Article
Biology
Matthew W. Parker, Jonchee A. Kao, Alvin Huang, James M. Berger, Michael R. Botchan
Summary: Researchers demonstrate that phase separation is driven by a synergy between electrostatic DNA-bridging interactions and hydrophobic inter-IDR contacts, dependent on sequence composition but not order. These interactions are resistant to 1,6-hexanediol and independent of aromaticity, revealing distinct mechanisms underlying condensate formation and specificity in different phase-separating systems.
Article
Biology
Dagmara Korona, Benedict Dirnberger, Carlo N. G. Giachello, Rayner M. L. Queiroz, Rebeka Popovic, Karin H. Mueller, David-Paul Minde, Michael J. Deery, Glynnis Johnson, Lucy C. Firth, Fergus G. Earley, Steven Russell, Kathryn S. Lilley, Stephan A. Pless
Summary: This study utilized a CRISPR/Cas9 strategy to generate null alleles for all ten nAChR subunit genes in Drosophila, and investigated their interactions with peptide neurotoxins. The findings have important implications for the development of more effective insecticides.
Article
Multidisciplinary Sciences
Sreesankar Easwaran, Matthew Van Ligten, Mackenzie Kui, Denise J. Montell
Summary: This study reveals that Drosophila enter adult reproductive diapause under specific environmental conditions, which leads to ovarian arrest but preserves fertility. Germline stem cells (GSCs) in diapause incur DNA damage and division reduction, yet they are able to recover. Mimicking reduced juvenile hormone production during diapause enhances GSC longevity in non-diapausing flies.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Chun-Ping Yu, Chen-Hao Kuo, Chase W. Nelson, Chi-An Chen, Zhi Thong Soh, Jinn-Jy Lin, Ru-Xiu Hsiao, Chih-Yao Chang, Wen-Hsiung Li
Summary: By developing a computational pipeline for analyzing ChIP-seq data, this study discovered and characterized a large number of previously unknown TFBSs, providing insights into the biological and genomic features of TFBSs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemical Research Methods
Qingqing Huang, Zhengtang Tan, Yanjing Li, Wenzhu Wang, Mei Lang, Changying Li, Zhiyun Guo
Summary: TFcancer is a database that collects experimentally supported associations between transcription factors and 33 TCGA cancers, providing valuable information on TF expression, molecular alterations, regulatory relationships, biological processes, and signaling pathways in cancers. It is a useful resource for researchers seeking to understand the functions and molecular mechanisms of TFs involved in human cancers.
Article
Biochemical Research Methods
Manuel Rueda, Roberto Ariosa, Mauricio Moldes, Jordi Rambla
Summary: Beacon v2 is an API specification that defines a standard for federated discovery of genomic and phenotypic data. B2RI is a set of open-source software tools that allow quick setup of a local Beacon instance.
Review
Cell Biology
Anjeli Mase, Jordan Augsburger, Katja Bruckner
Summary: Research shows that macrophages in fruit flies play key roles in development, organogenesis, regeneration, and homeostasis, with significant diversity in their functions. Their functional diversity is influenced by anatomical locations and systemic conditions.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biology
Matthew P. Bostock, Anadika R. Prasad, Alicia Donoghue, Vilaiwan M. Fernandes
Summary: This study reveals that the Hh pathway activity is gradiently distributed along the distal-proximal axis of lamina columns, which is determined by the gradient of Hh ligand. Manipulating the activity of the Hh pathway in lamina precursors and photoreceptors showed that different levels of activity specify unique cell identities, with more proximal cell types specified in response to lower Hh levels. These findings establish the role of Hh as a morphogen in patterning the lamina, and demonstrate a remarkable similarity with the pattern formation of the vertebrate neural tube.
Article
Agronomy
Yaluan Bi, Xuan Zhang, Xuefei Chang, Jiaxin Li, Shan Xiao, Bo Zhang, Cong Dang, Linlin Sun, Hongwei Yao, Qi Fang, Fang Wang, Gongyin Ye
Summary: This study investigated the olfactory behavior of two Drosophila species and their pupal parasitoid to volatiles from bananas. The results showed that overripe bananas were most attractive to both flies and certain compounds had inducing or repellent effects on fly and parasitoid behavior.
PEST MANAGEMENT SCIENCE
(2023)
Article
Genetics & Heredity
Sergio Casas-Tinto, Alberto Ferrus
Summary: The study found that haplolethals associated with the gene wupA result from the combined insufficiency of a large number of Troponin I isoforms. These findings reveal novel aspects of gene expression and may have implications for evolutionary gene splitting.
Article
Biochemical Research Methods
Yu-An Huang, Gui-Qing Pan, Jia Wang, Jian-Qiang Li, Jie Chen, Yang-Han Wu
Summary: The proposed deep learning model HGETGI shows high prediction performance in identifying TF-target gene interactions, with successful case studies on two important TFs. The method has the potential to be feasible and effective for large-scale predictions in biomedical research.
Review
Biotechnology & Applied Microbiology
Hehe He, Mingfei Yang, Siyu Li, Gaoyang Zhang, Zhongyang Ding, Liang Zhang, Guiyang Shi, Youran Li
Summary: This review comprehensively summarizes the mechanisms, identification methods, and applications of transcription factors in various biotechnological fields. It also discusses the current limitations of research and provides prospects for future investigations.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2023)
Article
Biology
Yang Joon Kim, Kaitlin Rhee, Jonathan Liu, Selene Jeammet, Meghan A. Turner, Stephen J. Small, Hernan G. Garcia
Summary: A challenge in quantitative biology is to predict gene expression patterns using knowledge of transcription factor patterns and binding sites on regulatory DNA. By studying transcriptional repression in early fruit fly embryos, researchers found that higher-order cooperativity between multiple molecular players is required, which cannot be determined from simpler regulatory architectures. This highlights the challenges in understanding transcriptional regulation in eukaryotes and calls for quantitative approaches to dissect their molecular nature.
Article
Biochemical Research Methods
Simon d'Oelsnitz, Joshua D. Love, Daniel J. Diaz, Andrew D. Ellington
Summary: Genetic biosensors play a crucial role in synthetic biology, particularly in high-throughput screening, dynamic feedback regulation, and diagnostic applications. To provide a reliable resource for engineering applications, we have developed GroovDB, a web-accessible database of ligand-inducible transcription factors that includes all the necessary information for building chemically responsive genetic circuits. Ligand-DNA interaction data have been verified and a custom tool allows visualization of the natural genetic context of biosensor entries.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Food Science & Technology
Jianfeng Huang, Xinxin Su, Qiyan Jia, Haoran Chen, Shaoxiao Zeng, Hui Xu
Summary: This study investigated the potential mechanism of action of tea polyphenols (TPs) to enhance heat resistance in Drosophila and the attenuating effect of heat treatment on their efficacy. The results showed that TPs were able to prolong the survival time of Drosophila under high-temperature stress, but this effect was significantly reduced with increasing heat-treatment time. The composition of TPs changed after heat treatment. Transcriptomic and metabolomic analysis revealed the pathways and processes involved in the heat tolerance improvement by TPs. The study provides important insights for the development and utilization of tea's heat-protection function.
