scholarly journals Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy

2014 ◽  
Vol 25 (22) ◽  
pp. 3699-3708 ◽  
Author(s):  
Anyimilehidi Mazo-Vargas ◽  
Heungwon Park ◽  
Mert Aydin ◽  
Nicolas E. Buchler
Keyword(s):  
Gene Expression ◽  
Fluorescent Proteins ◽  
Single Cells ◽  
Time Lapse ◽  
Photon Flux ◽  
Luminescence Microscopy ◽  
Cell Cycle Genes ◽  
Light Excitation ◽  
Better Than

Time-lapse fluorescence microscopy is an important tool for measuring in vivo gene dynamics in single cells. However, fluorescent proteins are limited by slow chromophore maturation times and the cellular autofluorescence or phototoxicity that arises from light excitation. An alternative is luciferase, an enzyme that emits photons and is active upon folding. The photon flux per luciferase is significantly lower than that for fluorescent proteins. Thus time-lapse luminescence microscopy has been successfully used to track gene dynamics only in larger organisms and for slower processes, for which more total photons can be collected in one exposure. Here we tested green, yellow, and red beetle luciferases and optimized substrate conditions for in vivo luminescence. By combining time-lapse luminescence microscopy with a microfluidic device, we tracked the dynamics of cell cycle genes in single yeast with subminute exposure times over many generations. Our method was faster and in cells with much smaller volumes than previous work. Fluorescence of an optimized reporter (Venus) lagged luminescence by 15–20 min, which is consistent with its known rate of chromophore maturation in yeast. Our work demonstrates that luciferases are better than fluorescent proteins at faithfully tracking the underlying gene expression.

scholarly journals C-terminal eYFP fusion impairs Escherichia coli MinE function

Open Biology ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 200010
Author(s):  
Navaneethan Palanisamy ◽  
Mehmet Ali Öztürk ◽  
Emir Bora Akmeriç ◽  
Barbara Di Ventura
Keyword(s):  
Escherichia Coli ◽  
In Silico ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Yellow Fluorescent Protein ◽  
Time Lapse ◽  
Enhanced Yellow Fluorescent Protein ◽  
Min Proteins

The Escherichia coli Min system plays an important role in the proper placement of the septum ring at mid-cell during cell division. MinE forms a pole-to-pole spatial oscillator with the membrane-bound ATPase MinD, resulting in MinD concentration being the lowest at mid-cell. MinC, the direct inhibitor of the septum initiator protein FtsZ, forms a complex with MinD at the membrane, mirroring its polar gradients. Therefore, MinC-mediated FtsZ inhibition occurs away from mid-cell. Min oscillations are often studied in living cells by time-lapse microscopy using fluorescently labelled Min proteins. Here, we show that, despite permitting oscillations to occur in a range of protein concentrations, the enhanced yellow fluorescent protein (eYFP) C-terminally fused to MinE impairs its function. Combining in vivo , in vitro and in silico approaches, we demonstrate that eYFP compromises the ability of MinE to displace MinC from MinD, to stimulate MinD ATPase activity and to directly bind to the membrane. Moreover, we reveal that MinE-eYFP is prone to aggregation. In silico analyses predict that other fluorescent proteins are also likely to compromise several functionalities of MinE, suggesting that the results presented here are not specific to eYFP.

Gene Expression in Synovial Membrane Cells After Intraarticular Delivery of Plasmid-Linked Superparamagnetic Iron Oxide Particles—A Preliminary Study in Sheep

2006 ◽  
Vol 6 (9) ◽  
pp. 2841-2852 ◽  
Author(s):  
Larry D. Galuppo ◽  
Sarah W. Kamau ◽  
Benedikt Steitz ◽  
Paul O. Hassa ◽  
Monika Hilbe ◽  
...  
Keyword(s):  
Gene Expression ◽  
Iron Oxide ◽  
Gene Delivery ◽  
Synovial Membrane ◽  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Superparamagnetic Iron Oxide ◽  
Oxide Nanoparticles ◽  
Positive Evidence

