35 research outputs found

### Effect of larval age on nursing behavior.

<p>Number of visits (A), total time spent visiting (B) and number of bees visiting cell (C). Data represent average Â± SE, sample size (number of groups) is in the base of each bar, p-values summarize the results of two-tailed t-test (A: <i>t</i><sub><i>(18)</i></sub> = 0.1, B: <i>t</i><sub><i>(18)</i></sub> = 3.75, C: <i>t</i><sub><i>(18)</i></sub> = 2.86).</p

### Worker response to a queen cell with a larva vs. an empty cell.

<p>Number of visits (inspections and nursing, A and B), total time spent visiting (C and D) and number of bees visiting cell (E and F), for bees from Colony 1 (A, C, E) and Colony 2 (B, D, F). Data represent average Â± SE, sample size (number of groups) is at the base of each bar, p-values summarize the results of paired t-test (A: <i>t</i><sub><i>(8)</i></sub> = 6.4; B: <i>t</i><sub><i>(8)</i></sub> = 7.1; C: <i>t</i><sub><i>(8)</i></sub> = 3.4; D: <i>t</i><sub><i>(9)</i></sub> = 3.0; E: <i>t</i><sub><i>(9)</i></sub> = 5.3; F: <i>t</i><sub><i>(9)</i></sub> = 3.1).</p

### Effect of adult worker genetic background on nursing behavior.

<p>Bees from three genetically different colonies were studied. Latency until first cell visit (A); total number of inspection visits (B); total number of nursing visits (C); total time spent visiting larvae (D); and number of bees visiting cell (E). The p-value summarizes the results of one-way ANOVA (F<sub>(2)</sub> â„ 10.4 for all measurements), different letter above the bars indicate significant pair-wise differences in LSD post-hoc test (p < 0.05).</p

### Effect of group size on nursing performances.

<p>Percentage of: cells with cocoons or capped / total number of queen cells tested (left); queens that eclosed / total number of queen cells (middle); and queens that eclosed / cells with cocoon or capped (right) in three experimental groups: 8-bees (blue; N = 65), single-bee (green; N = 38) and zero-bees (yellow; N = 24). The p-values summarize the results of Fisherâs exact test for independence, different letters in parentheses indicate a significant difference in proportion between the groups in a pairwise test (Fisher's exact test with Bonferroni correction for multiple testing p < 0.05).</p

### Worker response to a queen cell with only larva vs. a queen cell with royal jelly.

<p>Number of visits (A), total time spent visiting (B) and number of bees visiting cell (C). Scan sampling of 21 groups (10 bees in each group) during the first 5 minutes after the introduction of either a queen larva or royal jelly. Data represent average Â± SE, sample size (number of groups) is at the base of each bar, p-values summarize the results of paired t-test (A: <i>t</i><sub><i>(20)</i></sub> = 2.5; B: <i>t</i><sub><i>(20)</i></sub> = 2.9; C: <i>t</i><sub><i>(20)</i></sub> = 3.25).</p

### GO Biological Process and Molecular Function Trees (Benjamini-corrected p-value cutoff = 0.05) for the âEutheria-conservedâ Alarm_Pheromone Genesâ Human Orthologs.

<p>This figure shows the Biological Process (left) and Molecular Function (right) Trees. âEutheria-conservedâ means that genes have orthologs in all eutherian species included in InParanoid database. Nodes with red bounds are GO terms with p-value (Benjamini p-value) < = 0.01. Nodes with various green bounds are nodes with p-value between 0.01 and 0.05. Nodes with white bounds (or no bounds as it is the same as the background color) are not themselves enriched but are parents of enriched terms in the GO hierarchy. Enriched nodes are labeled with the names of the GO term. All nodes are numerically tagged. The correlations between the numerical tags and the names of the GO categories is given in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.t003" target="_blank">Table 3</a>. Separate GO analysis are done for all the up-regulated âEutheria-conservedâ Alarm_Pheromone Genesâ Human orthologs (Upâ), all the down-regulated orthologs (âDownâ), and all regardless of regulation (âCombinedâ). The results are indicated by the colors of the node faces as follows: GO category enriched in the up-regulated subset only is red; GO category enriched in the down-regulated subset only is green; GO category enriched in the complete set is deep blue; GO category enriched in the up-regulated subset and the complete set is purple; GO category enriched in the down-regulated subset and the complete set is light blue; GO category enriched in both subsets and in the total set is gray. For example, a Biological Process GO term indexed â29â and identified as âresponse to unfolded proteinâ is seen as significant in the analysis for up-regulated and for all genes (Hence it is in purple, the,âDown+Combinedâ color, and bordered in red because the p-value was below 0.01). All the names for the enriched GO terms and their parents are in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.t003" target="_blank">Table 3</a> (The tables and this tree are designed to be complementary to each other. The trees show the overall architecture of the relationships among GO categories while the tables provide more detail) and in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.s005" target="_blank">S2 Table</a>. Corresponding information in spreadsheet form is provided for the âMouse-and-human conservedâ and âAll-Vertebrate-Conservedâ sets in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.s005" target="_blank">S2 Table</a>.</p

### Normalized distribution of the number of all of the âArray-Unspottedâ Honey Bee genesâ orthologs in 54 species.

<p>âArray-Unspottedâ means that these genes are present in the InParanoid database but not spotted on the Honey Bee Oligonucleotide Microarray. There are 1631 such honey bee genes. X-axis is the number of orthologs in 54 species (53 metazoan species+ yeast). Y-axis is the percentage of these 1631 honey bee genes that have the corresponding number of orthologs. (Note vertical scale difference between Figs <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.g001" target="_blank">1</a> and 2).</p

