Article
Multidisciplinary Sciences
Daniel Camacho-Gomez, Ioritz Sorzabal-Bellido, Carlos Ortiz-de-Solorzan, Jose Manuel Garcia-Aznar, Maria Jose Gomez-Benito
Summary: We propose an artificial intelligence-based framework to enhance understanding of how cells coordinate their spatial and temporal functions. The framework integrates mechanical interactions and cell functions using a hybrid physics-based model and a data-driven model trained on image data metrics with a deep learning algorithm. Using data from 3D cultures of murine pancreatic ductal adenocarcinoma cells grown in Matrigel, we demonstrate how cells activate different cellular processes to self-organize in various patterns based on specific microenvironmental conditions. This framework expands the tools for simulating biological systems at the cellular level and provides a novel perspective for unraveling morphogenetic patterns.
Article
Optics
Yongsheng Gao, Fangjing Shi, Jing Zhang, Biao Cao, Boyuan Ma, Weile Zhai, Yangyu Fan
Summary: Microwave photonic mixing can achieve the conversion of microwave signals in the optical domain. In this paper, a wideband, large dynamic range, and reconfigurable microwave photonic mixer is proposed and demonstrated. Various reconfigurable functions including dispersion immune mixing, frequency down-conversion, image rejection mixing, and double-balanced mixing are realized, and the performance is improved by optimization techniques.
Article
Chemistry, Multidisciplinary
Javad Safaei, Yifu Gao, Mostafa Hosseinpour, Xiuyun Zhang, Yi Sun, Xiao Tang, Zhijia Zhang, Shijian Wang, Xin Guo, Yao Wang, Zhen Chen, Dong Zhou, Feiyu Kang, Lei Jiang, Guoxiu Wang
Summary: This study demonstrates that vacancy engineering is an effective strategy to enhance the permselectivity of 2D nanofluidic membranes for high-efficiency osmotic energy generation. By creating phosphorus vacancies on NbOPO4 (NbP) nanosheets, the negative surface charge is remarkably increased, resulting in fast transmembrane ion migration and high ionic selectivity. When applied in a natural river water|seawater osmotic power generator, the macroscopic-scale V-NbP membrane delivers a record-high power density of 10.7 W m(-2), surpassing the commercial benchmark of 5.0 W m(-2).
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Tuanwei Liu, Guodong Fu, Zhongjie Wu, Zhongjie Kang, Jinjian Wei, Zhide Zhang, Xinlin Yang, Dian-Shun Guo
Summary: Inspired by green plant photosynthesis, the photocatalytic reduction of CO2 into hydrocarbons is a promising approach to solve the environmental problem of excess CO2 in the atmosphere. The design of Ag@P(IVBC-co-DVB) yolk-shell nanoparticles (AIDNPs) enables efficient photoreduction of CO2 to HCOOH, achieving a competitive efficiency of 396 mu mol g(cat)(-1) h(-1) without the need for a photosensitizer or sacrificial reducing agent. This research provides a comprehensive model for efficient and economic CO2 photoreduction through the investigation of factors related to photocatalytic CO2 production and the proposed reduction mechanism.
Article
Biochemistry & Molecular Biology
Brian Charlesworth, Jeffrey D. Jensen
Summary: It has been proposed that lower mutation rates in gene bodies in Arabidopsis thaliana are an adaptive modification related to the rate of beneficial and deleterious mutations. However, the assumptions made in the population genomics analyses for this claim were questionable. Specifically, the difference in Tajima's D between gene bodies and less selectively constrained sequences can be explained by purifying selection rather than lower mutation rates.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Chemistry, Multidisciplinary
Mengke Cai, Xin Tong, Hongyang Zhao, Xin Li, Yimin You, Rui Wang, Li Xia, Nan Zhou, Lianzhou Wang, Zhiming M. Wang
Summary: This study successfully develops a cost-effective and high-efficiency photoelectrochemical water splitting system based on colloidal quantum dots. By optimizing the intrinsic charge dynamics of the photoelectrodes through rational ligand and heterojunction engineering, enhanced photo-induced charge transfer/injection is achieved, leading to improved system performance. The self-biased PEC water splitting process exhibits high STH efficiency and stability under one-sun illumination.
Article
Biology
Tianzhu Xiong, Xueyan Li, Masaya Yago, James Mallet
Summary: A study on hybridization between two species of swallowtail butterflies discovered unequal rates of genomic substitution between the parental species. This finding reveals a new process in hybridization, where genomic regions affected by gene flow evolve at similar rates between species, while regions with strong reproductive isolation evolve at different rates. The researchers also demonstrate that the degree of rate-mixing can be quantitatively predicted from sequence divergence between the hybridizing species. In addition, asymmetric rates of evolution provide an additional signature of loci involved in reproductive isolation.
Review
Fisheries
Nicole M. Phillips, Floriaan Devloo-Delva, Carly McCall, Toby S. Daly-Engel
Summary: Current studies indicate the presence of some degree of male-biased dispersal in elasmobranchs, but factors such as the pooling of different life stages during data analysis and the inherent characteristics of different marker types may lead to an overemphasis on male dispersal, potentially obscuring genetic signals of female and male reproductive philopatry.
