Review
Genetics & Heredity
Hartwig Visser, Adam D. Thomas
Summary: The DNA damage response plays a crucial role in determining cell fate, with miRNAs potentially influencing cell fate by regulating key DDR proteins. While miRNAs are dysregulated in cancerous tissues, further research is needed to establish their functional association in this context.
Article
Biochemistry & Molecular Biology
Sonia Paget, Marion Dubuissez, Adeline Page, Vanessa Dehennaut, Ingrid Loison, Nathalie Spruyt, Dominique Leprince
Summary: HIC1 is a tumor suppressor gene encoding a transcriptional repressor that plays a role in the DNA-damage response. Specific posttranslational modifications, such as phosphorylation and acetylation, are crucial for the function of HIC1 and its activity in DNA repair. These modifications are essential for HIC1-mediated cellular response to repairable DNA double strand breaks.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Huan Liu, Wenchao Zhang, Lijie Jin, Shasha Liu, Liying Liang, Yanfei Wei
Summary: This study investigates the anticancer mechanism of Plumbagin (PLB) and its potential connections with oxidative stress, genotoxicity, and cell cycle arrest. The results indicate that PLB significantly inhibits HCC cell viability and colony formation, induces G2/M cell cycle arrest, oxidative stress, and DNA damage. These effects can be attenuated by NAC pretreatment. PLB triggers a DNA damage response by activating ATM, Chk1, Chk2, and p53. Furthermore, the key modulator of the G2/M transition factor, cdc25C, is downregulated in an ROS-dependent manner. Inhibition of the ATM-p53 pathway can reduce the occurrence of G2/M cell cycle arrest. Therefore, ROS-mediated oxidative stress plays a crucial role in PLB-induced G2/M cell cycle arrest mediated by the ATM-p53 pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Food Science & Technology
Silu Hou, Yuqiang Cheng, Zhaofei Wang, Luming Xia, Jian Wang, Hengan Wang, Jianhe Sun, Jingjiao Ma, Yaxian Yan
Summary: This study investigated the toxic effects of deoxynivalenol (DON) on gastric mucosal epithelial cells and found that DON can inhibit cell activity, induce DNA damage, apoptosis, and cell cycle arrest. These findings are important for understanding the cytotoxicity and gastric diseases caused by DON.
FOOD AND CHEMICAL TOXICOLOGY
(2023)
Article
Multidisciplinary Sciences
Dimitris C. Kanellis, Jaime A. Espinoza, Asimina Zisi, Elpidoforos Sakkas, Jirina Bartkova, Anna-Maria Katsori, Johan Bostrom, Lars Dyrskjot, Helle Broholm, Mikael Altun, Simon J. Elsasser, Mikael S. Lindstrom, Jiri Bartek
Summary: eIF4A3 plays a role in ribosome biogenesis and p53 regulation, with its depletion leading to cell cycle arrest and changes in cell death regulation pathways. The expression and subnuclear localization of eIF4A3 among clinical cancer specimens correlate with RiBi status, impacting cancer pathogenesis and treatment.
Article
Oncology
Zhili Xia, Minzhen Li, Meng Hu, Yanyan Lin, Lawrence Lawer Atteh, Wenkang Fu, Long Gao, Mingzhen Bai, Chongfei Huang, Ping Yue, Yu Liu, Wenbo Meng
Summary: This study reveals the mechanism by which CB induces apoptosis of ICC cells through activating the ATM/CHK2/p53 signaling pathway and initiating DNA damage. This finding suggests that CB may serve as a potential chemotherapeutic drug candidate for ICC treatment.
FRONTIERS IN ONCOLOGY
(2022)
Article
Oncology
Amr Ghaleb, Lucia Roa, Natalia Marchenko
Summary: The biological consequences of low-dose radiation (LDR) in breast cancer are unclear, while high-dose radiation (HDR) promotes DNA repair and cell cycle arrest. Mutant p53 promotes mammary tumorigenesis following LDR, but has negligible effects on tumors carrying the wild-type p53 allele.
