Co-operative response of chemically excitable membrane III. Three-state model

The general three-state model is formulated first, which is the direct extension of the unified two-state model previously formulated (Kijima & Kijima, 1978). In this model, each protomer in a symmetrically interacting system (oligomers or lattices) can take three states, S, R and Q, where S and R states are the same as in the two-state model and Q state is another state either corresponding to a different open-state of ionophore from R open-state or corresponding to another closed state of ionophore. The model has no restriction on the value of Hill coefficient at the midpoint of the dose-response curves in contrast to two-state models. It is applied on GABA sensitive inhibitory synapse of crayfish muscle to account for anomalous behaviour of the membrane in I^? solution.The simplified versions of the above general three-state model are also formulated (simplified three-state model), in which it is assumed that R and Q state are equivalent in regard to the nearest neighbor interaction. By this assumption, R and Q state are collectively treated as state A and mathematical formula obtained on Ising model are applicable on this model. This model is applied on the insect sugar receptor which was shown to be incompatible with the two-state models (Kijima & Kijima, 1980). Further simplification of the above simplified model results in two convenient models: three-state KNF model and three-state MWC model, which have minimum parameters but sufficient to account for most experiments. They give plausible physico-chemical base on the “classical model” in which the existence of both inactive and active ligand-receptor complex is assumed.     

Nonrandom expression of lactate dehydrogenase isozymes in the lizard family xantusiidae

A preliminary study of allozyme evolution in the lizard family Xantusiidae revealed the complete absence of expression of the A₁B₃ lactate dehydrogenase heterotetramer isozyme in both muscle and liver tissue in 17 taxa surveyed. The four-banded LDH pattern resulting from this loss is postulated te be a derived (synapomorphic) character state for the entire family, perhaps shared with the Scincidae. Additional derived character states were observed to have evolved in parallel in several lineages within the Xantusiidae. Loss of the A₃B₁ asymmetrical heterotetramer appears to have occurred a minimum of four times, and one species, Lepidophyma tuxtlae, also appears to have lost the B₄ homotetramer, having only a two-banded LDH isozyme pattern (A₄ and A₂B₂).     

Epidemiology and risk factors associated with Anaplasma marginale infection of cattle in Peninsular Malaysia

Bovine anaplasmosis is a major concern to cattle farming in most parts of the world. Anaplasmosis negatively impacts the profitability of cattle farming by reducing the production, reproduction, and draft ability of cattle. Here, we report results from a one-year cross sectional study to determine the epidemiology and the risk factors for Anaplasma marginale infection of cattle in Peninsular Malaysia. Examination of one thousand and forty five blood samples of apparently healthy cattle from forty-three farms in all the states of Peninsular Malaysia by polymerase chain reaction (PCR) assay revealed an overall prevalence of A. marginale infection of cattle of 72.6%, showing high endemicity of this heamoprotozoan among cattle in the country. Cattle breeds, production type, herd owner, herd size, management system, farm size, farm age, prophylactic treatment against blood parasites, presence of ticks, frequency of deticking, zones, closeness to forest, closeness to waste area, closeness to human settlement and closeness to body of water were the risk factors significantly associated (P?<?0.05) with the detection of A. marginale in cattle. Results of this first molecular study on the epidemiology and risk factors for A. marginale infection of cattle from all the states of Peninsular Malaysia suggest policies and strategies for the prevention and control of the parasite to improve profitability of cattle farming in the country.     

Natural Selection Mediated Association of the Duffy (FY) Gene Polymorphisms with Plasmodium vivax Malaria in India

