Single-Species Microarrays and Comparative Transcriptomics

BACKGROUND: Prefabricated expression microarrays are currently available for only a few species but methods have been proposed to extend their application to comparisons between divergent genomes. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that the hybridization intensity of genomic DNA is a poor basis on which to select unbiased probes on Affymetrix expression arrays for studies of comparative transcriptomics, and that doing so produces spurious results. We used the Affymetrix Xenopus laevis microarray to evaluate expression divergence between X. laevis, X. borealis, and their F1 hybrids. When data are analyzed with probes that interrogate only sequences with confirmed identity in both species, we recover results that differ substantially analyses that use genomic DNA hybridizations to select probes. CONCLUSIONS/SIGNIFICANCE: Our findings have implications for the experimental design of comparative expression studies that use single-species microarrays, and for our understanding of divergent expression in hybrid clawed frogs. These findings also highlight important limitations of single-species microarrays for studies of comparative transcriptomics of polyploid species

Effect of sitagliptin on cardiovascular outcomes in type 2 diabetes

BACKGROUND: Data are lacking on the long-term effect on cardiovascular events of adding sitagliptin, a dipeptidyl peptidase 4 inhibitor, to usual care in patients with type 2 diabetes and cardiovascular disease. METHODS: In this randomized, double-blind study, we assigned 14,671 patients to add either sitagliptin or placebo to their existing therapy. Open-label use of antihyperglycemic therapy was encouraged as required, aimed at reaching individually appropriate glycemic targets in all patients. To determine whether sitagliptin was noninferior to placebo, we used a relative risk of 1.3 as the marginal upper boundary. The primary cardiovascular outcome was a composite of cardiovascular death, nonfatal myocardial infarction, nonfatal stroke, or hospitalization for unstable angina. RESULTS: During a median follow-up of 3.0 years, there was a small difference in glycated hemoglobin levels (least-squares mean difference for sitagliptin vs. placebo, -0.29 percentage points; 95% confidence interval [CI], -0.32 to -0.27). Overall, the primary outcome occurred in 839 patients in the sitagliptin group (11.4%; 4.06 per 100 person-years) and 851 patients in the placebo group (11.6%; 4.17 per 100 person-years). Sitagliptin was noninferior to placebo for the primary composite cardiovascular outcome (hazard ratio, 0.98; 95% CI, 0.88 to 1.09; P<0.001). Rates of hospitalization for heart failure did not differ between the two groups (hazard ratio, 1.00; 95% CI, 0.83 to 1.20; P = 0.98). There were no significant between-group differences in rates of acute pancreatitis (P = 0.07) or pancreatic cancer (P = 0.32). CONCLUSIONS: Among patients with type 2 diabetes and established cardiovascular disease, adding sitagliptin to usual care did not appear to increase the risk of major adverse cardiovascular events, hospitalization for heart failure, or other adverse events

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization

Abstract Background The mechanism by which duplicate genes originate – whether by duplication of a whole genome or of a genomic segment – influences their genetic fates. To study events that trigger duplicate gene persistence after whole genome duplication in vertebrates, we have analyzed molecular evolution and expression of hundreds of persistent duplicate gene pairs in allopolyploid clawed frogs (Xenopus and Silurana). We collected comparative data that allowed us to tease apart the molecular events that occurred soon after duplication from those that occurred later on. We also quantified expression profile divergence of hundreds of paralogs during development and in different tissues. Results Our analyses indicate that persistent duplicates generated by allopolyploidization are subjected to strong purifying selection soon after duplication. The level of purifying selection is relaxed compared to a singleton ortholog, but not significantly variable over a period spanning about 40 million years. Despite persistent functional constraints, however, analysis of paralogous expression profiles indicates that quantitative aspects of their expression diverged substantially during this period. Conclusion These results offer clues into how vertebrate transcriptomes are sculpted in the wake of whole genome duplication (WGD), such as those that occurred in our early ancestors. That functional constraints were relaxed relative to a singleton ortholog but not significantly different in the early compared to the later stage of duplicate gene evolution suggests that the timescale for a return to pre-duplication levels is drawn out over tens of millions of years – beyond the age of these tetraploid species. Quantitative expression divergence can occur soon after WGD and with a magnitude that is not correlated with the rate of protein sequence divergence. On a coarse scale, quantitative expression divergence appears to be more prevalent than spatial and temporal expression divergence, and also faster or more frequent than other processes that operate at the protein level, such as some types of neofunctionalization.</p

