Brachypodium distachyon. A new model system for functional genomics in grasses

John Draper, Luis A.J. Mur, Glyn Jenkins, Gadab C. Ghosh-Biswas, Pauline Bablak, Robert Hasterok,and Andrew P.M. Routledge (2001). Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiology, 127 (4), 1539-1555. Sponsorship: BBSRC / Gatsby Foundation RAE2008

Identification and analysis of mechanisms involved in a broad-spectrum disease resistant mutant of the winter wheat cv. Guardian

M66 an X-ray induced mutant of winter wheat (Triticum aestivum) cv. Guardian exhibits broad-spectrum resistance to powdery mildew (Blumeria graminis f. sp. tritici), yellow rust (Puccinia striiformis f. sp. tritici), and leaf rust (Puccinia recondita f. sp. tritici), along with partial resistance to stagnonospora nodorum blotch (caused by the necrotroph Stagonosporum nodorum) and septoria tritici blotch (caused by the hemibiotroph Mycosphaerella graminicola) compared to the parent plant ‘Guardian’. Analysis revealed that M66 exhibited no symptoms of infection following artificial inoculation with Bgt in the glasshouse after adult growth stage (GS 45). Resistance in M66 was associated with widespread leaf flecking which developed during tillering. Flecking also occurred in M66 leaves without Bgt challenge; as a result grain yields were reduced by approximately 17% compared to ‘Guardian’ in the absence of disease. At the seedling stage, M66 exhibited partial resistance. M66, along with Tht mutants (Tht 12, Tht13), also exhibit increased tolerance to environmental stresses (abiotic), such as drought and heat stress at seedling and adult growth stages, However, adult M66 exhibited increased susceptibility to the aphid Schizaphis graminum compared to ‘Guardian’. Resistance to Bgt in M66 was characterized with increased and earlier H2O2 accumulation at the site of infection which resulted in increased papilla formation in epidermal cells, compared to ‘Guardian’. Papilla formation was associated with reduced pathogen ingress and haustorium formation, indicating that the primary cause of resistance in M66 was prevention of pathogen penetration. Heat treatment at 46º C prior to challenge with Bgt also induced partial disease resistance to Blumeria graminis f. sp. tritici in ‘Guardian’ and M66 seedlings. This was characterized by a delay in primary infection, due to increased production of ROS species, such as hydrogen peroxide, ROS-scavenging enzymes and Hsp70, resulting in cross-linking of cell wall components prior to inoculation. This actively prevented the fungus from penetrating the epidermal cell wall. Proteomics analysis using 2-D gel electrophoresis identified primary and secondary disease resistance effects in M66 including detection of ROS scavenging enzymes (4, 24 hai), such as ascorbate peroxidase and a superoxidase dismutase isoform (CuZnSOD) in M66 which were absent from ‘Guardian’. Chitinase (PR protein) was also upregulated (24 hai) in M66 compared to ‘Guardian’.Monosomic and ditelosomic analysis of M66 revealed that the mutation in M66 is located on the long arm of chromosome 2B (2BL). Chromosome 2BL is known to have key genes involved in resistance to pathogens such as those causing stripe rust and powdery mildew. The TaMloB1 gene, an orthologue of the barley Mlo gene, is also located on chromosome 2BL. Sanger sequencing of part of the coding sequence revealed no deletions in the TaMloB1 gene between ‘Guardian’ and M66.

Profiling phytochemical and nutritional components of potato

Potatoes (Solanum Tuberosum L.) contain secondary metabolites that may have an impact on human health. The aim of this study was to assess the levels of some of these compounds in a wide range of varieties, including rare, heritage and commercial cultivars. Vitamin C, total carotenoids, phenolics, flavonoids, antioxidant activity and glycoalkaloids were determined, using spectroscopy and chromatography, in the skin and flesh of tubers grown in field trials. Transcript levels of key synthetic enzymes were assessed by qPCR. Accumulation of selected metabolites was higher in the skin than in the flesh of tubers, except ascorbate, which was undetected in the skin. Differences were on average 2.5 to 3-fold for carotenoids, 6-fold for phenolics, 15 to 16-fold for flavonoids, 21-fold for glycoalkaloids and 9 to 10-fold for antioxidant activity. Higher contents of carotenoids were associated with yellow skin or flesh, and higher values of phenolics, flavonoids and antioxidant activity with blue flesh. Variety ‘Burren’ had maxima values of carotenoids in skin and flesh, variety ‘Nicola’ of ascorbate, variety ‘Congo’ of phenolics, flavonoids and antioxidant activity in both tissues, except antioxidant activity in the skin, which was higher in ‘Edzell Blue’. Varieties ‘May Queen’ and ‘International Kidney’ had highest glycoalkaloid content in skin and flesh respectively. The effect of the environment was diverse: year of cultivation was significant for all metabolites, but site of cultivation was not for carotenoids and glycoalkaloids. Levels of expression of phenylalanine ammonia-lyase and chalcone synthase were higher in varieties accumulating high contents of phenolic compounds. However, levels of expression of phytoene synthase and L-galactono-1,4-lactone dehydrogenase were not different between varieties showing contrasting levels of carotenoids and ascorbate respectively. This work will help identify varieties that could be marketed as healthier and the most suitable varieties for extraction of high-value metabolites such as glycoalkaloids.

