Inline monitoring of high cell density cultivation of Scenedesmus rubescens in a mesh ultra-thin layer photobioreactor by photon density wave spectroscopy.

OBJECTIVE: Due to multiple light scattering that occurs inside and between cells, quantitative optical spectroscopy in turbid biological suspensions is still a major challenge. This includes also optical inline determination of biomass in bioprocessing. Photon Density Wave (PDW) spectroscopy, a technique based on multiple light scattering, enables the independent and absolute determination of optical key parameters of concentrated cell suspensions, which allow to determine biomass during cultivation. RESULTS: A unique reactor type, called "mesh ultra-thin layer photobioreactor" was used to create a highly concentrated algal suspension. PDW spectroscopy measurements were carried out continuously in the reactor without any need of sampling or sample preparation, over 3 weeks, and with 10-min time resolution. Conventional dry matter content and coulter counter measurements have been employed as established offline reference analysis. The PBR allowed peak cell dry weight (CDW) of 33.4 g L-1. It is shown that the reduced scattering coefficient determined by PDW spectroscopy is strongly correlated with the biomass concentration in suspension and is thus suitable for process understanding. The reactor in combination with the fiber-optical measurement approach will lead to a better process management.

Immunolabeling of Nuclei/Chromosomes in Arabidopsis thaliana.

The cell cycle is a complex sequence of events by which cells grow and divide mitotically or meiotically. Mitosis results in the generation of two identical daughter cells, while meiosis generates gametes as a prerequisite for sexual reproduction. To study the localization and dynamics of proteins involved in the regulation and proceeding of the cell cycle, life cell imaging of proteins fused to fluorescent tags can be performed. However, in some cases this approach cannot be applied, e.g., due to low fluorescence intensity, fast bleaching, or degradation of recombinant proteins by the proteasome pathway. Instead, immunolabeling with protein-specific antibodies offers a useful approach for the analysis of intact cells. Alternatively, immunolabeling can also be applied to isolated and/or flow-sorted nuclei of particular cell cycle stages (G1, S, and G2) or of different endopolyploidy levels. The following chapter will detail indirect immunolabeling protocols to analyze the subcellular localization and distribution of cell cycle-specific proteins in Arabidopsis thaliana.

Establishment of a simple method to evaluate mixing times in a plastic bag photobioreactor using image processing based on freeware tools.

OBJECTIVE: Accurate determination of the mixing time in bioreactors is essential for the optimization of the productivity of bioprocesses. The aim of this work was to develop a simple optical method to determine the mixing time in a photobioreactor. The image processing method should be based on freeware tools, should not require programming skills, and thus could be used in education within high schools and in early stages of undergraduate programs. RESULTS: An optical method has been established to analyze images from recorded videos of mixing experiments. The steps are: 1. Extraction of a sequence of images from the video file; 2. Cropping of the pictures; 3. Background removal; and 4. Image analysis and mixing time evaluation based on quantification of pixel-to-pixel heterogeneity within a given area of interest. The novel method was generally able to track the dependency between aeration rate and mixing time within the investigated photobioreactor. In direct comparison, a PEARSON correlation coefficient of rho = 0.99 was obtained. Gas flow rates between 10 L h-1, and 300 L h-1 resulted from mixing times of between 48 and 14 s, respectively. This technique is applicable without programming skills and can be used in education with inexperienced user groups.

Comparative life cycle assessment of a mesh ultra-thin layer photobioreactor and a tubular glass photobioreactor for the production of bioactive algae extracts.

This study aimed at the comparison of two different photobioreactors with focus on technology and sustainability. The mesh ultra-thin layer photobioreactor (MUTL-PBR) exhibited around 3-fold biomass based space-time-yield and an around 10-fold specific antioxidant capacity than the traditional reference photobioreactor. Life cycle assessment (LCA) was done under autotrophic conditions in both pilot scale reactors with focus on biomass production and on antioxidant capacity of the biomass, respectively. Biomass production within the reference reactor showed a lower environmental impact in most categories. A significantly higher energy demand for mixing and cooling of the cell suspension within the MUTL-PBR is the major reason for its environmental burden. This relates to high impacts in the categories "non-renewable energy" and "global warming potential" per kg biomass. Comparing algal antioxidant capacity, environmental impact of the MUTL cultivation was 5-10 times lower. This clearly illustrates the potential of MUTL-PBR for sustainable production of bioactive substances.

