Article
Biochemistry & Molecular Biology
Chandrakanta Potdar, Alka Kaushal, Aishwarya Raj, Rathijit Mallick, Indrani Datta
Summary: This study aimed to investigate the effect of siRNA silencing of casein kinase (CK)2 alpha on the functional performance of dopaminergic-neurons overexpressing A53T alpha-synuclein. The results showed that CK2 alpha siRNA could alleviate the cellular pathology induced by phosphorylated alpha-synuclein serine129 (pSyn-129) and improve the functional performance of the cells.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2022)
Article
Immunology
Albrecht Froehlich, Florian Olde Heuvel, Rida Rehman, Sruthi Sankari Krishnamurthy, Shun Li, Zhenghui Li, David Bayer, Alison Conquest, Anna M. Hagenston, Albert Ludolph, Markus Huber-Lang, Tobias Boeckers, Bernd Knoll, Maria Cristina Morganti-Kossmann, Hilmar Bading, Francesco Roselli
Summary: This study explores the effects of buffering neuronal nuclear calcium signals in the context of TBI, revealing that it leads to a significant increase in reactive microglial recruitment, accompanied by synaptic loss and reduced whisking activity.
JOURNAL OF NEUROINFLAMMATION
(2022)
Article
Physics, Multidisciplinary
Silvia Ghirga, Letizia Chiodo, Riccardo Marrocchio, Javier G. Orlandi, Alessandro Loppini
Summary: Understanding the functioning of neuronal networks is crucial in modern research in experimental and computational neurophysiology. While knowledge of neuronal and synaptic structure has increased, studying functional and effective networks involves emergent phenomena and nonlinear responses. Refinement in data analysis can help infer connectivity from neuronal activity, with techniques like Transfer Entropy being useful in predicting interactions between neurons.
Article
Biochemistry & Molecular Biology
Ya Wen, Zhifang Dong, Jun Liu, Peter Axerio-Cilies, Yehong Du, Junjie Li, Long Chen, Lu Zhang, Lidong Liu, Jie Lu, Ning Zhou, Dong Chuan Wu, Yu Tian Wang
Summary: Maintaining a proper balance between neuronal excitation and inhibition is crucial for brain function. This study reveals a novel interaction between glutamate and GABA(A) receptors, where glutamate can enhance the function of GABA(A) receptors by directly binding to them. Disruption of this interaction leads to increased neuronal excitability, suggesting its importance in maintaining the excitation-inhibition balance in the brain.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Cell Biology
Natalie J. Guzikowski, Ege T. Kavalali
Summary: Earlier studies explored the organization of proteins that drive neurotransmitter release and postsynaptic signaling at excitatory synapses, but the spatial organization of neurotransmission at inhibitory synapses remains unclear. This study used the specific interaction between antimalarial artemisinins and the inhibitory synapse scaffold protein, gephyrin, to investigate the functional organization of GABAAR-mediated neurotransmission. The results suggest that the GABAergic postsynaptic apparatus has a concentric center-surround organization, where the peripheral gephyrin clusters selectively maintain spontaneous GABAergic neurotransmission, facilitating its autonomous function in regulating Bdnf expression.
Article
Biochemistry & Molecular Biology
Silvia Gleitze, Andrea Paula-Lima, Marco T. Nunez, Cecilia Hidalgo
Summary: Iron plays a crucial role in the physiological function of biological systems, particularly in the development of normal cognitive functions in the brain, but its deregulation can lead to neuronal damage and death. Ferroptosis, a newly described iron-dependent cell death pathway, differs morphologically, biochemically, and genetically from other types of cell death. It involves iron-mediated lipid peroxidation, depletion of the endogenous antioxidant glutathione, and altered mitochondrial morphology.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Article
Biology
Ryan C. F. Siu, Anna Kotova, Ksenia Timonina, Christiane Zoidl, Georg R. Zoidl
Summary: The study highlights the interplay between Connexin-36 (Cx36), NMDA receptor, and Pannexin 1 in calcium signaling in neuronal cells. It shows that CaMKII binding to Cx36 increases gap junction opening, with NMDA receptor and Pannexin 1 playing crucial roles. The research emphasizes the importance of calcium-dependent signaling in modulating the efficacy of Cx36 channels.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biology
Bin Wang, Olga K. Dudko
Summary: A theory of action-potential-triggered neurotransmitter release is proposed and validated with existing data, showing a universal scaling law in synaptic transmission and the ability to extract unique kinetic and energetic parameters for each synapse. The theory also detects cooperativity among SNARE complexes and establishes connections between molecular constituents of synapses and synaptic function. Additionally, the theory reveals trade-off relations between transmission rate and fidelity, providing insights into the molecular-level properties of synapses in synaptic transmission functions.
