Hasil untuk "Microscopy"

M. Ovesný, P. Krízek, J. Borkovec et al.

Summary: ThunderSTORM is an open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy. ThunderSTORM offers an extensive collection of processing and post-processing methods so that users can easily adapt the process of analysis to their data. ThunderSTORM also offers a set of tools for creation of simulated data and quantitative performance evaluation of localization algorithms using Monte Carlo simulations. Availability and implementation: ThunderSTORM and the online documentation are both freely accessible at https://code.google.com/p/thunder-storm/ Contact: guy.hagen@lf1.cuni.cz Supplementary information: Supplementary data are available at Bioinformatics online.

J. Bancroft, M. Gamble

J. Griffith, L. Comeau, S. Rosenfield et al.

D. Gabor

J. Hren, J. Goldstein, D. Joy

M. Abercrombie, J. E. Heaysman, S. Pegrum

H. Leamy

Mohammad Reza Farhadinia, Nicolas Olivier

Providing quantitative interpretation of coherent nonlinear microscopy images, such as third-harmonic generation (THG), is generally hampered by the complex phase-matching conditions, especially in the presence of sample linear heterogeneity. We recently presented a numerical pipeline using the finite-difference time-domain (FDTD) method to take this heterogeneity into account. However, due to software restrictions, we only considered nonlinear materials with diagonal nonlinear susceptibilities. We now expand the recently developed FDTD approach to model nonlinear microscopy for anisotropic materials that obey Kleinman Symmetry, organized in layers along the optical axis, and validate our simulations on well-described geometries.

Jiangxue Shi, Wenyan Zhang, Yi Dong et al.

The intertidal sediments of Sanya Haitang Bay, a tropical coast, harbor abundant multicellular magnetotactic prokaryotes (MMPs). Using light and electron microscopy, micromanipulation sorting, and whole-genome amplification, we examined their diversity from morphological, phylogenetic, and ecological perspectives. Two types of MMPs were identified: ellipsoidal (eMMPs) and spherical (sMMPs). Their average abundance was 1.37 × 10³ ind./dm³ in autumn and 0.27 × 10³ ind./dm³ in spring, indicating strong seasonal variation. eMMPs averaged 9.74 × 8.15 µm, consisting of 80–100 cells arranged in layers, whereas sMMPs averaged 5.64 µm in diameter with 40–50 cells organized radially or spirally. Electron microscopy revealed bullet-shaped magnetosomes in both types: those in eMMPs averaged 90.1 × 34.0 nm, while those in sMMPs averaged 97.2 × 36.3 nm. Interestingly, Cu was homogenously detected in the magnetosomes of sMMPs. 16S rRNA gene analysis identified nine OTUs, including three potential new species in the Desulfobacteraceae family within Thermodesulfobacteriota phylum. Of these, two may represent a new genus, and one is affiliated with <i>Candidatus</i> Magnetananas. Global distribution analysis suggests that eMMPs prefer stable, nutrient-rich environments, whereas sMMPs occupy broader ecological niches. Together, these findings expand understanding of tropical MMP diversity and distribution, and the discovery of Cu-containing magnetosomes provides new insight into biomineralization mechanisms.

José Edson Fontes Figueiredo, Gisele de Fátima Dias Diniz, Mikaely Sousa Marins et al.

IntroductionBacillus velezensis is a ubiquitous bacterium with potent antifungal activity and a plant growth promoter. This study investigated the potential of B. velezensis CNPMS-22 as a biocontrol agent against phytopathogenic fungi under diverse experimental conditions and its potential as a plant growth promoter. Genome sequencing and analysis revealed putative genes involved in these traits.MethodsThis research performed in vitro experiments to evaluate the CNPMS-22 antagonistic activity against 10 phytopathogenic fungi using dual culture in plate (DCP) and inverted sealed plate assay (ISP). Greenhouse and field tests evaluated the ability of CNPMS-22 to control Fusarium verticillioides in maize plants in vivo. The CNPMS-22 genome was sequenced using the Illumina HiSeq 4,000 platform, and genomic analysis also included manual procedures to identify genes of interest accurately.ResultsCNPMS-22 showed antifungal activity in vitro against all fungi tested, with notable reductions in mycelial growth in both DCP and ISP experiments. In the ISP, volatile organic compounds (VOCs) produced by CNPMS-22 also altered the mycelium coloration of some fungi. Scanning electron microscopy revealed morphological alterations in the hyphae of F. verticillioides in contact with CNPMS-22, including twisted, wrinkled, and ruptured hyphae. Eight cluster candidates for synthesizing non-ribosomal lipopeptides and ribosomal genes for extracellular lytic enzymes, biofilm, VOCs, and other secondary metabolites with antifungal activity and plant growth promoters were identified by genomic analysis. The greenhouse and field experiments showed that seed treatment with CNPMS-22 reduced Fusarium symptoms in plants and increased maize productivity.ConclusionOur findings highlight the CNPMS-22’s potential as bioinoculant for fungal disease control and plant growth with valuable implications for a sustainable crop productivity.

