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.     

Monitoring and control of biotechnological production processes by Bio-FET-FIA-sensors

Summary Single and multisensor field effect transistors (FET) with a pH-sensitive Si/SiO₂/Si₃N₄/Ta₂O₅-gate and reference electrode (for single sensor) were developed and used for manufacturing the following biological (Bio)-FETs: for glucose analysis, glucose oxidase-FET (GOD-FET); for urea analysis, urease-FET; and for cephalosporin C analysis, cephalosporinase-FET. The GOD-FETs were integrated into flow injection analysis (FIA) of the Eppendorf variables analyser (EVA) system and used for monitoring the glucose concentration in microbial cultivation and production processes with recombinant Escherichia coli K12 MF, recombinant E. coli JM103, Saccharomyces cerevisiae H620, and Candida boidinii. Urease-FET-FIA was used to monitor the urea concentration in a simulated cultivation of Cephalosporium acremonium and urease-FET-FIA and GOD-FET-FIA for the monitoring of urea and glucose concentrations in simulated S. cerevisiae cultivations.     

Acoustic orientation in adult, female crickets (Gryllus bimaculatus de Geer) after unilateral foreleg amputation in the larva

Summary InGryllus bimaculatus females one foreleg was amputated at the coxa-trochanter joint in the 2nd, 4th or 8th/9th larval instar. A leg of up to normal length is regenerated (Fig. 1) but it lacks a functional ear. In spite of the, usually shorter, regenerated foreleg, the adult one-eared crickets show no impairments in walking when tested on a locomotion compensator. Without sound they walk erratically and most of them weakly circle towards the intact side (Fig. 2).With calling song presentation three response types can be distinguished:tracking (Fig. 3A), hanging on (Fig. 3B) or continuouscircling towards the intact side (Fig. 3C, D). Turning tendencies in monaurals increase with song intensity and exceed those of intact and bilaterally operated animals (Fig. 4). Course deviations towards the intact side also slightly increase with intensity (Fig. 5). Course stability is reduced compared to that of intact animals but exceeds that of bilaterally operated crickets (Figs. 5, 6). It is best at 60 dB and deteriorates at higher sound intensities (Fig. 6). The percentage of monaurals tracking or hanging on decreases with increasing intensity (Fig. 7B). Tracking is established in most animals but it is limited to a narrow intensity range (Fig. 7A, C). Apart from an increased percentage of tracking after early operations (Fig. 7D), there are no prominent changes in orientational parameters with the date of foreleg amputation.Reamputation of the regenerated leg in the adult monaurals does not significantly impair acoustic orientation (Figs. 8, 9), but occlusion of the ipsilateral prothoracic spiracle does (Figs. 10, 11).An attempt is made to correlate the behavioral performance with the activity of auditory interneurons which have undergone morphological and physiological changes (Fig. 12).     

The influence of animals on phosphorus cycling in lake ecosystems

Aquatic animals directly influence the cycling of phosphorus in lakes through feeding and excretion. Traditionally, animals (zooplankton, benthic invertebrates and fish) have been assigned only minor roles in the process of freshwater phosphorus cycling. They were regarded as consumers without much regulating influence. Today there is growing evidence that animals, predators and herbivores, directly or indirectly can control biomass of primary producers and internal cycling of phosphorus.This paper summarizes different mechanisms of transformation and translocation of phosphorus via different groups of organisms.     

Nutrient composition,ruminal degradability and whole tract digestibility of whole crop maize silage from nine current varieties

Since maize silage is an important forage in cattle nutrition, it is important to know its nutritive value. Much effort is put into breeding maize, and several new varieties are introduced on the market every year. This requires periodical analyses of the nutritive value of current maize varieties for the formulation of cattle rations. The aim of this study was to examine the nutritive value of whole crop maize silage (WCMS) from nine maize varieties in 3 consecutive years. For the analysis of nutrient composition and ruminal degradability of organic matter (OM), crude protein (CP), neutral detergent fibre (aNDFom) and non-fibre carbohydrates (NFC), varieties were harvested at three harvest dates (50%, 55% and 60% dry matter content in ear). Due to capacity limitations, the digestibility of WCMS was tested only for the middle harvest date. The CP and acid detergent fibre (ADFom) content was affected (p < 0.05) while aNDFom and NFC content was not influenced by variety. With advancing maturity, CP, aNDFom and ADFom content declined while NFC content increased. Variety influenced effective ruminal degradability (ED) of nutrients, except for CP. The ED of all examined nutrients decreased as maturity advanced from first to third harvest date. Digestibility of OM, ADFom and NFC was significantly and digestibility of aNDFom was tendentially (p = 0.064) influenced by variety. Additionally, an effect of year and a harvest date × year interaction was found for almost all examined parameters. In conclusion, variety, harvest date and year influence the nutritive value of WCMS. A comparison with earlier studies shows that current varieties have a higher fibre digestibility and a slower-ripening stover compared to older varieties.     

