Article
Biochemistry & Molecular Biology
Jeffrey A. Hussmann, Jia Ling, Purnima Ravisankar, Jun Yan, Ann Cirincione, Albert Xu, Danny Simpson, Dian Yang, Anne Bothmer, Cecilia Cotta-Ramusino, Jonathan S. Weissman, Britt Adamson
Summary: Cells repair DNA double-strand breaks using a complex set of pathways, with the study identifying unexpected relationships among DSB repair genes and demonstrating the importance of genetic dependencies in repair outcomes. The research lays a foundation for mapping DNA repair pathways and optimizing genome editing across a variety of modalities.
Article
Chemistry, Organic
Pradeep Shrestha, Atreyee Mukhopadhyay, Komadhie C. Dissanayake, Arthur H. Winter
Summary: The recent developments in more efficient BODIPY photocages have led to higher photosensitivity and better chemical yields. These photocages can release amines, alcohols, phenols, phosphates, halides, and carboxylic acid derivatives with high quantum yields. The quantum yield of photorelease is related to the quality of the leaving group and the color of the absorbing light.
JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Chemistry, Physical
Valmir B. Silva, Elisa S. Orth
Summary: This study investigates the alkaline hydrolysis of organophosphates and evaluates the impact of leaving and non-leaving groups. A linear correlation model is successfully established to predict optimal neutralization processes. The study finds that the contribution of non-leaving groups is as important as leaving groups, and the presence of heteroatoms affects the contribution of these groups.
Review
Biochemistry & Molecular Biology
Yu Chen, Zhifeng Zeng, Qunxin She, Wenyuan Han
Summary: CRISPR-Cas and pAgo are defense systems in prokaryotes that use nucleic acid (NA) guides to recognize and cleave invading NA targets. However, they also utilize the abortive infection (Abi) strategy to activate toxic effectors and kill infected cells, preventing the spread of invaders. This review summarizes the mechanisms of CRISPR-Cas and pAgo systems and highlights their crucial roles in the microbial arms race against invaders.
TRENDS IN MICROBIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Joanna Czescik, Susanna Zamolo, Tamis Darbre, Riccardo Rigo, Claudia Sissi, Adam Pecina, Laura Riccardi, Marco De Vivo, Fabrizio Mancin, Paolo Scrimin
Summary: Gold nanoparticles can efficiently catalyze chemical reactions as nanozymes, exhibiting the highest efficiency in cleaving plasmid DNA. By successfully mimicking the suggested structure of natural metallonucleases, this study provides important insights into the catalytic mechanism.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Organic
Ethan A. Gormong, Dorian S. Sneddon, Theresa M. Reineke, Thomas R. Hoye
Summary: The presence of a nearby tethered functional group significantly affects the cleavage rate of an Si-O bond. In this study, we investigated the relative rates of cleavage of model substrates with different Si-O substructures using in situ H-1 NMR spectroscopy. The computed trends in the relative rates correlated well with the experimental data. Additionally, we observed a siloxy-metathesis reaction facilitated by a pendant dimethylamino group.
JOURNAL OF ORGANIC CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Yu Feng, Yao Dong, Ke-Jie Du, Xi-Chun Liu, Shu-Qin Gao, Ying-Wu Lin
Summary: Natural and artificial nucleases are widely used in biotechnology and biomedicine. This study engineered four human cytochrome c (Cyt c) mutants with enhanced DNA cleavage activity and degradation, especially under acidic conditions. Mechanism assays revealed the importance of superoxide in the nuclease reaction, while kinetic assays showed that the peroxidase activity of the I81D Cyt c mutant was significantly enhanced. This study highlights the critical role of specific mutations in the nuclease activity of Cyt c and suggests potential applications in DNA damage and biomedicine.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2023)
Article
Green & Sustainable Science & Technology
Ruoqi Liu, Zhanbiao Yang, Guiyin Wang, Junren Xian, Ting Li, Yulin Pu, Yongxia Jia, Wei Zhou, Zhang Cheng, Shirong Zhang, Gang Xiang, Xiaoxun Xu
Summary: This study explored the simultaneous removal of NH4+ and PO43- from water using two Chinese medicinal herbal residues, ZB and ZG. It was found that ZG exhibited a more significant potential for removing and recovering NH4+ and PO43- from wastewater compared to ZB. The adsorption of NH4+ and PO43- was well described by pseudo-second-order and intra-particle diffusion models, with Langmuir isotherm model being the best fit for the adsorption equilibrium data.
