A neutral pH thermal hydrolysis method for quantification of structured RNAs

Riboswitch aptamers adopt diverse and complex tertiary structural folds that contain both single-stranded and double-stranded regions. We observe that this high degree of secondary structure leads to an appreciable hypochromicity that is not accounted for in the standard method to calculate extinction coefficients using nearest-neighbor effects, which results in a systematic underestimation of RNA concentrations. Here we present a practical method for quantifying riboswitch RNAs using thermal hydrolysis to generate the corresponding pool of mononucleotides, for which precise extinction coefficients have been measured. Thermal hydrolysis can be performed at neutral pH without reaction quenching, avoids the use of nucleases or expensive fluorescent dyes, and does not require generation of calibration curves. The accuracy of this method for determining RNA concentrations has been validated using quantitative ³¹P-NMR calibrated to an external standard. We expect that this simple procedure will be generally useful for the accurate quantification of any sequence-defined RNA sample, which is often a critical parameter for in vitro binding and kinetic assays.     

Mechanisms of chromosome banding

A thorough understanding of the mechanisms of R-, C-and G-banding will come only from studies of the binding of Giemsa dyes to isolated and characterized preparations of heterochromatin and euchromatin. Since such studies require an exact knowledge of the optical characteristics of Giemsa, the spectral adsorption curves and extinction coefficients of Giemsa and its component dyes at various concentrations in the presence and absence of DNA were determined. — Although Giemsa is a complex mixture of thiazin dyes plus eosin; methylene blue, and azure A, B or C alone gave good banding. Thionin, with no methyl groups, gave poor or no banding. Eosin was not a necessary component for banding. — The most striking characteristic of the thiazin dyes is that they are strongly metachromatic, i.e., their adsorption spectra and extinction coefficients change as the concentration of the dye increases or as they bind to positively charged compounds (chromotropes). These changes, especially for methylene blue, are described in detail and allow a distinction between concentration dependent binding to DNA by intercalation and binding by side stacking.     

Spectral analysis for base composition of DNA undergoing melting

A microcomputer-controlled spectrophotometer is described for obtaining the base composition of melting domains in DNA from derivative melting curves. Values have been determined for the differential molar extinction coefficients for the A-T and G-C base pair at the three wavelengths most useful for spectral analysis of base composition, 260, 270 and 282 nm. The average RMS error for these values was 29 l(mol X cm)-1 for the melting of 14 DNA specimens ranging in base composition from 0-0.72 F(G + C). A precision of approximately 1% in base composition of domains is possible. Such analysis is useful for confirming or establishing assignments of domains to particular subtransitional features in high resolution melting curves.     

用碱水解的方法测定蛋白质的消光系数

在蛋白质结构与功能的研究中,有时蛋白质溶液的浓度是一个重要的参数.紫外吸收法是测定蛋白质溶液浓度最为常用的方法,而已知蛋白质的消光系数是用紫外吸收法准确测定蛋白质溶液浓度的前提条件.在0.1 mol/L NaOH溶液中,蛋白质发生碱性水解,因而蛋白质溶液可以看作是色氨酸和酪氨酸的二元体系.以此为依据,给出了用碱水解的方法测定蛋白质消光系数的方法.这一方法操作步骤简便易行,蛋白质消光系数的计算公式简单明了.用这一碱水解的方法分别测定了几种氨基酸组成不同的蛋白质的消光系数,与文献数据对照,得到了令人满意的结果,测定误差均小于±5％.     

Quantification of Art v 1 and Act c 1 being major allergens of mugwort pollen and kiwi fruit extracts in mass-units by ion-exchange HPLC-UV method

A simple ion-exchange HPLC-UV method was developed for determination of major allergens from mugwort pollen and kiwi fruit extracts in mass-units. The separation of Art v 1 and Act c 1 from other components in the extracts was achieved in one step. The extinction coefficients used in the study were theoretically determined and compared to the extinction coefficients determined by gravimetry. We also reported a close correlation of the major allergen contents with the overall allergenic potency of the extracts determined by inhibition ELISA. This method could be a useful tool for standardization of allergenic extracts for clinical use.     

