diffusion coefficient D _20,w ⁰ , of monomeric human immunoglobulin G (IgG) has been studied by photon-correlation spectroscopy as a function of pH and protein concentration. At pH 7.6, we find D _20,w ⁰ =3.89×10^–7±0.02 cm²/sec, in good agreement with the value determined by classic mehods. This value corresponds to an effective hydrodynamic radius R, of 55.1±0.3 Å. As pH is increased to 8.9; with the same ionic strength, the molecule appears to expand slightly (3.5% increase in hydrodynamic radius). The concentration dependence of the IgG diffusion constant is interpreted in terms of solution electrostatic effects and shows that long-range repulsive interactions are negligible in the buffer used. The diffusion coefficient for dimeric IgG has also been determined to be D_20,w=2.81×10^–7±0.04 cm²/sec at 1.6 mg/ml, which corresponds to a hydrodynamic radius of 75 Å. For light-scattering studies of protein molecules in the dimension range of 5–10 nm (M_r=10⁵–10⁷) we find monomeric horse spleen ferritin well suited as a reference standard. Ferritin is a spherical molecule with a hydrodynamic radius R of 6.9±0.1 nm and is stable for years in our standard Tris-HCl-NaCl buffer even at room temperature.     

Effect of Soil Dose on Bioavailability of Lead from Mining Waste Soil in Rats

Abstract

The purpose of this study was to determine the extent of absorption of lead (Pb) in mining waste soil from Butte, Montana. It is the first study to fully investigate the bioavailability of lead in soils containing mine waste using a soil dose response approach. Young 7–8 week-old male and female Sprague-Dawley rats (5 animals/sex/group) were given mining waste soil [810 ppm lead (Test Soil I) or 3,908 ppm lead (Test Soil III)] mixed in a purified diet (AIN—76?) at four different dose levels (0.2, 0.5, 2 and 5% dietary soil) for 30 consecutive days. The test soil dose levels at 2 and 5% were chosen to bracket a pica-for-soil child's soil exposure levels. A pica-for-soil child is a young child who eats large quantities of soil (10 g day^?1). Standard groups included untreated controls and dosed feed soluble lead acetate groups (1, 10, 25, 100 and 250 μg Pb g^?1 feed). The concentrations of lead acetate were chosen to bracket the test soil dose levels of lead. Liver, blood and femur, representing the three compartments in which lead is distributed in the body, were analyzed for total lead concentration using graphite furnace atomic absorption spectroscopy. Clinical signs, body weight, food consumption and liver weights for treated and standard groups were similar to control. Tissue lead concentrations from test soil animals were significantly lower than the tissue concentrations for the dosed feed lead acetate group. Group mean whole blood, bone and liver lead concentrations increased with increasing dose levels for most treatment groups. The increases in blood, bone and liver lead concentrations were not proportional with increasing dose levels and plateaued at the high dose levels. Relative percent bioavailability values, based on dosed feed soluble lead as the standard, were independent of the two different test soils, dose levels or sex, and only slightly dependent on the tissue (blood > bone, liver). Overall relative percent bioavailability values were 20% based on the blood data; 9% based on the bone data; and 8% based on the liver data (2 and 5% dose levels only). The results of this study will provide the scientific validity needed to determine the significance of lead exposure from Butte soils in assessing human health risks as part of the Superfund Remedial Investigation/Feasibility Study process.     

Carbamates as potent calcitonin gene-related peptide antagonists with improved solution stability

The calcitonin gene-related peptide (CGRP) receptor has been implicated in the pathogenesis of migraine. A class of urethanamide derivatives has been identified as potent inhibitors of the CGRP receptor. Compound 20 was found to be among the most potent (IC₅₀ = 17 pM). It was shown to retain excellent aqueous solubility (>50 mg/mL, pH 7) while dramatically improving solution stability as compared to our previously disclosed development candidate, BMS-694153 (1).     

Cleavage site specificity of vertebrate collagenases

A series of synthetic peptide substrates for vertebrate collagenase having the structure Ac-Pro-Leu-Gly-X-Leu-Gly-OC2H5, where X is Leu, Ile, Val, Phe and Ala, have been prepared. Collagenolytic enzymes from various sources cleave these substrates with differing relative rate patterns. This series of peptides should be valuable for characterization of collagenases.