Article
Plant Sciences
Malgorzata Majewska, Lukasz Kuzma, Piotr Szymczyk
Summary: Salvia miltiorrhiza synthesises tanshinones with multidirectional therapeutic effects. In this study, a new sequence of the HMGR4 gene in S. miltiorrhiza was isolated and characterised, providing valuable information for understanding the transcription regulation of this gene and further exploring the medicinal value of S. miltiorrhiza.
Article
Plant Sciences
Xiangli Niu, Han Lu, Youhong Fan, Wenjie Wang, Yulin Yuan, Madigan Hawkins, Junhong Zhang, Zhibiao Ye, Min Miao, Yongsheng Liu, Fangming Xiao
Summary: The tomato transcription factor SlNAC1 plays a crucial role in abiotic stress response and its instability is attributed to the acidic amino acid-rich transactivation domain TAD1. By manipulating SlNAC1 at both gene and protein levels, the researchers were able to enhance tomato's tolerance to cold, drought, and salt stresses, providing a successful example for developing crops adapted to abiotic stress.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Biochemistry & Molecular Biology
Xiaomin Gao, Xiaolin Sun, Pei Xu, Xiang Shi, Ming Zhang, Xia Yuan, Jingyi Jiang, Kai Jin, Qisheng Zuo, Yani Zhang, Bichun Li
Summary: The study of chicken TDRD1 promoter revealed that the region from -161 to 0 bp is the core promoter region, and TCF7L2 and ZEB1 are key transcription factors in the regulation of TDRD1 transcription.
MOLECULAR GENETICS AND GENOMICS
(2022)
Article
Veterinary Sciences
Dawei Wei, Sayed Haidar Abbas Raza, Xingping Wang, Rajwali Khan, Zhaoxiong Lei, Guijie Zhang, Jiupan Zhang, Zhuoma Luoreng, Yun Ma, Muna O. Alamoudi, Bandar Hamad Aloufi, Ahmed Mohajja Alshammari, Ayman Hassan Abd El-Aziz, Majid Alhomrani, Abdulhakeem S. Alamri
Summary: This study investigated the tissue expression patterns and functional promoter of bovine LATS1, and identified the key transcription factors in the core promoter region. It revealed the regulatory mechanisms of bovine LATS1 transcription in mediating skeletal muscle growth. Bovine LATS1 was highly expressed in the longissimus thoracis and upregulated in infancy muscle.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Genetics & Heredity
Zhiyuan Sui, Yongjie Zhang, Zhishuai Zhang, Chenguang Wang, Xiaojun Li, Feng Xing, Mingxing Chu
Summary: The Lin28B gene plays a role in initiating puberty, but its regulatory mechanisms are not well understood. This study aimed to investigate the regulatory mechanism of the Lin28B promoter by cloning and analyzing its proximal promoter region. Deletion vectors were constructed based on bioinformatic analysis, and dual-fluorescent activity detection was performed. Mutations in transcription factor-binding sites and overexpression of transcription factors were used to analyze the transcriptional regulation mechanism of the Lin28B promoter region. The results showed that the -837 to -338 bp region had the highest transcriptional activity, and mutations in Egr1 and SP1 significantly decreased the transcriptional activity. Overexpression of Egr1 enhanced Lin28B transcription, indicating the importance of Egr1 and SP1 in regulating Lin28B. These findings provide a theoretical foundation for further research on the transcriptional regulation of sheep Lin28B during puberty initiation.
Article
Biotechnology & Applied Microbiology
Nancy M. Kim, Riley W. Sinnott, Lily N. Rothschild, Nicholas R. Sandoval
Summary: In this study, the sort-seq method was used to investigate the sequence-function relationship of a butanol-responsive TF-promoter pair and improve the biosensor characteristics. Site-specific mutations were identified to increase the sensor output. Essential sites required for proper biosensor function were also identified. This work enables high-throughput screening methods for strain development.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Cassidy T. Burke, Iuliia Vitko, Justyna Straub, Elsa O. Nylund, Agnieszka Gawda, Kathryn Blair, Kyle A. Sullivan, Lara Ergun, Matteo Ottolini, Manoj K. Patel, Edward Perez-Reyes
Summary: Epileptogenesis involves changes in neuronal firing and gene transcription networks, which can be targeted by the activity-dependent transcription factor EpiPro. The study successfully validated the effectiveness of EpiPro in multiple rodent models of epilepsy, highlighting its potential as a gene therapy driver for epilepsy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Yongpeng Li, Tiantian Chen, Wei Wang, Hang Liu, Xin Yan, Kuanyu Wu-Zhang, Wei Qin, Lihui Xie, Yaojie Zhang, Bowen Peng, Xinghao Yao, Chen Wang, Sadaf-Ilyas Kayani, Xueqing Fu, Ling Li, Kexuan Tang
Summary: A simple, rapid, efficient, and cost-effective transient transformation system in Artemisia annua was developed, which was demonstrated to be useful for gene functional studies such as gene subcellular localization, promoter activity, and transcription activation assays, providing a new approach to avoid aberrant phenotypes resulting from gene expression in a heterologous system.
