The design, synthesis, and evaluation of novel conformationally rigid analogues of sialyl Lewis

The design and synthesis of a series of analogues of sialyl Lewis^x (1) which incorporate conformationally rigid tetralin and naphthalene ring systems (2–4) has led to novel compounds which have similar potency to 1 as inhibitors of cell adhesion.     

Using neural networks for prediction of the subcellular location of proteins.

Neural networks have been trained to predict the subcellular location of proteins in prokaryotic or eukaryotic cells from their amino acid composition. For three possible subcellular locations in prokaryotic organisms a prediction accuracy of 81% can be achieved. Assigning a reliability index, 33% of the predictions can be made with an accuracy of 91%. For eukaryotic proteins (excluding plant sequences) an overall prediction accuracy of 66% for four locations was achieved, with 33% of the sequences being predicted with an accuracy of 82% or better. With the subcellular location restricting a protein's possible function, this method should be a useful tool for the systematic analysis of genome data and is available via a server on the world wide web.     

Locally efficient estimation of the quality-adjusted lifetime distribution with right-censored data and covariates

Zhao and Tsiatis (1997) consider the problem of estimation of the distribution of the quality-adjusted lifetime when the chronological survival time is subject to right censoring. The quality-adjusted lifetime is typically defined as a weighted sum of the times spent in certain states up until death or some other failure time. They propose an estimator and establish the relevant asymptotics under the assumption of independent censoring. In this paper we extend the data structure with a covariate process observed until the end of follow-up and identify the optimal estimation problem. Because of the curse of dimensionality, no globally efficient nonparametric estimators, which have a good practical performance at moderate sample sizes, exist. Given a correctly specified model for the hazard of censoring conditional on the observed quality-of-life and covariate processes, we propose a closed-form one-step estimator of the distribution of the quality-adjusted lifetime whose asymptotic variance attains the efficiency bound if we can correctly specify a lower-dimensional working model for the conditional distribution of quality-adjusted lifetime given the observed quality-of-life and covariate processes. The estimator remains consistent and asymptotically normal even if this latter submodel is misspecified. The practical performance of the estimators is illustrated with a simulation study. We also extend our proposed one-step estimator to the case where treatment assignment is confounded by observed risk factors so that this estimator can be used to test a treatment effect in an observational study.     

Phosphate Regulation of Nitrate Assimilation in Soybean

It is known that phosphorus deficiency results in alterationsin the assimilation of nitrogen. An experiment was conductedto investigate mechanisms involved in altered ¹⁵NO^–₃ uptake,endogenous ¹⁵N translocation, and amino acid accumulation insoybean (Glycine max L. Merrill, cv. Ransom) plants deprivedof an external phosphorus supply for 20 d in solution culture.Phosphorus deprivation led to decreased rates of ¹⁵NO^–₃uptake and increased accumulation of absorbed ¹⁵N in the root.Both effects became more pronounced with time. Asparagine, theprimary transport amino acid in soybean, accumulated in largeexcess in roots and stems. In roots of phosphorus-deprived plants,concentrations of ATP and inorganic phosphate declined rapidly,but dry weight accumulation was similar to or above that ofthe control even after 20 d of treatment. Arginine accumulationin leaves was greatly enhanced, even though ¹⁵N partitioninginto the insoluble reduced-N fraction of leaves was unaffected.The results suggest that decreases in NO^–₃ uptake in lowphosphorus plants could be caused by feedback control factorsand by limited ATP availability. The decline in endogenous Ntransport from the root to the shoot may be associated withchanges in membrane properties, which also result in paralleleffects on hydraulic conductance and the upward flow of waterthrough the plant. Key words: Phosphorus stress, nitrate uptake, nitrate translocation, arginine     

PCR-based assays of mendelian polymorphisms from anonymous single-copy nuclear DNA: techniques and applications for population genetics

This paper outlines a PCR-based approach for population genetics that offers several advantages over conventional Southern blotting methods for revealing restriction-fragment-length polymorphisms (RFLPs) in nuclear DNA. Primers are constructed from clones isolated from a nuclear DNA library, and these primers subsequently are employed in in vitro syntheses of homologous regions. Amplified products are then screened directly for RFLPs by using gel-staining procedures. Population applications for this PCR-based approach, including potential strengths and weaknesses, are exemplified by two RFLP data sets generated to estimate (a) male-mediated gene flow in the green turtle (Chelonia mydas) and (b) geographic population genetic structure in the American oyster (Crassostrea virginica). Restriction assays of amplified products from 14 or 15 independent primer pairs in each species revealed polymorphisms at several loci that proved highly informative in the population genetic analyses. In general, the Mendelian polymorphisms produced by this PCR-based approach will provide useful genetic markers for population studies, particularly in situations where simpler and less expensive allozyme methods have failed, for whatever reason, to provide adequate information.      

Cavities and packing at protein interfaces.

