Browse
Submit Data
Databases
API
Help

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A new method for quantitative analysis of M13 bacteriophage by atomic force microscopy.

ABSTRACT: Quantitative analysis is essential for virus research, especially in determining the virus titer. The classical method plaque assay is time-consuming, complex, and difficult for the phages that cannot form apparent plaque on the solid medium. In order to realize rapid and effective detection, a new method combining atomic force microscopy (AFM) observation and mathematical calculation is established. In this research, M13 phages with an appropriate dilution ratio were observed and counted by AFM. Based on the counting results, the titer of M13 phages can be calculated simply through mathematical substitution. Instead of cultivating overnight in plaque assay, this new method can be implemented within a few hours. Moreover, it is a method that can achieve visualization for titer determination and have the potential to determine the phages that fail to form apparent plaque, which is significant in virus quantitative assessment.

SUBMITTER: Wu Y

PROVIDER: S-EPMC9293941 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A new method for quantitative analysis of M13 bacteriophage by atomic force microscopy.

Wu Yuting Y Liu Shuai S Liu Zhiwei Z Liu Bing B Du Bin B Tong Zhaoyang Z Xu Jianjie J

Synthetic and systems biotechnology 20220713 4

Quantitative analysis is essential for virus research, especially in determining the virus titer. The classical method plaque assay is time-consuming, complex, and difficult for the phages that cannot form apparent plaque on the solid medium. In order to realize rapid and effective detection, a new method combining atomic force microscopy (AFM) observation and mathematical calculation is established. In this research, M13 phages with an appropriate dilution ratio were observed and counted by AFM ...[more]

PMID: 35891946

Similar Datasets

Quantitative atomic force microscopy provides new insight into matrix vesicle mineralization.

Project description:Matrix vesicles (MVs) are a class of extracellular vesicles that initiate mineralization in cartilage, bone, and other vertebrate tissues by accumulating calcium ions (Ca2+) and inorganic phosphate (Pi) within their lumen and forming a nucleation core (NC). After further sequestration of Ca2+ and Pi, the NC transforms into crystalline complexes. Direct evidence of the existence of the NC and its maturation have been provided solely by analyses of dried samples. We isolated MVs from chicken embryo cartilage and used atomic force microscopy peak force quantitative nanomechanical property mapping (AFM-PFQNM) to measure the nanomechanical and morphological properties of individual MVs under both mineralizing (+Ca2+) and non-mineralizing (-Ca2+) fluid conditions. The elastic modulus of MVs significantly increased by 4-fold after incubation in mineralization buffer. From AFM mapping data, we inferred the morphological changes of MVs as mineralization progresses: prior to mineralization, a punctate feature, the NC, is present within MVs and this feature grows and stiffens during mineralization until it occupies most of the MV lumen. Dynamic light scattering showed a significant increase in hydrodynamic diameter and no change in the zeta potential of hydrated MVs after incubation with Ca2+. This validates that crystalline complexes, which are strongly negative relative to MVs, were forming within the lumen of MVs. These data were substantiated by transmission electron microscopy energy dispersive X-ray and Fourier transform infrared spectroscopic analyses of dried MVs, which provide evidence that the complexes increased in size, crystallinity, and Ca/P ratio within MVs during the mineralization process.

| S-EPMC7104627 | biostudies-literature

Atomic force microscopy analysis of the Acinetobacter baumannii bacteriophage AP22 lytic cycle.

Project description:BackgroundAcinetobacter baumannii is known for its ability to develop resistance to the major groups of antibiotics, form biofilms, and survive for long periods in hospital environments. The prevalence of infections caused by multidrug-resistant A. baumannii is a significant problem for the modern health care system, and application of lytic bacteriophages for controlling this pathogen may become a solution.Methodology/principal findingsIn this study, using atomic force microscopy (AFM) and microbiological assessment we have investigated A. baumannii bacteriophage AP22, which has been recently described. AFM has revealed the morphology of bacteriophage AP22, adsorbed on the surfaces of mica, graphite and host bacterial cells. Besides, morphological changes of bacteriophage AP22-infected A. baumannii cells were characterized at different stages of the lytic cycle, from phage adsorption to the cell lysis. The phage latent period, estimated from AFM was in good agreement with that obtained by microbiological methods (40 min). Bacteriophage AP22, whose head diameter is 62±1 nm and tail length is 88±9 nm, was shown to disperse A. baumannii aggregates and adsorb to the bacterial surface right from the first minute of their mutual incubation at 37°C.Conclusions/significanceHigh rate of bacteriophage AP22 specific adsorption and its ability to disperse bacterial aggregates make this phage very promising for biomedical antimicrobial applications. Complementing microbiological results with AFM data, we demonstrate an effective approach, which allows not only comparing independently obtained characteristics of the lytic cycle but also visualizing the infection process.

| S-EPMC3469531 | biostudies-literature

Quantitative determination of atomic buckling of silicene by atomic force microscopy.

