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1. Genome-wide identification and analysis of TCP family genes in Medicago sativa reveal their critical roles in Na+/K+ homeostasis

Author

Mingxiao Zhang, Shangqian Qin, Jianping Yan, Lin Li, Mingzhi Xu, Yanrong Liu, and Wanjun Zhang

Subjects
Medicago sativa, MsTCPs, Salt tolerance, MIM319, Na+/K+ homeostasis, Botany, QK1-989
Abstract

Abstract Background Medicago sativa is the most important forage world widely, and is characterized by high quality and large biomass. While abiotic factors such as salt stress can negatively impact the growth and productivity of alfalfa. Maintaining Na+/K+ homeostasis in the cytoplasm helps reduce cell damage and nutritional deprivation, which increases a salt-tolerance of plant. Teosinte Branched1/ Cycloidea/ Proliferating cell factors (TCP) family genes, a group of plant-specific transcription factors (TFs), involved in regulating plant growth and development and abiotic stresses. Recent studies have shown TCPs control the Na+/K+ concentration of plants during salt stress. In order to improve alfalfa salt tolerance, it is important to identify alfalfa TCP genes and investigate if and how they regulate alfalfa Na+/K+ homeostasis. Results Seventy-one MsTCP s including 23 non-redundant TCP genes were identified in the database of alfalfa genome (C.V XinJiangDaYe), they were classified into class I PCF (37 members) and class II: CIN (28 members) and CYC/TB1 (9 members). Their distribution on chromosome were unequally. MsTCP s belonging to PCF were expressed specifically in different organs without regularity, which belonging to CIN class were mainly expressed in mature leaves. MsTCP s belongs to CYC/TB1 clade had the highest expression level at meristem. Cis-elements in the promoter of MsTCP s were also predicted, the results indicated that most of the MsTCP s will be induced by phytohormone and stress treatments, especially by ABA-related stimulus including salinity stress. We found 20 out of 23 MsTCP s were up-regulated in 200 mM NaCl treatment, and MsTCP3/14/15/18 were significantly induced by 10 μM KCl, a K+ deficiency treatment. Fourteen non-redundant MsTCPs contained miR319 target site, 11 of them were upregulated in MIM319 transgenic alfalfa, and among them four (MsTCP3/4/10A/B) genes were directly degraded by miR319. MIM319 transgene alfalfa plants showed a salt sensitive phenotype, which caused by a lower content of potassium in alfalfa at least partly. The expression of potassium transported related genes showed significantly higher expression in MIM319 plants. Conclusions We systematically analyzes the MsTCP gene family at a genome-wide level and reported that miR319-TCPs model played a function in K+ up-taking and/ or transportation especially in salt stress. The study provide valuable information for future study of TCP genes in alfalfa and supplies candidate genes for salt-tolerance alfalfa molecular-assisted breeding.

Published
2023
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2. CT Metrics of Airway Disease and Emphysema in Severe COPD

