Effects of different cryopreservation parameters on the differences between trypan blue and fluorescent SYTO 13/GelRed assays.

Post-thaw cell viability assessment is very important in cryopreservation because it is the main assessment method used to optimize cryopreservation protocols for each cell type; hence, having standardized accurate, quick, and reliable assays for post-thaw cell viability measurements is of utmost importance. The trypan blue exclusion assay and nucleic-acid-binding fluorescence-based assays are two different methods for cell viability assessment. Both assays identify cells with damaged membranes by whether they let a compound enter the cell. In this study, these two assays are compared in the context of cryopreservation and the impacts of important cryopreservation parameters on the differences in measurements are investigated. H9c2 myoblasts were cryopreserved with different freezing protocols. Cell membrane integrities were measured immediately after thaw as well as after cryoprotectant removal by a hemocytometer-based trypan blue dye exclusion assay and a dual fluorometric SYTO 13/GelRed assay; and the results were compared. This study quantifies how (i) the absence or presence of different cryoprotectants, (ii) different cell-cryoprotectant incubation conditions, and (iii) the presence or removal of cryoprotectants after thaw affect the differences between these two viability assays.

Methanol bioconversion in Methylotuvimicrobium buryatense 5GB1C through self-cycling fermentation.

Methanol is an abundant and low-cost next-generation carbon source. While many species of methanotrophic bacteria can convert methanol into valuable bioproducts in bioreactors, Methylotuvimicrobium buryatense 5GB1C stands out as one of the most promising strains for industrialization. It has a short doubling time compared to most methanotrophs, remarkable resilience against contamination, and a suite of tools enabling genetic engineering. When approaching industrial applications, growing M. buryatense 5GB1C on methanol using common batch reactor operation has important limitations; for example methanol toxicity leads to mediocre biomass productivity. Advanced bioreactor operation strategies, such as fed-batch and self-cycling fermentation, have the potential to greatly improve the industrial prospects of methanotrophs growing on methanol. Herein, implementation of fed-batch operation led to a 26-fold increase in biomass density, while two different self-cycling fermentation (SCF) strategies led to 3-fold and 10-fold increases in volumetric biomass productivity. Interestingly, while synchronization is a typical trait of microbial populations undergoing SCF, M. buryatense 5GB1C cultures growing under this mode of operation led to stable, reproducible cycles but no significant synchronization.

In vivo quantification of polyhydroxybutyrate (PHB) in the alphaproteobacterial methanotroph, Methylocystis sp. Rockwell.

Methane is a common industrial by-product that can be used as feedstock for production of the biopolymer polyhydroxybutyrate (PHB) by alphaproteobacterial methanotrophs. In vivo assessment of PHB production would shed light on the biosynthesis process and guide design of improved production strategies, but it is currently difficult to perform efficiently. In this study, the alphaproteobacterial methanotroph Methylocystis sp. Rockwell was grown on methane with three different nitrogen sources (ammonium, nitrate, and atmospheric nitrogen), and biomass samples were harvested at defined time points during lag, exponential, and stationary growth phases. PHB cell content was analyzed at these sampling points via a standard gas chromatography-flame ionization detector method, which requires hydrolysis of PHB and esterification of the resulting monomer under acidic conditions, and a novel, rapid, cost-effective approach based on fixation and staining of bacterial cells via Nile Blue A fluorescent dye enabling differential staining of cell membranes and intracellular PHB granules for single-cell analysis through fluorescence microscopy. Overall, the two PHB quantification approaches were in agreement at all stages of growth and in all three growing conditions tested. The PHB cell content was greatest with atmospheric nitrogen as a nitrogen source, followed by ammonium and nitrate. Under atmospheric nitrogen and ammonium conditions, PHB cell content decreased with growth progression, while under nitrate conditions PHB cell content remained unchanged in all growth phases. In addition to presenting a rapid, efficient method enabling in vivo quantification of PHB production, the present study highlights the impact of nitrogen source on PHB production by Methylocystis sp. Rockwell. KEY POINTS: • A novel fluorescence microscopy method to quantify PHB in single cells was developed • The microscopy method was validated by the derivation/gas chromatography method • Methylocystis sp. Rockwell synthesizes PHB granules without nutrient stress.

