14 results on '"Li, Amy S."'
Search Results
2. Disruption in glutathione metabolism and altered energy production in the liver and kidney after ischemic acute kidney injury in mice
- Author
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Baker, II, Peter R., Li, Amy S., Griffin, Benjamin R., Gil, Hyo-Wook, Orlicky, David J., Fox, Benjamin M., Park, Bryan, Sparagna, Genevieve C., Goff, Jared, Altmann, Christopher, Elajaili, Hanan, Okamura, Kayo, He, Zhibin, Stephenson, Daniel, D’Alessandro, Angelo, Reisz, Julie A., Nozik, Eva S., Sucharov, Carmen C., and Faubel, Sarah
- Published
- 2024
- Full Text
- View/download PDF
3. Putative Mode of Action of the Monoterpenoids Linalool, Methyl Eugenol, Estragole, and Citronellal on Ligand-Gated Ion Channels
- Author
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Li, Amy S., Iijima, Akimasa, Huang, Junhao, Li, Qing X., and Chen, Yongli
- Published
- 2020
- Full Text
- View/download PDF
4. Metformin does not slow cyst growth in the PCK rat model of polycystic kidney disease
- Author
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Oto, Ozgur A., primary, Atwood, Daniel J., additional, Chaudhary, Anjana, additional, He, Zhibin, additional, Li, Amy S., additional, Wempe, Michael F., additional, and Edelstein, Charles L., additional
- Published
- 2023
- Full Text
- View/download PDF
5. Immune checkpoint activity regulates polycystic kidney disease progression
- Author
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Kleczko, Emily K., primary, Nguyen, Dustin T., additional, Marsh, Kenneth H., additional, Bauer, Colin D., additional, Li, Amy S., additional, Monaghan, Marie-Louise T., additional, Berger, Michael D., additional, Furgeson, Seth B., additional, Gitomer, Berenice Y., additional, Chonchol, Michel B., additional, Clambey, Eric T., additional, Zimmerman, Kurt A., additional, Nemenoff, Raphael A., additional, and Hopp, Katharina, additional
- Published
- 2023
- Full Text
- View/download PDF
6. IL-6 mediates the hepatic acute phase response after prerenal azotemia in a clinically defined murine model.
- Author
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Kayo Okamura, Sizhao Lu, Zhibin He, Altmann, Chris, Montford, John R., Li, Amy S., Lucia, M. Scott, Orlicky, David J., Weiser-Evans, Mary, and Faubel, Sarah
- Subjects
ACUTE phase reaction ,GLOMERULAR filtration rate ,ACUTE kidney failure ,BLOOD proteins ,INTERLEUKIN-6 - Abstract
Prerenal azotemia (PRA) is a major cause of acute kidney injury and uncommonly studied in preclinical models. We sought to develop and characterize a novel model of PRA that meets the clinical definition: acute loss of glomerular filtration rate (GFR) that returns to baseline with resuscitation. Adult male C57BL/6J wild-type (WT) and IL-6
−/− mice were studied. Intraperitoneal furosemide (4 mg) or vehicle was administered at time = 0 and 3 h to induce PRA from volume loss. Resuscitation began at 6 h with 1 mL intraperitoneal saline for four times for 36 h. Six hours after furosemide administration, measured glomerular filtration rate was 25% of baseline and returned to baseline after saline resuscitation at 48 h. After 6 h of PRA, plasma interleukin (IL)-6 was significantly increased, kidney and liver histology were normal, kidney and liver lactate were normal, and kidney injury molecule-1 immunofluorescence was negative. There were 327 differentially regulated genes upregulated in the liver, and the acute phase response was the most significantly upregulated pathway; 84 of the upregulated genes (25%) were suppressed in IL-6−/− mice, and the acute phase response was the most significantly suppressed pathway. Significantly upregulated genes and their proteins were also investigated