This study evaluated in vivo gene delivery and subsequent gene expression within cells of the synovium in the presence of static and pulsating magnetic field application following intraarticular injection of superparamagnetic iron oxide nanoparticles linked to plasmids containing reporter genes encoding for fluorescent proteins. Plasmids encoding genes for either green fluorescent protein or red fluorescent protein were bound to superparamagnetic nanoparticles coated with polyethyleneimine. Larger (200–250 nm) and smaller (50 nm) nanoparticles were compared to evaluate the effects of size on transfection efficiency as well as any associated intraarticular reaction. Comparisons between groups were evaluated at 24, 72, and 120 h time periods. Inflammatory response was mild to moderate for all injected particles, but was present in the majority of synovial membrane samples evaluated. Larger particles tended to be associated with more inflammation than smaller ones. Nevertheless, intraarticular application of both experimental and control nanoparticles were well tolerated clinically. Gene expression as determined by observation of either green or red intracellular fluorescence was difficult to assess by both epifluorescent light, and confocal microscopy. An insufficient concentration of nanoparticles in relation to joint volume likely resulted in a limited number of samples with positive evidence of iron staining and with suspected positive evidence of cells expressing fluorescent proteins. Our results indicate that intraarticular administration of functionalized superparamagnetic iron oxide nanoparticles resulted in a mild to moderate synovitis and there was in conclusive evidence of gene expression. Further research is warranted to determine the best and most effective reporter assay for assessment of the in vivo gene delivery into the joints. In addition, the best suited concentration and size of nanoparticles, which will optimize gene delivery and expression, while minimizing intraarticular inflammation, needs to be determined.

scholarly journals In vivo single cell analysis reveals Gata2 dynamics in cells transitioning to hematopoietic fate

2017 ◽  
Vol 215 (1) ◽  
pp. 233-248 ◽  
Author(s):  
Christina Eich ◽  
Jochen Arlt ◽  
Chris S. Vink ◽  
Parham Solaimani Kartalaei ◽  
Polynikis Kaimakis ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Cell Fate ◽  
Regulatory Networks ◽  
Single Cell Analysis ◽  
Single Cells ◽  
Time Lapse ◽  
Hematopoietic Stem ◽  
And Function ◽  
In Cells

Cell fate is established through coordinated gene expression programs in individual cells. Regulatory networks that include the Gata2 transcription factor play central roles in hematopoietic fate establishment. Although Gata2 is essential to the embryonic development and function of hematopoietic stem cells that form the adult hierarchy, little is known about the in vivo expression dynamics of Gata2 in single cells. Here, we examine Gata2 expression in single aortic cells as they establish hematopoietic fate in Gata2Venus mouse embryos. Time-lapse imaging reveals rapid pulsatile level changes in Gata2 reporter expression in cells undergoing endothelial-to-hematopoietic transition. Moreover, Gata2 reporter pulsatile expression is dramatically altered in Gata2+/− aortic cells, which undergo fewer transitions and are reduced in hematopoietic potential. Our novel finding of dynamic pulsatile expression of Gata2 suggests a highly unstable genetic state in single cells concomitant with their transition to hematopoietic fate. This reinforces the notion that threshold levels of Gata2 influence fate establishment and has implications for transcription factor–related hematologic dysfunctions.

scholarly journals Organoid single-cell profiling identifies a transcriptional signature of glomerular disease

2018 ◽  
Author(s):  
Jennifer L. Harder ◽  
Rajasree Menon ◽  
Edgar A. Otto ◽  
Jian Zhou ◽  
Sean Eddy ◽  
...  
Keyword(s):  
Gene Expression ◽  
Kidney Disease ◽  
Single Cells ◽  
Gene Expression Signature ◽  
Human Kidney ◽  
Glomerular Disease ◽  
Podocyte Injury ◽  
Compensation Mechanisms ◽  
Kidney Organoids

ABSTRACTPodocyte injury is central to many forms of kidney disease, but transcriptional signatures reflecting podocyte injury and compensation mechanisms are challenging to analyze in vivo. Human kidney organoids derived from pluripotent stem cells (PSCs), a new model for disease and regeneration, present an opportunity to explore the transcriptional plasticity of podocytes. Here, transcriptional profiling of over 12,000 single cells from human PSC-derived kidney organoid cultures was used to identify robust and reproducible cell-lineage gene expression signatures shared with developing human kidneys based on trajectory analysis. Surprisingly, the gene expression signature characteristic of developing glomerular epithelial cells was also observed in glomerular tissue from a kidney disease cohort. This signature correlated with proteinuria and inverse eGFR, and was confirmed in an independent podocytopathy cohort. Three genes in particular were further identified as critical components of the glomerular disease signature. We conclude that cells in human PSC-derived kidney organoids reliably recapitulate the developmental transcriptional program of podocytes and other cell lineages in the human kidney, and that the early transcriptional profile seen in developing podocytes is reactivated in glomerular disease. Our findings demonstrate an innovative approach to identifying novel molecular programs involved in the pathogenesis of glomerulopathies.

scholarly journals Exploiting variability of single cells to uncover the in vivo hierarchy of miRNA targets

2015 ◽  
Author(s):  
Andrzej Jerzy Rzepiela ◽  
Arnau Vina-Vilaseca ◽  
Jeremie Breda ◽  
Souvik Ghosh ◽  
Afzal P Syed ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Single Cells ◽  
Human Embryonic Kidney Cells ◽  
Mirna Targets ◽  
Wide Range ◽  
Gene Expression Dynamics ◽  
Cell To Cell Variability ◽  
First Time

MiRNAs are post-transcriptional repressors of gene expression that may additionally reduce the cell-to-cell variability in protein expression, induce correlations between target expression levels and provide a layer through which targets can influence each other's expression as 'competing RNAs' (ceRNAs). Here we combined single cell sequencing of human embryonic kidney cells in which the expression of two distinct miRNAs was induced over a wide range, with mathematical modeling, to estimate Michaelis-Menten (KM)-type constants for hundreds of evolutionarily conserved miRNA targets. These parameters, which we inferred here for the first time in the context of the entire network of endogenous miRNA targets, vary over ~2 orders of magnitude. They reveal an in vivo hierarchy of miRNA targets, defined by the concentration of miRNA-Argonaute complexes at which the targets are most sensitively down-regulated. The data further reveals miRNA-induced correlations in target expression at the single cell level, as well as the response of target noise to the miRNA concentration. The approach is generalizable to other miRNAs and post-transcriptional regulators and provides a deeper understanding of gene expression dynamics.

Effective targeted antitumor activity of the antimicrobial agent taurolidine against relapsed/refractory neuroblastoma: Cytotoxicity, target modulation and tumor xenograft studies.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e21502-e21502
Author(s):  
Lucy Swift ◽  
Chunfen Zhang ◽  
Antony Pfaffle ◽  
Paul Chew ◽  
Olga Kovalchuk ◽  
...  
Keyword(s):  
Gene Expression ◽  
Clinical Trial ◽  
Early Phase ◽  
Phase Contrast ◽  
Time Lapse ◽  
Early Phase Clinical Trial ◽  
Phase Clinical Trial ◽  
Time Lapse Video

e21502 Background: Neuroblastoma (NB) is the most common extracranial solid tumor and one of the most complex and difficult to treat diseases in pediatrics. Currently, even with highly aggressive treatment protocols, the prognosis for patients with high-risk and relapsed NB remains poor. Hence, there is a clear need to identify new agents and novel therapeutic strategies for the treatment of these children. Taurolidine (TRD) is derived from the aminosulfoacid taurine and has known anti-microbial and anti-inflammatory properties. TRD has demonstrated anti-neoplastic activity against a range of aggressive human tumors. We present mechanistic evidence and supportive preclinical data from in vitro and animal models of refractory NB for the development of an early phase clinical trial incorporating TRD. Methods: For in vitro activity studies, a panel of cell lines derived from patients with relapsed NB (n = 6) and normal control cells were treated with increasing concentrations of TRD and cell viability was measured by alamar blue assay. Phase-contrast light microscopy, western blotting, time-lapse video microscopy and analysis of global gene expression by RNA-Seq were used to evaluate target modulation and induction of cell death pathways. Bioluminescence imaging of mice bearing NB xenografts treated with TRD was used to investigate the efficacy of TRD in vivo. Results: Cell survival data showed that TRD is cytotoxic against NB cell lines in vitro (mean IC50 value 100 µM, range 65-135 µM). Phase-contrast and time-lapse video microscopy confirmed the antitumor effects of TRD. Western blot analyses identified that TRD induced target modulation and an effective apoptotic cascade, resulting in PARP cleavage. Gene expression analyses and signaling pathway activation scores indicated alterations in the Notch, MAPK and IL-10 signaling pathways. Xenograft studies further validated the in vivo activity of TRD with decreased tumor burden in treated mice and a measurable improvement in survival. Conclusions: Our study provides key pre-clinical data on the activity and mechanism of action of TRD against NB. The findings support the rationale for further evaluation of TRD for the treatment of relapsed/refractory NB patients in an early phase clinical trial.

scholarly journals Phenotypic diversity and temporal variability in a bacterial signaling network revealed by single-cell FRET

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Johannes M Keegstra ◽  
Keita Kamino ◽  
François Anquez ◽  
Milena D Lazova ◽  
Thierry Emonet ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Phenotypic Diversity ◽  
Single Cells ◽  
Gene Expression Noise ◽  
Switching Regime ◽  
Molecular Noise ◽  
Entire Cell ◽  
Chemotaxis System

