Article
Biochemistry & Molecular Biology
Renying Wang, Peijing Zhang, Jingjing Wang, Lifeng Ma, E. Weigao, Shengbao Suo, Mengmeng Jiang, Jiaqi Li, Haide Chen, Huiyu Sun, Lijiang Fei, Ziming Zhou, Yincong Zhou, Yao Chen, Weiqi Zhang, Xinru Wang, Yuqing Mei, Zhongyi Sun, Chengxuan Yu, Jikai Shao, Yuting Fu, Yanyu Xiao, Fang Ye, Xing Fang, Hanyu Wu, Qile Guo, Xiunan Fang, Xia Li, Xianzhi Gao, Dan Wang, Peng-Fei Xu, Rui Zeng, Gang Xu, Lijun Zhu, Lie Wang, Jing Qu, Dan Zhang, Hongwei Ouyang, He Huang, Ming Chen, Shyh-Chang Ng, Guang-Hui Liu, Guo-Cheng Yuan, Guoji Guo, Xiaoping Han
Summary: By using single-cell RNA sequencing, researchers mapped organism-level cell landscapes for mice, zebrafish, and Drosophila. They identified structural inflammation and mitochondrial dysfunction as common hallmarks of organism aging.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Immunology
Xing-Xing Fan, Qiang Wu
Summary: Lung cancer is highly heterogeneous, and single-cell analysis can help us understand its molecular characteristics and cell types better. Recent findings may provide new directions for the treatment strategies of lung cancer.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Cell Biology
Ryohichi Sugimura, Yiming Chao
Summary: The tumor microenvironment contains various innate immune cells that have important roles in regulating tumor progression. Accurate characterization of these cells at the single-cell level using single-cell technology can enhance the potential of cancer immunotherapy.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Arne Werner
Summary: RNA double strand hybridization is a crucial process in gene expression regulation, and this study determined the dissociation constants of complementary equally sized RNA single strands using fluorescence correlation spectroscopy at the single molecule level. The dissociation constants for different lengths of dsRNA were measured, and the translational diffusion coefficients of RNA at infinite dilution were accurately predicted.
ANALYTICAL BIOCHEMISTRY
(2023)
Article
Peripheral Vascular Disease
Alessandra Pasut, Lisa M. Becker, Anne Cuypers, Peter Carmeliet
Summary: The plasticity of vascular endothelial cells drives physiological repair and pathological angiogenesis, posing challenges for targeted therapy due to their heterogeneity and unidentified phenotypes. Single-cell studies have revealed the diversity of EC types and states, offering insights into new subtypes and functions in health and disease. Metabolic gene signatures in different EC phenotypes may hold therapeutic potential for promoting tissue repair or inhibiting tumor angiogenesis in a tissue-specific manner.
Editorial Material
Biochemistry & Molecular Biology
Huan Yao, Ying Yang, Yun-Gui Yang
Summary: In this study, Tegowski et al. developed a single-cell DART-seq method to profile m(6)A sites and revealed fundamental features of m(6)A biology at the single-cell level. These findings enhance our understanding of the regulatory and functional mechanisms of m(6)A.
Article
Multidisciplinary Sciences
Fei Wang, Peiwen Ding, Xue Liang, Xiangning Ding, Camilla Blunk Brandt, Evelina Sjostedt, Jiacheng Zhu, Saga Bolund, Lijing Zhang, Laura P. M. H. de Rooij, Lihua Luo, Yanan Wei, Wandong Zhao, Zhiyuan Lv, Janos Hasko, Runchu Li, Qiuyu Qin, Yi Jia, Wendi Wu, Yuting Yuan, Mingyi Pu, Haoyu Wang, Aiping Wu, Lin Xie, Ping Liu, Fang Chen, Jacqueline Herold, Joanna Kalucka, Max Karlsson, Xiuqing Zhang, Rikke Bek Helmig, Linn Fagerberg, Cecilia Lindskog, Fredrik Ponten, Mathias Uhlen, Lars Bolund, Niels Jessen, Hui Jiang, Xun Xu, Huanming Yang, Peter Carmeliet, Jan Mulder, Dongsheng Chen, Lin Lin, Yonglun Luo
Summary: Using single-cell RNA sequencing, researchers generated a comprehensive map of single-cell transcriptomes from various organs of pigs. They identified a high degree of heterogeneity within cells and uncovered several functionally distinct cell types, including a subtype of endothelial cells in adipose tissues. Additionally, they predicted tissue- and cell type-specific communication between endothelial cells and other cell types through specific pathways. Furthermore, analysis of microglia transcriptomes across species revealed an evolutionally conserved regulon.