JOURNAL OF CLEANER PRODUCTION
(2021)
Article
Materials Science, Ceramics
Greta Ugolotti, Enrico Sassoni
Summary: This study explored different strategies to improve the consolidating efficacy of diammonium hydrogen phosphate (DAP) solution, including increasing pH or adding organic solvents. The results showed that apatite phases were formed as a result of all treatments, except when undesired ammonium calcium phosphate hydrate was formed at pH 12. Higher concentration DAP solutions provided greater strengthening ability.
CERAMICS INTERNATIONAL
(2023)
Article
Biochemistry & Molecular Biology
Yujing Ren, Beiming Yu, Lihui Zhou, Feng Wang, Yanfeng Wang
Summary: This study analyzed the phosphorylation mechanism of UCHL3 in its deubiquitinating activity and provided in vitro evidence of UCHL3's cleavage activity towards specific types of polyubiquitin chains.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Environmental Sciences
Xiaoxiao Wang, Yunfeng Ma, Xiaoqing Lin, Angjian Wu, Yifan Xiang, Xiaodong Li, Jianhua Yan
Summary: In this study, ADP and CaO were used as inhibitors to suppress the formation of PCDD/Fs. ADP showed significant inhibition effects, especially on toxic PCDFs. The synergistic effect of ADP and CaO further improved the inhibition on toxic PCDDs.
Article
Chemistry, Multidisciplinary
Duo Yang, Yu Song, Ming-Yue Zhang, Zengming Qin, Jie Liu, Xiao-Xia Liu
Summary: In this study, a novel manganese phosphate material (MP-20) was fabricated for NH4+ ion storage, exhibiting high charge storage capacity, and the important role of electrolyte in improving the material's performance was proposed.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Gulzar A. Bhat, Ramaswamy Murugavel
Summary: This study investigates the chemical properties of binuclear complexes formed by 2,6-diisopropylphenyl phosphate and group 12 metal acetates in the presence of hexadentate N-donor ligands, and characterizes them using various analytical techniques, with further determination of their molecular structures through X-ray diffraction.
JOURNAL OF MOLECULAR STRUCTURE
(2021)
Article
Chemistry, Analytical
Roshan Javanshad, Andre R. Venter
Summary: The study found that adding serine in DESI-MS significantly increased protein signal and demonstrated the importance of serine in protein dissolution. Compared to ESI-MS, DESI-MS serves as a novel tool for investigating protein solubility, dissolution, and the mechanisms of solubility-enhancing additives.
Article
Green & Sustainable Science & Technology
S. Arun, Surjith Ramasamy, Kannan Pakshirajan
Summary: A consortium of microalgae, ammonia-oxidizing bacteria, and nitrite-oxidizing bacteria showed high NH4+ removal efficiency at light intensities up to 1500 µmol m(-2) s(-1), but the removal process was affected at light intensities above 1500 µmol m(-2) s(-1). This indicates that the mechanism of ammonium removal is strongly influenced by the daily average light intensity.
