Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences

Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher order relationships. Such analyses are rightfully regarded as the ‘gold standard’ for phylogenetics. However, DNA retrieval requires modern or well-preserved tissue and is less likely to be preserved in archaeological or fossil specimens. By contrast, some proteins, such as collagen, are phylogenetically informative and can survive into deep time. Here, we test the utility of collagen type I amino acid sequences for phylogenetic estimation of ray-finned fishes. We estimate topology using Bayesian approaches and compare the congruence of our estimated trees with published genomic phylogenies. Furthermore, we apply a Bayesian molecular clock approach and compare estimated divergence dates with previously published genomic clock analyses. Our collagen-derived trees exhibit 77% of node positions as congruent with recent genomic-derived trees, with the majority of discrepancies occurring in higher order node positions, almost exclusively within the Percomorpha. Our molecular clock trees present divergence times that are fairly comparable with genomic-based phylogenetic analyses. We estimate the mean node age of Actinopteri at ∼293 million years (Ma), the base of Teleostei at ∼211 Ma and the radiation of percomorphs beginning at ∼141 Ma (∼350 Ma, ∼250–283 Ma and ∼120–133 Ma in genomic trees, respectively). Finally, we show that the average rate of collagen (I) sequence evolution is 0.9 amino acid substitutions for every million years of divergence, with the α3 (I) sequence evolving the fastest, followed by the α2 (I) chain. This is the quickest rate known for any vertebrate group. We demonstrate that phylogenetic analyses using collagen type I amino acid sequences generate tangible signals for actinopterygians that are highly congruent with recent genomic-level studies. However, there is limited congruence within percomorphs, perhaps due to clade-specific functional constraints acting upon collagen sequences. Our results provide important insights for future phylogenetic analyses incorporating extinct actinopterygian species via collagen (I) sequencing

Lack of Genetic Interaction between Tbx20 and Tbx3 in Early Mouse Heart Development

Members of the T-box family of transcription factors are important regulators orchestrating the complex regionalization of the developing mammalian heart. Individual mutations in Tbx20 and Tbx3 cause distinct congenital heart abnormalities in the mouse: Tbx20 mutations result in failure of heart looping, developmental arrest and lack of chamber differentiation, while hearts of Tbx3 mutants progress further, loop normally but show atrioventricular convergence and outflow tract defects. The two genes have overlapping areas of expression in the atrioventricular canal and outflow tract of the heart but their potential genetic interaction has not been previously investigated. In this study we produced compound mutants to investigate potential genetic interactions at the earliest stages of heart development. We find that Tbx20; Tbx3 double heterozygous mice are viable and fertile with no apparent abnormalities, while double homozygous mutants are embryonic lethal by midgestation. Double homozygous mutant embryos display abnormal cardiac morphogenesis, lack of heart looping, expression patterns of cardiac genes and time of death that are indistinguishable from Tbx20 homozygous mutants. Prior to death, the double homozygotes show an overall developmental delay similar to Tbx3 homozygous mutants. Thus the effects of Tbx20 are epistatic to Tbx3 in the heart but Tbx3 is epistatic to Tbx20 with respect to developmental delay

The Ursinus Weekly, January 10, 1908

Richard Wagner • Editorial: Resolution • Lecture • Alumni notes • College world • Personals • Seminary notes • Literary Supplement: A story from life; Richard Mansfield; A twentieth century satirist; Patrick Henry; Eulogy on Lincolnhttps://digitalcommons.ursinus.edu/weekly/2890/thumbnail.jp

Metabolomics Profile and Targeted Lipidomics in Multiple Tissues Associated with Feed Efficiency in Beef Steers

A study of multiple tissues was conducted to identify potential metabolic differences in cattle differing in feed efficiency. Individual feed intake and body weight was measured on 144 steers during 105 days on a high-concentrate ration. Steers were selected according to differences in average daily gain (ADG) with those with the greatest ADG (n = 8; 1.96 ± 0.02 kg/day) and least ADG (n = 8; 1.57 ± 0.02 kg/day), whose dry matter intake was within 0.32 SD of the mean intake (10.10 ± 0.05 kg/day). Duodenum, liver, adipose, and longissimus-dorsi were collected at slaughter, and metabolomics profiles were performed by ultra performance liquid chromatography quadrupole-time of-flight mass spectrometry. Principal components analyses, t-tests, and fold changes in tissues profile were used to identify differential metabolites between ADG groups. These were primarily involved in α-linolenic metabolism, which was downregulated in the greatest ADG as compared to least-ADG group in duodenum, adipose, and longissimus-dorsi. However, taurine and glycerophospholipids metabolisms were both upregulated in the greatest ADG compared with least-ADG group in the liver. The phospholipids and cholesterol were quantified in the tissues. Lipid transport and oxidation were the main common metabolic mechanisms associated with cattle feed efficiency. Combining analyses of multiple tissues may offer a powerful approach for defining the molecular basis of differences in performance among cattle for key production attributes

PSXII-19 Urine Metabolomics Analysis Associated with Feed Efficiency on Crossbred Steers during the Growing and Finishing Period on Forage- and Concentrate- Based Diets.

