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Micromachines May 2023A new generation of nanoscale photosensitizer agents has improved photothermal capabilities, which has increased the impact of photothermal treatments (PTTs) in cancer...
A new generation of nanoscale photosensitizer agents has improved photothermal capabilities, which has increased the impact of photothermal treatments (PTTs) in cancer therapy. Gold nanostars (GNS) are promising for more efficient and less invasive PTTs than gold nanoparticles. However, the combination of GNS and visible pulsed lasers remains unexplored. This article reports the use of a 532 nm nanosecond pulse laser and polyvinylpyrrolidone (PVP)-capped GNS to kill cancer cells with location-specific exposure. Biocompatible GNS were synthesized via a simple method and were characterized under FESEM, UV-visible spectroscopy, XRD analysis, and particle size analysis. GNS were incubated over a layer of cancer cells that were grown in a glass Petri dish. A nanosecond pulsed laser was irradiated on the cell layer, and cell death was verified via propidium iodide (PI) staining. We assessed the effectiveness of single-pulse spot irradiation and multiple-pulse laser scanning irradiation in inducing cell death. Since the site of cell killing can be accurately chosen with a nanosecond pulse laser, this technique will help minimize damage to the cells around the target cells.
PubMed: 37374759
DOI: 10.3390/mi14061173 -
PLoS Computational Biology Aug 2023Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize...
Harnessing the power of microbial consortia is integral to a diverse range of sectors, from healthcare to biotechnology to environmental remediation. To fully realize this potential, it is critical to understand the mechanisms behind the interactions that structure microbial consortia and determine their functions. Constraint-based reconstruction and analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as the state-of-the-art tool to simulate the behavior of microbial communities from their constituent genomes. In the last decade, many tools have been developed that use COBRA approaches to simulate multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these tools have not been systematically evaluated regarding their software quality, most suitable application, and predictive power. Hence, it is uncertain which tools users should apply to their system and what are the most urgent directions that developers should take in the future to improve existing capacities. This study conducted a systematic evaluation of COBRA-based tools for microbial communities using datasets from two-member communities as test cases. First, we performed a qualitative assessment in which we evaluated 24 published tools based on a list of FAIR (Findability, Accessibility, Interoperability, and Reusability) features essential for software quality. Next, we quantitatively tested the predictions in a subset of 14 of these tools against experimental data from three different case studies: a) syngas fermentation by C. autoethanogenum and C. kluyveri for the static tools, b) glucose/xylose fermentation with engineered E. coli and S. cerevisiae for the dynamic tools, and c) a Petri dish of E. coli and S. enterica for tools incorporating spatiotemporal variation. Our results show varying performance levels of the best qualitatively assessed tools when examining the different categories of tools. The differences in the mathematical formulation of the approaches and their relation to the results were also discussed. Ultimately, we provide recommendations for refining future GEM microbial modeling tools.
Topics: Microbial Consortia; Escherichia coli; Saccharomyces cerevisiae; Genome; Software
PubMed: 37578975
DOI: 10.1371/journal.pcbi.1011363 -
Microorganisms Jan 2024In this paper, an automatic colony counting system based on an improved image preprocessing algorithm and convolutional neural network (CNN)-assisted automatic counting...
In this paper, an automatic colony counting system based on an improved image preprocessing algorithm and convolutional neural network (CNN)-assisted automatic counting method was developed. Firstly, we assembled an LED backlighting illumination platform as an image capturing system to obtain photographs of laboratory cultures. Consequently, a dataset was introduced consisting of 390 photos of agar plate cultures, which included 8 microorganisms. Secondly, we implemented a new algorithm for image preprocessing based on light intensity correction, which facilitated clearer differentiation between colony and media areas. Thirdly, a U-Net was used to predict the probability distribution of the edge of the Petri dish in images to locate region of interest (ROI), and then threshold segmentation was applied to separate it. This U-Net achieved an F1 score of 99.5% and a mean absolute error (MAE) of 0.0033 on the validation set. Then, another U-Net was used to separate the colony region within the ROI. This U-Net achieved an F1 score of 96.5% and an MAE of 0.005 on the validation set. After that, the colony area was segmented into multiple components containing single or adhesive colonies. Finally, the colony components (CC) were innovatively rotated and the image crops were resized as the input (with 14,921 image crops in the training set and 4281 image crops in the validation set) for the ResNet50 network to automatically count the number of colonies. Our method achieved an overall recovery of 97.82% for colony counting and exhibited excellent performance in adhesion classification. To the best of our knowledge, the proposed "light intensity correction-based image preprocessing→U-Net segmentation for Petri dish edge→U-Net segmentation for colony region→ResNet50-based counting" scheme represents a new attempt and demonstrates a high degree of automation and accuracy in recognizing and counting single-colony and multi-colony targets.
PubMed: 38258027
DOI: 10.3390/microorganisms12010201 -
Scientific Reports Feb 2021Delivering appropriate stimuli remains a challenge in vision research, particularly for aquatic animals such as zebrafish. Due to the shape of the water tank and the...
