Erratum to: “Nano-characterization of Jagged-1-educated dendritic cells”

Paper by Xing et al. “Nano-characterization of Jagged-1-educated dendritic cells” in Volume 6, Issue 6, 981-989 / December 2011; DOI: 10.2478/s11535-011-0063-3 contains an error in the graphic file inserted as Figure 1 and also an incorrect figure caption. The corrected Figure 1, together with its caption is presented below.     

<Emphasis Type="Italic">Ab initio</Emphasis> and DFT investigation of electrophilic addition reaction of bromine to <Emphasis Type="Italic">endo,endo</Emphasis>-tetracyclo[4.2.1.1<Superscript>3,6</Superscript>.0<Superscript>2,7</Superscript>]dodeca-4,9-diene

Full geometric optimization of endo,endo-tetracyclo[4.2.1.1^3,6.0^2,7]dodeca-4,9-diene (TTDD) has been carried out by ab initio and DFT/B3LYP methods and the structure of the molecule investigated. The double bonds of TTDD molecule are endo pyramidalized. The structure of π-orbitals and their mutual interactions for TTDD molecule were investigated. The cationic intermediates and products obtained as a result of the addition reaction have been studied using the HF/6-311G(d), HF/6-311G(d,p) and B3LYP/6-311G(d) methods. The bridged bromonium cation isomerized into the more stable N- and U-type cations and the difference between the stability of these cations is small. The N- and U-type reaction products are obtained as a result of the reaction, which takes place via the cations in question. The stability of exo, exo and exo, endo isomers of N-type product are nearly the same and the formation of both isomers is feasible. The U-type product basically formed from the exo, exo-isomer. Although the U-type cation was 0.68 kcal mol⁻¹ more stable than the N-type cation, the U-type product was 4.79 kcal mol⁻¹ less stable than the N-type product. Figure The energy diagram of TTDD–Br₂ system (kcal mol⁻¹)(MP2/6-311G*//HF/6-311G*)     

Ab initio and DFT study on the electrophilic addition reaction of bromine to tetracyclo[5.3.0.02,6.03,10]deca–4,8–diene

The electronic and geometric structures of tetracyclo[5.3.0.0^2,6.0^3,10]deca-4,8-diene (hypostrophene) have been investigated by ab initio and DFT/B3LYP methods using the 6-31G* and 6-311G* basis sets. The double bonds of hypostrophene are endo-pyramidalized. The cationic intermediates and products formed in the addition reaction have been investigated using the HF/6-311G*, HF/6-311G**, and B3LYP/6-311G* methods. The bridged bromonium cation was more stable than the U-type cation. Considering that the bridged cation does not isomerize to the less stable U-type cation, it is not possible for the U-type product to be obtained in the reaction. The bridged bromonium cation transformed into the more stable N-type cation and the N-type product was obtained via this cation. The thermodynamic stability of the exo, exo and exo, endo isomers of the N-type dibromide molecule were almost identical. The N-type product was 16.6 kcal mol⁻¹ more stable than the U-type product. Figure General energy diagram of the hypostrophene–bromine (HS–Br₂) system (kcal mol⁻¹) (MP2/6-311G*//HF/6-311G*)     

Vibrational analysis of a solvated green fluorescent protein chromophore

Resonance Raman (RR) spectra of green fluorescent protein (GFP) model chromophores in solution have been simulated with the CASSCF/MM methodology. Although several reports on vibrational analysis of GFP model chromophores have been recently published, the RR spectra were simulated for the first time in explicit solution with the inclusion of the counterion, as these effects are crucial for unambiguously reproducing the vibrational band assignment in the anionic form of the GFP chromophore. This strategy allows for a one-to-one correspondence of the calculated vibrational modes to the observed RR bands, concerning both the location and intensity pattern. In addition, these simulations were complemented with total energy distribution calculations to aid in the unambiguous assignment of the measured spectra. The current study helps to clarify some of the previous RR bands assignments as well as producing some new assignment for the anionic form of GFP chromophore. The explicit solvent simulations and PCM-based calculations are compared to the measured spectra, and these results demonstrate that explicit solvent simulations provide better agreement with experiment, both in terms of vibrational frequencies and intensity distribution. Figure a Correlation of explicit hydration calculations (CASSCF/6-31G*/MM) for the HBI model chromophore and experimental RR data [21]; slope = 0.982, intercept = 27.210 and regression coefficient = 0.997. b Correlation of implicit PCM calculations (CASSCF/6-31G*) for the HBI model chromophore and experimental RR data [21], slope = 1.017, intercept = −48.838 and regression coefficient = 0.984     