The Duffy (Fy) antigens act as receptors for chemokines as well as for Plasmodium vivax to invade human RBCs. A recent study has correlated the occurrence of the FY*A allele of Duffy gene with decreased susceptibility to vivax malaria, but no epidemiological correlation between the distribution of FY*A allele and incidences of vivax malaria has been established so far. Furthermore, if such correlations exist, whether natural selection has mediated the association, is an important question. Since India is highly endemic to P. vivax malaria with variable eco-climatic and varying vivax malaria epidemiology across different regions, such a question could well be answered in Indians. For this, we have genotyped the FY gene at the −33^rd and the 125^th nucleotide positions in 250 Indians sampled from six different zonal plus one tribal population covering the whole of India and studied possible correlations with eco-climatic and vivax malaria incidences. No FY*O allele was found, however, both the FY*A and FY*B alleles forming FY*A/FY*A, FY*A/FY*B and FY*B/FY*B genotypes were widely distributed among Indians. Five out of seven population samples significantly deviated from the Hardy-Weinberg equilibrium expectation, and two alleles (FY*A and FY*B) and the homozygote genotype, FY*B/FY*B were clinally distributed over the population coordinates. Furthermore, vivax malaria incidences over the past five years were significantly negatively and positively associated with the frequencies of the FY*A and FY*B alleles, respectively. The Northern Indians were highly differentiated from the other zonal population samples at the FY gene, as evidenced from the reconstructed Neighbor-Joining phylogenetic tree. The results specify the role of natural selection in the distribution of FY gene polymorphism in India. Furthermore, the hypotheses on the part of the FY*A allele in conferring protection to vivax malaria could be validated following population genetic studies in a vivax malaria epidemiological setting, such as India.     

Role assessment,reserve strategy,and acquisition of information in asymmetric animal conflicts

It was formerly argued that alternative evolutionarily stable strategies (ESSs) are possible for animal contests characterized by some asymmetry that can be perceived with perfect accuracy. Where roles A and B refer to the asymmetry between opponents, ESSs are: ‘fight when A, retreat when B’, and vice versa. Either can be an ESS, but only if the ‘reserve strategy’ (=what an animal does when it fights) is sufficiently damaging. We examine the ‘war of attrition’ (winner = opponent that persists longer). In a population at either ESS, reserve strategy is never normally shown; it is therefore subject to drift unless the selective action of rare individuals which break the convention is considered. These could arise either by mutation or by mistakes in role assessment. When mutations and mistakes simply specify that occasionally an animal fights when it ‘should’ retreat, selection adjusts reserve strategy to a level where only one ESS (the ‘commonsense’ ESS) is possible, if the asymmetry is relevant to payoff. Thus for asymmetries in fighting ability or resource value, the individual with the lower score will retreat. However, we are particularly concerned with cases where both payoff-relevant aspects (fighting ability and resource value) are asymmetric. If opponents sustain contest costs at rates K_A and K_B, and their resource values are V_A and V_B, an ‘optimal assessor’ strategy defined by the interaction between the two asymmetries, is a unique ESS. It obeys the rule ‘fight on estimating role A, where V_A/K_A>V_B/K_B; retreat in B’. If mistakes can occur in both roles, but are very rate, the ESS is not fundamentally altered though there will be infinitesimal tendencies for persisting in role B. Selection to improve assessment abilities intensifies as abilities improve, but is weak if roles A and B are rather similar. Over a range of similarity between roles, an ‘owner wins’ convention may be adopted if ownership correlates positively with role A and an individual cannot tell when it would otherwise pay him to break the convention. We also examine a contest in which information about roles can be acquired only during a contest itself, and at a cost. Much depends on the rate at which information is acquired relative to the rate at which costs are expended, and on whether contests normally escalate in intensity, remain at the same level, or de-escalate. Selection favours short contests when costs are high relative to resource value, where the outcome of a round contains much information about fighting ability, and where the actual disparity in fighting ability is large.     

An analysis of the influence of age and school-attendance status on the spread of variola minor.

Definitions are proposed for the independent and joint contributions that the chemical groups A and B make to the free energy of association of the ligand A?B with a receptor. The definitions are independent of the choice of the standard state and are consistent with the basic thermodynamic cycle relating the association of the ligands A?B, A?Y and X?B to the receptor Rappaport 1976. The basic idea is the use of the excess free energy of association of the ligand A?Y over the free energy of association of the reference ligand X?Y as the measure of the “independent” contribution of the group A to the binding. This definition allows the free energy of association of the ligand A?B to be written as the sum of the independent contributions of the groups A and B, their joint contribution, and an invariant free energy of association of the reference ligand with any receptor. With the appropriate definition of the receptor-reference ligand complex, water can be chosen as the reference ligand. Using ΔG(A?OH)?AG(HOH), ΔG(H?B?H)?ΔG(HOH) and ΔG(HO?C)?ΔG(HOH) as the definitions of the “independent” contributions of the chemical groups A, B and C to the binding of the ligand A?B?C, the joint contribution of the groups A and C to the binding is ΔG(A?B?C) ? ΔG(A?B?H) ? ΔG(H-B-C) + ΔG(H?B?H).     

