Formal modeling of approximate relations in biochemical systems

Aiming to satisfy the need for the formalization of semiquantitative reasoning in the analysis of biochemical systems, the O[M] formalism for reasoning with orders of magnitude and approximate relations has been developed. It is based on seven primitive relations among quantities and compound relations which are formed as implicit disjunctions of primitives. O[M] can perform inferences by using formal approximate relations, algebraic equations, inequalities, if-then rules, assumptions, and goals. The applications discussed include Michaelis-Menten kinetics, different modes of inhibition of an enzymatic reaction, analysis of fluxes in biochemical networks, and identification of rate-limiting steps of biochemical pathways. In these applications, O[M] provides a medium for acquisition and formalization of previously informal concepts, analysis of systems at the order-of-magnitude level of detail, and automation of commonsense reasoning.     

Influence of the solvent on the conformational-dependent properties of random coil polypeptides. II. Mean square optical anisotropies and Kerr constants

Mean square optical anisotropies and molar Kerr constants were calculated for homopolypeptides of the 20 natural amino acids and of several enzymes and proteins in the random-coil state. The effect of hydration was taken into account in constructing the molecular potential that gives the conformational energies as a function of the rotational angles phi and psi of the backbone and chi(1) of the side chain. The Rotational Isomeric State model was used in calculated energies, the Valence Optical Scheme and the matrix calculus technique of Flory being employed in the evaluation of the optical properties. The results are compared with calculations for the same substances that were performed without taking into account the solvent, as well as with other similar studies. The Kerr constant is confirmed as being one of the most sensitive properties of a given polypeptide to the residue class and to the sequence of those residues.     

在双脉冲光刺激下瞳孔系统的采样控制特性

本文用实验揭示了瞳孔对光动态反应具有采样控制特性。实验中采用各种不同时间间隔的双脉冲光,以开环的方式(Maxwellian View)刺激瞳孔,当双脉冲之间间隔较长时,瞳孔反应相当于对双脉冲光的两次脉冲分别产生瞬态收缩;当双脉冲时间间隔短于0.6s 时,其反应就成了一次瞬态收缩,与单个光脉冲所引起的瞳孔反应一样。同—受试者的多次实验结果相同,不同受试者所得结果也基本一致。故瞳孔对脉冲刺激光引起反应后,必须至少约隔0.6s 才能对另一次脉冲光产生反应,这就说明了瞳孔动态反应具有离散的采样控制特性。实验还进一步证明,瞳孔系统的控制机制是双重模式的控制:不同的刺激条件下,瞳孔反应可呈现为瞬态反应(AC)或持续反应(DC),瞬态反应的 AC 通道为离散的采样控制,持续反应的 DC 通道为连续控制。     

Import of a precursor protein into chloroplasts is inhibited by the herbicide glyphosate

Import of the precursor to 5-enolpyruvylshikimate-3-phosphate synthase (pEPSPS) into chloroplasts is inhibited by the herbicide glyphosate. Inhibition of import is maximal at glyphosate concentrations of ≥10 μm and occurs only when pEPSPS is present as a ternary complex of enzyme–shikimate-3-phosphate–glyphosate. Glyphosate alone had no effect on the import of pEPSPS since it is not known to interact with the enzyme in the absence of shikimate-3-phosphate. Experiments with wild-type and glyphosate-resistant mutant forms of pEPSPS show that inhibition of import is directly proportional to the binding constants for glyphosate. Inhibition of import is thus a direct consequence of glyphosate binding to the enzyme–shikimate-3-phosphate complex. The potential for non-specific effects of glyphosate on the chloroplast transport mechanism has been discounted by showing that import of another chloroplast-designated protein was unaffected by high concentrations of glyphosate and shikimate-3-phosphate. The mechanism of import inhibition by glyphosate is consistent with a precursor unfolding/refolding model.     

Cryogenic changes in seminal protein of cattle and buffalo

The effect of subzero temperatures on the electrophoretic pattern of seminal plasma protein of cattle and buffalo was studied. The profiles of the seminal proteins of these two closely related species differed considerably. Cattle had 11 proteins in the anodic system (pH 8.6) and none in the cathodic system (pH 4.3), while buffalo have 19 in the anodic system (pH 8.6) and 2 proteins in the cathodic system (pH 4.3). Freezing of semen at -5 degrees C for 24 h caused aggregation of seminal proteins in both species. A higher aggregation and loss of proteins were observed when freezing was done in liquid nitrogen at -196 degrees C. The effect was more pronounced in buffalo than in cattle. Loss of more seminal plasma proteins due to cryoinjury in buffalo semen may account for its poorer freezability than that of cattle semen.     

Activity of alkaline phosphatase in uterine flushings of dairy cows affected with ovarian cysts or endometritis

Both uterine horns of 14 dairy cows with ovarian follicular cysts, and four animals affected with purulent endometritis were flushed via catheter using 30 ml phosphate buffered saline, following evisceration at a local abattori. Activity in the flushing media of alkaline phosphatase (ALP) and aspartate aminotransferase (GOT) were examined. Ovaries were prepared for light microscopy. Amount and morphological integrity of luteinized tissue found on the ovaries were reflected by correspondent levels in ALP activity, which was higher in the media taken from the ipsilateral to the luteal tissue situated uterine horns (651 +/- 228 vs 244 +/- 62 u/l, n = 3). Only cows having relatively large amounts of luteal tissue on the cystic ovaries (as in luteinized follicular cysts) exhibited very high ALP activity in uterine flushings (2693 +/- 1348 u/l, n = 2). Results suggest the existence of local relationships between luteal tissue in the ovary and the ipsilateral uterine horn in cows with ovarian follicular cysts.     

Expression and Secretion of a Cellulomonas fimi Exoglucanase in Saccharomyces cerevisiae

We used the yeast MEL1 gene for secreted alpha-galactosidase to construct cartridges for the regulated expression of foreign proteins from Saccharomyces cerevisiae. The gene for a Cellulomonas fimi beta-1,4-exoglucanase was inserted into one cartridge to create a fusion of the alpha-galactosidase signal peptide to the exoglucanase. Yeast transformed with plasmids containing this construction produced active extracellular exoglucanase when grown under conditions appropriate to MEL1 promoter function. The cells also produced active intracellular enzyme. The secreted exoglucanase was N-glycosylated and was produced continuously during culture growth. It hydrolyzed xylan, carboxymethyl cellulose, 4-methylumbelliferyl-beta-d-cellobiose, and p-nitrophenyl-beta-d-cellobiose. A comparison of the recombinant S. cerevisiae enzyme with the native C. fimi enzyme showed the yeast version to have an identical K(m) and pH optimum but to be more thermostable.