Brownian dynamics study of flux ratios in sodium channels.

Measurements of unidirectional fluxes in ion channels provide one of the experimental methods for studying the steps involved in ion permeation in biological pores. Conventionally, the number of ions in the pore is inferred by fitting the ratio of inward and outward currents to an exponential function with an adjustable parameter known as the flux ratio exponent. Here we investigate the relationship between the number of ions in the pore and the flux ratio exponent in a model sodium channel under a range of conditions.

Efficacy of external tetraethylammonium block of the KcsA potassium channel: molecular and Brownian dynamics studies.

Blockade of the KcsA potassium channel by externally applied tetraethylammonium is investigated using molecular dynamics calculations and Brownian dynamics simulations. In KcsA, the aromatic rings of four tyrosine residues located just external to the selectivity filter create an attractive energy well or a binding cage for a tetraethylammonium molecule. We first investigate the effects of re-orienting the four tyrosine residues such that the centers of the aromatic rings face the tetraethylammonium molecule directly.

Sex determination in mammals--before and after the evolution of SRY.

Therian mammals (marsupials and placentals) have an XX female: XY male sex chromosome system, which is homologous to autosomes in other vertebrates. The testis-determining gene, SRY, is conserved on the Y throughout therians, but is absent in other vertebrates, suggesting that the mammal system evolved about 310 million years ago (MYA). However, recent work on the basal monotreme mammals has completely changed our conception of how and when this change occurred.

Detecting genetic recombination.

Recombination is the major motor of evolution. While mutations result in gradual changes, recombination reshuffles entire functional modules and thus progresses evolution in leaps and bounds. We need to identify recombination breakpoints in sequences to understand the evolutionary process, the impact of recombination, and to reconstruct the phylogenetic history of genes and genomes.

The potyviruses of Australia.

Many potyviruses have been found in Australia. We analyzed a selected region of the coat protein genes of 37 of them to determine their relationships, and found that they fall into two groups. Half were isolated from cultivated plants and crops, and are also found in other parts of the world.

The crucial role of plant mitochondria in orchestrating drought tolerance.

Background: Around the world, the frequency and intensity of droughts is increasing as a result of global climate change, with important consequences for the growth and survival of agricultural and native plant species. Understanding how plants respond to water stress is thus crucial for predicting the impacts of climate change on the crop productivity and ecosystem functioning. In contrast to the large number of studies assessing drought impacts on photosynthesis, relatively little attention has been devoted to understanding how mitochondrial respiratory metabolism is altered under water stress conditions.

Expression and role of the early-response gene Oxr1 in the hyperoxia-challenged mouse retina.

Purpose: To examine the response of mouse retina to sustained hyperoxia. Hyperoxia is toxic to photoreceptors after sustained exposure (7-14 days in the C57BL/6J mouse) but has been reported to enhance photoreceptor function after short-term exposure.

Methods: Retinas from the hyperoxia-vulnerable C57BL/6J mouse and from the hyperoxia-resistant BALB/cJ mouse were examined after 0, 3, 7, 14, and 35 days' exposure to 75% oxygen.

Rapid and dynamic subcellular reorganization following mechanical stimulation of Arabidopsis epidermal cells mimics responses to fungal and oomycete attack.

Background: Plant cells respond to the presence of potential fungal or oomycete pathogens by mounting a basal defence response that involves aggregation of cytoplasm, reorganization of cytoskeletal, endomembrane and other cell components and development of cell wall appositions beneath the infection site. This response is induced by non-adapted, avirulent and virulent pathogens alike, and in the majority of cases achieves penetration resistance against the microorganism on the plant surface. To explore the nature of signals that trigger this subcellular response and to determine the timing of its induction, we have monitored the reorganization of GFP-tagged actin, microtubules, endoplasmic reticulum (ER) and peroxisomes in Arabidopsis plants - after touching the epidermal surface with a microneedle.

