Article
Chemistry, Physical
L. K. R. Duarte, A. V. N. C. Teixeira, L. G. Rizzi
Summary: A computational methodology is proposed to obtain the viscoelastic response of dilute solutions of semiflexible filaments, by evaluating the dynamical properties through the fluctuation-dissipation theorem, microrheological approach, and relaxation simulations. The effects of bending energy on viscoelasticity were assessed, and the methodology was validated by comparing numerical results with experimental data on DNA and collagen solutions.
Article
Cell Biology
Fabina Binth Kandiyoth, Alphee Michelot
Summary: The encapsulation of biomimetic systems for in vitro reconstitution of cellular processes is a major challenge due to technical and chemical evolution issues.
EUROPEAN JOURNAL OF CELL BIOLOGY
(2023)
Article
Genetics & Heredity
Joachim Berger, Silke Berger, Yu Shan G. Mok, Mei Li, Hakan Tarakci, Peter D. Currie
Summary: Sarcomere assembly is a complex process involving filament capping proteins. CapZ proteins, Lmod proteins, and Tmod proteins play different roles in thin filament assembly. Zebrafish mutants with deficiencies in these capping proteins exhibited sarcomere defects, suggesting their involvement in myofibril growth. However, the presence of residual organized sarcomeres in the mutants indicates that these proteins are not essential for initial myofibril assembly.
Article
Chemistry, Multidisciplinary
Kodai Fukumoto, Yuya Miyazono, Takuya Ueda, Yoshie Harada, Hisashi Tadakuma
Summary: Cellular transport systems are complex and efficient, and there is a need to design artificial transport systems using nanotechnology. However, the design principles have been difficult to establish due to the lack of understanding on how motor layout affects motile activity. In this study, a DNA origami platform was used to evaluate the effect of motor protein layout on transporter motility. The densely packed layout of kinesin motor protein was found to decrease the run length of the transporter, highlighting the importance of considering steric hindrance in transport system design.
NANOSCALE ADVANCES
(2023)
Article
Multidisciplinary Sciences
Agustina Belen Fernandez Casafuz, Maria Cecilia De Rossi, Luciana Bruno
Summary: By studying the interactions between mitochondria and the cytoskeleton in melanocytes, it was found that microtubules play a major role in organizing mitochondria, while vimentin and actin filaments affect their shape. Microtubules transmit jittering to mitochondria, while F-actin restricts their motion.
SCIENTIFIC REPORTS
(2023)
Article
Pharmacology & Pharmacy
Santimoy Sen, Sheetal Lagas, Abhishek Roy, Hemant Kumar
Summary: Cells rely on a balanced cytoskeleton to maintain cellular integrity and regulate signaling pathways. Dysregulation of the cytoskeleton can lead to various pathological conditions, and targeting cytoskeletal dynamics may provide new therapeutic approaches for these diseases.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2022)
Article
Engineering, Chemical
Szymon Skoneczny, Monika Cioch-Skoneczny
Summary: This paper focuses on the dynamical modeling of microbiological processes in biofilms formed on fine inert particles. Approximate models based on the Laplace-Carson transform and a family of approximate models based on the concept of pseudo-stationary substrate concentration profiles were proposed. The models were evaluated for their applicability to microbiological processes using Monod or Haldane kinetics under conditions of dynamic biofilm growth. The use of approximate models simplifies computations and eliminates stiffness compared to the exact model. The proposed models achieved higher accuracy than the previously published approximate model derived using the homotopy analysis method.
Article
Urology & Nephrology
Chengqing Qu, Robyn Roth, Pongpratch Puapatanakul, Charles Loitman, Dina Hammad, Guy M. Genin, Jeffrey H. Miner, Hani Y. Suleiman
Summary: A new visualization technique has been developed to reveal the detailed three-dimensional organization of actin networks in healthy podocytes, providing insights into how podocytes respond to mechanical cues from their surrounding environment.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2022)
Article
Mathematics
Farai Nyabadza, Josiah Mushanyu, Rachel Mbogo, Gift Muchatibaya
Summary: Human behavior plays a crucial role in controlling the spread of COVID-19, especially after the lifting of restrictions. This study develops a deterministic model that incorporates dynamic non-pharmaceutical interventions to simulate the effects of social processes. The findings have implications for understanding the trajectory of the pandemic in the presence of evolving societal processes.
Article
Chemistry, Physical
Sriramvignesh Mani, Harshwardhan H. Katkar, Gregory A. Voth
Summary: The study presents an Ultra-Coarse-Grained model of actin filaments that can simulate ATP hydrolysis, inorganic phosphate release, and depolymerization reactions. The effects of compressive and tensile strains on the rates of reactions are analyzed, with compressive strains decreasing the rate of ATP hydrolysis and increasing the Pi release rate, while tensile strain has the opposite effect. Incorporating these predictions into a Markov State Model reveals that strains alter the steady-state distribution of subunits with ADPPi and ADP nucleotide, potentially impacting the binding of regulatory proteins to actin filaments.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Computer Science, Hardware & Architecture
Zhen Chen, Tangbin Xia, Yaping Li, Ershun Pan
Summary: This paper proposes a new degradation model TEDP, which can flexibly describe the degradation paths of products and utilizes random-effect models for modeling. Variational inference, expectation maximization algorithm, and differential evolution algorithm are used to estimate model parameters. Additionally, two nonlinear TEDP models with accelerated factors and random effects are developed for accelerated degradation analysis.