Analysis of population structures of the microalga Acutodesmus obliquus during lipid production using multi-dimensional single-cell analysis.

Microalgae bear a great potential to produce lipids for biodiesel, feed, or even food applications. To understand the still not well-known single-cell dynamics during lipid production in microalgae, a novel single-cell analytical technology was applied to study a well-established model experiment. Multidimensional single-cell dynamics were investigated with a non-supervised image analysis technique that utilizes data from epi-fluorescence microscopy. Reliability of this technique was successfully proven via reference analysis. The technique developed was used to determine cell size, chlorophyll amount, neutral lipid amount, and deriving properties on a single-cellular level in cultures of the biotechnologically promising alga Acutodesmus obliquus. The results illustrated a high correlation between cell size and chlorophyll amount, but a very low and dynamic correlation between cell size, lipid amount, and lipid density. During growth conditions under nitrogen starvation, cells with low chlorophyll content tend to start the lipid production first and the cell suspension differentiated in two subpopulations with significantly different lipid contents. Such quantitative characterization of single-cell dynamics of lipid synthesizing algae was done for the first time and the potential of such simple technology is highly relevant to other biotechnological applications and to deeper investigate the process of microalgal lipid accumulation.

Autotrophic and heterotrophic microalgae and cyanobacteria cultivation for food and feed: life cycle assessment.

The lack of protein sources in Europe could be reduced with onsite production of microalgae with autotrophic and heterotrophic systems, owing the confirmation of economic and environmental benefits. This study aimed at the life cycle assessment (LCA) of microalgae and cyanobacteria cultivation (Chlorella vulgaris and Arthrospira platensis) in autotrophic and heterotrophic conditions on a pilot industrial scale (in model conditions of Berlin, Germany) with further biomass processing for food and feed products. The comparison of analysis results with traditional benchmarks (protein concentrates) indicated higher environmental impact of microalgae protein powders. However high-moisture extrusion of heterotrophic cultivated C. vulgaris resulted in more environmentally sustainable product than pork and beef. Further optimization of production with Chlorella pyrenoidosa on hydrolyzed food waste could reduce environmental impact in 4.5 times and create one of the most sustainable sources of proteins.

Multidimensional single-cell analysis based on fluorescence microscopy and automated image analysis.

A single-cell analytical technology was developed for evaluating fast-growing cultures of green algae. The main part of the single-cell analysis is an epifluorescence microscopy-based cytometric approach combined with an automated image analysis algorithm and a single-threshold discrimination procedure. The reliability of the technique in terms of object recognition, evaluating particle size, and determining chlorophyll was successfully proven via reference analyses. The microscopy technique was used to determine the size of single cells, the amount of chlorophyll, and the density of chlorophyll in a model algal culture (Acutodesmus o.). The algal cells showed unexpected heterogeneity in all single-cell parameters, and exhibited a high correlation between cell size and amount of chlorophyll but a very low correlation between cell size and chlorophyll density. For a given cell size, the cell-to-cell heterogeneity of the relative chlorophyll density showed a spread of 0.02-0.08. This points to large variations in the architecture and the physiological state of the photosynthetic apparatus in the cells. This complex situation should be considered in future systems biology approaches focusing on the relationships between biomass accumulation, photosynthetic activity, and central carbon metabolism. Graphical abstract Analysis of cell-to-cell heterogeneity obtained from microscopic images.

Targeting of Arabidopsis KNL2 to Centromeres Depends on the Conserved CENPC-k Motif in Its C Terminus.