An analysis of internal packing defects or "cavities" (both empty and water-containing) within protein structures has been undertaken and includes 3 cavity classes: within domains, between domains, and between protein subunits. We confirm several basic features common to all cavity types but also find a number of new characteristics, including those that distinguish the classes. The total cavity volume remains only a small fraction of the total protein volume and yet increases with protein size. Water-filled "cavities" possess a more polar surface and are typically larger. Their constituent waters are necessary to satisfy the local hydrogen bonding potential. Cavity-surrounding atoms are observed to be, on average, less flexible than their environments. Intersubunit and interdomain cavities are on average larger than the intradomain cavities, occupy a larger fraction of their resident surfaces, and are more frequently water-filled. We observe increased cavity volume at domain-domain interfaces involved with shear type domain motions. The significance of interfacial cavities upon subunit and domain shape complementarity and the protein docking problem, as well as in their structural and functional role in oligomeric proteins, will be discussed. The results concerning cavity size, polarity, solvation, general abundance, and residue type constituency should provide useful guidelines for protein modeling and design.     

In vitro hydrolysis of RR,SS-threo-methylphenidate by blood esterases--differential and enantioselective interspecies variability

Enantioselective in vitro hydrolysis of methylphenidate (MPH) by the blood esterases of seven mammalian species is reported. The species included rats, rabbits, dogs, cattle, horses, monkeys, and humans. In vitro incubations up to 8 h were carried out in plasma, red blood cells, and whole blood of the various species. Enantioselective differences were evident among the different species on comparison of the data obtained from the three biological fluids. The esterases present in plasma appeared to show greater activity in the hydrolysis of MPH in all species where comparison with the other two biofluids was possible. Only in the case of humans did esterases present in plasma and red blood cells demonstrate opposite enantioselectivity in the hydrolysis of MPH. Thus after 8 h incubation, the RR-MPH/SS-MPH ratios in plasma and red blood cells were 0.31 and 1.16, respectively.     

Terpenoid biosynthesis and the stereochemistry of enzyme-catalysed allylic addition-elimination reactions.

Allylic addition-elimination reactions are widely used in the enzyme-catalysed formation of terpenoid metabolites. It has earlier been shown that the isoprenoid chain elongation reaction catalysed by farnesyl pyrophosphate synthase involving successive condensations of dimethylallyl pyrophosphate (DMAPP) and geranyl pyrophosphate (GPP) with isopentenyl pyrophosphate (IPP) corresponds to such an SE' reaction with net syn stereochemistry for the sequential electrophilic addition and proton elimination steps. Studies of the enzymic cyclization of farnesyl pyrophosphate (FPP) to pentalenene have now established the stereochemical course of two additional biological SE' reactions. Incubation of both (9R)- and (9S)-[9-3H,4,8-14]FPP with pentalenene synthase and analysis of the resulting labelled pentalenene has revealed that H-9re of FPP becomes H-8 of pentalenene, while H-9si undergoes net intramolecular transfer to the adjacent carbon, becoming H-1re (H-1 alpha) of pentalenene, as confirmed by subsequent experiments with [10-2H, 11-13C]FPP. These results correspond to net anti-stereochemistry in the intramolecular allylic addition-elimination reaction. The stereochemical course of a second SE' reaction has now been examined by analogous incubations of (4S,8S)-[4,8-3H,4,8-14C]FPP and (4R,8R)-[4,8-3H, 4.8-14C]FPP with pentalenene synthase. Determination of the distribution of label in the derived pentalenenes showed stereospecific loss of the original H-8si proton. Analysis of the plausible conformation of the presumed reaction intermediates revealed that the stereochemical course of the latter reaction cannot properly be described as either syn or anti, since cyclization and subsequent double bond formation require significant internal motions to allow proper overlap of the scissile C-H bond with the developing carbocation.     

Atropine, diazepam, and physostigmine: thermoregulatory effects in the heat-stressed rat

We have previously reported that administration of atropine (A) to unrestrained, sedentary, heat-stressed rats resulted in a dose-dependent increase in heating rate (rate of rise of core temperature, degree C/min). Additionally, we have demonstrated that the decrements in treadmill endurance and increments in heating rate of physostigmine (PH)-treated running rats can both be restored to control levels by pretreating the animals with A and diazepam (D). Our objective in the present work was to determine if the administration of D + PH to A-treated unrestrained, sedentary, heat-stressed rats (N = 16/group, 510-530 g) could improve their thermal tolerance. The following drugs were administered singly (at 10 min intervals) via lateral tail vein: vehicle-control (C), A (200 micrograms/kg), D (500 micrograms/kg), and PH (200 micrograms/kg). After drug administration, the rats were heat-stressed (Tamb = 41.5 degrees C) until a core temperature of 42.6 degrees C was attained when they were removed to a 26 degrees C chamber. The heating rates (degrees C/min) and tolerance times (min) of the respective groups were: C- 0.02, 235; A- 0.08, 58; A D- 0.06, 94; and A + D + PH- 0.04, 143. Administration of D with A significantly decreased heating rate, and D + PH more than doubled the thermal tolerance of A-treated rats. Thus, the combination of A + D + PH not only restores PH-induced performance and thermoregulatory decrements of rats exercised in a moderate environment, but also reduces A-induced heat intolerance.