Article
Biochemistry & Molecular Biology
Katja Scharinger, Sebastian Maxeiner, Carmen Schalla, Stephan Rutten, Martin Zenke, Antonio Sechi
Summary: The bimolecular complex between LSP1 and myosin1e plays a crucial role in regulating actin cytoskeleton remodeling and focal adhesion dynamics in macrophages, impacting cell migration, lamellipodia formation, and focal adhesion turnover.
Article
Multidisciplinary Sciences
Bojian Ding, Heidy Y. Narvaez-Ortiz, Yuvraj Singh, Glen M. Hocky, Saikat Chowdhury, Brad J. Nolen
Summary: Arp2/3 complex nucleates branched actin filaments and provides pushing forces for cellular processes. This study reveals the contacts between Arp2/3 complex and the mother actin filament, suggesting that actin filaments stimulate subunit flattening for complex activation. However, limited contact between the bottom half of the complex and the mother filament may explain why actin filaments are required but insufficient to trigger nucleation during WASP-mediated activation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Daniel A. D. Flormann, Moritz Schu, Emmanuel Terriac, Divyendu Thalla, Lucina Kainka, Marcus Koch, Annica K. B. Gad, Franziska Lautenschlaeger
Summary: Advancements in advanced microscopy techniques have enhanced imaging quality and understanding of subcellular structures, but computational analysis techniques have not progressed at the same pace. A new algorithm for tracing filament networks has been developed, capable of extracting important parameters and distinguishing sub-networks in two-dimensional images. This algorithm can be widely applied in analyzing images obtained from different advanced microscopy methods.
Article
Biochemical Research Methods
Ruohua Shi, Keyan Bi, Kai Du, Lei Ma, Fang Fang, Lingyu Duan, Tingting Jiang, Tiejun Huang
Summary: Cell membrane segmentation in electron microscopy (EM) images is an important task. Current approaches perform well on low-resolution datasets but struggle with high-resolution datasets. Through eye movement and perceptual consistency experiments, we found that humans are more sensitive to membrane structure and can tolerate misalignment. Based on these findings, we propose a computational framework that incorporates human perception characteristics, including the perceptual Hausdorff distance (PHD) evaluation metric and a PHD-guided segmentation network (PS-Net).
Article
Biochemistry & Molecular Biology
Desiree Sauter, Martin Schroeter, Christoph Frey, Cornelia Weber, Ulrike Mersdorf, Jan-Willi Janiesch, Ilia Platzman, Joachim P. Spatz
Summary: This study introduces a method for assembling an artificial cytoskeleton in a synthetic cell model system, and investigates the temperature-mediated contraction/release behavior of the cytoskeleton. The results show that the deformation induced by hydrogel can be used to controllably manipulate the motility of droplet-based synthetic cells.
MACROMOLECULAR BIOSCIENCE
(2022)
Review
Pharmacology & Pharmacy
Antonina Alexandrova, Maria Lomakina
Summary: Tumor shrinkage is not the only indicator of treatment success, as cancer progression and metastasis formation play crucial roles. The plasticity of tumor cells in switching between different migration modes contributes to their ability to avoid treatment. Identifying specific markers for migratory plasticity is important for successful treatment.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Cell Biology
Maria-Graciela Delgado, Ana-Maria Lennon-Dumenil
Summary: Migration of immune cells is crucial for building an efficient defense system, playing important roles from early development to tissue patrolling and lymph node migration.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Nanoscience & Nanotechnology
Maxime Liboz, Antoine Allard, Michel Malo, Guillaume Lamour, Gaelle Letort, Benedicte Thiebot, Sid Labdi, Juan Pelta, Clement Campillo
Summary: The mechanical properties of living cells reflect their physiological and pathological state. Adhesive micropatterns can be used to standardize the mechanics and morphologies of cancer cells. Micropatterning cancer cells leads to distinct morphological and mechanical changes associated with differences in the organization of the cytoskeleton.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Biochemistry & Molecular Biology
Anton S. Shakhov, Polina A. Kovaleva, Alexandra S. Churkina, Igor I. Kireev, Irina B. Alieva
Summary: Actin cytoskeleton is crucial for cellular processes, and there are different isoforms in non-muscle cells, β-actin and γ-actin, which have distinct functions and localization in the cytoplasm. Based on super-resolution microscopy, this study demonstrates that β-actin and γ-actin are segregated in the cytoplasm of endothelial cells, with varying degrees of colocalization in different cellular regions. The segregation of actin isoforms is enhanced during the activation of cell lamella in endothelial barrier dysfunction.
