Article
Biochemistry & Molecular Biology
Jayaraju Dheekollu, Andreas Wiedmer, Kasirajan Ayyanathan, Julianna S. Deakyne, Troy E. Messick, Paul M. Lieberman
Summary: This study reveals that EBNA1 forms cell cycle-dependent DNA crosslinks with the EBV origin of plasmid replication and the tyrosine 518 residue is essential for this process. These crosslinks and single-strand cleavage are critical for replication termination and viral episome maintenance.
Article
Mechanics
Yu Lu, Guo-Hui Hu
Summary: In this study, the diffusion of linear polymers in the semi-flexible polymer network inside the cell is investigated using dissipative particle dynamics (DPD). The analysis of Rouse modes reveals that the geometric constraint length N-a plays a crucial role in describing the network effect on polymer diffusion. Based on the analysis of Rouse modes and mean square displacements, a non-dimensional conformational dynamics function dependent on time is proposed, along with a scaling law to predict the long time diffusivity of linear polymers in a semi-flexible polymer network with different mesh sizes.
Article
Biochemistry & Molecular Biology
Daniela Escher, M. Nur Hossain, Heinz-Bernhard Kraatz, Jens Mueller
Summary: Films of different DNA quadruplex-forming sequences were studied on gold surfaces using electrochemical impedance spectroscopy, showing unique electrochemical responses that allow for their identification. This method could be an alternative means for determining G4 sequences of unknown structure.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2021)
Article
Environmental Sciences
Tsun Fung Au, Justin T. T. Maxwell, Scott M. M. Robeson, Jinbao Li, Sacha M. O. Siani, Kimberly A. A. Novick, Matthew P. P. Dannenberg, Richard P. P. Phillips, Teng Li, Zhenju Chen, Jonathan Lenoir
Summary: With the global decline of old trees and reforestation efforts, younger trees are becoming increasingly important for carbon sequestration and forest ecosystem functioning. This study finds that younger trees in the upper canopy layer are more sensitive to drought and experience larger growth reductions. However, they also recover more quickly from drought, suggesting a potential positive impact on carbon stocks over time.
NATURE CLIMATE CHANGE
(2022)
Article
Biochemical Research Methods
Corbin J. England, Tanner C. Gray, Shubha R. L. Malla, Samantha A. Oliveira, Benjamin R. Martin, Gary W. Beall, L. Kevin Lewis
Summary: The precipitation of double-stranded DNA by group 2 metals at high pH levels was effective, particularly with calcium, leading to the retention of DNA structural integrity in the precipitates formed. Neutralization of negative surface charges and cation bridging were proposed as mechanisms for this process.
ANALYTICAL BIOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Nanjun Hu, Lulu Bai, Enyong Dai, Leng Han, Rui Kang, Hongjun Li, Daolin Tang
Summary: This study reveals the role of the nuclear protein pirin in mediating resistance to ferroptosis in human pancreatic cancer cells. The upregulation of PIR by the transcription factor NFE2L2 during ferroptosis limits oxidative damage and HMGB1 release, while depletion of PIR initiates autophagy and promotes ferroptosis through ACSL4 activation. Blocking PIR signaling enhances ferroptosis-induced tumor growth suppression, providing new insights into the molecular mechanisms of autophagy-dependent ferroptosis.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Mathematics, Interdisciplinary Applications
Jorge L. Suzuki, Tyler G. Tuttle, Sara Roccabianca, Mohsen Zayernouri
Summary: The study introduces a data-driven fractional modeling framework to analyze the behavior of complex materials, with a focus on bio-tissues such as the porcine urinary bladder. Anomalous relaxation characteristics, including nonlinear behavior and power-law-like patterns for short/long times, were identified through multi-step relaxation experiments. Fractional Maxwell model and fractional quasi-linear viscoelastic model were employed to capture the material behavior under small and large strains, demonstrating the framework's effectiveness in describing multiple stages of bladder functionality.
FRACTAL AND FRACTIONAL
(2021)
Article
Polymer Science
Anna Braghetto, Sumanta Kundu, Marco Baiesi, Enzo Orlandini
Summary: This study uses long-short-term memory neural networks (LSTM NNs) to simulate configurations of flexible knotted rings confined inside a spherical cavity and successfully distinguish different knot types. The results show that even for flexible, strongly confined, and highly geometrically entangled rings, LSTM NNs perform well in knot recognition. Coarse-graining on configurations of longer rings than those used for training improves the performance of LSTMs in knot identification.
