iLIR : a web resource for prediction of Atg8-family interacting proteins

Macroautophagy was initially considered to be a nonselective process for bulk breakdown of cytosolic material. However, recent evidence points toward a selective mode of autophagy mediated by the so-called selective autophagy receptors (SARs). SARs act by recognizing and sorting diverse cargo substrates (e.g., proteins, organelles, pathogens) to the autophagic machinery. Known SARs are characterized by a short linear sequence motif (LIR-, LRS-, or AIM-motif) responsible for the interaction between SARs and proteins of the Atg8 family. Interestingly, many LIR-containing proteins (LIRCPs) are also involved in autophagosome formation and maturation and a few of them in regulating signaling pathways. Despite recent research efforts to experimentally identify LIRCPs, only a few dozen of this class of—often unrelated—proteins have been characterized so far using tedious cell biological, biochemical, and crystallographic approaches. The availability of an ever-increasing number of complete eukaryotic genomes provides a grand challenge for characterizing novel LIRCPs throughout the eukaryotes. Along these lines, we developed iLIR, a freely available web resource, which provides in silico tools for assisting the identification of novel LIRCPs. Given an amino acid sequence as input, iLIR searches for instances of short sequences compliant with a refined sensitive regular expression pattern of the extended LIR motif (xLIR-motif) and retrieves characterized protein domains from the SMART database for the query. Additionally, iLIR scores xLIRs against a custom position-specific scoring matrix (PSSM) and identifies potentially disordered subsequences with protein interaction potential overlapping with detected xLIR-motifs. Here we demonstrate that proteins satisfying these criteria make good LIRCP candidates for further experimental verification. Domain architecture is displayed in an informative graphic, and detailed results are also available in tabular form. We anticipate that iLIR will assist with elucidating the full complement of LIRCPs in eukaryotes

Foraging and nesting behavior of the leaf-cutter bee Megachile rotundata (Fabricius)

The study provides the details of the ethology of Megachile rotundata (Fabricius), and presents preliminary observations on its foraging and nesting behavior. Development from prepupae to adults proceeds most rapidly at 32 degrees C., and is retarded when held at lower and higher temperatures. Male behavior is distinct from that of the female. Mating, including the copulation process arid sleeping, are described. Requirements necessary for nesting are presented. These included: types of nesting places, natural and artificial; size range of tunnels; and the effects of competition on nesting. Females used leaf sections from a variety of plant species in construction of their cells. Description included desirable leaf characteristics, cutting procedures used to remove leaf sections from plants and return of bees to given leaf sources. The construction of the cell cup is detailed as to leaf placement, number of leaves used, cell dimensions, and arrangement of cells under various nesting conditions. After formation of the cell cup it is provisioned with pollen and nectar. Procedures of pollen collection, removal of pollen from the scopa, and the use of nectar for moistening the pollen mass were included as were descriptions of oviposition and cell capping. Upon completion of a cell series, the entrance to the tunnel was sealed, using leaf cuttings. All procedures of cell construction were influenced by the age of the bee and behavioral changes noted toward the end of the flight season. It was found that orientation to the nesting site is largely through visual association with gross characteristics of the area and that markers aided in orientation. Preliminary observations on color discrimination indicated that bees could distinguish between colors. Foraging studies were conducted in the presence and absence of alfalfa and included notes on flower preference and pollen collecting. Flight range studies indicated that bees forage plants closest to their nesting site and increase their range as close bloom is no longer available. Attempts made to relocate bees in new areas met with only limited success. Morning and evening behavior of bees were characterized and climatic conditions responsible for commencement and cessation of flight outlined

Mechanisms of orientation in the leaf-cutter bee Megachile rotundata (Fabricius)

The leaf- cutter bee Megachile rotundata (Fabricius) is an important alfalfa pollinator in western North America. This study was designed to provide information on methods of orientation used by M. rotundata in order to make recommendations regarding the parameters within which adult nesting populations may be relocated. Preliminary studies suggest that this bee species may possess a sun compass although they depend predominantly on landmarks for orientation. Color discrimination experiments with bees conditioned to various colors (i.e., red, orange, yellow, green, blue and purple) showed that they could distinguish all colors except red from 22 shades of gray, black and white, Tests with yellow indicate that it was a much stronger stimulus for homing bees than other colors I) . tested. Bees appeared to be unable to distinguish red from black and therefore are thought to be color blind to red. Figure studies indicated that bees could discriminate between a variety of configurations including squares, circles, triangles, crosses, stars, I's and Y's. In these studies,bees were conditioned to a cross - shaped figure and tested for their ability to discriminate between it and triangles, squares and circles, all of three -inch maximum diameters. The data indicate that bees are quite able to make the distinction. Adult relocation studies indicated that population losses were high (50 per cent or more) when bees were moved from nesting sites possessing many landmarks (e. g., buildings, rows of trees) into alfalfa fields with few prominant landmarks; from field situations providing an abundance of foraging blossoms into fields with little bloom; and when strong winds prevailed. Conditions favoring minimum relocation population losses were moving bees with their original shelters into areas similar in landmark composition to original nesting sites; moving them in progressive steps of 20 -100 yards when relocating populations over short distances; color conditioning bees to shelters painted various colors before short distance moves; moving bees into areas with sufficient bloom to maintain themselves; and conducting moves when strong winds did not exist. General orientation was discussed with respect to flight range, landmark importance, nest entrance location and orientation inside the nest. With the advent of commercial nesting boards containing hundreds of similar nesting tunnels, bees experience major orientation difficulties. Recommendations are outlined in this study regarding methods to ameliorate proximate orientation problems using combinations of figures and colors applied to the surface of nesting boards

