Article
Environmental Sciences
Gabrielle Cristina dos Santos Goncalves Nascimento, Daniela Giovana da Cunha Barros, Lizandra Souza Ratuchinski, Caio Okon, Patricia Aline Bressiani, Diego Espirito Santo, Charla Chaionara Schults Duarte, Paulo Michel Pinheiro Ferreira, Osvaldo Valarini Valarini Junior, Juan Carlos Pokrywiecki, Elisangela Dusman, Regiane da Silva Gonzalez, Debora Cristina de Souza, Ana Paula Peron
Summary: Octocrylene, a compound commonly found in sunscreen, has potential phytotoxicity and oxidative stress effects on plants and soil animals. It negatively affects seed germination and root growth in some plant species and impairs their defense systems against oxidative damage. In soil animals, octocrylene increases oxidative stress and lipid peroxidation in their cells. Therefore, regulation of octocrylene release into the environment is urgently needed.
WATER AIR AND SOIL POLLUTION
(2023)
Review
Biochemistry & Molecular Biology
Geraldine Veeckmans, Emily Van San, Tom Vanden Berghe
Summary: Ferroptosis is a cell death mechanism that occurs through excessive peroxidation of polyunsaturated fatty acids within cellular membranes, catalyzed by iron. This process is tightly regulated by lipid, iron, and redox metabolic processes. This review provides an overview of how ferroptosis is executed, including the major classes of inducers and inhibitors, as well as methods for detection. The detrimental role of ferroptosis in disease is also briefly discussed.
Article
Biochemistry & Molecular Biology
Eduardo Esteban-Zubero, Laura Lopez-Pingarron, Jose Manuel Ramirez, Marcos Cesar Reyes-Gonzales, Francisco Javier Azua-Romeo, Marisol Soria-Aznar, Ahmad Agil, Jose Joaquin Garcia
Summary: This study evaluated the in vivo effects of melatonin treatment on oxidative damage in the liver in an experimental model of ischemia-reperfusion. Melatonin pretreatment reduced liver ischemia-reperfusion injury and oxidative stress response, making it a potential candidate for co-treatment in patients with hepatic vascular occlusion followed by reperfusion.
Article
Engineering, Mechanical
Choon-Peng Chng, Yoel Sadovsky, K. Jimmy Hsia, Changjin Huang
Summary: The peroxidation of lipids with polyunsaturated fatty acid tails modulates the biophysical properties of bilayer membrane in a site-specific manner, influencing membrane structure and properties. Specifically, peroxidation at different sites leads to distinct changes in the membrane, with peroxidation in the bilayer interior causing membrane disruption and softening, while peroxidation near the membrane-water interface results in a more ordered and stiffer membrane.
EXTREME MECHANICS LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Azza A. A. Attia, Jehan M. M. Sorour, Neama A. A. Mohamed, Tagreed T. T. Mansour, Rasha A. A. Al-Eisa, Nahla S. S. El-Shenawy
Summary: This study aimed to investigate the protective role of vitamin E in improving cardiotoxicity induced by cyclophosphamide in rats. The results showed that vitamin E could attenuate the elevation of cardiac markers, increase in lipid profiles, reduction in antioxidant enzyme activities, and increase in lipid peroxidation. In addition, vitamin E was found to improve the histopathological alterations caused by cyclophosphamide.
Article
Food Science & Technology
Fatemeh Karimi, Negin Rezaei-savadkouhi, Aysenur Aygun, Rima Nour Elhouda Tiri, Ismet Meydan, Elaheh Aghapour, Hamdullah Seckin, Derya Berikten, Tugba Gur, Fatih Sen, Mustafa Ucar
Summary: Nanotechnology, an interdisciplinary study, has been rapidly developing worldwide and has significant impact on human life. Plant-based nanoparticles are clean, non-toxic, and biocompatible, opening up new fields of research. The Hibiscus sabdariffa plant has attracted scientists due to its health benefits and other impacts.
FOOD AND CHEMICAL TOXICOLOGY
(2022)
Article
Food Science & Technology
Deocleciano C. de Santana Neto, Angela M. T. M. Cordeiro, Bruno R. L. A. Meireles, Iris B. S. Araujo, Mario Estevez, Valquiria C. S. Ferreira, Fabio A. P. Silva
Summary: Yellow mombin extract successfully maintained the red color of chicken patties and inhibited protein and lipid oxidation compounds generation, making it a potential natural preservative for meat products.
