Bulk Cultures Research Articles

Substrate functionalization by cold plasma treatments as an alternative process to the cultivation of microalgae in biofilm: Application to Botryococcus

Microalgae are renowned for their diverse production of molecules, including biofuels. However, biotechnological processes aiming at producing these biomolecules have yet to achieve economic sustainability due to the high costs associated with downstream processing, which can make up to 80 % of the total production costs. Since microalgae immobilized on a flat surface are characterized by a higher productivity and an easier harvesting than bulk culture systems, flat cultures may present better economic viability. Nevertheless, immobilizing filamentous or colonial microalgae on a flat surface is challenging due to their inherent 3D development. In this study, we explored the effectiveness of a plasma-modified polyethylene terephthalate flat surface for improving the immobilization of the green freshwater colonial microalga Botryococcus protuberans, a promising taxon for biofuel production. Plasma treatments were found to alter the wettability and surface energy of polyethylene terephthalate substrates. Botryococcus adhesion was enhanced significantly on O2 plasma-modified substrates compared to untreated substrates. The adhesion was strong enough to prevent colony development in the water column while allowing the development of a biofilm over one month, with minimal impact on their physiology.

A serum-free culture medium production system by co-culture combining growth factor-secreting cells and l-lactate-assimilating cyanobacteria for sustainable cultured meat production

Large-scale production of cultured meat requires bulk culture medium containing growth-promoting proteins from animal serum. However, animal serum for mammalian cell culture is associated with high costs, ethical concerns, and contamination risks. Owing to its growth factor content, conditioned medium from rat liver epithelial RL34 cells can replace animal serum for myoblast proliferation. More seeded cells and longer culture periods are thought to yield higher growth factor levels, resulting in more effective muscle cell proliferation. However, RL34 cells can deplete nutrients and release harmful metabolites into the culture medium over time, potentially causing growth inhibition and apoptosis. This issue highlights the need for waste clearance during condition medium production. To address this issue, we introduced a lactate permease gene (lldP) and an l-lactate-to-pyruvate conversion enzyme gene (lldD) to generate a recombinant l-lactate-assimilating cyanobacterium Synechococcus sp. KC0110 strain. Transwell co-culture of this strain with RL34 cells exhibited a marked reduction in the levels of harmful metabolites, lactate and ammonium, while maintaining higher concentrations of glucose, pyruvate, and pyruvate-derived amino acids than those seen with RL34 cell monocultures. The co-culture medium supported myoblast proliferation without medium dilution or additional nutrients, which was attributed to the waste clearance and nutrient replenishment effects of the KC0110 strain. This culture system holds potential for the production of low-cost, and animal-free cultured meat.

Single-Cell Phenotyping of Extracellular Electron Transfer via Microdroplet Encapsulation.

Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes. Studying this phenomenon in high-throughput is challenging since extracellular reduction cannot easily be traced back to its cell of origin within a mixed population. Here, we describe the development of a microdroplet emulsion system to enrich EET-capable organisms. We validated our system using the model electroactive organism S. oneidensis and describe the tooling of a benchtop microfluidic system for oxygen-limited processes. We demonstrated enrichment of EET-capable phenotypes from a mixed wild-type and EET-knockout population. As a proof-of-concept application, bacteria were collected from iron sedimentation from Town Lake (Austin, TX) and subjected to microdroplet enrichment. We observed an increase in EET-capable organisms in the sorted population that was distinct when compared to a population enriched in a bulk culture more closely akin to traditional techniques for discovering EET-capable bacteria. Finally, two bacterial species, C. sakazakii and V. fessus not previously shown to be electroactive, were further cultured and characterized for their ability to reduce channel conductance in an organic electrochemical transistor (OECT) and to reduce soluble Fe(III). We characterized two bacterial species not previously shown to exhibit electrogenic behavior. Our results demonstrate the utility of a microdroplet emulsions for identifying putative EET-capable bacteria and how this technology can be leveraged in tandem with existing methods.

