Characterization of the sugar alcohol-producing yeast Pichia anomala

Sugar alcohols have been widely applied in the field of food and medicine for their unique properties. Compared to chemical production, microbial production of sugar alcohol has become attractive for its environmental and sustainable pattern. In this study, a potential yeast isolated from soil of Beijing suburbs was identified as Pichia anomala TIB-x229, and its key enzyme of d-arabitol dehydrogenase for microbial production of sugar alcohols was functionally characterized. This yeast could simultaneously produce d-arabitol, xylitol, and/or ribitol from a different ratio of sugar substrates at a high efficiency by bioconversion, and no glucose repression happened when mixed sugars of xylose and glucose were used as the substrates during the bioconversion. This yeast could also efficiently convert complicated feedstock such as xylose mother liquor to d-arabitol, xylitol, and ribitol with 55 % yields. To elucidate the conversion relationship of the sugar alcohols, especially d-arabitol and xylitol, the key d-arabitol dehydrogenase gene from P. anomala was cloned, expressed and purified for further in vitro characterization. The results showed that this d-arabitol dehydrogenase could catalyze arabitol to xylulose further, which is significant for xylitol production from glucose. Our study laid the foundation for improving the production of sugar alcohols by metabolic and fermentation engineering strategies.     

Differentiation of strains of sugar beet yellows virus onTetragonia expansa Murr. and other indicator plants

Five different isolates of beet yellows virus were maintained without any changes in their properties onTetragonia expansa Murr. syn.T. tetragonoides Pall. for a long period of time. According to their characteristics and different properties especially in a diploid inbred line of sugar beet the isolates are considered to be strains of BYV and are classified into three groups: group of mild strains (the mild masked and mild strains), normal strains (the common strain) and necrotic strains (the severe necrotic and necrotic strains). The necrotic strains of BYV were relatively easily transmissible manually to sugar beet plants and other indicator species. The common strain can be transmitted to sugar beet,Chenopodium quinoa Willd. but not toC. capitatum L. Asch. Mild strains are transmissible with difficulty andC. quinoa is the only species which develops a larger number of local lesions after inoculation. In contrast to the mild masked and common strains it is manually transmissible toC. capitatum. The mild masked strain can not be transmitted to sugar beet.Nicotiana quadrivalvis Pursh. is not susceptible to mechanical inoculation with BYV. Aphid transmission withMyzus persicae (Sulz.) was positive in experiments with necrotic strains only. Mechanical transmission of BYV was successful also toC. foliosum (Moench) Asch.,C. murale L. andClaytonia perfoliata Donn. The last two species were susceptible to inoculation by aphids as well. Attempts to transmit the virus manually toT. expansa Murr. andC. giganteum Donn. failed.     

Fluorescent sensors based on BODIPY derivatives for aluminium ion recognition: an experimental and theoretical study

Two BODIPY derivative sensors for metal ion recognition containing 10-(4-hydroxyphenyl) (L1) and 10-(3,4-dihydroxyphenyl) (L2) were synthesized in a one-pot reaction of benzaldehyde derivative and 2,4-dimethylpyrrole in the presence of trifluoroacetic acid as catalyst. The binding abilities between these sensors and 50 equivalents of Na⁺, K⁺, Ag⁺, Ca²⁺, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Cd²⁺, Pb²⁺, Al³⁺ and Cr³⁺ ions were studied using UV–vis and fluorescent spectroscopic methods. Of all the metal ions tested, Al³⁺ ion showed the greatest decrease in intensity in the spectra of the sensors, and therefore Al³⁺ ion forms the strongest complex. The binding abilities of BODIPY receptors with Na⁺, Ag⁺, Ca²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺ and Al³⁺ ions were also investigated using density functional theory (DFT) calculations at B3LYP/LanL2DZ theoretical level. The calculated results point to the same conclusion. DFT calculations also provided the HOMO–LUMO energy levels, which can explain the spectrum change upon complexation.

Genetic analysis of bolting after winter in sugar beet (Beta vulgaris L.)

Key message

This study reveals for the first time a major QTL for post-winter bolting resistance in sugar beet ( Beta vulgaris L.). The knowledge of this QTL is a major contribution towards the development of a winter sugar beet with controlled bolting behavior.

