Optimization of staining conditions for microalgae with three lipophilic dyes to reduce precipitation and fluorescence variability

Influence of multi-stressor combinations of pCO2, temperature, and salinity on the toxicity of Heterosigma akashiwo (Raphidophyceae), a fish-killing flagellate

Climate change and global warming have led to more frequent harmful algal blooms in the last decade. Among these blooms, Heterosigma akashiwo, a golden-brown phytoflagellate, is one of the 40 species with a high potential to form harmful blooms, leading to significant fish mortality. Climate change leads to rising atmospheric and ocean temperatures. These changes, along with altered rainfall patterns and meltwater input, can cause fluctuations in ocean salinity. Elevated atmospheric carbon dioxide (CO2) levels increase water acidity as oceans absorb CO2. This study investigated the effects of temperature, salinity, and CO2 levels on lipid production, hemolytic activity, and toxicity of H. akashiwo using the design of experiment approach, which can be used to investigate the effect of two or more factors on the same response simultaneously in a precise manner with fewer experiments and materials but in a larger region of the factor space. The lipid content was measured using a high-throughput Nile Red method, and the highest level of lipid content was detected at 25°C, a salinity of 30, and a CO2 concentration of 400 ppm. Hemolytic activity was assessed using rabbit blood erythrocytes in a 96-well plate, and the optimal conditions for achieving the highest hemolytic activity were determined at 15°C, a salinity of 10, and a CO2 concentration of 400 ppm. As the chemical structure of the toxin is not known, we used the toxicity against the cell line RTgill-W1 as the cell toxicity proxy. The maximum toxicity was identified at 15°C, a salinity of 10, and a CO2 level of 700 ppm.

Nile red-based lipid fluorometry protocol and its use for statistical optimization of lipids in oleaginous yeasts

As lipogenic yeasts are becoming increasingly harnessed as biofactories of oleochemicals, the availability of efficient protocols for the determination and optimization of lipid titers in these organisms is necessary. In this study, we optimized a quick, reliable, and high-throughput Nile red-based lipid fluorometry protocol adapted for oleaginous yeasts and validated it using different approaches, the most important of which is using gas chromatography coupled to flame ionization detection and mass spectrometry. This protocol was applied in the optimization of the concentrations of ammonium chloride and glycerol for attaining highest lipid titers in Rhodotorula toruloides NRRL Y-6987 and Yarrowia lipolytica W29 using response surface central composite design (CCD). Results of this optimization showed that the optimal concentration of ammonium chloride and glycerol is 4 and 123 g/L achieving a C/N ratio of 57 for R. toruloides, whereas for Y. lipolytica, concentrations are 4 and 139 g/L with a C/N ratio of 61 for Y. lipolytica. Outside the C/N of 33 to 74 and 45 to 75, respectively, for R. toruloides and Y. lipolytica, lipid productions decrease by more than 10%. The developed regression models and response surface plots show the importance of the careful selection of C/N ratio to attain maximal lipid production. KEY POINTS: • Nile red (NR)-based lipid fluorometry is efficient, rapid, cheap, high-throughput. • NR-based lipid fluorometry can be well used for large-scale experiments like DoE. • Optimal molar C/N ratio for maximum lipid production in lipogenic yeasts is ~60.

Overexpression of putative glutathione peroxidase from Neopyropia-associated microorganisms in Chlamydomonas to respond to abiotic stress

Lipid accumulation in microalgae can be substantially enhanced by exposing the microalgae to abiotic stress, thus increasing biofuel production. However, this also generates reactive oxygen species (ROS), which disrupts cell metabolism and reduces their productivity. Previous mRNA sequencing analyses in Neopyropia yezoensis and its associated microorganisms elucidated a putative glutathione peroxidase (PuGPx) gene. Here, this putative glutathione peroxidase was overexpressed in the microalga Chlamydomonas reinhardtii, which increased cell growth and survival rates compared to the control group under abiotic stress. Additionally, increased lipid accumulation was observed under salinity stress, high-temperature stress, and hydrogen peroxide (H₂O₂)-induced oxidative stress. These results suggest that PuGPx plays a protective role against abiotic stress in C. reinhardtii and stimulates lipid accumulation, which could be considered advantageous in terms of biofuel production.

Alternative Methods as Tools for Obesity Research: In Vitro and In Silico Approaches

The study of adipogenesis is essential for understanding and treating obesity, a multifactorial problem related to body fat accumulation that leads to several life-threatening diseases, becoming one of the most critical public health problems worldwide. In this review, we propose to provide the highlights of the adipogenesis study based on in vitro differentiation of human mesenchymal stem cells (hMSCs). We list in silico methods, such as molecular docking for identification of molecular targets, and in vitro approaches, from 2D, more straightforward and applied for screening large libraries of substances, to more representative physiological models, such as 3D and bioprinting models. We also describe the development of physiological models based on microfluidic systems applied to investigate adipogenesis in vitro. We intend to identify the main alternative models for adipogenesis evaluation, contributing to the direction of preclinical research in obesity. Future directions indicate the association of in silico and in vitro techniques to bring a clear picture of alternative methods based on adipogenesis as a tool for obesity research.