58 United States Department of Agriculture National Animal Health Monitoring System Goat 2019 study: Distribution of gastrointestinal nematodes

Abstract One objective of the United States Department of Agriculture National Animal Health Monitoring System Goat 2019 study was to describe practices producers use to control gastrointestinal nematodes (GIN) and reduce anthelmintic resistance through the examination of anthelmintic treatment efficacy via fecal egg count reduction tests and fecal cultures. The fecal cultures were used to determine what GIN were present across the areas of the US included in the study (September 2019-April 2020). Bulk cultures were processed from 318 operations in 24 states and results were consolidated into 4 regions: Northwest (3 states, 34 operations), Northeast (9 states, 89 operations), Southeast (9 states, 132 operations) and Southwest (3 states, 63 operations). GIN identification included Haemonchus, Trichostrongylus, Teladorsagia, Oesophagostomumand Nematodirus. In addition to GIN, lungworm presence was also noted. Haemonchus were found on 18.6% of the operations (Northwest, 27.0%; Northeast, 13.1%; Southeast, 15.9% and Southwest, 29.2%). Trichostrongylus were found on 97.2% of the operations (Northwest, 100%; Northeast, 98%; Southeast, 97.0% and Southwest, 95.7%). Teladorsagia were found on 80.3% of the operations (Northwest, 97.1%; Northeast, 71.6%; Southeast, 88.6% and Southwest (75.7%). Oesophagostomum were found on 38.2% of the operations (Northwest, 73.1%; Northeast, 39.6%, Southeast, 46.4% and Southwest, 15.5%). Nematodiruswere found on 7% of the operations (Northwest, 7%; Northeast, 5.2%, Southeast, 20.8% and Southwest, 0%). Lungworms were found on 35.4% of the operations (Northwest, 69.1%; Northeast, 52.2%, Southeast, 33.4% and Southwest, 8.3%). Due to sampling logistics, fecal collection was conducted during autumn through early spring which may have influenced number of more pathogenic GIN. This study provided valuable insight into regional prevalence of GIN in goats. In depth analyses continues and will be forthcoming.

Therapeutic potential of dietary nutrients and medicinal foods against metabolic disorders: Targeting Akkermansia muciniphila

AbstractAs one of the most attractive next‐generation probiotics, mucin‐degrading Akkermansia muciniphila has emerged as an essential and integral factor in maintaining human health and affecting pathological outcomes. Its abundance is inversely associated with various metabolic diseases (e.g., obesity and type 2 diabetes), cardiovascular diseases, and intestinal inflammation. Supplementing A. muciniphila to restore the gut microbiota ecosystem is a promising approach for treating metabolic disorders. However, the direct utilization of this probiotic is limited by technological and regulatory hurdles, such as the in vitro bulk culture of A. muciniphila and the need for expensive animal‐derived materials. Therefore, enrichment of A. muciniphila using nutraceutical supplements is a feasible strategy. Dietary supplements, especially medicinal herbs, offer a vast and valuable resource as potential prebiotics for promoting the growth of A. muciniphila in the gut, ensuring reliable safety and efficacy. In this study, we first systemically reviewed the dietary substances and medicinal foods known to promote A. muciniphila from over 100 literature sources, aiming to establish a candidate basis for future exploration of prebiotics targeting A. muciniphila. Furthermore, we summarized and discussed the major regulatory factors and mechanisms responsible for the beneficial effect of A. muciniphila on metabolic disorders, hoping to open up exciting directions for in‐depth research on the pharmacological mechanism of A. muciniphila and pave the way for its clinical therapeutics.

Activation-neutral gene editing of tonsillar CD4 T cells for functional studies in human ex vivo tonsil cultures

The molecular and immunological properties of tissue-resident resting CD4 Tcells are understudied due to the lack of suitable gene editing methods. Here, we describe the exvivo culture and gene editing methodology ediTONSIL for CD4 Tcells from human tonsils. Optimized CRISPR-Cas9 RNP nucleofection results in knockout efficacies of over 90% without requiring exogenous activation. Editing can be performed on multiple cell types in bulk cultures or on isolated CD4 Tcells that can be labeled and reintroduced into their tissue environment. Importantly, CD4 Tcells maintain their tissue-specific properties such as viability, activation state, or immunocompetence following reassembly into lymphoid aggregates. This highly efficient and versatile gene editing workflow for tonsillar CD4 Tcells enables the dissection of molecular mechanisms in exvivo cultures of human lymphoid tissue and can be adapted to other tonsil-resident cell types.

