Improved recognition of figures containing fluorescence microscope images in online journal articles using graphical models

MOTIVATION: There is extensive interest in automating the collection, organization and analysis of biological data. Data in the form of images in online literature present special challenges for such efforts. The first steps in understanding the contents of a figure are decomposing it into panels and determining the type of each panel. In biological literature, panel types include many kinds of images collected by different techniques, such as photographs of gels or images from microscopes. We have previously described the SLIF system (http://slif.cbi.cmu.edu) that identifies panels containing fluorescence microscope images among figures in online journal articles as a prelude to further analysis of the subcellular patterns in such images. This system contains a pretrained classifier that uses image features to assign a type (class) to each separate panel. However, the types of panels in a figure are often correlated, so that we can consider the class of a panel to be dependent not only on its own features but also on the types of the other panels in a figure. RESULTS: In this article, we introduce the use of a type of probabilistic graphical model, a factor graph, to represent the structured information about the images in a figure, and permit more robust and accurate inference about their types. We obtain significant improvement over results for considering panels separately. AVAILABILITY: The code and data used for the experiments described here are available from http://murphylab.web.cmu.edu/software.     

Incorporating biological structure into machine learning models in biomedicine

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Schematic showing the main categories of models incorporating structured biological data covered in this review. The first panel shows an example of a model operating on sequence data, the second panel shows a model in which dimension reduction is influenced by the connections in a gene network, and the third panel shows a neural network with structure constrained by a phylogeny or ontology. The ‘x’ values in the data tables represent gene expression measurements.     

Holliday Junction Resolvases

Four-way DNA intermediates, called Holliday junctions (HJs), can form during meiotic and mitotic recombination, and their removal is crucial for chromosome segregation. A group of ubiquitous and highly specialized structure-selective endonucleases catalyze the cleavage of HJs into two disconnected DNA duplexes in a reaction called HJ resolution. These enzymes, called HJ resolvases, have been identified in bacteria and their bacteriophages, archaea, and eukaryotes. In this review, we discuss fundamental aspects of the HJ structure and their interaction with junction-resolving enzymes. This is followed by a brief discussion of the eubacterial RuvABC enzymes, which provide the paradigm for HJ resolvases in other organisms. Finally, we review the biochemical and structural properties of some well-characterized resolvases from archaea, bacteriophage, and eukaryotes.Homologous recombination (HR) is an essential process that promotes genetic diversity during meiosis (see Lam and Keeney 2014; Zickler and Kleckner 2014). However, in somatic cells, HR plays a key role in conserving genetic information by facilitating DNA repair, thereby ensuring faithful genome duplication and limiting the divergence of repetitive DNA sequences (see Mehta and Haber 2014). As shown in Figure 1, HR is initiated by a DNA double-strand break, the ends of which are resected to produce single-stranded (ss) 3′-overhangs (see Symington 2014). Homologous strand invasion by one of the 3′ overhangs (e.g., one catalyzed by Escherichia coli RecA or human RAD51) leads to the formation of a displacement loop (D-loop) (see Morrical 2014). The invading 3′ end of the D-loop can then be extended by a DNA polymerase, which uses the homologous strand as a template for DNA synthesis. Recombination then proceeds in one of several different ways, some of which involve second-end capture, such that the other resected 3′ end anneals to the displaced strand of the D-loop (Szostak et al. 1983). In the resulting recombination intermediate, the two interacting DNAs are linked by nicked Holliday junctions (HJs). Additional DNA synthesis and nick ligation lead to the formation of a double Holliday junction (dHJ) intermediate. In eukaryotes, dHJs are removed primarily by “dissolution” (Fig. 1, bottom left) (see Bizard and Hickson 2014). This pathway involves the combined activities of a DNA helicase and a type IA topoisomerase, which catalyze branch migration and decatenation of the dHJ into noncrossover products (Manthei and Keck 2014). In somatic cells, this is essential for the avoidance of sister-chromatid exchanges (SCEs) and loss of heterozygosity. Alternatively, dHJs can be processed by “resolution” in reactions mediated by canonical or noncanonical mechanisms of endonuclease-mediated cleavage into either crossover or noncrossover products (Fig. 1, bottom middle and right).Open in a separate windowFigure 1.Pathways for the formation and processing of Holliday junctions. Resected DNA double-strand breaks invade homologous duplex DNA to create a joint molecule, or displacement-loop structure. The invading 3′ end then serves as a primer for DNA synthesis, leading to second end capture and the formation of a double Holliday junction. In eukaryotes, these structures are removed by “dissolution” (bottom left panel) or “resolution” (bottom middle and right panels). Canonical Holliday junction resolvases introduce a pair of symmetrical and coordinated nicks across one of the helical axes (bottom middle panel) to generate nicked DNA duplexes that can be directly ligated. Alternatively, noncanonical resolvases cleave Holliday junctions with asymmetric nicks to produce gapped and flapped DNA duplexes that require further processing prior to ligation (bottom right panel). *Mitochondrial Holliday junction resolvase.     