Review
Cell Biology
Evelyn Garlick, Steven G. Thomas, Dylan M. Owen
Summary: Immune cells consist of a diverse set of cells that undergo complex biological processes, with the cellular cytoskeleton playing a key role in regulating these processes. Optical microscopy is well-suited for imaging and quantitatively describing the structure and dynamics of the cytoskeleton. The latest methodology, hardware, and software for labeling and analyzing cytoskeletal structures are reviewed, with highlighted challenges and areas for future development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Cell Biology
James M. Cowan, Jacob J. Duggan, Breanne R. Hewitt, Ryan J. Petrie
Summary: This review discusses the distinct modes of 3D cell migration and the role of non-muscle myosin II (NMII) in generating mechanical forces for migration. It also highlights the potential roles of tropomyosins and septins in regulating NMII activity during 3D cell migration. Investigating the mechanisms controlling NMII activity is important for understanding how cells transition between different modes of 3D migration in response to the physical environment.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biophysics
Marketa Kubankova, Bettina Hohberger, Jakob Hoffmanns, Julia Fuerst, Martin Herrmann, Jochen Guck, Martin Kraeter
Summary: Various physical parameters of blood cells, including lymphocyte stiffness, monocyte size, neutrophil size and deformability, and heterogeneity of erythrocyte deformation and size, were found to change significantly in COVID-19 patients. While some of these changes recovered after hospitalization, others persisted for months after discharge, demonstrating the long-term impact of COVID-19 on the body.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Daichi Takahashi, Ikuko Fujiwara, Yuya Sasajima, Akihiro Narita, Katsumi Imada, Makoto Miyata
Summary: MreB is a bacterial protein involved in cell wall synthesis and cell shape determination. This study investigates the structure and dynamics of MreB homologs in Spiroplasma eriocheiris. The results reveal different polymerization behaviors and the importance of a specific amino acid motif in the hydrolysis of ATP.
Article
Cell Biology
Sandeep M. Nalluri, Chinmay S. Sankhe, Joseph W. O'Connor, Paul L. Blanchard, Joelle N. Khouri, Steven H. Phan, Gage Virgi, Esther W. Gomez
Summary: Epithelial-mesenchymal transition (EMT) is a physiological process essential for embryogenesis and wound healing, but also implicated in pathologies like fibrosis and cancer. Regulation of phosphorylation status can impact cell physiology and gene expression changes during TGFβ1-induced EMT, highlighting the crucial role of intricate crosstalk between signaling cascades in regulating EMT processes.
JOURNAL OF CELLULAR PHYSIOLOGY
(2022)
Article
Biology
Jeong Min Chung, Osamu Sato, Reiko Ikebe, Sangmin Lee, Mitsuo Ikebe, Hyun Suk Jung
Summary: This study investigated the mechanism by which fascin-1 induces actin bundling and its localization along actin filaments. The researchers found that the N-terminal region of fascin-1 is responsible for actin bundling, while the C-terminal region is important for fascin-1 dimerization. Furthermore, they discovered that the intermolecular interactions of the C-terminal region are essential for actin bundling.
Article
Biochemistry & Molecular Biology
Lucien Fabre, Abigail T. Ntreh, Amira Yazidi, Inga Leus, Jon W. Weeks, Sudipta Bhattacharyya, Jakob Ruickoldt, Isabelle Rouiller, Helen Zgurskaya, Jurgen Sygusch
Summary: The structure of the inner membrane component TriABC and its substrate-free conformation were determined by cryoelectron microscopy, revealing an intermediate step in efflux complex assembly and identifying a tunnel network with constriction that impedes substrate efflux. Functional analyses were used to propose that selective substrate translocation involves conformational gating at the tunnel narrowing.
Article
Cell Biology
Xi He, Sarah E. Smith, Shiyuan Chen, Hua Li, Di Wu, Paloma Meneses-Giles, Yongfu Wang, Mark Hembree, Kexi Yi, Xia Zhao, Fengli Guo, Jay R. Unruh, Lucinda E. Maddera, Zulin Yu, Allison Scott, Anoja Perera, Yan Wang, Chongbei Zhao, KyeongMin Bae, Andrew Box, Jeffrey S. Haug, Fang Tao, Deqing Hu, Darrick M. Hansen, Pengxu Qian, Subhrajit Saha, Dan Dixon, Shrikant Anant, Da Zhang, Edward H. Lin, Weijing Sun, Leanne M. Wiedemann, Linheng Li
Summary: The study reveals a bidirectional crosstalk between treatment-resistant tumor-initiating stem cells (TrTSC) and the tumor microenvironment (TME), leading to a contexture that promotes tumor growth and immunosuppression.
