Recognition of super-secondary structure in proteins

A procedure to recognize super-secondary structure in protein sequences is described. An idealized template, derived from known super-secondary structures, is used to locate probable sites by matching with secondary structure probability profiles. We applied the method to the identification of βαβ units in β/α type proteins with 75% accuracy. The location of super-secondary structure was then used to refine the original (Garnier et al., 1978) secondary structure prediction resulting in an 8.8% improvement, which correctly assigned 83% of secondary structure elements in 14 proteins. Slight modifications to the Garnier et al. method arc suggested, producing a more accurate identification of protein class and a better prediction for β/α. type proteins. A method for the incorporation of hydrophobic information into the prediction is also described.     

Identification of adenovirus 12-encoded E1A tumor antigens synthesized in infected and transformed mammalian cells and in Escherichia coli

A 16-amino acid peptide, H2N-Arg-Glu-Gln-Thr-Val-Pro-Val-Asp-Leu-Ser-Val-Lys-Arg-Pro-Arg-Cys-COOH (peptide 204), targeted to the common C-terminus of human adenovirus 12 (Ad12) tumor antigens encoded by the E1A 13S mRNA and 12S mRNA, has been synthesized. Antibody prepared in rabbits against peptide 204 immunoprecipitated two proteins of apparent Mr 47,000 and 45,000 from extracts of [35S]methionine-labeled Ad12-early infected KB cells and a 47,000 protein from extracts of the Ad12-transformed hamster cell line, HE C19. Immunoprecipitation analysis of infected and transformed cells labeled with 32Pi showed that both major Ad12 E1A T antigens are phosphoproteins. Immunofluorescence microscopy of Ad12-early infected KB cells with antipeptide antibody showed the site of E1A protein concentration to be predominantly nuclear. E1A proteins were detected by immunofluorescence at 4 to 6 h postinfection and continued to increase until at least 18 h postinfection. Antipeptide 204 antibody was used to analyze the proteins synthesized in Escherichia coli cells transformed by plasmids containing cDNA copies of the Ad12 E1A 13S mRNA or 12S mRNA under the control of the tac promoter (D. Kimelman, L. A. Lucher, M. Green, K. H. Brackmann, J. S. Symington, and M. Ptashne, Proc. Natl. Acad. Sci. U.S.A., in press). A major protein of ca. 47,000 was immunoprecipitated from extracts of each transformed E. coli cell clone. Two-dimensional gel electrophoretic analysis of immunoprecipitates revealed that the T antigens synthesized in infected KB cells, transformed hamster cells, and transformed E. coli cells possess very similar molecular weights and acidic isoelectric points of 5.2 to 5.4.     

Some characteristics of monolayers of 1-palmitoyl-2-oleoyl-phosphatidylglycerol with and without dipalmitoylphosphatidylcholine during dynamic compression and expansion

Some properties of monolayers of $\text{1-}\text{palmitoyl}\text{-2-}\text{oleoyl}\text{-sn-}\text{glycero}\text{-3-}\text{phospho}\text{-rac-}\text{glycerol}$ (POPG) alone or of POPG in mixtures with $\text{1,2-}\text{dipalmitoyl}\text{-sn-}\text{glycero}\text{-3-}\text{phosphocholine}$ (DPPC) have been measured near 35°C during dynamic compression and expansion at 3.6 cm²·s^?1. (2) The mean values of minimum surface tension (corresponding to maximum surface pressure) which could be obtained with pure POPG monolayers at high compression ranged from 15 to 18 mN·m^?1 in the presence of Na⁺, Ca²⁺ or low pH (2.0) in the subphase. (3) The presence of Ca²⁺ or low pH in the subphase increased the collapse plateau ratios obtained on cyclic compression. This might represent enhanced respreading into the monolayer of pure POPG from a collapsed form during reexpansion of the surface. (4) Monolayers containing 10% or 30% POPG and 90% or 70% DPPC could be compressed to surface tensions approaching zero. (5) In such mixed monolayers, 10% or 30% POPG did not appear to enhance respreading, as measured by collapse plateau ratios, in the presence of Na⁺ or Ca²⁺ in the subphase.     

Initial Phases of Starvation and Activity of Bacteria at Surfaces

The activity of the hydrophilic Vibrio sp. strain DW1 and the hydrophobic Pseudomonas sp. strain S9, which both undergo starvation-induced responses, was examined at nutrient-enriched and nutrient-deficient interfaces. The initial period of response to a starvation regime (“dwarfing” phase) is a sequence of two processes: fragmentation and continuous size reduction of the fragmented cells. This dwarfing phase is also one of intense metabolic activity as supported by O₂ uptake measurements of the endogenous metabolism and the use of inhibitors of the proton flow, the electron transport chain, and membrane-bound ATPase. Hydrophilic bacteria become even smaller at nutrient-deficient surfaces than in the liquid phase upon starvation, and this is reflected in a higher endogenous metabolism exhibited by surface-associated cells compared with those in the liquid phase. On the other hand, hydrophobic bacteria dwarfing at surfaces did not exhibit a greater size reduction and exhibited an endogenous metabolism that was only slightly higher than that of cells in the liquid phase. Bacterial scavenging of surface-localized nutrients is related to the degree of irreversible binding of dwarf and starved bacteria, which in turn may be related to the degree of cell surface hydrophobicity.     