Ab initio analysis of the Cope rearrangement of germacrane sesquiterpenoids

The energetics of the Cope rearrangement of 17 germacrane sesquiterpenoids to their respective elemane forms have been calculated using both density functional theory (B3LYP/6-31G*) and post Hartee-Fock (MP2/6-31G**) ab initio methods. The calculations are in qualitative agreement with experimentally observed Cope rearrangements, but the two methods give slightly different results. MP2 calculations generally show more favorable elemene energies compared to the respective germacrenes (by around 3–4 kcal mol⁻¹) and smaller activation energies (by 2–3 kcal mol⁻¹). Additionally, neither method is accurate enough to consistently reproduce the germacrene/elemene equilibrium. Apparently, the generally small energy differences between the two forms in these sesquiterpenoids cannot be adequately reproduced at these levels of calculation. Figure The Cope rearrangement of the germacrane sesquiterpenoid bacchascandon to the elemane shyobunone     

Interactions in pseudorotoxanes based on crown ether-secondary ammonium motifs. A theoretical study

A theoretical analysis of the nature of the interactions in dibenzo[24]crown-8 (DB24C8)-n-dibutylammonium (DBM)—pseudorotaxane complex at the MP2 and DFT levels shows that the main contribution to the binding energy is the electrostatic interaction with moderate (20–25%) correlation stabilization. The total binding energy in the DB24C8-DBM complex represents a sum of the binding energies of two NH–O and one CH–O hydrogen bonds and the latter constitutes about 25% of the total interaction energy, giving the total binding energy of −41.2 kcal mol⁻¹ at the BHandHLYP/6-311++G** level. Deprotonation of the DB24C8-DBM complex reduces the binding energy by some 50 kcal mol⁻¹, giving metastable complexes DB24C8-DBA-1 or DB24C8-DBA-2, which will dissociate to give free crown ether and n-dibutylamine because of the strong exchange repulsion that prevails in neutral complexes. Figure Formation of DB24C8-DBM pseudorotoxane complex     

Molecular modeling studies of poly lactic acid initiation mechanisms

The two possible routes to synthesize poly (lactic acid) are polycondensation of the lactic acid and ring opening polymerization (ROP) of the lactide. This work involves molecular modeling of the polymerization initiation mechanisms using different initiators a) H₂SO₄ for polycondensation b) aluminum isopropoxide for coordination-insertion ROP c)methyl triflate for cationic ROP, and d) potassium methoxide for anionic ROP. For molecular modeling of PLA, we have benchmarked our approach using Ryner’s work on ROP of L-lactide using stannous (II) 2-ethylhexanoate (Sn(Oct)₂) and methanol as initiators. Our values of -15.2 kcal mol^-1 and -14.1 kcal mol^-1 for enthalpy changes in the two steps of activated complex formation match with Ryner’s. Geometric and frequency optimizations have been done on Gaussian’03 using B3LYP density functional theory along with the basis sets LANL2DZ for metal atoms and 6–31G* and 6–31G** for non metal atoms. The kinetic rate constant for each mechanism has been calculated using the values of energy of activation, change in enthalpy, Gibbs free energy, entropy and the partition functions from the Gaussian’03 output. Our polycondensation rate constant value of 1.07 × 10^–4 se^-1 compares well with 1.51 × 10^–4 se^-1 as reported by Wang. However, ROP rate constants could not be validated due to lack of experimental data. Figure Cationic Ring Opening Polymerization of L-Lactide

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Comparative studies on the metabolism of linoleic acid by rumen bacteria,protozoa, and their mixture in vitro