Transcriptomic and Metabolomic Responses to Carbon and Nitrogen Sources in Methylomicrobium album BG8.

Methanotrophs use methane as their sole carbon and energy source and represent an attractive platform for converting single-carbon feedstocks into value-added compounds. Optimizing these species for biotechnological applications involves choosing an optimal growth substrate based on an understanding of cellular responses to different nutrients. Although many studies of methanotrophs have examined growth rate, yield, and central carbon flux in cultures grown with different carbon and nitrogen sources, few studies have examined more global cellular responses to different media. Here, we evaluated global transcriptomic and metabolomic profiles of Methylomicrobium album BG8 when grown with methane or methanol as the carbon source and nitrate or ammonium as the nitrogen source. We identified five key physiological changes during growth on methanol: M. album BG8 cultures upregulated transcripts for the Entner-Doudoroff and pentose phosphate pathways for sugar catabolism, produced more ribosomes, remodeled the phospholipid membrane, activated various stress response systems, and upregulated glutathione-dependent formaldehyde detoxification. When using ammonium, M. album BG8 upregulated hydroxylamine dehydrogenase (haoAB) and overall central metabolic activity, whereas when using nitrate, cultures upregulated genes for nitrate assimilation and conversion. Overall, we identified several nutrient source-specific responses that could provide a valuable basis for future research on the biotechnological optimization of these species. IMPORTANCE Methanotrophs are gaining increasing interest for their biotechnological potential to convert single-carbon compounds into value-added products such as industrial chemicals, fuels, and bioplastics. Optimizing these species for biotechnological applications requires a detailed understanding of how cellular activity and metabolism vary across different growth substrates. Although each of the two most commonly used carbon sources (methane or methanol) and nitrogen sources (ammonium or nitrate) in methanotroph growth media have well-described advantages and disadvantages in an industrial context, their effects on global cellular activity remain poorly characterized. Here, we comprehensively describe the transcriptomic and metabolomic changes that characterize the growth of an industrially promising methanotroph strain on multiple combinations of carbon and nitrogen sources. Our results represent a more holistic evaluation of cellular activity than previous studies of core metabolic pathways and provide a valuable basis for the future biotechnological optimization of these species.

Cryopreservation of swine colostrum-derived cells.

Mesenchymal stromal cells (MSCs) have been demonstrated to possess anti-inflammatory and antimicrobial properties and are of interest in biotechnologies that will require cryopreservation. Recently, MSC-like cells were isolated from colostrum and milk. We used an interrupted slow freezing procedure to examine cryoinjury incurred during slow cooling and rapid cooling of MSC-like cells from swine colostrum. Cells were loaded with either dimethyl sulfoxide (Me2SO) or glycerol, cooled to a nucleation temperature, ice-nucleated, and further cooled at 1 °C/min. At several temperatures along the cooling path, cells were either thawed directly, or plunged into liquid nitrogen for storage and later thawed. The pattern of direct-thaw and plunge-thaw responses was used to guide optimization of cryopreservation protocol parameters. We found that both 5% Me2SO (0.65 M, loaded for 15 min on ice) or 5% glycerol (0.55 M, loaded for 1 h at room temperature) yielded cells with high post-thaw membrane integrity when cells were cooled to at least -30 °C before being plunged into, and stored in, liquid nitrogen. Cells cultured post-thaw exhibited osteogenic differentiation similar to fresh unfrozen control. Fresh and cryopreserved MSC-like cells demonstrated antimicrobial activity against S. aureus. Also, the antimicrobial activity of cell-conditioned media was higher when both fresh and cryopreserved MSC-like cells were pre-exposed to S. aureus. Thus, we were able to demonstrate cryopreservation of colostrum-derived MSC-like cells using Me2SO or glycerol, and show that both cryoprotectants yield highly viable cells with osteogenic potential, but that cells cryopreserved with glycerol retain higher antimicrobial activity post-thaw.

