Search

Bacillus anthracis is an etiological agent of anthrax, a severe zoonotic disease that can be transmitted to people and cause high mortalities. Bacteriophages and their lytic enzymes, endolysins, have potential therapeutic value in treating infections caused by this bacterium as alternatives or complements to antibiotic therapy. They can also be used to identify and detect B. anthracis. Endolysins of two B. anthracis Wbetavirus phages, J5a and F16Ba which were described by us recently, differ significantly from the best-known B. anthracis phage endolysin PlyG from Wbetavirus genus bacteriophage Gamma and a few other Wbetavirus genus phages. They are larger than PlyG (351 vs. 233 amino acid residues), contain a signal peptide at their N-termini, and, by prediction, have a different fold of cell binding domain suggesting different structural basis of cell epitope recognition. We purified in a soluble form the modified versions of these endolysins, designated by us LysJ and LysF, respectively, and depleted of signal peptides. Both modified endolysins could lyse the B. anthracis cell wall in zymogram assays. Their activity against the living cells of B. anthracis and other species of Bacillus genus was tested by spotting on the layers of bacteria in soft agar and by assessing the reduction of optical density of bacterial suspensions. Both methods proved the effectiveness of LysJ and LysF in killing the anthrax bacilli, although the results obtained by each method differed. Additionally, the lytic efficiency of both proteins was different, which apparently correlates with differences in their amino acid sequence. KEY POINTS: • LysJ and LysF are B. anthracis-targeting lysins differing from lysins studied so far • LysJ and LysF could be overproduced in E. coli in soluble and active forms • LysJ and LysF are active in killing cells of B. anthracis virulent strains., (© 2024. The Author(s).)

Undergraduate students majoring in the life sciences benefit from experience with data analyses that connect mathematical calculations to the biological systems they are studying. Monitoring the optical density and cell number of Saccharomyces cerevisiae liquid cultures allows students to gain quantitative experience generating standard curves and trendlines that capture the relationship between optical density and cell concentration for a given S. cerevisiae strain. Data comparisons across multiple strains can yield insights into the biophysical properties of cells that drive light absorbance and scattering. In this Tips and Tools article, we share a laboratory module that allows students to experience cell biology tools, laboratory measurements, and data analysis to determine the mathematical relationship between optical density and cell concentration in liquid microbial cultures. This module could be integrated into undergraduate classes ranging from general biology to upper-level cell biology or microbiology and can be a starting point for more complex investigations of microbial growth.

Background: Radiochromic film (RCF) dosimeters with their high spatial resolution and tissue equivalent properties are conveniently used for two-dimensional and small-field dosimetry. OC-1 is a new model of RCF dosimeter that was commercially introduced recently. Due to its novelty there is a need to characterize its response in various radiation beam types., Purpose: To study the response of OC-1 RCFs to megavoltage clinical x-ray, electron, and proton beams, as well as kilovoltage x-ray beams used in a small animal research irradiator., Materials and Methods: OC-1 RCFs were cut into ∼4 × 4 cm 2 pieces. RCF samples were irradiated at various dose levels in the range 0.5-120 Gy using different modalities; a small animal radiation research platform (SARRP) (220 kVp), a medical linear accelerator (6 MV, 10 MV, 15 MV, 6 MV FFF, 10 MV FFF photon beams, as well as 6 and 20 MeV electron beams), and a gantry-mounted proton therapy synchrocyclotron. In order to study any dependency on the fractionation scheme, same dose was delivered at several fractions to a set of films. Different dose rates in the range 200-600 MU/min were delivered to a set of films to investigate any dose rate dependency. The films were scanned pre-irradiation and at 48 h post-irradiation using a flatbed scanner. The net optical density (OD) was measured for red, green, and blue color channel for each film. The orientation dependency was studied by scanning the films at eight different orientations. In order to study the temporal evolution of the response of the films, film samples were irradiated at 10 and 50 Gy using 6 MV photon beams and were scanned upon irradiation at certain time intervals up to 3 months. The spectral response of the films were studied over the visible range using a spectrometer., Results: For megavoltage photon, electron, and plateau region of the proton beams, we did not observe a significant dependency on the beam quality, dose rate, and fractionation scheme. At the kV beam, an unusual over-response was observed in the films' net OD. An orientation dependency in the response of the films with a sinusoidal trend was observed. The response of the films increased with time following a double or triple exponential trend. The spectral absorption peaks were blue-shifted with dose., Conclusion: OC-1 RCFs were found to be reliable dosimeters with no significant energy dependency in MV range for photon and electron beams including the FFF beams. They over-respond when irradiated by kV x-ray beams compared to MV x-ray beams. Caution must be exercised to maintain the orientation of the films when scanning. Due to the temporal growth in the net OD of the films, same post-irradiation time interval must be used for scanning the calibration and test films., (© 2024 The Author(s). Medical Physics published by Wiley Periodicals LLC on behalf of American Association of Physicists in Medicine.)

Plasma polymerized methyl acrylate (PPMA) thin films were fabricated on a borosilicate glass substrate at a plasma power of 28 W to study nonlinear optical parameters and electronic properties. X-ray Diffraction analysis confirmed the amorphous nature of the PPMA films, while Attenuated total reflectance Fourier transform infrared spectroscopy indicated monomer fragmentation due to plasma polymerization. Field emission scanning electron microscope images of the films display a water wave-like structure. PPMA films demonstrated thermal stability up to approximately 574 K in both N 2 and air environments. The values of direct band gap energies increase from 3.30 to 3.41 eV with increasing film thicknesses, whereas the Urbach energy values show in an opposite manner. The Wemple-DiDomenico model was employed to analyze both the oscillator energies ranging from 5.54 to 6.44 eV and the dispersion energies ranging from 10.56 to 12.89 eV. The static linear refractive index showed typical dispersion behavior, with film thickness conforming to Moss's rule. The nonlinear refractive index and 2nd and 3rd order nonlinear susceptibilities decrease with increasing the studied films. The lattice dielectric constant values exceeded the high-frequency dielectric constant, indicating the presence of lattice vibrations and free carriers. Electronic parameters are fluctuating with increasing film thickness. The observed changes in nonlinear optical parameters and electronic properties highlight the potential of PPMA films for applications in photovoltaic and optoelectronics., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2024 The Authors.)

Introduction: Intra-ocular lens (IOL) calcification is a rare yet serious complication, presenting as clouding within the optics of IOL and necessitating IOL exchange., Patient and Clinical Findings: In this case, a 77-year-old male experienced gradual vision loss in his left eye (LE) over four years post-cataract surgery a decade before. His best corrected visual acuity (BCVA) was 3/60 in the LE, with the anterior segment displaying a clear cornea but an opacified IOL within the capsular bag. Ultrasound biomicroscopy (UBM) revealed hyperechoic reflections from the IOL in the LE. ImageJ software used on UBM images indicated a significant difference in optical density (OD) compared to the right eye (RE)., Results: The patient was diagnosed with IOL calcification in LE, and underwent anterior vitrectomy and IOL exchange with sulcus-placed IOL with optic capture in the capsular bag, resulting in an improved visual acuity of 6/18. Microscopic examination of explanted IOL revealed whitish calcium carbonate crystal deposits on the IOL, which were visible under polarized light., Conclusions and Significance: The innovative use of polarized light and ImageJ software can be used in resource-constraint settings to confirm the diagnosis in such cases. Based on ImageJ on the UBM image, OD can pick up even subtle changes in the optical clarity of the IOL optic preoperatively., Competing Interests: The authors state no conflict of interest., (© 2024 The Authors.)

