Fluorometric probing on the binding of hematoxylin to serum albumin

The binding of a cell nucleus stain, hematoxylin (HTL), to bovine serum albumin (BSA) was studied by spectroscopy including fluorescence spectra, UV–Visible absorption, circular dichroism (CD) spectra, synchronous and three-dimensional fluorescence spectra. The results indicated that the binding had led to static fluorescence quenching, with non-radiation energy transfer happening within single molecule. The observed binding constant was calculated to be 10^5.588 l mol^?1 at 311 K and one binding site had formed. The thermodynamic parameters of the interaction complied with ΔG ^θ < 0, ΔH ^θ < 0, ΔS ^θ < 0 and the results indicate that hydrogen bonds played major role in the reaction. The distance r between donor (BSA) and acceptor (HTL) was obtained according to the Förster theory of non-radiation energy transfer. The structural change of BSA molecules with addition of HTL was analyzed and the optimized geometry of HTL–BSA was investigated by fluorescence probe method.     

Synthesis of Morin–Zinc(II) Complex and its Interaction with Serum Albumin

A morin–zinc(II) complex (MZ) was synthesized and its interaction with bovine serum albumin (BSA) were studied by molecular spectroscopy including fluorescence emission spectra, UV-visible spectra, circular dichroism (CD) spectra, three-dimensional fluorescence spectra, and synchronous fluorescence spectra. The interaction mechanism of BSA and MZ was discussed by fluorescence quenching method and Förster non-radiation energy transfer theory. The thermodynamic parameters ΔH ^θ, ΔG ^θ, ΔS ^θ at different temperatures were calculated and the results indicate the interaction is an exothermic as well as entropy-driven process. Hydrogen bond forces played the most important role in the reaction. The fluorescence probe experiment showed that the binding site of MZ is in subdomain IIA of BSA and the distance between BSA and MZ is 3.17 nm at normal body temperature. The conformation changes of BSA in presence of MZ were investigated by CD spectra and three-dimensional fluorescence spectra.     

Photochemical studies on the binding of an organic fluoride to bovine serum albumin

The interaction of fipronil (FPN), a pesticide containing fluorine, to bovine serum albumin (BSA) was studied by spectroscopy including fluorescence spectra, UV–Visible absorption, scattering spectra, circular dichroism (CD) spectra, synchronous and three-dimensional fluorescence spectra. The number of binding sites n and observed binding constant Kb was measured by fluorescence quenching method. The thermodynamic parameters ΔH, ΔG, ΔS at different temperatures were calculated and the results indicate that hydrophobic forces played major role in the reaction. The distance r between donor (BSA) and acceptor (FPN) was obtained according to the Förster theory of non-radiation energy transfer. The structural change of BSA molecules with addition of FPN was analyzed and the results may be helpful to biologists, chemists and therapeutists.     

Chemicobiological effects of herbicide MCPA-Na on plasma proteins

Under physiological conditions, the potential hematological toxicity of herbicide 2-methyl-4-chlorophenoxyacetic acid sodium (MCPA-Na) was discussed by fluorescence probe technology and spectroscopy methods including three-dimensional (3D) fluorescence, UV absorption and circular dichroism (CD) spectra. In vitro, MCPA-Na bound with bovine serum albumin (BSA) and formed new complex at ground state by electrostatic force and hydrogen bond. During the process, non-radiation energy transfer from BSA to MCPA-Na occurred and the distance r between donor and acceptor was obtained based on Förster theory. The binding site was investigated by fluorescence probe method and the results implied MCPA-Na was absorbed on domain II of BSA molecule. The enthalpy change (ΔH ^θ), Gibbs free energy change (ΔG ^θ) and entropy change (ΔS ^θ) were calculated at four different temperatures according to Van’t Hoff isobar equation and Gibbs–Helmholtz equation. Negative value of ΔG ^θ indicated the process of binding was a spontaneous and irreversible process, which gave a broad hint that MCPA-Na was likely to be poisonous. CD spectra exhibited significant changes of secondary structures in BSA molecule and three-dimensional fluorescence spectra indicated the tryptophan residue in BSA was placed in a less hydrophobic environment, which presented additional evidence to caution the danger of MCPA-Na residue in food. Meanwhile, the mechanism and geometry of the binding was analyzed at molecular level.     