The hSSB1 orthologue Obfc2b is essential for skeletogenesis but dispensable for the DNA damage response in vivo

We recently became aware of panel duplications in Supplementary Figures S6 and S7, due to pasting errors of similar flow cytometry images during figure preparation. This concerned the first two panels in the top row of Suppl. Fig S6A; second and third panel in the bottom row of Suppl. Fig S7B; and third and fourth panel in the bottom row of Suppl. Fig S7C.Furthermore, we noted a typographical error in Suppl. Fig S7B (top row, sixth plot), where the indicated percentage was wrongly given as 1.4%, instead of 1.1%. These errors did not change the results or the interpretation of the data. We deeply apologize to the scientific community for any confusion these errors may have caused. The updated appendix is published with this corrigendum.The original FlowJo analysis plots related to the affected figures are published as source data with this corrigendum. Please note that initial labelling of the experiments in these files referred to the official gene name Obfc2b informally as hSSB1, and Obfc2a‐shRNAs as ‘sh1’ and sh4’.Open in a separate windowFigure S6AOriginalOpen in a separate windowFigure S6ACorrectedOpen in a separate windowFigure S7BOriginalOpen in a separate windowFigure S7BCorrectedOpen in a separate windowFigure S7COriginalOpen in a separate windowFigure S7CCorrected     

Multivessel myocardial infarction

A 56-year-old female patient with hypertension, obesity and chronic intermittent cauda equina compression suffered an acute myocardial infarction five days after a lumbar hernia operation. The electrocardiogram (ECG) showed ST-segment elevation in multiple leads, consistent with an extensive acute apical and lateral myocardial infarction (figure 1, panel A). Acute coronary angiography revealed occlusion of the end-arteries of the left coronary artery in the absence of significant atherosclerotic disease (figure 1, panel B).     

Settlement Dynamics of the Encrusting Epibenthic Macrofauna in Two Creeks of the Caeté Mangrove Estuary (North Brazil)

The epibenthic encrusting fauna of 2 creeks of the Caeté mangrove estuary, northern Brazil, was studied over a 13 month period using collectors fixed at 2.5 and 3.5 m above the creek bottom and in which upper and lower sides of ceramic and wooden panels were used as settlement substrates. The number of individuals of the most abundant organisms (barnacles, oysters and mussels) settling per panel was determined each month, for each substrate type, panel orientation and height above creek bottom. The barnacle, Fistulobalanus citerosum has a peak settlement period during the wet season whereas both peaks in the numbers of settlers of the oyster Crassostrea rhizophorae were recorded during the dry season and such discrete temporal patterns in settlement have also been observed for barnacles and oysters in other mangroves and estuaries. In contrast to other studies, settlement of the mussel Mytella falcata was generally low during the study period and may be related to over-exploitation of stocks in the region. Overall, settler density was usually greater on the underside of ceramic panels close to the creek bottom, similar to results of other studies of epibenthic settlement in diverse habitats.     

Cover Picture

Confocal images of myoblasts containing a normal or a mutated desmin network. Desmin is stained in green, actin in red and nuclei in blue. The presence of the mutation (bottom panel) is responsible for the collapse of the desmin network into aggregates.     

Correction to: Intrathecal Epigallocatechin Gallate Treatment Improves Functional Recovery After Spinal Cord Injury by Upregulating the Expression of BDNF and GDNF

Neurochemical Research - Since the publication of our article [1] it has come to our attention that there was an error in Figure 4 in which the bottom left immunochemistry panel Control/Bax was a...     

ERRATA

page 13, legend to figure 14 : insert c, before two page 137, paragraph on Ampulla : for pulieum read pulicum page 145, line 6 from bottom : for versicolor (Gmelin) readversicolor Gmelin      

Cover Picture

The cover figure illustrates schematically the molecular linkages of cytoskeletal filaments to epithelial cell‐cell junctions. Microtubules are shown on the left, with schematic motors/cargoes, and connection to the zonula adhaerens and desmosomes. Actin filaments (top) and intermediate filaments (bottom) are shown on the right, with their connections to tight junctions, zonula adhaerens and desmosomes, respectively. See review by Sluysmans et al for identification of molecules.     

New Specificity of Australia Antigen

THE immunodiffusion laboratory at the Institute for Cancer Research frequently acts as a reference laboratory to test anti-Australia antigen sera for our colleagues in many parts of the world. Because Australia antigen is known to possess different antigenic specificities^1–4, a panel was established which consisted of Australia antigen specimens selected from hepatitis and Down's syndrome patients and from clinically normal residents of the Lau area in Malaita, British Solomon Islands. Sera from normal blood donors without Australia antigen were included as negative controls. All antisera received after August 1971 were tested against this panel to detect heterogeneity among both the antibodies tested and the antigens included in the panel. Immunodiffusion was performed in a seven-hole Ouchterlony pattern with the antiserum in the centre well and a positive Australia antigen control serum from a Pennsylvania Down's syndrome patient in the top and bottom wells. The patterns were cut in a layer of 1.1% agarose in veronal buffer, pH 8.2, on glass lantern slides^6,7.     

