Article
Biochemistry & Molecular Biology
Liubov Dadinova, Roman Kamyshinsky, Yury Chesnokov, Andrey Mozhaev, Vladimir Matveev, Andrey Gruzinov, Alexander Vasiliev, Eleonora Shtykova
Summary: Two independent methods, SAXS and cryo-EM, were used to investigate the effect of Mg2+ and Fe2+ cations on the Dps-DNA complex structure. It was found that Mg2+ ions block the interaction between Dps and DNA, while the presence of Fe2+ leads to complex destruction and aggregation without restoration. Cryo-EM analysis also revealed the presence of iron nanoparticles inside the Dps cavity next to acidic pore.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Christine Browne, Vikram Singh Raghuwanshi, Maoqi Lin, Gil Garnier, Warren Batchelor
Summary: The combination of rheology and SAXS measurements can effectively characterize and select the type of CNCs materials. CNC1 is more suited for applications requiring highly ordered structures, while CNC2 is suitable for applications requiring viscosity control. Effective characterization of CNCs prior to use is crucial in selecting the appropriate properties for desired applications.
COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS
(2022)
Article
Chemistry, Multidisciplinary
Michal Hammel, Yuchen Fan, Apoorva Sarode, Amy E. Byrnes, Nanzhi Zang, Ponien Kou, Karthik Nagapudi, Dennis Leung, Casper C. Hoogenraad, Tao Chen, Chun-Wan Yen, Greg L. Hura
Summary: Using a high-throughput screening method combined with structural analysis and gene silencing assessment, we found that PEG-lipids can modify the core organization of ASO-loaded LNPs, affecting their gene silencing activity.
Article
Biochemistry & Molecular Biology
Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis
Summary: REBASE is a comprehensive database of information about restriction-modification (RM) system components, providing details on recognition and cleavage sites for restriction enzymes and DNA methyltransferases, their commercial availability, sensitivity to methylation, crystal and sequence data. The database is regularly updated and can be accessed through a website and FTP.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Physical
Navdeep Rana, Aditya Prasad Roy, Dipanshu Bansal, Gopal Dixit
Summary: This study demonstrates that inelastic scattering methods, combined with theoretical simulation, can image lattice dynamics similar to time-resolved diffraction and imaging measurements. The proposed method is useful for imaging in-situ lattice dynamics under different environmental conditions, and will have a profound impact in cases where time-resolved diffraction within the pump-probe setup is not feasible.
NPJ COMPUTATIONAL MATERIALS
(2021)
Article
Chemistry, Multidisciplinary
Matthias Filez, Martin Vesely, Ivan Garcia-Torregrosa, Marianna Gambino, Oezguen Attila, Florian Meirer, Eugene A. Katrukha, Maarten B. J. Roeffaers, Jan Garrevoet, Lukas C. Kapitein, Bert M. Weckhuysen
Summary: The study revealed the dynamic process of hierarchical porosity formation within a zeolite ZSM-5 crystal, showing that pores initiate at the crystal surface and propagate to the crystal core with decreasing rate. Additionally, hierarchical porosity only establishes in specific subunits which constitute ZSM-5, indicating that the spacedependent meso- and macroporosity within a zeolite crystal may lead to local discrepancies in diffusion, performance, and deactivation behaviors.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Review
Chemistry, Multidisciplinary
Rongxiu Zhai, Bin Fang, Yaqi Lai, Bo Peng, Hua Bai, Xiaowang Liu, Lin Li, Wei Huang
Summary: Mitochondria play an essential role in the development of diseases and cellular metabolism disorders. Super-resolution imaging is crucial for studying the ultrafine structures and functions of mitochondria. Small-molecule fluorogenic probes have unique properties that make them ideal for super-resolution imaging of mitochondria. This paper summarizes recent advances in small-molecule fluorogenic probes, focusing on their chemical and spectroscopic properties for mitochondrial imaging. Future challenges in this field, including the design principles of small-molecule fluorogenic probes and nanoscopic techniques, are also discussed.
