Article
Polymer Science
Gabriela S. Garcia-Briones, Richard Laga, Zulfiya Cernochova, Carely Arjona-Ruiz, Olga Janouskova, Miroslav Slouf, Ognen Pop-Georgievski, Dana Kubies
Summary: Polyelectrolyte nanoparticles (NPs) have been investigated as carriers for protein delivery. The formation of these NPs was studied using a newly synthesized polycationic diblock copolymer and heparin without the use of additives. The encapsulation of heparin-binding proteins achieved high entrapment efficiency and increased protein stability. The released proteins exhibited sustained release and preserved bioactivity. The NPs showed noncytotoxic performance, making them promising candidates for controlled delivery of bioactive proteins in biomedical applications.
EUROPEAN POLYMER JOURNAL
(2023)
Article
Chemistry, Analytical
Luke T. Richardson, Elizabeth K. Neumann, Richard M. Caprioli, Jeffrey M. Spraggins, Touradj Solouki
Summary: This study extends the capabilities of RKMD analysis for lipid annotation and chemical structure-based filtering in IMS datasets. The method allows for image reconstruction and visualization based on lipid features such as molecular class, carbon chain length, and degree of unsaturation. The results demonstrate that the RKMD method is highly specific for lipid components in the presence of confounding background ions.
ANALYTICAL CHEMISTRY
(2022)
Article
Polymer Science
Yu-Min Wang, Anna Kalosi, Yuriy Halahovets, Iryna Romanenko, Jiri Slaby, Jiri Homola, Jan Svoboda, Andres de los Santos Pereira, Ognen Pop-Georgievski
Summary: This study compared the anti-fouling properties of poly(HPMA) brushes prepared by chemisorption and surface-initiated polymerization methods, finding that the latter exhibited better anti-fouling performance due to higher grafting density.
Article
Chemistry, Multidisciplinary
Helene Pizzala, Magalie Claeys-Bruno, Valerie Monnier, Michelle Sergent, Laurence Charles
Summary: MALDI is a popular ionization technique for mass spectrometry of synthetic polymers, but reliable prediction for the optimal matrix/analyte/salt system is still not possible. Despite challenges, successful MALDI of an amphiphilic copolymer composed of PEO and PS segments was achieved for the first time through experimental design and analysis.
FRONTIERS IN CHEMISTRY
(2021)
Article
Polymer Science
Petr Salek, Daniela Zborilova, Ewa Pavlova, Olga Kockova, Rafal Konefal, Zuzana Moravkova, Olga Janouskova
Summary: In this study, a dispersion polymerization method was developed to prepare cross-linked poly[N-(2-hydroxypropyl) methacrylamide] (PHPMA)-based nanogels. The nanogels were characterized for their size, particle size distribution, morphology, and structure. The biocompatibility of the nanogels was tested using rat mesenchymal stem cells (rMSC) and human foreskin fibroblasts (BJ). The results showed that the nanogels were well-distributed in the cytosol and taken up into lysosomes.
JOURNAL OF APPLIED POLYMER SCIENCE
(2023)
Article
Engineering, Biomedical
Yanan Shi, Miaomiao Yin, Yina Song, Tengteng Wang, Shiqi Guo, Xuemei Zhang, Kaoxiang Sun, Youxin Li
Summary: Delivery of peptides or protein drugs via oral route is challenging, but nanoparticles containing chitosan and pHPMA have shown potential for improving the bioavailability of liraglutide. By introducing CSK and HA(2) into the particles, the oral bioavailability of liraglutide can be significantly enhanced, making them a promising option for oral administration of peptides and proteins.
JOURNAL OF BIOMATERIALS APPLICATIONS
(2021)
Article
Chemistry, Medicinal
Junhai Yang, Lauren Rendino, Steven Cassar, Wayne Buck, James Sawicki, Nari Talaty, David Wagner
Summary: The utility of zebrafish is increasing due to its cost-effectiveness and similarity to humans. Obtaining good quality zebrafish larvae sections for batch samples is challenging, but optimized fresh frozen sectioning using gelatin solutions can improve mass spectrometry imaging. The optimized method ensures well-preserved morphology and consistent sectioning of the larvae.
