Review
Biochemical Research Methods
Di Xiao, Carissa Chen, Pengyi Yang
Summary: This article reviews computational methods, tools, and systems approaches that have been developed for phosphoproteomics data analysis, categorizing them into data processing, functional analysis, phosphoproteome annotation, and integration with other omics. The article highlights potential research directions that could contribute significantly to this fast-growing field.
Article
Anesthesiology
Attila Keresztes, Keith Olson, Paul Nguyen, Marissa A. Lopez-Pier, Ryan Hecksel, Natalie K. Barker, Zekun Liu, Victor Hruby, John Konhilas, Paul R. Langlais, John M. Streicher
Summary: This study reveals a new function of opioid receptors as a negative feedback brake on opioid-induced analgesia. By using a selective antagonist for the mu and delta opioid receptors (MDOR), the researchers found that the antagonist could enhance the analgesic effect of oxymorphone in mice, suggesting a role for MDOR in regulating pain. Additionally, the study found that the enhancement effect was selective to MDOR and occurred through the repression of Src and CaMKII signal transduction. These findings suggest that MDOR antagonism could be a potential approach to improve clinical opioid therapy.
Article
Cell Biology
Joaquim Javary, Eugenie Goupil, Mathilde Soulez, Evgeny Kanshin, Antoine Bouchard, Ole-Morten Seternes, Pierre Thibault, Jean-Claude Labbe, Sylvain Meloche
Summary: ERK3, an atypical member of the mitogen-activated protein kinase family, has been poorly characterized in terms of its substrates and cellular functions. This study identifies supervillin (SVIL) as a direct substrate of ERK3 and demonstrates its role in regulating myosin II activation and cytokinesis completion in dividing cells. These findings unveil a new function of ERK3 in cell division and highlight its importance in the regulation of cellular processes.
JOURNAL OF CELLULAR PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Geoff P. O'Donoghue, Lukasz J. Bugaj, Warren Anderson, Kyle G. Daniels, David J. Rawlings, Wendell A. Lim
Summary: T cells are able to pick out antigenic signals and establish self-tolerance from complex temporal patterns of stimulus. By engineering T cells to respond to light as a stimulus, researchers found that T cells can filter out minute-scale oscillations of activation signal. CD69 expression reached a local minimum at a period of around 25 minutes, suggesting a potential frequency filtering mechanism downstream of the Erk signaling branch. This study highlights the ability of T cell signaling machinery to temporally filter and interpret time-variant input signals in discriminatory ways.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Geoff P. O'Donoghue, Lukasz J. Bugaj, Warren Anderson, Kyle G. Daniels, David J. Rawlings, Wendell A. Lim
Summary: T cells experience complex temporal patterns of stimulation through receptor-ligand-binding interactions with surrounding cells, enabling them to pick out antigenic signals and establish self-tolerance. This study demonstrates that T cells are able to respond to minute-scale oscillations of activation signal and interpret time-variant input signals through a frequency filtering mechanism downstream of the Erk signaling branch. Temporal filtering may play a functional role in vivo, as indicated by observed T cell encounters with self-peptide-presenting antigen-presenting cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Biochemistry & Molecular Biology
Bozena Klodova, Jan Fila
Summary: Angiosperm mature pollen enters quiescence before pollination, but rapidly activates and grows a pollen tube post-pollination, accompanied by metabolic activity and protein synthesis. Phosphoproteomic studies aim to compare different species' pollen development and discover common proteins involved in root hair growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Pavneet Kaur, Apeksha Anand, Adil Bhat, Jaswinder Singh Maras, Neena Goyal
Summary: The study identified LdMAPK1 target proteins in Leishmania through proteomics, revealing its role in regulating diverse biological processes such as metabolism, signal transduction, replication, transcription, translation, transporters and cytoskeleton/motor proteins. This implies the potential of LdMAPK1 as a therapeutic drug target for treating visceral leishmaniasis.
JOURNAL OF PROTEOMICS
(2021)
Article
Multidisciplinary Sciences
Patrick Binder, Nikolas D. Schnellbaecher, Thomas Hoefer, Nils B. Becker, Ulrich S. Schwarz
Summary: In multicellular organisms, the IFNAR receptor is able to robustly decode ligand types, improving ligand recognition accuracy and buffering against moderate concentration fluctuations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Jessica Fiebelkow, Andre Guendel, Beate Guendel, Nora Mehwald, Tomasz Jetka, Michal Komorowski, Steffen Waldherr, Fred Schaper, Anna Dittrich
Summary: The study shows that SHP2 not only increases robustness of basal and cytokine-induced STAT3 activity, but also ensures information transmission. SHP2 increases the dynamic range of pathway activation in JAK/STAT signalling, contributing to communication in multicellular organisms.
