Psychophysical study of image orientation perception

The experiment reported here investigates the perception of orientation of color photographic images. A collection of 1000 images (mix of professional photos and consumer snapshots) was used in this study. Each image was examined by at least five observers and shown at varying resolutions. At each resolution, observers were asked to indicate the image orientation, the level of confidence, and the cues they used to make the decision. The results show that for typical images, accuracy is close to 98% when using all available semantic cues from high-resolution images, and 84% when using only low-level vision features and coarse semantics from thumbnails. The accuracy by human observers suggests an upper bound for the performance of an automatic system. In addition, the use of a large, carefully chosen image set that spans the 'photo space' (in terms of occasions and subject matter) and extensive interaction with the human observers reveals cues used by humans at various image resolutions: sky and people are the most useful and reliable among a number of important semantic cues.     

DNA sequence heterogeneity in Fim tyrosine-integrase recombinase-binding elements and functional motif asymmetries determine the directionality of the fim genetic switch in Escherichia coli K-12

Phase-variable expression of type 1 fimbriae in Escherichia coli K-12 involves inversion by site-specific recombination of a 314 bp sequence containing the promoter for fim structural gene expression. The invertible sequence is flanked by 9 bp inverted repeats, and each repeat is in turn flanked by non-identical recombinase-binding elements (RBEs) to which the FimB or FimE site-specific recombinases bind. These proteins have distinct DNA inversion preferences: FimB inverts the switch in the ON-to-OFF and OFF-to-ON directions with similar efficiencies, whereas FimE inverts it predominantly in the ON-to-OFF direction. We have found that FimB and FimE invert the switch through a common mechanism. A genetic investigation involving base-by-base substitution combined with a biochemical study shows that the same DNA cleavage and religation sites are used within the 9 bp inverted repeats, and that each recombination involves a common 3 bp spacer region. A comprehensive programme of RBE exchanges and replacements reveals that FimB is much more tolerant of RBE sequence variation than FimE. The asymmetric location of conserved 5'-CA motifs at either side of each spacer region allows the inside and outside of the switch to be differentiated while the RBE sequence heterogeneity permits its ON and OFF forms to be distinguished by the recombinases.     

Focal adhesion kinase protein levels in gut epithelial motility

Mucosal healing requires migration and proliferation. Most studies of focal adhesion kinase (FAK), a protein that regulates motility, proliferation, and apoptosis, have focused on rapid phosphorylation. We reported lower FAK protein levels in motile Caco-2 colon cancer cells and postulated that this reduction in FAK available for activation might impact cell migration and mucosal healing. Therefore, total and active FAK (FAK(397)) immunoreactivity was assessed at the migrating fronts of human Caco-2 and rat IEC-6 intestinal epithelial cells. Caco-2 and IEC-6 motility, quantitated as migration into linear or circular wounds, was examined following FAK protein inhibition by small interfering RNA (siRNA). FAK protein stability and mRNA expression were ascertained by cycloheximide decay, RT-PCR, and in situ hybridization in static and migrating Caco-2 cells. Cells at the migrating front of Caco-2 and IEC-6 monolayers exhibited lower immunostaining for both total and activated FAK than cells immediately behind the front. Western blot analysis also demonstrated diminished FAK protein levels in motile cells by >/=30% in both the differential density seeding and multiple scrape models. siRNA FAK protein inhibition enhanced motility in both the linear scrape (20% in Caco-2) and circular wound (16% in Caco-2 and 19% in IEC-6 cells) models. FAK protein degradation did not differ in motile and static Caco-2 cells and was unaffected by FAK(397) phosphorylation, but FAK mRNA was lower in migrating Caco-2 cells. Thus FAK protein abundance appears regulated at the mRNA level during gut epithelial cell motility and may influence epithelial cell migration coordinately with signals that modify FAK phosphorylation.     

Store-operated calcium entry and non-capacitative calcium entry have distinct roles in thrombin-induced calcium signalling in human platelets

Phosphatidylserine (PS)-exposing platelets accelerate coagulation at sites of vascular injury. PS exposure requires sustained Ca²⁺ signalling. Two distinct Ca²⁺ entry pathways amplify and sustain platelet Ca²⁺ signalling, but their relative importance in human platelets is not known. Here we examined the relative roles of store-operated Ca²⁺ entry (SOCE) and non-capacitative Ca²⁺ entry (NCCE) in thrombin-induced Ca²⁺ signalling and PS exposure by using two Ca²⁺ channel blockers. BTP-2 showed marked selectivity for SOCE over NCCE. LOE-908 specifically blocked NCCE under our conditions. Using these agents we found that SOCE is important at low thrombin concentrations whereas NCCE became increasingly important as thrombin concentration was increased. PS exposure was reduced by LOE-908, and only activated at thrombin concentrations that also activate NCCE. In contrast, BTP-2 had no effect on PS exposure. We suggest that SOCE amplifies and sustains Ca²⁺ signalling in response to low concentrations of thrombin whereas both NCCE and SOCE are important contributors to Ca²⁺ signalling at higher thrombin concentrations. However, despite being involved in Ca²⁺ signalling at high thrombin concentrations, SOCE is not important for thrombin-induced PS exposure in human platelets. This suggests that the route of Ca²⁺ entry is an important regulator of thrombin-induced PS exposure in platelets.     

