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.     

Deoxyribose conformation in [d(GTATATAC)]2: evaluation of sugar pucker by simulation of double-quantum-filtered COSY cross-peaks

Exchangeable and nonexchangeable proton and phosphorus resonances (11.75 T) of [d(GTATATAC)]2 in aqueous solution were assigned by using proton two-dimensional nuclear Overhauser effect (2D NOE) spectra, homonuclear proton double-quantum-filtered COSY (2QF-COSY) spectra, proton spin-lattice relaxation time measurements, and 31P1H heteronuclear shift correlation spectra. Due to the large line widths, it was not possible to directly extract vicinal proton coupling constant values from any spectrum including ECOSY or 2QF-COSY. However, comparison of quantitative 2QF-COSY spectral simulations with experimental spectra enabled elucidation of coupling constants. The scope and limitations of this approach were explored by computation and by use of experimental data. It was found that proton line widths exhibit some variability from one residue to the next as well as from one proton to the next within a residue and the exact line width is critical to accurate evaluation of coupling constants. Experimental 2QF-COSY spectra were not consistent with a rigid deoxyribose conformation for any of the nucleotide residues. A classical two-state model, with rapid jumps between C2'-endo (pseudorotation angle P = 162 degrees) and C3'-endo (P = 9 degrees) conformations, was able to account for the spectral characteristics of terminal residue sugars: 60% C2'-endo and 40% C3'-endo. However, the 2QF-COSY cross-peaks from the -TATATA- core could be simulated only if the classical two-state model was altered such that the dominant conformer had a pseudorotation angle at 144 degrees instead of 162 degrees. In this case, the major conformer amounted to 80-85%. Alternatively, the spectral data were consistent with a three-state model in which C2'-endo and C3'-endo conformations had the largest and smallest populations, respectively, but a third conformer corresponding to C1'-exo (P = 126 degrees) was present, consistent with recent molecular dynamics calculations. This alternative yielded populations of 50% (P = 162 degrees), 35% (P = 126 degrees), and 15% (P = 9 degrees) for the -TATATA- sugars. The spectral results indicate little variation of sugar pucker between T and A. Small differences in cross-peak component intensities and characteristic spectral distortions, however, do suggest some unquantified variation. 31P1H heteronuclear chemical shift correlation spectra manifested alternating chemical shifts and coupling constants suggestive of phosphodiester backbone conformational differences between TA and AT junctions.     

Efferent neurons of the lateral-line system and the VIII cranial nerve in the brainstem of anurans

Summary The octavo-lateral efferent system of several anuran species was studied by means of retrograde transport of horseradish peroxidase. This system is organized similarly in all larval anurans and in all adult aglossids. All have two groups of efferent neurons in the nucleus reticularis medialis between the VIIIth and the IXth motor nucleus. The caudal group consists of efferent neurons that supply the posterior lateral-line nerve (NLLp) and a considerably smaller group of neurons supplying both the NLLp and the anterior lateral-line nerve (NLLa). The rostral group is composed of efferent neurons supplying the NLLa, neurons projecting to the inner ear and neurons supplying both the inner ear and the NLLa. Efferent neurons of the VIIIth cranial nerve exhibit a rostrocaudal cytoarchitectonic differentiation. Caudal perikarya, which are rounder in shape than those of the rostral part, have a dendritic projection to the superior olive. It is suggested that this differentiation reflects a functional differentiation of acoustic and vestibular efferent neurons.Labeled neurons were ipsilateral to the site of application of HRP. None were found in the vestibular nuclei or in the cerebellum.Efferent axons projecting to neuromasts of the NLLa leave the medulla with the VIIth nerve, axons projecting to neuromasts of the NLLp exit via the IXth nerve. Cell counts and the observation of axonal branching revealed that efferent units of both the lateral-line and the VIIIth-nerve system supply more than one receptor organ. In contrast to the lateral-line system, dendrites of efferent neurons of the VIIIth nerve project dorsally onto its nuclei, and afferents of the VIIIth nerve project onto efferent neurons. These structures most probably represent a feedback loop between the afferent and efferent systems of the VIIIth cranial nerve.     

Isolation and characterization of a genomic sequence of maize coding for a zein gene

Summary An EcoRI restriction endonuclease fragment of maize DNA coding for the 19,000 dalton zein protein was cloned in phage gt WES. The zein gene was identified by the electron microscopic analysis of RNA-DNA hybrids (R-loops) and DNA-DNA hybrids (D-loops). The R-loops were formed with poly(rA)-containing RNA isolated from 18 days post-pollination maize endosperm and showed no intervening non-hybridizing sequences (introns) within their 800 base length. A cDNA clone specific for the 19,000 dalton zein protein formed D-loops in the same position and orientation as the R-loops. The cloned fragment measured 4.4 kilobases (kb), the same size as an EcoRI fragment of maize DNA revealed by Southern analysis.     