Studies on the interaction between benzidine and bovine serum albumin by spectroscopic methods

The interaction between bovine serum albumin (BSA) and benzidine (BD) in aqueous solution was investigated by fluorescence spectroscopy, circular dichroism (CD) spectra and UV–Vis spectroscopy, as well as resonance light scattering spectroscopy (RLS). It was proved from fluorescence spectra that the fluorescence quenching of BSA by BD was a result of the formation of BD–BSA complex, and the binding constants (K _a) were determined according to the modified Stern–Volmer equation. The enthalpy change (ΔH) and entropy change (ΔS) were calculated to be ?34.11 kJ mol^?1 and ?25.89 J mol^?1 K^?1, respectively, which implied that van der Waals force and hydrogen bond played predominant roles in the binding process. The addition of increasing BD to BSA solution caused the gradual enhancement in RLS intensity, exhibiting the forming of the aggregate. Moreover, the competitive experiments of site markers suggested that the binding site of BD to BSA was located in the region of subdomain IIA (sudlow site I). The distance (r) between the donor (BSA) and the acceptor (BD) was 4.44 nm based on the Förster theory of non–radioactive energy transfer. The results of synchronous fluorescence and CD spectra demonstrated the microenvironment and the secondary conformation of BSA were changed.     

Multi-spectroscopic studies on the interaction between traditional Chinese herb,helicid with pepsin

Study on the binding properties of helicid by pepsin systematically using multi-spectroscopic techniques and molecular docking method, and these interactions comprise biological recognition at molecular level and backbone of biological significance in medicine concerned with the uses, effects, and modes of action of drugs. We investigated the mechanism of interaction between helicid and pepsin by using various spectroscopic techniques viz., fluorescence spectra, UV–Vis absorption spectra, circular dichroism (CD), 3D spectra, synchronous fluorescence spectra and molecular docking methods. The quenching mechanism associated with the helicid–pepsin interaction was determined by performing fluorescence measurements at different temperatures. From the experimental results show that helicid quenched the fluorescence intensity of pepsin via a combination of static and dynamic quenching process. The binding constants (K_a) at three temperatures (288, 298, and 308 K) were 7.940?×?10⁷, 2.082?×?10⁵ and 3.199?×?10⁵ L mol^?1, respectively, and the number of binding sites (n) were 1.44, 1.14, and 1.18, respectively. The n value is close to unity, which means that there is only one independent class of binding site on pepsin for helicid. Thermodynamic parameters at 298 K were calculated as follows: ΔH^o (??83.85 kJ mol^?1), ΔG^o (??33.279 kJ mol^?1), and ΔS^o (??169.72 J K^?1 mol^?1). Based on thermodynamic analysis, the interaction of helicid with pepsin is driven by enthalpy, and Van der Waals’ forces and hydrogen bonds are the main forces between helicid and pepsin. A molecular docking study further confirmed the binding mode obtained by the experimental studies. The conformational changes in the structure of pepsin was confirmed by 3D fluorescence spectra and circular dichroism.     

Hardness maximization or equalization? New insights and quantitative relations between hardness increase and bond dissociation energy

