Microarray Analysis of Late-season Velvetleaf (Abutilon theophrasti) Effect on Corn

Microarray analysis was used to identify changes in gene expression in corn leaves collected from plants at the V11–14 growth stage that resulted from competition with velvetleaf. The plants were grown in field plots under adequate N (addition of 220 kg N ha1) and irrigation to minimize N and water stress. Consequently, only differences resulting from competition for micronutrients, light, and perhaps allelopathic stress were anticipated. Genes involved in carbon and nitrogen utilization, photosynthesis, growth and development, oxidative stress, signal transduction, responses to auxin and ethylene, and zinc transport were repressed in corn growing in competition with velvetleaf. Very few genes were induced because of competition with velvetleaf, and those that were provided little indication of the physiological response of corn. No differences were observed in genes responsive to water stress or sequestering/transporting micronutrients other than zinc, indicating that these stresses were not a major component of velvetleaf competition with corn at the developmental stage tested

Heterologous Hybridization of Cotton Microarrays with Velvetleaf (Abutilon theophrasti) Reveals Physiological Responses Due to Corn Competition

Microarray analysis was used to identify changes in gene expression in velvetleaf that result from competition with corn. The plants were grown in field plots under adequate N (addition of 220 kg N ha−1) to minimize stress and sampled at the V6 growth stage of corn (late June). Leaf area, dry weight, and N and P concentration were similar in velvetleaf plants grown alone or with corn. Competition, however, did influence velvetleaf gene expression. Genes involved in carbon utilization, photosynthesis, red light signaling, and cell division were preferentially expressed when velvetleaf was grown in competition with corn. A less clear picture of the physiological impact of growth in monoculture was provided by the data. However, several genes involved in secondary metabolism and a gene preferentially expressed in response to phosphate availability were induced. No differences were observed in genes responsive to water stress or sequestering/transporting micronutrients

Heterologous Hybridization of Cotton Microarrays with Velvetleaf (Abutilon theophrasti) Reveals Physiological Responses Due to Corn Competition

Microarray analysis was used to identify changes in gene expression in velvetleaf that result from competition with corn. The plants were grown in field plots under adequate N (addition of 220 kg N ha21 ) to minimize stress and sampled at the V6 growth stage of corn (late June). Leaf area, dry weight, and N and P concentration were similar in velvetleaf plants grown alone or with corn. Competition, however, did influence velvetleaf gene expression. Genes involved in carbon utilization, photosynthesis, red light signaling, and cell division were preferentially expressed when velvetleaf was grown in competition with corn. A less clear picture of the physiological impact of growth in monoculture was provided by the data. However, several genes involved in secondary metabolism and a gene preferentially expressed in response to phosphate availability were induced. No differences were observed in genes responsive to water stress or sequestering/transporting micronutrients

Structure and stereochemistry of the base excision repair glycosylase MutY reveal a mechanism similar to retaining glycosidases.

MutY adenine glycosylases prevent DNA mutations by excising adenine from promutagenic 8-oxo-7,8-dihydroguanine (OG):A mismatches. Here, we describe structural features of the MutY active site bound to an azaribose transition state analog which indicate a catalytic role for Tyr126 and approach of the water nucleophile on the same side as the departing adenine base. The idea that Tyr126 participates in catalysis, recently predicted by modeling calculations, is strongly supported by mutagenesis and by seeing close contact between the hydroxyl group of this residue and the azaribose moiety of the transition state analog. NMR analysis of MutY methanolysis products corroborates a mechanism for adenine removal with retention of stereochemistry. Based on these results, we propose a revised mechanism for MutY that involves two nucleophilic displacement steps akin to the mechanisms accepted for 'retaining' O-glycosidases. This new-for-MutY yet familiar mechanism may also be operative in related base excision repair glycosylases and provides a critical framework for analysis of human MutY (MUTYH) variants associated with inherited colorectal cancer

Microarray and Growth Analyses Identify Differences and Similarities of Early Corn Response to Weeds, Shade, and Nitrogen Stress

