Article
Multidisciplinary Sciences
Daisuke Kurotaki, Kenta Kikuchi, Kairong Cui, Wataru Kawase, Keita Saeki, Junpei Fukumoto, Akira Nishiyama, Kisaburo Nagamune, Keji Zhao, Keiko Ozato, Pedro P. Rocha, Tomohiko Tamura
Summary: This study comprehensively determined higher-order chromatin structures by Hi-C in DC progenitors and cDC subpopulations. The results showed that chromatin activation was initially induced at the MDP stage during cDC differentiation, followed by a shift from inactive to active nuclear compartments in CDPs. This study also identified the transcription factor IRF8 as a mediator of chromatin activation and changes in the active compartments in DC progenitors. Furthermore, the study found preestablished chromatin structures of host defense-related gene loci in unstimulated cDCs, which may contribute to the rapid responses to pathogens.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Luis Altamirano-Pacheco, Pablo Navarro
Summary: Two new studies using mouse embryonic stem cells further clarify the important role of histone inheritance in early cell fate decisions.
Article
Physics, Fluids & Plasmas
Oran Szachter, Eytan Katzav, Mokhtar Adda-Bedia, Michael Moshe
Summary: The stress function method in elasticity theory is a powerful tool for analyzing physical systems. However, it has limitations in dealing with nonlinear elasticity. This paper develops a formalism for nonlinear stress functions, allowing for better analysis of nonlinear deformation.
Article
Biochemical Research Methods
Emily Biernat, Uzair Khan, Chhabi K. Govind
Summary: Nucleosomes are the repeating units of chromatin and hinder DNA-dependent processes. MNase digestion of chromatin followed by ChIP-seq can determine nucleosome occupancy, positioning, and the impact of chromatin interacting factors on chromatin accessibility.
Article
Astronomy & Astrophysics
Christopher J. Fewster, Eli Hawkins, Christoph Minz, Kasia Rejzner
Summary: The paper first discusses a numerical study of finite causal sets in Minkowski spacetime, focusing on the selection of rank 2 past subsets. It then explores (infinite) sprinkled causal sets on general spacetime manifolds, with particular attention to the unique selection of a preferred past that satisfies desirable properties.
Review
Biochemistry & Molecular Biology
Ankita Saha, Yamini Dalal
Summary: Histone H1s, a family of chromatin compacting proteins, play essential roles in higher-order chromatin organization. Recent research suggests that different H1 family members have distinct affinities for chromatin and may impact different functions. Advances in technology have improved our understanding of how H1 interacts with chromatin and its importance in epigenetics.
Article
Cardiac & Cardiovascular Systems
Tongbin Wu, Zhengyu Liang, Zengming Zhang, Canzhao Liu, Lunfeng Zhang, Yusu Gu, Kirk L. Peterson, Sylvia M. Evans, Xiang-Dong Fu, Ju Chen
Summary: Disruption of cardiomyocyte specification plays a key role in the pathogenesis of LVNC. The study sheds light on the underlying mechanisms of LV-specific transcriptional program governing LV chamber growth and maturation.
Article
Mathematics
H. Monobe, H. Ninomiya
Summary: This study focuses on the dynamics of an anisotropic curvature flow with external driving force, investigating the conditions for the existence of compact traveling waves. The research shows that all traveling waves are strictly convex and unstable, with a unique compact traveling wave if it exists. Different cases are considered to determine the existence of compact traveling waves, with a necessary and sufficient condition for axisymmetric compact traveling waves also obtained. Additionally, the study touches upon the inverse problem and non-convex compact traveling waves.
TRANSACTIONS OF THE AMERICAN MATHEMATICAL SOCIETY
(2021)
Article
Computer Science, Artificial Intelligence
Chen Wang, Jiang Zhong, Qizhu Dai, Rongzhen Li, Qien Yu, Bin Fang
Summary: This paper proposes a novel local structure consistency distillation (LSCD) method to improve the segmentation accuracy of compact networks. By transferring local structure consistency and pixel correlations at the patch level, it achieves better segmentation results.
APPLIED INTELLIGENCE
(2023)
Article
Multidisciplinary Sciences
Haiqian Yang, Estelle Berthier, Chenghai Li, Pierre Ronceray, Yu Long Han, Chase P. Broedersz, Shengqiang Cai, Ming Guo
Summary: Nonlinear stiffening is a widespread property of biopolymers in the extracellular matrices, and cells can locally stretch and stiffen the surrounding matrix through a spindle-like shape. By using optical tweezers, we studied the force-displacement response to localized monopole forces and proposed a scaling argument to characterize the stiffened region in the matrix.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Mathematics, Interdisciplinary Applications
Yao Pengfei
Summary: The optimal exponents of thickness in the geometry rigidity inequality of shells indicate the geometry rigidity of the shells. Lower bounds of the optimal exponents for hyperbolic, parabolic, and elliptic shells are found to be 4/3, 3/2, and 1 respectively through the construction of Ansatze.
