Hill Plots Research Articles

Evaluation of high yielding soybean germplasm under water limitation.

Limited information is available for soybean root traits and their plasticity under drought stress. To date, no studies have focused on examining diverse soybean germplasm for regulation of shoot and root response under water limited conditions across varying soil types. In this study, 17 genetically diverse soybean germplasm lines were selected to study root response to water limited conditions in clay (trial 1) and sandy soil (trial 2) in two target environments. Physiological data on shoot traits was measured at multiple crop stages ranging from early vegetative to pod filling. The phenotypic root traits, and biomass accumulation data are collected at pod filling stage. In trial 1, the number of lateral roots and forks were positively correlated with plot yield under water limitation and in trial 2, lateral root thickness was positively correlated with the hill plot yield. Plant Introduction (PI) 578477A and 088444 were found to have higher later root number and forks in clay soil with higher yield under water limitation. In sandy soil, PI458020 was found to have a thicker lateral root system and higher yield under water limitation. The genotypes identified in this study could be used to enhance drought tolerance of elite soybean cultivars through improved root traits specific to target environments.

Measuring Multivalent Binding Interactions by Isothermal Titration Calorimetry.

Multivalent glycoconjugate-protein interactions are central to many important biological processes. Isothermal titration calorimetry (ITC) can potentially reveal the molecular and thermodynamic basis of such interactions. However, calorimetric investigation of multivalency is challenging. Binding of multivalent glycoconjugates to proteins (lectins) often leads to a stoichiometry-dependent precipitation process due to noncovalent cross-linking between the reactants. Precipitation during ITC titration severely affects the quality of the baseline as well as the signals. Hence, the resulting thermodynamic data are not dependable. We have made some modifications to address this problem and successfully studied multivalent glycoconjugate binding to lectins. We have also modified the Hill plot equation to analyze high quality ITC raw data obtained from multivalent binding. As described in this chapter, ITC-driven thermodynamic parameters and Hill plot analysis of ITC raw data can provide valuable information about the molecular mechanism of multivalent lectin-glycoconjugate interactions. The methods described herein revealed (i) the importance of functional valence of multivalent glycoconjugates, (ii) that favorable entropic effects contribute to the enhanced affinities associated with multivalent binding, (iii) that with the progression of lectin binding, the microscopic affinities of the glycan epitopes of a multivalent glycoconjugate decrease (negative cooperativity), (iv) that lectin binding to multivalent glycoconjugates, especially to mucins, involves internal diffusion jumps, (bind and jump) and (v) that scaffolds of glycoconjugates influence their entropy of binding.

The anion recognition properties of a novel hydrazone based on colorimetric and potentiometric studies.

A novel hydrazone, 1,3-bis (2-formylphenoxy) propane bis (2,4-dinitrophenyl hydrazine) (S) has been synthesized and characterized by the NMR, IR, CHNS, UV-Vis, Raman, TEM and XPS analysis. Upon the addition of monohydrogen phosphate (MHP) ion, sudden color change from light yellow to dark violet has occurred. The binding constant of S-MHP was determined by Hill plot. Hydrazone also showed potential response with MHP ion. A number of polymeric membrane electrodes (PME) and coated graphite electrode (CGE) were also fabricated and found that the CGE has revealed better results in comparison to PME in terms of the detection limit of 7.58 × 10(-9) mol L(-1) and Nernstian response.

Can the KG1 cell line be used as a model of dendritic cells and discriminate the sensitising potential of chemicals?

The KG1 myeloid leukaemia was used as source of dendritic cells (DC) to discriminate between respiratory and contact sensitising chemicals. A cocktail of cytokines was used to differentiate KG1 to dendritic like cells (termed dKG1) and the effects of nine chemicals (respiratory and contact sensitisers) and an irritant control on surface marker expression, 'antigen presenting' function and cytokine expression investigated. The stability of these chemicals when dissolved was characterised using MALDI ToF MS. A Hill plot model was used with the cellular viability data to quantify the lethal dose 50% (LD50) and a maximum sub toxic concentration of each chemical defined. Cytokine expression by the treated dKG1 was quantified using multiplex immunobead analysis. Whilst dKG1 cells were morphologically similar to DCs, expression of specific surface markers was not typical for DCs derived from healthy precursor cells. When the chemicals were applied at defined sub toxic doses no effects on dKG1 phenotype, function, or cytokine expression, attributable to the sensitisation properties were discriminated. However, dKG1 cells were much more sensitive to the toxic effects of these chemicals compared to the parent KG1 cells. Only 4 of the 9 chemicals tested were stable when dissolved indicating that the effect of sensitising chemicals on antigen presenting cells may be related to species other than the parent compound.