Ana Yareli Flores-Ramírez, Martina Alejandra Chacón-López, René Antaño-López et al.

Magnetite nanoparticles (MNp) have demonstrated applications in different areas due to their properties, such as magnetism, adsorption, biocompatibility, low toxicity, and antimicrobial activity, which mainly depend on the synthesis methods. However, current methods have some drawbacks, such as the presence of maghemite, the oxidation process and the poor control of particle size and distribution. Therefore, the synthesis by electrochemical methods of MNp is proposed, applying three different anodic potentials (0.8, 0.3 and − 0.2 V vs. Hg|Hg2Cl2) and its surface modification with chitosan (CS). In addition, in order to identify the effect of the anodic potentials in obtaining MNp and MNp modified with chitosan (MNp-CS), the characterization of these magnetic materials by physicochemical methods was carried out, through which it was demonstrated the obtaining of MNp and MNp-CS by field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD) and UV–vis spectrophptometry, in addition, it was observed that the MNp-CS synthesized at the anodic potentials of 0. 8 V and 0.3 V vs. Hg|Hg2Cl2 show higher colloidal stability, pore volume, specific surface area and magnetic properties, which could contribute to their efficiency to adsorb metal ions, dyes, and microorganisms.

Yu Z, Zhou Z, Zhao Y

Zhecheng Yu,1– 4 Zeya Zhou,1– 4 Yunqi Zhao1– 4 1College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang, People’s Republic of China; 2Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Wenzhou, Zhejiang, People’s Republic of China; 3Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Wenzhou, Zhejiang, People’s Republic of China; 4Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, Union, NJ, USACorrespondence: Yunqi Zhao, College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou, Zhejiang, People’s Republic of China, Tel +86 577 5587 0000, Fax +86 577 5587 0101, Email yuzhao@kean.eduBackground: Cancer immunotherapy has achieved great success in breast cancer treatment in recent years. The Programmed Death-1 (PD-1) /Programmed Death-Ligand 1 (PD-L1) immune checkpoint pathway is among the most studied. BMS-1166, a PD-L1 inhibitor, can interfere with PD-1 and PD-L1 interaction. Transferrin Receptor 1 is a transmembrane glycoprotein overexpressed in various cancer cells, including breast cancer, and can specifically interact with the T7 (HAIYPRH) peptide.Purpose: This study hypothesized that BMS-1166-loaded T7-modified poly(ethylene glycol)-poly(&epsiv;-caprolactone) (PEG-PCL) polymeric micelles (BMS-T7) could block PD-L1 interaction with PD-1, serving as a targeted immunotherapy for TfR1-positive breast cancer.Methods: BMS-1166 was encapsulated in T7-PEG-PCL micelle. Particle size and zeta potential were determined by dynamic light scattering. Particle morphology was studied by transmission electron microscopy. The particles were characterized by Fourier transform infrared, thermogravimetric analysis, and differential scanning calorimetry. Drug encapsulation efficiency, loading degree, and release profile were examined by high-performance liquid chromatography. Human breast cancer MDA-MB-231 was used to test the cytotoxicity. Flow cytometry and immunofluorescence imaging were used to study the PD-L1 inhibition in cell surface and exosomes. MDA-MB-231 and Jurkat co-culture studied T-cell activation and apoptosis.Results: The particle size of the empty and drug-loaded micelles showed a size distribution with an average diameter of 54.62 ± 2.28 nm and 60.22 ± 2.56 nm, respectively. The encapsulation efficiency of BMS-T7 was 83.89 ± 5.59%. The release half-life of drug-loaded micelles was 48h. The IC50 of BMS-1166 was 28.77 μM in MDA-MB-231 cells. In addition, the BMS-T7 showed a better inhibitory effect on PD-L1 expression in breast cancer cells and exosomes than the naked drug. The formulation significantly restored T-cell function compared to the BMS-1166 treatment.Conclusion: These results provide preliminary evidence indicating that BMS-T7 may have the potential to deliver drugs to breast cancer cells via active targeting and hold great promise in cancer immunotherapy drug delivery applications.Keywords: PD-L1, BMS-1166, immunotherapy, breast cancer, micelles

Maheen Rashid, Shoichi Tachiyama, Shiwei Zhu et al.

