Exploiting a wheat EST database to assess genetic diversity

Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01

Modulation of crustal magmatic systems by external tectonic forcing

We develop a two dimensional model that simulates the response of the crust to prolonged mantle-derived intrusions in arc environments. The domain includes the entire crustal section and upper mantle and focuses on the evolving thermal structure due to intrusions and external tectonic forcing. We monitor the thermal response, melt fraction and volume for different environments after a definite time by considering geologically relevant melt flux and extensional tectonic rates. The amount of crustal melt versus fractionated primary mantle melts present in the crustal column helps determine crustal structure and growth through time. We observe that with a geophysically estimated flux and tectonic rate, the mantle-derived magma bodies can melt the surrounding volume of crust. We express the amount of crustal melting in terms of an efficiency; therefore we define the melting efficiency as the ratio of the melted volume of crustal material to the volume of melt expected from a strict enthalpy balance as explained by Dufek and Bergantz (2005). Melting efficiencies are less than 1.0 in real systems because heat diffuses to sections of the crust that never melt. The maximum calculated efficiency is 0.05 in our model while most of our simulations show zero efficiency. Additionally, maximum total melt amount is observed in relatively greater extensional environments (0.02 m/yr) and high intrusion rates (10⁻² m³/m²/yr) and in long time periods (2 x 10⁶ years). However, maximum crustal melting in the same environment is reached in 1.2 x 10⁶ years. The relative amounts of mantle-derived and crustal melts in the total volume of magma suggest that the majority of magma composition in crustal column is derived from the mantle material.MSCommittee Chair: Dufek, Josef; Committee Member: Newman, Andrew; Committee Member: Peng, Zhigan

Time and length scales of crust-magma interaction in rift settings

Understanding the processes that lead to magma emplacement and differentiation in the crust is of fundamental importance to science and society, as these magma bodies are important components of crustal growth and erupted products. During magma emplacement and residence in the Earth’s crust, magma thermally and chemically evolves as a function of several complex nonlinear magmatic processes. This thesis work focuses on rift settings and quantifying the time and length scales involved in the thermal and compositional evolution of crustal magmas. In order to give quantitative constraints, this research utilizes a novel thermal-petrographic numerical model that solves for conservation of mass and energy in response to magma emplacement and extensional tectonic forces. In particular, this work tests the sensitivity of tectonic extension rates on crustal magma evolution. General trends of magma evolution are characterized in various rift systems. In particular, the numerical model is applied to Salton Sea Geothermal Field as a natural setting. This work delivers detailed insights to the interaction of magma and crust in extensional tectonic settings. The outcomes address important topics in volcanology including the timescales of generation of evolved magmas, and the thermal and compositional conditions that lead to the compositional diversity observed in diverse settings.Ph.D

The genesis of arc dacites: the case of Mount St. Helens, WA

ISSN:0010-7999ISSN:1432-096

Sulfate radical formation by Cr(III) activation of peroxydisulfate Diphenylcarbazide spectrophotometric determination of sulfate radical and its scavenging activity

Even though sulfate anion radical (SO4 center dot) is a very reactive oxidant used in advanced oxidation processes, a reliably selective and simple colorimetric method for determining this radical can hardly be found. Peroxydisulfate (S2O82 center dot) or peroxymonosulfate (HSO5 center dot) can be activated with transition metal ions to produce SO4 center dot. We have discovered that Cr(III) can be an activator for persulfate, generating Cr(VI) along with SO4 center dot. By measuring the emerging chromate with diphenyl carbazide (DPC) spectrophotometry at 542 nm, we could measure both the formation of SO4 center dot and its scavenging with antioxidant compounds. We could also investigate a number of UV-absorbing SO4 center dot scavengers which could not be measured with other UV spectrometric methods. In addition to conventional antioxidants (phenolics such as quercetin, catechin, epicatechin, caffeic acid, thiols like cysteine and N-acetyl cysteine, and ascorbid acid), nitro-aromatics (represented by 2,4,6-trinitrophenol and 2,4-dinitrophenol) used in ammunition formulations could also be measured as scavengers. The presence of scavengers caused a reduction in the amount of Cr(VI) generated, where the difference in absorbance (Delta A) of chromate - with respect to the DPC method - in the absence and presence of scavengers was a linear function of SO4 center dot scavenging capacity. Ethanol and tert-butanol were tested as solvents to show the selectivity of the method for SO4 center dot. The method was statistically compared to a suitably modified ABTS/persulfate assay. The efficiency order of sulfate radical scavengers was determined and ranked (Spearman's test) using both the proposed method and modified ABTS/persulfate method to reveal a moderate correlation. (C) 2021 Elsevier B.V. All rights reserved

