Estimation of rate constants of drug binding to open channels of cardiac transient outward current

An improved approach to the evaluation of the rate constants of drugs binding to the open channel underlying the transient outward potassium current I(t0) is described. It is based on an analysis of a quantitative model formulated by a set of twelve differential equations. The rate constants are calculated from the time constants resulting from an approximation of the time course of apparent inactivation of the recorded I(t0) by two exponentials in the absence and by three exponentials in the presence of a blocking agent. The model study confirmed significantly higher accuracy in comparison with the existing electrophysiological method.     

Evidence for multiple open states of sodium channels in neuroblastoma cells

Summary Open times of voltage-gated sodium channels in neuroblastoma cells were measured during repolarization (following a short depolarizing conditioning pulse) and during moderate depolarization. Conditional and unconditional channel open-time histograms were best fitted by the sum of two exponentials. (The conditional open time was measured from the end of the conditioning pulse until an open channel shuts provided it was open att=0). Time constants of both histograms depended on the postpulse and were shifted to more positive potentials with increasing conditioning pulse potential. This shift could be explained by assuming more than two time constants in the histograms, which could not be separated. Channel open-time histograms from single-pulse experiments showed a maximum att>0. These histograms could be best fitted by an exponential function with three time constants. One term of this function included the difference of two exponentials resulting in a maximum att>0. Open-time histograms showed a definite time dependence. At 2 to 6.5 msec after the beginning of the depolarization the best fit could be obtained by the difference of two exponentials. To these components another term had to be added at 0 to 2 msec. Between 6.5 and 14.0 msec the sum of two exponentials, and after 14.0 msec a single exponential resulted in a good fit. The results support the hypothesis that sodium channels in neuroblastoma cells may have multiple open states. Two of these states are irreversibly coupled.     

Calibration of stopped-flow spectrophotometers using a two-step disulfide exchange reaction

A coupled two-step reaction of Ellman's reagent (5,5′-dithiobis(2-nitrobenzoic acid)) with excess thioglycerol produces a progress curve composed of two superimposed exponentials. The ratio of the two pseudo-first-order rate constants equals 22.5 and does not vary appreciably with ehanges of either pH value or temperature. Because the ratio of the two amplitudes is defined by the ratio of the rate constants, the reaction can be used to estimate both the apparent zero time of mixing (or the dead time) and the detector linearity of a stopped-flow instrument with a single mixing experiment. The reaction is used as a standard of performance for both absorbance and fluorescence measurements with a stopped-flow spectrophotometer.     

Leukocyte and platelet margination within microvasculature of rabbit lungs

These studies compare the behavior of radiolabeled neutrophils, monocytes, lymphocytes, and platelets during their first pass through the pulmonary circulation after a central venous injection and their distribution within the circulation 10 min later. Their first pass through the pulmonary circulation was compared with erythrocytes (RBCs) using the indicator-dilution technique, and their recovery within the circulation of the lung and other organs was determined at 10 min by counting the radioisotopes in each organ. The extraction of each cell relative to RBCs during the first pass through the lung correlated with cell size in that the neutrophils (volume 107-140 fl) showed 97.6 +/- 0.6% extraction, monocytes (volume 80-105 fl) showed 91.4 +/- 1.7% extraction, lymphocytes (volume 36-75 fl) showed 80.1 +/- 4.4% extraction, and platelets (volume 4-7 fl) showed 33.1 +/- 3.9% extraction. After 10 min of circulation, the proportion of injected cells remaining in the lung was similar for neutrophils and monocytes (27.4 +/- 1.8 vs. 31.4 +/- 1.6%) but lower for lymphocytes (18.6 +/- 2.9%) and platelets (3.1 +/- 0.5%). All of the leukocytes were found to have a substantial marginated pool within the lung, whereas the platelets did not. The exchange between the circulating and marginated pools of leukocytes in the lung was related to blood velocity, with the least retention occurring in lung regions with shortest RBC transit times. We conclude that cell size is a major factor determining the time that cells will be delayed by the pulmonary microvasculature.(ABSTRACT TRUNCATED AT 250 WORDS)     