It has been overlooked that the change of hardness, η, upon bonding is intimately connected to thermochemical cycles, which determine whether hardness is increased according to Pearson’s “maximum hardness principle” (MHP) or equalized, as expected by Datta’s “hardness equalization principle” (HEP). So far the performances of these likely incompatible “structural principles” have not been compared. Computational validations have been inconclusive because the hardness values and even their qualitative trends change drastically and unsystematically at different levels of theory. Here I elucidate the physical basis of both rules, and shed new light on them from an elementary experimental source. The difference, Δη = η _mol – <η _at>, of the molecular hardness, η _mol, and the averaged atomic hardness, <η _at>, is determined by thermochemical cycles involving the bond dissociation energies D of the molecule, D ⁺ of its cation, and D ^? of its anion. Whether the hardness is increased, equalized or even reduced is strongly influenced by ΔD = 2D – D ⁺  ? D ^?. Quantitative expressions for Δη are obtained, and the principles are tested on 90 molecules and the association reactions forming them. The Wigner-Witmer symmetry constraints on bonding require the valence state (VS) hardness, η _VS, instead of the conventional ground state (GS) hardness, η _GS. Many intriguingly “unpredictable” failures and systematic shortcomings of said “principles” are understood and overcome for the first time, including failures involving exotic and/or challenging molecules, such as Be_2, B₂, O₃, and transition metal compounds. New linear relationships are discovered between the MHP hardness increase Δη _VS and the intrinsic bond dissociation energy D _i . For bond formations, MHP and HEP are not compatible, and HEP does not qualify as an ordering rule.     

Spectroscopic Investigation of the Interaction Between Copper (II) 2-oxo-propionic Acid Salicyloyl Hydrazone Complex and Bovine Serum Albumin

The interaction between copper (II) 2-oxo-propionic acid salicyloyl hydrazone (Cu^IIL) and bovine serum albumin (BSA) under physiological conditions was investigated by the methods of fluorescence spectroscopy, UV-Vis absorption, and circular dichroism spectroscopy. Fluorescence data showed that the fluorescence quenching of BSA by Cu^IIL was the result of the formation of the BSA–Cu^IIL complex. The apparent binding constants (K _a) between Cu^IIL and BSA at four different temperatures were obtained according to the modified Stern–Volmer equation. The thermodynamic parameters, enthalpy change (ΔH) and entropy change (ΔS), for the reaction were calculated to be ?80.79 kJ mol^?1 and ?175.48 J mol^?1 K^?1 according to van’t Hoff equation. The results indicated that van der Waals force and hydrogen bonds were the dominant intermolecular force in stabilizing the complex. The binding distance (r) between Cu^IIL and the tryptophan residue of BSA was obtained to be 4.1 nm according to Förster’s nonradioactive energy transfer theory. The conformational investigation showed that the application of Cu^IIL increased the hydrophobicity of amino acid residues and decreased the α-helical content of BSA (from 62.71% to 37.31%), which confirmed some microenvironmental and conformational changes of BSA molecules.     

Analysis of photoprotection and apparent non-photochemical quenching of chlorophyll fluorescence in <Emphasis Type="Italic">Tradescantia</Emphasis> leaves based on the rate of irradiance-induced changes in optical transparence

The kinetics of irradiation-induced changes in leaf optical transparence (ΔT) and non-photochemical quenching (NPQ) of chlorophyll fluorescence in Tradescantia fluminensis and T. sillamontana leaves adapted to different irradiance in nature was analyzed. Characteristic times of a photoinduced increase and a dark decline of ΔT in these species were 12 and 20 min, respectively. The ΔT was not confirmed to be the main contributor to the observed middle phase of NPQ relaxation kinetics (τ = 10-28 min). Comparison of rate of photoinduced increase in ΔT and photosystem II quantum yield recovery showed that the former did not affect the tolerance of the photosynthetic apparatus (PSA) to irradiances up to 150 μmol PAR·m^–2·s^–1. Irradiance tolerance correlated with the rate of “apparent NPQ” induction. Considering that the induction of apparent NPQ involves processes significantly faster than ΔT, we suggest that the photoprotective mechanism induction rate is crucial for tolerance of the PSA to moderate irradiance during the initial stage of light acclimation (first several minutes upon the onset of illumination).     

The investigation of the interaction between ribavirin and bovine serum albumin by spectroscopic methods

The interaction between ribavirin (RIB) with bovine serum albumin (BSA) has been investigated by fluorescence quenching technique in combination with UV–vis absorption and circular dichroism (CD) spectroscopies under the simulative physiological conditions. The quenching of BSA fluorescence by RIB was found to be a result of the formation of RIB–BSA complex. The binding constants and the number of binding sites were calculated at three different temperatures. The values of thermodynamic parameters ?H, ?S, ?G at different temperatures indicate that hydrophobic and hydrogen bonds played important roles for RIB–BSA association. The binding distance r was obtained according to the theory of FÖrster’s non–radiation energy transfer. The displacement experiments was performed for identifying the location of the binding site of RIB on BSA. The effects of common ions on the binding constant of RIB and BSA were also examined. Finally, the conformational changes of BSA in the presence of RIB were also analyzed by CD spectra and Synchronous fluorescence spectra.     