Molecular modeling and biophysical analysis of the c-MYC NHE-III<Subscript>1</Subscript> silencer element

G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation of oncogenes. In this study, molecular models were created for the c-MYC NHE-III₁ (nuclease hypersensitivity element III₁) from two 39-base complementary sequences. The NHE modeled here consists of single folded conformers of the polypurine intramolecular G-Quadruplex and the polypyrimidine intramolecular i-Motif structures, flanked by short duplex DNA sequences. The G-Quadruplex was based on published NMR structural data for the c-MYC 1:2:1 loop isomer. The i-Motif structure is theoretical (with five cytosine–cytosine pairs), where the central intercalated cytosine core interactions are based on NMR structural data obtained for a tetramolecular [d(A₂C₄)₄] model i-Motif. The loop structures are in silico predictions of the c-MYC i-motif loops. The porphyrin meso-tetra(N-methyl-4-pyridyl)porphine (TMPyP4), as well as the ortho and meta analogs TMPyP2 and TMPyP3, were docked to six different locations in the complete c-MYC NHE. Comparisons are made for drug binding to the NHE and the isolated G-Quadruplex and i-Motif structures. NHE models both with and without bound cationic porphyrin were simulated for 100 ps using molecular dynamics techniques, and the non-bonded interaction energies between the DNA and porphyrins calculated for all of the docking interactions. Figure Molecular models of the average structure of the final 20 ps of the molecular dynamics simulation of the c-MYC NHE-III₁ (nuclease hypersensitivity element III₁) “silencer” element. The G-Quadruplex structure is at the top-center, and the i-Motif is at the bottom-center of each picture. a “Rotation #1” of the G-Quadruplex, with the T15 loop at the top and rear and the G19/A20 loop at the top and front of the picture. b “Rotation #2” of the G-Quadruplex, with the T15 loop at the top and front of the image, and the G19/A20 loop at the front and adjacent to the G-Quadruplex/i-Motif interface     

Quantifying the relative roles of selective and neutral processes in defining eukaryotic microbial communities

We have a limited understanding of the relative contributions of different processes that regulate microbial communities, which are crucial components of both natural and agricultural ecosystems. The contributions of selective and neutral processes in defining community composition are often confounded in field studies because as one moves through space, environments also change. Managed ecosystems provide an excellent opportunity to control for this and evaluate the relative strength of these processes by minimising differences between comparable niches separated at different geographic scales. We use next-generation sequencing to characterize the variance in fungal communities inhabiting adjacent fruit, soil and bark in comparable vineyards across 1000 kms in New Zealand. By compartmentalizing community variation, we reveal that niche explains at least four times more community variance than geographic location. We go beyond merely demonstrating that different communities are found in both different niches and locations by quantifying the forces that define these patterns. Overall, selection unsurprisingly predominantly shapes these microbial communities, but we show the balance of neutral processes also have a significant role in defining community assemblage in eukaryotic microbes.     

Impacts of a simulated heat wave on composition of a marine community

Extreme events, such as heat waves, are predicted to increase in frequency, duration, and severity as a consequence of climate change. However, global change research generally focuses on increases in mean temperatures and fails to address the potential impacts of increasingly severe heat waves. In addition, climate change may interact with another primary threat to biodiversity, non‐native species invasions. We assessed the impacts of a short‐term heat wave on the marine epibenthic fouling community of Bodega Harbor, California, USA, by exposing experimental mesocosms to a simulated heat wave in the laboratory and then monitoring community development in the field. We hypothesized that (1) juveniles would be more susceptible to heat waves than adults, (2) native species would be more susceptible than non‐native species, and (3) non‐native species would recover more quickly than native species. We observed no effect of the heat wave on juvenile species richness, either initially or during the recovery period, relative to communities at ambient seawater temperatures. In contrast, total adult species richness initially declined in response to the heat wave. Adult community composition also changed in heat‐wave treatments, with non‐natives representing the majority of species and occupying more cover than native species. The reduction in native richness associated with the heat wave persisted through the recovery period, whereas invasive richness was actually higher on heat‐wave versus ambient plates at 95 days. Heat waves have the potential to alter the composition of this community because of species‐, taxon‐, and/or origin‐specific responses; for example, non‐native bryozoans displayed greater resistance than native and non‐native tunicates. Recovery from the heat wave occurred via growth of resistant individuals and larval recruitment. Our study highlights the importance of considering species’ and community responses to heat waves, and not just mean predicted temperature increases, to evaluate the consequences of climate change.     

