W3 Is a New Wax Locus That Is Essential for Biosynthesis of beta-Diketone, Development of Glaucousness, and Reduction of Cuticle Permeability in Common Wheat

Citation: Zhang, Z. Z., Wei, W. J., Zhu, H. L., Challa, G. S., Bi, C. L., Trick, H. N., & Li, W. L. (2015). W3 Is a New Wax Locus That Is Essential for Biosynthesis of beta-Diketone, Development of Glaucousness, and Reduction of Cuticle Permeability in Common Wheat. Plos One, 10(10), 21. doi:10.1371/journal.pone.0140524The cuticle plays important roles in plant development, growth and defense against biotic and abiotic attacks. Crystallized epicuticular wax, the outermost layer of cuticle, is visible as white-bluish glaucousness. In crops like barley and wheat, glaucousness is trait of adaption to the dry and hot cultivation conditions, and hentriacontane-14,16-dione (beta-diketone) and its hydroxy derivatives are the major and unique components of cuticular wax in the upper parts of adult plants. But their biosynthetic pathway and physiological role largely remain unknown. In the present research, we identified a novel wax mutant in wheat cultivar Bobwhite. The mutation is not allelic to the known wax production gene loci W1 and W2, and designated as W3 accordingly. Genetic analysis localized W3 on chromosome arm 2BS. The w3 mutation reduced 99% of beta-diketones, which account for 63.3% of the total wax load of the wild-type. W3 is necessary for beta-diketone synthesis, but has a different effect on beta-diketone hydroxylation because the hydroxy-beta-diketones to beta-diketone ratio increased 11-fold in the w3 mutant. Loss of beta-diketones caused failure to form glaucousness and significant increase of cuticle permeability in terms of water loss and chlorophyll efflux in the w3 mutant. Transcription of 23 cuticle genes from five functional groups was altered in the w3 mutant, 19 down-regulated and four up-regulated, suggesting a possibility that W3 encodes a transcription regulator coordinating expression of cuticle genes. Biosynthesis of beta-diketones in wheat and their implications in glaucousness formation and drought and heat tolerance were discussed.Citation: Zhang, Z., . . . & Wanlong, Li. (2015). W3 Is a New Wax Locus That Is Essential for Biosynthesis of β-Diketone, Development of Glaucousness, and Reduction of Cuticle Permeability in Common Wheat. PLoS One, 10(10), 1-21. https://doi.org/10.1371/journal.pone.014052

Computational design of biomimetic nanopores: a molecular dynamics study

Molecular dynamics simulations are used to study the function of hydrophobic gates within models of biomimetic nanopores and in ligand-gated ion channels. A computational approach to building and simulating model β-barrel nanopores has been established to explore the effects of changing the shape and polarity of amino acids lining the pore lumen. Changing the position of such residues resulted in different water conductive states. In 14 β-strand pores, a computationally transplanted hydrophobic barrier to water and ions has been demonstrated and characterised in detail using free energy calculations. Electrowetting of such a hydrophobic gate within a model β-barrel nanopore is demonstrated in simulation, using two different methods to apply a transmembrane electric eld. An increase in the transmembrane voltage results in breakdown of the hydrophobic barrier, resulting in the ow of water and ions. The effect (electrowetting) is shown to be reversed upon the removal of the transmembrane voltage. An investigation into the possible hydrophobic gate of the 5-HT3 receptor channel via free energy calculations and simulations con firmed that the crystal structure is in a closed conformation with respect to the ow of ions. This demonstrates that simulations and free energy calculations may be used to functionally annotate crystal structures of ion channels

Associative Transcriptomics Study Dissects the Genetic Architecture of Seed Glucosinolate Content in Brassica napus

Breeding new varieties with low seed glucosinolate (GS) concentrations has long been a prime target in Brassica napus. In this study, a novel association mapping methodology termed 'associative transcriptomics' (AT) was applied to a panel of 101 B. napus lines to define genetic regions and also candidate genes controlling total seed GS contents. Over 100,000 informative single-nucleotide polymorphisms (SNPs) and gene expression markers (GEMs) were developed for AT analysis, which led to the identification of 10 SNP and 7 GEM association peaks. Within these peaks, 26 genes were inferred to be involved in GS biosynthesis. A weighted gene co-expression network analysis provided additional 40 candidate genes. The transcript abundance in leaves of two candidate genes, BnaA.GTR2a located on chromosome A2 and BnaC.HAG3b on C9, was correlated with seed GS content, explaining 18.8 and 16.8% of phenotypic variation, respectively. Resequencing of genomic regions revealed six new SNPs in BnaA.GTR2a and four insertions or deletions in BnaC.HAG3b. These deletion polymorphisms were then successfully converted into polymerase chain reaction-based diagnostic markers that can, due to high linkage disequilibrium observed in these regions of the genome, be used for marker-assisted breeding for low seed GS lines

Collaborative Research: What Limits Denitrification and Bacterial Growth in Lake Bonney, Taylor Valley, Antarctica?

