The block conjugate gradient algorithm and related methods

The development of the Lanczos algorithm for finding eigenvalues of large sparse symmetric matrices was followed by that of block forms of the algorithm. In this paper, similar extensions are carried out for a relative of the Lanczos method, the conjugate gradient algorithm. The resulting block algorithms are useful for simultaneously solving multiple linear systems or for solving a single linear system in which the matrix has several separated eigenvalues or is not easily accessed on a computer. We develop a block biconjugate gradient algorithm for general matrices, and develop block conjugate gradient, minimum residual, and minimum error algorithms for symmetric semidefinite matrices. Bounds on the rate of convergence of the block conjugate gradient algorithm are presented, and issues related to computational implementation are discussed. Variants of the block conjugate gradient algorithm applicable to symmetric indefinite matrices are also developed.     

Fluorogenic Probe Using a Mislow–Evans Rearrangement for Real‐Time Imaging of Hydrogen Peroxide

Hydrogen peroxide (H₂O₂) mediates the biology of wound healing, apoptosis, inflammation, etc. H₂O₂ has been fluorometrically imaged with protein‐ or small‐molecule‐based probes. However, only protein‐based probes have afforded temporal insights within seconds. Small‐molecule‐based electrophilic probes for H₂O₂ require many minutes for a sufficient response in biological systems. Here, we report a fluorogenic probe that selectively undergoes a [2,3]‐sigmatropic rearrangement (seleno‐Mislow‐Evans rearrangement) with H₂O₂, followed by acetal hydrolysis, to produce a green fluorescent molecule in seconds. Unlike other electrophilic probes, the current probe acts as a nucleophile. The fast kinetics enabled real‐time imaging of H₂O₂ produced in endothelial cells in 8 seconds (much earlier than previously shown) and H₂O₂ in a zebrafish wound healing model. This work may provide a platform for endogenous H₂O₂ detection in real time with chemical probes.     

Identification multiplex assay of 19 terrestrial mammal species present in New Zealand

An identification assay has been developed that allows accurate detection of 19 of the most common terrestrial mammals present in New Zealand (cow, red deer, goat, dog, horse, hedgehog, cat, tammar wallaby, mouse, weasel, ferret, stoat, sheep, rabbit, Pacific rat, Norway rat, ship rat, pig, and brushtail possum). This technique utilizes species‐specific primers that, combined in a multiplex PCR, target small fragments of the mitochondrial cytochrome b gene. Each species, except hedgehog, produces two distinctive species‐specific fragments, making the assay self‐confirmatory and enabling the identification of multiple species simultaneously in DNA mixtures. The multiplex assay detects as little as 100 copies of mitochondrial DNA, which makes it a very reliable tool for degraded and trace samples. Reliability, accuracy, reproducibility, and sensitivity tests to validate the technique were performed. The technique featured here enabled a prompt response in a predation specific event, but can also be useful for wildlife management and conservation, pest incursions detection, forensic, and industrial purposes in a very simple and cost‐effective manner.     

An evaluation of ferrihydrite- and Metsorb™-DGT techniques for measuring oxyanion species (As,Se, V,P): Effective capacity,competition and diffusion coefficients

This study investigated several knowledge gaps with respect to the diffusive gradients in thin films (DGT) technique for measurement of oxyanions (As(III), As(V), Se(IV), Se(VI), PO₄³⁻, and V(V)) using the ferrihydrite and Metsorb™ binding layers. Elution efficiencies for each binding layer were higher with 1:20 dilutions, as analytical interferences for ICP-MS were minimised. Diffusion coefficients measured by diffusion cell and by DGT time-series experiments were found to agree well and generally agreed with previously reported values, although a range of diffusion coefficients have been reported for inorganic As and Se species. The relative binding affinity for both ferrihydrite and Metsorb™ was PO₄³⁻ ≈ As(V) > V(V) ≈ As(III) > Se(IV) ? Se(VI) and effective binding capacities were measured in single ion solutions, and spiked synthetic freshwater and seawater, advising practical decisions about DGT monitoring. Under the conditions tested the performance of both ferrihydrite and Metsorb™ binding layers was directly comparable for As(V), As(III) Se(IV), V(V) and PO₄³⁻ over a deployment spanning ≤2 days for both freshwater and seawater. In order to return quantitative data for several analytes we recommend that the DGT method using either ferrihydrite or Metsorb™ be deployed for a maximum of 2 days in marine waters likely to contain high levels of the most strongly adsorbing oxyanions contaminants. The high pH, the competitive ions present in seawater and the identity of co-adsorbing ions affect the capacity of each binding layer for the analytes of interest. In freshwaters, longer deployment times can be considered but the concentration and identity of co-adsorbing ions may impact on quantitative uptake of Se(IV). This study found ferrihydrite-DGT outperformed Metsorb-DGT while previous studies have found the opposite, with variation in binding materials masses used being a likely reason. Clearly, preparation of both binding layers should always be optimised to produce the highest capacity possible, especially for seawater deployments.     

Quantification of water compartmentation in cell suspensions by diffusion-weighted and T(2)-weighted MRI

When studying water diffusion in biological systems, any specific signal attenuation curve may be reproduced by a broad range of mathematical functions. Our goals were to quantify the diffusion and T₂ relaxation properties of water in a simple biological system and to study the changes that occur in osmotically stressed cells.     

Neuropeptide delivery to the brain: a von Willebrand factor signal peptide to direct neuropeptide secretion

Background  

Multiple neuropeptides, sometimes with opposing functions, can be produced from one precursor gene. To study the roles of the different neuropeptides encoded by one large precursor we developed a method to overexpress minigenes and establish local secretion.