Cloning and Functional Analysis of <Emphasis Type="Italic">SaCLCc1</Emphasis>, a Gene Belonging to the Chloride Channel Family (<Emphasis Type="Italic">CLC</Emphasis>), from the Halophyte <Emphasis Type="Italic">Suaeda altissima</Emphasis> (L.) Pall.

One of the genes of the CLC (Chloride Channel) family, SaCLCc1, from the halophyte Suaeda altissima (L.) Pall. was cloned. To investigate the function of SaCLCc1, it was expressed in the S. cerevisiae deletion mutant Δgef1::LEU2 for the only gene of the CLC family in this organism. The growth of the transformed SaCLCc1-expressing mutant Δgef1 was restored when cells were grown in Fe²⁺-deficient YPEG medium, in minimal synthetic media SD and SR (pH 7.0), and in rich YPD medium containing Mn²⁺. The complementation of the Δgef1 mutant phenotype with the SaClCc1 gene indicates the involvement of the SaClCc1 protein in the transport of Cl^– ions.     

Effects of temperature and food quality on isotopic turnover and discrimination in a cladoceran

Our experimental study was designed to assess the effects of temperature on nitrogen isotope turnover and to measure the effects of temperature and food quality on the stable carbon and nitrogen isotope discrimination factors (Δ¹³C and Δ¹⁵N) in a cladoceran. For the first part of our study, Daphnia were fed with non-enriched or ¹⁵N-enriched Scenedesmus obliquus at 12, 15, 20, and 25 °C. For the second part, Daphnia were reared at 15, 20, and 25 °C on Scenedesmus or Cryptomonas sp. There were no clear effects of temperature on turnover rates of the nitrogen isotope of cladocerans. However, a general increase in Δ¹³C with increasing temperature was measured, regardless of the food source. Δ¹⁵N was also affected by temperature, but contrasting results were measured depending on the food source used. There were significant effects of food quality on Δ¹³C and Δ¹⁵N in Daphnia, as values obtained for Daphnia fed Scenedesmus were always higher than those obtained for Daphnia fed Cryptomonas. Our experiments produced discrimination factors that were very different from those usually considered in isotope studies and showed that the values used for isotope model implementation to analyze field data need to be adapted to environmental conditions.     

Short-term effects of crop rotation,residue management,and soil water on carbon mineralization in a tropical cropping system

The purpose of this study was to investigate the short-term effects of maize (Zea mays)-fallow rotation, residue management, and soil water on carbon mineralization in a tropical cropping system in Ghana. After 15 months of the trial, maize–legume rotation treatments had significantly (P?C ₀ (μg CO₂–C g^?1) than maize–elephant grass (Pennisetum purpureum) rotations. The C ₀ for maize–grass rotation treatments was significantly related to the biomass input (r?=?0.95; P?=?0.05), but that for the maize–legume rotation was not. The soil carbon mineralization rate constant, k (per day), was also significantly related to the rotation treatments (P?k values for maize–grass and maize–legume rotation treatments were 0.025 and 0.036 day^?1 respectively. The initial carbon mineralization rate, m ₀ (μg CO₂–C g^?1 day ^?1), was significantly (P?θ. The m ₀ ranged from 3.88 to 18.67 and from 2.30 to 15.35 μg CO₂–C g^?1 day^?1 for maize–legume and maize–grass rotation treatments, respectively, when the soil water varied from 28% to 95% field capacity (FC). A simple soil water content (θ)-based factor, f _w, formulated as: \(f_{\text{w}} = \left[ {\frac{{\theta - \theta _{\text{d}} }}{{\theta _{{\text{FC}}} - \theta _{\text{d}} }}} \right]\), where θ _d and θ _FC were the air-dry and field capacity soil water content, respectively, adequately described the variation of the m ₀ with respect to soil water (R ²?=?0.91; RMSE?=?1.6). Such a simple relationship could be useful for SOC modeling under variable soil water conditions.     