Revised UV extinction coefficients for nucleoside-5'-monophosphates and unpaired DNA and RNA

Ultraviolet absorption provides the nearly universal basis for determining concentrations of nucleic acids. Values for the UV extinction coefficients of DNA and RNA rely on the mononucleotide values determined 30-50 years ago. We show that nearly all of the previously published extinction coefficients for the nucleoside-5'-monophosphates are too large, and in error by as much as 7%. Concentrations based on complete hydrolysis and the older set of values are too low by approximately 4% for typical RNA and 2-3% for typical DNA samples. We also analyzed data in the literature for the extinction coefficients of unpaired DNA oligomers. Robust prediction of concentrations can be made using 38 microg/A260 unit for single-stranded DNA (ssDNA) having non-repetitive sequences and 40-80% GC. This is superior to currently used predictions that account for nearest-neighbor frequency or base composition. The latter result in concentrations that are 10-30% too low for typical ssDNA used as primers for PCR and other similar techniques. Methods are described here to accurately measure concentrations of nucleotides by nuclear magnetic resonance. NMR can be used to accurately determine concentrations (and extinction coefficients) of biomolecules within 1%.     

Simple computer method for evaluation of lateral diffusion coefficients from fluorescence photobleaching recovery kinetics.

A method is presented for the analysis of fluorescence photobleaching recovery curves. Based on the simplified kinetic expression of Yguerabide, J., J.A. Schmidt, and E.E. Yguerabide (1982, Biophys. J., 40:69-75), a linearization procedure is described that permits unequivocal determination of all diffusion parameters. The presence of additional membrane flow or multiple diffusion coefficients can easily be detected by this method, and simple corrections for the presence of these alternative recovery processes can be made by the use of a regular mini-computer. The validity of the method is tested on simulated recovery curves, varying the contribution of flow, multiple diffusion coefficients, and statistical noise due to counting error.     

Extinction,diversity and survivorship of taxa in the fossil record

Using data drawn from large-scale databases, a number of interesting trends in the fossil record have been observed in recent years. These include the average decline in extinction rates throughout the Phanerozoic, the average increase in standing diversity, correlations between rates of origination and extinction, and simple laws governing the form of survivorship curves and the distribution of the lifetimes of taxa. In this paper we derive a number of mathematical relationships between these quantities and show how these different trends are interrelated. We also derive a variety of constraints on the possible forms of these trends, such as limits on the rate at which extinction may decline and limits on the allowed difference between extinction and origination rates at any given time.     

Molecular extinction coefficients of lead sulfide and polymerized diaminobenzidine as final reaction products of histochemical phosphatase reactions.

Molar extinction coefficients of precipitated lead sulfide (PbS) and polymerized diaminobenzidine (polyDAB) have been determined at wavelengths of 450 nm and 480 nm, respectively, for quantitative histochemical analysis of phosphatase reactions. These values are essential for the conversion of cytophotometric (mean integrated) absorbance values to absolute units of substrate converted per unit time and volume of tissue. This conversion allows direct comparison of histochemical and biochemical data. The molar extinction coefficient of PbS at 450 nm was found to be 3,800 and therefore, per mole phosphate liberated, the molar extinction coefficient is 5,700 because 3 moles phosphate are captured by 2 moles lead at neutral or alkaline pH. Parallel experiments with the cerium-DAB method revealed that the molar extinction coefficient of polyDAB at 480 nm is 5,500 with respect to liberated phosphate. The molar extinction coefficients were applied for comparison of data from biochemical and histochemical assays of glucose-6-phosphatase activity in rat livers. A significant correlation was found between both sets of data. The values were in the same order of magnitude with histochemical values approximately 1.4 times higher than biochemical values.     

USING PHYLOGENETIC TREES TO STUDY SPECIATION AND EXTINCTION

One tool in the study of the forces that determine species diversity is the null, or simple, model. The fit of predictions to observations, good or bad, leads to a useful paradigm or to knowledge of forces not accounted for, respectively. It is shown how simple models of speciation and extinction lead directly to predictions of the structure of phylogenetic trees. These predictions include both essential attributes of phylogenetic trees: lengths, in the form of internode distances; and topology, in the form of internode links. These models also lead directly to statistical tests which can be used to compare predictions with phylogenetic trees that are estimated from data. Two different models and eight data sets are considered. A model without species extinction consistently yielded predictions closer to observations than did a model that included extinction. It is proposed that it may be useful to think of the diversification of recently formed monophyletic groups as a random speciation process without extinction.     

Investigating age‐dependency of species extinction rates using dynamic survivorship analysis

Survivorship curves with taxon lifespans normalised to variations in the real‐time extinction rate (the ‘Corrected Survivorship Score’ technique) are plotted for various fossil groups. Of five groups tested at the ‘species level’ (strictly speaking, Linnean morphospecies), only the calcareous nannoplankton are found to have had a constant extinction probability with respect to morphospecies age. The planktonic foraminifer, trilobite, conodont and graptolite data all show a significant age‐dependent effect (convexity of survivorship curves), which reveals in each case a progressively increasing extinction probability as morphospecies became older. This effect is found to be much reduced for trilobite genera and absent for ammonoid families, suggesting that age‐dependency of extinction probability is primarily a characteristic of the species level in some, but not all groups. However, the pattern may be partly an artefact of taxonomic methodology. Morphospecies range data, which are gathered primarily for biostratigraphic purposes, are far from ideal for the purpose of survivorship analysis. Therefore, survivorship curves for a specially‐developed lineage phylogeny of Palaeogene planktonic foraminifera are also presented. These do not indicate a similar age‐dependency to the extinction probability with respect to either the terminal or non‐terminal lineages.     