KINETOCHORE NULL2 (KNL2) is involved in recognition of centromeres and in centromeric localization of the centromere-specific histone cenH3. Our study revealed a cenH3 nucleosome binding CENPC-k motif at the C terminus of Arabidopsis thaliana KNL2, which is conserved among a wide spectrum of eukaryotes. Centromeric localization of KNL2 is abolished by deletion of the CENPC-k motif and by mutating single conserved amino acids, but can be restored by insertion of the corresponding motif of Arabidopsis CENP-C. We showed by electrophoretic mobility shift assay that the C terminus of KNL2 binds DNA sequence-independently and interacts with the centromeric transcripts in vitro. Chromatin immunoprecipitation with anti-KNL2 antibodies indicated that in vivo KNL2 is preferentially associated with the centromeric repeat pAL1 Complete deletion of the CENPC-k motif did not influence its ability to interact with DNA in vitro. Therefore, we suggest that KNL2 recognizes centromeric nucleosomes, similar to CENP-C, via the CENPC-k motif and binds adjoining DNA.

Immunolabeling of Nuclei/Chromosomes in Arabidopsis thaliana.

The cell cycle is a complex sequence of events by which cells grow and divide mitotically or meiotically. Mitosis results in the generation of two identical daughter cells, while meiosis generates gametes as a prerequisite for sexual reproduction. To study the localization and dynamics of proteins involved in the regulation and proceeding of the cell cycle, life cell imaging of proteins fused to fluorescent tags can be performed. However, in some cases this approach cannot be applied, e.g., due to low fluorescence intensity, fast bleaching or degradation of recombinant proteins by the proteasome pathway. Instead, immunolabeling with protein-specific antibodies represents a useful approach for the analysis of intact cells. Alternatively, immunolabeling can also be applied to isolated and/or flow-sorted nuclei of particular cell cycle stages (G1, S, and G2) or of different endopolyploidy levels. This chapter details indirect immunolabeling protocols to analyze the subcellular localization and distribution of cell cycle-specific proteins in Arabidopsis thaliana.

Centromeric chromatin and its dynamics in plants.

Centromeres are chromatin structures that are required for proper separation of chromosomes during mitosis and meiosis. The centromere is composed of centromeric DNA, often enriched in satellite repeats, and kinetochore complex proteins. To date, over 100 kinetochore components have been identified in various eukaryotes. Kinetochore assembly begins with incorporation of centromeric histone H3 variant CENH3 into centromeric nucleosomes. Protein components of the kinetochore are either present at centromeres throughout the cell cycle or localize to centromeres transiently, prior to attachment of microtubules to each kinetochore in prometaphase of mitotic cells. This is the case for the spindle assembly checkpoint (SAC) proteins in animal cells. The SAC complex ensures equal separation of chromosomes between daughter nuclei by preventing anaphase onset before metaphase is complete, i.e. the sister kinetochores of all chromosomes are attached to spindle fibers from opposite poles. In this review, we focus on the organization of centromeric DNA and the kinetochore assembly in plants. We summarize recent advances regarding loading of CENH3 into the centromere, and the subcellular localization and protein-protein interactions of Arabidopsis thaliana proteins involved in kinetochore assembly and function. We describe the transcriptional activity of corresponding genes based on in silico analysis of their promoters and cell cycle-dependent expression. Additionally, barley homologs of all selected A. thaliana proteins have been identified in silico, and their sequences and domain structures are presented.

Weak correlation of starch and volume in synchronized photosynthetic cells.

In cultures of unicellular algae, features of single cells, such as cellular volume and starch content, are thought to be the result of carefully balanced growth and division processes. Single-cell analyses of synchronized photoautotrophic cultures of the unicellular alga Chlamydomonas reinhardtii reveal, however, that the cellular volume and starch content are only weakly correlated. Likewise, other cell parameters, e.g., the chlorophyll content per cell, are only weakly correlated with cell size. We derive the cell size distributions at the beginning of each synchronization cycle considering growth, timing of cell division and daughter cell release, and the uneven division of cell volume. Furthermore, we investigate the link between cell volume growth and starch accumulation. This work presents evidence that, under the experimental conditions of light-dark synchronized cultures, the weak correlation between both cell features is a result of a cumulative process rather than due to asymmetric partition of biomolecules during cell division. This cumulative process necessarily limits cellular similarities within a synchronized cell population.

Systems-wide analysis of acclimation responses to long-term heat stress and recovery in the photosynthetic model organism Chlamydomonas reinhardtii.

