Detection and quantitation of the activity of DNA methyltransferases using a biotin/avidin microplate assay.

The biotin-avidin microplate assay is a sensitive method to measure methylation of biotinylated oligonucleotide substrates by DNA methyltransferases (MTases). The methylation reaction is carried out in solution using [methyl-3H]-AdoMet. Afterwards, the oligonucleotides are immobilized on an avidin-coated microplate, where the incorporation of [3H]-labeled methyl groups into the DNA is stopped by addition of unlabeled AdoMet to the binding buffer.

On the enzymatic properties of Dnmt1: specificity, processivity, mechanism of linear diffusion and allosteric regulation of the enzyme.

In this short review the enzymatic properties of Dnmt1 are summarized. Studies on the specificity of Dnmt1 have shown that it has 30-40 fold preference for hemimethylated target sites. It methylates hemimethylated DNA in a processive reaction, moving on the DNA in a random walk.

Cathepsin B is essential for regeneration of scratch-wounded normal human epidermal keratinocytes.

Migration, proliferation and differentiation of keratinocytes are important processes during tissue regeneration and wound healing of the skin. Here, we focussed on proteases that contribute to extracellular matrix (ECM) remodeling as a prerequisite of keratinocyte migration. In particular, we assessed the significance of the mammalian cysteine peptidase cathepsin B for human keratinocytes during regeneration from scratch wounding.

A temperature-sensing histidine kinase: function, genetics, and membrane topology.

Two-component systems provide a means for bacteria to sense and adapt to environmental signals in order to survive in a continuously changing environment. Understanding of the mechanism by which these systems function is important in combating bacterial infections because many bacterial two-component systems are associated with virulence. The plant pathogenic bacterium Pseudomonas syringae pv.

Dititanium-containing 19-tungstodiarsenate(III) [Ti2(OH)2As2W19O67(H2O)]8-: synthesis, structure, electrochemistry, and oxidation catalysis.

The dititanium-containing 19-tungstodiarsenate(III) [Ti(2)(OH)(2)As(2)W(19)O(67)(H(2)O)](8-) (1) has been synthesized and characterized by IR, TGA, elemental analysis, electrochemistry, and catalytic studies. Single-crystal X-ray analysis was carried out on Cs(8)[Ti(2)(OH)(2)As(2)W(19)O(67)(H(2)O)].2CsCl.

New neurons for the injured brain: mechanisms of neuronal regeneration in adult teleost fish.

In contrast to mammals, teleost fish exhibit an enormous potential to continuously produce new neurons in many areas of the adult brain, and to regenerate neural tissue after brain injury. The regenerative capability of the teleost fish brain is based upon a series of well-orchestrated individual processes, including: elimination of damaged cells by apoptosis, removal of cellular debris by the action of microglia/macrophages, proliferation of endogenous neural precursor cells, radial glia-mediated migration of their progeny to the site of the lesion, neuronal differentiation, promotion of cellular survival, and integration of the new neurons into existing neural circuits. Combination of a well-defined cerebellar lesion paradigm with differential proteome analysis has demonstrated that identification of the multitude of proteins mediating the regenerative potential of the adult fish brain is feasible in the foreseeable future.

Eyes of male and female Orgyia antiqua (Lepidoptera; Lymantriidae) react differently to an exposure with UV-A.

The structural organization of the eyes belonging to 12 winged male and 12 wingless female Orgyia antiqua moths, exposed for 1 h to UV-radiation (lambda(max)=351 nm) of 1.4 kW/m2, was compared with that of 12 male and 12 female non-irradiated control specimens. Following the UV-exposure, the screening pigments were found in a position indicative of extreme light-adaptation.

Social balance as a satisfiability problem of computer science.

Reduction of frustration was the driving force in an approach to social balance as it was recently considered by Antal [T. Antal, P. L.

Universality class of triad dynamics on a triangular lattice.

We consider triad dynamics as it was recently considered by Antal [Phys. Rev. E 72, 036121 (2005)] as an approach to social balance.

Directed evolution of oxygenases: screening systems, success stories and challenges.

