Analysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks

Summary Global relations between RNA sequences and secondary structures are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of allGC andAU sequences with chain lengths up to 30. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based on statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them that ofneutral networks (being sets of sequences folding into the same structure). Exhaustive enumeration allows to test several previously suggested relations: the number of (minimum free energy) secondary structures as a function of the chain length as well as the frequency distribution of structures at constant chain length (commonly resulting in generalized forms ofZipf's law).

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Analyse der Beziehungen zwischen RNA-Sequenzen und Sekundärstrukturen durch vollständige Faltung, 1. Mitt. Faltung, Neutrale Netzwerke

Zusammenfassung Die globalen Benziehungen zwischen RNA-Sequenzen und Sekundärstrukturen werden als Abbildungen aus einem Raum aller Sequenzen in einen Raum aller Strukturen aufgefaßt. Diese Abbildungen werden durch Falten aller binären Sequenzen desGC-undAU-Alphabets mit Kettenlängen bis zun=30 untersucht. Die berechneten Strukturdaten werden durch vollständiges Abzählen ausgewertet und als eine exakte Referenz zum Überprüfen analytischer Resultate aus mathematischen Modellen sowie zum Testen statistisch erhobener Proben verwendet. Einige neuartige Konzepte zur Beschreibung der Beziehungen zwischen Sequenzen und Strukturen werden eingehend untersucht, unter ihnen der Begriff derneutralen Netzwerke. Ein neutrales Netzwerk besteht aus allen Sequenzen, die eine bestimmte Struktur ausbilden. Vollständiges Abzählen ermöglicht beispielsweise die Bestimmung aller Strukturen minimaler freier Energie in Abhängigkeit von der Kettenlänge ebenso wie die Bestimmung der Häufigkeitsverteilungen der Strukturen bei konstanten Kettenlängen. Die letzteren folgen einer verallgemeinerten FormZipfschen Gesetzes.

     

P588, A SECOND RETINAL-CONTAINING PIGMENT IN HALOBACTERIUM HALOBIUM

Abstract— Halobacterium mutant strains with defects in the biosynthesis of various pigments have been isolated. One of these strains, mutant ET-15, is incapable of producing the light-driven proton pump bacteriorhodopsin and the carotenoid bacterioruberin. However, ET-15 synthesizes another photochemically active, retinal-containing pigment, P₅₈₈, which mediates light-induced proton uptake enhanced by uncouplers. P₅₈₈ and bacteriorhodopsin are simultaneously present in wild-type cells grown under normal conditions; however, they can be distinguished by the following criteria.

• 1 They can be separated by independent mutational events.
• 2 Proton ionophores such as FCCP diminish bacteriorhodopsin-driven proton translocation but enhance P₅₈₈-mediated proton flows. We define here proton translocations which can be diminished by the addition of uncouplers (e.g. FCCP) as ‘active’, others which can be enhanced by FCCP as ‘passive’.
• 3 The kinetic and spectral properties of the photocycle intermediates of bacteriorhodopsin and P₅₈₈ are different.
• 4 The action spectrum for photocycling of P₅₈₈ is red-shifted with respect to that for bacteriorhodopsin.

A comparison of action spectra for proton translocations with that for photocycling links pigment P₅₈₈ and light-driven, passive proton uptake by ET-15 envelope vesicles. When chemically bleached P₅₈₈ was regenerated with all-trans-retinal, both photochemical activity and light-induced proton inflow were restored to equal extents. This identifies P₅₈₈ with the energizer for the passive proton flows.     

1,2-Dialkoxyacenaphthylenes and 2,3,11,12-bis-(1,2-acenaphtho)-[18]crown-6

A general synthesis of 1,2-dialkoxyacenaphthylenes by dehydrogenation of the corresponding acenaphthene derivatives with high potential quinones is described. The new crown ether, 2,3,11,12-bis(1,2-acenaphtho)-[18]crown-6, 1, is obtained by this route. The surprisingly poor complexing ability of 1 is ascribed to electronic and geometrical effects of the acenaphthylene rings as shown by spectroscopic and voltammetric data and the crystal structure of the free ligand 1.     

An integral representation for decomposable measures of measurable functions

Summary We start with a measurem on a measurable space (,A), decomposable with respect to an Archimedeant-conorm on a real interval [0,M], which generalizes an additive measure. Using the integral introduced by the second author, a Radon-Nikodym type theorem, needed in what follows, is given.The integral naturally leads to a -decomposable measurem on the space of all measurable functions from to [0, 1]. The main result of the present paper is the converse of this, namely that, under natural conditions, any -decomposable measurem on can be represented as an integral of a certain Markov-kernelK. We extend this representation to measures on which have values in a set of distribution functions.These results generalize the work done by the first author in the case of additive measures.     

CEMS and DCEMS investigations of Al-implanted iron

-Fe surfaces were implanted with a nominal dose of 5×10¹⁷ Al ions/cm² at 50 keV and a current density of about 3.7 A/cm². Samples of different shapes and thicknesses have been used in order to test the influence of heat flow from specimen to target holder during implantation. Integral and energy differential (depth-selective)⁵⁷Fe conversion electron Mössbauer spectroscopy (CEMS and DCEMS) were employed. The spectra indicated a magnetic phase characterised by a broad hyperfine field distributionP(B _hf), a non-magnetic phase, and -Fe. The relative intensity of the non-magnetic phase was enhanced if the thermal contact during implantation became worse. An energy dependence of DCEM spectra in the L-electron range was observed. Model calculations using L-electron weight functions and experimental concentration profiles obtained by secondary neutral mass spectroscopy (SNMS) yielded fair agreement between calculated and experimental phase signals. The results demonstrate that the non-magnetic Fe-Al alloy phase with high Al concentration is located closer to the surface than the magnetic alloy phase, which extends to much larger depth than expected.