Macro- and micro-scale culture environment differentially regulate the effects of crowding on macrophage function.

Macrophages hold vital roles in immune defense, wound healing, and tissue homeostasis, and have the exquisite ability to sense and respond to dynamically changing cues in their microenvironment. Much of our understanding of their behavior has been derived from studies performed using in vitro culture systems, in which the cell environment can be precisely controlled. Recent advances in miniaturized culture platforms also offer the ability to recapitulate some features of the in vivo environment and analyze cellular responses at the single-cell level. Since macrophages are sensitive to their surrounding environments, the specific conditions in both macro- and micro-scale cultures likely contribute to observed responses. In this study, we investigate how the presence of neighboring cells influence macrophage activation following proinflammatory stimulation in both bulk and micro-scale culture. We found that in bulk cultures, higher seeding density negatively regulated the average TNF-α secretion from individual macrophages in response to inflammatory agonists, and this effect was partially caused by the reduced cell-to-media volume ratio. In contrast, studies conducted using microwells to isolate single cells and groups of cells revealed that increasing numbers of cells positively influences their inflammatory activation, suggesting that the absolute cell numbers in the system may be important. In addition, a single inflammatory cell enhanced the inflammatory state of a small group of cells. Overall, this work helps to better understand how variations of macroscopic and microscopic culture environments influence studies in macrophage biology and provides insight into how the presence of neighboring cells and the soluble environment influences macrophage activation.

Sleeping Beauty kit sets provide rapid and accessible generation of artificial antigen-presenting cells for natural killer cell expansion.

Artificial antigen-presenting cells (aAPCs) offer a cost effective and convenient tool for the expansion of chimeric antigen receptor (CAR)-bearing T cells and NK cells. aAPCs are particularly useful because of their ability to efficiently expand low-frequency antigen-reactive lymphocytes in bulk cultures. Commonly derived from the leukemic cell line K562, these aAPCs lack most major histocompatibility complex expression and are therefore useful for NK cell expansion without triggering allogeneic T-cell proliferation. To combat difficulties in accessing existing aAPC lines, while circumventing the iterative lentiviral gene transfers with antibody-mediated sorting required for the isolation of stable aAPC clones, we developed a single-step technique using Sleeping Beauty (SB)-based vectors with antibiotic selection options. Our SB vectors contain options of two to three genes encoding costimulatory molecules, membrane-bound cytokines as well as the presence of antibiotic-resistance genes that allow for stable transposition-based transfection of feeder cells. Transfection of K562 with SB vectors described in this study allows for the surface expression of CD86, 4-1BBL, membrane-bound (mb) interleukin (IL)-15 and mbIL-21 after simultaneous transposition and antibiotic selection using only two antibiotics. aAPCs successfully expanded NK cells to high purity (80-95%). Expanded NK cells could be further engineered by lentiviral CAR transduction. The multivector kit set is publicly available and will allow convenient and reproducible in-house production of effective aAPCs for the invitro expansion of primary cells.

Unfractionated Bulk Culture of Mouse Skeletal Muscle to Recapitulate Niche and Stem Cell Quiescence.

Skeletal muscle is the largest tissue of the body and performs multiple functions, from locomotion to body temperature control. Its functionality and recovery from injuries depend on a multitude of cell types and on molecular signals between the core muscle cells (myofibers, muscle stem cells) and their niche. Most experimental settings do not preserve this complex physiological microenvironment, and neither do they allow the ex vivo study of muscle stem cells in quiescence, a cell state that is crucial for them. Here, a protocol is outlined for the ex vivo culture of muscle stem cells with cellular components of their niche. Through the mechanical and enzymatic breakdown of muscles, a mixture of cell types is obtained, which is put in 2D culture. Immunostaining shows that within 1 week, multiple niche cells are present in culture alongside myofibers and, importantly, Pax7-positive cells that display the characteristics of quiescent muscle stem cells. These unique properties make this protocol a powerful tool for cell amplification and the generation of quiescent-like stem cells that can be used to address fundamental and translational questions.