Linoleic acid was differentially catabolized by the various rumen microbial fractions, such as rumen bacteria (B), protozoa (P), and their mixture (BP). The predominant isomer of conjugated linoleic acids (CLA) synthesized by B, P, and BP from linoleic acid was 9c11t-CLA. The formation of 9c11t-CLA was higher (P < 0.05) in P suspension (53.6 μg/mg microbial nitrogen) compared with B (38.3 μg/mg microbial nitrogen) and BP (28.8 μg/mg microbial nitrogen) suspensions by 12 h of incubation. The second most abundant CLA isomer was 10t12c. The accumulation of 10t12c-CLA in BP suspension was 2.3 times lower (P < 0.05) than that in B suspension (84.8 μg/mg microbial nitrogen) by 12 h of incubation. The accumulation of 10t-18:1 in BP suspension during 6- and 12-h incubation periods were not different (P > 0.05) than that in B suspension (6.8 and 14.0 μg/mg microbial nitrogen, respectively). However, the accumulation of 11t-18:1 in BP suspension at 6- and 12-h incubations were 2.7 and 3.3 times higher (P < 0.05), respectively, than that in B suspension. There were no significant accumulations of 11t-18:1, 10t-18:1, and 18:0 in P suspension throughout the incubation period. It was concluded that B, P, and BP metabolized linoleic acid to different isomers of CLA, whereas B, including BP, was only capable of biohydrogenating the CLA isomers to 18:0 by the reduction of 18:1 isomers. P was incapable of biohydrogenating LA, but its association with B in the BP suspension altered the biohydrogenation of LA significantly compared with B alone.     

Accumulation of cyclohexenone derivatives in barley, wheat and maize roots in response to inoculation with different arbuscular mycorrhizal fungi

Glomus intraradices , Glomus mosseae, and Gigaspora rosea leads to the accumulation of cyclohexenone derivatives. Mycorrhizal roots of all plants accumulate in response to all three fungi blumenin [9-O-(2′-O-glucuronosyl)-β-glucopyranoside of 6-(3-hydroxybutyl)-1,1,5-trimethyl-4-cyclohexen-3-one], 13-carboxyblumenol C 9-O-gentiobioside, nicoblumin [9-O-(6′-O-β-glucopyranosyl)-β-glucopyranoside of 13-hydroxy-6-(3-hydroxybutyl)-1,1,5-trimethyl-4-cyclohexen-3-one] and another, as yet unidentified, cyclohexenone derivative. The accumulation of all four compounds in three tested mycorrhizal plants colonized by the three arbuscular mycorrhizal fungi indicates no fungus-specific induction of these compounds. Accepted: 6 October 1999     

Molecular cloning and characterization of a novel γ-CGTase from alkalophilic Bacillus sp.

We found a novel cyclodextrin glucanotransferase (CGTase) from alkalophilic Bacillus sp. G-825-6. The enzyme was expressed in the culture broth by recombinant Bacillus subtilis KN2 and was purified and characterized. The enzyme named CGTase825-6 showed 95% amino acid sequence identity with a known enzyme β-/γ-CGTase from Bacillus firmus/lentus 290-3. However, the product specificity of CGTase825-6 differed from that of β-/γ-CGTase. CGTase825-6 produced γ-cyclodextrin (CD) as the main product, but degradation of γ-CD was observed with prolonged reaction. The product specificity of the enzyme was positioned between γ-CGTase produced by Bacillus clarkii 7364 and B. firmus/lentus 290-3 β-/γ-CGTase. It showed that the difference of product specificity was dependent on only 28 amino acid residues in 671 residues in CGTase825-6. We compared the amino acid sequence of CGTase825-6 and those of other CGTases and constructed a protein structure model of CGTase825-6. The comparison suggested that the diminished loop (Val138-Asp142) should provide subsite -8 for γ-CD production and that Asp142 might have an important role in product specificity. CGTase825-6 should be a useful tool to produce γ-CD and to study the differences of producing mechanisms between γ-CD and β-CD.     