Mechanism of primary and secondary ion-radical pair formation in photosystem I complexes

The mechanisms of the ultrafast charge separation in reaction centers of photosystem I (PS I) complexes are discussed. A kinetic model of the primary reactions in PS I complexes is presented. The model takes into account previously calculated values of redox potentials of cofactors, reorganization energies of the primary P700⁺A ₀ ^- and secondary P700⁺A ₁ ^- ion-radical pairs formation, and the possibility of electron transfer via both symmetric branches A and B of redox-cofactors. The model assumes that the primary electron acceptor A₀ in PS I is represented by a dimer of chlorophyll molecules Chl2A/Chl3A and Chl2B/Chl3B in branches A and B of the cofactors. The characteristic times of formation of P700⁺A ₀ ^- and P700⁺A ₁ ^- calculated on the basis of the model are close to the experimental values obtained by pump-probe femtosecond absorption spectroscopy. It is demonstrated that a small difference in the values of redox potentials between the primary electron acceptors A_0A and A_0B in branches A and B leads to asymmetry of the electron transfer in a ratio of 70: 30 in favor of branch A. The secondary charge separation is thermodynamically irreversible in the submicrosecond range and is accompanied by additional increase in asymmetry between the branches of cofactors of PS I.     

A method to calculate binding equilibrium concentrations in the allosteric ternary complex model that supports ligand depletion

The allosteric ternary complex model is frequently used in pharmacology to represent the interaction of a receptor R with two ligands A and B. Certain well-known formulas are routinely used to calculate the fractions of the receptor bound at equilibrium with A only, B only, and both A and B. However, it is often omitted that these classical formulas presume that there is no ligand depletion, i.e. that the equilibrium concentrations [A] and [B] of the ligands are well approximated by their total concentrations [A]_T and [B]_T. We present a calculation method which is applicable without this or any restrictions. The equilibrium concentration [R] of the receptor is implicitly characterized by an equation which is solved with a very simple convergent numerical algorithm. The concentrations [A] and [B] are given by explicit formulas in terms of [R]. The required parameters are the equilibrium dissociation constants K_A and K_B, the cooperativity factor α, and the total concentrations [R]_T, [A]_T and [B]_T.     

Effect of temperature on the photoreduction of centres A and B in Photosystem I,and the kinetics of recombination

When spinach Photosystem I particles, frozen in the dark with ascorbate, are illuminated at low temperatures, one electron is transferred from P-700 to either iron-sulphur centre A or B. It was found that the proportion of centre A or B reduced depended on the temperature of illumination. At 25 K, reduction of centre A, as detected by ESR spectroscopy, was strongly preferred. At higher temperatures, at about 150K, there was an increased proportion of reduced centre B. Reduction of B was more strongly preferred in particles frozen in 50% glycerol. The kinetics of dark reoxidation of A^? and B^? at various temperatures were followed by observing the radical signal of P-700⁺, and also by periodically cooling to 25 K to measure the ESR spectra of the iron-sulphur centres. The recombination of A^? and P-700⁺ occurred at lower temperatures than that at of B^?; at 150–200 K, centre B was the more stable electron trap. Dark reoxidation of both centres was more rapid in samples that were illuminated at 25 K than in samples illuminated at 150–215 K. In no case was net electron transfer between centres A and B observed. Differences in g values of the ESR spectra in particles illuminated at 25 and 200 K indicate that the iron-sulphur centres are in altered conformational states. It is concluded firstly that, in the frozen state, the rates of dark electron transfer decrease in the sequence A^? → P-700⁺ > B^? → P-700⁺ > B^? → A; secondly, that when centres A or B are photoreduced, a temperature-dependent conformational change takes place which slows down the rate of recombination with P-700⁺.     

