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6. Changes in CpG Methylation of the Vitellogenin 1 Promoter in Adult Male Zebrafish after Exposure to 17α‐Ethynylestradiol.

Author

Kolli, Ramya T., Glenn, Travis C., Bringolf, Robert B., Henderson, Matthew, Cummings, Brian S., and Kenneke, John F.

Subjects
*VITELLOGENINS, *SEWAGE, *BRACHYDANIO, *DNA methylation, *AGRICULTURE, *ESTROGEN receptors, *EGG yolk, *MESSENGER RNA
Abstract

Numerous pharmaceutical and industrial chemicals are classified as endocrine‐disrupting chemicals (EDCs) that interfere with hormonal homeostasis, leading to developmental disorders and other pathologies. The synthetic estrogen 17α‐ethynylestradiol (EE2) is used in oral contraceptives and other hormone therapies. EE2 and other estrogens are inadvertently introduced into aquatic environments through municipal wastewater and agricultural effluents. Exposure of male fish to estrogens increases expression of the egg yolk precursor protein vitellogenin (Vtg), which is used as a molecular marker of exposure to estrogenic EDCs. The mechanisms behind Vtg induction are not fully known, and we hypothesized that it is regulated via DNA methylation. Adult zebrafish were exposed to either dimethyl sulfoxide or 20 ng/L EE2 for 14 days. Messenger RNA (mRNA) expression and DNA methylation were assessed in male zebrafish livers at 0, 0.25, 0.5, 1, 4, 7, and 14 days of exposure; and those of females were assessed at 13 days (n ≥ 4/group/time point). To test the persistence of any changes, we included a recovery group that received EE2 for 7 days and did not receive any for the following 7 days, in the total 14‐day study. Methylation of DNA at the vtg1 promoter was assessed with targeted gene bisulfite sequencing in livers of adult male and female zebrafish. A significant increase in vtg1 mRNA was observed in the EE2‐exposed male fish as early as 6 h. Interestingly, DNA methylation changes were observed at 4 days. Decreases in the overall methylation of the vtg1 promoter in exposed males resulted in levels comparable to those in female controls, suggesting feminization. Importantly, DNA methylation levels in males remained significantly impacted after 7 days post–EE2 removal, unlike mRNA levels. These data identify an epigenetic mark of feminization that may serve as an indicator of not only estrogenic exposure but also previous exposure to EE2. Environ Toxicol Chem 2024;43:1547–1556. © 2024 SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA. [ABSTRACT FROM AUTHOR]

Published
2024
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7. Earth history and the passerine superra

Author

Oliveros, Carl H., Field, Daniel J., Ksepka, Daniel T., Barker, F. Keith, Aleixo, Alexandre, Andersen, Michael J., Alström, Per, Benz, Brett W., Braun, Edward L., Braun, Michael J., Bravo, Gustavo A., Brumfield, Robb T., Chesser, R. Terry, Claramunt, Santiago, Cracraft, Joel, Cuervo, Andrés M., Derryberry, Elizabeth P., Glenn, Travis C., Harvey, Michael G., Hosner, Peter A., Joseph, Leo, Kimball, Rebecca T., Mack, Andrew L., Miskelly, Colin M., Peterson, A. Townsend, Robbins, Mark B., Sheldon, Frederick H., Silveira, Luís Fábio, Smith, Brian Tilston, White, Noor D., Moyle, Robert G., and Faircloth, Brant C.

Published
2019

10. Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture.

Author

Álvarez Narváez, Sonsiray, Beaudry, Megan S., Norris, Connor G., Bartlett, Paula B., Glenn, Travis C., and Sanchez, Susan

Subjects
GUT microbiome, CAUSES of death, GASTROINTESTINAL system, RIBOSOMAL RNA, HORSES, DYSBIOSIS, HORSE breeds
Abstract