Article
Food Science & Technology
Phung Diep Huy Vu, Akkaratch Rodklongtan, Pakamon Chitprasert
Summary: The study found that the encapsulant weight ratio of whey protein isolate-lignin complex significantly affects the survival rate of spray-dried probiotics, with the 9:1 ratio offering the best protection. Lignin improves the survival of probiotics by enhancing the structure and antioxidant properties of WPI.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Environmental Sciences
Megha Murali, T. Shivanandappa
Summary: Endosulfan exposure causes high levels of oxidative stress in the liver and brain, leading to reduced antioxidant enzyme activity and increased ROS and lipid peroxidation. The brain is more susceptible to oxidative stress than the liver, likely due to its lower antioxidant defenses and higher oxygen consumption.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2022)
Article
Biochemistry & Molecular Biology
Michal J. Sabat, Anna M. Wisniewska-Becker, Michal Markiewicz, Katarzyna M. Marzec, Jakub Dybas, Justyna Furso, Pawel Pabisz, Mariusz Duda, Anna M. Pawlak
Summary: TUDCA is a hydrophilic bile acid that has been used as a therapeutic compound in traditional Chinese medicine. It has gained interest as a neuroprotective agent and has antioxidant activity, as well as stabilizing effects on mitochondrial and plasma membranes. Additionally, TUDCA induces slight changes in the polarity and fluidity of model membranes.
Article
Environmental Sciences
Hamdullah Seckin, Rima Nour Elhouda Tiri, Ismet Meydan, Aysenur Aygun, Meliha Koldemir Gunduz, Fatih Sen
Summary: The study successfully synthesized Pt-Pd nanoparticles through a green synthesis method and characterized and tested them. The results showed that these nanoparticles exhibited good activities in antioxidant, antibacterial, and lipid peroxidation inhibition properties. The photocatalytic activity of the nanoparticles was also demonstrated through the degradation of dyes.
ENVIRONMENTAL RESEARCH
(2022)
Article
Agriculture, Dairy & Animal Science
Alireza Behnamifar, Shaban Rahimi, Mohammad Amir Karimi Torshizi, Mohsen Sharafi, J. L. Grimes
Summary: This study investigated the effects of alpha-lipoic acid supplementation on the semen quality and fertility parameters of aging breeder roosters, finding that appropriate levels of ALA can improve sperm quality, while higher doses do not result in further improvement.
Article
Biochemistry & Molecular Biology
Anja Sadzak, Zlatko Brkljaca, Mihael Erakovic, Manfred Kriechbaum, Nadica Maltar-Strmecki, Jan Pribyl, Suzana Segota
Summary: Products of lipid peroxidation can cause detrimental structural changes in cell membranes, including the formation of water pores. However, the influence of dicarboxylic acids on cell membranes is still not well understood. This study focused on dodecanedioic acid (DDA) as a model product and investigated the impact of different flavonoids on DDA aggregation. The results showed that the addition of flavonoids disrupted the formation of DDA aggregates, leading to a decrease in DDA concentration in cell membranes.
JOURNAL OF LIPID RESEARCH
(2023)
Article
Multidisciplinary Sciences
Tomas Sabirovas, Ausra Valiuniene, Gintaras Valincius
Summary: In this study, biomimetic electrodes suitable for probing protein/phospholipid interactions were created on metallurgically polished aluminum surfaces. The fusion of multilamellar vesicles on the aluminum surface formed a hybrid bilayer lipid membrane (hBLM), with its complex capacitance being typical for intact phospholipid bilayers. The presence of cholesterol in hBLMs inhibited membrane damage caused by the peptide melittin, which showed a concentration-dependent interaction with the hBLMs.
SCIENTIFIC REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Onchuma Mueangson, Aongart Mahittikorn, Nsoh Godwin Anabire, Wanida Mala, Manas Kotepui
Summary: This study examined the relationship between malondialdehyde (MDA) concentrations and Plasmodium infections. The results showed that MDA concentrations were significantly elevated in patients with malaria compared to uninfected controls, indicating an increase in oxidative stress and lipid peroxidation. MDA levels can be a valuable biomarker for evaluating these processes in individuals with malaria.