Article
Chemistry, Physical
Daniel Horak, Karolina Turnovcova, Zdenek Plichta, Dana Marekova, Vladimir Proks, Radek Kaiser, David Netuka, Pavla Jendelova
Summary: In this study, a block copolymer consisting of PHP and PMAH was synthesized and conjugated with Dox and/or RGDS targeting peptide to create nanoparticles that can reduce glioblastoma tumor growth. The nanoparticles were found to effectively decrease tumor size and induce more apoptosis in treated cells compared to untreated cells.
COLLOID AND POLYMER SCIENCE
(2022)
Article
Biochemical Research Methods
Michiel Vandenbosch, Sylvia P. Nauta, Anastasiya Svirkova, Martijn Poeze, Ron M. A. Heeren, Tiffany Porta Siegel, Eva Cuypers, Martina Marchetti-Deschmann
Summary: In this study, the sample preparation protocol for undecalcified bone samples was optimized for targeted and untargeted applications in forensic and preclinical research. The combination of gelatin and carboxymethyl cellulose (CMC) was found to best support the bone tissue during sectioning. Different cutting methods were successfully applied to rat, mouse, and human bone samples, demonstrating the versatility of the developed sectioning method. The detection of targeted substances (methadone and EDDP) and untargeted substances (unknown lipids) was achieved using specific matrix materials, showcasing the potential for future forensic and preclinical investigations.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Engineering, Biomedical
Qi Li, Zhuoran Jiang, Liang Ma, Jun Yin, Ziqi Gao, Luqi Shen, Huayong Yang, Zhanfeng Cui, Hua Ye, Hongzhao Zhou
Summary: This study presents a new embedding medium with adjustable thermoresponsive rheological properties to address the limitations of conventional bioprinting. The proposed medium allows for the freeform writing of complex tubular structures with high shape fidelity and cell viability. It is compatible with multiple bioinks and crosslinking methods, demonstrating its potential in heterogeneous tissue regeneration.
Article
Materials Science, Multidisciplinary
Niklas Huber, Masis Sirim, Zhuangfei Qian, Calum T. J. Ferguson, Wenxin Wei, Kai A. I. Zhang
Summary: The use of polymeric photocatalytic materials for the visible light driven conversion of organic substances in environmentally friendly reaction media, especially in water, has attracted much attention recently. However, most current conjugated polymer photocatalysts are not suitable for applications in water due to their hydrophobic nature. In this study, water-compatible poly(methyl methacrylate) (PMMA)-based polymer photocatalysts were designed by controlling the comonomers with specific functions. The properties and water compatibility of PMMA photocatalysts could be tuned by the monomer composition. The photocatalytic degradation of various contaminants in water was successfully conducted using the PMMA photocatalysts.
ACS APPLIED POLYMER MATERIALS
(2022)
Article
Engineering, Biomedical
Sarah R. Brady, Simone B. Gohsman, Keven Sepulveda, Jessica D. Weaver
Summary: Hydrogel injection molding is a useful biofabrication method for rapidly generating complex cell-laden hydrogel structures in tissue engineering applications. This study explores the feasibility of using synthetic PEG-based hydrogels functionalized with strain promoted azide-alkyne cycloaddition click chemistry groups for injection molding. Mechanical properties, such as gelation time and successful generation of complex geometries, as well as the binding and retention of adhesive ligand RGD and cell viability and function, are evaluated. The results demonstrate the potential utility of injection molding synthetic PEG-based hydrogels in tissue engineering applications and biomanufacturing.
