Understanding the reactivity of captodative ethylenes in polar cycloaddition reactions. A theoretical study

The electrophilic/nucleophilic character of a series of captodative (CD) ethylenes involved in polar cycloaddition reactions has been studied using DFT methods at the B3LYP/6-31G(d) level of theory. The transition state structures for the electrophilic/nucleophilic interactions of two CD ethylenes toward a nucleophilically activated ethylene, 2-methylene-1,3-dioxolane, and an electrophilically activated ethylene, 1,1-dicyanoethyelene, have been studied, and their electronic structures have been characterized using both NBO and ELF methods. Analysis of the reactivity indexes of the CD ethylenes explains the reactivity of these species. While the electrophilicity of the molecules accounts for the reactivity toward nucleophiles, it is shown that a simple index chosen for the nucleophilicity, Nu, based on the HOMO energy is useful explaining the reactivity of these CD ethylenes toward electrophiles.

Estrogenicity of resin-based composites and sealants used in dentistry

We tested some resin-based composites used in dentistry for their estrogenic activity. A sealant based on bisphenol-A diglycidylether methacrylate (bis-GMA) increased cell yields, progesterone receptor expression, and pS2 secretion in human estrogen-target, serum-sensitive MCF7 breast cancer cells. Estrogenicity was due to bisphenol-A and bisphenol-A dimethacrylate, monomers found in the base paste of the dental sealant and identified by mass spectrometry. Samples of saliva from 18 subjects treated with 50 mg of a bis-GMA-based sealant applied on their molars were collected 1 hr before and after treatment. Bisphenol-A (range 90-931 micrograms) was identified only in saliva collected during a 1-hr period after treatment. The use of bis-GMA-based resins in dentistry, and particularly the use of sealants in children, appears to contribute to human exposure to xenoestrogens.

Applications of the Conceptual Density Functional Theory Indices to Organic Chemistry Reactivity

Theoretical reactivity indices based on the conceptual Density Functional Theory (DFT) have become a powerful tool for the semiquantitative study of organic reactivity. A large number of reactivity indices have been proposed in the literature. Herein, global quantities like the electronic chemical potential μ, the electrophilicity ω and the nucleophilicity N indices, and local condensed indices like the electrophilic P k + and nucleophilic P k - Parr functions, as the most relevant indices for the study of organic reactivity, are discussed.

The nucleophilicity N index in organic chemistry

The nucleophilicity N index (J. Org. Chem. 2008, 73, 4615), the inverse of the electrophilicity, 1/ω, and the recently proposed inverse of the electrodonating power, 1/ω⁻, (J. Org. Chem. 2010, 75, 4957) have been checked toward (i) a series of single 5-substituted indoles for which rate constants are available, (ii) a series of para-substituted phenols, and for (iii) a series of 2,5-disubstituted bicyclic[2.2.1]hepta-2,5-dienes which display concurrently electrophilic and nucleophilic behaviors. While all considered indices account well for the nucleophilic behavior of organic molecules having a single substitution, the nucleophilicity N index works better for more complex molecules. Unlike, the inverse of the electrophilicity, 1/ω, (R(2) = 0.71), and the inverse of the electrodonating power, 1/ω⁻ (R(2) = 0.83), a very good correlation of the nucleophilicity N index of twelve 2-substituted-6-methoxy-bicyclic[2.2.1]hepta-2,5-dienes versus the activation energy associated with the nucleophilic attack on 1,1-dicyanoethylene is found (R(2) = 0.99). This comparative study allows to assert that the nucleophilicity N index is a measure of the nucleophilicity of complex organic molecules displaying concurrently electrophilic and nucleophilic behaviors.