Nonequilibrium as a source of unmixing

The intermediates, U and V, of a simple model reaction system (the so-called Brusselator) are shown to have both uniform and patterned steady states in a membrane. The patterned distribution of U and V has the symmetry of hexagons in the plane and is stable for B #62; B_m, B being the controlled concentration of one of the parametric species. The uniform solution is stable for B < B_c, and, since B_c #62; B_m, the increase and subsequent decrease of B over an interval that includes (B_m,B_c) can produce a hysteresis in which the transitions from mixed (i.e. uniform) to unmixed (i.e. hexagonlly patterned) states happen quite suddenly at the two critical values. Since the transfer or reactive properties of the membrane might be different in the two states, this model provides a bistable membrane element that might have prototypical value in a theory of biochemical control.     

Association of PDE4B Polymorphisms with Susceptibility to Schizophrenia: A Meta-Analysis of Case-Control Studies

Background

The PDE4B single nucleotide polymorphisms (SNPs) have been reported to be associated with schizophrenia risk. However, current findings are ambiguous or even conflicting. To better facilitate the understanding the genetic role played by PDE4B in susceptibility to schizophrenia, we collected currently available data and conducted this meta-analysis.

Methods

A comprehensive electronic literature searching of PubMed, Embase, Web of Science and Cochrane Library was performed. The association between PDE4B SNPs and schizophrenia was evaluated by odds ratios (ORs) and 95% confidence intervals (CIs) under allelic, dominant and recessive genetic models. The random effects model was utilized when high between-study heterogeneity (I² > 50%) existed, otherwise the fixed effects model was used.

Results

Five studies comprising 2376 schizophrenia patients and 3093 controls were finally included for meta-analysis. The rs1040716 was statistically significantly associated with schizophrenia risk in Asian and Caucasian populations under dominant model (OR = 0.87, 95% CI: 0.76–0.99, P = 0.04). The rs2180335 was significantly related with schizophrenia risk in Asian populations under allelic (OR = 0.82, 95% CI: 0.72–0.93, P = 0.003) and dominant (OR = 0.75, 95% CI: 0.64–0.88, P < 0.001) models. A significant association was also observed between rs4320761 and schizophrenia in Asian populations under allelic model (OR = 0.87, 95% CI: 0.75–1.00, P = 0.048). In addition, a strong association tendency was found between rs6588190 and schizophrenia in Asian populations under allelic model (OR = 0.87, 95% CI: 0.76–1.00, P = 0.055).

Conclusion

This meta-analysis suggests that PDE4B SNPs are genetically associated with susceptibility to schizophrenia. However, due to limited sample size, more large-scale, multi-racial association studies are needed to further clarify the genetic association between various PDE4B variants and schizophrenia.     

Varying degrees of nonlinear mechanical behavior arising from geometric differences of urogynecological meshes

Synthetic polypropylene meshes were designed to restore pelvic organ support for women suffering from pelvic organ prolapse; however, the FDA released two notifications regarding potential complications associated with mesh implantation. Our aim was to characterize the structural properties of Restorelle and UltraPro subjected to uniaxial tension along perpendicular directions, and then model the tensile behavior of these meshes utilizing a co-rotational finite element model, with an imbedded linear or fiber-recruitment local stress–strain relationship. Both meshes exhibited a highly nonlinear stress–strain behavior; Restorelle had no significant differences between the two perpendicular directions, while UltraPro had a 93% difference in the low (initial) stiffness (p=0.009) between loading directions. Our model predicted that early alignment of the mesh segments in the loading direction and subsequent stretching could explain the observed nonlinear tensile behavior. However, a nonlinear stress–strain response in the stretching regime, that may be inherent to the mesh segment, was required to better capture experimental results. Utilizing a nonlinear fiber recruitment model with two parameters A and B, we observed improved agreement between the simulations and the experimental results. An inverse analysis found A=120 MPa and B=1.75 for Restorelle (RMSE=0.36). This approach yielded A=30 MPa and B=3.5 for UltraPro along one direction (RMSE=0.652), while the perpendicular orientation resulted in A=130 MPa and B=4.75 (RMSE=4.36). From the uniaxial protocol, Restorelle was found to have little variance in structural properties along these two perpendicular directions; however, UltraPro was found to behave anisotropically.     

