Analysis of starch amylolysis using plots for first-order kinetics

Investigators often study product release from starches during prolonged incubations with α-amylase in vitro. The reaction time courses usually fit to a linear form of a first order rate equation, i.e., ln[(C_∞ − C_t)/C_∞] = −kt. This equation calls for an accurate estimate of C_∞, i.e., the concentration of product at the end of the reaction. Estimates of C_∞ from digestibility curves can be unreliable. The Guggenheim method does not require prior knowledge of C_∞ but seems not to have been applied to starch hydrolysis data. An alternative method is also available in which the logarithm of the slope (LOS) of a digestibility curve at various time points is plotted against time. This allows estimations of both k and C_∞ and can also reveal whether changes occur in digestion rate from rapid to slow as digestion proceeds. We describe the Guggenheim and LOS methods and provide examples of their application to starch digestibility data.     

Ligand bias in receptor tyrosine kinase signaling

Ligand bias is the ability of ligands to differentially activate certain receptor signaling responses compared with others. It reflects differences in the responses of a receptor to specific ligands and has implications for the development of highly specific therapeutics. Whereas ligand bias has been studied primarily for G protein–coupled receptors (GPCRs), there are also reports of ligand bias for receptor tyrosine kinases (RTKs). However, the understanding of RTK ligand bias is lagging behind the knowledge of GPCR ligand bias. In this review, we highlight how protocols that were developed to study GPCR signaling can be used to identify and quantify RTK ligand bias. We also introduce an operational model that can provide insights into the biophysical basis of RTK activation and ligand bias. Finally, we discuss possible mechanisms underpinning RTK ligand bias. Thus, this review serves as a primer for researchers interested in investigating ligand bias in RTK signaling.     

Revisiting the Ramachandran plot based on statistical analysis of static and dynamic characteristics of protein structures

Ramachandran plots, which describe protein structures by plotting the dihedral angle pairs of the backbone on a two-dimensional plane, have played an important role in structural biology over the past few decades. However, despite continued discovery of new protein structures to date, the Ramachandran plot is still constructed by only a small number of data points, and further it cannot reflect the steric information of proteins. Here, we investigated the secondary structure of proteins in terms of static and dynamic characteristics. As for static feature, the Ramachandran plot was revisited for the dataset consisting of 9,148 non-redundant high-resolution protein structures released in the protein data bank until April 1, 2022. By calculating amino acid propensities, it was found that the proportion of secondary structures with respect to residue depth is directly related to their hydrophobicity. As for dynamic feature, normal mode analysis (NMA) based on an elastic network model (ENM) was carried out for the dataset using our KOSMOS web server (http://bioengineering.skku.ac.kr/kosmos/). All ENM-based NMA results were stored in the KOSMOS database, allowing researchers to use them in various ways. In this process, it was commonly found that high B-factors appeared at the edge of the alpha helix region, which was elucidated by introducing residue depth. In addition, by investigating the change in dihedral angle, it was possible to quantitatively survey the contribution of structural change of protein on the Ramachandran plot. In conclusion, our statistical analysis of protein characteristics will provide insight into a range of protein structural studies.     

A graphical method for determining inhibition constants

A new simple graphical method is described for the determination of inhibition type and inhibition constants of an enzyme reaction without any replot. The method consists of plotting experimental data as (V–v)/v versus the inhibitor concentration at two or more concentrations of substrate, where V and v represent the maximal velocity and the velocity in the absence and presence of inhibitor with given concentrations of the substrate, respectively. Competitive inhibition gives straight lines that converge on the abscissa at a point where [I]?=??K_i. Uncompetitive inhibition gives parallel lines with the slope of 1/K’_i. For mixed type inhibition, the intersection in the plot is given by [I]?=??K_i and (V–v)/v?=??K_i/K’_i in the third quadrant, and in the special case where K_i?=?K’_i (noncompetitive inhibition) the intersections occur at the point where [I]?=??K_i and (V–v)/v?=??1. The present method, the “quotient velocity plot,” provides a simple way of determining the inhibition constants of all types of inhibitors.     

