Article
Multidisciplinary Sciences
Eudald Pascual-Carreras, Carlos Herrera-Ubeda, Maria Rossello, Pablo Coronel-Cordoba, Jordi Garcia-Fernandez, Emili Salo, Teresa Adell
Summary: The Fox genes encode transcription factors that control key aspects of development, with ancestral origins in all eukaryotes. This study identified a new Fox gene family and corrected annotation errors, showcasing the evolutionary and functional studies of Fox genes in lophotrochozoan species and specifically in planarians. The findings highlight family diversification and specific gene appearances in Platyhelminthes, as well as the evolutionary conserved role of specific Fox genes such as foxO in controlling cell death.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Michael Pryszlak, Mallory Wiggans, Xin Chen, Julia E. Jaramillo, Sarah E. Burns, Laura M. Richards, Trevor J. Pugh, David R. Kaplan, Xi Huang, Peter B. Dirks, Bret J. Pearson
Summary: By using a comparative genomics approach, researchers have identified and demonstrated the role of DEAD-box helicase DDX56 in regulating stemness in different cell systems. DDX56 affects ribosomal RNA expression and nucleolar integrity in planarians, mouse neural stem cells, human GSCs, and a fruit fly model, ultimately leading to stem cell death.
Article
Multidisciplinary Sciences
Axel Poulet, Arcadia J. Kratkiewicz, Danyan Li, Josien C. van Wolfswinkel
Summary: The chromatin organization of stem cell genes in the planarian Schmidtea mediterranea is distinct from tissue-specific genes and resembles constitutive genes. The promoters of stem cell-specific genes have a sequence feature that decreases nucleosome binding affinity, making pluripotency-related gene expression the default state. This state is maintained by the activity of chromatin remodelers ISWI and SNF2 in the stem cells.
Article
Neurosciences
Leticia Tavares-Gomes, Camille Monney, Geraldine Neuhaus, David Francisco, Diana Solis, Artur Summerfield, Daniel Erny, Vidhya Jagannathan, Anna Oevermann
Summary: Microglia and MDM play different roles in neuroinfections, with potential data from studies on bovine neuroinfections being applicable to human infections.
Article
Plant Sciences
Shiyu Sun, Duoxiang Wang, Jingbin Li, Yaqi Lei, Gang Li, WenGuo Cai, Xiangxiang Zhao, Wanqi Liang, Dabing Zhang
Summary: This study used a transcriptomics approach to identify key genes and regulatory networks affecting pollen maturation in rice anthers in response to different day lengths. A total of 11,726 differentially expressed genes were revealed, with GO enrichment analysis showing enrichment in transport, carbohydrate, and lipid metabolic processes, as well as signaling pathways. Co-expression network analysis identified four modules strongly correlated with photoperiod, with 496 hub genes playing a key role in connecting photoperiod-sensitive genes affecting male fertility.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
H. B. Mahesh, Meghana Deepak Shirke, Guo-Liang Wang, Malali Gowda
Summary: Transcriptional re-programming occurs in both host and pathogen during leaf and neck infection, resulting in tissue-specific and infection-specific gene expression patterns. Different sets of genes are uniquely expressed in leaf and neck tissues, with certain genes being up-regulated during infection in each tissue. MicroRNA sequencing reveals differential expression of microRNAs targeting specific transcripts in response to infection, providing insights into the dual-epidemics of blast disease.
Article
Physiology
Wenhong Li, Zhimo Li, Xiang Yang, Xinyi Wang, Mingwei Yang, Chunyang Huang, Yueping He
Summary: In this study, neuropeptide signaling genes of the predatory stink bug Picromerus lewisi were comprehensively identified, providing valuable information for understanding its biology and behavior, as well as for developing improved pest management strategies.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kunxi Zhang, Xiaofei Chen, Penghao Yuan, Chunhui Song, Shangwei Song, Jian Jiao, Miaomiao Wang, Pengbo Hao, Xianbo Zheng, Tuanhui Bai
Summary: Apple is one of the most cultivated fruit crops in China, but it frequently suffers from waterlogging stress, leading to yellowing leaves and decreased fruit quality and yield. This study investigated the response of two apple rootstocks (M. hupehensis and M. toringoides) to waterlogging stress and found that M. toringoides showed more severe leaf chlorosis and had higher ethylene production. Transcriptomic analysis revealed differentially expressed genes related to flavonoid biosynthesis and hormone signaling between the two rootstocks under waterlogging stress. These findings provide important insights for understanding the mechanisms of waterlogging tolerance in apple and for future molecular breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Song Guo, Adnan Arshad, Lan Yang, Yusheng Qin, Xiaohuan Mu, Guohua Mi
Summary: In this study, we analyzed the molecular responses of different regions of maize leaves to low nitrogen supply using hydroponics and a transcriptome approach. We identified developmental stage-specific genes and common genes that play important roles in the biological processes and metabolic processes of maize leaves. Coexpression modules further revealed the core metabolic and regulatory networks in maize leaves under low nitrogen conditions.