Optimized Protocol for Microalgae DNA Staining with SYTO9/SYBR Green I, Based on Flow Cytometry and RSM Methodology: Experimental Design, Impacts and Validation

Multiple fluorochromes are extensively used to investigate different microalgal aspects, such as viability and physiology. Some of them can be used to stain nucleic acids (DNA). Well-known examples are SYBR Green I and SYTO 9, the latter of which offers several advantages, especially when combined with flow cytometry (FCM)—a powerful method for studying microalgal population heterogeneity and analyzing their cell cycles. However, the effects of these dyes on the microalgae cell physiology have not been fully elucidated yet. A statistical experimental design, using response surface methodology (RSM) with FCM was applied in this study to optimize the DNA staining of a non-conventional microalgae, Chromochloris zofingiensis, with SYBR Green I and SYTO 9, and to optimize the variables affecting staining efficiency, i.e., the dye concentration, incubation time and staining temperature. We found that none of these factors affects the staining efficiency, which was not less than 99.65%. However, for both dyes, the dye concentration was shown to be the most significant factor causing cell damage (p-values: 0.0003; <0.0001) for SYBR Green I and SYTO 9, respectively. The staining temperature was only significant for SYTO 9 (p-value: 0.0082), and no significant effect was observed regarding the incubation time for both dyes. The values of the optimized parameters (0.5 µM, 05 min and 25 °C) for SYTO 9 and (0.5 X, 5 min and 25 °C) for SYBR Green I resulted in the maximum staining efficiency (99.8%; 99.6%), and the minimum damaging effects (12.86%; 13.75%) for SYTO 9 and SYBR Green I, respectively. These results offer new perspectives for improving the use of DNA staining fluorochromes and provides insights into their possible side effects on microalgae.

In situ quantification of poly(3-hydroxybutyrate) and biomass in Cupriavidus necator by a fluorescence spectroscopic assay

Abstract

Fluorescence spectroscopy offers a cheap, simple, and fast approach to monitor poly(3-hydroxybutyrate) (PHB) formation, a biodegradable polymer belonging to the biodegradable polyester class polyhydroxyalkanoates. In the present study, a fluorescence and side scatter-based spectroscopic setup was developed to monitor in situ biomass, and PHB formation of biotechnological applied Cupriavidus necator strain. To establish PHB quantification of C. necator, the dyes 2,2-difluoro-4,6,8,10,12-pentamethyl-3-aza-1-azonia-2-boranuidatricyclo[7.3.0.03,7]dodeca-1(12),4,6,8,10-pentaene (BODIPY^493/503), ethyl 5-methoxy-1,2-bis(3-methylbut-2-enyl)-3-oxoindole-2-carboxylate (LipidGreen2), and 9-(diethylamino)benzo[a]phenoxazin-5-one (Nile red) were compared with each other. Fluorescence staining efficacy was obtained through 3D-excitation-emission matrix and design of experiments. The coefficients of determination were ≥ 0.98 for all three dyes and linear to the high-pressure liquid chromatography obtained PHB content, and the side scatter to the biomass concentration. The fluorescence correlation models were further improved by the incorporation of the biomass-related side scatter. Afterward, the resulting regression fluorescence models were successfully applied to nitrogen-deficit, phosphor-deficit, and NaCl-stressed C. necator cultures. The highest transferability of the regression models was shown by using LipidGreen2. The novel approach opens a tailor-made way for a fast and simultaneous detection of the crucial biotechnological parameters biomass and PHB content during fermentation.

Key points

• Intracellular quantification of PHB and biomass using fluorescence spectroscopy.

• Optimizing fluorescence staining conditions and 3D-excitation-emission matrix.

• PHB was best obtained by LipidGreen2, followed by BODIPDY^493/503 and Nile red.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-021-11670-8.

Improved tolerance of recombinant Chlamydomonas rainhardtii with putative 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase from Pyropia yezoensis to nitrogen starvation

In a previous study, a putative 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase (ACMSD) was highly expressed in a mutant strain of Pyropia yezoensis, which exhibited an improved growth rate compared to its wild strain. To investigate the functional role of the putative ACMSD (Pyacmsd) of P. yezoensis, the putative Pyacmsd was cloned and expressed in Chlamydomonas reinhardtii. Recombinant C. reinhardtii cells with Pyacmsd (Cr_Pyacmsd) exhibited enhanced tolerance compared to control C. reinhardtii cells (Cr_control) under nitrogen starvation. Notably, Cr_Pyacmsd cells showed accumulation of lipids in nitrogen-enriched conditions. These results demonstrate the role of Pyacmsd in the generation of acetyl-coenzyme A. Thus, it can be used to enhance the production of biofuel using microalgae such as C. reinhardtii and increase the tolerance of other biological systems to nitrogen-deficient conditions.

GlycoBODIPYs: Sugars Serving as a Natural Stock for Water-soluble Fluorescent Probes of Complex Chiral Morphology

A range of unprocessed, reducing sugar substrates (mono-, di-, and trisaccharides) is shown to take part in a straightforward four-step synthetic route to water-soluble, uncharged BODIPY derivatives with unimpaired chiral integrity and high fluorescence efficiency. A wide compatibility with several postfunctionalizations is demonstrated, thus suggesting a universal utility of the multifunctional glycoconjugates, which we call GlycoBODIPYs. Knoevenagel condensations are able to promote a red-shift in the spectra, thereby furnishing strongly fluorescent red and far-red glycoconjugates of high hydrophilicity. The synthetic outcome was studied by X-ray crystallography and by comprehensive photophysical investigations in several solvent systems. Furthermore, cell experiments illustrate efficient cell uptake and demonstrate differential cell targeting as a function of the integrated chiral information.