Rapid determination of enzyme kinetics from fluorescence: overcoming the inner filter effect

Fluorescence change is convenient for monitoring enzyme kinetics. Unfortunately, it loses linearity as the absorbance of the fluorescent substrate increases with concentration. When the sum of absorbance at excitation and emission wavelengths exceeds 0.08, this inner filtering effect (IFE) alters apparent initial velocities, K(m), and k(cat). The IFE distortion of apparent initial velocities can be corrected without doing fluorophore dilution assays. Using the substrate's extinction coefficients at excitation and emission wavelengths, the inner filter effect can be modeled during curve fitting for more accurate Michaelis-Menten parameters. A faster and simpler approach is to derive k(cat) and K(m) from progress curves. Strategies to obtain reliable and reproducible estimates of k(cat) and K(m) from only two or three progress curves are illustrated using matrix metalloproteinase 12 and alkaline phosphatase. Accurate estimates of concentration of enzyme-active sites and specificity constant k(cat)/K(m) (from one progress curve with [S]相似文献   

Quantitative determination of individual teicoplanin components in human plasma and cerebrospinal fluid by high-performance liquid chromatography with electrochemical detection

We have developed a simple, rapid and highly sensitive method for determining a plasma or cerebrospinal fluid (CSF) concentrations of individual teicoplanin components using reversed-phase high-performance liquid chromatography followed by electrochemical detection. A linear relationship was observed between concentrations and peak heights for the teicoplanin concentration range of 0.025-10microg/mL. The correlation coefficients of all standard curves were greater than or equal to 0.999. The limit of detection for the major component of teicoplanin was 1.0ng/mL (signal/noise ratio >3). Daily fluctuations of standard curves (n=5) were small, with coefficients of variation of 3.3%. The intra-assay precision was 5.9% (n=5). Inter-assay precision ranged from 2.6 to 6.8%. The method described here is suitable for clinical monitoring of teicoplanin levels in plasma or CSF level and for use in studies involving pharmacokinetics of individual teicoplanin component.     

Statistical determination of the average values of the extinction coefficients of tryptophan and tyrosine in native proteins.

Spectroscopic measurement of protein concentration requires knowledge of the value of the relevant extinction coefficient. If the amino acid composition of a protein is known, however, extinction coefficients can be calculated approximately, provided that the values of the molar absorptivities for tryptophan and tyrosine residues in the protein are known. We have applied a matrix linear regression procedure and a mapping of average absolute deviations between experimental and calculated values to find molar extinction coefficients (epsilon M, 1 cm, 280 nm) of 5540 M-1 cm-1 for tryptophan and 1480 M-1 cm-1 for tyrosine residues in an "average" protein, as defined by a set of experimentally determined extinction coefficients for more than 30 proteins. Use of these values provides a significant improvement in extinction coefficient estimation over that obtained with the commonly used values obtained from solutions of model compounds in guanidine-HCl. The consistency of these results when compared to the large deviations often observed between experimentally determined extinction coefficients suggest that this method may offer acceptable accuracy in the initial estimation of molar absorptivities of globular proteins.     

Simplification traps

When experiments are analyzed with simple functions, one gets simple results. A trap springs when experiments show deviations from the expected simplicity. When kinetic experiments do not follow exponential curves, they simply are not of the first or pseudofirst order. They can and have to be calculated on the base of plausible reaction schemes. When dose–response curves are analyzed with logistic functions (“4-parameter fit”) and give Hill coefficients different from one, this is an experimental result stating that more than one molecule is involved in eliciting the response. If one ignores that result, one usually finds forgiving referees, but one will loose real money when one tries to develop such an unspecific compound into a drug.

Electronic supplementary material

The online version of this article (doi:10.1007/s12154-011-0069-3) contains supplementary material, which is available to authorized users.     