Photosynthesis and transpiration ofPinus radiata D. Don under natural conditions in a forest stand

Summary Gas-exchange ofPinus radiata foliage was measured with climatised cuvettes under natural light in the sun-crown of 8 m tall trees in a forest stand. Measurement began during a period of drought (_WS –8.2 bar, _We –10.5 bar) and continued after elimination of soil moisture-deficit by watering (_WS –0.5 bar, _We –5.5 bar). Soil and air moisture-deficits severely restricted gas-exchange. Watering resulted in an immediate decline in stomatal resistance (r _s ) and an increase in net photosynthesis (P _N ) of 13%. A slower progressive gas-exchange recovery occurred additionally during the 10 days after watering leading to a further decline inr _s to 3 s cm^-1 and an ultimate increase inP _N of 38% when measured under comparable conditions at 8 mb v.p.d. Radiata pine had a high photosynthetic capacity with a measured maximumP _N of 10.2 mg CO₂ dm^-2 h^-1 total needle surface (11.4 mg CO₂ g^-1 DM h^-1).Optimum temperature forP _N in March (late summer) occurred at ca. 18°C. Rate ofP _N was 95% saturated at irradiance of 900 E m^-2 s^-1 and 50% saturated at only 270 E m^-2 s^-1. Radiata pine needles responded directly to changes in atmospheric humidity by adjusting their stomatal diffusive resistance. As a result, between 8 and 18 mb v.p.d.P _N declined by 2.3% mb^-1 increase.     

Production of 3-acetoxyscirpene-4,15-diol from anguidine (4,15-diacetoxyscirpene-3-ol) by Fusarium oxysporum f.sp. vasinfectum.

Growing cells of Fusarium oxysporum f.sp. vasinfectum (ATCC 7808) formed 3-acetoxyscirpene-4,15-diol from anguidine (4,15-diacetoxyscirpene-3-ol) by way of the intermediates triacetoxyscirpene, 3,4-diacetoxyscirpene-15-ol and 3,15-diacetoxyscirpene-4-ol. The new 3-acetoxy analog was found to be less active than anguidine and the other monoacetoxy derivatives when tested against a series of fungal strains and against HeLa cells in vitro.     

The interaction of RNA polymerase and lac repressor with the lac control region.

We have examined the interactions of lac repressor and RNA polymerase with the DNA of the lac control region, using a method for direct visualization of the regions of DNA protected by proteins from DNAase attack. The repressor protects the operator essentially as reported by Gilbert and Maxam (1) with some small modifications. However, the evidence reported here concerning the binding of RNA polymerase to the DNA of the promoter mutant UV5 indicates that : 1) the RNA polymerase molecule binds asymmetrically to the promoter DNA, 2) RNA polymerase protects DNA sequences to within a few bases of the CAP binding site, suggesting direct interaction between polymerase and the CAP protein at this site, 3) RNA polymerase still binds to the promoter when repressor is bound to the operator, but fails to form the same extensive complex.     

Die Morphologie der Schleimsekretion im Fruchtknoten vonAptenia cordifolia

Zusammenfassung Der Fruchtknoten vonAptenia cordifolia enthÄlt wÄhrend der Samenentwicklung einen proteinreichen Polysaccharidschleim. Verschieden alte schleimproduzierende Placentarpapillen werden einer elektronenmikroskopischen Analyse unterzogen. Kurz vor dem Einsetzen der Schleimproduktion ist das rauhe ER noch spÄrlich entwickelt. Der Golgi-Apparat ist unauffÄllig und wenig aktiv. Zu Beginn der Schleimbildung sind als hauptsÄchliche Strukturkomponenten hypersekretorische Dictyosomen und ER-umschlossene Vakuolen (storage vesicles) zu beobachten. Es wird angenommen, da\ diese Komplexe aus rauhem ER und vermutlich mitèinander verschmolzenen Golgi-Vesikeln die charakteristischen Synthese-Einheiten für den Polysaccharid-Protein-Schleim darstellen, da sie nachweislich neben Polysacchariden auch Proteine enthalten. Membranfusionen zwischen Vesikeln und dem Plasmalemma deuten auf Exocytose-Prozesse unter Beteiligung des Golgi-Apparates hin. Daneben wird eine holocrine Ausscheidung des in den storage vesicles zunÄchst gespeicherten Polysaccharid-Protein-Schleimes bei Degeneration des Protoplasten vermutet.

---

Morphology of slime secretion in the seed vessels ofAptenia cordifolia

Summary During seed development the gynaeceum ofAptenia cordifolia produces a mucilage rich in carbohydrates and protein. The mucilage-producing placentary papillae are analyzed in different developmental stages by electron microscopy. Just before mucilage production is started, the rough ER occurs but sparsely. At that time the dictyosomes are inconspicuous and of low activity. When mucilage production commences, one can observe hypersecretory dictyosomes and ER-ensheathed vacuoles (storage vesicles) as the main structural components. It is suggested that the complexes of rough ER and probably fused Golgi vesicles are the synthetizing units of the carbohydrate protein mucilage, since in these complexes both components can be identified cytochemically. Fusion sites of plasmalemma and vesicles indicate processes of exocytosis-probably involving the Golgi apparatus. In addition, a holocrine excretion of the mucilage initially enclosed in the storage vesicles via degeneration of the protoplast is assumed.

     

Diagnosis and Treatment of Amanita Phalloides-Type Mushroom Poisoning: Use of Thioctic Acid

The number of cases of mushroom poisoning is increasing as a result of the increasing popularity of “wild” mushroom consumption. Amanitin and phalloidin cytotoxins found in some Amanita and Galerina species produce the most severe and frequent life-threatening symptoms of Amanita phalloidestype poisoning. Delay in onset of symptoms, individual susceptibility variation and lack of rapid and reliable identification have contributed to the significant morbidity and mortality of this type of poisoning.A rapid chromatographic assay for identifying the potent cytotoxins and apparently successful management using thioctic acid of two cases of A. phalloides-type mushroom poisoning are reported. All known cases of A. phalloides-type mushroom poisoning treated with thioctic acid in the United States are summarized.     

Populations- und syn?kologische Modelle in der Ornithologie

Ohne Zusammenfassung

---

Population models and synecological models in ornithology