Article
Cell Biology
Sheema Almozyan, James Coulton, Roya Babaei-Jadidi, Abdolrahman S. Nateri
Summary: Recent studies have indicated that FLYWCH1 may play a critical role in facilitating the recruitment of DNA-damage response proteins in the context of DNA damage and repair.
Article
Biology
Yang Wei, Ruilin Bao, Le Hu, Yanqing Geng, Xuemei Chen, Yixian Wen, Yingxiong Wang, Mao Qin, Yue Zhang, Xueqing Liu
Summary: This study evaluated the reproductive toxicity of two-dimensional ultrathin Ti3C2 nanosheets in the testes. It found that exposure to Ti3C2 nanosheets caused defects in spermatogenic function, possibly due to oxidative stress and DNA damage.
Review
Biotechnology & Applied Microbiology
Abir Zebian, Maya El-Dor, Abdullah Shaito, Frederic Mazurier, Hamid Reza Rezvani, Kazem Zibara
Summary: XPC plays a crucial role in DNA damage recognition and repair, as well as DNA damage response and cell fate decisions. Its interactions with other proteins can influence cell apoptosis, senescence, or tumorigenesis. Understanding the status of XPC is important for successful cancer treatment and patient survival.
MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH
(2022)
Article
Biology
Anna K. Uryga, Mandy O. J. Grootaert, Abel M. Garrido, Sebnem Oc, Kirsty Foote, Joel Chappell, Alison Finigan, Francesca Rossiello, Fabrizio D'Adda di Fagagna, Dimitra Aravani, Helle F. Jorgensen, Martin R. Bennett
Summary: Accumulation of vascular smooth muscle cells (VSMCs) is a hallmark of multiple vascular pathologies. The study suggests that persistent telomere damage in VSMCs inducing cell senescence has a major role in driving persistent inflammation in vascular disease. The findings indicate that telomere injury and DNA damage can be primary causes of premature senescence and persistent inflammation in VSMCs.
COMMUNICATIONS BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Elena Oropeza, Sinem Seker, Sabrina Carrel, Aloran Mazumder, Daniel Lozano, Athena Jimenez, Sabrina N. VandenHeuvel, Dillon A. Noltensmeyer, Nindo B. Punturi, Jonathan T. Lei, Bora Lim, Susan E. Waltz, Shreya A. Raghavan, Matthew N. Bainbridge, Svasti Haricharan
Summary: The mode of cell cycle dysregulation determines cancer subtype, metastatic potential, and treatment responsiveness. ATM mutation is associated with older women diagnosed with primary estrogen receptor (ER)(+)/human epidermal growth factor (HER)2(-) cancer, CHK2 dysregulation induces formation of metastatic, premenopausal ER+/HER2(-) breast cancer that is treatment-resistant, and ATR/TP53 co-mutation is enriched in ER+/HER2(-) disease and associated with metastatic progression.
Article
Oncology
Xiaoqing Zhang, Matias A. Bustos, Rebecca Gross, Romela Irene Ramos, Teh-Ling Takeshima, Gordon B. Mills, Qiang Yu, Dave S. B. Hoon
Summary: Our study reveals that ILF2 amplification on chromosome 1q21.3 is linked to melanoma progression and activates a downstream pathway in metastatic melanoma that increases drug resistance. ILF2 expression is positively correlated with copy number variation and is associated with poor overall survival in metastatic melanoma patients. Overexpression of ILF2 promotes cell proliferation in metastatic melanoma, while knockdown of ILF2 inhibits proliferation by blocking the cell cycle.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Article
Biology
Iraia Garcia-Santisteban, Alba Llopis, Lenno Krenning, Jon Vallejo-Rodriguez, Bram van den Broek, Ana M. Zubiaga, Rene H. Medema
Summary: ATM becomes dispensable for G1 checkpoint maintenance as early as 1 hour after DSB induction, while CHK2 kinase activity is necessary to maintain G1 arrest independently of other proteins, suggesting that the G1 arrest is sustained in a lesion-independent manner.