Article
Chemistry, Physical
Marketa Paloncyova, Martin Srejber, Petra Cechova, Petra Kuhrova, Filip Zaoral, Michal Otyepka
Summary: RNA-based therapies have shown promise in various applications. Encapsulation of RNA into lipid nanoparticles allows for safe and targeted delivery. Simulations of pH-sensitive RNA-carrying nanoparticles reveal their self-assembly process and internal structure, providing insights into their composition and potential interactions for improving RNA-based medicine.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Michal Langer, Lukas Zdrazil, Miroslav Medved, Michal Otyepka
Summary: The establishment of structure-photoluminescence (PL) relationships in carbon dots (CDs) is still a challenge. The core, surface, and molecular states are the main sources of PL, but their interaction and effects on each other are not well understood. By performing TD-DFT calculations, researchers found that different structural arrangements support the communication between PL centers. This study provides insights for designing CDs with desired surface/core characteristics.
Article
Chemistry, Medicinal
Petra Kuhrova, Vojtech Mlynsky, Michal Otyepka, Jiri Sponer, Pavel Banas
Summary: RNA molecules play a key role in biochemical processes and interact closely with ions and water molecules. Double-stranded RNA is important for RNA folding and the design of RNA-based nanostructures. This study used molecular dynamics simulations to investigate the effects of ion concentrations and solvation box size on A-RNA structure.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Medicine, Research & Experimental
Martin Balouch, Katerina Storchmannova, Frantisek Stepanek, Karel Berka
Summary: Encapsulation into liposomes is a formulation strategy that improves drug efficacy and reduces side effects. However, some drugs are not suitable for liposomal formulations due to their properties. Several options for solving this issue include changing the lipid bilayer composition, adding permeability enhancers, or modifying the chemical structure of the drug.
MOLECULAR PHARMACEUTICS
(2023)
Article
Biochemistry & Molecular Biology
Aliaksei Chareshneu, Adam Midlik, Crina-Maria Ionescu, Alexander Rose, Vladimir Horsky, Alessio Cantara, Radka Svobodova, Karel Berka, David Sehnal
Summary: Segmentation is important for interpreting imaging data in a biological context. Mol*VS is a web-based tool that allows interactive visualization of 3D volume segmentations, supporting cellular imaging data and biological annotations.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ondrej Schindler, Karel Berka, Alessio Cantara, Ales Krenek, Dominik Tichy, Tomas Racek, Radka Svobodova
Summary: The AlphaFold2 prediction algorithm has allowed for the exploration of protein structural space on a large scale. A web application called alpha Charges has been introduced for the quick calculation of partial atomic charges for protein structures from AlphaFoldDB.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Aby Cheruvathoor Poulose, Miroslav Medved, Vasudeva Rao Bakuru, Akashdeep Sharma, Deepika Singh, Suresh Babu Kalidindi, Hugo Bares, Michal Otyepka, Kolleboyina Jayaramulu, Aristides Bakandritsos, Radek Zboril
Summary: This study presents a reusable graphene catalyst that can convert glycerol, produced from biomass fermentation, to high-value chemicals at room temperature without solvents. The catalyst shows excellent activity and selectivity for glycerol conversion to solketal, and it can also convert oils to biodiesel.
NATURE COMMUNICATIONS
(2023)
Article
Nanoscience & Nanotechnology
Akshay Kumar K. Padinjareveetil, Juan V. Perales-Rondon, Dagmar Zaoralova, Michal Otyepka, Osamah Alduhaish, Martin Pumera
Summary: Electrochemical reduction of nitrate into ammonia is a promising solution to address the challenges of growing global energy demand. Metal-organic framework (MOF)-based catalysts are being investigated for their enhanced structural and compositional integrity, making them effective in catalytic reduction reactions.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Sujit Deshmukh, Kalyan Ghosh, Martin Pykal, Michal Otyepka, Martin Pumera
Summary: Microsupercapacitors with mechanical flexibility offer potential applications in portable biomonitoring devices. Researchers have developed high-energy-density micro-SCs integrated with a force sensing device using picosecond pulsed laser technology, and demonstrated their effectiveness in monitoring human body's radial artery pulses.