Author

James Walter, David Godwin, Joyce Canterbury, Thomas E. Hartman, Yen Pin Chiang, Jeanne Smith, John J. Reilly, Hope Livingston, Abby M. Krichman, Mahasti Rittinger, Karma L. Kreizenbeck, Kymberley Anable, Ameena Al-Amin, Colleen Witt, Karen McVearry, Claude Deschamps, Selim M. Arcasoy, Liz Roessler, James K. Stoller, Yahya M. Berkmen, Paul J. Friedman, Enrique Fernandez, Laura Kotler-Klein, Chris Piker, Robert E. Hyatt, Mark J. Krasna, Priscilla McCreight, Jo Anna Baldwin, Jennifer M Lamb, Francisco Alvarez, Janet R. Maurer, Rodney Simcox, Gerald O'Brien, Iris Moskowitz, Marianne C. Fahs, Judd Gurney, A. Mark Fendrick, Mike Mantinaos, Sanjay Kalra, Robert M. Kaplan, Kevin R. Flaherty, Timothy Gilbert, James K. Garrett, Kathy Mieras, Kapreena Owens, Trina Limberg, Patricia Belt, Rolf D. Hubmayr, Roger Barnette, James Carter, Phillip M. Boiselle, Brian Woodcock, Anne Marie Kuzma, Brian F. Mullan, Dean Follmann, Mary Ellen Kleinhenz, Judith Harle, Ubaldo J. Martin, Bonnie Edwards, Fernando I. Martinez, Sandy Do, Alejandro A. Diaz, F.C. Sciurba, William Russell, David J. Sugarbaker, Theresa Alcorn, Susan Borosh, Patricia McDowell, Carolyn Wheeler, Blake Wood, Edwin K. Silverman, Alan J. Moskowitz, John F. Plankeel, William F. Bria, Susan Clark, Patricia Ward, Scott D. Ramsey, Barry J. Make, David H Kupferberg, Chinh T. Q. Nguyen, Stanley Aukberg, Elisabeth L. George, Steven Piantadosi, Geoffrey McLennan, Carl D. Mottram, Martin Zamora, Marvin Pomerantz, Ella A. Kazerooni, Jennifer Propst, Bessie Kachulis, Carol Fanning, Valentina Yegyan, Kenneth Silver, James P. Kiley, Sabine Duffy, David H. Harpole, Junfeng Guo, Donald C. Oxorn, Andrew L. Ries, Paramjit Gill, Bruce H. Culver, Todd M. Officer, Catherine Wood Larsen, John Hansen-Flaschen, Patrick Ross, Mindi Steiger, Lori Hanson, Rose Butanda, Paul F. Simonelli, Neil W. Brister, Amy Chong, Charles L. White, Eric A. Jensen, Cynthia Raymond, Mark K. Ferguson, Moulay Meziane, Mary Milburn-Barnes, James D. Luketich, Douglas E. Wood, A. John McSweeny, Woo Jin Kim, Kim Stavrolakes, John A. Waldhausen, Gregory L. Aughenbaugh, Chul Kwak, Sara L. Bartling, Joan Osterloh, Larry R. Kaiser, John S. Howe, Michael I. Lewis, Andrew Bowdle, Mark A. Gerhardt, Richard O'Connell, Brian R. Lawlor, Neil R. MacIntyre, David A. Lynch, Milton Joyner, Louie Boitano, James P. Utz, Everett Hood, Paul J. Smith, Joshua O. Benditt, John Apostolakis, Frances L. Brogan, Robert McKenna, Berend Mets, Phyllis Dibbern, Kevin Carney, Joan M. Lacomis, Kevin McCarthy, A. Laurie Shroyer, Mitchell K. O’Shea, Barry Make, Dora Greene, Janice Willey, Catherine Ramirez, Gwendolyn B. Vance, Philip R. Karsell, David DeMets, Angela DiMango, Peter Rising, Erik J. Kraenzler, Michael F. Keresztury, Laurie Ney Silfies, Michael Magliocca, Vivian Knieper, Betsy Ann Bozzarello, Marlene Edgar, Madelina Lorenzon, Deb Andrist, Sophia Chatziioannou, Darryl Atwell, Sally Frese, Ruth Etzioni, Stephen I. Marglin, Maria Shiau, Thomas Schroeder, Vincent J. Carey, Vladmir Formanek, Robert Levine, Cindy Chwalik, David Rittinger, Kenneth Martay, Brett A. Simon, Nancy Kurokawa, Anne L. Fuhlbrigge, Peter J. Julien, Michelle T. Toshima, Sean D. Sullivan, Joanne Deshler, Margaret Wu, Anthony Norris, David A. Lipson, Scott J. Swanson, Diane Lockhart, Omar A. Minai, Joseph l. Reeves-Viets, Raed A. Dweik, Keith S. Naunheim, Angela Delsing, Minnie Ellisor, Jane Whalen-Price, Victor F. Tapson, Leonard Rossoff, Susan M. Peterson, Deborah Nowakowski, David M. Shade, Susanne Snedeker, Susan Craemer, Anne Marie G. Sykes, Jennifer Norten, Manmohan S. Biring, Diane C. Strollo, Beth Elliot, Kedren Williams, Heather Sheaffer, Sheila Shearer, Robert P. Hoffman, Robert Quaife, J. Mendez, Donald A. Mahler, Janice Cook-Granroth, Scott Marlow, Zab Mosenifar, Malcolm