JOURNAL OF SYSTEMS SCIENCE & COMPLEXITY
(2021)
Article
Engineering, Electrical & Electronic
Zhecheng Wang, Shuai Wan, Lei Wei
Summary: Point cloud compression is important for storing and transmitting point clouds efficiently. This study proposes two local geometry-based prediction methods: binary prediction and ternary prediction. The binary prediction achieves a BD-rate of -0.8% and a bpip of 100.09% for lossy compression, reducing decoding time by more than 20%. The ternary prediction achieves a BD-rate of -1.2% and a bpip of 97.19% for lossy compression, while saving about 18% decoding time.
IEEE TRANSACTIONS ON CIRCUITS AND SYSTEMS FOR VIDEO TECHNOLOGY
(2023)
Article
Mechanics
Meral Tuna, Patrizia Trovalusci
Summary: The study compared the micropolar and Eringen's models with classical model on infinite plates weakened by elliptic holes, showing that non-local effects reduce maximum stress more prominently with increasing aspect ratio of the ellipse.
COMPOSITE STRUCTURES
(2021)
Article
Biochemistry & Molecular Biology
Grigoriy A. Armeev, Anna K. Gribkova, Alexey K. Shaytan
Summary: This article discusses the diversity of known nucleosome structures, analyzes data and model quality, variations in histone/DNA content of nucleosomes, and their interacting systems. It outlines the explored and unexplored parts of the nucleosome structurome.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Engineering, Electrical & Electronic
Shengyao Xu, Weijie Chang, Yiyang Luo, Perry Ping Shum, Lei Wei, Yangan Zhang, Xueguang Yuan, Zhenggang Lian, Yongqing Huang
Summary: The compact and cost-effective vector bending sensor proposed in this study utilizes a specially designed SSAF structure to achieve sensitive detection of bending with orientation dependence, without the need for complex alignment procedures or fiber grating inscription.
IEEE SENSORS JOURNAL
(2021)
Article
Biophysics
Sunny S. Lou, Andrew S. Kennard, Elena F. Koslover, Edgar Gutierrez, Alexander Groisman, Julie A. Theriot
Summary: The study reveals a dynamic wrinkling phenotype in the lamellipodium of fish keratocytes, where the generation of wrinkles is dependent upon myosin contractility. Despite rapid actin turnover, the lamellipodial cytoskeleton behaves as an elastic material on the timescale of cell migration. The cells maintain a constant wrinkle wavelength that is directly related to actin network density and inversely related to cell adhesion.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Owen K. Smith, Charles Limouse, Kelsey A. Fryer, Nicole A. Teran, Kousik Sundararajan, Rebecca Heald, Aaron F. Straight
Summary: The study successfully identified the repetitive sequences of Xenopus laevis centromeres using a combination of Cenpa ChIP-seq and k-mer analysis, and mapped the centromere positions on each chromosome through in situ hybridization and analysis of centromere-enriched k-mers distribution. This approach enables previously unapproachable centromere genomic studies and could be broadly applicable for analyzing repetitive sequences in any organism.
Article
Biochemistry & Molecular Biology
David Jukam, Rishabh R. Kapoor, Aaron F. Straight, Jan M. Skotheim
Summary: In multicellular animals, the switch from maternal to zygotic control of development after fertilization is known as zygotic genome activation (ZGA). DNA is identified as an important component of the N/C ratio, which serves as a critical regulator of zygotic genome activation in Xenopus embryos.
Article
Biophysics
Saurabh S. Mogre, Jenna R. Christensen, Samara L. Reck-Peterson, Elena F. Koslover
Summary: Cellular functions like autophagy, cell signaling, and vesicular trafficking involve retrograde transport of cargo along microtubules, where the spatial arrangement of microtubule plus ends affects the efficiency of cargo capture. Optimal microtubule configurations minimize mean cargo capture times, showing that a single microtubule plus end near the distal tip and broadly distributed other plus ends allow for efficient capture in different scenarios for retrograde transport. Live-cell imaging of microtubule plus ends in fungal hyphae confirms these optimal features, highlighting important coupling effects between microtubule distributions and cargo transport efficiency.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemical Research Methods
Nicolas Altemose, Annie Maslan, Owen K. Smith, Kousik Sundararajan, Rachel R. Brown, Reet Mishra, Angela M. Detweiler, Norma Neff, Karen H. Miga, Aaron F. Straight, Aaron Streets
Summary: In this study, we developed a method called DiMeLo-seq, which utilizes long-read sequencing to perform in situ methylation of DNA and obtain genome-wide information about protein-DNA interactions. DiMeLo-seq involves methylating DNA near the binding sites of specific proteins using antibody-tethered enzymes, and simultaneously detecting the exogenous methylation marks along with the endogenous CpG methylation on unamplified DNA. Using DiMeLo-seq, researchers successfully mapped chromatin-binding proteins and histone modifications across the human genome, and identified the localization and density of centromere protein A in highly repetitive regions that were not readily mappable with short-read sequencing.