We applied a top-down systems biology approach to understand how Chlamydomonas reinhardtii acclimates to long-term heat stress (HS) and recovers from it. For this, we shifted cells from 25 to 42°C for 24 h and back to 25°C for ≥8 h and monitored abundances of 1856 proteins/protein groups, 99 polar and 185 lipophilic metabolites, and cytological and photosynthesis parameters. Our data indicate that acclimation of Chlamydomonas to long-term HS consists of a temporally ordered, orchestrated implementation of response elements at various system levels. These comprise (1) cell cycle arrest; (2) catabolism of larger molecules to generate compounds with roles in stress protection; (3) accumulation of molecular chaperones to restore protein homeostasis together with compatible solutes; (4) redirection of photosynthetic energy and reducing power from the Calvin cycle to the de novo synthesis of saturated fatty acids to replace polyunsaturated ones in membrane lipids, which are deposited in lipid bodies; and (5) when sinks for photosynthetic energy and reducing power are depleted, resumption of Calvin cycle activity associated with increased photorespiration, accumulation of reactive oxygen species scavengers, and throttling of linear electron flow by antenna uncoupling. During recovery from HS, cells appear to focus on processes allowing rapid resumption of growth rather than restoring pre-HS conditions.

Centromeres and kinetochores of Brassicaceae.

The centromere-the primary constriction of monocentric chromosomes-is essential for correct segregation of chromosomes during mitosis and meiosis. Centromeric DNA varies between different organisms in sequence composition and extension. The main components of centromeric and pericentromeric DNA of Brassicaceae species are centromeric satellite repeats. Centromeric DNA initiates assembly of the kinetochore, the large protein complex where the spindle fibers attach during nuclear division to pull sister chromatids apart. Kinetochore assembly is initiated by incorporation of the centromeric histone H3 cenH3 into centromeric nucleosomes. The spindle assembly checkpoint acts during mitosis and meiosis at centromeres and maintains genome stability by preventing chromosome segregation before all kinetochores are correctly attached to microtubules. The function of the spindle assembly checkpoint in plants is still poorly understood. Here, we review recent advances of studies on structure and functional importance of centromeric DNA of Brassicaceae, assembly and function of cenH3 in Arabidopsis thaliana and characterization of core SAC proteins of A. thaliana in comparison with non-plant homologues.

Arabidopsis kinetochore null2 is an upstream component for centromeric histone H3 variant cenH3 deposition at centromeres.

The centromeric histone H3 variant cenH3 is an essential centromeric protein required for assembly, maintenance, and proper function of kinetochores during mitosis and meiosis. We identified a kinetochore null2 (KNL2) homolog in Arabidopsis thaliana and uncovered features of its role in cenH3 loading at centromeres. We show that Arabidopsis KNL2 colocalizes with cenH3 and is associated with centromeres during all stages of the mitotic cell cycle, except from metaphase to mid-anaphase. KNL2 is regulated by the proteasome degradation pathway. The KNL2 promoter is mainly active in meristematic tissues, similar to the cenH3 promoter. A knockout mutant for KNL2 shows a reduced level of cenH3 expression and reduced amount of cenH3 protein at chromocenters of meristematic nuclei, anaphase bridges during mitosis, micronuclei in pollen tetrads, and 30% seed abortion. Moreover, knl2 mutant plants display reduced expression of suppressor of variegation 3-9 homologs2, 4, and 9 and reduced DNA methylation, suggesting an impact of KNL2 on the epigenetic environment for centromere maintenance.

Cell-to-cell diversity in a synchronized Chlamydomonas culture as revealed by single-cell analyses.

In a synchronized photoautotrophic culture of Chlamydomonas reinhardtii, cell size, cell number, and the averaged starch content were determined throughout the light-dark cycle. For single-cell analyses, the relative cellular starch was quantified by measuring the second harmonic generation (SHG). In destained cells, amylopectin essentially represents the only biophotonic structure. As revealed by various validation procedures, SHG signal intensities are a reliable relative measure of the cellular starch content. During photosynthesis-driven starch biosynthesis, synchronized Chlamydomonas cells possess an unexpected cell-to-cell diversity both in size and starch content, but the starch-related heterogeneity largely exceeds that of size. The cellular volume, starch content, and amount of starch/cell volume obey lognormal distributions. Starch degradation was initiated by inhibiting the photosynthetic electron transport in illuminated cells or by darkening. Under both conditions, the averaged rate of starch degradation is almost constant, but it is higher in illuminated than in darkened cells. At the single-cell level, rates of starch degradation largely differ but are unrelated to the initial cellular starch content. A rate equation describing the cellular starch degradation is presented. SHG-based three-dimensional reconstructions of Chlamydomonas cells containing starch granules are shown.

