Molecular Cues for Phenological Events in the Flowering Cycle in Avocado.

Reproductively mature horticultural trees undergo an annual flowering cycle that repeats each year of their reproductive life. This annual flowering cycle is critical for horticultural tree productivity. However, the molecular events underlying the regulation of flowering in tropical tree crops such as avocado are not fully understood or documented.

Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes.

The labelling of DNA oligonucleotides with signalling groups that give a unique response to duplex formation depending on the target sequence is a highly effective strategy in the design of DNA-based hybridisation sensors. A key challenge in the design of these so-called base discriminating probes (BDPs) is to understand how the local environment of the signalling group affects the sensing response. The work herein describes a comprehensive study involving a variety of photophysical techniques, NMR studies and molecular dynamics simulations, on anthracene-tagged oligonucleotide probes that can sense single base changes (point variants) in target DNA strands.

Pattern-oriented modelling as a novel way to verify and validate functional-structural plant models: a demonstration with the annual growth module of avocado.

Background And Aims: Functional-structural plant (FSP) models have been widely used to understand the complex interactions between plant architecture and underlying developmental mechanisms. However, to obtain evidence that a model captures these mechanisms correctly, a clear distinction must be made between model outputs used for calibration and thus verification, and outputs used for validation. In pattern-oriented modelling (POM), multiple verification patterns are used as filters for rejecting unrealistic model structures and parameter combinations, while a second, independent set of patterns is used for validation.

BTN3A1 Discriminates γδ T Cell Phosphoantigens from Nonantigenic Small Molecules via a Conformational Sensor in Its B30.2 Domain.

Human Vγ9/Vδ2 T-cells detect tumor cells and microbial infections by recognizing small phosphorylated prenyl metabolites termed phosphoantigens (P-Ag). The type-1 transmembrane protein Butyrophilin 3A1 (BTN3A1) is critical to the P-Ag-mediated activation of Vγ9/Vδ2 T-cells; however, the molecular mechanisms involved in BTN3A1-mediated metabolite sensing are unclear, including how P-Ag's are discriminated from nonantigenic small molecules. Here, we utilized NMR and X-ray crystallography to probe P-Ag sensing by BTN3A1.

Single Site Discrimination of Cytosine, 5-Methylcytosine, and 5-Hydroxymethylcytosine in Target DNA Using Anthracene-Tagged Fluorescent Probes.

The ability to discriminate between epigenetic variants in DNA is a necessary tool if we are to increase our understanding of the roles that they play in various biological processes and medical conditions. Herein, it is demonstrated how a simple two-step fluorescent probe assay can be used to differentiate all three major epigenetic variants of cytosine at a single locus site in a target strand of DNA.

NMR and molecular dynamics study of the size, shape, and composition of reverse micelles in a cetyltrimethylammonium bromide (CTAB)/n-hexane/pentanol/water microemulsion.

The size, shape, and composition of reverse micelles (RMs) in a cetyltrimethylammonium bromide (CTAB)/pentanol/n-hexane/water microemulsion were investigated using pulsed gradient stimulated echo (PGSTE) nuclear magnetic resonance (NMR) measurements and molecular modeling. PGSTE data were collected at observation times (Δ) of 10, 40, and 450 ms. At long observation times, CTAB and pentanol exhibited single diffusion coefficients.

De novo design of Ln(III) coiled coils for imaging applications.

A new peptide sequence (MB1) has been designed which, in the presence of a trivalent lanthanide ion, has been programmed to self-assemble to form a three stranded metallo-coiled coil, Ln(III)(MB1)3. The binding site has been incorporated into the hydrophobic core using natural amino acids, restricting water access to the lanthanide. The resulting terbium coiled coil displays luminescent properties consistent with a lack of first coordination sphere water molecules.

The influence of surface topography of a porous perfluoropolyether polymer on corneal epithelial tissue growth and adhesion.

Design principles for corneal implants are challenging and include permeability which inherently involves pore openings on the polymer surface. These topographical cues can be significant to a successful clinical outcome where a stratified epithelium is needed over the device surface, such as with a corneal onlay or corneal repair material. The impact of polymer surface topography on the growth and adhesion of corneal epithelial tissue was assessed using porous perfluoropolyether membranes with a range of surface topography.

The effect of leaving group on mechanistic preference in phosphate monoester hydrolysis.

