ORE-Seq: Genome-Wide Absolute Occupancy Measurement by Restriction Enzyme Accessibilities.

Digestion with restriction enzymes is a classical approach for probing DNA accessibility in chromatin. It allows to monitor both the cut and the uncut fraction and thereby the determination of accessibility or occupancy (= 1 - accessibility) in absolute terms as the percentage of cut or uncut molecules, respectively, out of all molecules. The protocol presented here takes this classical approach to the genome-wide level.

Large-scale analysis of Drosophila core promoter function using synthetic promoters.

The core promoter plays a central role in setting metazoan gene expression levels, but how exactly it "computes" expression remains poorly understood. To dissect its function, we carried out a comprehensive structure-function analysis in Drosophila. First, we performed a genome-wide bioinformatic analysis, providing an improved picture of the sequence motifs architecture.

Synthesis, C-H bond functionalisation and cycloadditions of 6-styryl-1,2-oxathiine 2,2-dioxides.

A series of 6-styryl-1,2-oxathiine 2,2-dioxides have been efficiently obtained by a two-step protocol from readily available (1E,4E)-1-(dimethylamino)-5-arylpenta-1,4-dien-3-ones involving a regioselective sulfene addition and subsequent Cope elimination. Pd-Mediated direct C-H bond functionalisation of the 6-styryl-1,2-oxathiine 2,2-dioxides and a wider selection of 5,6-diaryl substituted 1,2-oxathiine 2,2-dioxides proceeded smoothly to afford C-3 (hetero)aryl substituted analogues and the results are contrasted with those of a complementary bromination - Suzuki cross-coupling sequence. Whilst the cycloaddition of benzyne, derived from in situ fluoride initiated decomposition of 2-(trimethylsilyl)phenyl trifluoromethanesulfonate, to the substituted 1,2-oxathiine 2,2-dioxides resulted in low yields of substituted naphthalenes, the addition of 4-phenyl-1,2,4-triazoline-3,5-dione to the 6-styryl-1,2-oxathiine 2,2-dioxides afforded novel 5,9-dihydro-1H-[1,2]oxathiino[5,6-c][1,2,4]triazolo[1,2-a]pyridazine-1,3(2H)-dione 8,8-dioxides through a silica-mediated isomerisation of the initial [4 + 2] adducts.

Quenching of the phosphorescence of thermally reversible photochromic naphthopyran Re(i) complexes initiated by either visible or ultraviolet radiation.

Re(i) complexes bearing thermally reversible photochromic naphthopyran axial ligands undergo highly efficient, reversible phosphorescence quenching actuated by either visible or UV irradiation. The photoinduced quenching of the triplet metal-to-ligand charge-transfer (MLCT) emission is interpreted based on changes in the relative energies of the excited states.

Synthesis and Photochromism of Novel Pyridyl-Substituted Naphthopyrans.

Multitarget synthetic strategies to access novel photochromic 3-naphtho[2,1-]pyrans decorated with pyridyl units are described. The new pyridyl-substituted 3-naphtho[2,1-]pyrans display good photochromic properties with reversible generation of photomerocyanines, which exhibit mainly orange/red hues. Photochromic parameters including photocolorability and persistence of color vary tremendously on structural modification of the naphthopyran core.

Base-Mediated Ring-Contraction of Pyran Systems Promoted by Palladium and Phase-Transfer Catalysis.

A study of the ring-contraction of a model 3-naphtho[2,1-]pyran is described to elucidate and optimize the ring-contraction of naphthopyrans. Two efficient base-mediated protocols to access multiple naphthofurans, naphthodifurans, and a benzo-fused indole in generally good yields are reported. Furthermore, a protocol to selectively prepare (hetero)aryl-substituted naphthofurans via a Suzuki-coupling-ring-contraction process is presented.

Absolute nucleosome occupancy map for the genome.

Mapping of nucleosomes, the basic DNA packaging unit in eukaryotes, is fundamental for understanding genome regulation because nucleosomes modulate DNA access by their positioning along the genome. A cell-population nucleosome map requires two observables: nucleosome positions along the DNA ("Where?") and nucleosome occupancies across the population ("In how many cells?"). All available genome-wide nucleosome mapping techniques are yield methods because they score either nucleosomal (e.