Reaction center and UQH2:cytc 2 oxidoreductase act as independent enzymes inRps. sphaeroides

Turnover of the ubiquinol oxidizing site of the UQH₂:cyt c₂ oxidoreductase (b/c ₁ complex) ofRps. sphaeroides can be assayed by measuring the rate of reduction of cytb ₅₆₁ in the presence of antimycin (AA). Oxidation of ubiquinol is a second-order process, with a value ofk ₂ of about 3 × 10⁵ M^–1. The reaction shows saturation at high quinol concentrations, with an apparentK _m of about 6–8 mM (with respect to the concentration of quinol in the membrane). When the quinone pool is oxidized before illumination, reduction of the complex shows a substantial lag (about 1 ms) after a flash, indicating that the quinol produced as a result of the photochemical reactions is not immediately available to the complex. We have suggested that the lag may be due to several factors, including the leaving time of the quinol from the reaction center, the diffusion time to the complex, and the time for the head group to cross the membrane. We have suggested aminimal value for the diffusion coefficient of ubiquinone in the membrane (assuming that the lag is due entirely to diffusion) of about 10^–9 cm^–2 sec^–1. The lag is reduced to about 100 µsec when the pool is significantly reduced, showing that quinol from the pool is more rapidly available to the complex than that from the reaction center. With the pool oxidized, similar kinetics are seen when the reduction of cytb ₅₆₁ occurs through the AA-sensitive site (with reactions at the quinol oxidizing site blocked by myxothiazol). These results show that there is no preferential reaction pathway for transfer of reducing equivalents from reaction center tob/c ₁ complex. Oxidation of cytb ₅₆₁ through the AA-sensitive site can be assayed from the slow phase of the carotenoid electrochromic change, and by comparison with the kinetics of cytb ₅₆₁. As long as the quinone pool is significantly oxidized, the reaction is not rate-determining for the electrogenic process. On reduction of the pool below 1 quinone per complex, a slowing of the electrogenic process occurs, which could reflect a dependence on the concentration of quinone. If the process is second-order, the rate constant must be about 2–5 times greater than that for quinol oxidation, since the effect on rate is relatively small compared with the effect seen at the quinol oxidizing site when the quinol concentration is changed over theE _h range where the first few quinols are produced on reductive titration. When the quinone pool is extracted (experiments in collaboration with G. Venturoli and B. A. Melandri), the slowing of the electrochromic change on reduction of the pool is not enhanced; we assume that this is due to the fact that a minimum of one quinone per active complex is produced by turnover of the quinol oxidizing site. Two lines of research lead us to revise our previous estimate for the minimal value of the quinone diffusion coefficient. These relate to the relation between the diffusion coefficient and the rate constants for processes involving the quinones: (a) The estimated rate constant for reaction of quinone at the AA-site approaches the calculated diffusion limited rate constant, implying an improbably efficient reaction. (b) From a preliminary set of experiments, the activation energy determined by measuring the variation of the rate constant for quinol oxidation with temperature, is about 8 kcal mol^–1. Although we do not know the contribution of entropic terms to the pre-exponential factor, the result is consistent with a considerably larger value for the diffusion coefficient than that previously suggested.     

Kinetic study on unzippering of polynucleotides and order-order transition in polypeptides