We present 2-dimensional potential energy surfaces and optimised transition states (TS) for water attack on a series of substituted phosphate monoester monoanions at the DFT level of theory, comparing a standard 6-31++g(d,p) basis set with a larger triple-zeta (augmented cc-pVTZ) basis set. Small fluorinated model compounds are used to simulate increasing leaving group stability without adding further geometrical complexity to the system. We demonstrate that whilst changing the leaving group causes little qualitative change in the potential energy surfaces (with the exception of the system with the most electron withdrawing leaving group, CF(3)O(-), in which the associative pathway changes from a stepwise A(N) + D(N) pathway to a concerted A(N)D(N) pathway), there is a quantitative change in relative gas-phase and solution barriers for the two competing pathways.

A perfluoropolyether corneal inlay for the correction of refractive error.

This study assessed the long-term biological response of a perfluoropolyether-based polymer developed as a corneal inlay to correct refractive error. The polymer formulation met chemical and physical specifications and was non-cytotoxic when tested using standard in vitro techniques. It was cast into small microporous membranes that were implanted as inlays into corneas of rabbits (n = 5) and unsighted humans (n = 5 + 1 surgical control) which were monitored for up to 23 and 48 months respectively.

Magnetic resonance studies of a redox probe in a reverse sodium bis(2-ethylhexyl)sulfosuccinate/octane/water microemulsion.

The location and dynamics of the [Ru(bpy)(3)](2+) complex inside sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/octane/water microemulsions were studied, over a range of droplet sizes, using magnetic resonance spectroscopy, dynamic light scattering, and molecular modeling. The T(1) magnetic resonance relaxation times of water inside the AOT reverse micelles (RMs) were measured in both the presence and the absence of the [Ru(bpy)(3)](2+) complex. Large size droplet RMs (ω(0) > 20) were found to be sensitive to the presence of the [Ru(bpy)(3)](2+) complex, which was detected through a decrease in the T(1) relaxation time of the water inside the RM core, as compared to RMs containing no [Ru(bpy)(3)](2+).

Functionalised polysiloxanes as injectable, in situ curable accommodating intraocular lenses.

The aged eye's ability to change focus (accommodation) may be restored by replacing the hardened natural lens with a soft gel. Functionalised polysiloxane macromonomers, designed for application as an injectable, in situ curable accommodating intraocular lens (A-IOL), were prepared via a two-step synthesis. Prepolymers were synthesised via ring opening polymerisation (ROP) of octamethylcyclotetrasiloxane (D(4)) and 2,4,6,8-tetramethylcyclotetrasiloxane (D(4)(H)) in toluene using trifluoromethanesulfonic acid (TfOH) as catalyst.

Mechanism of CB1954 reduction by Escherichia coli nitroreductase.

NTR (nitroreductase NfsB from Escherichia coli) is a flavoprotein with broad substrate specificity, reducing nitroaromatics and quinones using either NADPH or NADH. One of its substrates is the prodrug CB1954 (5-[aziridin-1-yl]-2,4-dinitrobenzamide), which is converted into a cytotoxic agent; so NTR/CB1954 has potential for use in cancer gene therapy. However, wild-type NTR has poor kinetics and binding with CB1954, and the mechanism for the reduction of CB1954 by NTR is poorly understood.

Regulation of floral initiation in horticultural trees.

The intention of this review is to discuss floral initiation of horticultural trees. Floral initiation is best understood for herbaceous species, especially at the molecular level, so a brief overview of the control of floral initiation of Arabidopsis (Arabidopsis thaliana (L.) Heynh.

Anion complexation via C-H...X interactions using a palladacyclic receptor.

A novel organometallic receptor binds anions in solution and in the solid state, with complexes stabilised through a series of C-HX interactions, as evidenced by 1H NMR spectroscopy, X-ray crystallography and computational models.

Synthesis and ex vivo profiling of chemically modified cytomegalovirus CMVpp65 epitopes.

The effect of substituting unnatural hydrophobic amino acids into the critical MHC binding residues of an HLA-A*0201-restricted cytomegalovirus CMVpp65 epitope, NLVPMVATV, has been investigated. A new set of peptides containing the amino acids tert-butyl glycine (Tgl), cyclohexyl glycine (Chg), neo-pentyl glycine (Npg), cyclohexyl alanine (Cha) and cyclo leucine (Cyl), at either position 2, to mimic Leu, or position 9, to mimic Val, have been synthesised. Immunological profiling using class I MHC stabilisation assays to assess MHC binding affinity, and enzyme-linked immunospot (ELISPOT) assays to assess the ability of the modified peptides to re-stimulate a specific cytotoxic T-lymphocyte (CTL) response, compared to the native epitope, have been performed.