CHEMICAL SOCIETY REVIEWS
(2023)
Article
Materials Science, Multidisciplinary
Hirokazu Sasaki, Shunta Akiya, Yojiro Oba, Masato Onuma, A. D. Giddings, Tadakatsu Ohkubo
Summary: The strengthening effect of Cu-Ni-Si alloy by dispersing Ni-Si-based compound as a precipitate was investigated through various analytical methods, including transmission electron microscopy, small-angle X-ray scattering, small-angle neutron scattering, and atom probe tomography. The results showed that the precipitated phase became coarser with increasing aging temperature, providing insights into the diffusion layer at the interface between the Cu parent phase and the precipitated phase.
MATERIALS TRANSACTIONS
(2021)
Article
Pharmacology & Pharmacy
Celine Jaudoin, Maria Maue Gehrke, Isabelle Grillo, Fabrice Cousin, Malika Ouldali, Ana-Andreea Arteni, Evelyne Ferrary, Florence Siepmann, Juergen Siepmann, Fanny Simeliere, Amelie Bochot, Florence Agnely
Summary: Mixtures of hyaluronic acid and liposomes with high lipid concentration have great potential in drug delivery. The characteristics of liposomes, including their surface and size, influence their release from these hybrid systems. Various techniques were used to characterize the liposomes, and it was found that both size and surface properties governed liposome release, with multiple mechanisms involved.
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2023)
Article
Chemistry, Physical
Meltem Bayrak, Jitendra Mata, Jared K. Raynes, Mark Greaves, Jacinta White, Charlotte E. Conn, Juliane Floury, Amy Logan
Summary: This study investigated the structural devolution of RG and TG gels during simulated gastric digestion, finding that gel firmness and disintegration behavior are closely related. Gel firmness and brittleness were greater in D2O samples compared to H2O.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2021)
Review
Chemistry, Analytical
Seema Thakral, Kyungtae Kim
Summary: Small-angle scattering (SAS) is a versatile analytical technique that provides detailed structural information at the nanometer scale. It has diverse applications in pharmaceutical material characterization, including identification of liquid-crystalline mesophase of drugs, study of excipient microstructure influence, and optimization of solid dispersions and protein-based therapeutics formulations.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Alessandra Gianoncelli, Katarina Vogel-Mikus, Murielle Salome, Ernesto Pascotto, Giuseppe Ricci, Lorella Pascolo
Summary: Although cryogenic conditions are ideal for single-cell and plant analyses, it is still challenging to cryo-fix human or animal soft tissue for X-ray fluorescence analysis. In this study, we compare and discuss the analysis of bovine ovarian tissues under cryogenic or room temperature conditions, with the latter being either chemically fixed or freeze-dried.
JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Eugen Mircea Anitas
Summary: The fractal characteristics of DNA sequences are studied using the frequency chaos game representation (FCGR) and small-angle scattering (SAS) technique. The FCGR allows representation of the frequencies of occurrence of k-mers (oligonucleotides of length k) in the form of images. The numerically encoded data are then used in a SAS analysis to enhance hidden features in DNA sequences. It is shown that the simulated SAS intensity allows us to obtain the fractal dimensions and scaling factors at various scales. These structural parameters can be used to distinguish unambiguously between the scaling properties of complex hierarchical DNA sequences. The validity of this approach is illustrated on several sequences from: Escherichia coli, Mouse mitochondrion, Homo sapiens mitochondrion and Human cosmid.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Applied
Rajath Alexander, Amit Kaushal, Jyoti Prakash, P. T. Rao, Debasis Sen, Kinshuk Dasgupta
Summary: This study reports on how the S/Fe ratio in the feedstock controls the density and pore structure of self-assembled carbon nanotube aerogel in the floating catalyst chemical vapor deposition process. Decreasing the S/Fe ratio increases the density of the aerogel, while decreasing its porosity and increasing bundle dimensions. The study also found that the carbon nanotubes have a multi-walled structure and improved crystallinity with increasing S/Fe ratio. The formed aerogels were then converted into carbon nanotube fibers, achieving high electrical conductivity and tensile strength with an S/Fe ratio of 0.2.