The novel MYH6-E1584K tail domain variant associated with hypoplastic left heart syndrome leads to hypercontractility in vitro

Hypoplastic left heart syndrome (HLHS) is a complex form of congenital heart disease (CHD) characterized by hypoplasia of the left ventricle and proximal aorta, as well as stenosis or atresia of the mitral and aortic valves. Our lab previously identified that rare, predicted-damaging variants in the gene encoding for α-myosin heavy chain ( MYH6, α-MHC), a key contractile protein in the heart, are enriched in HLHS. It has been shown that pathological variants in the MHC head domain directly alter force generation, but mechanisms by which tail domain variants cause contractile defects are less clear.In double-blind analyses, patient-specific induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) carrying the MYH6 E1584K tail domain variant (VAR) showed significant structural and functional deficits compared to wild-type (WT). Consistent with our previously reported findings in atrial tissue from a patient carrying MYH6 E1584K, VAR iPSC-CMs exhibited sarcomere disarray (p<0.001) and altered sarcomeric gene expression (p<0.05). VAR iPSC-CMs display a hypercontractile phenotype compared to WT, with increased amplitude (2.16μm VAR, 1.32μm WT; p<0.05) and duration (233 msec VAR, 173 msec WT; p<0.05) of contraction and elongated relaxation times (270 msec VAR, 190 msec WT; p<0.01). Hypercontractility was also observed in bulk culture, where VAR iPSC-CMs demonstrated increased amplitude (1413.4 a.u. VAR, 993.6 a.u. WT, p<0.05) and velocity of contraction (1493.7 a.u./msec VAR, 982.2 a.u./msec WT, p<0.05). Notably, this is different than our previous reports of iPSC-CMs carrying the head domain variant MYH6 R443P, which exhibited decreased contraction velocity.Our data demonstrate the mechanism of MYH6 pathogenicity is distinct between variants, emphasizing the importance of mechanistic studies to inform clinical decision-making. Furthermore, this work will direct future investigations into the genetic etiology and physiology of CHD and provide a framework upon which personalized treatment strategies can be developed. Future studies will examine the effect of myosin modulators omecamtiv mecarbil (OM) and mavacamten on MYH6 variant iPSC-CMs. Advancing a Healthier Wisconsin Endowment This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Plastic responses lead to increased neurotoxin production in the diatom Pseudo-nitzschia under ocean warming and acidification.

Ocean warming (OW) and acidification (OA) are recognized as two major climatic conditions influencing phytoplankton growth and nutritional or toxin content. However, there is limited knowledge on the responses of harmful algal bloom species that produce toxins. Here, the study provides quantitative and mechanistic understanding of the acclimation and adaptation responses of the domoic acid (DA) producing diatom Pseudo-nitzschia multiseries to rising temperature and pCO2 using both a one-year in situ bulk culture experiment, and an 800-day laboratory acclimation experiment. Ocean warming showed larger selective effects on growth and DA metabolism than ocean acidification. In a bulk culture experiment, increasing temperature +4 °C above ambient seawater temperature significantly increased DA concentration by up to 11-fold. In laboratory when the long-term warming acclimated samples were assayed under low temperatures, changes in growth rates and DA concentrations indicated that P. multiseries did not adapt to elevated temperature, but could instead rapidly and reversibly acclimate to temperature shifts. However, the warming-acclimated lines showed evidence of adaptation to elevated temperatures in the transcriptome data. Here the core gene expression was not reversed when warming-acclimated lines were moved back to the low temperature environment, which suggested that P. multiseries cells might adapt to rising temperature over longer timescales. The distinct strategies of phenotypic plasticity to rising temperature and pCO2 demonstrate a strong acclimation capacity for this bloom-forming toxic diatom in the future ocean.