### Heat maps and statistical analysis of the p-values of number of orthologs for each species and each set.

<p>Each row of the heat maps in Figs 3a and 3b represents one of the honey bee experimental sets. Each column represents one species. Fig 3a is based on the InParanoid ortholog database and 3 b is based on the OrthoMCL database. The white represents the honey bee. The species are ordered along the x-axis by evolutionary distance from the honey bee based on NCBI taxonomy common tree (<a href="http://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi" target="_blank">http://www.ncbi.nlm.nih.gov/Taxonomy/CommonTree/wwwcmt.cgi</a>). The order is further refined based on the tree from Flybase (<a href="http://flybase.org/blast/species_tree.png" target="_blank">http://flybase.org/blast/species_tree.png</a>), WormBook [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.ref042" target="_blank">42</a>] and UCSC Genome Browser [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.ref043" target="_blank">43</a>]. The evolutionary relationships are illustrated by the cladogram along the base of each heat map. Those species to the left of the honey bee (the white vertical column) belong to lineages that diverged from the insects earlier than the insects diverged from the lineage leading to the mammals. The species immediately to the right of the honey bee are insects and other arthropods. The species at the far right are mammals. Between the insects and the mammals are marine invertebrates, marine chordates, fish, amphibians, and birds. The shading code (vertical bar on the right hand side of the figure) represents the p-value for statistical significance of enrichment of orthology in each species relative to the degree of orthology of all the genes on the microarray. The numerical data for these plots are in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.s004" target="_blank">S1 Table</a>. Panel c represents the enhanced orthology between the honey bee alarm pheromone set and the placental mammals by means of boxplots. Reading from left to right the boxplots show: i) the distribution of individual species p-values for orthology enhancement between the honey bees and the placental mammals using the InParanoid database, ii) the distribution of individual species p-values for orthology enhancement between the honey bees and their fellow arthropods using the InParanoid data base, iii) the same as i) but using the OrthoMCL database, and iv) the same as ii) but using the OrthoMCL database. It is seen that the p-values for orthology enhancement of the honey bee alarm pheromone set are much much lower (and therefore more favorable) for placental mammals than for arthropods. This is in spite of the fact that overall the honey bee is much more closely related to the other arthropods than to the mammals, as indicated by cladograms in Fig 3a and 3b. The relative positions of the boxplots in Fig 3c are just the opposite of what would pertain if the degree of orthology followed the species relationship. Fig 3d shows the Kolmogorov-Smirnov cumulative fraction difference plot for the distributions of p-values for orthology enrichment of the Alarm Pheromone gene set against the placental mammals (solid trace) and against the arthropods, using the InParanoid orthology database. The horizontal axis is p-values. Each vertical position on each trace is the fraction of p-values making up that trace whose p-value is below the indicated value. One important feature of such a plot is the maximum vertical distance between the two traces, D. In this figure, D is 0.75. P, the likelihood that this difference would be achieved by chance for a distribution with this number of data points, is 0.001 Fig 3e shows the same graph as Fig 3d using the OrthoMCL orthology database. In this graph the value of D is 1.0, since there is no overlap between the distributions at all. P, the likelihood that this degree of separation would occur by chance among members of the same underlying distribution, is vanishingly small. Based on the Kolmogorov-Smirnov statistics, depicted in Fig 3d and 3e we can say with confidence that the Alarm Pheromone honey bee gene set is relatively more enriched in orthologs to placental mammals than in orthologs to other arthropods. Fig 3f shows the Kolmogrov-Smirnov cumulative fraction plot for the differences between the p-values for orthology enrichment for the soldier cg and soldier wg sets. It is seen that the degree of conservation is dramatically higher for the cg than the wg set, which can also be inferred qualitatively from the shading in the heat map of Fig 3a. The value of D, the greatest vertical distance between the two traces shown by the double-headed arrow, is 0.81. P, the probability that the difference between the two traces is due to chance, is < .0005.</p

### Examples of Behavior/neural-related âEutheria-conservedâ Alarm_Pheromone Genesâ Human Orthologs (Part 1).

<p>Examples of Behavior/neural-related âEutheria-conservedâ Alarm_Pheromone Genesâ Human Orthologs (Part 1).</p

### GO Cellular Component Trees (Benjamini-corrected p-value cutoff = 0.05) for the âEutheria-conservedâ Alarm_Pheromone Genesâ Human Orthologs.

<p>This figure shows the Cellular Component tree. âEutheria-conservedâ defined as in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.g004" target="_blank">Fig 4</a> legend. Nodes with red bounds are GO terms with p-value (Benjamini p-value) < = 0.01. Nodes with red bounds are GO terms with p-value < = 0.01. Nodes with various green bounds are nodes with p-value between 0.01 and 0.05. Nodes with white bounds (or no bounds as it is the same as the background color) are not themselves enriched but are parents of enriched terms in the GO hierarchy. Separate GO analysis are done for all the up-regulated âVertebrate-conservedâ Alarm_Pheromone Genesâ Human orthologs (âUpâ), all the down-regulated ones (âDownâ), and all regardless of regulation (âCombinedâ). The results are indicated by the colors of the node faces as follows: GO category enriched in the up-regulated subset only is red; GO category enriched in the down-regulated subset only is green; GO category enriched in the complete set is deep blue; GO category enriched in the up-regulated subset and the complete set is purple; GO category enriched in the down-regulated subset and the complete set is light blue; GO category enriched in both subsets and in the total set is gray. The exact names for these indexed GO terms are in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.t004" target="_blank">Table 4</a> and in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.s005" target="_blank">S2 Table</a>. Corresponding information about the âmouse-and-human-conservedâ and âvertebrate-conservedâ gene sets is found in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004921#pcbi.1004921.s005" target="_blank">S2 Table</a>.</p