Simple Summary: Gastrointestinal tract disorders (GITDs) are a serious problem for both adult and young horses. In many cases, the sources of these disorders are unknown, and a link with alterations of the gastrointestinal (GI) microbiome (i.e., GI dysbiosis) is suspected. New alternatives to conventional amplicon sequencing are needed to decipher the real connection between GITDs and dysbiosis. This study compares the performance of target enrichment by hybridization capture (TEHC), a new approach for microbiome sequencing, with conventional amplicon sequencing for the characterization of the equine fecal microbiome. GITDs are among the most common causes of death in adult and young horses in the United States (US). Previous studies have indicated a connection between GITDs and the equine gut microbiome. However, the low taxonomic resolution of the current microbiome sequencing methods has hampered the identification of specific bacterial changes associated with GITDs in horses. Here, we have compared TEHC, a new approach for 16S rRNA gene selection and sequencing, with conventional 16S rRNA gene amplicon sequencing for the characterization of the equine fecal microbiome. Both sequencing approaches were used to determine the fecal microbiome of four adult horses and one commercial mock microbiome. Our results show that TEHC yielded significantly more operational taxonomic units (OTUs) than conventional 16S amplicon sequencing when the same number of reads were used in the analysis. This translated into a deeper and more accurate characterization of the fecal microbiome when the samples were sequenced with TEHC according to the relative abundance analysis. Alpha and beta diversity metrics corroborated these findings and demonstrated that the microbiome of the fecal samples was significantly richer when sequenced with TEHC compared to 16S amplicon sequencing. Altogether, our study suggests that the TEHC strategy provides a more extensive characterization of the fecal microbiome of horses than the current alternative based on the PCR amplification of a portion of the 16S rRNA gene. [ABSTRACT FROM AUTHOR]

Published
2024
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11. River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex.

Author

Pierson, Todd W, Kozak, Kenneth H, Glenn, Travis C, and Fitzpatrick, Benjamin M

Subjects
SALAMANDERS, DNA analysis, SPECIES, GENE flow, MITOCHONDRIAL DNA, DRAINAGE, PHYLOGEOGRAPHY
Abstract

The origin and eventual loss of biogeographic barriers can create alternating periods of allopatry and secondary contact, facilitating gene flow among distinct metapopulations and generating reticulate evolutionary histories that are not adequately described by a bifurcating evolutionary tree. One such example may exist in the two-lined salamander (Eurycea bislineata) species complex, where discordance among morphological and molecular datasets has created a "vexing taxonomic challenge." Previous phylogeographic analyses of mitochondrial DNA (mtDNA) suggested that the reorganization of Miocene paleodrainages drove vicariance and dispersal, but the inherent limitations of a single-locus dataset precluded the evaluation of subsequent gene flow. Here, we generate triple-enzyme restriction site-associated DNA sequencing (3RAD) data for > 100 individuals representing all major mtDNA lineages and use a suite of complementary methods to demonstrate that discordance among earlier datasets is best explained by a reticulate evolutionary history influenced by river drainage reorganization. Systematics of such groups should acknowledge these complex histories and relationships that are not strictly hierarchical. [Amphibian; hybridization; introgression; Plethodontidae; stream capture.] [ABSTRACT FROM AUTHOR]

Published
2024
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15. Security in a Safety Pin

Author

Glenn, Travis

Subjects
Discrimination against gays -- Personal narratives -- Health aspects, Medical personnel -- Training, Family and marriage, Health, Psychology and mental health
Abstract

A narrative about realizations as a young, gay, cis-gender man going through the medical system then through medical training. Keywords: narrative, LGBTQ, LGBTQ healthcare, Being raised in a conservative and religious family, I struggled to accept my identity as a gay man. In that struggle, I also found it difficult to be honest with [...]

Published
2020
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23. New T2T assembly of Cryptosporidium parvum IOWA annotated with reference genome gene identifiers

Author

de Paula Baptista, Rodrigo, Xiao, Rui, Li, Yiran, Glenn, Travis C., and Kissinger, Jessica C.

Subjects
Article
Abstract

Cryptosporidium parvum is a significant pathogen causing gastrointestinal infections in humans and animals, that is spread through the ingestion of contaminated food and water. Despite its global impact on public health, generating a C. parvum genome sequence has always been challenging due to a lack of in vitro cultivation systems and challenging sub-telomeric gene families. A gapless telomere to telomere genome assembly has been created for Cryptosporidium parvum IOWA obtained from Bunch Grass Farms, named here as CpBGF. There are 8 chromosomes that total 9,259,183 bp. The new hybrid assembly which was generated with Illumina and Oxford Nanopore resolves complex sub-telomeric regions of chromosomes 1, 7 and 8. To facilitate ease of use and consistency with the literature, whenever possible, chromosomes have been oriented and genes in this annotation have been given the same gene IDs used in the current reference genome sequence generated in 2004. The annotation of this assembly utilized considerable RNA expression evidence, thus, untranslated regions, long noncoding RNAs and antisense RNAs are annotated. The CpBGF genome assembly serves as a valuable resource for understanding the biology, pathogenesis, and transmission of C. parvum , and it facilitates the development of diagnostics, drugs, and vaccines against cryptosporidiosis.

