Analyzing steady states of dynamics of bio-molecules from the structure of regulatory networks.

Regulatory relations between biological molecules constitute complex network systems and realize diverse biological functions through the dynamics of molecular activities. However, we currently have very little understanding of the relationship between the structure of a regulatory network and its dynamical properties. In this paper we introduce a new method, named "linkage logic" to analyze the dynamics of network systems.

Gqalpha-linked phospholipase Cbeta1 and phospholipase Cgamma are essential components of the pheromone biosynthesis activating neuropeptide (PBAN) signal transduction cascade.

Sex pheromone production for most moths is regulated by pheromone biosynthesis activating neuropeptide (PBAN). In Bombyx mori, PBAN binding triggers the opening of store-operated Ca(2+) channels, suggesting the involvement of a receptor-activated phospholipase C (PLC). In this study, we found that PLC inhibitors U73122 and compound 48/80 reduced sex pheromone production and that intracellular levels of (3)H-inositol phosphate species increased following PBAN stimulation.

Marine antifungal theonellamides target 3beta-hydroxysterol to activate Rho1 signaling.

Linking bioactive compounds to their cellular targets is a central challenge in chemical biology. Here we report the mode of action of theonellamides, bicyclic peptides derived from marine sponges. We generated a chemical-genomic profile of theonellamide F using a collection of fission yeast strains in which each open reading frame (ORF) is expressed under the control of an inducible promoter.

Measurement of two-photon excitation spectra of fluorescent proteins with nonlinear Fourier-transform spectroscopy.

We present measurements of two-photon excitation (TPE) spectra of various fluorescent proteins with nonlinear Fourier-transform spectroscopy. By using an ultrabroadband laser pulse with a spectrum ranging from 700 to 1100 nm, the absolute TPE spectra of six typical fluorescent proteins (SeBFP, Sapphire, eGFP, eCFP, Venus, DsRed) were measured with high spectral resolution.

Application of proteomic profiling based on 2D-DIGE for classification of compounds according to the mechanism of action.

The development of new anticancer agents derived from natural resources requires a rapid identification of their molecular mechanism of action. To make this step short, we have initiated the proteomic profiling of HeLa cells treated with anticancer drugs representing a wide spectrum of mechanisms of action using two-dimensional difference gel electrophoresis (2D-DIGE). Unique proteome patterns were observed in HeLa cells treated with the HSP90 inhibitor geldanamycin, and were similar to the patterns induced by radicicol, a structurally different HSP90 inhibitor.

Introduction of new tools for chemical biology research on microbial metabolites.

Recently, high-throughput screening (HTS) has become the mainstream technique for drug discovery. Compounds that are synthesized by combinatorial chemistry might be more suitable than natural products to apply to HTS, because the purification procedure is a drawback of using natural products. Nevertheless, natural products remain an extremely important source of drugs.

Theoretical Investigation of Solvent Effects on Glycosylation Reactions: Stereoselectivity Controlled by Preferential Conformations of the Intermediate Oxacarbenium-Counterion Complex.

The mechanism of solvent effects on the stereoselectivity of glycosylation reactions is investigated using quantum-mechanical (QM) calculations and molecular dynamics (MD) simulations, considering a methyl-protected glucopyranoside triflate as a glycosyl donor equivalent and the solvents acetonitrile, ether, dioxane, or toluene, as well as gas-phase conditions (vacuum). The QM calculations on oxacarbenium-solvent complexes do not provide support to the usual solvent-coordination hypothesis, suggesting that an experimentally observed β-selectivity (α-selectivity) is caused by the preferential coordination of a solvent molecule to the reactive cation on the α-side (β-side) of the anomeric carbon. Instead, explicit-solvent MD simulations of the oxacarbenium-counterion (triflate ion) complex (along with corresponding QM calculations) are compatible with an alternative mechanism, termed here the conformer and counterion distribution hypothesis.

Selective ammonolysis of half-sandwich rare-earth metal dialkyl and polyhydride complexes: synthesis of polyamido rare-earth complexes having novel structures.

The scandium dialkyl complex [Cp'Sc(CH(2)SiMe(3))(2)(THF)] (1-Sc, Cp' = C(5)Me(4)SiMe(3)) reacts rapidly with ammonia at room temperature to afford selectively a trinuclear hexaamido complex [Cp'Sc(mu-NH(2))(2)](3) (3-Sc) with release of SiMe(4). The reaction of the lutetium dialkyl complex [Cp'Lu(CH(2)SiMe(3))(2)(THF)] (1-Lu) with ammonia under the same conditions gives the analogous hexaamido Lu complex [Cp'Lu(mu-NH(2))(2)](3) (3-Lu) as a major product (92%) together with a tetranuclear octaamido complex [Cp'Lu(mu-NH(2))(2)](4) (4-Lu) as a minor product (8%). In contrast, reaction of tetranuclear rare-earth metal octahydride complexes [Cp'Ln(mu-H)(2)](4)(THF) (Ln = Y (2-Y), Lu (2-Lu)) with ammonia under similar conditions yields selectively the heptaamido/monohydrido complexes [(Cp'Ln)(4)(mu-NH(2))(6)(mu(3)-NH(2))(mu(4)-H)] (Ln = Y (5-Y), Lu (5-Lu)), in which a mu(4)-H ligand remains at the center of the tetrahedral metal framework.

