High-throughput characterization of the filamentous cyanobacterium Anabaena sp. using flow cytometry.

In stirred-tank photobioreactors agitation causes fragmentation of filamentous cyanobacteria. Here, we introduce a flow cytometric approach for high-throughput measurements of trichome dimensions, heterocysts and metabolic activity of Anabaena sp. cultures. The longest characterized trichome had 1135 µm chain length. This technology could potentially be used for monitoring and control purposes.

Coelastrella terrestris for Adonixanthin Production: Physiological Characterization and Evaluation of Secondary Carotenoid Productivity.

A novel strain of Coelastrella terrestris (Chlorophyta) was collected from red mucilage in a glacier foreland in Iceland. Its morphology showed characteristic single, ellipsoidal cells with apical wart-like wall thickenings. Physiological characterization revealed the presence of the rare keto-carotenoid adonixanthin, as well as high levels of unsaturated fatty acids of up to 85%. Initial screening experiments with different carbon sources for accelerated mixotrophic biomass growth were done. Consequently, a scale up to 1.25 L stirred photobioreactor cultivations yielded a maximum of 1.96 mg·L-1 adonixanthin in free and esterified forms. It could be shown that supplementing acetate to the medium increased the volumetric productivity after entering the nitrogen limitation phase compared to autotrophic control cultures. This study describes a promising way of biotechnological adonixanthin production using Coelastrella terrestris.

In Situ Quantification of Polyhydroxybutyrate in Photobioreactor Cultivations of Synechocystis sp. Using an Ultrasound-Enhanced ATR-FTIR Spectroscopy Probe.

Polyhydroxybutyrate (PHB) is a very promising alternative to most petroleum-based plastics with the huge advantage of biodegradability. Biotechnological production processes utilizing cyanobacteria as sustainable source of PHB require fast in situ process analytical technology (PAT) tools for sophisticated process monitoring. Spectroscopic probes supported by ultrasound particle traps provide a powerful technology for in-line, nondestructive, and real-time process analytics in photobioreactors. This work shows the great potential of using ultrasound particle manipulation to improve spectroscopic attenuated total reflection Fourier-transformed mid-infrared (ATR-FTIR) spectra as a monitoring tool for PHB production processes in photobioreactors.

Make microalgal cultures axenic again - a fast and simple workflow utilizing fluorescence-activated cell sorting.

Since the removal of contaminations in microalgal cultures is extremely laborious and time-consuming, we developed a rapid workflow to obtain axenicity by a combination of fluorescence-activated cell sorting (FACS) and plate spreading. During method development, several cyanobacteria and green algae strains were successfully made axenic. At the end, method transferability to another FACS device was demonstrated. Our workflow offers great time-savings with less hands-on laboratory work compared to conventional isolation techniques.

Tetraedron minimum, First Reported Member of Hydrodictyaceae to Accumulate Secondary Carotenoids.

We isolated a novel strain of the microalga Tetraedron minimum in Iceland from a terrestrial habitat. During long-term cultivation, a dish culture turned orange, indicating the presence of secondary pigments. Thus, we characterized T. minimum for growth and possible carotenoid production in different inorganic media. In a lab-scale photobioreactor, we confirmed that nitrogen starvation in combination with salt stress triggered a secondary carotenoid accumulation. The development of the pigment composition and the antioxidant capacity of the extracts was analyzed throughout the cultivations. The final secondary carotenoid composition was, on average, 61.1% astaxanthin and 38.9% adonixanthin. Moreover, the cells accumulated approx. 83.1% unsaturated fatty acids. This work presents the first report of the formation of secondary carotenoids within the family Hydrodictyaceae (Sphaeropleales, Chlorophyta).

Morphological and physiological characterization of filamentous Lentzea aerocolonigenes: Comparison of biopellets by microscopy and flow cytometry.

Cell morphology of filamentous microorganisms is highly interesting during cultivations as it is often linked to productivity and can be influenced by process conditions. Hence, the characterization of cell morphology is of major importance to improve the understanding of industrial processes with filamentous microorganisms. For this purpose, reliable and robust methods are necessary. In this study, pellet morphology and physiology of the rebeccamycin producing filamentous actinomycete Lentzea aerocolonigenes were investigated by microscopy and flow cytometry. Both methods were compared regarding their applicability. To achieve different morphologies, a cultivation with glass bead addition (Ø = 969 µm, 100 g L-1) was compared to an unsupplemented cultivation. This led to two different macro-morphologies. Furthermore, glass bead addition increased rebeccamycin titers after 10 days of cultivation (95 mg L-1 with glass beads, 38 mg L-1 without glass beads). Macro-morphology and viability were investigated through microscopy and flow cytometry. For viability assessment fluorescent staining was used additionally. Smaller, more regular pellets were found for glass bead addition. Pellet diameters resulting from microscopy followed by image analysis were 172 µm without and 106 µm with glass beads, diameters from flow cytometry were 170 and 100 µm, respectively. These results show excellent agreement of both methods, each considering several thousand pellets. Furthermore, the pellet viability obtained from both methods suggested an enhanced metabolic activity in glass bead treated pellets during the exponential production phase. However, total viability values differ for flow cytometry (0.32 without and 0.41 with glass beads) and confocal laser scanning microscopy of single stained pellet slices (life ratio in production phase of 0.10 without and 0.22 with glass beads), which is probably caused by the different numbers of investigated pellets. In confocal laser scanning microscopy only one pellet per sample could be investigated while flow cytometry considered at least 50 pellets per sample, resulting in an increased statistical reliability.