Published
2023

28. Addressing ecological effects of radiation on populations and ecosystems to improve protection of the environment against radiation: Agreed statements from a Consensus Symposium

Author

Bréchignac, François, Oughton, Deborah, Mays, Claire, Barnthouse, Lawrence, Beasley, James C., Bonisoli-Alquati, Andrea, Bradshaw, Clare, Brown, Justin, Dray, Stéphane, Geras'kin, Stanislav, Glenn, Travis, Higley, Kathy, Ishida, Ken, Kapustka, Lawrence, Kautsky, Ulrik, Kuhne, Wendy, Lynch, Michael, Mappes, Tapio, Mihok, Steve, Møller, Anders P., Mothersill, Carmel, Mousseau, Timothy A., Otaki, Joji M., Pryakhin, Evgeny, Rhodes, Olin E., Jr., Salbu, Brit, Strand, Per, and Tsukada, Hirofumi

Published
2016
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35. Whole-genome analyses resolve early branches in the tree of life of modern birds

Author

Jarvis, Erich D., Mirarab, Siavash, Aberer, Andre J., Li, Bo, Houde, Peter, Li, Cai, Ho, Simon Y. W., Faircloth, Brant C., Nabholz, Benoit, Howard, Jason T., Suh, Alexander, Weber, Claudia C., da Fonseca, Rute R., Li, Jianwen, Zhang, Fang, Li, Hui, Zhou, Long, Narula, Nitish, Liu, Liang, Ganapathy, Ganesh, Boussau, Bastien, Bayzid, Md. Shamsuzzoha, Zavidovych, Volodymyr, Subramanian, Sankar, Gabaldón, Toni, Capella-Gutiérrez, Salvador, Huerta-Cepas, Jaime, Rekepalli, Bhanu, Munch, Kasper, Schierup, Mikkel, Lindow, Bent, Warren, Wesley C., Ray, David, Green, Richard E., Bruford, Michael W., Zhan, Xiangjiang, Dixon, Andrew, Li, Shengbin, Li, Ning, Huang, Yinhua, Derryberry, Elizabeth P., Bertelsen, Mads Frost, Sheldon, Frederick H., Brumfield, Robb T., Mello, Claudio V., Lovell, Peter V., Wirthlin, Morgan, Schneider, Maria Paula Cruz, Prosdocimi, Francisco, Samaniego, José Alfredo, Velazquez, Amhed Missael Vargas, Alfaro-Núñez, Alonzo, Campos, Paula F., Petersen, Bent, Sicheritz-Ponten, Thomas, Pas, An, Bailey, Tom, Scofield, Paul, Bunce, Michael, Lambert, David M., Zhou, Qi, Perelman, Polina, Driskell, Amy C., Shapiro, Beth, Xiong, Zijun, Zeng, Yongli, Liu, Shiping, Li, Zhenyu, Liu, Binghang, Wu, Kui, Xiao, Jin, Yinqi, Xiong, Zheng, Qiuemei, Zhang, Yong, Yang, Huanming, Wang, Jian, Smeds, Linnea, Rheindt, Frank E., Braun, Michael, Fjeldsa, Jon, Orlando, Ludovic, Barker, F. Keith, Jønsson, Knud Andreas, Johnson, Warren, Koepfli, Klaus-Peter, O'Brien, Stephen, Haussler, David, Ryder, Oliver A., Rahbek, Carsten, Willerslev, Eske, Graves, Gary R., Glenn, Travis C., McCormack, John, Burt, Dave, Ellegren, Hans, Alström, Per, Edwards, Scott V., Stamatakis, Alexandros, Mindell, David P., Cracraft, Joel, Braun, Edward L., Warnow, Tandy, Jun, Wang, Gilbert, M. Thomas P., and Zhang, Guojie