REVIEWS IN FISH BIOLOGY AND FISHERIES
(2021)
Article
Environmental Sciences
Tingting Li, Yihan Zhang, Shiqi Liu, Moli Li, Ruixing Yao, Senyu Niu, Jingyao Yuan, Huizhen Wang, Jingjie Hu, Zhenmin Bao, Xiaoli Hu
Summary: In this study, transcriptomic analysis was conducted to investigate the genes and pathways related to carotenoid accumulation in the adductor muscle of Yesso scallop. The study identified several carotenoid accumulation-related gene modules, as well as a hub gene (PyBCO-like 1) that showed connectivity with a transcriptional factor involved in retinoic acid regulation. Additionally, several up-regulated genes and pathways were found to potentially play a regulatory role in response to carotenoid accumulation. These findings contribute to a better understanding of the regulatory and response mechanisms of carotenoid accumulation in marine animals.
FRONTIERS IN MARINE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Long Xiao, Duchangjiang Fan, Huan Qi, Yulin Cong, Zhuo Du
Summary: Developmental processes are robust and capable of maintaining normal-like states in response to genetic and environmental changes. Through large-scale gene perturbation experiments, it was found that individual gene knockdowns frequently induce cellular defects, which are often transient and can be corrected through cellular plasticity. Developmentally related cell modules may also buffer the phenotypic effects of individual cell position changes.
Article
Multidisciplinary Sciences
Benjamin D. Sunkel, Meng Wang, Stephanie LaHaye, Benjamin J. Kelly, James R. Fitch, Frederic G. Barr, Peter White, Benjamin Z. Stanton
Summary: This study quantitatively examines the role of PFs in childhood rhabdomyosarcoma and finds that PAX3-FOXO1 has the ability to localize in inactive chromatin and nucleosome motifs.
Article
Multidisciplinary Sciences
Haoyang Li, Juexiao Zhou, Zhongxiao Li, Siyuan Chen, Xingyu Liao, Bin Zhang, Ruochi Zhang, Yu Wang, Shiwei Sun, Xin Gao
Summary: Spatial transcriptomics technologies are utilized to analyze transcriptomes while preserving spatial information, providing high-resolution characterization of transcriptional patterns and tissue architecture reconstruction. Cellular heterogeneity plays a crucial role in deciphering spatial patterns of cell types, and various related methods have been proposed. In this study, we benchmarked 18 existing methods for cellular deconvolution using 50 real-world and simulated datasets, evaluating their accuracy, robustness, and usability. CARD, Cell2location, and Tangram showed the best performance for the cellular deconvolution task. Additionally, we provide decision-tree-style guidelines and recommendations for method selection and their additional features, facilitating users in choosing the optimal method for their specific needs. This comprehensive evaluation of 18 state-of-the-art methods for cellular deconvolution in spatial transcriptomics and the accompanying decision-tree-style guidelines and recommendations are valuable resources for researchers in this field.
NATURE COMMUNICATIONS
(2023)
Article
Pharmacology & Pharmacy
Alaa Sayed Abou-Elhamd, Gauthaman Kalamegam, Farid Ahmed, Mourad Assidi, Abdulmajeed Fahad Alrefaei, Peter Natesan Pushparaj, Muhammad Abu-Elmagd
Summary: Khat is a stimulant plant containing cathinone and cathine, which can induce excitement and euphoria but also have adverse effects like oral cancer and high blood pressure. Research showed that khat extracts affect ovarian adenocarcinoma cells, causing cellular defects, apoptosis, and alterations in gene expression. In silico analysis revealed potential implications in signaling pathways and neurological diseases.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Multidisciplinary Sciences
Wen-Xin Jiang, Ping-Yi Li, Xiu-Lan Chen, Yi-Shuo Zhang, Jing-Ping Wang, Yan-Jun Wang, Qi Sheng, Zhong-Zhi Sun, Qi-Long Qin, Xue-Bing Ren, Peng Wang, Xiao-Yan Song, Yin Chen, Yu-Zhong Zhang
Summary: This study describes a complete pathway for oxidative chitin utilization in marine bacteria. The pathway involves LPMOs-mediated chitin breakdown, oxidation of chitooligosaccharides, and extracellular hydrolysis, and differs from the known hydrolytic chitin utilization pathway in enzymes, transporters, and regulatory factors.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Reiko Martin, Reiko Watanabe, Kosuke Hashimoto, Kazuma Higashisaka, Yuya Haga, Yasuo Tsutsumi, Kenji Mizuguchi
Summary: Developing a generalized model for predicting nanotoxicity is critical for designing safe nanoparticles. However, the complex toxicity mechanisms and evaluation bias hinder reliable predictions. Using literature data mining and machine learning, we propose an evidence-based prediction method for distinguishing between cytotoxic and noncytotoxic nanoparticles and apply it to amorphous silica nanoparticles (SiO2-NPs), identifying key attributes for toxicity.