High-throughput single nucleotide polymorphism typing by fluorescent single-strand conformation polymorphism analysis with capillary electrophoresis

In this study, we performed high-throughput and precise single nucleotide polymorphism (SNP) typing by fluorescent capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis. A system composed of a multicapillary DNA analyzer, a newly developed sieving matrix, four different colors of fluorescent labels, and a multiplex polymerase chain reaction (PCR) enabled low-cost and highly reliable SNP typing. Moreover, this system enabled the estimation of SNP allele frequencies using pooled DNA samples, which should be beneficial for large-scale association studies. Thus, fluorescent CE-SSCP analysis is a useful method for large-scale SNP typing.     

Spongelike Macroporous TiO2 Monoliths Prepared from Starch Gel Template

TiO₂ materials with a hierarchical meso/macropore organization were fabricated by using titanium dioxide nanoparticles and starch gel templates. Starch sponges with high internal macroporosities were prepared by freezing and thawing of starch gels and were then infiltrated with colloidal suspensions of titania nanoparticles and air-dried to produce TiO₂-starch foams with pores up to 200 m across depending on the starch concentration and the TiO₂ loading. The TiO₂ nanoparticles were deposited as coherent layers on the thin walls of the starch framework, which was removed by calcination without significant disruption of the TiO₂ framework. The three dimensional macroporous structures of TiO₂-starch sponge composite and TiO₂ sponge induced extremely high photocatalytic activity.     

The Clostridium cellulovorans cellulosome: an enzyme complex with plant cell wall degrading activity

Cellulose comprises a major portion of biomass on the earth, and the turnover of this material contributes to the CO2 cycle. Cellulases, which play a major role in the turnover of cellulosic materials, have been found either as free enzymes that work synergistically, or as an enzyme complex called the cellulosome. This review summarizes some of the general properties of cellulosomes, and more specifically, the properties of the Clostridium cellulovorans cellulosome. The C cellulovorans cellulosome is an extracellular enzyme complex with a molecular weight of about 1 x 10(6), and is comprised of at least ten subunits. The major subunit is the scaffolding protein CbpA, with a molecular weight of 189,000. This nonenzymatic subunit contains a cellulose binding domain (CBD) that binds the cellulosome to the substrate, nine conserved cohesins or enzyme binding domains, and four conserved surface layer homologous (SLH) domains. It is postulated that the SLH domains help to bind the cellulosome to the cell surface. The cellulosomal enzymes include cellulases (family 5 and 9 endoglucanases and a family 48 exoglucanase), a mannanase, a xylanase, and a pectate lyase. The cellulosome is capable of converting Arabidopsis and tobacco plant cells to protoplasts. One of the endoglucanases, EngE, contains three tandemly repeated SLHs at its N-terminus, and therefore appears capable of binding to the scaffolding protein CbpA as well as to the cell surface. Cellulosomes can attack crystalline cellulose, but the free cellulosomal enzymes can attack only soluble and amorphous celluloses. Nine genes for the cellulosome are found in a gene cluster cbpA-exgS-engH-engK-hbpA-engL-manA-engM-engN. Other cellulosomal genes such as engB, engE, and engY are not linked to the major gene cluster or to each other. By determining the structure and function of the cellulosome, we hope to increase the efficiency of the cellulosome by genetic engineering techniques.     

N-Allyl-N-tert-butyldimethylsilylamine for chiral ligand-controlled asymmetric conjugate addition to tert-butyl alkenoates

The chiral ligand controlled asymmetric conjugate addition reaction of lithium N-allyl-N-(tert-butyldimethylsilyl)amide to alkenoates proceeded smoothly to give, after protodesilylation, the corresponding 3-allylaminoalkanoates with high enantioselectivities in high yields. The allyl group on the nitrogen atom was easily removable to afford 3-aminoalkanoates.     

Molecular dynamics simulation study on the phase behavior of the Gay-Berne model with a terminal dipole and a flexible tail

To study the effect of the alkyl tail and the terminal dipole on the stability of the liquid crystalline phase of mesogens, we have carried out molecular dynamics simulations for 1CB(4-methyl-4'-cyanobiphenyl) and 5CB(4-n-pentyl-4'-cyanobiphenyl) by using a coarse-grained model. In the coarse-grained model, a 5CB molecule is divided into the rigid part of 1CB moiety, which is represented by an ellipsoid, and the remaining flexible part which is represented by a chain of united atoms. The nonbonded potential between coarse-grained segments is represented by the generalized Gay-Berne (GB) potential and the potential parameters are determined by directly comparing the GB potential with the atomistic potentials averaged over the rotation of the mesogen around its axis. In addition, a dipole moment is placed at one end of the ellipsoid opposite to the flexible tail. The ordered state obtained in the polar 5CB model was assigned as the nematic phase, and the experimental static and dynamical properties were reproduced well by using this coarse-grained model. Both the dipole-dipole interactions and the thermal fluctuation of the flexible tail increase the positional disorder in the director direction, and stabilize the nematic phase. Thus, the nematic phase in the polar 5CB is induced by a cooperative effect of the flexible tail and the terminal dipole. It is noted that a local bilayer structure with head-to-head association is formed in the nematic phase, as experimentally observed by x-ray diffraction measurements.     