Fast and Highly Efficient Affinity Enrichment of Azide-A-DSBSO Cross-Linked Peptides.

Cross-linking mass spectrometry is an increasingly used, powerful technique to study protein-protein interactions or to provide structural information. Due to substochiometric reaction efficiencies, cross-linked peptides are usually low abundance. This results in challenging data evaluation and the need for an effective enrichment. Here we describe an improved, easy to implement, one-step method to enrich azide-tagged, acid-cleavable disuccinimidyl bis-sulfoxide (DSBSO) cross-linked peptides using dibenzocyclooctyne (DBCO) coupled Sepharose beads. We probed this method using recombinant Cas9 and E. coli ribosome. For Cas9, the number of detectable cross-links was increased from ∼100 before enrichment to 580 cross-links after enrichment. To mimic a cellular lysate, E. coli ribosome was spiked into a tryptic HEK background at a ratio of 1:2-1:100. The number of detectable unique cross-links was maintained high at ∼100. The estimated enrichment efficiency was improved by a factor of 4-5 (based on XL numbers) compared to enrichment via biotin and streptavidin. We were still able to detect cross-links from 0.25 µg cross-linked E. coli ribosomes in a background of 100 µg tryptic HEK peptides, indicating a high enrichment sensitivity. In contrast to conventional enrichment techniques, like SEC, the time needed for preparation and MS measurement is significantly reduced. This robust, fast, and selective enrichment method for azide-tagged linkers will contribute to mapping protein-protein interactions, investigating protein architectures in more depth, and helping to understand complex biological processes.

Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents.

Cross-linking mass spectrometry is becoming increasingly popular, and current advances are widening the applicability of the technique so that it can be utilized by nonspecialist laboratories. Specifically, the use of novel mass-spectrometry-cleavable (MS-cleavable) reagents dramatically reduces the complexity of the data by providing (i) characteristic reporter ions and (ii) the mass of the individual peptides rather than that of the cross-linked moiety. However, optimum acquisition strategies to obtain the best-quality data for such cross-linkers with higher energy C-trap dissociation (HCD) alone are yet to be achieved. Therefore, we have carefully investigated and optimized MS parameters to facilitate the identification of disuccinimidyl-sulfoxide-based cross-links on HCD-equipped mass spectrometers. From the comparison of nine different fragmentation energies, we chose several stepped-HCD fragmentation methods that were evaluated on a variety of cross-linked proteins. The optimal stepped-HCD method was then directly compared with previously described methods using an Orbitrap Fusion Lumos Tribrid instrument using a high-complexity sample. The final results indicate that our stepped-HCD method is able to identify more cross-links than other methods, mitigating the need for multistage MS-enabled (MSn) instrumentation and alternative dissociation techniques. Data are available via ProteomeXchange with identifier PXD011861.

Elevated pCO2 affects the lactate metabolic shift in CHO cell culture processes.

The shift from lactate production to consumption in CHO cell metabolism is a key event during cell culture cultivations and is connected to increased culture longevity and final product titers. However, the mechanisms controlling this metabolic shift are not yet fully understood. Variations in lactate metabolism have been mainly reported to be induced by process pH and availability of substrates like glucose and glutamine. The aim of this study was to investigate the effects of elevated pCO2 concentrations on the lactate metabolic shift phenomena in CHO cell culture processes. In this publication, we show that at elevated pCO2 in batch and fed-batch cultures, the lactate metabolic shift was absent in comparison to control cultures at lower pCO2 values. Furthermore, through metabolic flux analysis we found a link between the lactate metabolic shift and the ratio of NADH producing and regenerating intracellular pathways. This ratio was mainly affected by a reduced oxidative capacity of cultures at elevated pCO2. The presented results are especially interesting for large-scale and perfusion processes where increased pCO2 concentrations are likely to occur. Our results suggest, that so far unexplained metabolic changes may be connected to increased pCO2 accumulation in larger scale fermentations. Finally, we propose several mechanisms through which increased pCO2 might affect the cell metabolism and briefly discuss methods to enable the lactate metabolic shift during cell cultivations.

The impact of pH inhomogeneities on CHO cell physiology and fed-batch process performance - two-compartment scale-down modelling and intracellular pH excursion.

Due to high mixing times and base addition from top of the vessel, pH inhomogeneities are most likely to occur during large-scale mammalian processes. The goal of this study was to set-up a scale-down model of a 10-12 m3 stirred tank bioreactor and to investigate the effect of pH perturbations on CHO cell physiology and process performance. Short-term changes in extracellular pH are hypothesized to affect intracellular pH and thus cell physiology. Therefore, batch fermentations, including pH shifts to 9.0 and 7.8, in regular one-compartment systems are conducted. The short-term adaption of the cells intracellular pH are showed an immediate increase due to elevated extracellular pH. With this basis of fundamental knowledge, a two-compartment system is established which is capable of simulating defined pH inhomogeneities. In contrast to state-of-the-art literature, the scale-down model is included parameters (e.g. volume of the inhomogeneous zone) as they might occur during large-scale processes. pH inhomogeneity studies in the two-compartment system are performed with simulation of temporary pH zones of pH 9.0. The specific growth rate especially during the exponential growth phase is strongly affected resulting in a decreased maximum viable cell density and final product titer. The gathered results indicate that even short-term exposure of cells to elevated pH values during large-scale processes can affect cell physiology and overall process performance. In particular, it could be shown for the first time that pH perturbations, which might occur during the early process phase, have to be considered in scale-down models of mammalian processes.