Weed interference with crop growth is often attributed to water, nutrient, or light competition; however, specific physiological responses to these stresses are not well described. This study\u27s objective was to compare growth, yield, and gene expression responses of corn to nitrogen (N), low light (40% shade), and weed stresses. Corn vegetative parameters from V2 to V12 stages, yield parameters, and gene expression using transcriptome (2008) and quantitative polymerase chain reaction (qPCR) (2008/09) analyses at V8 were compared among the stresses and with nonstressed corn. N stress did not affect vegetative parameters, although grain yield was reduced by 40% compared with nonstressed plants. Shade, present until V2, reduced biomass and leaf area \u3e 50% at V2, and recovering plants remained smaller than nonstressed plants at V12. However, grain yields of shade-stressed and nonstressed plants were similar, unless shade remained until V8. Weed stress reduced corn growth and yield in 2008 when weeds remained until V6. In 2009, weed stress until V2 reduced corn vegetative growth, but yield reductions occurred only if weed stress remained until V6 or later. Principle component analysis of differentially expressed genes indicated that shade and weed stress had more similar gene expression patterns to each other than they did to nonstressed or N-stressed tissues. However, corn grown in N-stressed conditions shared 252 differentially expressed genes with weed-stressed plants. Ontologies associated with light/photosynthesis, energy conversion, and signaling were down-regulated in response to all three stresses. Shade and weed stress clustered most tightly together, based on gene expression, but shared only three ontologies, O-METHYLTRANSFERASE activity (lignification processes), POLY(U)-BINDING activity (posttranscriptional gene regulation), and stomatal movement. Based on morphologic and genomic observations, weed stress to corn was not explained by individual effects of N or light stress. Therefore, we hypothesize that these stresses share limited signaling mechanisms

Syndemics and the PrEP Cascade: Results from a Sample of Young Latino Men Who Have Sex with Men.

Young Latino men who have sex with men (MSM) are a highly vulnerable population for HIV infection. Pre-exposure prophylaxis (PrEP) is a novel biomedical HIV prevention tool that may aid in reducing the disparity in HIV incidence among Latino MSM. However, PrEP use is disproportionally low among Latino MSM and, therefore, identifying barriers along the PrEP continuum of care (the "PrEP cascade") would provide insight into how to best deploy PrEP interventions. Syndemics theory is a prominent framework employed in HIV prevention; however, to date, no known studies have applied this theory to PrEP. Thus, the aim of the current study was to explore the association between syndemics and the PrEP cascade, including the degree to which psychosocial and structural syndemic constructs are related to the PrEP cascade. Participants were 151 young Latino MSM (M age = 24 years; SD = 3) residing in San Diego, California, who completed a battery of online self-report measures. Results indicated high levels of syndemic indicators and varying levels of engagement across the PrEP cascade. As syndemic indicators increased, the odds of engagement across the PrEP cascade were significantly lowered. Psychosocial and structural syndemic factors accounted for unique variance in the PrEP cascade. Results highlight the need for combination interventions that address both psychosocial and structural barriers to PrEP use and persistence among young Latino MSM

Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.)

<p>Abstract</p> <p>Background</p> <p>Dormancy of buds is a critical developmental process that allows perennial plants to survive extreme seasonal variations in climate. Dormancy transitions in underground crown buds of the model herbaceous perennial weed leafy spurge were investigated using a 23 K element cDNA microarray. These data represent the first large-scale transcriptome analysis of dormancy in underground buds of an herbaceous perennial species. Crown buds collected monthly from August through December, over a five year period, were used to monitor the changes in the transcriptome during dormancy transitions.</p> <p>Results</p> <p>Nearly 1,000 genes were differentially-expressed through seasonal dormancy transitions. Expected patterns of gene expression were observed for previously characterized genes and physiological processes indicated that resolution in our analysis was sufficient for identifying shifts in global gene expression.</p> <p>Conclusion</p> <p>Gene ontology of differentially-expressed genes suggests dormancy transitions require specific alterations in transport functions (including induction of a series of mitochondrial substrate carriers, and sugar transporters), ethylene, jasmonic acid, auxin, gibberellic acid, and abscisic acid responses, and responses to stress (primarily oxidative and cold/drought). Comparison to other dormancy microarray studies indicated that nearly half of the genes identified in our study were also differentially expressed in at least two other plant species during dormancy transitions. This comparison allowed us to identify a particular MADS-box transcription factor related to the <it>DORMANCY ASSOCIATED MADS-BOX </it>genes from peach and hypothesize that it may play a direct role in dormancy induction and maintenance through regulation of <it>FLOWERING LOCUS T</it>.</p