JOURNAL OF CLEANER PRODUCTION
(2021)
Article
Chemistry, Physical
Valerio Mazzilli, Katsuhiko Satoh, Giacomo Saielli
Summary: In this study, the phase behavior of mixtures of discotic Gay-Berne (GB) particles with spherical Lennard-Jones (LJ) particles was investigated using molecular dynamics simulations. It was observed that the GB-rich systems undergo a nematic-to-isotropic transition as the fraction of LJ solutes is increased, leading to phase separation. On the other hand, for LJ-rich systems, mixing and the transition to the nematic phase occur simultaneously. There is also a clear correlation between the orientational order parameter of the LC phase and the solubility of LJ particles within the LC phase.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Chiara Bellini, Salvatore Antonucci, Lucia Morillas-Becerril, Sara Scarpa, Regina Tavano, Fabrizio Mancin, Fabio Di Lisa, Emanuele Papini
Summary: The study demonstrated the effectiveness of utilizing two formulations of poly(lipoic acid)-based nanoparticles (NPs) in combating radical damage and ROS formation in various cell types. Results indicate that NPs could effectively protect against myocardial cell damage induced by ischemic reperfusion injury.
Article
Chemistry, Physical
Nicola Peruffo, Fabrizio Mancin, Elisabetta Collini
Summary: The ultrafast dynamics of plexcitonic materials, influenced by other states, have longer time constants than typical values found in literature and can be modulated, opening up potential prospects for modifying rates of chemical reactions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Nanoscience & Nanotechnology
Chiara Castellani, Claudia Maria Radu, Lucia Morillas-Becerril, Ilaria Barison, Federica Menato, Tomaz Michele Do Nascimento, Marny Fedrigo, Alessia Giarraputo, Grazia Maria Virzi, Paolo Simioni, Cristina Basso, Emanuele Papini, Regina Tavano, Fabrizio Mancin, Giorgio Vescovo, Annalisa Angelini
Summary: This study investigated the biodistribution, safety, and molecular delivery ability of F127@PLA-NPs in healthy rats. The results showed that F127@PLA-NPs accumulated the most in the heart and had the ability to target cardiomyocytes. No histopathological lesions or thrombogenicity were observed after NPs injection.
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE
(2022)
Article
Chemistry, Multidisciplinary
Krishnendu Das, Haridas Kar, Rui Chen, Ilaria Fortunati, Camilla Ferrante, Paolo Scrimin, Luca Gabrielli, Leonard J. Prins
Summary: This article describes a self-assembly of surfactant-based structures that rely on a combination of a thermodynamically controlled and a dissipative pathway for their formation. Adenosine triphosphate (ATP) acts as a high-affinity template and triggers the formation of assemblies at low surfactant concentrations. The presence of these assemblies allows for the activation of a dissipative self-assembly process by a weak-affinity substrate. The induced recruitment of additional surfactants by the substrate leads to the spontaneous formation of catalytic hotspots in the ATP-stabilized assemblies, resulting in substrate cleavage. Catalysis can be observed at a surfactant concentration where low catalytic activity is observed in the absence of ATP.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Francesco Lanero, Bianca Maria Bresolin, Anna Scettri, Marco Nogarole, Elisabetta Schievano, Stefano Mammi, Giacomo Saielli, Alessia Famengo, Alessandra Semenzato, Giovanni Tafuro, Paolo Sgarbossa, Roberta Bertani
Summary: Vegetable oils, as bio-based and sustainable starting materials, can be used to develop chemicals for industrial processes. This study investigated the functionalization of grape, hemp, and linseed oils with maleic anhydride using conventional heating or microwave activation. The resulting products could enhance the water dispersion of oils for industrial applications.
Article
Chemistry, Organic
Flavio della Sala, Elisa Ceresara, Fabrizio Micheli, Stefano Fontana, Leonard J. Prins, Paolo Scrimin
Summary: Cationic, monolayer-protected gold nanoparticles with a multivalent charged surface and a hydrophobic monolayer can effectively bind to phosphatidylinositol (3,4,5)-trisphosphate, a relevant biomarker, with a dissociation constant in the picomolar range. This suggests that these gold nanoparticles can be used for the selective extraction of this molecule from biological fluids.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Luca Fusaro, Nikolay Tumanov, Giacomo Saielli, Riccardo Montis
Summary: Crystalline materials and crystallization processes are important in various scientific fields. The choice of solvent system is crucial for crystallization. In this study, we investigated the role of a binary solvent mixture in the crystallization of a simple salt. The results showed that the presence of acetone led to the formation of a complex structure belonging to the FK phases, which was never observed before. The interaction between acetone and the solute played a key role in promoting specific molecular aggregations.
