Matrix-assisted laser desorption/ionisation mass spectrometry imaging and its development for plant protein imaging

Matrix-Assisted Laser Desorption/Ionisation (MALDI) mass spectrometry imaging (MSI) uses the power of high mass resolution time of flight (ToF) mass spectrometry coupled to the raster of lasers shots across the cut surface of tissues to provide new insights into the spatial distribution of biomolecules within biological tissues. The history of this technique in animals and plants is considered and the potential for analysis of proteins by this technique in plants is discussed. Protein biomarker identification from MALDI-MSI is a challenge and a number of different approaches to address this bottleneck are discussed. The technical considerations needed for MALDI-MSI are reviewed and these are presented alongside examples from our own work and a protocol for MALDI-MSI of proteins in plant samples

Insights into female sperm storage from the spermathecal fluid proteome of the honeybee Apis mellifera

A proteomic and metabolic network analysis of honeybee queen spermathecal fluid provides insights into female long-term sperm storage mechanisms

Statistical Error in Particle Simulations of Hydrodynamic Phenomena

We present predictions for the statistical error due to finite sampling in the presence of thermal fluctuations in molecular simulation algorithms. Specifically, we establish how these errors depend on Mach number, Knudsen number, number of particles, etc. Expressions for the common hydrodynamic variables of interest such as flow velocity, temperature, density, pressure, shear stress and heat flux are derived using equilibrium statistical mechanics. Both volume-averaged and surface-averaged quantities are considered. Comparisons between theory and computations using direct simulation Monte Carlo for dilute gases, and molecular dynamics for dense fluids, show that the use of equilibrium theory provides accurate results.Comment: 24 pages postscript (including 16 figures

Genome sequences of six Phytophthora species threatening forest ecosystems

AbstractThe Phytophthora genus comprises of some of the most destructive plant pathogens and attack a wide range of hosts including economically valuable tree species, both angiosperm and gymnosperm. Many known species of Phytophthora are invasive and have been introduced through nursery and agricultural trade. As part of a larger project aimed at utilizing genomic data for forest disease diagnostics, pathogen detection and monitoring (The TAIGA project: Tree Aggressors Identification using Genomic Approaches; http://taigaforesthealth.com/), we sequenced the genomes of six important Phytophthora species that are important invasive pathogens of trees and a serious threat to the international trade of forest products. This genomic data was used to develop highly sensitive and specific detection assays and for genome comparisons and to make evolutionary inferences and will be useful to the broader plant and tree health community. These WGS data have been deposited in the International Nucleotide Sequence Database Collaboration (DDBJ/ENA/GenBank) under the accession numbers AUPN01000000, AUVH01000000, AUWJ02000000, AUUF02000000, AWVV02000000 and AWVW02000000

Diel- and temperature-driven variation of leaf dark respiration rates and metabolite levels in rice

Leaf respiration in the dark (R-dark) is often measured at a single time during the day, with hot-acclimation lowering R-dark at a common measuring temperature. However, it is unclear whether the diel cycle influences the extent of thermal acclimation of R-dark, or how temperature and time of day interact to influence respiratory metabolites. To examine these issues, we grew rice under 25 degrees C : 20 degrees C, 30 degrees C : 25 degrees C and 40 degrees C : 35 degrees C day : night cycles, measuring R-dark and changes in metabolites at five time points spanning a single 24-h period. R-dark differed among the treatments and with time of day. However, there was no significant interaction between time and growth temperature, indicating that the diel cycle does not alter thermal acclimation of R-dark. Amino acids were highly responsive to the diel cycle and growth temperature, and many were negatively correlated with carbohydrates and with organic acids of the tricarboxylic acid (TCA) cycle. Organic TCA intermediates were significantly altered by the diel cycle irrespective of growth temperature, which we attributed to light-dependent regulatory control of TCA enzyme activities. Collectively, our study shows that environmental disruption of the balance between respiratory substrate supply and demand is corrected for by shifts in TCA-dependent metabolites.Peer reviewe

An oligofluorene truxene based distributed feedback laser for biosensing applications

The first example of an all-organic oligofluorene truxene based distributed feedback laser for the detection of a specific protein–small molecule interaction is reported. The protein avidin was detected down to View the MathML source1μgmL−1 using our biotin-labelled biosensor platform. This interaction was both selective and reversible when biotin was replaced with desthiobiotin. Avidin detection was not perturbed by Bovine Serum Albumin up to View the MathML source50,000μgmL−1. Our biosensor offers a new detection platform that is both highly sensitive, modular and potentially re-usable

Frailty and Risk of Falls, Fracture, and Mortality in Older Women: The Study of Osteoporotic Fractures

Background. A standard phenotype of frailty was associated with an increased risk of adverse outcomes including mortality in a recent study of older adults. However, the predictive validity of this phenotype for fracture outcomes and across risk subgroups is uncertain. Methods. To determine whether a standard frailty phenotype was independently associated with risk of adverse health outcomes in older women and to evaluate the consistency of associations across risk subgroups defined by age and body mass index (BMI), we ascertained frailty status in a cohort of 6724 women ≥ 69 years and followed them prospectively for incident falls, fractures, and mortality. Frailty was defined by the presence of three or more of the following criteria: unintentional weight loss, weakness, self-reported poor energy, slow walking speed, and low physical activity. Incident recurrent falls were defined as at least two falls during the subsequent year. Incident fractures (confirmed with x-ray reports), including hip fractures, and deaths were ascertained during an average of 9 years of follow-up. Results. After controlling for multiple confounders such as age, health status, medical conditions, functional status, depressive symptoms, cognitive function, and bone mineral density, frail women were subsequently at increased risk of recurrent falls (multivariate odds ratio = 1.38, 95% confidence interval [CI], 1.02-1.88), hip fracture (multivariate hazards ratio [MHR] = 1.40, 95% CI, 1.03-1.90), any nonspine fracture (MHR = 1.25, 95% CI, 1.05-1.49), and death (MHR = 1.82, 95% CI, 1.56-2.13). The associations between frailty and these outcomes persisted among women ≥ 80 years. In addition, associations between frailty and an increased risk of falls, fracture, and mortality were consistently observed across categories of BMI, including BMI ≥ 30 kg/m2. Conclusion. Frailty is an independent predictor of adverse health outcomes in older women, including very elderly women and older obese wome

Algorithmic Complexity for Short Binary Strings Applied to Psychology: A Primer

Since human randomness production has been studied and widely used to assess executive functions (especially inhibition), many measures have been suggested to assess the degree to which a sequence is random-like. However, each of them focuses on one feature of randomness, leading authors to have to use multiple measures. Here we describe and advocate for the use of the accepted universal measure for randomness based on algorithmic complexity, by means of a novel previously presented technique using the the definition of algorithmic probability. A re-analysis of the classical Radio Zenith data in the light of the proposed measure and methodology is provided as a study case of an application.Comment: To appear in Behavior Research Method