STEM-08. MODELING AND UNDERSTANDING GLIOBLASTOMA EDGE CELLS

Abstract Glioblastoma is a devastating disease with an overall median survival of 8 months from diagnosis. The majority of patients die of a tumor relapse in close proximity of the resected primary tumor. Glioblastoma is intensely researched but most studies have been performed on tissues and cultures derived from the bulk tumor while it is the remaining edge cells that cause lethality. Investigations of edge cells are rare and few experimental models exist. Here we have established and analyzed a series of matched cell cultures derived from the tumor bulk and outer edge of six IDH wildtype glioblastoma patients with the purpose to understand glioblastoma edge cell biology. Tumor samples were resected guided by 5-ALA fluorescence using neuro-navigation and stringent procedures to not contaminate edge samples with bulk tumor cells. First bulk tumor samples were resected from 5-ALA fluorescent tissue. After removal of all fluorescent areas and careful irrigation of the cavity the edge sample was resected 1-2 cm outside of the fluorescent border in a non-eloquent area. Following dissociation the samples were used in sphere assays and for explantation. There was a significant difference in self-renewal across all patients between matched bulk and edge cultures, in line with results from sphere assays on acute cells, suggesting maintenance of glioblastoma cell properties in established cultures. Invasion analysis showed a reverse significant difference between matched bulk and edge cultures strengthening a general functional distinction between tumor bulk and edge cells across patients. To investigate the molecular basis of our findings we performed whole exome sequencing (WES) and combined single cell RNA- and ATAC-sequencing (10X Multiome). Analyses are ongoing but WES data does not support genetic causes for their differences while the 10X Multiome data indicate that epigenetic regulation may underlie the different properties of bulk and edge glioblastoma cells.

Clinically encountered growth phenotypes of tuberculosis-causing bacilli and their in vitro study: A review.

The clinical manifestations of tuberculosis (TB) vary widely in severity, site of infection, and outcomes of treatment-leading to simultaneous efforts to individualize therapy safely and to search for shorter regimens that can be successfully used across the clinical spectrum. In these endeavors, clinicians and researchers alike employ mycobacterial culture in rich media. However, even within the same patient, individual bacilli among the population can exhibit substantial variability in their culturability. Bacilli in vitro also demonstrate substantial heterogeneity in replication rate and cultivation requirements, as well as susceptibility to killing by antimicrobials. Understanding parallels in clinical, ex vivo and in vitro growth phenotype diversity may be key to identifying those phenotypes responsible for treatment failure, relapse, and the reactivation of bacilli that progresses TB infection to disease. This review briefly summarizes the current role of mycobacterial culture in the care of patients with TB and the ex vivo evidence of variability in TB culturability. We then discuss current advances in in vitro models that study heterogenous subpopulations within a genetically identical bulk culture, with an emphasis on the effect of oxidative stress on bacillary cultivation requirements. The review highlights the complexity that heterogeneity in mycobacterial growth brings to the interpretation of culture in clinical settings and research. It also underscores the intricacies present in the interplay between growth phenotypes and antimicrobial susceptibility. Better understanding of population dynamics and growth requirements over time and space promises to aid both the attempts to individualize TB treatment and to find uniformly effective therapies.

Modeling single-cell phenotypes links yeast stress acclimation to transcriptional repression and pre-stress cellular states.

Stress defense and cell growth are inversely related in bulk culture analyses; however, these studies miss substantial cell-to-cell heterogeneity, thus obscuring true phenotypic relationships. Here, we devised a microfluidics system to characterize multiple phenotypes in single yeast cells over time before, during, and after salt stress. The system measured cell and colony size, growth rate, and cell-cycle phase along with nuclear trans-localization of two transcription factors: stress-activated Msn2 that regulates defense genes and Dot6 that represses ribosome biogenesis genes during an active stress response. By tracking cells dynamically, we discovered unexpected discordance between Msn2 and Dot6 behavior that revealed subpopulations of cells with distinct growth properties. Surprisingly, post-stress growth recovery was positively corelated with activation of the Dot6 repressor. In contrast, cells lacking Dot6 displayed slower growth acclimation, even though they grow normally in the absence of stress. We show that wild-type cells with a larger Dot6 response display faster production of Msn2-regulated Ctt1 protein, separable from the contribution of Msn2. These results are consistent with the model that transcriptional repression during acute stress in yeast provides a protective response, likely by redirecting translational capacity to induced transcripts.