Article
Multidisciplinary Sciences
Carlos Anerillas, Allison B. Herman, Martina Rossi, Rachel Munk, Elin Lehrmann, Jennifer L. Martindale, Chang-Yi Cui, Kotb Abdelmohsen, Supriyo De, Myriam Gorospe
Summary: This study analyzed the response of human fibroblasts to different doses of the genotoxin etoposide and found that SRC is a crucial kinase in determining whether the cells undergo apoptosis or senescence. SRC is activated by low levels of DNA damage, leading to cell survival and senescence, but not by high levels, resulting in apoptosis. Inhibition of SRC prevents the accumulation of senescent cells in tissues exposed to DNA damage, suggesting that targeting SRC could improve health outcomes by promoting apoptosis over senescence.
Article
Mathematics, Applied
Francesca R. Guarguaglini, Roberto Natalini
Summary: In this paper, we investigate linear parabolic equations on a finite oriented star-shaped network with transmission conditions at the inner node. We demonstrate that as the diffusion coefficient approaches zero, the family of solutions converges to the unique solution of the first-order equations with appropriate transmission conditions at the inner node.
JOURNAL OF EVOLUTION EQUATIONS
(2021)
Article
Mathematics
Elishan Christian Braun, Gabriella Bretti, Roberto Natalini
Summary: This work is inspired by recent laboratory experiments on chips that enable culturing of multiple cell species. The model is based on coupled reaction-diffusion-transport equations with chemotaxis, focusing on cell interactions and drug testing effects. Challenges include introducing mass-preserving and positivity-preserving conditions, balancing fluxes between 2D and 1D domains, and developing numerical conditions for external boundaries and interfaces.
Review
Biology
M. Kuznetsov, J. Clairambault, V. Volpert
Summary: Despite advancements in oncological research, cancer remains a leading cause of death globally. Optimizing cancer treatment through mathematical modeling, which can address complexity and suggest potentially effective protocols, is an important goal in oncology.
PHYSICS OF LIFE REVIEWS
(2021)
Article
Mechanics
Elishan C. Braun, Gabriella Bretti, Roberto Natalini
Summary: This study investigates the interaction between immune and cancer cells on a microfluidic chip called Organ-on-Chip (OOC) based on laboratory experiments. By using a mathematical model and real data, the study aims to estimate the model parameters and evaluate the effect of tumor cell-produced chemoattractant on immune cells.
INTERNATIONAL JOURNAL OF NON-LINEAR MECHANICS
(2022)
Article
Biophysics
Nicole Roselli, Alessia Castagnino, Giuseppe Pontrelli, Roberto Natalini, Abdul Barakat
Summary: Endothelial cell migration is crucial for various processes, and different migration patterns are associated with distinct profiles of cell length. In this study, a mathematical model based on differences in intracellular ATP levels is developed, and it successfully captures the different cell length profiles observed experimentally.
BIOMECHANICS AND MODELING IN MECHANOBIOLOGY
(2022)
Article
Mathematics, Applied
Roberta Bianchini, Roberto Natalini
Summary: In the context of hyperbolic systems of balance laws, the Shizuta-Kawashima coupling condition guarantees dissipativity of all variables, even in partially dissipative systems. This condition is crucial for the global existence of classical solutions. However, it is common to find physically based models that violate this condition. In this paper, we study two examples of partially dissipative hyperbolic systems that violate the Shizuta-Kawashima condition, and prove that as long as the source term is nonresonant in the non-dissipative directions, singularities formation is prevented and smooth solutions exist globally in time.
JOURNAL OF EVOLUTION EQUATIONS
(2022)
Article
Mathematics, Interdisciplinary Applications
Gabriella Bretti, Maurizio Ceseri, Roberto Natalini, Maria Carla Ciacchella, Maria Laura Santarelli, Giulia Tiracorrendo
Summary: This paper introduces a mathematical model to describe the intermediate chemical reactions in the carbonation process of concrete. Through simulation algorithms, researchers are able to accurately describe the effects of the interaction between concrete and CO2 on the porosity of the material, which is in substantial accordance with experimental results. Additionally, the dissolution of calcium carbonate under an acid environment is considered, and a trend inversion in the evolution of porosity is observed for long exposure times, significantly affecting the durability of the concrete.