Implications of long-distance flavonoid movement in Arabidopsis thaliana.

Flavonoid synthesis is modulated by developmental and environmental signals that control the amounts and localization of the diverse flavonoids found in plants. Flavonoids are implicated in regulating a number of physiological processes including UV protection, fertilization, auxin transport, plant architecture, gravitropism and pathogenic and symbiotic interactions with other organisms. Recently we showed that flavonoids can move long distances in plants, which may facilitate these molecules reaching positions in the plant where these processes are regulated.

Evidence for counting in insects.

Here we investigate the counting ability in honeybees by training them to receive a food reward after they have passed a specific number of landmarks. The distance to the food reward is varied frequently and randomly, whilst keeping the number of intervening landmarks constant. Thus, the bees cannot identify the food reward in terms of its distance from the hive.

Features of the primary wall CESA complex in wild type and cellulose-deficient mutants of Arabidopsis thaliana.

Evidence from genetics, co-precipitation and bimolecular fluorescence complementation suggest that three CESAs implicated in making primary wall cellulose in Arabidopsis thaliana form a complex. This study shows the complex has a M(r) of approximately 840 kDa in detergent extracts and that it has undergone distinctive changes when extracts are prepared from some cellulose-deficient mutants. The mobility of CESAs 1, 3, and 6 in a Triton-soluble microsomal fraction subject to blue native polyacrylamide gel electrophoresis was consistent with a M(r) of about 840 kDa.

Evolving improved Synechococcus Rubisco functional expression in Escherichia coli.

The photosynthetic CO2-fixing enzyme Rubisco [ribulose-P(2) (D-ribulose-1,5-bisphosphate) carboxylase/oxygenase] has long been a target for engineering kinetic improvements. Towards this goal we used an RDE (Rubisco-dependent Escherichia coli) selection system to evolve Synechococcus PCC6301 Form I Rubisco under different selection pressures. In the fastest growing colonies, the Rubisco L (large) subunit substitutions I174V, Q212L, M262T, F345L or F345I were repeatedly selected and shown to increase functional Rubisco expression 4- to 7-fold in the RDE and 5- to 17-fold when expressed in XL1-Blue E.

Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes.

In therian mammals (placentals and marsupials), sex is determined by an XX female: XY male system, in which a gene (SRY) on the Y affects male determination. There is no equivalent in other amniotes, although some taxa (notably birds and snakes) have differentiated sex chromosomes. Birds have a ZW female: ZZ male system with no homology with mammal sex chromosomes, in which dosage of a Z-borne gene (possibly DMRT1) affects male determination.

Conduction of Na+ and K+ through the NaK channel: molecular and Brownian dynamics studies.

Conduction of ions through the NaK channel, with M0 helix removed, was studied using both Brownian dynamics and molecular dynamics. Brownian dynamics simulations predict that the truncated NaK has approximately a third of the conductance of the related KcsA K+ channel, is outwardly rectifying, and has a Michaelis-Menten current-concentration relationship. Current magnitude increases when the glutamine residue located near the intracellular gate is replaced with a glutamate residue.

Processing of sting pheromone and its components in the antennal lobe of the worker honeybee.

In the honeybee Apis mellifera, a sting pheromone produced by sting glands plays an important role in coordinating defensive behavior. This pheromone is a blend constituted by several components. Little is known about the neural substrates underlying sting pheromone processing in the bee brain.

The pipe and the pinwheel: is pressure an effective stimulus for the 9+0 primary cilium?

Almost universally, the effective stimulus for mammalian 9+0 primary cilia has been taken to be bending. In this article I point out that in several physiological contexts there is great advantage in detecting pressure differences across the cell wall, i.e.

Application of the ERICA Integrated Approach to the Drigg coastal sand dunes.