QTL mapping for downy mildew resistance in cucumber via bulked segregant analysis using next-generation sequencing and conventional methods

Key message

QTL mapping using NGS-assisted BSA was successfully applied to an F ₂ population for downy mildew resistance in cucumber. QTLs detected by NGS-assisted BSA were confirmed by conventional QTL analysis.

Abstract

Downy mildew (DM), caused by Pseudoperonospora cubensis, is one of the most destructive foliar diseases in cucumber. QTL mapping is a fundamental approach for understanding the genetic inheritance of DM resistance in cucumber. Recently, many studies have reported that a combination of bulked segregant analysis (BSA) and next-generation sequencing (NGS) can be a rapid and cost-effective way of mapping QTLs. In this study, we applied NGS-assisted BSA to QTL mapping of DM resistance in cucumber and confirmed the results by conventional QTL analysis. By sequencing two DNA pools each consisting of ten individuals showing high resistance and susceptibility to DM from a F₂ population, we identified single nucleotide polymorphisms (SNPs) between the two pools. We employed a statistical method for QTL mapping based on these SNPs. Five QTLs, dm2.2, dm4.1, dm5.1, dm5.2, and dm6.1, were detected and dm2.2 showed the largest effect on DM resistance. Conventional QTL analysis using the F₂ confirmed dm2.2 (R ² = 10.8–24 %) and dm5.2 (R ² = 14–27.2 %) as major QTLs and dm4.1 (R ² = 8 %) as two minor QTLs, but could not detect dm5.1 and dm6.1. A new QTL on chromosome 2, dm2.1 (R ² = 28.2 %) was detected by the conventional QTL method using an F₃ population. This study demonstrated the effectiveness of NGS-assisted BSA for mapping QTLs conferring DM resistance in cucumber and revealed the unique genetic inheritance of DM resistance in this population through two distinct major QTLs on chromosome 2 that mainly harbor DM resistance.

     

Theoretical Aspects of Differential Scanning Calorimetry as a Tool for the Studies of Equilibrium Thermodynamics in Pharmaceutical Solid Phase Transitions

Although differential scanning calorimetry (DSC) is a non-equilibrium technique, it has been used to gain energetic information that involves phase equilibria. DSC has been widely used to characterize the equilibrium melting parameters of small organic pharmaceutical compounds. An understanding of how DSC measures an equilibrium event could make for a better interpretation of the results. The aim of this mini-review was to provide a theoretical insight into the DSC measurement to obtain the equilibrium thermodynamics of a phase transition especially the melting process. It was demonstrated that the heat quantity obtained from the DSC thermogram (ΔH) was related to the thermodynamic enthalpy of the phase transition (ΔH ^P ) via: ΔH?=?ΔH ^P /(1?+?K ^??1) where K was the equilibrium constant. In melting, the solid and liquefied phases presumably coexist resulting in a null Gibbs free energy that produces an infinitely larger K. Thus, ΔH could be interpreted as ΔH ^P. Issues of DSC investigations on melting behavior of crystalline solids including polymorphism, degradation impurity due to heating in situ, and eutectic melting were discussed. In addition, DSC has been a tool for determination of the impurity based on an ideal solution of the melt that is one of the official methods used to establish the reference standard.     