Article
Biochemistry & Molecular Biology
Nikita Zhilyakov, Arsenii Arkhipov, Artem Malomouzh, Dmitry Samigullin
Summary: Cholinergic neurotransmission plays a key role in both the peripheral and central nervous systems, but certain aspects of its regulation remain unclear. Studies suggest that nicotine can decrease ACh release by enhancing calcium influx through Ca(v)1 channels.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Zachary L. Newman, Dariya Bakshinskaya, Ryan Schultz, Samuel J. Kenny, Seonah Moon, Krisha Aghi, Cherise Stanley, Nadia Marnani, Rachel Li, Julia Bleier, Ke Xu, Ehud Y. Isacoff
Summary: Super-resolution quantal imaging reveals the variability of transmission and identifies responsible presynaptic proteins. The study highlights the importance of balancing and nanoscale distribution of presynaptic proteins in regulating synaptic transmission and generating high signal-to-noise ratio evoked transmission.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
Jonathan Lezmy
Summary: Astrocytes play a crucial role in synapse processing by controlling formation, strength, and termination of synapses. They release ATP, which has diverse effects, and recent studies have revealed its modulation of cellular mechanisms in nearby neurons and glia, signal transmission, and behavioral outputs. A flowchart of astrocytic ATP signaling is provided, suggesting its tendency to inhibit neural circuits to match energy demands.
CURRENT OPINION IN NEUROBIOLOGY
(2023)
Article
Physics, Multidisciplinary
Tatiana Cardoso e Bufalo, R. Bufalo, Lucas P. G. de Figueiredo, Qiuping A. Wang, Fabio Lucio Alves
Summary: We propose a formulation of the Stochastic Least Action Principle that incorporates heavy-tailed distributions to describe random movements in non-dissipative systems, specifically black swan events. We demonstrate that these rare and drastic events in physical systems are related to nonlocal correlations, suggesting the use of Tsallis entropy instead of the conventional Shannon-Boltzmann-Gibbs entropy for their description. Consequently, we assess the validity of the path probability distribution obtained using the non-additive Tsallis entropy.
EUROPEAN PHYSICAL JOURNAL PLUS
(2023)
Article
Neurosciences
Tianyu Gao, Zhengyao Zhang, Yunong Yang, Hangyu Zhang, Na Li, Bo Liu
Summary: Accurate signal transmission between neurons in the central nervous system relies on precise vesicle release within the active zone (AZ). RIM-binding proteins (RIM-BPs) play a crucial role in regulating vesicle release by interacting with other proteins, stabilizing the AZ structure, collecting ion channels, and ultimately controlling the fusion and release of neuronal vesicles.
BRAIN RESEARCH BULLETIN
(2021)
Article
Multidisciplinary Sciences
J. Y. Hu, N. Dauphas, F. L. H. Tissot, R. Yokochi, T. J. Ireland, Z. Zhang, A. M. Davis, F. J. Ciesla, L. Grossman, B. L. A. Charlier, M. Roskosz, E. E. Alp, M. Y. Hu, J. Zhao
Summary: Research found that group II calcium-aluminum-rich inclusions are formed through a two-stage process involving fast evaporation and near-equilibrium recondensation, contrary to the expected scenario of equilibrium condensation. Calculated time scales are consistent with heating events similar to FU Orionis or EX Lupi-type outbursts of eruptive pre-main-sequence stars.
Article
Neurosciences
Marijn Kuijpers, Gaga Kochlamazashvili, Alexander Stumpf, Dmytro Puchkov, Aarti Swaminathan, Max Thomas Lucht, Eberhard Krause, Tanja Maritzen, Dietmar Schmitz, Volker Haucke
Summary: This study demonstrates that loss of neuronal autophagy leads to selective accumulation of tubular endoplasmic reticulum (ER) in axons, resulting in increased excitatory neurotransmission and compromised postnatal viability in vivo. The elevated excitatory neurotransmission is caused by increased calcium release from ER stores via ryanodine receptors accumulated in axons and at presynaptic sites. Neuronal autophagy controls axonal ER calcium stores to regulate neurotransmission in healthy neurons and in the brain.
Article
Chemistry, Physical
K. Basnayake, D. Holcman
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Physics, Multidisciplinary
Suney Toste, David Holcman
Summary: This study derives asymptotic formulas for the mean exit time of the fastest Brownian particle among N identical ones to an absorbing boundary under various initial distributions. The results show a continuous algebraic decay law for the mean exit time, differing from classical Weibull or Gumbel results. Formulas are derived for 1-dimensional and 2-dimensional cases, compared with stochastic simulations, and a discussion on applications in cell biology involving long-tail initial distributions is provided.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2021)
Article
Biochemistry & Molecular Biology
Andrea Papale, David Holcman
Summary: The stability of chromatin loops inside the nucleus is dependent on the balance between binding and unbinding events, with the number of cross-linkers playing a key role. The time scale of loop stability can vary from minutes to the entire cell cycle lifetime as the number of cross-linkers increases.
Article
Biology
A. Tricot, I. M. Sokolov, D. Holcman
Summary: The distribution of voltage in sub-micron cellular domains is poorly understood, especially in terms of maintaining electro-neutrality. Through studying the voltage distribution in a generic domain, it was found that long-range voltage drop changes may have significance in neuronal microcompartments and the activation of voltage-gated channels on the surface membrane.