Published
2014

36. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Author

Green, Richard E., Braun, Edward L., Armstrong, Joel, Earl, Dent, Nguyen, Ngan, Hickey, Glenn, Vandewege, Michael W., St. John, John A., Capella-Gutiérrez, Salvador, Castoe, Todd A., Kern, Colin, Fujita, Matthew K., Opazo, Juan C., Jurka, Jerzy, Kojima, Kenji K., Caballero, Juan, Hubley, Robert M., Smit, Arian F., Platt, Roy N., Lavoie, Christine A., Ramakodi, Meganathan P., Finger, John W., Suh, Alexander, Isberg, Sally R., Miles, Lee, Chong, Amanda Y., Jaratlerdsiri, Weerachai, Gongora, Jaime, Moran, Christopher, Iriarte, Andrés, McCormack, John, Burgess, Shane C., Edwards, Scott V., Lyons, Eric, Williams, Christina, Breen, Matthew, Howard, Jason T., Gresham, Cathy R., Peterson, Daniel G., Schmitz, Jürgen, Pollock, David D., Haussler, David, Triplett, Eric W., Zhang, Guojie, Irie, Naoki, Jarvis, Erich D., Brochu, Christopher A., Schmidt, Carl J., McCarthy, Fiona M., Faircloth, Brant C., Hoffmann, Federico G., Glenn, Travis C., Gabaldón, Toni, Paten, Benedict, and Ray, David A.

Published
2014

40. Phylogeography of the blacklegged tick (Ixodes scapularis) throughout the USA identifies candidate loci for differences in vectorial capacity.

Author

Frederick, Julia C., Thompson, Alec T., Sharma, Prisha, Dharmarajan, Guha, Ronai, Isobel, Pesapane, Risa, Smith, Ryan C., Sundstrom, Kellee D., Tsao, Jean I., Tuten, Holly C., Yabsley, Michael J., and Glenn, Travis C.

Subjects
IXODES scapularis, TICK infestations, POPULATION differentiation, LYME disease, LOCUS (Genetics), GENETIC variation, PHYLOGEOGRAPHY
Abstract

The blacklegged tick (Ixodes scapularis (Journal of the Academy of Natural Sciences of Philadelphia, 1821, 2, 59)) is a vector of Borrelia burgdorferi sensu stricto (s.s.) (International Journal of Systematic Bacteriology, 1984, 34, 496), the causative bacterial agent of Lyme disease, part of a slow‐moving epidemic of Lyme borreliosis spreading across the northern hemisphere. Well‐known geographical differences in the vectorial capacity of these ticks are associated with genetic variation. Despite the need for detailed genetic information in this disease system, previous phylogeographical studies of these ticks have been restricted to relatively few populations or few genetic loci. Here we present the most comprehensive phylogeographical study of genome‐wide markers in I. scapularis, conducted by using 3RAD (triple‐enzyme restriction‐site associated sequencing) and surveying 353 ticks from 33 counties throughout the species' range. We found limited genetic variation among populations from the Northeast and Upper Midwest, where Lyme disease is most common, and higher genetic variation among populations from the South. We identify five spatially associated genetic clusters of I. scapularis. In regions where Lyme disease is increasing in frequency, the I. scapularis populations genetically group with ticks from historically highly Lyme‐endemic regions. Finally, we identify 10 variable DNA sites that contribute the most to population differentiation. These variable sites cluster on one of the chromosome‐scale scaffolds for I. scapularis and are within identified genes. Our findings illuminate the need for additional research to identify loci causing variation in the vectorial capacity of I. scapularis and where additional tick sampling would be most valuable to further understand disease trends caused by pathogens transmitted by I. scapularis. [ABSTRACT FROM AUTHOR]

Published
2023
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45. The drivers of tropical speciation

Author

Smith, Brian Tilston, McCormack, John E., Cuervo, Andrés M., Hickerson, Michael. J., Aleixo, Alexandre, Cadena, Carlos Daniel, Pérez-Emán, Jorge, Burney, Curtis W., Xie, Xiaoou, Harvey, Michael G., Faircloth, Brant C., Glenn, Travis C., Derryberry, Elizabeth P., Prejean, Jesse, Fields, Samantha, and Brumfield, Robb T.

Published
2014
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