Evolutionary genomics of LysM genes in land plants

<p>Abstract</p> <p>Background</p> <p>The ubiquitous LysM motif recognizes peptidoglycan, chitooligosaccharides (chitin) and, presumably, other structurally-related oligosaccharides. LysM-containing proteins were first shown to be involved in bacterial cell wall degradation and, more recently, were implicated in perceiving chitin (one of the established pathogen-associated molecular patterns) and lipo-chitin (nodulation factors) in flowering plants. However, the majority of <it>LysM </it>genes in plants remain functionally uncharacterized and the evolutionary history of complex <it>LysM </it>genes remains elusive.</p> <p>Results</p> <p>We show that LysM-containing proteins display a wide range of complex domain architectures. However, only a simple core architecture is conserved across kingdoms. Each individual kingdom appears to have evolved a distinct array of domain architectures. We show that early plant lineages acquired four characteristic architectures and progressively lost several primitive architectures. We report plant <it>LysM </it>phylogenies and associated gene, protein and genomic features, and infer the relative timing of duplications of <it>LYK </it>genes.</p> <p>Conclusion</p> <p>We report a domain architecture catalogue of LysM proteins across all kingdoms. The unique pattern of LysM protein domain architectures indicates the presence of distinctive evolutionary paths in individual kingdoms. We describe a comparative and evolutionary genomics study of <it>LysM </it>genes in plant kingdom. One of the two groups of tandemly arrayed plant <it>LYK </it>genes likely resulted from an ancient genome duplication followed by local genomic rearrangement, while the origin of the other groups of tandemly arrayed <it>LYK </it>genes remains obscure. Given the fact that no animal <it>LysM </it>motif-containing genes have been functionally characterized, this study provides clues to functional characterization of plant <it>LysM </it>genes and is also informative with regard to evolutionary and functional studies of animal <it>LysM </it>genes.</p

Target detection against narrow band noise backgrounds

AbstractWe studied the detectability of narrow band random noise targets embedded in narrow band random noise backgrounds as a function of differences in center frequency, spatial frequency bandwidth and orientation bandwidth between target and the immediately adjacent background. Unlike most target detection experiments the targets were not added to the background; they replaced the underlying background texture. Simulations showed that target detection probabilities could be accounted for by a simple transformation on the summed outputs of a two layer filter model similar to the complex channels model proposed by Graham, Beck and Sutter (Graham, N., Beck, J., & Sutter, A. (1992). Vision Research, 32, 719–743). Subsequently, the model was tested on the detection of camouflaged vehicle targets with encouraging results

Detection of an Optical Counterpart to the ALFALFA Ultra-compact High Velocity Cloud AGC 249525

We report on the detection at $>$98% confidence of an optical counterpart to AGC 249525, an Ultra-Compact High Velocity Cloud (UCHVC) discovered by the ALFALFA blind neutral hydrogen survey. UCHVCs are compact, isolated HI clouds with properties consistent with their being nearby low-mass galaxies, but without identified counterparts in extant optical surveys. Analysis of the resolved stellar sources in deep $g$- and $i$-band imaging from the WIYN pODI camera reveals a clustering of possible Red Giant Branch stars associated with AGC 249525 at a distance of 1.64$\pm$0.45 Mpc. Matching our optical detection with the HI synthesis map of AGC 249525 from Adams et al. (2016) shows that the stellar overdensity is exactly coincident with the highest-density HI contour from that study. Combining our optical photometry and the HI properties of this object yields an absolute magnitude of $-7.1 \leq M_V \leq -4.5$, a stellar mass between $2.2\pm0.6\times10^4 M_{\odot}$ and $3.6\pm1.0\times10^5 M_{\odot}$, and an HI to stellar mass ratio between 9 and 144. This object has stellar properties within the observed range of gas-poor Ultra-Faint Dwarfs in the Local Group, but is gas-dominated.Comment: 9 pages, 4 figures; accepted to ApJ

Quarterly Technical Progress Report for January - March 2003

Application and testing of the new combustion Large Eddy Simulation (LES) code for the design of advanced gaseous combustion systems is described in this 10th quarterly report. CFD Research Corporation has developed the LES module within the parallel, unstructured solver included in the commercial CFD-ACE+ software. In this quarter, validation and testing of the combustion LES code was performed for the DOE-Simval combustor. Also, Beta testing by consortium members was performed for various burner and combustor configurations. In the two quarters ahead, CFDRC will validate the code on the new DOE SimVal experiments. Experimental data from DOE should be available in June 2003, though LES calculations are currently being performed. This will ensure a truly predictive test of the software. CFDRC will also provide help to the consortium members on running their cases, and incorporate improvements to the software suggested by the beta testers. The beta testers will compare their predictions with experimental measurements and other numerical calculations. At the end of this project (October, 2003), a final released version of the software will be available for licensing to the general public

Prehistoric Irrigation in Central Utah: Chronology, Agricultural Economics, and Implications