and included serum amyloid A2, serum amyloid A1, lipocalin 2, chemokine (C-X-C motif) ligand 1, and haptoglobin; hepatic gene expression and plasma protein levels were all increased in wild-type PRA and were all reduced in IL-6−/− PRA. This work demonstrates previously unknown systemic effects of PRA that includes IL-6-mediated upregulation of the hepatic acute phase response. NEW & NOTEWORTHY Prerenal azotemia (PRA) accounts for a third of acute kidney injury (AKI) cases yet is rarely studied in preclinical models. We developed a clinically defined murine model of prerenal azotemia characterized by a 75% decrease in measured glomerular filtration rate (GFR), return of measured glomerular filtration rate to baseline with resuscitation, and absent tubular injury. Numerous systemic effects were observed, such as increased plasma interleukin-6 (IL-6) and upregulation of the hepatic acute phase response. [ABSTRACT FROM AUTHOR]- Published
- 2023
- Full Text
- View/download PDF
7. IL-6 mediates the hepatic acute phase response after prerenal azotemia in a clinically defined murine model
- Author
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Okamura, Kayo, Lu, Sizhao, He, Zhibin, Altmann, Chris, Montford, John R., Li, Amy S., Lucia, M. Scott, Orlicky, David J., Weiser-Evans, Mary, and Faubel, Sarah
- Published
- 2023
- Full Text
- View/download PDF
8. Immune Checkpoint Activity Regulates Polycystic Kidney Disease Progression
- Author
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Kleczko, Emily K., primary, Nguyen, Dustin T., additional, Marsh, Kenneth H., additional, Bauer, Colin D., additional, Li, Amy S., additional, Furgeson, Seth B., additional, Gitomer, Berenice Y., additional, Chonchol, Michel B., additional, Clambey, Eric T., additional, Zimmerman, Kurt A., additional, Nemenoff, Raphael A., additional, and Hopp, Katharina, additional
- Published
- 2022
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9. Comment from the Field: Disability Studies in Science Fiction and Fantasy
- Author
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Li, Amy S., primary
- Published
- 2020
- Full Text
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10. Retrotransposons Are the Major Contributors to the Expansion of theDrosophila ananassaeMuller F Element
- Author
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Leung, Wilson, primary, Shaffer, Christopher D, additional, Chen, Elizabeth J, additional, Quisenberry, Thomas J, additional, Ko, Kevin, additional, Braverman, John M, additional, Giarla, Thomas C, additional, Mortimer, Nathan T, additional, Reed, Laura K, additional, Smith, Sheryl T, additional, Robic, Srebrenka, additional, McCartha, Shannon R, additional, Perry, Danielle R, additional, Prescod, Lindsay M, additional, Sheppard, Zenyth A, additional, Saville, Ken J, additional, McClish, Allison, additional, Morlock, Emily A, additional, Sochor, Victoria R, additional, Stanton, Brittney, additional, Veysey-White, Isaac C, additional, Revie, Dennis, additional, Jimenez, Luis A, additional, Palomino, Jennifer J, additional, Patao, Melissa D, additional, Patao, Shane M, additional, Himelblau, Edward T, additional, Campbell, Jaclyn D, additional, Hertz, Alexandra L, additional, McEvilly, Maddison F, additional, Wagner, Allison R, additional, Youngblom, James, additional, Bedi, Baljit, additional, Bettincourt, Jeffery, additional, Duso, Erin, additional, Her, Maiye, additional, Hilton, William, additional, House, Samantha, additional, Karimi, Masud, additional, Kumimoto, Kevin, additional, Lee, Rebekah, additional, Lopez, Darryl, additional, Odisho, George, additional, Prasad, Ricky, additional, Robbins, Holly