Delivering appropriate stimuli remains a challenge in vision research, particularly for aquatic animals such as zebrafish. Due to the shape of the water tank and the associated optical paths of light rays, the stimulus can be subject to unwanted refraction or reflection artifacts, which may spoil the experiment and result in wrong conclusions. Here, we employ computer graphics simulations and calcium imaging in the zebrafish optic tectum to show, how a spherical glass container optically outperforms many previously used water containers, including Petri dish lids. We demonstrate that aquatic vision experiments suffering from total internal reflection artifacts at the water surface or at the flat container bottom may result in the erroneous detection of visual neurons with bipartite receptive fields and in the apparent absence of neurons selective for vertical motion. Our results and demonstrations will help aquatic vision neuroscientists on optimizing their stimulation setups.
Topics: Animals; Artifacts; Calcium Signaling; Computer Graphics; Female; Male; Photic Stimulation; Superior Colliculi; Vision, Ocular; Zebrafish
PubMed: 33547357
DOI: 10.1038/s41598-021-81904-2 -
Nanomaterials (Basel, Switzerland) Oct 2022Given the demanding use of controlled drug delivery systems, our attention was focused on developing a magnetic film that can be triggered in the presence of a magnetic...
Given the demanding use of controlled drug delivery systems, our attention was focused on developing a magnetic film that can be triggered in the presence of a magnetic field for both drug delivery and the actuating mechanism in micropump biomedical microelectromechanical systems (BioMEMS). Magnetic alginate films were fabricated in three steps: the co-precipitation of iron salts in an alkaline environment to obtain magnetite nanoparticles (FeO), the mixing of the obtained nanoparticles with a sodium alginate solution containing glycerol as a plasticizer and folic acid as an active substance, and finally the casting of the final solution in a Petri dish followed by cross-linking with calcium chloride solution. Magnetite nanoparticles were incorporated in the alginate matrix because of the well-established biocompatibility of both materials, a property that would make the film convenient for implantable BioMEMS devices. The obtained film was analyzed in terms of its magnetic, structural, and morphological properties. To demonstrate the hypothesis that the magnetic field can be used to trigger drug release from the films, we studied the release profile in an aqueous medium (pH = 8) using a NdFeB magnet as a triggering factor.
PubMed: 36296787
DOI: 10.3390/nano12203598 -
Frontiers in Microbiology 2022A modified cultivation technique was developed and applied to resource mining of uncultured microbes from marine sediments of Meishan Island in the East China Sea. Two...
A modified cultivation technique was developed and applied to resource mining of uncultured microbes from marine sediments of Meishan Island in the East China Sea. Two novel strains NBU2968 and NBU2984 were isolated by this method but not standard Petri dish, which indicated the modified technique was more effective compared to conventional approaches for isolating uncultured microbes and could be popularized and applied to other aquatic environments. The two novel strains were identified by the polyphasic taxonomic approach. Cells of both strains were observed to be Gram-staining-negative, rod-shaped, nonmotile, aerobic, and yellow-pigmented. Catalase and oxidase activities and hydrolysis of Tweens 40, 60, and 80 of two novel strains were positive. Methyl red reaction, HS production, and hydrolysis of Tween 20 were negative. According to 16S rRNA gene sequence analysis, two novel strains shared the highest similarities (96.4-97.7%) to the species with a validated name in the genus , while shared lower sequence similarities (<95.6%) to all other genera. Phylogenetic analysis revealed that strains NBU2968 and NBU2984 were affiliated with the genus . ANI and dDDH values between the two novel strains and species were 77.4-78.3% and 20.4-20.9%, respectively, which were below the thresholds for species delineation. The 16S rRNA gene sequence similarity, ANI, and dDDH values between the two novel strains were 99.3, 88.9, and 36.3%, respectively, indicating that the two strains represent different species. The genomes of NBU2968 and NBU2984 were 3.28 Mbp with a G+C content of 34.2% and 3.09 Mbp with a G+C content of 34.4%, respectively. The only respiratory quinone was menaquinone-6 (MK-6). The major cellular fatty acids were iso-C, iso-CG, and iso-C 3-OH. The major polar lipids of the two strains were phosphatidylethanolamine, unidentified amino lipids, and unidentified lipids. Based on the above polyphasic characteristics, strains NBU2968 and NBU2984 represent two novel species within the genus , for which the names sp. nov. and sp. nov. are proposed. The type strains are NBU2968 (= MCCC 1K06392= KCTC 82913) and NBU2984 (= MCCC 1K07472= KCTC 92511), respectively.
PubMed: 35935200
DOI: 10.3389/fmicb.2022.957397 -
Evolution; International Journal of... Oct 2022Oceanic archipelagos have long been treated as a Petri dish for studies of evolutionary and ecological processes. Like archipelagos, cities exhibit similar patterns and...