ABSTRACT Francisella tularensis is a gram-negative, intracellular pathogen that causes the zoonotic disease tularemia. Due to its ease of dissemination and high lethality, F. tularensis is classified as a tier 1 select agent with potential for misuse as a bioweapon. The mechanisms by which Francisella replicates intracellularly and interacts with the host during infection are not well understood. Francisella produces spherical outer membrane vesicles (OMVs) and novel tubular extensions of its cell surface that are also released extracellularly. These OMV and outer membrane tubes (OMTs) contain Francisella virulence factors and are produced in response to amino acid starvation and during infection of macrophages. To investigate how the OMTs are formed, we used cryogenic electron tomography to examine the model Francisella spp., Francisella novicida, during in vitro culture and within the macrophage phagosome. OMT formation involved progressive alterations of the bacterial envelope, resulting in extensions of both the inner and outer membranes. A dynamic cytoplasmic structure was present at the base of the OMT that extended into the tubes during elongation, together with cytoplasmic material. OMT produced within the macrophage phagosome was associated with changes to the phagosomal membrane, suggesting a role in phagosomal escape. Consistent with this, using confocal microscopy, we observed co-localization of the Francisella type VI secretion system with the OMT, both within bacteria and in released tubular vesicles. These findings reveal the cellular transformations that occur during membrane tubulation by Francisella and provide insights into the function of membrane-derived structures during host-pathogen interactions.IMPORTANCEFrancisella tularensis is an intracellular bacterial pathogen that causes the zoonotic disease tularemia. Following uptake by host cells, the bacteria rapidly escape the phagosome and replicate intracellularly. In previous studies, we found that Francisella produces tubular extensions of its cell surface in response to specific cues and during macrophage infection. In the present study, we used cryogenic electron tomography to examine tube formation by the model Francisella sp., F. novicida. This analysis revealed that tube formation involves extensive bacterial envelope alterations and a dynamic cytoplasmic organelle. Furthermore, tubes produced by bacteria within infected macrophages were associated with the breakdown of the phagosomal membrane. In addition, we found that the Francisella type VI secretion system, which is essential for phagosomal escape, co-localized with the bacterial tubes. These findings reveal the cellular transformations that occur during membrane tubulation by Francisella and suggest a role for the tubes in phagosomal escape.

Ashesh Ashesh, Florian Jug

Fluorescence microscopy, while being a key driver for progress in the life sciences, is also subject to technical limitations. To overcome them, computational multiplexing techniques have recently been proposed, which allow multiple cellular structures to be captured in a single image and later be unmixed. Existing image decomposition methods are trained on a set of superimposed input images and the respective unmixed target images. It is critical to note that the relative strength (mixing ratio) of the superimposed images for a given input is a priori unknown. However, existing methods are trained on a fixed intensity ratio of superimposed inputs, making them not cognizant of the range of relative intensities that can occur in fluorescence microscopy. In this work, we propose a novel method called scSplit that is cognizant of the severity of the above-mentioned mixing ratio. Our idea is based on InDI , a popular iterative method for image restoration, and an ideal starting point to embrace the unknown mixing ratio in any given input. We introduce (i) a suitably trained regressor network that predicts the degradation level (mixing ratio) of a given input image and (ii) a degradation-specific normalization module, enabling degradation-aware inference across all mixing ratios. We show that this method solves two relevant tasks in fluorescence microscopy, namely image splitting and bleedthrough removal, and empirically demonstrate the applicability of scSplit on 5 public datasets. The source code with pre-trained models is hosted at https://github.com/juglab/scSplit/.

Hao Chen, Julian Najera, Dagmawit Geresu et al.

Multimodal and multi-information microscopy techniques such as Fluorescence Lifetime Imaging Microscopy (FLIM) extend the informational channels beyond intensity-based fluorescence microscopy but suffer from reduced image quality due to complex noise patterns. For FLIM, the intrinsic relationship between intensity and lifetime information means noise in each channel is a multivariate function across channels without necessarily sharing structural features. Based on this, we present a novel Zero-Shot Denoising Framework with an Intensity-Guided Learning approach. Our correlation-preserving strategy maintains important biological information that might be lost when channels are processed independently. Our framework implements separate processing paths for each channel and utilizes a pre-trained intensity denoising prior to guide the refinement of lifetime components across multiple channels. Through experiments on real-world FLIM-acquired biological samples, we show that our approach outperforms existing methods in both noise reduction and lifetime preservation, thereby enabling more reliable extraction of physiological and molecular information.