Lyn, additional, Sandhu, Tanveer, additional, Selfridge, Tracy, additional, Tsukashima, Kara, additional, Yosif, Hani, additional, Kokan, Nighat P, additional, Britt, Latia, additional, Zoellner, Alycia, additional, Spana, Eric P, additional, Chlebina, Ben T, additional, Chong, Insun, additional, Friedman, Harrison, additional, Mammo, Danny A, additional, Ng, Chun L, additional, Nikam, Vinayak S, additional, Schwartz, Nicholas U, additional, Xu, Thomas Q, additional, Burg, Martin G, additional, Batten, Spencer M, additional, Corbeill, Lindsay M, additional, Enoch, Erica, additional, Ensign, Jesse J, additional, Franks, Mary E, additional, Haiker, Breanna, additional, Ingles, Judith A, additional, Kirkland, Lyndsay D, additional, Lorenz-Guertin, Joshua M, additional, Matthews, Jordan, additional, Mittig, Cody M, additional, Monsma, Nicholaus, additional, Olson, Katherine J, additional, Perez-Aragon, Guillermo, additional, Ramic, Alen, additional, Ramirez, Jordan R, additional, Scheiber, Christopher, additional, Schneider, Patrick A, additional, Schultz, Devon E, additional, Simon, Matthew, additional, Spencer, Eric, additional, Wernette, Adam C, additional, Wykle, Maxine E, additional, Zavala-Arellano, Elizabeth, additional, McDonald, Mitchell J, additional, Ostby, Kristine, additional, Wendland, Peter, additional, DiAngelo, Justin R, additional, Ceasrine, Alexis M, additional, Cox, Amanda H, additional, Docherty, James E B, additional, Gingras, Robert M, additional, Grieb, Stephanie M, additional, Pavia, Michael J, additional, Personius, Casey L, additional, Polak, Grzegorz L, additional, Beach, Dale L, additional, Cerritos, Heaven L, additional, Horansky, Edward A, additional, Sharif, Karim A, additional, Moran, Ryan, additional, Parrish, Susan, additional, Bickford, Kirsten, additional, Bland, Jennifer, additional, Broussard, Juliana, additional, Campbell, Kerry, additional, Deibel, Katelynn E, additional, Forka, Richard, additional, Lemke, Monika C, additional, Nelson, Marlee B, additional, O'Keeffe, Catherine, additional, Ramey, S Mariel, additional, Schmidt, Luke, additional, Villegas, Paola, additional, Jones, Christopher J, additional, Christ, Stephanie L, additional, Mamari, Sami, additional, Rinaldi, Adam S, additional, Stity, Ghazal, additional, Hark, Amy T, additional, Scheuerman, Mark, additional, Silver Key, S Catherine, additional, McRae, Briana D, additional, Haberman, Adam S, additional, Asinof, Sam, additional, Carrington, Harriette, additional, Drumm, Kelly, additional, Embry, Terrance, additional, McGuire, Richard, additional, Miller-Foreman, Drew, additional, Rosen, Stella, additional, Safa, Nadia, additional, Schultz, Darrin, additional, Segal, Matt, additional, Shevin, Yakov, additional, Svoronos, Petros, additional, Vuong, Tam, additional, Skuse, Gary, additional, Paetkau, Don W, additional, Bridgman, Rachael K, additional, Brown, Charlotte M, additional, Carroll, Alicia R, additional, Gifford, Francesca M, additional, Gillespie, Julie Beth, additional, Herman, Susan E, additional, Holtcamp, Krystal L, additional, Host, Misha A, additional, Hussey, Gabrielle, additional, Kramer, Danielle M, additional, Lawrence, Joan Q, additional, Martin, Madeline M, additional, Niemiec, Ellen N, additional, O'Reilly, Ashleigh P, additional, Pahl, Olivia A, additional, Quintana, Guadalupe, additional, Rettie, Elizabeth A S, additional, Richardson, Torie L, additional, Rodriguez, Arianne E, additional, Rodriguez, Mona O, additional, Schiraldi, Laura, additional, Smith, Joanna J, additional, Sugrue, Kelsey F, additional, Suriano, Lindsey J, additional, Takach, Kaitlyn E, additional, Vasquez, Arielle M, additional, Velez, Ximena, additional, Villafuerte, Elizabeth J, additional, Vives, Laura T, additional, Zellmer, Victoria