JOURNAL OF POROUS MATERIALS
(2023)
Article
Biochemistry & Molecular Biology
Oscar E. Torres Montaguth, Stephen J. Cross, Kincaid W. A. Ingram, Laura Lee, Fiona M. Diffin, Mark D. Szczelkun
Summary: Mapping the precise position of DNA cleavage events is crucial in studying the mechanism and function of endonucleases. ENDO-Pore is a high-throughput nanopore-based method that allows time-resolved mapping of single molecule DNA cleavage events in vitro, enabling the analysis of different endonucleases and cleavage patterns.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Wojciech Potrzebowski, Ingemar Andre
Article
Biochemical Research Methods
Grzegorz Chojnowski, Tomasz Walen, Pawel Piatkowski, Wojciech Potrzebowski, Janusz M. Bujnicki
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2015)
Article
Biochemistry & Molecular Biology
Nisha Kanwar, Gareth A. Roberts, Laurie P. Cooper, Augoustinos S. Stephanou, David T. F. Dryden
NUCLEIC ACIDS RESEARCH
(2016)
Article
Multidisciplinary Sciences
Chih-Chao Liang, Zhuolun Li, David Lopez-Martinez, William V. Nicholson, Catherine Venien-Bryan, Martin A. Cohn
Nature Communications
(2016)
Article
Biochemistry & Molecular Biology
Laurie P. Cooper, Gareth A. Roberts, John H. White, Yvette A. Luyten, Edward K. M. Bower, Richard D. Morgan, Richard J. Roberts, Jodi A. Lindsay, David T. F. Dryden
NUCLEIC ACIDS RESEARCH
(2017)
Article
Biochemistry & Molecular Biology
Kai Chen, Marcel Reuter, Bansi Sanghvi, Gareth A. Roberts, Laurie P. Cooper, Matthew Tilling, Garry W. Blakely, David T. F. Dryden
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2014)
Article
Biophysics
Rita De Zorzi, William V. Nicholson, Jean-Michel Guigner, Francoise Erne-Brand, Henning Stahlberg, Catherine Venien-Bryan
BIOPHYSICAL JOURNAL
(2013)
Correction
Biophysics
R. De Zorzi, W. Nicholson, J. M. Guigner, F. Erne-Brand, H. Stahlberg, C. Benien-Bryan
BIOPHYSICAL JOURNAL
(2013)
Article
Biochemistry & Molecular Biology
Gareth A. Roberts, Kai Chen, Edward K. M. Bower, Julia Madrzak, Arcadia Woods, Amy M. Barker, Laurie P. Cooper, John H. White, Garry W. Blakely, Iain Manfield, David T. F. Dryden
Article
Biochemistry & Molecular Biology
Elzbieta Nowak, Wojciech Potrzebowski, Petr V. Konarev, Jason W. Rausch, Marion K. Bona, Dmitri I. Svergun, Janusz M. Bujnicki, Stuart F. J. Le Grice, Marcin Nowotny
NUCLEIC ACIDS RESEARCH
(2013)
Article
Biochemistry & Molecular Biology
Edward K. M. Bower, Laurie P. Cooper, Gareth A. Roberts, John H. White, Yvette Luyten, Richard D. Morgan, David T. F. Dryden
NUCLEIC ACIDS RESEARCH
(2018)
Article
Biochemical Research Methods
James E. N. Taylor, Anna Swiderska, G. Geoff Kneale
PROTEIN EXPRESSION AND PURIFICATION
(2013)
Article
Allergy
Martina S. Elias, Sheila C. Wright, Judit Remenyi, James C. Abbott, Susan E. Bray, Christian Cole, Sharon Edwards, Marek Gierlinski, Mateusz Glok, John A. McGrath, William V. Nicholson, Lavinia Paternoster, Alan R. Prescott, Sara Ten Have, Phillip D. Whitfield, Angus I. Lamond, Sara J. Brown
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2019)
Article
Cell Biology
Gareth A. Roberts, Burak Ozkan, Ivana Gachulincova, Michael R. O'Dwyer, Elisa Hall-Ponsele, Manoj Saxena, Philip J. Robinson, Abdenour Soufi
Summary: Through systematic mutagenesis mapping, it was found that OCT4 dynamically regulates chromatin accessibility during cell fate changes and pluripotency maintenance by interacting with nucleosomes. Stable interactions between OCT4 and nucleosomes are crucial for maintaining the accessibility of pluripotency enhancers in stem cells.
NATURE CELL BIOLOGY
(2021)
Article
Plant Sciences
Oliver Smith, William Nicholson, Logan Kistler, Emma Mace, Alan Clapham, Pamela Rose, Chris Stevens, Roselyn Ware, Siva Samavedam, Guy Barker, David Jordan, Dorian Q. Fuller, Robin G. Allaby