Base-pair probability profiles of RNA secondary structures

Dynamic programming algorithms are able to predict optimal andsuboptimal secondary structures of RNA. These suboptimal oralternative secondary structures are important for the biologicalfunction of RNA. The distribution of secondary structures presentin solution is governed by the thermodynamic equilibrium betweenthe different structures. An algorithm is presented which approximatesthe total partition function by a Boltzmann–weighted summationof optimal and suboptimal secondary structures at several temperatures.A clear representation of the equilibrium distribution of secondarystructures is derived from a two-dimensional bonding matrixwith base–pairing probability as the third dimension.The temperature dependence of the equilibrium distribution givesthe denaturation behavior of the nucleic acid, which may becompared to experimental optical denaturation curves after correctionfor the hypochromicities of the different base-pairs. Similarly,temperature-induced mobility changes detected in temperature-gradientgel electrophoresis of nucleic acids may be interpreted on thebasis of the temperature dependence of the equilibrium distribution.Results are illustrated for natural circular and synthetic linearpotato spindle tuber viroid RNA respectively, and are comparedto experimental data.     

Spatial distribution of resting stages,rate of emergence from diapause and times to adulthood and to the appearance of the first clutch in 3 species of cyclopoid copepods

The spatial distribution of dormant copepodids of 3 species of cyclopoid copepods — Cyclops vicinus, Mesocyclops leuckarti and Thermocyclops crassus — was studied in 4 small lakes in South Germany. The rate of emergence from diapause and times from the resting stage to adulthood and from adulthood to the appearance of the first clutch was studied at 4 constant temperatures (5, 10, 15, 20 °C) in the laboratory. Resting stages of C. vicinus were always concentrated in the deepest parts of the lakes and were found relatively deep in the mud. M. leuckarti- and T. crassus-copepodids preferred shallow areas in deep lakes but were concentrated in the deep areas in shallow lakes. Copepodids of both species were always concentrated in the uppermost mud layers.Rate of emergence from diapause was strongly temperature-dependent. At high temperatures (20 °C) copepodids of all species under study emerged within 2 weeks. At lower temperatures C. vicinus copepodids showed the highest rate of emergence. At 5 to 10 °C only few M. leuckarti- and T. crassus-copepodids had emerged after the investigation period (7 weeks). Both C. vicinus and T. crassus showed the highest rate of emergence at the natural end of diapause but even at that time only few T. crassus-copepodids emerged at 5 °C. Times to adulthood at 5 °C were shortest in C. vicinus. At higher temperatures this species was passed by M. leuckarti. Times from adulthood to the appearance of the first clutch at 5–15 °C were shortest in C. vicinus. T. crassus produced no clutch at 5 and 10 °C.     

The effect of temperature on the development,reproduction, and longevity of two common cyclopoid copepods — Eucyclops serrulatus (Fischer) and Cyclops strenuus (Fischer)

The embryonic and postembryonic development times, time interval between clutches, and longevity of two common cyclopoid copepods — Eucyclops serrulatus and Cyclops strenuus — were studied at constant temperatures (5°, 10°, 15°, 20° and 25 °C), using algae and protozoans as food. Both, E. serrulatus and C. strenuus showed a considerable temperature tolerance and adaptability. Embryonic development times were similar in both species but postembryonic development times were shorter in E. serrulatus. Time intervals between successive clutches were relatively variable at all temperatures in both species. Longevity was shorter in E. serrulatus than in C. strenuus. The embryonic and postembryonic development of E. serrulatus was short relative to that of littoral copepods; the development of C. strenuus was similar or shorter than that of other species of the genus Cyclops.     

Effect of pH and butyrate concentration on the production of acetone and butanol by Clostridium acetobutylicum grown in continuous culture

Summary When Clostridium acetobutylicum was grown in continuous culture under glucose limitation at neutral pH and varying dilution rates the only fermentation products formed were acetate, butyrate, carbon dioxide and molecular hydrogen. The Y _glucose ^max and (Y _ATP ^max ) _gluc ^exp values were 48.3 and 23.8 dry weight/mol, respectively. Acetone and butanol were produced when the pH was decreased below 5.0 (optimum at pH 4.3). The addition of butyric acid (20 to 80 mM) to the medium with a pH of 4.3 resulted in a shift of the fermentation from acid, to solvent formation.A preliminary report of part of this work was presented at a symposium Trends in the Biology of Fermentations for Fuels and Chemicals held December 7–11, 1980, at Brookhaven National Laboratory, Upton, New York; Gottschalk and Bahl 1981     