The physiological aging process is well known for functional decline in visual abilities. Among the components of the visual system, the dorsal lateral geniculate nucleus (DLG) and superior colliculus (SC) provide a good model for aging investigations, as these structures constitute the main visual pathways for retinal inputs reaching the visual cortex. However, there are limited data available on quantitative morphological and neurochemical aspects in DLG and SC across lifespan. Here, we used optical density to determine immunoexpression of glial fibrillary acidic protein (GFAP) and design-based stereological probes to estimate the neuronal number, total volume, and layer volume of the DLG and SC in marmosets (Callithrix jacchus), ranging from 36 to 143 months of age. Our results revealed an age-related increase in total volume and layer volume of the DLG, with an overall stability in SC volume. Furthermore, a stable neuronal number was demonstrated in DLG and superficial layers of SC (SCv). A decrease in GFAP immunoexpression was observed in both visual centers. The results indicate region-specific variability in volumetric parameter, possibly attributed to structural plastic events in response to inflammation and compensatory mechanisms at the cellular and subcellular level. Additionally, the DLG and SCv seem to be less vulnerable to aging effects in terms of neuronal number. The neuropeptidergic data suggest that reduced GFAP expression may reflect morphological atrophy in the astroglial cells. This study contributes to updating the current understanding of aging effects in the visual system and stablishes a crucial foundation for future research on visual perception throughout the aging process., (© 2024 Wiley Periodicals LLC.)

Purpose: The Beer-Lambert law suggests that visual pigment optical density (OD) should be linearly related to the length of photoreceptor outer segments (POSs). Mammalian studies indicate that visual pigment concentration increases with POS length, but the nature of this relationship may vary due to factors such as visual pigment packing density or retinal eccentricity, and may not necessarily be linearly related. The purpose of this study was to establish the relationship between OD and POS length in humans., Methods: Spectral domain optical coherence tomography (OCT) was used to image POS, and imaging retinal densitometry (IRD) was used to measure OD at corresponding locations in 19 healthy participants (age range 25-82 years). POS length and OD measurements were extracted from OCT and IRD images at 23 discrete locations spanning the central 9° of the retina. The averaged data from all participants were fitted with models based on the Beer-Lambert law to establish the relationship between OD and POS length., Results: Visual pigment OD increased monotonically with POS length, but the relationship was non-linear, and a straight-line fit, based on a simple interpretation of the Beer-Lambert law, provided a poor description. A model allowing for different rod and cone visual pigment concentrations provided a superior fit. Specifically, the data were well described by a model where the molar concentration of visual pigment in cones and rods were 3.8 × 10 -3 mol/L and 1.8 × 10 -3 mol/L, respectively., Conclusions: In accordance with the Beer-Lambert law, the results indicate that OD increases monotonically with POS length in humans, but the precise relationship is dependent on photoreceptor type. These results suggest that visual pigment concentration in rods is only about 48% of that found in cones. This may be due to the ubiquitous nature of artificial light that works to reduce the concentration of rhodopsin in rod photoreceptors., (© 2024 The Authors. Ophthalmic and Physiological Optics published by John Wiley & Sons Ltd on behalf of College of Optometrists.)

Chlorella vulgaris is of great importance in numerous exploratory or industrial applications (e.g., medicals, food, and feed additives). Rapid quantification of algal biomass is crucial in photobioreactors for the optimization of nutrient management and the estimation of production. The main goal of this study is to provide a simple, rapid, and not-resource-intensive estimation method for determining the algal density of C. vulgaris according to the measured parameters using UV-Vis spectrophotometry. Comparative assessment measurements were conducted with seven different methods (e.g., filtration, evaporation, chlorophyll a extraction, and detection of optical density and fluorescence) to determine algal biomass. By analyzing the entire spectra of diluted algae samples, optimal wavelengths were determined through a stepwise series of linear regression analyses by a novel correlation scanning method, facilitating accurate parameter estimation. Nonlinear formulas for spectrometry-based estimation processes were derived for each parameter. As a result, a general formula for biomass concentration estimation was developed, with recommendations for suitable measuring devices based on algae concentration levels. New values for magnesium content and the average single-cell weight of C. vulgaris were established, in addition to the development of a rapid, semiautomated cell counting method, improving efficiency and accuracy in algae quantification for cultivation and biotechnology applications.

The hyphal surface of cells of filamentous fungi is covered with cell wall, which is mainly composed of polysaccharides. Since the cell wall is the first structure to come in contact with the infection host, the environment, and the fungus itself, the elucidation of the cell wall structure and biogenesis is essential for understanding fungal ecology. Among filamentous fungi, the genus Aspergillus is an important group in the industrial, food, and medical fields. It is known that Aspergillus species form hyphal pellets in shake liquid culture. The authors previously found the role of α-1,3-glucan in hyphal aggregation in Aspergillus species. In addition, extracellular polysaccharide galactosaminogalactan contributed to hyphal aggregation as well, and dual disruption of biosynthesis genes of α-1,3-glucan and galactosaminogalactan resulted in complete hyphal dispersion in shake liquid culture. The characteristic of mycelia to form pellets under liquid culture conditions was the main reason why the growth measurement methods used for unicellular organisms could not be applied. We reported that hyphal growth of the dual disruption mutant could be measured by optical density. A real-time plate reader could be used to determine the growth curve of the mycelial growth of the dual disruption mutant. This measurement approach not only provides basic microbiological insights in filamentous fungi, but also has the potential to be applied to high-throughput screening of anti-Aspergillus drugs.

The Aim of the Study: Was to investigate the dynamics of mandibular density in cancer patients during therapy with zolendronic acid., Materials and Methods: The study comprised 14 patients who received zolendronic acid at a dosage of 4 mg once every 28 days for bone metastases. In all 14 patients, measurements of mandibular density values on CT scans were performed over time., Results: Using multiple linear regression analysis, a model was developed to predict the effect of the number of zolendronic acid injections «X 1 » on the dynamics of mandibular density «Y». The resulting formula for predicting mandibular density is Y = 5.9 X 1 + 49 HU., Conclusion: The model has limitations due to the study design but still can be used by oncologists and dentists to assess mandibular density in patients taking zolendronic acid.

The Aim the Study: To analyze the density of the mandible in cancer patients during treatment with zoledronic acid., Materials and Methods: A retrospective cohort study included 45 patients with cancer aged 26-81 years (average age 55±12.88 years), of whom 14 patients had bone metastases ( n =14) and took 4 mg of zolendronic acid once every 28 days. The patients underwent standard PET-CT examinations in the «whole body» mode, and the density of the mandible was examined on CT. Radiation therapy was performed by intracavitary administration of strontium 89 chloride; remote radiation therapy with cisplatin radiomodification. In the presence of bone metastases, patients received complex supportive therapy with zolendronic acid. The effect of zolendronic acid on the density of the mandible in the frontal and lateral sections was studied by multidimensional dispersion analysis., Results: Statistically significant differences ( p =0.002) were revealed for density indicators according to CT scans of the mandible in the frontal region against the background of zolendronic acid therapy. We attribute the absence of statistically significant differences for the density of the mandible in the lateral sections ( p =0.101 and p =0.082) against the background of zolendronic acid therapy to a measurement bias. We attribute the absence of statistically significant differences in density indices against the background of hormonal, radiation, targeted and chemotherapy to the design of the study., Conclusion: Density measurement based on CT examination data can be recommended for use as an additional tool in assessing the effect of zolendronic acid on the density of the mandible. However, the method of measuring the density of the mandible in the lateral sections requires improvement to prevent measurement bias.

Purpose: To develop a method to measure the macular pigment optical density (MPOD) using scanning laser ophthalmoscopic images in young adults and children., Study Design: Cross-sectional study., Methods: Blue light reflectance fundus images of 32 healthy subjects were used. A profile of the linear reflectance changes across the center of the fovea on a grayscale fundus image was generated. The ratio of the macula-to-periphery reflection was designated as the peak value of the MPOD (MPOD [FR] ) based on established fundamentals. In the MPOD profile, the basal width of the pixels at MPOD < 0 (wMP) and width at one-half value of the MPOD [FR] (wMP 0.5 ) were determined. The MOPD at eccentricity of 0.5° was measured by heterochromatic flicker photometry (MPOD [HFP] ), and the correlation between the MPOD [FR] and MPOD [HFP] was evaluated., Results: The MPOD [FR] ranged from 0.17 to 0.73 with a mean of 0.40 ± 0.13. The wMP ranged from 88 to 173 pixels with a mean of 121.7 ± 24.2 pixels, and the wMP 0.5 ranged from 38 to 83 pixels with a mean of 54.1 ± 10.3 pixels. A significant correlation was found between the MPOD [FR] and MPOD [HFP] (r = 0.41, P = 0.02)., Conclusions: This simplified method can provide accurate and reliable values of the MPOD comparable to heterochromatic flicker photometry. Obtaining the fundus images in this fast and easy way should be suitable for children thus enabling clinicians to determine the MPODs for children., (© 2023. Japanese Ophthalmological Society.)