The role of metal ions in phosphate ester hydrolysis.

Many phosphatases make use of metal ions to aid catalysis of phosphate ester hydrolysis. Here, we investigate the impact of metal ions on the potential energy surface (PES), and hence the preferred reaction mechanism, for a simple model for hydrolysis of phosphate ester monoanions. We show that, while both associative (A(N) + D(N)) and dissociative (D(N) + A(N)) mechanisms are represented on the potential energy surfaces both in the presence and absence of metal ions, the D(N) + A(N) process is favoured when there are no metal ions present and the A(N) + D(N) process is favoured in the presence of two metal ions.

Structures of the dI2dIII1 complex of proton-translocating transhydrogenase with bound, inactive analogues of NADH and NADPH reveal active site geometries.

Transhydrogenase couples the redox reaction between NADH and NADP+ to proton translocation across a membrane. The enzyme comprises three components; dI binds NAD(H), dIII binds NADP(H), and dII spans the membrane. The 1,4,5,6-tetrahydro analogue of NADH (designated H2NADH) bound to isolated dI from Rhodospirillum rubrum transhydrogenase with similar affinity to the physiological nucleotide.

Discovery of (Z)-2-phenyl-3-(1H-pyrrol-2-yl)acrylonitrile derivatives active against Haemonchus contortus and Ctenocephalides felis (cat flea).

A series of 2-phenyl-3-(1H-pyrrol-2-yl)acrylonitrile derivatives were synthesized and evaluated for in vitro activity against the endoparasite Haemonchus contortus and the ectoparasite Ctenocephalides felis. Some compounds had significant in vitro activity against these parasites.

Two-year preclinical testing of perfluoropolyether polymer as a corneal inlay.

Purpose: To assess the long-term biocompatibility and optical clarity of a perfluoropolyether (PFPE) polymer as a corneal inlay.

Methods: A 4-mm-diameter PFPE inlay was implanted under a microkeratome flap in the corneas of rabbits (n = 16) and maintained for predetermined time points of 6, 12, or 24 months. These were compared with normal (n = 3) and time-matched sham-wounded rabbit corneas (n = 8).

Approaches to improving the biocompatibility of porous perfluoropolyethers for ophthalmic applications.

Porous perfluoropolyether (PFPE) membranes for ophthalmic applications were prepared with a zwitterion monomer, 3-[[2-(methacryloxy) ethyl](N,N-dimethyl)ammonio]-propane-1-sulphonate, copolymerized in weight ratios of 0-10%. The polymer samples were assessed for a range of physical properties, including equilibrium water content, bovine serum albumin permeability, transparency, refractive index and the ability to support corneal epithelial cell and tissue attachment, growth and migration. In vitro assessment of the polymers using bovine corneal epithelial cells and tissue showed that a zwitterion incorporation level of between 0% and 6% in the PFPE membranes supported the migration of an intact sheet of epithelial tissue without compromising epithelial cell attachment and growth, with 4-6% being the optimal level for these properties.

A design for life: prokaryotic metal-binding MerR family regulators.

The MerR family of metal-binding, metal-responsive proteins is unique in that they activate transcription from unusual promoters and coordinate metals through cysteine (and in the case of ZntR, histidine) residues. They have conserved primary structures yet can effectively discriminate metals in vivo.

Progress in the development of a synthetic corneal onlay.

Purpose: This study evaluated an improved perfluoropolyether polymer formulation designed for use as a corneal onlay to correct refractive error.

Methods: Collagen I coated perfluoropolyether lenticules were implanted in feline corneas exposing a 6-mm diameter area of lenticule surface for epithelial growth. A parallel series of sham-wounded corneas were also studied.

The use of corneal organ culture in biocompatibility studies.

This study investigated the potential of a corneal organ culture system in the evaluation of polymers for ophthalmic devices that require epithelialisation. Two different polymers were tested in lenticule form to explore the sensitivity of this in vitro assay. Polycarbonate and perfluoropolyether-based lenticules were surgically implanted into bovine corneas and compared with a parallel series of sham-wounded corneas.