Amphidinol C, a major polyketide from an Irish strain of the dinoflagellate Amphidinium carterae

An Irish strain of the dinoflagellate Amphidinium carterae was previously shown to produce antibacterial amphidinol derivatives of unknown masses. Inspection of the major metabolites present in a bulk culture of this strain led to the isolation and structure elucidation of a new amphidinol derivative named amphidinol C featuring an unprecedented tetrahydropyran ring between the positions C-7 and C-11. The structure was determined using extensive analyses of NMR and MS data and comparison with data of analogues. The new ring was proposed to stem from a nucleophilic substitution of the sulphate present on the side chain of Amphidinol B. The major metabolites isolated were tested for their antibacterial and antifungal activities and Amphidinol C showed moderate fungicidal activity against yeast and filamentous fungi at 8–16 µg mL −1 . • Amphidinol C was isolated from an Irish strain of the dinoflagellate Amphidinium carterae. • Amphidinol C features an unusual tetrahydropyrane ring between the positions C-7 and C-11. • The tetrahydropyrane ring could result from the substitution of the sulphate group of amphidinol B. • Amphidinol C exhibited moderate fungicidal activity.

Alcaligenes ammonioxydans HO-1 antagonizes Bacillus velezensis via hydroxylamine-triggered population response.

Antagonism is a common behavior seen between microbes in nature. Alcaligenes ammonioxydans HO-1 converts ammonia to nitrogen under aerobic conditions, which leads to the accumulation of extracellular hydroxylamine (HA), providing pronounced growth advantages against many bacterial genera, including Bacillus velezensis V4. In contrast, a mutant variant of A. ammonioxydans, strain 2-29, that cannot produce HA fails to antagonize other bacteria. In this article, we demonstrate that cell-free supernatants derived from the antagonistic HO-1 strain were sufficient to reproduce the antagonistic behavior and the efficiency of this inhibition correlated strongly with the HA content of the supernatant. Furthermore, reintroducing the capacity to produce HA to the 2-29 strain or supplementing bacterial co-cultures with HA restored antagonistic behavior. The HA-mediated antagonism was dose-dependent and affected by the temperature, but not by pH. HA caused a decline in biomass, cell aggregation, and hydrolysis of the cell wall in exponentially growing B. velezensis bulk cultures. Analysis of differential gene expression identified a series of genes modulating multicellular behavior in B. velezensis. Genes involved in motility, chemotaxis, sporulation, polypeptide synthesis, and non-ribosomal peptide synthesis were all significantly downregulated in the presence of HA, whereas autolysis-related genes showed upregulation. Taken together, these findings indicate that HA affects the population response of coexisting strains and also suggest that A. ammonioxydans HO-1 antagonize other bacteria by producing extracellular HA that, in turn, acts as a signaling molecule.

Combined noncanonical NF-κB agonism and targeted BET bromodomain inhibition reverse HIV latency ex vivo.

Latency reversal strategies for HIV cure using inhibitor of apoptosis protein (IAP) antagonists (IAPi) induce unprecedented levels of latent reservoir expression without immunotoxicity during suppressive antiretroviral therapy (ART). However, full targeting of the reservoir may require combinatorial approaches. A Jurkat latency model screen for IAPi combination partners demonstrated synergistic latency reversal with bromodomain (BD) and extraterminal domain protein inhibitors (BETi). Mechanistic investigations using CRISPR-CAS9 and single-cell RNA-Seq informed comprehensive ex vivo evaluations of IAPi plus pan-BET, bD-selective BET, or selective BET isoform targeting in CD4+ T cells from ART-suppressed donors. IAPi+BETi treatment resulted in striking induction of cell-associated HIV gag RNA, but lesser induction of fully elongated and tat-rev RNA compared with T cell activation–positive controls. IAPi+BETi resulted in HIV protein induction in bulk cultures of CD4+ T cells using an ultrasensitive p24 assay, but did not result in enhanced viral outgrowth frequency using a standard quantitative viral outgrowth assay. This study defines HIV transcriptional elongation and splicing as important barriers to latent HIV protein expression following latency reversal, delineates the roles of BET proteins and their BDs in HIV latency, and provides a rationale for exploration of IAPi+BETi in animal models of HIV latency.

