Article
Biochemistry & Molecular Biology
Li -Tao Guo, Kazuaki Amikura, Han -Kai Jiang, Takahito Mukai, Xian Fu, Yane-Shih Wang, Patrick O'Donoghue, Dieter Soell, Jeffery M. Tharp
Summary: The pyrrolysyl-tRNA synthetase (PylRS) is a major route to install noncanonical amino acids into proteins in living cells due to its tolerance for diverse amino acid substrates and orthogonality in multiple organisms. A novel class of PylRS enzymes was identified in a subset of methanogenic archaea, lacking the N-terminal tRNA-binding domain yet remaining active and orthogonal in bacteria and eukaryotes. Molecular phylogeny analysis revealed the coevolutionary history of PylRS and tRNAPyl, with the emergence of tRNAPyl sequences containing unique discriminator bases that may enable further genetic code expansion efforts.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Jingxuan Tai, Lin Wang, Wai Shan Chan, Jiahui Cheng, Yuk Hei Chan, Marianne M. Lee, Michael K. Chan
Summary: Macrocyclization is an effective strategy to improve the stability and efficacy of protein therapeutics. In this study, a scalable and robust system based on endogenous biosynthesis of a noncanonical amino acid coupled with the pyrrolysine translational machinery is described for generating lasso-grafted proteins. With this system, cyclization of a therapeutic P16 peptide engrafted on a fusion protein was achieved in under 3 hours, resulting in improved binding affinity and serum stability.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biology
Jiaxin Li, Patrick T. Kang, Ruisheng Jiang, Jodie Y. Lee, Jitesh A. Soares, Joseph A. Krzycki, Michael K. Chan
Summary: This study reveals the important role of pyrrolysine in methyl group transfer from trimethylamine to the corrinoid cofactor in Methanosarcina barkeri trimethylamine methyltransferase (MttB).
COMMUNICATIONS BIOLOGY
(2023)
Article
Microbiology
Veronika Kivenson, Blair G. Paul, David L. Valentine
Summary: Marine benthic environments can be influenced by anthropogenic and localized events, affecting microbial community composition that may only become evident decades later. Marine sediments are home to diverse taxa and can provide insights into unique evolutionary strategies. Genetic code expansion in abundant Deltaproteobacteria found in deep-sea industrial waste dump sites enhances their metabolic versatility, potentially impacting microbial interactions with ocean-dumped wastes.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Immunology
Samuel A. Myers, Rachel A. Gottschalk
Summary: Cells integrate various cytokine cues and inflammatory stimuli by activating the STAT family of transcription factors. The availability of signaling components and the strength of receptor-STAT interactions play crucial roles in determining immune function. Understanding context-dependent STAT function will guide therapeutic efforts to selectively modulate STAT-regulated responses.
CURRENT OPINION IN IMMUNOLOGY
(2022)
Editorial Material
Plant Sciences
Stanislav Kopriva, Andreas P. M. Weber
Summary: In order to guarantee food security for future generations, new approaches to enhance crop productivity are needed as a result of global climate change and the growing human population causing resource scarcity and productivity declines.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Neurosciences
Devyn E. Smith, Isabelle L. Moore, Nicole M. Long
Summary: This study identifies brain states using scalp EEG from male and female human subjects and shows the extent to which temporal overlap promotes interference and induces retrieval. Greater temporal overlap leads to impaired memory for the past event selectively when the top-down goal is to encode the present event. Additionally, greater temporal overlap leads to automatic retrieval of a past event, independent of top-down goals. These findings provide insight into the role of temporal overlap on interference and memory formation.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Juan Carlos Gonzalez-Sanchez, Mustafa F. R. Ibrahim, Ivo C. Leist, Kyle R. Weise, Robert B. Russell
Summary: Advances in DNA sequencing and proteomics require researchers to regularly examine thousands of gene/protein changes to identify those relevant for potential clinical applications or biological insights. The developed tool, Mechnetor, allows users to explore and visualize integrated mechanistic data for proteins or interactions of interest, providing a finer resolution interaction network for immediate clues on intervention points or mechanistic understanding. The tool is demonstrated with topical examples in human genetic diseases and cancer genomics.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Psychology, Multidisciplinary
Christopher R. Madan, Marcia L. Spetch, Fernanda M. D. S. Machado, Alice Mason, Elliot A. Ludvig
Summary: Both memory and choice are influenced by context. In the study, it was found that risky choices were context dependent, with individuals choosing differently depending on outcomes experienced in that context. Memory tests showed biases specific to distinct contexts, challenging theories of choice that rely on retrieval as guiding choice.
PSYCHOLOGICAL SCIENCE
(2021)
Article
Cell Biology
Tatiana C. Coverdell, Ruei-Jen Abraham-Fan, Chen Wu, Stephen B. G. Abbott, John N. Campbell
Summary: By analyzing gene expression and using single-cell RNA sequencing technology, this study identified molecular subtypes of nucleus ambiguus neurons and revealed their role in controlling esophageal muscle function. The results suggest that activating specific neurons may lead to esophageal muscle contraction, while activating other neurons may significantly suppress heart rate.
Article
Multidisciplinary Sciences
Kei Kudo, Takehiro Nishimura, Ikuko Kozone, Junko Hashimoto, Noritaka Kagaya, Hikaru Suenaga, Haruo Ikeda, Kazuo Shin-ya
Summary: Engineering polyketide synthases can generate a variety of polyketide derivatives, potentially aiding in the development of improved drugs in the future. By utilizing the "module editing" technique, novel rapamycin derivatives were produced through the engineering of the rapamycin PKS, providing important insights into the mechanisms of rapamycin skeletal formation.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Weilun Sun, Ilseob Choi, Stoyan Stoyanov, Oleg Senkov, Evgeni Ponimaskin, York Winter, Janelle M. P. Pakan, Alexander Dityatev
Summary: The study demonstrates that neurons in the retrosplenial cortex are capable of encoding multiple task-related dimensions across learning, particularly showing enhanced performance in tasks requiring cognitive flexibility. Chemogenetic inactivation of the RSC disrupts behavioral context discrimination during learning phases, but does not affect recall of previously formed associations, suggesting a crucial role for the RSC in context-value updating.
NATURE COMMUNICATIONS
(2021)
Article
Computer Science, Artificial Intelligence
Yuemeng Li, Hongming Li, Yong Fan
Summary: Our study introduces an ACEnet network to incorporate 3D spatial and anatomical contexts in 2D deep learning methods for brain structure segmentation from MR scans. Experimental results demonstrate that our method achieves promising performance in terms of both computational efficiency and segmentation accuracy.
MEDICAL IMAGE ANALYSIS
(2021)
Article
Neurosciences
Fernanda Talarico, Giovany Oliveira Costa, Vanessa Kiyomi Ota, Marcos Leite Santoro, Cristiano Noto, Ary Gadelha, Rodrigo Bressan, Hatylas Azevedo, Sintia Iole Belangero
Summary: Treatment-resistant schizophrenia (TRS) may be associated with genetic variations that contribute to poor antipsychotic response. Cluster analysis and functional enrichment analysis reveal the functional and spatiotemporal context of these genes, providing insights into the mechanism of TRS.
MOLECULAR NEUROBIOLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Mengyu Liu, Hujun Yin
Summary: The lightweight feature pyramid encoding network (FPENet) proposed in this study achieves a good balance between accuracy and speed for semantic segmentation tasks. By utilizing feature pyramid encoding blocks and an encoder-decoder attention mechanism, it effectively improves the performance of semantic segmentation.
IMAGE AND VISION COMPUTING
(2021)