Nile Red assay development for the estimation of neutral lipids in Chlorella emersonii and Pseudokirchneriella subcapitata

Fluorescent dyes offer a useful method for the measurement of intracellular lipids. They are inexpensive and require simple optical measurement instrumentation, whilst simultaneously providing high throughput application. Nile Red is a hydrophobic, metachromatic dye which has been widely used for detection of intracellular lipids. However, Nile Red fluorescence depends on its concentration, microenvironment polarity, incubation time and, therefore, requires strain specific optimization. Hence, neutral lipids in Chlorella emersonii and Pseudokirchneriella subcapitata cannot be quantified using existing Nile Red methods developed for other microalgae strains and, therefore an optimised procedure for these strains is required. In this method development, the optimal excitation and emission wavelengths were selected based on the solvent used for Nile Red dissolution. The effect of Nile Red concentration, microalgae cell concentration, incubation time on fluorescence intensity was explored and optimised. Quintuplet assay repeats were executed for increased assay robustness for two microalgae strains, Chlorella emersonii and Pseudokirchneriella subcapitata, with protocol reliability confirmed by fluorescence microscopy. In brief, 20% (v/v) DMSO containing 10μg/ml and 5μg/ml Nile red was found to be ideal concentration for neutral lipid estimation in Chlorella emersonii and Pseudokirchneriella subcapitata respectively when an incubation time of 60mins and 40mins at 40°C was used. This optimised Nile Red protocol is a robust, simple and cost-effective method for neutral lipid quantification in Chlorella emersonii and Pseudokirchneriella subcapitata.

Microalgae Lipid Staining with Fluorescent BODIPY Dye

The staining of lipids in algae cells with BODIPY dyes is much less studied compared to Nile red; therefore, a complex of issues concerning staining details and fluorescence measurements still should be clarified for the species that vary in cell wall complexity. Nevertheless, some general guidelines could be given, and a preliminary protocol of the method is provided based on the existing data. The semiquantification of lipid could be reliable if the staining protocol will be developed and adapted for particular microalgae species.

Using flow cytometry and multistage machine learning to discover label-free signatures of algal lipid accumulation

Most applications of flow cytometry or cell sorting rely on the conjugation of fluorescent dyes to specific biomarkers. However, labeled biomarkers are not always available, they can be costly, and they may disrupt natural cell behavior. Label-free quantification based upon machine learning approaches could help correct these issues, but label replacement strategies can be very difficult to discover when applied labels or other modifications in measurements inadvertently modify intrinsic cell properties. Here we demonstrate a new, but simple approach based upon feature selection and linear regression analyses to integrate statistical information collected from both labeled and unlabeled cell populations and to identify models for accurate label-free single-cell quantification. We verify the method’s accuracy to predict lipid content in algal cells (Picochlorum soloecismus) during a nitrogen starvation and lipid accumulation time course. Our general approach is expected to improve label-free single-cell analysis for other organisms or pathways, where biomarkers are inconvenient, expensive, or disruptive to downstream cellular processes.

Estimation of lipid reserves in different life stages of Meloidogyne incognita using image analysis of Nile Red-stained nematodes

Biochemical analyses of nematodes have revealed that neutral lipids (especially triglycerides) are the main source of energy reserves, which is depleted as the nematodes age. Several methodologies have been developed to visualise triglyceride-rich fat stores in plant-parasitic nematodes using non-fluorescent, lipophilic dyes, such as Oil Red O. Here, we propose a robust and reproducible fluorescence-based Nile Red staining method (followed by image analysis) for rapid detection of neutral lipid droplets in Meloidogyne incognita. This unique lipophilic dye selectively fluoresces in red and green spectra in a lipid-rich environment. The neutral lipid content of M. incognita juveniles gradually diminished during different periods of food deprivation, and this was significantly correlated with reduction in parasitic success of M. incognita in eggplant. Additionally, variation in fat reserves in different developmental stages of M. incognita infecting adzuki bean was also demonstrated. This investigation may aid future metabolic research, including functional analysis of lipid regulatory genes in plant-parasitic nematodes.

Quantification of Tetradesmus obliquus (Chlorophyceae) cell size and lipid content heterogeneity at single-cell level

Much of our current knowledge of microbial growth is obtained from studies at a population level. Driven by the realization that processes that operate within a population might influence a population's behavior, we sought to better understand Tetradesmus obliquus (formerly Scenedesmus obliquus) physiology at the cellular level. In this work, an accurate pretreatment method to quantitatively obtain single cells of T. obliquus, a coenobia-forming alga, is described. These single cells were examined by flow cytometry for triacylglycerol (TAG), chlorophyll, and protein content, and their cell sizes were recorded by coulter counter. We quantified heterogeneity of size and TAG content at single-cell level for a population of T. obliquus during a controlled standard batch cultivation. Unexpectedly, variability of TAG content per cell within the population increased throughout the batch run, up to 400 times in the final stage of the batch run, with values ranging from 0.25 to 99 pg · cell^-1 . Two subpopulations, classified as having low or high TAG content per cell, were identified. Cell size also increased during batch growth with average values from 36 to 70 μm³  · cell^-1 ; yet cell size variability increased only up to 16 times. Cell size and cellular TAG content were not correlated at the single-cell level. Our data show clearly that TAG production is affected by cell-to-cell variation, which suggests that its control and better understanding of the underlying processes may improve the productivity of T. obliquus for industrial processes such as biodiesel production.

AC-202, a highly effective fluorophore for the visualization of lipid droplets in green algae and diatoms

BACKGROUND

Lipid-specific live cell dyes are an important tool for the study of algal lipid metabolism, the monitoring of lipid production, and the identification of algal strains with high lipid yields. Nile Red and BODIPY have emerged as the principal dyes for these purposes. However, they suffer from a number of shortcomings including for specificity, penetration, interference from chlorophyll autofluorescence, and incompatibility with widely used genetically encoded reporters in the green and blue regions of the spectrum such as the green fluorescent protein and the red fluorescent protein.

