“Phase capture” in amblyopia: The influence function for sampled shape

AbstractThis study was concerned with what stimulus information humans with amblyopia use to judge the shape of simple objects. We used a string of four Gabor patches to define a contour. A fifth, center patch served as the test pattern. The observers’ task was to judge the location of the test pattern relative to the contour. The contour was either a straight line, or an arc with positive or negative curvature. We asked whether phase shifts in the inner or outer pairs of patches distributed along the contour influence the perceived shape. That is, we measured the phase shift influence function. Our results, consistent with previous studies, show that amblyopes are imprecise in shape discrimination, showing elevated thresholds for both lines and curves. We found that amblyopes often make much larger perceptual errors (biases) than do normal observers in the absence of phase shifts. These errors tend to be largest for curved shapes and at large separations. In normal observers, shifting the phase of inner patches of the string by 0.25 cycle results in almost complete phase capture (attraction) at the smallest separation (2λ), and the capture effect falls off rapidly with separation. A 0.25 cycle shift of the outer pair of patches has a much smaller effect, in the opposite direction (repulsion). While several amblyopic observers showed reduced capture by the phase of the inner patches, to our surprise, several of the amblyopes were sensitive to the phase of the outer patches. We used linear multiple regression to determine the weights of all cues to the task: the carrier phase of the inner patches, carrier phase of the outer patches and the envelope of the outer patches. Compared to normal observers, some amblyopes show a weaker influence of the phase of the inner patches, and a stronger influence of both the phase and envelope of the outer patches. We speculate that this may be a consequence of abnormal “crowding” of the inner patches by the outer ones

Oligosaccharyltransferase is highly specific for the hydroxy amino acid in Asn-Xaa-Thr/Ser

AbstractPig liver oligosaccharyltransferase (OST), which is involved in the en bloc transfer of the Dol-PP-linked GlcNAc2-Man9-Glc3 precursor on to asparagine residues in the Asn-Xaa-Thr/Ser sequence, is highly stereospecific for the conformation of the 3-carbon atom in the hydroxy amino acid. Moreover, substitution of the hydroxy group by either SH as in cysteine, or NH2 as in β,γ-diamino-butanoic acid as reported previously [Bause, E. et al., Biochem. J. 312 (1995) 979–985], followed by the determination of the pH optimum for enzymatic activity, indicates that neither a negative nor a positive charge in the hydroxy amino acid position is tolerated by the enzyme. Binding of the threonine β-methyl group by OST is also specific, with serine, L-threo-β-hydroxynorvaline and L-β-hydroxynorleucine containing tripeptides all bound much less efficiently than the threonine peptide itself. The data are interpreted in terms of a highly stereospecific hydrophobic binding pocket for the threonine CH3-CH(OH) group

EC03-101 Nebraska Seed Guide, 2004

This circular is a progress report of corn hybrid performance tests conducted by the Agronomy/Horticulture Department and the Northeast, South Central, West Central and Panhandle Research and Extension Centers of Nebraska and University of Wyoming at Torrington. Conduct of experiments and publication of results is a joint effort of the Agricultural Research Division and the Cooperative Extension Service

Simplicity of eigenvalues in Anderson-type models

We show almost sure simplicity of eigenvalues for several models of Anderson-type random Schr\"odinger operators, extending methods introduced by Simon for the discrete Anderson model. These methods work throughout the spectrum and are not restricted to the localization regime. We establish general criteria for the simplicity of eigenvalues which can be interpreted as separately excluding the absence of local and global symmetries, respectively. The criteria are applied to Anderson models with matrix-valued potential as well as with single-site potentials supported on a finite box.Comment: 20 page

EC03-101 Nebraska Seed Guide, 2004

This circular is a progress report of corn hybrid performance tests conducted by the Agronomy/Horticulture Department and the Northeast, South Central, West Central and Panhandle Research and Extension Centers of Nebraska and University of Wyoming at Torrington. Conduct of experiments and publication of results is a joint effort of the Agricultural Research Division and the Cooperative Extension Service

Digital image processing to detect subtle motion in stony coral

Coral reef ecosystems support significant biological activities and harbor huge diversity, but they are facing a severe crisis driven by anthropogenic activities and climate change. An important behavioral trait of the coral holobiont is coral motion, which may play an essential role in feeding, competition, reproduction, and thus survival and fitness. Therefore, characterizing coral behavior through motion analysis will aid our understanding of basic biological and physical coral functions. However, tissue motion in the stony scleractinian corals that contribute most to coral reef construction are subtle and may be imperceptible to both the human eye and commonly used imaging techniques. Here we propose and apply a systematic approach to quantify and visualize subtle coral motion across a series of light and dark cycles in the scleractinian coral Montipora capricornis. We use digital image correlation and optical flow techniques to quantify and characterize minute coral motions under different light conditions. In addition, as a visualization tool, motion magnification algorithm magnifies coral motions in different frequencies, which explicitly displays the distinctive dynamic modes of coral movement. Specifically, our assessment of displacement, strain, optical flow, and mode shape quantify coral motion under different light conditions, and they all show that M. capricornis exhibits more active motions at night compared to day. Our approach provides an unprecedented insight into micro-scale coral movement and behavior through macro-scale digital imaging, thus offering a useful empirical toolset for the coral research community

