Identification of a small-molecule inhibitor of DNA topoisomerase II by proteomic profiling.

BNS-22, a chemically synthesized derivative of the natural plant product GUT-70, has antiproliferative activity against human cancer cells, the mechanism of which is unknown. Here, we identify a target of BNS-22 by proteomic profiling analysis, which suggests that BNS-22 belongs to the same cluster as ICRF-193, a DNA topoisomerase II (TOP2) catalytic inhibitor. BNS-22 inhibits kinetoplast DNA decatenation that is mediated by human TOP2α and TOP2β in vitro at an IC(50) of 2.

A proof of the DBRF-MEGN method, an algorithm for deducing minimum equivalent gene networks.

Background: We previously developed the DBRF-MEGN (difference-based regulation finding-minimum equivalent gene network) method, which deduces the most parsimonious signed directed graphs (SDGs) consistent with expression profiles of single-gene deletion mutants. However, until the present study, we have not presented the details of the method's algorithm or a proof of the algorithm.

Results: We describe in detail the algorithm of the DBRF-MEGN method and prove that the algorithm deduces all of the exact solutions of the most parsimonious SDGs consistent with expression profiles of gene deletion mutants.

Branched RNA nanostructures for RNA interference.

Branched RNAs with three- or four-way junctions were designed by assembling single-stranded RNA for RNA interference. Human Dicer transformed branched RNAs into about 20 base pairs of double-stranded RNA, which is a standard siRNA species. Our tetramer design provides a potent silencing effect over a period of 5 days.

ECHO probes: a concept of fluorescence control for practical 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. This critical review points out the recent advances in exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) probes, which have a fluorescence-labeled nucleotide in which two molecules of thiazole orange or its derivatives are linked covalently. ECHO probes show absorption shift and emission switching depending on hybridization with the target nucleic acid.

The occurrence of 'bulbs', a complex configuration of the vacuolar membrane, is affected by mutations of vacuolar SNARE and phospholipase in Arabidopsis.

The plant vacuole fulfills a variety of functions, and is essential for plant growth and development. We previously identified complex and mobile structures on the continuous vacuolar membrane, which we refer to as 'bulbs'. To ascertain their biological significance and function, we searched for markers associated with bulbs, and mutants that show abnormalities with respect to bulbs.

Reveromycin A biosynthesis uses RevG and RevJ for stereospecific spiroacetal formation.

Spiroacetal compounds are ubiquitous in nature, and their stereospecific structures are responsible for diverse pharmaceutical activities. Elucidation of the biosynthetic mechanisms that are involved in spiroacetal formation will open the door to efficient generation of stereospecific structures that are otherwise hard to synthesize chemically. However, the biosynthesis of these compounds is poorly understood, owing to difficulties in identifying the responsible enzymes and analyzing unstable intermediates.

Synthesis of cubic SrCoO3 single crystal and its anisotropic magnetic and transport properties.

A large-size single crystal of nearly stoichiometric SrCoO(3) was prepared with a two-step method combining the floating-zone technique and subsequent high oxygen pressure treatment. SrCoO(3) crystallizes in a cubic perovskite structure with space group Pm3m, and displays an itinerant ferromagnetic behavior with the Curie temperature of 305 K. The easy magnetization axis is found to be along the [111] direction, and the saturation moment is 2.

Metabolism of free oligosaccharides is facilitated in the och1Δ mutant of Saccharomyces cerevisiae.

In eukaryotic cells, it is known that N-glycans play a pivotal role in quality control of carrier proteins. Although "free" forms of oligosaccharides (fOSs) are known to be accumulated in the cytosol, the precise mechanism of their formation, degradation and biological relevance remains poorly understood. It has been shown that, in budding yeast, almost all fOSs are formed from misfolded glycoproteins.

Furaquinocins I and J: novel polyketide isoprenoid hybrid compounds from Streptomyces reveromyceticus SN-593.

