Subunit polypeptide composition of rubisco and the origin of allopolyploid Arabidopsis suecica (Brassicaceae)

The polypeptide composition of the large and small subunits of Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) from Arabidopsis thaliana, A. suecica and Cardaminopsis arenosa have been studied by IEF (isoelectric focusing) analysis. The putative recent alopolyploid origin of A. suecica is supported. The chloroplast encoded large subunits served to identify solely A. thaliana as the maternal parent whereas the nuclear encoded small subunits indicate C. arenosa as the paternal species.     

NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes

The explosion of bioinformatics technologies in the form of next generation sequencing (NGS) has facilitated a massive influx of genomics data in the form of short reads. Short read mapping is therefore a fundamental component of next generation sequencing pipelines which routinely match these short reads against reference genomes for contig assembly. However, such techniques have seldom been applied to microbial marker gene sequencing studies, which have mostly relied on novel heuristic approaches. We propose NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA for short), a fast and highly accurate novel method enabling reference-based marker gene matching (picking Operational Taxonomic Units, or OTUs). NINJA takes advantage of the Burrows-Wheeler (BW) alignment using an artificial reference chromosome composed of concatenated reference sequences, the “concatesome,” as the BW input. Other features include automatic support for paired-end reads with arbitrary insert sizes. NINJA is also free and open source and implements several pre-filtering methods that elicit substantial speedup when coupled with existing tools. We applied NINJA to several published microbiome studies, obtaining accuracy similar to or better than previous reference-based OTU-picking methods while achieving an order of magnitude or more speedup and using a fraction of the memory footprint. NINJA is a complete pipeline that takes a FASTA-formatted input file and outputs a QIIME-formatted taxonomy-annotated BIOM file for an entire MiSeq run of human gut microbiome 16S genes in under 10 minutes on a dual-core laptop.     

Benzylpenicillin-induced filament formation of Clostridium perfringens

Growth of Clostridium perfringens with low concentrations of benzylpenicillin inhibited septum formation and division of the organisms. This resulted in continued growth of the organisms as aseptate filaments. The effect was reversed on removal of the antibiotic. The composition of walls isolated from organisms grown with the antibiotic was similar to that of walls from untreated bacteria. In addition, both contained non-N-acetylated glucosamine residues in their peptidoglycan. No differences were detected in the degree of cross-linkage of peptidoglycan. Clostridium perfringens contains six membrane-associated penicillin-binding proteins (PBPs) which have different affinities for [3H]benzylpenicillin. Concentrations of the antibiotic which were sufficient to cause filamentation of apparently all organisms in a culture caused almost complete saturation of PBPs 3, 4, 5 and 6. At these concentrations there was no measurable interaction with PBPs 1 and 2. Thus interaction of the antibiotic with the lower molecular weight PBPs is correlated with the inhibition of septum formation in C. perfringens.     

X-ray diffraction and time-resolved fluorescence analyses of Aequorea green fluorescent protein crystals

The energy transfer protein, green fluorescent protein, from the hydromedusan jellyfish Aequorea victoria has been crystallized in two morphologies suitable for x-ray diffraction analysis. Hexagonal plates have been obtained in the P6122 or P6522 space group with a = b = 77.5, c = 370 A, and no more than three molecules per asymmetric unit. Monoclinic parallel-epipeds have been obtained in the C2 space group with a = 93.3, b = 66.5, c = 45.5 A, beta = 108 degrees, and one molecule per asymmetric unit. The monoclinic form is better suited for use in a structure determination, and a data set was collected from the native crystal. Time-resolved fluorescence measurements of large single crystals are possible due to the unique, covalently bound chromophore present in this molecule. Fluorescence emission spectra of Aequorea green fluorescent protein in solution and from either the hexagonal or monoclinic single crystal show similar profiles suggesting that the conformations of protein in solution and in the crystal are similar. Multifrequency phase fluorimetric data obtained from a single crystal were best fit by a single fluorescence lifetime very close to that exhibited by the protein in solution. The complementary structural data obtained from fluorescence spectroscopy and x-ray diffraction crystallography will aid in the elucidation of this novel protein's structure-function relationship.     

Das pyroelektrische Verhalten und das permanente elektrische Moment von menschlichem und tierischem Sehnengewebe

Zusammenfassung Bei menschlichem und tierischem Sehnengewebe wurde pyroelektrisches Verhalten festgestellt. Pyroelektrisches Verhalten bedeutet, daß eine permanente makroskopische elektrische Polarisation und somit ein permanentes elektrisches Moment in Richtung der pyroelektrischen Achse vorhanden ist.Die pyroelektrische (und daher auch piezoelektrische) Achse verläuft in der Längsrichtung der Sehnenfasern bzw. ihrer Kollagenfibrillen. Sie stimmt überein mit der optischen Faserachse, in deren Verlauf positiv einachsige Doppelbrechung bekannt ist. Sehnen mit leidlicher Parallelausrichtung ihrer Faserbündel zeigen dementsprechend makroskopisch eine pyroelektrische Achse parallel zur physiologischen Sehnenlängsachse. Bei seilartiger Bündelung der Fibrillen oder anderen histologischen Unregelmäßigkeiten im Faserverlauf zeigen sich korrespondierende Unregelmäßigkeiten des pyroelektrischen Achsenverlaufs.In genau korrespondierenden Abschnitten der gleichen Sehne verschiedener Individuen fand sich eine sehr erhebliche biologische Streubreite der pyro- und piezoelektrischen Effekte.In situ hatte das permanente elektrische Moment der untersuchten menschlichen und Rinder-Sehnen, sowie der Schwanzsehnen von Ratten eine festliegende gleichsinnige Vektorrichtung bei allen Individuen. Die Vektorrichtung war bei den untersuchten korrespondierenden Sehnen von Mensch und Rind sowie bei den Rattenschwanz-Sehnen analog.Die Vektorrichtung der permanenten elektrischen Polarisation bei Sehnengewebe, und wahrscheinlich auch bei anderen kollagenhaltigen Strukturen, scheint in Beziehung zur morphogenetischen Entwicklungsrichtung der Tiere zu stehen.

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Summary Tendons are pyroelectric. Pyroelectrical behaviour is identical with a permanent electrical moment in the direction of the pyroelectrical axis. There exists a pyroelectrical (and consequently also piezoelectrical) axis corresponding to the longitudinal axis of the tendon fibres and their collagen fibrils, and also corresponding to their optical axis, in the direction of which a positive birefringence is known.Accordingly in tendons with an approximately parallel alignment of the collagen fibres the pyroelectrical (and piezoelectrical) axis corresponds to the physiological longitudinal tendon axis. In rope-like or any other histological irregular forms of the collagen fibre alignment corresponding irregularities of the electrical axis direction were found.The pyro- and piezoelectric effects show large biological variations in corresponding tendons of different individuals.In situ the permanent electrical moment in the examined tendons of men and ox and of rat-tail respectively is always in the same vector direction in each individual. This vector direction is analogical in all examined corresponding tendons of men, ox, and also in rat-tail. The permanent electrical moment of tendons (as well as of other collagen-containing tissues) seems to correspond to the morphogenetical development axis of animals.The results of this investigation may be understood by the assumption that the rod-like collagen molecule (i.e. tropocollagen) represents an electrical dipole with a permanent electrical moment in the longitudinal direction of the rod.

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Unterstützt durch Sachbeihilfen der Deutschen Forschungsgemeinschaft.