PURE AND APPLIED CHEMISTRY
(2023)
Article
Materials Science, Multidisciplinary
Nicola Peruffo, Fabrizio Mancin, Elisabetta Collini
Summary: Two-dimensional electronic spectroscopy (2DES) is employed to study the quantum coherent interactions of colloidal plexciton nanohybrids, revealing the nonlinear photophysical processes and advancing the understanding and exploitation of these nanomaterials.
ADVANCED OPTICAL MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Giacomo Saielli
Summary: We investigated the NMR chemical shift of Tl-205 in various thallium compounds, spanning from small covalent Tl(I) and Tl(III) molecules to supramolecular complexes with large organic ligands and some thallium halides. NMR calculations were performed at the ZORA relativistic level using different GGA and hybrid functionals, and solvent effects were also examined. The computational protocol at the ZORA-SO-PBE0 (COSMO) level showed excellent performance in determining the structural conformations based on the agreement between the calculated chemical shift and the experimental value.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Sebastian Franco-Ulloa, Andrea Cesari, Laura Riccardi, Federico De Biasi, Daniele Rosa-Gastaldo, Fabrizio Mancin, Marco De Vivo, Federico Rastrelli
Summary: Nanoparticle-assisted nuclear magnetic resonance (NMR) chemosensing is a technique that uses monolayer-protected nanoparticles as supramolecular hosts to detect small molecules in complex mixtures. The structure-sensitivity relationships that determine the detection limits of this technique are still not well understood. This study combines NMR spectroscopy and atomistic molecular dynamics simulations to investigate the factors that affect the sensitivity of different NMR chemosensing experiments. The results show that the intensity of the observed signals is correlated with the spin-spin interactions between the analytes and the nanoparticles, as well as the analytes and the nanoparticles' solvation molecules.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Ziqi Cheng, Shen Li, Elena Tocci, Giacomo Saielli, Annarosa Gugliuzza, Yanting Wang
Summary: This study uses molecular dynamics simulations to investigate the effect of an ionic liquid (IL) on water vapor transport through PEBAX membranes. The simulation shows that the IL forms a pathway for water transport in the membrane, with the width of the pathway and the water-accessible area increasing as the IL concentration increases. This leads to higher diffusion coefficients for water molecules and ions.
Article
Chemistry, Physical
Jie Yao, Giacomo Saielli, Fanlong Meng, Yanting Wang
Summary: We performed molecular dynamics simulations to investigate the transition processes of [C-22/C(1)MIm](+)[NO3](-) binary mixtures by varying the cation ratio of C-22 to C-1 at a fixed temperature of 400 K. The results showed that the system undergoes a first-order phase transition from a homogeneous liquid to a nano-fragment liquid with increasing C-22 percentage, during which some cationic alkyl side chains aggregate to form small bundles floating in the solvent. As the C-22 percentage further increases, another first-order phase transition occurs, bringing the system into an ionic liquid crystal phase.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Valerio Mazzilli, Katsuhiko Satoh, Giacomo Saielli
Summary: The phase behavior of mixtures of soft disks and soft spheres with opposite charge has been investigated. Different compositions and charges lead to a rich mesomorphism with the formation of isotropic, discotic nematic, hexagonal columnar, and crystal phases. The morphology of the hexagonal columnar phase varies depending on the composition, with lamellar structures observed in the 1:2 stoichiometry and a frustrated phase with alternating tilt direction in the 2:1 stoichiometry.
Article
Chemistry, Physical
Valerio Mazzilli, Yanting Wang, Giacomo Saielli
Summary: By using molecular dynamics simulations, the structural and dynamic properties of mixtures of [C(1)C(1)im][Tf2N] and [C(12)C(1)im][Tf2N] were investigated. It was found that the pre-peak of the structure factor S(q) shifted to higher q values and increased in intensity with the concentration of the long-chain component C-12. The diffusion of ions showed a simple behavior consistent with the increased viscosity of the mixture.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