NATURE COMMUNICATIONS
(2022)
Editorial Material
Cell Biology
Mary Mohrin, Heinrich Jasper
Summary: In this issue of Developmental Cell, Zou et al. use eyelid samples to study human skin aging at the single-cell level. They identify photo- and inflammation-related changes starting in middle age and suggest that restoring youthful expression of KLF6 and HES1 may help mitigate some age-associated changes.
DEVELOPMENTAL CELL
(2021)
Article
Multidisciplinary Sciences
Zhuo Ma, Xiaofei Zhang, Wen Zhong, Hongyan Yi, Xiaowei Chen, Yinsuo Zhao, Yanlin Ma, Eli Song, Tao Xu
Summary: In this study, the authors used single-cell RNA sequencing and single-cell assay for transposase accessible chromatin sequencing to explore the molecular heterogeneity, developmental trajectory, and regulatory networks of early human pancreas development. They identified differences in gene expression patterns between dorsal and ventral pancreatic multipotent cells in humans, and identified pancreato-biliary progenitors that generate ventral multipotent cells. Notch and MAPK signals from mesenchymal cells were found to regulate the differentiation of multipotent cells into trunk and duct cells. They also discovered different subclusters of endocrine progenitors with varying differentiation potentials. While the developmental trajectories were largely conserved between humans and mice, distinct gene expression patterns were also identified.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Fuzhou Wang, Hamid Alinejad-Rokny, Jiecong Lin, Tingxiao Gao, Xingjian Chen, Zetian Zheng, Lingkuan Meng, Xiangtao Li, Ka-Chun Wong
Summary: A lightweight framework called scGSLoop is introduced to detect chromatin loops on single-cell Hi-C data. Leveraging graph-based deep learning, scGSLoop operates on sparse matrices, avoiding resource-intensive data densification. This model not only achieves computational efficiency but also accurately predicts loops genome-wide. It preserves single-cell information, enabling the investigation of looping variability and multi-connected hubs.
Article
Oncology
Douglas R. Green
Summary: Genetically identical cells in a tissue can exhibit different responses to environmental stress, influencing their decision to repair or die, and affecting surrounding cells. These responses play a role in controlling the health and fitness of individual cells and their competition with other genetically identical cells.
CANCER IMMUNOLOGY RESEARCH
(2021)
Article
Immunology
Rongguo Wei, Zheng Qin, Qi Huang, Lulu Liu, Fang Cheng, Songdong Meng, Lin Wang
Summary: This study reveals the immune abnormalities at the single-cell level in COVID-19 patients and investigates the impact of cytokine storms on immune response. The study also identifies pathways and cell subsets associated with inflammation. These findings are important for understanding the immune mechanisms of COVID-19.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Panos Louridas, Diomidis Spinellis
Summary: People exhibit their status through conspicuous consumption of particular goods or experiences. Higher income is often associated with higher status, but can also lead to unethical behavior. Some individuals engage in illegal activities, like bribery, to acquire restricted goods as a status symbol, as seen in the case of obtaining special license plates in Greece.
Article
Chemistry, Analytical
Jiri Dietvorst, Amparo Ferrer-Vilanova, Sharath Narayana Iyengar, Aman Russom, Nuria Vigues, Jordi Mas, Lluisa Vilaplana, Maria-Pilar Marco, Gonzalo Guirado, Xavier Munoz-Berbel
Summary: This study introduces a cyanotype-based photochemical amplification reaction for detecting low bacterial concentrations efficiently and simply, which is expected to have a significant impact on clinical diagnosis of infectious diseases.
ANALYTICAL CHEMISTRY
(2022)
Editorial Material
Oncology
Thomas S. B. Schmidt, Peer Bork
Summary: This study provides a detailed description of the role of microorganisms in pancreatic tumors, identifying their intracellular presence associated with cell-type-specific transcriptional shifts and clinical prognosis.
