Synthesis, structure, and biological activity of dumbbell-shaped nanocircular RNAs for RNA interference.

RNA interference (RNAi) is one of the most promising new approaches for disease therapy. The design of a dumbbell-shaped nanocircular RNA allows it to act as a short interfering RNA (siRNA) precursor. To optimize the design, we studied the relationship between the nanostructure and RNAi activity by synthesizing various RNA dumbbells.

Actin stress fiber retraction and aggresome formation is a common cellular response to actin toxins.

F-actin-stabilizing drugs induce actin aggresome formation. In this study, we found that an actin-depolymerizing drug, latrunculin A (LatA), induced actin aggresomes. Actin stress fibers were retracted and disappeared in minutes, but a large aggresome formed in consequence of LatA treatment.

Identification of novel oxidized levuglandin D2 in marine red alga and mouse tissue.

In animals, the product of cyclooxygenase reacting with arachidonic acid, prostaglandin(PG)H(2), can undergo spontaneous rearrangement and nonenzymatic ring cleavage to form levuglandin(LG)E(2) and LGD(2). These LGs and their isomers are highly reactive γ-ketoaldehydes that form covalent adducts with proteins, DNA, and phosphatidylethanolamine in cells. Here, we isolated a novel oxidized LGD(2) (ox-LGD(2)) from the red alga Gracilaria edulis and determined its planar structure.

13C-NMR quantification of proton exchange at LewisX hydroxyl groups in water.

NMR-based analysis of glycans by directly observing hydroxyl protons has been difficult because of their inherently fast exchange with water. We observed hydroxyl proton exchanges in a LewisX-LewisX interaction by using deuterium isotope shifts on (13)C-NMR. This strategy is suitable for analyzing weak interactions by identifying involved protons.

The effects of covalently immobilized hyaluronic acid substrates on the adhesion, expansion, and differentiation of embryonic stem cells for in vitro tissue engineering.

We investigated the in vitro effects of the molecular weight (MW) of hyaluronic acid (HA) on the maintenance of the pluripotency and proliferation of murine embryonic stem (ES) cells. High (1000 kDa) or low (4-8 kDa) MW HA was derivatized using an ultraviolet-reactive compound, 4-azidoaniline, and the derivative was immobilized onto cell culture cover slips. Murine ES cells were cultured on these HA surfaces for 5 days.

Dynamics of coherent and incoherent emission from an artificial atom in a 1D space.

We study dynamics of a two-level superconducting quantum system, analogous to a natural atom in an open space, by measuring the evolution of its coherent and incoherent emission. The emitted waves containing full information about the states of the artificial atom are efficiently collected due to strong atom-transmission-line coupling. This allows us to do simultaneous measurements of all the quantum state projections and perform a full characterization of the system.

Fluorescence image screening for chemical compounds modifying cholesterol metabolism and distribution.

An automated fluorescence microscopy assay using a nontoxic cholesterol binding protein, toxin domain 4, (D4), was developed in order to identify chemical compounds modifying intracellular cholesterol metabolism and distribution. Using this method, we screened a library of 1,056 compounds and identified 35 compounds that decreased D4 binding to the cell surface. Among them, 8 compounds were already reported to alter the biosynthesis or the intracellular distribution of cholesterol.

Sphingomyelin synthase 1-generated sphingomyelin plays an important role in transferrin trafficking and cell proliferation.

Transferrin (Tf) endocytosis and recycling are essential for iron uptake and the regulation of cell proliferation. Tf and Tf receptor (TfR) complexes are internalized via clathrin-coated pits composed of a variety of proteins and lipids and pass through early endosomes to recycling endosomes. We investigated the role of sphingomyelin (SM) synthases (SMS1 and SMS2) in clathrin-dependent trafficking of Tf and cell proliferation.

Activating transcription factor-6 (ATF6) mediates apoptosis with reduction of myeloid cell leukemia sequence 1 (Mcl-1) protein via induction of WW domain binding protein 1.