Genomic prediction in CIMMYT maize and wheat breeding programs

Genomic selection (GS) has been implemented in animal and plant species, and is regarded as a useful tool for accelerating genetic gains. Varying levels of genomic prediction accuracy have been obtained in plants, depending on the prediction problem assessed and on several other factors, such as trait heritability, the relationship between the individuals to be predicted and those used to train the models for prediction, number of markers, sample size and genotype × environment interaction (GE). The main objective of this article is to describe the results of genomic prediction in International Maize and Wheat Improvement Center's (CIMMYT's) maize and wheat breeding programs, from the initial assessment of the predictive ability of different models using pedigree and marker information to the present, when methods for implementing GS in practical global maize and wheat breeding programs are being studied and investigated. Results show that pedigree (population structure) accounts for a sizeable proportion of the prediction accuracy when a global population is the prediction problem to be assessed. However, when the prediction uses unrelated populations to train the prediction equations, prediction accuracy becomes negligible. When genomic prediction includes modeling GE, an increase in prediction accuracy can be achieved by borrowing information from correlated environments. Several questions on how to incorporate GS into CIMMYT's maize and wheat programs remain unanswered and subject to further investigation, for example, prediction within and between related bi-parental crosses. Further research on the quantification of breeding value components for GS in plant breeding populations is required.

Purification and characterization of a phenoloxidase (laccase) from the lignin-degrading basidiomycete PM1 (CECT 2971)

A new lignin-degrading basidiomycete, strain PM1 (= CECT 2971), was isolated from the wastewater of a paper factory. The major ligninolytic activity detected in the basidiomycete PM1 culture supernatant was a phenoloxidase (laccase). This activity was produced constitutively in defined or complex media and appeared as two protein bands in native gel electrophoresis preparations. No enzyme induction was found after treatment with certain potential laccase inducers. Laccase I was purified to homogeneity by gel filtration chromatography, anion-exchange chromatography, and hydrophobicity chromatography. The enzyme is a monomeric glycoprotein containing 6.5% carbohydrate and having a molecular weight of 64,000. It has an isoelectric point of 3.6, it is stable in a pH range from 3 to 9, and its optimum pH is 4.5. The laccase optimal reaction temperature is 80 degrees C, the laccase is stable for 1 h at 60 degrees C, and its activity increases with temperature. Spectroscopic analysis revealed that the enzyme has four bound copper atoms, a type I copper, a type II copper, and a type III binuclear copper. The amino-terminal sequence of the protein is very similar to the amino-terminal sequences of laccases from Coriolus hirsutus and Phlebia radiata.

Origin of the synchronicity on the transition structures of polar Diels-Alder reactions. Are these reactions [4 + 2] processes?

The transition structures (TSs) for a series of related Diels-Alder reactions between cyclopentadiene and mono-, di-, tri-, and tetracyanoethylene derivatives have been studied with use of DFT methods at the B3LYP/6-31G computational level. The increase of the electron-withdrawing substitution on ethylene increases the rate of these polar cycloadditions. However, the symmetric arrangement of cis and trans 1,2-di- and tetracyanoethylenes decreases the effectiveness of the substitution, which can be related to the symmetry found at the corresponding TSs. A DFT analysis of the global and local electrophilicity power of these series of cyano ethylenes provides a sound explanation about the nature of these synchronous processes. The present theoretical study is in agreement with the experimental outcomes.

Fission yeast alpha-glucan synthase Mok1 requires the actin cytoskeleton to localize the sites of growth and plays an essential role in cell morphogenesis downstream of protein kinase C function

In fission yeast protein kinase C homologues (Pck1 and Pck2) are essential for cell morphogenesis. We have isolated mok1(+) in a genetic screen to identify downstream effectors for Pck1/2. mok1(+) is essential for viability and encodes a protein that has several membrane-spanning domains and regions homologous to glucan metabolic enzymes. mok1 mutant shows abnormal cell shape, randomization of F-actin and weak cell wall. Biochemical analysis shows that Mok1 appears to have alpha-glucan synthase activity. Mok1 localization undergoes dramatic alteration during the cell cycle. It localizes to the growing tips in interphase, the medial ring upon mitosis, a double ring before and dense dot during cytokinesis. Double immunofluorescence staining shows that Mok1 exists in close proximity to actin. The subcellular localization of Mok1 is dependent upon the integrity of the F-actin cytoskeleton. Conversely, overexpression of mok1(+) blocks the translocation of cortical actin from one end of the cell to the other. pck2 mutant is synthetically lethal with mok1 mutant, delocalizes Mok1 and shows a lower level of alpha-glucan. These results indicate that Mok1 plays a crucial role in cell morphogenesis interdependently of the actin cytoskeleton and works as one of downstream effectors for Pck1/2.