Article
Genetics & Heredity
Mingqian Li, Hainan Li, Anni Sun, Liwei Wang, Chuanyou Ren, Jiang Liu, Xining Gao
Summary: This study investigated the response mechanism underlying soybean resistance to drought stress. Differentially expressed genes and key metabolic pathways related to soybean drought resistance were identified, and the impact of severe drought on soybean yield was evaluated.
FRONTIERS IN GENETICS
(2022)
Article
Environmental Sciences
Clarissa P. Ferreira, Renato S. Moreira, Guilherme Toledo-Silva, Declan C. Schroeder, Afonso C. D. Bainy, Karim H. Luchmann
Summary: This study utilized transcriptome data from the mangrove oyster to generate a reference assembly, identifying numerous transcripts and potential genes related to metal transport, storage, and detoxification. This provides insights into the molecular pathways underlying metal tolerance and susceptibility in bivalves, serving as an auxiliary tool for biomonitoring metal contamination in dynamic estuarine environments.
Article
Multidisciplinary Sciences
Shengchao Ma, Li Long, Xixia Huang, Kechuan Tian, Yuezhen Tian, Cuiling Wu, Zhiwen Zhao
Summary: This study compared the expression pattern difference of genome-wide genes between the skin transcriptomes of Subo and Chinese Merinos and screened 16 candidate differentially expressed genes (DEGs) that may associate with wool fineness. These genes were located in signaling pathways that regulate hair follicle development, cycle, or hair growth. Among the 16 DEGs, COL1A1 gene has the highest expression level in Merino skins, and the fold change of LOC101116863 gene is the highest, and the structures of these two genes are both highly conserved in different species. These two genes may play a key role in regulating wool fineness and have similar and conserved functions in different species.
Article
Plant Sciences
Binbin Wen, Xingyao Gong, Xiude Chen, Qiuping Tan, Ling Li, Hongyu Wu
Summary: This study identified differentially expressed genes in apple leaves under early and late nitrogen deficiency stress. Functional analysis revealed the involvement of these genes in pathways and metabolic networks related to apple adaptation to nitrogen deficiency stress. Furthermore, MdNAC4 was identified as a key transcription factor regulating nitrogen deficiency stress.
JOURNAL OF PLANT PHYSIOLOGY
(2022)
Article
Neurosciences
Liang Li, Fang Fang, Xue Feng, Pei Zhuang, Haoliang Huang, Pingting Liu, Liang Liu, Adam Z. Xu, Lei S. Qi, Le Cong, Yang Hu
Summary: Axon regeneration in CNS axonopathies, such as glaucoma, holds great potential for neural repair. In this study, a strategy was developed to specifically label and purify regenerating retinal ganglion cells (RGCs) and non-regenerating RGCs from the same mice. Transcriptome analysis revealed novel genes, including Anxa2, that significantly promote axon regeneration. Anxa2, along with its downstream effectors ILK and Mpp1, were found to protect RGCs and axons, preserving visual function in a glaucoma model. This innovative strategy shows exciting potential for identifying effective candidates for neural repair.
Article
Plant Sciences
Hongxiang Cao, Zhangshuai Yang, Shu Song, Min Xue, Guanyu Liang, Ning Li
Summary: Banded leaf and sheath blight (BLSB) caused by Rhizoctonia solani is a devastating disease in maize fields. This study reveals the transcriptome features of maize plants in response to R. solani infection, identifying differentially expressed genes (DEGs) and defense-related processes. Overexpression of certain candidate genes enhances resistance in rice.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Vladimir Presnyak, Najwa Alhusaini, Ying-Hsin Chen, Sophie Martin, Nathan Morris, Nicholas Kline, Sara Olson, David Weinberg, Kristian E. Baker, Brenton R. Graveley, Jeff Coller
Article
Biochemistry & Molecular Biology
Marcus H. Stoiber, Sara Olson, Gemma E. May, Michael O. Duff, Jan Manent, Robert Obar, K. G. Guruharsha, Peter J. Bickel, Spyros Artavanis-Tsakonas, James B. Brown, Brenton R. Graveley, Susan E. Celniker