B. Rothenhäusler, W. Knoll

Hossein Bayahia

FeNbO4 monoclinic nanocomposite semiconductors were synthesised using hydrothermal and sol gel methods; photocatalysts were then calcined at 800 °C. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), UV–Vis spectroscopy (UV/Vis) and X-ray diffraction (XRD) technologies were used to investigate crystallinity, morphology and optical properties of the photocatalysts. Fourier transform infrared spectroscopy (FTIR) was used to determine the functional groups of both treated and untreated FeNbO4. It was found that the S. molle extract-treated FeNbO4 prepared using the hydrothermal method (FeNbO4-HT + S. molle) has the smallest nanoparticles (22.8 nm) with the smallest band gap energy (2.78 eV). X-ray photoelectron spectroscopy verified the presence of the elements of FeNbO4 as well as their oxidation states. The photodegradation reactions of 10-ppm methyl orange dye solutions using FeNbO4-sol gel, FeNbO4-HT and FeNbO4-HT + S. molle were carried out under visible light (>420 nm) for 50 min. The reactions resulted in degradation percent of 74 %, 78 % and 96 % by using FeNbO4-sol gel, FeNbO4-HT and FeNbO4-HT + S. molle respectively. The photocatalytic activity of FeNbO4 treated with S. molle extract demonstrated superior light absorption and photostability, which is attributed to the consistency in the photocatalysts’ morphology, optical band gap, particle size distribution, and porosity. The photocatalysts remained stable and effective for five degradation cycles.

Imdad Ali

PVC gels are in high demand for actuators, so choosing the optimal route for preparing PVC gel is crucial. In this study, PVC gel samples were prepared using polymer PVC, plasticizer Di-butyl adipate (DBA), and solvent tetrahydrofuran (THF) at temperatures ranging from 40°C to 70°C. The samples obtained at different temperatures were labeled as PVC40, PVC50, PVC60, and PVC70. Rheological properties of all PVC gel samples were analyzed, revealing, that the rheological behavior of the PVC70 gel sample differed significantly from the others due to THF evaporation at 70°C, resulting in inadequate PVC gel preparation. However, PVC40, PVC50, and PVC60 gel samples were chosen for further characterizations, including scanning electron microscopy (SEM), actuation, and mechanical properties evaluation. Moreover, a self-assembled setup was fabricated using electrodes and PVC gel to test the performance of the planar actuator. The maximum displacement of PVC60 was measured at approximately 0.74 mm, with a response time of 0.75 sec under an applied voltage of 1000V. It was observed that the homogeneity of the gel and the solubility of the raw materials, based on resin were influenced by the reaction temperature, suggesting that uniformity could be achieved through dipole-dipole interactions or hydrogen bonding between PVC and DBA (Cl-H…. O=C). Finally, our findings have the potential to contribute to the development of innovative PVC gel actuators.

GONG Xuan, LIU Jiachen, CUI Yan, LI Qiang

In order to enhance the wear resistance of aluminum alloy surfaces，Ni-P/diamond composite coatings were prepared on 2014 aluminum alloy surfaces using electroplating method.The effects of varying diamond particle content in the coating on the coating’s elemental composition， surface morphology， microhardness， corrosion resistance and wear resistance were investigated using wavelength dispersive X-ray fluorescence spectroscopy， scanning electron microscopy (SEM)， Vickers hardness testing， electrochemical workstation and friction-wear testing machine.Results showed that as the concentration of diamond particles in the plating solution increased from 0 to 1.0 g/L，the corrosion current density decreased and the corrosion potential increased.The micro Vickers hardness improved from 526 to 786 HV0.5.When the diamond particle concentration was 1.0 g/L， the coating exhibited the lowest wear rate.With the increase in diamond content， the wear mechanism of the coating transitioned from fatigue wear to a combination of fatigue and adhesive wear， eventually shifting to predominantly adhesive wear.

Raymond Wightman

Movement of cellulose synthase particles have so far been observed on the plant epidermis that are amenable to confocal imaging, yielding appreciable signal and resolution to observe small plasma membrane-localised particles. Presented here is a method, using airyscan confocal microscopy, that permits similar information to be obtained at depth within the developing protoxylem vessels of intact roots.