RESULTS

We tested a new blue fluorescent dye, AC-202, in both the green algae Chlamydomonas reinhardtii and the pennate diatom Phaeodactylum tricornutum. We show that AC-202 is effective in both algae and that after minimal sample preparation, it can label lipid droplets induced by nitrogen starvation or by inhibitors of the TOR (target of rapamycin) kinase. We found that AC-202 benefits from a low background signal and is therefore more sensitive than BODIPY for semiquantitative in vivo fluorescence measurements. Finally, a co-staining experiment indicated that AC-202 can be used for multicolor imaging in combination with both red and green fluorophores.

CONCLUSIONS

AC-202 is an alternative and highly effective fluorophore for algal research that resolves drawbacks encountered with other neutral lipid dyes. AC-202 can be used to rapidly and sensitively visualize lipid droplets, and will contribute to the identification of metabolic and signaling pathways involved in lipid droplet formation, monitoring lipid production, and in the development of screens for algal strains suitable for biofuel production.

Imaging the accumulated intracellular microalgal lipids as a response to temperature stress

Over the last few decades, many scientists considered microalgae as promising actors for future biofuels because of the high lipid productivity inside their cells. Moreover, much attention has been paid to algal lipids as they can be used in biodiesel production. In this study, we optimized the different suitable conditions such as incubation time, incubation temperature, Dimethylesulfoxide and Nile red concentrations of the lipophilic fluorescence dye Nile red as an excellent and fast vital stain to detect and quantify intracellular lipids. This was achieved using the green alga Nannochloropsis salina. In addition, investigating the accumulation of lipid vesicles inside different isolated microalgal species as a response to temperature stress. Furthermore, the confocal laser scanning microscopy (LS510) for imaging and measuring the size and volume of the accumulated lipid vesicles was used.

Morphological and ultrastructural characterization of the acidophilic and lipid-producer strain Chlamydomonas acidophila LAFIC-004 (Chlorophyta) under different culture conditions

Chlamydomonas acidophila LAFIC-004 is an acidophilic strain of green microalgae isolated from coal mining drainage. In the present work, this strain was cultivated in acidic medium (pH 3.6) under phototrophic, mixotrophic, and heterotrophic regimes to determine the best condition for growth and lipid production, simultaneously assessing possible morphological and ultrastructural alterations in the cells. For heterotrophic and mixotrophic treatments, two organic carbon sources were tested: 1 % glucose and 1 % sodium acetate. Lipid content and fatty acid profiles were only determined in phototrophic condition. The higher growth rates were achieved in phototrophic conditions, varying from 0.18 to 0.82 day^-1. Glucose did not result in significant growth increase in either mixotrophic or heterotrophic conditions, and acetate proved to be toxic to the strain in both conditions. Oil content under phototrophic condition was 15.9 % at exponential growth phase and increased to 54.63 % at stationary phase. Based on cell morphology (flow cytometry and light microscopy) and ultrastructure (transmission electron microscopy), similar characteristics were observed between phototrophic and mixotrophic conditions with glucose evidencing many lipid bodies, starch granules, and intense fluorescence. Under the tested conditions, mixotrophic and heterotrophic modes did not result in increased neutral lipid fluorescence. It can be concluded that the strain is a promising lipid producer when grown until stationary phase in acidic medium and under a phototrophic regime, presenting a fatty acid profile suitable for biodiesel production. The ability to grow this strain in acidic mining residues suggests a potential for bioremediation with production of useful biomass.

High-throughput, label-free, single-cell, microalgal lipid screening by machine-learning-equipped optofluidic time-stretch quantitative phase microscopy

The development of reliable, sustainable, and economical sources of alternative fuels to petroleum is required to tackle the global energy crisis. One such alternative is microalgal biofuel, which is expected to play a key role in reducing the detrimental effects of global warming as microalgae absorb atmospheric CO₂ via photosynthesis. Unfortunately, conventional analytical methods only provide population-averaged lipid amounts and fail to characterize a diverse population of microalgal cells with single-cell resolution in a non-invasive and interference-free manner. Here high-throughput label-free single-cell screening of lipid-producing microalgal cells with optofluidic time-stretch quantitative phase microscopy was demonstrated. In particular, Euglena gracilis, an attractive microalgal species that produces wax esters (suitable for biodiesel and aviation fuel after refinement), within lipid droplets was investigated. The optofluidic time-stretch quantitative phase microscope is based on an integration of a hydrodynamic-focusing microfluidic chip, an optical time-stretch quantitative phase microscope, and a digital image processor equipped with machine learning. As a result, it provides both the opacity and phase maps of every single cell at a high throughput of 10,000 cells/s, enabling accurate cell classification without the need for fluorescent staining. Specifically, the dataset was used to characterize heterogeneous populations of E. gracilis cells under two different culture conditions (nitrogen-sufficient and nitrogen-deficient) and achieve the cell classification with an error rate of only 2.15%. The method holds promise as an effective analytical tool for microalgae-based biofuel production. © 2017 International Society for Advancement of Cytometry.