Generation of 5.0 fs, 5.0 mJ pulses at 1kHz using hollow-fiber pulse compression.

We demonstrate methods to increase the energy incident on hollow fibers for spectral broadening by self-phase modulation. We used chirped pulses for spectral broadening, lowering the optical intensity to avoid ionization of the gaseous medium. We also used helium as a nonlinear medium and demonstrated the generation of 5.

Identification of an Htm1 (EDEM)-dependent, Mns1-independent Endoplasmic Reticulum-associated Degradation (ERAD) pathway in Saccharomyces cerevisiae: application of a novel assay for glycoprotein ERAD.

Endoplasmic reticulum (ER)-associated degradation (ERAD) is a quality control system for newly synthesized proteins in the ER; nonfunctional proteins, which fail to form their correct folding state, are then degraded. The cytoplasmic peptide:N-glycanase is a deglycosylating enzyme that is involved in the ERAD and releases N-glycans from misfolded glycoproteins/glycopeptides. We have previously identified a mutant plant toxin protein, RTA (ricin A-chain nontoxic mutant), as the first in vivo Png1 (the cytoplasmic peptide:N-glycanase in Saccharomyces cerevisiae)-dependent ERAD substrate.

A stable doubly hydrogen-bridged butterfly-shaped diborane(4) compound.

In contrast to the common multiple bonding between carbon atoms, multiply bonded boron compounds have still been a synthetic challenge due to the electron deficiency of boron. We now report that a stable doubly hydrogen-bridged diborane(4), EindB(mu-H)(2)BEind, is produced by the two-electron oxidation of a hydrogen-substituted diborane(4) dianion [Li(+)(thf)](2)[Eind(H)BB(H)Eind](2-), where Eind denotes the 1,1,3,3,5,5,7,7-octaethyl-s-hydrindacen-4-yl. The X-ray crystallography reveals a short B-B distance of 1.

Excitonic interaction: another photophysical process for fluorescence-controlled nucleic acid sensing.

An excitonic interaction caused by the H-aggregation of fluorescent dyes is a new type of useful photophysical process for fluorescence-controlled nucleic acid sensing. We designed a fluorescence-labeled nucleotide in which two thiazole orange dyes were linked covalently. A DNA strand containing this fluorescence-labeled nucleotide showed absorption at 480 nm before hybridization, whereas an absorption band at 510 nm became predominant when the DNA was hybridized with the complementary strand.

Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics.

Activation of ErbB receptors by epidermal growth factor (EGF) or heregulin (HRG) determines distinct cell-fate decisions, although signals propagate through shared pathways. Using mathematical modeling and experimental approaches, we unravel how HRG and EGF generate distinct, all-or-none responses of the phosphorylated transcription factor c-Fos. In the cytosol, EGF induces transient and HRG induces sustained ERK activation.

Perfluoro-functionalized PEDOT films with controlled morphology as superhydrophobic coatings and biointerfaces with enhanced cell adhesion.

Perfluoro-functionalized PEDOT thin films with various surface morphologies were prepared electrochemically by applying different potential pulse sequences using ionic liquids as electrolyte and solvent, and these films could display superhydrophobicity with enhanced capability of cell adhesion.

Evidence for an essential deglycosylation-independent activity of PNGase in Drosophila melanogaster.

Background: Peptide:N-glycanase (PNGase) is an enzyme which releases N-linked glycans from glycopeptides/glycoproteins. This enzyme plays a role in the ER-associated degradation (ERAD) pathway in yeast and mice, but the biological importance of this activity remains unknown.

Principal Findings: In this study, we characterized the ortholog of cytoplasmic PNGases, PNGase-like (Pngl), in Drosophila melanogaster.

Live imaging system for visualizing nuclear pore complex (NPC) formation during interphase in mammalian cells.

Nuclear pore complexes (NPCs) are 'supramolecular complexes' on the nuclear envelope assembled from multiple copies of approximately 30 different proteins called nucleoporins (Nups) that provide aqueous channels for nucleocytoplasmic transport during interphase. Although the structural aspects of NPCs have been characterized in detail, NPC formation and its regulation, especially during interphase, are poorly understood. In this study, using the temperature-sensitive RCC1 mutant tsBN2, a baby hamster kidney 21 cell line, we found that a lack of RCC1 activity inhibited NPC formation during interphase, suggesting that RanGTP is required for NPC formation during interphase in mammalian cells.