Oceanic archipelagos have long been treated as a Petri dish for studies of evolutionary and ecological processes. Like archipelagos, cities exhibit similar patterns and processes, such as the rapid phenotypic divergence of a species between urban and nonurban environments. However, on a local scale, cities can be highly heterogenous, where geographically close populations can experience dramatically different environmental conditions. Nevertheless, we are yet to understand the evolutionary and ecological implications for populations spread across a heterogenous cityscape. To address this, we compared neutral genetic divergence to quantitative trait divergence within three native riparian and four city park populations of an iconic urban adapter, the eastern water dragon. We demonstrated that selection is likely acting to drive divergence of snout-vent length and jaw width across native riparian populations that are geographically isolated and across city park populations that are geographically close yet isolated by urbanization. City park populations as close as 0.9 km exhibited signs of selection-driven divergence to the same extent as native riparian populations isolated by up to 114.5 km. These findings suggest that local adaptation may be occurring over exceptionally small geographic and temporal scales within a single metropolis, demonstrating that city parks can act as archipelagos for the study of rapid evolution.
Topics: Animals; Cities; Urbanization; Genetic Drift; Lizards; Water
PubMed: 35971751
DOI: 10.1111/evo.14596 -
Brazilian Journal of Otorhinolaryngology 2022Three-dimensional (3D) cell cultures have many applications such as stem cell biology research, new drug discovery, cancer, and Chronic Rhinosinusitis with Nasal Polyps...
OBJECTIVES
Three-dimensional (3D) cell cultures have many applications such as stem cell biology research, new drug discovery, cancer, and Chronic Rhinosinusitis with Nasal Polyps (CRSwNP). This disease is characterized by a significant impact on quality of life and productivity. The diversity of factors that act in the progression of CRSwNP point to the creation of a cell culture model that allows the integration of different cell types with extracellular matrix. This work aimed to create a cell culture model in 3 dimensions (spheroids) for the study of Nasal Polyposis.
METHODS
Nasal polyp tissue from patients diagnosed with CRSwNP was mechanically dissociated using tweezers and a scalpel and the solution containing cells and small aggregates of nasal polyps was transferred to a Petri dish containing 5 mL of culture medium at the concentration of 10 cells/mL.
RESULTS
The spheroids were cultivated for 20 days, fixed and analyzed using confocal microscopy. In a 3D culture environment, the spheroids were formed both by clustering cells and from small tissue fragments. In the cultures analyzed, the ciliary beat was present from the dissociation of the cells up to 20 days in culture.
CONCLUSION
Our findings also point to these characteristics showing the environment generated in our study, the cells remained differentiated for a longer time and with ciliary beating. Thus, this work shows that nasal polyp-derived cells can be maintained in a 3D environment, enabling better strategies for understanding CRSwNP in situations similar to those found in vivo.
LEVEL OF EVIDENCE
Laboratory studies.
Topics: Humans; Nasal Polyps; Rhinitis; Quality of Life; Sinusitis; Chronic Disease; Cell Culture Techniques, Three Dimensional
PubMed: 34924329
DOI: 10.1016/j.bjorl.2021.11.001 -
Mathematical Medicine and Biology : a... Mar 2023A traditional method of in vitro cell culture involves a monolayer of cells at the base of a petri dish filled with culture medium. While the primary role of the culture...
A traditional method of in vitro cell culture involves a monolayer of cells at the base of a petri dish filled with culture medium. While the primary role of the culture medium is to supply nutrients to the cells, drug or other solutes may be added, depending on the purpose of the experiment. Metabolism by cells of oxygen, nutrients and drug is typically governed by Michaelis-Menten (M-M) kinetics. In this paper, a mathematical model of solute transport with M-M kinetics is developed. Upon non-dimensionalization, the reaction/diffusion system is re-characterized in terms of Volterra integral equations, where a parameter $\beta $, the ratio of the initial solute concentration to the M-M constant, proves important: $\beta \ll 1$ is relevant to drug metabolism for the liver, whereas $\beta \gg 1$ is more appropriate in the case of oxygen metabolism. Regular perturbation expansions for both cases are obtained. A small-time expansion and steady-state solution are also presented. All results are compared against the numerical solution of the Volterra integral equations, and excellent agreement is found. The utility of the model and analytical solutions are discussed in the context of assisting experimental researchers to better understand the environment within in vitro cell culture experiments.
Topics: Models, Biological; Kinetics; Models, Theoretical; Cell Culture Techniques; Oxygen
PubMed: 36201433
DOI: 10.1093/imammb/dqac014 -
Cancer Management and Research 2020Detection of circulating tumor cells (CTC) is an important liquid biopsy technique that has advanced considerably in recent years. To further advance the development of... (Review)
Review
Detection of circulating tumor cells (CTC) is an important liquid biopsy technique that has advanced considerably in recent years. To further advance the development of technology for curing cancer, several CTC technologies have been proposed by various research groups. Despite their potential role in early cancer diagnosis and prognosis, CTC methods are currently used for research purposes only, and very few methods have been accepted for clinical applications because of difficulties, including CTC heterogeneity, CTC separation from the blood, and a lack of thorough clinical validation. Although current CTC technologies have not been truly implemented, they possess high potential as future clinical diagnostic techniques for individualized cancer. Here, we review current developments in CTC separation technology. We also explore new CTC detection methods based on telomerase and nanomaterials, such as in vivo flow cytometry. In addition, we discuss the difficulties that must be overcome before CTC can be applied in clinical settings.
PubMed: 32884342
DOI: 10.2147/CMAR.S248380