Solutions are presented for N + 1 sequential and reversible first-order reactions for which the magnitude of the reverse rate constant, k_b, for all steps except the last is identical. Also the magnitude of the forward rate constant, k_f, for all steps except the first and last is identical. The initial and final steps are nucleation reactions; therefore, the initial and final k_f are modified by the factors σ′ and γ respectively. The final k_b is modified by the factor γ σ. The ratio k_b/k_f is defined as s, which has the same meaning as s in the Zimm-Bragg theory. The mathematical model is intended to apply to polymeric molecules of N segments and allows the calculation of the mole fraction of molecules in state i at any time t, C_i(t). A molecule in state i has i unreacted segments and N – i reacted ones. Because the reactions are sequential, all reacted segments are contiguous. Our numerical results show that when σ′ is much less than unity and the forward reaction is favored, the relaxation curve is sigmoidal. If, however, the forward and reverse reactions are equally favored (i.e., s ? 1) the relaxation curve is a straight line. When s and σ′ are near unity, the curve is exponential for a considerably large fraction of the reaction. Further, in the exponential for a considerably large fraction of the reaction. Further, in the exponential phase of the reaction, the relaxation time is proportional to N² for highly cooperative systems (i.e., Nσ ? 1). As found by Pipkin and Gibbs, if N is sufficiently large and s is less than unity (e.g., N ? 50 and s ?0.9) the relaxation curve is largely linear with a slope inversely proportional to N. Applications are given for the unwinding of double-helical poly(A·U) and the order–order transition in poly-L -proline.     

Allosteric interactions of the membrane-bound acetylcholine reception: kinetic studies with alpha-bungarotoxin.

The specific and irreversible reaction of a snake neurotoxin, α-bungarotoxin, with the acetylcholine receptor of electroplax membrane preparations from $\text{Electrophorus electricus}$ proceeds by an initial fast phase followed by a slower one. The fraction of the reaction in the fast phase increases with increasing initial toxin concentrations, while the fraction going slowly decreases correspondingly. Both phases are affected by compounds which initiate or inhibit nerve impulse transmissions. The time course of the reaction can be fitted to the sum of two exponentials. The dependence on initial toxin concentration of the two exponentials, and of the fraction of reaction governed by the exponentials, can be fitted to a minimum reaction mechanism which involves at least two types of toxin binding sites with different dissociation constants and ligand-induced conversion of one type of site into the other. The mechanism is consistent with our previous data which showed that activators and inhibitors of membrane electrical potential changes occupy separate sites, only half of which interact. This type of mechanism has been seen in a number of allosteric regulatory enzymes.     

Marginated pool of neutrophils in rabbit lungs

The size and location of the marginated pool of neutrophils (PMNs) in rabbit lungs were evaluated, and the rate of exchange of the PMNs with the circulating pool was determined. 99mTc-labeled erythrocytes (99mTc-RBCs) and 125I-labeled macroaggregated albumin (125I-MAA) were used to determine RBC transit times in the pulmonary circulation. Radiolabeled PMNs were studied on their first passage through the lungs. After 10 min of circulation, the lungs were fixed, gamma counted, and prepared for morphometric and autoradiographic studies; 74 +/- 3% of the PMNs was retained in the lungs on the first passage, and 23 +/- 2% was within the pulmonary marginated pool 10 min later. The regional PMN retention and the rate of exchange between the marginated and circulating PMN pools in the lung were directly related to RBC transit time. The radiolabeled PMNs distributed similarly to the unlabeled cells within the microvasculature and had a similar exchange rate between the marginated and circulating pools (1.4 +/- 0.2%/s using labeled cells and 1.5 +/- 0.5%/s using unlabeled cells). The marginated pool was located primarily within alveolar capillaries and contained two to three times as many PMNs as the total circulating pool.     

Analysis of venous flow transients for estimation of vascular resistance, compliance, and blood flow distribution