Design,synthesis, and characterization of 2,2-bis(2,4-dinitrophenyl)-2-(phosphonatomethylamino)acetate as a herbicidal and biological active agent

The present study was designed to synthesize the bioactive molecule 2,2-bis(2,4-dinitrophenyl)-2-(phosphonatomethylamino)acetate (1), having excellent applications in the field of plant protection as a herbicide. Structure of newly synthesized molecule 1 was confirmed by using the elemental analysis, mass spectrometric, NMR, UV-visible, and FTIR spectroscopic techniques. To obtain better structural insights of molecule 1, 3D molecular modeling was performed using the GAMESS programme. Microbial activities of 1 were checked against the pathogenic strains Aspergillus fumigatus (NCIM 902) and Salmonella typhimurium (NCIM 2501). Molecule 1 has shown excellent activities against fungal strain A. fumigates (35 μg/l) and bacterial strain S. typhimurium (25 μg/l). To check the medicinal significance of molecule 1, interactions with bovine serum albumin (BSA) protein were checked. The calculated value of binding constant of molecule 1–BSA complex was 1.4 × 10⁶ M^?1, which were similar to most effective drugs like salicylic acid. More significantly, as compared to herbicide glyphosate, molecule 1 has exhibited excellent herbicidal activities, in pre- and post-experiments on three weeds; barnyard grass (Echinochloa Crus), red spranglitop (Leptochloa filiformis), and yellow nuts (Cyperus Esculenfus). Further, effects of molecule 1 on plant growth-promoting rhizobacterial (PGPR) strains were checked. More interestingly, as compared to glyphosate, molecule 1 has shown least adverse effects on soil PGPR strains including the Rhizobium leguminosarum (NCIM 2749), Pseudomonas fluorescens (NCIM 5096), and Pseudomonas putida (NCIM 2847).     

Evaluation of microbial globin promoters for oxygen-limited processes using <Emphasis Type="Italic">Escherichia coli</Emphasis>

Oxygen-responsive promoters can be useful for synthetic biology applications, however, information on their characteristics is still limited. Here, we characterized a group of heterologous microaerobic globin promoters in Escherichia coli. Globin promoters from Bacillus subtilis, Campylobacter jejuni, Deinococcus radiodurans, Streptomyces coelicolor, Salmonella typhi and Vitreoscilla stercoraria were used to express the FMN-binding fluorescent protein (FbFP), which is a non-oxygen dependent marker. FbFP fluorescence was monitored online in cultures at maximum oxygen transfer capacities (OTR_max) of 7 and 11 mmol L^?1 h^?1. Different FbFP fluorescence intensities were observed and the OTR_max affected the induction level and specific fluorescence emission rate (the product of the specific fluorescence intensity multiplied by the specific growth rate) of all promoters. The promoter from S. typhi displayed the highest fluorescence emission yields (the quotient of the fluorescence intensity divided by the scattered light intensity at every time-point) and rate, and together with the promoters from D. radiodurans and S. coelicolor, the highest induction ratios. These results show the potential of diverse heterologous globin promoters for oxygen-limited processes using E. coli.     

Comparative study of daytime and nighttime sap flow of <Emphasis Type="Italic">Populus euphratica</Emphasis>

In order to quantify and characterize the variance in desert riparian forest tree sap flow, we measured the sap flow from Populus euphratica and compared the daytime and nighttime patterns and responses to environmental variables. Results showed that daytime sap flow velocity was significantly higher (P?<?0.05). Daytime and nighttime mean sap flow velocities were 7.65 and 4.01 cm h^?1 in spring, 21.38 and 9.60 cm h^?1 in summer, and 11.04 and 5.21 cm h^?1 in autumn, respectively. Moreover, results indicated that the stoma remained partially open (15% minimum) throughout the night, providing sufficient evidence for the existance of nighttime transpiration. The vapor pressure deficit (VPD), stomatal conductance (Cs), photosynthetically active radiation (PAR), air temperature (Ta), wind speed (WS), and soil moisture (θ) all had significant positive effects on P. euphratica sap flow velocity (P?<?0.05). Furthermore, the relationship between daytime sap flow velocity and VPD showed clockwise hysteresis, while the relationship between nighttime sap flow velocity and VPD showed counter-clockwise hysteresis. It was evident that PAR and VPD were the key factors impacting daytime sap flow velocity, while Cs and θ were the key factors impacting nighttime sap flow velocity. Furthermore, linear regression results showed that daytime sap flow had a significant positive effect on nighttime sap flow throughout the growing season (P?<?0.05).