Deconstructing PML‐induced premature senescence

The authors contacted the journal after being alerted to errors in Fig 6C. The authors provided the source data, which show that the panel had been assembled and presented incorrectly. Fig 6C is herewith corrected. The authors note that the corrected panel shows similar results, although less pronounced for the induction of p53 acetylation by PMLIV, consistent with what had been reported previously in PML+/+ MEFs (Fig 3C in Pearson et al, 2000). PMLIV‐induced increase in p53 acetylation is also shown in human fibroblasts (Fig 5B). The authors state that this correction does not affect the message of Fig 6, nor does it impact the overall conclusions of the article.The authors apologize for this oversight and any confusion it may have caused. The source data are available with this notice together with the corrected figure. Figure 6C. Original. Figure 6C. Corrected.. Source data are available online for this figure      

Propidium Iodide Competes with Ca2+ to Label Pectin in Pollen Tubes and Arabidopsis Root Hairs

We have used propidium iodide (PI) to investigate the dynamic properties of the primary cell wall at the apex of Arabidopsis (Arabidopsis thaliana) root hairs and pollen tubes and in lily (Lilium formosanum) pollen tubes. Our results show that in root hairs, as in pollen tubes, oscillatory peaks in PI fluorescence precede growth rate oscillations. Pectin forms the primary component of the cell wall at the tip of both root hairs and pollen tubes. Given the electronic structure of PI, we investigated whether PI binds to pectins in a manner analogous to Ca²⁺ binding. We first show that Ca²⁺ is able to abrogate PI growth inhibition in a dose-dependent manner. PI fluorescence itself also relies directly on the amount of Ca²⁺ in the growth solution. Exogenous pectin methyl esterase treatment of pollen tubes, which demethoxylates pectins, freeing more Ca²⁺-binding sites, leads to a dramatic increase in PI fluorescence. Treatment with pectinase leads to a corresponding decrease in fluorescence. These results are consistent with the hypothesis that PI binds to demethoxylated pectins. Unlike other pectin stains, PI at low yet useful concentration is vital and specifically does not alter the tip-focused Ca²⁺ gradient or growth oscillations. These data suggest that pectin secretion at the apex of tip-growing plant cells plays a critical role in regulating growth, and PI represents an excellent tool for examining the role of pectin and of Ca²⁺ in tip growth.The apical wall of tip-growing cells participates directly in the process of growth regulation (McKenna et al., 2009; Winship et al., 2010), yet few methods permit monitoring the wall properties of living cells. Despite this, several recent studies have enhanced our understanding of the apical cell wall. Chemical analyses of isolated pollen tube wall material have revealed a complex mixture of pectic polysaccharides with regions comprising long sequences of polygalacturonic acid. Important patterns of pectin methoxylation have been detected using immunocytochemical approaches, but these are limited to fixed cells (Dardelle et al., 2010). In a recent study, Parre and Geitmann (2005) used microindentation to show significant correlations between wall strength and growth rate. None of these techniques allow for easy investigation of the cell wall during growth.In an earlier study, we found that propidium iodide (PI) vitally stains pollen tubes of lily (Lilium formosanum) and tobacco (Nicotiana tabacum) and in particular reveals with great clarity the thickened apical cell wall (Fig. 1; McKenna et al., 2009). In addition, the apical PI fluorescence oscillates and in lily pollen tubes correlates tightly with oscillations in wall thickness measured by differential interference contrast (DIC) optics. Finally, these studies indicated that the PI fluorescence predicted cell growth rates with high confidence, suggesting that PI binding may provide useful information about the physical and chemical properties of the cell wall.Open in a separate windowFigure 1.PI fluorescence and growth rate oscillate in lily pollen tubes (A and B), Arabidopsis root hairs (C–E), and Arabidopsis pollen tubes (F and G). A, The top panel shows a DIC image of a lily pollen tube, and the bottom panel shows PI fluorescence of the same tube. The PI fluorescence is pseudocolored, with white representing high signal and blue representing low signal. Bar = 10 μm. B, Growth rate (blue) and PI fluorescence (red) are plotted on a line graph. Both oscillate with the same period but with different phases. C, DIC image (top panel) and PI fluorescence image (bottom panel) of an Arabidopsis root hair. Bar = 10 μm. D, Two PI fluorescence images of the same root hair focused on the apex representing peak (top) and trough (bottom) PI signals. Bar = 5 μm. E, A line graph showing the growth rate (blue) and peak PI fluorescence at the apex (red) for the same root hair shown in C and D. F, The top panel shows a DIC image of an Arabidopsis pollen tube, and the bottom panel shows PI fluorescence of the same tube. The PI fluorescence is pseudocolored, with white representing high signal and blue representing low signal. Bar = 5 μm. G, Growth rate (blue) and PI fluorescence (red) are plotted on a line graph. Both oscillate with the same period but with different phases. The growth rate between individual 3-s frames was smaller than the pixel size for our optics in both Arabidopsis cell types; to remove the noise this generated, a four-image (pollen) or five-image (root hair) running average is shown. A.U., Arbitrary units.PI is commonly used to visualize plant cell walls by wide-field fluorescence and confocal microscopy (Fiers et al., 2005; Tian et al., 2006; Estevez et al., 2008) and to select viable cells during cell sorting (Deitch et al., 1982; Jones and Senft, 1985). A positively charged phenanthridine derivative, the propidium ion stains cell walls but does not pass through the intact cell membranes of living cells. It readily diffuses into dead cells and forms highly fluorescent complexes by intercalation between base pairs of double-stranded nucleic acids, thus acting as an excellent indicator for cell vitality (Hudson et al., 1969). Binding to cell walls presumably occurs by a different mechanism, since it is not accompanied by the dramatic increase in fluorescence and shift in absorption and emission maxima observed when PI binds to nucleic acids. The mechanism of PI binding needs further exploration, as does the potential for broader use in other tip-growing plant cells.In this report, we test two hypotheses: first, that PI stains other tip-growing cells with pectin-containing cell walls; and second, that PI and Ca²⁺ bind to the same sites in these walls. This binding would occur through the interaction of partial positive charges caused by localized deficits in π-orbital electrons associated with three of the four nitrogen atoms of PI (Luedtke et al., 2005) coordinating with negatively charged carboxyl and hydroxyl groups on homogalacturonans (HGs), as has been suggested in Oedogonium bharuchae (Estevez et al., 2008).Our findings indicate that both hypotheses are satisfied. Notably, oscillatory changes in apical PI fluorescence occur and are observed to anticipate oscillations in growth rate in Arabidopsis (Arabidopsis thaliana) root hairs and Arabidopsis pollen tubes. In addition, competition studies indicate that PI and Ca²⁺ bind to the same sites in cell walls. Supporting these studies, we demonstrate that pectin methyl esterase (PME) creates more sites for PI binding, presumably by demethoxylating HGs as they are secreted, and that pectinase reduces PI fluorescence dramatically. However, unlike other pectin-binding dyes, PI does not block Ca²⁺ channels at the concentration used in live cell studies, nor does it alter oscillatory growth characteristics. Our findings provide evidence that PI may be employed as a quantitative measure of Ca²⁺-binding sites and thus may have use as an indicator of the degree of cross-linking of HGs and of cell wall extensibility.     

