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Plants (Basel, Switzerland) Aug 2021The present study was aimed at investigating the allelopathic effects of a crude extract from (L.) R.M.King and H.Rob. (Siam weed). The effects of 70% crude ethanol...
The present study was aimed at investigating the allelopathic effects of a crude extract from (L.) R.M.King and H.Rob. (Siam weed). The effects of 70% crude ethanol extract from the whole plant, leaf, stem, and root on the germination and growth of and seedlings were evaluated using Petri-dish tests under laboratory conditions. Crude extracts from the leaf showed the highest inhibitory activity. The leaf extract (OR) was further separated by sequential solvent extraction to provide hexane (HX), ethyl acetate (ET), and butanol (BU) fractions, which were also evaluated using Petri-dish tests. The hexane fraction was significantly the most active; therefore, it was selected for formulation in a concentrated suspension and tested for its herbicidal characteristics. The formulation showed greater early post-emergence than post- and pre-emergence activities, respectively. The physiological mechanism of the formulation was tested against and showed that chlorophyll a and b and the carotenoid contents of the leaf dramatically decreased when the concentration was increased, suggesting its ability to disrupt the process of photosynthesis. As thiobarbituric acid reactive substances also occurred in the leaf of , this suggests lipid peroxidation and cell disruption. These results represent the possibility that extract contains inhibitory compounds with herbicidal activity and could be used as an early post-emergence herbicide for weed control.
PubMed: 34451653
DOI: 10.3390/plants10081609 -
Frontiers in Microbiology 2019is an ascomycete fungus that infects and contaminates corn, peanuts, cottonseed, and treenuts with acutely toxic and carcinogenic aflatoxins. The ecological function of...
is an ascomycete fungus that infects and contaminates corn, peanuts, cottonseed, and treenuts with acutely toxic and carcinogenic aflatoxins. The ecological function of aflatoxin production is not well understood; though not phytotoxic, aflatoxin may be involved in resisting oxidative stress responses from infection or drought stress in plants. Observation of aflatoxin stimulation in 48-well plates in response to increasing inoculated wells sparked an investigation to determine if volatiles influence aflatoxin production in neighboring colonies. Experiments controlling several culture conditions demonstrated a stimulation of aflatoxin production with increased well occupancy independent of pH buffer, moisture, or isolate. However, even with all wells inoculated, aflatoxin production was less in interior wells. Only one isolate stimulated aflatoxin production in a large Petri-dish format containing eight small Petri dishes with shared headspace. Other isolates consistently inhibited aflatoxin production when all eight Petri dishes were inoculated with . No contact between cultures and only shared headspace implied the fungus produced inhibitory and stimulatory gases. Adding activated charcoal between wells and dishes prevented inhibition but not stimulation indicating stimulatory and inhibitory gases are different and/or gas is inhibitory at high concentration and stimulatory at lower concentrations. Characterizing stimulatory and inhibitory effects of gases in headspace as well as the apparently opposing results in the two systems deserves further investigation. Determining how gases contribute to quorum sensing and communication could facilitate managing or using the gases in modified atmospheres during grain storage to minimize aflatoxin contamination.
PubMed: 32010096
DOI: 10.3389/fmicb.2019.03038 -
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 -
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 -
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 -
Plants (Basel, Switzerland) Jul 2023Salinization is a global agricultural problem with many negative effects on crops, including delaying germination, inhibiting growth, and reducing crop yield and...
Salinization is a global agricultural problem with many negative effects on crops, including delaying germination, inhibiting growth, and reducing crop yield and quality. This study compared the salt tolerance of 20 soybean varieties at the germination stage to identify soybean germplasm with a high salt tolerance. Germination tests were conducted in Petri dishes containing 0, 50, 100, 150, and 200 mmol L NaCl. Each Petri dish contained 20 soybean seeds, and each treatment was repeated five times. The indicators of germination potential, germination rate, hypocotyl length, and radicle length were measured. The salt tolerance of 20 soybean varieties was graded, and the theoretical identification concentration was determined by cluster analysis, the membership function method, one-way analysis of variance, and quadratic equation analysis. The relative germination rate, relative germination potential, relative root length, and relative bud length of the 20 soybean germplasms decreased when the salt concentration was >50 mmol L, compared with that of the Ctrl. The half-lethal salt concentration of soybean was 164.50 mmol L, and the coefficient of variation was 18.90%. Twenty soybean varieties were divided into three salt tolerance levels following cluster analysis: Dongnong 254, Heike 123, Heike 58, Heihe 49, and Heike 68 were salt-tolerant varieties, and Xihai 2, Suinong 94, Kenfeng 16, and Heinong 84 were salt-sensitive varieties, respectively. This study identified suitable soybean varieties for planting in areas severely affected by salt and provided materials for screening and extracting parents or genes to breed salt-tolerant varieties in areas where direct planting is impossible. It assists crop breeding at the molecular level to cope with increasingly serious salt stress.
PubMed: 37570942
DOI: 10.3390/plants12152789 -
Dental and Medical Problems 2019Recently, a new generation of calcium silicate-based root canal sealers has been developed. These new types of sealers have the ability to set in wet environment, have...
BACKGROUND
Recently, a new generation of calcium silicate-based root canal sealers has been developed. These new types of sealers have the ability to set in wet environment, have high alkalinity and present potential antimicrobial activity.
OBJECTIVES
The aim of this study was to determine the chemical composition and microstructure of 2 novel calcium silicate-containing root canal sealers - TotalFill® BC Sealer and GuttaFlow® Bioseal.