Prophylaxis of Mycobacterium tuberculosis H37Rv Infection in a Preclinical Mouse Model via Inhalation of Nebulized Bacteriophage D29.

Globally, more people die annually from tuberculosis than from any other single infectious agent. Unfortunately, there is no commercially-available vaccine that is sufficiently effective at preventing acquisition of pulmonary tuberculosis in adults. In this study, pre-exposure prophylactic pulmonary delivery of active aerosolized anti-tuberculosis bacteriophage D29 was evaluated as an option for protection against Mycobacterium tuberculosis infection. An average bacteriophage concentration of approximately 1 PFU/alveolus was achieved in the lungs of mice using a nose-only inhalation device optimized with a dose simulation technique and adapted for use with a vibrating mesh nebulizer. Within 30 minutes of bacteriophage delivery, the mice received either a low dose (∼50-100 CFU), or an ultra-low dose (∼5-10 CFU), of M. tuberculosis H37Rv aerosol to the lungs. A prophylactic effect was observed with bacteriophage aerosol pre-treatment significantly decreasing M. tuberculosis burden in mouse lungs 24 hours and 3 weeks post-challenge (p < 0.05). These novel results indicate that a sufficient dose of nebulized mycobacteriophage aerosol to the lungs may be a valuable intervention to provide extra protection to health care professionals and other individuals at risk of exposure to M. tuberculosis.

Polyhydroxybutyrate (PHB) biodegradation using bacterial strains with demonstrated and predicted PHB depolymerase activity.

The biodegradation of polyhydroxybutyrate (PHB) has been broadly investigated, but studies typically focus on a single strain or enzyme and little attention has been paid to comparing the interaction of different PHB depolymerase (PhaZ)-producing strains with this biopolymer. In this work, we selected nine bacterial strains-five with demonstrated and four with predicted PhaZ activity-to compare their effectiveness at degrading PHB film provided as sole carbon source. Each of the strains with demonstrated activity were able to use the PHB film (maximum mass losses ranging from 12% after 2 days for Paucimonas lemoignei to 90% after 4 days for Cupriavidus sp.), and to a lower extent Marinobacter algicola DG893 (with a predicted PhaZ) achieved PHB film mass loss of 11% after 2 weeks of exposure. Among the strains with proven PhaZ activity, Ralstonia sp. showed the highest specific activity since less biomass was required to degrade the polymer in comparison to the other strains. In the case of Ralstonia sp., PHB continued to be degraded at pH values as low as pH 3.3-3.7. In addition, analysis of the extracellular fractions of the strains with demonstrated activity showed that Comamonas testosteroni, Cupriavidus sp., and Ralstonia sp. readily degraded both PHB film and PHB particles in agar suspensions. This study highlights that whole cell cultures and enzymatic (extracellular) fractions display different levels of activity, an important factor in the development of PHB-based applications and in understanding the fate of PHB and other PHAs released in the environment. Furthermore, predictions of PhaZ functionality from genome sequencing analyses remain to be validated by experimental results; PHB-degrading ability could not be proven for three of four investigated species predicted by the polyhydroxyalkanoates (PHA) depolymerase engineering database.

Anti-Tuberculosis Bacteriophage D29 Delivery with a Vibrating Mesh Nebulizer, Jet Nebulizer, and Soft Mist Inhaler.

