Antigen�Cantibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation

Effective interactions between amino acid residues in antigen?Cantibody complex of influenza virus hemagglutinin (HA) protein can be evaluated in terms of the inter-fragment interaction energy (IFIE) analysis with the fragment molecular orbital (FMO) method, in which each fragment contains the side chain of corresponding amino acid residue. We have carried out the FMO-MP2 (second-order Moeller?CPlesset) calculation for the complex of HA antigen and Fab antibody of influenza virus H3N2 A/Aichi/2/68 and obtained the IFIE values between each amino acid residue in HA and the whole antibody as the sums over the residues contained in the latter. Combining this IFIE data with experimental data for hemadsorption activity of HA mutants, we succeeded in theoretically explaining the mutations in HA observed after the emergence of influenza virus H3N2 A/Aichi/2/68 in an earlier study, except for those of THR83. In the present study, we employ an alternative way of fragment division in the FMO calculation at the carbonyl C site of the peptide bond instead of the C_?? site used in the previous work, which provides revised IFIE values consistent with all the historical mutation data in the antigenic region E of HA including the case of THR83 in the present prediction scheme for probable mutations in HA.     

Ribonuclease protection assay on microchip electrophoresis

We describe the potential of microchip electrophoresis with a Hitachi SV1210, which can be used to evaluate the integrity of total RNA, for the analysis of mRNA expression. The ribonuclease (RNase) protection assay was performed by using microchip electrophoresis with cyanine 5 (Cy5) labeled 248-base antisense RNA probe (riboprobe) encoding adipose-type fatty acid binding protein (A-FABP) as the riboprobe. The fluorescence intensity corresponding to the protected RNA fragment increased in a dose-dependent manner with respect to the complementary strand RNA. Results were obtained in 120 s, and the same amount of Cy5-labeled antisense riboprobe as used in the conventional method can be used. Furthermore, 8 times more sensitive detection of mRNA by microchip electrophoresis could be obtained. An obvious increase in the mRNA expression of A-FABP, which is known as a differentiation marker of adipocytes, occurred during the adipocyte differentiation of 3T3-L1 cells. These results clearly indicate the potential of microchip electrophoresis for the analysis of mRNA expression in cells.     

A fluorescent single domain antibody against plumbagin expressed in silkworm larvae for fluorescence-linked immunosorbent assay (FLISA)

A fluorescent single-domain antibody (fluobody), a chimera of a green fluorescent protein (AcGFP) with a single chain variable fragment antibody (scFv), against plumbagin (5-hydorxy-2-methyl-1,4-naphthoquinone; PL) was successfully expressed in the hemolymph of silkworm larvae using a Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid DNA system to develop a rapid, simple, and sensitive fluorescence-linked immunosorbent assay (FLISA). In this study, two kinds of fluobody, in which the PL-scFv was fused at the N-terminus (N-fluobody) or C-terminus of AcGFP (C-fluobody), were expressed in silkworm larvae for comparative purposes. Interestingly, both fluobodies expressed in the BmNPV bacmid DNA system retained both of their original functions as an AcGFP and a PL-scFv, although the functions of the N-fluobody were found to be inferior to those of C-fluobody when they were expressed in Escherichia coli. Moreover, an improvement in the limit of quantification for PL measurement was observed in FLISA (24 ng mL(-1)) compared with conventional ELISA (0.2 μg mL(-1)). Since both the C-fluobody and N-fluobody are useful probes for FLISA and the time-, cost-consuming refolding step required in the conventional bacterial expression system can be avoided when they are expressed in the BmNPV bacmid DNA system, the silkworm expression system is useful for expressing fluobodies when developing FLISA.     

Sequence‐Specific DNA Recognition by Cyclic Pyrrole–Imidazole Cysteine‐Derived Polyamide Dimers

Pyrrole–imidazole (PI) polyamides bind to the minor groove of the DNA duplex in a sequence‐specific manner and thus have the potential to regulate gene expression. To date, various types of PI polyamides have been designed as sequence‐specific DNA binding ligands. One of these, cysteine cyclic PI polyamides containing two β‐alanine molecules, were designed to recognize a 7 bp DNA sequence with high binding affinity. In this study, an efficient cyclization reaction between a cysteine and a chloroacetyl residue was used for dimerization in the synthesis of a unit that recognizes symmetrical DNA sequences. To evaluate specific DNA binding properties, dimeric PI polyamide binding was measured by using a surface plasmon resonance (SPR) method. Extending this molecular design, we synthesized a large dimeric PI polyamide that can recognize a 14 bp region in duplex DNA.     