Protein Dielectric Environment Modulates the Electron-Transfer Pathway in Photosynthetic Reaction Centers

The replacement of tyrosine by aspartic acid at position M210 in the photosynthetic reaction center of Rhodobacter sphaeroides results in the generation of a fast charge recombination pathway that is not observed in the wild-type. Apparently, the initially formed charge-separated state (cation of the special pair, P, and anion of the A-side bacteriopheophytin, H_A) can decay rapidly via recombination through the neighboring bacteriochlorophyll (B_A) soon after formation. The charge-separated state then relaxes over tens of picoseconds and recombination slows to the hundreds-of-picoseconds or nanosecond timescale. This dielectric relaxation results in a time-dependent blue shift of B_A^– absorption, which can be monitored using transient absorbance measurements. Protein dynamics also appear to modulate the electron transfer between H_A and the next electron carrier, Q_A (a ubiquinone). The kinetics of this reaction are complex in the mutant, requiring two kinetic terms, and the spectra associated with the two terms are distinct; a red shift of the H_A ground-state bleaching is observed between the shorter and longer H_A-to-Q_A electron-transfer phases. The kinetics appears to be pH-independent, suggesting a negligible contribution of static heterogeneity originating from protonation/deprotonation in the ground state. A dynamic model based on the energy levels of the two early charge-separated states, P⁺B_A^– and P⁺H_A^–, has been developed in which the energetics of these states is modulated by fast protein dielectric relaxations and this in turn alters both the kinetic complexity of the reaction and the reaction pathway.     

Competitive blocking of apical sodium channels in epithelia

Apical sodium-selective channels in frog skin, when blocked by amiloride or triamterene, exhibit fluctuations in current, the spectra of which are Lorentzian. These effects have been modeled previously with two-state and three-state models by Lindemann and Van Driessche. A recent observation by Hoshiko and Van Driessche that corner frequencies are lowered by increasing the apical sodium concentration cannot be accounted for by these models. We explore the possibility that sodium (S) and amiloride (A) compete for a site at the mouth of the channel. A new three-state channel model (sodium-occupied, open/unoccupied, open/amiloride-blocked) is analyzed. Its corner frequency is of the form f_c = f_co[1 + (A/K_A)/(1 + S/K_S)], consistent with the observed sodium dependence of the corner frequency. The minimum frequency, f_co, and the inhibition constants, K_A and K_S, are expressed in terms of the rate constants of the model. To account for sodium self-inhibition, we postulate that two sodium ions in the channel may result in clogging — a fourth state. The two corner frequencies are calculated; so are the plateau values of the noise power. The noise power shows a maximum as a function of blocker concentration, as observed previously using triamterene. The four-state model predicts the observed suppression by small amounts of blocker of the low-frequency sodium (clogging) noise.     

Electron transfer in reaction centers of Rhodopseudomonas sphaeroides. I. Determination of the charge recombination pathway of D+QAQ−B and free energy and kinetic relations between Q−AQB and QAQ−B

The electron-transfer reactions and thermodynamic equilibria involving the quinone acceptor complex in bacterial reaction centers from R. sphaeroides were investigated. The reactions are described by the scheme: We found that the charge recombination pathway of D⁺Q_AQ^?_B proceeds via the intermediate state D⁺Q^?_AQ_B, the direct pathway contributing less than approx. 5% to the observed recombination rate. The method used to obtain this result was based on a comparison of the kinetics predicted for the indirect pathway (given by the product k_AD-times the fraction of reaction centers in the Q^?_AQ_B state) with the observed recombination rate, k^obs_{D⁺ →D}. The kinetic measurements were used to obtain the pH dependence (6.1 ? pH ? 11.7) of the free energy difference between the states Q^?_AQ_B and Q_AQ^?_B. At low pH (less than 9) Q_AQ^?_B is stabilized relative to Q^?_AQ_B by 67 meV, whereas at high pH Q^?_AQ_B is energetically favored. Both Q^?_A and Q^?_B associate with a proton, with pK values of 9.8 and 11.3, respectively. The stronger interaction of the proton with Q^?_B provides the driving force for the forward electron transfer.     