Selenium modified oxalate chelated titania: Characterization, mechanistic and photocatalytic studies

In order to enhance the visible photocatalytic activity of titanium dioxide (TiO2), selenium (Se) doped TiO2 was prepared by sol–gel method using oxalic acid as a chelating agent. To characterize and describe the effect of Se+4 ions on the structural, optical and photocatalytic properties of TiO2, the powders were characterized by XRD, FTIR, UV-DRS, HR-TEM, PL, Raman, XPS and BET measurements. XRD analysis showed that doped powders consist of anatase phase, while undoped TiO2 is a composite mixture of anatase and rutile at a calcination temperature of 550°C. Williamson–Hill plot results indicated the presence of tensile strain on the addition of 0.02, 0.04 and 0.06mol% Se content, while compressive strain was specified on the addition of 0.08, 0.1 and 0.2mol% Se content in TiO2 lattice. FTIR analysis revealed the chelating behaviour of oxalic acid with titanium ions in forming titanium oxalate stretches. Diffuse reflectance measurements showed that visible light absorption is induced by dopant localized/intermediate electronic states, probably originating from Se 4s and 4p states within the band gap of TiO2. Raman peak broadening and the small frequency shifting for the peaks (1-Eg and B1g) were attributed to oxygen vacancies and crystal lattice distortions. Photoluminescence (PL) analysis showed that electron hole recombination was decreased with the incorporation of Se+4 ions in TiO2, which act as trapping sites for the photogenerated electrons. Moreover, PL analysis demonstrated that Se doping produces Ti+3 centers, oxygen defects and localized electronic states in TiO2 band gap, which become responsible for the TiO2 response towards the visible light. The activity of the prepared photocatalysts powder were tested by investigating the kinectics of the photocatalytic decoloration of methylene blue (MB) under UV irradiations and decomposition of 4-chlorophenol (4-CP) under visible light irradiation. It was observed that the TSe0.08 powder with Brönsted acid sites, calcined at 550°C showed highest photocatalytic activity under both UV and visible light irradiations for the selected pollutants. In the decoloration of MB, TSe0.08 powder attain a rate constant (kapp) value of 0.045min−1 which is higher than Degussa P25 (0.033min−1) as well two times higher than undoped TiO2 (0.021min−1). Based on the obtained results, a UV/vis light irradiated photocatalytic mechanism has been proposed for the Se+4 doped anatase TiO2.

Thermodynamic Study on Reaction of Tetra Sulfona to Phenyl Porphyrin Iron (II) Complex With Different Nitrogenous Ligands

The binding characteristics of number of axial aliphatic amines ligands were studied with Fe(ll)TPPS4 complex in aqueous solutions at hiqh PHs > 12.5 . All formed low spin octahedral complexes . Electronic absorption , ΔH , ΔG , and ΔS of these complexes have been reported and Calculated . The Path way for the axial ligation on addition of ligand to Fe(ll)TPPS4 is shown in one step . Hill Plots used to obtain the formation constants ( KF) and ( n ) number of axial ligands bonded to the iron(ll) ion . It has been found low values of the KF for these ligands comparing to those recorded in organic solvents may be due to the polar solvent , and these values ( KF) more higher than that recorded for aromatic amine with the same complex and solvents due to steric effect of the size of porphyrin ring .

A parametric alternative to the Hill estimator for heavy-tailed distributions

Abstract Despite its wide use, the Hill estimator and its plot remain to be difficult to use in Extreme Value Theory (EVT) due to substantial sampling variations in extreme sample quantiles. In this paper, we propose a new plot we call the eigenvalue plot which can be seen as a generalization of the Hill plot. The theory behind the plot is based on a heavy-tailed parametric distribution class called the scaled Log phase-type (LogPH) distributions, a generalization of the ordinary LogPH distribution class which was previously used to model insurance claims data. We show that its tail property and moment condition are well aligned with EVT. Based on our findings, we construct the eigenvalue plot from fitting a shifted PH distribution to the excess log data with a minimal phase size. Through various numerical examples we illustrate and compare our method against the Hill plot.