Article
Multidisciplinary Sciences
Tobias Herrmann, Raul Torres, Eric N. Salgado, Cristina Berciu, Daniel Stoddard, Daniela Nicastro, Simon Jenni, Stephen C. Harrison
Summary: Studies using electron cryomicroscopy have revealed that rotaviruses attach to target cells through the outer-layer protein VP4, which rearranges after cleavage to facilitate membrane perforation and delivery of the viral genome. The VP4 of rotaviruses undergoes a transition from an 'upright' to a 'reversed' conformation activated by cleavage, projecting a 'foot' domain outward into the host cell membrane. This mechanism defines the first steps of rotavirus penetration into target cell membranes, suggesting similarities with mechanisms of other viruses.
Article
Chemistry, Physical
Theodore Lupinski, Markus Ludwig, Seth Fraden, Nathan Tompkins
Summary: Constant pressure pumps play a crucial role in microfluidic flow systems, stabilizing fluid pressure and adapting to systems requiring pressure stability. These pumps are cost-effective and suitable for use in undergraduate institutions and laboratories with limited research budgets.
EUROPEAN PHYSICAL JOURNAL E
(2021)
Article
Biochemistry & Molecular Biology
Gang Fu, Chasity Scarbrough, Kangkang Song, Nhan Phan, Maureen Wirschell, Daniela Nicastro
Summary: The study investigates the molecular architecture of the I1 dynein ICLC complex using biochemical and genetic approaches in Chlamydomonas. The research highlights the importance of TCTEX2B dynein light chain in the stable assembly of TCTEX1 and inner dynein arm interacting proteins. Structural defects observed in the study reveal potential protein-protein interactions involved in the pathway by which I1 regulates ciliary motility.
Article
Chemistry, Multidisciplinary
Sarah E. Zuraw-Weston, Mahsa Siavashpouri, Maria E. Moustaka, Thomas Gerling, Hendrik Dietz, Seth Fraden, Alexander E. Ribbe, Anthony D. Dinsmore
Summary: This experimental study explores the impact of nanorods binding to lipid bilayer vesicles and altering membrane shape. By adjusting adhesion strength, membrane tension, and particle concentration, it was found that increasing adhesion strength led to membrane deformation, vesicle-vesicle adhesion, and vesicle rupture. These findings provide insight into the physical mechanisms behind membrane remodeling and may inspire the development of new bioinspired materials.
Article
Cell Biology
Yanhe Zhao, Justine Pinskey, Jianfeng Lin, Weining Yin, Patrick R. Sears, Leigh A. Daniels, Maimoona A. Zariwala, Michael R. Knowles, Lawrence E. Ostrowski, Daniela Nicastro
Summary: The study provides insights into the potential structural basis for primary ciliary dyskinesia by examining the structure of RSPH4A(-/-) human respiratory cilia, highlighting the benefits of using cryo-electron tomography directly on patient samples for molecular structure determination.
MOLECULAR BIOLOGY OF THE CELL
(2021)
Article
Chemistry, Physical
Maria Eleni Moustaka, Michael M. Norton, Baptiste Blanc, Viktor Horvath, S. Ali Aghvami, Seth Fraden
Summary: Experiments and models were used to investigate the permeation and reaction of aqueous bromine in PDMS, revealing the diffusion, reversible binding, and irreversible reaction processes between bromine and PDMS.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Christian Sigl, Elena M. Willner, Wouter Engelen, Jessica A. Kretzmann, Ken Sachenbacher, Anna Liedl, Fenna Kolbe, Florian Wilsch, S. Ali Aghvami, Ulrike Protzer, Michael F. Hagan, Seth Fraden, Hendrik Dietz
Summary: This study introduces a programmable icosahedral canvas for the self-assembly of icosahedral shells with viral trapping and antiviral properties. It demonstrates the potential of a new broad-spectrum antiviral platform that could alleviate many threats to global public health.
Article
Cell Biology
Kai Cai, Yanhe Zhao, Lei Zhao, Nhan Phan, Yuqing Hou, Xi Cheng, George B. Witman, Daniela Nicastro
Summary: The study identified two proteins, FAP42 and FAP246, localized to the L-shaped C1b projection of the central apparatus (CA) and their interaction with the candidate CA protein FAP413. The complex of FAP246-FAP413-FAP42 is essential for stable assembly of the C1b, C1f, and C2b projections, and their loss leads to ciliary motility defects.