We analysed venous flow transients using a long venous circuit and right heart bypass in 17 dogs after a rapid decrease in atrial pressure. A biphase curve was obtained which we decomposed into a two-compartment model, one with a fast time constant for venous return (0.069 min) and 52% of total circulating flow (Q), and one with a slower time constant (0.456 min) and 48% of Q. Subsequently, separate drainage from splanchnic and peripheral beds (with the renal venous return in the peripheral bed drainage) allowed comparison of time constants and venous outflow in these beds. The sum of the venous outflow volumes over time during separate drainage was indistinguishable from the single biphasic venous outflow volume curve over time observed with a long circuit and single reservoir. The fast time constant of the biphasic curve was not different from that determined by separate drainage from the peripheral circulation. The slow time constant of the single biphasic curve of 0.456 min was hybrid of two time constants, 0.216 min in the splanchnic bed and 0.862 min in the peripheral bed. Separate drainage from peripheral and splanchnic vascular beds demonstrated that the peripheral bed constituted 70% of venous outflow in the fast time constant compartment using Caldini's technique, whereas the splanchnic bed constituted 63% of venous outflow in the slow time constant compartment. It is concluded that, although Caldini's technique demonstrates biphasic venous flow transients, neither the fast nor the slow time constant compartments resolved from this analysis represent a particular anatomical region or vascular bed.     

The Design of Pooling Experiments for Screening a Clone Map

We consider nonadaptive pooling designs for unique-sequence screening of a 1530-clone map ofAspergillus nidulans.The map has the properties that the clones are, with possibly a few exceptions, ordered and no more than 2 of them cover any point on the genome. We propose two subdesigns of the Steiner systemS(3, 5, 65), one with 65 pools and approximately 118 clones per pool, the other with 54 pools and about 142 clones per pool. Each design allows 1 or 2 positive clones to be detected, even in the presence of substantial experimental error rates. More efficient designs are possible if the overlap information in the map is exploited, if there is no constraint on the number of clones in a pool, and if no error tolerance is required. An information theory lower bound requires at least 12 pools to satisfy these minimal criteria, and an “interleaved binary” design can be constructed on 20 pools, with about 380 clones per pool. However, the designs with more pools have important properties of robustness to various possible errors and general applicability to a wider class of pooling experiments.     

Gating current kinetics in Myxicola giant axons. Order of the back transition rate constants.

Gating current, Ig, was recorded in Myxicola axons with series resistance compensation and higher time resolution than in previous studies. Ig at ON decays as two exponentials with time constants, tau ON-F and tau ON-S, very similar to squid values. No indication of an additional very fast relaxation was detected, but could be still unresolved. Ig at OFF also displays two exponentials, neither reflecting recovery from charge immobilization. Deactivation of the two I(ON) components may proceed with well-separated exponentials at -100 mV. INa tail currents at OFF also display two exponentials plus a third very slow relaxation of 5-9% of the total tail current. The very slow component is probably deactivation of a very small subpopulation of TTX sensitive channels. A -100 mV, means for INa tail component time constants (four axons) are 76 microseconds (range: 53-89 microseconds) and 344 microseconds (range: 312-387 microseconds), and for IOFF (six axons) 62 microseconds (range: 34-87 microseconds) and 291 microseconds (range: 204-456 microseconds) in reasonable agreement. INa ON activation time constant, tau A, is clearly slower than tau ON-F at all potentials. Except for the interval -30 to -15 mV, tau A is clearly faster than tau ON-S, and has a different dependency on potential. tau ON-S is several fold smaller than tau h. Computations with a closed2----closed1----open activation model indicated Na tail currents are consistent with a closed1----open rate constant greater than the closed2----closed1.     

Theoretical fluorescence induction curves derived from coupled differential equations describing the primary photochemistry of photosystem II by an exciton-radical pair equilibrium

