Article
Biology
Diyan Li, Mengnan He, Qianzi Tang, Shilin Tian, Jiaman Zhang, Yan Li, Danyang Wang, Long Jin, Chunyou Ning, Wei Zhu, Silu Hu, Keren Long, Jideng Ma, Jing Liu, Zhihua Zhang, Mingzhou Li
Summary: The three-dimensional architecture of the genome plays a crucial role in gene expression regulation and conservation across species. This study compares the 3D genomes of fish, chickens, and 10 mammalian species, and reveals that genome size and chromosome length influence the higher hierarchical organization of the genome, while local transcriptional availability is selected through vertebrate evolution. Additionally, conservation of topologically associating domains is associated with modularity of expression profiles, and LINE and SINE transposable elements contribute to heterochromatin and euchromatin organization during genome evolution.
Article
Biochemistry & Molecular Biology
Juan C. Opazo, Michael W. Vandewege, Federico G. Hoffmann, Kattina Zavala, Catalina Melendez, Charlotte Luchsinger, Viviana A. Cavieres, Luis Vargas-Chacoff, Francisco J. Morera, Patricia Burgos, Cheril Tapia-Rojas, Gonzalo A. Mardones
Summary: Studying the evolutionary history of gene families is important for understanding gene origin, evolution, and their implications for functional studies. The sirtuin gene family, involved in aging-related functions, has a complex duplicative history, but our results provide a well-resolved phylogeny and shed light on the repertoire of sirtuin genes among vertebrates. We identified a new member (SIRT3.2) that was lost in amniotes but retained in other jawed vertebrates, and its experimental analysis revealed its mitochondrial location and deacetylase activity similar to mammalian SIRT3.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Biology
Giovanni Annona, Iori Sato, Juan Pascual-Anaya, David Osca, Ingo Braasch, Randal Voss, Jan Stundl, Vladimir Soukup, Allyse Ferrara, Quenton Fontenot, Shigeru Kuratani, John H. Postlethwait, Salvatore D'Aniello
Summary: Nitric oxide (NO) is a crucial signaling molecule in biological systems, playing important roles in cardiovascular, neurological, and immune functions. Understanding the evolution of NO synthases (Nos) genes, which produce NO in vivo, is still a puzzle, especially in fish compared to tetrapods. Recent studies have found the presence of nos3 gene, previously considered lost, in spotted gar, changing our perspective on the origin of nos genes. This study explored nos gene evolution in different vertebrate species and revealed lineage-specific gene duplications and losses, independent losses of nos3 in teleost lineages, and the expression of nos genes in the gills of certain gnathostome species. These findings provide insights into the roles and evolutionary history of nos genes.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Developmental Biology
Juan C. Opazo, Federico G. Hoffmann, Kattina Zavala, Scott Edwards
Summary: The DAN gene family plays fundamental roles in development and is associated with diseases in adulthood. This study investigates the evolutionary history of the DAN gene family in vertebrates, identifying two new gene lineages and reconstructing the ancestral repertoire of DAN genes in gnathostomes.
DEVELOPMENTAL BIOLOGY
(2022)
Article
Genetics & Heredity
Yuqi Huang, Minghao Sun, Lenan Zhuang, Jin He
Summary: This study provides a comprehensive molecular phylogenetic analysis of vertebrate AIGs, revealing loss or gain of AIG members in different species during evolution. The findings can be used for future functional characterization of AIGs.
Article
Developmental Biology
Adrian Garcia-Concejo, Dan Larhammar
Summary: PKC, one of the earliest identified kinases in human cells, forms a family of kinases that respond to various signaling molecules with diverse functions. Evolutionary analysis reveals a vertebrate predecessor with five PKC genes, leading to a total of 21 genes in jawed vertebrates due to genome doublings. The genome duplications account for the complexity of the PKC gene family in jawed vertebrates and greatly impact their evolution.
DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ying Xiong, Fumin Lei
Summary: The study reveals that avian genomes lack important genes related to glucose transport, but functional compensation is retained through biochemical or physiological means. Classification of the SLC2 gene family shows positive selection for SLC2A4 and SLC2A12 in birds and mammals, with the latter gene being closely associated with insulin sensitivity and basal metabolic rate in birds.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Endocrinology & Metabolism
Yorgui Santiago-Andres, Matan Golan, Tatiana Fiordelisio
Summary: The pituitary gland, a master endocrine gland in vertebrates, has recently been found to consist of tightly wired large-scale networks of cells that communicate with each other in homo and heterotypic manners, optimizing hormone pulse generation in response to changing physiological demands. The development of 3D imaging methods and transgenic models has allowed for further research into functional pituitary networks across different vertebrate classes.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Biology
Alexandre P. Thiery, Ariane S. Standing, Rory L. Cooper, Gareth J. Fraser
Summary: Tooth development in mammals is regulated by the enamel knot signalling center. While there are differences in signalling, the presence of an enamel knot in non-mammalian vertebrates is still debated. Through studying sharks, researchers found similarities in the expression of fgf3, fgf10, and shh, as well as changes in tooth phenotypes following perturbations of canonical Wnt signalling, which supports the conservation of the enamel knot-like signalling center throughout vertebrates. This suggests that tooth types in different animals follow a similar developmental plan, and the lineage-specific differences in signalling do not refute the homology of this signalling center.