Necessary and sufficient conditions for Von Kries chromatic adaptation to give color constancy

Necessary and sufficient spectral conditions are presented for Von Kries chromatic adaptation to give color constancy. Von-Kries-invariant reflectance spectra are computed for illuminant spectral power distributions that are arbitrary linear combinations of the first three daylight phases. Experiments are suggested to test models of color constancy using computed spectra (either exact or approximate) within the illuminant-invariant framework.     

Isolation and identification of spirorenone metabolites from the monkey (Macaca fascicularis)

The plasma level of spirorenone was determined 3 h after 1, 8, 22 and 46 daily oral administrations of 20 mg/kg to two female and two male monkeys ($\text{Macaca fascicularis}$). A fifth animal, female, was treated with eight daily doses of tritium-labelled drug and was completely bled from the carotid vein 4 h after the last administration in order to isolate and identify plasma metabolites.After repeated daily doses of spirorenone the mean plasma level of unchanged drug was 711 ± 213 ng/ml. In the plasma of the fifth animal four radioactively labelled compounds could be detected after extraction and subsequent HPLC separation. Mass spectrometric identification of three of the substances indicated 1,2-dihydrospirorenone, hydroxy-1,2-dihydrospirorenone and the unchanged drug itself.     

Phytochrome control of plastid mRNA in mustard (Sinapis alba L.)

The steady-state levels of plastid RNA sequences in dark-grown and light-grown mustard (Sinapis alba L.) seedlings have been compared. Total cellular RNAs were labeled in vitro with ³²P and hybridized to separated restriction fragments of plastid DNA. Cloned DNA fragments which encode the large subunit (LS) of ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxylase (dimerizing), EC 4.1.1.39] and a 35,000 plastid polypeptide were used as probes to assess the levels of these two plastid mRNAs. The 1.22-kilobase-pair mRNA for the 35,000 polypeptide is almost undetectable in dark-grown seedlings, but is a major plastid mRNA in light-grown seedlings. The hybridization analysis of RNA from seedlings which were irradiated with red and far-red light indicates that the level of this mRNA, but not of LS mRNA, is controlled by phytochrome.Abbreviations LS large subunit - RuBP ribulose-1,5-bisphosphate - ptDNA plastid DNA     

Hemoglobins,XLVIIII

Summary Hagfish hemoglobin has three main components, one of which is Hb III. It is monomeric and consists of 148 amino acid residues (M = 17 350). Its complete primary structure, previously published, is discussed here. The proximal amino acid (F8) of the heme linkage is histidine as always in the hemoglobins, but the regularly expected distal histidine E7 is substituted by glutamine. This substitution, leading to a new kind of heme linkage, has hitherto only been demonstrated in opossum hemoglobin. It is suggested that E7, Gln, is directed out of the heme pocket, and that the adjacent Ell, Ile, is directed toward the inside of the pocket, giving the distal heme contact instead of histidine.Myxine Hb III has an additional tail of 9 amino acid residues at its N-terminal end, as has the hemoglobin ofLampetra fluviatilis. The genetic codes ofMyxine andLampetra hemoglobins show 117 differences, in spite of many morphological resemblances between hagfish and lamprey. Their primary hemoglobin structures show differences substantial enough to bo compatible with the divergence of the two families some 400–500 million years ago.     

In Vitro Release of Endogenous β- Alanine, GABA, and Glutamate, and Electrophysiological Effect of β-Alanine in Pigeon Optic Tectum

The efflux of 20 amino acids, induced by either high K+ concentration or veratrine, was determined in pigeon tectal slices. Ca2+-dependent, K+-induced release of beta-alanine, gamma-aminobutyric acid (GABA), and glutamate was observed. Veratrine caused release of the same amino acids plus glycine in a tetrodotoxin-sensitive manner. beta-Alanine had a strong inhibitory effect on the activity of tectal neurons which was blocked by strychnine but not by bicuculline. The results indicated a transmitter function for beta-alanine in the optic tectum, and were consistent with the previously proposed transmitter role of GABA and glutamate in this structure.