Determination of Major Phytohormones in Fourteen Different Seaweeds Utilizing SPE-LC-MS/MS

Analysis of plant growth regulators (PGRs) should be approached by considering their extremely low concentrations and serious interfering effects that result from the matrix of various plant tissues. In the current research, the separation and simultaneous determination of different classes of phytohormones in 14 seaweeds collected from Turkey seashores were achieved by using solid-phase extraction (SPE) followed by a rapid and sensitive liquid chromatography tandem mass detection method. OASIS HLB (Hydrophilic-Lipophilic Balance) cartridges were successfully used for SPE process to eliminate the matrix effect and enhance the PGRs including zeatin, benzyl amino purine, indole-3-acetic acid, abscisic acid and gibberellic acid within partially different polarities. Based on the optimized experimental conditions, the method presented excellent performance related to linearity (r, 0.9996-0.9999) within the ranges of 0.5-500 ng/mL, relative standard deviation values ((1.43-2.01) for intraday and (2.36-3.50) for interday)), the limit of detection (0.01-0.84 mu g/L) and the limit of quantification (0.02-2.76 mu g/L). The obtained results confirm that the SPE-liquid chromatography/tandem mass spectrometry method performed is highly effective and convenient for routine analyses of trace amounts of the tested phytohormones in seaweeds and any other plant samples as well

Mantle versus crustal contributions in crustal‐scale magmatic systems (Sesia Magmatic System, northern Italy) from coupling Hf isotopes and numerical modelling

The growth and evolution of crustal-scale magmatic systems play a key role in the generation of the continental crust, the largest eruptions on Earth, and the formation of metal resources vital to our society. However, such systems are rarely exposed on the Earth’s surface, limiting our knowledge about the magmatic processes occurring throughout the crust to indirect geo- chemical and petrographic data obtained from the shallowest part of the system. The Hf isotopic composition of accessory zircon is widely used to quantify crust-mantle evolution and mass transfers to and within the crust. Here we combine single- grain zircon Hf isotopic analysis by LA-MC-ICP-MS with thermal modelling to one of the best-studied crustal-scale igneous systems (Sesia Magmatic System, northern Italy), to quantify the relative contribution of crustal- and mantle-derived magmas in the entire system. Zircons from the deep gabbroic units define a tight range of εHf (−2.5 ± 1.5). Granites and rhyolites overlap with this range but tail towards significantly more negative values (down to −9.5). This confirms that the entire system consists of hybrid magmas that stem from both differentiation of mantle-derived magmas and melting of the crust. Thermal modelling suggests that crustal melting and assimilation predominantly occurs during emplacement and evolution of magmas in the lower crust, although melt production is heterogeneous within the bodies both spatially and temporally. The spatial and temporal heterogeneity resolved by the thermal model is consistent with the observed Hf isotope variations within and between samples, and in agreement with published bulk-rock Sr–Nd isotopic data. On average, the crustal con- tribution to the entire system determined by mixing calculations based on Hf isotopic data range between 10 and 40%, even with conservative assumptions, whereas the thermal model suggests that this space- and time-averaged contribution does not exceed 20%. However, spatial and temporal variations in the crustal melt proportion (from 0 up to 80% as observed in the thermal model) may impart significant isotopic variability to different batches of magma observed on the outcrop scale, emphasizing the need to consider a magmatic system as a whole, i.e., by integrating all spatial and temporal scales, to more precisely quantify crustal growth vs. reworking

Identification and quantification of some phytohormones in seaweeds using UPLC-MS/MS

The aim of this work was to identify main plant growth regulators (PGRs), such as, indole-3-acetic acid (IAA), abscisic acid (ABA), gibberellic acid (GA), zeatin, kinetin and 6-benzyl amino purine (BAP) and to determine corresponding quantity in nine seaweed varieties. The samples were extracted by methanol-water (75%) solvent from lyophilized seaweeds for 16 h at -20 degrees C. A rapid and sensitive UPLC-MS/MS method was developed and validated. Both individual and mixed standards were used to study the peak separation and identification of hormones. The precision of the method was tested with good RSD values of 0.67-2.01 for intra-day and 1.21-3.50 for inter-day in six and four replicates, respectively. Accuracy was in the range of 82.75-98.94% by spiking phytohormone standards to eliminate plant matrix. Excellent linearities were found within the ranges of 0.5-50 ng mL(-1) for zeatin and 0.5-10 ng mL(-1) for BAP, 5-500 ng mL(-1) for GA and kinetin, and 2.5-500 ng mL(-1) for IAA and ABA. The results showed that the applied SPE-UPLC-MS/MS method was very sensitive and can be used extensively for the routine analysis of trace amounts of multi-class phytohormones in seaweeds. The method developed greatly reduced both sample preparation and total analysis time