In synthetic biology, Fluorescent reporters are frequently used to characterize the expression levels obtained from both genetic parts such as promoters and ribosome binding sites as well as from complex genetic circuits. To this end, plate readers offer an easy and high-throughput way of characterizing both the growth and fluorescence expression levels of cell cultures. However, despite the similar mode of action used in different devices, their output is not comparable due to intrinsic differences in their setup. Additionally, the generated output is expressed using arbitrary units, limiting reliable comparison of results to measurements taken within one single experiment using one specific plate reader, hampering the transferability of data across different plate readers and laboratories. This article presents an easy and accessible calibration method for transforming the device-specific output into a standardized output expressing the amount of fluorescence per well as a known equivalent fluorophore concentration per cell for fluorescent reporters spanning the visible light spectrum. This calibration method follows a 2-fold approach determining both the estimated number of cells and the equivalent chemical fluorophore concentration per well. It will contribute to the comparison of plate reader experiments between different laboratories across the world and will therefore greatly improve the reliability and exchange of both results and genetic parts between research groups.

Purpose: To evaluate alterations of the choroid in patients with a neurodegenerative disease versus healthy controls, a custom algorithm based on superpixel segmentation was used., Design: A cross-sectional study was conducted on data obtained in a previous cohort study., Subjects: Swept-source optical coherence tomography (OCT) B-scan images obtained using a Triton (Topcon, Japan) device were compiled according to current OSCAR IB and APOSTEL OCT image quality criteria. Images were included from three cohorts: multiple sclerosis (MS) patients, Parkinson disease (PD) patients, and healthy subjects. Only patients with early-stage MS and PD were included., Methods: In total, 104 OCT B-scan images were processed using a custom superpixel segmentation (SpS) algorithm to detect boundary limits in the choroidal layer and the optical properties of the image. The algorithm groups pixels with similar structural properties to generate clusters with similar meaningful properties., Main Outcomes: SpS selects and groups the superpixels in a segmented choroidal area, computing the choroidal optical image density (COID), measured as the standard mean gray level, and the total choroidal area (CA), measured as px 2 ., Results: The CA and choroidal density (CD) were significantly reduced in the two neurodegenerative disease groups (higher in PD than in MS) versus the healthy subjects ( p < 0.001); choroidal area was also significantly reduced in the MS group versus the healthy subjects. The COID increased significantly in the PD patients versus the MS patients and in the MS patients versus the healthy controls ( p < 0.001)., Conclusions: The SpS algorithm detected choroidal tissue boundary limits and differences optical density in MS and PD patients versus healthy controls. The application of the SpS algorithm to OCT images potentially acts as a non-invasive biomarker for the early diagnosis of MS and PD.

Microalgae biomass and pigments have a high economic value due to their many biological and commercial applications. In this sense, Spirulina platensis was grown under different (LEDs) light-emitting diodes. The current examination aims to increase the biomass production of S. platensis by formulating an optimal growth condition under different LED lights. Light-emitting diodes have a precise wavelength that has an encouraging effect on microalgae biomass production. For this purpose, the light intensity of 3000 lx was used to illuminate the culture medium, resulting in enhanced S. platensis biomass production. The highest optical density of 0.576 and dry cell weight of 0.343 g/L was recorded for the white light-emitting diode, and the red light-emitting diode, the optical density of 0.479 and dry cell weight of 0.321 g/L was recorded. The highest protein content of 66.10 ± 0.44% was registered with a blue light-emitting diode, followed by a white light-emitting diode with a protein content of 60.86 ± 0.39%. This research is an essential step in defining the light condition that might be useful to increase the biomass production of S. platensis. The study's findings demonstrated that exposure to various light-emitting diode colors could enhance both the quality and quantity of biomass produced in S. platensis cultures and encourage the use of light-emitting diodes as a light source for S. platensis farming without any undesirable effects on growth., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

A novel chemical assay, the so-called Kdo-DMB-liquid chromatography (LC) assay, was used for the accurate and cost-effective determination of the endotoxin content in supernatants of Gram-negative bacteria bioreactor samples. During mild acid hydrolysis, the endotoxin-specific sugar acid 3-deoxy-D-manno-oct-2-ulsonic acid (Kdo) is quantitatively released. Kdo is reacted with 1,2-diamino-4,5-methylenedioxybenzene (DMB) to obtain the highly fluorescent derivate Kdo-DMB. It is separated from the reaction mixture by reversed phase-(U)HPLC and detected by fluorescence. From the Kdo content the endotoxin content of the sample is calculated. For three batch cultivations of Escherichia coli K12 and a fed-batch cultivation of Pseudomonas putida KT2440, the evolution of the endotoxin content in dependence on the cultivation time was monitored. Under optimal, constant cultivation conditions a linear correlation between the endotoxin content and the easy-to-access bioreactor parameters optical density at 600 nm and dry cell weight was found for both endotoxin kinds. Under stress cultivation conditions the E. coli K12 cultivation showed a stronger increase of the endotoxin content at harvest in comparison to optimal conditions. Optical density and dry cell weight may be used for production reactors as an economic real-time estimation tool to determine the endotoxin content at different cultivation time points and conditions. The optical density can further be used to establish straightforward sample dilution schemes for endotoxin quantification in samples of unknown endotoxin content. The endotoxin content [ng mL -1 ] measured by the Kdo-DMB-LC assay and the endotoxin activity [EU mL -1 ] obtained by the compendial Limulus Amoebocyte Lysate assay show a high correlation for the bacterial bioreactor samples tested., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

Doxorubicin (DRB) is an anthracycline oncogenic drug extracted from cultures of Streptomyces peucetius var. caesius. It is frequently recommended as an anti-neoplastic agent for the treatment of diverse malignancies. It exerts its antineoplastic effect either via inhibiting the enzyme topoisomerase II and/or via intercalation to DNA or reactive oxygen species generation. In the present article, the direct, simple, one-pot, somewhat eco-safe, and non-extractive spectrophotometric system was executed to track doxorubicin, a chemotherapeutic remedy, in the presence of paclitaxel, a naturally occurring Taxan antineoplastic radical, through the greenness rated method. DRB's optical density was studied in various mediums and solvents to develop the current approach. An acidic ethanolic solution was found to increase the optical density of the sample significantly. At 480 nm., the most remarkable optical density was obtained. Various experimental factors, including intrinsic media, solvent, pH, and stability time, were investigated and controlled. The current approach achieved linearity within the 0.6-40.0 µg mL-1 range, accompanied by a limit of both detection and quantification (LOD and LOQ) of 0.18 and 0.55 µg mL-1, correspondingly. The approach was validated under the ICH guidelines (Quality Guidelines). The system's greenness and enhancement degree were estimated., (© 2023. The Author(s).)

The purpose of this study is to calculate microbiological composition of aligners after a day of wearing them. To date, the dental market for orthodontists offers many ways to correct bites. Aligners are transparent and almost invisible from the teeth. They are used for everyday wear to correct the incorrect position of the teeth, which was once considered the prerogative of braces. Scientists worldwide have repeatedly considered questions regarding the interaction between aligners and the oral cavity's microflora; however, the emphasis has mainly shifted toward species composition and antibiotic resistance. The various properties of these microorganisms, including biofilm formation, adhesion to various cells, and the ability to phagocytize, have not been studied so widely. In addition, these characteristics, as well as the microorganisms themselves, have properties that change over time, location, and in certain conditions. In this regard, the problem of biofilm formation in dental practice is always relevant. It requires constant monitoring since high contamination of orthodontic materials can reduce the effectiveness of local anti-inflammatory therapy and cause relapses in caries and inflammatory diseases of the oral cavity. Adhesive properties, one of the key factors in forming the architectonics of biofilms, provide the virulence factors of microorganisms and are characterized by an increase in optical density, determining the duration and retrospectivity of diagnostic studies. This paper focuses on the isolation of clinical microbial isolates during aligner therapy and their ability to form biofilms. In the future, we plan to use the obtained strains of microorganisms to create an effective and safe biofilm-destroying agent. We aimed to study morphometric and densitometric indicators of biofilms of microorganisms persisting on aligners.