Article
Biochemistry & Molecular Biology
Karina Lindbog Madsen, Oke Gerke, Poul F. Hoilund-Carlsen, Birgitte Brinkmann Olsen
Summary: Cancer stem cells (CSCs) are resistant to conventional therapy and responsible for cancer relapse. Auger electron emitters show promising potential in eradicating resistant lung cancer CD44(+) populations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Danahe Mohammed, Chan Young Park, Jeffrey J. Fredberg, David A. Weitz
Summary: This study reveals that mesenchymal tumorigenic clusters are less sensitive to moderate osmotic stress compared to non-tumorigenic cells. The findings also suggest that the lower sensitivity in tumorigenic cells is associated with a reduced expression of E-cadherin, highlighting the importance of cadherin-based junctions in the response to osmotic stress.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Golam Mustafa, Sajad Shiekh, G. C. Keshav, Sanjaya Abeysirigunawardena, Hamza Balci
Summary: The accessibility of telomeric DNA is influenced by its length, with longer telomeres forming more compact structures that are less accessible to binding molecules. Intermediate regions of telomeric DNA were found to be more accessible compared to the ends, suggesting a gradient of accessibility along the telomere length. These findings highlight the importance of telomere structure in regulating accessibility to critical genomic sites.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Developmental Biology
Matthias Godart, Carla Frau, Diana Farhat, Maria Virginia Giolito, Catherine Jamard, Clementine Le Neve, Jean-Noel Freund, Luiz O. Penalva, Maria Sirakov, Michelina Plateroti
Summary: The thyroid hormone T3 and its nuclear receptor TRα1 have a rapid and strong effect on intestinal stem cells, modulating the number of stem cells, the expression of their specific markers, and the commitment of progenitors into lineage-specific differentiation, which broadens perspectives in T3/TRα1-dependent signaling research in these cells.
Article
Automation & Control Systems
Jonas Kirchhoff
Summary: This paper introduces the new concept of relative generic subsets and shows that the set of controllable linear finite-dimensional port-Hamiltonian systems is a relative generic subset of the set of all linear finite-dimensional port-Hamiltonian systems, implying that a random, continuously distributed port-Hamiltonian system is almost surely controllable.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2022)
Article
Chemistry, Multidisciplinary
Christopher R. Lucas, Patrick D. Halley, Amjad A. Chowdury, Bonnie K. Harrington, Larry Beaver, Rosa Lapalombella, Amy J. Johnson, Erin K. Hertlein, Mitch A. Phelps, John C. Byrd, Carlos E. Castro
Summary: The study demonstrates that DNA origami (DO) nanotechnology can be used to construct precise nanostructures capable of functionalization and has a wide range of biomedical applications. DO structures distribute well systemically, eliciting a gradually diminishing mild pro-inflammatory response, while being non-toxic.
Article
Computer Science, Hardware & Architecture
Seyed Mohammadhossein Tabatabaee, Anne Bouillard, Jean-Yves Le Boudec
Summary: In this study, worst-case delay bounds were obtained in feed-forward time-sensitive networks with Deficit Round-Robin (DRR) by combining Total Flow Analysis (TFA) with the strict service curve characterization of DRR by Tabatabaee et al. The study introduces Polynomial-size Linear Programming (PLP) to improve the TFA bounds and stability region for DRR networks and proposes a generic method, called PLP-DRR, for combining iterations sequentially or in parallel. The obtained bounds are always valid and consistent regardless of the combination of iterations.