Article
Biochemistry & Molecular Biology
Yuko Shimada, Takuya Kato, Yasutaka Sakurai, Hitoe Watanabe, Mayu Nonaka, Natsumi Nanaura, Masaaki Ichinoe, Yoshiki Murakumo
Summary: This study characterized the promoter region of the REV7 gene and identified two transcriptional activation regions. They found that BLIMP-1 may be a potential transcriptional regulator of REV7 in mammalian cells.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Plant Sciences
Himanshu Tak, Sanjana Negi, Thumballi R. Ganapathi
Summary: Increasing crop productivity is crucial for global food supply, and closing stomata plays a key role in pathogen resistance and drought tolerance. Novel research has uncovered insights into stomatal closure networks that can enhance crop endurance.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Biochemical Research Methods
Fidan Erden-Karaogian, Mert Karaogian, Gurkan Yilmaz, Semiramis Yilmaz, Mehmet Inan
Summary: This study investigated the regulation of the ADH genes in P. pastoris, identifying the UAS and URS sequences of the ADH2 promoter. Five synthetic promoters were constructed by altering regulatory sites, leading to improved xylanase production. The highest activity synthetic promoter, SNT5, was further evaluated at the fermenter scale, with potential implications for industrial processes.
BIOTECHNOLOGY JOURNAL
(2022)
Review
Biotechnology & Applied Microbiology
Xiaohan Huang, Qiaoqiao Song, Shuqi Guo, Qiang Fei
Summary: This review summarizes several transcription regulation strategies applied in methylotrophs and discusses their applications and prospects.
BIORESOURCES AND BIOPROCESSING
(2022)
Article
Chemistry, Physical
Emmanuelle Bignon, Angelo Spinello, Tom Miclot, Luisa D'Anna, Cosimo Ducani, Stephanie Grandemange, Giampaolo Barone, Antonio Monari, Alessio Terenzi
Summary: This article investigates the interplay among three G4 sequences in the c-KIT proto-oncogene promoter and finds that their structural linkage favors the formation of a parallel structure for WSP. Using molecular dynamics simulations and enhanced sampling methods, they provide the first computationally resolved structure of a well-organized G4 cluster in the promoter of a crucial gene involved in cancer development. The study suggests that neighboring G4s influence their mutual three-dimensional arrangement and provide a powerful tool for predicting and interpreting complex DNA structures, which can be used as a starting point for drug discovery.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Plant Sciences
Tianli Wu, Yun Zhong, Min Chen, Bo Wu, Ting Wang, Bo Jiang, Guangyan Zhong
Summary: The study identified 18 CcGASA proteins in Citrus clementina, which shared a conserved GASA domain but varied considerably in primary sequences and motif compositions. The proteins could be classified into three major phylogenetic groups, and are predicted to be involved in defense against biotic and abiotic stresses as well as growth and development. Both segmental and tandem duplications played a role in the expansion of the CcGASA gene family in Citrus, indicating structural and functional divergence among family members.
Article
Microbiology
Sumeet Patiyal, Nitindeep Singh, Mohd Zartab Ali, Dhawal Singh Pundir, Gajendra P. S. Raghava
Summary: The study developed a model for predicting sigma70 promoters with high accuracy using various features, achieving 97.38% accuracy on the training dataset and 90.41% accuracy on an independent dataset. The model is available as a webserver and standalone packages for free use.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Mathematics, Applied
Ll Alseda, B. Vidiella, R. Sole, J. T. Lazaro, J. Sardanyes
COMMUNICATIONS IN NONLINEAR SCIENCE AND NUMERICAL SIMULATION
(2020)
Article
Multidisciplinary Sciences
Andreas K. Brodel, Rui Rodrigues, Alfonso Jaramillo, Mark Isalan
Article
Cell Biology
Bruno Lamas, Leticia Hernandez-Galan, Heather J. Galipeau, Marco Constante, Alexandra Clarizio, Jennifer Jury, Natalia M. Breyner, Alberto Caminero, Gaston Rueda, Christina L. Hayes, Justin L. McCarville, Miriam Bermudez Brito, Julien Planchais, Nathalie Rolhion, Joseph A. Murray, Philippe Langella, Linda M. P. Loonen, Jerry M. Wells, Premysl Bercik, Harry Sokol, Elena F. Verdu
SCIENCE TRANSLATIONAL MEDICINE
(2020)
Article
Biochemical Research Methods
Salva Duran-Nebreda, Jordi Pla, Blai Vidiella, Jordi Pinero, Nuria Conde-Pueyo, Ricard Sole
Summary: This article discusses the characteristics of multicellular entities and their spatial patterns related to functions, as well as the repeating distributions in biological structures. It introduces patterning modules and synthetic gene circuits, along with the phenomenon of symmetry-breaking demonstrated through experimental results.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Biology
Ricard Sole, Guim Aguade-Gorgorio
Summary: Differentiation therapy (DTH) is a promising approach to cancer treatment, showing success in specific types of cancer. Mathematical framework and ecological models provide insights for therapy design, but challenges remain in its application to solid tumors.