The field of directed evolution of oxygenases (mono-, di- and epoxygenases) is rapidly advancing as an increasing number of success stories indicate. A significant number of screening systems have been developed to specifically improve oxygenase properties. Oxygenases will become very valuable biocatalysts for synthetic applications in industry when stability, cofactor and activity properties match industrial demands.

The monolanthanide-containing silicotungstates [Ln(beta2-SiW11O39)2]13- (Ln = La, Ce, Sm, Eu, Gd, Tb, Yb, Lu): a synthetic and structural investigation.

We have synthesized and structurally characterized the monolanthanide-containing polyanions [Ln(beta2-SiW11O39)2]13- (Ln = La (1), Ce (2), Sm (3), Eu (4), Gd (5), Tb (6), Yb (7), Lu (8)). Synthesis was accomplished by reaction of the respective lanthanide ion with the monolacunary Keggin-type precursor [beta2-SiW11O39]8- in a 1:2 molar ratio in 1 M KCl medium at pH 5. Polyanions 1-8 were isolated as potassium salts and then characterized by IR, single-crystal X-ray diffraction, and elemental as well as thermogravimetric analysis.

Enantioselective hydrogenation of ethyl pyruvate over diop modified Pt nanoclusters. Determination of geometry of the ligand adsorption mode via DRIFTS.

Immobilization of chiral ligands on the surface of metal nanoparticles is one concept for heterogenation of enantioselective catalysts. Diop modified Pt nanoclusters were found to be able to induce enantioselectivity and enhancement of the reaction rate in hydrogenation of ethyl pyruvate. The model of geometry of the diop adsorption has been proposed based on DRIFTS and molecular modelling investigations.

Glowworms: a review of Arachnocampa spp. and kin.

The term 'glowworm' is used in connection with the flightless females of lampyrid fireflies and to describe the luminescent larvae of certain fungus gnats that belong to the subfamilies Arachnocampinae, Keroplatinae and Macrocerinae of the dipteran family Keroplatidae. This review focuses on the luminescent larval fungus gnats. The weakly luminescent species of the Holarctic feed mainly on fungal spores, but some, such as Orfelia fultoni, have turned to a carnivorous diet.

Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation.

Comparative explicit solvent molecular dynamics (MD) simulations have been performed on a complete nucleosome core particle with and without N-terminal histone tails for more than 20 ns. Main purpose of the simulations was to study the dynamics of mobile elements such as histone N-terminal tails and how packing and DNA-bending influences the fine structure and dynamics of DNA. Except for the tails, histone and DNA molecules stayed on average close to the crystallographic start structure supporting the quality of the current force field approach.

Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles.

MHC class I molecules load antigenic peptides in the endoplasmic reticulum and present them at the cell surface. Efficiency of peptide loading depends on the class I allele and can involve interaction with tapasin and other proteins of the loading complex. Allele HLA-B*4402 (Asp at position 116) depends on tapasin for efficient peptide loading, whereas HLA-B*4405 (identical to B*4402 except for Tyr116) can efficiently load peptides in the absence of tapasin.

Sensing lipid bilayer formation and expansion with a microfabricated cantilever array.

We show that cantilever array sensors can sense the formation of supported phospholipid bilayers on their surface and that they can monitor changes in mechanical properties of lipid bilayers. Supported lipid bilayers were formed on top of microfabricated cantilevers by vesicle fusion. The formation of bilayers led to a bending of the cantilevers of 70-590 nm comparable to a surface stress of 27-224 mN/m.

Directed evolution of glucose oxidase from Aspergillus niger for ferrocenemethanol-mediated electron transfer.

A directed evolution protocol was developed for glucose oxidase (GOx) from Aspergillus niger that mimics applications conditions and employs a well-known mediator, oxidized ferrocenemethanol, in a medium throughput screen (96-well plate format). Upon reduction, oxidized ferrocenemethanol shows a color change from blue to pale yellow that can be recorded at 625 nm. Under optimized screening conditions, a CV of less than 20% was achieved in 96-well microtiter plates.

High-throughput liberation of water-soluble yeast content by irreversible electropermeation (HT-irEP).