PURPOSE: To compare titer reduction and delivery rate of active anti-tuberculosis bacteriophage (phage) D29 with three inhalation devices. METHODS: Phage D29 lysate was amplified to a titer of 11.8 ± 0.3 log10(pfu/mL) and diluted 1:100 in isotonic saline. Filters captured the aerosolized saline D29 preparation emitted from three types of inhalation devices: 1) vibrating mesh nebulizer; 2) jet nebulizer; 3) soft mist inhaler. Full-plate plaque assays, performed in triplicate at multiple dilution levels with the surrogate host Mycobacterium smegmatis, were used to quantify phage titer. RESULTS: Respective titer reductions for the vibrating mesh nebulizer, jet nebulizer, and soft mist inhaler were 0.4 ± 0.1, 3.7 ± 0.1, and 0.6 ± 0.3 log10(pfu/mL). Active phage delivery rate was significantly greater (p < 0.01) for the vibrating mesh nebulizer (3.3x108 ± 0.8x108 pfu/min) than for the jet nebulizer (5.4x104 ± 1.3x104 pfu/min). The soft mist inhaler delivered 4.6x106 ± 2.0x106 pfu per 11.6 ± 1.6 µL ex-actuator dose. CONCLUSIONS: Delivering active phage requires a prudent choice of inhalation device. The jet nebulizer was not a good choice for aerosolizing phage D29 under the tested conditions, due to substantial titer reduction likely occurring during droplet production. The vibrating mesh nebulizer is recommended for animal inhalation studies requiring large amounts of D29 aerosol, whereas the soft mist inhaler may be useful for self-administration of D29 aerosol.

Enzymatic degradation of dimensionally constrained polyhydroxybutyrate films.

The effect of dimensional constraint, imparted by a variation in film thickness, on the enzymatic degradation of polyhydroxybutyrate (PHB) is reported. The characterization of the crystalline structure and the surface topography of solvent-cast PHB thin films revealed strong correlations between film thickness and both crystallinity and crystal anisotropy, with the polymer film becoming more amorphous with decreasing thickness. The enzymatic degradation of the PHB films was characterized using a high precision diffraction metrology, which enabled the visualization of small variations in the degradation behavior. The results show that the degradation rate increases with decreasing thickness due to the corresponding decrease in crystallinity. However, in a nanoscopic ultra-thin PHB specimen, produced by µ-transfer molding, enzymatic degradation was impeded. The enzymatic degradation rate of the PHB films therefore was found to exhibit a discontinuous trend with respect to film thickness: initially increasing as film thickness was reduced, and then decreasing dramatically once the thickness was reduced to tens of nanometers. In this regime, enzymatic degradation was hindered by the absence of crystalline regions in the films. These results show that a nano-dimensional constraint on PHB films can result in specimens with a tunable response to extracellular enzymes.

Industrializing methanotrophs and other methylotrophic bacteria: from bioengineering to product recovery.

Microbes that use the single-carbon substrates methanol and methane offer great promise to bioindustry along with substantial environmental benefits. Methanotrophs and other methylotrophs can be engineered and optimized to produce a wide range of products, from biopolymers to biofuels and beyond. While significant limitations remain, including delivery of single-carbon feedstock to bioreactors, efficient growth, and scale-up, these challenges are being addressed and notable improvements have been rapid. Development of expression chassis, use of genome-scale and regulatory models based on omics data, improvements in bioreactor design and operation, and development of green product recovery schemes are enabling the rapid development of single-carbon bioconversion in the industrial space.

Sensitivity of visible range multi-wavelength algorithms for retinal tissue oximetry to acquisition parameters.

This study examined the sensitivity of broadband spectroscopy algorithms for retinal tissue oximetry to spectral acquisition parameters. Monte Carlo simulations were conducted on a 4-layer retinal model to assess the impact of various parameters. The optimal spectral range for accurate measurements was determined to be 530 nm to 585 nm. Decreased spectral resolution below 4 nm significantly reduced accuracy. Using an acquisition area larger than the blood vessel resulted in an underestimation of oxygen saturation, especially for high values. A threshold was observed where increased light intensity had no significant impact on measurement variability. The study highlights the importance of informed parameter selection for accurately assessing retinal microcapillary oxygenation and studying local hemodynamics.

Adapted feeding strategies in fed-batch fermentation improve sugar delivery and ethanol productivity.