Campylobacter growth kinetic parameters can be used to refine the sensitivity and efficiency of microbial growth-based methods. Therefore, the aim of this study was to construct growth curves for C. jejuni , C. coli , and C. lari in pure culture and calculate growth kinetics for each Campylobacter species in the same environmental conditions. Campylobacter jejuni , C. coli and C. lari were grown over 48 h and inoculated into 15 mL Hungate tubes ( N  = 3 trials per species; 5 biological replicates per trial; 3 species; 1 strain per species). Absorbance measurements were taken in 45 min intervals over 24 h. Optical density readings were plotted versus time to calculate growth kinetic parameters. C. jejuni exhibited the longest lag phase ( p  < 0.001) at 15 h 20 min ± 30 min, versus C. coli at 11 h 15 min ± 17 min, and C. lari at 9 h 27 min ± 15 min. The exponential phase duration was no longer than 5 h for all species, and doubling times were all less than 1h 30 min. The variation in growth kinetics for the three species of Campylobacter illustrates the importance of determining individual Campylobacter spp. growth responses for optimizing detection based on low bacterial levels. This study provides kinetics and estimates to define enrichment times necessary for low concentration Campylobacter detection.

Reliable and scalable seroepidemiology methods are needed to estimate SARS-CoV-2 incidence and monitor the dynamics of population-level immunity as the pandemic evolves. We aimed to evaluate the reliability of SARS-CoV-2 normalized ELISA optical density (nOD) at a single dilution compared to titers derived from serial dilutions. We conducted serial serosurveys within a community-based cohort in Salvador, Brazil. Anti-S IgG ELISA (Euroimmun AG) was performed with 5 serial 3-fold dilutions of paired sera from 54 participants. Changes in nOD reliably predicted increases and decreases in titers (98.1% agreement, κ = 95.8%). Fitting the relationship between nOD and interpolated titers to a log-log curve yields highly accurate predictions of titers (r 2  = 0.995) and changes in titers (r 2  = 0.975), using only 1 to 2 dilutions. This approach can significantly reduce the time, labor and resources needed for large-scale serosurveys to ascertain population-level changes in exposure and immunity., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

This paper reports the characterization and antibacterial performance evaluation of some spherical and stable crystalline silver (Ag)/copper (Cu) nanocomposites (Ag-CuNCs) prepared in deionized water (DIW) using pulse laser ablation in liquid (PLAL) method. The influence of various laser fluences (LFs) on the structural, morphological, optical and antibacterial properties of these NCs were determined. The UV-Vis absorbance of these NCs at 403 nm and 595 nm was gradually increased accompanied by a blue shift. XRD patterns disclosed the nucleation of highly crystalline Ag-CuNCs with their face centered cubic lattice structure. TEM images showed the existence of spherical NCs with size range of 3-20 nm and lattice fringe spacing of approximately 0.145 nm. EDX profiles of Ag-CuNCs indicated their high purity. The antibacterial effectiveness of the Ag-CuNCs was evaluated by the inhibition zone diameter (IZD) and optical density (OD600) tests against Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria. The proposed NCs revealed the IZD values in the range of 22-26 mm and 20-25 mm when tested against E. coli and S. aureus bacteria, respectively. The Ag-CuNCs prepared at LF of 14.15 J/cm 2 revealed the best bactericidal activity. It is established that by controlling the laser fluence the bactericidal effectiveness of the Ag-CuNCs can be tuned., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Objective: Histochemical characterization of proteoglycan content in articular cartilage is important for the understanding of osteoarthritis pathogenesis. However, cartilage cells may interfere with the measurement of matrix proteoglycan content in small animal models (e.g. mice and rats) due to the high cell volume fraction (38%) in mice compared to human tissue (~1%). We investigated whether excluding the cells from image analysis affects the histochemically measured proteoglycan content of rat knee joint cartilage and assessed the effectiveness of a deep learning algorithm-based tool named U-Net in cell segmentation., Design: Histological sections were stained with Safranin-O, after which optical densities were measured using digital densitometry to estimate proteoglycan content. U-Net was trained with 600 annotated Safranin-O cartilage images for exclusion of cells from the cartilage extracellular matrix. Optical densities of the ECM with and without cells were compared as a function of normalized tissue depth., Results: U-Net cell segmentation was accurate, with the measured cell area fraction following largely that of ground-truth images (average difference: 4.3%). Cell area fraction varied as a function of tissue depth and took up 8-21% of the tissue area. The exclusion of cells from the analysis led to an increase in the analyzed depth-dependent optical density of cartilage by approximately 0.6-1.8% ( p < 0.01)., Conclusions: Although the effect of cells on the analyzed proteoglycan content is small, it should be considered for improved sensitivity, especially at the onset of the disease during which cells may proliferate in small animals.

Objective: The aim of this study was to develop a tool to visualize and quantify hemodynamic information, such as hemoglobin concentration and hematocrit, within microvascular networks recorded in vivo using intravital video microscopy. Additionally, we aimed to facilitate the 3-D reconstruction of the microvascular networks., Methods: Digital images taken from an intravital video microscopy preparation of the extensor digitorum longus muscle in rats for 25 capillary segments were used. The developed algorithm was used to delineate capillaries of interest, calculate the optical density for each pixel in the image, and reconstruct the 3-D capillary geometry using the calculated light path-lengths. Subsequently, the mean corpuscular hemoglobin concentration (MCHC), hemoglobin concentration, and hematocrit for these capillaries were calculated. We evaluated the hematocrit values determined by our methodology by comparing them to those obtained using a previously published method., Results: The hematocrit values from the proposed optical method were strongly correlated with those calculated using published methods r 2 (25) = .92, p < .001, and demonstrated excellent agreement with a mean difference of 1.3% and a coefficient of variation (CV) of 11%. The average MCHC, hemoglobin concentration, and light path-lengths were 23.83 g/dl, 8.06 g/dl, and 3.92 µm, respectively., Conclusion: The proposed methodology can quantify hemodynamic measurements and produce functional images for visualization of the microcirculation in vivo., (© 2022 John Wiley & Sons Ltd.)

Background and Aim: The resistance of susceptible fish populations and the adaptive potential of heterogeneous biofilms, which cause multiple antibacterial resistance and long-term persistence of microorganisms, mediate the development and outcome of the infectious process. The study of the fish immunological parameters in interaction with biofilm-forming bacteria is of practical importance for assessing the stability of the homeostasis of the fish. This study aimed to determine the immunobiological parameters of Cyprinus carpio Linnaeus when interacting with biofilm-forming bacteria Aeromonas hydrophila ., Materials and Methods: Clinically healthy fish C. carpio L. (Linnaeus, 1758) of both sexes, aged 4 years, and weighing 1.0-1.5 kg (n = 10), were used in this study. The fish were taken from the pond of the VNIIR experimental base in the period of 2020-2022. The standard method was employed to determine the phagocytic activity of blood cells, the total redox activity of neutrophils, and the bactericidal activity of blood serum., Results: After 24-48 h of cultivation in nutrient broth, the implementation of the processes of intercellular communication of bacteria had common patterns of formation of the heterogeneous structure of biofilms. Moreover, analyzing the optical density indices (density, D), it was observed that A. hydrophila was a strong producer of biofilms, as the optical density of the sample (density of sample, Ds) exceeded the optical density of the control (density of control, Dc) by more than 4 times (D = 0.464 ± 0.07). The ratio of the average number of microorganisms attached to the surface of one erythrocyte (average adhesion index) and the percentage (%) of erythrocytes having bacteria on their surface (adhesion coefficient [AC]) was 14.05 ± 0.72, and the adhesion index, AI was ≥4.00, indicating A. hydrophila to be highly adhesive. In addition, the AC of erythrocytes having bacteria on the surface was 14.05% ± 0.72%. A direct correlation was established (R 2 = 0.94) between the AC (14.05% ± 0.11%-13.29% ± 0.08%) and the phagocytic index (11.3% ± 0.29%-32.0% ± 0.8%). The indicators of spontaneous nitro blue tetrazolium were 103.20 ± 11.70 when estimating the total redox activity of neutrophils. The optical density increased to 182.10 ± 21.12 with the addition of 20.0 mL of A. hydrophila bacteria (1 billion/mL) and the activity of neutrophils also increased., Conclusion: Among the markers of homeostasis stability, immunological indicators most fully reflect the mechanisms of initiation, development, and outcome of the infectious process mediated by the interaction of adhesive molecules of multicellular eukaryotes and adhesives of infectious disease pathogens. The research will contribute to further understanding the potential mechanism of quorum-sensing molecules and the search for new anti-adhesive drugs that reduce the formation of biofilms., Competing Interests: The authors declare that they have no competing interests., (Copyright: © Lenchenko, et al.)