The article describes a high-throughput method for the liberation of water-soluble cell contents by exploiting the phenomenon of irreversible membrane electropermeation (HT-irEP). The method is exemplified in recombinant proteins and plasmid liberation from yeast Saccharomyces cerevisiae on the detectable level. Obtained extracts are pure enough to be readily applied for further analytical analysis such as enzyme assay, PCR, and so on.

Why two "Distractors" are better than one: modeling the effect of non-target auditory and tactile stimuli on visual saccadic reaction time.

Saccadic reaction time (SRT) was measured in a focused attention task with a visual target stimulus (LED) and auditory (white noise burst) and tactile (vibration applied to palm) stimuli presented as non-targets at five different onset times (SOAs) with respect to the target. Mean SRT was reduced (i) when the number of non-targets was increased and (ii) when target and non-targets were all presented in the same hemifield; (iii) this facilitation first increases and then decreases as the time point of presenting the non-targets is shifted from early to late relative to the target presentation. These results are consistent with the time-window-of-integration (TWIN) model (Colonius and Diederich in J Cogn Neurosci 16:1000-1009, 2004) which distinguishes a peripheral stage of independent sensory channels racing against each other from a second stage of neural integration of the input and preparation of an oculomotor response.

Eye ultrastructure in the pollen-feeding beetle, Xanthochroa luteipennis (Coleoptera: Cucujiformia: Oedemeridae).

The pollen-consuming beetle Xanthochroa luteipennis, which belongs to the family Oedemeridae, possesses a nearly spherical eye of approximately 400 microm in diameter. The eye contains 750-800, mostly hexagonal ommatidia, which are of the acone apposition type and have an open rhabdom. A well-developed pupil mechanism controls the light flux to the rhabdom.

Structure and putative function of dark- and light-adapted as well as UV-exposed eyes of the food store pest Psyllipsocus ramburi Sélys-longchamps (Insecta: Psocoptera: Psyllipsocidae).

The psocopteran Psyllipsocus ramburi Sélys-Longchamps can render food stuffs unpalatable and may serve as an intermediate host for cestodes. Its two circular compound eyes consist of about 26 facets, capped by strongly convexly curved corneae of 10-18 microm in diameter. Corneal nipples or interommatidial hairs are not developed.

Reversible inactivation of the CG specific SssI DNA (cytosine-C5)-methyltransferase with a photocleavable protecting group.

Caging of proteins by conjugation with a photocleavable group is a powerful approach for reversibly blocking enzymatic activity. Here we describe the covalent modification of the bacterial SssI DNA methyltransferase (M.SssI) with the cysteine-specific reagent 4,5-dimethoxy-2-nitrobenzylbromide (DMNBB).

Are transversion mutations better? A Mutagenesis Assistant Program analysis on P450 BM-3 heme domain.

Directed evolution represents a versatile tool to tailor enzyme properties to needs in industrial applications and to understand structure-function relationships. Genetic diversity is commonly generated using error-prone PCR. Exploration of sequence space by random mutagenesis strongly favors transitions when enzyme-based mutagenesis methods are employed (Wong, T.

A novel hexatungstate fragment stabilized by dimethyltin groups: [{(CH3)2Sn}2(W6O22)]4-.

Reaction of Na2WO4 and (CH3)2SnCl2 in water (pH 7) led to the formation of the hybrid organic-inorganic polyanion [{(CH3)2Sn}2(W6O22)]4- (1), which is composed of a novel hexatungstate core stabilized by two dimethyltin groups. Selective crystallization of 1 with guanidinium cations resulted in [C(NH2)3]4[{CH3)2Sn}2(W6O22)]2H2O (1a), which exhibits a 1D arrangement via distorted trigonal-bipyramidal cis-(CH3)2SnO3 moieties.

Entanglement entropy of black holes and anti-de Sitter space/conformal-field-theory correspondence.

A recent proposal by Ryu and Takayanagi for a holographic interpretation of entanglement entropy in conformal field theories dual to supergravity on anti-de Sitter space is generalized to include entanglement entropy of black holes living on the boundary of anti-de Sitter space. The generalized proposal is verified in boundary dimensions d=2 and d=4 for both the uv-divergent and uv-finite terms. In dimension d=4 an expansion of entanglement entropy in terms of size L of the subsystem outside the black hole is considered.