Article
Biochemical Research Methods
Sunkyu Choi, Rudolf Engelke, Neha Goswami, Frank Schmidt
Summary: This study used SILAC-based proteomic profiling to investigate the effects of metformin on 3T3-L1 adipocytes. The results showed that metformin not only affects glucose and lipid metabolism, but also has an impact on protein folding, endoplasmic reticulum stress, negative regulation of appetite, and one-carbon folate metabolism in adipocytes.
Article
Biochemical Research Methods
Lindsay K. Pino, Josue Baeza, Richard Lauman, Birgit Schilling, Benjamin A. Garcia
Summary: The study presents a workflow combining SILAC and DIA-MS using free software, showing that DIA achieves similar peptide detection numbers as DDA but with improved quantitative accuracy and precision for SILAC by an order of magnitude. Application of SILAC-DIA-MS to determine protein turnover rates reveals more sensitive protein turnover models and identifies known proteins degraded by the ubiquitinproteasome pathway, as well as proteins with slower turnover rates implicated in invasive breast cancer. The improved quantification from DIA is expected to make SILAC-based experiments like protein turnover more sensitive.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Neurosciences
Patricia Morcillo, Hector Cordero, Omamuyovwi M. Ijomone, Akinyemi Ayodele, Julia Bornhorst, Leslie Gunther, Frank P. Macaluso, Aaron B. Bowman, Michael Aschner
Summary: The study found that manganese can disrupt mitochondrial dynamics by affecting mitochondrial fission and fusion, leading to impaired respiratory capacity and structure of mitochondria. It also interferes with mitochondrial trafficking and communication, which may be a common pathway underlying neurodegenerative diseases.
MOLECULAR NEUROBIOLOGY
(2021)
Article
Physics, Multidisciplinary
Marcel Hain, Markus Stabel, Thomas Halfmann
Summary: We demonstrate the experimental storage of light at the single photon level for a long time in a Pr3+:Y2SiO5 crystal using electromagnetically induced transparency. Decoherence control and a filter crystal are used to improve storage efficiency and filter selectivity. The findings have significant implications for implementing true quantum memory in other protocols and media.
NEW JOURNAL OF PHYSICS
(2022)
Article
Materials Science, Multidisciplinary
Seyed Mehrdad Zamzamian, Seyed Amirhossein Feghhi, Mohammad Samadfam
Summary: A novel time-dependent model for the displacement cascade in cementite was proposed in this paper, showing satisfactory agreement with results of molecular dynamics simulations based on the Fe-C MEAM potential developed by Liyanage et al. (2014). The comparison of results based on different interatomic potentials revealed fundamental differences, leading to the conclusion that the potential developed by Liyanage et al. (2014) has the best performance for studying radiation damage. Furthermore, nudged elastic band calculations indicated that vacancies in cementite most likely migrate to interstitial sites due to lower migration energies.
JOURNAL OF NUCLEAR MATERIALS
(2021)
Article
Microbiology
Jiayin Lu, Wei Liu, Xue-Zhu Chen, Yiwen Wang, Tianlei Ying, Liang Qiao, Yan-Jun Liu, Baohong Liu
Summary: This study used temporal proteomics to uncover the molecular changes during VACV-induced cell migration, identifying the importance of cell motility and cytoskeleton regulation. The results provide potential biomedical targets for treating viral diseases.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Karmveer Yadav, Syed Azmal Ali, Ashok Kumar Mohanty, Eshwarmoorthy Muthusamy, Kesavan Subaharan, Gautam Kaul
Summary: The study suggests that different types of nanoparticles have varied effects on CHO-K1 cells, with MSN helping prevent protein aggregation, MWCNT causing elongated cell appearance and cytoskeleton remodeling, and ZnO resulting in rounded cell morphology and activation of endocytic, ubiquitination, and proteasomal pathway proteins.
JOURNAL OF NANOBIOTECHNOLOGY
(2021)
Article
Cell Biology
Yihong Yang, Dong Li, Xiaoting Chao, Shashi P. Singh, Peter Thomason, Yonghong Yan, Mengqiu Dong, Lei Li, Robert H. Insall, Huaqing Cai
Summary: This study identifies a novel polarity regulator, Leep1, in the model system Dictyostelium, which selectively localizes at the leading edge of cells by binding to PIP3 to negatively regulate the Scar/WAVE complex, thereby modulating the dynamics of protrusive structures at the leading edge.