Endoplasmic reticulum (ER) stress is involved in both physiological and pathological apoptosis. ER stress triggers the unfolded protein response (UPR), which can then initiate apoptosis, when the cell fails to restore ER homeostasis. However, the mechanism employed by the UPR to lead cells into apoptosis is unknown.

Drosophila GTPase nucleostemin 2 changes cellular distribution during larval development and the GTP-binding motif is essential to nucleoplasmic localization.

Nucleostemin (NS), a nucleolar guanosine triphosphate (GTP)-binding protein, plays significant roles in cell cycle progression and ribosomal biogenesis. Drosophila Nucleostemin 2 (NS2), a member of the Drosophila NS family, regulates early eye development and is essential to cell survival in vivo, but the underlying mechanisms have yet to be clarified. Biochemical analysis using the recombinant NS2 protein indicated that NS2 has GTPase activity.

Polypeptide aptamer selection using a stabilized ribosome display.

A newly developed ribosome display protocol was applied to the in vitro selection of polypeptide aptamers to small molecular weight chemicals, 6-[hydroxy(4-nitrobenzyl)phosphonyl]hexanoic acid and vitamin B12, chosen from a peptide library of random sequences. New peptide sequences binding to the targets were found after six rounds of this protocol.

[Modeling the transition state of enzyme-catalyzed phosphoryl transfer reaction using QM/MM method].

Reversible phosphorylation of proteins is a post-translational modification that regulates diverse biological processes. The molecular mechanism underlying phosphoryl transfer catalyzed by enzymes, in particular the nature of transition state (TS), remains a subject of active debate. Structural evidence supports an associative TS, whereas physical organic studies point to a dissociative character.

Condensins I and II are essential for construction of bivalent chromosomes in mouse oocytes.

In many eukaryotes, condensins I and II associate with chromosomes in an ordered fashion during mitosis and play nonoverlapping functions in their assembly and segregation. Here we report for the first time the spatiotemporal dynamics and functions of the two condensin complexes during meiotic divisions in mouse oocytes. At the germinal vesicle stage (prophase I), condensin I is present in the cytoplasm, whereas condensin II is localized within the nucleus.

On-chip DNA methylation analysis using osmium complexation.

The development of a reaction for detecting the presence/absence of one methyl group in a long DNA strand is a chemically and biologically challenging research subject. A newly designed chemical assay on a chip for the typing of DNA methylation has been developed. A methylation-detection probe fixed at the bottom of microwells was crosslinked with methylated DNA mediated by osmium complexation and contributes to selective amplification of methylated DNA.

Efficient microwelding of glass substrates by ultrafast laser irradiation using a double-pulse train.

Efficient microwelding of glass substrates by irradiation by a double-pulse train of ultrafast laser pulses is demonstrated. Temporal beam shaping techniques such as double-pulse irradiation enabled increased flexibility for high-quality, high-efficiency material processing. The bonding strength of two photostructurable glass substrates welded by double-pulse irradiation was evaluated to be 22.

N-glycosylation is critical for the stability and intracellular trafficking of glucose transporter GLUT4.

The facilitative glucose transporter GLUT4 plays a key role in regulating whole body glucose homeostasis. GLUT4 dramatically changes its distribution upon insulin stimulation, and insulin-resistant diabetes is often linked with compromised translocation of GLUT4 under insulin stimulation. To elucidate the functional significance of the sole N-glycan chain on GLUT4, wild-type GLUT4 and a GLUT4 glycosylation mutant conjugated with enhanced GFP were stably expressed in HeLa cells.

Cy5-conjugated hybridization-sensitive fluorescent oligonucleotides for ratiometric analysis of nuclear poly(A)+ RNA.

Subnuclear poly(A)(+) RNA localization in living mammalian cells was visualized by ratiometric analysis using hybridization-sensitive fluorescent oligonucleotide probes. Probes were oligonucleotides, which contained a Cy5 fluorescent dye at the strand end and a thiazole orange double-labeled nucleotide inside strand. A ratiometric analysis using poly(A)-targeting probes revealed a distribution of the probe itself as red fluorescence and localization of the target RNA sequence in cell nuclei as green fluorescence.