CELL COMMUNICATION AND SIGNALING
(2021)
Article
Mechanics
Rati Sharma
Summary: This study investigates the effect of extrinsic noise on mRNA translation and reveals its impact on ribosome residence time, ribosomal traffic, and protein production through stochastic simulations and statistical analysis. The results show that noise in the translation initiation rate significantly affects the distribution of ribosome residence times on mRNA, while the presence of slow codons increases the average residence time.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Multidisciplinary Sciences
Amanda N. Johnson, Guoliang Li, Hossein Jashnsaz, Alexander Thiemicke, Benjamin K. Kesler, Dustin C. Rogers, Gregor Neuert
Summary: Our study shows that signaling is dependent on a rate threshold combined with stimulus concentration to determine the timing of MAPK signaling during rate-varying stimulus treatments. Additionally, we found that the stimulation rate threshold and stimulation rate-dependent cell survival are sensitive to changes in the expression levels of the Ptp2 phosphatase. This suggests that stimulation rate is a regulated determinant of cell behavior and can guide the dissection of major stimulation rate dependent mechanisms in other systems.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Ryan J. Butcher, Jeffrey J. Tabor
Summary: This article mainly introduces a method to monitor the dynamics of RR dimerization in live bacteria in real time through the depolarization of excitation light. Mathematical modeling reveals that TCS phosphosignaling accelerates with SHK expression but decelerates with RR expression and SHK phosphatase activity. Pulsatile activation of the SHK NarX is observed in response to addition and depletion of the extracellular electron acceptor nitrate. The combination of this method with polarized light microscopy enables single-cell measurements of RR dimerization under changing stimulus conditions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Plant Sciences
Lourdes Infantes, Maria Rivera-Moreno, Miguel Daniel-Mozo, Juan Luis Benavente, Javier Ocana-Cuesta, Alberto Coego, Jorge Lozano-Juste, Pedro L. Rodriguez, Armando Albert
Summary: Modulating the activity of plant phytohormone receptors through genetic or chemical strategies has biotechnological relevance. Designing receptors with single point mutations can enhance plant responses to phytohormones. Structural studies on receptors can lead to the discovery of antagonist molecules for plant hormones.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Dentistry, Oral Surgery & Medicine
D. Wu, Y. Weng, Y. Feng, B. Liang, H. Wang, L. Li, Z. Wang
Summary: In periodontitis, Trem1 regulates polarization of M1 macrophages through the STAT3/HIF-1α signaling pathway. Studies suggest that targeting Trem1 could be a potential strategy for the treatment of periodontitis by modulating macrophage polarization.
JOURNAL OF DENTAL RESEARCH
(2022)
Review
Physiology
Peng Tan, Lian He, Yun Huang, Yubin Zhou
Summary: Optogenetics combines light and genetics to precisely control living cells, tissues, and organisms. It has advantages such as noninvasiveness, rapid responsiveness, tunability, and high spatiotemporal resolution. This review summarizes the fundamental photochemical properties of optogenetic tools and highlights applications in cellular physiology. It also discusses the progress and future trends in wireless optogenetics.
PHYSIOLOGICAL REVIEWS
(2022)
Article
Chemistry, Physical
Elisabetta Collini, Hugo Gattuso, R. D. Levine, F. Remacle
Summary: Through experimental and theoretical studies, ultrafast electronic coherences in semiconducting colloidal quantum dot assemblies at room temperature have been characterized, demonstrating potential for quantum information processing. Close interdot spacing in dimers allows for efficient delocalization of excitons across two QDs. Rich electronic coherent dynamics occur within a 200 fs time scale.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
K. Komarova, F. Remacle, R. D. Levine
Summary: This study algebraically describes molecules in a coherent superposition of several electronic states and identifies key observables to characterize the density matrix of the system accurately.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Manabu Kanno, Benoit Mignolet, Francoise Remacle, Hirohiko Kono
Summary: The study investigates the internal conversion process from S-2 to S-1 state in pyrazine, combining nuclear wave packet simulations and photoelectron spectrum calculations. The results support the conventional two-state picture and experimental observations, further confirming the existence of the rapid internal conversion pathway from S-2 to S-1 in pyrazine.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
K. Komarova, Francoise Remacle, R. D. Levine
Summary: This method simplifies the algebraic procedure for determining dominant constraints by vectorizing the density matrix and using SVD. It is applicable for handling the time evolution of quantum systems and has been successfully applied in molecular dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Martin Blavier, Natalia Gelfand, R. D. Levine, F. Remacle
Summary: In this study, a matricization of the wave function is used to generate an exact separable expression for the entangled molecular wave function. The most compact approximation is obtained through Singular Value Decomposition.