Retrieval of Salt Marsh Above-ground Biomass From High-spatial Resolution Hyperspectral Imagery Using PROSAIL

Salt marsh vegetation density varies considerably on short spatial scales, complicating attempts to evaluate plant characteristics using airborne remote sensing approaches. In this study, we used a mast-mounted hyperspectral imaging system to obtain cm-scale imagery of a salt marsh chronosequence on Hog Island, VA, where the morphology and biomass of the dominant plant species, Spartina alterniflora, varies widely. The high-resolution hyperspectral imagery allowed the detailed delineation of variations in above-ground biomass, which we retrieved from the imagery using the PROSAIL radiative transfer model. The retrieved biomass estimates correlated well with contemporaneously collected in situ biomass ground truth data ( R2=0.73 ). In this study, we also rescaled our hyperspectral imagery and retrieved PROSAIL salt marsh biomass to determine the applicability of the method across spatial scales. Histograms of retrieved biomass changed considerably in characteristic marsh regions as the spatial scale of the imagery was progressively degraded. This rescaling revealed a loss of spatial detail and a shift in the mean retrieved biomass. This shift is indicative of the loss of accuracy that may occur when scaling up through a simple averaging approach that does not account for the detail found in the landscape at the natural scale of variation of the salt marsh system. This illustrated the importance of developing methodologies to appropriately scale results from very fine scale resolution up to the more coarse-scale resolutions commonly obtained in airborne and satellite remote sensing

A study of denotative similarity with restricted word associations

Data for this study were collected in two parts. In the first, 70 Ss responded to a list of stimuli in seven tasks of restricted association. The second part of the study employed stimuli consisting of 11 of these original stimuli plus their primary responses in each of the seven tasks. These were given to 50 new Ss under the same seven task instructions. The seven tasks were Superordinates, Coordinates, Similars, Contrasts, Functions, Qualities, and Parts. The main analysis of data was the derivation of matrices of response overlap for the seven semantic relationships corresponding to the restricted-association tasks.Primary interest centered on similarity relationships. High overlap along the diagonal of the response-overlap matrix characterized the Similars. Overlap in five of these diagonal cells was found to discriminate Similars from the other relationships. A measure of the degree of Restricted-Association Similarity (RAS) was derived, based on this discriminating overlap.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/33281/1/0000673.pd

Products as Affective Modifiers of Identities

© The Author(s) 2015. Are salesclerks seen as better, more powerful, or more active when they drive Mustangs? What about entrepreneurs? What about driving a mid-sized car? Intuitively, we have ideas about these, but much of the research on the affective nature of products is on purchasing, desires, and self-fulfillment. Drawing on symbolic interactionism, we argue that people's association with products has some basis in the impression management of their identity. For this to occur, there must be some cultural consensus about the way that products modify identities. Drawing on affect control theory's (ACT) methodology and equations, we measure the goodness, powerfulness, and activeness of several products, identities, and the associated product-modified identities to explore how products function as affective modifiers of identities. We find consistent effects across several types of technology products, whereby products pull the modified identity in the direction of the products' affective qualities. Support is established for the ACT equations that predict how traits modify identities as also having utility for predicting how products modify identities. This suggests that the opening questions can be answered empirically by measuring cultural-specific sentiments of the identity and the product and by developing equations to predict the identity modification process

In Vivo Role of 20-hydroxyecdysone in the Regulation of the Vitellogenin mRNA and Egg Development in the American Dog Tick, Dermacentor variabilis (Say)

Injection of the hormone 20-hydroxyecdysone (20-E) into partially fed (virgin) female adults of the American dog tick, Dermacentor variabilis, while they are attached and feeding on the rabbit host, initiated the expression of the vitellogenin (Vg) gene, and Vg protein secretion and uptake by the ovary. The induction of egg production by 20-E in this bioassay was dose dependent in the range of 1-50 times the concentration normally found in a replete, vitellogenic female. Ticks examined 4d after the 50x treatment were still attached to the host, had numerous enlarged vitellin-filled (brown) oocytes in their ovaries, but had not engorged to repletion. The ovaries reached weights similar to those found in untreated, replete (mated) females (pre-oviposition) while solvent-injected controls demonstrated no increase in oocyte size or increase in ovary weight. An increase in the levels of a putative Vg protein was observed in hemolymph samples collected 1, 2 and 3d post-20-E injection but was not observed in the corresponding solvent controls as determined by native PAGE. Analysis of the ecdysteroid-induced protein by tryptic digestion-mass fingerprinting and BLASTP found that the putative Vg had the strongest match to GP80 (U49934), the partial sequence for the vitellogenin protein from Boophilus microplus. A partial Vg cDNA was cloned and sequenced from replete females of D. variabilis with a high similarity to GP80. Using this message as a probe, Northern blots conducted with RNA collected from partially fed, virgin females 1, 2 and 3d post-20-E injection showed upregulation of the Vg mRNA on all 3 days. Controls injected with solvent only showed no Vg mRNA. Injections with juvenile hormone III did not stimulate Vg expression, oocyte growth or full engorgement. These studies indicate that ecdysteroids and not JH can initiate expression of the Vg gene, Vg protein synthesis and release into hemolymph, and Vg uptake into developing oocytes under bioassay conditions mimicking normal feeding on the host