Article
Multidisciplinary Sciences
Fengli Guo, Melainia McClain, Xia Zhao, Kexi Yi, Tari Parmely, Jay Unruh, Brian Slaughter, Leonid Kruglyak, Longhua Guo, Alejandro Sanchez Alvarado
Summary: This research protocol utilizes a brief fixation step to facilitate the localization and dissection of planarian ovaries for downstream analysis. The dissected ovaries are suitable for ultrastructural examination using transmission electron microscopy and antibody immunostaining.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Biochemistry & Molecular Biology
Christopher W. Akey, Digvijay Singh, Christna Ouch, Ignacia Echeverria, Ilona Nudelman, Joseph M. Varberg, Zulin Yu, Fei Fang, Yi Shi, Junjie Wang, Daniel Salzberg, Kangkang Song, Chen Xu, James C. Gumbart, Sergey Suslov, Jay Unruh, Sue L. Jaspersen, Brian T. Chait, Andrej Sali, Javier Fernandez-Martinez, Steven J. Ludtke, Elizabeth Villa, Michael P. Rout
Summary: This study provides a structure of the isolated yeast NPC and reveals how flexible connectors tie together different structural and functional layers. It also suggests an evolutionary and mechanistic link between assembly and transport. Additionally, the study identifies three major NPC variants that may signify functional specializations at the nuclear periphery.
Article
Biochemistry & Molecular Biology
Remi Vuillemot, Osamu Miyashita, Florence Tama, Isabelle Rouiller, Slavica Jonic
Summary: This article presents a new flexible fitting method, NMMD, which combines normal mode analysis (NMA) and molecular dynamics simulation (MD), to obtain atomic models of cryo-EM maps more efficiently and accurately.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Parasitology
George Kobakhidze, Ashish Sethi, Sepideh Valimehr, Stuart A. Ralph, Isabelle Rouiller
Summary: This article reviews the current knowledge on the structure, function, and conservation of p97 in pathogens and discusses the potential of using p97 as a drug target against these pathogens. It also explores strategies in designing novel inhibitors.
TRENDS IN PARASITOLOGY
(2022)
Article
Biology
Joseph M. Varberg, Jay R. Unruh, Andrew J. Bestul, Azqa A. Khan, Sue L. Jaspersen
Summary: The number and distribution of nuclear pore complexes (NPCs) in the nuclear envelope vary between cell types and change in cellular differentiation and disease. In this study, the researchers used structured illumination microscopy to analyze the NPC number and distribution in the fission yeast Schizosaccharomyces pombe. They found that NPC density is maintained across a wide range of nuclear sizes, and regions of reduced NPC density are observed over the nucleolus and surrounding the spindle pole body (SPB). They also discovered that Lem2-mediated tethering of the centromeres to the SPB is required to maintain NPC exclusion near SPB.
LIFE SCIENCE ALLIANCE
(2022)
Article
Multidisciplinary Sciences
Karla T. Falcon, Kristin E. N. Watt, Soma Dash, Ruonan Zhao, Daisuke Sakai, Emma L. Moore, Sharien Fitriasari, Melissa Childers, Mihaela E. Sardiu, Selene Swanson, Dai Tsuchiya, Jay Unruh, George Bugarinovic, Lin Li, Rita Shiang, Annita Achilleos, Jill Dixon, Michael J. Dixon, Paul A. Trainor
Summary: This study investigates the importance of ribosomal RNA (rRNA) transcription in craniofacial development and the implications of disruptions in this process. The researchers discovered that high expression of Pol I subunits in neuroepithelium and neural crest cells (NCCs) sustains elevated rRNA transcription, supporting the high levels of protein translation in these cells. However, disruptions in rRNA synthesis in NCCs can lead to p53 protein accumulation, NCC apoptosis, and craniofacial anomalies. Compound mutations in Pol I subunits further exacerbate these anomalies. Mechanistically, diminished rRNA synthesis causes an imbalance between rRNA and ribosomal proteins, affecting the binding of these proteins with Mdm2 and p53. This study highlights the critical role of rRNA transcription in craniofacial development and its specific sensitivities to disruptions in certain congenital craniofacial disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Alejandro Rodriguez Gama, Tayla Miller, Jeffrey J. Lange, Jay R. Unruh, Randal Halfmann
Summary: This study investigates the molecular mechanism of immune cell activation and the assembly mechanism of the signalosome. The researchers discovered that the switch-like activation of immune cells is achieved through large protein assemblies known as signalosomes. They also found that the assembly of the signalosome involves a nucleation barrier and that the structure of the proteins in the signalosome is not critical for its activity.
