Article
Biology
Daniel Richard, Steven Pregizer, Divya Venkatasubramanian, Rosanne M. Raftery, Pushpanathan Muthuirulan, Zun Liu, Terence D. Capellini, April M. Craft
Summary: To fill in the knowledge gaps of molecular regulation in human articular and growth plate cartilage development, researchers used directed differentiation approach to generate these cartilage tissues from human embryonic stem cells. The transcriptomic profiles of the resulting cartilage cells were similar to fetal chondrocytes, in terms of both known and unknown genes related to cartilage biology. By mapping chromatin accessibility in the chondrocyte lineages, researchers identified lineage-specific gene regulatory networks, and validated the functional interactions of two transcription factors with their predicted genomic targets. This work provides a framework for studying chondrocyte differentiation and sheds new light on human cartilage development and biology.
Article
Plant Sciences
Yang Zhao, Qiye Wei, Tianci Chen, Lijuan Xu, Jing Liu, Xingen Zhang, Guomin Han, Qing Ma
Summary: This study identified heat-responsive miRNAs in maize and predicted their target genes, constructing a regulatory network and discovering 16 significantly differentially expressed miRNAs. The findings provide insights into the miRNA-mediated regulatory network and mechanisms involved in heat stress response in maize.
PLANT GROWTH REGULATION
(2022)
Article
Plant Sciences
Zhelong Lin, Leina Zhou, Shuyang Zhong, Xiaojian Fang, Hangqin Liu, Yan Li, Can Zhu, Jiacheng Liu, Zhongwei Lin
Summary: The genetic regulation of tiller development in maize involves a complex network of genes, with Tin8 and Tb1 identified as key genes controlling the expression of 13 tiller-related genes. Tin8, encoding a kinase, is downregulated and interacts with Tb1 to impact hormonal responses and tiller number.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Multidisciplinary Sciences
Matthieu Dos Santos, Akansha M. Shah, Yichi Zhang, Svetlana Bezprozvannaya, Kenian Chen, Lin Xu, Weichun Lin, John R. McAnally, Rhonda Bassel-Duby, Ning Liu, Eric N. Olson
Summary: Researchers used single-nucleus RNA and ATAC sequencing to create an atlas of skeletal muscle development, identifying gene programs and transcription factors that control muscle fiber development and maturation. They discovered that specific gene programs and transcriptional switches play crucial roles in myofiber formation, maturation, and contraction.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Organic
Lea Winand, Pascal Schneider, Sebastian Kruth, Nico-Joel Greven, Wolf Hiller, Marcel Kaiser, Joerg Pietruszka, Markus Nett
Summary: By combining chemical synthesis with pathway refactoring, a series of physostigmine analogues with altered specificity and toxicity profiles were produced in the heterologous host. Among the compounds generated, the promising drug candidate phenserine was included, which was previously only accessible through total synthesis. This study provides a new approach for the development of novel therapeutics.
Article
Biotechnology & Applied Microbiology
Julio A. Freyre-Gonzalez, Juan M. Escorcia-Rodriguez, Luis F. Gutierrez-Mondragon, Jeronimo Marti-Vertiz, Camila N. Torres-Franco, Andrea Zorro-Aranda
Summary: Synthetic biology applies engineering principles to design and construct biological systems with functions that do not exist in nature. Understanding the interconnections, workings, and evolution of molecular entities in bacterial gene regulatory networks is crucial for this field. The network structure plays a vital role in reconstructing regulatory networks, and network inference based on structural properties has shown improvements.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Hironori Hojo
Summary: Skeletal development is regulated by chondrocytes and osteoblasts derived from skeletal progenitors. Runx2 plays a crucial role in chondrocyte hypertrophy and osteoblast differentiation. Advances in molecular biology and next-generation sequencing have provided insights into the multi-layer regulatory mechanisms of Runx2. This review summarizes these emerging mechanisms and discusses their potential applications in treating skeletal diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Ryoji Kawakami, Yohko Kitagawa, Kelvin Y. Chen, Masaya Arai, Daiya Ohara, Yamami Nakamura, Keiko Yasuda, Motonao Osaki, Norihisa Mikami, Caleb A. Lareau, Hitomi Watanabe, Gen Kondoh, Keiji Hirota, Naganari Ohkura, Shimon Sakaguchi
Summary: The transcription factor Foxp3 plays crucial roles in Treg cell development and function by controlling Foxp3 transcription. Deletion of CNS0 and CNS3 completely abrogates Treg cell generation and impairs Foxp3 expression stability in residual Treg cells, leading to lethal systemic autoimmunity and inflammation. Hierarchical and coordinated activation of Foxp3 CNS0 and CNS3 initiates and stabilizes Foxp3 gene expression, crucially controlling Treg cell development and self-tolerance.