M. DeCamp, Paul J. Christensen, Rosetta Jackson, Wissam Chatila, Robert Schilz, Glenda DeMercado, Peter B. O'Donovan, Kimberly Dubose, Robert J. Keenan, Satoshi Furukawa, Theodore Kopp, Gerald T. Ayres, Betty Collison, Stephen J. Swensen, Jennifer Stone-Wynne, Nicole Jenson, Stanley S. Siegelman, Tina Bees, Owen B. Wilson, R. Duane Davis, Pierre A. DeVilliers, Marcia Katz, Carolyn M. Clancy, Eddie L. Hoover, Bryan Benedict, Karen Kirsch, Philip M. Hartigan, Simon C. Body, Mark Stafford-Smith, David A. Zisman, Jeanne M. Hoffman, Fernando J. Martinez, Clarence Weir, Jeffrey D. Edelman, William Stanford, Zab Mohsenifar, Michael P. Donahoe, Michele Donithan, Catherine A. Meldrum, William A. Slivka, Lori Zaremba, Michael W. Smith, Martin D. Abel, Robert B Gerber, Sarah Hooper, Steven M. Scharf, Karen A. Hanson, Katherine P. Grichnik, J. Sanford Schwartz, Margaret L. Snyder, Charles J. Hearn, Joe Chin, Tammy Ojo, Gregory D.N. Pearson, Vera Edmonds, George R. Washko, Christine Young, Jennifer Minkoff-Rau, Ron Daniele, Chun Yip, Gregory L. Foster, Harold I. Palevsky, Joan E. Sexton, Dev Pathak, Pamela Fox, Paul E. Kazanjian, Karen King, Jacqueline Pfeffer, Imran Nizami, Judith Wagner, Catherine Wrona, John H. M. Austin, Karla Conejo-Gonzales, Sharon Bendel, Amir Sharafkhaneh, Carol Geaga, Denise Vilotijevic, Thomas H. Sisson, Steven H. Sheingold, Ryan Colvin, Elaine Baker, Karen Collins, Charles F. Emery, Mark Ginsburg, Abass Alavi, David D. Frankville, Joseph M. Reinhardt, Jan Drake, John M. Travaline, Rafael Espada, Kathy Lautensack, Leslie E. Quint, Jeffrey T. Chapman, Rosemary Lann, Steven M. Berkowitz, Alice L. Sternberg, Thurman Gillespy, Nadia Howlader, Frank J. Papatheofanis, Robert Frantz, Manuel L. Brown, Sarah Shirey, Yvonne Meli, Andra E. Ibrahim, Patricia A. Jellen, Rebecca Crouch, Warren B. Gefter, Michael J. Reardon, Jonathan B. Orens, Neal S. Kleiman, Marilyn L. Moy, Daniel L. Miller, Julie Fuller, Reuben M. Cherniack, Claudette Sikora, Lynn Bosco, Harry Handelsman, R. Edward Coleman, Judith M. Aronchick, James Tonascia, Delmar J. Gillespie, Patricia Berkoski, David P. Kapelanski, Cesar A. Keller, Amanda L. Blackford, Charles C. Miller, Kelly M. Campbell, Jill Meinert, Carl R. Fuhrman, Gordon R. Bernard, Connie Hudson, Roger Russell, Lewis Poole, Dale Williams, Magdy Younes, Shing Lee, Steven L. Sax, Martin Carlos, Diane C. Saunders, John Dodge, Matthew N. Bartels, Amy Jahn, Karen Taylor, Gregg L Ruppel, Wallace T. Miller, Mary Gilmartin, Tanisha Carino, Alfred P. Fishman, Gerene Bauldoff, Frank C. Sciurba, Gerard J. Criner, John Haddad, Mark D. Iannettoni, Terri Durr, Gordon F. Harms, Susan Golden, Norman E. Torres, Lisa Geyman, Alan Hibbit, Paul Rysso, Gilbert E. D'Alonzo, Henry E. Fessler, Mark L. Van Natta, Peter Wahl, James H. Harrell, Willard Chamberlain, Roger D. Yusen, Boleyn Hammel, Dawn E. Sassi-Dambron, Mark S. Allen, Jennifer Cutler, Shangqian Qi, Susan Rinaldo-Gallo, John D. Newell, June Hart, Raúl San José Estépar, Kerri McKeon, Staci Opelman, Eric S. Edell, Kathy Winner, Joe R. Rodarte, Mark A. King, Eric A. Hoffman, Laura A. Wilson, Phil Cagle, Jennifer Meyers, Kristin Berry, Mark P. Steele, Katherine Hale, Peter Barnard, Charles Soltoff, Melissa Weeks, Arfa Khan, Cary Stolar, Jeanine P. Wiener-Kronish, Jeannie Ricketts, Nancy Battaglia, Francine L. Jacobson, Satish G. Jhingran, Robert B. Teague, Mary Louise Dempsey, Leighton Chan, Philip T. Diaz, David Hicks, David E. Midthun, Charlene Levine, Andetta R. Hunsaker, Tomeka Simon, Jered Sieren, Susan Lubell, Scott A. Schartel, H P McAdams, Francis Cordova, Kris Bradt, Jeffery J. Johnson, Kenneth White, Mercedes True, Erin A. Sullivan, Byron Thomashow, Gail Weinmann, Robert A. Wise, Donna Tsang, Robert M. Kotloff, Atul C. Mehta, Gregory Tino, and Angela Wurster