Abstract

In cool temperate climates, sugar beets are currently grown as a spring crop. They are sown in spring and harvested in autumn. Growing sugar beet as a winter crop with an extended vegetation period fails due to bolting after winter. Bolting after winter might be controlled by accumulating genes for post-winter bolting resistance. Previously, we had observed in field experiments a low post-winter bolting rate of 0.5 for sugar beet accession BETA 1773. This accession was crossed with a biennial sugar beet with regular bolting behavior to develop a F₃ mapping population. The population was grown in the greenhouse, exposed to artificial cold treatment for 16 weeks and transplanted to the field. Bolting was recorded twice a week from May until October. Post-winter bolting behavior was assessed by two different factors, bolting delay (determined as days to bolt after cold treatment) and post-winter bolting resistance (bolting rate after winter). For days to bolt, means of F₃ families ranged from 25 to 164 days while for bolting rate F₃ families ranged from 0 to 1. For each factor one QTL explaining about 65 % of the phenotypic variation was mapped to the same region on linkage group 9 with a partially recessive allele increasing bolting delay and post-winter bolting resistance. The results are discussed in relation to the potential use of marker-assisted breeding of winter sugar beets with controlled bolting.     

Optical chemosensors for Cu(II) ion based on BODIPY derivatives: an experimental and theoretical study

Two BODIPY derivatives for Cu²⁺ ion chemosensors containing 4-[2-(diethylamino)-2-oxoethoxy]phenyl (BDP1) and 3,4-bis[2-(diethylamino)-2-oxoethoxy]phenyl (BDP2) were synthesized by coupling appropriate N,N-diethyl-2-(4-formylphenoxy)acetamide and 2,4-dimethylpyrrole moieties in the presence of trifluoroacetic acid and anhydrous dichloromethane at room temperature. The binding abilities between these chemosensors and 50 equivalents of Na⁺, K⁺, Ag⁺, Ca²⁺, Fe²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Cd²⁺, Hg²⁺ and Pb²⁺ ions were studied using UV-vis and fluorescence spectrophotometry. The results show that, compared to other ions, both the UV-vis absorption and fluorescence emission intensity of BDP2 decreased dramatically when Cu²⁺ ion was added. To explain this behavior, ab initio quantum chemical calculations were performed using correlated second-order Møller-Plesset perturbation theory (MP2/LanL2DZ). The calculated orbital energies indicated that the decrease in UV-vis absorption intensity and the quenching of fluorescene emission were due to the single-electron reduction of Cu²⁺ to Cu⁺ ion.

Simulations on the possibility of formation of complexes between fluorouracil drug and cucurbit[n]urils: ab initio van der Waals DFT study

The binding geometry of fluorouracil/cucurbit[n]urils (CB[n]s) complexes with n?=?5–8 is investigated using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such host-guest complexes are typically calculated using conventional DFT method, which significantly underestimates non-local dispersion forces (or vdW contributions) and therefore affects interactions between respected entities. We address here the role of vdW forces for the fluorouracil and CB[n]s molecules which can form directional hydrogen bonds with each other. It was found that the inclusion of dispersion interactions significantly affects the host-guest binding properties and the hydrogen bonding between the molecules provides the main binding mechanism, while results in the same geometries for the considered complexes. The 0.84 eV binding energy, for the thermodynamically favorable state, reveals that the interaction of fluorouracil with CB[n]s is an exothermic interaction and typical for strong hydrogen bonding. Furthermore, we have investigated the binding nature of these host-guest systems in aqueous solution with ab initio MD simulations adopting vdW-DF method. These findings afford evidence for the applicability of the vdW-DF approach and provide a realistic benchmark for the investigation of the host-guest complexes.

First-principles vdW-DF investigation on the interaction between the oxazepam molecule and C60 fullerene

The interaction between oxazepam and C₆₀ fullerene was explored using first-principles vdW-DF calculations. It was found that oxazepam binds weakly to the fullerene cage via its carbonyl group. The binding of oxazepam to C₆₀ is affected drastically by nonlocal dispersion interactions, while vdW forces affect the corresponding geometries only a little. Furthermore, aqueous solution affects the geometries of the oxazepam approaching to fullerene slightly, while oxazepam binds slightly farther away from the nanocage. The results presented provide evidence for the applicability of the vdW-DF method and serve as a practical benchmark for the investigation of host–guest interactions in biological systems.

