The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB.

The DNA-binding mode of archaeal feast/famine-regulatory proteins (FFRPs), i.e. paralogs of the Esherichia coli leucine-responsive regulatory protein (Lrp), was studied.

Molecular motions and ion diffusions of the room-temperature ionic liquid 1,2-dimethyl-3-propylimidazolium bis(trifluoromethylsulfonyl)amide (DMPImTFSA) studied by 1H, 13C, and 19F NMR.

The diffusive properties of an imidazolium room-temperature ionic liquid (RTIL), 1,2-dimethyl-3-propylimidazolium bis(trifluoromethylsulfonyl)amide (DMPImTFSA), are studied from the ionic conductivity and the ion diffusion coefficients measured by pulsed field gradient spin echo NMR. The temperature-dependent (1)H, (19)F, and (13)C NMR spin-lattice relaxation time T(1) values were observed, and the (1)H T(1) for DMPIm showed T(1) minima for various protons. According to the Bloemberger-Purcell-Pound (BPP) equation, the correlation time tau(c) values were directly calculated from (1)H NMR.

Conformational analysis of 1-butyl-3-methylimidazolium by CCSD(T) level ab initio calculations: effects of neighboring anions.

Conformational energies for the butyl group of 1-butyl-3-methylimidazolium (bmim) were calculated by high-level ab initio methods. Estimated relative energies for the TT, GT and G'T rotamers of an isolated bmim cation at the CCSD(T)/cc-pVTZ level are 0.0 -0.

Permeation regulation of charged species by the component change of polyion complex membranes.

Three kinds of polyion complex membranes were prepared on a glassy carbon electrode: polycation (poly-L-lysine)-rich membrane, polyanion (DNA)-rich membrane, and equivalent membrane. The permeation of electroactive species (e.g.

Transcription regulation by feast/famine regulatory proteins, FFRPs, in archaea and eubacteria.

Feast/famine regulatory proteins (FFRPs) comprise a single group of transcription factors systematically distributed throughout archaea and eubacteria. In the eubacterial domain in Escherichia coli, autotrophic pathways are activated and heterotrophic pathways are repressed by an FFRP, the leucine-responsive regulatory protein (Lrp), in some cases in interaction with other transcription factors. By sensing the concentration of leucine, Lrp changes its association state between hexadecamers and octamers to adapt the autotrophic or heterotrophic mode.

Quaternary ammonium room-temperature ionic liquid including an oxygen atom in side chain/lithium salt binary electrolytes: ionic conductivity and 1H, 7Li, and 19F NMR studies on diffusion coefficients and local motions.

A room-temperature ionic liquid (RTIL) of a quaternary ammonium cation having an ether chain, N,N-diethyl-N-methyl-N-(2-methoxyethyl)ammonium bis(trifluoromethylsulfonyl)amide (DEME-TFSA), is a candidate for use as an electrolyte of lithium secondary batteries. In this study, the electrochemical ionic conductivity, sigma, of the neat DEME-TFSA and DEME-TFSA-Li doped with five different concentrations of lithium salt (LiTFSA) was measured and correlated with NMR measurements of the diffusion coefficients D and the spin-lattice relaxation times T1 of the individual components DEME (1H), TFSA (19F), and lithium ion (7Li). The ion conduction of charged ions can be activated with less thermal energy than ion diffusion which contains a contribution from paired ions in DEME-TFSA.

Feast/famine regulation by transcription factor FL11 for the survival of the hyperthermophilic archaeon Pyrococcus OT3.

Transcriptional repressor FL11 from the hyperthermophilic archaeon, Pyrococcus OT3, was crystallized in its dimer form in complex with a DNA duplex, TGAAAWWWTTTCA. Chemical contacting of FL11 to the terminal 5 bps, and DNA bending by propeller twisting at WWW confirmed specificity of the interaction. Dimer-binding sites were identified in promoters of approximately 200 transcription units coding, for example, H+-ATPase and NAD(P)H dehydrogenase.

A structural code for discriminating between transcription signals revealed by the feast/famine regulatory protein DM1 in complex with ligands.

Feast/famine regulatory proteins (FFRPs) comprise the largest group of archaeal transcription factors. Crystal structures of an FFRP, DM1 from Pyrococcus, were determined in complex with isoleucine, which increases the association state of DM1 to form octamers, and with selenomethionine, which decreases it to maintain dimers under some conditions. Asp39 and Thr/Ser at 69-71 were identified as being important for interaction with the ligand main chain.