IEEE-ACM TRANSACTIONS ON NETWORKING
(2023)
Article
Computer Science, Interdisciplinary Applications
Solomon Barkley, Thomas G. Dimiduk, Jerome Fung, David M. Kaz, Vinothan N. Manoharan, Ryan McGorty, Rebecca W. Perry, Anna Wang
COMPUTING IN SCIENCE & ENGINEERING
(2020)
Article
Instruments & Instrumentation
Ruilin You, Ryan McGorty
Summary: Differential dynamic microscopy (DDM) is a method increasingly used in soft matter physics and biophysics to extract the dynamics of microscopic objects by optical microscopy. By sequentially illuminating the sample with spectrally distinct light and imaging with a color camera, the two-color DDM method allows for measuring dynamics occurring much faster than the camera frame rate.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2021)
Article
Multidisciplinary Sciences
Gloria Lee, Gregor Leech, Michael J. Rust, Moumita Das, Ryan J. McGorty, Jennifer L. Rosso, Rae M. Robertson-Anderson
Summary: The cytoskeleton is a dynamic network of proteins that enables essential cellular processes, with microtubules providing flexural rigidity and enhanced connectivity to actin networks for self-organized myosin-driven contraction.
Article
Multidisciplinary Sciences
Jan Smrek, Jonathan Garamella, Rae Robertson-Anderson, Davide Michieletto
Summary: The study reveals that larger supercoiling in dense supercoiled DNA increases the size of entangled plasmids and enhances DNA mobility. These findings suggest a way to tune DNA mobility via supercoiling, enabling topological control over the (micro)rheology of DNA-based complex fluids.
Article
Mechanics
Pawan Khanal, Karthik R. Peddireddy, Juexin Marfai, Ryan McGorty, Rae M. Robertson-Anderson
Summary: Polymer architecture plays a critical role in both bulk rheological properties and microscale macromolecular dynamics in entangled polymer solutions and composites. This study investigates the influence of DNA topology (rings versus linear chains) and the relative volume fractions of DNA and dextran on the viscoelasticity and molecular-level transport properties of DNA-dextran composites. The results show nonmonotonic dependences on the fraction of DNA comprising the composites, with characteristics strongly dependent on the DNA topology.
JOURNAL OF RHEOLOGY
(2022)
Article
Multidisciplinary Sciences
Karthik R. Peddireddy, Ryan Clairmont, Philip Neill, Ryan McGorty, Rae M. Robertson-Anderson
Summary: The authors propose a new method to connect polymer dynamics to force response by integrating optical tweezers with differential dynamic microscopy. They find that blends of ring and linear DNA exhibit a resonant response, which is suppressed by the presence of microtubules. This study provides insights into the relationship between polymer dynamics and force response.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Mehdi Shafiei Aporvari, Steven Dang, Juexin Marfai, Kara Coursey, Ryan McGorty, Rae M. Robertson-Anderson
Summary: This study uses differential dynamic microscopy to investigate the diffusion of large DNA molecules confined in cell-sized droplets and crowded by dextran polymers. The results show that confined and crowded DNA molecules exhibit universal anomalous subdiffusion, with the degree of confinement and crowding having minimal impact. However, as droplet size decreases, the effective DNA diffusion coefficients decrease significantly, and this effect is enhanced by increased crowding.
Article
Chemistry, Physical
Steven Dang, John Brady, Ryle Rel, Sreenidhi Surineni, Conor O'Shaughnessy, Ryan McGorty
Summary: Microcapsules can encapsulate various cargoes and be controlled by temperature-responsive microgel particles and a polymer mixture, leading to liquid-liquid phase separation and the formation of unique core-shell structures with stimuli-sensitive properties for potential biological applications.
Article
Chemistry, Physical
S. J. Anderson, J. Garamella, S. Adalbert, R. J. McGorty, R. M. Robertson-Anderson
Summary: Anomalous diffusion in complex environments, specifically within the cytoskeleton, is influenced by crosslinking of actin and microtubules. The presence of crosslinking enhances non-Gaussian and non-ergodic subdiffusion, with actin-microtubule crosslinking having the most pronounced impact. Subtle changes in actin-microtubule interactions can lead to complex impacts on particle diffusion, indicating that reduced filament mobility and more variance in actin mobilities contribute to more strongly anomalous particle transport.
Article
Chemistry, Physical
Jonathan Garamella, Kathryn Regan, Gina Aguirre, Ryan J. McGorty, Rae M. Robertson-Anderson
Article
Physics, Fluids & Plasmas
Anna Wang, Jos W. Zwanikken, David M. Kaz, Ryan McGorty, Aaron M. Goldfain, W. Benjamin Rogers, Vinothan N. Manoharan
Article
Chemistry, Physical
Jing Wang, Ryan McGorty