Stereoselectivity of chalcone isomerase with chalcone derivatives: a computational study

Chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcones into flavonoids. The activity of CHI is essential for the biosynthesis of flavonoids precursors of floral pigments and phenylpropanoid plant defense compounds. In the present study, we explored the detailed binding structures and binding free energies for two different active site conformations of CHI with s-cis/s-trans conformers of three chalcone compounds by performing molecular dynamics (MD) simulations and binding free energy calculations. The computational results indicate that s-cis/s-trans conformers of chalcone compounds are orientated in the similar binding position in the active site of CHI and stabilized by the different first hydrogen bond network and the same second hydrogen bond network. The first hydrogen bond network results in much lower binding affinity of s-trans conformer of chalcone compound with CHI than that of s-cis conformer. The conformational change of the active site residue T48 from indirectly interacting with the substrate via the second hydrogen bond network to directly forming the hydrogen bond with the substrates cannot affect the binding mode of both conformers of chalcone compounds, but remarkably improves the binding affinity. These results show that CHI has a strong stereoselectivity. The calculated binding free energies for three chalcone compounds with CHI are consistent with the experimental activity data. In addition, several valuable insights are suggested for future rational design and discovery of high-efficiency mutants of CHI.

A molecular dynamics study on sI hydrogen hydrate

A molecular dynamics simulation is carried out to explore the possibility of using sI clathrate hydrate as hydrogen storage material. Metastable hydrogen hydrate structures are generated using the LAMMPS software. Different binding energies and radial distribution functions provide important insights into the behavior of the various types of hydrogen and oxygen atoms present in the system. Clathrate hydrate cages become more stable in the presence of guest molecules like hydrogen.

Cytotoxic effect and molecular docking of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide—a novel topoisomerase II inhibitor

The preliminary cytotoxic effect of 4-ethoxycarbonylmethyl-1-(piperidin-4-ylcarbonyl)-thiosemicarbazide hydrochloride (1)—a potent topoisomerase II inhibitor—was measured using a MTT assay. It was found that the compound decreased the number of viable cells in both estrogen receptor-positive MCF-7 and estrogen receptor-negative MDA-MB-231breast cancer cells, with IC₅₀ values of 146?±?2 and 132?±?2 μM, respectively. To clarify the molecular basis of the inhibitory action of 1, molecular docking studies were carried out. The results suggest that 1 targets the ATP binding pocket.

The identification of allergen proteins in sugar beet (Beta vulgaris) pollen causing occupational allergy in greenhouses

Background

During production of sugar beet (Beta vulgaris) seeds in greenhouses, workers frequently develop allergic symptoms. The aim of this study was to identify and characterize possible allergens in sugar beet pollen.

Methods

Sera from individuals at a local sugar beet seed producing company, having positive SPT and specific IgE to sugar beet pollen extract, were used for immunoblotting. Proteins in sugar beet pollen extracts were separated by 1- and 2-dimensional electrophoresis, and IgE-reactive proteins analyzed by liquid chromatography tandem mass spectrometry.

Results

A 14 kDa protein was identified as an allergen, since IgE-binding was inhibited by the well-characterized allergen Che a 2, profilin, from the related species Chenopodium album. The presence of 17 kDa and 14 kDa protein homologues to both the allergens Che a 1 and Che a 2 were detected in an extract from sugar beet pollen, and partial amino acid sequences were determined, using inclusion lists for tandem mass spectrometry based on homologous sequences.

Conclusion

Two occupational allergens were identified in sugar beet pollen showing sequence similarity with Chenopodium allergens. Sequence data were obtained by mass spectrometry (70 and 25%, respectively for Beta v 1 and Beta v 2), and can be used for cloning and recombinant expression of the allergens. As for treatment of Chenopodium pollinosis, immunotherapy with sugar beet pollen extracts may be feasible.     

Probing mechanism of metal catalyzed hydrolysis of Thymidylyl (3′-O, 5′-S) thymidine phosphodiester derivatives

Hydrolysis of nucleic acids is of fundamental importance in biological sciences. Kinetic and theoretical studies on different substrates wherein the phosphodiester bond combined with alkyl or aryl groups and sugar moiety have been the focus of attention in recent literature. The present work focuses on understanding the mechanism and energetics of alkali metal (Li, Na, and K) catalyzed hydrolysis of phosphodiester bond in modeled substrates including Thymidylyl (3′-O, 5′-S) thymidine phosphodiester (Tp-ST) (1), 3′-Thymidylyl (1-trifluoroethyl) phosphodiester (Tp-OCH₂CF₃) (2), 3′-Thymidylyl (o-cholorophenyl) phosphodiester (Tp-OPh(o-Cl)) (3) and 3′-Thymidylyl(p-nitrophenyl) phosphodiester (Tp-OPh(p-NO₂)) (4) employing density functional theory. Theoretical calculations reveal that the reaction follows a single-step (A_ND_N) mechanism where nucleophile attack and leaving group departure take place simultaneously. Activation barrier for potassium catalyzed Tp-ST hydrolysis (12.0 kcal mol^?1) has been nearly twice as large compared to that for hydrolysis incorporating lithium or sodium. Effect of solvent (water) on activation energies has further been analyzed by adding a water molecule to each metal ion of the substrate. It has been shown that activation barrier of phosphodiester hydrolysis correlates well with basicity of leaving group.