A genomic approach for the identification and classification of genes involved in cell wall formation and its regulation in Saccharomyces cerevisiae

Using a hierarchical approach, 620 non-essential single-gene yeast deletants generated by EUROFAN I were systematically screened for cell-wall-related phenotypes. By analyzing for altered sensitivity to the presence of Calcofluor white or SDS in the growth medium, altered sensitivity to sonication, or abnormal morphology, 145 (23%) mutants showing at least one cell wall-related phenotype were selected. These were screened further to identify genes potentially involved in either the biosynthesis, remodeling or coupling of cell wall macromolecules or genes involved in the overall regulation of cell wall construction and to eliminate those genes with a more general, pleiotropic effect. Ninety percent of the mutants selected from the primary tests showed additional cell wall-related phenotypes. When extrapolated to the entire yeast genome, these data indicate that over 1200 genes may directly or indirectly affect cell wall formation and its regulation. Twenty-one mutants with altered levels of beta1,3-glucan synthase activity and five Calcofluor white-resistant mutants with altered levels of chitin synthase activities were found, indicating that the corresponding genes affect beta1,3-glucan or chitin synthesis. By selecting for increased levels of specific cell wall components in the growth medium, we identified 13 genes that are possibly implicated in different steps of cell wall assembly. Furthermore, 14 mutants showed a constitutive activation of the cell wall integrity pathway, suggesting that they participate in the modulation of the pathway either directly acting as signaling components or by triggering the Slt2-dependent compensatory mechanism. In conclusion, our screening approach represents a comprehensive functional analysis on a genomic scale of gene products involved in various aspects of fungal cell wall formation.

Global and local reactivity indices for electrophilic/nucleophilic free radicals

A set of five DFT reactivity indices, namely, the global electrophilicity ω° and nucleophilicity N° indices, the radical Parr function P, and the local electrophilicity ω and nucleophilicity N indices, for the study of free radicals (FRs) are proposed. Global indices have been tested for a series of 32 FRs having electrophilic and/or nucleophilic activations. As expected, no correlation between the proposed global electrophilicity ω° and global nucleophilicity N° has been found. Analysis of the local electrophilicity ω and nucleophilicity N indices for FRs, together with analysis of the local electrophilicity ωk and nucleophilicity Nk indices for alkenes, allows for an explanation of the regio- and chemoselectivity in radical additions of FRs to alkenes. Finally, an ELF bonding analysis for the C-C bond formation along the nucleophilic addition of 2-hydroxyprop-2-yl FR 28 to methyl acrylate 35 evidences that the new C-C bond is formed by C-to-C coupling of two radical centres, which are properly characterized through the use of the Parr functions.

Comparison between experimental and theoretical scales of electrophilicity in benzhydryl cations

The theoretical electrophilicity pattern of a series of benzhydryl cations as described in terms of a model based on global reactivity indexes is compared with an experimental scale recently proposed by Mayr et al. [J. Am. Chem. Soc. 2001, 123, 9500]. A good correlation between both theoretical and experimental quantities is found. The effect of chemical substitution on the electrophilic power of these charged electrophiles may also be assessed as local responses at the active site, in terms of a global contribution described by changes in global electrophilicity with reference to the dianisylcarbenium ion, and a local contribution described by the variations in electrophilic Fukui function at that site.