Fluorescence induction curves were calculated from a molecular model for the primary photophysical and photochemical processes of photosystem II that includes reversible exciton trapping by open (PHQ_A) and closed (PHQ^-_A) reaction centers (RCs), charge stabilization as well as quenching by oxidized (P⁺HQ^(-)_A) RCs. For the limiting case of perfectly connected photosynthetic units (“lake model”) and thermal equilibrium between the primary radical pair (P⁺H^-) and the excited singlet state, the primary reactions can be mathematically formulated by a set of coupled ordinary differential equations (ODE). These were numerically solved for weak flashes in a recursive way to simulate experiments with continuous illumination. Using recently published values for the molecular rate constants, this procedure yielded the time dependence of closed RCs as well as of the fluorescence yield (= fluorescence induction curves). The theoretical curves displayed the same sigmoidal shapes as experimental fluorescence induction curves. From the time development of closed RCs and the fluorescence yield, it was possible to check currently assumed proportionalities between the fraction of closed RCs and either (a) the variable fluorescence, (b) the complementary area above the fluorescence induction curve, or (c) the complementary area normalized to the variable fluorescence. By changing selected molecular rate constants, it is shown that, in contrast to current beliefs, none of these correlations obeys simple laws. The time dependence of these quantities is strongly nonexponential. In the presence of substances that quench the excited state, the model predicts straight lines in Stern-Volmer plots. We further conclude that it is impossible to estimate the degree of physical interunit energy transfer from the sigmoidicity of the fluorescence induction curve or from the curvature of the variable fluorescence plotted versus the fraction of closed RCs.     

A mathematical model of the food-consumer system I. A case without food replenishment

A simple mathematical model was proposed to describe the dynamics of a food-consumer system. The model was based on the Logistic Theory and consisted of Eqs. (4), (5) and (6). The model was divided into the following three cases for further analyss; i) without food supply except at the initial time, ii) with continuous food supply at a constant rate, and iii) with food supply at varying rates. Only the first model was dealth with in this paper. The assumptions of the model 1 are that a definite amount of food is given only once at the initial time and only the feeding by animals is responsible for the decrease of food, and that the rate of decrease is proportional to the amount of animals. It is also assumed that the growth of animal population is represented by the logistic curve, and that the upper limit of the population is proportional to the amount of food at that time. For simplicity the parameters of basic differential equations are assumed to be constant throughout the time course. Analytical solutions of this non-linear model were given by Eqs. (8), (9), (10) and (11). The properties of time course of the food amount and consumer population were discussed from the mathematical and biological points of view. The method of the estimation of the three constants λ,b, and c from the experimental data was also suggested. Since we had no available data for animal populations, we applied the model, regarding reserve substance as x and new plant body as y, to the data of the initial growth of Azuki bean plant in the dark. This model is very simple, but it may be useful for analyzing the behavior of food-consumer system. And it may give some clue to the analysis of the more complex systems.     

Oxygen evolution from single- and multiple-turnover light pulses: temporal kinetics of electron transport through PSII in sunflower leaves

Oxygen evolution per single-turnover flash (STF) or multiple-turnover pulse (MTP) was measured with a zirconium O₂ analyzer from sunflower leaves at 22°C. STF were generated by Xe arc lamp, MTP by red LED light of up to 18000 μmol quanta m⁻² s⁻¹. Ambient O₂ concentration was 10–30 ppm, STF and MTP were superimposed on far-red background light in order to oxidize plastoquinone (PQ) and randomize S-states. Electron (e⁻) flow was calculated as 4 times O₂ evolution. Q _A → Q _B electron transport was investigated firing double STF with a delay of 0 to 2 ms between the two. Total O₂ evolution per two flashes equaled to that from a single flash when the delay was zero and doubled when the delay exceeded 2 ms. This trend was fitted with two exponentials with time constants of 0.25 and 0.95 ms, equal amplitudes. Illumination with MTP of increasing length resulted in increasing O₂ evolution per pulse, which was differentiated with an aim to find the time course of O₂ evolution with sub-millisecond resolution. At the highest pulse intensity of 2.9 photons ms⁻¹ per PSII, 3 e⁻ initially accumulated inside PSII and the catalytic rate of PQ reduction was determined from the throughput rate of the fourth and fifth e⁻. A light response curve for the reduction of completely oxidized PQ was a rectangular hyperbola with the initial slope of 1.2 PSII quanta per e⁻ and V _m of 0.6 e⁻ ms⁻¹ per PSII. When PQ was gradually reduced during longer MTP, V _m decreased proportionally with the fraction of oxidized PQ. It is suggested that the linear kinetics with respect to PQ are apparent, caused by strong product inhibition due to about equal binding constants of PQ and PQH₂ to the Q _B site. The strong product inhibition is an appropriate mechanism for down-regulation of PSII electron transport in accordance with rate of PQH₂ oxidation by cytochrome b₆f.     