The effect of number of cells deposited on decrease in hydraulic conductivity of porous media using CaCO 3 precipitation induced by Sporosarcina pasteurii (ATCC 11,859) was examined in columns packed with glass beads in the range of 0.25 mm and 3 mm in diameter. After resting Sporosarcina pasteurii cells were introduced into the columns, a precipitation solution, which consisted of 500 mM CaCl 2 and 500 mM urea, was introduced under continuous flow conditions. It was shown that hydraulic conductivity was decreased by formation of microbially induced CaCO 3 precipitation from between 8.37 * 10 -1 and 6.73 * 10 -2  cm/s to between 3.69 * 10 -1 and 1.01 * 10 -2  cm/s. The lowest hydraulic conductivity was achieved in porous medium consisting of the smallest glass beads (0.25 mm in diameter) using the highest density of cell suspension (OD 600 2.25). The number of the deposited cells differed depending on the glass bead size of the columns. According to the experiments, 7 * 10 -9  g CaCO 3 was produced by a single resting cell. The urease activity, which led CaCO 3 precipitation, depended on presence of high number of cells deposited in the column because the nutrients were not included in the precipitation solution and consequently, the amount of CaCO 3 precipitated was proportional with the cell number in the column. A mathematical model was also developed to investigate the experimental results, and statistical analysis was also performed., (© 2022. The Author(s).)

Many studies have shown that algal growth is enhanced by organic carbon and algal mixotrophy is relevant for physiology and commercial cultivation. Most studies have tested only a single organic carbon concentration and report different growth parameters which hampers comparisons and improvements to algal cultivation methodology. This study compared growth of green algae Chlorella vulgaris and Chlamydomonas reinhardtii across a gradient of photoautotrophic-mixotrophic-heterotrophic culture conditions, with five acetate concentrations. Culture growth rates and biomass achieved were compared using different methods of biomass estimation. Both species grew faster and produced the most biomass when supplied with moderate acetate concentrations (1-4 g L -1 ), but light was required to optimize growth rates, biomass yield, cell size and cell chlorophyll content. Higher acetate concentration (10 g L -1 ) inhibited algal production. The choice of growth parameter and method to estimate biomass (optical density (OD), chlorophyll a fluorescence, flow cytometry, cell counts) affected apparent responses to organic carbon, but use of OD at 600, 680 or 750 nm was consistent. There were apparent trade-offs among exponential growth rate, maximum biomass, and culture time spent in exponential phase. Different cell responses over 1-10 g L -1 acetate highlight profound physiological acclimation across a gradient of mixotrophy. In both species, cell size vs cell chlorophyll relationships were more constrained in photoautotrophic and heterotrophic cultures, but under mixotrophy, and outside exponential growth phase, these relationships were more variable. This study provides insights into algal physiological responses to mixotrophy but also has practical implications for choosing parameters for monitoring commercial algal cultivation., Competing Interests: John A. Berges is an Academic Editor for PeerJ., (© 2022 Young et al.)

Ethnobotanical studies have reported the traditional medicinal uses of Acacia senegal (L.) Willd. and Argania spinosa (L.) Skeels against kidney stone formation and other chronic kidney diseases. The present work is undertaken to study the litholytic activity and the inhibiting activity of calcium oxalate crystallization by bioactive compounds identified in Argania spinosa (L.) Skeels press-cake (residue of Argan oil) and in Acacia senegal (L.) Willd. The litholytic activity was studied in vitro on cystine and uric acid stones using a porous bag and an Erlenmeyer glass. The study of the inhibiting activity of calcium oxalate crystallization, was based on temporal measurements of the optical density, registered at a 620 nm wavelength for 30 min using an ultraviolet−visible spectrophotometer. The silylation method was performed to identify phytochemicals, followed by gas chromatography coupled with mass spectrophotometry (GC/MS) analysis. The results show significant litholytic activity of Argania Spinosa press-cake hydro-ethanolic extract on uric acid and cystine stones, respectively, with dissolution rates (DR) of 86.38% and 60.42% versus 3.23% and 9.48% for the hydro-ethanolic extract of Acacia senegal exudate. Furthermore, the percentages of nucleation inhibition are 83.78% and 43.77% (p ˂ 0.05) for Argania spinosa and Acacia senegal, respectively. The results point to the detection of 17 phytochemicals in Argania spinosa press-cake extract, the majority of which are phenolic acids and have potent anti-urolithiatic action.

The development of antimicrobial devices and surfaces requires the setup of suitable materials, able to store and release active principles. In this context, zeolites, which are microporous aluminosilicate minerals, hold great promise, since they are able to serve as a reservoir for metal-ions with antimicrobial properties. Here, we report on the preparation of Linde Type A zeolites, partially exchanged with combinations of metal-ions (Ag + , Cu 2+ , Zn 2+ ) at different loadings (0.1-11.9 wt.%). We combine X-ray fluorescence, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and X-ray diffraction to monitor the metal-ion contents, distribution, and conservation of the zeolite structure after exchange. Then, we evaluate their antimicrobial activity, using agar dilution and optical-density monitoring of Escherichia coli cultures. The results indicate that silver-loaded materials are at least 70-fold more active than the copper-, zinc-, and non-exchanged ones. Moreover, zeolites loaded with lower Ag + concentrations remain active down to 0.1 wt.%, and their activities are directly proportional to the total Ag content. Sequential exchanges with two metal ions (Ag + and either Cu 2+ , Zn 2+ ) display synergetic or antagonist effects, depending on the quantity of the second metal. Altogether, this work shows that, by combining analytical and quantitative methods, it is possible to fine-tune the composition of bi-metal-exchanged zeolites, in order to maximise their antimicrobial potential, opening new ways for the development of next-generation composite zeolite-containing antimicrobial materials, with potential applications for the design of dental or bone implants, as well as biomedical devices and pharmaceutical products.

Bacterial studies based on growth curves are common in microbiology and related fields. Compared to the standard photometer and cuvette based protocols, bacterial growth curve measurements with microplate readers provide better temporal resolution, higher efficiency, and are less laborious, while analysis and interpretation of the microplate-based measurements are less straightforward. Recently, we developed a new analysis method for evaluating bacterial growth with microplate readers based on time derivatives. Here, we describe a detailed protocol for this development and provide the homemade program for the new analysis method., Competing Interests: Competing interestsNo competing interest is declared., (Copyright © 2022 The Authors; exclusive licensee Bio-protocol LLC.)

The engineering practices for applying the microbial precipitation of carbonates require a design of the blending biocement solution (BCS). The BCS is usually blended with concentrated strains NO-A10, reaction media, such as urea and CaCl 2 , and a solvent, i.e., water or seawater. To characterize the BCS, the unknown microbial characteristics, such as the cell viability, are complex factors. Therefore, the optical density (OD) was redefined as Rcv OD*, in which OD* was the tentative OD of the BCS used and Rcv was the conversion rate concerning the cell viability. To determine Rcv values, a standard precipitation curve based on the precipitation rate at 24 h was determined. It was found that the curve was expressed by λ 1 OD+ λ 2 OD 2 , in which λ 1 and λ 2 were 8.46 M and -17.633 M, respectively. With this, the Rcv and OD values of unknown BCS were estimated from the results of precipitation tests using arbitrary OD* values. By extending the testing time, the second order term of OD or OD* was negligible. Accordingly, the precipitation amount is expressed as 8.46 OD, in which the OD can be estimated by precipitation tests using arbitrary OD* values of BCSs. Unless the Ca 2+ value is dominant, the optimum blending of BCS can be determined by OD. Thus, it is concluded that the blending design of BCS is achieved using 8.46 OD, or 8.46 Rcv OD*, and the standard precipitation curve was defined in this study.