Definition of a Nucleophilicity Scale

This work deals with exploring some empirical scales of nucleophilicity. We have started evaluating the experimental indices of nucleophilicity proposed by Legon and Millen on the basis of the measure of the force constants derived from vibrational frequencies using a probe dipole H-X (X = F,CN). The correlation among some theoretical parameters with this experimental scale has been evaluated. The theoretical parameters have been chosen as the minimum of the electrostatic potential V(min), the binding energy (BE) between the nucleophile and the H-X dipole, and the electrostatic potential measured at the position of the hydrogen atom V(H) when the complex nucleophile and dipole H-X is in the equilibrium geometry. All of them present good correlations with the experimental nucleophilicity scale. In addition, the BEs of the nucleophiles with two other Lewis acids (one hard, BF(3), and the other soft, BH(3)) have been evaluated. The results suggest that the Legon and Millen nucleophilicity scale and the electrostatic potential derived scales can describe in good approximation the reactivity order of the nucleophiles only when the interactions with a probe electrophile is of the hard-hard type. For a covalent interaction that is orbital controlled, a new nucleophilicity index using information of the frontier orbitals of both, the nucleophile and the electrophile has been proposed.

An understanding of the electrophilic/nucleophilic behavior of electro-deficient 2,3-disubstituted 1,3-butadienes in polar diels-alder reactions. A density functional theory study

The electrophilic/nucleophilic behavior of dimethyl 2,3-dimethylenesuccinate 1, an electron-deficient 2,3-disubstituted 1,3-butadiene, in polar Diels-Alder reactions has been studied using DFT methods at the B3LYP/6-31G(d) level of theory. The electronic nature of bonding of the transition structures involved in the cycloaddition reactions of the diene 1 toward the nucleophilically activated dienophile 6 and the strong electrophilically activated dienophile 7 has been carefully examined within the natural bond orbital (NBO) and the topological analysis of the electron localization function (ELF) frameworks. Additionally, a study of the global electrophilicity pattern of the reagents at the ground state was performed. This evidence allows us to rationalize the participation of electron-deficient 2-susbtituted and 2,3-disubstituted 1,3-butadienes as nucleophiles in polar Diels-Alder reactions.

NGF binding to the trk tyrosine kinase receptor requires the extracellular immunoglobulin-like domains

Neurotrophins initiate their biological effects by activating members of the trk tyrosine kinase subfamily. The extracellular region of trk receptors is distinguished by several common structural features, including leucine-rich repeats, clusters of cysteine-rich domains, and two immunoglobulin-like domains. However, the receptor sequences required for ligand binding have not been localized. In order to define the domains involved in NGF binding, a series of chimeric receptors was constructed using cDNA sequences from rat trkA and trkB. The chimeric constructs were expressed after transient transfection in 293 cells and the expression of each receptor was verified by immunoprecipitation and immunoblot analysis. Equilibrium binding of transfected cells revealed that the two IgG domains of trkA are essential for NGF binding. The requirement for the two IgG domains was further confirmed by Scatchard analysis and affinity crosslinking with 125I-NGF. These results indicate that NGF binding is crucially dependent upon interactions with the IgG domains of the trkA receptor.

H-bonded N-heterocyclic base-pair phototautomerizational potential barrier and mechanism: The 7-azaindole dimer

A theoretical analysis of the double proton transfer (PT) in a hydrogen-bonded N-heterocyclic base pair is presented. The calculated (time-dependent density functional theory) double PT barrier calculated for the concerted process of the 7-azaindole C(2h) dimer in the first excited singlet electronic state S(1) conforms well to the kinetic data and the photophysical evidence reported in this article. The calculated PT energy barrier of 4.8 kcal/mol height, and the corresponding zero point energy value, yield for the S(1) state an activation energy barrier of 0.3 kcal/mol. This finding implies that the double PT concerted process is almost barrierless, confirming previous experiments. Upon N-H deuteration of the 7-azaindole dimer, the theoretical excited-state activation energy for the double deuterium transfer is determined to be 1.4 kcal/mol, in agreement with experiment, which in low-temperature spectroscopy is shown to negate excited-state double-deuteron transfer.