Investigation of the intermolecular proton transfer in the supersystems adenine-methanol/ethanol/i-propanol: MP2 and DFT levels study

Twelve H-bonded supersystems constructed between the adenine tautomers and methanol, ethanol, and i-propanol were studied at the B3LYP and MP2 levels of theory using 6-311G(d,p) and 6-311++G(d,p) basis functions. The thermodynamic parameters of the complex formations were calculated in order to estimate the exact stability of the supersystems. It was proven that the calculated energy barriers of the alcohol-assisted proton transfers are about 60% lower than those of the intramolecular proton transfers in adenine found earlier (Gu and Leszczynski in J Phys Chem A 103:2744–2750, 1999). Figure H-bonded complex between i-propanol and adenine     

An overview of halogen bonding

Halogen bonding (XB) is a type of noncovalent interaction between a halogen atom X in one molecule and a negative site in another. X can be chlorine, bromine or iodine. The strength of the interaction increases in the order Cl<Br<I. After a brief review of experimental evidence relating to halogen bonding, we present an explanation for its occurrence in terms of a region of positive electrostatic potential that is present on the outermost portions of some covalently-bonded halogen atoms. The existence and magnitude of this positive region, which we call the σ-hole, depends upon the relative electron-attracting powers of X and the remainder of its molecule, as well as the degree of sp hybridization of the s unshared electrons of X. The high electronegativity of fluorine and its tendency to undergo significant sp hybridization account for its failure to halogen bond. Some computed XB interaction energies are presented and discussed. Mention is also made of the importance of halogen bonding in biological systems and processes, and in crystal engineering. Figure The computed B3PW91/6-31G(d,p) electrostatic potential, in kcal mol⁻¹, on the 0.001 electrons/bohr³ surface of NC–C≡C–Cl. The chlorine atom is at the right. The color ranges are: red, more positive than 15; yellow between 7 and 15; green, between 0 and 7; blue, between −10 and 0; purple, more positive than −10. Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005.     

Metabolic pathways of quinoline, indole and their methylated analogs by Desulfobacterium indolicum (DSM 3383)

The transformation of quinoline, isoquinoline and 3-, 4-, 6- and 8-methylquinoline by Desulfobacterium indolicum was compared with that of the N-containing analogues indole and 1-, 2-, 3- and 7-methylindole. The metabolites were identified using high-performance liquid chromatography with UV detection, thin-layer chromatography, combined gas chromatography/mass spectrometry and proton NMR spectroscopy. All degraded compounds were initially hydroxylated at position 2 by D. indolicum. A new degradation product of quinoline was observed in the second transformation step, where 3,4-dihydro-2-quinolinone accumulated. This ring-reduced compound was further transformed into unidentified products. The transformation pathway of indole was characterized by well-known steps through oxindole, isatin, and anthranilic acid. No further transformation of the hydroxylated methyl analogues: 3- and 7-methyloxindole and 3- and 4-methyl-2-quinolinone, was observed within 162 days of incubation. These degradation products accumulated in stoichiometric amounts, while 6- and 8-methyl-2-quinolinone were further degraded to 6- and 8-methyl-3,4-dihydro-2-quinolinone in stoichiometric amounts. Isoquinoline, 2-methylquinoline and 1- and 2-methylindole were not degraded by D. indolicum. These observations indicate that a methyl group at or close to position 2 results in blockage of the microbial attack, and that transformation of hydroxyquinolines methylated at the heterocyclic ring also was blocked or sterically inhibited. An incomplete transformation of some methylated compounds was observed, e.g. for 3- and 6-methylquinoline and 3- and 7-methylindole, with residual concentrations of 0.5–4 mg/l in relation to initial concentrations of 10–15 mg/l. Received: 23 July 1996 / Received revision: 4 October 1996 / Accepted: 25 October 1996     

Effect of nutrition on fatty acid profiles of riverine, lacustrine, and aquaculture-raised salmonids of pre-alpine habitats

