scholarly journals Live Imaging Followed by Single Cell Tracking to Monitor Cell Biology and the Lineage Progression of Multiple Neural Populations

10.3791/56291 ◽  
2017 ◽  
Author(s):  
Rosa Gómez-Villafuertes ◽  
Lucía Paniagua-Herranz ◽  
Sergio Gascon ◽  
David de Agustín-Durán ◽  
María de la O Ferreras ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Biology ◽  
Cell Tracking ◽  
Live Imaging ◽  
Neural Populations

scholarly journals Live imaging of mouse embryos during pre-implantation and peri-implantation development

2019 ◽  
Author(s):  
Neophytos Christodoulou ◽  
Antonia Weberling ◽  
Magdalena Zernicka-Goetz
Keyword(s):  
Single Cell ◽  
Embryo Development ◽  
Cell Tracking ◽  
Live Imaging ◽  
Mouse Embryos ◽  
Pharmacological Manipulations

Abstract Live visualisation of embryo development is a powerful tool for scientists to understand how morphogenetic events shape the embryo. Here, we report on a culturing technique that allows live imaging of pre- and peri-implantation mouse embryos throughout the process of blastocyst to egg cylinder transition, enabling single cell tracking and delineation of the tissue dynamics accompanying this morphogenetic stage. At the same time, this protocol can be used for pharmacological manipulations of mouse embryos.

scholarly journals Cell region fingerprints enable highly precise single-cell tracking and lineage reconstruction

2021 ◽  
Author(s):  
Andreas P. Cuny ◽  
Aaron Ponti ◽  
Tomas Kuendig ◽  
Fabian Rudolf ◽  
Joerg Stelling
Keyword(s):  
Single Cell ◽  
Cell Biology ◽  
Cell Tracking ◽  
Structural Information ◽  
Experimental Studies ◽  
Size Control ◽  
Population Level ◽  
Distance Measures ◽  
Cell Region ◽  
Low Frequencies

Experimental studies of cell growth, inheritance, and their associated processes by microscopy require accurate single-cell observations of sufficient duration to reconstruct the genealogy. However, cell tracking - assigning identical cells on consecutive images to a track - is often challenging due to imperfect segmentation, moving cells, or focus drift, resulting in laborious manual verification. Here, we propose fingerprints to identify problematic assignments rapidly. A fingerprint distance measures the similarity between cells in two consecutive images by comparing the structural information contained in the low frequencies of a Fourier transform. We show that it is broadly applicable across cell types and image modalities, provided the image has sufficient structural information. Our tracker (TracX) uses the concept to reject unlikely assignments, thereby substantially increasing tracking performance on published and newly generated long-term data sets from various species. For S.cerevisiae, we propose a comprehensive model for cell size control at the single-cell and population level centered on the Whi5 regulator. It demonstrates how highly precise tracking can help uncover previously undescribed single-cell biology.

scholarly journals Optical and genetic tools for in vivo single cell tracking

2021 ◽  
Vol 358 ◽  
pp. 109192
Author(s):  
Yajie Liang ◽  
Liset M. de la Prida
Keyword(s):  
Single Cell ◽  
Cell Tracking ◽  
Genetic Tools

Statistical mechanics meets single-cell biology

2021 ◽  
Author(s):  
Andrew E. Teschendorff ◽  
Andrew P. Feinberg
Keyword(s):  
Statistical Mechanics ◽  
Single Cell ◽  
Cell Biology

scholarly journals Single-cell biology to decode the immune cellular composition of kidney inflammation

2021 ◽  
Author(s):  
Yu Zhao ◽  
Ulf Panzer ◽  
Stefan Bonn ◽  
Christian F. Krebs
Keyword(s):  
Single Cell ◽  
Cell Biology ◽  
Computational Analysis ◽  
Immune Cell ◽  
Therapeutic Interventions ◽  
Experimental Setup ◽  
Disease Etiology ◽  
Rna Profiling ◽  
Immune Mediated ◽  
Health And Disease