JOURNAL OF MATHEMATICAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
U. Dobramysl, D. Holcman
Summary: A computational approach is developed to locate the source of a steady-state gradient of diffusing particles, with a fast numerical scheme accelerating simulation time without computing Brownian trajectories explicitly. Results show that analytical formulae and numerical simulation agree on a large range of parameters for reconstructing the source location, while also investigating the uncertainties and window configurations' influence on source reconstruction. Possible applications for cell navigation in biology are discussed as well.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2021)
Article
Multidisciplinary Sciences
Kanishka Basnayake, David Mazaud, Lilia Kushnireva, Alexis Bemelmans, Nathalie Rouach, Eduard Korkotian, David Holcman
Summary: The study reveals that replenishment of dendritic spines involves store-operated calcium entry pathway. Key conditions for replenishment without depletion include small amplitude and slow timescale of calcium influx, as well as close proximity between the spine apparatus and plasma membranes. The nanoscale organization of dendritic spines separates replenishment from depletion.
Article
Engineering, Biomedical
Matteo Dora, David Holcman
Summary: This paper proposes a new wavelet-based method for removing artifacts from single-channel EEGs. The method adaptively attenuates artifacts of different nature through data-driven renormalization of wavelet components and demonstrates superior performances on different kinds of artifacts and signal-to-noise levels. The proposed method provides a valuable tool to remove artifacts in real-time EEG applications with few electrodes, such as monitoring in special care units.
IEEE TRANSACTIONS ON NEURAL SYSTEMS AND REHABILITATION ENGINEERING
(2022)
Article
Multidisciplinary Sciences
F. Paquin-Lefebvre, D. Holcman
Summary: This study investigates the diffusion behavior of Brownian particles injected on the surface of a bounded domain, analyzing the distribution of concentration between different windows. The solution is obtained using Green's function techniques and second-order asymptotic analysis, with the results depending on factors such as influx amplitude, diffusion properties, and the geometrical organization of the windows.
PROCEEDINGS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES
(2021)
Article
Biochemical Research Methods
Lou Zonca, David Holcman
Summary: This study investigates how connected neuronal networks contribute to the emergence of the alpha-band, finding that the alpha-band is generated by network behavior near the attractor of the Up-state. By modeling the interaction of excitatory and inhibitory networks, the study shows that short-term plasticity in well-connected neuronal networks can explain the emergence and fragmentation of the alpha-band.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Mathematics, Applied
Lou Zonca, David Holcman
Summary: This study examines the exit time of two-dimensional dynamical systems perturbed by small noise, revealing that the maximum of the probability density function of trajectories is not located at the point attractor and that exiting the basin of attraction does not guarantee full escape. By applying these results to neuronal networks, the study sheds light on bursting events and explains the non-Poissonian long interburst durations observed in neuronal dynamics.
JOURNAL OF NONLINEAR SCIENCE
(2022)
Review
Physics, Condensed Matter
S. Toste, D. Holcman
Summary: The article investigates the switching behavior of stochastic particles between two states and estimates the fastest arrival time through solving Fokker-Planck equations. The results reveal that the fastest particle avoids switching when the switching rates are low, but it switches twice when the diffusion in state 2 is much faster than in state 1.
EUROPEAN PHYSICAL JOURNAL B
(2022)
Article
Mathematics, Applied
Matteo Dora, Stephane Jaffard, David Holcman
Summary: Wavelet quantile normalization (WQN) is a nonparametric algorithm designed to remove transient artifacts from single-channel EEG in real-time while preserving the continuity of monitoring. The algorithm regularizes the signal by transporting the wavelet coefficient distributions of artifacted epochs into a reference distribution. The WQN algorithm preserves the distribution of wavelet coefficients compared to classical wavelet thresholding methods.
APPLIED AND COMPUTATIONAL HARMONIC ANALYSIS
(2022)
Review
Physics, Multidisciplinary
Ulrich Dobramysl, David Holcman
Summary: Computational methods are powerful and complementary in applied sciences like biology, exploring the gap between molecular and cellular scales. Recent progress includes diffusion modeling, asymptotic analysis, hybrid methods, and simulations for cell sensing and guidance via external gradients. The focus is on reconstructing point source location, estimating uncertainty in source reconstruction, and discussing the impact of window configurations on source position recovery.
REPORTS ON PROGRESS IN PHYSICS
(2022)
Article
Multidisciplinary Sciences
Jurgen Reingruber, Andrea Papale, Stephane Ruckly, Jean-Francois Timsit, David Holcman
Summary: Before vaccines, countries used social restrictions to prevent healthcare system saturation and regain control over COVID-19. Computational approaches are key to efficiently control a pandemic. This study develops a data-driven computational framework to control the pandemic with non-pharmaceutical interventions, using a compartmental model and recalibration based on new data.
Article
Physics, Fluids & Plasmas
F. Paquin-Lefebvre, S. Toste, D. Holcman
Summary: This article introduces the redundancy principle and its application in studying rare events. The authors propose a criterion based on splitting probabilities to estimate large n and obtain explicit computations, which are compared with stochastic simulations. They also provide examples of extreme trajectories with killing in dimension 2 and suggest that optimal trajectories should avoid penetrating inside the killing region for large n. Finally, some applications to cell biology are discussed.