Differences in the interaction of Escherichia coli RNase P RNA with tRNAs containing a short or a long extra arm.

The phosphorothioate footprinting technique was applied to the investigation of phosphate moieties in tRNA substrates involved in interactions with M1 RNA, the catalytic subunit of Escherichia coli RNase P. In general agreement with previous data, all affected sites were localized in acceptor stem and T arm. But the analyzed examples for class I (Saccharomyces cerevisiae pre-tRNA(Phe) with short variable arm) and class II tRNAs (E. coli pre-tRNA(Tyr) with large variable arm) revealed substantial differences. In the complex with pre-tRNA(Phe), protection was observed at U55, C56, and G57, along the top of the T loop in the tertiary structure, whereas in pre-tRNA(Tyr), the protected positions were G57, A58, and A59, at the bottom of the T loop. These differences suggest that the size of the variable arm affects the spatial arrangement of the T arm, providing a possible explanation for the discrepancy in reports about the D arm requirement in truncated tRNA substrates for eukaryotic RNase P enzymes. Enhanced reactivities were found near the junction of acceptor and T stem (U6, 7, 8 in pre-tRNA(Phe) and G7, U63, U64 in pre-tRNA(Tyr)). This indicates a partial unfolding of the tRNA structure upon complex formation with RNase P RNA.     

Example of a system which is computation universal but not effectively programmable

The incorporation of a chaotic component in a computing system is incompatible with its being effectively programmable. The example presented shows that concepts of programming suitable for biological systems may differ from those which have grown out of our experience with present day digital computers.     

Polar lobe formation and cytokinesis in fertilized eggs of Ilyanassa obsoleta: III. Large bleb formation caused by Sr2+, ionophores X537A and A23187, and compound 4880

Fertilized eggs of Ilyanassa obsoleta form a protuberance which resembles a normal polar lobe when injected with Sr²⁺ or Ca²⁺ by microiontophoresis. Eggs also form a lobe-like protuberance when exposed to any of three drugs: compound $\text{48}\text{80}$, ionophore X537A, and ionophore A23187. Protuberances form more quickly and at lower drug concentrations if additional exogenous Ca²⁺ is added, whereas higher concentrations of Mg²⁺ do not have such an effect. When eggs are exposed to these drugs in Ca²⁺-, Mg²⁺-“free” seawater, with or without 10 mM EDTA, the eggs are still able to undergo extensive shape changes and form protuberances. Drug-induced shape changes are prevented by cytochalasin B, but will still occur in the presence of colchicine. Approximately 75% of Ilyanassa eggs are capable of forming and resorbing their third polar lobe and undergoing cytokinesis in Ca²⁺-, Mg²⁺-“free” artificial seawater (even containing 10 mM EDTA), solutions which by atomic absorption spectroscopy are shown to contain low concentrations of Ca²⁺ (3–5 μM) and Mg²⁺ (1.0–3.5 μM). The data suggest that if Ca²⁺ is required for normal polar lobe formation and cytokinesis, it is derived from intracellular sources or is required in only very low exogenous concentrations (i.e., less than 10^?2 μM free Ca²⁺, in the presence of 10 mM EDTA).     

Effects of temperature on the size and shape of Escherichia coli cells

Two substrains of Escherichia coli B/r were grown to steady-state in batch cultures at temperatures between 22 and 42° C in different growth media. The size and shape of the cells were measured from light and electron micrographs and with the Coulter channelizer. The results indicate that cells are shorter and somewhat thicker at the lower temperatures, especially in rich growth media; cell volume is then slightly smaller. A lower temperature was further found to increase the relative duration of the constriction period. The shapes of the cell size distributions are indistinguishable, indicating that the pattern of growth of the cells is the same at all temperatures. The adaptation of the cells to a temperature shift lasted several generations, indicating that the morphological effects of temperature are mediated by the cell's physiology.     

Rapidly-secreting,cultured oat cells serve as a model system for the study of cellular exocytosis. Characterization of cells and isolated secretory vesicles

Summary Callus-derived suspension cultures of oats dramatically increase the viscosity of the culture media after one month in culture. Colorimetric assays for sugars and protein, as well as measurements of viscosity, suggest that the released material is a long-chain polysaccharide, probably a pectinaceous substance. These cells grow slowly in liquid culture, yet despite their low cell density, they are able to increase the viscosity of the media several fold within seven days after media transfer. Ultrastructural observations show that oat cells have features common to actively-secreting cells; especially evident are numerous dictyosomes with hypertrophied cisternae. Using a combination of filtering and centrifugation techniques we were able to recover large numbers of intact secretory vesicles. The interior of the vesicles stain with periodic acid-silver hexamine, and colormetric analysis of the vesicle pellet for total sugars confirms the presence of polysaccharides in this vesicle fraction. Because of the uniformity of these cells, the high rate of secretion, and the accessability of a large vesicle population, this culture system is'a useful model for studying the secretory process in plant cells.Scientific Article No. A-3128, Contribution No. 6196 of the Maryland Agricultural Experiment Station, College Park, MD.     

Levels of indole-3-acetic acid in intact and decapitated coleoptiles as determined by a specific and highly sensitive solid-phase enzyme immunoassay

A specific solid-phase enzyme immunoassay for the detection of as little as 3–4 pg of indole-3-acetic acid (IAA) is described. The assay involves minimal procedural efforts and requires only standard laboratory equipment. Up to 50 samples in triplicate, processed simultaneously, can be assayed and evaluated in 2.5 h. As little as 1 mg oat coleoptile tissue is sufficient for a quantitative IAA analysis and little or no extract purification is necessary. Using this assay, levels of IAA have been determined in coleoptiles of maize and oat. The distribution of IAA within single coleoptiles was quantitated and the production of IAA during the regeneration of the physiological tip in Avena coleoptiles was investigated. The changes in levels of IAA and other major phytohormones were quantitated during the growth of oat coleoptiles.Abbreviations ABA abscisic acid - BHT butylated hydroxytoluene - BSA bovine serum albumin - IAA indole-3-acetic acid - TBS Trishydroxymethylaminomethane buffered saline Part 21 in the series Use of Immunoassay in Plant Science     

Limits on the computing power of biological systems

The theory of computational complexity and certain explicitly-stated hypotheses imply limitations on the information processing power of biological systems. Parallelism, special purpose organization, and analog mechanisms may provide speedup critical for life processes, but have little power in the face of exponential growth. We show that “polynomially simulatable” biological systems cannot exhibit dynamic behavior which produces the solution of an intractable problem. The argument implies that parallelism does not allow biological systems to defeat the exponential explosion, but rather is important because it allows polynomial time algorithms to be used more efficiently.