Genomic mechanisms of adaptation to drought-stress in maize

Maize is a globally important crop, that can be devastated by drought stress. Therefore, there is a demand for increasing the adaptability of maize to drought stress. The activity of transposable elements (TEs) can cause long-lasting genetic changes, causing potential adaptation benefits. DNA methylation is an epigenetic process known to regulate the activity of TEs, and can also respond to external stress. This thesis is an investigation into the link between promoter region methylation, TE methylation and drought stress, in the drought tolerant B76 and drought susceptible B73 maize varieties. There were three major aims: 1) To test if there is a difference in methylation in gene promoter regions caused by drought in both varieties, 2) To ascertain methylation differences found in the TE fraction caused by drought in both varieties, 3) To discover if differentially methylated TEs were found in differentially methylated promoter regions of potentially important drought-tolerance genes. The primary method of investigation in chapters 3 and 4 involved the generation of bisulfite-treated DNA sequencing. Differential methylation analysis of this data showed that there is a methylation drought stress response found in B76, that is not found in B73. Methylation differences were also found in the majority of TE families in both varieties. However, the huck TE sub-family was found to be differentially methylated after drought stress and overrepresented within differentially methylated promoter regions of the B76 variety, suggesting a possible role in drought tolerance through the restriction of expression of particular genes. This research adds to the knowledge surrounding methylation changes after drought stress in the TE fraction, while also highlighting potential drought tolerance candidate gene, thereby providing a jumping off point for future adaptation studies in maize

Kinematics of Nearby Subdwarf Stars

We present an analysis of the space motions of 742 subdwarf stars based on the sample of Carney et al. (1994, CLLA). Hipparcos parallaxes, TYC2+HIP proper motions and Tycho2 proper motions were combined with radial velocities and metallicities from CLLA. The kinematical behavior is discussed in particular in relation to their metallicities. The majority of these sample stars have metal abundances of [Fe/H] >-1 and represent the thick disk population. The halo component, with [Fe/H] <-1.6, is characterized by a low mean rotation velocity and a radially elongated velocity ellipsoid. In the intermediate metallicity range (-1.6 < [Fe/H] <-1), we find a significant number of subdwarfs with disklike kinematics. We interpret this population of stars as a metal-weak thick disk population.Comment: 6 pages, 7 figures, accepted by Astronomy & Astrophysic

The changing face of floodplains in the Mississippi River Basin detected by a 60-year land use change dataset

Floodplains provide essential ecosystem functions, yet \u3e80% of European and North American floodplains are substantially modified. Despite floodplain changes over the past century, comprehensive, long-term land use change data within large river basin floodplains are limited. Long-term land use data can be used to quantify floodplain functions and provide spatially explicit information for management, restoration, and flood-risk mitigation. We present a comprehensive dataset quantifying floodplain land use change along the 3.3 million km2 Mississippi River Basin (MRB) covering 60 years (1941–2000) at 250-m resolution. We developed four unique products as part of this work, a(n): (i) Google Earth Engine interactive map visualization interface, (ii) Python code that runs in any internet browser, (iii) online tutorial with visualizations facilitating classroom code application, and (iv) instructional video demonstrating code application and database reproduction. Our data show that MRB’s natural floodplain ecosystems have been substantially altered to agricultural and developed land uses. These products will support MRB resilience and sustainability goals by advancing data-driven decision making on floodplain restoration, buyout, and conservation scenarios

Developing a trapping assay to assess the viability of Trogodermavariabileas a behavioral surrogate species for the biosecurity threat, Trogodermagranarium(Coleoptera: Dermestidae)

The Khapra beetle (KB), Trogoderma granarium, is a pest that threatens the biosecurity of the United States. This species has not established itself in this country, however in the past few years there has been an alarming increase in the number of interceptions of adults at borders and ports in the U.S. Because researchers in the U.S. are only able to work with KB in specially designated APHIS quarantine facilities, understanding the full extent of the threat from this species would proceed much faster if a behavioral surrogate species could be used that was already widespread in the country. One potential surrogate species is Trogodermavariabile, the warehouse beetle (Fig. 1), which is closely related to KB, occurs throughout the U.S., and is a destructive pest of stored products in its own right

Analysis of Immune Checkpoint Drug Targets and Tumor Proteotypes in Non-Small Cell Lung Cancer

New therapeutics targeting immune checkpoint proteins have significantly advanced treatment of non-small cell lung cancer (NSCLC), but protein level quantitation of drug targets presents a critical problem. We used multiplexed, targeted mass spectrometry (MS) to quantify immunotherapy target proteins PD-1, PD-L1, PD-L2, IDO1, LAG3, TIM3, ICOSLG, VISTA, GITR, and CD40 in formalin-fixed, paraffin-embedded (FFPE) NSCLC specimens. Immunohistochemistry (IHC) and MS measurements for PD-L1 were weakly correlated, but IHC did not distinguish protein abundance differences detected by MS. PD-L2 abundance exceeded PD-L1 in over half the specimens and the drug target proteins all displayed different abundance patterns. mRNA correlated with protein abundance only for PD-1, PD-L1, and IDO1 and tumor mutation burden did not predict abundance of any protein targets. Global proteome analyses identified distinct proteotypes associated with high PD-L1-expressing and high IDO1-expressing NSCLC. MS quantification of multiple drug targets and tissue proteotypes can improve clinical evaluation of immunotherapies for NSCLC