Bioethanol is a renewable fuel widely used in road transportation and is generally regarded as a clean energy source. Although fermentation is one of the major processes in bioethanol production, studies on improving its efficiency through operational design are limited, especially compared to other steps (pretreatment and hydrolysis/saccharification). In this study, two adapted feeding strategies, in which feed medium addition (sugar delivery) was adjusted to increase the supply of fermentable sugar, were developed to improve ethanol productivity in 5-L fed-batch fermentation by Saccharomyces cerevisiae. Specifically, a linear adapted feeding strategy was established based on changes in cell biomass, and an exponential adapted feeding strategy was developed based on cell biomass accumulation. By implementing these two feeding strategies, the overall ethanol productivity reached 0.88±0.04 and 0.87±0.06 g/L/h, respectively. This corresponded to ~20% increases in ethanol productivity compared to fixed pulsed feeding operations. Additionally, there was no residual glucose at the end of fermentation, and final ethanol content reached 95±3 g/L under the linear adapted operation and 104±3 g/L under the exponential adapted feeding strategy. No statistical difference was observed in the overall ethanol yield (ethanol-to-sugar ratio) between fixed and adapted feeding strategies (~91%). These results demonstrate that sugar delivery controlled by adapted feeding strategies was more efficient than fixed feeding operations, leading to higher ethanol productivity. Overall, this study provides novel adapted feeding strategies to improve sugar delivery and ethanol productivity. Integration into the current practices of the ethanol industry could improve productivity and reduce production costs of fermentation processes.

Accelerating the Biodegradation of Poly(lactic acid) through the Inclusion of Plant Fibers: A Review of Recent Advances.

As the global demand for plastics continues to grow, plastic waste is accumulating at an alarming rate with negative effects on the natural environment. The industrially compostable biopolymer poly(lactic acid) (PLA) is therefore being adopted for use in many applications, but the degradation of this material is slow under many end-of-life conditions. This Perspective explores the feasibility of accelerating the degradation of PLA through the formation of PLA-plant fiber composites. Topics include: (a) key properties of PLA, plant-based fibers, and biocomposites; (b) mechanisms of both hydrolytic degradation and biodegradation of PLA-fiber composites; (c) end-of-life degradation of PLA and PLA-plant fiber composites in aerobic and anaerobic conditions, relevant to compost, soil and seawater (aerobic), and landfills (anaerobic); and (d) sustainability and environmental impact of PLA and PLA-plant fiber composites, as evaluated using life cycle assessment. Additional degradation modes, including thermal and photodegradation, which are relevant during processing and use, have been omitted for clarity, as have other types of PLA biocomposites. Multiple studies have shown that the addition of some types of plant fibers to PLA (to form PLA biocomposites) accelerates both water transport in the material and hydrolysis, presenting a possible avenue for improving the end-of-life degradation of these materials. To facilitate the continued development of materials with enhanced biodegradability, we identify a need to implement testing protocols that can distinguish between different degradation mechanisms.

Targeted spectroscopy in the eye fundus.

Significance: The assessment of biomarkers in the eye is rapidly gaining traction for the screening, diagnosis, and monitoring of ocular and neurological diseases. Targeted ocular spectroscopy is a technology that enables concurrent imaging of the eye fundus and analysis of high-quality spectra from a targeted region within the imaged area. This provides structural, compositional, and functional information of specific regions of the eye fundus from a non-invasive approach to ocular biomarker detection. Aim: The aim of our study was to demonstrate the multimodal functionality and validation of targeted ocular spectroscopy. This was done in vitro, using a reference target and a model eye, and in vivo. Approach: Images and spectra from different regions of a reference target and a model eye were acquired and analyzed to validate the system. Targeted ocular fluorescence spectroscopy was also demonstrated with the same model. Subsequently, in vivo imaging and diffuse reflectance spectra were acquired to assess blood oxygen saturation in the optic nerve head and the parafovea of healthy subjects. Results: Tests conducted with the reference target showed accurate spectral analysis within specific areas of the imaging space. In the model eye, distinct spectral signatures were observed for the optic disc, blood vessels, the retina, and the macula, consistent with the variations in tissue composition and functions between these regions. An ocular oximetry algorithm was applied to in vivo spectra from the optic nerve head and parafovea of healthy patients, showing significant differences in blood oxygen saturation. Finally, targeted fluorescence spectral analysis was performed in vitro. Conclusions: Diffuse reflectance and fluorescence spectroscopy in specific regions of the eye fundus open the door to a whole new range of monitoring and diagnostic capabilities, from assessment of oxygenation in glaucoma and diabetic retinopathy to photo-oxidation and photodegradation in age-related macular degeneration.