GEM-INTERNATIONAL JOURNAL ON GEOMATHEMATICS
(2022)
Article
Biology
Jan Elias, Hirofumi Izuhara, Masayasu Mimura, Bao Q. Tang
Summary: The study proposes a mathematical model to describe the social behavior of cockroaches, taking into consideration the dispersion behavior due to overcrowding effect. It is found that, due to competition between aggregation towards areas of higher pheromone concentration and dispersion avoiding overcrowded areas, cockroaches aggregate more at the transition area of pheromone.
JOURNAL OF MATHEMATICAL BIOLOGY
(2022)
Article
Biology
Frank Ernesto Alvarez, Jose Antonio Carrillo, Jean Clairambault
Summary: In this study, we examine the biological problem of managing plasticity in cell populations and propose a rational approach. Through numerical approximations and simulations, we demonstrate the model's capacity to exhibit divergence of traits, which can be theoretically interpreted as a physiological step in animal evolution and a representation of resistance behavior in cancer cell populations.
JOURNAL OF MATHEMATICAL BIOLOGY
(2022)
Article
Mathematics, Applied
Roberto Natalini, Thierry Paul
Summary: In this paper, a general class of hybrid mathematical models is proposed to study the collective motions of cells under chemical stimuli. The models combine discrete entities represented by ODEs for cells and a continuous signal described by a diffusive equation for chemoattractant. The mean-field limit of this model is proved in the Wasserstein distance to a system comprised of a Vlasov-type equation coupled with the chemoattractant equation. The research is not based on empirical measures but instead focuses on the marginals of individual densities, and the limit system is shown to have explicit bounds with existence and uniqueness.
SIAM JOURNAL ON MATHEMATICAL ANALYSIS
(2023)
Article
Mathematics, Applied
Elena Bonetti, Cecilia Cavaterra, Francesco Freddi, Maurizio Grasselli, Roberto Natalini
Summary: In this paper, a mathematical model is proposed and analyzed to describe the sulphation process of marble in a specific material. The model considers rugosity and damaging effects. However, there are technical difficulties that hinder the theoretical advancement. Physically reasonable modifications are introduced to establish the existence of a suitable solution. Numerical simulations are presented and discussed for further research.
NONLINEAR ANALYSIS-REAL WORLD APPLICATIONS
(2023)
Article
Mathematics
Victor A. Kovtunenko, Jan Elias, Pavel Krejci, Giselle A. Monteiro, Judita Runczikova
Summary: This study examines the long-term dynamics of granular materials in the hypo-plastic theory of Kolymbas type. It is assumed that the granular hardness allows for exponential degradation, resulting in densification of the material. The governing system for rate-independent strain under stress control is described by implicit differential equations. An explicit form of finite ratcheting for the void ratio is derived under cyclic loading by periodic pressure, which converges to a limiting periodic process (attractor) as the number of cycles tends to infinity.
ARCHIVUM MATHEMATICUM
(2023)
Article
Mathematics, Applied
Gabriella Bretti, Maurizio Ceseri, Roberto Natalini
Summary: This paper focuses on modeling and simulating the carbonation process in concrete. It introduces free boundary problems to describe the evolution of calcium carbonate stones under the attack of CO2 dispersed in the atmosphere, taking into account the shrinkage of concrete and the influence of humidity. Two different regimes are described based on the relative humidity in the environment, and the numerical simulations presented in this study are in line with experimental results from literature.
DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS-SERIES S
(2022)
Article
Mathematics, Applied
Roberto Natalini, Thierry Paul
Summary: In this paper, we study generalizations of the Cucker-Smale dynamical system and rigorously derive the mean-field limit of the Vlasov-type equation in Wasserstein's type topologies. Unlike previous approaches, our method does not rely on empirical measures but uses an Eulerian point of view to provide explicit constants in the limit. We also offer insights on the flocking behavior of solutions to the Vlasov equation for non strictly Cucker-Smale particles dynamics and its relation to the unknown a priori flocking properties of the original particle system.
DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS-SERIES B
(2022)
Article
Mathematics, Applied
Gabriella Bretti, Adele De Ninno, Roberto Natalini, Daniele Peri, Nicole Roselli
Summary: This study aims to develop a mathematical model to mimic the mechanisms observed in lab-on-chip experiments, replicating in vivo scenarios on microfluidic chips. The Cancer-on-Chip experiment involves treating tumor cells with chemotherapy drugs and attracting multiple immune cell species. The proposed in silico model works towards creating a digital twin of experimental immune cells in the chip environment to enhance understanding of immunosurveillance mechanisms.