In 1928, Noel Morss was shown “irrigation ditches” along Pleasant Creek on the Dixie National Forest near Capitol Reef National Park, Utah, by a local guide who contended they were ancient. We relocated the site and mapped the route of an unusual mountain irrigation canal. We conducted excavations and employed OSL and AMS 14C showing historic irrigation, and an earlier event between AD 1460 and 1636. Geomorphic evidence indicates that the canal existed prior to this time, but we cannot date its original construction. The canal is 7.2 km long, originating at 2,450 m asl and terminating at 2,170 m asl. Less than half of the system was hand constructed. We cannot ascribe the prehistoric use-event to an archaeological culture, language, or ethnic group, but the 100+ sites nearby are largely Fremont in cultural affiliation. We also report the results of experimental modeling of the capital and maintenance costs of the system, which holds implications for irrigation north of the Colorado River and farming during the Little Ice Age. The age of the prehistoric canal is consistent with a fragmentary abandonment of farming and continuity between ancient and modern tribes in Utah

Applying Small-Scale DNA Signatures as an Aid in Assembling Soybean Chromosome Sequences

Previous work has established a genomic signature based on relative counts of the 16 possible dinucleotides. Until now, it has been generally accepted that the dinucleotide signature is characteristic of a genome and is relatively homogeneous across a genome. However, we found some local regions of the soybean genome with a signature differing widely from that of the rest of the genome. Those regions were mostly centromeric and pericentromeric, and enriched for repetitive sequences. We found that DNA binding energy also presented large-scale patterns across soybean chromosomes. These two patterns were helpful during assembly and quality control of soybean whole genome shotgun scaffold sequences into chromosome pseudomolecules

Gaze cueing and affective judgments of objects: I like what you look at

When we see another person look somewhere, we automatically attend to the same location in space. This joint attention emerges early in life and has a great impact on social interactions in development and in everyday adult life. The direction of another's gaze indicates what object is of current interest, which may be the target for a subsequent action. In this study, we found that objects that are looked at by other people are liked more than objects that do not receive the attention of other people (Experiment 1). This suggests that observing averted gaze can have an impact on the affective appraisals of objects in the environment. This liking effect was absent when an arrow was used to cue attention (Experiment 2). This underlines the importance of other people's interactions with objects for generating our own impressions of such stimuli in the world

Changes in Twelve Homoeologous Genomic Regions in Soybean following Three Rounds of Polyploidy

With the advent of high-throughput sequencing, the availability of genomic sequence for comparative genomics is increasing exponentially. Numerous completed plant genome sequences enable characterization of patterns of the retention and evolution of genes within gene families due to multiple polyploidy events, gene loss and fractionation, and differential evolutionary pressures over time and across different gene families. In this report, we trace the changes that have occurred in 12 surviving homoeologous genomic regions from three rounds of polyploidy that contributed to the current Glycine max genome: a genome triplication before the origin of the rosids (;130 to 240 million years ago), a genome duplication early in the legumes (;58 million years ago), and a duplication in the Glycine lineage (;13 million years ago). Patterns of gene retention following the genome triplication event generally support predictions of the Gene Balance Hypothesis. Finally, we find that genes in networks with a high level of connectivity are more strongly conserved than those with low connectivity and that the enrichment of these highly connected genes in the 12 highly conserved homoeologous segments may in part explain their retention over more than 100 million years and repeated polyploidy events

DiagHunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization

The DiagHunter and GenoPix2D applications work together to enable genomic comparisons and exploration at both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within or between genomes. DiagHunter works efficiently with diverse, large datasets to predict extended and interrupted synteny blocks and to generate graphical and text output quickly. GenoPix2D allows interactive display of synteny blocks and other genomic features, as well as querying by annotation and by sequence similarity

The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana

BACKGROUND: Most genes in Arabidopsis thaliana are members of gene families. How do the members of gene families arise, and how are gene family copy numbers maintained? Some gene families may evolve primarily through tandem duplication and high rates of birth and death in clusters, and others through infrequent polyploidy or large-scale segmental duplications and subsequent losses. RESULTS: Our approach to understanding the mechanisms of gene family evolution was to construct phylogenies for 50 large gene families in Arabidopsis thaliana, identify large internal segmental duplications in Arabidopsis, map gene duplications onto the segmental duplications, and use this information to identify which nodes in each phylogeny arose due to segmental or tandem duplication. Examples of six gene families exemplifying characteristic modes are described. Distributions of gene family sizes and patterns of duplication by genomic distance are also described in order to characterize patterns of local duplication and copy number for large gene families. Both gene family size and duplication by distance closely follow power-law distributions. CONCLUSIONS: Combining information about genomic segmental duplications, gene family phylogenies, and gene positions provides a method to evaluate contributions of tandem duplication and segmental genome duplication in the generation and maintenance of gene families. These differences appear to correspond meaningfully to differences in functional roles of the members of the gene families