A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation.

The role of chromosomal inversions in adaptation and speciation is controversial. Historically, inversions were thought to contribute to these processes either by directly causing hybrid sterility or by facilitating the maintenance of co-adapted gene complexes. Because inversions suppress recombination when heterozygous, a recently proposed local adaptation mechanism predicts that they will spread if they capture alleles at multiple loci involved in divergent adaptation to contrasting environments. Many empirical studies have found inversion polymorphisms linked to putatively adaptive phenotypes or distributed along environmental clines. However, direct involvement of an inversion in local adaptation and consequent ecological reproductive isolation has not to our knowledge been demonstrated in nature. In this study, we discovered that a chromosomal inversion polymorphism is geographically widespread, and we test the extent to which it contributes to adaptation and reproductive isolation under natural field conditions. Replicated crosses between the prezygotically reproductively isolated annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus, revealed that alternative chromosomal inversion arrangements are associated with life-history divergence over thousands of kilometers across North America. The inversion polymorphism affected adaptive flowering time divergence and other morphological traits in all replicated crosses between four pairs of annual and perennial populations. To determine if the inversion contributes to adaptation and reproductive isolation in natural populations, we conducted a novel reciprocal transplant experiment involving outbred lines, where alternative arrangements of the inversion were reciprocally introgressed into the genetic backgrounds of each ecotype. Our results demonstrate for the first time in nature the contribution of an inversion to adaptation, an annual/perennial life-history shift, and multiple reproductive isolating barriers. These results are consistent with the local adaptation mechanism being responsible for the distribution of the two inversion arrangements across the geographic range of M. guttatus and that locally adaptive inversion effects contribute directly to reproductive isolation. Such a mechanism may be partially responsible for the observation that closely related species often differ by multiple chromosomal rearrangements.

Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy.

Time-lapse fluorescence microscopy is an important tool for measuring in vivo gene dynamics in single cells. However, fluorescent proteins are limited by slow chromophore maturation times and the cellular autofluorescence or phototoxicity that arises from light excitation. An alternative is luciferase, an enzyme that emits photons and is active upon folding. The photon flux per luciferase is significantly lower than that for fluorescent proteins. Thus time-lapse luminescence microscopy has been successfully used to track gene dynamics only in larger organisms and for slower processes, for which more total photons can be collected in one exposure. Here we tested green, yellow, and red beetle luciferases and optimized substrate conditions for in vivo luminescence. By combining time-lapse luminescence microscopy with a microfluidic device, we tracked the dynamics of cell cycle genes in single yeast with subminute exposure times over many generations. Our method was faster and in cells with much smaller volumes than previous work. Fluorescence of an optimized reporter (Venus) lagged luminescence by 15-20 min, which is consistent with its known rate of chromophore maturation in yeast. Our work demonstrates that luciferases are better than fluorescent proteins at faithfully tracking the underlying gene expression.

Monitoring maternal Beta carotene and retinol consumption may decrease the incidence of neurodevelopmental disorders in offspring.

Retinoic acids (13-cis and 13-trans) are known teratogens, and their precursor is retinol, a form of vitamin A. In 1995, Rothman et al demonstrated an association between excessive vitamin A, >10,000 IU/day, during the first trimester of pregnancy and teratogenic effects, particularly in the central nervous system. However, vitamin A deficiency has long been known to be deleterious to the mother and fetus. Therefore, there may be a narrow therapeutic ratio for vitamin A during pregnancy that has not previously been fully appreciated. Neurodevelopmental disorders may not be apparent by macroscopic brain examination or imaging, and proving the existence of a behavioral teratogen is not straightforward. However, an excess of retinoic acid and some neurodevelopmental disorders are both associated with abnormalities in cerebellar morphology. Physical and chemical evidence strongly supports the notion that beta carotene crosses the placenta and is metabolized to retinol. Only very limited amounts of beta carotene are stored in fetal fat cells as evidenced by the fact that maternal fat is yellow from beta carotene, whereas non-brown neonatal fat is white. Furthermore, newborns of carotenemic mothers do not share the yellow complexion of their mothers. The excess 13-trans retinoic acid derived from metabolized beta carotene in the fetus increases the concentration of the more teratogenic 13-cis retinoic acid since the isomerization equilibrium is shifted to the left. Therefore, this paper proposes that consideration be given to monitoring all potential sources of fetal 13-cis and 13-trans retinoic acid, including nutritional supplements, dietary retinol, and beta carotene, particularly in the first trimester of pregnancy.