Enhancing the Activity of a Protein by Stereospecific Unfolding: CONFORMATIONAL LIFE CYCLE OF INSULIN AND ITS EVOLUTIONARY ORIGINS*S??

A central tenet of molecular biology holds that the function of a protein is mediated by its structure. An inactive ground-state conformation may nonetheless be enjoined by the interplay of competing biological constraints. A model is provided by insulin, well characterized at atomic resolution by x-ray crystallography. Here, we demonstrate that the activity of the hormone is enhanced by stereospecific unfolding of a conserved structural element. A bifunctional β-strand mediates both self-assembly (within β-cell storage vesicles) and receptor binding (in the bloodstream). This strand is anchored by an invariant side chain (Phe^B24); its substitution by Ala leads to an unstable but native-like analog of low activity. Substitution by d-Ala is equally destabilizing, and yet the protein diastereomer exhibits enhanced activity with segmental unfolding of the β-strand. Corresponding photoactivable derivatives (containing l- or d-para-azido-Phe) cross-link to the insulin receptor with higher d-specific efficiency. Aberrant exposure of hydrophobic surfaces in the analogs is associated with accelerated fibrillation, a form of aggregation-coupled misfolding associated with cellular toxicity. Conservation of Phe^B24, enforced by its dual role in native self-assembly and induced fit, thus highlights the implicit role of misfolding as an evolutionary constraint. Whereas classical crystal structures of insulin depict its storage form, signaling requires engagement of a detachable arm at an extended receptor interface. Because this active conformation resembles an amyloidogenic intermediate, we envisage that induced fit and self-assembly represent complementary molecular adaptations to potential proteotoxicity. The cryptic threat of misfolding poses a universal constraint in the evolution of polypeptide sequences.How insulin binds to the insulin receptor (IR)² is not well understood despite decades of investigation. The hormone is a globular protein containing two chains, A (21 residues) and B (30 residues) (Fig. 1A). In pancreatic β-cells, insulin is stored as Zn²⁺-stabilized hexamers (Fig. 1B), which form microcrystal-line arrays within specialized secretory granules (1). The hexamers dissociate upon secretion into the portal circulation, enabling the hormone to function as a zinc-free monomer. The monomer is proposed to undergo a change in conformation upon receptor binding (2). In this study, we investigated a site of conformational change in the B-chain (Phe^B24) (arrow in Fig. 1A). In classical crystal structures, this invariant aromatic side chain (tawny in Fig. 1B) anchors an antiparallel β-sheet at the dimer interface (blue in Fig. 1C). Total chemical synthesis is exploited to enable comparison of corresponding d- and l-amino acid substitutions at this site, an approach designated “chiral mutagenesis” (3-5). In the accompanying article, the consequences of this conformational change are investigated by photomapping of the receptor-binding surface (6). Together, these studies redefine the interrelation of structure and activity in a protein central to the hormonal control of metabolism.Open in a separate windowFIGURE 1.Sequence and structure of insulin. A, sequences of the B-chain (upper) and A-chain (lower) with disulfide bridges as indicated. The arrow indicates invariant Phe^B24. The B24-B28 β-strand is highlighted in blue. B, crystal structure of the T₆ zinc insulin hexamer (Protein Data Bank code 4INS): ribbon model (left) and space-filling model (right). The B24-B28 β-strand is shown in blue, and the side chain of Phe^B24 is highlighted in tawny. The B-chain is otherwise dark gray; the A-chain, light gray; and zinc ions, magenta. Also shown at the left are the side chains of His^B10 at the axial zinc-binding sites. C, cylinder model of the insulin dimer showing the B24-B26 antiparallel β-sheet (blue) anchored by the B24 side chain (tawny circle). The A- and B-chains are shown in light and dark gray, respectively. The protomer at the left is shown in the R-state, in which the central α-helix of the B-chain is elongated (B3-B19 in the frayed R^f protomer of T₃R^f₃ hexamers and B1-B19 in the R protomer of R₆ hexamers). The three types of zinc insulin hexamers share similar B24-B26 antiparallel β-sheets as conserved dimerization elements.The structure of an insulin monomer in solution resembles a crystallographic protomer (Fig. 2A) (7-9). The A-chain contains an N-terminal α-helix, non-canonical turn, and second helix; the B-chain contains an N-terminal segment, central α-helix, and C-terminal β-strand. The β-strand is maintained in an isolated monomer wherein the side chain of Phe^B24 (tawny in Fig. 2A), packing against the central α-helix of the B-chain, provides a “plug” to seal a crevice in the hydrophobic core (Fig. 2B). Anomalies encountered in previous studies of insulin analogs suggest that Phe^B24 functions as a conformational switch (4, 7, 10-14). Whereas l-amino acid substitutions at B24 generally impair activity (even by such similar residues as l-Tyr) (15), a seeming paradox is posed by the enhanced activities of nonstandard analogs containing d-amino acids (10-12).

TABLE 1

Previous studies of insulin analogs

Integration of IgA and IgG Autoantigens Improves Performance of Biomarker Panels for Early Diagnosis of Lung Cancer

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Highlights

• •HuProt array-based identification of autoantigens in serum of early lung cancer.
• •Independent validation of early lung cancer biomarker candidates with ELISA.
• •Bioinformatics-aided identification of a biomarker panel.
• •Independent verification of the panel with ELISA and immunohistochemistry.

     

THEORY AND MEASUREMENT OF VISUAL MECHANISMS : XI. ON FLICKER WITH SUBDIVIDED FIELDS

In Vol. 27, No. 5, May 20, 1944, page 403, in the eighth line from the bottom of the page, the comma after "intensity" should be a semicolon. On page 413, in the second formula from the bottom of the page, for See PDF for Equation read See PDF for Equation On the same page, formula 2 should read See PDF for Equation On page 414, line 3, at the end of the line add "or" to read "of the level of I or of F." On page 422, in the first line below the figure legend, for "illuminate" read "illuminated." On page 430, line 22, for "lighteb dars" read "lighted bars."     

Ganglioside GT1b Is a Putative Host Cell Receptor for the Merkel Cell Polyomavirus