Expedient synthesis of highly substituted 3,4-dihydro-1,2-oxathiine 2,2-dioxides and 1,2-oxathiine 2,2-dioxides: revisiting sulfene additions to enaminoketones.

Diversely substituted 1,2-oxathiine 2,2-dioxides, including 3,5,6-triaryl-, 3,6-diaryl-, 3,5-diaryl-, 5,6-diaryl- and selected fused heterocyclic analogues, have been efficiently obtained by the application of a mild Cope elimination of a 4-amino moiety from the requisite 4-amino-3,4-dihydro-1,2-oxathiine 2,2-dioxides, which themselves were readily obtained by the addition of sulfenes to enaminoketones.

Synthesis and photochromism of some mono and bis (thienyl) substituted oxathiine 2,2-dioxides.

1,2-Oxathiine 2,2-dioxides have been obtained from their respective 3,4-dihydro-4-dimethylamino precursors, for the first time, by a mild Cope elimination of the 4-dimethylamino function. The application of the 1,2-oxathiine 2,2-dioxide scaffold in materials chemistry is exemplified by the efficient P-type photochromism of the 5,6-bis(2,5-dimethyl-3-thienyl) substituted oxathiine 2,2-dioxides.

Optical Communication among Oscillatory Reactions and Photo-Excitable Systems: UV and Visible Radiation Can Synchronize Artificial Neuron Models.

Neuromorphic engineering promises to have a revolutionary impact in our societies. A strategy to develop artificial neurons (ANs) is to use oscillatory and excitable chemical systems. Herein, we use UV and visible radiation as both excitatory and inhibitory signals for the communication among oscillatory reactions, such as the Belousov-Zhabotinsky and the chemiluminescent Orban transformations, and photo-excitable photochromic and fluorescent species.

Processing Binary and Fuzzy Logic by Chaotic Time Series Generated by a Hydrodynamic Photochemical Oscillator.

This work demonstrates the computational power of a hydrodynamic photochemical oscillator based on a photochromic naphthopyran generating aperiodic time series. The chaotic character of the time series is tested by calculating its largest Lyapunov exponent and the correlation dimension of its attractor after building its phase space through the Takens' theorem. Then, the chaotic dynamic is shown to be suitable to implement all the fundamental Boolean two-inputs-one-output logic gates.

Extending human perception of electromagnetic radiation to the UV region through biologically inspired photochromic fuzzy logic (BIPFUL) systems.

Photochromic fuzzy logic systems have been designed that extend human visual perception into the UV region. The systems are founded on a detailed knowledge of the activation wavelengths and quantum yields of a series of thermally reversible photochromic compounds. By appropriate matching of the photochromic behaviour unique colour signatures are generated in response differing UV activation frequencies.

Spectroscopic studies (FT-IR, FT-Raman, UV-Visible), normal co-ordinate analysis, first-order hyperpolarizability and HOMO, LUMO studies of 3,4-dichlorobenzophenone by using Density Functional Methods.

The vibrational frequencies of 3,4-dichlorobenzophenone (DCLBP) were obtained from the FT-IR and Raman spectral data, and evaluated based on the Density Functional Theory using the standard method B3LYP with 6-311+G(d,p) as the basis set. On the basis of potential energy distribution together with the normal-co-ordinate analysis and following the scaled quantum mechanical force methodology, the assignments for the various frequencies were described. The values of the electric dipole moment (μ) and the first-order hyperpolarizability (β) of the molecule were computed.

The first structural and spectroscopic characterisation of a ring-opened form of a 2H-naphtho[1,2-b]pyran: a novel photomerocyanine.

Heating 4-methoxy-1-naphthol with a 1,1-diarylprop-2-yn-1-ol gave the 2,2-diaryl-6-methoxy-2H-naphtho[1,2-b]pyran together with the novel merocyanine, (E)-2-[3',3'-bis(aryl)allylidene]-4-methoxynaphthalen-1(2H)-one. Brief UV-irradiation of the pyran favoured the formation of the (Z)-merocyanine with longer irradiation and/or acidic conditions favouring the (E)-isomer.

RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress.

RECQL5 is the sole member of the RECQ family of helicases associated with RNA polymerase II (RNAPII). We now show that RECQL5 is a general elongation factor that is important for preserving genome stability during transcription. Depletion or overexpression of RECQL5 results in corresponding shifts in the genome-wide RNAPII density profile.

Homology-based inference sets the bar high for protein function prediction.

Background: Any method that de novo predicts protein function should do better than random. More challenging, it also ought to outperform simple homology-based inference.

Methods: Here, we describe a few methods that predict protein function exclusively through homology.

A large-scale evaluation of computational protein function prediction.

Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. If computational predictions are to be relied upon, it is crucial that the accuracy of these methods be high.

DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation.

Alternative messenger RNA splicing is the main reason that vast mammalian proteomic complexity can be achieved with a limited number of genes. Splicing is physically and functionally coupled to transcription, and is greatly affected by the rate of transcript elongation. As the nascent pre-mRNA emerges from transcribing RNA polymerase II (RNAPII), it is assembled into a messenger ribonucleoprotein (mRNP) particle; this is the functional form of the nascent pre-mRNA and determines the fate of the mature transcript.

Intrinsically thermochromic fluorans.

A Suzuki coupling strategy has been employed to access a series of novel fluorans substituted with a phenolic moiety. These fluorans display good thermochromism in methyl stearate and obviate the need for traditional complex formulations containing acidic colour developers.

Benzopentalenonaphthalenones from the intramolecular capture of a merocyanine derived from a naphthopyran.

Novel, highly coloured benzopentalenonaphthalenones result from a cascade process initiated by the thermally-induced ring-opening of diarylmethanol substituted 2H-naphtho[1,2-b]pyrans in the presence of acid.

The influence of a 1,1-diarylvinyl moiety on the photochromism of naphthopyrans.

1,1,3-Triarylpent-4-en-1-yn-3-ols, efficiently obtained in two steps from 1,1,3-triarylprop-2-yn-1-ols by a Meyer-Schuster rearrangement and subsequent addition of lithium trimethylsilylacetylide, react with either a 1- or 2- naphthol to afford photochromic 1,1-diarylvinyl substituted naphtho[1,2-b]- or naphtho[2,1-b]-pyrans respectively. Irradiation of solutions of these naphthopyrans results in reversible electrocyclic ring-opening to afford photomerocyanines which possess an extended conjugated system and show a bathochromically-shifted λ(max) relative to the non-vinyl substituted analogues.

Synthesis and Characterization of Co-polymers Based on Methyl Methacrylate and 2-Hexyl Acrylate Containing Naphthopyrans for a Light-Sensitive Contact Lens.

Three different naphthopyrans were incorporated in co-polymers of methyl methacrylate (MMA) and 2-ethylhexyl acrylate (EHA), with and without cross-linking with ethyleneglycol dimethacrylate (EGDMA), by a free radical polymerization method. The obtained materials were characterised in terms of some of their chemical and physical properties that could be important for the final functional properties of the envisaged application. Despite other important functional properties that should be evaluated in the near future, the system based in the physical entrapment of 3,3-bis(4-methoxyphenyl)-3H-naphtho [2,1-b]pyran presented a good potential for its application as novel light-sensitive contact lenses.

Ring contraction during the 6pi-electrocyclisation of naphthopyran valence tautomers.

The thermal and photochemical ring-opening of spiro(3H-naphtho[2,1-b]pyran-3,9'-thioxanthene-10,10-dioxide) results in the facile ring-contraction to 9-(naphtho[2,1-b]furan-2-yl)-9H-thioxanthene-10,10-dioxide . Similar behaviour is displayed by the isomeric spiro(2H-naphtho[1,2-b]pyran-2,9'-thioxanthene-10,10-dioxide) affording 9-(naphtho[1,2-b]furan-2-yl)-9H-thioxanthene-10,10-dioxide , though more severe reaction conditions were required. The comparative ease of this rearrangement for the isomers and was rationalised on the basis of the relative isomer populations of the ring-opened naphthopyrans.