Impact of light quality on a native Louisiana Chlorella vulgaris/Leptolyngbya sp. co-culture

Light effect on cultures of microalgae has been studied mainly on single species cultures. Cyanobacteria have photosynthetic pigments that can capture photons of wavelengths not available to chlorophylls. A native Louisiana microalgae (Chlorella vulgaris) and cyanobacteria (Leptolyngbya sp.) co-culture was used to study the effects of light quality (blue-467 nm, green-522 nm, red-640 nm and white-narrow peak at 450 nm and a broad range with a peak at 550 nm) at two irradiance levels (80 and 400 μmol m^-2 s^-1) on the growth, species composition, biomass productivity, lipid content and chlorophyll-a production. The co-culture shifted from a microalgae dominant culture to a cyanobacteria culture at 80 μmol m^-2 s^-1. The highest growth for the cyanobacteria was observed at 80 μmol μmol m^-2 s^-1 and for the microalgae at 400 μmol m^-2 s^-1. Red light at 400 μmol m^-2 s^-1 had the highest growth rate (0.41 d^-1), biomass (913 mg L^-1) and biomass productivity (95 mg L^-1 d^-1). Lipid content was similar between all light colors. Green light had the highest chlorophyll-a content (1649 μg/L). These results can be used to control the species composition of mixed cultures while maintaining their productivity.

Lipid nanoparticles assessment by flow cytometry

BACKGROUND

Liposomes are promising carriers for drugs and bioactive compounds. Size and structure are their crucial parameters. Thus, it is essential to assess individual vesicles as prepared. Currently available techniques fail to measure liposome's size and structure simultaneously, with a high throughput. To solve this problem, we have developed a novel, flow cytometric method quantifying liposomes.

METHODS

Firstly, the following fluorescent staining combinations were tested: DiD/TO, Rh123/DiD, Syto9/DiD. Further, chosen fluorochromes were used to compare three populations of vesicles: raw (R), obtained by thin film hydration and extruded ones (populations E10 and E21). Dynamic light scattering (DLS) was used for determination of average diameter and size distribution of nanocarriers. Structural differences between the raw and the extruded liposomes, as well as additional information concerning vesicles size were acquired employing atomic force microscopy (AFM).

RESULTS

DLS analysis indicated that, three distinct populations of vesicles were obtained. Liposomes were characterized by mean diameter of 323nm, 220nm and 170nm for population R, E10 and E21 respectively. All the populations were stable and revealed zeta potential of -29mV. AFM confirmed that raw and extruded liposomes were differed in structure.

CONCLUSIONS AND GENERAL SIGNIFICANCE

DiD/TO was the optimal fluorochrome combination that enabled to resolve distinctly the sub-populations of liposomes. Results obtained by flow cytometry were in a good agreement with those from DLS and AFM. It was proved that, flow cytometry, when proper fluorescent dyes are used, is an adequate method for liposomes assessment. The proposed method enables fast and reliable analysis of liposomes in their native environment.

Robust at-line quantification of poly(3-hydroxyalkanoate) biosynthesis by flow cytometry using a BODIPY 493/503-SYTO 62 double-staining

Poly(3-hydroxyalkanoates) (PHAs) are bio-based and biodegradable polyesters which have been considered as a promising alternative to petrol-based plastics. Their bacterial production is a dynamic process in which intracellular polymerization and depolymerization are closely linked and depend on the availability of carbon substrates and other nutrients. These dynamics require a fast and quantitative method to determine the optimal harvest-time of PHA containing cells or to adjust carbon supply. In principle, flow cytometry (FCM) is an ideal tool that suits these requirements and, in addition, provides data on the PHA content of different cell populations. However, FCM-based PHA quantification methods have often relied on laborious sample preparation including washing steps and long incubation times. Here, we introduce a fast method based on double-staining using BODIPY 493/503 for PHA staining and SYTO 62 for DNA that allows acquiring reliable fluorescence and cell count data in <10min. Finally, fed-batch experiments with Pseudomonas putida KT2440 and Rhodospirillum rubrum S1 revealed that the method was robust and independent of the strain and type of PHA (medium-chain-length [mcl-] and short-chain-length [scl-] PHA, respectively). Interestingly, the specific PHA fluorescence was in case of mcl-PHA larger than for scl-PHA, probably reflecting the different material properties (e.g., specific density, hydrophilicity and crystallinity).

Quantification of the asymmetric migration of the lipophilic dyes, DiO and DiD, in homotypic co-cultures of chondrosarcoma SW-1353 cells

DiO and DiD are lipophilic cell labelling dyes used in the staining of cells in vivo and in vitro. The aim of the present study was to quantify the asymmetrical distribution of dyes in co-cultured cells and to measure the intercellular transfer of DiO and DiD. DiO and DiD were applied separately to stain two identical populations of SW-1353 human chondrosarcoma cells that were subsequently co-cultured (homotypic co-culture). The intercellular migration of dyes in the co-cultured cells was measured by flow cytometry and recorded under a fluorescent microscope. DiD and DiO caused no effect on the proliferation of cells, the degradation rate of the two dyes was comparable and crossover effects between dyes were negligible. The results of the present study suggested that asymmetrical intercellular migration of DiD and DiO was responsible for the asymmetrical distribution of these dyes in co-cultured cells. To take advantage of the lipophilic dyes migration in the double-stained co-cultured cells we suggest to apply mixed-dyes controls prior to the flow cytometric analysis. These controls are performed by staining cells with a 1:1 mix of the two dyes and would enable the estimation of the intensity of intercellular contact in co-culture systems. A 1:1 premix of DiO and DiD was applied to estimate cellular effect on intercellular exchange of lipid dyes in co-cultures incubated with cycloheximide and cytochalasin B. The cellular effect contributed 6–7% of intercellular migration of the lipophilic dyes, DiO and DiD. The majority of the observed intercellular transfer of these dyes was due to non-cellular, passive transfer.