Subjects
Adult, Male, Pulmonary and Respiratory Medicine, medicine.medical_specialty, Pathology, Critical Care and Intensive Care Medicine, Risk Assessment, Sensitivity and Specificity, Severity of Illness Index, Cohort Studies, Pulmonary Disease, Chronic Obstructive, Predictive Value of Tests, Forced Expiratory Volume, Internal medicine, medicine, Humans, Lung volumes, Respiratory system, Aged, Probability, Original Research, Analysis of Variance, Univariate analysis, COPD, business.industry, Total Lung Capacity, Respiratory disease, Middle Aged, respiratory system, Airway obstruction, medicine.disease, Respiratory Function Tests, respiratory tract diseases, Airway Obstruction, Dyspnea, medicine.anatomical_structure, Pulmonary Emphysema, Multivariate Analysis, Cardiology, Female, Pulmonary Ventilation, Tomography, X-Ray Computed, Cardiology and Cardiovascular Medicine, business, Airway, Respiratory tract
Abstract

Background CT scan measures of emphysema and airway disease have been correlated with lung function in cohorts of subjects with a range of COPD severity. The contribution of CT scan-assessed airway disease to objective measures of lung function and respiratory symptoms such as dyspnea in severe emphysema is less clear. Methods Using data from 338 subjects in the National Emphysema Treatment Trial (NETT) Genetics Ancillary Study, densitometric measures of emphysema using a threshold of −950 Hounsfield units (%LAA-950) and airway wall phenotypes of the wall thickness (WT) and the square root of wall area (SRWA) of a 10-mm luminal perimeter airway were calculated for each subject. Linear regression analysis was performed for outcome variables FEV 1 and percent predicted value of FEV 1 with CT scan measures of emphysema and airway disease. Results In univariate analysis, there were significant negative correlations between %LAA-950 and both the WT ( r = −0.28, p = 0.0001) and SRWA ( r = −0.19, p = 0.0008). Airway wall thickness was weakly but significantly correlated with postbronchodilator FEV 1 % predicted (R = −0.12, p = 0.02). Multivariate analysis showed significant associations between either WT or SRWA (β = −5.2, p = 0.009; β = −2.6, p = 0.008, respectively) and %LAA-950 (β = −10.6, p = 0.03) with the postbronchodilator FEV 1 % predicted. Male subjects exhibited significantly thicker airway wall phenotypes (p = 0.007 for WT and p = 0.0006 for SRWA). Conclusions Airway disease and emphysema detected by CT scanning are inversely related in patients with severe COPD. Airway wall phenotypes were influenced by gender and associated with lung function in subjects with severe emphysema.

Published
2009
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3. An Optimized Tobacco Hairy Root Induction System for Functional Analysis of Nicotine Biosynthesis-Related Genes

Author

Shangqian Qin, Yanrong Liu, Jianping Yan, Shiwen Lin, Wanjun Zhang, and Bingwu Wang

Subjects
Rhizobium rhizogenes, hairy root, nicotine biosynthesis, tobacco, Agriculture
Abstract

Rhizobium rhizogenes-mediated plant hairy root induction is a convenient method for functional study of root-specific genes. To develop an optimized tobacco hairy root induction system and study gene function in nicotine biosynthesis, we investigated hairy root induction by three R. rhizogenes strains, R1601, K599, and LBA9402, on different media with leaf discs from plants of different ages, and we observed that the strain LBA9402 used for explant infection exhibited the highest hairy root induction rate with 4 and 8 week old leaf discs of the tobacco ‘Coker176’ on 2/3MS medium, and it could also be used as a cargo delivering foreign genes to hairy roots. Overexpression of MsSPL12 gene, an alfalfa (Medicago sativa) SQUAMOSA promoter binding protein-like (SPL) transcription factor, significantly improved nicotine production in transgenic hairy roots, reaching 1.38–1.85 mg/g compared to 0.5 mg/g of the controls. Expression analysis of the nicotine biosynthesis and transport-related genes responding to methyl-jasmonate (MeJA) treatment revealed a significant upregulation of NtMPO2 responsible for increased nicotine biosynthesis in MsSPL12 transgenic hairy roots. Our results establish a high-throughput approach for gene functional characterization in the hairy roots of a tobacco elite cultivar, ‘Coker176’, as well as suggest a system for efficiently manipulating tobacco nicotine biosynthesis.

Published
2022
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