The EC-funded project 'Environmental Risks from Ionising Contaminants: Assessment and Management' (ERICA) developed an 'Integrated Approach' for assessing the impact of ionising radiation on ecosystems. This paper presents the application of the ERICA Integrated Approach, supported by a software programme (the ERICA Tool) and guidance documentation, to an assessment of the Drigg coastal sand dunes (Cumbria, UK). Targeted sampling provided site-specific data for sand dune biota, including amphibians and reptiles.

On the effect of heavy water (DO) on carbon isotope fractionation in photosynthesis.

Internal conductance to carbon dioxide is a key aspect of leaf photosynthesis although is still not well understood. It is thought that it comprises two components, namely, a gas phase component (diffusion from intercellular spaces to cell walls) and a liquid phase component (dissolution, diffusion in water, hydration equilibrium). Here we use heavy water (DO), which is known to slow down CO hydration by a factor of nearly three.

Genetic variation in tolerance to the osmotic stress componentof salinity stress in durum wheat.

Salinity affects plant growth by the osmotic stress of the salt around the roots as well as by toxicity caused by excessive accumulation of salt in leaves. The aim of this study was to determine whether there is significant genetic variation in tolerance to osmotic stress that can be useful in improving the salinity tolerance of crop plants. Durum wheat is a salt-sensitive crop whose yield is reduced by moderately saline soils.

The effects of Rubisco activase on C4 photosynthesis and metabolism at high temperature.

The activation of Rubisco in vivo requires the presence of the regulatory protein Rubisco activase. This enzyme facilitates the release of sugar phosphate inhibitors from Rubisco catalytic sites thereby influencing carbamylation. T(1) progeny of transgenic Flaveria bidentis (a C(4) dicot) containing genetically reduced levels of Rubisco activase were used to explore the role of the enzyme in C(4) photosynthesis at high temperature.

C4 photosynthetic isotope exchange in NAD-ME- and NADP-ME-type grasses.

Monitoring photosynthetic isotope exchange is an important tool for predicting the influence of plant communities on the global carbon cycle in response to climate change. C(4) grasses play an important role in the global carbon cycle, but their contribution to the isotopic composition of atmospheric CO(2) is not well understood. Instantaneous measurements of (13)CO(2) (Delta(13)C) and C(18)OO (Delta(18)O) isotope exchange in five NAD-ME and seven NADP-ME C(4) grasses have been conducted to investigate the difference in photosynthetic CO(2) isotopic fractionation in these subgroups.

Nutritional control of reproductive status in honeybees via DNA methylation.

Fertile queens and sterile workers are alternative forms of the adult female honeybee that develop from genetically identical larvae following differential feeding with royal jelly. We show that silencing the expression of DNA methyltransferase Dnmt3, a key driver of epigenetic global reprogramming, in newly hatched larvae led to a royal jelly-like effect on the larval developmental trajectory; the majority of Dnmt3 small interfering RNA-treated individuals emerged as queens with fully developed ovaries. Our results suggest that DNA methylation in Apis is used for storing epigenetic information, that the use of that information can be differentially altered by nutritional input, and that the flexibility of epigenetic modifications underpins, profound shifts in developmental fates, with massive implications for reproductive and behavioral status.

Directional selectivity in the simple eye of an insect.

Among other sensory modalities, flight stabilization in insects is performed with the aid of visual feedback from three simple eyes (ocelli). It is thought that each ocellus acts as a single wide-field sensor that detects changes in light intensity. We challenge this notion by providing evidence that, when light-adapted, the large retinal L-neurons in the median ocellus of the dragonfly respond in a directional way to upward moving bars and gratings.

An innovative molybdenum column liner for oxygen and hydrogen stable isotope analysis by pyrolysis.

The most widely used method for pyrolysing samples for hydrogen or oxygen isotopic analysis involves heating them to greater than 1300 degrees C in a helium stream passed through a glassy carbon tube in an alumina casing. There are a number of difficulties with this. Glassy carbon tubes are expensive and interaction between the carbon tube and the outer casing produces unwanted carbon monoxide by reduction of the alumina at high temperatures.