Advances in techniques for assessment of microalgal lipids

Microalgae are a varied group of organisms with considerable commercial potential as sources of various biochemicals, storage molecules and metabolites such as lipids, sugars, amino acids, pigments and toxins. Algal lipids can be processed to bio-oils and biodiesel. The conventional method to estimate algal lipids is based on extraction using solvents and quantification by gravimetry or chromatography. Such methods are time consuming, use hazardous chemicals and are labor intensive. For rapid screening of prospective algae or for management decisions (e.g. decision on timing of harvest), a rapid, high throughput, reliable, accurate, cost effective and preferably nondestructive analytical technique is desirable. This manuscript reviews the application of fluorescent lipid soluble dyes (Nile Red and BODIPY 505/515), nuclear magnetic resonance (NMR), Raman, Fourier transform infrared (FTIR) and near infrared (NIR) spectroscopy for the assessment of lipids in microalgae.

High-Throughput Genetics Strategies for Identifying New Components of Lipid Metabolism in the Green Alga Chlamydomonas reinhardtii

Microalgal lipid metabolism is of broad interest because microalgae accumulate large amounts of triacylglycerols (TAGs) that can be used for biodiesel production (Durrett et al Plant J 54(4):593-607, 2008; Hu et al Plant J 54(4):621-639, 2008). Additionally, green algae are close relatives of land plants and serve as models to understand conserved lipid metabolism pathways in the green lineage. The green alga Chlamydomonas reinhardtii (Chlamydomonas hereafter) is a powerful model organism for understanding algal lipid metabolism. Various methods have been used to screen Chlamydomonas mutants for lipid amount or composition, and for identification of the mutated loci in mutants of interest. In this chapter, we summarize the advantages and caveats for each of these methods with a focus on screens for mutants with perturbed TAG content. We also discuss technical opportunities and new tools that are becoming available for screens of mutants altered in TAG content or perturbed in other processes in Chlamydomonas.

A lipophilic fluorescent LipidGreen1-based quantification method for high-throughput screening analysis of intracellular poly-3-hydroxybutyrate

Poly-3-hydroxybutyrate (PHB), the most abundant type of polyhydroxyalkanoates (PHA) is synthesized inside a variety of microorganisms as a primary candidate for industrial PHB production. Lipophilic dyes such as Nile red and BODIPY have been used to quantify intracellular PHB, but their uses have often been limited in terms of sensitivity and accuracy. In this study, a newly developed lipophilic fluorescent dye LipidGreen1 was used to quantify intracellular PHB. LipidGreen1 stained viable colonies by adding the dye into the medium which enabled the effective selection of PHB-positive cells. Furthermore, the fluorescence intensity of LipidGreen1 maintained its fluorescence intensity much longer than that of Nile red. The fluorescence intensities of intracellular PHB stained by LipidGreen1 accurately agreed with PHB contents measured by gas chromatography. In addition, internalization of LipidGreen1 in Escherichia coli cell was not necessary to obtain quantitative measurements. PHB-synthase mutants were differentiated by fluorescence intensities with a good correlation to increased levels of PHB production. These results show that LipidGreen1 is sensitive and accurate in high-throughput screening of newly isolated and genetically modified bacteria with enhanced PHB production.

LipiD-QuanT: a novel method to quantify lipid accumulation in live cells

Lipid droplets (LDs) are the main storage organelles for triglycerides. Elucidation of lipid accumulation mechanisms and metabolism are essential to understand obesity and associated diseases. Adipogenesis has been well studied in murine 3T3-L1 and human Simpson-Golabi-Behmel syndrome (SGBS) preadipocyte cell lines. However, most techniques for measuring LD accumulation are either not quantitative or can be destructive to samples. Here, we describe a novel, label-free LD quantification technique (LipiD-QuanT) to monitor lipid dynamics based on automated image analysis of phase contrast microscopy images acquired during in vitro human adipogenesis. We have applied LipiD-QuanT to measure LD accumulation during differentiation of SGBS cells. We demonstrate that LipiD-QuanT is a robust, nondestructive, time- and cost-effective method compared with other triglyceride accumulation assays based on enzymatic digest or lipophilic staining. Further, we applied LipiD-QuanT to measure the effect of four potential pro- or antiobesogenic substances: DHA, rosiglitazone, elevated levels of D-glucose, and zinc oxide nanoparticles. Our results revealed that 2 µmol/l rosiglitazone treatment during adipogenesis reduced lipid production and caused a negative shift in LD diameter size distribution, but the other treatments showed no effect under the conditions used here.

Measurement of lipid accumulation in Chlorella vulgaris via flow cytometry and liquid-state ¹H NMR spectroscopy for development of an NMR-traceable flow cytometry protocol

In this study, we cultured Chlorella vulgaris cells with a range of lipid contents, induced via nitrogen starvation, and characterized them via flow cytometry, with BODIPY 505/515 as a fluorescent lipid label, and liquid-state ¹H NMR spectroscopy. In doing so, we demonstrate the utility of calibrating flow cytometric measurements of algal lipid content using triacylglyceride (TAG, also known as triacylglycerol or triglyceride) content per cell as measured via quantitative ¹H NMR. Ensemble-averaged fluorescence of BODIPY-labeled cells was highly correlated with average TAG content per cell measured by bulk NMR, with a linear regression yielding a linear fit with r² = 0.9974. This correlation compares favorably to previous calibrations of flow cytometry protocols to lipid content measured via extraction, and calibration by NMR avoids the time and complexity that is generally required for lipid quantitation via extraction. Flow cytometry calibrated to a direct measurement of TAG content can be used to investigate the distribution of lipid contents for cells within a culture. Our flow cytometry measurements showed that Chlorella vulgaris cells subjected to nitrogen limitation exhibited higher mean lipid content but a wider distribution of lipid content that overlapped the relatively narrow distribution of lipid content for replete cells, suggesting that nitrogen limitation induces lipid accumulation in only a subset of cells. Calibration of flow cytometry protocols using direct in situ measurement of TAG content via NMR will facilitate rapid development of more precise flow cytometry protocols, enabling investigation of algal lipid accumulation for development of more productive algal biofuel feedstocks and cultivation protocols.