We examined trophic positions and fatty acid concentrations of riverine, lacustrine, and aquaculture diet and fish in Austrian pre-alpine aquatic ecosystems. It was hypothesized that dietary fatty acid (FA) profiles largely influence the FA composition of the salmonids Salvelinus alpinus, Salmo trutta, and Oncorhynchus mykiss. We analyzed trophic positions using stable isotopes (δ¹⁵N) and tested for correlations with polyunsaturated fatty acid (PUFA) concentrations. Gut content analysis revealed benthos (rivers), pellets (aquaculture), and zooplankton (lakes) as the predominant diet source. Results of dorsal muscle tissues analysis showed that the omega-3 PUFA, docosahexaenoic acid (DHA; 22:6n − 3), was the mostly retained PUFA in all fish of all ecosystems, yet with the highest concentrations in S. alpinus from aquaculture (mean: 20 mg DHA/g dry weight). Moreover, we found that eicosapentaenoic acid (EPA; 20:5n − 3) in fish of natural habitats (rivers, lakes) was the second most abundant PUFA (3–5 mg/g DW), whereas aquaculture-raised fish had higher concentrations of the omega-6 linoleic acid (18:2n – 6; 9–11 mg/g DW) than EPA. In addition, PUFA patterns showed that higher omega-3/-6 ratios in aquacultures than in both riverine and lacustrine fish. Data of this pilot field study suggest that salmonids did not seem to directly adjust their PUFA to dietary PUFA profiles in either natural habitats or aquaculture and that some alterations of PUFA are plausible. Finally, we suggest that trophic positions of these freshwater salmonids do not predict PUFA concentrations in their dorsal muscle tissues.     

Molecular surface electrostatic potentials and anesthetic activity

General anesthetics apparently act through weak, noncovalent and reversible interactions with certain sites in appropriate brain proteins. As a means of gaining insight into the factors underlying anesthetic potency, we have analyzed the computed electrostatic potentials V _S(r) on the surfaces of 20 molecules with activities that vary between zero and high. Our results are fully consistent with, and help to interpret, what has been observed experimentally. We find that an intermediate level of internal charge separation is required; this is measured by Π, the average absolute deviation of V _S(r), and the approximate window is 7 < Π < 13 kcal mol⁻¹. This fits in well with the fact that anesthetics need to be lipid soluble, but also to have some degree of hydrophilicity. We further show that polyhalogenated alkanes and ethers, which include the most powerful known anesthetics, have strong positive potentials, V _S,max, associated with their hydrogens, chlorines and bromines (but not fluorines). These positive sites may impede the functioning of key brain proteins, for example by disrupting their normal hydrogen-bond patterns. It has indeed been recognized for some time that the most active polyhalogenated alkanes and ethers contain hydrogens usually in combination with chlorines and/or bromines. Figure The computed HF/6-31G* electrostatic potential, in kcal mol⁻¹, on the 0.001 electrons/bohr³ surface of halothane, CF₃CHBrCl. The color ranges are: red, more positive than 25; yellow, between 15 and 25; green between 0 and 15; blue, between −10 and 0. The strongly positive (red) potential is due to the hydrogen; the yellow and green positive regions at the right are on the bromine surface Proceedings of “Modeling Interactions in Biomolecules II”, Prague, September 5th–9th, 2005.     

Theoretical investigations of a high density cage compound 10-(1-nitro-1, 2, 3, 4-tetraazol-5-yl)) methyl-2, 4, 6, 8, 12-hexanitrohexaazaisowurtzitane

A new polynitro cage compound with the framework of HNIW and a tetrazole unit, i.e., 10-(1-nitro-1, 2, 3, 4-tetraazol-5-yl)) methyl-2, 4, 6, 8, 12-hexanitrohexaazaisowurtzitane (NTz-HNIW) has been proposed and studied by density functional theory (DFT) and molecular mechanics methods. Properties such as IR spectrum, heat of formation, thermodynamic properties, and crystal structure were predicted. The compound belongs to the Pbca space group, with the lattice parameters a = 15.07 ?, b = 12.56 ?, c = 18.34 ?, Z = 8, and ρ = 1.990 g·cm^-3. The stability of the compound was evaluated by the bond dissociation energies and results showed that the first step of pyrolysis is the rupture of the N–NO₂ bond in the side chain. The detonation properties were estimated by the Kamlet-Jacobs equations based on the calculated crystal density and heat of formation, and the results were 9.240 km·s^-1 for detonation velocity and 40.136 GPa for detonation pressure. The designed compound has high thermal stability and good detonation properties and is probably a promising high energy density compound (HEDC).     