JOURNAL OF CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Chenyun Guo, Haoran Zhang, Weiliang Lin, Hanyu Chen, Ting Chang, Zhihua Wu, Jiaxin Yu, Donghai Lin
Summary: This study provides insights into the structural basis of hAK1 catalyzing ADP to ATP and AMP, and uncovers the driving force behind the conformational transition of hAK1, enhancing our understanding of the molecular mechanisms of hAK1 functions.
Article
Physics, Applied
Athena Economides, Georgios Arampatzis, Dmitry Alexeev, Sergey Litvinov, Lucas Amoudruz, Lina Kulakova, Costas Papadimitriou, Petros Koumoutsakos
Summary: Simulation of blood flows in microfluidic devices and physiological systems is crucial, and calibrating model parameters from experimental data is essential for accurate predictions. Single-level and hierarchical Bayesian models show different advantages in calibration, and proper integration of experimental data is necessary for developing robust and transferable RBC models.
PHYSICAL REVIEW APPLIED
(2021)
Article
Physics, Applied
G. H. R. Bittencourt, R. Moreno, R. Cacilhas, S. Castillo-Sepulveda, O. Chubykalo-Fesenko, D. Altbir, V. L. Carvalho-Santos
Summary: The study investigates the dynamics of a transverse domain wall in a bent nanostripe under external conditions. In addition to the standard Walker breakdown phenomenon, a second Walker-like critical field is observed, depending on the curvature and cross-section geometry of the nanostripe. The results show that the inclusion of local curvatures in nanostripes is key for controlling the domain wall phase using external stimuli.
APPLIED PHYSICS LETTERS
(2021)
Article
Polymer Science
Yangyang Wang, Weiyu Wang, Kunlun Hong, Yun Liu
Summary: This study quantitatively investigates the large concentration fluctuations of polymeric liquids under deformation and flow using small-angle neutron scattering and spherical harmonic expansion technique. The methodology allows for real-space analysis of anisotropic scattering length density correlation, providing a concrete venue for quantitative studies of phase behavior of fluids under deformation and flow. The emergence of butterfly patterns is shown to be caused by the change of sign in the leading anisotropic component of the small-angle spectrum, indicating intermolecular correlation associated with flow-induced demixing.
Article
Multidisciplinary Sciences
Danai Laskaratou, Guillermo Solis Fernandez, Quinten Coucke, Eduard Fron, Susana Rocha, Johan Hofkens, Jelle Hendrix, Hideaki Mizuno
Summary: FADED is a novel method for measuring FRET based on anisotropy rather than proximity, allowing for quantification of the relative angle between donor and acceptor. By suppressing donor bleed-through, purer sensitized acceptor anisotropy measurements can be obtained, making it suitable for live cell imaging.
NATURE COMMUNICATIONS
(2021)
Article
Neurosciences
Sybil C. L. Hrstka, Soneela Ankam, Busranur Agac, Jon P. Klein, Raymond A. Moore, Bhavya Narapureddy, Isabella Schneider, Ronald F. Hrstka, Surendra Dasari, Nathan P. Staff
Summary: This study identified proteomic changes in human induced pluripotent stem cell-derived sensory neurons exposed to bortezomib, with significant impact on microtubule dynamics, cytoskeletal organization, and molecular transport. Pathway analysis revealed enrichment in unfolded protein response and integrated stress response signaling pathways, while alterations in MAP2 suggested its influential role in bortezomib-induced neurotoxicity.
EXPERIMENTAL NEUROLOGY
(2021)
Article
Materials Science, Multidisciplinary
Xiaojiang Li, Peisong Peng, Hichem Dammak, Gregory Geneste, Alireza Akbarzadeh, Sergey Prosandeev, L. Bellaiche, Diyar Talbayev
Summary: We present a study of second harmonic generation and Kerr effect induced by terahertz electric fields in KTaO3. The terahertz pulses induce the decay of phonon mode and a polarization response that lasts for picoseconds. We observe a transient Kerr effect that lasts for 43 picoseconds. The slow dynamics of the Kerr effect may be associated with the rotational motion of polar nanoregions.