Article
Biochemical Research Methods
Hsiao Ju Chiang, Daniel E. S. Koo, Masahiro Kitano, Sean Burkitt, Jay R. R. Unruh, Cristina Zavaleta, Le A. A. Trinh, Scott E. E. Fraser, Francesco Cutrale
Summary: Hybrid Unmixing enables enhanced imaging of multiplexed fluorescence labels by reducing illumination intensities. It can cleanly separate and distinguish multiple fluorescent labels from background autofluorescence, enabling dynamic imaging in complex systems. HyU permits high dynamic range imaging, allowing simultaneous imaging of bright exogenous labels and dim endogenous labels, providing more accurate insights into the complexity of biological systems.
Article
Developmental Biology
Zainab Afzal, Jeffrey J. Lange, Christof Nolte, Sean McKinney, Christopher Wood, Ariel Paulson, Bony De Kumar, Jay Unruh, Brian D. Slaughter, Robb Krumlauf
Summary: Signaling pathways regulate the patterns of Hox gene expression in axial identity specification. Little is known about the properties of cis-regulatory elements and transcriptional mechanisms that control Hox expression through graded signaling inputs. This study optimized a single molecule fluorescent in situ hybridization (smFISH) technique to evaluate the role of three retinoic acid response element (RARE)-dependent enhancers in regulating nascent transcription patterns of Hoxb genes. The results suggest that these enhancers have differential impacts on global and local patterns of transcription, and their competitive interactions are important for maintaining proper levels and patterns of Hoxb transcription.
Article
Multidisciplinary Sciences
Qingqing Liu, Benjamin Fong, Seungmin Yoo, Jay R. Unruh, Fengli Guo, Zulin Yu, Jingjing Chen, Kausik Si, Rong Li, Chuankai Zhou
Summary: Eukaryotic cells organize cellular contents into membrane-bound organelles and membrane-less condensates. However, the mechanism behind the spatially localized protein aggregates on organellar surfaces, like mitochondria, remains unknown. In this study, it was found that the mitochondrial import receptor Tom70 is involved in the localized condensation of protein aggregates in yeast and human cells. Misfolded cytosolic proteins are recruited to the condensation sites initiated by Tom70's substrates on the organellar membrane using multivalent hydrophobic interactions. Disruption of the mitochondrial association of aggregates impairs their asymmetric retention during mitosis and reduces the mitochondrial import of misfolded proteins, suggesting a proteostasis role of the organelle-condensate interactions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Vivekanandan Ramalingam, Xinyang Yu, Brian D. Slaughter, Jay R. Unruh, Kaelan J. Brennan, Anastasiia Onyshchenko, Jeffrey J. Lange, Malini Natarajan, Michael Buck, Julia Zeitlinger
Summary: Lola-I, a Drosophila zinc finger transcription factor, can regulate the promoter state independently of gene activation. It makes the target promoters accessible and acquire paused RNA polymerase II throughout the embryo. This promoter transition is crucial for tissue-specific target gene activation. Lola-I mediates this function by depleting promoter nucleosomes.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Juliana Conkright-Finchaml, Chieri Tomomori-Sato, Rich McGhee, Ella M. Leslie, Carolyn J. Beucherl, Lauren E. Weems, Shigeo Sato, William B. Redwine, Kyle J. Weaver, Brandon D. Miller, Kym M. Delventhal, John J. Kary, Andrew B. Koebbe, Alexander Deans, Jessica L. Witt, Laura M. Remy, Tani J. Parmely, Chongbei Zhao, Yan Wang, Joan W. Conaway, Jay R. Unruh
Summary: This article presents a protocol for a high-throughput colorimetric ELISA assay to detect IgG antibodies against the SARS-CoV-2 spike protein. The assay reliably measures antibody levels quantitatively and improves sensitivity by controlling for non-specific binding and eliminating background contributions.
Article
Genetics & Heredity
Shary N. Shelton, Sarah E. Smith, Jay R. Unruh, Sue L. Jaspersen
Summary: The INM proteome differs between gametes and mitotic cells, with gametes requiring a unique set of INM proteins for gamete formation, synthesized de novo. This suggests changes in the nuclear permeability barrier and inheritance pattern of INM components during gametogenesis.
G3-GENES GENOMES GENETICS
(2021)
