Identification, characterization, and gene expression analysis of nucleotide binding site (NB)-type resistance gene homologues in switchgrass

Abstract Background Switchgrass (Panicum virgatum L.) is a warm-season perennial grass that can be used as a second generation bioenergy crop. However, foliar fungal pathogens, like switchgrass rust, have the potential to significantly reduce switchgrass biomass yield. Despite its importance as a prominent bioenergy crop, a genome-wide comprehensive analysis of NB-LRR disease resistance genes has yet to be performed in switchgrass. Results In this study, we used a homology-based computational approach to identify 1011 potential NB-LRR resistance gene homologs (RGHs) in the switchgrass genome (v 1.1). In addition, we identified 40 RGHs that potentially contain unique domains including major sperm protein domain, jacalin-like binding domain, calmodulin-like binding, and thioredoxin. RNA-sequencing analysis of leaf tissue from ‘Alamo’, a rust-resistant switchgrass cultivar, and ‘Dacotah’, a rust-susceptible switchgrass cultivar, identified 2634 high quality variants in the RGHs between the two cultivars. RNA-sequencing data from field-grown cultivar ‘Summer’ plants indicated that the expression of some of these RGHs was developmentally regulated. Conclusions Our results provide useful insight into the molecular structure, distribution, and expression patterns of members of the NB-LRR gene family in switchgrass. These results also provide a foundation for future work aimed at elucidating the molecular mechanisms underlying disease resistance in this important bioenergy crop

Feedback Tracking and Correlation Spectroscopy of Fluorescent Nanoparticles and Biomolecules

The best way to study dynamic fluctuations in single molecules or nanoparticles is to look at only one particle at a time, and to look for as long as possible. Brownian motion makes this difficult, as molecules move along random trajectories that carry them out of any fixed field of view. We developed an instrument that tracks the Brownian motion of single fluorescent molecules in three dimensions and in real-time while measuring fluorescence with nanosecond time resolution and single-photon sensitivity. The apparatus increases observation times by approximately three orders of magnitude while improving data-collecting efficiency by locking tracked objects to a high-intensity region of the excitation laser. As a first application of our technique, we tracked and studied the fluorescence statistics of semiconductor quantum dots. Our measurements were well resolved at 10ns correlation times, allowing measurement of photon anti-bunching on single particles in solution for the first time. We observed variations of (34 ± 16)% in the fluorescence lifetimes and (23 ± 18)% in the absorption cross-sections within an aqueous quantum dot sample, confirming that these variations are real, not artifacts of the immobilization methods previously used to study them. Additionally, we studied quantum dot fluorescence intermittency and its dependence on 2-mercaptoethanol, finding evidence that the chemical suppresses blinking on short time-scales (&#60;1s) by reducing the lifetime of the dark state. Finally, we studied the translational and intramolecular Brownian motion of λ-phage DNA molecules. Our apparatus decouples these motions almost completely, and yielded a translational diffusion coefficient estimate D=(0.71 ± 0.05)μm²/s lying between previous measurements for this molecule under identical solution conditions but with less precise techniques. Our measurements show clear evidence of intramolecular motion of the polymer chain in the form of statistical correlations on time-scales up to 1s, but we have not yet been able to determine the influence of solvent interactions on these dynamics.</p

Bush versus Kerry: A Functional Analysis of Campaign 2004

Bush versus Kerry analyzes the 2004 presidential campaign using the functional theory of political campaign communication. After an introduction and explication of political campaign communication theory, chapters investigate the content of candidate messages - for example, television spots, debates, webpages, and acceptance addresses - and media coverage of the campaign.https://epublications.marquette.edu/marq_fac-book/1004/thumbnail.jp

The Comma Sign: The Coracohumeral Ligament and Superior Glenohumeral Ligament Exhibit Similar Quantitative Characteristics With Terminal Confluence at the Subscapularis Insertion.

PURPOSE: The purpose of this morphologic cadaveric study was to quantitatively define the composition of the previously described comma tissue along with its relation to the subscapularis tendon insertion. METHODS: Fresh frozen cadaveric shoulder specimens were included for analysis. The coracohumeral ligament (CHL) was exposed at its origin along the base of the coracoid process and freed laterally along its course to the lesser tuberosity adjacent to the bicipital groove. The superior glenohumeral ligament (SGHL) was identified and traced along its course deep to the CHL within the rotator interval with insertion onto the superior aspect of the lesser tuberosity. The midpoint diameters of the SGHL and CHL and their composite insertional diameters on the subscapularis tendon insertion and lesser tuberosity were measured with digital calipers. The mean diameter was determined from 3 measurements taken of each ligament. RESULTS: Eight specimens were included. With the use of digital calipers, the mean midpoint diameters of the SGHL and CHL were identified as 5.99 mm (range, 5.25-6.91 mm) and 5.13 mm (range, 4.28-5.72 mm), respectively. The composite insertional diameter of the SGHL and CHL on both the lesser tuberosity and humeral insertion of the subscapularis tendon was 9.93 mm (range, 6.69-12.05 mm). At its insertion, the SGHL and CHL comprised 54% and 46% of the comma tissue, respectively. Additionally, all specimens were identified as showing a confluence of the SGHL and CHL composite insertion with the subscapularis tendon at the point of its humeral head insertion. CONCLUSIONS: The comma tissue is a pivotal structure for the identification, mobilization, and repair of retracted subscapularis tendon tears. Therefore, quantitative knowledge of the midpoint diameter, insertional diameter, and composite distribution of the CHL and SGHL provided by this morphologic cadaveric analysis may aid surgeons in their efforts to restore the native anatomy. CLINICAL RELEVANCE: Subscapularis tendon tears have often been under-addressed during rotator cuff repair. The comma tissue has been described as an anatomic structure that can aid in the identification, mobilization, and repair of retracted subscapularis tendon tears. Therefore, quantitative knowledge of this important arthroscopic landmark may aid surgeons in their efforts to restore the native anatomy

Identifying potential sources of variability between vegetation carbon storage estimates for urban areas

understudied ecosystems. Research into urban ecosystem service provision is still an emerging field, yet evidence is accumulating rapidly to suggest that the biological carbon stores in cities are more substantial than previously assumed. However, as more vegetation carbon densities are derived, substantial variability between these estimates is becoming apparent. Here, we review procedural differences evident in the literature, which may be drivers of variation in carbon storage assessments. Additionally, we quantify the impact that some of these different approaches may have when extrapolating carbon figures derived from surveys up to a city-wide scale. To understand how/why carbon stocks vary within and between cities, researchers need to use more uniform methods to estimate stores and relate this quantitatively to standardised ‘urbanisation’ metrics, in order to facilitate comparisons

Improved maize reference genome with single-molecule technologies

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes