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Sensors (Basel, Switzerland) Aug 2021Automatic tracking of () in standard Petri dishes is challenging due to high-resolution image requirements when fully monitoring a Petri dish, but mainly due to...
Automatic tracking of () in standard Petri dishes is challenging due to high-resolution image requirements when fully monitoring a Petri dish, but mainly due to potential losses of individual worm identity caused by aggregation of worms, overlaps and body contact. To date, trackers only automate tests for individual worm behaviors, canceling data when body contact occurs. However, essays automating contact behaviors still require solutions to this problem. In this work, we propose a solution to this difficulty using computer vision techniques. On the one hand, a skeletonization method is applied to extract skeletons in overlap and contact situations. On the other hand, new optimization methods are proposed to solve the identity problem during these situations. Experiments were performed with 70 tracks and 3779 poses (skeletons) of . Several cost functions with different criteria have been evaluated, and the best results gave an accuracy of 99.42% in overlapping with other worms and noise on the plate using the modified skeleton algorithm and 98.73% precision using the classical skeleton algorithm.
Topics: Algorithms; Animals; Caenorhabditis elegans; Skeleton
PubMed: 34451062
DOI: 10.3390/s21165622 -
Plant Methods 2019Bacterial volatiles promote plant growth and elicit immunity responses in plants grown in two-compartment Petri dishes. Due to the limitations of bacterial volatile...
Beyond the two compartments Petri-dish: optimising growth promotion and induced resistance in cucumber exposed to gaseous bacterial volatiles in a miniature greenhouse system.
BACKGROUND
Bacterial volatiles promote plant growth and elicit immunity responses in plants grown in two-compartment Petri dishes. Due to the limitations of bacterial volatile compound (BVC) treatments such as their high evaporation rates, it is convenient to apply BVCs in closed systems such as greenhouses. However, the concentrations of BVCs must be optimised. We therefore attempted to optimise BVC emissions from bacteria grown on solid medium and synthetic BVC treatment in order to maximise plant growth and induced resistance in a miniature greenhouse system.
RESULTS
We cultivated the model BVC emitter GB03 on complex medium for continuous treatment, which we placed near 1-week-old cucumber seedlings in a miniature greenhouse. Aboveground and belowground plant growth parameters were significantly increased at 1 and 2 weeks after treatment with BVCs released by GB03. Moreover, this treatment protected cucumber seedlings against the angular leaf spot pathogen pv. . In addition, cucumber shoot growth was promoted in response to the slow release of BVCs from filter paper that had absorbed 1000 and 10 µM synthetic 2,3-butanediol, a key BVC from strain GB03. However, induced resistance was only elicited when 10 plates containing 10 µM 2,3-butanediol were utilised in the miniature greenhouse. The mechanism of induced resistance appears to involve the activation of the jasmonic acid signalling pathway.
CONCLUSIONS
To overcome the difficulties associated with treatment using a single application of BVC in the greenhouse, we optimised conditions for BVC application via consistent exposure in a slow-release system.
PubMed: 30733821
DOI: 10.1186/s13007-019-0395-y -
BMC Musculoskeletal Disorders Sep 2018Fibroblast behavior and cell-matrix interactions of cells from normal and idiopathic carpal tunnel syndrome (CTS) subsynovial connective tissue (SSCT) with and without...
BACKGROUND
Fibroblast behavior and cell-matrix interactions of cells from normal and idiopathic carpal tunnel syndrome (CTS) subsynovial connective tissue (SSCT) with and without Triamcinolone Acetonide (TA) were compared in this study. A cell-seeded gel contraction model was applied to investigate the effect of steroid treatment on SSCT fibroblast gene expression and function.
METHODS
SSCT cells were obtained from CTS patients and fresh cadavers. Cells were isolated by mechanical and collagenase digestion. Collagen gels (1 mg/ml) were prepared with SSCT cells (1 × 10/mL). A sterile Petri dish with a cloning ring in the center was prepared. The area between the ring and outer dish was filled with cell-seeded collagen solution and gelled for 1 h. The gel was released from the outer way of the petri dish to allow gel contraction. Cell seeded gels were treated with 10 M triamcinolone acetonide (TA) or vehicle (DMSO) in modified MEM. Every 4 h for 3 days the contracting gels were photographed and areas calculated. Duplicate contraction tests were performed with each specimen, and the averages were used in the analyses, which were conducted using two-factor analysis of variance in a generalized linear model framework utilizing generalized estimating equations (GEE) to account for the correlation between samples. The contraction rate was determined by the area change over time, and the decay time constant was calculated. A customized mechanical test system was used to determine gel stiffness and tensile strength. Gene expression was assessed using Human Fibrosis and Cell Motility PCR arrays.