Editorial Material
Multidisciplinary Sciences
Matt Friedman
Summary: Scarce evidence suggests that important evolutionary developments for jawed vertebrates may have taken place during or prior to the Silurian period. Fossil discoveries unveil insights into this particular interval.
Review
Ecology
M. E. McNamara, V Rossi, T. S. Slater, C. S. Rogers, A-L Ducrest, S. Dubey, A. Roulin
Summary: This study integrates fossil data with current understanding of melanin function, biochemistry, and genetics to identify potential genomic controls on melanin evolution. Taxonomic trends in the anatomical location, geometry, and chemistry of vertebrate melanosomes are linked to the evolution of endothermy, suggesting fundamental links between melanization and vertebrate ecology. Tissue-specific and taxonomic trends in melanin chemistry support evidence for evolutionary tradeoffs between function and cytotoxicity.
TRENDS IN ECOLOGY & EVOLUTION
(2021)
Article
Genetics & Heredity
Yang Mao, Taotao Peng, Feng Shao, Qingyuan Zhao, Zuogang Peng
Summary: Adaptation to altitude and oxygen level is crucial for vertebrate evolution. Hemoglobin, a protein in red blood cells, plays a vital role in oxygen delivery for aerobic metabolism. However, the evolutionary history of hemoglobin genes in different taxa remains unclear. Through genome-wide analyses of 97 species, we investigated the conservation and variability of hemoglobin genes across vertebrates. Our results suggest that purifying selection has significantly influenced the evolution of hemoglobin genes in all vertebrates. Additionally, gene duplication, gene loss, and gene conversion have played important roles in shaping the complexity of the vertebrate hemoglobin gene family.
Article
Ecology
Aya Kuretani, Takayoshi Yamamoto, Masanori Taira, Tatsuo Michiue
Summary: In this study, by phylogenetic and synteny analyses, the orthologous and paralogous relationships of hes genes in various species including humans, mice, chicken, gecko, zebrafish, medaka, coelacanth, spotted gar, elephant shark, and three species of frogs were elucidated. It was found that hes5 clusters were not duplicated in mammals, however, they were conserved in teleost with fewer genes compared to frogs. The hes5 cluster-like structure was also identified in the elephant shark genome, but not in cyclostomes.
BMC ECOLOGY AND EVOLUTION
(2021)
Review
Ecology
Diego Safian, Geert F. Wiegertjes, Bart J. A. Pollux
Summary: Fish are an interesting model for studying regeneration, with the Poeciliidae family proposed as a new model system to investigate the evolution of fin regeneration. Current research has focused on the mechanisms and evolutionary pressures of fin regeneration, introducing three new theories for the evolution of this capacity.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Yun-Hai Lu, Intikhab Alam, Yan-Qing Yang, Ya-Cen Yu, Wen-Chao Chi, Song-Biao Chen, Boulos Chalhoub, Li-Xi Jiang
Summary: The YABBY gene family, present in all seed plants, plays crucial roles in plant growth and development, including polarity establishment, leaf and flower formation, and response to hormonal signals and environmental stress. Through identification of 364 YABBY genes in 37 Brassicaceae genomes, it was found that these genes are largely conserved across species but exhibit considerable functional divergence.
Article
Medicine, General & Internal
Tonglian Wang, Jing Hu, Lutong Xu, Hongbo Zhao, Yuanyue Li, Tao Shou, Xueshan Xia, Qiang Chen
IRANIAN RED CRESCENT MEDICAL JOURNAL
(2018)
Article
Biotechnology & Applied Microbiology
Hongbo Zhao, Hui Pan, Huixue Wang, Peiwei Chai, Shengfang Ge, Renbing Jia, Xianqun Fan
ONCOTARGETS AND THERAPY
(2019)
Article
Physics, Multidisciplinary
Hongbo Zhao, Brian D. Storey, Richard D. Braatz, Martin Z. Bazant
PHYSICAL REVIEW LETTERS
(2020)
Article
Medicine, General & Internal
Zhaohui Jin, Zhengtang Liu, Lei Kang, Aoran Yang, Hongbo Zhao, XiaoYan Yan, Tianqing Zhang, Lei Gao, Aixian Liu, Boyan Fang
Article
Chemistry, Physical
Jungjin Park, Hongbo Zhao, Stephen Dongmin Kang, Kipil Lim, Chia-Chin Chen, Young-Sang Yu, Richard D. Braatz, David A. Shapiro, Jihyun Hong, Michael F. Toney, Martin Z. Bazant, William C. Chueh
Summary: Layered oxides electrodes in lithium-ion batteries are designed to be cycled under conditions avoiding phase transitions, but phase separation during delithiation has been observed, which is shown to be a dynamical artefact occurring in a many-particle system driven by autocatalytic electrochemical reactions.