Article
Biochemistry & Molecular Biology
Keda Zhou, Magdalena Gebala, Dustin Woods, Kousik Sundararajan, Garrett Edwards, Dan Krzizike, Jeff Wereszczynski, Aaron F. Straight, Karolin Luger
Summary: CENP-N interacts with neighboring nucleosomes through its alpha 6 helix to facilitate the stacking of CENP-A-containing mononucleosomes and nucleosomal arrays at the centromere.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Cell Biology
Sydney E. Cason, Saurabh S. Mogre, Erika L. F. Holzbaur, Elena F. Koslover
Summary: In this study, a quantitative model and mathematical modeling were used to investigate the process of autophagosome maturation in neurons. The results showed that fusion between autophagosomes and lysosomes is less frequent during axonal transport, and the breakdown of the inner autophagosomal membrane is slower in neurons, highlighting the importance of this late maturation step.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Biochemical Research Methods
Ximena G. Arceo, Elena F. Koslover, Brian M. Zid, Aidan Brown
Summary: For nuclear-encoded mitochondrial genes, mRNA localization to the mitochondrial surface is co-translational with the help of mitochondrial targeting sequences (MTS) and the mitochondrial import complex. The localization of these mRNAs can be dependent on the metabolic state of the cell or constitutive. A stochastic, quantitative model was developed to understand mRNA localization to mitochondria in yeast cells. The model suggests that yeast cells can regulate mRNA localization by controlling mitochondrial volume fraction and gene translation kinetics.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Zitao Yang, Elena F. Koslover
Summary: The function of intracellular structures depends on the release of particles through pores or channels in the membrane. A simple model is proposed to estimate the release rate from different shapes of channels. The results show that even a low density of channels can achieve substantial release rates for small pores.
Article
Cell Biology
Julio C. Flores C. Servin, Rachel R. Brown, Aaron F. Straight
Summary: Flores Servin, Brown, and Straight discovered that vertebrate CENP-A assembly is restricted to G1 phase due to the inhibitory activities of HJURP phosphorylation and M18BP1.S competitive binding to CENP-C. These inhibitory activities prevent the metaphase centromere localization of HJURP and thus hinder CENP-A assembly. Removal of these inhibitory activities allows CENP-A assembly in metaphase.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Pragya Sidhwani, Aaron F. Straight
Summary: Centromeres are crucial for chromosome segregation during cell division. Understanding their epigenetic regulation and boundary establishment is important for genome stability. While boundaries between centromeres and heterochromatin have been identified in yeast, the mechanisms in humans remain unclear.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Charles Limouse, Owen K. Smith, David Jukam, Kelsey A. Fryer, William J. Greenleaf, Aaron F. Straight
Summary: This study provides insights into the global network of interactions between non-coding RNAs (ncRNAs) and chromatin in human embryonic stem cells. The researchers find that ncRNAs predominantly interact with genes in close three-dimensional proximity to their encoding loci. They also identify numerous unannotated RNAs that dynamically interact with chromatin. The study suggests that activation or repression of individual genes is unlikely to be controlled by a single ncRNA.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Multidisciplinary
Yunhao Sun, Zexi Yu, Christopher J. Obara, Keshav Mittal, Jennifer Lippincott-Schwartz, Elena F. Koslover
Summary: The analysis of single-particle trajectories is important for understanding dynamics in complex environments such as living cells. This study focuses on particles undergoing Brownian motion in narrow tubules within cellular organelles. A computational algorithm is developed to accurately extract the diffusion coefficient and differentiate between different types of particle motion. The algorithm is validated with simulated trajectories and applied to analyze the motion of membrane proteins in mammalian cells.
PHYSICAL REVIEW RESEARCH
(2022)
Meeting Abstract
Biophysics
Ximena Garcia Arceo, Brian M. Zid, Aidan Brown, Elena F. Koslover
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Brian M. Zid, Ximena Garcia Arceo, Tatsuhisa Tsuboi, Aidan I. Brown, Elena F. Koslover
BIOPHYSICAL JOURNAL
(2022)