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.

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 (OD 260 ). Here, we describe a method for direct determination of OD 260 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., Competing Interests: Competing Interests The authors declare that they have no competing interests.

A method of mathematically processing the digital images of targets is developed. The theoretical and mathematical justification and the experimental validation of the possibility of estimating the amount of gunshot residue (GSR) and determining the GSR distribution over the target on the basis of its digital image is provided. The analysis of the optical density in selected concentric rings in the images reveals the radial dependence of soot distribution in the cross section of a gas-gunpowder jet. The analysis of the optical density in selected sectors of the circle reveals the angular dependence of the soot distribution in the gas-gunpowder jet cross section. It is shown that the integral optical density averaged over a selected area in the target image characterizes the mass of GSP deposited on it. It is possible to quantify the differences in the radial and angular distributions of the thickness of the GSR layer on various targets obtained both with the help of weapons of different types at the same distances and with the help of weapons of the same type at different distances, by calculating the distribution of optical density on their digital images.

Optical properties of the cornea are responsible for correct vision; the ultrastructure allows optical transparency, and the biomechanical properties govern the shape, elasticity, or stiffness of the cornea, affecting ocular integrity and intraocular pressure. Therefore, the optical aberrations, corneal transparency, structure, and biomechanics play a fundamental role in the optical quality of human vision, ocular health, and refractive surgery outcomes. However, the inter-relationships of those properties are not yet reported at a macroscopic scale within the hierarchical structure of the cornea. This work explores the relationships between the biomechanics, structure, and optical properties (corneal aberrations and optical density) at a macro-structural level of the cornea through dual Placido-Scheimpflug imaging and air-puff tonometry systems in a healthy young adult population. Results showed correlation between optical transparency, corneal macrostructure, and biomechanics, whereas corneal aberrations and in particular spherical terms remained independent. A compensation mechanism for the spherical aberration is proposed through corneal shape and biomechanics.

The applicability of the Kramers-Kronig relation for attenuated total reflection (ATR) from a metal-dielectric interface that can excite surface plasmon polaritons (SPP) is theoretically investigated. The plasmon-induced attenuation of reflected light can be taken as the resonant absorption of light through a virtual absorptive medium. The optical phase shift of light reflected from the SPP-generating interface is calculated using the KK relation, for which the spectral dependence of ATR is used at around the plasmonic resonance. The KK relation-calculated phase shift shows good agreement with that directly obtained from the reflection coefficient, calculated by a field transfer matrix formula at around the resonance. This indicates that physical causality also produces the spectral dependence of the phase of the leakage field radiated by surface plasmons that would interfere with the reflected part of light incident to the interface. This is analogous with optical dispersion in an absorptive medium where the phase of the secondary field induced by a medium polarization, which interferes with a polarization-stimulating incident field, has a spectral dependence that stems from physical causality.

Sphingomyelin (SM) and cholesterol complexation gives rise to detergent-resistant liquid-ordered domains. The persistence of these domains and subsequent mixed micelle formation was examined in the presence of bile under physiological digestive in vitro conditions for vesicles comprising either SM/cholesterol, porcine brain phosphatidylcholine (BPC)/cholesterol, or soy phosphatidylcholine (SPC)/cholesterol bilayers, the latter two systems having no liquid-ordered domains. Micellization of these digested phospholipid multilamellar vesicle systems was confirmed by transmission electron microscopy. Bovine bile was found to consist of large multilamellar sheets which subsumed phospholipid vesicles to form aggregated superstructures. Budding off from these superstructures were vesicle-to-micelle transition intermediates: unilamellar vesicles and cylindrical micelles. The presence of cholesterol (60/40 phospholipid/cholesterol mol/mol) delayed the initial rapid onset of digestion, but not for BPC and SPC vesicle systems. Acyl chain order/disorder before and after vesicle-to-micelle transition of all three phospholipid/cholesterol systems was examined using Raman spectroscopy. The addition of bovine bile to both PC/cholesterol vesicle systems reduced the overall ratio of acyl chain disorder to order. In SM/cholesterol vesicles with ≤ 20% mol cholesterol, only the lateral inter-acyl chain packing was reduced, whereas for SM/cholesterol vesicles with ≥ 30% mol cholesterol, a higher proportion of gauche-to-trans isomerization was apparent, demonstrating that SM/cholesterol complexes modify the acyl chain structure of micelles., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Standard methods of monitoring the growth kinetics of anaerobic microorganisms are generally impractical when there is a protracted or indeterminate period of active growth, and when high numbers of samples or replications are required. As part of our studies of the adaptive evolution of a simple anaerobic syntrophic mutualism, requiring the characterization of many isolates and alternative syntrophic pairings, we developed a multiplexed growth monitoring system using a combination of commercially available electronics and custom designed circuitry and materials. This system automatically monitors up to 64 sealed, and as needed pressurized, culture tubes and reports the growth data in real-time through integration with a customized relational database. The utility of this system was demonstrated by resolving minor differences in growth kinetics associated with the adaptive evolution of a simple microbial community comprised of a sulfate reducing bacterium, Desulfovibrio vulgaris, grown in syntrophic association with Methanococcus maripaludis, a hydrogenotrophic methanogen., (Copyright © 2021. Published by Elsevier B.V.)

Bacterial growth is classically assessed by measuring the increases in optical density of pure cultures in shaken liquid media. Measuring growth using optical density has severe limitations when studying multistrain interactions, as it is not possible to measure the growth of individual strains within mixed cultures. Here, we demonstrated that constitutively expressed fluorescent proteins can be used to track the growth of individual strains in different liquid media. Fluorescence measurements were highly correlated with optical density measurements and cell counts. This allowed us to assess bacterial growth not only in pure cultures but also in mixed bacterial cultures and determine the impact of a competitor on a focal strain, thereby assessing relative fitness. Furthermore, we were able to track the growth of two different strains simultaneously by using fluorescent proteins with differential excitation and emission wavelengths. Bacterial densities measured by fluorescence yielded more consistent data between technical replicates than optical density measurements. Our setup employs fluorescence microplate readers that allow high throughput and replication. IMPORTANCE We expand on an important limitation of the concept of measuring bacterial growth, which is classically limited to one strain at a time. By adopting our approach, it is possible to measure the growth of several bacterial strains simultaneously with high temporal resolution and in a high-throughput manner. This is important to investigate bacterial interactions, such as competition and facilitation.

The turbidity of milk prohibits the use of optical density measurements for strain characterizations. This often limits research to laboratory media. Here, we cleared milk through centrifugation to remove insoluble milk solids. This resulted in a clear liquid phase, termed milk serum, in which optical density measurements can be used to track microbial growth until a pH of 5.2 is reached. At pH 5.2 coagulation of the soluble protein occurs, making the medium opaque again. We found that behavior in milk serum was predictive of that in milk for 39 Lactococcus lactis (R 2 = 0.81) and to a lesser extent for 42 Lactiplantibacillus plantarum (formerly Lactobacillus plantarum; R 2 = 0.49) strains. Hence, milk serum can be used as an optically clear alternative to milk for comparison of microbial growth and metabolic characteristics. Characterization of the growth rate, specific acidification rate for optical density at a wavelength of 600 nm, and the amount of acid produced per unit of biomass for all these strains in milk serum, showed that almost all strains could grow in milk, with higher specific acidification and growth rates of Lc. lactis strains compared with Lb. plantarum strains. Nondairy Lc. lactis isolates had a lower growth and specific acidification rate than dairy isolates. The amount of acid produced per unit biomass was relatively high and similar for Lc. lactis dairy and nondairy isolates, as opposed to Lb. plantarum isolates. Lactococcus lactis ssp. lactis showed slightly lower growth and acidification rates when compared with ssp. cremoris. For Lc. lactis strains a doubling of the specific acidification rate occurred with a doubling of the maximum growth rate. This relation was not found for Lb. plantarum strains, where the acidification rate remained relatively constant across 39 strains with growth rates ranging from 0.2 h -1 to 0.3 h -1 . We conclude that milk serum is a valuable alternative to milk for high-throughput strain characterization during milk fermentation., (The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).)