Review
Chemistry, Physical
Hongyi Xu, Juner Zhu, Donal P. Finegan, Hongbo Zhao, Xuekun Lu, Wei Li, Nathaniel Hoffman, Antonio Bertei, Paul Shearing, Martin Z. Bazant
Summary: The electrochemical and mechanical properties of lithium-ion battery materials heavily rely on their 3D microstructure characteristics. A quantitative understanding of the role played by stochastic microstructures is crucial for predicting material properties and guiding synthesis processes. Tailoring microstructure morphology is also a viable way to achieve optimal electrochemical and mechanical performance of lithium-ion cells. This review presents spatially and temporally resolved imaging of microstructure and electrochemical phenomena, microstructure statistical characterization and stochastic reconstruction, microstructure-resolved modeling for property prediction, and machine learning for microstructure design to facilitate the establishment of microstructure-resolved modeling and design methods. Perspectives on the unresolved challenges and opportunities in applying experimental data, modeling, and machine learning to improve understanding of materials and identify paths toward enhanced performance of lithium-ion cells are also discussed.
ADVANCED ENERGY MATERIALS
(2021)
Article
Electrochemistry
Marc D. Berliner, Hongbo Zhao, Supratim Das, Michael Forsuelo, Benben Jiang, William H. Chueh, Martin Z. Bazant, Richard D. Braatz
Summary: Porous electrode theory is commonly used to model battery behavior, but most effective parameters are not practically identifiable from cycling data in lithium-ion batteries. The only identifiable parameter from C/10 discharge data is the effective solid diffusion coefficient. Additional experiments are required to uniquely determine the full set of parameters.
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2021)
Article
Medical Laboratory Technology
Hui Shen, Dan Wang, Mengyun Zhan, Hanping Ding, Hongbo Zhao
Summary: MiR-146a and MiR-146b are decreased in psoriasis patients and negatively correlated with PASI scores; their gradually elevated expressions during etanercept treatment are associated with PASI75 response.
JOURNAL OF CLINICAL LABORATORY ANALYSIS
(2022)
Article
Chemistry, Physical
Haitao D. Deng, Hongbo Zhao, Norman Jin, Lauren Hughes, Benjamin H. Savitzky, Colin Ophus, Dimitrios Fraggedakis, Andras Borbely, Young-Sang Yu, Eder G. Lomeli, Rui Yan, Jueyi Liu, David A. Shapiro, Wei Cai, Martin Z. Bazant, Andrew M. Minor, William C. Chueh
Summary: This study developed a generalizable, physically constrained image-learning framework to learn the chemo-mechanical constitutive law from correlative microscopy images at the nanoscale. By applying this framework to LiXFePO4 battery positive electrode material, the researchers discovered the composition-eigenstrain relation and validated Vegard's law at the nanoscale. The study also visualized the residual strain field and identified heterogeneities arising from misfit dislocations.
Article
Multidisciplinary Sciences
Hongbo Zhao, Haitao Dean Deng, Alexander E. Cohen, Jongwoo Lim, Yiyang Li, Dimitrios Fraggedakis, Benben Jiang, Brian D. Storey, William C. Chueh, Richard D. Braatz, Martin Z. Bazant
Summary: This study demonstrates the learning of heterogeneous reaction kinetics from in situ scanning transmission X-ray microscopy images. The consistency of the learned model with theoretical models was verified, and the spatial heterogeneity of the reaction rate was also learned. These findings offer new possibilities for studying nonequilibrium material properties and characterizing heterogeneous reactive surfaces.
Article
Physics, Multidisciplinary
Hongbo Zhao, Andrej Kosmrlj, Sujit S. Datta
Summary: Research shows that there is a strong competition between collective chemotaxis and motility-induced phase separation (MIPS). Collective chemotaxis can suppress or inhibit phase separation, and it can also generate new dynamic instabilities. These findings contribute to the understanding and clarification of the rich physics underlying active matter systems, ranging from cells to robots.
PHYSICAL REVIEW LETTERS
(2023)
Article
Environmental Studies
Hongbo Zhao, Tianshun Gu, Li Yue, Xiaoman Xu
Summary: This study investigates the spatial associations of luxury hotels using GIS tools and the MGWR model. By analyzing the case of Shanghai City, the study identifies the key determinants that influence the distribution of luxury hotels, including institutional proximity, room rate, green space, and the World Expo.
Article
Medicine, General & Internal
Ting Li, Ling Zhou, Hongbo Zhao, Jing Song, Xiuwen Wang, Shiyuan Liu, Huji Xu
FRONTIERS IN MEDICINE
(2019)
Article
Physics, Fluids & Plasmas
Hongbo Zhao, Martin Z. Bazant
Article
Electrochemistry
Edwin Khoo, Hongbo Zhao, Martin Z. Bazant
JOURNAL OF THE ELECTROCHEMICAL SOCIETY
(2019)