R, additional, Hauke, Jeanette, additional, Hauser, Charles R, additional, Barker, Karolyn, additional, Cannon, Laurie, additional, Parsamian, Perouza, additional, Parsons, Samantha, additional, Wichman, Zachariah, additional, Bazinet, Christopher W, additional, Johnson, Diana E, additional, Bangura, Abubakarr, additional, Black, Jordan A, additional, Chevee, Victoria, additional, Einsteen, Sarah A, additional, Hilton, Sarah K, additional, Kollmer, Max, additional, Nadendla, Rahul, additional, Stamm, Joyce, additional, Fafara-Thompson, Antoinette E, additional, Gygi, Amber M, additional, Ogawa, Emmy E, additional, Van Camp, Matt, additional, Kocsisova, Zuzana, additional, Leatherman, Judith L, additional, Modahl, Cassie M, additional, Rubin, Michael R, additional, Apiz-Saab, Susana S, additional, Arias-Mejias, Suzette M, additional, Carrion-Ortiz, Carlos F, additional, Claudio-Vazquez, Patricia N, additional, Espada-Green, Debbie M, additional, Feliciano-Camacho, Marium, additional, Gonzalez-Bonilla, Karina M, additional, Taboas-Arroyo, Mariela, additional, Vargas-Franco, Dorianmarie, additional, Montañez-Gonzalez, Raquel, additional, Perez-Otero, Joseph, additional, Rivera-Burgos, Myrielis, additional, Rivera-Rosario, Francisco J, additional, Eisler, Heather L, additional, Alexander, Jackie, additional, Begley, Samatha K, additional, Gabbard, Deana, additional, Allen, Robert J, additional, Aung, Wint Yan, additional, Barshop, William D, additional, Boozalis, Amanda, additional, Chu, Vanessa P, additional, Davis, Jeremy S, additional, Duggal, Ryan N, additional, Franklin, Robert, additional, Gavinski, Katherine, additional, Gebreyesus, Heran, additional, Gong, Henry Z, additional, Greenstein, Rachel A, additional, Guo, Averill D, additional, Hanson, Casey, additional, Homa, Kaitlin E, additional, Hsu, Simon C, additional, Huang, Yi, additional, Huo, Lucy, additional, Jacobs, Sarah, additional, Jia, Sasha, additional, Jung, Kyle L, additional, Wai-Chee Kong, Sarah, additional, Kroll, Matthew R, additional, Lee, Brandon M, additional, Lee, Paul F, additional, Levine, Kevin M, additional, Li, Amy S, additional, Liu, Chengyu, additional, Liu, Max Mian, additional, Lousararian, Adam P, additional, Lowery, Peter B, additional, Mallya, Allyson P, additional, Marcus, Joseph E, additional, Ng, Patrick C, additional, Nguyen, Hien P, additional, Patel, Ruchik, additional, Precht, Hashini, additional, Rastogi, Suchita, additional, Sarezky, Jonathan M, additional, Schefkind, Adam, additional, Schultz, Michael B, additional, Shen, Delia, additional, Skorupa, Tara, additional, Spies, Nicholas C, additional, Stancu, Gabriel, additional, Vivian Tsang, Hiu Man, additional, Turski, Alice L, additional, Venkat, Rohit, additional, Waldman, Leah E, additional, Wang, Kaidi, additional, Wang, Tracy, additional, Wei, Jeffrey W, additional, Wu, Dennis Y, additional, Xiong, David D, additional, Yu, Jack, additional, Zhou, Karen, additional, McNeil, Gerard P, additional, Fernandez, Robert W, additional, Menzies, Patrick Gomez, additional, Gu, Tingting, additional, Buhler, Jeremy, additional, Mardis, Elaine R, additional, and Elgin, Sarah C R, additional
- Published
- 2017
- Full Text
- View/download PDF
11. Plasma Cystatin C Predicts Kidney Function Recovery in Patients Requiring Continuous Kidney Replacement Therapy (CKRT) for AKI
- Author
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Haeger, Sarah, Okamura, Kayo, He, Zhibin, Li, Amy S., Colbert, James F., Campbell, Ruth E., Griffin, Benjamin R., and Faubel, Sarah
- Published
- 2023
- Full Text
- View/download PDF
12. Cystatin C and Kidney Function Recovery in Patients Requiring Continuous Kidney Replacement Therapy for Acute Kidney Injury.