The Merkel cell polyomavirus (MCPyV) was identified recently in human Merkel cell carcinomas, an aggressive neuroendocrine skin cancer. Here, we identify a putative host cell receptor for MCPyV. We found that recombinant MCPyV VP1 pentameric capsomeres both hemagglutinated sheep red blood cells and interacted with ganglioside GT1b in a sucrose gradient flotation assay. Structural differences between the analyzed gangliosides suggest that MCPyV VP1 likely interacts with sialic acids on both branches of the GT1b carbohydrate chain. Identification of a potential host cell receptor for MCPyV will aid in the elucidation of its entry mechanism and pathophysiology.Members of the polyomavirus (PyV) family, including simian virus 40 (SV40), murine PyV (mPyV), and BK virus (BKV), bind cell surface gangliosides to initiate infection (2, 8, 11, 15). PyV capsids are assembled from 72 pentamers (capsomeres) of the major coat protein VP1, with the internal proteins VP2 and VP3 buried within the capsids (7, 12). The VP1 pentamer makes direct contact with the carbohydrate portion of the ganglioside (10, 12, 13) and dictates the specificity of virus interaction with the cell. Gangliosides are glycolipids that contain a ceramide domain inserted into the plasma membrane and a carbohydrate domain that directly binds the virus. Specifically, SV40 binds to ganglioside GM1 (2, 10, 15), mPyV binds to gangliosides GD1a and GT1b (11, 15), and BKV binds to gangliosides GD1b and GT1b (8).Recently, a new human PyV designated Merkel cell PyV (MCPyV) was identified in Merkel cell carcinomas, a rare but aggressive skin cancer of neuroendocrine origin (3). It is as yet unclear whether MCPyV is the causative agent of Merkel cell carcinomas (17). A key to understanding the infectious and transforming properties of MCPyV is the elucidation of its cellular entry pathway. In this study, we identify a putative host cell receptor for MCPyV.Because an intact infectious MCPyV has not yet been isolated, we generated recombinant MCPyV VP1 pentamers in order to characterize cellular factors that bind to MCPyV. VP1 capsomeres have been previously shown to be equivalent to virus with respect to hemagglutination properties (4, 16), and the atomic structure of VP1 bound to sialyllactose has demonstrated that the capsomere is sufficient for this interaction (12, 13). The MCPyV VP1 protein (strain w162) was expressed and purified as described previously (1, 6). Briefly, a glutathione S-transferase-MCPyV VP1 fusion protein was expressed in Escherichia coli and purified using glutathione-Sepharose affinity chromatography. The fusion protein was eluted using glutathione and cleaved in solution with thrombin. The thrombin-cleaved sample was then rechromatographed on a second glutathione-Sepharose column to remove glutathione transferase and any uncleaved protein. The unbound VP1 was then chromatographed on a P-11 phosphocellulose column, and peak fractions eluting between 400 and 450 mM NaCl were collected. The purified protein was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), followed by Coomassie blue staining (Fig. ​(Fig.1A,1A, left) and immunoblotting using an antibody (I58) that generally recognizes PyV VP1 proteins (Fig. ​(Fig.1A,1A, right) (9). Transmission electron microscopy (Philips CM10) analysis confirmed that the purified recombinant MCPyV VP1 formed pentamers (capsomeres), which did not assemble further into virus-like particles (Fig. ​(Fig.1B).1B). In an initial screening of its cell binding properties, we tested whether the MCPyV VP1 pentamers hemagglutinated red blood cells (RBCs). The MCPyV VP1 pentamers were incubated with sheep RBCs and assayed as previously described (5). SV40 and mPyV recombinant VP1 pentamers served as negative and positive controls, respectively. We found that MCPyV VP1 hemagglutinated the RBCs with the same efficiency as mPyV VP1 (protein concentration/hemagglutination unit) (Fig. ​(Fig.1C,1C, compare rows B and C from wells 1 to 11), suggesting that MCPyV VP1 engages a plasma membrane receptor on the RBCs. The recombinant murine VP1 protein used for comparison was from the RA strain, a small plaque virus (4). Thus, MCPyV VP1 has the hemagglutination characteristics of a small plaque mPyV (12, 13).Open in a separate windowFIG. 