RESULTS
TA-treated gels had a significantly higher contraction rate, tensile strength and stiffness than the untreated gels. Proteinases involved in remodeling had increased expression in TA-treated gels of the patient group. Pro-fibrotic genes and ECM regulators, such as TGF-β, collagens and integrins, were down-regulated by TA, indicating that TA may work in part by decreasing fibrotic gene expression.
CONCLUSIONS
This study showed that TA affects cell-matrix interaction and suppresses fibrotic gene expression in the SSCT cells of CTS patients.
Topics: Carpal Tunnel Syndrome; Collagen; Female; Fibroblasts; Glucocorticoids; Humans; Male; Middle Aged; Polymerase Chain Reaction; Primary Cell Culture; Transforming Growth Factor beta; Triamcinolone Acetonide
PubMed: 30243295
DOI: 10.1186/s12891-018-2260-y -
Medical Mycology Journal 2021We postulated that disinfection of viable Trichophyton species in shoes would help reduce the number of patients with tinea pedis in Japan and that this might be...
We postulated that disinfection of viable Trichophyton species in shoes would help reduce the number of patients with tinea pedis in Japan and that this might be accomplished safely using volatile components of essential oils. As vapor of lemongrass (Cymbopogon citratus) oil and citral have strong antimicrobial activities against Trichophyton, we examined the conditions under which lemongrass oil or citral show optimal antimicrobial activity in shoes. First, we investigated whether or not a strong antimicrobial effect could be obtained by combining with terpene aldehydes or aromatic aldehydes. When combined with citral, perillaldehyde showed superior antimicrobial activity to citronellal, cinnamaldehyde, cuminaldehyde, hydroxycitronellal, and vanillin. The combined effects of citral and perillaldehyde against Trichophyton mentagrophytes, Bacillus subtilis, and Candida albicans as volatile components dotted on filter paper placed away from the petri dish inoculated with fungi or bacteria were examined. Citral (2.5 mg/mL) and perillaldehyde (2.5 mg/mL) showed a greater inhibitory effect on growth of C. albicans than either solution alone in the aromatogram (disc diffusion) descent method (fractional inhibitory concentration [FIC] index of 0.58). Citral (2.5 mg/mL) and perillaldehyde (1.25 mg/mL) vapors in a closed box synergistically inhibited growth of B. subtilis and T. mentagrophytes (FIC indexes of 0.5 and 0.38, respectively). These results suggested that this combination would be safe and useful for disinfection of shoes.
Topics: Anti-Infective Agents; Cymbopogon; Humans; Oils, Volatile; Perilla; Trichophyton
PubMed: 34853254
DOI: 10.3314/mmj.21-00011 -
Physical Review. E May 2021Cell plating, the spreading out of a liquid suspension of cells on a surface followed by colony growth, is a common laboratory procedure in microbiology. Despite this,...
Cell plating, the spreading out of a liquid suspension of cells on a surface followed by colony growth, is a common laboratory procedure in microbiology. Despite this, the exact impact of its parameters on colony growth has not been extensively studied. A common protocol involves the shaking of glass beads within a Petri dish containing solid growth media. We investigated the effects of multiple parameters in this protocol: the number of beads, the shape of movement, and the number of movements. Standard suspensions of Escherichia coli were spread while varying these parameters to assess their impact on colony growth. Results were assessed by a variety of metrics: the number of colonies, the mean distance between closest colonies, and the variability and uniformity of their spatial distribution. Finally, we devised a mathematical model of shifting billiard to explain the heterogeneities in the observed spatial patterns. Exploring the parameters that affect the most fundamental techniques in microbiology allows us to better understand their function, giving us the ability to precisely control their outputs for our exact needs.
Topics: Culture Media; Escherichia coli; Movement
PubMed: 34134194
DOI: 10.1103/PhysRevE.103.052410 -
ELife Jun 2020Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and...
Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and yield biased sampling of environmental microbes due to ecological and evolutionary factors. New strategies are needed for ample representation of rare taxa and slow-growers that are often outcompeted by fast-growers in cultivation experiments. Here we describe a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts them based on colony density to enhance slow-growing organisms. We applied our strategy to a fecal microbiota transplant (FMT) donor stool using multiple growth media, and found significant increase in taxonomic richness and larger representation of rare and clinically relevant taxa among droplet-grown cells compared to conventional plates. Furthermore, screening the FMT donor stool for antibiotic resistance revealed 21 populations that evaded detection in plate-based assessment of antibiotic resistance. Our method improves cultivation-based surveys of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.
