Article
Genetics & Heredity
Daowu Hu, Yuting Ge, Yinhua Jia, Shoupu He, Xiaoli Geng, Liru Wang, Zhaoe Pan, Zubair Iqbal, Tahir Mahmood, Hongge Li, Baojun Chen, Xiaoyang Wang, Baoyin Pang, Xiongming Du
Summary: GIF genes are crucial in regulating plant growth and development, and this study identified 35 GIF genes in cotton. The expression of GhGIF4 was found to be associated with lateral root numbers in cotton. This research provides a foundation for further investigation of the role of GIF genes in upland cotton.
FRONTIERS IN GENETICS
(2022)
Article
Plant Sciences
Fan Qi, Fu Wang, Chunxiao Xiaoyang, Zhenhui Wang, Yujie Lin, Zhanwu Peng, Jun Zhang, Ningning Wang, Jian Zhang
Summary: This study conducted transcriptome analysis to analyze the gene expression profiles of different organs in flax. The results identified differentially expressed genes and organ-specific expression patterns. Gene ontology enrichment analysis revealed the biological processes and molecular functions associated with organ growth. The study also investigated the role of AP2 transcription factors in regulating flax organ development and stress response. Overall, this research provides valuable insights into the molecular mechanisms of flax organ development and has implications for genetic improvement of flax crops.
Article
Multidisciplinary Sciences
Lauren Cole, Sebastian Kurscheid, Maxim Nekrasov, Renae Domaschenz, Daniel L. Vera, Jonathan H. Dennis, David J. Tremethick
Summary: In this study, the authors present high-depth maps of the position and accessibility of H2A.Z-containing nucleosomes for human Pol II promoters and provide evidence that H2A.Z has multiple and distinct roles in regulating gene expression dependent upon its location in a promoter.
NATURE COMMUNICATIONS
(2021)
Article
Entomology
Dan-Mei Yao, Chi Zou, Yan-Ni Shu, Shu-Sheng Liu
Summary: WRKY transcription factors play important roles in many plant metabolic processes, including defense against pests like whiteflies. This study demonstrates that WRKYs contribute to plant defense by interacting with MAPK cascade pathways. Understanding these interactions provides new insights into plant defenses against insect infestation.
Article
Biochemistry & Molecular Biology
Jianyan Huang, Xiaobo Zhao, Marco Burger, Yurong Wang, Joanne Chory
Summary: The study revealed the positive role of ethylene signaling, ERF95, and ERF97 in basal thermotolerance of Arabidopsis thaliana and established the relationship between them. EIN3 physically binds to the promoters of ERF95 and ERF97, enhancing plant response to heat stress. ERF95 and ERF97 function genetically downstream of EIN3 and increase basal thermotolerance by regulating a common set of target genes.
Article
Multidisciplinary Sciences
Can Lu, Yuan Cai, Wei Liu, Bi Peng, Qiuju Liang, Yuanliang Yan, Desheng Liang, Zhijie Xu
Summary: This study identified the upregulation of lysine-specific demethylase 1 (LSD1/KDM1A) in lung cancer cells, which is associated with resistance to ferroptosis. Knockdown of KDM1A in human lung cancer cells resulted in increased levels of c-Myc and concentrations of malondialdehyde (MDA) and iron, facilitating ferroptosis. The study elucidates the role of the KDM1A/c-Myc regulatory axis in ferroptosis resistance of lung cancer cells.
SCIENTIFIC REPORTS
(2022)
Article
Biology
Shutong Fan, Xixi Li, Siyu Lin, Yunpeng Li, Huixin Ma, Zhifeng Zhang, Zhenkui Qin
Summary: This study used the Y1H system to screen transcription factors binding to the high transcriptional activity region of Foxl2 promoter in Zhikong scallop gonads for the first time. The highly transcriptional activity promoter sequence of Cf-Foxl2 was determined, and 11 candidate factors involved in the transcriptional regulation of Cf-Foxl2 were verified. These findings provide valuable data for understanding the specific transcriptional regulation mechanism of Foxl2 in the ovary.
Review
Biotechnology & Applied Microbiology
Anu Jose Mattam, Yogesh Babasaheb Chaudhari, Harshad Ravindra Velankar
Summary: The growing demand for biofuels has led to the search for alternative feedstock, and lignocellulosic biomass is a promising candidate. The conversion of lignocellulosic biomass to bioethanol involves a complex process with multiple unit operations. The expression of cellulases, which are necessary for saccharification, is controlled by transcription factors and sugar transporters, and genetic engineering efforts have been made to modulate their expression.