IEEE TRANSACTIONS ON RELIABILITY
(2022)
Article
Biochemistry & Molecular Biology
Pingzhou Du, Yu Liu, Lu Deng, Dong Qian, Xiuhua Xue, Ting Yang, Tonghui Li, Yun Xiang, Haiyun Ren
Summary: The newly discovered AtMAC protein is involved in the regulation of phragmoplast organization during centrifugal phragmoplast expansion, playing a crucial role in cytokinesis.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Tamara C. Bidone, David J. Odde
Summary: Computational models have provided insights into how cells establish connections with the external environment, but how individual adhesion proteins regulate the dynamics of whole adhesion complexes remains unclear. This is due to the differences in time and length scales and limitations in accurately extracting key information from molecular simulation approaches. This review discusses the models of integrin-based adhesion complexes and highlights important findings related to conformational transitions and the molecular clutch mechanism.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Review
Mathematics
Yikai Liu, Ruozheng Wu, Aimin Yang
Summary: Mathematical modeling is crucial in the medical field as it enhances the understanding and exploration of physiological and pathological processes in the human body. It facilitates accurate medical predictions and diagnoses through neural network, machine learning, and statistical models. The applications of mathematical modeling range from simulating the cardiovascular system to analyzing medical images, screening and optimizing active compounds in drug development, and mining and analyzing medical data for disease risk assessment and prediction. Overall, mathematical modeling has become an integral part of modern medical research.
Article
Cell Biology
George M. Langford
Summary: The speaker is deeply honored to receive the 2022 ASCB Public Service Award and highlights their research on the cytoskeleton and molecular motors. They also emphasize their dedication to addressing issues of diversity, equity, and inclusion in the scientific community. The speaker founded the PAIR-UP Imaging Science Program for Black Imaging Scientists to improve the professional work environment for Black scientists and promote a strong cultural identity.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Biochemistry & Molecular Biology
Caroline Laplante, Julien Berro, Erdem Karatekin, Ariel Hernandez-Leyva, Rachel Lee, Thomas D. Pollard
Article
Biochemistry & Molecular Biology
Ronan Fernandez, Julien Berro
Article
Biochemistry & Molecular Biology
Michelle L. Hutchings, Cambria J. Alpha-Cobb, David A. Hiller, Julien Berro, Scott A. Strobel
JOURNAL OF BIOLOGICAL CHEMISTRY
(2017)
Article
Cell Biology
Michael M. Lacy, David Baddeley, Julien Berro
MOLECULAR BIOLOGY OF THE CELL
(2017)
Review
Biochemistry & Molecular Biology
Michael M. Lacy, Rui Ma, Neal G. Ravindra, Julien Berro
Article
Cell Biology
Rajesh Arasada, Wasim A. Sayyad, Julien Berro, Thomas D. Pollard
MOLECULAR BIOLOGY OF THE CELL
(2018)
Article
Biochemical Research Methods
Rui Ma, Julien Berro
PLOS COMPUTATIONAL BIOLOGY
(2018)
Article
Cell Biology
Matthew Akamatsu, Julien Berro, Kai-Ming Pu, Irene R. Tebbs, Thomas D. Pollard
JOURNAL OF CELL BIOLOGY
(2014)
Article
Cell Biology
Julien Berro, Thomas D. Pollard
MOLECULAR BIOLOGY OF THE CELL
(2014)
Article
Cell Biology
Rui Ma, Julien Berro
Article
Biophysics
Jean-Louis Martiel, Alphee Michelot, Rajaa Boujemaa-Paterski, Laurent Blanchoin, Julien Berro
BIOPHYSICAL JOURNAL
(2020)
Article
Biology
Michael M. Lacy, David Baddeley, Julien Berro
Article
Biophysics
Rui Ma, Julien Berro
Summary: This study examined how a patch of membrane is deformed against turgor pressure by force and by curvature-generating proteins, and found that the amount of force needed varies depending on how the base of the membrane is constrained and how the membrane is coated with curvature-generating proteins.
BIOPHYSICAL JOURNAL
(2021)
Article
Cell Biology
Masoud Nickaeen, Julien Berro, Thomas D. Pollard, Boris M. Slepchenko
Summary: This study compared the differences in endocytosis between fission yeast and budding yeast and found that differences in turgor pressure can explain the differences in endocytic motility observed experimentally.
MOLECULAR BIOLOGY OF THE CELL
(2022)
Article
Chemistry, Multidisciplinary
Nathan D. Williams, Ane Landajuela, Ravi Kiran Kasula, Wenjiao Zhou, John T. Powell, Zhiqun Xi, Farren J. Isaacs, Julien Berro, Derek Toomre, Erdem Karatekin, Chenxiang Lin