Review
Biochemistry & Molecular Biology
Alia dos Santos, Christopher P. Toseland
Summary: The nucleus in eukaryotic cells houses the cell's genomic material. Factors like chromatin structure and the nuclear lamina play essential roles in the mechanical properties of the nucleus. Nuclear stiffness impacts and is impacted by cellular processes such as DNA damage and repair.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Eliya Bitman-Lotan, Amir Orian
Summary: Active and continued supervision is required to regulate the differentiated identity, as inability to do so is a hallmark of aging and aging-related disease. A network of nuclear regulators, including transcription factors, epigenetic regulators, and the localization of silent genes, is dedicated to maintaining cellular identity. Recent discoveries focus on mechanisms involving H3K9me3-decorated heterochromatin and the importance of nuclear lamins in cell identity, with relevance to aging and age-related disease discussed.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2021)
Article
Multidisciplinary Sciences
Fazlur Rashid, Wenjie Liu, Qianchun Wang, Baohua Ji, Joseph Irudayaraj, Ning Wang
Summary: It has been found that external mechanical forces have an impact on the structure and function of living cells and tissues in both physiological and pathological conditions. However, the mechanisms underlying changes in structures after force cessation are not well understood. This study used single-molecule imaging techniques to demonstrate that local forces applied via integrins cause chromatin decondensation and increased protein mobility in the nucleus, leading to elevated diffusivity of individual protein molecules in the nucleoplasm. The increased protein diffusivity was found to be regulated by nuclear pore complexes, suggesting a mechanomemory effect in the nucleus that persists for tens of minutes after force cessation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Eugene Jia Hao Soh, Hippolyte P. A. G. Astier, Dan Daniel, Jia Qing Isaiah Chua, Ali Miserez, Zian Jia, Ling Li, Sean J. O'Shea, Harish Bhaskaran, Nikodem Tomczak, Christian A. Nijhuis
Summary: In this study, we demonstrate the direct manipulation and control of liquid metal droplets using an atomic force microscope, achieving repeated contact and separation with self-assembled monolayers in different environments. We successfully create well-defined contact areas of liquid droplets on alkanethiolate SAMs in ethanol, and achieve smaller geometric contact areas in air compared to previous studies.
Article
Biochemistry & Molecular Biology
Anat Vivante, Irit Shoval, Yuval Garini
Summary: Lamin A plays a crucial role in maintaining nuclear organization and integrity, with its dynamics and distribution changing throughout the cell cycle. Analysis of lamin A concentration and distribution reveals its dynamic changes in different phases of the cell cycle, shedding light on its functions in nuclear assembly and disassembly.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Engineering, Biomedical
S-M. Yu, B. Li, F. Amblard, S. Granick, Y-K. Cho
Summary: This study investigated the mechanobiological characteristics of individual cells on a torus structure with different Gaussian curvatures. Cells on the torus surface exhibited topological sensing ability and demonstrated significant adjustments in nuclear area and position depending on the local Gaussian curvature. Spatial heterogeneity of intermediate filament proteins revealed local Gaussian curvature as a key factor of cellular adaptation on curved surfaces.
Review
Biochemistry & Molecular Biology
Laura Gil, Sandra A. Nino, Carmen Guerrero, Maria E. Jimenez-Capdeville
Summary: Cellular identity is determined by complex gene expression patterns, with chromatin regulation mainly controlled by the histone code. The challenges faced by cells include maintaining functionality and identity despite accumulating DNA damage during aging. The role of tau protein in protecting DNA, organizing chromatin, and its involvement in Alzheimer's disease and other tauopathies is discussed, focusing on chromatin dysregulation and the destabilization of tau-chromatin interaction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Kateryna Fal, Niklas Korsbo, Juan Alonso-Serra, Jose Teles, Mengying Liu, Yassin Refahi, Marie-Edith Chaboute, Henrik Jonsson, Olivier Hamant
Summary: The study reveals that organogenesis in plants generates compression that has global effects on chromatin in individual cells, providing further evidence of the role of forces on chromatin changes. The research also shows that the presence of active nuclear compression in the domain where organ outgrowth occurs, suggesting a link between mechanical stress and chromatin alterations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Engineering, Biomedical
Xinxin Xu, He Zhang, Yuzhou Li, Fengyi Liu, Zheng Jing, Mingxing Ren, Tao Chen, Yiru Fu, Yanqiu Wu, Ping Ji, Sheng Yang
Summary: This study investigates the effect of matrix stiffness on DNA accessibility and cell differentiation. It was found that a stiff matrix promotes osteogenic differentiation by activating the Wnt pathway, while a soft matrix leads to chromatin condensation and downregulation of beta-catenin target genes. Experimental manipulation of histone acetylation and lamin A/C expression successfully activated beta-catenin signaling in cells cultured on a soft matrix.