AbstractSingle-cell biology is transforming the ability of researchers to understand cellular signaling and identity across medical and biological disciplines. Especially for immune-mediated diseases, a single-cell look at immune cell subtypes, signaling, and activity might yield fundamental insights into the disease etiology, mechanisms, and potential therapeutic interventions. In this review, we highlight recent advances in the field of single-cell RNA profiling and their application to understand renal function in health and disease. With a focus on the immune system, in particular on T cells, we propose some key directions of understanding renal inflammation using single-cell approaches. We detail the benefits and shortcomings of the various technological approaches outlined and give advice on potential pitfalls and challenges in experimental setup and computational analysis. Finally, we conclude with a brief outlook into a promising future for single-cell technologies to elucidate kidney function.

scholarly journals Melanoma Single-Cell Biology in Experimental and Clinical Settings

2021 ◽  
Vol 10 (3) ◽  
pp. 506
Author(s):  
Hans Binder ◽  
Maria Schmidt ◽  
Henry Loeffler-Wirth ◽  
Lena Suenke Mortensen ◽  
Manfred Kunz
Keyword(s):  
T Cell ◽  
Single Cell ◽  
Intracellular Signaling ◽  
Cell Biology ◽  
Immune Cell ◽  
Malignant Tumors ◽  
Checkpoint Inhibitor ◽  
Treatment Resistance ◽  
Resistance Mechanisms ◽  
Cellular Heterogeneity

Cellular heterogeneity is regarded as a major factor for treatment response and resistance in a variety of malignant tumors, including malignant melanoma. More recent developments of single-cell sequencing technology provided deeper insights into this phenomenon. Single-cell data were used to identify prognostic subtypes of melanoma tumors, with a special emphasis on immune cells and fibroblasts in the tumor microenvironment. Moreover, treatment resistance to checkpoint inhibitor therapy has been shown to be associated with a set of differentially expressed immune cell signatures unraveling new targetable intracellular signaling pathways. Characterization of T cell states under checkpoint inhibitor treatment showed that exhausted CD8+ T cell types in melanoma lesions still have a high proliferative index. Other studies identified treatment resistance mechanisms to targeted treatment against the mutated BRAF serine/threonine protein kinase including repression of the melanoma differentiation gene microphthalmia-associated transcription factor (MITF) and induction of AXL receptor tyrosine kinase. Interestingly, treatment resistance mechanisms not only included selection processes of pre-existing subclones but also transition between different states of gene expression. Taken together, single-cell technology has provided deeper insights into melanoma biology and has put forward our understanding of the role of tumor heterogeneity and transcriptional plasticity, which may impact on innovative clinical trial designs and experimental approaches.

scholarly journals Graph Representation Learning for Single Cell Biology

2021 ◽  
Author(s):  
Leon Hetzel ◽  
David S. Fischer ◽  
Stephan Günnemann ◽  
Fabian J. Theis
Keyword(s):  
Single Cell ◽  
Cell Biology ◽  
Representation Learning ◽  
Graph Representation

scholarly journals Microfluidic Based Physical Approaches towards Single-Cell Intracellular Delivery and Analysis

Micromachines ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 631
Author(s):  
Kiran Kaladharan ◽  
Ashish Kumar ◽  
Pallavi Gupta ◽  
Kavitha Illath ◽  
Tuhin Subhra Santra ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Biology ◽  
Transfection Efficiency ◽  
Intracellular Delivery ◽  
Diagnostic Tools ◽  
Delivery Methods ◽  
Physical Methods ◽  
Cell Measurement ◽  
Therapeutic Development ◽  
Single Living

The ability to deliver foreign molecules into a single living cell with high transfection efficiency and high cell viability is of great interest in cell biology for applications in therapeutic development, diagnostics, and drug delivery towards personalized medicine. Various physical delivery methods have long demonstrated the ability to deliver cargo molecules directly to the cytoplasm or nucleus and the mechanisms underlying most of the approaches have been extensively investigated. However, most of these techniques are bulk approaches that are cell-specific and have low throughput delivery. In comparison to bulk measurements, single-cell measurement technologies can provide a better understanding of the interactions among molecules, organelles, cells, and the microenvironment, which can aid in the development of therapeutics and diagnostic tools. To elucidate distinct responses during cell genetic modification, methods to achieve transfection at the single-cell level are of great interest. In recent years, single-cell technologies have become increasingly robust and accessible, although limitations exist. This review article aims to cover various microfluidic-based physical methods for single-cell intracellular delivery such as electroporation, mechanoporation, microinjection, sonoporation, optoporation, magnetoporation, and thermoporation and their analysis. The mechanisms of various physical methods, their applications, limitations, and prospects are also elaborated.

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