- Author
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Haeger SM, Okamura K, Li AS, He Z, Park BD, Budnick IM, Foulon N, Kennis M, Blaine R, Miyazaki M, Campbell R, Jalal DI, Colbert JF, Brinton JT, Griffin BR, and Faubel S
- Abstract
Background: Plasma cystatin C is a reliable marker to estimate kidney function; however, it is unknown whether this remains true in patients receiving continuous kidney replacement therapy (CKRT). Herein, we tested the hypothesis that lower concentrations of plasma cystatin C during the first three days of CKRT would predict kidney function recovery., Methods: We performed a retrospective observational study of 72 patients from a 126-patient, single-center CKRT study. We studied two a priori defined cohorts of patients without advanced CKD who had acute kidney injury requiring CKRT (AKI-CKRT): 1) with early kidney function recovery defined as liberation from KRT within seven days of CKRT initiation versus 2) with delayed kidney function recovery defined as receipt of KRT for >21 days or death while on KRT. Subsequent analysis included patients with advanced CKD and intermediate kidney function recovery (liberation between 8 and 21 days). Cystatin C was then measured on stored plasma, urine, and dialysis effluent collected prior to CKRT initiation and on days 1, 2, and 3 of CKRT., Results: Plasma cystatin C was significantly lower in patients with early kidney function recovery in comparison to patients with delayed kidney function recovery on days 1 (1.79 vs. 2.39mg/L), 2 (1.91 vs. 2.38mg/L) and 3 (2.04 vs. 2.67mg/L) of CKRT. Sieving coefficient and CKRT clearance of cystatin C were similar for patients with early and delayed kidney function recovery. The lowest plasma cystatin C concentration on days 1-3 of CKRT predicted early kidney function recovery with an area under the receiver operating curve of 0.77 (P = 0.002), positive likelihood ratio of 5.60 for plasma cystatin C <1.30mg/L, and negative likelihood ratio of 0.17 for plasma cystatin C ≥1.88mg/L., Conclusion: Lower plasma cystatin C concentrations during the first three days of CKRT are associated with early kidney function recovery., (Copyright © 2024 by the American Society of Nephrology.)
- Published
- 2024
- Full Text
- View/download PDF
13. IL-6 mediates the hepatic acute phase response after prerenal azotemia in a clinically defined murine model.
- Author
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Okamura K, Lu S, He Z, Altmann C, Montford JR, Li AS, Lucia MS, Orlicky DJ, Weiser-Evans M, and Faubel S
- Subjects
- Animals, Male, Mice, Acute-Phase Reaction complications, Biomarkers, Disease Models, Animal, Furosemide, Glomerular Filtration Rate physiology, Interleukin-6 genetics, Interleukin-6 metabolism, Lipocalin-2 genetics, Liver metabolism, Mice, Inbred C57BL, Acute Kidney Injury metabolism, Azotemia complications
- Abstract
Prerenal azotemia (PRA) is a major cause of acute kidney injury and uncommonly studied in preclinical models. We sought to develop and characterize a novel model of PRA that meets the clinical definition: acute loss of glomerular filtration rate (GFR) that returns to baseline with resuscitation. Adult male C57BL/6J wild-type (WT) and IL-6