Project description:The atomic buckling in 2D "Xenes" (such as silicene) fosters a plethora of exotic electronic properties such as a quantum spin Hall effect and could be engineered by external strain. Quantifying the buckling magnitude with subangstrom precision is, however, challenging, since epitaxially grown 2D layers exhibit complex restructurings coexisting on the surface. Here, we characterize using low-temperature (5 K) atomic force microscopy (AFM) with CO-terminated tips assisted by density functional theory (DFT) the structure and local symmetry of each prototypical silicene phase on Ag(111) as well as extended defects. Using force spectroscopy, we directly quantify the atomic buckling of these phases within 0.1-Å precision, obtaining corrugations in the 0.8- to 1.1-Å range. The derived band structures further confirm the absence of Dirac cones in any of the silicene phases due to the strong Ag-Si hybridization. Our method paves the way for future atomic-scale analysis of the interplay between structural and electronic properties in other emerging 2D Xenes.

| S-EPMC6955330 | biostudies-literature

Easy and direct method for calibrating atomic force microscopy lateral force measurements.

Project description:We have designed and tested a new, inexpensive, easy-to-make and easy-to-use calibration standard for atomic force microscopy (AFM) lateral force measurements. This new standard simply consists of a small glass fiber of known dimensions and Young's modulus, which is fixed at one end to a substrate and which can be bent laterally with the AFM tip at the other end. This standard has equal or less error than the commonly used method of using beam mechanics to determine a cantilever's lateral force constant. It is transferable, thus providing a universal tool for comparing the calibrations of different instruments. It does not require knowledge of the cantilever dimensions and composition or its tip height. This standard also allows direct conversion of the photodiode signal to force and, thus, circumvents the requirement for a sensor response (sensitivity) measurement.

| S-EPMC3018784 | biostudies-literature

Atomic force microscopy based nanoassay: a new method to study α-Synuclein-dopamine bioaffinity interactions.

Project description:Intrinsically Disordered Proteins (IDPs) are characterized by the lack of well-defined 3-D structure and show high conformational plasticity. For this reason, they are a strong challenge for the traditional characterization of structure, supramolecular assembly and biorecognition phenomena. We show here how the fine tuning of protein orientation on a surface turns useful in the reliable testing of biorecognition interactions of IDPs, in particular α-Synuclein. We exploited atomic force microscopy (AFM) for the selective, nanoscale confinement of α-Synuclein on gold to study the early stages of α-Synuclein aggregation and the effect of small molecules, like dopamine, on the aggregation process. Capitalizing on the high sensitivity of AFM topographic height measurements we determined, for the first time in the literature, the dissociation constant of dopamine-α-Synuclein adducts.

| S-EPMC4064358 | biostudies-literature

Interactions of bacteriophage T4 adhesin with selected lipopolysaccharides studied using atomic force microscopy.

Project description:The interaction between the T4 bacteriophage gp37 adhesin and the bacterial lipopolysaccharide (LPS) is a well-studied system, however, the affinity and strength of the interaction haven't been analyzed so far. Here, we use atomic force microscopy to determine the strength of the interaction between the adhesin and its receptor, namely LPS taken from a wild strain of E. coli B. As negative controls we used LPSs of E. coli O111:B and Hafnia alvei. To study the interaction an AFM tip modified with the gp37 adhesin was used to scan surfaces of mica covered with one of the three different LPSs. Using the correlation between the surface topography images and the tip-surface interaction we could verify the binding between the specific LPS and the tip in contrast to the very weak interaction between the tip and the non-binding LPSs. Using force spectroscopy we could then measure the binding strength by pulling on the AFM tip until it lifted off from the surface. The force necessary to break the interaction between gp37 and LPS from E. coli B, LPS from E. coli O111:B and LPS from H. alvei were measured to be 70 ± 29 pN, 46 ± 13 pN and 45 ± 14 pN, respectively. The latter values are likely partially due to non-specific interaction between the gp37 and the solid surface, as LPS from E. coli O111:B and LPS from H. alvei have been shown to not bind to gp37, which is confirmed by the low correlation between binding and topography for these samples.

| S-EPMC6053362 | biostudies-literature

Direct quantitative analysis of HCV RNA by atomic force microscopy without labeling or amplification.