MICROBIAL CELL FACTORIES
(2022)
Article
Fisheries
Bingjie Jiang, Lanmei Wang, Jianjun Fu, Wenbin Zhu, Mingkun Luo, Zaijie Dong
Summary: A recombinant expression vector for Mitfa expression was successfully constructed and nearly 600 μg of Mitfa protein was purified. Ten proteins that interact with Mitfa protein were identified, including five proteins involved in melanogenesis and tyrosine metabolism pathways. Injection of purified Mitfa recombinant protein into red tilapia resulted in increased expression levels of mitfa, tyr, tyrp1, and dct genes, as well as increased melanin content and tyrosinase activity.
Article
Biochemistry & Molecular Biology
Shuping Zhao, Tao Jiang, Yao Zhang, Kailing Zhang, Kai Feng, Peng Wu, Liangjun Li
Summary: This study systematically characterized all NAC genes in Nelumbo nucifera and investigated their response mechanisms to salt stress. The results showed that NAC genes are responsive to biotic and abiotic stresses, light, low temperature, and plant hormones, and have tissue expression specificity. Three NAC proteins induced by NaCl and ABA were found to have transcriptional activation capabilities. The co-expression network analysis suggested that NAC proteins may form complexes with other proteins to function together.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Himani Punia, Jayanti Tokas, Anurag Malik, Sonali Sangwan, Anju Rani, Shikha Yashveer, Saleh Alansi, Maha J. Hashim, Mohamed A. El-Sheikh
Summary: Salinity stress is a major concern for global food security, and understanding the mechanisms that enable plants to survive under salt stress is crucial. Sorghum has become a focus of research in this area, with a systematic analysis of differentially expressed genes and their functions revealing involvement in important metabolic processes under high salinity. The findings highlight the potential for developing salt-resistant sorghum lines by targeting genes involved in response to salinity.
Article
Biochemistry & Molecular Biology
Csaba Papp, Vineeth T. Mukundan, Piroon Jenjaroenpun, Fernaldo Richtia Winnerdy, Ghim Siong Ow, Anh Tuan Phan, Vladimir A. Kuznetsov
Summary: The composition of DNA sequences determines the structure and stability of G-quadruplexes (G4s). In this study, a large family of computationally defined and experimentally verified potential G4-B forming sequences (pG4-BS) was introduced. These sequences are preferentially localized in transcription regulatory regions and are associated with brain tissue, immune, and developmental processes. The ability of these sequences to form G4 structures was predicted with 91.5% accuracy in vitro.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Mengdi Li, Danhui Ma, Zhijie Chang
Summary: CREPT and p15RS are RPRD proteins that regulate cell proliferation and tumorigenesis, with opposite functions. Aberrant expression of both proteins is found in cancers. They both interact with RNA polymerase II, but CREPT also plays a key role in DNA damage repair.
Article
Medicine, Research & Experimental
Hyun-Soo Kim, Yoon Jeon, Yoon Ok Jang, Ho Lee, Yong Shin, Chang-Woo Lee
Summary: This study reveals that mammalian Ssu72 plays a crucial role in the transcriptional regulation of various genes through transcriptional elongation rather than polyadenylation or RNA processing. Depletion of Ssu72 leads to Pol II pausing and elongation defects, and reduced transcriptional elongation efficiency primarily affects the expression levels of actively transcribed genes.
Article
Multidisciplinary Sciences
Miaomiao Li, Tao Yao, Wanru Lin, Will E. E. Hinckley, Mary Galli, Wellington Muchero, Andrea Gallavotti, Jin-Gui Chen, Shao-shan Carol Huang
Summary: This study presents a new method to investigate how proteins interact to regulate gene activity. It reveals that certain proteins can expand their ability to recognize specific DNA sequences when they form complexes, leading to the regulation of a broader range of genes.