The EΠ-XΔ Transition of Jet-Cooled TiO Observed in Absorption

The (0,0) and (1,0) bands of the E³Π-X³Δ transition of TiO in the near-infrared have been recorded by frequency modulated laser absorption spectroscopy in a laser ablation/free jet expansion source. The observed linewidths (FWHM) varied from 300 to 500 MHz according to the expansion conditions and are dominated by residual Doppler broadening in the unskimmed source. Data for the (0,0) band have been obtained for TiO molecules containing all the naturally occurring Ti isotopes but, for the weaker (1,0) band, only for ⁴⁸TiO. Rotational constants for the two upper state vibrational levels were derived by fitting the data to an effective Hamiltonian; equilibrium parameters have been calculated. The experimental results are compared to the results of ab initio calculations on the E-X system. Ab initio results for the b-a system and for the lowest ³Σ⁻ state are also presented. They indicate that the D³Σ⁻ state is not a very low-lying state.     

Highly permeable mesoporous silica membranes synthesized by vapor infiltration of tetraethoxysilane into non-ionic alkyl poly(oxyethylene) surfactant films

Mesoporous silica membranes were prepared on porous alumina substrates by a vapor infiltration of tetraethoxysilane (TEOS) into a non-ionic poly(oxyethylene) (Brij56) surfactant film. Periodic mesostructured silica membranes were formed on both α- and γ-alumina substrates pre-treated with polystyrene. The polystyrene polymer plugged the pores of the alumina substrates and inhibited the deposition of silica in the alumina pores, resulting in the formation of a very thin silica membrane without a silica/alumina composite layer at the interface between mesoporous silica and the alumina substrates. The calcined mesoporous silica membrane showed very high nitrogen permeance (>10⁻⁶ mol m⁻² s⁻¹ Pa⁻¹). The single gas permeation was governed by the Knudsen diffusion mechanism. The durability of the mesoporous silica membrane against moisture in air was improved by a silylation with trimethylethoxysiliane.     

An improved method for the measurement of the isotope ratio of ethanol in various samples, including alcoholic and non-alcoholic beverages

The isotope ratios of ethanol, an important constituent or ingredient of some foods and various beverages and fuels, provide information about biological and geographical origin and quality. We have developed an improved method for measuring the isotope ratio of ethanol in various samples by gas chromatography-high temperature conversion or combustion-isotope ratio mass spectrometry (GC-TC/C-IRMS) with headspace solid-phase microextraction (HS-SPME). A HS-SPME method was developed by optimizing several different parameters, including salt addition, incubation temperature and time, and extraction time. The HS-SPME method enabled us to determine the isotope ratio at low ethanol concentrations (0.08 mM) in 50 min with good precision (+/-0.3 per thousand for delta(13)C and +/-5 per thousand for deltaD). An advantage of this technique is that it can be adapted for use with samples which have high viscosity and contain many matrix compounds, such as alcoholic and non-alcoholic beverages.     

Water-mediated interactions in the CRP–cAMP–DNA complex: Does water mediate sequence-specific binding at the DNA primary-kink site?

The cyclic AMP receptor protein (CRP) of Escherichia coli binds preferentially to DNA sequences possessing a T:A base pair at position 6 (at which the DNA becomes kinked), but with which it does not form any direct interactions. It has been proposed that indirect readout is involved in CRP-DNA binding, in which specificity for this base pair is primarily related to sequence effects on the energetic susceptibility of the DNA to kink formation. In the current study, the possibility of contributions to indirect readout by water-mediated hydrogen bonding of CRP with the T:A base pair was investigated. A 1.0 ns molecular dynamics simulation of the CRP-cAMP-DNA complex in explicit solvent was performed, and assessed for water-mediated CRP-DNA hydrogen bonds; results were compared to several X-ray crystal structures of comparable complexes. While several water-mediated CRP-DNA hydrogen bonds were identified, none of these involved the T:A base pair at position 6. Therefore, the sequence specificity for this base pair is not likely enhanced by water-mediated hydrogen bonding with the CRP.     

Total synthesis of (+)- and (-)-sundiversifolide via intramolecular acylation and determination of the absolute configuration

Intramolecular acylation of an organolithium leads to an efficient stereocontrolled total synthesis of both enantiomers of sundiversifolide. The absolute configuration was determined by HPLC analysis and allelopathy assay. The gamma-lactone moiety resulted from a butenolide was obtained by the condensation of a bicyclic alpha-hydroxyhemiacetal with Ph3P=CMe(CO2R).     

Synthesis of 3D pore mesostructured silica films by vapor infiltration of tetraethoxysilane

Nonionic alkyl poly(oxyethylene) surfactants (Brij 56) films on a silicon substrate were treated with a tetraethoxysilane (TEOS) vapor. Mesostructured silica films were formed through a nano-phase transition under the infiltration of TEOS into the surfactant films. It was found that the calcined film had a 3D pore structure from the field emission scanning electron microscope (FE-SEM) observations in a different orientation. Grazing angle of incidence small angle X-ray scattering (GISAXS) measurement results showed that the symmetry of the film was an Fmmm space group oriented with the (010) plane parallel to the surface. The ordered structure of the films showed higher thermal stability than the films prepared by a conventional solvent-evaporation method.