This protocol describes the application of atomic force microscopy for structural analysis of prokaryotic and organellar nucleoids. It is based on a simple cell manipulation procedure that enables stepwise dissection of the nucleoid. The procedure includes (i) on-substrate lysis of cells and (ii) enzyme treatment, followed by atomic force microscopy. This type of dissection analysis permits analysis of nucleoid structure ranging from the fundamental units assembled on DNA to higher-order levels of organization. The combination with molecular-genetic and biochemical techniques further permits analysis of the functions of key nucleoid factors relevant to signal-induced structural reorganization or building up of basic structures, as seen for Dps in Escherichia coli and TrmBL2 in Thermococcus kodakarensis. These systems are described here as examples of the successful application of AFM for this purpose. Moreover, we describe the procedures needed for quantitative analysis of the data.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-0716-3930-6_13 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Co-Atomic Interface Minimizing Charge Transfer Barrier in Polytypic Perovskites for CO Photoreduction.
Adv Sci (Weinh)
January 2025
School of Resources and Environment, University of Electronic Science and Technology of China, Chengdu, 611731, China.
Heterojunctions, known for their decent separation of photo-generated electrons and holes, are promising for photocatalytic CO reduction. However, a significant obstacle in traditional post-assembled heterojunctions is the high interfacial barrier for charge transfer caused by atomic lattice mismatch at multiphase interfaces. Here, as research prototypes, the study creates a lattice-matched co-atomic interface within CsPbBr-CsPbBr polytypic nanocrystals (113-125 PNs) through the proposed in situ hybrid strategy to elucidate the underlying charge transfer mechanism within this unique interface.
View Article and Find Full Text PDFAnalyzing Atomic Interactions in Molecules as Learned by Neural Networks.
J Chem Theory Comput
January 2025
BIFOLD─Berlin Institute for the Foundations of Learning and Data, 10587 Berlin, Germany.
While machine learning (ML) models have been able to achieve unprecedented accuracies across various prediction tasks in quantum chemistry, it is now apparent that accuracy on a test set alone is not a guarantee for robust chemical modeling such as stable molecular dynamics (MD). To go beyond accuracy, we use explainable artificial intelligence (XAI) techniques to develop a general analysis framework for atomic interactions and apply it to the SchNet and PaiNN neural network models. We compare these interactions with a set of fundamental chemical principles to understand how well the models have learned the underlying physicochemical concepts from the data.
View Article and Find Full Text PDFEpoxy-Affixed ZIF-8/CS/Cellulase: a Sustainable Approach for Hydrolysis of Agricultural Waste to Reducing Sugars.
Appl Biochem Biotechnol
January 2025
Department of Botany, Maharshi Dayanand University, Rohtak, 124001, India.
Cellulase was effectively immobilized onto an epoxy-bound chitosan-modified zinc metal-organic framework (epoxy/ZIF-8/CS/cellulase) support, yielding a conjugation rate of 0.64 ± 0.02 mg/cm2 and retaining 80.
View Article and Find Full Text PDFMechanical Properties of Eye Lens Cortical and Nuclear Membranes and the Whole Lens.
Invest Ophthalmol Vis Sci
January 2025
Department of Physics, Boise State University, Boise, Idaho, United States.
Purpose: To elucidate the mechanical properties of the bovine lens cortical membrane (CM), the nuclear membrane (NM) containing cholesterol bilayer domains (CBDs), and whole bovine lenses.
Methods: The total lipids (lipids plus cholesterol) from the cortex and nucleus of a single bovine lens were isolated using the monophasic methanol extraction method. Supported CMs and NMs were prepared from total lipids extracted from the cortex and nucleus, respectively, using a rapid solvent exchange method and probe-tip sonication, followed by the fusion of unilamellar vesicles on a flat, freshly cleaved mica surface.
Nanoscale Titanium Oxide Memristive Structures for Neuromorphic Applications: Atomic Force Anodization Techniques, Modeling, Chemical Composition, and Resistive Switching Properties.
Nanomaterials (Basel)
January 2025
Research Laboratory Neuroelectronics and Memristive Nanomaterials (NEUROMENA Lab), Institute of Nanotechnologies, Electronics and Electronic Equipment Engineering, Southern Federal University, Taganrog 347922, Russia.
This paper presents the results of a study on the formation of nanostructures of electrochemical titanium oxide for neuromorphic applications. Three anodization synthesis techniques were considered to allow the formation of structures with different sizes and productivity: nanodot, lateral, and imprint. The mathematical model allowed us to calculate the processes of oxygen ion transfer to the reaction zone; the growth of the nanostructure due to the oxidation of the titanium film; and the formation of TiO, TiO, and TiO oxides in the volume of the growing nanostructure and the redistribution of oxygen vacancies and conduction channel.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!