Two novel furaquinocin (FQ) analogues, I (1) and J (2), were isolated from Streptomyces reveromyceticus SN-593 strain NRM2. Their structures were elucidated by MS and NMR analyses. Similar to the previously described FQ D (3), both 1 and 2 possessed a dihydrofuran ring fused to a polyketide naphthoquinone skeleton.

Free-energy landscapes of protein domain movements upon ligand binding.

The conformation and functions of proteins are closely linked, and many proteins undergo conformational changes upon ligand binding. The X-ray crystallographic studies have revealed conformational differences in proteins between the liganded and unliganded states. Currently, the conformational transitions that originate in the ligand binding are explained on the basis of two representative models, the induced-fit and preexisting equilibrium dynamics models.

Why so few drug targets: a mathematical explanation?

The apparently paradoxical lack of correlation between the huge increase in the discovery of new potential drug targets made possible by the post-genomic sciences and new drugs development has stimulated many different interpretations. Here we illustrate the general principle of redundancy of biological pathways on hand of simplified mathematical approaches applied to different models of biological regulation. The simulation was based on the analysis of the 'degree of autonomy' of network architectures in which the possibility for an external stimulus (e.

Design and synthesis of protein kinase Cα activators based on 'out of pocket' interactions.

Novel types of PKCα activators based on isobenzofuranone bearing a myo-inositol moiety were designed and synthesized. The derivatives with bulky substituents on the myo-inositol moiety significantly activated PKCα, but their binding sites were not the same as that of phorbol ester.

Hormone signaling linked to silkmoth sex pheromone biosynthesis involves Ca2+/calmodulin-dependent protein kinase II-mediated phosphorylation of the insect PAT family protein Bombyx mori lipid storage droplet protein-1 (BmLsd1).

Species-specific sex pheromones released by female moths to attract conspecific male moths are synthesized de novo in the pheromone gland (PG) via the fatty acid biosynthetic pathway. This pathway is regulated by a neurohormone termed pheromone biosynthesis activating neuropeptide (PBAN), a 33-amino acid peptide that originates in the subesophageal ganglion. In the silkmoth, Bombyx mori, cytoplasmic lipid droplets, which store the sex pheromone (bombykol) precursor fatty acid, accumulate in PG cells.

Free fatty acids induce transglutaminase 2-dependent apoptosis in hepatocytes via ER stress-stimulated PERK pathways.

Non-alcoholic steatohepatitis (NASH), a progressive form of fatty liver, shares histological similarities with alcoholic steatohepatitis (ASH), including accumulated fat, hepatic apoptosis, and fibrous tissues in the liver, but the molecular mechanisms responsible for hepatic apoptosis remain unclear. We previously reported that transglutaminase 2 (TG2), induced in the nuclei of ethanol-treated hepatocytes, crosslinks and inactivates the transcription factor Sp1, leading to hepatic apoptosis. In this study, we investigated whether a similar change is involved in NASH, and if so, how TG2 and crosslinked Sp1 (CLSp1) are induced.

3D microfluidic chips with integrated functional microelements fabricated by a femtosecond laser for studying the gliding mechanism of cyanobacteria.

Phormidium, a genus of filamentous cyanobacteria, forms endosymbiotic associations with seedling roots that accelerate the growth of the vegetable seedlings. Understanding the gliding mechanism of Phormidium will facilitate improved formation of this association and increased vegetable production. To observe the gliding movements, we fabricated various microfluidic chips termed nanoaquariums using a femtosecond (fs) laser.

Indomethacin Analogues that Enhance Doxorubicin Cytotoxicity in Multidrug Resistant Cells without Cox Inhibitory Activity.

Conformationally restricted indomethacin analogues were designed and prepared from the corresponding 2-substituted indoles, which were synthesized by a one-pot isomerization/enamide-ene metathesis as the key reaction. Conformational analysis by calculations, NMR studies, and X-ray crystallography suggested that these analogues were conformationally restricted in the s-cis or the s-trans form due to the 2-substituent as expected. Their biological activities on cyclooxygenase-1 (COX-1) inhibition, cyclooxygenase-2 (COX-2) inhibition, and modulation of MRP-1-mediated multidrug resistance (MDR) are described.