We present in vivo single-cell FRET measurements in the Escherichia coli chemotaxis system that reveal pervasive signaling variability, both across cells in isogenic populations and within individual cells over time. We quantify cell-to-cell variability of adaptation, ligand response, as well as steady-state output level, and analyze the role of network design in shaping this diversity from gene expression noise. In the absence of changes in gene expression, we find that single cells demonstrate strong temporal fluctuations. We provide evidence that such signaling noise can arise from at least two sources: (i) stochastic activities of adaptation enzymes, and (ii) receptor-kinase dynamics in the absence of adaptation. We demonstrate that under certain conditions, (ii) can generate giant fluctuations that drive signaling activity of the entire cell into a stochastic two-state switching regime. Our findings underscore the importance of molecular noise, arising not only in gene expression but also in protein networks.

scholarly journals Spectral recording of gene expression history by fluorescent timer protein

BioTechniques ◽  
2019 ◽  
Vol 67 (4) ◽  
pp. 154-164
Author(s):  
Anna R Tröscher ◽  
Barbara Werner ◽  
Nadia Kaouane ◽  
Wulf Haubensak
Keyword(s):  
Gene Expression ◽  
Fluorescent Proteins ◽  
Single Cells ◽  
Temporal Patterns ◽  
Spectral Shift ◽  
Early Gene ◽  
Proof Of Concept ◽  
Spatio Temporal ◽  
Living Organisms ◽  
Post Hoc

Monitoring spatio-temporal patterns of gene expression by fluorescent proteins requires longitudinal observation, which is often difficult to implement. Here, we fuse a fluorescent timer (FT) protein with an immediate early gene (IEG) promoter to track live gene expression in single cells. This results in a stimulus- and time-dependent spectral shift from blue to red for subsequent monitoring with fluorescence activated cell sorting (FACS) and live cell imaging. This spectral shift enables imputing the time point of activity post-hoc to dissociate early and late responders from a single snapshot in time. Thus, we provide a tool for tracking stimulus-driven IEG expression and demonstrate proof of concept exploiting promoter::FT fusions, adding new dimensions to experiments that require reconstructing spatio-temporal patterns of gene expression in cells, tissues or living organisms.

scholarly journals A human cell atlas of fetal chromatin accessibility

Science ◽  
2020 ◽  
Vol 370 (6518) ◽  
pp. eaba7612 ◽  
Author(s):  
Silvia Domcke ◽  
Andrew J. Hill ◽  
Riza M. Daza ◽  
Junyue Cao ◽  
Diana R. O’Day ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Cell ◽  
Single Cells ◽  
Complex Trait ◽  
Cell Types ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Cell Type ◽  
Cell Type Specific

The chromatin landscape underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of chromatin accessibility and gene expression in fetal tissues. For chromatin accessibility, we devised a three-level combinatorial indexing assay and applied it to 53 samples representing 15 organs, profiling ~800,000 single cells. We leveraged cell types defined by gene expression to annotate these data and cataloged hundreds of thousands of candidate regulatory elements that exhibit cell type–specific chromatin accessibility. We investigated the properties of lineage-specific transcription factors (such as POU2F1 in neurons), organ-specific specializations of broadly distributed cell types (such as blood and endothelial), and cell type–specific enrichments of complex trait heritability. These data represent a rich resource for the exploration of in vivo human gene regulation in diverse tissues and cell types.

scholarly journals Preventing Photomorbidity in Long-Term Multi-color Fluorescence Imaging of Saccharomyces cerevisiae and S. pombe

2020 ◽  
Vol 10 (12) ◽  
pp. 4373-4385
Author(s):  
Gregor W. Schmidt ◽  
Andreas P. Cuny ◽  
Fabian Rudolf
Keyword(s):  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Single Cells ◽  
Time Lapse ◽  
Light Dose ◽  
Live Cells ◽  
Excitation Light ◽  
Minimal Impact ◽  
Imaging Conditions

Time-lapse imaging of live cells using multiple fluorescent reporters is an essential tool to study molecular processes in single cells. However, exposure to even moderate doses of visible excitation light can disturb cellular physiology and alter the quantitative behavior of the cells under study. Here, we set out to develop guidelines to avoid the confounding effects of excitation light in multi-color long-term imaging. We use widefield fluorescence microscopy to measure the effect of the administered excitation light on growth rate (here called photomorbidity) in yeast. We find that photomorbidity is determined by the cumulative light dose at each wavelength, but independent of the way excitation light is applied. Importantly, photomorbidity possesses a threshold light dose below which no effect is detectable (NOEL). We found, that the suitability of fluorescent proteins for live-cell imaging at the respective excitation light NOEL is equally determined by the cellular autofluorescence and the fluorescent protein brightness. Last, we show that photomorbidity of multiple wavelengths is additive and imaging conditions absent of photomorbidity can be predicted. Our findings enable researchers to find imaging conditions with minimal impact on physiology and can provide framework for how to approach photomorbidity in other organisms.

Sign in / Sign up

Export Citation Format

Share Document