MATERIAL AND METHODS
The tested sealers were prepared according to the manufacturers' instructions. Sixteen cylindrical dishes (inner diameter: 4 mm; height: 3 mm) were placed on a glass Petri dish and packed with the materials. The Petri dish was transferred to an incubator. After the sealers set, excess material was removed with diamond discs and polishing paste. The materials were assessed using scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS) X‑ray microanalysis.
RESULTS
Both TotalFill BC Sealer and GuttaFlow Bioseal contained calcium, zirconium, oxygen, carbon, silicon, and a trace of sodium. In the case of TotalFill BC Sealer, trace amounts of copper and technetium were also present, and for GuttaFlow Bioseal, iron, zinc, and a trace of magnesium and hafnium were noted. No bismuth was found. Both of the assessed sealers contained fine particles embedded in the matrix; however, GuttaFlow Bioseal also had larger particles with a diameter of 2-10 μm.
CONCLUSIONS
TotalFill BC Sealer represents a higher degree of purity in comparison with GuttaFlow Bioseal. The clinical implications of heavy metals present in GuttaFlow Bioseal need to be investigated. Both materials have a fine particle structure, which is desirable for root canal sealers.
Topics: Calcium Compounds; Dental Pulp Cavity; Dimethylpolysiloxanes; Drug Combinations; Gutta-Percha; Microscopy, Electron, Scanning; Root Canal Filling Materials
PubMed: 31140764
DOI: 10.17219/dmp/105561 -
Microbial Cell Factories Jan 2022With the steady increase of antibiotic resistance, several strategies have been proposed in the scientific community to overcome the crisis. One of many successful...
BACKGROUND
With the steady increase of antibiotic resistance, several strategies have been proposed in the scientific community to overcome the crisis. One of many successful strategies is the re-evaluation of known compounds, which have been early discarded out of the pipeline, with state-of-the-art know-how. Xanthoepocin, a polyketide widespread among the genus Penicillium with an interesting bioactivity spectrum against gram-positive bacteria, is such a discarded antibiotic. The purpose of this work was to (i) isolate larger quantities of this metabolite and chemically re-evaluate it with modern technology, (ii) to explore which factors lead to xanthoepocin biosynthesis in P. ochrochloron, and (iii) to test if it is beside its known activity against methicillin-resistant Staphylococcus aureus (MRSA), also active against linezolid and vancomycin-resistant Enterococcus faecium (LVRE)-a very problematic resistant bacterium which is currently on the rise.
RESULTS
In this work, we developed several new protocols to isolate, extract, and quantify xanthoepocin out of bioreactor batch and petri dish-grown mycelium of P. ochrochloron. The (photo)chemical re-evaluation with state-of-the-art techniques revealed that xanthoepocin is a photolabile molecule, which produces singlet oxygen under blue light irradiation. The intracellular xanthoepocin content, which was highest under ammonium-limited conditions, varied considerably with the applied irradiation conditions in petri dish and bioreactor batch cultures. Using light-protecting measures, we achieved MIC values against gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA), which were up to 5 times lower than previously published. In addition, xanthoepocin was highly active against a clinical isolate of linezolid and vancomycin-resistant Enterococcus faecium (LVRE).
CONCLUSIONS
This interdisciplinary work underlines that the re-evaluation of known compounds with state-of-the-art techniques is an important strategy in the combat against multiresistant bacteria and that light is a crucial factor on many levels that needs to receive more attention. With appropriate light protecting measures in the susceptibility tests, xanthoepocin proved to be a powerful antibiotic against MRSA and LVRE. Exploring the light response of other polyketides may be pivotal for re-introducing previously discarded metabolites into the antibiotic pipeline and to identify photosensitizers which might be used for (antimicrobial) photodynamic therapies.
Topics: Anti-Bacterial Agents; Drug Resistance, Multiple, Bacterial; Dynamic Light Scattering; Epoxy Compounds; Gram-Positive Bacteria; Light; Microbial Sensitivity Tests; Penicillium; Photolysis; Pyrones
PubMed: 34983506
DOI: 10.1186/s12934-021-01718-9 -
Physical Biology 2012Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed...
Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a chemostat. Since spatial organization can significantly affect evolutionary dynamics, the need is growing for evolutionary experiments in spatially structured environments. The surface of a Petri dish provides such an environment, but a more detailed understanding of microbial growth on Petri dishes is necessary to interpret such experiments. We formulate a simple deterministic reaction-diffusion model, which successfully predicts the spatial patterns created by two competing species during colony expansion. We also derive the shape of these patterns analytically without relying on microscopic details of the model. In particular, we find that the relative fitness of two microbial strains can be estimated from the logarithmic spirals created by selective sweeps. The theory is tested with strains of the budding yeast Saccharomyces cerevisiae for spatial competitions with different initial conditions and for a range of relative fitnesses. The reaction-diffusion model also connects the microscopic parameters like growth rates and diffusion constants with macroscopic spatial patterns and predicts the relationship between fitness in liquid cultures and on Petri dishes, which we confirmed experimentally. Spatial sector patterns therefore provide an alternative fitness assay to the commonly used liquid culture fitness assays.
Topics: Biological Evolution; Genetic Fitness; Genotype; Models, Biological; Saccharomyces cerevisiae; Selection, Genetic
PubMed: 22476106
DOI: 10.1088/1478-3975/9/2/026008