Circadian clock, cancer and lipid metabolism.

Genetic analysis has revealed that mammalian circadian oscillator is driven by a cell autonomous transcription/translation-based negative feedback loop, wherein positive elements (CLOCK and BMAL1) induce the expression of negative regulators (Periods, CRY1 and CRY2) that inhibit the transactivation of positive regulators. Recent research reveals that this clock feedback loop affects many aspects of our physiology, such as cell cycle and lipid metabolism. In this review, I summarize the molecular links between the circadian clock mechanism and the cell cycle, and between the clock and lipid metabolism.

Alcohol and proton transport in perfluorinated ionomer membranes for fuel cells.

To clarify the transport mechanisms of alcohols and proton in perfluorosulfonated ionomer (PFSI) membranes for fuel cells, four membranes having different equivalent weight (EW) values were examined. Membranes were immersed in methanol, ethanol, and 2-propanol to prepare a total of 12 samples, and membrane swelling, mass (alcohol and proton) transports, and interactions between alcohols and proton were investigated systematically in the fully penetrated state. The membrane expansion fraction theta and alcohol content lambda increased with decreasing the EW value for all the samples.

Temperature dependence of ion and water transport in perfluorinated ionomer membranes for fuel cells.

To clarify the mechanisms of transport of ions and water molecules in perfluorosulfonated ionomer membranes for fuel cells, the temperature dependence of their transport behaviors was investigated in detail. Two types of Flemion membranes having different equivalent weight values (EW) were utilized along with Nafion 117 as the perfluorinated ionomer membranes, and H-, Li-, and Na-form samples were prepared for each membrane by immersion in 0.03 M HCl, LiCl, and NaCl aqueous solutions, respectively.

Synthesis of tubular titanate via a self-assembly and self-removal process.

Novel morphology titanate tubes were successfully synthesized via a self-assembly and self-removal process. After the product was treated by calcinating and washing, crystalline TiO2 tubes were obtained. In this study, two new concepts are applied to design the synthetic route: (i) titanium glycolate rods obtained from an ethylene glycol-mediated process and titanate sheets synthesized using the hydrothermal process were used as the template and the precursor, respectively, and ii) the template was directly removed in the reaction without posttreatment.

A SELEX study of the DNA-binding specificity of archaeal FFRPs: 2. FL4 (pot1613368).

The DNA-binding specificity of a transcription factor, the FFRP FL4 (pot1613368) from Pyrococcus sp. OT3, was studied. Using SELEX (systematic evolution of ligands by exponential environment) experiments, from a set of fragments, ∼150 bps, of the genomic DNA of P.

Feast/famine regulatory proteins (FFRPs): Escherichia coli Lrp, AsnC and related archaeal transcription factors.

Feast/famine regulatory proteins comprise a diverse family of transcription factors, which have been referred to in various individual identifications, including Escherichia coli leucine-responsive regulatory protein and asparagine synthase C gene product. A full length feast/famine regulatory protein consists of the N-terminal DNA-binding domain and the C-domain, which is involved in dimerization and further assembly, thereby producing, for example, a disc or a chromatin-like cylinder. Various ligands of the size of amino acids bind at the interface between feast/famine regulatory protein dimers, thereby altering their assembly forms.

Water disinfection by electrochemical treatment.

The electrochemical disinfection of germinated brown rice (GBR) circulating water and cooling tower water containing Legionella bacteria was investigated. Results showed the total aerobic plate counts (APC) in the treated GBR circulating water decreased significantly and the turbidity was largely improved at a pulse voltage of 1.0 kV; Legionella bacteria were also disinfected effectively at 1.

A new type of sample tube for reducing convection effects in PGSE-NMR measurements of self-diffusion coefficients of liquid samples.

Pulsed gradient spin-echo (PGSE) NMR measurements of the self-diffusion coefficients of low viscosity liquids are greatly hampered by the effects of convection especially away from ambient temperature. Here we report on a new NMR tube designed to minimize the deleterious effects of convection. In this tube, which derives from a Shigemi symmetrical NMR tube, the sample is contained in an annulus formed from a concentric cylinder of susceptibility matched glass.