1.Characterization of MCPyV VP1. Recombinant MCPyV VP1 forms pentamers and hemagglutinates sheep RBCs. (A) Coomassie blue-stained SDS-PAGE and an immunoblot of the purified recombinant MCPyV VP1 protein are shown. Molecular mass markers are indicated. (B) Electron micrograph of the purified MCPyV VP1. MCPyV VP1 (shown in panel A) was diluted to 100 μg/ml and absorbed onto Formvar/carbon-coated copper grids. Samples were washed with phosphate-buffered saline, stained with 1% uranyl acetate, and visualized by transmission electron microscopy at 80 kV. Bar = 20 nm. (C) Sheep RBCs (0.5%) were incubated with decreasing concentrations of purified recombinant SV40 VP1 (row A), mPyV VP1 (row B), and MCPyV VP1 (row C). Wells 1 to 11 contain twofold serial dilutions of protein, starting at 2 μg/ml (well 1). Well 12 contains buffer only and serves as a negative control. Well 7 (rows B and C) corresponds to 128 hemagglutination units per 2 μg/ml VP1 protein.To characterize the chemical nature of the putative receptor for MCPyV, total membranes from RBCs were purified as described previously (15). The plasma membranes (30 μg) were incubated with MCPyV VP1 (0.5 μg) and floated on a discontinuous sucrose gradient (15). After fractionation, the samples were analyzed by SDS-PAGE, followed by immunoblotting with I58. VP1 was found in the bottom of the gradient in the absence of the plasma membranes (Fig. ​(Fig.2A,2A, first panel). In the presence of plasma membranes, a fraction of the VP1 floated to the middle of the gradient (Fig. ​(Fig.2A,2A, second panel), supporting the hemagglutination results that suggested that MCPyV VP1 binds to a receptor on the plasma membrane.Open in a separate windowFIG. 2.MCPyV VP1 binds to a protease-resistant, sialic acid-containing receptor on the plasma membrane. (A) Purified recombinant MCPyV VP1 was incubated with or without the indicated plasma membranes. The samples were floated in a discontinuous sucrose gradient, and the fractions were collected from the top of the gradient, subjected to SDS-PAGE, and immunoblotted with the anti-VP1 antibody I58. (B) Control and proteinase K-treated plasma membranes were subjected to SDS-PAGE, followed by Coomassie blue staining. (C) HeLa cells treated with proteinase K (4 μg/ml) were incubated with MCPyV at 4°C, and the resulting cell lysate was probed for the presence of MCPyV VP1. (D) As described in the legend to panel C, except 293T cells were used. (E) Purified MCPyV VP1 was incubated with plasma membranes pretreated with or without α2-3,6,8 neuraminidase and analyzed as described in the legend to panel A.To determine whether the receptor is a protein or a lipid, plasma membrane preparations (30 μg) were incubated with proteinase K (Sigma), followed by analysis with SDS-PAGE and Coomassie blue staining. Under these conditions, the majority of the proteins in the plasma membranes were degraded by the protease (Fig. ​(Fig.2B,2B, compare lanes 1 and 2). Despite the lack of proteins, the proteinase K-treated plasma membranes bound MCPyV VP1 as efficiently as control plasma membranes (Fig. ​(Fig.2A,2A, compare the second and third panels), demonstrating that MCPyV VP1 interacts with a protease-resistant receptor. The absence of VP1 in the bottom fraction in Fig. ​Fig.2A2A (third panel) is consistent with the fact that the buoyant density of the membranes is lowered by proteolysis. Of note, a similar result was seen with binding of the mPyV to the plasma membrane (15). Binding of MCPyV to the cell surface of two human tissue culture cells (i.e., HeLa and 293T) was also largely unaffected by pretreatment of the cells with proteinase K (Fig. 2C and D, compare lanes 1 and 2), further indicating that a nonproteinaceous molecule on the plasma membrane engages the virus.We next determined whether the protease-resistant receptor contains a sialic acid modification. Plasma membranes (10 μg) were incubated with a neuraminidase (α2-3,6,8 neuraminidase; Calbiochem) to remove the sialic acid groups. In contrast to the control plasma membranes, the neuraminidase-treated membranes did not bind MCPyV VP1 (Fig. ​(Fig.2E,2E, compare first and second panels), indicating that the MCPyV receptor includes a sialic acid modification.Gangliosides are lipids that contain sialic acid modifications. We asked if MCPyV VP1 binds to gangliosides similar to other PyV family members. The structures of the gangliosides used in this analysis (gangliosides GM1, GD1a, GD1b, and GT1b) are depicted in Fig. ​Fig.3A.3A. To assess a possible ganglioside-VP1 interaction, we employed a liposome flotation assay established previously (15). When liposomes (consisting of phosphatidyl-choline [19 μl of 10 mg/ml], -ethanolamine [5 μl of 