A STUDY OF THE BACTERICIDAL ACTION OF ULTRA VIOLET LIGHT : III. THE ABSORPTION OF ULTRA VIOLET LIGHT BY BACTERIA

The simple conclusion of former investigators that the shorter the wave length of ultra violet light the greater the bactericidal action is in error. A study with measured monochromatic energy reveals a characteristic curve of bactericidal effectiveness with a striking maximum between 260 and 270 m.µ. The reciprocal of this abiotic energy curve suggests its close relation to specific light absorption by some single essential substance in the cell. Methods are described for determining the absorption curve, or absorption coefficients, of intact bacteria. These curves for S. aureus and B. coli have important points of similarity and of difference with the reciprocals of the curves of bactericidal incident energy, and point the way in a further search for the specific substance, or substances, involved in the lethal reaction.     

Chaotic dynamics may determine the effect of inter-patch migration on metapopulation survival

A simple, strategic model of a system of habitat fragments connected by conservation corridors is presented. The intrinsic dynamics of the population on each fragment are stochastic. In addition, at each generation there is a probability of a catastrophic event occurring which affects all the habitat fragments by greatly reducing the size of the population on each. Global extinction is considered to occur when all the populations simultaneously fall below a threshold value. If the intrinsic dynamics on each fragment are simple cycles or a stable equilibrium, then the addition of conservation corridors does not reduce the frequency of global extinction. This is because migration between fragments induces their populations to have values which are similar to each other. However, if the intrinsic population dynamics are chaotic then the probability of global extinction is greatly reduced by the introduction of conservation corridors. Although local extinction is likely, the chaos acts to oppose the synchronising effect of migration. Often a subset of the populations survive a catastrophe and can recolonize the other patches.     

A sharp threshold for disease persistence in host metapopulations

A sharp threshold is established that separates disease persistence from the extinction of small disease outbreaks in an S→E→I→R→S type metapopulation model. The travel rates between patches depend on disease prevalence. The threshold is formulated in terms of a basic replacement ratio (disease reproduction number), ?(0), and, equivalently, in terms of the spectral bound of a transmission and travel matrix. Since frequency-dependent (standard) incidence is assumed, the threshold results do not require knowledge of a disease-free equilibrium. As a trade-off, for ?(0)>1, only uniform weak disease persistence is shown in general, while uniform strong persistence is proved for the special case of constant recruitment of susceptibles into the patch populations. For ?(0)<1, Lyapunov's direct stability method shows that small disease outbreaks do not spread much and eventually die out.     

EXPLOSIVE EVOLUTIONARY RADIATIONS: DECREASING SPECIATION OR INCREASING EXTINCTION THROUGH TIME?

A common pattern in time-calibrated molecular phylogenies is a signal of rapid diversification early in the history of a radiation. Because the net rate of diversification is the difference between speciation and extinction rates, such "explosive-early" diversification could result either from temporally declining speciation rates or from increasing extinction rates through time. Distinguishing between these alternatives is challenging but important, because these processes likely result from different ecological drivers of diversification. Here we develop a method for estimating speciation and extinction rates that vary continuously through time. By applying this approach to real phylogenies with explosive-early diversification and by modeling features of lineage-accumulation curves under both declining speciation and increasing extinction scenarios, we show that a signal of explosive-early diversification in phylogenies of extant taxa cannot result from increasing extinction and can only be explained by temporally declining speciation rates. Moreover, whenever extinction rates are high, "explosive early" patterns become unobservable, because high extinction quickly erases the signature of even large declines in speciation rates. Although extinction may obscure patterns of evolutionary diversification, these results show that decreasing speciation is often distinguishable from increasing extinction in the numerous molecular phylogenies of radiations that retain a preponderance of early lineages.     

Graphical analysis of mass and anisotropy changes observed by plasmon-waveguide resonance spectroscopy can provide useful insights into membrane protein function

Plasmon-waveguide resonance spectroscopy is a recently developed optical method that allows characterization of mass and structural changes in two-dimensionally ordered thin films (e.g., proteolipid membranes) deposited onto a sensor surface. Full analysis of these systems involves fitting theoretical curves (obtained using Maxwell's equations) to experimental spectra measured using s- and p-polarized excitation. This allows values to be obtained for refractive indices and optical extinction coefficients in these two directions, as well as a value for film thickness, thereby providing information about mass density and anisotropy changes. This is a time-consuming process that works well for simple systems in which only a single conformational event occurs, but cannot distinguish between events involving multiple conformations that proceed either sequentially or in a parallel series of events. This article describes a graphical method that can distinguish between mass density and anisotropy changes in a simpler, more rapid procedure, even for processes that proceed via multiple conformational events. This involves measurement of plasmon-waveguide resonance spectral shifts obtained upon molecular interactions occurring in deposited films with both s- and p-polarized excitation, and transforming these from an (s-p) coordinate system into a (mass-structure) coordinate system. This procedure is illustrated by data obtained upon the binding of a small peptide, penetratin, to solid-supported lipid bilayer membranes.