Revisiting with a relative-density calibration approach the determination of growth rates of microorganisms by use of optical density data from liquid cultures.
Ontology highlight
ABSTRACT:
SUBMITTER: Lin HL
PROVIDER: S-EPMC2832404 | biostudies-literature | 2010 Mar
REPOSITORIES: biostudies-literature
Publications
Revisiting with a relative-density calibration approach the determination of growth rates of microorganisms by use of optical density data from liquid cultures.
Lin Hsiu-Li HL Lin Chien-Chung CC Lin Yi-Jen YJ Lin Hsiu-Chen HC Shih Chwen-Ming CM Chen Chi-Rong CR Huang Rong-Nan RN Kuo Tai-Chih TC
Applied and environmental microbiology 20100115 5
To solve the problems of measuring the growth rates of microorganisms from optical density (OD)-growth time plots, we used relative-density (RD) plots. The relationship of OD and RD was built from the diluted grown cultures. This method was satisfactorily applied to study the growth of Escherichia coli and the cyanobacterium Anabaena spiroides. ...[more]
Similar Datasets
Project description:Oligodeoxynucleotides (ODNs) are typically purified and analysed with HPLC equipped with a UV-Vis detector. Quantities of ODNs are usually determined using a UV-Vis spectrometer separately after HPLC, and are reported as optical density at 260 nm (OD260). Here, we describe a method for direct determination of OD260 of ODNs using the area of the peaks in HPLC profiles. It is expected that the method will save significant time for researchers in the area of nucleic acid research, and minimize the loss of oligonucleotide samples.
| S-EPMC9288849 | biostudies-literature
Project description:Along the last two centuries, the story of semiconductor materials ranged from a mix of disbelief and frustration to one of the most successful technological achievements ever seen. Such a progress comprised the development of materials and models that, allied to the knowledge provided by spectroscopic techniques, resulted in the (nowadays) omnipresent electronic gadgets. Within this context, optically-based methods were of special importance since, amongst others, they presented details about the electronic states and energy bandgap Egap of semiconductors which, ultimately, decided about their application in devices. Stimulated by these aspects, this work investigated the semiconductors silicon, germanium, and gallium-arsenide in the crystalline (bulk and powder) and amorphous (film) forms. The detailed analysis of the experimental results indicates that accurate Egap values can be obtained by fitting a sigmoid (Boltzmann) function to their corresponding optical absorption spectra. The method is straightforward and, contrary to the traditional approaches to determine Egap, it is exempt from errors due to experimental spectra acquisition and data processing. Additionally, it complies with the requirements of direct, indirect, and amorphous bandgap semiconductors, and it is able to probe the (dis)order of the material as well. In view of these characteristics, a new-unified methodology based on the fitting of the absorption spectrum with a Boltzmann function is being proposed to efficiently determine the optical bandgap of semiconductor materials.
| S-EPMC6677798 | biostudies-literature
Project description:Poisson's ratio (?) defines a material's propensity to laterally expand upon compression, or laterally shrink upon tension for non-auxetic materials. This fundamental metric has traditionally, in some fields, been assumed to be a material-independent constant, but it is clear that it varies with composition across glasses, ceramics, metals, and polymers. The intrinsically elastic metric has also been suggested to control a range of properties, even beyond the linear-elastic regime. Notably, metallic glasses show a striking brittle-to-ductile (BTD) transition for ?-values above ~0.32. The BTD transition has also been suggested to be valid for oxide glasses, but, unfortunately, direct prediction of Poisson's ratio from chemical composition remains challenging. With the long-term goal to discover such high-? oxide glasses, we here revisit whether previously proposed relationships between Poisson's ratio and liquid fragility (m) and atomic packing density (Cg) hold for oxide glasses, since this would enable m and Cg to be used as surrogates for ?. To do so, we have performed an extensive literature review and synthesized new oxide glasses within the zinc borate and aluminoborate families that are found to exhibit high Poisson's ratio values up to ~0.34. We are not able to unequivocally confirm the universality of the Novikov-Sokolov correlation between ? and m and that between ? and Cg for oxide glass-formers, nor for the organic, ionic, chalcogenide, halogenide, or metallic glasses. Despite significant scatter, we do, however, observe an overall increase in ? with increasing m and Cg, but it is clear that additional structural details besides m or Cg are needed to predict and understand the composition dependence of Poisson's ratio. Finally, we also infer from literature data that, in addition to high ?, high Young's modulus is also needed to obtain glasses with high fracture toughness.
| S-EPMC6696245 | biostudies-literature
Project description:A procedure for microbial cell density determination with a high-throughput densitometric assay was developed to allow a precise quantification of both free and sessile cells, such as those of a biofilm, with a large range from low to high cell densities. Densitometry was chosen because it allows fast, rapid and cost-effective measures; it is non-disruptive; and has an easy learning curve. The method setup, and the further validation, was carried out with strains of Candida albicans, C. tropicalis and C. parapsilosis. Equations were developed at the level of the single strains, of the three species and finally a general one applicable to all three species. In the cross validation, with strains absent from the training set, the method was shown to be robust and flexible. The best results were obtained with species specific equations, although the global equation performed almost as well in terms of correlation between real and estimated density values. In all cases, a correlation around 0.98 between effective and predicted density was obtained with figures ranging from 10² to 10⁸ cells mL-1. The entire analytical part of the procedure can be accomplished with a MS Excel macro provided free of charge.