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization

BACKGROUND: The mechanism by which duplicate genes originate – whether by duplication of a whole genome or of a genomic segment – influences their genetic fates. To study events that trigger duplicate gene persistence after whole genome duplication in vertebrates, we have analyzed molecular evolution and expression of hundreds of persistent duplicate gene pairs in allopolyploid clawed frogs (Xenopus and Silurana). We collected comparative data that allowed us to tease apart the molecular events that occurred soon after duplication from those that occurred later on. We also quantified expression profile divergence of hundreds of paralogs during development and in different tissues. RESULTS: Our analyses indicate that persistent duplicates generated by allopolyploidization are subjected to strong purifying selection soon after duplication. The level of purifying selection is relaxed compared to a singleton ortholog, but not significantly variable over a period spanning about 40 million years. Despite persistent functional constraints, however, analysis of paralogous expression profiles indicates that quantitative aspects of their expression diverged substantially during this period. CONCLUSION: These results offer clues into how vertebrate transcriptomes are sculpted in the wake of whole genome duplication (WGD), such as those that occurred in our early ancestors. That functional constraints were relaxed relative to a singleton ortholog but not significantly different in the early compared to the later stage of duplicate gene evolution suggests that the timescale for a return to pre-duplication levels is drawn out over tens of millions of years – beyond the age of these tetraploid species. Quantitative expression divergence can occur soon after WGD and with a magnitude that is not correlated with the rate of protein sequence divergence. On a coarse scale, quantitative expression divergence appears to be more prevalent than spatial and temporal expression divergence, and also faster or more frequent than other processes that operate at the protein level, such as some types of neofunctionalization

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization-0

) Regression of Ka/Ks versus Ks in the early and later stages indicates that selection (relaxed purifying + positive) is not more common in the early stage of duplicate gene evolution (blue dots) than the later stage (red dots). The Y-intercept of these regression lines was set to zero and Ka/Ks ratios greater 2 (including undefined ratios) were given a value of 2. In (A) and (B), a dashed line indicates the neutral expectation. Fragments with Ka/Ks > 2 are, on average, half of the size of those with Ka/Ks < 2. Ka/Ks ratios above 2 may therefore be attributable in part to stochastic variance in Ks [43].<p><b>Copyright information:</b></p><p>Taken from "Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization"</p><p>http://www.biomedcentral.com/1471-2148/8/43</p><p>BMC Evolutionary Biology 2008;8():43-43.</p><p>Published online 8 Feb 2008</p><p>PMCID:PMC2275784.</p><p></p

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization-1

Ction of expression and three probe specificities were compared that are labeled low, medium, and high (see Methods). We report paralogous profiles whose presence/absence scores in all five treatments were identical in the medium and high specificity analysis (shaded in gray on the left of each chart). 1789 and 1462 genes had consistent present/absent expression profiles in the medium and high specificity analyses using the standard and conservative thresholds. These sets of genes included 841 and 632 paralogous pairs, respectively. The tables on the right compare paralogous profiles by tabulating whether they are both present and absent in the same treatments (identical), the expression profile of one overlaps entirely with the other (overlap), or paralogs in which each duplicate has a unique component (distinct).<p><b>Copyright information:</b></p><p>Taken from "Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization"</p><p>http://www.biomedcentral.com/1471-2148/8/43</p><p>BMC Evolutionary Biology 2008;8():43-43.</p><p>Published online 8 Feb 2008</p><p>PMCID:PMC2275784.</p><p></p

Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization-2

Ofiles (white bars) and between paralogous expression profiles (black bars). Ninety percent of the non-paralogous expression profiles have a Pearson correlation coefficient that is greater than -0.861 but less than 0.865. The Pearson correlation coefficients of 62% of the paralogous expression profiles are less than 0.865, and 0.3% of them are less than -0.861.<p><b>Copyright information:</b></p><p>Taken from "Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization"</p><p>http://www.biomedcentral.com/1471-2148/8/43</p><p>BMC Evolutionary Biology 2008;8():43-43.</p><p>Published online 8 Feb 2008</p><p>PMCID:PMC2275784.</p><p></p