Profiling of generic anti-phosphopeptide antibodies and kinases with peptide microarrays using radioactive and fluorescence-based assays

Kinases represent one of the largest enzyme families and key regulatory proteins in the cell. Only a small subset of these enzymes has been characterised so far. We have prepared different types of phosphopeptide and peptide microarrays displaying peptides deduced from annotated human phosphorylation sites and cytoplasmic domains of all annotated human membrane proteins. This approach was enabled by fully-automated high throughput micro-scale synthesis of peptides by the SPOT technology combined with chemo-selective immobilisation on modified glass slides. The phosphopeptide microarrays displaying 2923 peptides in total have been used for the characterisation of commercially available generic anti-phosphopeptide antibodies. This enabled us to detect Abl kinase activity on a microarray with anti-phosphotyrosine antibodies yielding results comparable to those obtained from a radioactive assay. More than 13 000 peptides deposited on six glass slides were used to profile casein kinase 2 (CK2) using a radioactive assay, since no generic antibody for the reliable detection of serine or threonine phosphorylation could be identified. All previously identified substrates were detected in the microarray experiment. In order to confirm whether substrates on the microarray are substrates in solution phase assays, more than 700 peptides were synthesised and tested with CK2 in a solution phase assay. All substrates identified in the solution phase assay were also detected on the microarray.     

A mixed ladderane/n-alkyl glycerol diether membrane lipid in an anaerobic ammonium-oxidizing bacterium

A novel glycerol diether containing ladderane and tetradecyl moieties has been identified in an anaerobic ammonium-oxidizing bacterium by GC/MS and high-field NMR spectroscopy.     

Field-induced thermal metal-to-insulator transition in underdoped La(2-x)Sr(x)CuO(4+delta)

The transport of heat and charge in cuprates was measured in single crystals of La(2-x)Sr(x)CuO(4+delta) (LSCO) across the doping phase diagram at low temperatures. In underdoped LSCO, the thermal conductivity is found to decrease with increasing magnetic field in the T-->0 limit, in striking contrast to the increase observed in all superconductors, including cuprates at higher doping. In heavily underdoped LSCO, where superconductivity can be entirely suppressed with an applied magnetic field, we show that a novel thermal metal-to-insulator transition takes place upon going from the superconducting state to the field-induced normal state.     

Lewis acid mediated cyclisations of silylated methylenecyclopropyl hydrazones

Silylated methylenecyclopropyl hydrazones on treatment with BF3 x Et2O cyclise to give heterocyclic products involving a novel sequence of hydride and silyl shifts via a series of increasingly stable cationic intermediates.     

Palladium catalysed cyclisation-carbonylation of enynes to give cyclic gamma,delta-unsaturated acids

In the presence of acetic acid, trifurylphosphine and CO (2 atm), palladium catalyses the conversion of a range of enynes to cyclic delta,gamma-unsaturated carboxylic acids in good yield.     

Recycling solid supports – A head-to-tail linker

The concept of a `head-to-tail linker' designed to allow the regeneration and reuse of a variety of solid supports is introduced. The synthesis of this linker, its coupling to various solid supports, its application in a number of standard solid phase reactions and resin regeneration are presented.     

Fluorinated polymerizable phosphonium salts from PH3: Surface properties of photopolymerized films

An array of highly fluorinated polymerizable phosphonium salts (HFPPS) were synthesized from PH₃ and utilized in UV‐curable formulations. Inclusion of these salts at very low loading (0.1–1 wt %) into hexanediol diacrylate (HDDA) resulted in hydrophobic surfaces. The water repellency was achieved with short C₄F₉ fluorocarbon appendages in the monomer as opposed to the bioaccumulative C₈F₁₇ appended polymers. The physical properties of these new monomers were also characterized. The molecular architecture of the monomers had a pronounced effect on both their physical properties along with the degree of hydrophobicity imparted in the polymer. Salts utilizing the bis(trifluoromethylsulfonyl)imide anion displayed excellent compatibility with HDDA, while the chloride salts were insoluble. Time‐of‐flight secondary ion mass spectrometry (TOF‐SIMS) confirmed the presence of the HFPPS at the surface of the polymer coating. For the first time this demonstrates how these salts may be used to functionalize the surface of a UV‐cured film with ionic species. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 2782–2792     

Interaction between salinity intrusion and vegetation succession: A modeling approach

Predicting potential changes in groundwater salinity in low-lying coastal regions due to climate change is important, where coastal vegetation is abundant, succession competition between halophytes and glycophytes plays a significant role in the salinity budget. Sea level rise enhances salinity intrusion, contributing an additional dimension to vegetation competition. A new simulation model known as mangrove-hardwood hammock model coupled with saturated-unsaturated transport (MANTRA) has recently been developed by the authors to simulate groundwater salinity regimes in the presence of vegetation competition, subject to climate change. MANTRA is based upon linking two existing Unites States geological survey (USGS) simulation models known as mangrove-hardwood hammock model (MANHAM) and saturated-unsaturated transport (SUTRA). MANHAM simulates the evolution of vegetation succession subject to changing groundwater salinity. SUTRA simulates saturated and unsaturated transport of solutes and salinity in groundwater given sea salinity. MANTRA improves the simulation robustness to simultaneously simulate groundwater hydrology, salinity and coastal vegetation succession subject to sea level rise. Some simulation results will be presented to demonstrate the impact of sea level rise on coastal vegetation succession and groundwater salinity.     

Iterative Thresholding for Sparse Approximations

Sparse signal expansions represent or approximate a signal using a small number of elements from a large collection of elementary waveforms. Finding the optimal sparse expansion is known to be NP hard in general and non-optimal strategies such as Matching Pursuit, Orthogonal Matching Pursuit, Basis Pursuit and Basis Pursuit De-noising are often called upon. These methods show good performance in practical situations, however, they do not operate on the ? ₀ penalised cost functions that are often at the heart of the problem. In this paper we study two iterative algorithms that are minimising the cost functions of interest. Furthermore, each iteration of these strategies has computational complexity similar to a Matching Pursuit iteration, making the methods applicable to many real world problems. However, the optimisation problem is non-convex and the strategies are only guaranteed to find local solutions, so good initialisation becomes paramount. We here study two approaches. The first approach uses the proposed algorithms to refine the solutions found with other methods, replacing the typically used conjugate gradient solver. The second strategy adapts the algorithms and we show on one example that this adaptation can be used to achieve results that lie between those obtained with Matching Pursuit and those found with Orthogonal Matching Pursuit, while retaining the computational complexity of the Matching Pursuit algorithm.