La ultraestructura de los panza blanca, moteados y vitreos, en tres especies de trigos cultivados : en la región semiárida trigera Argentina

p.65-72

Exact colorations of graphs and digraphs

A coloration is an exact regular coloration if whenever two vertices are colored the same they have identically colored neighborhoods. For example, if one of the two vertices that are colored the same is connected to three yellow vertices, two white and red, then the other vertex is as well. Exact regular colorations have been discussed informally in the social network literature. However they have been part of the mathematical literature for some time, though in a different format. We explore this concept in terms of social networks and illustrate some important results taken from the mathematical literature. In addition we show how the concept can be extended to ecological and perfect colorations, and discuss how the CATREGE algorithm can be extended to find the maximal exact regular coloration of a graph.

Canna tandilensis Ciciar. (Cannaceae-Zingiberales), a new species from Argentina.

Canna tandilensis is proposed as a species new to science. Plants grow wild terrestrial, in rocky places exposed to solar radiation forming dense colonies whose individuals of small to medium length, produce reduced inflorescences with large and few yellow to bright orange flowers and narrow and reflexed staminodes. The specific epithet refers to the city of Tandil at the south of Buenos Aires Province where the holotype comes from. It is related to other species having reduced inflorescences, narrow leaves and staminodes, and nectar guides in androecium pieces such as C. lineata. A detailed description of the new species is given, along with a study of the morphological vegetative and floral characters. These characters were compared with those from two other species C. glauca and C. lineata. According to these new evidences two groups of similar species of the genus are suggested. The number of species surveyed until now in Argentina rises to sixteen.

Adsorption isotherm models for basic dye adsorption by peat in single and binary component systems

Coloured effluents from textile industries are a problem in many rivers and waterways. Prediction of adsorption capacities of dyes by adsorbents is important in design considerations. The sorption of three basic dyes, namely Basic Blue 3, Basic Yellow 21 and Basic Red 22, onto peat is reported. Equilibrium sorption isotherms have been measured for the three single component systems. Equilibrium was achieved after twenty-one days. The experimental isotherm data were analysed using Langmuir, Freundlich, Redlich-Peterson, Temkin and Toth isotherm equations. A detailed error analysis has been undertaken to investigate the effect of using different error criteria for the determination of the single component isotherm parameters and hence obtain the best isotherm and isotherm parameters which describe the adsorption process. The linear transform model provided the highest R2 regression coefficient with the Redlich-Peterson model. The Redlich-Peterson model also yielded the best fit to experimental data for all three dyes using the non-linear error functions. An extended Langmuir model has been used to predict the isotherm data for the binary systems using the single component data. The correlation between theoretical and experimental data had only limited success due to competitive and interactive effects between the dyes and the dye-surface interactions.

Deposition of Uranium Precipitates in Dolomitic Gravel Fill

Uranium-containing precipitates have been observed in a dolomitic gravel fill near the Department of Energy (DOE) S-3 Ponds former waste disposal site as a result of exposure to acidic (pH 3.4) groundwater contaminated with U (33 mg L-1), Al3+ (900 mg L-1), and NO3- (14?000 mg L-1). The U containing precipitates fluoresce a bright green under ultraviolet (UV) short-wave light which identify U-rich coatings on the gravel. Scanning electron microscopy (SEM) microprobe analysis show U concentration ranges from 1.6-19.8% (average of 7%) within the coatings with higher concentrations at the interface of the dolomite fragments. X-ray absorption near edge structure spectroscopy (XANES) indicate that the U is hexavalent and extended X-ray absorption fine structure spectroscopy (EXAFS) shows that the uranyl is coordinated by carbonate. The exact nature of the uranyl carbonates are difficult to determine, but some are best described by a split K+-like shell similar to grimselite [K4Na(UO2)(CO3)3·H2O] and other regions are better described by a single Ca2+-like shell similar to liebigite [Ca2(UO2)(CO3)3·11(H2O)] or andersonite [Na2CaUO2(CO3)3 · 6H2O]. The U precipitates are found in the form of white to light yellow cracked-formations as coatings on the dolomite gravel and as detached individual precipitates, and are associated with amorphous basalumnite [Al4(SO4)(OH)10·4H2O].

A structural and electrochemical investigation of 1-alkyl-3-methylimidazollum salts of the nitratodioxouranate(VI) anions [{UO2(NO3)(2)}(2)(mu(4)-C2O4)](2-), [UO2(NO3)(3)](-), and [UO2(NO3)(4)](2-)

The properties of the 1-butyl-3-methylimidazolium salt of the dinuclear mu(4)-(O,O,O',O'-ethane-1,2-dioato)bis[bis-(nitrato-O,O)dioxouranate(VI)] anion have been investigated using electrochemistry, single-crystal X-ray crystallography, and extended X-ray absorbance fine structure spectroscopy: the anion structures from these last two techniques are in excellent agreement with each other. Electrochemical reduction of the complex leads to the a two-electron metal-centered reduction of U(VI) to U(IV), and the production Of UO2, or a complex containing UO2. Under normal conditions, this leads to the coating of the electrode with a passivating film. The presence of volatile organic compounds in the ionic liquids 1-alkyl-3-methylimidazolium nitrate (where the 1-alkyl chain was methyl, ethyl, propyl, butyl, pentyl, hexyl, dodecyl, hexadecyl, or octadecyl) during the oxidative dissolution of uranium(IV) oxide led to the formation of a yellow precipitate. To understand the effect of the cation upon the composition and structure of the precipitates, 1-alkyl-3-methylimidazolium salts of a number of nitratodioxouranate(VI) complexes were synthesized and then analyzed using X-ray crystallography. It was demonstrated that the length of the 1-alkyl chain played an important role, not only in the composition of the complex salt, but also in the synthesis of dinuclear anions containing the bridging mu(4)-(O,O,O',O'-ethane-1,2-dioato), or oxalato, ligand, by protecting it from further oxidation.

Microcolumn studies of dye adsorption onto manganese oxides modified diatomite

The method described here cannot fully replace the analysis of large columns by small test columns (microcolumns). The procedure, however, is suitable for speeding up the determination of adsorption parameters of dye onto the adsorbent and for speeding up the initial screening of a large adsorbent collection that can be tedious if a several adsorbents and adsorption conditions must be tested. The performance of methylene blue (MB), a basic dye, Cibacron reactive black (RB) and Cibacron reactive yellow (RY) was predicted in this way and the influence of initial dye concentration and other adsorption conditions on the adsorption behaviour were demonstrated.

The removal of dyes from textile wastewater: a study of the physical characteristics and adsorption mechanisms of diatomaceous earth

The feasibility of using diatomite for the removal of the problematic reactive dyes as well as basic dyes from textile wastewater was investigated. Methylene blue, Cibacron reactive black and reactive yellow dyes were considered. Physical characteristics of diatomite such as pH(solution), pH(ZPC), surface area, Fourier transform infrared, and scanning electron microscopy were investigated. The surface area of diatomite was found to be 27.80 m(2) g(-1) and the pH(ZPC) occurred around pH of 5.4. The results indicated that the surface charge of diatomite decreased as the pH of the solution increased with the maximum methylene blue removal from aqueous solution occurring at basic pH of around (1011). Adsorption isotherms of diatomite with methylene blue, hydrolysed reactive black and yellow dyes were constructed at different pH values, initial dye concentrations and particle sizes. The experimental results were fitted to the Langmuir, Freundlich, and Henry models. The study indicated that electrostatic interactions play an important role in the adsorption of dyes onto diatomite. A model of the adsorption mechanism of methylene blue onto diatomite is proposed. (C) 2003 Elsevier Ltd. All rights reserved.

Comparison of optimised isotherm models for basic dye adsorption by kudzu

This study assesses the use of dried (5% w/w moisture) kudzu (Peuraria lobata ohwi) as an adsorbent medium for the removal of two basic dyes, Basic Yellow 21 and Basic Red 22, from aqueous solutions. The extent of adsorption was measured through equilibrium sorption isotherms for the single component systems. Equilibrium was achieved after 21 days. The experimental isotherm data were analysed using Langmuir, Freundlich, Redlich-Peterson, Temkin and Toth isotherm equations. A detailed error analysis was undertaken to investigate the effect of using different error criteria for the determination of the single component isotherm parameters. The performance of the kudzu was compared with an activated carbon (Chemviron F-400). Kudzu was found to be an effective adsorbent for basic dye colour removal, though its capacity for colour removal was not as high as an activated carbon, the potential appeared to exist to use it as an alternative to activated carbon where carbon cost was prohibitive. (C) 2002 Elsevier Science Ltd. All rights reserved.