MATERIALS TODAY BIO
(2023)
Article
Plant Sciences
Joseph F. McKenna, Hardeep K. Gumber, Zachary M. Turpin, Alexis M. Jalovec, Andre C. Kartick, Katja Graumann, Hank W. Bass
Summary: The study demonstrates that nucleoskeletal proteins NCH1, NCH2, and MKAKU41 in maize have characteristic properties of LINC-associated plant nucleoskeletal proteins, impacting the nuclear periphery structure and overall nuclear architecture.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Chemistry, Analytical
Georges Adam, Subramanian Chidambaram, Sai Swarup Reddy, Karthik Ramani, David J. Cappelleri
Summary: In the modern world of increasing technological complexity, microrobots and microscale systems are challenging to fabricate using standard techniques, leading to a trend of assembling them in parts. A comprehensive micromanipulation platform has been developed, with four manipulators for complex tasks, a vision-based force sensor for manipulation assistance, and integration of virtual reality for future immersive micromanipulation experiences.
Article
Optics
U. M. S. Andrade, A. M. Garcia, M. S. Rocha
Summary: The study introduces a Bessel beam optical tweezers setup that can stably trap superparamagnetic beads, with trap stiffness practically independent of beam radius and bead height. Despite the absorption coefficient of the beads, trap stiffness linearly increases with laser power. A geometric optics model accurately predicts optical forces and trap stiffness, advancing the field of optical trapping of absorbing magnetic particles.
Article
Biochemistry & Molecular Biology
Megan E. Dempsey, Graylen R. Chickering, Rafael D. Gonzalez-Cruz, Vera C. Fonseca, Eric M. Darling
Summary: This study demonstrates a workflow for surface protein discovery associated with cellular mechanophenotype. The method allows for the sorting and enrichment of live cells based on their mechanophenotype using surface protein biomarkers, followed by further characterization and differentiation studies.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Engineering, Biomedical
Geonhui Lee, Seong-Beom Han, Dong-Hwee Kim
Summary: Cell polarization, crucial in dynamic cellular processes, is precisely controlled by interactions between the nucleus and microtubule organizing center, involving cellular adhesion to extracellular matrix and nucleus-cytoskeletal connections. The localization of individual adhesive spots is more influential than cell shape in inducing intracellular polarization, with disruption of nuclear lamin A/C significantly reducing cell polarization. Geometrical cues guide intracellular polarization, determining directional cell migration through local activation of Cdc42.
Article
Chemistry, Analytical
Zenghua Fan, Zixiao Liu, Congcong Huang, Wei Zhang, Zhe Lv, Lefeng Wang
Summary: This study investigates capillary bridges and forces between spherical concave grippers and spherical particles. The analysis includes parameters such as contact angle, radius ratio, and liquid bridge volume to discuss the influence on dimensionless capillary force. The effectiveness of the theoretical approach is verified through simulation models and experiments.
Article
Biology
Edward J. Banigan, Aafke A. van den Berg, Hugo B. Brandao, John F. Marko, Leonid A. Mirny
Review
Cell Biology
Edward J. Banigan, Leonid A. Mirny
CURRENT OPINION IN CELL BIOLOGY
(2020)
Review
Cell Biology
Chad M. Hobson, Andrew D. Stephens
Article
Biology
Edward J. Banigan, Leonid A. Mirny
Article
Genetics & Heredity
Houda Belaghzal, Tyler Borrman, Andrew D. Stephens, Denis L. Lafontaine, Sergey V. Venev, Zhiping Weng, John F. Marko, Job Dekker
Summary: Liquid chromatin Hi-C technique reveals the stability of interactions between chromatin loci, showing that compartmentalization is stabilized when fragments are larger than 10-25 kb and smaller chromatin fragments can lead to gradual loss of genome organization. Lamin-associated domains are more stable compared to speckle- and polycomb-associated loci, and cohesin-mediated loops dissolve after fragmentation. This technique provides a genome-wide view of chromosome interaction dynamics.