Self-cycling operation increases productivity of recombinant protein in Escherichia coli.

Self-cycling fermentation (SCF), a cyclical, semi-continuous process that induces cell synchrony, was incorporated into a recombinant protein production scheme. Escherichia coli CY15050, a lac(-) mutant lysogenized with temperature-sensitive phage λ modified to over-express ß-galactosidase, was used as a model system. The production scheme was divided into two de-coupled stages. The host cells were cultured under SCF operation in the first stage before being brought to a second stage where protein production was induced. In the first stage, the host strain demonstrated a stable cycling pattern immediately following the first cycle. This reproducible pattern was maintained over the course of the experiments and a significant degree of cell synchrony was obtained. By growing cells using SCF, productivity increased 50% and production time decreased by 40% compared to a batch culture under similar conditions. In addition, synchronized cultures induced from the end of a SCF cycle displayed shorter lysis times and a more complete culture-wide lysis than unsynchronized cultures. Finally, protein synthesis was influenced by the time at which the lytic phase was induced in the cell life cycle. For example, induction of a synchronized culture immediately prior to cell division resulted in the maximum protein productivity, suggesting protein production can be optimized with respect to the cell life cycle using SCF.

Effects of di-(2-ethylhexyl) phthalate and four of its metabolites on steroidogenesis in MA-10 cells.

Phthalate plasticizers are used in the plastics industry to aid in processing and impart flexibility to plastics. Due to the broad use of plastics, and the tendency of plasticizers to leach out of polymers, plasticizers have become ubiquitous in the environment. Concerns about the testicular toxicity of phthalate plasticizers, in particular di-(2-ethylhexyl) phthalate (DEHP), have arisen due to their ability to cause male reproductive tract abnormalities in animal models. It has been assumed that the DEHP metabolite, mono-(2-ethylhexyl) phthalate (MEHP), is the active compound, however, metabolites such as 2-ethylhexanol, 2-ethylhexanal and 2-ethylhexanoic acid, have not been thoroughly investigated. The aim of this study was to evaluate the anti-androgenic potential of these metabolites in vitro with a mouse Leydig tumor cell line, MA-10 cells. DEHP, MEHP and 2-ethylhexanal were found to decrease cell viability, as well as steroidogenic potential. The latter was assessed using an enzyme-linked immunosorbent assay (ELISA) to quantify steroid production and quantitative real-time polymerase chain reaction (qRT-PCR) to assess gene expression analysis of key steroidogenic enzymes. 2-Ethylhexanal proved to be the most potent steroidogenic disruptor, offering intriguing implications in the search for the mechanism of phthalate testicular toxicity. Overall, the study suggests the involvement of multiple active metabolites in the testicular toxicity of DEHP.

The influence of self-cycling fermentation long- and short-cycle schemes on Saccharomyces cerevisiae and Escherichia coli.

Self-cycling fermentation (SCF), a cyclic process in which cells, on average, divide once per cycle, has been shown to lead to whole-culture synchronization and improvements in productivity during bioconversion. Previous studies have shown that the completion of synchronized cell replication sometimes occurs simultaneously with depletion of the limiting nutrient. However, cases in which the end of cell doubling occurred before limiting nutrient exhaustion were also observed. In order to better understand the impact of these patterns on bioprocessing, we investigated the growth of Saccharomyces cerevisiae and Escherichia coli in long- and short-cycle SCF strategies. Three characteristic events were identified during SCF cycles: (1) an optimum in control parameters, (2) the time of completion of synchronized cell division, and (3) the depletion or plateau of the limiting nutrient. Results from this study and literature led to the identification of three potential trends in SCF cycles: (A) co-occurrence of the three key events, (B) cell replication ending prior to the co-occurrence of the other two events, and (C) depletion or plateau of the limiting nutrient occurring later than the co-occurrence of the other two events. Based on these observations, microbial physiological differences were analyzed and a novel definition for SCF is proposed.