Project description:Force-based atomic force microscopy (AFM) was used to detect HCV (hepatitis C virus) RNA directly and to quantitatively analyse it without the need for reverse transcription or amplification. Capture and detection DNA probes were designed. The former was spotted onto a substrate with a conventional microarrayer, and the latter was immobilized on an AFM probe. To control the spacing between the immobilized DNAs on the surface, dendron self-assembly was employed. Force-distance curves showed that the mean force of the specific unbinding events was 32 ± 5 pN, and the hydrodynamic distance of the captured RNA was 30-60 nm. Adhesion force maps were generated with criteria including the mean force value, probability of obtaining the specific curves and hydrodynamic distance. The maps for the samples whose concentrations ranged from 0.76 fM to 6.0 fM showed that cluster number has a linear relationship with RNA concentration, while the difference between the observed number and the calculated one increased at low concentrations. Because the detection limit is expected to be enhanced by a factor of 10 000 when a spot of 1 micron diameter is employed, it is believed that HCV RNA of a few copy numbers can be detected by the use of AFM.

| S-EPMC3526272 | biostudies-literature

Localization atomic force microscopy.

Project description:Understanding structural dynamics of biomolecules at the single-molecule level is vital to advancing our knowledge of molecular mechanisms. Currently, there are few techniques that can capture dynamics at the sub-nanometre scale and in physiologically relevant conditions. Atomic force microscopy (AFM)1 has the advantage of analysing unlabelled single molecules in physiological buffer and at ambient temperature and pressure, but its resolution limits the assessment of conformational details of biomolecules2. Here we present localization AFM (LAFM), a technique developed to overcome current resolution limitations. By applying localization image reconstruction algorithms3 to peak positions in high-speed AFM and conventional AFM data, we increase the resolution beyond the limits set by the tip radius, and resolve single amino acid residues on soft protein surfaces in native and dynamic conditions. LAFM enables the calculation of high-resolution maps from either images of many molecules or many images of a single molecule acquired over time, facilitating single-molecule structural analysis. LAFM is a post-acquisition image reconstruction method that can be applied to any biomolecular AFM dataset.

| S-EPMC8697813 | biostudies-literature

Analysis of force-deconvolution methods in frequency-modulation atomic force microscopy.

Project description:In frequency-modulation atomic force microscopy the direct observable is the frequency shift of an oscillating cantilever in a force field. This frequency shift is not a direct measure of the actual force, and thus, to obtain the force, deconvolution methods are necessary. Two prominent methods proposed by Sader and Jarvis (Sader-Jarvis method) and Giessibl (matrix method) are investigated with respect to the deconvolution quality. Both methods show a nontrivial dependence of the deconvolution quality on the oscillation amplitude. The matrix method exhibits spikelike features originating from a numerical artifact. By interpolation of the data, the spikelike features can be circumvented. The Sader-Jarvis method has a continuous amplitude dependence showing two minima and one maximum, which is an inherent property of the deconvolution algorithm. The optimal deconvolution depends on the ratio of the amplitude and the characteristic decay length of the force for the Sader-Jarvis method. However, the matrix method generally provides the higher deconvolution quality.

| S-EPMC3323913 | biostudies-literature

Electrostatic Discovery Atomic Force Microscopy.

Project description:While offering high resolution atomic and electronic structure, scanning probe microscopy techniques have found greater challenges in providing reliable electrostatic characterization on the same scale. In this work, we offer electrostatic discovery atomic force microscopy, a machine learning based method which provides immediate maps of the electrostatic potential directly from atomic force microscopy images with functionalized tips. We apply this to characterize the electrostatic properties of a variety of molecular systems and compare directly to reference simulations, demonstrating good agreement. This approach offers reliable atomic scale electrostatic maps on any system with minimal computational overhead.

| S-EPMC8793147 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data