Highly active copper-network catalyst for the direct aldol reaction.

The development of a highly active solid-phase catechol-copper network catalyst for direct aldol reaction is described. The catalyst was prepared from an alkyl-chain-linked bis(catechol) and a copper(II) complex. The direct aldol reaction between carbonyl compounds (aldehydes and ketones) and methyl isocyanoacetate was carried out using 0.

Carboxylation of alkylboranes by N-heterocyclic carbene copper catalysts: synthesis of carboxylic acids from terminal alkenes and carbon dioxide.

Caught in the act: N-Heterocyclic carbene copper(I) complexes (1; IPr=1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) serve as an excellent catalyst for the carboxylation of alkylboranes (2; R=alkyl) with CO(2) to afford a variety of functionalized carboxylic acids (3) in high yields. A novel copper methoxide/alkylborane adduct (A) and its subsequent CO(2) insertion product (B) have been isolated and shown to be true active catalyst species.

Efficient synthesis of 3,4-ethylenedioxythiophene (EDOT)-based functional π-conjugated molecules through direct C-H bond arylations.

A variety of 3,4-ethylenedioxythiophene (EDOT)-based π-conjugated molecules were efficiently synthesized in good yields through Pd-catalyzed direct C-H bond arylations, wherein a detailed synthetic investigation, including the screening of various kinds of palladium catalysts, ligands, additives, and solvents, was carried out. In addition, the spectroscopic and electrochemical properties of these EDOT-containing molecules were also investigated.

The relative ratio of condensin I to II determines chromosome shapes.

To understand how chromosome shapes are determined by actions of condensins and cohesin, we devised a series of protocols in which their levels are precisely changed in Xenopus egg extracts. When the relative ratio of condensin I to II is forced to be smaller, embryonic chromosomes become shorter and thicker, being reminiscent of somatic chromosomes. Further depletion of condensin II unveils its contribution to axial shortening of chromosomes.

In-water dehydrative alkylation of ammonia and amines with alcohols by a polymeric bimetallic catalyst.

An in-water dehydrative alkylation with a novel heterobimetallic polymeric catalyst is described. Thus, a boron-iridium heterobimetallic polymeric catalyst was prepared by ionic convolution of a poly(catechol borate) and an iridium complex. The alkylation of ammonia and amines with alcohols, alkylating agents, was performed with 1 mol % Ir of the heterogeneous catalyst in water without the use of organic solvents under aerobic conditions to give the corresponding alkylated amines.

Poly(aspartate) hydrolases: biochemical properties and applications.

Thermally synthesized poly(aspartate) (tPAA) shows potential for use in a wide variety of products and applications as a biodegradable replacement for non-biodegradable polycarboxylates, such as poly(acrylate). The tPAA molecule has unnatural structures, and the relationship between its biodegradability and structures has been investigated. Two tPAA-degrading bacteria, Sphingomonas sp.

Boron-boron σ-bond formation by two-electron reduction of a H-bridged dimer of monoborane.

Diborane(6) as a H-bridged dimer of monoborane can be converted cleanly by two-electron reduction into diborane(6) dianion, which is isoelectronic with ethane, through B-B σ-bond formation when each boron atom has a bulky ligand on it. The existence of the B-B σ bond is supported by the X-ray molecular structure [B-B bond length of 1.924(3) Å], NMR studies, magnetic susceptibility measurements, and DFT calculations.

Co-expression of four baculovirus proteins, IE1, LEF3, P143, and PP31, elicits a cellular chromatin-containing reticulate structure in the nuclei of uninfected cells.

Baculovirus DNA replication, transcription, and nucleocapsid assembly occur within a subnuclear structure called the virogenic stroma (VS) that consists of two subcompartments. Specific components of the VS sub-compartments have not been identified except for PP31, a DNA-binding protein that localizes specifically to the electron-dense region of VS. Here, we investigate the dynamic structure of VS using a GFP-tagged PP31 molecule (GFP-PP31).