The use of fluorescent Nile red and BODIPY for lipid measurement in microalgae

Microalgae are currently emerging as one of the most promising alternative sources for the next generation of food, feed, cosmetics and renewable energy in the form of biofuel. Microalgae constitute a diverse group of microorganisms with advantages like fast and efficient growth. In addition, they do not compete for arable land and offer very high lipid yield potential. Major challenges for the development of this resource are to select lipid-rich strains using high-throughput staining for neutral lipid content in microalgae species. For this purpose, the fluorescent dyes most commonly used to quantify lipids are Nile red and BODIPY 505/515. Their fluorescent staining for lipids offers a rapid and inexpensive analysis tool to measure neutral lipid content, avoiding time-consuming and costly gravimetric analysis. This review collates and presents recent advances in algal lipid staining and focuses on Nile red and BODIPY 505/515 staining characteristics. The available literature addresses the limitations of fluorescent dyes under certain conditions, such as spectral properties, dye concentrations, cell concentrations, temperature and incubation duration. Moreover, the overall conclusion of the present review study gives limitations on the use of fluorochrome for screening of lipid-rich microalgae species and suggests improved protocols for staining recalcitrant microalgae and recommendations for the staining quantification.

Nile Red Staining for Oil Determination in Microalgal Cells: A New Insight through Statistical Modelling

In the wake of global warming and rapid fossil fuel depletion, microalgae emerge as promising feedstocks for sustainable biofuel production. Nile red staining acts as a rapid diagnostic tool to measure the amount of biodiesel-convertible lipid that the cells accumulate. There is a need for the development of a more uniform staining procedure. In its first phase, this study examined the dependence of microalgal Nile red fluorescence (Tetraselmis suecica) in terms of its most pertinent staining variables. A quadratic surface model that successfully described the Nile red fluorescence intensity as a composite function of its variables was generated (r2=0.86). Cell concentration was shown to have a significant effect on the fluorescence intensity. Up to a certain threshold, fluorescence intensity was shown to increase with Nile red dye concentration. In its second phase, the study reviewed findings from previous Nile red studies to elucidate some of the fundamental mechanism underlying the diffusion of Nile red dye molecules into the microalgal cells and their subsequent interaction with intracellular lipids. Through the review process, we were able to develop a simple framework that provided a set of guidelines for the standardization of the Nile red staining procedure across different microalgal species.

A fluorescence-activated cell sorting-based strategy for rapid isolation of high-lipid Chlamydomonas mutants

There is significant interest in farming algae for the direct production of biofuels and valuable lipids. Chlamydomonas reinhardtii is the leading model system for studying lipid metabolism in green algae, but current methods for isolating mutants of this organism with a perturbed lipid content are slow and tedious. Here, we present the Chlamydomonas high-lipid sorting (CHiLiS) strategy, which enables enrichment of high-lipid mutants by fluorescence-activated cell sorting (FACS) of pooled mutants stained with the lipid-sensitive dye Nile Red. This method only takes 5 weeks from mutagenesis to mutant isolation. We developed a staining protocol that allows quantification of lipid content while preserving cell viability. We improved separation of high-lipid mutants from the wild type by using each cell's chlorophyll fluorescence as an internal control. We initially demonstrated 20-fold enrichment of the known high-lipid mutant sta1 from a mixture of sta1 and wild-type cells. We then applied CHiLiS to sort thousands of high-lipid cells from a pool of about 60,000 mutants. Flow cytometry analysis of 24 individual mutants isolated by this approach revealed that about 50% showed a reproducible high-lipid phenotype. We further characterized nine of the mutants with the highest lipid content by flame ionization detection and mass spectrometry lipidomics. All mutants analyzed had a higher triacylglycerol content and perturbed whole-cell fatty acid composition. One arbitrarily chosen mutant was evaluated by microscopy, revealing larger lipid droplets than the wild type. The unprecedented throughput of CHiLiS opens the door to a systems-level understanding of green algal lipid biology by enabling genome-saturating isolation of mutants in key genes.

High frequency dielectrophoretic response of microalgae over time

The high frequency dielectrophoresis (>20 MHz) response of microalgae cells with different lipid content was monitored over time. Chlamydomonas reinhardtii was cultured in regular medium and under nitrogen-depleted conditions in order to produce populations of cells with low and high lipid content, respectively. The electrical conductivity of the culture media was also monitored over the same time. The upper crossover frequency decreased for high-lipid cells over time. The single-shell model predicts that the upper crossover frequency is dictated primarily by the dielectric properties of the cytoplasm. The high frequency DEP response of the high-lipid cells' cytoplasm was changed by lipid accumulation. DEP response of the low-lipid cells also varied with the conductivity of the culture media due to nutrient consumption. Relative lipid content was estimated with BODIPY 505/515 dye by calculating the area-weighted intensity average of fluorescent images. Finally, microalgae cells were successfully separated based on lipid content at 41 MHz and DEP media conductivity 106 ± 1 μS/cm.