The archaeal feast/famine regulatory protein: potential roles of its assembly forms for regulating transcription.

The classification feast/famine regulatory proteins (FFRPs) encompasses archaeal DNA-binding proteins with Escherichia coli transcription factors, the leucine-responsive regulatory protein and the asparagine synthase C gene product. In this paper, we describe two forms of the archaeal FFRP FL11 (pot0434017), both assembled from dimers. When crystallized, a helical cylinder is formed with six dimers per turn.

Origins of protein stability revealed by comparing crystal structures of TATA binding proteins.

The crystal structure of TATA binding protein (TBP) from a mesothermophilic archaeon, Sulfolobus acidocaldarius, has been determined at a resolution of 2.0 A with an R factor of 20.9%.

Development of a high performance electrochemical wastewater treatment system.

In order to construct a high performance electrochemical system for practical use in industrial and municipal wastewater treatment, laboratory scale electrochemical experiments were performed to select anode materials by applying pulse voltage. Based on the results obtained from laboratory experiments, a pilot plant of electrochemical treatment system (0.3 m3 h(-1)) was successfully developed, in which electrocoagulation and electrooxidation processes were used.

Bacillus krulwichiae sp. nov., a halotolerant obligate alkaliphile that utilizes benzoate and m-hydroxybenzoate.

Obligate alkaliphilic strains, AM31D(T) and AM11D, that utilize benzoate and m-hydroxybenzoate were isolated from soil obtained from Tsukuba, Ibaraki, Japan. The isolates grew at pH 8-10, but not at neutral pH. They were Gram-positive, facultatively anaerobic, straight rods with peritrichous flagella and produced ellipsoidal spores.

Trigger lipids inducing pH-dependent liposome fusion.

Aspartic acid-derived artificial lipids (ADLs; s indicates the number of the methylene groups, s=2, 4, 6, 8, 10, 12) (Scheme 1) with various carboxyl alkyl chains as head groups are designed and synthesized, which are incorporated into liposome membranes by sonication. Fluorescence resonance energy transfer (FRET) measurements indicate that ADL6, ADL8 and ADL10 have high lipid-mixing ability in the acidic solution. The other ADLs, however, do not induce remarkable liposome fusion at acidic nor neutral pH.

Long-term durability of porous hydroxyapatite with low-pressure system to support osteogenesis of mesenchymal stem cells.

In this study, we hypothesize that loading more marrow-derived mesenchymal stem cells (MSCs) into porous material by using a low-pressure system during subculture, creating a composite which combines MSCs and a novel mechanical reinforced porous hydroxyapatite, can result in more bone tissue formation in vivo. Within 26 weeks postimplantation, we examined in vivo bone formation of the experimental group with 100 mmHg pressure applied to porous HA blocks loaded with MSCs. For in vivo testing, the 2-week subcultured HA/MSC composites were implanted into subcutaneous sites of syngeneic rats.

Dynamic light scattering and circular dichroism studies on heat-induced gelation of hard-keratin protein aqueous solutions.

Animal hairs consist of aggregates of dead cells filled with keratin protein gel. We succeeded in preparing water-soluble hard-keratin proteins and reconstructing the keratin gels by heat-induced disulfide linkages in vitro. Here, the roles of intermolecular hydrophobic interaction and disulfide bonding between the proteins in the gel were discussed.

Mononuclear platinum(II) complex with 2-phenylpyridine ligands showing high cytotoxicity against mouse sarcoma 180 cells acquiring high cisplatin resistance.

Mouse sarcoma 180 cell with a 25-fold higher cisplatin (CDDP) resistance, termed S-180cisR, is newly established. S-180cisR cells grow quite slowly in the presence of CDDP with high concentration. This may show that S-180cisR cells modulate the cell cycle to acquire CDDP resistance.

Promoter analysis for daily expression of Drosophila timeless gene.

Drosophila circadian clock gene timeless (tim) displays circadian oscillation in its mRNA level, and such oscillation is transcriptionally regulated. The promoter region up to -756 of tim is suggested to promote the circadian mRNA expression, however, the role of the sequence upstream of tim promoter region in the transcriptional regulation is still unrevealed. We novelly isolated and determined tim 5'-flanking sequence -2764 to -757, and found a putative cAMP-response element, six regions of the half site for PAR-basic leucine zipper transcription factors and six nonpalindromic E-boxes.