A discovery project to identify non‐invasive biomarkers that can detect subtle metabolic discrepancies for cattle feed efficiency was performed using untargeted and targeted urine metabolomics by ultra-performance liquid chromatography-mass spectrometry. Individual feed intake and body weight gain were measured in crossbred steers (n = 80) on a forage-based growing ration (stage-1) followed by a high-concentrate diet finishing ration (stage- 2). Urine was collected on study days 0, 21, 42, 63, and 83 for each dietary stage. In total, 28 steers with the greatest and the least average daily-gain (ADG) within 0.32 SD of the mean of dry-matter-intake (DMI) were used. A principal component analysis of the untargeted metabolites fully segregated the highest-ADG and lowest-ADG animals, with overlap across diets (both stages). The urinary untargeted metabolites that segregated the ADG-groups (n = 199; P \u3c 0.05), included steroid-hormones, bile-acids, alpha-linolenic acid metabolites, vitamin-B6, along with products of glycine, serine and threonine metabolism (metabolic pathway analysis: impact-value \u3e 0.50; FDR \u3c 0.10). Bile acids and steroids were then quantified in urine and their associations with animal performance and carcass composition evaluated by correlation and multiple logistic regression AUC-ROC curve analyses. In stage-1, urine concentration of cortisone was associated (P \u3c 0.05) with ADG (r = -0.28), DMI (r = -0.40) and ribeye-area (r = -0.28); cortisol was associated with DMI (r = -0.32; P \u3c 0.01) and testosterone was associated with ADG (r = -0.28; P \u3c 0.01). The urine concentrations of 18 measured bile acids were negatively associated (P \u3c 0.05) with DMI, and secondary bile acids were negatively associated (P \u3c 0.01) with marbling and hot-carcass-weight. In stage-2, negative association between the bile acids glycocholic acid and deoxycholic acid with marbling and hot-carcass-weight were identified. Urine metabolomics provide new insight into the physiological mechanisms and potential biomarkers of cattle feed efficiency. USDA is an equal opportunity provider and employer

Conflict of interest in science communication: more than a financial issue. Report from Esteve Foundation discussion group, April 2009

A systematic review and meta-analysis suggests that around 2% of scientists admit to have falsified research at least once. Up to 33% admit other questionable practices such as plagiarism, duplicate publication, undisclosed changes in pre-research protocols or dubious ethical behavior. There can be no doubt that discovered cases of research and publication misconduct represent a tip of an iceberg and many cases go unreported

Portfolio Vol. V N 3

Koons, Marilyn. Apology . Poem. 5. Koons, Marilyn. A Woman\u27s Request Poem. 5. Davidson, Sally. Of the Present . Poem. 5. Koons, Marilyn. Escape in Memory . Poem. 5. Stander, Marianna. Self Portrait . Picture. 5. Morton, John. Consumer\u27s Victory . Prose. 6. Rhu, Helen. Prize Winning Poem . Poem. 8. Rhu, Helen. To the Victor . Poem. 8. Rhu, Helen. Fantasy at Midnight . Poem. 8. Tomlin, Bonnie. The Drag . Picture. 8. Morse, Kay. In Spite of all... Prose. 9. Metcalf, Carolyn. Isolation . Cartoon. 12. Koons, Marilyn. In Black and White . Prose. 14. Harvey, Dick. Through Enemy Eyes . Prose. 15. Vercoe, Mary. Storm .Poem. 16. Vercoe, Mary. Refuge .Poem. 16. Vercoe, Mary. Recovery .Poem. 16. Vercoe, Mary. Temporary Address .Poem. 16. Hill, Jacque. Weary Words . Poem. 17. Brannon, Earl W. The Fall . Poem. 17. T.W. Gardenias . Poem. 17. Hayne, Barbara. Window Tears . Poem. 17. Burrows, Pete. Family Portrait . Prose. 18. Seagrave, Leslie. Retribution . Prose. 19. Benson, Virginia. The Moon Came Up . Prose. 21. Reynolds, Virginia. Matter Over Mind . Prose. 22