Primate multidien enamel rhythms and body size.

<p>Multidien rhythms measured from the enamel of numerous primates are regressed against body size (Kg). This association was our first indication that some systemic physiological event linked to development perturbed the enamel forming cells, altering their matrix production and manifesting a periodic growth line [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145919#pone.0145919.ref011" target="_blank">11</a>]. Lemur outliers have been isolated from other primates on Madagascar for 31 million years, and evolved their limited multidien variability and life history strategy to cope with island ecological instability [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145919#pone.0145919.ref012" target="_blank">12</a>]. Fig 2 is modified from an earlier publication [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145919#pone.0145919.ref010" target="_blank">10</a>]. The following statement is a PLOS requirement: "Tim Bromage pictured in Fig 2 and representing "human", has given written informed consent to himself to publish this image". Closed circles = New World monkeys; Open squares = Old World monkeys, apes; Open triangles = lemurs.</p

IPA 'direct' associated gene network underlying the 5-day multidien growth rhythm.

<p>The directed links for all genes and enzyme-catalysis reactions (ecr) identified in the IPA analysis of the day 2 acrophase metabolite group were entered into Cytoscape [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145919#pone.0145919.ref025" target="_blank">25</a>] to produce this network architecture. Gene hubs containing from 7–17 in- and out-degree links are highlighted, and include ATP-pyrophosphate ecr (17 links), APP (14), L-glutamic acid (11), SNCA (11), ATP (9), phosphate (8), cholesterol (7), and NADP-NADPH ecr (7). Genes included in the sncRNA IPA Gene Interaction Network (TP53, MYC, FOXO1, VIM) are also indicated (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145919#pone.0145919.g011" target="_blank">Fig 11</a>).</p

Enamel incremental periodicity.

<p>Top: Daily (circadian) growth lines, or cross-striations (short arrows) are observed between adjacent long-period (multidien) striae of Retzius (long arrows) (distance between the adjacent striae of Retzius shown = 30 μm). Bottom: Striae of Retzius may be seen to course across the horizontal field of view (FW = 450 μm). The number of cross-striations between adjacent striae of Retzius is termed the "repeat period" (RP). In this instance the molar enamel from one of the authors (TGB), the RP = 8 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145919#pone.0145919.g002" target="_blank">Fig 2</a>).</p

24 hr rhythm of Arginine concentration.

<p>A. The cosinor time plot for the metabolite Arginine. Blue points and their connecting lines are original data for each animal in the study; the bold black line is the mean of the data point time series. Red lines are cosinor waves fit over the data for each individual. The bold yellow line is the mean of the individual cosinor time series. On the X-axis, data points are given in decimal fractions of each day and in local time; dark and light bars denote lights-off and lights on illumination conditions. First peak (acrophase) occurs at about 0.75 days (18:00), next peak appearing at 1.75 days on day 2. (All individuals are represented except #12, which was eliminated from the analysis because of having too few measurements for this animal). B. The cosinor polar plot for Fig 4A, illustrating the distribution of first acrophase for each individual, most individuals peaking between 16:00 and 20:00 hr local time. C. The cosinor time plot for a representative individual in the sample from Fig 4A. D. The cosinor polar plot for Fig 4C, illustrating a local time for first acrophase occurring roughly between 17:00 and 18:00 hr.</p

Multidien rhythm of sncRNA concentration.

<p><b>A</b>. The cosinor time plot for 18 of 19 sncRNA representing the degradation rhythm (one very high concentration sncRNA was removed to expand the scale for visualizing the mean cosinor rhythm). Blue points and their connecting lines are original data for each pooled sncRNA in the study; the bold black line is the mean of the data point time series. Red lines are cosinor waves fit over the data for each pooled sncRNA. The bold yellow line is the mean of the individual cosinor time series. First peak (acrophase) occurs at about early day 5, then next peak at early day 10. Most sncRNA in the study have a concentrated distribution of first peaks within day 5. B. The cosinor polar plot for Fig 10A, illustrating the distribution of first acrophase for each individual, most individuals peaking during day 5.</p

5-day multidien rhythm of Alanine concentration.

<p><b>A</b>. The cosinor time plot for the metabolite Alanine. Blue points and their connecting lines are original data for each animal in the study; the bold black line is the mean of the data point time series. Red lines are cosinor waves fit over the data for each individual. The bold yellow line is the mean of the individual cosinor time series. First peak (acrophase) occurs at about day 2, then next peak at day 7, and then day 12. Most metabolites in the study have a more concentrated distribution of first peaks within the day, but this interindividual variability leads to some level of statistical significance for days bordering the rhythm having the highest statistical power. B. The cosinor polar plot for Fig 5A, illustrating the distribution of first acrophase for each individual, most individuals peaking throughout day 2 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145919#pone.0145919.s002" target="_blank">S2 Fig</a> for detail). C. The cosinor time plot for a representative individual in the sample from Fig 5A. D. The cosinor polar plot for Fig 5C, illustrating a local time for first acrophase occurring near to day 2.</p

Pattern of 5-day multidien biological functions.

<p>The top canonical pathways identified by IPA are: <u>5-day growth rhythm</u>—Proline Biosynthesis II (from Arginine), tRNA Charging, Citrulline Biosynthesis, Glycine Biosynthesis III, Superpathway of Citrulline Metabolism. <u>5-day degradation rhythm</u>—Adenine and Adenosine Salvage III, Sucrose Degradation V (Mammalian), Purine Ribonucleosides Degradation to Ribose-1-phosphate, Adenosine Nucleotides Degradation II, Purine Nucleotides Degradation II (Aerobic).</p

Two-way hierarchical clustering of the cross-correlation matrix of the levels of 70 5-day oscillating sncRNAs and 55 5-day oscillating metabolites across 14 sampling points.

<p>Pairwise metabolite-sncRNA Spearman correlations were generated using quantile-normalized metabolite and sncRNA levels. The range of Spearman correlation values is shown to the right of the figure (brown to blue). The sign of correlation values indicate positive (+) and negative (-) correlation. The heat map shows the clustering of metabolites or sncRNAs based on similarity and highlights the presence of major groups of sncRNAs that oscillate in a similar fashion (positive/red-brown or negative/blue) relative to few major groups of metabolites.</p