Interaction of glyceraldehyde-3-phosphate dehydrogenase in the light-induced rod alpha-transducin translocation

The light-dependent subcellular translocation of rod alpha-transducin (GNAT-1, or rod Tα) has been well documented. In dark-adapted animals, rod Tα (rTα) is predominantly located in the rod outer segment (ROS) and translocates into the rod inner segment (RIS) upon exposure to the light. Neither the molecular participants nor the mechanism(s) involved in this protein trafficking are known. We hypothesized that other proteins must interact with rTα to affect the translocations. Using the MBP-rTα fusion pulldown assay, the yeast two-hybrid assay and the co-immunoprecipitation assay, we identified glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and rTα as interacting proteins. Immunoprecipitation also showed β-actin associates with rTα in the dark but not in the light. To further investigate the involvement of GAPDH in light-induced rod Tα translocation, GAPDH mRNA was knocked down in vivo by transient expression of siRNAs in rat photoreceptor cells. Under completely dark- and light-adapted conditions, the translocation of rTα was not significantly different within the 'GAPDH knock-down photoreceptor cells' compared to the non-transfected control cells. However, under partial dark-adaptation, rTα translocated more slowly in the 'GAPDH knock-down cells' supporting the conclusion that GAPDH is involved in rTα translocation from the RIS to the ROS during dark adaptation.     

Cancer-prone mice expressing the Ki-rasG12C gene show increased lung carcinogenesis after CT screening exposures

A >20-fold increase in X-ray computed tomography (CT) use during the last 30 years has caused considerable concern because of the potential carcinogenic risk from these CT exposures. Estimating the carcinogenic risk from high-energy, single high-dose exposures obtained from atomic bomb survivors and extrapolating these data to multiple low-energy, low-dose CT exposures using the Linear No-Threshold (LNT) model may not give an accurate assessment of actual cancer risk. Recently, the National Lung Cancer Screening Trial (NLST) reported that annual CT scans of current and former heavy smokers reduced lung cancer mortality by 20%, highlighting the need to better define the carcinogenic risk associated with these annual CT screening exposures. In this study, we used the bitransgenic CCSP-rtTA/Ki-ras mouse model that conditionally expresses the human mutant Ki-ras(G12C) gene in a doxycycline-inducible and lung-specific manner to measure the carcinogenic risk of exposure to multiple whole-body CT doses that approximate the annual NLST screening protocol. Irradiated mice expressing the Ki-ras(G12C) gene in their lungs had a significant (P = 0.01) 43% increase in the number of tumors/mouse (24.1 ± 1.9) compared to unirradiated mice (16.8 ± 1.3). Irradiated females had significantly (P < 0.005) more excess tumors than irradiated males. No tumor size difference or dose response was observed over the total dose range of 80-160 mGy for either sex. Irradiated bitransgenic mice that did not express the Ki-ras(G12C) gene had a low tumor incidence (≤ 0.1/mouse) that was not affected by exposure to CT radiation. These results suggest that (i) estimating the carcinogenic risk of multiple CT exposures from high-dose carcinogenesis data using the LNT model may be inappropriate for current and former smokers and (ii) any increased carcinogenic risk after exposure to fractionated low-dose CT-radiation may be restricted to only those individuals expressing cancer susceptibility genes in their tissues at the time of exposure.     

Elevated Corticosterone Levels and Changes in Amphibian Behavior Are Associated with Batrachochytrium dendrobatidis (Bd) Infection and Bd Lineage

Few studies have examined the role hormones play in mediating clinical changes associated with infection by the parasite Batrachochytrium dendrobatidis (Bd). Glucocorticoid (GC) hormones such as corticosteroids (CORT) regulate homeostasis and likely play a key role in response to infection in amphibians. We explore the relationship between CORT release rates and Bd infection in tadpoles of the common midwife toad, Alytes obstetricians, using a non-invasive water-borne hormone collection method across seven populations. We further examined whether tadpoles of A. muletensis infected with a hypervirulent lineage of Bd, BdGPL, had greater CORT release rates than those infected with a hypovirulent lineage, BdCAPE. Finally, we examined the relationship between righting reflex and CORT release rates in infected metamorphic toads of A. obstetricans. We found an interaction between elevation and Bd infection status confirming that altitude is associated with the overall severity of infection. In tandem, increasing elevation was associated with increasing CORT release rates. Tadpoles infected with the hypervirulent BdGPL had significantly higher CORT release rates than tadpoles infected with BdCAPE showing that more aggressive infections lead to increased CORT release rates. Infected metamorphs with higher CORT levels had an impaired righting reflex, our defined experimental endpoint. These results provide evidence that CORT is associated with an amphibian’s vulnerability to Bd infection, and that CORT is also affected by the aggressiveness of infection by Bd. Together these results indicate that CORT is a viable biomarker of amphibian stress.