Denitrification is the main process by which fixed nitrogen is lost from ecosystems and the regulation of this process may directly affect primary production and carbon cycling over short and long time scales. Previous investigations of the role of bioactive metals in regulating denitrification in bacteria from permanently ice-covered Lake Bonney in the Taylor Valley of East Antarctica indicated that denitrifying bacteria can be negatively affected by metals such as copper, iron, cadmium, lead, chromium, nickel, silver and zinc; and that there is a distinct difference in denitrifying activity between the east and west lobes of the lake. Low iron concentrations were found to exacerbate the potential toxicity of the other metals, while silver has the potential to specifically inhibit denitrification because of its ability to interfere with copper binding in redox proteins, such as nitrite reductase and nitrous oxide reductase. High silver concentrations might prevent the functioning of nitrous oxide reductase in the same way that simple copper limitation does, thereby causing the buildup of nitrous oxide and resulting in a nonfunctional nitrogen cycle. Other factors, such as oxygen concentration, are likely also to affect bacterial activity in Lake Bonney. This project will investigate silver toxicity, general metal toxicity and oxygen concentration to determine their effect on denitrification in the lake by using a suite of sentinel strains of denitrifying bacteria (isolated from the lake) incubated in Lake Bonney water and subjected to various treatments. The physiological responses of these strains to changes in metal and oxygen concentration will be quantified by flow cytometric detection of single cell molecular probes whose sensitivity and interpretation have been optimized for the sentinel strains. Understanding the relationships between metals and denitrification is expected to enhance our understanding of not only Lake Bonney\u27s unusual nitrogen cycle, but more generally, of the potential role of metals in the regulation of microbial nitrogen transformations.The broader impacts of this work include not only a better understanding of regional biogeochemistry and global perspectives on these processes; but also the training of graduate students and a substantial outreach effort for school children

CATMA: a complete Arabidopsis GST database

The Complete Arabidopsis Transcriptome Micro Array (CATMA) database contains gene sequence tag (GST) and gene model sequences for over 70% of the predicted genes in the Arabidopsis thaliana genome as well as primer sequences for GST amplification and a wide range of supplementary information. All CATMA GST sequences are specific to the gene for which they were designed, and all gene models were predicted from a complete reannotation of the genome using uniform parameters. The database is searchable by sequence name, sequence homology or direct SQL query, and is available through the CATMA website at http://www.catma.or

Age-related changes in global motion coherence: conflicting haemodynamic and perceptual responses

Our aim was to use both behavioural and neuroimaging data to identify indicators of perceptual decline in motion processing. We employed a global motion coherence task and functional Near Infrared Spectroscopy (fNIRS). Healthy adults (n = 72, 18-85) were recruited into the following groups: young (n = 28, mean age = 28), middle-aged (n = 22, mean age = 50), and older adults (n = 23, mean age = 70). Participants were assessed on their motion coherence thresholds at 3 different speeds using a psychophysical design. As expected, we report age group differences in motion processing as demonstrated by higher motion coherence thresholds in older adults. Crucially, we add correlational data showing that global motion perception declines linearly as a function of age. The associated fNIRS recordings provide a clear physiological correlate of global motion perception. The crux of this study lies in the robust linear correlation between age and haemodynamic response for both measures of oxygenation. We hypothesise that there is an increase in neural recruitment, necessitating an increase in metabolic need and blood flow, which presents as a higher oxygenated haemoglobin response. We report age-related changes in motion perception with poorer behavioural performance (high motion coherence thresholds) associated with an increased haemodynamic response

Collaborative Research: The Effect of Iron-Complexing Ligands on Iron Availability to Phytoplankton in HNLC Waters of the Subarctic Pacific Ocean

Scientists from the University of Maine and San Francisco State University propose to do deck-board incubation experiments in high nutrient, low chlorophyll (HNLC) waters of the eastern (Ocean Station PAPA) and the western (Ocean Station KNOT) Subarctic Pacific Ocean to determine how Fe supply affects phytoplankton species composition. Specifically, this team of scientists plans to address the following specific objectives: (1) assess how the relative availability of Fe bound to weaker and stronger classes of ligands differs among different phytoplankton groups (cyanobacteria, diatoms, dinoflagellates, prymnesiophytes) and how these differences influence the evolution of the phytoplankton community after Fe enrichment in HNLC waters; (2) ascertain if new ligands produced in response to Fe enrichment of HNLC waters behave similarly to ambient ligands, or if they have significantly different effect on regulating how an ecosystem evolves over the long term; and (3) determine whether phytoplankton assemblages in HNLC waters having different proximity or history of Fe inputs respond differently to the same suite of Fe ligand blends, or whether conditioning has led to their adaptation of alternate uptake capabilities. In addition, measurements of growth rates, macronutrient utilization rates, fluorescence, cell size determinations, Fe use efficiencies, rates of Fe and carbon uptake and flow cytometry sorting will be done to assess how specific organisms will respond to Fe supplied in different chemical forms