Binding and release kinetics of inhibitors of Q−A oxidation in thylakoid membranes

Oxygen flash yield patterns of dark adapted thylakoid membranes as measured with a Joliot-type O₂-electrode indicate that inhibitors that block the oxidation of the reduced primary quinone Q^?_A of Photosystem II vary greatly in the rate of binding to and release from the inhibitor / Q_B binding environment. The ‘classical’ Photosystem-II herbicides like diuron and atrazine exhibit slow binding and release kinetics, whereas, for example, phenolic inhibitors, o-phenanthroline and synthetic quinones are exchanging quite rapidly with Q_B (about once per second or faster at inhibitor concentrations causing about 50% inhibition of O₂ evolution). No general relationship between the efficiency of the inhibitor and the exchange rate is observed; it depends mainly on the type of inhibitor. Based on the classical Kok model, equations are derived in order to calculate oxygen yields evolved by thylakoids in single-turnover flashes as a function of the rate constants of inhibitor binding to and release from the inhibitor / Q_B binding environment in the presence of an oxidized or semireduced Q_A · Q_B or Q_A · inhibitor complex. Fitting of theoretical and experimental values yields that o-phenanthroline binds much faster to an oxidized than to a semireduced Q_A · Q_B complex. This fits very well with the hypothesis that the Q^?_B affinity to the site is much higher than that of Q_B. In the case of i-dinoseb, however, inhibitor / quinone exchange seems to occur mainly in the semiquinone state. Possibilities to explain this result are discussed.     

Biparental contributions of the H2A.B histone variant control embryonic development in mice

Histone variants expand chromatin functions in eukaryote genomes. H2A.B genes are testis-expressed short histone H2A variants that arose in placental mammals. Their biological functions remain largely unknown. To investigate their function, we generated a knockout (KO) model that disrupts all 3 H2A.B genes in mice. We show that H2A.B KO males have globally altered chromatin structure in postmeiotic germ cells. Yet, they do not show impaired spermatogenesis or testis function. Instead, we find that H2A.B plays a crucial role postfertilization. Crosses between H2A.B KO males and females yield embryos with lower viability and reduced size. Using a series of genetic crosses that separate parental and zygotic contributions, we show that the H2A.B status of both the father and mother, but not of the zygote, affects embryonic viability and growth during gestation. We conclude that H2A.B is a novel parental-effect gene, establishing a role for short H2A histone variants in mammalian development. We posit that parental antagonism over embryonic growth drove the origin and ongoing diversification of short histone H2A variants in placental mammals.

The unusual short histone variant H2A.B is a novel parental-effect gene that plays an important role in early mammalian development. Parental antagonism over embryonic growth resource allocation may have driven the origin and ongoing diversification of short histone H2A variants in placental mammals.     

The dependence of reaction center and antenna triplets on the redox state of Photosystem I

The formation of chlorophyll triplet states during illumination of Photosystem I reaction center samples depends upon the redox state of P-700, X and ferredoxin Centers A and B. When the reaction centers are in the states P-700⁺A₁XFd_BFd^?_A and P-700 A₁XFd^?_BFd^?_A prior to illumination, we observe electron paramagnetic resonance (EPR) spectra from a triplet species which has zero-field splitting parameters (|D| and |E|) larger than those of either the chlorophyll a or chlorophyll b monomer triplet, and a polarization which results from population of the triplet spin sublevels by an intersystem crossing mechanism. We interpret this triplet as arising from photoexcited chlorophyll antenna species associated with reaction centers in the states P-700⁺Fd^?_A and P-700⁺X^?, respectively, which undergo de-excitation via intersystem crossing. When the reaction centers are in the states P-700A₁XFd^?_BFd^?_A and P-700A₁X^?Fd^?_BFd^?_A prior to illumination, we observe a triplet EPR signal with a polarization which results from population of the triplet spin sublevels by radical pair recombination, and which has a |D| value similar to that of chlorophyll a monomer. We interpret this triplet (the radical pair-polarized triplet) as arising from ³P-700 which has been populated by the process $\text{P-700}{}^{\mathrm{+}}\text{A}{}^{\mathrm{?}}{}_1\text{→}{}^3\text{P-700}\text{A}{}_1$. We observe both the radical pair-polarized triplet and the chlorophyll antenna triplet when the reaction centers are in the state P-700 A₁XFd^?_BFd^?_A, presumably because the processes P-700⁺A^?₁X → P-700⁺A₁X^? and $\text{P-700}{}^{\mathrm{+}}\text{A}{}^{\mathrm{?}}{}_1\text{X}\text{→}{}^3\text{P-700}\text{A}{}_1\text{X}$ have similar rate constants when Centers A and B are reduced, i.e., the forward electron transfer time from A^?₁ to X is apparently much slower in the redox state P-700 A₁XFd^?_BFd^?_A than it is in state P-700 A₁XFd_BFd_A. The amplitude of the radical pair-polarized triplet EPR signal does not decrease in the presence of a 13.5-G-wide EPR signal centered at g 2.0 which was recorded in the dark prior to triplet measurements in samples previously frozen under intense illumination. This g 2.0 signal, which has been attributed to phototrapped A^?₁ (Heathcote, P., Timofeev, K.N. and Evans, M.C.W. (1979) FEBS Lett. 101, 105–109), corresponds to as many as 12 spins per P-700 and can be photogenerated during freezing without causing any apparent attenuation of the radical pair-polarized triplet amplitude. We conclude that species other than A^?₁ contribute to the g 2.0 signal.     