Theoretical study on aluminum carbide endohedral fullerene-Al4C@C80

The possibility of a new endohedral fullerene with a trapped aluminum carbide cluster, Al₄C @C₈₀-I _h , was theoretical investigated. The geometries and electronic properties of it were investigated using density functional theory methods. The Al₄C unit formally transfers six electrons to the C₈₀ cage which induces stabilization of Al₄C@C₈₀. A favorable binding energy, relatively large HOMO-LUMO gap, electron affinities and ionization potentials suggested the Al₄C@C₈₀ is rather stable. The analysis of vertical ionization potential and vertical electron affinity indicate Al₄C@C₈₀ is a good electron acceptor.

X-ray structure of a galactose-specific lectin from Spatholobous parviflorous

A galactose-specific seed lectin from Spatholobous parviflorus (SPL) has been purified, crystallized and its X-ray structure solved. It is the first lectin purified and crystallized from the genus Spatholobus (family: Fabaceae). The crystals belong to the space group P1, with a = 60.792 Å, b = 60.998 Å, c = 78.179 Å, α = 78.68°, β = 88.62°, γ = 104.32°. The data were collected at 2.04 Å resolution under cryocondition, on a MAR image-plate detector system, mounted on a rotating anode X-ray generator. The coordinates of Dolichos biflorus lectin (1lu1) were successfully used for the structure solution by molecular replacement method. The primary structure of the SPL was not known earlier and it was unambiguously visible in the electron density. S. parviflorus lectin is a hetero-dimeric-tetramer with two alpha and two beta chains of 251 and 239 residues respectively. SPL has two metal ions, Ca²⁺ and Mn²⁺, bound to a loop region of each chain. The SPL monomers are in jelly roll form.     

Quantitative characterization of protein tertiary motifs

Dimerization of 2-naphthalenecarbonitrile (2-NpCN) mediated by cucurbit[8]uril (CB[8]) has been investigated employing the density functional theory. Different structures of 2-NpCN dimers were generated by combining monomers in anti-head-to-head (A), anti-head-to-tail (B) and syn-head-to-tail (C) fashion. All these dimeric structures possess rigid cube-like architecture. On confinement within the CB[8] dimer A turns out to be the lowest energy structure. Calculated ¹H NMR spectra revealed that the 2-NpCN dimer exhibits large shielding for aromatic protons consistent with the experiment. The protons attached to cubane moiety on the other hand, led to down-field signals. Dimerization mediated with CB[8] cavitand is further accompanied by the frequency up-shift (blue shift) of methylene stretching vibration in its infrared spectra.

A comparative DFT study on aquation and nucleobase binding of ruthenium (II) and osmium (II) arene complexes

The potential energy surfaces of the reactions of organometallic arene complexes of the type [(η ⁶-arene)M^II(pic)Cl] (where pic = 2-picolinic acid, M = Ru or Os) were examined by a DFT computational study. Among the seven density functional methods, hybrid exchange functional B3LYP outperforms the others to explain the aquation of the complexes. The reactions and binding energies of Ru^II and Os^II arene complexes with both 9EtG and 9EtA were studied to gain insight into the reactivity of these types of organometallic complexes with DNA. The obtained data rationalize experimental observation, contributing to partly understanding the potential biological and medical applications of organometallic complexes.

Ethylene is differentially regulated during sugar beet germination and affects early root growth in a dose-dependent manner

Main conclusion

By integrating molecular, biochemical, and physiological data, ethylene biosynthesis in sugar beet was shown to be differentially regulated, affecting root elongation in a concentration-dependent manner. There is a close relation between ethylene production and seedling growth of sugar beet (Beta vulgaris L.), yet the exact function of ethylene during this early developmental stage is still unclear. While ethylene is mostly considered to be a root growth inhibitor, we found that external 1-aminocyclopropane-1-carboxylic acid (ACC) regulates root growth in sugar beet in a concentration-dependent manner: low concentrations stimulate root growth while high concentrations inhibit root growth. These results reveal that ethylene action during root elongation is strongly concentration dependent. Furthermore our detailed study of ethylene biosynthesis kinetics revealed a very strict gene regulation pattern of ACC synthase (ACS) and ACC oxidase (ACO), in which ACS is the rate liming step during sugar beet seedling development.