Alignment of chain-like molecules

The steric obstruction model, that describes the enhanced alignment of folded proteins by anisotropic medium, is extended to account for the residual dipolar couplings of chain-like polypeptides. The average alignment of each chain segment is calculated from an ensemble of conformations represented by a spatial probability distribution. The segmental alignment depends on chain length, flexibility and segment's position in the chain. Residual dipolar couplings in turn depend on internuclear vector directions within each fragment. The results of calculations and simulations explain salient features of the experimental data. With this insight residual dipolar couplings can be interpreted to assess the degree of denaturation, local structures and spatial organization of weakly structured proteins.     

Refilling of a hydraulically isolated embolized xylem vessel: model calculations

When they are hydraulically isolated, embolized xylem vessels can be refilled, while adjacent vessels remain under tension. This implies that the pressure of water in the refilling vessel must be equal to the bubble gas pressure, which sets physical constraints for recovery. A model of water exudation into the cylindrical vessel and of bubble dissolution based on the assumption of hydraulic isolation is developed. Refilling is made possible by the turgor of the living cells adjacent to the refilling vessel, and by a reflection coefficient below 1 for the exchange of solutes across the interface between the vessel and the adjacent cells. No active transport of solutes is assumed. Living cells are also capable of importing water from the water-conducting vessels. The most limiting factors were found to be the osmotic potential of living cells and the ratio of the volume of the adjacent living cells to that of the embolized vessel. With values for these of 1.5 MPa and 1, respectively, refilling times were in the order of hours for a broad range of possible values of water conductivity coefficients and effective diffusion distances for dissolved air, when the xylem water tension was below 0.6 MPa and constant. Inclusion of the daily pattern for xylem tension improved the simulations. The simulated gas pressure within the refilling vessel was in accordance with recent experimental results. The study shows that the refilling process is physically possible under hydraulic isolation, while water in surrounding vessels is under negative pressure. However, the osmotic potentials in the refilling vessel tend to be large (in the order of 1 MPa). Only if the xylem water tension is, at most, twice atmospheric pressure, the reflection coefficient remains close to 1 (0.95) and the ratio of the volume of the adjacent living cells to that of the embolized vessel is about 2, does the osmotic potential stay below 0.4 MPa.     

Pellet manufacturing by extrusion-spheronization using process analytical technology

The aim of this study was to investigate the phase transitions occurring in nitrofurantoin and theophylline formulations during pelletization by extrusion-spheronization. An at-line process analytical technology (PAT) approach was used to increase the understanding of the solid-state behavior of the active pharmaceutical ingredients (APIs) during pelletization. Raman spectroscopy, near-infrared (NIR) spectroscopy, and X-ray powder diffraction (XRPD) were used in the characterization of polymorphic changes during the process. Samples were collected at the end of each processing stage (blending, granulation, extrusion, spheronization, and drying). Batches were dried at 3 temperature levels (60°C, 100°C, and 135°C). Water induced a hydrate formation in both model formulations during processing. NIR spectroscopy gave valuable real-time data about the state of water in the system, but it was not able to detect the hydrate formation in the theophylline and nitrofurantoin formulations during the granulation, extrusion, and spheronization stages because of the saturation of the water signal. Raman and XRPD measurement results confirmed the expected pseudopolymorphic changes of the APIs in the wet process stages. The relatively low level of Raman signal with the theophylline formulation complicated the interpretation. The drying temperature had a significant effect on dehydration. For a channel hydrate (theophylline), dehydration occurred at lower drying temperatures. In the case of isolated site hydrate (nitrofurantoin), dehydration was observed at higher temperatures. To reach an understanding of the process and to find the critical process parameters, the use of complementary analytical techniques are absolutely necessary when signals from APIs and different excipients overlap each other. Published: September 30, 2005     

Genome-wide selection of unique and valid oligonucleotides

Functional genomics methods are used to investigate the huge amount of information contained in genomes. Numerous experimental methods rely on the use of oligo- or polynucleotides. Nucleotide strand hybridization forms the underlying principle for these methods. For all these techniques, the probes should be unique for analyzed genes. In addition to being unique for the studied genes, the probes should fulfill a large number of criteria to be usable and valid. The criteria include for example, avoidance of self-annealing, suitable melting temperature and nucleotide composition. We developed a method for searching unique and valid oligonucleotides or probes for genes so that there is not even a similar (approximate) occurrence in any other location of the whole genome. By using probe size 25, we analyzed 17 complete genomes representing a wide range of both prokaryotic and eukaryotic organisms. More than 92% of all the genes in the investigated genomes contained valid oligonucleotides. Extensive statistical tests were performed to characterize the properties of unique and valid oligonucleotides. Unique and valid oligonucleotides were relatively evenly distributed in genes except for the beginning and end, which were somewhat overrepresented. The flanking regions in eukaryotes were clearly underrepresented among suitable oligonucleotides. In addition to distributions within genes, the effects on codon and amino acid usage were also studied.     

Some Factors Causing Mortality among Female Minks during the Puerperium and Lactation Periods

The purpose of this study, in which the farm was used as the statistical unit, was to find factors affecting mink mortality under farm conditions. Mortality was hypothesised to be affected by factors including, among others, variables describing the amount (level) and variation in composition and quality of the feed. Other explanatory variables applied in the study included farm size and age. Factor analyses were performed for variables of feed composition and quality in order to condense the variable information and to facilitate the selection of explanatory variables. This report presents a preliminary regression model for female mink mortality factors describing feed level and variation, and farm size, as explanatory variables. The regression model emphasized among other factors the importance of a constant albumin quality and a constant energy level.     

Whitefish stocking in acidified lakes: ecological and physiological responses

In autumn 1986, six small lakes at different stages of acidification were stocked with one-summer-old whitefish, Coregonus pallasi Valenciennes 1848, in order to see whether whitefish stocking would be a suitable method for the mitigation of acidification effects. In two of the lakes the introduction was a complete failure: the whitefish did not survive, evidently due to high acidity and high aluminium concentrations of the lake waters. In one of the most acidified lakes (pH 4.3–4.8, Al_lab 29–125 g 1^–1) and in two less acidic lakes (pH 5.0–5.2 and 5.4–6.4), introduction was successful. Three years after the introduction, the mean weights of the fish in those three lakes were 580, 250 and 360 g respectively, with the weight and also the condition factor of stocked whitefish being highest in the most acidified lake. In that lake there were few or no fish present during the introduction, whereas in the less acid lakes there were dense populations of perch and therefore a potential interspecific competition for food. Different availability of food in the lakes was presumed to be the main reason for the growth differences. Plasma Na⁺ and Cl^– concentrations of whitefish were lower in the acidic lakes than in the lake with pH around 6 three years after stocking. This suggests that, despite the good growth and highest condition factor of whitefish in the most acid lake, the fish still experienced some acid stress.