Article
Biochemistry & Molecular Biology
Trang Van Tran, Hoa Nguyen, Luyen Vu, ChangWoo Lee
Summary: Glutaredoxin 3 (Grx3) is a redox protein that maintains structural integrity and glutathione (GSH) binding capabilities across different temperatures. This study investigates the roles of specific bonds in Grx3's structure and function, and how psychrophilic Grx3 variants adapt to cold environments. The highly conserved Arg51-Asp69 salt bridge and Gln56-His63 hydrogen bond are crucial for stabilizing the structure and catalytic activity of Grx3. Psychrophilic variants of Grx3 have adapted to cold environments by reducing GSH binding and increasing structural flexibility.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Amanda Lais de Souza Coto, Arthur Alexandre Pereira, Sabrina Dorta Oliveira, Milene Nobrega de Oliveira Moritz, Arthur Moraes Franco da Rocha, Paulo Roberto Dores-Silva, Noeli Soares Melo da Silva, Ana Rita de Araujo Nogueira, Lisandra Marques Gava, Thiago Vagas Seraphim, Julio Cesar Borges
Summary: J-domain proteins form a large molecular chaperone family involved in proteostasis processes, with hDjC20 playing a vital role in mitochondria and being heavily influenced by the presence of Zn+2.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Meiling Zhang, Jiaxiang Zhang, Yan Liang, Shicheng Tian, Shuyang Xie, Tong Zhou, Qin Wang
Summary: This study determined the crystal structures of RGLG2 VWA domain in Arabidopsis thaliana, revealing that Ca2+ ions act as regulators and affect the conformational change of RGLG2-VWA domain.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Alexandra Bork, Sander H. J. Smits, Lutz Schmitt
Summary: This study reveals the structure and calcium ion binding properties of CBL1 protein, and proposes a binding model of CBL1 for Ca2+. Additionally, it provides preliminary insights into the formation of the dimer interface of CBL1.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Evgeniia V. Leisi, Andrey V. Moiseenko, Sofia S. Kudryavtseva, Denis V. Pozdyshev, Vladimir I. Muronetz, Lidia P. Kurochkina
Summary: The pathogenesis of prion diseases involves the transformation of prion protein into an insoluble form. This study found that two phage chaperonins can promote the fibrillation of prion protein in an ATP-dependent manner, resulting in the formation of less toxic large clusters. These fibrils differ in morphology and properties from those formed spontaneously in acidic pH with denaturants.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Gaurab Chowdhury, Saroj Biswas, Yuthika Dholey, Puja Panja, Sumit Das, Subrata Adak
Summary: Magnesium is an important divalent cation for regulating enzyme activity. The binding of Mg2+ through the PAS domain inhibits phosphoglycerate kinase (PGK) activity in LmPAS-PGK at neutral pH, but PGK activity is derepressed at acidic pH. Mutation studies revealed that the Asp-4 residue is crucial for Mg2+ binding at neutral pH.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Shima Ghaedizadeh, Majid Zeinali, Bahareh Dabirmanesh, Behnam Rasekh, Khosrow Khajeh, Ali Mohammad Banaei-Moghaddam
Summary: Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies can increase the rate of CO2 absorption from industrial flue gases. This study successfully improved the thermostability of a known hyperthermostable carbonic anhydrase through rational engineering of a single-point mutation.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)
Article
Biochemistry & Molecular Biology
Khaled A. Elnahriry, Dorothy C. C. Wai, Lauren M. Ashwood, Muhammad Umair Naseem, Tibor G. Szanto, Shaodong Guo, Gyorgy Panyi, Peter J. Prentis, Raymond S. Norton
Summary: Sea anemone venom contains a peptide called Tst2, which shows sequence similarity to peptides that interact with various ion channels. Recombinant Tst2 was successfully produced and its structure and function were studied. The results showed that Tst2 is an inhibitor of the TRPV1 channel.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2024)