Article
Biochemistry & Molecular Biology
Jan Chasak, Lauren Oorts, Milan Dak, Veronika Slachtova, Vaclav Bazgier, Karel Berka, Linda De Vooght, Natalia Smiejkowska, Kevin Van Calster, Laurence Van Moll, Davie Cappoen, Paul Cos, Lucie Brulikova
Summary: This study aims to develop new antimycobacterial agents against drug-resistant tuberculosis by inhibiting mycobacterial ATP synthase. Squaric acid analogues were synthesized and explored, with phenyl-substituted compounds showing the best inhibition effect. Deeper insights into their mechanisms of action were gained, and a single point mutation in the atpB gene responsible for ATP synthase subunit a was validated as the molecular basis of resistance to squaramides. The study also highlights the potential synergy between squaramides and clofazimine, providing a promising avenue for enhancing the effectiveness of existing treatments.
BIOORGANIC & MEDICINAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Remi Coulon, Barbora Papouskova, Elmira Mohammadi, Michal Otyepka, Sreekar Wunnava, Jiri Sponer, Judit E. Sponer
Summary: 3',5'-Cyclic nucleotides play a fundamental role in modern biochemical processes and may have played a central role in the origin of early terrestrial life. A formamide-based systems chemistry could explain their availability on early Earth, as demonstrated by the formation of 3',5'-cyclic nucleotides in liquid formamide environments at elevated temperatures.
Article
Chemistry, Physical
Rabindranath Lo, Martin Pykal, Andreas Schneemann, Radek Zboril, Roland A. Fischer, Kolleboyina Jayaramulu, Michal Otyepka
Summary: Covalent hybrids of graphene and metal-organic frameworks (MOFs) have great potential in various technologies, especially catalysis and energy applications, due to their combination of conductivity and porosity. The formation of an amide bond between carboxylate-functionalized graphene acid (GA) and amine-functionalized UiO-66-NH2 MOF is an efficient strategy for creating such hybrids. This study used density functional theory (DFT) calculations to elucidate the mechanism of amide bond formation between GA and UiO-66-NH2, highlighting the crucial role of zirconium within UiO-66 as a catalyst. Insight into the binding interactions between graphene derivatives and MOFs can lead to tailored synthesis strategies for these nanocomposite materials.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Multidisciplinary
Yang Qiuyue, Emily P. Nguyen, David Panacek, Veronika Sedajova, Vitezslav Hruby, Giulio Rosati, de Carvalho Castro Silva Cecilia, Aristides Bakandritsos, Michal Otyepka, Arben Merkoci
Summary: Heavy metal pollutants are highly toxic and pose great concern in environmental monitoring. Electrochemical detection, hindered by mutual interferences of heavy metal ions, is a main technique with limited sensitivity to Cd2+ ions. This study introduces a metal-free and sustainable nanomaterial, cysteamine covalently functionalized graphene (GSH), which significantly enhances the sensitivity of screen-printed carbon electrode (SPCE) to Cd2+ ions while maintaining sensitivity to other heavy metals. The enhancement is attributed to the grafted thiols on the GSH sheets with strong affinity to Cd2+ ions, based on Pearson's principle. The GSH-modified SPCE also exhibits high reusability and outperforms existing SPCEs modified by non-covalently functionalized graphene derivatives. The GSH-SPCE is successfully validated in tap water.
Article
Chemistry, Physical
Vojtech Mlynsky, Petra Kuhrova, Petr Stadlbauer, Miroslav Krepl, Michal Otyepka, Pavel Banas, Jiri Sponer
Summary: Molecular dynamics simulations are commonly used to study RNA molecules. By adjusting the nonbonded parameters, the widely used AMBER OL3 ff in RNA simulations can be improved. The modified simulations show better agreement with experimental results.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biochemistry & Molecular Biology
Anna Spackova, Ondrej Vavra, Tomas Racek, Vaclav Bazgier, David Sehnal, Jiri Damborsky, Radka Svobodova, David Bednar, Karel Berka
Summary: ChannelsDB 2.0 is an updated database that provides structural information about the position, geometry, and physicochemical properties of protein channels and pores. It incorporates data calculated by CAVER and MOLE tools, as well as additional information from AlphaFill database, resulting in significantly expanded channel annotations. The database stores information such as geometrical features and physico-chemical properties based on channel-lining amino acids, and is interlinked with UniProt mutation annotation data. ChannelsDB 2.0 serves as an important resource for in-depth analysis of the role of biomacromolecular tunnels and pores.
NUCLEIC ACIDS RESEARCH
(2023)