A Molecular Electron Density Theory Study of the Reactivity and Selectivities in [3 + 2] Cycloaddition Reactions of C,N-Dialkyl Nitrones with Ethylene Derivatives

The zw-type [3 + 2] cycloaddition (32CA) reactions of C,N-dialkyl nitrones with a series of ethylenes of increased electrophilic character have been studied within the Molecular Electron Density Theory (MEDT) at the MPWB1K/6-311G(d,p) computational level. Both, reactivity and selectivities are rationalized depending on the polar character of the reaction. Due to the strong nucleophilic character of C,N-dialkyl nitrones, the corresponding zw-type 32CA reactions are accelerated with the increased electrophilic character of the ethylene, which also plays a crucial role in the reaction mechanism, thus determining the regio- and stereoselectivities experimentally observed. While, in the 32CA reactions with nucleophilic ethylenes, the reaction begins with the formation of the C-C single bond, determining the ortho regioselectivity, in the 32CA reactions with strong electrophilic ethylenes, the reaction begins with the formation of the C-O single bond involving the β-conjugated carbon of the ethylene, determining the meta regioselectivity. The present MEDT study also provides an explanation for the unexpected ortho regioselectivity experimentally found in the 32CA reactions involving weak electrophilic ethylenes such as ethyl acrylate and acrylonitrile.

Understanding the mechanism of non-polar Diels-Alder reactions. A comparative ELF analysis of concerted and stepwise diradical mechanisms

The electron-reorganization along the concerted and stepwise pathways associated with the non-polar Diels-Alder reaction between cyclopentadiene (Cp, 1) and ethylene (2) has been studied using the topological analysis of the electron localization function (ELF) at the B3LYP/6-31G(d) level of theory. ELF results for the concerted mechanism stresses that the electron-reorganization demanded on the diene and ethylene reagents to reach two pseudo-diradical structures is responsible for the high activation energy. A comparative ELF analysis of some relevant points of the non-polar Diels-Alder reaction between Cp and styrene (10) suggests that these concerted mechanisms do not have a pericyclic electron-reorganization.

Condensed-to-atoms electronic Fukui functions within the framework of spin-polarized density-functional theory

A simple formalism devised to calculate the condensed-to-atoms Fukui function [R. R. Contreras, P. Fuentealba, M. Galván, and P. Pérez, Chem. Phys. Lett. 304, 405 (1999)] has been further analyzed within a spin-polarized density-functional theory framework. The model is based on a frozen-core approximation to these local reactivity indices [M. Galván, A. Vela, and J. L. Gázquez, J. Phys. Chem. 92, 6470 (1988)], giving us an extended local reactivity description of systems based on the frontier spin-up and spin-down molecular orbitals. Degenerate molecular spin orbitals have been explicitly included in our model equations. Computational results for the nitric oxide (NO) and some simple carbene systems are presented in order to test the model. These quantities have been discussed in the context of changes both in charge density and spin density within the context of electron charge transfer or spin-polarization processes.

COVID-19 vaccine candidates based on modified vaccinia virus Ankara expressing the SARS-CoV-2 spike induce robust T- and B-cell immune responses and full efficacy in mice