The multilayer perceptron (MLP) topology of an artificial neural network (ANN) was applied to create two predictor models in Agrobacterium -mediated gene transformation of tobacco. Agrobacterium -mediated transformation parameters, including Agrobacterium strain, Agrobacterium cell density, acetosyringone concentration, and inoculation duration, were assigned as inputs for ANN-MLP, and their effects on the percentage of putative and PCR-verified transgenic plants were investigated. The best ANN models for predicting the percentage of putative and PCR-verified transgenic plants were selected based on basic network quality statistics. Ex-post error calculations of the relative approximation error (RAE), the mean absolute error (MAE), the root mean square error (RMS), and the mean absolute percentage error (MAPE) demonstrated the prediction quality of the developed models when compared to stepwise multiple regression. Moreover, significant correlations between the ANN-predicted and the actual values of the percentage of putative transgenes ( R 2 = 0.956) and the percentage of PCR-verified transgenic plants ( R 2 = 0.671) indicate the superiority of the established ANN models over the classical stepwise multiple regression in predicting the percentage of putative ( R 2 = 0.313) and PCR-verified ( R 2 = 0.213) transgenic plants. The best combination of the multiple inputs analyzed in this investigation, to achieve maximum actual and predicted transgenic plants, was at OD 600 = 0.8 for the LB4404 strain of Agrobacterium × 300 μmol/L acetosyringone × 20 min immersion time. According to the sensitivity analysis of ANN models, the Agrobacterium strain was the most important influential parameter in Agrobacterium -mediated transformation of tobacco. The prediction efficiency of the developed model was confirmed by the data series of Agrobacterium -mediated transformation of an important medicinal plant with low transformation efficiency. The results of this study are pivotal to model and predict the transformation of other important Agrobacterium -recalcitrant plant genotypes and to increase the transformation efficiency by identifying critical parameters. This approach can substantially reduce the time and cost required to optimize multi-factorial Agrobacterium -mediated transformation strategies., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Niedbała, Niazian and Sabbatini.)

Purpose: In this study, we propose a method to grade corneal stromal opacity using optical density measurements by anterior segment optical coherence tomography (AS-OCT) and validate the approach in Fuchs endothelial corneal dystrophy (FECD)., Methods: A retrospective analysis of human corneal OCT scans was performed on 48 eyes of 32 patients with FECD and 33 control eyes of 21 patients using the Carl Zeiss Cirrus HD-OCT 5000. In addition, corneal edema in fresh rabbit cadaver eyes was artificially induced by distilled water and imaged with the Thorlabs TELESTO-II spectral domain OCT at different time points during saturation. The increase of opacity due to corneal edema was proposed to directly correlate with enhanced reflectivity sites in the OCT images, corresponding to higher optical density. The increase was determined as the image area above a statistically established gray-scale value using ImageJ and correlated with other disease characteristics., Results: Optical densities in human corneas showed significant differences between FECD patients and the control group ( p  = 0.002). The increased optical densities determined in FECD corneas correlated well with other disease characteristics such as corneal pachymetry or visual acuity. Likewise, rabbit corneas showed a time dependent increase in thickness and in corneal optical density during soaking in distilled water., Conclusion: This study presents corneal optical density by AS-OCT as an objective value for corneal changes in FECD. Complementing other diagnostic tools in FECD the assessment of corneal optical density may identify progression of FECD, gauge novel therapeutic strategies and support risk and benefit analyses for corneal surgery.

In this article, the Ni-Cu nanoparticles (NPs) in the amorphous carbon hydrogenated thin films with different copper percentage by co-deposition of RF-plasma enhanced chemical vapor deposition were prepared using acetylene gas and Ni and Cu targets. The films deposited with 5% Cu have minimum value of the average diameter of Multi-walled Carbon Nanotubes, MWCNTs, in about of 100 nm. It can be seen that the lateral size values of the nanoparticles for films with 5% Cu have minimum value of 5.34 nm. Films deposited with 75% Cu have maximum value of optical density specially in high energy. The spectral density power of all films indicated the presence of fractal components in prominent topographies. Films deposited without Cu NPs have minimum value of fractal dimension in about of 2.96. The diagram of the bearing area versus the nanoparticles height has shown the percentage of cavities and single-layers. The single-layer contents of all films were about 95%., (© 2020 Wiley Periodicals LLC.)

Background and Aim: Different Candida species isolated in humans and animals have different types of parasite activity. The most pathogenic species is Candida albicans followed by Candida tropicalis . However, the effects of the morphology of Candida krusei, Candida guilliermondii , and Candida glabrata biofilms on the pathogenicity of these species have not been fully characterized. To the best of our knowledge, there is no literature on the effect of farnesol on rare Candida species. This study aimed to check the effect of different farnesol concentrations on the species C. krusei, C. guilliermondii , and C. glabrata compared with the strain C. albicans ATCC 10231, which has been widely studied, and is a strong producer of biofilms., Materials and Methods: We studied the morphological and densitometric parameters of biofilms produced by Candida species under the influence of the drug farnesol (Sigma-Aldrich, St. Louis, MO). We used a heart brain broth with the addition of 2% bovine blood serum in 96-well plates. To each well, we added 100 mL of C. albicans, C. krusei, C. guilliermondii , or C. glabrata culture, and 0.2-400 mM farnesol. The microliter plates were cultured with the lid closed at 37°C for 48 h. Then, the liquid was removed, and the wells were washed 3 times with 200 mL phosphate buffer solution (pH 7.3). Biofilm fixation was performed using 150 mL of 96% ethanol for 15 min. Then, the microliter plates were dried for 20 min at 37°C, a 0.5% solution of crystalline violet was added, and the plates were placed in an incubator at 37°C. After 5 min, the contents of the wells were removed, washed 3 times with 200 mL of phosphate buffer solution (pH 7.2), and dried. The dye was extracted by washing with 200 mL of 96% ethanol for 30 min. The results were obtained using a photometric analyzer of enzyme immunoassay reactions at an optical density (OD) wavelength of 450 nm., Results: All of Candida spp. strains tested were susceptible to farnesol at concentrations ranging from 0.8 to 400 mM for C. albicans, C. krusei , and C. guilliermondii , and 12.5 to 400 mM for C. glabrata ., Conclusion: This study provides new insights into the use of farnesol against biofilms produced by Candida species, but further studies in vivo are necessary to evaluate the effectiveness of the reduction of OD. To the best of our knowledge, the antimicrobial activity of farnesol against C. krusei, C. guilliermondii , and C. glabrata has not been reported previously, although studies have confirmed the inhibitory effect of farnesol on the growth of different microorganisms., (Copyright: © Sachivkina, et al.)