Article
Agronomy
Blaise Pascal Muvunyi, Xiang Lu, Junhui Zhan, Sang He, Guoyou Ye
Summary: This study conducted a meta-analysis of previous RNA-Seq studies to elucidate the genetic mechanisms regulating zinc deprivation response in rice. By using weighted gene co-expression network analysis (WGCNA), modules of co-expressed genes were identified, along with conserved differentially expressed genes (DEGs) and their molecular pathways. The findings provide a comprehensive insight into zinc deficiency response and may facilitate gene and pathway prioritization for improving zinc use efficiency and zinc biofortification in rice.
Article
Microbiology
Maeve Mclaughlin, Penelope I. Higgs
Summary: MrpC, a member of the CRP/Fnr transcription factor superfamily, is necessary for the synchronized transition of cells in the bacterium Myxococcus xanthus from aggregation to sporulation. Disruption of MrpC binding sites leads to increased cell-to-cell variation in mrpC expression and the formation of a new developmental state termed "developmental swarms", where cells lose synchronized transition and remain in a cohesive swarming state.
FRONTIERS IN MICROBIOLOGY
(2023)
Review
Mathematics, Applied
Manuela A. D. Aguiar, Ana P. S. Dias, Haibo Ruan
Summary: This paper discusses the synchronization mechanisms in GRNs as well as the impact of gene duplication and redundancy on them, presenting results on robust synchrony patterns for SUM and MULT dynamical models. It also explores the concepts of quotient network and network lifting, and their relationship to gene duplication and the phenomenon of functional divergence.
PHYSICA D-NONLINEAR PHENOMENA
(2022)
Article
Forestry
Jiabao Ye, Ke Yang, Yuting Li, Feng Xu, Shuiyuan Cheng, Weiwei Zhang, Yongling Liao, Xiaoyan Yang, Lina Wang, Qijian Wang
Summary: In this study, the transcriptomic analysis of different organs of G. biloba revealed the TTL regulatory network. Weighted gene co-expression network analysis and Cytoscape visualization identified transcription factors, structural genes, and CYP450 involved in TTL accumulation. This study provides molecular evidence for revealing the comprehensive regulatory network involved in TTL metabolism in G. biloba.
Review
Biochemical Research Methods
Mengyuan Zhao, Wenying He, Jijun Tang, Quan Zou, Fei Guo
Summary: The study focuses on the importance of GRN reconstruction technologies in biology and medical science, discussing different method classifications and their performance in networks of varying scales. The aim is to discover potential drug targets and identify cancer biomarkers.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Erik K. Zhivkoplias, Oleg Vavulov, Thomas Hillerton, Erik L. L. Sonnhammer
Summary: The regulatory relationships between genes and proteins in a cell form a gene regulatory network (GRN) that controls cellular response. Methods have been developed to reverse engineer GRNs from expression data, but realistic simulations are necessary due to the lack of ground-truth GRNs. Analysis shows that the feed-forward loop (FFL) motif is significantly enriched in real GRNs, leading to the development of a novel preferential attachment algorithm, FFLatt, for network generation.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
Ji-Sun Park, Su-Jin Park, Suk-Yoon Kwon, Ah-Young Shin, Ki-Beom Moon, Jeong Mee Park, Hye Sun Cho, Sang Un Park, Jae-Heung Jeon, Hyun-Soon Kim, Hyo-Jun Lee
Summary: Temperature is a major environmental factor affecting tuberization in potatoes, with high temperatures suppressing tuber development. This study reveals that potatoes have temporally distinct molecular mechanisms to finely control tuber development in response to temperature.