NF539 Yield Suppressions of Glyphosate-Resistant (Roundup Ready) Soybeans

Research description and results of testing for effect of glyphosate herbicide application and the effect of the glyphosate-resistant gene in soybean production. Glyphosate is a popular postemergence herbicide. Glyphosate-resistant soybean technology is gaining acceptance in Nebraska and in U.S. cropping systems; however, potential yield suppression from either genetic differences among varieties, the glyphosate-resistant gene/gene insertion process, or glyphosate is a concern. The first of these could contribute to a yield lag; the latter two could contribute to a yield drag. Research Goals We designed experiments to test for both elements of yield drag: the effect of glyphosate herbicide application and the effect of the glyphosate-resistant gene. Since we could not distinguish between yield drag associated with the glyphosate-resistant gene or effects of its insertion, reference to this gene in the following could mean either or both of these possibilities. Two experiments were conducted at each of four Nebraska locations for two years with the intent to: 1) investigate the glyphosate herbicide effect on 12-13 varieties; and 2) look at the effect of the glyphosate-resistant (glyphosate-resistant) gene on five pairs of glyphosate- resistant, nonglyphosate-resistant sister cultivars (eight other cultivars were included as checks). Summary: Yield suppressions were observed. Yield drag from glyphosate application was not observed. Yield drag from glyphosate-resistant gene = 5 percent. Yield lag from variety genetic differences =

EC94-872-S Nebraska Crop Budgets

Resource Persons • Crops Budgeting Procedure • Prices Used for 1994 Panhandle • Gravity Irrigated Crops • Sugar Beets • Dry Edible Beans • Corn for Grain • Corn for Silage • Establish Alfatfa with Oats • Alfalfa Hay Gravity Irrigated • Center Pivot Irrigated Crops • Sugar Beets • Dry Edible Beans • Corn for Grain • Winter Wheat • Alfalfa Hay • Non-Irrigated Crops • Winter Wheat Stubble Much Fallow • Winter Wheat, Eco-Fallow (Chemical and Tillage Combination) • Sunflower, Wheat-Sunflower-Fallow Rotation • Millet, Wheat, Fallow, Millet, Fallow Southwest • Corn for Grain, Gravity Irrigated • Corn for Silage, Gravity Irrigated • Corn for Grain, Ditch Irrigated, Platte Valley • Corn for Grain, Ridge Planted, Gravity Irrigated • Corn for Grain, Center Pivot Irrigated, Fine Texture Soil • Corn for Grain, Center Pivot Irrigated, Sandy Soil • Pinto Beans, Center Pivot Irrigated • Soybeans, Center Pivot Irrigated • Fall Seed Alfalfa, Center Pivot Irrigated • Alfalfa Hay, Center Pivot Irrigated • Alfalfa Hay, Sub-Irrigated, Platte Valley • Fall Seed Grass, Center Pivot Irrigated • Pasture, Center Pivot Irrigated • Wheat, Center Pivot Irrigated • Wheat, Stubble Mulch Fallow • Wheat, Clean Till Fallow • Wheat, Continuous, Chemical Weed Control • Wheat, Followed by Corn, 3 Year Rotation, Eco-Fallow • Corn, Following Eco-Fallow Wheat • Grain Sorghum, Non-Irrigated • Grain Sorghum, Non-Irrigated, No-TUI Continuous • Cane Hay, Non-Irrigated North • Corn for Grain, Center Pivot Irrigated • Corn for Silage, Center Pivot Irrigated • Establish Alfalfa, Center Pivot Irrigated • Alfalfa Hay, Center Pivot Irrigated • Establish Grass, Center Pivot Irrigated • Pasture, Center Pivot Irrigated • Native Hay, Wet Meadow • Native Hay, Upland Central • Corn for Grain Center Pivot Irrigated • Corn for Silage Center Pivot Irrigated • Grain Sorghum for Grain, Limited Irrigation, Center Pivot • Corn for Grain, Gravity Irrigated • Corn for Silage Gravity Irrigated • Soybeans, Gravity Irrigated , • Establish Alfalfa, Gravity Irrigated • Alfalfa for Hay, Gravity Irrigated • Corn for Grain, Non-Irrigated • Corn for Grain, Eco-Fallow, Follows Wheat in 3 Year Rotation • Corn for Silage, Non-Irrigated • Grain Sorghum for Grain, Non-Irrigated • Grain Sorghum for Grain, Eco-Fallow, Follows Wheat in 3 Year Rotation • Grain Sorghum for Grain, Continuous, No Till, Non-Irrigated • Soybeans, Non-Irrigated • Wheat for Grain, Continuous Cropped, Non-Irrigated • Wheat for Grain, Continuous, No Till, Non-Irrigated • Wheat for Grain, Fallow Every Third Year • Establish Alfalfa, Non-Irrigated • Alfalfa for Hay, Non-Irrigated • Establish and Maintain Cover Crop on Set Aside Acres Northeast • Corn for Grain, Center Pivot Irrigated, Sandy Soils • Corn for Grain, Center Pivot Irrigated, Rolling Hills • Corn for Grain, Till-Plant, Rolling Hills • Soybeans, Non-Irrigated • Soybeans, Center Pivot Irrigated • Oats, Non-Irrigated 8 • Oats With Spring Alfalfa Seeding • Alfalfa Seeding • Establish Alfalfa, Sandy Soil, Fall Seeding • Alfalfa Hay, Large Round Baler • Alfalfa Hay Small Square Baler • East Central • Corn for Grain, Center Pivot Irrigated • Soybeans, Center Pivot Irrigated • Corn tor Grain, Non-Irrigated • No-Till Com in Soybean Residue • Grain Sorghum, Non-Irrigated • Soybeans, Non-Irrigated • Soybeans, After Corn Reduced Till • Wheat • Establish Alfalfa, Fall Seeded • Establish Alfalfa, Spring With Herbicide • Alfalfa Hay, Large Round Baler • Alfalfa Hay, Field Stacker • Oats, Non-Irrigated Southeast • Corn for Grain, Center Pivot Irrigated • Corn for Silage, Center Pivot Irrigated • Corn for Grain, Non-Irrigated • Grain Sorghum, Non-Irrigated • Forage Sorghum Silage, Non-Irrigated • Soybeans, Non-Irrigated • Wheat • Alfalfa Hay, Large Round Bale

Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome

With the ease of gene sequencing and the technology available to study and manipulate non-model organisms, the extension of the methodological toolbox required to translate our understanding of model organisms to non-model organisms has become an urgent problem. For example, mining of large coral and their symbiont sequence data is a challenge, but also provides an opportunity for understanding functionality and evolution of these and other non-model organisms. Much more information than for any other eukaryotic species is available for humans, especially related to signal transduction and diseases. However, the coral cnidarian host and human have diverged over 700 million years ago and homologies between proteins in the two species are therefore often in the gray zone, or at least often undetectable with traditional BLAST searches. We introduce a two-stage approach to identifying putative coral homologues of human proteins. First, through remote homology detection using Hidden Markov Models, we identify candidate human homologues in the cnidarian genome. However, for many proteins, the human genome alone contains multiple family members with similar or even more divergence in sequence. In the second stage, therefore, we filter the remote homology results based on the functional and structural plausibility of each coral candidate, shortlisting the coral proteins likely to have conserved some of the functions of the human proteins. We demonstrate our approach with a pipeline for mapping membrane receptors in humans to membrane receptors in corals, with specific focus on the stony coral, P. damicornis. More than 1000 human membrane receptors mapped to 335 coral receptors, including 151 G protein coupled receptors (GPCRs). To validate specific sub-families, we chose opsin proteins, representative GPCRs that confer light sensitivity, and Toll-like receptors, representative non-GPCRs, which function in the immune response, and their ability to communicate with microorganisms. Through detailed structure-function analysis of their ligand-binding pockets and downstream signaling cascades, we selected those candidate remote homologues likely to carry out related functions in the corals. This pipeline may prove generally useful for other non-model organisms, such as to support the growing field of synthetic biology

Applying model approaches in non-model systems: A review and case study on coral cell culture

Model systems approaches search for commonality in patterns underlying biological diversity and complexity led by common evolutionary paths. The success of the approach does not rest on the species chosen but on the scalability of the model and methods used to develop the model and engage research. Fine-tuning approaches to improve coral cell cultures will provide a robust platform for studying symbiosis breakdown, the calcification mechanism and its disruption, protein interactions, micronutrient transport/exchange, and the toxicity of nanoparticles, among other key biological aspects, with the added advantage of minimizing the ethical conundrum of repeated testing on ecologically threatened organisms. The work presented here aimed to lay the foundation towards development of effective methods to sort and culture reef-building coral cells with the ultimate goal of obtaining immortal cell lines for the study of bleaching, disease and toxicity at the cellular and polyp levels. To achieve this objective, the team conducted a thorough review and tested the available methods (i.e. cell dissociation, isolation, sorting, attachment and proliferation). The most effective and reproducible techniques were combined to consolidate culture methods and generate uncontaminated coral cell cultures for ~7 days (10 days maximum). The tests were conducted on scleractinian corals Pocillopora acuta of the same genotype to harmonize results and reduce variation linked to genetic diversity. The development of cell separation and identification methods in conjunction with further investigations into coral cell-type specific metabolic requirements will allow us to tailor growth media for optimized monocultures as a tool for studying essential reef-building coral traits such as symbiosis, wound healing and calcification at multiple scales