Comparison of techniques for the detection of avian infectious bronchitis virus as a contaminant of vaccines

Techniques for detecting various levels of both field and vaccine strains of infectious bronchitis virus in a deliberately contaminated Newcastle disease vaccine were compared using chick embryos, chick kidney cells, chick tracheal organ cultures and chickens with a view to determining the most appropriate method for screening vaccines for freedom from IBV contamination. Techniques examined included detection of abnormalities and deaths in embryos, cytopathic effect in chick kidney cells, ciliostasis in chick tracheal organ cultures and clinical signs and virus isolation in chickens as well as the fluorescent antibody test, negative contrast electron microscopy and serology where appropriate. Results showed that the techniques capable of detecting both strains of infectious bronchitis virus were, in order of sensitivity, the fluorescent antibody test on allantoic cells from infected embryos, ciliostasis and direct electron microscopy of allantoic fluid. One surprising feature was the poor results obtained using chickens. Some detection was achieved with tracheal virus isolation and tracheal organ cultures prepared from inoculated birds and to a lesser extent with histology and clinical signs, but no technique detected the field strain.     

The mineralization and hardness of the radular teeth of the limpet Patella vulgata L.

Summary A study of the Patella vulgata radula has been made using: the scanning electron microscope in its normal and compositional contrast modes of operation, the electron microprobe analyser, ion etching with argon ions and microhardness testing.Only iron, silicon and small amounts of sulphur were detected in the radula. The teeth can be subdivided into a cusp, a junctional area where the cusp is joined to the base, and the base which is embedded in the radular membrane. From a study of longitudinal vertical and transverse sections of the mature teeth it was found that the cusp could be subdivided into a posterior iron-rich area (44–51% Fe, 1–6% Si) and an anterior silicon-rich area (22–30% Fe, 27–32% Si). The junctional zone consisted of a poorly mineralised layer at its border with the cusp and an iron-rich layer where it joined the base. The upper part of the base (5% Fe, 16% Si) could be clearly differentiated from the silicon-rich anterior and lower parts of the base (3–4% Fe, 28–35% Si). No minerals were detected in the membrane. The changes in the mineral content of the teeth cusps along the length of the radula were studied. Iron appeared in the cusps at the 25th row and the concentration increased to 28% at the 50th row. The iron was here evenly distributed throughout the cusp. Silicon appeared in the anterior part of the cusp at the 50th row and as it increased in concentration so the iron was displaced, and at the same time the concentration of iron increased in the posterior part of the cusp. Mineralization appeared to be complete by the 150th row.The teeth cusps appear to consist of 800 Å fibres grouped into 1 thick bundles and the tooth appears to be covered by a thin enamel-like layer. It is suggested that the fibres contain the silicon-rich phase and the matrix the iron-rich phase.The significance of the arrangement of the fibres and the distribution of the minerals are discussed with relation to the function of the teeth.We wish to thank Mr. A. Rees and Mr. A. Davies for their technical assistance; Prof. Lewis and Dr. James for the use of the Electron Microprobe; and the S.R.C. for their financial support.     

A neural model for conditioned avoidance learning

A mathematical model for learning of a conditioned avoidance behavior is presented. An identification of the net excitation of a neural model (Rashevsky, N., 1960.Mathematical Biophysics. Vol. II. New York: Dover Publications, Inc.) with the instantaneous probability of response is introduced and its usefulness in discussing block-trial learning performances in the conditioned avoidance situation is outlined for normal and brain-operated animals, using experimental data collected by the author. Later, the model is applied to consecutive trial learning and connection is made with the approach of H. D. Landahl (1964. “An Avoidance Learning Situation. A Neural Net Model.”Bull. Math. Biophysics,26, 83–89; and 1965, “A Neural Net Model for Escape Learning.”Bull. Math. Biophysics,27, Special Edition, 317–328) wherein lie further data with which the model can be compared.     

Exudation of amino acids by intact and damaged roots of wheat and peas

Summary Wheat and pea seedlings were grown aseptically in solution-culture and the total free amino nitrogen released by the roots was determined by a quantitative ninhydrin test. Amino nitrogen from wheat plants after 14 days growth was not detected by the test, indicating the release of less than 3 µg of amino nitrogen from a culture of 15 plants. Pea plants of the same age released from 2 to 7 µg per plant. Paper chromatograms of highly concentrated undisturbed solution-cultures revealed up to 13 amino compounds from wheat and 11 from pea. The pattern of amino acids in exudates was similar to that in crushed roots, except for an unidentified amino compound which was detected only in exuded material. The total amino nitrogen and relative proportions of several amino acids in the root exudates of sand-grown peas was influenced by several ratios of oxygen and carbon dioxide supplied to the root zone. Roots, experimentally damaged by swirling and rinsing in sand, released in 1 hour amino nitrogen of from 73 to 120 per cent of that released by normal exudation over a 2-week period. Our findings suggest that experimental and environmental root damage may be responsible for a large proportion of organic materials released by growing plant roots.Trade names are used in this publication to provide specific information. Their use does not constitute a guarantee of the products named and does not signify that they are approved by the U.S. Department of Agriculture to the exclusion of others of suitable composition.