Low density lipoprotein turnover in swine.

The catabolism of intravenously injected 125I-labelled low density lipoproteins (LDL) was followed in normal miniature swine for 2 weeks. When compared with the two-exponential model, the decay curve of the plasma radioactivity associated with the LDL fraction was best described by a three-exponential model. In this system, the half-lives were 4.5 +/- 3.7, 19.7 +/- 6.6, and 127 +/- 70 h (mean of four studies). Assuming a kinetic model with metabolism of LDL in the rapidly equilibrating compartment and two slower equilibrating compartments (a model requiring three exponentials), the mean fractional catabolic rate for apo-LDL was calculated to be 0.015 h-1. Therefore, if at steady state, the synthetic rate for apo-LDL in the same pigs would be 5.6 +/- 4.1 mg/h. Different kinetic models using two or three exponentials would provide different values for the synthetic rate of apo-LDL. However, in view of the known existence of at least three major equilibrating pools for LDL in plasma, liver, and lymph, and in view of the present results, the kinetic model for LDL metabolism should be better represented by a three-exponential system.     

Exponential Sum-Fitting of Dwell-Time Distributions without Specifying Starting Parameters

Fitting dwell-time distributions with sums of exponentials is widely used to characterize histograms of open- and closed-interval durations recorded from single ion channels, as well as for other physical phenomena. However, it can be difficult to identify the contributing exponential components. Here we extend previous methods of exponential sum-fitting to present a maximum-likelihood approach that consistently detects all significant exponentials without the need for user-specified starting parameters. Instead of searching for exponentials, the fitting starts with a very large number of initial exponentials with logarithmically spaced time constants, so that none are missed. Maximum-likelihood fitting then determines the areas of all the initial exponentials keeping the time constants fixed. In an iterative manner, with refitting after each step, the analysis then removes exponentials with negligible area and combines closely spaced adjacent exponentials, until only those exponentials that make significant contributions to the dwell-time distribution remain. There is no limit on the number of significant exponentials and no starting parameters need be specified. We demonstrate fully automated detection for both experimental and simulated data, as well as for classical exponential-sum-fitting problems.     

Is red blood cell survival limited by the activity of a critical enzyme?

Erythrocyte glutathione reductase is responsible for generating reduced glutathione, which has been implicated in maintaining the integrity of the red blood cell.Erythrocytes from peripheral blood were separated into fractions of increasing age and the activity of glutathione reductase and aspartate amino transferase determined in each fraction.The age-related decline in activity of both enzymes was confirmed, but with detailed resolution of the cells by age a significant secondary rise in only glutathione reductase activity was found in very old cells. As red blood cells from the same cohort survive in the circulation for varying periods they must vary in some way from one another. It is postulated that glutathione reductase is a critical enzyme which limits erythrocyte survival and that the rate of decline in activity varies from cell to cell. A simple mathematical model based on this postulate accounted quantitatively for both the pattern of glutathione reductase activity and the erythrocyte survival curve. In addition, a simplified model of the passage of erythrocytes through the circulation was designed and run. The predicted erythrocyte survival curve and pattern of glutathione reductase activity were very similar to observed patterns. This model may be useful in other situations where a finite resource is degraded at different rates by random passages through different pathways.     