Steady-State Predictions from a Compact Cooperative Kinetic Model of Cardiac Sarcomere Dynamics

A compact model of cardiac sarcomere dynamics is useful when developing integrated models of whole ventricular function. Kinetic models can be simplified by separating slower from faster processes. The representation of faster processes can then be reduced to their equivalent equilibrium relationships. Analysis of cooperativity within a cardiac sarcomere is also aided by dealing with equilibria, which can be analyzed using statistical thermodynamics. These principles guided the formulation of a compact kinetic model of cardiac sarcomere dynamics. In this scheme there were three slower processes: (1) reversible transitions between weak and strong crossbridges, (2) detachment of strong crossbridges, (3) dissociation of calcium from regulatory units (RUs) having a strong crossbridge. In the overall kinetic scheme, an individual RU could exist in 6 states: 3 states of crossbridge binding (none, weak, strong) interacting with 2 states of calcium binding (yes, no). Exchanges between the 4 states without strong crossbridges occurred by rapid equilibria. Thus, in the reduced model only 3 kinetic states remained: (1) strong crossbridges attached to RUs where calcium was bound, (2) strong crossbridges remaining attached even after calcium had dissociated, (3) the equilibrium mixture of the 4 remaining states. Since strong crossbridges appear to act independently, rate constants between these 3 states were considered independent of neighboring RUs. However, cooperativity between neighboring RUs exerted major impacts on the mixture of 4 states interacting rapidly as equilibria. Applying the linear Ising Model of statistical thermodynamics, the grand partition function characterizing interactions between neighboring RUs included activating effects from strong crossbridges as well as free calcium ions. This model predicted steady-state relationships between force and pCa (given as Hill plots) that reproduced the experimentally observed bend toward less cooperative slope near half activation.

On the tail index inference for heavy-tailed GARCH-type innovations

In this study, we investigate the smoothing Hill plot and change point test for the tail index of power-transformed and threshold generalized autoregressive conditional heteroscedasticity (PTTGARCH) and autoregressive and moving average (ARMA)–GARCH innovations. It is shown that their asymptotic properties are the same as those in the i.i.d. sample case. For illustration, we provide a simulation study and real data analysis.

Computational tools for fitting the Hill equation to dose–response curves

IntroductionMany biological response curves commonly assume a sigmoidal shape that can be approximated well by means of the 4-parameter nonlinear logistic equation, also called the Hill equation. However, estimation of the Hill equation parameters requires access to commercial software or the ability to write computer code. Here we present two user-friendly and freely available computer programs to fit the Hill equation — a Solver-based Microsoft Excel template and a stand-alone GUI-based “point and click” program, called HEPB. MethodsBoth computer programs use the iterative method to estimate two of the Hill equation parameters (EC50 and the Hill slope), while constraining the values of the other two parameters (the minimum and maximum asymptotes of the response variable) to fit the Hill equation to the data. In addition, HEPB draws the prediction band at a user-defined confidence level, and determines the EC50 value for each of the limits of this band to give boundary values that help objectively delineate sensitive, normal and resistant responses to the drug being tested. ResultsBoth programs were tested by analyzing twelve datasets that varied widely in data values, sample size and slope, and were found to yield estimates of the Hill equation parameters that were essentially identical to those provided by commercial software such as GraphPad Prism and nls, the statistical package in the programming language R. DiscussionThe Excel template provides a means to estimate the parameters of the Hill equation and plot the regression line in a familiar Microsoft Office environment. HEPB, in addition to providing the above results, also computes the prediction band for the data at a user-defined level of confidence, and determines objective cut-off values to distinguish among response types (sensitive, normal and resistant). Both programs are found to yield estimated values that are essentially the same as those from standard software such as GraphPad Prism and the R-based nls. Furthermore, HEPB also has the option to simulate 500 response values based on the range of values of the dose variable in the original data and the fit of the Hill equation to that data.