Organization of polyhydroxyalkanoate synthase for in vitro polymerization as revealed by atomic force microscopy

Individual polyhydroxyalkanoate synthase molecules from Ralstonia eutropha (PhaCRe) were directly visualized on highly oriented pyrolytic graphite (HOPG) by atomic force microscopy (AFM). PhaCRe molecule was observed as a spherical particle of 2.9 +/- 0.4 nm in height and 28 +/- 4 nm in width. In vitro polymerization reaction on HOPG was carried out for 5 min by reacting the PhaCRe molecules with (R)-3-hydroxybutyryl-CoA monomers. The reaction product was then observed after the removal of water solution. Several PhaCRe molecules associated with each other to form an assembly, which was attached to a fibrillar structure of ca. 0.2-0.3 nm in height. The fibrillar structure that elongated from the PhaCRe assembly was interpreted as the poly[(R)-3-hydroxybutyrate] polymer chain. High resolution AFM suggested that the PhaCRe assembly was composed of 3-4 subunits of PhaCRe molecules. This was further supported by SDS-PAGE analysis of the cross-linked PhaCRe enzyme. These results suggest that more than two subunits of PhaCRe are necessary for the in vitro polymerization of PHB molecular chains.     

Alternating polyampholytes prepared by hydrolysis of copolymer of maleic anhydride and N-vinylsuccinimide

Alternating polyampholytes (MA-VA) containing two acidic groups and one basic group were prepared by the copolymerization of maleic anhydride (M₁) and N-vinylsuccinimide (M₂) at 60°C with AIBN as the initiator, followed by acid hydrolysis with 1N hydrochloric acid at 140°C for 24 hr. The monomer reactivity ratios r₁ and r₂ are 0.025 and 0.06, respectively. The structure of polymers was discussed on the basis of the data of their elementary, infrared (IR), and thermal analyses and the binding ability of heavy metal ion. Polyampholytes were soluble in strong acidic and basic media but were precipitated in the pH range 3–4. An isoelectric point at pH 3 was determined by potentiometric titration and the turbidimetric method. By thermal treatment above 205°C the polyampholyte turned quantitatively into a cyclized lactam. This suggests that the polyampholyte MA–VA has an intramolecular hydrogen bond between the amino and γ-carboxyl groups. The binding of Cu²⁺ and Hg²⁺ by the polyelectrolyte was evaluated by equilibrium dialysis.     

Magnetic susceptibility and specific heat of uranium double perovskite oxides Ba2MUO6 (M=Co, Ni)

Double perovskites Ba₂MUO₆ (M=Co, Ni) were prepared by the solid-state reaction. X-ray diffraction measurements show that both cobalt (nickel) and uranium ions are ordered in the NaCl type over the six-coordinate B sites of the perovskite ABO₃. Detailed magnetic susceptibility and specific heat measurements show that Ba₂CoUO₆ and Ba₂NiUO₆ order ferromagnetically at 9.1 and 25 K, respectively. From the analysis of the magnetic specific heat, the ground states of the Co²⁺ and Ni²⁺ ions were determined.     

Interaction between poly[(R)-3-hydroxybutyrate] depolymerase and biodegradable polyesters evaluated by atomic force microscopy

Adsorption of PHB depolymerase from Ralstonia pickettii T1 to biodegradable polyesters such as poly[(R)-3-hydroxybutyrate] (PHB) and poly(l-lactic acid) (PLLA) was investigated by atomic force microscopy (AFM). The substrate-binding domain (SBD) with histidines within the N-terminus was prepared and immobilized on the AFM tip surface via a self-assembled monolayer with a nitrilotriacetic acid group. Using the functionalized AFM tips, the force-distance measurements for polyesters were carried out at room temperature in a buffer solution. In the case of AFM tips with immobilized SBD and their interaction with polyesters, multiple pull-off events were frequently recognized in the retraction curves. The single rupture force was estimated at approximately 100 pN for both PLLA and PHB. The multiple pull-off events were recognized even in the presence of a surfactant, which will prevent nonspecific interactions, but reduced when using polyethylene instead of polyesters as a substrate. The present results provide that the PHB depolymerase adsorbs specifically to the surfaces of polyesters and that the single unbinding event evaluated here is mainly associated with the interaction between one molecule of SBD and the polymer surface.