-/- mice were studied. Intraperitoneal furosemide (4 mg) or vehicle was administered at time = 0 and 3 h to induce PRA from volume loss. Resuscitation began at 6 h with 1 mL intraperitoneal saline for four times for 36 h. Six hours after furosemide administration, measured glomerular filtration rate was 25% of baseline and returned to baseline after saline resuscitation at 48 h. After 6 h of PRA, plasma interleukin (IL)-6 was significantly increased, kidney and liver histology were normal, kidney and liver lactate were normal, and kidney injury molecule-1 immunofluorescence was negative. There were 327 differentially regulated genes upregulated in the liver, and the acute phase response was the most significantly upregulated pathway; 84 of the upregulated genes (25%) were suppressed in IL-6-/- mice, and the acute phase response was the most significantly suppressed pathway. Significantly upregulated genes and their proteins were also investigated and included serum amyloid A2, serum amyloid A1, lipocalin 2, chemokine (C-X-C motif) ligand 1, and haptoglobin; hepatic gene expression and plasma protein levels were all increased in wild-type PRA and were all reduced in IL-6-/- PRA. This work demonstrates previously unknown systemic effects of PRA that includes IL-6-mediated upregulation of the hepatic acute phase response. NEW & NOTEWORTHY Prerenal azotemia (PRA) accounts for a third of acute kidney injury (AKI) cases yet is rarely studied in preclinical models. We developed a clinically defined murine model of prerenal azotemia characterized by a 75% decrease in measured glomerular filtration rate (GFR), return of measured glomerular filtration rate to baseline with resuscitation, and absent tubular injury. Numerous systemic effects were observed, such as increased plasma interleukin-6 (IL-6) and upregulation of the hepatic acute phase response.- Published
- 2023
- Full Text
- View/download PDF
14. Retrotransposons Are the Major Contributors to the Expansion of the Drosophila ananassae Muller F Element.
- Author
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Leung W, Shaffer CD, Chen EJ, Quisenberry TJ, Ko K, Braverman JM, Giarla TC, Mortimer NT, Reed LK, Smith ST, Robic S, McCartha SR, Perry DR, Prescod LM, Sheppard ZA, Saville KJ, McClish A, Morlock EA, Sochor VR, Stanton B, Veysey-White IC, Revie D, Jimenez LA, Palomino JJ, Patao MD, Patao SM, Himelblau ET, Campbell JD, Hertz AL, McEvilly MF, Wagner AR, Youngblom J, Bedi B, Bettincourt J, Duso E, Her M, Hilton W, House S, Karimi M, Kumimoto K, Lee R, Lopez D, Odisho G, Prasad R, Robbins HL, Sandhu T, Selfridge T, Tsukashima K, Yosif H, Kokan NP, Britt L, Zoellner A, Spana EP, Chlebina BT, Chong I, Friedman H, Mammo DA, Ng CL, Nikam VS, Schwartz NU, Xu TQ, Burg MG, Batten SM, Corbeill LM, Enoch E, Ensign JJ, Franks ME, Haiker B, Ingles JA, Kirkland LD, Lorenz-Guertin JM, Matthews J, Mittig CM, Monsma N, Olson KJ, Perez-Aragon G, Ramic A, Ramirez JR, Scheiber C, Schneider PA, Schultz DE, Simon M, Spencer E, Wernette AC, Wykle ME, Zavala-Arellano E, McDonald MJ, Ostby K, Wendland P, DiAngelo JR, Ceasrine AM, Cox AH, Docherty JEB, Gingras RM, Grieb SM, Pavia MJ, Personius CL, Polak GL, Beach DL, Cerritos HL, Horansky EA, Sharif KA, Moran R, Parrish S, Bickford K, Bland J, Broussard J, Campbell K, Deibel KE, Forka R, Lemke MC, Nelson MB, O'Keeffe C, Ramey SM, Schmidt L, Villegas P, Jones CJ, Christ SL, Mamari S, Rinaldi AS, Stity G, Hark AT, Scheuerman M, Silver Key SC, McRae BD, Haberman AS, Asinof S, Carrington H, Drumm K, Embry T, McGuire R, Miller-Foreman D, Rosen S, Safa N, Schultz D, Segal M, Shevin Y, Svoronos P, Vuong T, Skuse G, Paetkau DW, Bridgman RK, Brown CM, Carroll AR, Gifford FM, Gillespie JB, Herman SE, Holtcamp KL, Host MA, Hussey G, Kramer DM, Lawrence