JOURNAL OF THEORETICAL BIOLOGY
(2021)
Article
Green & Sustainable Science & Technology
Josep M. Anto, Jose Luis Marti, Jaume Casals, Paul Bou-Habib, Paula Casal, Marc Fleurbaey, Howard Frumkin, Manel Jimenez-Morales, Jacint Jordana, Carla Lancelotti, Humberto Llavador, Lela Melon, Ricard Sole, Francesc Subirada, Andrew Williams
Summary: We are living in a time that requires massive and novel coordinated scientific and societal efforts to address pressing challenges threatening catastrophic change to the natural environment. Universities and academic institutions have the opportunity and responsibility to take a leading role in this era. The Planetary Wellbeing Initiative aims to promote the highest attainable standard of wellbeing for both human and non-human beings, requiring collaboration across various fields to tackle the challenges of global complexity, interdisciplinarity, and urgency.
Article
Multidisciplinary Sciences
Blai Vidiella, Antoni Guillamon, Josep Sardanyes, Victor Maull, Jordi Pla, Nuria Conde, Ricard Sole
Summary: This paper presents an engineered gene network that displays self-organized criticality (SOC) behavior in living cells, poising them close to a critical state. The authors discuss the potential implications of this state on cellular dynamics and behavior.
NATURE COMMUNICATIONS
(2021)
Correction
Multidisciplinary Sciences
Blai Vidiella, Antoni Guillamon, Josep Sardanyes, Victor Maull, Jordi Pla, Nuria Conde, Ricard Sole
NATURE COMMUNICATIONS
(2021)
Article
Biology
Guim Aguade-Gorgorio, Stuart Kauffman, Ricard Sole
Summary: Phenotypic switching in cancer cells is a common phenomenon across tumor types and plays a crucial role in tumor evolution and therapy resistance. A mathematical framework has been developed to understand the dynamics of phenotypic switching, which provides insights for the success of combination therapies targeting both replication and phenotypic transitions.
BULLETIN OF MATHEMATICAL BIOLOGY
(2022)
Article
Ecology
Miguel Berdugo, Blai Vidiella, Ricard V. Sole, Fernando T. Maestre
Summary: With ongoing climate change, the probability of exceeding aridity thresholds in drylands and experiencing abrupt ecosystem changes is higher than ever. By identifying different mechanisms causing aridity thresholds and potential amplification mechanisms, we can develop specific hypotheses to bridge knowledge gaps and focus on monitoring and adapting to abrupt ecosystem changes in global drylands.
FUNCTIONAL ECOLOGY
(2022)
Review
Physics, Multidisciplinary
Ricard Sole, Josep Sardanyes, Santiago F. Elena
Summary: Viruses have complex relationships with other organisms, sometimes parasitizing them and causing diseases, while also playing a pivotal role in the evolution of their hosts.
REPORTS ON PROGRESS IN PHYSICS
(2021)
Review
Biotechnology & Applied Microbiology
Martina Oliver Huidobro, Jure Tica, Georg K. A. Wachter, Mark Isalan
Summary: Engineering multicellular patterning and spatial control over gene expression have the potential to revolutionize developmental biology and medicine. Classifying engineered patterns into four levels of complexity and identifying diffusive signals to regulate gene expression can help synthetic biologists engineer increasingly intricate spatial structures.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Ecology
Patrick Fraser, Ricard Sole, Gemma de las Cuevas
Summary: The article discusses why the brain can understand self-reference and introduces the "Strange Loop Model" to explain this phenomenon. This model involves causal feedback between two brain modules to avoid paradoxes of self-reference and negation. It also suggests that the brain's metastable dynamics can limit endless reasoning. Finally, the representation of logical inconsistencies in the model leads to causal incongruence between brain subsystems.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Multidisciplinary Sciences
Alicia Broto, Erika Gaspari, Samuel Miravet-Verde, Vitor A. P. Martins dos Santos, Mark Isalan
Summary: This study provides a robust genetic toolkit for Mycoplasma, demonstrating the application of gene circuit engineering to control and limit the growth of Mycoplasma. The synthetic gene circuits developed were found to be stable and robust in the long-term, laying the foundation for developing viable biosafety systems using a synthetic Mycoplasma chassis.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Lara Selles Vidal, Mark Isalan, John T. Heap, Rodrigo Ledesma-Amaro
Summary: Directed evolution is a powerful tool for protein engineering, allowing for the rapid selection of biomolecule variants with desired properties. Since its initial development in 1967, various techniques have been developed to facilitate genetic diversification and variant isolation. This review discusses the advantages, drawbacks, and recent developments in directed evolution methodologies, highlighting the ability to handle larger library sizes and address new research questions.
RSC CHEMICAL BIOLOGY
(2023)