| S-EPMC6406537 | biostudies-literature
Project description:Filamentous fungi form multicellular hyphae, which generally form pellets in liquid shake cultures, during the vegetative growth stage. Because of these characteristics, growth-monitoring methods commonly used in bacteria and yeast have not been applied to filamentous fungi. We have recently revealed that the cell wall polysaccharide α-1,3-glucan and extracellular polysaccharide galactosaminogalactan (GAG) contribute to hyphal aggregation in Aspergillus oryzae. Here, we tested whether Aspergillus fumigatus shows dispersed growth in liquid media that can be quantitatively monitored, similar to that of yeasts. We constructed a double disruptant mutant of both the primary α-1,3-glucan synthase gene ags1 and the putative GAG synthase gene gtb3 in A. fumigatus AfS35 and found that the hyphae of this mutant were fully dispersed. Although the mutant lost α-1,3-glucan and GAG, its growth and susceptibility to antifungal agents were not different from those of the parental strain. Mycelial weight of the mutant in shake-flask cultures was proportional to optical density for at least 18 h. We were also able to quantify the dose response of hyphal growth to antifungal agents by measuring optical density. Overall, we established a convenient strategy to monitor A. fumigatus hyphal growth. Our method can be directly used for screening for novel antifungals against Aspergillus species. IMPORTANCE Filamentous fungi generally form hyphal pellets in liquid culture. This property prevents filamentous fungi so that we may apply the methods used for unicellular organisms such as yeast and bacteria. In the present study, by using the fungal pathogen Aspergillus fumigatus strain with modified hyphal surface polysaccharides, we succeeded in monitoring the hyphal growth quantitatively by optical density. The principle of this easy measurement by optical density could lead to a novel standard of hyphal quantification such as those that have been used for yeasts and bacteria. Dose response of hyphal growth by antifungal agents could also be monitored. This method could be useful for screening for novel antifungal reagents against Aspergillus species.
| S-EPMC8729762 | biostudies-literature
Project description:Previous growth-rate studies covering 14 dinosaur taxa, as represented by 31 data sets, are critically examined and reanalyzed by using improved statistical techniques. The examination reveals that some previously reported results cannot be replicated by using the methods originally reported; results from new methods are in many cases different, in both the quantitative rates and the qualitative nature of the growth, from results in the prior literature. Asymptotic growth curves, which have been hypothesized to be ubiquitous, are shown to provide best fits for only four of the 14 taxa. Possible reasons for non-asymptotic growth patterns are discussed; they include systematic errors in the age-estimation process and, more likely, a bias toward younger ages among the specimens analyzed. Analysis of the data sets finds that only three taxa include specimens that could be considered skeletally mature (i.e., having attained 90% of maximum body size predicted by asymptotic curve fits), and eleven taxa are quite immature, with the largest specimen having attained less than 62% of predicted asymptotic size. The three taxa that include skeletally mature specimens are included in the four taxa that are best fit by asymptotic curves. The totality of results presented here suggests that previous estimates of both maximum dinosaur growth rates and maximum dinosaur sizes have little statistical support. Suggestions for future research are presented.
| S-EPMC3864909 | biostudies-literature
Project description:We review the optical properties of the FMO complex as found by spectroscopic studies of the Q ( y ) band over the last two decades. This article emphasizes the different methods used, both experimental and theoretical, to elucidate the excitonic structure and dynamics of this pigment-protein complex.
| S-EPMC2882565 | biostudies-literature
Project description:Tuning and calibration are processes for improving the representativeness of a computer simulation code to a physical phenomenon. This article introduces a statistical methodology for simultaneously determining tuning and calibration parameters in settings where data are available from a computer code and the associated physical experiment. Tuning parameters are set by minimizing a discrepancy measure while the distribution of the calibration parameters are determined based on a hierarchical Bayesian model. The proposed Bayesian model views the output as a realization of a Gaussian stochastic process with hyperpriors. Draws from the resulting posterior distribution are obtained by the Markov chain Monte Carlo simulation. Our methodology is compared with an alternative approach in examples and is illustrated in a biomechanical engineering application. Supplemental materials, including the software and a user manual, are available online and can be requested from the first author.
| S-EPMC2879656 | biostudies-literature
Project description:For modern security, devices, individuals, and communications require unprecedentedly unique identifiers and cryptographic keys. One emerging method for guaranteeing digital security is to take advantage of a physical unclonable function. Surprisingly, native silk, which has been commonly utilized in everyday life as textiles, can be applied as a unique tag material, thereby removing the necessary apparatus for optical physical unclonable functions, such as an objective lens or a coherent light source. Randomly distributed fibers in silk generate spatially chaotic diffractions, forming self-focused spots on the millimeter scale. The silk-based physical unclonable function has a self-focusing, low-cost, and eco-friendly feature without relying on pre-/post-process for security tag creation. Using these properties, we implement a lens-free, optical, and portable physical unclonable function with silk identification cards and study its characteristics and reliability in a systemic manner. We further demonstrate the feasibility of the physical unclonable functions in two modes: authentication and data encryption.
| S-EPMC8752800 | biostudies-literature
Project description:We study a stochastic model of urban growth generating spatial distributions of population densities at an intermediate mesoscopic scale. The model is based on the antagonist interplay between the two opposite abstract processes of aggregation (preferential attachment) and diffusion (urban sprawl). Introducing indicators to quantify urban form, the model is first statistically validated and intensively explored to understand its complex behavior across the parameter space. We then compute real morphological indicators on local areas of size 50km covering all European Union, and show that the model can reproduce most of these existing urban morphologies. It implies that the morphological dimension of urban growth processes at this scale are sufficiently captured by the two abstract processes of aggregation and diffusion.
| S-EPMC6126859 | biostudies-literature