The K (+) battery-regulating Arabidopsis K (+) channel AKT2 is under the control of multiple post-translational steps.

Potassium (K (+) ) is an important nutrient for plants. It serves as a cofactor of various enzymes and as the major inorganic solute maintaining plant cell turgor. In a recent study, an as yet unknown role of K (+) in plant homeostasis was shown. It was demonstrated that K (+) gradients in vascular tissues can serve as an energy source for phloem (re)loading processes and that the voltage-gated K (+) channels of the AKT2-type play a unique role in this process. The AKT2 channel can be converted by phosphorylation of specific serine residues (S210 and S329) into a non-rectifying channel that allows a rapid efflux of K (+) from the sieve element/companion cells (SE/CC) complex. The energy of this flux is used by other transporters for phloem (re)loading processes. Nonetheless, the results do indicate that post-translational modifications at S210 and S329 alone cannot explain AKT2 regulation. Here, we discuss the existence of multiple post-translational modification steps that work in concert to convert AKT2 from an inward-rectifying into a non-rectifying K (+) channel.

Potassium (K+) gradients serve as a mobile energy source in plant vascular tissues.

The essential mineral nutrient potassium (K(+)) is the most important inorganic cation for plants and is recognized as a limiting factor for crop yield and quality. Nonetheless, it is only partially understood how K(+) contributes to plant productivity. K(+) is used as a major active solute to maintain turgor and to drive irreversible and reversible changes in cell volume. K(+) also plays an important role in numerous metabolic processes, for example, by serving as an essential cofactor of enzymes. Here, we provide evidence for an additional, previously unrecognized role of K(+) in plant growth. By combining diverse experimental approaches with computational cell simulation, we show that K(+) circulating in the phloem serves as a decentralized energy storage that can be used to overcome local energy limitations. Posttranslational modification of the phloem-expressed Arabidopsis K(+) channel AKT2 taps this "potassium battery," which then efficiently assists the plasma membrane H(+)-ATPase in energizing the transmembrane phloem (re)loading processes.

Rehabilitation robotics: pilot trial of a spatial extension for MIT-Manus.

BACKGROUND: Previous results with the planar robot MIT-MANUS demonstrated positive benefits in trials with over 250 stroke patients. Consistent with motor learning, the positive effects did not generalize to other muscle groups or limb segments. Therefore we are designing a new class of robots to exercise other muscle groups or limb segments. This paper presents basic engineering aspects of a novel robotic module that extends our approach to anti-gravity movements out of the horizontal plane and a pilot study with 10 outpatients. Patients were trained during the initial six-weeks with the planar module (i.e., performance-based training limited to horizontal movements with gravity compensation). This training was followed by six-weeks of robotic therapy that focused on performing vertical arm movements against gravity. The 12-week protocol includes three one-hour robot therapy sessions per week (total 36 robot treatment sessions). RESULTS: Pilot study demonstrated that the protocol was safe and well tolerated with no patient presenting any adverse effect. Consistent with our past experience with persons with chronic strokes, there was a statistically significant reduction in tone measurement from admission to discharge of performance-based planar robot therapy and we have not observed increases in muscle tone or spasticity during the anti-gravity training protocol. Pilot results showed also a reduction in shoulder-elbow impairment following planar horizontal training. Furthermore, it suggested an additional reduction in shoulder-elbow impairment following the anti-gravity training. CONCLUSION: Our clinical experiments have focused on a fundamental question of whether task specific robotic training influences brain recovery. To date several studies demonstrate that in mature and damaged nervous systems, nurture indeed has an effect on nature. The improved recovery is most pronounced in the trained limb segments. We have now embarked on experiments that test whether we can continue to influence recovery, long after the acute insult, with a novel class of spatial robotic devices. This pilot results support the pursuit of further clinical trials to test efficacy and the pursuit of optimal therapy following brain injury.