10 mg/ml], -serine [1 μl of 10 mg/ml], and -inositol [3 μl of 10 mg/ml]) were incubated with MCPyV VP1 and subjected to the sucrose flotation assay, the VP1 remained in the bottom fraction (Fig. ​(Fig.3B,3B, first panel), indicating that VP1 does not interact with these phospholipids. However, when liposomes containing GT1b (1 μl of 1 mM), but not GM1 (1 μl of 1 mM) or GD1a (1 μl of 1 mM), were incubated with MCPyV VP1, the vesicles bound this VP1 (Fig. ​(Fig.3B).3B). A low level of virus floated partially when incubated with liposomes containing GD1b (Fig. ​(Fig.3B),3B), perhaps reflecting a weak affinity between MCPyV and GD1b. Importantly, MCPyV binds less efficiently to neuraminidase-treated GT1b-containing liposomes than to GT1b-containing liposomes (Fig. ​(Fig.3B,3B, sixth panel), suggesting that the GT1b sialic acids are involved in virus binding. This finding is consistent with the ability of neuraminidase to block MCPyV binding to the plasma membrane (Fig. ​(Fig.2E).2E). The level of virus flotation observed in the neuraminidase-treated GT1b-containing liposomes is likely due to the inefficiency of the neuraminidase reaction with a high concentration of GT1b used to prepare the vesicles.Open in a separate windowFIG. 3.MCPyV VP1 binds to ganglioside GT1b. (A) Structures of gangliosides GM1, GD1a, GD1b, and GT1b. The nature of the glycosidic linkages is indicated. (B) Purified MCPyV VP1 protein was incubated with liposomes only or with liposomes containing the indicated gangliosides. The samples were analyzed as described in the legend to Fig. ​Fig.2A.2A. Where indicated, GT1b-containing liposomes were pretreated with α2-3,6,8 neuraminidase and analyzed subsequently for virus binding. (C to E) The indicated viruses were incubated with liposomes and analyzed as described in the legend to panel B.As controls, GM1-containing liposomes bound SV40 (Fig. ​(Fig.3C),3C), GD1a-containing liposomes bound mPyV (Fig. ​(Fig.3D),3D), and GD1b-containing liposomes bound BKV (Fig. ​(Fig.3E),3E), demonstrating that the liposomes were functionally intact. We note that, while all of the MCPyV VP1 floated when incubated with liposomes containing GT1b (Fig. ​(Fig.3B,3B, sixth panel), a significant fraction of SV40, mPyV, and BKV VP1 remained in the bottom fraction despite being incubated with liposomes containing their respective ganglioside receptors (Fig. 3C to E, second panels). This result is likely due to the fact that in contrast to MCPyV, which are assembled as pentamers (Fig. ​(Fig.1B),1B), the SV40, mPyV, and BKV used in these experiments are fully assembled particles: their larger and denser nature prevents efficient flotation. Nonetheless, we conclude that MCPyV VP1 binds to ganglioside GT1b efficiently.The observation that GD1a does not bind to MCPyV VP1 suggests that the monosialic acid modification on the right branch of GT1b (Fig. ​(Fig.3A)3A) is insufficient for binding. Similarly, the failure of GD1b to bind MCPyV VP1 suggests that the sialic acid on the left arm of GT1b is necessary for binding. Together, these observations suggest that MCPyV VP1 interacts with sialic acids on both branches of GT1b (Fig. ​(Fig.4).4). A recent structure of SV40 VP1 in complex with the sugar portion of GM1 (10) demonstrated that although SV40 VP1 binds both branches of GM1 (Fig. ​(Fig.4),4), only a single sialic acid in GM1 is involved in this interaction. In the case of mPyV, structures of mPyV VP1 in complex with different carbohydrates (12, 13) revealed that the sialic acid-galactose moiety on the left branch of GD1a (and GT1b) is sufficient for mPyV VP1 binding (Fig. ​(Fig.4).4). Although no structure of BKV in complex with the sugar portion of GD1b (or GT1b) is available, in vitro binding studies (8) have suggested that the disialic acid modification on the right branch of GD1b (and GT1b) is responsible for binding BKV VP1 (Fig. ​(Fig.4).4). Thus, it appears that the unique feature of the MCPyV VP1-GT1b interaction is that the sialic acids on both branches of this ganglioside are likely involved in capsid binding.Open in a separate windowFIG. 4.A potential model of the different VP1-ganglioside interactions (see the text for discussion).The identification of a potential cellular receptor for MCPyV will facilitate the study of its entry mechanism. An important issue for further study is to determine whether MCPyV targets Merkel cells preferentially, and if so, whether GT1b is found in higher levels in these cells to increase susceptibility.     