CHEMICAL PHYSICS LETTERS
(2022)
Article
Chemistry, Physical
Matteo Lucchini, Benoit Mignolet, Mario Murari, Cayo E. M. Goncalves, Giacinto D. Lucarelli, Fabio Frassetto, Luca Poletto, Francoise Remacle, Mauro Nisoli
Summary: The dissociation of the ethylene cation is a complex process with unknown mechanisms. This study uses femtosecond extreme-ultraviolet and infrared pulses to investigate the excited-state dynamics and nonradiative relaxation. The results show that the infrared pulse can excite the cationic ground state to higher excited states, leading to enhanced fragmentation yield.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Multidisciplinary
Manuel Cardosa-Gutierrez, Guillaume De Bo, Anne-Sophie Duwez, Francoise Remacle
Summary: Substituted furan-maleimide Diels-Alder adducts connected by dynamic covalent bonds exhibit high attractiveness in mechanophores. Thermally activated [4 + 2] retro-Diels-Alder (DA) reactions proceed mainly through a concerted mechanism. An asymmetric mechanical force along the anchoring bonds in proximal dimethyl furan-maleimide adducts favors a sequential pathway. The findings provide a basis for the rational design of DA mechanophores in polymer science and photochemistry.
Article
Astronomy & Astrophysics
Natalia Gelfand, Ksenia Komarova, Francoise Remacle, Raphael D. D. Levine
Summary: The photodissociation of nitrogen in the vacuum ultraviolet is a major source of reactive nitrogen atoms in the upper atmosphere of Earth and throughout the solar system. Recent studies have shown that the photodissociation branching ratios exhibit strong energy dependence and oscillations in the 108,000-116,000 cm(-1) energy range, leading to different reactive products. High-level quantum chemistry calculations are used to investigate the potential curves of excited states and their couplings, providing insights into the photodissociation mechanism.
ASTROPHYSICAL JOURNAL
(2023)
Article
Chemistry, Physical
Natalia Gelfand, Ksenia Komarova, Francoise Remacle, Raphael D. Levine
Summary: Understanding multi-state electronic dynamics at higher excitation energies is crucial for studying various energy rich situations. Quantum chemistry provides the necessary background for energetics and coupling, while quantum dynamics is employed for the propagation in time. A demonstration of coupled electron-nuclear quantum dynamics through 47 electronic states is reported, achieving close agreement with experimental results. The non-monotonic branching between two exit channels in VUV photodissociation is reproduced and interpreted.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Natalia Gelfand, Francoise Remacle, Raphael D. Levine
Summary: After a singlephoton VUV absorption, the N-2 molecule dissociates into N atoms of different reactivities. Singlets are bound and dissociation occurs through the transfer induced by spin-orbit to the triplets. With the help of a time-reversed quantum dynamical approach, we can trace the path along the nonadiabatic couplings toward a specific exit channel.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
James R. Hamilton, Edoardo Amarotti, Carlo N. Dibenedetto, Marinella Striccoli, Raphael D. Levine, Elisabetta Collini, Francoise Remacle
Summary: In this study, electronic coherence signatures are directly identified in the time-frequency maps measured in 2DES, and the advantages of this approach are discussed. The fast-femtosecond beatings of electronic coherences in ensemble dimers of quantum dots (QDs) are applied and characterized at room temperature in solution. The time-frequency maps allow exploiting electronic coherences without additional post-processing and with fewer 2DES measurements.
Article
Chemistry, Physical
Matteo Lucchini, Benoit Mignolet, Mario Murari, Cayo E. M. Goncalves, Giacinto D. Lucarelli, Fabio Frassetto, Luca Poletto, Francoise Remacle, Mauro Nisoli
Summary: The dissociation of the ethylene cation is a complex process whose exact mechanisms of energy conversion are still not fully understood. By using femtosecond extreme-ultraviolet and infrared pulses for excitation and probing, this study reveals that excitation leads to a thermal ground state in the ethylene cation, resulting in enhanced fragmentation yield. The probing results also provide information about the type of conical intersection involved in the ultrafast excited-state dynamics and nonradiative relaxation.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Quantum Science & Technology
James R. Hamilton, Edoardo Amarotti, Carlo Nazareno Dibenedetto, Marinello Striccoli, R. D. Levine, Elisabetta Collini, F. Remacle
Summary: Ensembles of quasi-homodimers assembled with sub-nm ligands from colloidal 3 nm CdSe quantum dots (QDs) show robust photoinduced electronic coherences even in the presence of dephasing. The coherence periods range from 40 to 300 fs and are observed in both solution and solid-state samples. A theoretical model explains the electronic coherences and guides the optimization of these coherences by tuning the interplay between dimer electronic delocalization, optical activity, and size dispersion. The persistence of many QD electronic coherences in the solid-state and in solution opens up possibilities for quantum technology applications.
ADVANCED QUANTUM TECHNOLOGIES
(2022)
Article
Chemistry, Physical
Martin Blavier, R. D. Levine, F. Remacle
Summary: Broad energy optical pulses induce ultrafast molecular dynamics with entanglement between nuclear and electronic degrees of freedom. Singular Value Decomposition (SVD) provides a representation of this entangled system, equivalent to a Schmidt decomposition. The level of entanglement is determined by the ordering and number of singular values. Non-adiabatic transitions also contribute to the entanglement in the system.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Cayo E. M. Goncalves, R. D. Levine, F. Remacle
Summary: The ultrafast structural dynamics in CH4+ and CD4+ cations exhibit a strong isotope effect, with the high ratio being attributed to the faster electronic coherence dynamics in CH4+.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)