Although optical hyperthermia could be a promising anticancer therapy, the need for high concentrations of light-absorbing metal nanoparticles and high-intensity lasers, or large exposure times, could discourage its use due to the toxicity that they could imply. In this article, we explore a possible role of silica microparticles that have high biocompatibility and that scatter light, when used in combination with conventional nanoparticles, to reduce those high concentrations of particles and/or those intense laser beams, in order to improve the biocompatibility of the overall procedure. Our underlying hypothesis is that the scattering of light caused by the microparticles would increase the optical density of the irradiated volume due to the production of multiple reflections of the incident light: the nanoparticles present in the same volume would absorb more energy from the laser than without the presence of silica particles, resulting either in higher heat production or in the need for less laser power or absorbing particles for the same required temperature rise. Testing this new optical hyperthermia procedure, based on the use of a mixture of silica and metallic particles, we have measured cell mortality in vitro experiments with murine glioma (CT-2A) and mouse osteoblastic (MC3T3-E1) cell lines. We have used gold nanorods (GNRs) that absorb light with a wavelength of 808 nm, which are conventional in optical hyperthermia, and silica microparticles spheres (hereinafter referred to as SMSs) with a diameter size to scatter the light of this wavelength. The obtained results confirm our initial hypothesis, because a high mortality rate is achieved with reduced concentrations of GNR. We found a difference in mortality between CT2A cancer cells and cells considered non-cancer MC3T3, maintaining the same conditions, which gives indications that this technique possibly improves the efficiency in the cell survival. This might be related with differences in the proliferation rate. Since the experiments were carried out in the 2D dimensions of the Petri dishes, due to sedimentation of the silica particles at the bottom, whilst light scattering is a 3D phenomenon, a large amount of the energy provided by the laser escapes outside the medium. Therefore, better results might be expected when applying this methodology in tissues, which are 3D structures, where the multiple reflections of light we believe will produce higher optical density in comparison to the conventional case of no using scattering particles. Accordingly, further studies deserve to be carried out in this line of work in order to improve the optical hyperthermia technique.

The traditional needle cricothyroidotomy procedure is performed blindly without any medical equipment. Complications including posterior tracheal wall perforation, accidental vessel puncture, and missed tracheal puncture are reported. Therefore, we proposed a dual-wavelength fiber-optic technique based on the technique of near-infrared spectroscopy to assist operators performing needle cricothyroidotomy in a swine model. We embedded optical fibers in a 16-gauge intravenous needle catheter. Real-time data were displayed on an oscilloscope, and we used the program to analyze the data immediately. The change of optical density corresponding to 690-nm and 850-nm wavelengths and hemoglobin parameters (HbO 2 and Hb concentrations) was analyzed immediately using the program in the laptop. Unique and significant optical differences were presented in this experiment. We could easily identify every different tissue by the change of optical density corresponding to 690-nm and 850-nm wavelengths and hemoglobin parameters (HbO 2 and Hb concentrations). Statistical method (Kruskal-Wallis H test) was used to compare differences in tissues at each time-point, respectively. The p values in every tissue in optical density change corresponding to 690 nm and 850 nm were all < 0.001. Furthermore, the p values in every tissue in Hb and HbO 2 were also all < 0.001. The results were statistically significant. This is the first and novel study to introduce a dual-wavelength embedded fibers into a standard cricothyroidotomy needle. This proposed system might be helpful to provide us real-time information of the advanced needle tip to decrease possible complications.

Pumping experiments were performed in a 2D tank in order to estimate the recovery yield of pure heavy chlorinated organic compounds (DNAPL; dense non-aqueous phase liquids) by varying different parameters: permeability of the saturated zone, pumping flow rates, addition of surfactant and heating. Surfactant was added to decrease capillary forces involved in the entrapment of DNAPL in porous media while temperature was increased to reduce DNAPL viscosity (and hence increase its mobility). Chemical enhancement was performed with the addition of Sodium Dodecyl Benzene Sulfonate (SDBS) (at its Critical Micelle Concentration, to avoid DNAPL dissolution) and thermal enhancement was performed at 50 °C (to avoid DNAPL volatilization). The experiments were monitored with photography allowing, on the basis of image interpretation, to convert optical densities (OD) into water saturations (S w ). Image interpretations were compared with modelling results. The two-phase flow modelling was performed with the pressure-pressure formulation using capillary pressure and relative permeability functions based on the van Genuchten-Mualem equations. Measured volumes of DNAPL recovered as well as the displacement of the DNAPL-water interface (radius and height of the cone of depression) are consistent with the modelling results. Furthermore, chemical enhancement results in a significant increase in the recovery rates of DNAPL. The observed improvement in the recovery of DNAPL with chemical enhancement is due to the fact that: (i) the residual saturation inside the cone of depression is lower and (ii) the cone of depression radius and height increase. Thermal enhancement had no beneficial effect on DNAPL recovery rate or yield. This study shows that it is possible to accurately determine water and DNAPL saturations by image interpretation during pumping tests in a 2D tank in the laboratory. For field-scale applications, the two-phase flow model allows to determine remediation yields as well as the volumes of the cone of depression according to the different operating conditions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Aim: To investigate the association of the pair box 6 gene (PAX6) and hsa-miR-328-3p with optical density of macular pigment., Materials and Methods: We evaluated 112 individuals (34 with moderate myopia, eight with high-degree myopia, and 70 healthy individuals). The optical density of macular pigment was measured using single-wavelength reflectometry. DNA and RNA were extracted from whole blood samples. Expression of hsa-miR-328-3p and genotyping of single-nucleotide polymorphism of PAX6 (rs662702) were performed using Applied Biosystems 7900HT real-time polymerase chain reaction system. Optical density of retinal pigment epithelial cells was evaluated using Fundus plus camera., Results: In the group with myopia, with increasing ∆Ct hsa-miR-328-3p, the median optical density of the retinal pigment epithelium decreased statistically significantly (p<0.032). No statistically significant association was found between SNP rs662702 genotype variant of the PAX6 gene and the optical density of the retinal pigment epithelium., Conclusion: The increased expression of hsa-miR-328-3p in the blood indicates a decrease in the optical density of the retinal pigment epithelium in those with myopia., (Copyright© 2021, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)

Spectrophotometric monitoring of 4-nitrophenol (4-NP) reduction by sodium borohydride (NaBH 4 ) using gold nanoparticles (GNPs) as a catalyst has been extensively studied, but the stability of GNPs in terms of change in the surface plasmon resonance (SPR) at different temperatures has not been explored. In the present investigation, our aim was to evaluate the SPR stability of GNPs as a catalyst during the reduction of 4-NP at different elevated temperatures (i.e. 30-60 °C) and sodium borohydride concentrations. Sensitivity of this degradation process toward concentration of GNPs at a range of temperatures is also evaluated. The spectrophotometric results reveal that up to 45 °C, 12 ± 1.5 nm catalyst has a consistent optical density (OD) during the entire 4-NP reduction process, which is related to the surface integrity of catalyst atoms. As the temperature approached 50 °C, the OD gradually decreased and showed a blue shift as the reaction proceeded, which could be related to a decrease in particle size or surface dissolution of gold atoms. The present study may find application in the design of catalysts for the reduction of organic pollutants in industrial wastewater at a range of temperatures., Competing Interests: CONFLICT OF INTEREST: The authors declare no conflict of interest regarding the publication of this work., (Copyright © 2021 The Author(s).)

Echinops kebericho Mesfin is traditionally used for the treatment of various infectious diseases. This study investigated antibacterial activity of the essential oil (EO) and the different fractions of ethanol extract. The most active component was isolated and identified. Isolation and purification was accomplished using chromatographic techniques while identification was done by spectroscopic method. Minimum inhibitory concentration (MIC) was determined using the broth micro-dilution method. In bioactive-guided isolation, percent inhibition was determined using optical density (OD) measurement. The MICs of the essential oil ranged from 78.125 μg/ml to 625 μg/ml, and its activity was observed against methicillin-resistant Staphylococcus aureus (MRSA, NCTC 12493). Ethyl acetate fraction showed high activity against MRSA (NCTC 12493), MIC = 39.075 μg/ml followed by Enterococcus faecalis (ATCC 49532), MIC = 78.125 μg/ml and was least active against Klebsiella pneumoniae (ATCC 700603), MIC = 1,250 μg/ml. MIC of hexane fraction ranged from 156.2 µg/ml to Escherichia coli (ATCC 49532) to 1,250 μg/ml to E. coli (NCTC 11954). The MICs of chloroform fraction ranged from 312.5 to 2500 μg/ml; while butanol fraction could be considered pharmacologically inactive as its MIC value was 2,500 μg/ml for all and no activity against E. coli (NCTC 11954). Dehydrocostus lactone was successfully isolated and identified whose MIC was 19.53 μg/ml against MRSA. Dehydrocostus lactone isolated from E. kebericho M. showed noteworthy antibacterial activity which lends support to ethnopharmacological use of the plant. Further optimization should be done to improve its antibacterial activities and pharmacokinetic profile., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Deyno, Mtewa, Hope, Bazira, Makonnen and Alele.)