High-Throughput Screening Assays for Estrogen Receptor by Using Coumestrol, a Natural Fluorescence Compound

Estrogen receptor (ER) is a ligand-inducible transcriptional factor involving in cell growth, differentiation, and diseases, so detection and identification of compounds having estrogenic effects are of great importance in the drug discovery industry. We have developed and validated a rapid, simple, and homogeneous method that can detect estrogenic compounds. This human ERα/β binding assay uses fluorescence polarization (FP) by applying an autofluorescent phytoestrogen, coumestrol (CS). A nonspecific adsorption assay shows that no obvious nonspecific adsorption is detected between CS and ERs. In the Scatchard plot analysis, the convex curve exhibits a positive cooperative binding, indicating that the binding of CS induces a conformational change of the ER to form a dimer and increases the affinity for the additional CS. In the Hill plot analysis, CS shows moderate binding affinity with both ERα and ERβ, and the measured Kd of CS is 32.66 µM and 36.14 µM, respectively, indicating that CS is applicable to the ER binding assay for determination of potent ligands of moderate binding affinity. Four typical ligands are selected to verify the ER binding assays, and the results are consistent with the reported data. All of above make the FP method based on CS suitable for high-throughput screening.

Melting temperatures deduced from molar volumes: a consequence of the combination of enthalpy/entropy compensation with linear cohesive free-energy densities

Enthalpy/entropy compensation is a general issue of intermolecular binding processes when the interaction between the partners can be roughly modelled with a single harmonic potential. Whereas linear H/S correlations are wished for by experimentalists, and often graphically justified, no inflexible law of thermodynamics supports the latter statement. On the contrary, the non-directional Ford's approach suggests logarithmic H/S relationships, which can be linearized only over narrow enthalpy/entropy ranges. Predictions covering larger domains require mathematical mapping obeying specific boundary conditions which are not compatible with linear plots. The analysis of solvent-free melting processes operating in six different classes of organic and inorganic materials shows that reciprocal Hill plots are acceptable functions for correlating melting enthalpies and entropies. The combination of H/S compensation with the observed linear dependence of the cohesive free energy densities with respect to the melting temperature eventually provides an unprecedented interdependence between melting temperatures and molar volumes. This procedure is exploited for the prediction of melting temperatures in substituted cyanobiphenyls.

Naked eye and fluorescent detections of Hg2+ ions and Cysteine via J-aggregation and deaggregation of a perylene bisimide derivative

Selective naked eye and fluorescent sensor responses of a 1,6,7,12-tetra(4-tert-butylphenoxy)perylene-3,4:9,10-tetracarboxylic acid bisimide (PBI) derivative are reported for the first time toward Hg2+ ions and Cysteine (Cys) via J-aggregation and deaggregation mechanisms. The J-aggregation and deaggregation of PBI induced by Hg2+ and Cys were well established by UV–vis/PL and 1H NMR titrations. The 1:1 stoichiometry of PBI-Hg2+ and Cys-Hg2+/PBI ensembles were elucidated from the jobs plots based on their UV–vis spectral changes. The linear complex formation by PBI-Hg2+ ensemble was confirmed through FT-IR and 1H NMR spectral studies and well supported by its reversible nature upon the addition of pentamethyl diethylene triamine (PMDTA). The positive cooperativities of Hg2+ and Cys (with PBI) in PBI-Hg2+ and Cys-Hg2+/PBI ensembles were evidenced from the Hill plots based on their fluorescence binding isotherms. The detection limits of Hg2+ ions and Cys were calculated as 36.6 and 91.3nM, respectively, by standard deviations and linear fittings of their Stern–Volmer (KSV) constants and relative fluorescence intensity changes, respectively. Furthermore, the sensor properties of PBI were well investigated by KSV constants, pH values, time effects, and time resolved photoluminescence (TRPL) spectra.