Estimation of population allele frequencies from next‐generation sequencing data: pool‐versus individual‐based genotyping

Molecular markers produced by next‐generation sequencing (NGS) technologies are revolutionizing genetic research. However, the costs of analysing large numbers of individual genomes remain prohibitive for most population genetics studies. Here, we present results based on mathematical derivations showing that, under many realistic experimental designs, NGS of DNA pools from diploid individuals allows to estimate the allele frequencies at single nucleotide polymorphisms (SNPs) with at least the same accuracy as individual‐based analyses, for considerably lower library construction and sequencing efforts. These findings remain true when taking into account the possibility of substantially unequal contributions of each individual to the final pool of sequence reads. We propose the intuitive notion of effective pool size to account for unequal pooling and derive a Bayesian hierarchical model to estimate this parameter directly from the data. We provide a user‐friendly application assessing the accuracy of allele frequency estimation from both pool‐ and individual‐based NGS population data under various sampling, sequencing depth and experimental error designs. We illustrate our findings with theoretical examples and real data sets corresponding to SNP loci obtained using restriction site–associated DNA (RAD) sequencing in pool‐ and individual‐based experiments carried out on the same population of the pine processionary moth (Thaumetopoea pityocampa). NGS of DNA pools might not be optimal for all types of studies but provides a cost‐effective approach for estimating allele frequencies for very large numbers of SNPs. It thus allows comparison of genome‐wide patterns of genetic variation for large numbers of individuals in multiple populations.     

Variant Identification in Multi-Sample Pools by Illumina Genome Analyzer Sequencing

Multi-sample pooling and Illumina Genome Analyzer (GA) sequencing allows high throughput sequencing of multiple samples to determine population sequence variation. A preliminary experiment, using the RET proto-oncogene as a model, predicted ≤30 samples could be pooled to reliably detect singleton variants without requiring additional confirmation testing. This report used 30 and 50 sample pools to test the hypothesized pooling limit and also to test recent protocol improvements, Illumina GAIIx upgrades, and longer read chemistry. The SequalPrep^TM method was used to normalize amplicons before pooling. For comparison, a single ‘control’ sample was run in a different flow cell lane. Data was evaluated by variant read percentages and the subtractive correction method which utilizes the control sample. In total, 59 variants were detected within the pooled samples, which included all 47 known true variants. The 15 known singleton variants due to Sanger sequencing had an average of 1.62±0.26% variant reads for the 30 pool (expected 1.67% for a singleton variant [unique variant within the pool]) and 1.01±0.19% for the 50 pool (expected 1%). The 76 base read lengths had higher error rates than shorter read lengths (33 and 50 base reads), which eliminated the distinction of true singleton variants from background error. This report demonstrated pooling limits from 30 up to 50 samples (depending on error rates and coverage), for reliable singleton variant detection. The presented pooling protocols and analysis methods can be used for variant discovery in other genes, facilitating molecular diagnostic test design and interpretation.     

The reaction cycle of bacteriorhodopsin: an analysis using visible absorption,photocurrent and infrared techniques

The light activated absorbance changes and photo-electric events of bacteriorhodopsin (bR) were simultaneously measured. The results were compared with the kinetics of the time resolved infrared signals which are characteristic for protonation changes of Asp residues, chromophore vibrations, and amide I vibrations. Each data set was analyzed separately. Assuming first order reactions the experimental curves in the time range from L back to bR could be fitted by a sum of five exponentials. However, for the photocurrent signal only four exponentials were necessary. The corresponding half-life times were of the same order of magnitude. Simultaneous fits of the traces from absorption changes in the visible range and the photocurrent signal provided evidence that the photocurrent data could also be described by the same sum of exponentials as the data obtained in the visible range. The rate constants obtained from the different methods applied were, within the limits of error, identical. These results demonstrate that retinal monitors not only charge displacements but also conformational movements of the protein moiety. The reprotonation of the Schiff base occurs synchronously with a protonation change of an internal aspartic acid which absorbs at 1755 cm^–1. From the IR-signals, amplitude spectra could be derived which provided evidence that Asp-residues absorbing at 1765 cm^–1 (Asp85) and 1755 cm^–1 are still protonated in the O-intermediate. Major conformational changes of the peptide back bone occur in the time range of the L M transition and with opposite sign during the decay of the O-intermediate. Offprint requests to: M. Engelhard