Microfluidic Platforms Designed for Morphological and Photosynthetic Investigations of Chlamydomonas reinhardtii on a Single-Cell Level.

Chlamydomonas reinhardtii is a model organism of increasing biotechnological importance, yet, the evaluation of its life cycle processes and photosynthesis on a single-cell level is largely unresolved. To facilitate the study of the relationship between morphology and photochemistry, we established microfluidics in combination with chlorophyll a fluorescence induction measurements. We developed two types of microfluidic platforms for single-cell investigations: (i) The traps of the “Tulip” device are suitable for capturing and immobilizing single cells, enabling the assessment of their photosynthesis for several hours without binding to a solid support surface. Using this “Tulip” platform, we performed high-quality non-photochemical quenching measurements and confirmed our earlier results on bulk cultures that non-photochemical quenching is higher in ascorbate-deficient mutants (Crvtc2-1) than in the wild-type. (ii) The traps of the “Pot” device were designed for capturing single cells and allowing the growth of the daughter cells within the traps. Using our most performant “Pot” device, we could demonstrate that the FV/FM parameter, an indicator of photosynthetic efficiency, varies considerably during the cell cycle. Our microfluidic devices, therefore, represent versatile platforms for the simultaneous morphological and photosynthetic investigations of C. reinhardtii on a single-cell level.

Flow Cytometry Approaches to Obtain Medulloblastoma Stem Cells from Bulk Cultures.

Cancer stem cells are considered the reservoir cancer cells that are resistant to most of the forms of cancer therapies and cause relapse of the tumor. Medulloblastoma (MB), a primary CNS tumor, is a very fast-growing tumor affecting younger population. In order to characterize medulloblastoma cancer stem cells or studying the drug resistance in MB mediated through the cancer stem cells, it becomes essential to isolate and study them. Isolation and characterization of tumor cells is a critical step in understanding the cancer progression and to devise novel approaches against them as drug targets. Typically, characterization of stem cells is done through surface marker analysis and with the advent of flow cytometry based techniques, this has become incredibly straightforward. Flow cytometry employs a uniformly linear flow of cells created by complex hydraulics of the flow cytometer followed by illuminating flow path with a LASER beam. This gives very valuable information about cell composition in forward scatter (FSC) and side scatter (SSC). The surface molecules of the cells can further be stained with various florescent dyes which upon excitation with the LASER beam will give the signal that will be detected by the instrument. Flow cytometer is high-throughput equipment and requires careful operation to get valuable information about the samples. In this chapter, we describe how from a bulk cell sample of medulloblastoma cells, cancer stem cells are isolated.

Assessment of Endothelial-to-Hematopoietic Transition of Individual Hemogenic Endothelium and Bulk Populations in Defined Conditions.

Endothelial-to-hematopoietic transition (EHT) is a unique morphogenic event in which flat, adherent hemogenic endothelial (HE) cells acquire round, non-adherent blood cell morphology. Investigating the mechanisms of EHT is critical for understanding the development of hematopoietic stem cells (HSCs) and the entirety of the adult immune system, and advancing technologies for manufacturing blood cells from human pluripotent stem cells (hPSCs). Here we describe a protocol to (a) generate and isolate subsets of HE from hPSCs, (b) assess EHT and hematopoietic potential of HE subsets in bulk cultures and at the single-cell level, and (c) evaluate the role of NOTCH signaling during HE specification and EHT. The generation of HE from hPSCs and EHT bulk cultures are performed in xenogen- and feeder-free system, providing the unique advantage of being able to investigate the role of individual signaling factors during EHT and the definitive lympho-myeloid cell specification from hPSCs.