The effects of acute inflammation on cognitive functioning and emotional processing in humans: A systematic review of experimental studies

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record Objective The cognitive neuropsychological model of depression proposes that negative biases in the processing of emotionally salient information have a central role in the development and maintenance of depression. We have conducted a systematic review to determine whether acute experimental inflammation is associated with changes to cognitive and emotional processing that are thought to cause and maintain depression. Methods We identified experimental studies in which healthy individuals were administered an acute inflammatory challenge (bacterial endotoxin/vaccination) and standardised tests of cognitive function were performed. Results Fourteen references were identified, reporting findings from 12 independent studies on 345 participants. Methodological quality was rated strong or moderate for 11 studies. Acute experimental inflammation was triggered using a variety of agents (including endotoxin from E. coli, S. typhi, S. abortus Equi and Hepatitis B vaccine) and cognition was assessed over hours to months, using cognitive tests of i) attention/executive functioning, ii) memory and iii) social/emotional processing. Studies found mixed evidence that acute experimental inflammation caused changes to attention/executive functioning (2 of 6 studies showed improvements in attention executive function compared to control), changes in memory (3 of 5 studies; improved reaction time: reduced memory for object proximity: poorer immediate and delayed memory) and changes to social/emotional processing (4 of 5 studies; reduced perception of emotions, increased avoidance of punishment/loss experiences, and increased social disconnectedness). Conclusions Acute experimental inflammation causes negative biases in social and emotional processing that could explain observed associations between inflammation and depression.National Institute for Health Research (NIHR

The hijacking of a receptor kinase-driven pathway by a wheat fungal pathogen leads to disease

Citation: Shi, G. J., Zhang, Z. C., Friesen, T. L., Raats, D., Fahima, T., Brueggeman, R. S., . . . Faris, J. D. (2016). The hijacking of a receptor kinase-driven pathway by a wheat fungal pathogen leads to disease. Science Advances, 2(10), 9. https://doi.org/10.1126/sciadv.1600822Necrotrophic pathogens live and feed on dying tissue, but their interactions with plants are not well understood compared to biotrophic pathogens. The wheat Snn1 gene confers susceptibility to strains of the necrotrophic pathogen Parastagonospora nodorum that produce the SnTox1 protein. We report the positional cloning of Snn1, a member of the wall-associated kinase class of receptors, which are known to drive pathways for biotrophic pathogen resistance. Recognition of SnTox1 by Snn1 activates programmed cell death, which allows this necrotroph to gain nutrients and sporulate. These results demonstrate that necrotrophic pathogens such as P. nodorum hijack host molecular pathways that are typically involved in resistance to biotrophic pathogens, revealing the complex nature of susceptibility and resistance in necrotrophic and biotrophic pathogen interactions with plants

Pyrolysis of medium-density fiberboard: optimized search for kinetics scheme and parameters via a genetic algorithm driven by Kissinger's method

The pyrolysis kinetics of charring materials plays an important role in understanding material combustions especially for construction materials with complex degradation chemistry. Thermogravimetric analysis (TGA) is frequently used to study the heterogeneous kinetics of solid fuels; however, there is no agreed method to determine the pyrolysis scheme and kinetic parameters for charring polymers with multiple components and competing reaction pathways. This study develops a new technique to estimate the possible numbers of species and sub-reactions in pyrolysis by analyzing the second derivatives of thermogravimetry (DDTG) curves. The pyrolysis of a medium-density fiberboard (MDF) in nitrogen is studied in detail, and the DDTG curves are used to locate the temperature of the peak mass-loss rate for each sub-reaction. Then, on the basis of the TG data under multiple heating rates, Kissinger’s method is used to quickly find the possible range of values of the kinetic parameters (<i>A</i> and <i>E</i>). These ranges are used to accelerate the optimization of the inverse problem using a genetic algorithm (GA) for the kinetic and stoichiometric parameters. The proposed method and kinetic scheme found are shown to match the experimental data and are able to predict accurately results at different heating rates better than Kissinger’s method. Moreover, the search method (K–K method) is highly efficient, faster than the regular GA search alone. Modeling results show that, as the TG data available increase, the interdependence among kinetic parameters becomes weak and the accuracy of the first-order model declines. Furthermore, conducting TG experiment under multiple heating rates is found to be crucial in obtaining good kinetic parameters