Structure, dynamics and domain organization of the repeat protein Cin1 from the apple scab fungus

Venturia inaequalis is a hemi-biotrophic fungus that causes scab disease of apple. A recently-identified gene from this fungus, cin1 (cellophane-induced 1), is up-regulated over 1000-fold in planta and considerably on cellophane membranes, and encodes a cysteine-rich secreted protein of 523 residues with eight imperfect tandem repeats of ~60 amino acids. The Cin1 sequence has no homology to known proteins and appears to be genus-specific; however, Cin1 repeats and other repeat domains may be structurally similar. An NMR-derived structure of the first two repeat domains of Cin1 (Cin1-D1D2) and a low-resolution model of the full-length protein (Cin1-FL) using SAXS data were determined. The structure of Cin1-D1D2 reveals that each domain comprises a core helix-loop-helix (HLH) motif as part of a three-helix bundle, and is stabilized by two intra-domain disulfide bonds. Cin1-D1D2 adopts a unique protein fold as DALI and PDBeFOLD analysis identified no structural homology. A (15)N backbone NMR dynamic analysis of Cin1-D1D2 showed that a short stretch of the inter-domain linker has large amplitude motions that give rise to reciprocal domain-domain mobility. This observation was supported by SAXS data modeling, where the scattering length density envelope remains thick at the domain-domain boundary, indicative of inter-domain dynamics. Cin1-FL SAXS data models a loosely-packed arrangement of domains, rather than the canonical parallel packing of adjacent HLH repeats observed in α-solenoid repeat proteins. Together, these data suggest that the repeat domains of Cin1 display a "beads-on-a-string" organization with inherent inter-domain flexibility that is likely to facilitate interactions with target ligands.     

Organization of the superficial neuromast system in goldfish, Carassius auratus

Distribution, morphology, and orientation of superficial neuromasts and polarization of the hair cells within superficial neuromasts of the goldfish (Carassius auratus) were examined using fluorescence labeling and scanning electron microscopy. On each body side, goldfish have 1,800-2,000 superficial neuromasts distributed across the head, trunk and tail fin. Each superficial neuromast had about 14-32 hair cells that were arranged in the sensory epithelium with the axis of best sensitivity aligned perpendicular to the long axis of the neuromast. Hair cell polarization was rostro-caudal in most superficial neuromasts on trunk scales (with the exception of those on the lateral line scales), or on the tail fin. On lateral line scales, the most frequent hair cell polarization was dorso-ventral in 45% and rostro-caudal in 20% of the superficial neuromasts. On individual trunk scales, superficial neuromasts were organized in rows which in most scales showed similar orientations with angle deviations smaller than 45 degrees . In about 16% of all trunk scales, groups of superficial neuromasts in the dorsal and ventral half of the scale were oriented orthogonal to each other. On the head, most superficial neuromasts were arranged in rows or groups of similar orientation with angle deviations smaller than 45 degrees . Neighboring groups of superficial neuromasts could differ with respect to their orientation. The most frequent hair cell polarization was dorso-ventral in front of the eyes and on the ventral mandible and rostro-caudal below the eye and on the operculum.     

Current perspectives in pulmonary surfactant — Inhibition, enhancement and evaluation

Pulmonary surfactant (PS) is a complicated mixture of approximately 90% lipids and 10% proteins. It plays an important role in maintaining normal respiratory mechanics by reducing alveolar surface tension to near-zero values. Supplementing exogenous surfactant to newborns suffering from respiratory distress syndrome (RDS), a leading cause of perinatal mortality, has completely altered neonatal care in industrialized countries. Surfactant therapy has also been applied to the acute respiratory distress syndrome (ARDS) but with only limited success. Biophysical studies suggest that surfactant inhibition is partially responsible for this unsatisfactory performance. This paper reviews the biophysical properties of functional and dysfunctional PS. The biophysical properties of PS are further limited to surface activity, i.e., properties related to highly dynamic and very low surface tensions. Three main perspectives are reviewed. (1) How does PS permit both rapid adsorption and the ability to reach very low surface tensions? (2) How is PS inactivated by different inhibitory substances and how can this inhibition be counteracted? A recent research focus of using water-soluble polymers as additives to enhance the surface activity of clinical PS and to overcome inhibition is extensively discussed. (3) Which in vivo, in situ, and in vitro methods are available for evaluating the surface activity of PS and what are their relative merits? A better understanding of the biophysical properties of functional and dysfunctional PS is important for the further development of surfactant therapy, especially for its potential application in ARDS.     

Detection of microsatellite instability during somatic embryogenesis of oak (Quercus robur L.)

Five microsatellite loci (QpZAG1/5, QpZAG9, QpZAG36, MSQ4, MSQ13) were used to test for genetic stability of three somatic embryogenic culture lines of Quercus robur L. and plantlets derived therefrom. DNA variation was detected among somatic embryos within all embryogenic lines, whereas no genetic instability was found among the regenerated plants. Two microsatellite loci revealed variation, and a locus-dependent instability was observed. The most polymorphic and useful microsatellite locus for detecting genetic variation was QpZAG9, with 28.5% of the investigated loci being variable.