JQ, Martin MM, Niemiec EN, O'Reilly AP, Pahl OA, Quintana G, Rettie EAS, Richardson TL, Rodriguez AE, Rodriguez MO, Schiraldi L, Smith JJ, Sugrue KF, Suriano LJ, Takach KE, Vasquez AM, Velez X, Villafuerte EJ, Vives LT, Zellmer VR, Hauke J, Hauser CR, Barker K, Cannon L, Parsamian P, Parsons S, Wichman Z, Bazinet CW, Johnson DE, Bangura A, Black JA, Chevee V, Einsteen SA, Hilton SK, Kollmer M, Nadendla R, Stamm J, Fafara-Thompson AE, Gygi AM, Ogawa EE, Van Camp M, Kocsisova Z, Leatherman JL, Modahl CM, Rubin MR, Apiz-Saab SS, Arias-Mejias SM, Carrion-Ortiz CF, Claudio-Vazquez PN, Espada-Green DM, Feliciano-Camacho M, Gonzalez-Bonilla KM, Taboas-Arroyo M, Vargas-Franco D, Montañez-Gonzalez R, Perez-Otero J, Rivera-Burgos M, Rivera-Rosario FJ, Eisler HL, Alexander J, Begley SK, Gabbard D, Allen RJ, Aung WY, Barshop WD, Boozalis A, Chu VP, Davis JS, Duggal RN, Franklin R, Gavinski K, Gebreyesus H, Gong HZ, Greenstein RA, Guo AD, Hanson C, Homa KE, Hsu SC, Huang Y, Huo L, Jacobs S, Jia S, Jung KL, Wai-Chee Kong S, Kroll MR, Lee BM, Lee PF, Levine KM, Li AS, Liu C, Liu MM, Lousararian AP, Lowery PB, Mallya AP, Marcus JE, Ng PC, Nguyen HP, Patel R, Precht H, Rastogi S, Sarezky JM, Schefkind A, Schultz MB, Shen D, Skorupa T, Spies NC, Stancu G, Vivian Tsang HM, Turski AL, Venkat R, Waldman LE, Wang K, Wang T, Wei JW, Wu DY, Xiong DD, Yu J, Zhou K, McNeil GP, Fernandez RW, Menzies PG, Gu T, Buhler J, Mardis ER, and Elgin SCR
- Subjects
- Animals, Base Composition genetics, Base Sequence, Codon genetics, Female, Gene Expression Profiling, Genes, Insect, Histones metabolism, Protein Processing, Post-Translational genetics, Wolbachia genetics, Chromosomes genetics, Drosophila genetics, Retroelements genetics
- Abstract
The discordance between genome size and the complexity of eukaryotes can partly be attributed to differences in repeat density. The Muller F element (∼5.2 Mb) is the smallest chromosome in Drosophila melanogaster , but it is substantially larger (>18.7 Mb) in D. ananassae To identify the major contributors to the expansion of the F element and to assess their impact, we improved the genome sequence and annotated the genes in a 1.4-Mb region of the D. ananassae F element, and a 1.7-Mb region from the D element for comparison. We find that transposons (particularly LTR and LINE retrotransposons) are major contributors to this expansion (78.6%), while Wolbachia sequences integrated into the D. ananassae genome are minor contributors (0.02%). Both D. melanogaster and D. ananassae F-element genes exhibit distinct characteristics compared to D-element genes ( e.g. , larger coding spans, larger introns, more coding exons, and lower codon bias), but these differences are exaggerated in D. ananassae Compared to D. melanogaster , the codon bias observed in D. ananassae F-element genes can primarily be attributed to mutational biases instead of selection. The 5' ends of F-element genes in both species are enriched in dimethylation of lysine 4 on histone 3 (H3K4me2), while the coding spans are enriched in H3K9me2. Despite differences in repeat density and gene characteristics, D. ananassae F-element genes show a similar range of expression levels compared to genes in euchromatic domains. This study improves our understanding of how transposons can affect genome size and how genes can function within highly repetitive domains., (Copyright © 2017 Leung et al.)
- Published
- 2017
- Full Text
- View/download PDF
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