Dentition and tooth replacement of <i>Dicraeosaurus hansemanni</i> (Dinosauria, Sauropoda, Diplodocoidea) from the Tendaguru Formation of Tanzania

<div><p>ABSTRACT</p><p>Computed tomographic scan data of three premaxillae, a maxilla, and a dentary of <i>Dicraeosaurus hansemanni</i> allow reconstruction of the tooth replacement pattern in this taxon. Four or five replacement teeth are present in each of the four tooth families of the premaxilla. The interalveolar septum is labially interrupted, and an alveolar trough is formed. In the maxilla, the number of replacement teeth decreases in a caudal direction from four to one per tooth family. The dentary bears 16 alveoli, and the number of replacement teeth decreases caudally from three to one per tooth family. Replacement rates are around 20 days for the premaxillary and rostral maxillary teeth of <i>Dicraeosaurus</i>, which confirms the presence of high tooth replacement rates in Diplodocoidea. Replacement teeth of the dentary are less than half as large as those of the upper jaw, and replacement rates are around 50 days for the rostral dentary teeth. Hypothetical reconstruction of Zahnreihen yields a potential z-spacing of 1 with simultaneous front-to-back tooth replacement. Most probably, the rostral-most teeth in <i>Dicraeosaurus</i> were used for food acquisition, whereas the more caudally positioned teeth served only as a guide and as a lateral limit for the food within the mouth. The teeth of the dentary were less prone to wear than those of the upper jaws. These findings are in agreement with the reconstructions of <i>Dicraeosaurus</i> as a selective mid-height browser.</p><p>SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at <a href="http://www.tandfonline.com/UJVP" target="_blank">www.tandfonline.com/UJVP</a></p><p>Citation for this article: Schwarz, D., J. C. D. Kosch, G. Fritsch, and T. Hildebrandt. 2015. Dentition and tooth replacement of <i>Dicraeosaurus hansemanni</i> (Dinosauria, Sauropoda, Diplodocoidea) from the Tendaguru Formation of Tanzania. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2015.1008134 .</p></div

Structural Parameters Controlling the Fluorescence Properties of Phytochromes

Phytochromes constitute a class of photoreceptors that can be photoconverted between two stable states. The tetrapyrrole chromophore absorbs in the red spectral region and displays fluorescence maxima above 700 nm, albeit with low quantum yields. Because this wavelength region is particularly advantageous for fluorescence-based deep tissue imaging, there is a strong interest to engineer phytochrome variants with increased fluorescence yields. Such targeted design efforts would substantially benefit from a deeper understanding of those structural parameters that control the photophysical properties of the protein-bound chromophore. Here we have employed resonance Raman (RR) spectroscopy and molecular dynamics simulations for elucidating the chromophore structural changes in a fluorescence-optimized mutant (iRFP) derived from the PAS-GAF domain of the bacteriophytochrome RpBphP2 from Rhodopseudomas palustris. Both methods consistently reveal the structural consequences of the amino acid substitutions in the vicinity of the biliverdin chromophore that may account for lowering the propability of nonradiative excited state decays. First, compared to the wild-type protein, the tilt angle of the terminal ring <i>D</i> with respect to ring <i>C</i> is increased in iRFP, accompanied by the loss of hydrogen bond interactions of the ring <i>D</i> carbonyl function and the reduction of the number of water molecules in that part of the chromophore pocket. Second, the overall flexibility of the chromophore is significantly reduced, particularly in the region of rings <i>D</i> and <i>A</i>, thereby reducing the conformational heterogeneity of the methine bridge between rings <i>A</i> and <i>B</i> and the ring <i>A</i> carbonyl group, as concluded from the RR spectra of the wild-type proteins

Additional file 2: of Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging

Table S1. Age at death for NMRs and GPs. Table S2. Number of analyzed biological replicates per group. Table S3. Reason for exclusion of samples from further analysis. Table S4. Number of uniquely aligned RNA-seq reads. Table S5. Mean pairwise Pearson correlation coefficients between biological replicates in (A) naked mole-rat and (B) guinea pig. Table S22. Proportion of mitochondrial transcriptonal output. Table S25. Enrichment of age-related genes (Digital Ageing Atlas) in status-related DEGs. Only tissues having at least 50 DEGs were tested for enrichment. Table S27. Fisher’s exact test for overlap between DAA and upper quintile of status-related expression differences. Table S10, S12, S15–17, S19–21, S28, S29. Functional gene set enrichments analyses—see Overview tab for detailed description. Table S7–9, S11, S13, S14, S18, S23, S24, S26. Differentially expressed genes—see Overview tab for detailed description. (XLSX 313 kb

Additional file 5: of Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging

Supplementary Data S12-S47 containing test results for differential expression between female vs. male in each species, group, and tissue (DESeq2). (XLSX 28655 kb

Additional file 6: of Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging

Supplementary Data S48-S87 containing test results for differential expression between breeder vs. non-breeder in each species, sex, and tissue (DESeq2). (XLSX 31326 kb

Additional file 4: of Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging

Supplementary Data S1-S11 containing test results for differential expression between NMR vs. GP. (XLSX 5404 kb

Additional file 1: of Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging

Figure S1. Identity of protein-coding sequences between human, mouse, GP, and NMR. Figure S2. Schema of collected tissues. Figure S3. Hierarchical clustering of gene expression profiles. Figure S4. Top 15 highest ranked GO sets based on enrichment analysis of cross-species DEGs between NMR and GP. Figure S5. Top 15 highest ranked GO sets based on enrichment analysis of sex-related DEGs that are shared between GP breeder and non-breeder. Figure S6. Top 15 highest ranked GO sets based on enrichment analysis of status-related DEGs in the ovary of NMR females. Figure S7. Top 15 highest ranked GO sets based on enrichment analysis of status-related DEGs in adrenal gland of NMR females. Figure S8. Top 15 highest ranked GO sets based on enrichment analysis of status-related DEGs in cerebellum of NMR females. Figure S9. Top 15 highest ranked GO sets based on enrichment analysis of status-related DEGs in testis of NMR males. Figure S10: Top 15 highest ranked GO sets based on enrichment analysis of status-related DEGs in skin of NMR males. Figure S11. Mitonuclear ratios in non-breeders and breeders per sex, tissue, and species. Figure S12. Top 15 highest ranked GO sets based on enrichment analysis of the non-redundant set of aging-related 20% quantiles that show the greatest interspecies difference in males (Tes, Skn). Figure S13. Top 15 highest ranked GO sets based on enrichment analysis of the non-redundant set of aging-related 20% quantiles that show the greatest interspecies difference in females (Hrt, Pit, Ovr). (PDF 1241 kb

Additional file 7: of Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging

Gene annotation track for guinea pig. (GFF 19536 kb

Additional file 8: of Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging

Gene annotation track for naked mole-rat. (GFF 18958 kb

Additional file 3: of Naked mole-rat transcriptome signatures of socially suppressed sexual maturation and links of reproduction to aging

Text S1. Detailed description of expression changes in genes involved in steroidogenesis. Text S2. Detailed description of expression changes in gonadotropin-related genes (PDF 296 kb