Frequency analysis of precipitation extremes in Heihe River basin based on generalized Pareto distribution

Precipitation extremes could cause a series of social, environmental and ecological problems. This paper, taking Heihe River basin, the second largest inland river basin in China, as the study area, focused on the frequency analysis of precipitation extremes based on the historical daily precipitation records (1960–2010) at nine stations. Generalized Pareto distribution (GPD) was employed for fitting the peaks over threshold (POT) series, in which Hill plot, percentile method and the average annual occurrence number were used to select the threshold in GPD. Maximum likelihood estimate and L-moment were used to estimate the parameters. The inherent assumptions for POT series were investigated by auto-correlation coefficient, Mann–Kendall test, Spearman’s ρ test, cumulative deviation test and Worsley likelihood ratio test. 10, 20, 50 and 100 year precipitation extremes for Heihe River basin were calculated and analyzed as well. It was found the POT series derived from several methods involved were approximately independent and stationary, and GPD could give a satisfactory fit to the POT series for each station. For the upper and lower reaches, the frequency of precipitation extremes at long return periods (20, 50 year or longer) presented increasing in recent years, and the intensity of the highest precipitation were getting stronger as well. The intensity of the highest precipitation extremes for the lower reach (21 and 35 %) increased higher than those for the upper reach (10 and 11 %). For the middle reach, the frequency of precipitation extremes (over 20 year return level) was not found to be increased. The uneven spatial and temporal distribution of precipitation extremes for the basin especially for the upper and lower reaches were getting more and more serious, which would bring great challenges for the local water allocation and management.

A Schiff-based sensor with turn-on fluorescence for selective detection of Hg2+.

A simple Schiff-base colorimetric receptor 1 was prepared. It exhibits an ‘off–on-type’ mode with high sensitivity in the presence of Hg2+. The change in color is very easily observed by the naked eye in the presence of Hg2+, whereas other metal cations do not induce such a change. A Job plot indicated a 1 : 1 complexation stoichiometry between receptor 1 and Hg2+. The association constant for 1–Hg2+ in Tetrahydrofuran (THF) was determined to be 1.3 × 10(9)M-1 using a Hill plot.

Autoxidation and Oxygen Binding Properties of Recombinant Hemoglobins with Substitutions at the αVal-62 or βVal-67 Position of the Distal Heme Pocket

The E11 valine in the distal heme pocket of either the α- or β-subunit of human adult hemoglobin (Hb A) was replaced by leucine, isoleucine, or phenylalanine. Recombinant proteins were expressed in Escherichia coli and purified for structural and functional studies. (1)H NMR spectra were obtained for the CO and deoxy forms of Hb A and the mutants. The mutations did not disturb the α1β2 interface in either form, whereas the H-bond between αHis-103 and βGln-131 in the α1β1 interfaces of the deoxy α-subunit mutants was weakened. Localized structural changes in the mutated heme pocket were detected for the CO form of recombinant Hb (rHb) (αV62F), rHb (βV67I), and rHb (βV67F) compared with Hb A. In the deoxy form the proximal histidyl residue in the β-subunit of rHb (βV67F) has been altered. Furthermore, the interactions between the porphyrin ring and heme pocket residues have been perturbed in rHb (αV62I), rHb (αV62F), and rHb (βV67F). Functionally, the oxygen binding affinity (P50), cooperativity (n50), and the alkaline Bohr Effect of the three α-subunit mutants and rHb (βV67L) are similar to those of Hb A. rHb (βV67I) and rHb (βV67F) exhibit low and high oxygen affinity, respectively. rHb (βV67F) has P50 values lower that those reported for rHb (αL29F), a B10 mutant studied previously in our laboratory (Wiltrout, M. E., Giovannelli, J. L., Simplaceanu, V., Lukin, J. A., Ho, N. T., and Ho, C. (2005) Biochemistry 44, 7207-7217). These E11 mutations do not slow down the autoxidation and azide-induced oxidation rates of the recombinant proteins. Results from this study provide new insights into the roles of E11 mutants in the structure-function relationship in hemoglobin.

A Schiff-Based Colorimetric Fluorescent Sensor with the Potential for Detection of Fluoride Ions

A simple Schiff-based colorimetric fluorescent receptor 1 was prepared. It exhibits a "turn-on-type" mode with high sensitivity in the presence of F(-). The change in color is very easily observed by the naked eye in the presence of F(-), whereas other anions do not induce such a change. Job plot indicated a 1:2 complexation stoichiometry between receptor 1 and F(-). The association constant for 1-F(-) in CH3CN was determined as 1.32*10(5)M(-2) by a Hill plot.