Species composition and above ground phytomass in chalk grassland with different management

During the last decades chalk grasslands lost their agricultural importance in the greater part of their distribution area in W Europe. Due to their botanical richness a number of chalk grassland sites were established as Nature Reserve. As a consequence of the semi-natural character of these grasslands an appropriate management is necessary to maintain or to re-create this vegetation including a great number of rare and endangered species.This paper deals with the results of three different management practices, viz. mowing in autumn, sheep grazing and abandoning, of a medium term (8–11 yr) permanent plot experiment. Sheep grazing was considered the best management since it resulted in the highest number of species, phanerogams as well as bryophytes, and the highest number of characteristic chalk grassland species. Abandoning resulted in a decrease in species number and a dominance of a few species only.The changes in species number are related to the above ground biomass. Under the canopy in the abandoned plot light intensity and the Red/Far-red ratio are very low, which partly explains the decrease in species number as such conditions are not favourable to seedling emergence and survival.Plant nomenclature follows Heukels & Van Ooststroom (1975) for phanerogams, Margadant & During (1976) and van der Wijk et al. (1969) for bryophytes, and Westhoff & den Held (1969) for syntaxa.Presented at the Symposium on Vegetation Dynamics, organized by the International Society for Vegetation Science at Montpellier, 15–20 September 1980. I am grateful to Dr. H. J. During for useful comments.     

Orientational polarisability of lipid membrane surfaces

Here we present a fluorescence method based on the Stokes shift of the voltage-sensitive dye di-8-ANEPPS to quantify the orientational polarisability of lipid membrane surfaces, i.e. the polarisability due to molecular reorientation. Di-8-ANEPPS is already an established probe of membrane dipole potential. Its use, therefore, as a probe of both the dipole potential and orientational polarisability allows a direct comparison of these two properties in an identical region of the lipid bilayer. We applied the new technique on phosphatidylcholine vesicles to study the effects of different degrees of hydrocarbon saturation and of the incorporation of cholesterol and some of its oxidized derivatives. We found that lipids with unsaturated chains had a lower orientational polarisability than those with saturated chains. This could be explained by a reduction in membrane dipole potential as a result of a decrease in lipid packing density. Cholesterol derivatives were found to either increase or decrease the orientational polarisability depending on their molecular structure. The varying effects could be explained by antagonistic effects of the dipole potential and membrane order, which are both changed to varying degrees by the cholesterol derivatives and which lead to increases and decreases in orientational polarisability, respectively.     

Reconstructing the history of log-drifting in the Reichraminger Hintergebirge, Austria

The watersheds of the rivers Enns and Steyer border the Reichraminger Hintergebirge. This area has a long tradition in the iron processing industry. Because mineral coal was not available, charcoal has been produced for the iron industry for the past 500 years, leading to a heavy exploitation of the vast forests (180 km²).

From the logging sites in the mountains the timber had to be transported up to 12 km to the forges in the lowland. Most of the small rivers had insufficient water to drift logs efficiently. Therefore, at gorges or at places where there were narrow steep sided valleys wooden dams (klausen) were built to block the water, using the first cut trees of a newly targeted harvesting area. By abruptly opening the dams, the rapid flow of the raised water level carried the logs to the next klausen. Up to seven klausen were built in a valley before the rechen (rake-like grids within the river to collect the logs) of the Enns and Steyer were reached.

To reconstruct the history of log drifting in the Reichraminger Hintergebirge, 33 klausen and rechen were visited and dendrochronologically sampled. The remaining wood of the dam constructions showed progressive stages of degradation, and in some cases only a few logs remained preserved under the water. With cores from living trees added to the dataset, master chronologies were established for spruce (576 years), fir (569 years) and larch (342 years). The construction history of the klausen can be sequentially traced back to 1563 AD. The time spans of the individual chronologies varied between 40 and 392 years. All available conifer species were utilized to build the dams, except during the 19th century, when the most suitable species - larch - was used to a higher degree.     

Uniformly minimum variance unbiased estimators in split plot designs

Explicit forms of the uniformly minimum variance unbiased estimators (UMVUE) of estimable linear functions of the fixed effects and the UMVUE of variance components in the fixed linear normal model of the complete randomized block design in which there are several levels of plots splitting are found.