Vaccines against SARS-CoV-2, the causative agent of the COVID-19 pandemic, are urgently needed. We developed two COVID-19 vaccines based on modified vaccinia virus Ankara (MVA) vectors expressing the entire SARS-CoV-2 spike (S) protein (MVA-CoV2-S); their immunogenicity was evaluated in mice using DNA/MVA or MVA/MVA prime/boost immunizations. Both vaccines induced robust, broad and polyfunctional S-specific CD4+ (mainly Th1) and CD8+ T-cell responses, with a T effector memory phenotype. DNA/MVA immunizations elicited higher T-cell responses. All vaccine regimens triggered high titers of IgG antibodies specific for the S, as well as for the receptor-binding domain; the predominance of the IgG2c isotype was indicative of Th1 immunity. Notably, serum samples from vaccinated mice neutralized SARS-CoV-2 in cell cultures, and those from MVA/MVA immunizations showed a higher neutralizing capacity. Remarkably, one or two doses of MVA-CoV2-S protect humanized K18-hACE2 mice from a lethal dose of SARS-CoV-2. In addition, two doses of MVA-CoV2-S confer full inhibition of virus replication in the lungs. These results demonstrate the robust immunogenicity and full efficacy of MVA-based COVID-19 vaccines in animal models and support its translation to the clinic.IMPORTANCE The continuous dissemination of the novel emerging SARS-CoV-2 virus, with more than 78 million infected cases worldwide and higher than 1,700,000 deaths as of December 23, 2020, highlights the urgent need for the development of novel vaccines against COVID-19. With this aim, we have developed novel vaccine candidates based on the poxvirus modified vaccinia virus Ankara (MVA) strain expressing the full-length SARS-CoV-2 spike (S) protein, and we have evaluated their immunogenicity in mice using DNA/MVA or MVA/MVA prime/boost immunization protocols. The results showed the induction of a potent S-specific T-cell response and high titers of neutralizing antibodies. Remarkably, humanized K18-hACE2 mice immunized with one or two doses of the MVA-based vaccine were 100% protected from SARS-CoV-2 lethality. Moreover, two doses of the vaccine prevented virus replication in lungs. Our findings prove the robust immunogenicity and efficacy of MVA-based COVID-19 vaccines in animal models and support its translation to the clinic.

Effect of bile on the lipid composition and surface properties of bifidobacteria

AIM

The changes produced on the bacterial surface of Bifidobacteria cells when they are grown in bile were compared with those provoked by bile added to bacteria grown in the absence of bile.

METHODS AND RESULTS

The adhesive properties, the zeta potential and the lipid composition of Bifidobacterial strains, isolated from human faeces and grown in MRS medium, were determined. Bacteria grown in MRS with bile showed a loss of adherence and autoaggregation in correlation with a decrease in the surface hydrophobicity in comparison to those grown in MRS without bile, concomitant with the absence of two glycolipids, the increase of sugar content and minor changes in fatty acid composition. The surface changes caused by bile shock on bacteria grown in bile-free medium were much less pronounced and, in addition, no effect on the lipid composition was apparent.

CONCLUSIONS

The comparison of the results indicates that bile action on surface properties is related to metabolic changes.

SIGNIFICANCE AND IMPACT OF THE STUDY

Long-term exposure of bacteria to bile may cause metabolic changes affecting their adhesive properties irreversibly. This may be taken as a criterion to define the probiotic properties of different strains.

Rapid and sensitive diagnosis of human adenovirus infections by a generic polymerase chain reaction

A new adenovirus specific nested polymerase chain reaction (PCR) method is described. It was designed inside the hexon protein gene of the adenovirus genome, and was able to detect DNA of all 47 human adenovirus types in a wide range of clinical samples. A sensitive internal control system able to assure proper analytical conditions for the amplification of as few as 100 molecules of a heterologous DNA was included to avoid false negative results. Sensitivity was estimated at about 10 molecules per tube of a plasmid containing an insert of the first amplification product. The method was able to detect adenovirus infection in 31/43 conjunctival scrapings from patients with acute kerato conjunctivitis 10/40 nasopharyngeal aspirates from patients admitted to hospital with acute respiratory disease and 2/26 urine samples from patients with haemorrhagic cystitis with better sensitivity than cell culture or rapid diagnosis by antigen detection by immunofluorescence (IF) in the case of respiratory specimens. Only two of 17 stools positive for a group F adenovirus specific latex immunoassay were PCR negative. The internal control system avoided a false negative result on another two stool samples. In conclusion, the method described below was shown to be useful for rapid diagnosis of adenovirus infections with higher sensitivity than antigen detection by IF.