Flow Analysis of the Cleveland Clinic Centrifugal Pump

An implantable ventricular assist rotordynamic blood pump is being developed by the Cleveland Clinic Foundation in cooperation with the NASA Lewis Research Center. At the nominal design condition, the pump provides blood flow at the rate of 5 liters per minute at a pressure rise of 100 mm of mercury and a rotative speed of 3000 RPM. Bench testing of the centrifugal pump in a water/glycerin mixture has provided flow and pressure data at several rotative speeds. A one-dimensional empirical based pump flow analysis computer code developed at NASA Lewis Research Center has been used in the design process to simulate the flow in the primary centrifugal pump stage. The computer model was used to size key impeller and volute geometric parameters that influence pressure rise and flow. Input requirements to the computer model include a simple representation of the pump geometry. The model estimates the flow conditions at the design and at off-design operating conditions at the impeller leading and trailing edges and the volute inlet and exit. The output from the computer model is compared to flow and pressure data obtained from bench testing

Varying Weed Densities Alter the Corn Transcriptome, Highlighting a Core Set of Weed-Induced Genes and Processes with Potential for Manipulating Weed Tolerance

The phenological responses of corn (Zea mays L.) to competition with increasing densities of winter canola (Brassica napus L.) as the weedy competitor were investigated. Changes in the corn transcriptome resulting from varying weed densities were used to identify genes and processes responsive to competition under controlled conditions where light, nutrients, and water were not limited. Increasing densities of weeds resulted in decreased corn growth and development and increased the number and expression intensity of competition-responsive genes. The physiological processes identified in corn that were consistently induced by competition with weeds included protein synthesis and various transport functions. Likewise, numerous genes involved in these processes, as well as several genes implicated in phytochrome signaling and defense responses, were noted as differentially expressed. The results obtained in this study, conducted under controlled (greenhouse) conditions, were compared with a previously published study where the response of corn to competition with other species was evaluated under field conditions. Approximately one-third of the genes were differentially expressed in response to competition under both field and controlled conditions. These competition-responsive genes represent a resource for investigating the signaling processes by which corn recognizes and responds to competition. These results also highlight specific physiological processes that might be targets for mitigating the response of crops to weeds or other competitive plants under field conditions

Corn Response to Competition: Growth Alteration vs. Yield Limiting Factors

Competition mechanisms among adjacent plants are not well understood. This study compared corn growth and yield responses to water, N, and shade at 74,500 plants ha−1 (1×) with responses to water and N when planted at 149,000 plant ha−1 Plant biomass, leaf area, chlorophyll content, reflectance, and enzyme expression (transcriptome analysis) were measured at V-12. Grain and stover yields were measured with grain analyzed for 13C isotopic discrimination (Δ) and N concentration. At V-12, 60% shade plants had increased chlorophyll and reduced leaf area and height compared to full sun plants. In the 2× treatment, plants had 11% less chlorophyll than 1× plants with leaf area and height similar to 60% shade plants. At harvest, plants in the 2× treatment were smaller, had increased water and N use efficiency, and an 11% per hectare yield increase compared with the 1× unstressed treatment. Per-plant yields from 60% shade and 2× treatments were 50% less than 1× unstressed treatment. Yield reduction in shaded plants was attributed to light stress. Lower yield in the 2× treatment was attributed to a population-density induced 20% decrease in the red/near-infrared (NIR) ratio, which resulted in downregulation of C4 carbon metabolism enzymes (phosphoenolpyruvate carboxykinase, phosphoenolpyruvate carboxylase, and pyruvate orthophosphate dikinase). Although the net impact of high plant density and shade stress on per-plant yield were similar, the stress compensation mechanisms differed