Membrane potentials,electrolyte contents,cell pH,and some enzyme activities of fibroblasts

Summary The resting membrane potential of the cultured fibroblasts derived from rabbit subcutaneous tissues was −10.2±0.20 mV (n=390). This potential was affected by the potassium concentration in the culture medium, but not by other chemical or hormonal preparations, such as dibutyryladenosine 3′,5′-cyclic monophosphate (0.5 to 5.0 mmol/l), sodium fluoride (10⁻⁵ to 10⁻⁴ M), hydrocortisone (10⁻⁷ to 10⁻⁶ M), parathyroid extract (0.5 to 1.0 U/ml), or thyrotrophin (5 to 10 mU/ml). The Na⁺, K⁺, and Cl⁻ concentrations of the cultured fibroblasts were 35.4, 85.7, and 22.6 mmol/l cell water, respectively. The water and protein contents of these cells were 82.1 and 9.18 g/100-g cells, respectively. The intracellular pH of fibroblasts as determined by [¹⁴C] dimethyloxazolidine-2, 4-dione, and³H₂O ranged between 6.9 and 7.1 when the pH of the culture medium was maintained at 7.4. The activiities of Na⁺, K⁺-, HCO₃ ⁻-, and Ca⁺⁺, Mg⁺⁺-ATPases in these cultured cells were 19.0±2.1, 13.6±2.1, and 6.6±1.2 nmol pi/mg protein per minute, respectively, and the carbonic anhydrase activity was 0.054 U/mg protein. Calculations based on the values for the membrane potential and the electrolyte concentrations observed in this study indicate that Na⁺, K⁺, Cl⁻, and H⁺ are not distributed according to their electrochemical gradients across the cell membrane. Na⁺, Cl⁻, and H⁺ are actively transported out of the cells and K⁺ into the cells. This study was supported by Grant AM20935 from the NIAMDD, NIH, Bethesda, Maryland, and National Aeronautics & Space Administration NASA-Ames Grant NAG 2-108 and U.S. Department of Energy Contract DE-AC02-76-EV-00119. D. M. W. is the recipient of a Research Career Award (5-K6-NB-13838), NINCDS, NIH.     

Aromatic C20F20 cage and its endohedral complexes X@C20F20 (X = H-, F-, Cl-, Br-, H, He)

The structure and stability of endohedral X@C₂₀F₂₀ complexes (X = H⁻, F⁻, Cl⁻, Br⁻, H, He) have been computed at the B3LYP level of theory. All complexes in I _h symmetry were found to be energy minimum structures. H⁻@C₂₀F₂₀ and F⁻@C₂₀F₂₀ complexes have negative inclusion energies, while other complexes have positive inclusion energies. Similarity between C₂₀F₂₀ and C₂₀H₂₀ has been found for X = H and He. On the basis of the computed nucleus independent chemical shift values at the cage center, both C₂₀F₂₀ and C₂₀F₂₀ are aromatic. Figure Endohedral X@C₂₀F₂₀ complexes     

Structural analysis of cell wall mannan of <Emphasis Type="Italic">Candida sojae</Emphasis>, a new yeast species isolated from defatted soybean flakes

We investigated the structural and immunochemical characteristics of cell wall mannan obtained from Candida sojae JCM 1644, which is a new yeast species isolated from defatted soybean flakes. The results of a slide-agglutination test and of an enzyme-linked immunosorbent assay using anti-factor sera to the pathogenic Candida species indicated that the cells and the C. sojae mannan were cross-reactive to the specific anti-factor sera against Candida albicans serotype A (FAb 6) and Candida guilliermondii (FAb 9). Two-dimensional homonuclear Hartmann–Hahn analysis indicated that the mannan consisted of various linked oligomannosyl side chains containing α-1,2-, α-1,3-, α-1,6- and β-1,2-linked mannose residues. However, although the determinants of antigenic factors 6 and 9 could be not found in this mannan, branched side chains, Manβ1-2Manα1-3[Manα1-6]Manα1-(2Manα1-)n2Man and a linear α-1,6-linked polymannosyl backbone, which are cross-reacted by FAbs 6 and 9, respectively, were identified. The mannan was subjected to acetolysis in order to determine the polymerization length of the α-1,2-linked oligomannosyl residue in the side chains. The result of ¹H-nuclear magnetic resonance analysis of the released oligosaccharides showed that the remarkable regularity in the length of α-1,2-linked oligomannosyl side chains, which were previously found in mannans of other Candida species, is not observed in this mannan.