JOURNAL OF BIOMEDICAL MATERIALS RESEARCH PART A
(2023)
Article
Biotechnology & Applied Microbiology
Hangjun Huang, Haiqiang Liu, Weiwei Ma, Liang Qin, Lulu Chen, Hua Guo, Hualei Xu, Jinrong Li, Chenyu Yang, Hao Hu, Ran Wu, Difan Chen, Jinchao Feng, Yijun Zhou, Junli Wang, Xiaodong Wang
Summary: A novel metabolomics analysis technique called MALDI-MSI-PTMA was developed to detect and image metabolites from plant tissues. This technique overcomes the limitation of intact plant tissues by homogenizing plant tissues, preparing PTMA moulds, and spraying matrix on PTMA sections. The technique has advantages such as no need of sample separation and enrichment, high-throughput metabolite detection and imaging, high-stability mass spectrometry data acquisition and imaging reconstruction, and high reproducibility of data.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Pharmacology & Pharmacy
Yamini Bobde, Milan Paul, Tarun Patel, Swati Biswas, Balaram Ghosh
Summary: Delivery of combination chemotherapeutic agents to tumors using nanovesicles shows promise for enhanced tumor suppression and reduced toxicity. These novel micelles exhibit improved anti-tumor efficacy and cytotoxicity, with higher induction of apoptosis and cellular arrest in G2 and S phase compared to traditional drugs.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2021)
Article
Chemistry, Multidisciplinary
Ethan Yang, Xinyi Elaine Shen, Hoku West-Foyle, Tae-Hun Hahm, Maxime A. Siegler, Dalton R. Brown, Cole C. Johnson, Jeong Hee Kim, LaToya Ann Roker, Caitlin M. Tressler, Ishan Barman, Scot C. Kuo, Kristine Glunde
Summary: The authors report that co-crystallization of fluorophores with MALDI imaging matrices significantly enhances fluorophore brightness, enabling the amplification of innate tissue autofluorescence. This allows the development of FluoMALDI, which combines fluorescence microscopy and MALDI imaging to image the same biological sample. FluoMALDI has demonstrated the feasibility of imaging with endogenous and exogenous fluorophores, as well as autofluorescence-based imaging of brain and kidney tissue sections.
Article
Allergy
Veronika Kanderova, Tamara Svobodova, Simon Borna, Martina Fejtkova, Vendula Martinu, Jana Paderova, Michael Svaton, Jarmila Kralova, Eva Fronkova, Adam Klocperk, Stepanka Pruhova, Min Ae Lee-Kirsch, Ludmila Hornofova, Miroslav Koblizek, Petr Novak, Olga Zimmermannova, Zuzana Parackova, Anna Sediva, Tomas Kalina, Ales Janda, Jana Kayserova, Marcela Dvorakova, Milan Macek, Petr Pohunek, Petr Sedlacek, Ashleigh Poh, Matthias Ernst, Tomas Brdicka, Ondrej Hrusak, Jan Lebl
Summary: This article reports a new monogenic autoinflammatory disorder caused by a de novo activating mutation in the HCK gene, characterized by cutaneous vasculitis and chronic pulmonary inflammation. The study shows the aberrant functions of mutant HCK and the therapeutic efficacy of the Janus kinase 1/2 inhibitor Ruxolitinib in treating inflammatory lung disease.
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2022)
Article
Chemistry, Analytical
Marek Polak, Ghazaleh Yassaghi, Daniel Kavan, Frantisek Filandr, Jan Fiala, Zdenek Kukacka, Petr Halada, Dmitry S. Loginov, Petr Novak
Summary: The combination of covalent labeling techniques with mass spectrometry is a progressive approach for studying protein surfaces and protein-ligand interactions. In this study, the interaction interface between the DNA binding domain of the FOXO4 protein and the DNA binding element was mapped. Different approaches were used to confirm the results and compare with other studies, showing consistent findings. This method is important for understanding the structure and dynamics of protein-DNA interactions.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Dmitry S. Loginov, Jan Fiala, Peter Brechlin, Gary Kruppa, Petr Novak
Summary: Structural mass spectrometry methods, particularly FPOP, are widely used for studying protein structure and dynamics. In this study, FPOP analysis of the Hb-Hp complex revealed specific residues affected by the complex formation and provided insights into the interacting amino acids. The data, available via ProteomeXchange, can be further utilized for investigating protein-protein interactions.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2022)
Review
Spectroscopy
Rutuja H. Patil, Dominika Luptakova, Vladimir Havlicek
Summary: Infection metallomics is a mass spectrometry platform that utilizes microbial metallophores as specific biomarkers for invasive infectious diseases. It has potential applications in diagnosis and treatment of infections, and shows promising prospects in the post-COVID era.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Chemistry, Analytical
Ghazaleh Yassaghi, Zdenek Kukacka, Jan Fiala, Daniel Kavan, Petr Halada, Michael Volny, Petr Novak
Summary: Fast photochemical oxidation of proteins (FPOP) footprinting is a method that uses chemical reactions to label protein structures. It provides information about protein conformation, dynamics, and interactions. FPOP samples can be analyzed using either bottom-up or top-down mass spectrometry approaches. The top-down approach allows for more specific selection of protein subpopulations, but is limited to smaller proteins. Comparison with bottom-up data confirms the usefulness of the top-down approach in oxidative protein footprinting.