Article
Biology
M. Pineda, C. J. Weijer, R. Eftimie
JOURNAL OF THEORETICAL BIOLOGY
(2015)
Article
Multidisciplinary Sciences
Gernot Gloeckner, Hajara M. Lawal, Marius Felder, Reema Singh, Gail Singer, Cornelis J. Weijer, Pauline Schaap
NATURE COMMUNICATIONS
(2016)
Review
Biology
Till Bretschneider, Hans G. Othmer, Cornelis J. Weijer
Article
Biochemical Research Methods
Daniel L. Barton, Silke Henkes, Cornelis J. Weijer, Rastko Sknepnek
PLOS COMPUTATIONAL BIOLOGY
(2017)
Article
Developmental Biology
Valentina Ferro, Manli Chuai, David McGloin, Cornelis J. Weijer
Article
Multidisciplinary Sciences
Mattia Serra, Sebastian Streichan, Manli Chuai, Cornelis J. Weijer, L. Mahadevan
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Developmental Biology
Guillermo Serrano Najera, Cornelis J. Weijer
MECHANISMS OF DEVELOPMENT
(2020)
Article
Multidisciplinary Sciences
Yuri Belotti, David McGloin, Cornelis J. Weijer
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Biographical-Item
Developmental Biology
Robert R. Kay, Cornelis J. Weijer
Article
Mathematics, Applied
Y. H. Gao, P. Lin, X. L. Lu, T. J. Sun, C. J. Weijer
Summary: In this study, we propose an inverse problem to derive the stress distributions that drive tissue flows during gastrulation in the epiblast of the chick embryo. We assume that the embryonic tissue can be described as a highly viscous fluid, characterized by the Stokes equations. By using the theory of optimal control, stress distributions are determined by minimizing an objective functional that matches the numerical velocity of the flow with experimental velocity data. We employ the Lagrange multiplier method to derive the optimality system and solve the optimal control problem using the finite element method and the conjugate gradient algorithm.
INTERNATIONAL JOURNAL OF COMPUTER MATHEMATICS
(2022)
Article
Multidisciplinary Sciences
Manli Chuai, Guillermo Serrano Najera, Mattia Serra, Lakshminarayanan Mahadevan, Cornelis J. Weijer
Summary: The morphology of gastrulation differs among vertebrate species, ranging from involution of epithelial sheets of cells in amphibians to ingression of mesenchymal cells through a primitive streak in amniotes. By manipulating signaling pathways in the chick embryo, we were able to change the formation of the primitive streak into modes seen in other species. This suggests that the evolution of gastrulation movements is largely influenced by changes in critical cell behaviors and controlled by a few signaling pathways.
Article
Developmental Biology
Guillermo Serrano Najera, Cornelis J. Weijer
Summary: During gastrulation, the topology of germ layers in early embryos is specified and reorganized, and recent experiments have shown that different alternative modes of gastrulation can be generated in single organisms, such as early cnidarian, arthropod and vertebrate embryos. This process is not rigidly constrained by evolutionary pressures, allowing for high variability in gastrulation morphology throughout the animal kingdom. This review discusses the mechanisms underlying the plasticity of vertebrate gastrulation, its effects on yolk volume, and two crucial innovations during amniote gastrulation: the transition from a ring-shaped mesoderm domain to a crescent-shaped domain, and the evolution of the reptilian blastoporal plate/canal into the avian primitive streak.
Article
Biology
Rastko Sknepnek, Ilyas Djafer-Cherif, Manli Chuai, Cornelis Weijer, Silke Henkes
Summary: Convergence-extension in embryos is regulated by chemical and mechanical signaling through T1 transitions. A model with positive feedback between myosin motors recruitment and mechanical tension in cell junctions is proposed and analyzed. The model generates active T1 events, resulting in tissue elongation perpendicular to the main direction of tissue stress. Our findings demonstrate that active intercalations activate T1 events and cause tension-dependent tissue reorganization, consistent with experiments on gastrulation in chick embryos.
Article
Biology
Gail Singer, Tsuyoshi Araki, Cornelis J. Weijer
COMMUNICATIONS BIOLOGY
(2019)
Proceedings Paper
Optics
Sascha L. Reidt, Ricardo B. C. Correia, Mark Donnachie, Cornelis J. Weijer, Michael P. MacDonald
OPTICAL TRAPPING AND OPTICAL MICROMANIPULATION XIV
(2017)