A new method to assess the influence of odor on food selection in dogs

Previous research provides evidence that odor is a key driver in food selection in dogs. Dogs' flavor preferences are generally assessed through paired comparison tests based on food intake. Methods for evaluating odor preference in canines are lacking. In this study, the paired comparison test was modified by replacing standard bowls with false‐bottom bowls (FBBs). Made of two compartments separated by a drilled, stainless‐steel plate, FBBs enable odorant compounds to be placed under the food that is presented to the dogs. Several paired comparison trials were conducted on a trained canine panel with FBBs containing various odorant substances under the kibbles. Results showed that dogs were able to perceive the hidden substances and to distinguish between the bowls accordingly. These results demonstrate that the false‐bottom bowl paired comparison method could be helpful in evaluating the role of odor in dogs' food preferences, thus, also as a way of assessing food odor performance.

Practical applications

The false‐bottom bowl method is an adaptation of the paired comparison test that enables the influence of odor on dog behavior to be isolated from that stimulated by vision, taste or textural parameters. The odor impact of a hidden substance is tested under pet meal conditions. This new method could be useful in pet food industry to measure the odor potential of a new ingredient, or to understand the key food selection drivers for dogs and cats. In addition, as the olfactory stimulus is not eaten by the animal, the influence of odor in non‐food products for dogs, such as pet care and pet medicines, could also be evaluated using this method.     

La grotte de Niaux,théâtre des illusions

Niaux Cavern, one of the great decorated caves, has been continuously open to the public. Despite its apparent accessibility, there is much that remains beyond our comprehension. One of the most inaccessible images is in the much visited Salon Noir. It is panel number four which contains a powerful but puzzling figure sometimes referred to as the Crossed Bison. This paper is an attempt to reach into the mind of the individual who produced that image to show how that artist's evident understanding of optical illusions, as well as an intuitive understanding of the theory of mind, propelled its creation for a specific graphic purpose.