NATURE COMMUNICATIONS
(2023)
Article
Computer Science, Interdisciplinary Applications
Jeffrey T. Palmer, Steven M. Gallo, Thomas R. Furlani, Matthew D. Jones, Robert L. DeLeon, Joseph P. White, Nikolay Simakov, Abani K. Patra, Jeanette Sperhac, Thomas Yearke, Ryan Rathsam, Martins Innus, Cynthia D. Cornelius, James C. Browne, William L. Barth, Richard T. Evans
COMPUTING IN SCIENCE & ENGINEERING
(2015)
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Computer Science, Software Engineering
Nikolay A. Simakov, Joseph P. White, Robert L. DeLeon, Amin Ghadersohi, Thomas R. Furlani, Matthew D. Jones, Steven M. Gallo, Abani K. Patra
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE
(2015)
Article
Biochemical Research Methods
Biao Liu, Jessica L. Childs-Disney, Brent M. Znosko, Dan Wang, Mohammad Fallahi, Steven M. Gallo, Matthew D. Disney
BMC BIOINFORMATICS
(2016)
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Computer Science, Software Engineering
Thomas R. Furlani, Matthew D. Jones, Steven M. Gallo, Andrew E. Bruno, Charng-Da Lu, Amin Ghadersohi, Ryan J. Gentner, Abani Patra, Robert L. DeLeon, Gregor von Laszewski, Fugang Wang, Ann Zimmerman
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE
(2013)
Article
Biochemistry & Molecular Biology
Sai Pradeep Velagapudi, Steven M. Gallo, Matthew D. Disney
NATURE CHEMICAL BIOLOGY
(2014)
Article
Biochemistry & Molecular Biology
Steven M. Gallo, Dave T. Gerrard, David Miner, Michael Simich, Benjamin Des Soye, Casey M. Bergman, Marc S. Halfon
NUCLEIC ACIDS RESEARCH
(2011)
Article
Health Care Sciences & Services
Robin M. Lally, Kevin Kupzyk, Steve Gallo, Donna Berry
JOURNAL OF MEDICAL INTERNET RESEARCH
(2020)
Proceedings Paper
Computer Science, Theory & Methods
Robert Settlage, Alan Chalker, Eric Franz, Doug Johnson, Steve Gallo, Edgar Moore, David Hudak
HIGH PERFORMANCE COMPUTING: ISC HIGH PERFORMANCE 2019 INTERNATIONAL WORKSHOPS
(2020)
Proceedings Paper
Computer Science, Hardware & Architecture
Steven M. Gallo, Joseph P. White, Robert L. DeLeon, Thomas R. Furlani, Helen Ngo, Abani K. Patra, Matthew D. Jones, Jeffrey T. Palmer, Nikolay Simakov, Jeanette M. Sperhac, Martins Innus, Thomas Yearke, Ryan Rathsam
2015 IEEE INTERNATIONAL CONFERENCE ON CLUSTER COMPUTING - CLUSTER 2015
(2015)
Proceedings Paper
Computer Science, Hardware & Architecture
James C. Browne, Robert L. DeLeon, Charng-Da Lu, Matthew D. Jones, Steven M. Gallo, Amin Ghadersohi, Abani K. Patra, William L. Barth, John Hammond, Thomas R. Furlani, Robert T. McLay
2013 INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS (SC)
(2013)
Proceedings Paper
Computer Science, Theory & Methods
Jonathan J. Bednasz, Steven M. Gallo, Russ Miller, Catherine L. Ruby, Charles M. Weeks
FRONTIERS OF HIGH PERFORMANCE COMPUTING AND NETWORKING - ISPA 2007 WORKSHOPS
(2007)
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Biochemical Research Methods
SM Gallo, L Li, Z Hu, MS Halfon
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Biochemistry & Molecular Biology
Obi L. Griffith, Stephen B. Montgomery, Bridget Bernier, Bryan Chu, Katayoon Kasaian, Stein Aerts, Shaun Mahony, Monica C. Sleumer, Mikhail Bilenky, Maximilian Haeussler, Malachi Griffith, Steven M. Gallo, Belinda Giardine, Bart Hooghe, Peter Van Loo, Enrique Blanco, Amy Ticoll, Stuart Lithwick, Elodie Portales-Casamar, Ian J. Donaldson, Gordon Robertson, Claes Wadelius, Pieter De Bleser, Dominique Vlieghe, Marc S. Halfon, Wyeth Wasserman, Ross Hardison, Casey M. Bergman, Steven J. M. Jones
NUCLEIC ACIDS RESEARCH
(2008)
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Biochemistry & Molecular Biology
Marc S. Halfon, Steven M. Gallo, Casey M. Bergman
NUCLEIC ACIDS RESEARCH
(2008)