Recombinant hBMP4 incorporated with non-canonical amino acid for binding to hydroxyapatite.

A novel growth factor containing non-canonical amino acids was designed and synthesized to enhance the binding to hydroxyapatite (HA). The designed protein was human bone morphogenetic protein 4 (hBMP4) incorporating diphosporylated serines (pSpS) that was found in salivary protein statherin and was reported to be responsible for binding to HA. Recombinant hBMP4 and a short peptide sequences containing pSpS were ligated by enzymatice reaction of sortase A, which exchanges the terminal amino acids of two polypeptides.

Recombinant human gelatin substitute with photoreactive properties for cell culture and tissue engineering.

The human recombinant collagen I α1 chain monomer (rh-gelatin) was modified by the incorporation of an azidophenyl group to prepare photoreactive human gelatin (Az-rh-gelatin), with approximately 90% of the lysine residues conjugated with azidobenzoic acid. Slight changes in conformation (circular dichroism spectra) and thermal properties (gelation and melting points) were noticed after modification. Ultraviolet (UV) irradiation could immobilize the Az-rh-gelatin on polymer surfaces, such as polystyrene and polytetrafluoroethylene.

Real-time imaging of histone H4K12-specific acetylation determines the modes of action of histone deacetylase and bromodomain inhibitors.

Histone acetylation constitutes an epigenetic mark for transcriptional regulation. Here we developed a fluorescent probe to visualize acetylation of histone H4 Lys12 (H4K12) in living cells using fluorescence resonance energy transfer (FRET) and the binding of the BRD2 bromodomain to acetylated H4K12. Using this probe designated as Histac-K12, we demonstrated that histone H4K12 acetylation is retained in mitosis and that some histone deacetylase (HDAC) inhibitors continue to inhibit cellular HDAC activity even after their removal from the culture.

Air- and moisture-stable p-monothiobenzoquinones incorporated in an octaalkyl-s-hydrindacene skeleton.

p-Monothiobenzoquinones incorporated in a fused-ring octaalkyl-s-hydrindacene skeleton have been synthesized as air- and moisture-stable reddish orange crystals by the oxidation of mercaptophenol derivatives with DDQ, which have been characterized by X-ray crystallography to show a planar quinoid framework.

Synthesis, structure and efficient electroluminescence of a heteroleptic dipyridylamido/bis(pyridylphenyl)iridium(III) complex.

A neutral 2,2'-dipyridylamido (dpa)-supported bis(cyclometalated) iridium(III) complex [Ir(ppy)(2)(dpa)] (ppy = o-(2-pyridyl)phenyl) has been synthesized and structurally characterized for the first time, which emits green electroluminescence with high current efficiency (123.5 cd A(-1)) and high power efficiency (43.2 lm W(-1)).

Dual-chirped optical parametric amplification for generating few hundred mJ infrared pulses.

An ultrafast high-power infrared pulse source employing a dual-chirped optical parametric amplification (DC-OPA) scheme based on a Ti:sapphire pump laser system is theoretically investigated. By chirping both pump and seed pulses in an optimized way, high-energy pump pulses can be utilized for a DC-OPA process without exceeding the damage threshold of BBO crystals, and broadband signal and idler pulses at 1.4 μm and 1.

Two-dimensional optical feedback control of Euglena confined in closed-type microfluidic channels.

We examined two-dimensional (2D) optical feedback control of phototaxis flagellate Euglena cells confined in closed-type microfluidic channels (microaquariums), and demonstrated that the 2D optical feedback enables the control of the density and position of Euglena cells in microaquariums externally, flexibly, and dynamically. Using three types of feedback algorithms, the density of Euglena cells in a specified area can be controlled arbitrarily and dynamically, and more than 70% of the cells can be concentrated into a specified area. Separation of photo-sensitive/insensitive Euglena cells was also demonstrated.