Use of uncoated magnetic beads to capture Mycobacterium smegmatis and Mycobacterium avium paratuberculosis prior detection by mycobacteriophage D29 and real-time-PCR.

Uncoated tosyl-activated magnetic beads were evaluated to capture Mycobacterium smegmatis and Mycobacterium avium subspecies paratuberculosis (MAP) from spiked feces, milk, and urine. Centrifugation and uncoated magnetic beads recovered more than 99% and 93%, respectively, of 1.68 × 107 CFU/mL, 1.68 × 106 CFU/mL and 1.68 × 105 CFU/mL M. smegmatis cells resuspended in phosphate buffer saline. The use of magnetic beads was more efficient to concentrate cells from 1.68 × 104 CFU/mL of M. smegmatis than centrifugation. Likewise, the F57-qPCR detection of MAP cells was different whether they were recovered by beads or centrifugation; cycle threshold (Ct) was lower (p < 0.05) for the detection of MAP cells recovered by beads than centrifugation, indicative of greater recovery. Magnetic separation of MAP cells from milk, urine, and feces specimens was demonstrated by detection of F57 and IS900 sequences. Beads captured no less than 109 CFU/mL from feces and no less than 104 CFU/mL from milk and urine suspensions. In another detection strategy, M. smegmatis coupled to magnetic beads were infected by mycobacteriophage D29. Plaque forming units were observed after 24 h of incubation from urine samples containing 2 × 105 and 2 × 103 CFU/mL M. smegmatis. The results of this study provide a promising tool for diagnosis of tuberculosis and Johne's disease.

Monte-Carlo simulation and tissue-phantom model for validation of ocular oximetry.

Ocular oximetry, in which blood oxygen saturation is evaluated in retinal tissues, is a promising technique for the prevention, diagnosis and management of many diseases and conditions. However, the development of new tools for evaluating oxygen saturation in the eye fundus has often been limited by the lack of reference tools or techniques for such measurements. In this study, we describe a two-step validation method. The impact of scattering, blood volume fraction and lens yellowing on the oximetry model is investigated using a tissue phantom, while a Monte Carlo model of the light propagation in the eye fundus is used to study the effect of the fundus layered-structure. With this method, we were able to assess the performance of an ocular oximetry technique in the presence of confounding factors and to quantify the impact of the choroidal circulation on the accuracy of the measurements. The presented strategy will be useful to anyone involved in studies based on the eye fundus diffuse reflectance.

Metabolome profiles of the alphaproteobacterial methanotroph Methylocystis sp. Rockwell in response to carbon and nitrogen source.

Methanotrophs use methane as a sole carbon source and thus play a critical role in its global consumption. Intensified interest in methanotrophs for their low-cost production of value-added products and large-scale industrialization has led to investigations of strain-to-strain variation in parameters for growth optimization and metabolic regulation. In this study, Methylocystis sp. Rockwell was grown with methane or methanol as a carbon source and ammonium or nitrate as a nitrogen source. The intracellular metabolomes and production of polyhydroxybutyrate, a bioplastic precursor, were compared among treatments to determine how the different combinations of carbon and nitrogen sources affected metabolite production. The methane-ammonium condition resulted in the highest growth, followed by the methane-nitrate, methanol-nitrate and methanol-ammonium conditions. Overall, the methane-ammonium and methane-nitrate conditions directed metabolism toward energy-conserving pathways, while methanol-ammonium and methanol-nitrate directed the metabolic response toward starvation pathways. Polyhydroxybutyrate was produced at greater abundances in methanol-grown cells, independent of the nitrogen source. Together, the results revealed how Methylocystis sp. Rockwell altered its metabolism with different combinations of carbon and nitrogen source, with implications for production of industrially relevant metabolites.