Article
Biophysics
Tetiana Zaichuk, John F. Marko
Summary: The study using single-molecule magnetic force spectroscopy techniques found that cytosine methylation increases DNA flexibility and results in longer contour length. Under physiological conditions, DNA tends to form plectonemes rather than unwound single-stranded bubbles. The flexibility and high structural stability of methylated DNA are likely to have significant consequences on protein recognition and DNA packaging.
BIOPHYSICAL JOURNAL
(2021)
Article
Physics, Multidisciplinary
Kuang Liu, Alison E. Patteson, Edward J. Banigan, J. M. Schwarz
Summary: This study shows that the dynamics of chromosomes and nuclear shape in the cell nucleus come from motor activity, with a model of an active, cross-linked Rouse chain identifying the physical mechanisms. System-sized motions require both motor activity and cross-links, with contractile motors enhancing chromosome dynamics. Nuclear shape fluctuations are dependent on factors such as motor strength, cross-linking, and chromosome-lamina binding.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biology
Monica S. Guo, Ryo Kawamura, Megan L. Littlehale, John F. Marko, Michael T. Laub
Summary: The GapR-seq method allows high-resolution mapping of positive supercoiling in genomes, revealing its widespread presence, association with transcription, and enrichment between certain genes. This approach provides new insights into chromosome structure and organization that are not accessible with existing methods like Hi-C.
Article
Biology
Amy R. Strom, Ronald J. Biggs, Edward J. Banigan, Xiaotao Wang, Katherine Chiu, Cameron Herman, Jimena Collado, Feng Yue, Joan C. Ritland Politz, Leah J. Tait, David Scalzo, Agnes Telling, Mark Groudine, Clifford P. Brangwynne, John F. Marko, Andrew D. Stephens
Summary: HP1 alpha plays a critical role in chromatin-based mechanics by maintaining chromatin stiffness and nuclear morphology, supporting cellular functions.
Article
Biochemistry & Molecular Biology
Stefanos K. Nomidis, Enrico Carlon, Stephan Gruber, John F. Marko
Summary: Structural Maintenance of Chromosomes (SMC) complexes play critical roles in genome organization. Researchers developed a molecular dynamics model to investigate the control of SMC complex activities by ATP binding and hydrolysis. The model revealed the sensitivity of this process to DNA tension and the ability of the SMC complex to perform loop extrusion by tethering DNA to an additional binding site.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Cell & Tissue Engineering
Marilena L. Currey, Viswajit Kandula, Ronald Biggs, John F. Marko, Andrew D. Stephens
Summary: This article introduces a universal micromanipulation apparatus for inverted microscopes, which allow for force measurements and investigation of the mechanical components of the nucleus. The apparatus separates the contributions of chromatin and lamin A and has been used to develop new techniques in nuclear mechanobiology.
CELLULAR AND MOLECULAR BIOENGINEERING
(2022)
Article
Engineering, Biomedical
Satzhan Sitmukhambetov, Bryan Dinh, Youfang Lai, Edward J. Banigan, Zui Pan, Xun Jia, Yujie Chi
Summary: In this study, a metaphase chromosome model representing the complete genome of a human lymphocyte cell was successfully developed for Monte Carlo simulation-based radiation-induced DNA damage studies. The model consists of voxelized chromatid segments connected with pre-constructed nucleosomes and linker DNAs, and was used to compute DNA damage under different radiation conditions. The obtained results were consistent with experimental measurements, suggesting the effectiveness and accuracy of the model.
PHYSICS IN MEDICINE AND BIOLOGY
(2023)
Article
Cell Biology
Isabel K. Berg, Marilena L. Currey, Sarthak Gupta, Yasmin Berrada, Bao Nguyen, Mai Pho, Alison E. Patteson, J. M. Schwarz, Edward J. Banigan, Andrew D. Stephens
Summary: Chromatin plays a crucial role in maintaining nuclear shape and function, but transcription activity can also affect nuclear shape through its impact on chromatin structure and dynamics. In this study, we found that transcription inhibition suppresses nuclear blebbing and rupture, independent of chromatin rigidity.
JOURNAL OF CELL SCIENCE
(2023)