ANALYTICAL CHEMISTRY
(2022)
Article
Microbiology
Radim Dobias, Petr Jahn, Katarina Tothova, Olga Dobesova, Denisa Visnovska, Rutuja Patil, Anton Skriba, Pavla Jaworska, Misa Skoric, Libor Podojil, Michaela Kantorova, Jakub Mrazek, Eva Krejci, David A. Stevens, Vladimir Havlicek
Summary: Invasive pulmonary aspergillosis (IPA) can be a rare cause of granulomatous pneumonia in horses. This study highlights the importance of direct diagnostic tools for horses, such as bronchoalveolar lavage fluid (BALF) and serum samples analysis. The results show significant differences in the levels of Aspergillus spp. DNA, fungal galactomannan (GM), ferricrocin (Fc), triacetylfusarinin C (TafC), and gliotoxin (Gtx) in BALF samples from healthy controls, IPA cases, and horses with equine asthma.
Letter
Hematology
Natividad Alquezar-Artieda, Daniela Kuzilkova, Jennie Roberts, Katerina Hlozkova, Alena Pecinova, Petr Pecina, Martina Zwyrtkova, Eliska Potuckova, Daniel Kavan, Ivana Hermanova, Marketa Zaliova, Petr Novak, Tomas Mracek, Lucie Sramkova, Daniel A. Tennant, Jan Trka, Julia Starkova
Article
Multidisciplinary Sciences
Pieter-Jan Vermeire, Anastasia V. Lilina, Hani M. Hashim, Lada Dlabolova, Jan Fiala, Steven Beelen, Zdenek Kukacka, Jeremy N. Harvey, Petr Novak, Sergei V. Strelkov
Summary: Intermediate filaments (IFs) are essential components of the metazoan cytoskeleton and can self-assemble from soluble tetrameric species into typical 10-12 nm wide filaments. The molecular structure of mature IFs is poorly understood, but this study reveals that the formation of tetramers is dependent on the presence of the coil1A domain and is synergistically stabilized by interactions between coil1B domains, coil1A, coil2, and the head and rod domains. Additionally, small-angle X-ray scattering experiments show that elongated A(11) tetramers are dominant in low ionic strength solutions with structural flexibility in the terminal domains.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Josef Dvorak, Jana Novakova, Lucie Kraftova, Vendula Studentova, Martin Matejovic, Jaroslav Radej, Thomas Karvunidis, Jan Horak, Marcela Kralovcova, Jaroslav Hrabak, Zuzana Kalaninova, Michael Volny, Petr Novak, Petr Pompach
Summary: A rapid PCT detection method using MALDI-TOF mass spectrometry was developed and validated against LC-MS bottom-up workflow. The new method detects intact PCT and uncovers its alterations in septic patients' serum.
CLINICAL PROTEOMICS
(2023)
Article
Ecology
Brennen Heames, Filip Buchel, Margaux Aubel, Vyacheslav Tretyachenko, Dmitry Loginov, Petr Novak, Andreas Lange, Erich Bornberg-Bauer, Klara Hlouchova
Summary: A comparison between de novo genes and synthetic random sequences reveals no difference in biophysical properties, but in vitro expression demonstrates de novo proteins' higher solubility, indicating their better integration into the cellular system. The emergence of de novo genes provides a pathway for the formation of new proteins from previously non-coding DNA. While the likelihood of assuming a soluble and stable tertiary structure in de novo proteins remains unclear, evidence suggests that native-like biophysical properties are abundant in sequence space. Experimental characterization of putative de novo proteins in human and fly shows that their solubility and structure propensity are moderately higher compared to synthetic random proteins. The DnaK chaperone system further enhances the solubility of de novo proteins. Therefore, de novo proteins may be better integrated into the cellular system than random sequences due to their higher solubility.