Urea-based polyacetylenes as an optical sensor for fluoride ions

Novel acetylenes carrying urea groups, 1-(4-ethynylphenyl)-3-(4-nitrophenyl) urea (1), 1-(4-propargyl)-3-(4-nitrophenyl) urea (2), were synthesized and polymerized with rhodium catalyst. Polymers [poly(1) and poly(2)] with moderate molecular weights were obtained in good yields. The anion sensing ability of poly(1) and poly(2) was estimated using the tetra-n-butylammonium (TBA) salts of a series of anions in DMF. Upon the addition of F−, the color of the DMF solution of poly(1) and poly(2) immediately turned to a different color, while the color of solution changed slightly upon addition of Cl−, HSO4−, Br−, and NO3−, indicating the F− sensing ability of poly(1) and poly(2). The 1H-NMR titrations of poly(1) revealed that the colorimetric response of poly(1) was triggered by the urea/F− interaction through the hydrogen bonding and/or deprotonation process. The absorption spectra titration and Hill plot analysis were carried out to measure the F− binding ability, and the Hill coefficient in the poly(1)/F− complexation was found to be 5.8. This result clearly indicated that this binding mode between poly(1) and F− was based on a positive homotropic allosterism.

1053 – In vitro receptor-binding profile of lurasidone and other commonly-used antipsychotics

Introduction Atypical antipsychotics bind to multiple receptor types and subtypes. Improved outcomes in schizophrenia are linked to activity at D2 and serotonin receptors 5-HT7, 5-HT2A and 5-HT1A. Objectives To characterize the receptor-binding profile of lurasidone and other antipsychotics. Aims To compare receptor-binding profiles of antipsychotics. Methods Replicated, side-by-side receptor-binding assays used human recombinant receptors (for 5-HT7, α2A, and α2C) or membrane-fractions of animal CNS tissue. Affinities were determined via Hill plot analysis for IC50values; Ki values were determined using Ki=IC50/(1+ S/Kd) (S=concentration of competing radioligand, Kd=dissociation constant). Results Lurasidone displayed potent binding and full antagonism at dopamine D2(Ki, 1.68nM) and serotonin 5-HT2A(Ki, 2.03nM) receptors (the highest D2affinity of all tested agents). Lurasidone's dopamine binding was selective for D2receptors. Unlike other antipsychotics tested, lurasidone had very high affinity and full antagonism at serotonin 5-HT7(Ki, 0.49nM), and nanomolar affinity (Ki=6.75nM) with weak-moderate partial agonism at serotonin 5-HT1Areceptors., Lurasidone showed higher affinity for 5-HT7, 5-HT2A, and 5-HT1Areceptors relative to D2receptor-binding than other agents. Lurasidone displayed moderate affinity for α2C adrenoceptors (Ki, 10.8nM); moderate-weak affinity for α1adrenoceptors (Ki, 48nM); and minimal or unappreciable affinity for receptors associated with undesirable effects (5-HT2C [Ki, 415nM], histamine H1[IC50>1000nM] and muscarinic [cholinergic] M1[IC50>1000nM] receptors). Conclusions The unique pharmacological profile of lurasidone is consistent with observed antipsychotic efficacy, low-tomoderate likelihood of EPS, low weight-gain potential, and possible mood, anxiety, and cognitive benefits.

Amperometric biosensor based on polypyrrole and tyrosinase for the detection of tyramine in food samples

An electrochemical tyrosinase electrode for detection of tyramine was developed via cross-linking immobilization method over phosphate-doped polypyrrole film. The enzyme tyrosinase immobilized over the polypyrrole thin film preserves well its biocatalytic activity. Tyramine was determined by the direct reduction of biocatalytically formed dopaquinone at −0.250V. The analytical characteristics of this biosensor, including linear range, detection limit, repeatability and storage stability are described. The kinetics of the enzymatic reaction fitted into a Michaelis–Menten type kinetic, as confirmed by the h parameter close to 1 obtained from the Hill's plot. Under the optimum conditions, the current response had a linear relationship with the concentration of tyramine in the range of 4–80×10−6M, with a sensitivity of 0.1069AM−1 and a limit of detection of 5.7×10−7M. The biosensor exhibited high repeatability and long term stability. Determination of tyramine in real samples showed good recovery. The selective detection is related to specific action of tyrosinase toward phenolic group from tyramine (1-hydroxy-4-ethylaminobenzene). The developed biosensor was applied to the determination of the tyramine content in sauerkraut samples.