Effects of frozen conditions on stereoselectivity and velocity of O-glycosylation reactions.

Rate acceleration of O-glycosylation had been observed in p-xylene under frozen conditions, when thioglycosides were activated by methyl trifluoromethane sulfonate. Curiously, significant perturbation of stereoselectivity was observed. Effects of various factors, such as solvent, concentration, anomeric configuration and protective groups of the donor, were systematically examined to clarify the mechanistic implications of stereoselectivity on glycosylation under frozen system.

The fabrication and single electron transport of Au nano-particles placed between Nb nanogap electrodes.

We have fabricated Nb nanogap electrodes using a combination of molecular lithography and electron beam lithography. Au nano-particles with anchor molecules were placed in the gap, the width of which could be controlled on a molecular scale (approximately 2 nm). Three different anchor molecules which connect the Au nano-particles and the electrodes were tested to investigate their contact resistance, and a local gate was fabricated underneath the Au nano-particles.

Photoactivatable fluorescein derivatives with azidomethyl caging groups for tracing oligonucleotides in living human cells.

A new photocaged fluorescent compound, azidomethyl fluorescein, was successfully utilized to monitor the dynamics of oligonucleotides in living human cells.

Phosphatidylglucoside forms specific lipid domains on the outer leaflet of the plasma membrane.

Phosphatidylglucoside (PtdGlc) is a recently discovered unique glycophospholipid involved in granulocytic differentiation of human promyelocytic leukemia cell line HL60 and in astrocytic differentiation in developing rodent brains. Using a PtdGlc-specific monoclonal antibody in immunofluorescence and immunoelectron microscopy, we showed that PtdGlc forms distinct lipid domains on the outer leaflet of the plasma membrane of HL60 cells and the human alveolar epithelial cell line, A549. Similar to glycosphingolipid, glucosylceramide (GlcCer), the natural form of PtdGlc exhibited a high main phase transition temperature in differential scanning calorimetry (DSC).

A DNA-binding surface of SPO11-1, an Arabidopsis SPO11 orthologue required for normal meiosis.

Meiotic recombination is initiated by DNA double-stranded breaks introduced by the SPO11 protein. Despite a decade of research, the biochemical functions of SPO11 remain largely unknown, perhaps because of difficulties in studying the functionally active SPO11. Arabidopsis thaliana encodes three SPO11-related proteins, two of which (SPO11-1 and SPO11-2) are required for, and cooperate in, meiosis.

Unconventional s-wave superconductivity in Fe(Se,Te).

The superconducting state is characterized by a pairing of electrons with a superconducting gap on the Fermi surface. In iron-based superconductors, an unconventional pairing state has been argued for theoretically. We used scanning tunneling microscopy on Fe(Se,Te) single crystals to image the quasi-particle scattering interference patterns in the superconducting state.

Synthesis and binding analysis of unique AG2 pentasaccharide to human Siglec-2 using NMR techniques.

Siglec-2 is a mammalian sialic acid binding protein expressed on B-cell surfaces and is involved in the modulation of B-cell mediated immune response. We synthesized a unique starfish ganglioside, AG2 pentasaccharide Galfbeta(1-3)Galpalpha(1-4)Neu5Acalpha(2-3)Galpbeta(1-4)Glcp, and found that the synthetic pentasaccharide binds to human Siglec-2 by performing (1)H NMR experiments. Saturation transfer difference NMR experiments indicated that the C7-C9 side-chain and the acetamide moiety of the central sialic acid residue were located in the binding face of human Siglec-2.

Molecular frame image restoration and partial wave analysis of photoionization dynamics of NO by time-energy mapping of photoelectron angular distribution.

The benchmark system of molecular photoionization dynamics, the (1+1{'}) two-photon ionization of NO via the A state, is investigated using the time-energy mapping of the photoelectron angular distribution in a laboratory frame. The molecular frame photoelectron angular distribution and partial wave composition are determined from time-energy maps and compared with those obtained by Schwinger variational calculation (SVC) and state-to-state photoelectron spectroscopy. Good agreement is found with SVC.

The YlmG protein has a conserved function related to the distribution of nucleoids in chloroplasts and cyanobacteria.

Background: Reminiscent of their free-living cyanobacterial ancestor, chloroplasts proliferate by division coupled with the partition of nucleoids (DNA-protein complexes). Division of the chloroplast envelope membrane is performed by constriction of the ring structures at the division site. During division, nucleoids also change their shape and are distributed essentially equally to the daughter chloroplasts.