Lipid accumulation during the establishment of kleptoplasty in Elysia chlorotica

The establishment of kleptoplasty (retention of "stolen plastids") in the digestive tissue of the sacoglossan Elysia chlorotica Gould was investigated using transmission electron microscopy. Cellular processes occurring during the initial exposure to plastids were observed in laboratory raised animals ranging from 1-14 days post metamorphosis (dpm). These observations revealed an abundance of lipid droplets (LDs) correlating to plastid abundance. Starvation of animals resulted in LD and plastid decay in animals <5 dpm that had not yet achieved permanent kleptoplasty. Animals allowed to feed on algal prey (Vaucheria litorea C. Agardh) for 7 d or greater retained stable plastids resistant to cellular breakdown. Lipid analysis of algal and animal samples supports that these accumulating LDs may be of plastid origin, as the often algal-derived 20∶5 eicosapentaenoic acid was found in high abundance in the animal tissue. Subsequent culturing of animals in dark conditions revealed a reduced ability to establish permanent kleptoplasty in the absence of photosynthetic processes, coupled with increased mortality. Together, these data support an important role of photosynthetic lipid production in establishing and stabilizing this unique animal kleptoplasty.

Bioprospecting for acidophilic lipid-rich green microalgae isolated from abandoned mine site water bodies

With fossil fuel sources in limited supply, microalgae show tremendous promise as a carbon neutral source of biofuel. Current microalgae biofuel strategies typically rely on growing high-lipid producing laboratory strains of microalgae in open raceways or closed system photobioreactors. Unfortunately, these microalgae species are found to be sensitive to environmental stresses or competition by regional strains. Contamination by invasive species can diminish productivity of commercial algal processes. A potential improvement to current strategies is to identify high-lipid producing microalgae, which thrive in selected culture conditions that reduce the risk of contamination, such as low pH. Here we report the identification of a novel high-lipid producing microalgae which can tolerate low pH growth conditions. Lig 290 is a Scenedesmus spp. isolated from a low pH waterbody (pH = 4.5) in proximity to an abandoned lignite mine in Northern Ontario, Canada. Compared to a laboratory strain of Scendesmus dimorphus, Lig 290 demonstrated robust growth rates, a strong growth profile, and high lipid production. As a consequence, Lig 290 may have potential application as a robust microalgal species for use in biofuel production.

Optimization of the C11-BODIPY(581/591) dye for the determination of lipid oxidation in Chlamydomonas reinhardtii by flow cytometry

Lipid oxidation is a recognized end point for the study of oxidative stress and is an important parameter to describe the mode of micropollutant action on aquatic microorganisms. Therefore, the development of quick and reliable methodologies probing the oxidative stress and damage in living cells is highly sought. In the present proof-of-concept work, we examined the potential of the fluorescent dye C11-BODIPY(591/581) to probe lipid oxidation in the green microalga Chlamydomonas reinhardtii. C11-BODIPY(591/581) staining was combined with flow cytometry measurements to obtain multiparameter information on cellular features and oxidative stress damage within single cells. First, staining conditions were optimized by exploring the capability of the dye to stain algal cells under increasing cell and dye concentrations and different staining procedures. Then lipid oxidation in algae induced by short- and long-term exposures to the three metallic micropollutants, copper, mercury, and nanoparticulate copper oxide, and the two organic contaminants, diethyldithiocarbamate (DDC) and diuron was determined. In this work we pointed out C11-BODIPY(591/581) applicability in a wide range of exposure conditions, including studies of oxidation as a function of time and that it is suitable for in vivo measurements of lipid oxidation due to its high permeation and stability in cells and its low interference with algal autofluorescence. © 2013 International Society for Advancement of Cytometry.

Microfluidic cytometer for high-throughput measurement of photosynthetic characteristics and lipid accumulation in individual algal cells

Commercially viable algal biofuel production requires discovery of new strains, genetic engineering for higher productivity and optimization of growth conditions. To accelerate research in these areas, we developed a microfluidic cytometer that measures forward light scatter, chlorophyll fluorescence induction and lipophilic stain fluorescence at a rate of 100 cells s(-1). The chlorophyll fluorescence data is processed in real-time to measure the fluorescence-based maximum quantum yield, reported as Fv/Fm, to quantify the photochemical energy conversion of each cell. To demonstrate instrument performance, Fv/Fm measurements are obtained for unstressed (nutrient-replete) and stressed (nutrient-limited) cultures of the marine diatom Phaeodactylum tricornutum and are correlated to values obtained in bulk samples using traditional pulse-amplitude-modulating fluorometry. We then use the cytometer to characterize unstressed and stressed P. tricornutum and show that lipid content (as measured by Nile Red fluorescence) is inversely correlated with Fv/Fm. We believe these findings to be the first time that both photosynthetic efficiency and lipid accumulation have been simultaneously evaluated at the single cell level, and that in doing so, the diversity within these populations was revealed.

Soft nanomaterial-based targeting polymersomes for near-infrared fluorescence multispectral in vivo imaging

We report here the soft nanomaterial-based targeting polymersomes for near-infrared (NIR) fluorescence imaging to carry out in vivo tumor detection. Two polymersome-based NIR fluorescent probes were prepared through the self-assembly of amphiphilic block copolymers, poly(butadiene-b-ethylene oxide) (PEO-b-PBD). Each of them was encapsulated with distinct hydrophobic near-infrared dyes (DiD and DiR) and modified with different targeting ligands (anti-CEA antibody and anti-EGFR antibody), respectively. After simultaneous injection of these two probes into the tumor-bearing mice via tail vein, multispectral near-infrared fluorescence images were obtained. The results indicate that both probes are successfully directed to the tumor foci, where two distinguishable fluorescent signals were detected through the unmixed fluorescence images. By taking advantage of two targeting polymersome-based probes with distinct fluorescent features, the proposed multispectral near-infrared fluorescence imaging method can greatly improve the specificity and accuracy for in vivo tumor detection.