JOURNAL OF CELL SCIENCE
(2021)
Article
Plant Sciences
Ethan Weiner, Justine M. Pinskey, Daniela Nicastro, Marisa S. Otegui
Summary: Recent developments in instrumentation and image analysis algorithms have advanced the capabilities of 3D-EM, allowing for automated image collections and near-atomic resolution imaging of macromolecular complexes. This review focuses on the applications of cryo-ET in plant and algal cell biology research, highlighting its unique ability to reveal the organization of eukaryotic organelles. Challenges in sample preparation for cryo-ET are also discussed, along with the development of correlative light and electron microscopy approaches.
Article
Multidisciplinary Sciences
John Berezney, Bruce L. Goode, Seth Fraden, Zvonimir Dogic
Summary: This study investigates a reconstituted composite system composed of an active microtubule network and a passive F-actin filament network. By increasing the concentration of actin filaments, the system's dynamics transition from turbulent-like flows to bulk contractions. At intermediate concentrations, the composite separates into layered asters that coexist with a background turbulent fluid. These structures self-organize and have a defined lifetime.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Yanhe Zhao, Huafeng Wang, Caroline Wiesehoefer, Naman B. Shah, Evan Reetz, Jae Yeon Hwang, Xiaofang Huang, Tse-en Wang, Polina V. Lishko, Karen M. Davies, Gunther Wennemuth, Daniela Nicastro, Jean-Ju Chung
Summary: The study visualizes the native in-cell 3D structure and higher-order organization of the CatSper calcium channels using cryo-electron tomography. The authors discover that the CatSper channels form long zigzag rows along the sperm tail and interact with other molecules. Moreover, the loss of EFCAB9-CATSPER zeta alters the architecture and interactions of the channels, disrupting flagellar movement in sperm.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Sean Rogers, Long Gui, Anastasiia Kovalenko, Valeria Zoni, Maxime Carpentier, Kamran Ramji, Kalthoum Ben Mbarek, Amelie Bacle, Patrick Fuchs, Pablo Campomanes, Evan Reetz, Natalie Ortiz Speer, Emma Reynolds, Abdou Rachid Thiam, Stefano Vanni, Daniela Nicastro, W. Mike Henne
Summary: The study reveals that yeast glucose restriction can induce liquid crystalline phase transitions and lipid demixing in lipid droplets, leading to selective remodeling of their proteome.
JOURNAL OF CELL BIOLOGY
(2022)
Article
Biology
Justine M. Pinskey, Adhya Lagisetty, Long Gui, Nhan Phan, Evan Reetz, Amirrasoul Tavakoli, Gang Fu, Daniela Nicastro
Summary: This study used cryo-electron microscopy to investigate flagella in the aquatic eukaryote choanoflagellates, and found that their flagellar structures are more similar to those of multicellular organisms. Additionally, unique features of choanoflagellate flagella were described, and unknown functional structures were reported on the extracellular surface of the flagellar membrane.
Proceedings Paper
Materials Science, Multidisciplinary
U. Hommerich, J. Barnett, A. Kabir, K. Ghebreyessus, K. Hampton, S. Uba, I Uba, D. Geddis, C. Yang, S. Trivedi, S. Fraden, Ali Aghvami
Summary: Manganese doped CsPbCl3 bulk crystals and nanoparticles were prepared and their emission properties were compared in this study. The results showed significant differences in excitation spectra, emission characteristics, and emission lifetimes between the two forms.
OPTICAL COMPONENTS AND MATERIALS XVIII
(2021)
Article
Physics, Fluids & Plasmas
Yi Fan, Kun-Ta Wu, S. Ali Aghvami, Seth Fraden, Kenneth S. Breuer
Summary: This study investigates the dynamics and structure of kinesin-driven microtubule active fluids as the height of the container increases. The activity level, characterized by velocity fluctuations, increases with system size while maintaining small-scale isotropy. The velocity-velocity temporal correlation develops a strong positive correlation at longer times as the confinement level decreases.