Article
Biochemistry & Molecular Biology
Angela N. Brooks, Michael O. Duff, Gemma May, Li Yang, Mohan Bolisetty, Jane Landolin, Ken Wan, Jeremy Sandler, Benjamin W. Booth, Susan E. Celniker, Brenton R. Graveley, Steven E. Brenner
Article
Biochemistry & Molecular Biology
Joseph D. Coolon, Kraig R. Stevenson, C. Joel McManus, Bing Yang, Brenton R. Graveley, Patricia J. Wittkopp
MOLECULAR BIOLOGY AND EVOLUTION
(2015)
Article
Multidisciplinary Sciences
Michael O. Duff, Sara Olson, Xintao Wei, Sandra C. Garrett, Ahmad Osman, Mohan Bolisetty, Alex Plocik, Susan E. Celniker, Brenton R. Graveley
Editorial Material
Biochemistry & Molecular Biology
Brenton R. Graveley
Article
Biochemistry & Molecular Biology
Sonali Majumdar, Peng Zha, Neil T. Pfister, Mark Compton, Sara Olson, Claiborne V. C. Glover, Lance Wells, Brenton R. Graveley, Rebecca M. Terns, Michael P. Terns
Article
Biology
Shahar Alon, Sandra C. Garrett, Erez Y. Levanon, Sara Olson, Brenton R. Graveley, Joshua J. C. Rosenthal, Eli Eisenberg
Article
Biochemistry & Molecular Biology
C. Joel McManus, Joseph D. Coolon, Jodi Eipper-Mains, Patricia J. Wittkopp, Brenton R. Graveley
Article
Biochemistry & Molecular Biology
Jason Carte, Ross T. Christopher, Justin T. Smith, Sara Olson, Rodolphe Barrangou, Sylvain Moineau, Claiborne V. C. Glover, Brenton R. Graveley, Rebecca M. Terns, Michael P. Terns
MOLECULAR MICROBIOLOGY
(2014)
Article
Multidisciplinary Sciences
James B. Brown, Nathan Boley, Robert Eisman, Gemma E. May, Marcus H. Stoiber, Michael O. Duff, Ben W. Booth, Jiayu Wen, Soo Park, Ana Maria Suzuki, Kenneth H. Wan, Charles Yu, Dayu Zhang, Joseph W. Carlson, Lucy Cherbas, Brian D. Eads, David Miller, Keithanne Mockaitis, Johnny Roberts, Carrie A. Davis, Erwin Frise, Ann S. Hammonds, Sara Olson, Sol Shenker, David Sturgill, Anastasia A. Samsonova, Richard Weiszmann, Garret Robinson, Juan Hernandez, Justen Andrews, Peter J. Bickel, Piero Carninci, Peter Cherbas, Thomas R. Gingeras, Roger A. Hoskins, Thomas C. Kaufman, Eric C. Lai, Brian Oliver, Norbert Perrimon, Brenton R. Graveley, Susan E. Celniker
Article
Multidisciplinary Sciences
Mark B. Gerstein, Joel Rozowsky, Koon-Kiu Yan, Daifeng Wang, Chao Cheng, James B. Brown, Carrie A. Davis, LaDeana Hillier, Cristina Sisu, Jingyi Jessica Li, Baikang Pei, Arif O. Harmanci, Michael O. Duff, Sarah Djebali, Roger P. Alexander, Burak H. Alver, Raymond Auerbach, Kimberly Bell, Peter J. Bickel, Max E. Boeck, Nathan P. Boley, Benjamin W. Booth, Lucy Cherbas, Peter Cherbas, Chao Di, Alex Dobins, Jorg Drenkows, Brent Ewing, Gang Fang, Megan Fastucas, Elise A. Feingold, Adam Frankish, Guanjun Gao, Peter J. Good, Roderic Guigo, Ann Hammonds, Jen Harrow, Roger A. Hoskins, Cedric Howald, Long Hu, Haiyan Huang, Tim J. P. Hubbard, Chau Huynh, Sonali Jhas, Dionna Kasper, Masaomi Kato, Thomas C. Kaufman, Robert R. Kitchen, Erik Ladewig, Julien Lagarde, Eric Lai, Ling Leng, Zhi Lu, Michael MacCoss, Gemma May, Rebecca McWhirter, Gennifer Merrihew, David M. Miller, Ali Mortazavi, Rabi Murad, Brian Oliver, Sara Olson, Peter J. Park, Michael J. Pazin, Norbert Perrimon, Dmitri Pervouchine, Valerie Reinke, Alexandre Reymond, Garrett Robinson, Anastasia Samsonova, Gary I. Saunders, Felix Schlesingers, Anurag Sethi, Frank J. Slack, William C. Spencer, Marcus H. Stoiber, Pnina Strasbourger, Andrea Tanzer, Owen A. Thompson, Kenneth H. Wan, Guilin Wang, Huaien Wang, Kathie L. Watkins, Jiayu Wen, Kejia Wen, Chenghai Xue, Li Yang, Kevin Yip, Chris Zaleskis, Yan Zhang, Henry Zheng, Steven E. Brenner, Brenton R. Graveley, Susan E. Ceniker, Thomas R. Gingeras, Robert Waterston
Article
Biotechnology & Applied Microbiology
Scott I. Adamson, Lijun Zhan, Brenton R. Graveley
Article
Biotechnology & Applied Microbiology
Mohan T. Bolisetty, Gopinath Rajadinakaran, Brenton R. Graveley
Article
Biology
Christian K. Roy, Sara Olson, Brenton R. Graveley, Phillip D. Zamore, Melissa J. Moore