Topics: Bacteria; Bacteriological Techniques; Drug Resistance, Bacterial; Gastrointestinal Microbiome; High-Throughput Screening Assays
PubMed: 32553109
DOI: 10.7554/eLife.56998 -
International Journal of Infectious... Sep 2007
Topics: Agar; Animals; Diarrhea; Female; Humans; Larva Migrans; Strongyloides stercoralis; Strongyloidiasis
PubMed: 17331785
DOI: 10.1016/j.ijid.2006.12.007 -
PloS One 2020Spissistilus festinus (Say) (Hemiptera: Membracidae) was shown to transmit Grapevine red blotch virus (GRBV) in a greenhouse study. Grapevines infected with GRBV exhibit...
Spissistilus festinus (Say) (Hemiptera: Membracidae) was shown to transmit Grapevine red blotch virus (GRBV) in a greenhouse study. Grapevines infected with GRBV exhibit reduced sugar accumulation, altered secondary metabolite production and delayed berry maturation that negatively impacts wine quality and economics. Augmentative biocontrol may be a useful integrated pest management (IPM) tool for suppressing S. festinus populations in vineyards, but minimal research has been conducted on testing potential predators against the different life stages of S. festinus. The susceptibility of S. festinus adults and nymphs (1st through 5th instar) to predation by six commercially available biocontrol agents in petri dish and bell bean plant arenas was determined under greenhouse conditions. No significant mortality of S. festinus nymphs or adults occurred when exposed to Cryptolaemus montrouzieri adults, C. montrouzieri larvae and Sympherobius barberi adults in petri dish or bell bean plant arenas. Significant mortality of 1st and 2nd instar nymphs of S. festinus in the presence of Zelus renardii nymphs was observed in petri dish but not in bell bean arenas. Hippodamia convergens adults and Chrysoperla rufilabris larvae both consumed a significant number of S. festinus nymphs in petri dish and bell bean arenas. No significant predation of S. festinus adults was documented in this experiment. Results of this study aid in identifying predators that may be suitable candidates for additional field testing to determine their potential efficacy as biocontrol agents of S. festinus in a vineyard setting.
Topics: Animals; Coleoptera; Food Chain; Geminiviridae; Hemiptera; Models, Biological; Nymph; Predatory Behavior
PubMed: 33253247
DOI: 10.1371/journal.pone.0242775 -
Scientific Reports Jul 2023The mechanisms governing chemotaxis in Chlamydomonas reinhardtii are largely unknown compared to those regulating phototaxis despite equal importance on the migratory...
The mechanisms governing chemotaxis in Chlamydomonas reinhardtii are largely unknown compared to those regulating phototaxis despite equal importance on the migratory response in the ciliated microalga. To study chemotaxis, we made a simple modification to a conventional Petri dish assay. Using the assay, a novel mechanism governing Chlamydomonas ammonium chemotaxis was revealed. First, we found that light exposure enhances the chemotactic response of wild-type Chlamydomonas strains, yet phototaxis-incompetent mutant strains, eye3-2 and ptx1, exhibit normal chemotaxis. This suggests that Chlamydomonas transduces the light signal pathway in chemotaxis differently from that in phototaxis. Second, we found that Chlamydomonas collectively migrate during chemotaxis but not phototaxis. Collective migration during chemotaxis is not clearly observed when the assay is conducted in the dark. Third, the Chlamydomonas strain CC-124 carrying agg1, the AGGREGATE1 gene (AGG1) null mutation, exhibited a more robust collective migratory response than strains carrying the wild-type AGG1 gene. The expression of a recombinant AGG1 protein in the CC-124 strain suppressed this collective migration during chemotaxis. Altogether, these findings suggest a unique mechanism; ammonium chemotaxis in Chlamydomonas is mainly driven by collective cell migration. Furthermore, it is proposed that collective migration is enhanced by light and suppressed by the AGG1 protein.
Topics: Chlamydomonas reinhardtii; Chemotaxis; Ammonium Compounds; Chlamydomonas; Cell Movement; Light
PubMed: 37402785
DOI: 10.1038/s41598-023-36818-6 -
Advanced Science (Weinheim,... Dec 2020There is an unmet demand for microfluidics in biomedicine. This paper describes contactless fabrication of microfluidic circuits on standard Petri dishes using just a...
There is an unmet demand for microfluidics in biomedicine. This paper describes contactless fabrication of microfluidic circuits on standard Petri dishes using just a dispensing needle, syringe pump, three-way traverse, cell-culture media, and an immiscible fluorocarbon (FC40). A submerged microjet of FC40 is projected through FC40 and media onto the bottom of a dish, where it washes media away to leave liquid fluorocarbon walls pinned to the substrate by interfacial forces. Such fluid walls can be built into almost any imaginable 2D circuit in minutes, which is exploited to clone cells in a way that beats the Poisson limit, subculture adherent cells, and feed arrays of cells continuously for a week. This general method should have wide application in biomedicine.
PubMed: 33304750
DOI: 10.1002/advs.202001854