A Process for Co-Designing Educational Technology Systems for Refugee Children

There is a growing interest in the potential for technology to facilitate emergency education of refugee children. However, designing in this space requires knowledge of the displaced population and the contextual dynamics surrounding it. Design should therefore be informed by both existing research across relevant disciplines, and from the practical experience of those who are on the ground facing the problem in real life. This paper describes a process for designing appropriate technology for these settings. The process draws on literature from emergency education, student engagement and motivation, educational technology, and participatory design. We emphasise a thorough understanding of the problem definition, the nature of the emergency, and of socio-cultural aspects that can inform the design process. We describe how this process was implemented leading to the design of a digital learning space for children living in a refugee camp in Greece. This drew on involving different groups of participants such as social-workers, parents, and children

Acetaminophen Combinations Protect Against Iron-Induced Cardiac Damage in Gerbils

This study tested if acetaminophen, N-methyl-D-glucamine dithiocarbamate (NMGDTC), deferoxamine, and combinations of these agents reduce excess iron content, prevent iron-induced pathology, reduce cardiac arrhythmias, and reduce mortality in iron-overloaded gerbils. Eight groups of 16 gerbils received iron dextran injections (ferric hydroxide dextran complex, 120 mg/kg, ip) or saline solution (controls) twice/wk for 8 wk. The 8 groups were treated every Monday, Wednesday, and Friday with one of the following: saline control, acetaminophen, 150 mg/kg, ip), acetaminophen (150 mg/kg, po), deferoxamine, 83 mg/kg, ip), NMGDTC (200 mg/kg, ip), or combinations of acetaminophen (75 mg/kg) with deferoxamine (42 mg/kg, each ip, separately) or acetaminophen (75 mg/kg) with NMGDTC (100 mg/kg, each ip, separately). The treatments were given 4 hr after each iron injection on days when both iron administration and treatment occurred during iron overloading (8 wk) and were continued 4 wk thereafter. Echocardiography (ECHO) was used to evaluate iron-induced cardiac changes and detect arrhythmias. Acetaminophen and NMGDTC, or combinations thereof, reduced cardiac and hepatic excess iron content as measured by inductively coupled plasma atomic emission spectrometry (ICP-AES). Acetaminophen was effective whether administered po or ip. Acetaminophen treatment had a positive inotropic effect on cardiac function. Acetaminophen-deferoxamine combination conferred equal cardioprotection as acetaminophen or deferoxamine alone, was equally able to remove hepatic iron, and was superior to either acetaminophen or deferoxamine in removing cardiac iron from iron-overloaded gerbils. Acetaminophen-NMGDTC combination was also effective in removing cardiac and hepatic iron and protecting against iron-induced cardiac damage. ECHO evaluation of iron-overloaded, untreated gerbils demonstrated a high incidence of cardiac arrhythmias, usually PVCs (10/16 = 63%), and mortality prior to completion of the experiment (4/16 = 25%). All treatments except deferoxamine, alone, reduced the incidence of cardiac arrhythmias and deaths. All treatments reduced iron-induced increases in hepatic and cardiac weights. This study demonstrates injection alternates that are equally or more effective than deferoxamine injections and shows oral acetaminophen to be effective in treatment of iron-overload and associated cardiac complications

Tomographic Magnification of Lyman Break Galaxies in The Deep Lens Survey

Using about 450,000 galaxies in the Deep Lens Survey, we present a detection of the gravitational magnification of z > 4 Lyman Break Galaxies by massive foreground galaxies with 0.4 < z < 1.0, grouped by redshift. The magnification signal is detected at S/N greater than 20, and rigorous checks confirm that it is not contaminated by any galaxy sample overlap in redshift. The inferred galaxy mass profiles are consistent with earlier lensing analyses at lower redshift. We then explore the tomographic lens magnification signal by splitting our foreground galaxy sample into 7 redshift bins. Combining galaxy-magnification cross-correlations and galaxy angular auto-correlations, we develop a bias-independent estimator of the tomographic signal. As a diagnostic of magnification tomography, the measurement of this estimator rejects a flat dark matter dominated Universe at > 7.5{\sigma} with a fixed \sigma_8 and is found to be consistent with the expected redshift-dependence of the WMAP7 {\Lambda}CDM cosmology.Comment: 12 pages, 9 figures, Accepted to MNRA