NATURE ECOLOGY & EVOLUTION
(2023)
Review
Infectious Diseases
Radim Dobias, David A. Stevens, Vladimir Havlicek
Summary: Aspergillus fumigatus is a critical priority fungal pathogen identified by the World Health Organization. Commercially available diagnostics for various forms of aspergillosis often rely on fungal metabolites, including intracellular molecules, cell wall components, and extracellular secretomes. This review highlights the limitations of antibody tests compared to tests of fungal products in body fluids, and discusses the application of beta-D-glucan, galactomannan, and pentraxin 3 in bronchoalveolar lavage fluids. It also explores the detection of nucleic acids, next-generation sequencing, and recent studies on Aspergillus metallophores.
Article
Chemistry, Analytical
Marek Polak, Michael Palasser, Alan Kadek, Daniel Kavan, Christopher A. Wootton, Marc-Andre Delsuc, Kathrin Breuker, Petr Novak, Maria A. van Agthoven
Summary: Two-dimensional mass spectrometry (2D MS) is a multiplexed tandem mass spectrometry method that uses modulation of precursor ion radii to show the fragmentation patterns of analytes. This study introduces quadrupolar detection in 2D MS and discusses its advantages, as well as adapts existing data processing techniques for accurate frequency-to-mass conversion. The method is applied to the top-down analysis of covalently labeled ubiquitin and the label-free relative quantification of biomolecule isoforms.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Thomas Lambert, Marius Gramlich, Luisa Stutzke, Luke Smith, Dingyu Deng, Philipp D. Kaiser, Ulrich Rothbauer, Justin L. P. Benesch, Cornelia Wagner, Maximiliane Koenig, Petr Pompach, Petr Novak, Anne Zeck, Kasper D. Rand
Summary: Protein glycosylation is a common protein modification, but determining the HDX of glycosylated protein segments has been challenging. In this study, we developed a column containing PNGase Rc that can be integrated into a conventional HDX-MS setup to improve glycoprotein analysis. The PNGase Rc column enables efficient online removal of N-linked glycans and determination of glycosylated regions' HDX in complex glycoproteins. We also demonstrated the column's use in mapping the binding epitope of a mAb to c-Met, a complex glycoprotein drug target. Overall, our work shows that HDX-MS with the integrated PNGase Rc column allows fast and efficient deglycosylation under harsh quench conditions and provides comprehensive analysis of complex glycoproteins.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Eliska Koutna, Vanda Lux, Tomas Kouba, Jana Skerlova, Jiri Novacek, Pavel Srb, Rozalie Hexnerova, Hana Svachova, Zdenek Kukacka, Petr Novak, Milan Fabry, Simon Poepsel, Vaclav Veverka
Summary: This study reports the ability of the PWWP domain of transcriptional coactivator LEDGF to bind to specific histone modifications and reveals the role of the intrinsically disordered region in nucleosome binding. The interplay between the H3K36 methylation reader and protein binding module of LEDGF facilitates productive transcription elongation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Jessica P. Burns, Christopher Wilding, Lukas Krasny, Xixuan Zhu, Madhumeeta Chadha, Yuen Bun Tam, P. S. H. Hari, Aswanth Mahalingam, Alexander T. J. Lee, Amani Arthur, Nafia Guljar, Emma Perkins, Valeriya Pankova, Andrew Jenks, Vanessa Djabatey, Cornelia Szecsei, Frank McCarthy, Chanthirika Ragulan, Martina I. Milighetti, Theodoros Roumeliotis, Stephen Crosier, Martina S. Finetti, Jyoti Choudhary, Ian Judson, Cyril F. Fisher, Eugene Schuster, Anguraj W. Sadanandam, Tom Chen, Daniel Williamson, Khin L. Thway, Robin Jones, Maggie C. U. H. Cheang, Paul Huang
Summary: This study conducted comprehensive proteomic profiling of tumor specimens from 321 STS patients and identified three proteomic subtypes within leiomyosarcomas with distinct myogenesis and immune features, anatomical site distribution and survival outcomes. The complement cascade is suggested as a candidate immunotherapeutic target for undifferentiated pleomorphic sarcomas and dedifferentiated liposarcomas. The study also defines functional signatures called Sarcoma Proteomic Modules that are independent prognostic factors for distant metastasis.
NATURE COMMUNICATIONS
(2023)