Estimation of coalescence probabilities and population divergence times from SNP data

We present a method called the G(A|B) method for estimating coalescence probabilities within population lineages from genome sequences when one individual is sampled from each population. Population divergence times can be estimated from these coalescence probabilities if additional assumptions about the history of population sizes are made. Our method is based on a method presented by Rasmussen et al. (2014) to test whether an archaic genome is from a population directly ancestral to a present-day population. The G(A|B) method does not require distinguishing ancestral from derived alleles or assumptions about demographic history before population divergence. We discuss the relationship of our method to two similar methods, one introduced by Green et al. (2010) and called the F(A|B) method and the other introduced by Schlebusch et al. (2017) and called the TT method. When our method is applied to individuals from three or more populations, it provides a test of whether the population history is treelike because coalescence probabilities are additive on a tree. We illustrate the use of our method by applying it to three high-coverage archaic genomes, two Neanderthals (Vindija and Altai) and a Denisovan.Subject terms: Rare variants, Evolutionary genetics

One of the goals of population genetics is to estimate the divergence time of isolated populations. We will review several methods that have been proposed and present a new method that is closely related to two existing methods. We will emphasize the assumptions made when using different methods. It will be useful to make the distinction between estimating coalescence probabilities within populations and estimating population divergence times. We will also introduce a test for a treelike population history based on our method.For distantly related populations, the numbers of mutational differences between sequences indicate relative times of divergence. Relative times are converted to absolute times by assuming a mutation rate. This method traces to Zuckerkandl and Pauling (1962, 1965) and has been used and refined extensively. This class of methods estimates genomic divergence times. Using it to estimate population or species divergence times assumes that those times are so large that the difference between them can be ignored.For recently diverged populations, the numbers of mutational differences probably do not provide a reliable estimate of population divergence times both because there may be too few mutations that differentiate populations and because the difference between the genomic and population divergence times may be substantial. To overcome this problem, Green et al. (2010) (in Supplement 14) introduced a method that accounts for the difference between genomic and population divergence. This method was used in later papers from the same group (Meyer et al. 2012; Prüfer et al. 2014, 2017).The Green et al. (2010) method is applicable when one genome is sampled from each of two populations. It depends on the statistic F(A|B), which is the fraction of sites in population A that carry the derived allele when that site is heterozygous in population B. Green et al. (2010) showed by simulation that the expectation of F(A|B) decreases roughly exponentially with the separation time of A and B. The rate of decrease depends on the history of population sizes both in B and in the population ancestral to A and B. Green et al. (2010) estimated population divergence times by interpolating their simulation results.More recently, Schlebusch et al. (2017), in Section 9.1 of their supplementary materials, introduced a similar method, called the TT method. Their method is based on analytic expressions for the configuration probabilities of SNPs that are polymorphic in the two populations. The TT method assumes that ancestral and derived alleles can be distinguished and the population before divergence was of constant size. The TT method is developed and elaborated on by Sjödin et al. (2020).In the present paper, we present a new method that is closely related to the F(A|B) and TT methods. We call it the G(A|B) method to emphasize its similarity to F(A|B). Our method is based on a method presented by Rasmussen et al. (2014) to test whether an ancient DNA sequence is from a population directly ancestral to a present-day population. We will show that our method provides a way to test whether the history of three or more populations is accurately represented by a population tree even if the demographic histories of those populations are not known.